1
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Narayanan KK, Amaya M, Tsang N, Yin R, Jays A, Broder CC, Shukla D, Procko E. Sequence basis for selectivity of ephrin-B2 ligand for Eph receptors and pathogenic henipavirus G glycoproteins. J Virol 2023; 97:e0062123. [PMID: 37931130 PMCID: PMC10688352 DOI: 10.1128/jvi.00621-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/13/2023] [Indexed: 11/08/2023] Open
Abstract
IMPORTANCE Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and regulates multiple cell developmental and signaling processes. It also functions as the cell entry receptor for Nipah virus and Hendra virus, zoonotic viruses that can cause respiratory and/or neurological symptoms in humans with high mortality. Here, we investigate the sequence basis of EFNB2 specificity for binding the Nipah virus attachment G glycoprotein over Eph receptors. We then use this information to engineer EFNB2 as a soluble decoy receptor that specifically binds the attachment glycoproteins of the Nipah virus and other related henipaviruses to neutralize infection. These findings further mechanistic understanding of protein selectivity and may facilitate the development of diagnostics or therapeutics against henipavirus infection.
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Affiliation(s)
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Natalie Tsang
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Alka Jays
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda, Maryland, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois, Urbana, Illinois, USA
- Cyrus Biotechnology, Seattle, Washington, USA
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2
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Havranek B, Lindsey GW, Higuchi Y, Itoh Y, Suzuki T, Okamoto T, Hoshino A, Procko E, Islam SM. A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo. Commun Biol 2023; 6:513. [PMID: 37173421 PMCID: PMC10177734 DOI: 10.1038/s42003-023-04860-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
SARS-CoV-2, especially B.1.1.529/omicron and its sublineages, continues to mutate to evade monoclonal antibodies and antibodies elicited by vaccination. Affinity-enhanced soluble ACE2 (sACE2) is an alternative strategy that works by binding the SARS-CoV-2 S protein, acting as a 'decoy' to block the interaction between the S and human ACE2. Using a computational design strategy, we designed an affinity-enhanced ACE2 decoy, FLIF, that exhibited tight binding to SARS-CoV-2 delta and omicron variants. Our computationally calculated absolute binding free energies (ABFE) between sACE2:SARS-CoV-2 S proteins and their variants showed excellent agreement to binding experiments. FLIF displayed robust therapeutic utility against a broad range of SARS-CoV-2 variants and sarbecoviruses, and neutralized omicron BA.5 in vitro and in vivo. Furthermore, we directly compared the in vivo therapeutic efficacy of wild-type ACE2 (non-affinity enhanced ACE2) against FLIF. A few wild-type sACE2 decoys have shown to be effective against early circulating variants such as Wuhan in vivo. Our data suggest that moving forward, affinity-enhanced ACE2 decoys like FLIF may be required to combat evolving SARS-CoV-2 variants. The approach described herein emphasizes how computational methods have become sufficiently accurate for the design of therapeutics against viral protein targets. Affinity-enhanced ACE2 decoys remain highly effective at neutralizing omicron subvariants.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA
- ComputePharma, LLC., Chicago, IL, USA
| | | | - Yusuke Higuchi
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Atsushi Hoshino
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801, USA
- Cyrus Biotechnology, Inc., Seattle, WA, USA
| | - Shahidul M Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- ComputePharma, LLC., Chicago, IL, USA.
- Department of Chemistry, Delaware State University, Dover, DE, 19901, USA.
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3
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Narayanan KK, Amaya M, Tsang N, Yin R, Jays A, Broder CC, Shukla D, Procko E. The Sequence Basis for Selectivity of Ephrin-B2 Ligand for Eph Receptors and Pathogenic Henipavirus G Glycoproteins: Selective Ephrin-B2 Decoys for Nipah and Hendra Virus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.26.538420. [PMID: 37162958 PMCID: PMC10168364 DOI: 10.1101/2023.04.26.538420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ephrin-B2 (EFNB2) is a ligand for six Eph receptors in humans and functions as a cell entry receptor for several henipaviruses including Nipah virus (NiV), a pathogenic zoonotic virus with pandemic potential. To understand the sequence basis of promiscuity for EFNB2 binding to the attachment glycoprotein of NiV (NiV-G) and Eph receptors, we performed deep mutagenesis on EFNB2 to identify mutations that enhance binding to NiV-G over EphB2, one of the highest affinity Eph receptors. The mutations highlight how different EFNB2 conformations are selected by NiV-G versus EphB2. Specificity mutations are enriched at the base of the G-H binding loop of EFNB2, especially surrounding a phenylalanine hinge upon which the G-H loop pivots, and at a phenylalanine hook that rotates away from the EFNB2 core to engage Eph receptors. One EFNB2 mutant, D62Q, possesses pan-specificity to the attachment glycoproteins of closely related henipaviruses and has markedly diminished binding to the six Eph receptors. However, EFNB2-D62Q has high residual binding to EphB3 and EphB4. A second deep mutational scan of EFNB2 identified combinatorial mutations to further enhance specificity to NiV-G. A triple mutant of soluble EFNB2, D62Q-Q130L-V167L, has minimal binding to Eph receptors but maintains binding, albeit reduced, to NiV-G. Soluble EFNB2 decoy receptors carrying the specificity mutations were potent neutralizers of chimeric henipaviruses. These findings demonstrate how specific residue changes at the shared binding interface of a promiscuous ligand (EFNB2) can influence selectivity for multiple receptors, and may also offer insight towards the development of henipavirus therapeutics and diagnostics.
