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Dick JK, Hicks D, Krishna VD, Sangala JA, Zandstra BT, Baehr C, Verbeek JS, Cragg MS, Cheeran MCJ, Pravetoni M, Hart GT. ACE2 decoy Fc-fusions and bi-specific killer engager (BiKEs) require Fc engagement for in vivo efficacy against SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599956. [PMID: 38948747 PMCID: PMC11212978 DOI: 10.1101/2024.06.20.599956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
SARS-CoV-2 virus has continued to evolve over time necessitating the adaptation of vaccines to maintain efficacy. Monoclonal antibodies (mAbs) against SARS-CoV-2 were a key line of defense for unvaccinated or immunocompromised individuals. However, these mAbs are now ineffective against current SARS-CoV-2 variants. Here, we tested three aspects of αSARS-CoV-2 therapeutics. First, we tested whether Fc engagement is necessary for in vivo clearance of SARS-CoV-2. Secondly, we tested bi-specific killer engagers (BiKEs) that simultaneously engage SARS-CoV-2 and a specific Fc receptor. Benefits of these engagers include the ease of manufacturing, stability, more cell-specific targeting, and high affinity binding to Fc receptors. Using both mAbs and BiKEs, we found that both neutralization and Fc receptor engagement were necessary for effective SARS-CoV-2 clearance. Thirdly, due to ACE2 being necessary for viral entry, ACE2 will maintain binding to SARS-CoV-2 despite viral evolution. Therefore, we used an ACE2 decoy Fc-fusion or BiKE, instead of an anti-SARS-CoV-2 antibody sequence, as a potential therapeutic that would withstand viral evolution. We found that the ACE2 decoy approach also required Fc receptor engagement and, unlike traditional neutralizing antibodies against specific variants, enabled the clearance of two distinct SARS-CoV-2 variants. These data show the importance of Fc engagement for mAbs, the utility of BiKEs as therapies for infectious disease, and the in vivo effectiveness of the ACE2 decoy approach. With further studies, we predict combining neutralization, the cellular response, and this ACE2 decoy approach will benefit individuals with ineffective antibody levels. Abbreviations ACE2, scFv, mAb, BiKE, COVID-19, Fc, CD16, CD32b, CD64, d.p.i. Key points With equal dosing, both neutralization and Fc engagement are necessary for the optimal efficacy of in vivo antibodies and bi-specific killer engagers (BiKEs) against SARS-CoV-2. BiKEs can clear SARS-CoV-2 virus and protect against severe infection in the hACE2-K18 mouse model. ACE2 decoys as part of Fc-fusions or BiKEs provide in vivo clearance of two disparate SARS-CoV-2 variants.
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2
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Chen H, Peng J, Wang T, Wen J, Chen S, Huang Y, Zhang Y. Counter-regulatory renin-angiotensin system in hypertension: Review and update in the era of COVID-19 pandemic. Biochem Pharmacol 2023; 208:115370. [PMID: 36481346 PMCID: PMC9721294 DOI: 10.1016/j.bcp.2022.115370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Cardiovascular disease is the major cause of mortality and disability, with hypertension being the most prevalent risk factor. Excessive activation of the renin-angiotensin system (RAS) under pathological conditions, leading to vascular remodeling and inflammation, is closely related to cardiovascular dysfunction. The counter-regulatory axis of the RAS consists of angiotensin-converting enzyme 2 (ACE2), angiotensin (1-7), angiotensin (1-9), alamandine, proto-oncogene Mas receptor, angiotensin II type-2 receptor and Mas-related G protein-coupled receptor member D. Each of these components has been shown to counteract the effects of the overactivated RAS. In this review, we summarize the latest insights into the complexity and interplay of the counter-regulatory RAS axis in hypertension, highlight the pathophysiological functions of ACE2, a multifunctional molecule linking hypertension and COVID-19, and discuss the function and therapeutic potential of targeting this counter-regulatory RAS axis to prevent and treat hypertension in the context of the current COVID-19 pandemic.
