Investigating lithium-ion battery cathode materials for new generation improvements in sustainable energy solutions
“Ensuring access to affordable, reliable, sustainable and modern energy for all will open a new world of opportunities for billions of people through new economic opportunities and jobs, empowered women, children and youth, better education and health, more sustainable, equitable and inclusive communities, and greater protections from, and resilience to, climate change.”UN Sustainable Development Goal 7 – Energy.
Lithium-ion batteries are used around the world in everyday portable electronics, in electric vehicles as well as in small power grids. Scientists from the Energy Materials Research Group at the University of the Witwatersrand (Wits), South Africa, study the materials needed to improve the performance, safety, affordability and environmental footprint of lithium-ion batteries in line with important sustainable development goals (SDGs). A range of different cathode materials, as well as battery chemistry is studied to increase the understanding of the materials themselves: how various synthetic routes introduce impurity phases in these materials and how this can be avoided, and what the effects are of intentional doping and co-doping of these materials to explore the impact they have on the structure, performance and impurities formed.
In this work, however, laboratory-based measurements do not often reveal a clear picture of the overall structure of the material, particularly when it contains lower concentrations of impurity phases which are either below the limit at which it can be detected or cannot be resolved from the major phase. It is therefore important to firstly, employ multiple techniques to provide complementary information and secondly, to obtain high-resolution measurements from synchrotron-based techniques which expose far more in terms of other phases in the samples. This is where the GCRF START grant plays a vital part.
“A synchrotron is millions of times more capable than the equipment in our labs in terms of brightness and detail, which makes access through the GCRF START grant to the UK’s national synchrotron, Diamond Light Source (Diamond), so significant.”GCRF START Co-I, Prof. David Billing, Professor in the School of Chemistry and Co-PI of the Energy Materials Research Group at Wits.
“Thus far we have data from various synchrotrons for high resolution X-ray diffraction and total scattering, as well as X-ray absorption spectrometry,” says Group Co-PI, Prof. Caren Billing, lecturer and Associate Professor in the School of Chemistry. “The GCRF START grant provides us with these important experimental opportunities, alongside vital skills training and knowledge exchange for building capacity and training emerging scientists in the energy materials field.”
The ultimate aim of the Group is to address global energy, climate, and health challenges which, amongst other aims, includes enabling better “access to clean and safe cooking fuels and technologies and expanding the use of renewable energy beyond the electricity sector, as well as to increase electrification in sub-Saharan Africa”. To this end, improved battery storage solutions are one of a creative mix of options the Group is examining, with the help of their collaborators, including the GCRF START grant.
“GCRF START asks us to consider questions in our research around the global challenges like: am I using components that are sustainable? Are we using elements which are abundant, affordable, and environmentally compatible?”, explains Prof. Dave Billing. “In doing so, we are mindful that the economic and social situations in Europe are different to Africa: different resources, different engineers, and different environments where the solutions have to work. Everything costs energy, fundamentally, and the whole solution has to fit the community – these are the bigger picture questions that START encourages us to ask.”
Some of the Group’s early career scientists focus on various lithium metal ion phosphate materials, where they are studied with the idea of using earth abundant metal ions of benefit for cost effective production and materials with a possible impact on local mining opportunities to support local economies. Two of these scientists – Michelle Thiebaut from South Africa and Michelle Nyoni from Zimbabwe – are PhD research students at Wits working on lithium iron phosphate and lithium vanadium phosphate respectively, examining them as cathode materials. Both students are supervised and mentored by Prof. Dave Billing and Prof. Caren Billing, and are part of a growing number of female scientists in the Energy Materials Research Group at Wits. Michelle Thiebaut and Michelle Nyoni describe the aims, techniques and motivation for their projects in the case studies below.
Michelle Thiebaut’s research: studying Lithium iron phosphate for battery cathode materials
“When Michelle Thiebaut first started in the group, she referred to herself as “an analogue girl in a digital world”. Michelle is now the forerunner in the group in processing XAS data and has been the only chemistry student to operate the Mössbauer spectroscopy instrument in the School of Physics at Wits.” – Prof. Caren Billing, Prof. Caren Billing, University of the Witwatersrand.
Being a new researcher in a field such as energy materials is both daunting and exciting because this field is always changing and improving. One needs to change and improve one’s skill set just as quickly but the key to continue is finding one’s motivation. My main motivation is seeing how people in South Africa and in other developing countries are struggling with everyday tasks, especially people in the rural areas – tasks like coming home and doing their homework. These tasks are things many people take for granted but I think it is unacceptable that people should be struggling to get by without proper, cheap and a long-lasting access to clean energy and electricity.
My second motivation is our planet. Every person has an obligation to the planet and to live an environmentally cleaner life. By pushing science in the energy materials field means also pushing towards a greener tomorrow. Trying to break through in this field as a young female is still a bit tough with people questioning your skill set and abilities but I do think we owe former female scientists a great deal of respect for paving the way for us.
My research field is energy materials, specifically investigating the cathode material LiFePO4 found in lithium-ion batteries. My focus with this material is to find a low cost, low energy synthetic route and to possibly improve the performance. LiFePO4 is a naturally occurring mineral but can also be synthesised in a lab. This naturally occurring mineral is not phase pure, meaning that the iron is commonly mixed with other metals such as manganese, magnesium and calcium which lowers the electrochemical performance. Cathode materials are the positive electrodes of batteries and host the mobile ions (in this case lithium). The mobile ions are the ions that are removed from the structure when the battery is being charged and when the battery discharges (depletes) the ions are inserted back into the structure. Current cathode materials are not only expensive to produce but also have some safety issues like overheating and short-circuiting associated with them – challenges we want to overcome.
Compared with other cathode materials, LiFePO4 has the advantage of being environmentally friendly, meaning there are no toxic materials presents, relatively cost efficient (no expensive metals/rare earth metals needed to synthesise the material) and is structurally and thermally stable. This means that the structure does not collapse with the removal of the mobile ions and the structure prevents the battery from overcharging as well as overheating, making this material safer to use. However, one of the main disadvantages of LiFePO4 is the electrochemical performance such as the ionic (movement of ions through the crystal lattice) and electronic (the ability to conduct or resist electric current), which are both important properties for cathode material. The mobile ions are restricted to movement through a 1-dimensional channel. Overcoming these problems has been the main focus for most research groups.
In my research, the electrochemical performance can be improved by doping with a selection of different metal ions. Inserting small amounts of metal ions into the structure can improve the battery performance differently depending on the metal. For example, nickel improves the stability of the structure and enhances the movement of lithium through the structure; copper improves the conductivity and improves the reversibility of the lithium ions in the structure; and manganese improves the reversibility as well as the stability of the structure.
Exploring materials through multiple techniques and collaborative efforts
To fully understand my material, it is very important to understand how the structure changes with small changes in my synthetic method and it is the collaborative effort between the Chemistry and Physics Departments at my university – the University of the Witwatersrand – which makes this possible, and through access to world class synchrotron sources to utilise the benefits of synchrotron data to further characterise my materials. Selected samples were sent to the Synchrotron source at Brookhaven National Laboratory (NSLS-II) in the USA and to Diamond Light Source, the UK’s national synchrotron (Diamond), with access to Diamond provided by the GCRF START grant. We have obtained data from synchrotron X-ray diffraction and total scattering, as well as X-ray absorption spectroscopy. Having remote access to state-of-the-art synchrotron equipment in this COVID-19 travel restricted world is heaven-sent as the research can continue even when no travelling is allowed.
To thoroughly characterise my synthesised materials, I have made use of our lab-based diffractometers in the Chemistry department at Wits as well as the Mössbauer spectrometer and the Raman spectrometer in the Physics department. Mössbauer spectroscopy and Raman spectroscopy are very useful for identifying crystalline (presence of long-range order of the atoms – regular arrangement of atoms over a longer distance) as well as amorphous (only the presence of short-range order of atoms – regular arrangement of atoms but only over a short distance) species in my samples. It is important to identify all the crystalline and amorphous species in the sample as impurities can occur in both forms and could negatively affect the battery performance.
Mössbauer spectroscopy is also useful for identifying the different local iron (Fe) environments present in my sample and to determine the form of iron – (oxidation state – Fe2+ is the desired state in my samples). Raman spectroscopy aids as a structural fingerprint that can be used to determine the identity of one’s material and is also useful in identifying any impurities present that the lab diffractometers could not detect due poor detection limits or due to the phase being amorphous. Synthesised samples can have a mixture of the desired product as well as impurities. There could be multiple sources for the formation of impurities but the most common causes can be either synthesis related (impurities that are formed due to a specific synthetic route) or impurities formed due to sensitivity to air (being exposed to air could cause some small changes like a change in oxidation state of a metal). Impurities can block the channel and subsequently the movement of the mobile ion and negatively affect the performance of the material and the battery.
Michelle Nyoni’s research: investigating Lithium vanadium phosphate for improved battery cathode materials
“Michelle Nyoni is a lady who, against many odds, is striving to obtain her PhD in energy materials. Impacted currently by Covid19 travel restrictions, Michelle is normally an ‘out-of-seat’ student who works full time at Chinhoyi University of Technology (CUT) in Zimbabwe and comes to South Africa for laboratory experiments at the University of the Witwatersrand during her teaching breaks as facilities for her research topic at CUT are limited. She has worked hard during her visits here to gather sufficient data so that she can process it when she returns home and brings with her a great deal of positivity and energy on each visit.” – Prof. Caren Billing, Prof. Caren Billing, University of the Witwatersrand.
While working in the farming sector in my home country of Zimbabwe, I realised that we are blessed with abundant renewable sources of energy – wind and solar – yet hindered by the challenge of how to store this energy effectively. This is where the subject of batteries came into my life and where my current PhD research area fits in. I am investigating lithium vanadium phosphates as cathode materials for lithium-ion batteries. I began my PhD studies part-time, in 2017, at the University of the Witwatersrand in South Africa under the supervision of Prof. Caren Billing and Prof. Dave Billing, while working as a Chemistry Lecturer at CUT in Zimbabwe.
The inspiration for my research is the fact that South Africa is one of the biggest vanadium producers in the world and Zimbabwe is one of the biggest lithium producers in the world. Therefore, if the raw materials are locally available it will hopefully mean reduced cost of battery production. My research is directly linked to Sustainable Development Goal (SDG) 7 concerning affordable and clean energy but by contributing to SDG 7, my research also contributes to achieving SDGs 1-6 and 8-9.
The aim of my research is to do much of the material characterisation by focussing on understanding what is happening at the atomic level, asking questions like: what is happening with the structure and the material? Lithium vanadium phosphate materials have been made but is this synthesis method reproducible? Does it work for upscaling to commercial levels? How do slight changes within the synthesis (preparation method) affect the material? How does adding a dopant manipulate the electrochemical properties of my material?