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Affiliation(s)
| | - Moushimi Amaya
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
| | - Natalie Tsang
- Department of Biochemistry, University of Illinois, Urbana IL, USA
| | - Randy Yin
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD, USA
| | - Alka Jays
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda MD, USA
| | - Christopher C. Broder
- Department of Microbiology and Immunology, Uniformed Services University, Bethesda MD, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana IL, USA
| | - Erik Procko
- Department of Biochemistry, University of Illinois, Urbana IL, USA
- Cancer Center at Illinois, University of Illinois, Urbana IL, USA
- Cyrus Biotechnology, Seattle WA, USA
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4
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Singh M, Pushpakumar S, Bard N, Zheng Y, Homme RP, Mokshagundam SPL, Tyagi SC. Simulation of COVID-19 symptoms in a genetically engineered mouse model: implications for the long haulers. Mol Cell Biochem 2023; 478:103-119. [PMID: 35731343 PMCID: PMC9214689 DOI: 10.1007/s11010-022-04487-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 05/30/2022] [Indexed: 01/24/2023]
Abstract
The ongoing pandemic (also known as coronavirus disease-19; COVID-19) by a constantly emerging viral agent commonly referred as the severe acute respiratory syndrome corona virus 2 or SARS-CoV-2 has revealed unique pathological findings from infected human beings, and the postmortem observations. The list of disease symptoms, and postmortem observations is too long to mention; however, SARS-CoV-2 has brought with it a whole new clinical syndrome in "long haulers" including dyspnea, chest pain, tachycardia, brain fog, exercise intolerance, and extreme fatigue. We opine that further improvement in delivering effective treatment, and preventive strategies would be benefited from validated animal disease models. In this context, we designed a study, and show that a genetically engineered mouse expressing the human angiotensin converting enzyme 2; ACE-2 (the receptor used by SARS-CoV-2 agent to enter host cells) represents an excellent investigative resource in simulating important clinical features of the COVID-19. The ACE-2 mouse model (which is susceptible to SARS-CoV-2) when administered with a recombinant SARS-CoV-2 spike protein (SP) intranasally exhibited a profound cytokine storm capable of altering the physiological parameters including significant changes in cardiac function along with multi-organ damage that was further confirmed via histological findings. More importantly, visceral organs from SP treated mice revealed thrombotic blood clots as seen during postmortem examination. Thus, the ACE-2 engineered mouse appears to be a suitable model for studying intimate viral pathogenesis thus paving the way for identification, and characterization of appropriate prophylactics as well as therapeutics for COVID-19 management.
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Affiliation(s)
- Mahavir Singh
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
| | - Sathnur Pushpakumar
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Nia Bard
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Yuting Zheng
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Rubens P Homme
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Sri Prakash L Mokshagundam
- Division of Endocrinology, Metabolism and Diabetes and Robley Rex VA Medical Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Suresh C Tyagi
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
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5
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Torchia JA, Tavares AH, Carstensen LS, Chen DY, Huang J, Xiao T, Mukherjee S, Reeves PM, Tu H, Sluder AE, Chen B, Kotton DN, Bowen RA, Saeed M, Poznansky MC, Freeman GJ. Optimized ACE2 decoys neutralize antibody-resistant SARS-CoV-2 variants through functional receptor mimicry and treat infection in vivo. SCIENCE ADVANCES 2022; 8:eabq6527. [PMID: 36475798 PMCID: PMC9728973 DOI: 10.1126/sciadv.abq6527] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/01/2022] [Indexed: 05/14/2023]
Abstract
As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) evolves to escape natural antibodies, it also loses sensitivity to therapeutic antibody drugs. By contrast, evolution selects for binding to ACE2, the cell-surface receptor required for SARS-CoV-2 infection. Consistent with this, we find that an ACE2 decoy neutralizes antibody-resistant variants, including Omicron, with no loss in potency. To identify design features necessary for in vivo activity, we compare several enzymatically inactive, Fc effector-silenced ACE2-Fc decoys. Inclusion of the ACE2 collectrin-like domain not only improves affinity for the S protein but also unexpectedly extends serum half-life and is necessary to reduce disease severity and viral titer in Syrian hamsters. Fc effector function is not required. The activity of ACE2 decoy receptors is due, in part, to their ability to trigger an irreversible structural change in the viral S protein. Our studies provide a new understanding of how ACE2 decoys function and support their development as therapeutics to treat ACE2-dependent coronaviruses.
