The Binding Mechanism and Inhibition of SARS-CoV-2 Spike Glycoprotein to Host Cell

"Assoc. Prof. Mert Gur of the Mechanical Engineering Department uses all-atom molecular dynamics simulations to investigate the binding mechanism of the spike glycoprotein to the ACE2 receptor of the host cell, elucidate how this binding mechanism is altered in SARS-CoV-2 variants, and explore strategies to inhibit spike-ACE2 interactions. Furthermore, he tests SARS-CoV-2 neutralizing nanobodies against SARS-COV-2 variants and also engineers novel nanobodies effective against SARS-CoV-2 variants in silico.

Host cell recognition and fusion between host cell and viral membranes are the most critical steps determining the pathogenesis and viral infectivity. In SARS-CoV-2, large trimeric spike glycoproteins located on its membrane interact with the angiotensin-converting enzyme 2 (ACE2) receptors of human host cells. Following binding to ACE2, the spike protein undergoes large-scale conformational changes that mediate interactions between the SARS-CoV-2 and host cell membranes, and hence facilitate the fusion process. As a result of the membrane fusion, the genetic material of SARS-CoV-2 enters the human cell and the human cell becomes infected. The spike protein is among the primary drug targets to inhibit viral entry and all available vaccines promote antibody production against the SARS-CoV-2 spike glycoprotein.  

Inhibiting spike proteins is a challenging process as the SARS-CoV-2 spike protein is shielded against antibodies and other molecules by the glycan molecules coating its surface.  Mutations in the SARS-CoV-2 variants can make spike protein inhibition by antibodies even more challenging by decreasing antibody binding strengths while increasing spike-ACE2 interaction strength. Most vaccine induced antibodies showed reduced or completely lost neutralization activity against the Spike protein of the Delta variant 1-4. The recently published report estimates that effectiveness of Pfizer-BionTech, Moderna and Janssen has declined from 91% to 66% on average since the Delta variant became predominant 5. Similar results were reported for other available vaccines, such as Sputnik, and AstraZeneca 6,7. Due to the loss in neutralization activity against the spike protein of vaccine induced antibodies, at least one additional booster vaccine shot has started to become a standard practice globally. With the booster shot higher levels of antibodies are maintained so that higher numbers of antibodies make up for the lost antibody effectivity. New variants are expected to emerge due to the natural course of the pandemic, posing the danger of reducing antibody binding efficiency further to critically low levels.  Therefore, developing effective vaccines, antibodies and drugs against the SARS-CoV-2 variants is critical for the long term fight against the COVID-19.

By utilizing molecular dynamics simulations, Gur and his research group aim to reveal novel strategies and mechanisms to inhibit the spike protein that can be used in drug design, determine how SARS-CoV-2 variations affect the function and also inhibition of spike protein, and to engineer novel nanobody specific to SARS-CoV-2 variants. While experiments can provide critical information about protein functions and interactions, they are not able explore and visualize these processes in real time at atomic resolution. For example, electron microscopy can provide near-atomic structure of proteins, by trapping the protein at one state along the process. Even if multiple structures along the process could be obtained, it is hard to connect atomic structures to obtain the full dynamic picture of the process of. This is similar to taking multiple pictures of a person on a bicycle along various location. Based on a few pictures, it could be theoretically claimed that the bicycle might be jumping or sliding to go from one location to the other. However, in reality the person on the bike is moving her/his legs and turning the tires through a mechanism. In collaboration with his experimental collaborators, Gur and his research group are performing molecular dynamics simulations to explore the atomistic details of protein functions.

Gur has been acting as the co-PI of three COVID-19 High Performance Computing Consortium projects performed in collaboration with UC Berkeley (USA) with the aim of exploring the binding and fusion mechanism of SARS-COV-2 spike glycoprotein, revealing the nanobody inhibitory mechanism spike glycoprotein, and identifying and reengineering effective nanobodies against SARS-COV-2 omicron variant. TÜBİTAK supported 5 graduate students within the 2247-C STAR-Intern Researcher Scholarship Program to work in two of these projects.

Gur and his research group were the first to model and publish the transition of the spike protein from its closed state to the open state with all atom molecular dynamics simulations in the presence of explicit solvent. Furthermore, Gur and his colleagues determined critical residues for the binding of the spike protein to ACE2 by a comprehensive mutagenesis analysis utilizing molecular dynamics simulations to test the effect of the mutations.  Blocking interactions of these specified residues was proposed to decrease binding affinity of spike to ACE2 that could serve as a design parameter in the development of novel drugs. Gur and is colleagues were also the first to explore the binding and inhibition mechanisms of nanobodies to the spike via all atom molecular dynamics simulations. Furthermore, effect of mutations in the SARS-CoV-2 Alpha, Beta and Delta variants onto nanobody-spike and ACE2-spike interactions were modeled via molecular dynamics simulations. Nanobodies ability to abrogate ACE2-spike binding was tested for Alpha, Beta and Delta variants showing concerning decrease nanobody effectivity for the Delta variant. Critical design parameters for novel nanobody design against Delta variant were obtained. Gur and his colleagues are currently investigating the nanobody effectivity against the omicron variant and are engineering novel nanobodies specific to the Omicron variant.

Gur and his colleagues work on SARS-CoV-2 have been covered in national newspapers (such as Habertürk, Milliyet and Anadolu Agency) and also on various platforms (such as, HPCwire and ScienceDaily). His student’s master thesis was among the first three master thesis on SARS-CoV-2 research in Turkey. 
Gur and his research group are performing in silico pulling experiment (steered molecular dynamics simualtions) with pulling speeds and loading rates directly comparable to high speed atomic force microscopy experiments to explore the ACE2 and nanobody binding mechanisms and strengths to spike protein, and also the effect of SARS-COV-2 variations on them. These steered molecular dynamic simulations require at least 40-100 times more simulations lengths than standard steered molecular dynamic simulations performed in the literature. Considering the large number of nanonbodies and also variants, only a limited number of research groups have the massive resources to perform steered molecular dynamics simulations with parameters comparable to experiments to a such large extent. The require massive computational resources are provided to the Gur by the COVID-19 High Performance Computing Consortium.



Figure 1. The atomic model of the SARS-CoV-2 S protein bound to the ACE2 receptor on the host cell membrane. The receptor binding domain of the S protein (RBD, green) interacts with the peptidase domain of ACE2 (PD, blue). (This study was published on the cover of The Journal of Physical Chemistry B, volume 125, issue 21. Taka, E., Yilmaz, S. Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2021). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptorThe Journal of Physical Chemistry B. 125 (21), 5537-5548.)


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UHeM, COVID-19 HPC Consortium (Grant No. TG-MCB200070)

Lab members involved:

Elhan Taka, Mert Gölcük, Sema Zeynep Yılmaz, Ceren Kılınç ve Umut Aktaş


Ahmet Yıldız (UC Berkeley)

Related Articles:

1. Gur, M., Taka, E., Yilmaz, S. Z., Kilinc, C., Aktas, U., Golcuk, M. (2020). Conformational transition of SARS-CoV-2 spike glycoprotein between its closed and open states. The Journal of Chemical Physics, 153(7), 075101.

2. Taka, E., Yilmaz, S. Z., Golcuk, M., Kilinc, C., Aktas, U., Yildiz, A., Gur, M. (2020). Critical interactions between the SARS-CoV-2 spike glycoprotein and the human ACE2 receptorThe Journal of Physical Chemistry B. 125 (21), 5537-5548.