Lithium vanadium phosphates are potentially effective because their various properties are attractive – they have a high thermodynamic and kinetic stability, and studies have shown they possess the potential to have very good electrochemical properties, which means they will have high specific energy, high working voltage, and good cycle stability. Normally, as batteries get older, the cycling gets poorer and poorer but lithium vanadium phosphate materials have good cycle stability and a lower price tag so they are not as expensive as some of the alternative materials that can be used. There are also other advantages. Lithium vanadium phosphate materials provide improved safety, phosphates are more environmentally friendly than some other materials, and the vanadium contributes to the energy density as well as the voltage of the cells – in fact, our Lithium vanadium phosphate materials can reach voltages of over 4 volts! A key application is in electric vehicles which will benefit from increased length of travel due to the cycle stability of Lithium vanadium phosphate materials and the higher specific energy density, amongst other improvements due to the advantages described above.
The cathode material determines the voltage and capacity of a battery and the cathode in a lithium-ion battery is the positive electrode, which is normally a metal oxide that is responsible for being the source of lithium ions that carry the electric current when a battery is in use (discharging). There are various components that contribute to the cost of the battery with the cathode material within the battery usually one of the biggest costs, along with the separator. The lithium vanadium phosphate materials that I am working with are cathode materials, therefore if we can source these locally within the SADC region of Africa, which includes 15 member states, this would make them a lot more affordable and accessible – which is the goal I am driving at.
Cutting edge techniques to determine material characterisation and impact
The techniques I will use in my PhD studies aim to test the lithium vanadium phosphate materials in depth so that I can contribute to research that is already available to help find viable products that can be used in Africa. Techniques include powder X-ray diffraction for the phase identification and Raman spectroscopy to enable me to determine the structural finger-print to ensure I am making the same product each time so that when I do change a parameter, the resulting effect will be clear. The GCRF START grant enables us to use the Diamond synchrotron for variable temperature experiments. Therefore, I would want to look out for how the material changes when we vary the temperature. I would also use XAFS– X-ray absorption fine structure spectroscopy at the B18 beamline at Diamond to study the changes in the neighbourhoods of particular atoms.
Another technique is transition electron microscopy – the determination of particle size and the distribution of those particles as well as the general morphology of the fine particles within the material. Additionally, I want to use STA – Simultaneous Thermal Analysis – to look at the thermal stability to ask a series of questions: how stable is my material and what happens under temperature changes? Does it break down or decompose? How does this effect the overall electrochemical properties because when we use these batteries they will heat up? What is the impact, for example, if I were to leave my phone device with a battery using these materials in the sun – how would the warmth of the sun affect it? Would the structure and performance be impacted? Therefore, I would do extensive electrochemical testing which includes cyclic voltammetry and electrochemical impedance tests, amongst others, to ensure the batteries with these materials are viable in the varied environmental conditions found across Africa, including very warm environments.
The GCRF START grant: a bridge to sustainable growth and life-changing possibility
“Being part of the GCRF START collaboration has certainly taken our work in energy materials in South Africa to the next level!”Prof. Caren Billing, University of the Witwatersrand
Many of the Group’s research projects are now at the point where data has been measured and obtained and the next learning curve of how to process the data is underway. Progress has been made, Prof. Caren Billing reports, which, without funding from the GCRF START Grant, would have been an even larger hurdle to overcome.The resultis cutting-edge science and capacity building, knowledge exchange and access to the latest techniques and technology, and a new generation of gifted scientists working towards the shared vision of developing novel, green and affordable energy solutions to inspire life-changing possibility in Africa and beyond.
“This is where the GCRF START grant comes in,” says Prof. David Billing, “it provides that bridge. Yes, there’s a skills gap here in Africa but for me that gap is possibly smaller than others; as long as we are staying current on the XRD side we can transition easily and tackle the more challenging newer techniques – there’s a whole suite of them but that will grow – and START gets us there! This is also what you need to get to the higher impact journals; it also to gets us closer to current answers and future possibilities rather than just ‘the best we can do’ with 30-year-old technology.”
“In terms of energy solutions, take the scenario of load shedding (electricity cuts) which poses a huge challenge across countries in Africa. The thought of being able to go off grid is vital. If you think about a rural village which is cooking using wood or charcoal and lighting in the form of paraffin or candles – this is energy poverty. If you can find a cheap, clean, sustainable source of energy to replace these – that would be life changing!”GCRF START Co-I, Prof. David Billing, Professor in the School of Chemistry and Co-PI of the Energy Materials Research Group at Wits.
 Introducing small amounts of other metal ions into the structure during synthesis without changing the structure of the material
 Prof. David Billing is also Assistant Dean in the Faculty of Science at the University of the Witwatersrand, South Africa.
 An easy way to picture this is in terms of ores. Generally, an ore will contain a mixture of minerals and hence is not ‘phase pure’.
 Information on the natural occurring triphylite (mineral data): https://www.mindat.org/min-4020.html as well as an electrochemical comparison: https://www.sciencedirect.com/science/article/pii/S0378775301007273?casa_token=zcBRvEsb5SMAAAAA:Lrk2oIjOY-9W73OBWasFIrxQaP7mhWNfQ4HrYjzx7Ib_r95Pq4ix8eORm0IBm29G-izoI18
 How Lithium batteries work in: https://www.explainthatstuff.com/how-lithium-ion-batteries-work.html
 Advantages and disadvantages of Lithium-iron-phosphate v lithium ion: https://blog.epectec.com/lithium-iron-phosphate-vs-lithium-ion-differences-and-advantages
 See Figure 1. How the lithium ions move in a battery in: https://www.spectroscopyonline.com/view/techniques-raman-analysis-lithium-ion-batteries; see also: The channels through which lithium has to move in LiFePO4 in the paper: Yi, T., Li, X., Liu, H. et al. Recent developments in the doping and surface modification of LiFePO4 as cathode material for power lithium ion battery. Ionics 18, 529–539 (2012). https://doi.org/10.1007/s11581-012-0695-y
 Jingkun Li, Zi-Feng. Past and Present of LiFePO4: From Fundamental Research to Industrial Applications. Chem. Volume 5, Issue 1, 10 January 2019, Pages 3-6 (2019), Elsevier. https://doi.org/10.1016/j.chempr.2018.12.012;
V.S.L. Satyavani,A. Srinivas Kumar,P.S.V. Subba Rao.Methods of synthesis and performance improvement of lithium iron phosphate for high rate Li-ion batteries: A review. Engineering Science and Technology 19, Issue 1, March 2016, Pages 178-188. Elsevier. https://doi.org/10.1016/j.jestch.2015.06.002;
Yi, T., Li, X., Liu, H. et al. Recent developments in the doping and surface modification of LiFePO4 as cathode material for power lithium ion battery. Ionics 18, 529–539 (2012). https://doi.org/10.1007/s11581-012-0695-y
 Hameed, S.A., Reddy, M.V., Sakar, N., Chowdari, B.V.R. & Vittal, J.J.; Royal Society of Chemistry Advances 2015, 5, 60630-60637
 See: ‘The four components of a Lithium battery’: https://www.samsungsdi.com/column/technology/detail/55272.html?pageIndex=1&idx=55272&brdCode=001&listType=list&searchKeyword=
 See: Figure 3. ‘Total material costs of all 10 considered cell chemistries plus Panasonic NCA Use Case differentiated in combined CAM cost, anode cost, and secondary material costs’ in: Wentker, M.; Greenwood, M.; Leker, J. A Bottom-Up Approach to Lithium-Ion Battery Cost Modeling with a Focus on Cathode Active Materials. Energies 2019, 12, 504. https://doi.org/10.3390/en12030504
“Over the past two years, being involved in the GCRF START grant has allowed me to mature and to become much more independent as a scientist.”Dr Camien Tolmie, University of the Free State, South Africa
The molecular workings of the natural world have always interested me, especially how we can use these processes to sustainably improve human health and agriculture. My name is Carmien Tolmie and I grew up in the small city of Bloemfontein, in the Free State province of South Africa. From a young age, I enjoyed maths, science and languages, and I participated in various extracurricular academic activities in STEM. As a result, I decided at an early age to pursue a career in science, starting with a BSc degree in Molecular Biology and Biotechnology at the University of Stellenbosch, and returning to Bloemfontein for my postgraduate studies (BSc Honours degree, MSc and finally PhD) at the University of the Free State (UFS), where I chose Biochemistry as my discipline.
Structural Biology is an incredibly powerful and multi-functional field with various applications in human health, agriculture and sustainable ‘green’ chemistry (environmentally friendly chemistry). Passionate about addressing the challenges I see in Africa, I was motivated to undertake my PhD with Prof. Dirk Opperman who is a GCRF START Co-Investigator (Co-I) in UFS’s Biocatalysis and Structural Biology research group, working on enzymes (proteins that act as biological catalysts) from Aspergillus flavus. The Aspergillus flavus fungus grows on agricultural crops, produces cancer-causing compounds and can also cause infectious fungal disease. Studying the atomic structures of proteins from fungi like the Aspergillus flavus reveals a wealth of information, such as how the three-dimensional structure looks and changes during the chemical reactions it catalyses, the possible mechanism of how the protein works, and how it binds to small molecules. If the protein is a drug target, the structure can be used in Structure-Based Drug Discovery to develop new medications, ‘green’ pesticides for agriculture, and other applications.
Passing on the love of learning to other young scientists
I love learning and discovering new things, working in the lab, as well as passing on the knowledge to others. Therefore, I decided to build a career in academia with a focus on Structural Biology. I have recently been appointed as a full-time academic in UFS’s Department of Microbial, Biochemical and Food Biotechnology (January 2020) where I have a joint research and teaching position as Lecturer in Biochemistry. In my new fungal drug discovery projects, which I have just started (delayed because of Covid19 lockdown), I am the main Principal Investigator (PI) in collaboration with Prof. Opperman and Prof. Martie Smit.
My new research projects will look specifically at developing inhibitor compounds against fungal metabolic targets with the aim of discovering new antifungal compounds. Existing anti-fungal medication and pesticides have been so widely used that fungi have evolved and developed ways to combat the anti-fungals, thereby becoming drug resistant. Our research may help in the future to develop sustainable solutions through novel antifungal drugs to improve the health, wellbeing and prognosis of people who suffer from infectious fungal disease, particularly immune-compromised patients, where fungal infections can cause serious health complications and can be life threatening.
To conduct the research, I will use the structure-based drug discovery method of X-ray crystallographic fragment screening at the UK’s national synchrotron, Diamond Light Source (Diamond). This method uses protein crystals of the target enzyme to identify small molecule fragments that bind to the enzyme. These fragments are then elaborated into larger molecules with higher potency, which will hopefully not only inhibit the specific enzyme, but also the growth of pathogenic fungi. I was introduced to the concept and power of fragment screening techniques during GCRF START meetings and learnt more about the experimental workflow of XChem and the I-04 beamline during my research visit to Diamond Light Source in the UK last year, which inspired me to embark on XChem projects for antifungal drug discovery.
