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Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
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Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Notin P, Rollins N, Gal Y, Sander C, Marks D. Machine learning for functional protein design. Nat Biotechnol 2024; 42:216-228. [PMID: 38361074 DOI: 10.1038/s41587-024-02127-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024]
Abstract
Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. New methods promise to escape the constraints of natural and laboratory evolution, accelerating the generation of proteins for applications in biotechnology and medicine. To make sense of the exploding diversity of machine learning approaches, we introduce a unifying framework that classifies models on the basis of their use of three core data modalities: sequences, structures and functional labels. We discuss the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more. We then highlight trends shaping the future of this field, from large-scale assays to more robust benchmarks, multimodal foundation models, enhanced sampling strategies and laboratory automation.
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Affiliation(s)
- Pascal Notin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Computer Science, University of Oxford, Oxford, UK.
| | | | - Yarin Gal
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Debora Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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Loi LK, Yang CC, Lin YC, Su YF, Juan YC, Chen YH, Chang HC. Decoy peptides effectively inhibit the binding of SARS-CoV-2 to ACE2 on oral epithelial cells. Heliyon 2023; 9:e22614. [PMID: 38107325 PMCID: PMC10724569 DOI: 10.1016/j.heliyon.2023.e22614] [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: 06/08/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
The entry of SARS-CoV-2 into host cells involves the interaction between the viral spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. Given that the spike protein evolves rapidly to evade host immunity, therapeutics that block ACE2 accessibility, such as spike decoys, could serve as an alternative strategy for attenuating viral infection. Here, we constructed a drug screening platform based on oral epithelial cells to rapidly identify peptides or compounds capable of blocking the spike-ACE2 interaction. We engineered short decoy peptides, 8 to 14 amino acids in length, using the spike protein's receptor-binding motif (RBM) and demonstrated that these peptides can effectively inhibit virus attachment to host cells. Additionally, we discovered that diminazene aceturate (DIZE), an ACE2 activator, similarly inhibited virus binding. Our research thus validates the potential of decoy peptides as a new therapeutic strategy against SARS-CoV-2 infections, opening avenues for further development and study.
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Affiliation(s)
- Lai-Keng Loi
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Cheng-Chieh Yang
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Stomatology, Oral & Maxillofacial Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yee-Fun Su
- iStat Biomedical Co., Ltd, New Taipei City, Taiwan
| | - Yi-Chen Juan
- iStat Biomedical Co., Ltd, New Taipei City, Taiwan
| | - Yi-Hsin Chen
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsiu-Chuan Chang
- Institute of Oral Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
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Llewellyn GN, Chen HY, Rogers GL, Huang X, Sell PJ, Henley JE, Cannon PM. Comparison of SARS-CoV-2 entry inhibitors based on ACE2 receptor or engineered Spike-binding peptides. J Virol 2023; 97:e0068423. [PMID: 37555663 PMCID: PMC10506483 DOI: 10.1128/jvi.00684-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
With increasing resistance of SARS-CoV-2 variants to antibodies, there is interest in developing entry inhibitors that target essential receptor-binding regions of the viral Spike protein and thereby present a high bar for viral resistance. Such inhibitors could be derivatives of the viral receptor, ACE2, or peptides engineered to interact specifically with the Spike receptor-binding pocket. We compared the efficacy of a series of both types of entry inhibitors, constructed as fusions to an antibody Fc domain. Such a design can increase protein stability and act to both neutralize free virus and recruit effector functions to clear infected cells. We tested the reagents against prototype variants of SARS-CoV-2, using both Spike pseudotyped vesicular stomatitis virus vectors and replication-competent viruses. These analyses revealed that an optimized ACE2 derivative could neutralize all variants we tested with high efficacy. In contrast, the Spike-binding peptides had varying activities against different variants, with resistance observed in the Spike proteins from Beta, Gamma, and Omicron (BA.1 and BA.5). The resistance mapped to mutations at Spike residues K417 and N501 and could be overcome for one of the peptides by linking two copies in tandem, effectively creating a tetrameric reagent in the Fc fusion. Finally, both the optimized ACE2 and tetrameric peptide inhibitors provided some protection to human ACE2 transgenic mice challenged with the SARS-CoV-2 Delta variant, which typically causes death in this model within 7-9 days. IMPORTANCE The increasing resistance of SARS-CoV-2 variants to therapeutic antibodies has highlighted the need for new treatment options, especially in individuals who do not respond to vaccination. Receptor decoys that block viral entry are an attractive approach because of the presumed high bar to developing viral resistance. Here, we compare two entry inhibitors based on derivatives of the ACE2 receptor, or engineered peptides that bind to the receptor-binding pocket of the SARS-CoV-2 Spike protein. In each case, the inhibitors were fused to immunoglobulin Fc domains, which can further enhance therapeutic properties, and compared for activity against different SARS-CoV-2 variants. Potent inhibition against multiple SARS-CoV-2 variants was demonstrated in vitro, and even relatively low single doses of optimized reagents provided some protection in a mouse model, confirming their potential as an alternative to antibody therapies.
