José Nelson Onuchic | PAS Academician

Using physics to improve human health: From protein folding to understanding Covid-19 and designing new vaccines


We explore how, utilizing a theoretical framework coming from the physical sciences, we can quantitatively understand the underlying mechanisms governing biological processes with applications to medicine. Here we specifically focus on how a virus may infect cells with emphasis on COVID-19. We discuss how the spike protein has to go through a major structural rearrangement during cell invasion. We also describe how a combined theoretical and experimental effort is used to propose a possible new vaccine for COVID-19 utilizing a phage display-based approach. Such a spray-based vaccine is cost-effective, needle-free, and can be stored at room temperature.

1.     Introduction – A physical mechanism for virus infection

Viral infection is a serious public health issue contributing significantly to morbidity and mortality in society. Understanding the mechanisms by which a virus may infect cells should provide us with the needed understanding to develop new therapies. Several viruses have developed a fusion mechanism that utilize proteins involved in merging the host and viral membranes [1,2], a process by which the viral genetic material to invades the cell and begin the process of replication. During this invasion, these proteins undergo a large and global structural rearrangement. Understanding these major conformational changes is central to fully comprehend viral cell invasion and the associated infection.

In this presentation, we focus on the currently most serious viral disease, SARS-CoV-2. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and its transmission involves a series of processes that may be targeted by vaccines and therapeutics. The host cell invasion involves a large conformational change of the Spike protein that leads to membrane fusion between the host cell and the virus. This fusion creates transmembrane pores through which the viral genome infects the host cell.

2.     Understanding COVID-19 cell invasion – a physical model

This physical mechanism is a based on a global transformation of the spike protein. The invasion starts when the Spike 1 (S1) domain that covers the spike 2 (S2) head identifies the receptor ACE2. ACE2 is located on the surface of many cells in the respiratory track. When S1 recognizes this receptor, the S1 dissociates and S2 starts a configurational transformation toward the viral capsid. During this process, S2 releases the fusion peptides that bind to the host cell. This binding process is followed by a zippering of S2 and the associated membrane fusion, the mechanism by which invasion becomes possible. S2 is covered by sugars called glycans. These glycans slow the conformational transition, providing the fusion peptides sufficient time for the fusion peptides bind before the free energy is released, allowing for the fusion of the membranes. If the glycans are not bound to the Spike protein, this free energy is released too early before the invasion could take place.

Removing the glycans from S2 probably makes the virus ineffective. Possible therapies may be inspired on this principle. Understanding this rearrangement, therefore, provides several other possibilities that can be potentially targeted to deal with this disease. These simulations start to provide enough understanding to generate new ways to defeat the SARS-CoV-2 virus.

2.a A physical mechanism for cell invasion

To investigate the pre-to-post membrane fusion rearrangement, simulations were performed employing an all-atom structure-based model [3,4]. To obtain the physical mechanism governing the transition between the pre-to-post rearrangement, this structure-based model was utilized to perform thousands of simulations between these two states [5]. A physical mechanism and associated intermediates were identified and are described in the schematic representation shown in figure 1.

From figure 1E, it can be noticed that the intermediate states are required to be sufficiently long-lived to allow for the fusion peptides to have sufficient time to capture the cell membrane. This is achieved by creating a sufficiently long-lived sterically-caged intermediate of the Spike protein during the conformational change. This is achieved by the steric presence of glycans which may substantially increase the life of this intermediate. This glycan-induced delay is essential to provide the opportunity for the fusion peptides to capture the host cell. Therefore, the absence of glycans makes it much more difficult for the viral genome to enter the host cell. These results suggest a possible mechanism by which the glycosylation state may regulate infectivity [7].

Understanding this mechanism creates opportunities for searching new therapies inspired in this invasion mechanism which may help to reduce the negative impact of SARS-CoV-2 in society.

3. Creating new COVID-19 vaccines

In view of creating new COVID-19 vaccines, we have proposed a strategy that employs modified bacteriophages which can be inhaled to deliver protection via the lungs to the immune system. Exploring the unique features of phage (a bacterial virus), we are trying to develop phage display-based vaccine candidates against COVID-19. This will be achieved by utilizing engineered ligand-directed phage particles displaying structurally defined epitopes of the Spike protein.