Investing in African Early Career networks through GCRF START grant
“Carmien is not only passionate about Structural Biology, but also teaching. She has been a vital part of START, helping and teaching the postgraduate students not just in our lab, but also reached out and helped other GCRF START groups in South Africa.”Prof. Dirk Opperman, University of the Free State
Being involved in the START grant has made a very concrete contribution to my career as a young scientist. At the beginning of the START project, I was a PhD student with Prof. Opperman. The START grant has contributed to the running cost of our laboratory, funded my postdoctoral salary for 2019, as well as my travel cost of attending a CCP4 workshop in Brazil (2018), the Biophysics and Structural Biology at Synchrotrons workshop, and various START meetings. The grant also enabled and funded my research exchange to the UK last year (2019). Through START, we have met numerous top-notch scientists that can advise us on our experiments. We have START meetings for early career scientists, both in the Structural Biology and Energy Materials strands of the START project. We routinely collect data with other members of the South African Structural Biology Consortium at Diamond (various universities and START collaborating laboratories), albeit through remote access – a process that was greatly improved by a Data Collection Workshop run by Diamond’s beamline scientists in Pretoria last year, and which enhanced our data collection skills and deepened our relations within the network established by START.
Interestingly, this international collaboration has been instrumental in establishing a network of early-career structural biologists in South Africa, including postgraduate students and postdoctoral researchers. Getting to know peers who are working in Structural Biology, and who are using the same techniques as I am, and who have similar research interests has provided a feeling of connectedness. These projects are often very demanding and having the support and motivation of a friend who has encountered similar setbacks (or being that friend to someone else) can really help one endure in difficult times. My hope is that this network will be the basis for many future collaborations.
Exposure to international research collaborations and facilities
GCRF START has exposed me to many esteemed international scientists and facilities. The START events have introduced me to scientists at Diamond who are very supportive and who have invested in both the START project and the development of the people involved in the project, such as START Co-I, Prof. Frank von Delft, who has research groups at both Diamond and the Structural Genomics Consortium at the University of Oxford. I was hosted by the Structural Genomics Consortium for a two-month research exchange last year to develop new experimental skills and this kind of exposure has greatly improved my skills and the way I think about my research.
At the time of writing, I am currently involved in organising a crystallographic data processing workshop in South Africa – the first of its kind to be held on the continent – with START and CCP4. The workshop was supposed to be in April of this year (2020) but had to be postponed because of the Covid19 pandemic. I am one of the main local organisers, and this has given me the opportunity to improve both my grant-writing skills and organisational skills. In addition to funding by CCP4 and START, we have secured funding from the International Union for Crystallography, the International Union for Pure and Applied Physics, the National Research Foundation of South Africa, and the University of Cape Town.
Gaining the competitive edge!
Over the past two years, being involved in the grant has allowed me to mature and to become much more independent as a scientist. My appointment as a Lecturer in Biochemistry means starting with my own, independent research projects in Structure-Based Drug Discovery, which is very exciting, and scary at the same time! I will be responsible for the second-year undergraduate Biochemistry module – Enzymology and introduction to metabolism. Although this is a difficult year to start teaching a module, I have a great support system at the department. I truly believe that the experience and exposure of START gave me a competitive edge in being selected for the position, and I am very grateful for this opportunity.
“The opportunities that were afforded to Carmien through the GCRF START grant enabled her to transition to academia. For the momentum we have gained through the grant to continue, we must transition our START Post Graduate Research Assistants into permanent academic positions. This allows us to retain the ‘critical mass’ required for structural biology to be successful in South Africa.”Prof. Dirk Opperman, University of the Free State, South Africa
Click here to read more about the UN’s Sustainable Development Goals
I would firstly like to thank Dirk for the motivation, support and academic mentoring throughout the years; I would not have been the researcher I am today without him. I would like to thank Prof. Trevor Sewell (Director of the Aaron Klug Centre for Imaging and Analysis, University of Cape Town), Dr Ruslan Nukri Sanishvili (formerly of Argonne National Laboratory, Chicago, USA), Dr Gwyndaf Evans (Deputy Director Life Science, Diamond Light Source), Dr Dave Hall (MX Group leader, Diamond Light Source), and the CCP4 staff for their help in organising the CCP4 workshop. I would also like to thank Prof. Frank von Delft (Diamond Light Source, University of Oxford) and Dr Nicola Burgess-Brown (University of Oxford) for hosting me in their research groups. Finally, I would like to thank the University of the Free State and especially Prof. Martie Smit (HOD, Dept. of Microbial, Biochemical and Food Biotechnology) for giving me the opportunity to further my academic career.
Tolmie C, Do Aido Machado R, Ferroni FM, Smit MS and DJ Opperman (2020). Natural variation in the ‘control loop’ of BVMOAFL210 and its influence on regioselectivity and sulfoxidation. Catalysts 10(3): 339. doi: 10.3390/catal10030339 (Impact factor 3.444): https://www.mdpi.com/2073-4344/10/3/339
Carmien’s profile on Research Gate Profile
“The atomic structure of proteins provides an intimate insight into these magnificent macromolecules. This knowledge is crucial to truly understand how they function; whether it is to answer a burning question or to manipulate them – either to enhance if their reactions are desirable, or to inhibit if they are harmful.”Prof. Dirk Opperman, University of the Free State, South Africa
Our research studies the structures of bacterial and fungal oxidoreductases (enzymes) which are possible drug targets to combat infectious disease. The current focus is fungal drug targets for fungal infectious diseases which can be very serious, especially for immune-compromised patients, such as those who are HIV/AIDS positive, organ transplant receivers, patients undergoing chemotherapy, and many more. This research is performed at the University of the Free State’s (UFS’s) Department of Microbial, Biochemical and Food Biotechnology1 and is led by the two Principal Investigators (PIs) of the Biocatalysis group at UFS, Prof. Dirk Opperman, who is a GCRF START Co-Investigator (Co-I), and Prof. Martie Smit. In our laboratory, we have solved the structures of a number of bacterial and fungal enzymes by X-ray crystallography over the past few years, two of the most recent – solving the structures of fungal cytochrome P450 reductase (Dec 2019) and Baeyer-Villiger monooxygenase (Feb 2020) – were assisted by the GCRF START grant and published in the journals Scientific reports2 and Catalysts3 respectively, as described later in this article.
The scale of the Fungal infection and drug resistance challenge
Currently, there are three classes of anti-fungal drugs that are used to combat infectious fungal disease, but there is an increasing number of drug resistant (and even multi-drug resistant) fungi against these drugs meaning that these pathogenic fungi have become or are becoming resistant to the current medication used to treat patients. If no drugs are effective against invasive opportunistic fungi, the prognosis for immune-compromised patients is very poor, and many people will die.
“It is therefore imperative that we search for and develop new antifungal compounds to address the growing challenge [of drug-resistance to opportunistic fungi], which impacts countries across Africa, as well as globally. This is especially urgent if the world is to meet the UN’s Sustainable Development Goals of Health and Wellbeing and Food Security by 2030.”Dr Carmien Tolmie, University of the Free State, South Africa
Fungal infections are often underreported and because of this the extent of the situation is not fully known. In South Africa, this is of particular concern because of our high incidence of HIV/AIDS. For example, one group4 reported that 90 % of HIV/AIDS positive patients on prolonged treatment contract oropharyngeal candidiasis (also called Thrush), an infection caused by a yeast, which is a type of fungus called Candida (Dos Santos Abrantes, McArthur and Africa 2014). However, this is only one statistic, and the problem is much wider. In another example, Cryptococcal meningitis is a deadly brain infection caused by the soil-dwelling fungus Cryptococcus. Worldwide, nearly 220,000 new cases of cryptococcal meningitis occur each year, resulting in 181,000 deaths, most of which occur in sub-Saharan Africa (CDC, 2020).
Using the powerful beams of Diamond’s synchrotron light to determine protein structures
Our quest to find new drug targets involves examining the chemical processes that happen in the fungal cell in order to keep the cell alive. We choose an enzyme – a special type of protein involved in these processes – which will be a good target for anti-fungal medication. The experiments we do to produce our protein crystals include molecular biology, protein expression, purification and crystallisation. We clone the gene that encodes the enzyme and insert it into a suitable host to produce the protein, such as the bacterium Escherichia coli, by protein expression methods. Escherichia coli is easy to manipulate and inexpensive to culture in large volumes. We then isolate the enzyme by protein purification methods which exploit the physicochemical properties of the enzyme to separate the target from the host proteins, and crystallise it before we examine it by X-ray crystallography.
We use an in-house crystallisation robot at UFS to prepare the crystallisation trials and we regularly collect crystal diffraction data via remote access at the macromolecular beamlines of the UK’s national synchrotron – Diamond Light Source (Diamond). This is a great help as we can control the beamline equipment from our offices, so we don’t incur the expense of travelling to the UK to use synchrotron techniques essential for our research. While we have X-ray diffractometers at the University of the Free State, they are not nearly as powerful as the beamlines of the Diamond synchrotron. Diamond’s beamline hardware has been developed to such an advanced stage that data collection can proceed very rapidly, enabling us to collect data much faster (minutes) than at our home sources (days). This high throughput is essential when searching for and identify tiny molecules that might potentially bind to the protein and possibly act as inhibitors, as large libraries of fragments must be screened.
“The brilliant light generated by Diamond (10 billion times brighter than the sun!) enables us to determine the structure of the proteins to extremely high resolutions, as well as structures from small or weakly diffracting crystals that we cannot study with our own laboratory techniques.”Dr Carmien Tolmie, University of the Free State, South Africa
We use the protein structure to search for small molecules that will bind to the enzyme and possibly stop it from working (act as inhibitors). In Biocatalysis, knowledge of the protein structure can identify ways in which one can change, or mutate, the enzyme to perform the specific reactions desired. If the protein is a drug target, the structure can be used in Structure-Based Drug Discovery to develop new medications. This process can also be used for other applications like developing new pesticides for agriculture. Therefore, the next step in the research process is to use fragment screening methods to identify lead compounds that can be further developed into inhibitors, thus helping develop a next generation drug. The fragment screening is done in collaboration with Prof. Frank von Delft and the XChem group on the I04-1 beamline at Diamond through the GCRF START grant and will be undertaken once Covid19 travel restrictions are lifted.
Solving the structures of fungal cytochrome P450 reductase and Baeyer-Villiger monooxygenase
Recently, we were able to solve and gain new insights into the structures and mechanisms of the fungal cytochrome P450 reductase (CPR) from Candida tropicalis and the Baeyer-Villiger monooxygenase BVMOAFL210 from Aspergillus flavus, research that was made possible by the GCRF START grant. The results were published in the journals Scientific reports and Catalysts respectively, and the research on the CPR was done in collaboration with scientists from the University of Cape Town5, who are also part of the START project. The publications were co-authored by START PDRAs Ana Ebrecht (first author on CPR paper) and Rodolpho do Aido Machado (co-author on BVMOAFL210).
The CPR plays a pivotal role in primary and secondary metabolism of different species, from bacteria to animals and plants. In fungi, it supplies electrons to enzymes that are vital for the survival of the organism. The CPR mechanism is complex and involves conformational changes that need to be finely tuned to optimise the process. The structural characterisation of the CPR helps to understand how this process occurs and what are the differences with the human homolog, opening the possibility to use it as a drug target. The structure and mutation data of BVMOAFL210 allowed us to better understand the role of the amino acid at a specific position in the enzyme, in terms of regioselectivity (the position in the substrate where the oxygen atom is inserted) as well as the sulfoxidation (the number of oxygen atoms inserted in a sulfur-containing compound). This residue may be used in future studies for directed evolution experiments to evolve the enzyme to catalyse a desired reaction.