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Affiliation(s)
- Hongyin Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518000, Guangdong, China
| | - Jiangyun Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China,Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan 528200, Guangdong, China
| | - Tengyao Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China,Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan 528200, Guangdong, China
| | - Jielu Wen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China,Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan 528200, Guangdong, China
| | - Sifan Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, Guangdong, China,Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan 528200, Guangdong, China
| | - Yu Huang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China,Corresponding authors
| | - Yang Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen 518000, Guangdong, China,Corresponding authors
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3
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Zhu R, Canena D, Sikora M, Klausberger M, Seferovic H, Mehdipour AR, Hain L, Laurent E, Monteil V, Wirnsberger G, Wieneke R, Tampé R, Kienzl NF, Mach L, Mirazimi A, Oh YJ, Penninger JM, Hummer G, Hinterdorfer P. Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nat Commun 2022; 13:7926. [PMID: 36566234 PMCID: PMC9789309 DOI: 10.1038/s41467-022-35641-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Recent waves of COVID-19 correlate with the emergence of the Delta and the Omicron variant. We report that the Spike trimer acts as a highly dynamic molecular caliper, thereby forming up to three tight bonds through its RBDs with ACE2 expressed on the cell surface. The Spike of both Delta and Omicron (B.1.1.529) Variant enhance and markedly prolong viral attachment to the host cell receptor ACE2, as opposed to the early Wuhan-1 isolate. Delta Spike shows rapid binding of all three Spike RBDs to three different ACE2 molecules with considerably increased bond lifetime when compared to the reference strain, thereby significantly amplifying avidity. Intriguingly, Omicron (B.1.1.529) Spike displays less multivalent bindings to ACE2 molecules, yet with a ten time longer bond lifetime than Delta. Delta and Omicron (B.1.1.529) Spike variants enhance and prolong viral attachment to the host, which likely not only increases the rate of viral uptake, but also enhances the resistance of the variants against host-cell detachment by shear forces such as airflow, mucus or blood flow. We uncover distinct binding mechanisms and strategies at single-molecule resolution, employed by circulating SARS-CoV-2 variants to enhance infectivity and viral transmission.
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Affiliation(s)
- Rong Zhu
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Daniel Canena
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Faculty of Physics, University of Vienna, Vienna, Austria
- Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Kraków, Poland
| | - Miriam Klausberger
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Hannah Seferovic
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Ahmad Reza Mehdipour
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Center for Molecular Modeling, University of Ghent, Ghent, Belgium
| | - Lisa Hain
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Elisabeth Laurent
- Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
- Core Facility Biomolecular & Cellular Analysis, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Vanessa Monteil
- Department of Laboratory Medicine, Unit of Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | | | - Ralph Wieneke
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt, Germany
| | - Nikolaus F Kienzl
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Lukas Mach
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Ali Mirazimi
- Department of Laboratory Medicine, Unit of Clinical Microbiology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- National Veterinary Institute, Uppsala, Sweden
| | - Yoo Jin Oh
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
| | - Peter Hinterdorfer
- Department of Experimental Applied Biophysics, Johannes Kepler University Linz, Linz, Austria.
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4
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Zhang L, Zhang Y, Qin X, Jiang X, Zhang J, Mao L, Jiang Z, Jiang Y, Liu G, Qiu J, Chen C, Qiu F, Zou Z. Recombinant ACE2 protein protects against acute lung injury induced by SARS-CoV-2 spike RBD protein. Crit Care 2022; 26:171. [PMID: 35681221 PMCID: PMC9178547 DOI: 10.1186/s13054-022-04034-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/27/2022] [Indexed: 01/08/2023] Open
Abstract
Abstract
Background
SARS-CoV-2 infection leads to acute lung injury (ALI) and acute respiratory distress syndrome (ARDS). Both clinical data and animal experiments suggest that the renin–angiotensin system (RAS) is involved in the pathogenesis of SARS-CoV-2-induced ALI. Angiotensin-converting enzyme 2 (ACE2) is the functional receptor for SARS-CoV-2 and a crucial negative regulator of RAS. Recombinant ACE2 protein (rACE2) has been demonstrated to play protective role against SARS-CoV and avian influenza-induced ALI, and more relevant, rACE2 inhibits SARS-CoV-2 proliferation in vitro. However, whether rACE2 protects against SARS-CoV-2-induced ALI in animal models and the underlying mechanisms have yet to be elucidated.