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Affiliation(s)
- James A. Torchia
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Alexander H. Tavares
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Laura S. Carstensen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Da-Yuan Chen
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University, Boston Medical Center, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Tianshu Xiao
- Division of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia Mukherjee
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Patrick M. Reeves
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Hua Tu
- LakePharma Inc., San Carlos, CA 94070, USA
| | - Ann E. Sluder
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Bing Chen
- Division of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University, Boston Medical Center, and The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mohsan Saeed
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Gordon J. Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
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6
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Feng L, Fu S, Zhang P, Zhang Y, Zhao Y, Yao Y, Luo L, Ping P. Potential use of the S-protein-Angiotensin converting enzyme 2 binding pathway in the treatment of coronavirus disease 2019. Front Public Health 2022; 10:1050034. [PMID: 36518573 PMCID: PMC9742547 DOI: 10.3389/fpubh.2022.1050034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/15/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen that causes coronavirus disease 2019 (COVID-19), infects humans through a strong interaction between the viral spike protein (S-protein) and angiotensin converting enzyme 2 (ACE2) receptors on the cell surface. The infection of host lung cells by SARS-CoV-2 leads to clinical symptoms in patients. However, ACE2 expression is not restricted to the lungs; altered receptors have been found in the nasal and oral mucosa, vessel, brain, pancreas, gastrointestinal tract, kidney, and heart. The future of COVID-19 is uncertain, however, new viral variants are likely to emerge. The SARS-CoV-2 Omicron variant has a total of 50 gene mutations compared with the original virus; 15 of which occur in the receptor binding domain (RBD). The RBD of the viral S-protein binds to the human ACE2 receptor for viral entry. Mutations of the ACE2-RBD interface enhance tight binding by increasing hydrogen bond interactions and expanding the accessible surface area. Extracorporeal membrane oxygenation, hyperbaric oxygen, and aggressive dialysis for the treatment of COVID-19 have shown various degrees of clinical success. The use of decoy receptors based on the ACE2 receptor as a broadly potent neutralizer of SARS-CoV-2 variants has potential as a therapeutic mechanism. Drugs such as 3E8 could block binding of the S1-subunit to ACE2 and restrict the infection of ACE2-expressing cells by a variety of coronaviruses. Here, we discuss the development of ACE2-targeted strategies for the treatment and prevention of COVID-19.
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Affiliation(s)
- Long Feng
- Department of Anesthesia, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Shihui Fu
- Department of Geriatric Cardiology, Chinese People's Liberation Army General Hospital, Beijing, China
- Department of Cardiology, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Pei Zhang
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yujie Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yali Zhao
- Central Laboratory, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China
| | - Yao Yao
- Center for Healthy Aging and Development Studies, National School of Development, Peking University, Beijing, China
| | - Leiming Luo
- Department of Geriatric Cardiology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Ping Ping
- General Station for Drug and Instrument Supervision and Control, Joint Logistic Support Force of Chinese People's Liberation Army, Beijing, China
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7
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Tang H, Ke Y, Wang L, Wu M, Sun T, Zhu J. Recombinant Decoy Exhibits Broad Protection against Omicron and Resistance Potential to Future Variants. Pharmaceuticals (Basel) 2022; 15:1002. [PMID: 36015150 PMCID: PMC9413901 DOI: 10.3390/ph15081002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022] Open
Abstract
The Omicron variant has swept through most countries and become a dominant circulating strain, replacing the Delta variant. The evolutionary history of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suggests that the onset of another variant (possibly another variant of concern (VOC) is inevitable. Therefore, the development of therapeutics that enable treatments for all Omicron-included VOCs/variants of interest (VOIs) and future variants is desired. Recently, the recombinant receptor decoy therapeutic angiotensin-converting enzyme 2 (ACE2)-Fc has exhibited good safety in a phase 1 clinical trial; therefore, its variant-resistant profile needs to be understood. Here, we conducted a comprehensive evaluation of its neutralization breadth against the Omicron variant and other VOCs/VOIs. Furthermore, to evaluate its resistance to future variants, we investigated its ability to neutralize various single-residue mutated variants. Next, we demonstrated its resistance to evasion via an experiment that rapidly and effectively stimulates virus evolution with a replication-competent virus model. In addition, we evaluated its efficacy for cocktail therapy. The combination of ACE2-Fc and neutralizing antibodies showed both efficacy and breadth in the simulation experiment. The underlying mechanism was revealed to be a synergistic effect in the cocktails. Collectively, this study deepens the understanding of the resistance profile of recombinant receptor decoy therapeutics and highlights the potential value of ACE2-Fc and neutralizing antibody cocktails in the subsequent anti-SARS-CoV-2 campaign. Furthermore, we also provide an effective method to study the resistance profile of antiviral agents and rapidly screen for potential cocktails to combat future variants.