In order to achieve the results, we first needed to produce pure protein. The proteins were crystallised by the vapour-diffusion method with the Douglas Oryx Nano crystallization robot located in our crystallography lab in our department. In these experiments, a library of 384 crystallisation conditions were screened and a few conditions yielded crystals. These crystals were cryo-cooled and shipped at liquid nitrogen conditions in a specialised container to Diamond where we collected data on the macromolecular crystallography beamlines through remote access. We processed the data and solved the structure with programs from the CCP4 suite of macromolecular data processing software. The proteins were characterised further by investigating their kinetic properties with several spectrophotometric assays using a UV/Visible light spectrophotometer.
For BVMOAFL210, we created mutations at a specific position and determined how these mutations alter the biocatalytic profile of the enzyme using whole-cell biotransformation experiments, followed by Gas-Chromatography Mass Spectrometry (GC-MS) analyses. In terms of the fungal cytochrome P450 reductase (CPR), the next steps will be to use the CPR for fragment screening to gain further, more detailed insights. This method uses protein crystals of the target enzyme to identify small molecule fragments that bind to the enzyme. These fragments are then elaborated into larger molecules with higher potency, which will hopefully not only inhibit the specific enzyme, but also the growth of pathogenic fungi.
Benefitting from increased research capacity through the GCRF START grant
The grant has contributed greatly to the research capacity of the Biocatalysis and Structural Biology Research group, making it possible to appoint a START Postdoctoral Research Assistant (PDRA) who focused on structural biology research, the research itself partially funded by START. START also helped to develop the skills of the researchers in the group by funding workshops, as well as workshop attendance, and a research exchange of the START PDRA to the UK in 2019. In addition, START has introduced us to world-class scientists at Diamond and other institutions who we can consult if we need advice on our experiments.
“With this sharing of knowledge, capacity building and cutting-edge research enabled by the GCRF START grant, it is our fervent aim to make a lasting, positive impact in terms of sustainable health, well-being and food security solutions now, and well into the future.”Dr Carmien Tolmie, University of the Free State, South Africa
Click here to read more about the UN’s Sustainable Development Goals
We would like to thank Prof. Trevor Sewell from the START Centre of Excellence at the University of Cape Town’s Aaron Klug Centre for Imaging and Analysis for the pivotal role he has played both in GCRF START and Structural Biology in South Africa. The START Centre of Excellence is a collaborative, shared resource where participants in the START programme can access everything they need to get started with their research, such as advice and the necessary equipment which may not be available in their own laboratories elsewhere. This also includes the technological support and expertise to access the UK’s national synchrotron – Diamond Light Source – through the GCRF START grant (such as support with sample preparation, shipping, and remote access experiments).
Dr Carmien Tolmie: https://orcid.org/0000-0001-9095-3048
Prof.Dirk Opperman: https://orcid.org/0000-0002-2737-8797
 Research in the Department falls broadly into three main areas: (i) production of safe and novel food products, (ii) biocatalytic production of chemicals or bioremediation of chemical pollution, and (iii) improvement of human and animal health. Our Biocatalysis Group focuses heavily on biocatalysis which involves the use of one or more enzymes, either as cell-free enzymes or enzymes in whole cells, to convert a substrate into a value-added product. This includes converting alkanes, alcohols, fatty acids or monoterpenes into value added building blocks of pharmaceuticals, bio-plastics, cosmetics, flavours and/or fragrances.
 Ebrecht AC, Van der Bergh N, Harrison STL, Smit MS, Sewell BT and DJ Opperman (2019). Biochemical and structural insights into the cytochrome P450 reductase from Candida tropicalis. Scientific Reports 9:20088. doi: 10.1038/s41598-019-56516-6: https://www.nature.com/articles/s41598-019-56516-6
 Tolmie C,Do Aido Machado R, Ferroni FM, Smit MS and DJ Opperman (2020). Natural variation in the ‘control loop’ of BVMOAFL210 and its influence on regioselectivity and sulfoxidation. Catalysts 10(3): 339. doi: 10.3390/catal10030339: https://www.mdpi.com/2073-4344/10/3/339
 Dos Santos Abrantes PM, McArthur CP, Africa CWJ. Multi-drug resistant oral Candida species isolated from HIV-positive patients in South Africa and Cameroon. Diagn Microbiol Infect Dis 2014;79:222–7.
“I think we, as African scientists, have a lot to offer. We are very connected and very close to the problems of the world. On a daily basis, we witness many of the global challenges first-hand and see the impact of diseases like HIV/AIDS, TB, Malaria, cancers and other communicable, as well as non-communicable diseases. We can see directly how our research can be life-saving. This is a big motivator!”Melissa Marx, University of Cape Town, South Africa
To me, the GCRF START grant means the ability to learn new techniques which I can apply in my research on the human papillomavirus (HPV) 16 pseudovirions (PsVs) at the University of Cape Town (UCT). I’m using the structural biology technique cryo-electron microscopy (cryo-EM) to image HPV16-PsVs particles in order to obtain a better idea of the entry mechanisms used by the virus to infect host cells. With the help of the START grant, I can use techniques for research that could potentially contribute to the development of inhibitors for HPV infection, thereby decreasing HPV-associated cancer incidence down the line. This is really exciting and topical because cervical cancer – almost always caused by oncogenic HPV infection – is one of the most common cancers in women globally and the HPV is the second most frequent cause of cancer among women in Africa and in my own country of South Africa. My research and the START grant are therefore very important to me personally, as well as for women in Africa in general.
As a ‘newbie scientist’ in the early stages of my career, it is important to be exposed to different techniques that we wouldn’t normally be exposed to here in Africa. In my undergraduate degree, I had almost no exposure to electron microscopy and computer software in general. Fast forward to the present as a first year MSc student, and after only one year of experience in this field (and lots of help), I’ve managed to make three reconstructions of HPV particles using two different reconstruction programs and have made large numbers of grids on which we mount the samples! Within South Africa, there isn’t a lot of information about cryo-EM and other techniques we need to use for our research. Through the grant, I have been able to learn things like negative staining, vitrification, sample purification, sample preparation, and data analysis using RELION, and I even had the opportunity to go overseas to visit the UK’s national synchrotron, Diamond Light Source (Diamond).
Why developing Inhibitors for HPV could be the way forward
“Melissa’s project is the result of a fruitful collaboration with the Electron Microscopy Unit at the University of Cape Town which adds exciting new approaches to study and target viral entry mechanisms.”Dr Georgia Schäfer, University of Cape Town, South Africa
Human Papillomavirus (HPV) is one of the most commonly diagnosed sexually transmitted viruses worldwide, and infection with high risk types has been linked to several cancer types, most notably cervical cancer, as mentioned above. In Africa, an estimated 372.2 million women aged 15 years and older are at risk of developing cervical cancer; every year, 119,284 women across Africa are diagnosed with cervical cancer and 81,687 women die from the disease, as reported by the HPV Centre report on HPV in Africa, 2019. In my own country of South Africa, cervical cancer is the first most common female cancer in women aged 15 to 44 years and one of the leading causes of cancer related deaths [1-6]. Although HPV vaccinations exist and are safe, these vaccines are only protective to HPV uninfected adolescents, making them ineffective for persons already infected with HPV [7,8].
The vaccines are also relatively expensive and need repeat doses [7,9,10]. This creates a difficult situation for many people, who may not be able to afford repeat treatments or do not have easy access to health care facilities. In addition, rural communities in South Africa are largely unaware of HPV infection as a risk factor for cervical cancer, which has made vaccine distribution ineffective, with little of the South African population vaccinated between 2009 and 2014 . Developing medication to prevent HPV infection by blocking the entry of HPV into susceptible human cells could be an alternative to vaccination, and another opportunity to reduce the amount of HPV associated cancers within South Africa and worldwide.
In our laboratories at the University of Cape Town we have identified two human proteins, surfactant protein A (SP-A) and vimentin, which decrease HPV infection by modulating viral entry into susceptible cells  or by activating the innate immune system, respectively. This research took place in UCT’s Electron Microscope Unit at the Aaron Klug Centre for Imaging and Analysis and Division of Medical Biochemistry and Structural Biology (Institute of Infectious Disease and Molecular Medicine). To determine which portions of these two proteins interact with HPV, electron microscopy imaging and 3D reconstruction studies of HPV particles pre-incubated with each of these two proteins are being conducted. From this, and further biochemical tests, we can determine the relevance of these interactions for HPV infection, with the potential to develop inhibitors for HPV infection of susceptible human cells.
Using Diamond Light Source synchrotron to image our HPV samples
In order to carry out this research access to state-of-the-art imaging equipment is vital. The GCRF START grant has made this possible, by providing our researchers and collaborators with access to the Electron Bio-imaging Centre (eBIC) embedded at Diamond Light Source. My visit to the Diamond synchrotron to conduct experiments for my research took place from the 9 – 11 October 2019. We had done the sample preparation at the University of Cape Town and had shipped the HPV samples in liquid nitrogen to Diamond a few weeks previously, so they were there once we arrived. The HPV samples were loaded onto the Diamond M06 Titan Krios electron microscope with the help of eBIC staff before imaging them using the transmission electron microscopy (TEM) technique.
Unfortunately, there are no equivalent facilities available on the African continent, and only a handful available worldwide, so I feel unbelievably fortunate to have been to Diamond – not just as someone from overseas on a tour but to have the experience as a researcher of working in and around such an innovative environment. The research and the equipment available are cutting edge and incredibly motivating to a young scientist. In addition to this, the scientists and staff are friendly and easy to engage with, and I found myself having conversations with researchers from all fields, not just biology.
Having a central research hub with scientists from different academic backgrounds, such as the materials sciences, biology, physical sciences, chemistry and others, creates a co-operative space and is likely to benefit anyone who participates. Being at Diamond Light Source and the Harwell Campus made me realise that having such a research hub is essential to science, aside from making things easier logistically! It was an incredible experience to be at Diamond Light Source, and I don’t think I could thank everyone involved enough for all the support and guidance along the way.
Most importantly, I would like to thank Dr Jeremy Woodward, who is a GCRF START Co-Investigator – for the time and effort he was willing to put into this project; I really wouldn’t be anywhere without him. I am also grateful to my supervisor, Dr Georgia Schäfer, for her help and encouragement, especially when producing the HPV16 particles at such short notice! I am also grateful to GCRF START Co-Investigator, Prof. Trevor Sewell, and Dr Andani Mulelu (previously a GCRF START-funded Postdoctoral Research Fellow), and to Dr Lubbe (currently a START-funded Postdoctoral Research Assistant); thanks also to Dr Sarron for all the advice and reassurance – which really helps! Lastly, I would like to thank the staff of the Electron Microscopy Unit at the University of Cape Town, especially Mohammed Jaffer, and the eBIC staff – James Gilchrist and Alistair Siebert – all of whom were very cheerful and accommodating when using the different microscopes. I even had a good enough sample for me to travel to Diamond, with the help of my two brilliant supervisors, Dr Georgia Schafer and Dr Jeremy Woodward, without whom, I might have been completely lost!