Methods and Results
Here, we demonstrated that the SARS-CoV-2 spike receptor-binding domain (RBD) protein aggravated lipopolysaccharide (LPS)-induced ALI in mice. SARS-CoV-2 spike RBD protein directly binds and downregulated ACE2, leading to an elevation in angiotensin (Ang) II. AngII further increased the NOX1/2 through AT1R, subsequently causing oxidative stress and uncontrolled inflammation and eventually resulting in ALI/ARDS. Importantly, rACE2 remarkably reversed SARS-CoV-2 spike RBD protein-induced ALI by directly binding SARS-CoV-2 spike RBD protein, cleaving AngI or cleaving AngII.
Conclusion
This study is the first to prove that rACE2 plays a protective role against SARS-CoV-2 spike RBD protein-aggravated LPS-induced ALI in an animal model and illustrate the mechanism by which the ACE2-AngII-AT1R-NOX1/2 axis might contribute to SARS-CoV-2-induced ALI.
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5
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Remesh SG, Merz GE, Brilot AF, Chio US, Rizo AN, Pospiech TH, Lui I, Laurie MT, Glasgow J, Le CQ, Zhang Y, Diwanji D, Hernandez E, Lopez J, Pawar KI, Pourmal S, Smith AM, Zhou F, DeRisi J, Kortemme T, Rosenberg OS, Glasgow A, Leung KK, Wells JA, Verba KA. Computational pipeline provides mechanistic understanding of Omicron variant of concern neutralizing engineered ACE2 receptor traps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.09.503400. [PMID: 35982665 PMCID: PMC9387132 DOI: 10.1101/2022.08.09.503400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The SARS-CoV-2 Omicron variant, with 15 mutations in Spike receptor binding domain (Spike-RBD), renders virtually all clinical monoclonal antibodies against WT SARS-CoV-2 ineffective. We recently engineered the SARS-CoV-2 host entry receptor, ACE2, to tightly bind WT-Spike-RBD and prevent viral entry into host cells ("receptor traps"). Here we determine cryo-EM structures of our receptor traps in complex with full length Spike. We develop a multi-model pipeline combining Rosetta protein modeling software and cryo-EM to allow interface energy calculations even at limited resolution and identify interface side chains that allow for high affinity interactions between our ACE2 receptor traps and Spike-RBD. Our structural analysis provides a mechanistic rationale for the high affinity (0.53 - 4.2nM) binding of our ACE2 receptor traps to Omicron-RBD confirmed with biolayer interferometry measurements. Finally, we show that ACE2 receptor traps potently neutralize Omicron- and Delta-pseudotyped viruses, providing alternative therapeutic routes to combat this evolving virus.
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Affiliation(s)
- Soumya G. Remesh
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Gregory E. Merz
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Axel F. Brilot
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Un Seng Chio
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Alexandrea N. Rizo
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Thomas H. Pospiech
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Irene Lui
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
| | - Mathew T. Laurie
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA - 94158, USA
| | - Jeff Glasgow
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
| | - Chau Q. Le
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
| | - Yun Zhang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
| | - Devan Diwanji
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Evelyn Hernandez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Jocelyne Lopez
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Komal Ishwar Pawar
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Sergei Pourmal
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Amber M. Smith
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Fengbo Zhou
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | | | - Joseph DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA - 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA - 94158, USA
| | - Tanja Kortemme
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA - 94158, USA
- The University of California, Berkeley–University of California, San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA - 94158, USA
| | - Oren S. Rosenberg
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
| | - Anum Glasgow
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Kevin K. Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
| | - James A. Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA - 94158, USA
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA - 94158, USA
| | - Kliment A. Verba
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA
- QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA
- QBI, University of California, San Francisco, CA 94158, USA
- Lead contact
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6
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Wang SC, Zhang F, Zhu H, Yang H, Liu Y, Wang P, Parpura V, Wang YF. Potential of Endogenous Oxytocin in Endocrine Treatment and Prevention of COVID-19. Front Endocrinol (Lausanne) 2022; 13:799521. [PMID: 35592777 PMCID: PMC9110836 DOI: 10.3389/fendo.2022.799521] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/14/2022] [Indexed: 01/09/2023] Open
Abstract