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Affiliation(s)
- Haoneng Tang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education of China, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yong Ke
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education of China, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education of China, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingyuan Wu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education of China, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tao Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China
| | - Jianwei Zhu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education of China, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Jecho Biopharmaceuticals Co., Ltd., Tianjin 300467, China
- Jecho Laboratories, Inc., Frederick, MD 21704, USA
- Jecho Institute, Co., Ltd., Shanghai 200240, China
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8
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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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9
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Wines BD, Kurtovic L, Trist HM, Esparon S, Lopez E, Chappin K, Chan LJ, Mordant FL, Lee WS, Gherardin NA, Patel SK, Hartley GE, Pymm P, Cooney JP, Beeson JG, Godfrey DI, Burrell LM, van Zelm MC, Wheatley AK, Chung AW, Tham WH, Subbarao K, Kent SJ, Hogarth PM. Fc engineered ACE2-Fc is a potent multifunctional agent targeting SARS-CoV2. Front Immunol 2022; 13:889372. [PMID: 35967361 PMCID: PMC9369017 DOI: 10.3389/fimmu.2022.889372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/27/2022] [Indexed: 01/26/2023] Open
Abstract
Joining a function-enhanced Fc-portion of human IgG to the SARS-CoV-2 entry receptor ACE2 produces an antiviral decoy with strain transcending virus neutralizing activity. SARS-CoV-2 neutralization and Fc-effector functions of ACE2-Fc decoy proteins, formatted with or without the ACE2 collectrin domain, were optimized by Fc-modification. The different Fc-modifications resulted in distinct effects on neutralization and effector functions. H429Y, a point mutation outside the binding sites for FcγRs or complement caused non-covalent oligomerization of the ACE2-Fc decoy proteins, abrogated FcγR interaction and enhanced SARS-CoV-2 neutralization. Another Fc mutation, H429F did not improve virus neutralization but resulted in increased C5b-C9 fixation and transformed ACE2-Fc to a potent mediator of complement-dependent cytotoxicity (CDC) against SARS-CoV-2 spike (S) expressing cells. Furthermore, modification of the Fc-glycan enhanced cell activation via FcγRIIIa. These different immune profiles demonstrate the capacity of Fc-based agents to be engineered to optimize different mechanisms of protection for SARS-CoV-2 and potentially other viral pathogens.