My science career so far..
I’ve always had an interest in biology, and I was fortunate enough to have parents who encouraged my interest, although they didn’t always know what I was doing! I began my scientific journey by completing a Bachelor of Science at Stellenbosch University (South Africa) in biochemistry and physiology. I then moved to the University of Cape Town for my Honour’s and Masters’ degrees. I was exposed to structural biology during my Honour’s degree, but I was somewhat intimidated by all the physics and maths involved. So, I only became involved in structural biology during the first year of my Master’s degree, at the Biophysics and Structural Biology at Synchrotrons 2019 conference (Cape Town, South Africa). I am currently completing my MSc in Medical Biochemistry and Structural Biology, under the supervision of Dr Georgia Schäfer and Dr Jeremy Woodward, within the Electron Microscopy Unit at UCT.
Click here to read more about the UN’s Sustainable Development Goals
1. Trottier, H. and E.L. Franco, The epidemiology of genital human papillomavirus infection. Vaccine, 2006. 24 Suppl 1: p. S1-15.
2. de Villiers, E.M., et al., Classification of papillomaviruses. Virology, 2004. 324(1): p. 17-27.
3. Chikandiwa, A., et al., Patterns and trends of HPV-related cancers other than cervix in South Africa from 1994-2013. Cancer Epidemiol, 2019. 58: p. 121-129.
4. Munoz, N., et al., Epidemiologic classification of human papillomavirus types associated with cervical cancer. N Engl J Med, 2003. 348(6): p. 518-27.
5. Walboomers, J.M., et al., Human papillomavirus is a necessary cause of invasive cervical cancer worldwide. J Pathol, 1999. 189(1): p. 12-9.
6. Bruni, L., et al., Global estimates of human papillomavirus vaccination coverage by region and income level: a pooled analysis. Lancet Glob Health, 2016. 4(7): p. e453-63.
7. Draper, E., et al., A randomized, observer-blinded immunogenicity trial of Cervarix((R)) and Gardasil((R)) Human Papillomavirus vaccines in 12-15 year old girls. PLoS One, 2013. 8(5): p. e61825.
8. Hildesheim, A., et al., Impact of human papillomavirus (HPV) 16 and 18 vaccination on prevalent infections and rates of cervical lesions after excisional treatment. Am J Obstet
9. Schiller, J.T., et al., An update of prophylactic human papillomavirus L1 virus-like particle vaccine clinical trial results. Vaccine, 2008. 26 Suppl 10: p. K53-61.
10 Biryukov, J. and C. Meyers, Papillomavirus Infectious Pathways: A Comparison of Systems. Viruses, 2015. 7(8): p. 4303-25
11. Phasa.org. Implementation of HPV vaccination in South Africa. 2015; Available from: https://phasa.org.za/2015/02/26/implementation-hpv-vaccination-south-africa/.
12. Schafer, G., et al., Vimentin Modulates Infectious Internalization of Human Papillomavirus 16 Pseudovirions. J Virol, 2017. 91(16).
“The GCRF START grant has been a game-changer for young African scientists, particularly from underrepresented groups such as female, and black scientists, enabling them to enter the field of Structural Biology and thrive. This has been achieved by collaborations from Africa and the UK, outstanding workshops on research techniques, international conferences, symposia hosted in Africa, and the recruitment of African scientific officers and postdoctoral fellows.”Prof. Edward D. Sturrock, University of Cape Town, South Africa.
GCRF START – belonging to a diverse group of African scientists
My name is Lizelle Lubbe and I am a GCRF START Postdoctoral Research Fellow. My field of research is Structural Biology, which is a scarce skill in Africa with only a handful of scientists trained in single particle cryo-EM – a cutting-edge technique for determining the structure of proteins. START provides me with the opportunity to learn from these science pioneers in Africa, as well as from experts in the UK by establishing networks for discussion and organising workshops for hands-on training. Furthermore, GCRF START provides us with the resources to conduct outreach, not only to make science accessible for the community but also to inspire the future generation of scientists. I find it very stimulating to be a part of such a diverse group of scientists who are all working together towards achieving common goals to uplift communities and find solutions to global challenges.
Structural Biology combines concepts of Biology, Chemistry and Physics and therefore can be quite daunting to enter. For example, the design of drugs for the treatment of disease requires one to understand how the disease develops, identify a drug target in this process, use medicinal chemistry to design a small molecule capable of blocking that target, and validate the process using structural techniques. Although this has traditionally been a more male-dominated field, the hardships endured by women in science throughout history have led to ground-breaking discoveries and a paradigm shift, so that today I have the privilege of doing my postdoctoral research using revolutionary techniques like cryo-EM.
As a result of the GCRF START grant, I am funded to do my research which includes associated travel costs for data collection, access to mentoring from experts in their field, and the use of state-of-the-art equipment and facilities such as the UK’s national synchrotron, Diamond Light Source, and the GCRF START Centre for Excellence in the University of Cape Town’s (UCT’s) Aaron Klug Centre for Imaging and Analysis. START has made it possible to gain valuable and much sought-after experience and skills in biophysical and synchrotron techniques.
Improving the health of patients with hypertension and other diseases
My research is focused on a protein called angiotensin-converting enzyme (ACE) which is well-known for its role in blood pressure1 regulation. It is found in many organs throughout the human body where it catalyses a reaction to produce a peptide (string of amino acids) that causes constriction of blood vessels, thereby regulating blood pressure and circulation. In some cases, however, this process goes awry, and the blood pressure becomes elevated, increasing the force of blood against the artery walls. This condition is known as hypertension and typically does not produce any noticeable symptoms.
According to the World Health Organisation, 1.13 billion people suffer from hypertension globally2, with many countries in Africa3 experiencing the highest prevalence of hypertension in the world at 27% (WHO, 2019). Conditions caused by hypertension include stroke, heart failure, heart attack, kidney failure and loss of vision. There are many risk factors to hypertension, and these include family history, increasing age, stress, being overweight/obese, a diet high in salt, smoking tobacco, drinking too much alcohol, and a lack of exercise. Given the important role of ACE in blood pressure regulation, ACE inhibitors are commonly used in the clinic to effectively treat hypertension and heart/kidney disease. The use of ACE inhibitors is unfortunately linked to the development of side effects in some patients. It can be mild (loss of taste, skin rash or persistent dry cough) but also life-threatening in the case of angioedema. Angioedema is a condition where the patient develops severe swelling below the skin surface which can affect the throat, tongue and lips and obstruct the airway.
I am motivated by the potential of the research we are doing to improve the lives of patients living with hypertension and other diseases associated with ACE by increasing our understanding of the disease-causing protein. This would ultimately allow us to design ACE inhibitors with less side-effects. It is also very exciting to learn structural biology techniques such as cryo-EM and to help establish this expertise in Africa for the benefit of our community. By gaining valuable experience in the scarce field of Structural Biology, I hope to strengthen research in Africa and motivate others towards a career in science.
Inspired into biochemistry – persistence pays off!
The motivation I describe above started at a young age, and I was greatly inspired by my parents who both studied science – my mother studied Microbiology and my father, Mechanical Engineering. I grew up on a small farm outside Pretoria in the Gauteng province of South Africa and have been interested in the mechanism of action of therapeutic drugs from a young age. Opportunities for women in science were scarce in the early 1990’s and my mother could unfortunately no longer pursue her career after my birth. Her interest in the world of microorganisms remained, however, and inspired me to enter the field of Biochemistry where one could not only study microorganisms and other factors in relation to disease but also design therapies.
I had very limited hands-on exposure to science at the farm school I attended. My siblings and I spent many afternoons in the community library and at some point, I started reading encyclopaedias and became fascinated with science. After that, I saved some money and bought myself a second-hand toy light-microscope which occupied me for hours. However, these years were not without hardship. After obtaining his degree in Mechanical Engineering, my father single-handedly established a small business and it was very challenging to secure an income, so we were often left without certain essentials. Our school tuition was funded by government subsidies and as we could not afford private healthcare, I spent many school days in long queues since before the crack of dawn at the local District Hospital.
During my final year at high school (matric), the Physical Sciences teacher told me about the field of Biochemistry and although my parents could not afford to pay for my tertiary education, I was determined to obtain a degree and arranged to get a student loan. Persistence paid off and I obtained my undergraduate Bachelor of Science (BSc) degree at the University of Pretoria majoring in Biochemistry and Chemistry in 2011.
Great mentors – learning key Structural Biology techniques from GCRF START experts
These challenges and hardships only cemented my determination to continue in the field I am passionate about and having experienced mentors has really helped. My PhD at the University of Cape Town was supervised and co-supervised by Prof. Ed Sturrock and Prof. Trevor Sewell, respectively. They are both Co-Investigators on the GCRF START grant and, after finalising my PhD thesis, Prof. Sturrock offered me a GCRF START Postdoctoral Fellowship on a related research project in his laboratory. I started as a GCRF START postdoc in October 2018 and, in October 2019, I travelled to the UK to the Harwell Campus, and collected a dataset of ACE at the Electron Bio-Imaging Centre (eBIC) at Diamond Light Source using a Titan Krios transmission electron microscope with K3 detector. I am in the data analysis stage right now.
Professor Sturrock4 is a leader in the design of anti-hypertensive drugs and was an excellent mentor during my BSc (Med)(Hons) in Medical Biochemistry (completed in 2012) and PhD in Chemical Biology (completed in 2018) studies. He has taught me how to think critically about the problem at hand and to persevere despite the numerous setbacks one experiences as a scientist. For example, Structural Biology techniques such as X-ray crystallography, molecular dynamics (MD) simulations and cryo-electron microscopy (cryo-EM) are key to understanding proteins involved in disease and how to target them.
However, because advanced Mathematics or Physics modules were not included in my undergraduate training, it was really difficult for me to learn the theoretical aspects of these techniques and how it is applied in practice. I am therefore very grateful for the START project which has given me the opportunity to learn from experts in the field of Structural Biology – experts such as Dr Jeremy Woodward and Prof.Trevor Sewell from the UCT Aaron Klug Centre for Imaging and Analysis. A further challenge throughout my PhD was my limited background in Computational Science. The computer skills I learned from high school were very elementary which meant a particularly steep learning curve when I decided to use MD simulations to answer key research questions.
Studying ACE for the future design of ACE inhibitors
ACE is a dumbbell-shaped protein comprised of two domains (the N- and C-domain) which perform diverse physiological functions: the C-domain is mainly responsible for blood pressure regulation while the N-domain is important for regulating scar tissue formation. The main focus of Prof. Sturrock’s research is to design inhibitors that selectively bind to the N- or C-domain. Selectivity is very important since the side-effects associated with current ACE inhibitors are due to equal inhibition of both domains. At the end of my BSc (Med)(Hons) year, Prof. Sturrock (in collaboration with Prof. Kelly Chibale at UCT) discovered a molecule (33RE) which binds with 1000-times greater affinity to the N-domain than the C-domain of ACE5. N-selective ACE inhibitors are antifibrotic and as such, show potential for the treatment of fibrosis (excessive scar tissue formation). X-ray crystallography was used to study the binding of 33RE to the N-domain but the reason for its selectivity remained a mystery. One limitation of this technique is that it only gives you a static ‘snapshot’ of the protein’s structure while proteins are naturally very dynamic when in solution (as in the body).