Coronavirus disease 2019 or COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a significant threat to the health of human beings. While wearing mask, maintaining social distance and performing self-quarantine can reduce virus spreading passively, vaccination actively enhances immune defense against COVID-19. However, mutations of SARS-CoV-2 and presence of asymptomatic carriers frustrate the effort of completely conquering COVID-19. A strategy that can reduce the susceptibility and thus prevent COVID-19 while blocking viral invasion and pathogenesis independent of viral antigen stability is highly desirable. In the pathogenesis of COVID-19, endocrine disorders have been implicated. Correspondingly, many hormones have been identified to possess therapeutic potential of treating COVID-19, such as estrogen, melatonin, corticosteroids, thyroid hormone and oxytocin. Among them, oxytocin has the potential of both treatment and prevention of COVID-19. This is based on oxytocin promotion of immune-metabolic homeostasis, suppression of inflammation and pre-existing comorbidities, acceleration of damage repair, and reduction of individuals' susceptibility to pathogen infection. Oxytocin may specifically inactivate SARS-COV-2 spike protein and block viral entry into cells via angiotensin-converting enzyme 2 by suppressing serine protease and increasing interferon levels and number of T-lymphocytes. In addition, oxytocin can promote parasympathetic outflow and the secretion of body fluids that could dilute and even inactivate SARS-CoV-2 on the surface of cornea, oral cavity and gastrointestinal tract. What we need to do now is clinical trials. Such trials should fully balance the advantages and disadvantages of oxytocin application, consider the time- and dose-dependency of oxytocin effects, optimize the dosage form and administration approach, combine oxytocin with inhibitors of SARS-CoV-2 replication, apply specific passive immunization, and timely utilize efficient vaccines. Meanwhile, blocking COVID-19 transmission chain and developing other efficient anti-SARS-CoV-2 drugs are also important. In addition, relative to the complex issues with drug applications over a long term, oxytocin can be mobilized through many physiological stimuli, and thus used as a general prevention measure. In this review, we explore the potential of oxytocin for treatment and prevention of COVID-19 and perhaps other similar pathogens.
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Affiliation(s)
- Stephani C. Wang
- Division of Cardiology, Department of Medicine, University of California-Irvine, Irvine, CA, United States
| | - Fengmin Zhang
- Department of Microbiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Hui Zhu
- Department of Physiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Haipeng Yang
- Neonatal Division of the Department of Pediatrics, Harbin Medical University The Fourth Affiliated Hospital, Harbin, China
| | - Yang Liu
- Department of Physiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Ping Wang
- Department of Genetics, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
| | - Vladimir Parpura
- Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Yu-Feng Wang
- Department of Physiology, School of Basic Medical Sciences, Harbin Medical University, Harbin, China
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7
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Valério M, Borges-Araújo L, Melo MN, Lousa D, Soares CM. SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. FRONTIERS IN MEDICAL TECHNOLOGY 2022; 4:1009451. [PMID: 36277437 PMCID: PMC9581196 DOI: 10.3389/fmedt.2022.1009451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 6 million people and is having a devastating social and economic impact around the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss of vaccine and natural immunity, as well as increased transmissibility. All VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes. The spike glycoprotein binds to angiotensin-converting enzyme 2 (ACE2) via its receptor binding domain (RBD) initiating the infection process. Attempting to understand the effect of RBD mutations in VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect the RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of four VOCs (Alpha, Beta, Delta, and Omicron). Our results show that the wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The Alpha and Beta variants shift the open/closed equilibrium towards the open conformation by roughly 20%, likely increasing ACE2 binding affinity. Simulations of the Delta and Omicron variants showed extreme results, with the closed conformation being rarely observed. The Delta variant also differed substantially from the other variants, alternating between the open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge. This alternate conformation could provide a fitness advantage due to increased availability for ACE2 binding, and by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the Omicron and Delta variants, impact RBD conformational dynamics in a direction that promotes efficient binding to ACE2 and, in the case of Delta, may assist antibody escape.
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Affiliation(s)
- Mariana Valério
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Luís Borges-Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
| | - Diana Lousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
| | - Cláudio M. Soares
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Associated Laboratory LS4FUTURE, ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
- Correspondence: Manuel N. Melo Diana Lousa Cláudio M. Soares
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