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Affiliation(s)
- George N. Llewellyn
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Hsu-Yu Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Geoffrey L. Rogers
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Xiaoli Huang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Philip J. Sell
- The Hastings Foundation and The Wright Foundation Laboratories, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Jill E. Henley
- The Hastings Foundation and The Wright Foundation Laboratories, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Paula M. Cannon
- Department of Molecular Microbiology and Immunology, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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Lu M, Yao W, Li Y, Ma D, Zhang Z, Wang H, Tang X, Wang Y, Li C, Cheng D, Lin H, Yin Y, Zhao J, Zhong G. Broadly Effective ACE2 Decoy Proteins Protect Mice from Lethal SARS-CoV-2 Infection. Microbiol Spectr 2023; 11:e0110023. [PMID: 37395664 PMCID: PMC10434153 DOI: 10.1128/spectrum.01100-23] [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: 03/14/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been causing increasingly serious drug resistance problem, development of broadly effective and hard-to-escape anti-SARS-CoV-2 agents is an urgent need. Here, we describe further development and characterization of two SARS-CoV-2 receptor decoy proteins, ACE2-Ig-95 and ACE2-Ig-105/106. We found that both proteins had potent and robust in vitro neutralization activities against diverse SARS-CoV-2 variants, including BQ.1 and XBB.1, that are resistant to most clinically used monoclonal antibodies. In a stringent lethal SARS-CoV-2 infection mouse model, both proteins lowered the lung viral load by up to ~1,000-fold, prevented the emergence of clinical signs in >75% animals, and increased the animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously described ACE2-Ig constructs, we found that two constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the receptor binding domain (RBD)-binding interface should be avoided or performed with extra caution. Furthermore, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to the level of grams per liter, demonstrating the developability of them as biologic drug candidates. Stress condition stability testing of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses. IMPORTANCE Engineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to creating broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This article describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants, including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously described ACE2 decoy constructs was performed here. Two previously described constructs with relatively more ACE2 surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Furthermore, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broad anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses.
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Affiliation(s)
- Mengjia Lu
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Weitong Yao
- Hubei JiangXia Laboratory, Wuhan, Hubei, China
| | - Yujun Li
- Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Danting Ma
- Tianjin Medical University Chu Hsien-I Memorial Hospital, Tianjin, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haimin Wang
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Xiaojuan Tang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chao Li
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Dechun Cheng
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Hua Lin
- Biomedical Research Center of South China, Fujian Normal University, Fuzhou, Fujian, China
| | - Yandong Yin
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Guocai Zhong
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, China
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
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Gagne M, Flynn BJ, Honeycutt CC, Flebbe DR, Andrew SF, Provost SJ, McCormick L, Van Ry A, McCarthy E, Todd JPM, Bao S, Teng IT, Marciano S, Rudich Y, Li C, Pessaint L, Dodson A, Cook A, Lewis MG, Andersen H, Zahradník J, Nason MC, Foulds KE, Kwong PD, Roederer M, Schreiber G, Seder RA, Douek DC. RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544432. [PMID: 37503026 PMCID: PMC10370179 DOI: 10.1101/2023.06.09.544432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.
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Chen Y, Cao B, Zhou Q, Liu Y, He Q, Zhao M. Bibliometric evaluation of 2020-2022 publications on COVID-19-related cardiovascular disease. Front Cardiovasc Med 2023; 9:1070336. [PMID: 36712251 PMCID: PMC9880207 DOI: 10.3389/fcvm.2022.1070336] [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: 10/14/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Objective This study aimed to investigate the international scientific output regarding the relationship between COVID-19 and cardiovascular diseases (CVDs) through a bibliometric analysis and explore research hotspots in this field. Methods We searched the Web of Science Core Collection for publications and used different types of software, such as R, CiteSpace, and VOSviewer, to analyze and visualize the data. Results A total of 10,055 publications were retrieved as of the 13 December 2022, based on the inclusion criteria after screening. The USA and China lead in the quantity and quality of publications in this field. Based on Bradford's law, 63 journals were considered core journals in the field. Co-cited references and keywords analysis indicated that researchers paid particular attention to cardiovascular comorbidities, outcomes, and COVID-19 regenerative medicine. In summary, with increasing COVID-19 research related to CVD, more attention might be drawn to the relationship between these two diseases. Conclusion The hotspots in this field may continue to revolve around cardiovascular comorbidities, outcomes, and COVID-19 regenerative medicine. Owing to the different situations faced by different groups with COVID-19, further exploration of the related factors specific to each of these groups, e.g., history or no history of heart failure, is needed, with a view to providing a reference for intervention measures in COVID-19 research.
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Affiliation(s)
- Yiru Chen
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, China
| | - Buzi Cao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Medical School, Hunan Normal University, Changsha, China
| | - Quan Zhou
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, China
| | - Yantong Liu
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, China
| | - Qingnan He
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Qingnan He ✉
| | - Mingyi Zhao
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Mingyi Zhao ✉
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