For my PhD research, I therefore decided to study ACE using MD simulations. In this technique, the atoms in the crystal structure are allowed to move which can provide more insight into how the drug interacts with the protein. My results were really interesting and showed that subtle amino acid differences between the two domains caused drastic changes in their dynamics and thereby, their affinity for 33RE6.
GCRF START ensures the continuation of postdoctoral research
As a GCRF START postdoc, I am continuing this research in collaboration with Prof. K Ravi Acharya7 at the University of Bath and we have recently discovered that these differences in dynamics also affect the binding and selectivity of ACE inhibitors from different classes8 9. This has great implications for the future design of ACE inhibitors and emphasizes the importance of using a range of biophysical techniques when studying proteins. The workshops funded by the GCRF START grant has equipped me with valuable skills and I am very excited to discover even more insight into the workings of ACE by applying these skills.
The biggest challenge on my road to becoming a scientist has been financing ten years of tertiary study. Although I was fortunate enough to receive merit and government bursaries to fund my PhD, I am still paying off the student loan from my undergraduate and honours years. Therefore, funding through the GCRF START grant has been invaluable, ensuring the continuation of my postdoctoral research.
Commenting on Lizelle’s achievements and the impact of the GCRF START grant on emerging African scientists like Lizelle, Prof. Ed Sturrock said,
“The GCRF START grant has had a significant impact on Lizelle’s career development, career opportunities and personal growth. Her progress with a very challenging research project and her involvement in other GCRF START activities, such as the START outreach project to uplift the community and promote science through art, bear testament to this. I have been enormously impressed by what Lizelle has achieved as a START postdoctoral research fellow in a relatively short period of time.”
Read more about Hypertension here.
Read more about the UN’s Sustainable Development Goal 3 for Health and Wellbeing here.
I am very grateful to Mrs Sylva L. U. Schwager (Chief Scientific Officer in Prof. Sturrock’s laboratory at the University of Cape Town) for her guidance and assistance with key experiments during my postgraduate and postdoctoral years.
- Cozier, G.E., Lubbe, L.*, Sturrock, E.D., Acharya, K.R. ACE-domain selectivity extends beyond direct interacting residues at the active site. Biochem J 477 (7), 1241–1259 (2020) https://doi.org/10.1042/BCJ20200060
- Sturrock, E.D., Lubbe, L., Cozier, G.E., Schwager, S.L.U., Arowolo, A.T., Arendse, L.B., Belcher, E., Acharya, K.R. Structural basis for the C-domain-selective angiotensin-converting enzyme inhibition by bradykinin-potentiating peptide b (BPPb). Biochem J 476 (10), 1553–1570 (2019) https://doi.org/10.1042/BCJ20190290
 Hypertension, also known as high or raised blood pressure, is a condition in which the blood vessels have persistently raised pressure. For more information: https://www.who.int/health-topics/hypertension/#tab=tab_1
“The GCRF START grant has initiated a beautiful story and this story involves developing African scientists, especially in terms of Synchrotron Radiation Technology and Research. We hope to continue this highly fruitful collaboration for many years to come.”Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand
I love teaching and research, especially contributing towards human development through innovative research in medicine and biology. My research focuses on the Biochemistry and Structural Biology of druggable proteins of human Neglected Tropical Diseases (NTD’s) and ESKAPE pathogens (Healthcare Acquired Infections) at the University of the Witwatersrand’s Protein Structure-Function Research Unit (PSFRU). I owe my motivation for biochemistry to very good teachers and mentors from an early point in my education.
I was educated to undergraduate level in biochemistry at Nigeria’s Abia State University, Uturu, Abia State and as an undergraduate, found pleasure in being taught by biochemistry lecturers who were able to ‘self-de-elevate’ and inspire us. These teachers were easy to have rapport with and I was able to extract as much as they could offer, both as my teachers, as well as my mentors and motivators. I remember Dr Okechukwu Ukairo, a young and admirable biochemistry lecturer who taught us carbohydrate metabolism and bioenergetics. His persona as a biochemistry lecturer and researcher enabled him to de-mystify what was a difficult course in biochemistry by being down to earth, but not to be trampled upon!
Subsequently, I spent four years in Lesotho as an educator, teaching in secondary schools after briefly working as an analytical chemist at Lesotho Pharmaceuticals in Mafeteng. My desire to do my Master’s in Biochemistry was fulfilled, however, at the University of KwaZulu-Natal in Durban, South Africa, where I gained my PhD in 2008. Working with Prof Heini Dirr at Wits University (March 2009) strengthened my aspiration in Structural Biology and three years later, I joined The University of the Witwatersrand. Currently, I am a Senior Researcher and the Interim South African Research Chair (SARChI) in Protein Biochemistry and Structural Biology.
When I look back at my career journey so far, it was the experience of having inspiring teachers and mentors that stayed with me to the present day and drives my vision as head of my group in teaching, supervising and mentoring the students on my watch. Therefore, the GCRF START grant with its emphasis on equipping and mentoring the next generation of scientists in Africa to tackle local and global challenges, means everything to me, especially in terms of structural biology.
African scientists have a critical role to play in the search to solve Africa’s challenges
“My vision is to see young people rise-up and flourish in the sciences on the African continent and apply the African, UK and global perspectives we share in the GCRF START network to the global challenges we face.” – Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand
With the START grant I believe we can create a new narrative of excellence in African science and structural biology and fulfil our vision to equip our students in the latest techniques to solve our continent’s health, energy and socio-economic challenges. For example, at the PSRU, we have many gifted post-docs and undergraduates with the potential to go far and make a positive difference on our continent and beyond. I supervise 12 students (four PhD and seven MSc. students, and one Post-Doctoral Fellow), some of whom already benefit from the exposure to state-of-the-art synchrotron techniques at the UK’s national synchrotron – Diamond Light Source (Diamond) – as a result of the GCRF START grant. Often from previously disadvantaged backgrounds and female, these students have attended START funded workshops, have collected data remotely, and are being trained by scientists from the Diamond beamlines. They would love to one day visit Diamond to see a synchrotron for themselves and want to develop careers in structural biology and biochemistry.
Our dream is that each university in South Africa and beyond our borders will have new generation structural biology, synchrotron and drug discovery techniques taking place as a matter of course. In South Africa, our vision is to include lesser known universities like Venda, Fort Hare, and Johannesburg ensuring that those previously unable to access to opportunities will be able to do so. Already, in just over two years, the START network has grown in South Africa to encompass a wide range of university groups/hubs covering a broad variety of research disciplines to address challenges across Africa, as well as globally.
Take viruses like COVID-19, for example, we have every potential to be able to produce the targeted, appropriate vaccines and drugs needed for our unique situations. Instead of researchers from Europe and America coming to us to collect samples to take over to Europe/America to do their studies, we could be on an equal footing and able to do every stage of the research right here in Africa so that we are well prepared for outbreaks when they occur.
In terms of our journey at the PSFRU, the GCRF START grant and Diamond Light Source came at the right time for our group, and for me personally. When I got involved with START in 2018, most of my protein crystal structures were solved in-house using a home-source XRD Wits University commissioned in 2008. However, over the years, the life of the machine started depreciating and we had to look for an alternative light source. Prof. Yasien Sayed, Director of the PSFRU, was contacted by START Co-I, Prof. Trevor Sewell, from the University of Cape Town to champion the University of the Witwatersrand’s Structural Biology collaboration with Diamond as part of the South African broader collaboration with the facility, and because Prof. Sayed and I work in the same research unit, he involved my research in his application.
The common denominator is science!
“I know some people say that the priorities in Africa are all about hunger, and that doing scientific research is not a priority but if you look at all the challenges here, the common denominator is science!” – Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand
We can’t do without the science and the latest scientific equipment in terms of tackling Africa’s sustainable development goals. Take hunger and the goal of food security, for example. We need drought resistant crops and pest resistance; we need clean water sources and uncontaminated land; we need disease solutions for the animals and a healthy variety of nutritional and affordable crops; we need people who are sufficiently healthy to grow the food, distribute, manufacture and sell it. Indeed, some of the pathogens I am working on right now, such as Schistosomiasis (Bilharzia), affect a prime source of food security on our continent – cattle. The poultry industry is another example where multiple pathogens kill the poultry which people rely on for food. Therefore, investing in science in Africa is imperative for the health of our continent and the world.
However, sustainable sources of funding are needed to conduct world class science. Even in terms of small things like shipping samples, it costs over 3500 Rand (£160.00) each time we ship our protein crystals to and from Diamond. This would be prohibitive for many science groups if it were not for grants like GCRF START. The fact that START grant enables us to do the experiments remotely at Diamond, means we can save money – we don’t have to fly abroad to conduct our experiments and we speak the same language so there are no ‘lost in translation’ issues!
To demonstrate some of the diverse and world class science research we do at the PSFRU I have outlined three examples below, which benefit from the GCRF START grant.
Exploring language and cognition: untangling the neuromolecular networks in the brain
Dr Sylvia Fanucchi’s research looks in detail at a particular node of interaction that is implicated in Autism. This involves investigating the FOXP family of transcription factors which are associated with language and cognition. Her studies aim at untangling the neuromolecular networks in the brain by identifying the nodes of interactions associated with these proteins. In order to do this, Dr Fanucchi explores protein-protein interactions and protein-nucleic acid interactions and how they influence each other in these large neuromolecular complexes. Through the GCRF START grant using the Diamond synchrotron, Dr Fanucchi can investigate the structures of both protein-DNA and protein-protein complexes. This information is highly valuable in dissecting the interactions within these neuromolecular complexes at atomic resolution and is critical to answering the questions posed by Dr Fanucchi in her research.
New insights into the South African HIV-1 subtype C protease
Another example of success is Prof. Yasien Sayed’s research on the HIV C protease1 – the strain of the HIV virus we have in South Africa, whereby Prof Sayed and his team are the first to solve the type C protease at unparalleled resolution. This is a significant success (pending publication) which has been made possible with access synchrotron techniques at Diamond with the GCRF START grant2. This paves the way to repurpose AntiRetrovirals (ARV’s) that are tailor-made for the type of HIV we have here in South Africa so that in years to come, HIV prevention and treatment can be far more effective than they are now. Currently, the ARV’s employed here in South Africa are not tailored specifically for our strain of the HIV virus, which means that the side effects are more than they should be (leading to problems with ARV adherence) and drug resistance.
