Importance of interactions between ACE2 and variants of SARS-CoV-2 spike protein

“The successful expression, purification, and characterisation of ACE2 and SARS-CoV-2 spike RBD was a huge milestone.”

Sedzani Mbedzi, University of Cape Town, South Africa

The problem

The disease caused by a novel SARS corona virus (SARS-CoV-2) is a global health threat associated with high mortality rates and increased length of stay in hospital for patients with underlying comorbidities such as hypertension, obesity, and diabetes1. SARS-CoV-2 uses the metalloprotease ACE2 as its receptor, like SARS-CoV-1, but with higher binding affinity, which may account for its increased transmissibility2. Mutations in the spike protein of SARS-CoV-2 introduce novel variants of COVID-19. A new lineage of SARS-CoV-2 (501Y.V2; also known as B.1.351 or 20H) that has eight mutations in the spike protein and is associated with increased transmissibility was first detected in South Africa3. COVID-19 infection and reinfection are a major health burden, and previous COVID-19 exposure does not always result in complete immunity.

The challenge

Image: University of Cape Town MSc student, Sedzani Mbedzi, looking at an ACE2 protein chromatogram from high pressure liquid chromatography. Photo credit: Lucas Raphela. ©University of Cape Town

Development of therapeutic agents for COVID-19 is extremely challenging because the mutations at key residues in the spike protein result in immune evasion and thus reduce the efficacy of the vaccines posing a significant challenge to prevention and control strategies.  Two spike antigens are currently widely used for drug and vaccine development: the receptor binding domain (RBD) and a larger soluble spike ectodomain. The spike RBD can be reproducibly and effectively produced and can be crystallised as a complex with ACE2.

The solution

As soon as the SARS-CoV-2 genome sequence was made publicly available, structural biologists worldwide focused on determining the 3D structures of the proteins that comprise the virus. Structural Biology has played a crucial role in impacting our understanding of how different viral proteins interact with human host proteins and small molecule ligands. Research has focused on studying the effects of mutations that are present in the viral population circulating in South Africa and scientists at the University of Cape Town (UCT) are performing protein-protein binding experiments and structural studies to elucidate this binding at an atomic level. Structural studies are currently underway to determine the interacting domains of the ACE2-RBD complex using X-ray crystallography.  

Sedzani Mbedzi is an MSc student in the field of medical biochemistry at UCT’s Faculty of Health Sciences in the Department of Integrative Biomedical Sciences. Assisted by the Sylva Schwager – the Chief Scientific Officer of the Sturrock group – Sedzani has been involved in preparing and characterising the SARS-CoV-2 spike protein, the RBD and ACE2, for her MSc research project, prior to using the UK’s Diamond Light Source synchrotron for her experiments.   

“The successful expression, purification, and characterisation of ACE2 and SARS-CoV-2 spike RBD was a huge milestone. Thanks to START: Health & Bio Science, the crystallisation of the interacting domains of ACE2 and RBD and the determination of the structures by X-ray diffraction will ultimately play a significant role in this project’s development. There is still much to learn from structural studies, and it has made me realise the power of this technology for giving important details about a virus, sickness, or any other underlying traits of an organism.”

Sedzani Mbedzi, University of Cape Town, South Africa


RBD binding to ACE2 affects infectivity and disease severity of SARS-CoV-2, and by studying the binding of different variants we can understand the interactions between the RBD and ACE2 at a molecular level. ​ This will further our understanding of SARS-CoV-2 infectivity in different variants and allow us to predict the binding affinity of new variants.​ This will also provide a good lead for development of SARS-CoV-2 therapeutics that can inhibit COVID-19 and any future coronaviruses.

Capacity building

Image: Sedzani Mbedzi, MSc student at the University of Cape Town. Photo credit: Lucas Raphela. ©University of Cape Town

Sedzani started her career journey under the supervision of Professor Edward Sturrock and Professor Trevor Sewell. Her involvement has led on an exciting journey in which she discovered her interest in Structural Biology. In October 2022, Sedzani first learned about START: Health and Bio Science by attending the Legacy of START conference at UCT, where she learnt about the latest Structural Biology and synchrotron techniques and heard about START’s successes. Sedzani describes listening to the presentations at the conference and being fascinated by the Structural Biology research being conducted in Africa and elsewhere. She reports that her research project has advanced favourably because of attending the Legacy of START conference.

“I have always loved science and had wonderful mentors – like my high school teacher, the late Mr Ramovha, and Professor N.E. Madala at the University of Venda – who helped me along the way. As a young girl, I always dreamt of studying pharmacy or working for a pharmaceutical company. After completing matric, I enrolled at the University of Venda to pursue a BSc in microbiology and biochemistry. In 2021, I registered for an Honours degree in medical biochemistry at UCT. During this degree, I was able to appreciate how my medical biochemistry training could enable me to pursue a career in the pharmaceutical industry. Now my MSc research brings me closer to my career goals.”  

Sedzani Mbedzi, University of Cape Town, South Africa


1 Rabaan AA, Al-Ahmed SH, Haque S, Sah R, Tiwari R, Malik YS, Dhama K, Yatoo MI, Bonilla-Aldana DK and Rodriguez-Morales AJ (2020) SARS-CoV-2, SARS-CoV, and MERS-COV: A comparative overview. Infez Med 28:174-184.

2 Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, Doolabh D, Pillay S, San EJ, Msomi N, Mlisana K, von Gottberg A, Walaza S, Allam M, Ismail A, Mohale T, Glass AJ, Engelbrecht S, Van Zyl G, Preiser W, Petruccione F, Sigal A, Hardie D, Marais G, Hsiao NY, Korsman S, Davies MA, Tyers L, Mudau I, York D, Maslo C, Goedhals D, Abrahams S, Laguda-Akingba O, Alisoltani-Dehkordi A, Godzik A, Wibmer CK, Sewell BT, Lourenco J, Alcantara LCJ, Kosakovsky Pond SL, Weaver S, Martin D, Lessells RJ, Bhiman JN, Williamson C and de Oliveira T (2021) Detection of a SARS-CoV-2 variant of concern in South Africa. Nature 592:438-443. doi: 10.1038/s41586-021-03402-9

3 Laffeber C, de Koning K, Kanaar R and Lebbink JHG (2021) Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants. J Mol Biol 433:167058. doi: 10.1016/j.jmb.2021.167058