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Affiliation(s)
- Bruce D. Wines
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia,Life Sciences, Burnet Institute, Melbourne, VIC, Australia,Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, Australia
| | - Liriye Kurtovic
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia,Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Halina M. Trist
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
| | - Sandra Esparon
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
| | - Ester Lopez
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Klasina Chappin
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia
| | - Li-Jin Chan
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Francesca L. Mordant
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Sheila K. Patel
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Gemma E. Hartley
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Phillip Pymm
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James P. Cooney
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James G. Beeson
- Life Sciences, Burnet Institute, Melbourne, VIC, Australia,Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia,Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia,Department of Microbiology, Monash University, Clayton VIC, Australia
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Louise M. Burrell
- Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Menno C. van Zelm
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia,Department of Allergy, Immunology and Respiratory Medicine, Central Clinical School, Alfred Hospital, Melbourne, VIC, Australia
| | - Adam K. Wheatley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia,Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Melbourne, VIC, Australia
| | - Amy W. Chung
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Wai-Hong Tham
- Infectious Diseases and Immune Defence Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia,World Health Organization (WHO) Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephen J. Kent
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia,Australian Research Council Centre for Excellence in Convergent Bio-Nano Science and Technology, The University of Melbourne, Melbourne, VIC, Australia,Melbourne Sexual Health Centre and Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - P. Mark Hogarth
- Immune therapies Laboratory, Burnet Institute, Melbourne, VIC, Australia,Life Sciences, Burnet Institute, Melbourne, VIC, Australia,Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia,*Correspondence: P. Mark Hogarth,
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10
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Gutman H, Aftalion M, Melamed S, Politi B, Nevo R, Havusha-Laufer S, Achdout H, Gur D, Israely T, Dachir S, Mamroud E, Sagi I, Vagima Y. Matrix Metalloproteinases Expression Is Associated with SARS-CoV-2-Induced Lung Pathology and Extracellular-Matrix Remodeling in K18-hACE2 Mice. Viruses 2022; 14:1627. [PMID: 35893698 PMCID: PMC9332556 DOI: 10.3390/v14081627] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 infection induced lung inflammation characterized by cytokine storm and fulminant immune response of both resident and migrated immune cells, accelerating alveolar damage. In this work we identified members of the matrix metalloprotease (MMPs) family associated with lung extra-cellular matrix (ECM) destruction using K18-hACE2-transgenic mice (K18-hACE2) infected intranasally with SARS-CoV-2. Five days post infection, the lungs exhibited overall alveolar damage of epithelial cells and massive leukocytes infiltration. A substantial pulmonary increase in MMP8, MMP9, and MMP14 in the lungs post SARS-CoV-2 infection was associated with degradation of ECM components including collagen, laminin, and proteoglycans. The process of tissue damage and ECM degradation during SARS-CoV-2 lung infection is suggested to be associated with activity of members of the MMPs family, which in turn may be used as a therapeutic intervention.
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Affiliation(s)
- Hila Gutman
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
- Department of Biological Regulation, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
- Department of Biomolecular Sciences, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Moshe Aftalion
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Sharon Melamed
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Boaz Politi
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Reinat Nevo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Sapir Havusha-Laufer
- Department of Biological Regulation, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Hagit Achdout
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - David Gur
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Tomer Israely
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Shlomit Dachir
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Emanuelle Mamroud
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Herzel 234, Rehovot P.O. Box 26, Israel;
| | - Yaron Vagima
- Israel Institute for Biological Research, Ness Ziona P.O. Box 19, Israel; (H.G.); (M.A.); (S.M.); (B.P.); (H.A.); (D.G.); (T.I.); (S.D.); (E.M.)
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11
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Chen Y, Sun L, Ullah I, Beaudoin-Bussières G, Anand SP, Hederman AP, Tolbert WD, Sherburn R, Nguyen DN, Marchitto L, Ding S, Wu D, Luo Y, Gottumukkala S, Moran S, Kumar P, Piszczek G, Mothes W, Ackerman ME, Finzi A, Uchil PD, Gonzalez FJ, Pazgier M. Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities. SCIENCE ADVANCES 2022; 8:eabn4188. [PMID: 35857504 PMCID: PMC9278865 DOI: 10.1126/sciadv.abn4188] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/27/2022] [Indexed: 05/27/2023]
Abstract
Soluble angiotensin-converting enzyme 2 (ACE2) constitutes an attractive antiviral capable of targeting a wide range of coronaviruses using ACE2 as their receptor. Using structure-guided approaches, we developed a series of bivalent ACE2-Fcs harboring functionally and structurally validated mutations that enhance severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain recognition by up to ~12-fold and remove angiotensin enzymatic activity. The lead variant M81 potently cross-neutralized SARS-CoV-2 variants of concern (VOCs), including Omicron, at subnanomolar half-maximal inhibitory concentration and was capable of robust Fc-effector functions, including antibody-dependent cellular cytotoxicity, phagocytosis, and complement deposition. When tested in a stringent K18-hACE2 mouse model, Fc-enhanced ACE2-Fc delayed death by 3 to 5 days or effectively resolved lethal SARS-CoV-2 infection in both prophylactic and therapeutic settings via the combined effects of neutralization and Fc-effector functions. These data add to the demonstrated utility of soluble ACE2 as a valuable SARS-CoV-2 antiviral and indicate that Fc-effector functions may constitute an important component of ACE2-Fc therapeutic activity.
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Affiliation(s)
- Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Irfan Ullah
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | | | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Lorie Marchitto
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuhong Luo
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Sean Moran
- Biomedical Instrumentation Center, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Priti Kumar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
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