Schistosomiasis/Bilharzia – solving the 3D structure of the Schistosoma japonicum Glutathione S-transferase (GST ) protein
“Access to facilities at Diamond has enabled young and emerging researchers, such as Dr. Achilonu in my Unit to realise their potential by publishing their research in internationally peer-reviewed journals.” –Prof. Yasien Sayed, Director of the Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand, South Africa
There are several milestones yet to be reached but my journey with the GCRF START grant is already yielding fruitful outcomes for Africa. My publication3 titled “Molecular basis of inhibition of Schistosoma japonicum glutathione transferase by ellagic acid: insights into biophysical and structural studies” is one of those milestones achieved over the past three years. Using I03 & I04 beamlines at Diamond, we were recently able to solve the 3D structure of the Schistosoma japonicum GST protein at an unprecedented resolution of 1.53 Å- amongst the highest resolution in the current global protein database for this enzyme!
The resulting publication emphasises the need to exploit the unique structural diversity between Schistosoma GST and other human GSTs for a rational approach to design new generation anthelminthics. Without the high-resolution structure of the Schistosoma GST-in-complex with the potential natural product (Ellagic Acid) – which we aim to study for the design of new anti-Schistosoma drugs – it would have been difficult understanding several empirical observations made in our research. Achieving these results means we can now progress further to find effective drug targets, something only possible to the level we need using synchrotron techniques. I am very grateful to the GCRF START grant and Diamond for this opportunity.
Our vision to collaborate with groups in other African countries is also progressing. One such group is a medical research institute working on Schistosoma in Kenya with whom we hope to have a collaboration up and running by early next year. Now that we have new insights afforded by the solved structure of the Schistosoma japonicum GST protein, we need to know that the drug target we are investigating is active against an entire parasite – either as a parasite on its own or in an animal. A collaboration with the Kenyan group offers exciting opportunities to explore this. I also have students from Nigeria, Zimbabwe and Namibia who will be joining us next year; and one from India, therefore our group is truly pushing the boundaries geographically as well as scientifically!
Towards an African Light Source
For many, the ultimate vision is having an African Synchrotron Light Source on the African continent. However, it may take years before this is possible and therefore, in the meantime, the START grant enables us to move closer to fulfilling our vision to inspire creative and collaborative scientific research and equip the next generation of scientists in structural biology (and energy materials) to use synchrotron equipment and techniques. I pray and hope that GCRF START and Diamond continue this incredible journey with us, long into the future.
Read more here about the UN’s Sustainable Development Goals.
More about Dr Achilonu
Dr Ikechukwu Anthony Achilonu is Senior Researcher and the Interim South African Research Chair (NRF/SARChI) in Protein Biochemistry and Structural Biology at the Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand in South Africa.
“Africa is a bank when it comes to diseases. The beauty of the GCRF START grant is that it offers us the opportunity to deal with these challenges in Africa, while enabling international collaboration and access to amazing synchrotron facilities with world class results.”Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand, South Africa
Neglected Tropical Diseases (NTD’s) and Antimicrobial Resistance (AMR) are major challenges threatening the world’s sustainability and development efforts across the spectrum of the UN’s Sustainable Development Goals, causing millions of deaths each year1. My name is Dr Ikechukwu Achilonu and I work in the PSFRU at the University of the Witwatersrand, in South Africa, where I focus on rational design and discovery of new generation anthelminthic and anti-bacterial drug targets to tackle NTD’s and Nosocomial infections by ESKAPE2 pathogens.
To design inhibitors to serve as potential drugs against these pathogens, high-resolution 3D protein structures are needed to test the ability of certain drugs to interact with and inhibit the properties of the proteins being studied. This is made possible with the GCRF START grant which provides us with access to state-of-the-art synchrotron techniques, equipment and expertise at the UK’s world class national synchrotron, Diamond Light Source (Diamond), enabling the X-ray diffraction from protein crystals generated in our research. The GCRF START grant is currently our only conduit to the UK to enable us to conduct these ultra-high-quality experiments.
My recent research success is solving the Schistosomiasis joponicum Glutathione S-transferase (GST) enzyme has been recently published and is a tribute to the value of collaborating with Diamond and GCRF START. The solved structure is among the crystal structures with the highest resolution in the global protein database for this enzyme with two different ligands. Of the authors, Dr Ramesh Pandian is a GCRF START postdoctoral fellow (Host: Prof. Yasian Sayed), and Dr Sylvia Fanucchi, Prof. Yasien Sayed, Prof. Heine W. Dirr, and I – Dr Ikechukwu Achilonu – are collaborators on the GCRF START grant.
The resulting publication emphasises the need to exploit the unique structural diversity between Schistosoma GST and other human GSTs for a rational approach to design new generation anthelminthics. This research, outlined later in this article, will pave the way for the next exciting step in the structural validation of druggable targets for this debilitating and life-threatening Schistosomiasis (Bilharzia), a NTD which infects large numbers of people across several countries each year4.
The extent of the challenge: NTD’s and ESKAPE pathogens
AMR is described by the World Health Organization5 as “one of the biggest threats to global health, food security, and development today…compromising our ability to treat infectious diseases, as well as undermining many other advances in health and medicine.”
NTD’s are a diverse group of communicable diseases caused by a variety of pathogens prevalent in tropical and subtropical conditions, such as viruses, bacteria, protozoa and parasitic worms (helminths). More than a billion people in over 149 countries are impacted by NTD’s with huge costs to developing economies of billions of US dollars every year. My research on NTD’s focuses on Schistosoma and Wuchereria (Wuchereria is a human parasitic worm (Filariworm) that is the major cause of lymphatic filariasis) – both of which display AMR. Populations living in poverty, without adequate sanitation and in close contact with infectious vectors and domestic animals and livestock, are those worst affected by NTD’s6.
The six nosocomial ESKAPE pathogens that exhibit multidrug resistance and virulence are often acquired in health care settings like hospitals (Health Care Acquired Infection/HAI) and feature on the World Health Organization’s ‘Priority Pathogens list’7. The persistent use of antibiotics has provoked the emergence of multidrug resistant (MDR) and extensively drug resistant (XDR) bacteria, which can make even the most effective drugs ineffective. These bacteria have built-in abilities to find new ways to become resistant and can pass on genetic materials which enable other bacteria to become drug resistant. Like NTD’s, this situation is made worse by limited or non-existent infection prevention and control (IPC) programmes, combined with an inadequate water supply, poor sanitation, and a weak hygiene infrastructure in health facilities, which make the burden of HAI several fold higher in low- and middle-income countries than in high-income ones.
World class results! Solving the Schistosomiasis japonicum GST enzyme
Over the past three years, I have been working on the Schistosoma GST enzyme, which is a protein that is involved in detoxification of foreign molecules in the Schistosome parasite that causes the disease Schistosomiasis/Bilharzia. This enzyme very critical to the survival of the parasite. If the enzyme is not functioning properly, the parasite cannot move from egg stage to lava stage. Therefore, if the enzyme could be effectively inhibited, one would have a drug against the parasite.
In my research, I used a molecule which is a natural product found in pomegranate juice called Ellagic Acid. One of my MSc. students, Ms Blessing Akumadu, carried out the study I had conceptualised, showing that this molecule can inhibit the activity of the Schistosoma GST by 66%. The concept was based on an earlier study that ellagic acid and its derivative inhibits Plasmodium GST (duly acknowledged in the forthcoming paper). To be more confident about making extrapolations from the structure of the Schistosoma japonicum GST enzyme, we needed to see that our wet lab results had meaning in 3D high resolution. Using the I038 and I04 beamlines at Diamond, we were able to solve the structure of the 26 kilodalton GST at 1.53 Å resolution and were amazed when we saw the results! We had achieved the highest resolution of any of the several variants of the Schistosoma japonicum GST in the global protein database!
What we observed is the Schistosoma 26 kilodalton GST enzyme (Sj26GST), which is a dimeric protein (it has two similar subunits joined together) with an interface where the subunits are joined. The unique thing about this protein is that the dimer interface can be exploited for drug interaction, unlike other GST’s in humans. The results have enabled us to see where the Ellagic Acid molecule (the potential drug) can bind to the protein. In this parasite we only have two classes of GSTs (in humans there are several) – the 26 kilodalton (kDa) GST and the 28 kDa GST. Having studied the 26 kDa GST, we are now currently working on the 28 kDa GST across the three species of the Schistosoma parasite that infect humans (mansoni, haematobium and japonicum) to see if the Ellagic Acid molecule can also inhibit the 28 kDa GST of the Schistosoma parasite.
The implications of these results mean we can go on and redesign this potential drug molecule because we can see the type of interaction this drug is making with the protein in the 3D images. The more the drug interacts, the stronger the binding. Therefore, we can start to redesign this drug for better binding so that the binding and the efficiency is improved beyond the 66% to maybe 75% or even to 99 % in order to completely shut down the activity of the enzyme at a very low amounts of the drug. Without the high-resolution 3D crystal structure solved using Diamond, we could not do this. We can now exploit this interaction by adding a bond here or a functional group there to improve the strength of the interaction and potency of the drug, and produce new high resolution structures until we have a drug that shuts down the enzyme and produces a new drug target to which the Schistosoma parasite is not resistant to.
The benefit of studying multiple NTD and ESKAPE pathogens simultaneously – the case of nicotinamide adenine transferase enzyme in klebsiella pneumonia and Enterococcus faecium.
In my experience, the techniques one applies to studying one protein can also be applied to the others, which is why I study a range of druggable proteins from several human NTD and ESKAPE pathogens simultaneously. For example, my students and I are examining the nicotinate-nucleotide adenylyltransferaseenzyme which is important in the redox metabolism in both klebsiella pneumonia and Enterococcus faecium. Klebsiella pneumonia is a Gram-negative bacterium resistant to multiple drugs and increasingly resistant to most available antibiotics (it has a thin cell wall surrounded by a protective cell membrane which makes it harder for antibodies to penetrate). In health care settings, patients who require devices like ventilators or intravenous catheters, and patients who are taking long courses of certain antibiotics are most at risk for Klebsiella infections.
The Gram-positive Enterococcus faecium is a human pathogen that causes nosocomial bacteremia, surgical wound infection, endocarditis, and urinary tract infections (it has thick cell walls but no outer membrane). Studying both simultaneously has led to us noticing that the Gram-negative function of the nicotinamide adenine transferase enzyme performs differently from the Gram-positive function of the same enzyme which is exciting because this enables us to infer structural and functional differences between this enzymes from different bacteria that are supposed to perform similar activities in these bacterial pathogens. This has serious implication in the design of a broad-spectrum antibiotics that will target this enzyme in different organisms.
The process of solving protein structures – systematic integration of multi-facted ‘new generation’ theoretical and empirical studies
The approaches we use in the research outlined above are multi-faceted and multi-disciplinary involving the integration of sophisticated ‘new generation’ theoretical and empirical studies and, as already indicated, a range of cutting-edge equipment. To design drugs against disease pathogens, the three-dimensional architecture of the druggable protein is needed. Druggable proteins are proteins that are key to the survival of the pathogen which enables it to replicate inside the human host, either intracellularly or extracellularly. In the case of bacteria, for example, they need to manufacture their own energy and without the enzyme (protein) that makes this possible, the bacteria would not survive. Therefore, if we know the protein’s DNA sequence, we should be able to predict that we can synthesis this protein and develop the druggable target.