The phages are engineered with an epitope from the SARS-CoV-2 spike protein, along with a small ligand peptide that helps the phage cross from the lungs into the patient’s bloodstream. Once absorbed, they activated the immune system to defend against COVID-19. To facilitate the selection of these epitopes, the part of the antigen molecules that bind to specific biological targets, simulations were performed to determine their effectiveness in producing protecting antibodies [8]. The initial results are presented in figure 2.

Figure 2. A) Four epitopes spanning the SARS-CoV-2 S protein were selected based on their ability to be introduced into phage-type virus coating proteins. Then, altered phages with the epitopes included were used to trigger an immune response against SARS-COV-2 virus in mice. Only epitope four was able to trigger a significant immune response. B) Explicit solvent simulations of the epitopes in an exposed environment, show that epitope 4 is the most stable ranging low values of RMSD (<4A) when comparing it with the SARS-COV-2 structure. Then, it was hypothesized that working epitopes for this immunization strategy would require stable epitopes in exposed environments.

Experimental studies determining of the immunogenicity of the Spike protein epitopes demonstrated that epitope 4 is the most immunogenic among the selected epitopes [8]. Therefore, it provides strong support to our hypothesis that epitopes that display their native conformation when transferred to the phage will produce stronger specific immune response as predicted by the theoretical studies.

The success of these early results now provides a combined theoretical and experimental strategy towards the development of new SARS-CoV-2 vaccines. These phage vaccines have the potential of become powerful tools against this deadly disease.

4. Conclusion – The synergy of physical models and biological experiments as a transformative approach to medical science.

The two examples in this presentation, 1) the mechanism for viral infection and 2) the development of phage vaccines, describe how approaches coming from theoretical and computational physical modeling can be used synergistically with biological and medical experiments to address challenges of current diseases affecting society. The complexity of these problems requires a combined multi-disciplinary approach in order to achieve successes and the physical sciences are becoming more and more part of the solution.


[1] J.M. White, S.E. Delos, M. Brecher, and K. Schornberg. “Structures and Mechanisms of Viral Membrane Fusion Proteins”, Critical Reviews in Biochemistry and Molecular Biology, 43(3), 189-219, 2008.

[2] S.C. Harrison. “Viral membrane fusion”, Virology, 479-480, 498-507, 2015.

[3] Paul C. Whitford, Jeffrey K. Noel, Shachi Gosavi, Alexander Schug, Kevin Y. Sanbonmatsu, and José N. Onuchic. “An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields”, Proteins: Structure, Function, and Bioinformatics, 75(2), 430-441, 2009.

[4] Antonio B. de Oliveira Jr, Vinícius G. Contessoto, Asem Hassan, Sandra Byju, Ailun Wang, Yang Wang, Esteban Dodero-Rojas, Udayan Mohanty, Jeffrey K. Noel, and Jose N. Onuchic. “Smog 2 and opensmog: Extending the limits of structure-based models”, Protein Science, 31(1), 158-172, 2021.

[5] E. Dodero-Rojas, J.N. Onuchic, and P. Whitford. “Sterically-confined rearrangements of Sarscov-2 spike protein control cell invasions”, eLife, 10, e70362 2021.

[6] A.C. Walls, Y.J. Park, M.A. Tortorici, A. Wall, A.T. McGuire and D. Vessler. “Structure, Function, and Antigenicity of the SARS- CoV-2 Spike Glycoprotein”, Cell, 181(2), 281-292, 2020.

[7] Yasunori Watanabe, Joel D. Allen, Daniel Wrapp, Jason S. McLellan, and Max Crispin. “Site-specific glycan analysis of the sars-cov-2 spike,” Science, 369(6501), 330-333, 2020.

[8] Daniela I. Staquicini, Fenny H.F. Tang, Christopher Markosian, Virginia J. Yao, Fernanda I. Staquicini, Esteban Dodero-Rojas, Vinicius G. Contessoto, Deodate Davis, Paul O’Brien, Nazia Habib. Tracey L. Smitha, Natalie Bruiners, Richard L. Sidman, Maria L. Gennaro, Edmund C. Lattime, Steven K. Libuttig, Paul C. Whitford, Stephen K. Burley, José N. Onuchic, Wadih Arap, and Renata Pasqualini. “Design and proof-of-concept for targeted phage-based Covid-19 vaccination strategies with a streamlined cold-free supply chain”, Proceedings of the National Academy of Sciences, 118(30), e2105739118, 2021.