To elucidate the crystal structure of these druggable proteins it is possible to use home X-ray sources. Ultimately, however, there is a major advantage of using a powerful synchrotron light source like Diamond over most home X-ray sources because the amount of inferences made from a protein crystal with resolutions in the range of 1.3 – 1.7 Å is unprecedented. Such crystals can be further studied using computational algorithms and can also serve as models for replacement when solving the crystal structure of a protein that is very similar in structure.
In order to generate the recombinant proteins that are druggable targets, we need large amounts of these proteins. For this we use E. coli bacteria like a factory to synthesize our target proteins and carry out a rigorous ‘quality assurance’ process to ensure the proteins we make are pure, stable and homogenous for successful crystallisation experiments. If the protein is an enzyme, it should be able to catalyze the same function it does naturally in an organism (in vivo), inside a test tube (in vitro), which means that whatever we send off to Diamond for X-ray diffraction experiments, we need to be sure that the biological function is intact. To do this, the proteins are assayed (measured) for catalytic activity in vitro (if they are enzymes) and are further characterised using several biophysical techniques to test their structure and the function to the point we are satisfied that the proteins are active, properly folded and can perform the function they are supposed to perform properly (biological activity is maintained).
We purify the proteins to homogeneity using an ensemble of protein chromatography techniques. For ‘quality assurance’, we check the secondary structure content (Far-UV circular dichroism), the tertiary structure (intrinsic and extrinsic fluorescence spectroscopy); and the quaternary structure (using size exclusion HPLC). Every physical interaction between two biomolecules generates heat or absorbs heat as part of the function of the protein to interact with another molecule (molecular recognition). Therefore, to estimate the thermodynamics of protein-ligand interaction (interaction ability), we use isothermal titration calorimetry.
Once we are satisfied that the proteins are of good quality and quantity, we begin protein crystallisation. I like to use the analogy that structural biologists are akin to photographers and using X-ray diffraction is like taking a snapshot of the protein which has been forced to assemble as repeating units in a crystalline form. There are several approaches we use. We can either conduct crystallisation manually, or we can do it robotically using our in-house Douglas Instrument Oryx 8 crystallography robot for high throughput protein crystallisation.
To solve the protein structure – sometimes in complex with potential drugs – X-ray light is invaluable. However, X-rays have very short wavelengths and if you keep bombarding a protein crystal with X-rays, it will heat it up and gradually fall apart because of X-ray damage. By changing the protein from solution to a crystal, and then embedding it in a liquid able to resist the intense bombardment of X-ray (cryo-protection) by freezing it at the temperature of liquid nitrogen (-196 degrees Celsius), the sample stays stable and the X-rays will last 100x longer in the X-ray beam! Our crystal samples are therefore sent to Diamond in special containers which keep the samples crystals frozen. GCRF START makes it very easy to ship our crystals to the UK without lots of red tape. We use DHL and we have an easy system which means it only takes a few days to get to Diamond ready for the experiments; the GCRF START grant helps this process at no cost to us.
We can use an X-ray diffractometer such as a small in-house diffractometer to solve the protein structure, or the ultimate technique for X-ray crystallography – a massive synchrotron like Diamond! Diamond’s I03 and I04 beamlines are used to fire X-rays onto our crystal samples. The X-ray will be scattered based on the structure of the protein/molecule (X-ray diffraction). Then, using mathematical modelling and other techniques, the 3D structure of the protein is resolved, either on its own or in a complex with a drug or other biomolecules such as DNA.
My theoretical (computational) studies involve several molecular modelling techniques to model the atomistic behaviour of our proteins of interest, especially how the dynamics of these proteins are altered upon drug binding. We also screen various in silico (virtual) libraries (including PubChem, ZINC and Drug Bank databases) for potential hits that we further extend to the theoretical studies, including high-throughput virtual screening, induced-fit ligand docking, molecular dynamic simulation and free binding energy calculations.
Sometimes, however, the process provides a few surprises, which was the case in our journey to solving the structure of the Schistosoma japonicum GST enzyme. We usually send our crystals to Diamond at the same time as the other groups in South Africa because we have the same slots for data collection. Two weeks before we were supposed to ship our crystals, we found that none were ready yet to ship. This wasn’t good. Therefore, to hurry things along, I asked one of my MSc students, Jessica Olfsen, who knows the crystallization robot very well to generate the crystals we needed within one week. This she did, but they were very ugly looking crystals! I did not think we would get any data out of these crystals but at least we had crystals to send. I so doubted their usefulness that when I collected the data, I didn’t even want to look at it, let alone solve the protein structure. In my disappointment I asked one of our new post-docs (Dr Pandian) who needed a task to look at it. The resulting 3D high resolution structure blew him away! When we both looked at it, we saw just how beautiful it was. I had written the paper already, but it had needed more experimental data for publishing so now I had it! The structure was solved at unprecedented resolution and the paper was accepted for publishing.
As a structural biologist, drug discovery and protein biochemistry are completely intertwined and multidisciplinary in the sense that I cannot do without a synthetic chemist (organic chemist). These are the people who will synthesize the drug. For example, once we add the extra functional groups, it will improve the binding capacity of the drug. The synthetic chemist will then go into the laboratory, resynthesize the drug before I will return to my lab and see if the inhibition improves. When an improvement in the inhibition is apparent, we go through the whole process again: recrystallize the protein with the proposed drug, and then use Diamond again to produce another high-resolution 3D structure of the re-modelled drug molecule and protein interaction.
“This whole drug discovery process can take some time, so it is vital that we have access to world class synchrotron facility like Diamond for the lifetime of this research we until we have the results needed to tackle the NTD’s and ESKAPE pathogens which impact countless lives.”Dr Ikechukwu Anthony Achilonu, Protein Structure-Function Research Unit (PSFRU), University of the Witwatersrand, South Africa
Read more here about the UN’s Sustainable Development Goals.
More about Dr Achilonu
Dr Ikechukwu Anthony Achilonu is Senior Researcher and the Interim South African Research Chair (NRF/SARChI) in Protein Biochemistry and Structural Biology at the Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand in South Africa.
 Transforming our world: the 2030 Agenda for Sustainable Development – A/RES/70/1. New York, USA: United Nations; 2015.
 ESKAPE is an acronym for the group of bacteria, encompassing both Gram-positive and Gram-negative species, made up of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species.
 Authors: Blessing O. Akumadu, Ramesh Pandian, Jessica Olfsen, Roland Worth, Monare Thulo, Tshireletso Mentor, Sylvia Fanucchi, Yasien Sayed, Heini W. Dirr, Ikechukwu Achilonu. Title: Molecular basis of inhibition of Schistosoma japonicum glutathione transferase by ellagic acid: insights into biophysical and structural studies. Publication: Molecular and Biochemical Parasitology (2020);Elsevier. https://doi.org/10.1016/j.molbiopara.2020.111319
 World Health Organization Global action plan on AntiMicrobial Resistance (AMR). Geneva: World Health Organization; 2015. https://www.who.int/antimicrobial-resistance/global-action-plan/en/
Cape Town, 16-17 December 2019
A warm South African welcome and stunning Cape Town backdrop greeted the 20 participants of the GCRF START Energy Materials Workshop, which was funded by GCRF START. The event took place from the 16-17 December 2019 and was hosted by the Catalysis Institute and c*change (DSI-NRF Centre of Excellence in Catalysis) at the University of Cape Town in South Africa.
The event kicked off with an introductory dinner at the stunning Steenberg Farm. Nationalities from Swaziland and South Africa through to the UK and Germany were represented. The Post-docs (PDRA’s), MSc. and PhD students, University lecturers, Principal Investigators (PI’s) and Co-Investigators (Co-I’s), Communications and grant staff hailed from the University of Cape Town’s Catalysis Institute (SA), University of the Witwatersrand (SA) Diamond Light Source (UK), the ISIS Neutron Source (UK), the University of Oxford (UK), Cardiff Catalysis Institute, Cardiff University (UK), the University of Southampton (UK), University of Sheffield (UK), The African Neutron and Synchrotron Data Analysis Competency (ANSDAC), and the DST-NRF Centre of Excellence in Catalysis – c*change (SA).
Tours of the Centre for Catalysis were given by Professor Claeys showcasing the excellent laboratory facilities and equipment available for use. GCRF START project Investigators and PDRA’s presented research covering topics including:
- Photo Voltaic’s – PV, batteries, fuel cells, solar cells
- Organic solar cells and Microstructures
- Organic semiconductors
- Global optimisation of Cu clusters
- Catalysis (controlling nanomaterials and structures)
- CO2 hydrogenation
- X-ray Spectroscopy
Presentations by Nico Fischer at ANSDAC, Michael Claeys from c*Change, and Daniel Bowron from the ISIS Neutron Source, provided insights into the collaboration opportunities through GCRF START.
Passing the mid-point of the GCRF grant is a good time to reflect on what has been achieved thus far, and is a useful time to plan ahead – both within the time of the remaining grant and how to continue the momentum into the future. With established PI’s, Co-I’s, and Post-docs attending the workshop, there was ample opportunity to share ideas for a potential GCRF START phase II, and to agree a vision and strategy for forging new ways to collaborate on the African continent in keeping with the UN Sustainable Development Goals and Pan-African 50-year mission – AGENDA 2063.
In particular, the discussion considered ways to facilitate beamtime applications within Energy Materials research. Access to Diamond can either be through an individual proposal, or through a ‘Block Allocation Group’ (BAG). GCRF START is an excellent vehicle to bring together a BAG for Energy Materials research, which also increases the networking between scientists. Indeed, there is already a successful BAG access in Structural Biology. In addition, beamlines with robotic support allow for remote access, meaning scientists can take control of the beamline without having to travel thousands of miles to take part.
Another key point was how to increase the amount of outreach activity we do to further the impact of the grant and help foster an enthusiasm for salient science within the local population. There are already many examples of excellent practice from individuals and institutions within the grant network such as SciArt with local crafters from the Keiskamma Art Project, as well as outreach to schools and graduates through to government ministers.
Finally, the network has grown for the grant to further increase its scope, expanding to include more researchers, institutions and organisations. There is a great opportunity to be had in teaching more about applying synchrotron science to a wider pool of researchers who may find that using the powerful X-ray beams and laboratory equipment available through GCRF START collaborators can enhance their current work and skills set.
An important aspect of all START events is networking and knowledge sharing, and participants took full advantage of the time available between presentations at coffee breaks and mealtimes to share their experiences and cement collaborations. At the end of the event, a traditional South African ‘Braai’ (Barbeque) in the grounds of the University of Cape Town aptly rounded off a thoroughly enjoyable and fruitful workshop. Interviews, photos and videos captured the buzz of the workshop to be used to share more of START’s ongoing work, achievements and impact with our current and potential stakeholders.
Photo Credit Rebekka Stredwick, ©Diamond Light Source
Across the continent, GCRF START is working with Africa to support the Pan-African 50-year mission: AGENDA 2063 .
Click here for more information about the UN’s Sustainable Development Goal for Energy.