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Chen L, He Y, Liu H, Shang Y, Guo G. Potential immune evasion of the severe acute respiratory syndrome coronavirus 2 Omicron variants. Front Immunol 2024; 15:1339660. [PMID: 38464527 PMCID: PMC10924305 DOI: 10.3389/fimmu.2024.1339660] [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: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic. The Omicron variant (B.1.1.529) was first discovered in November 2021 in specimens collected from Botswana, South Africa. Omicron has become the dominant variant worldwide, and several sublineages or subvariants have been identified recently. Compared to those of other mutants, the Omicron variant has the most highly expressed amino acid mutations, with almost 60 mutations throughout the genome, most of which are in the spike (S) protein, especially in the receptor-binding domain (RBD). These mutations increase the binding affinity of Omicron variants for the ACE2 receptor, and Omicron variants may also lead to immune escape. Despite causing milder symptoms, epidemiological evidence suggests that Omicron variants have exceptionally higher transmissibility, higher rates of reinfection and greater spread than the prototype strain as well as other preceding variants. Additionally, overwhelming amounts of data suggest that the levels of specific neutralization antibodies against Omicron variants decrease in most vaccinated populations, although CD4+ and CD8+ T-cell responses are maintained. Therefore, the mechanisms underlying Omicron variant evasion are still unclear. In this review, we surveyed the current epidemic status and potential immune escape mechanisms of Omicron variants. Especially, we focused on the potential roles of viral epitope mutations, antigenic drift, hybrid immunity, and "original antigenic sin" in mediating immune evasion. These insights might supply more valuable concise information for us to understand the spreading of Omicron variants.
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Affiliation(s)
- Luyi Chen
- Chongqing Nankai Secondary School, Chongqing, China
| | - Ying He
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Hongye Liu
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Yongjun Shang
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
| | - Guoning Guo
- Department of Orthopedics, Kweichow MouTai Hospital, Renhuai, Zunyi, Guizhou, China
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Zhang Y, Wang D, Xiang Q, Hu X, Zhang Y, Wu L, Zhang Z, Wang Y, Zhao J, McCormick PJ, Fu J, Fu Y, Zhang J, Jiang H, Li J. A potent neutralizing nanobody targeting a unique epitope on the receptor-binding domain of SARS-CoV-2 spike protein. Virology 2024; 589:109925. [PMID: 37984151 DOI: 10.1016/j.virol.2023.109925] [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: 06/13/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
SARS-CoV-2 and its variants continue to threaten public health. Nanobodies that block the attachment of the RBD to host cell angiotensin-converting enzyme 2 (ACE2) represent promising drug candidates. In this study, we reported the identification and structural biological characterization of a nanobody from a RBD-immunized alpaca. The nanobody, termed as 2S-1-19, shows outstanding neutralizing activity against both pseudotyped and authentic SARS-CoV-2 viruses. The crystal structure of 2S-1-19 bound to SARS-CoV-2 RBD reveals an epitope that overlaps with the binding site for ACE2. We also showed that 2S-1-19 reserves promising, though compromised, neutralizing activity against the Delta variant and that the trivalent form of 2S-1-19 remarkably increases its neutralizing capacity. Despite this, neither the monomeric or trimeric 2S-1-19 could neutralize the Omicron BA.1.1 variant, possibility due to the E484A and Q493K mutations found within this virus variant. These data provide insights into immune evasion caused by SARS-CoV-2 variants.
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Affiliation(s)
- Yuting Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Dan Wang
- Key Lab for Agro-product Processing and Quality Control of Nanchang City, College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qi Xiang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaohui Hu
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Yuting Zhang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, 518118, China
| | - Lijie Wu
- IHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Zhaoyong Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 511436, China; Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, 510060, China; Guangzhou Laboratory, Bio-island, Guangzhou, Guangdong, 510320, China; Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Peter J McCormick
- William Harvey Research Institute, Bart's and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Jinheng Fu
- Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, 330047, China.
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
| | - Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China.
| | - Jian Li
- College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, China.
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Ben Geoffrey AS, Gracia J. A Bayesian walker coupled with a computational workflow that generates the micro-evolution of SARS-CoV-2 and makes predictions of new mutations that can emerge. J Biomol Struct Dyn 2023:1-9. [PMID: 37771150 DOI: 10.1080/07391102.2023.2263798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/22/2023] [Indexed: 09/30/2023]
Abstract
In this work, a Bayesian walker was constructed that generates mutations that are more prone as per UNIPROT variant data. The Bayesian walker was used to search the mutational landscape of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) and a computational workflow was followed to evaluate whether a particular mutation would satisfy natural selection's fitness criteria. For SARS-CoV-2, the empirical known fitness criteria derived from SARS-CoV-2 micro-evolution data is 3-fold criteria. Mutations that have emerged on the Spike protein of SARS-CoV-2 are ones that preserve the structural integrity of the Spike, retain, or increase infectivity and are Immune evasive as per literature reports. Based on the molecular mechanism of infectivity and Immune evasion of SARS-CoV-2, a molecular modelling workflow was adopted to investigate the evolutionary feasibility of the mutations generated by the walker, to check whether the mutations satisfy the 3-fold fitness criteria for SARS-CoV-2 micro-evolution. It was found that the walker (mutation generator) coupled with the computational workflow to evaluate the evolutionary fitness of the generated mutations, re-generated the mutants corresponding to the Alpha, Beta and Gamma variants of SARS-CoV-2 demonstrating the ability of the methodology to generate the micro-evolution of SARS-CoV-2. Having demonstrated the ability of the methodology to generate the micro-evolution of SARS-CoV-2, the computational methodology was used to make predictions for new mutants that could emerge.Communicated by Ramaswamy H. Sarma.
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Chu M, Ji H, Li K, Liu H, Peng M, Wang Z, Zhu X. Investigating the potential mechanism of quercetin against cervical cancer. Discov Oncol 2023; 14:170. [PMID: 37704909 PMCID: PMC10499770 DOI: 10.1007/s12672-023-00788-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Cervical cancer is emerging as a potential target of increased susceptibility to coronavirus disease-2019 (COVID-19), leading to compromised survival rates. Despite this critical link, efficacious anti-cervical cancer/COVID-19 interventions remain limited. Quercetin, known for its efficacy against both cancer and viral infections, holds promise as a therapeutic agent. This study aims to elucidate quercetin's anti-cervical cancer/COVID-19 mechanisms and potential targets. METHODS We initiated our investigation with differential gene expression analysis using cervical cancer transcriptome data from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx), focusing on intersections with COVID-19-related genes. Network pharmacology was employed to identify the shared targets between cervical cancer/COVID-19 DEGs and quercetin's targets. Subsequently, Cox proportional hazards analyses were employed to establish a risk score based on these genes. Molecular docking techniques were applied to predict quercetin's therapeutic targets and mechanisms for mitigating cervical cancer and COVID-19. RESULTS Our findings unveiled 45 potential quercetin targets with anti-cervical cancer/COVID-19 actions. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses highlighted significant enrichment in immune pathways and COVID-19-related pathways. A refined risk score model, comprising PLA2G7, TNF, TYK2, F2, and NRP1, effectively stratified cervical cancer patients into distinct risk groups. Importantly, molecular docking analyses illuminated quercetin's remarkable binding affinity to the primary protease of the coronavirus. CONCLUSIONS In summation, our study suggests that quercetin holds promise as a potential therapeutic agent for mitigating coronavirus function, specifically through its interaction with the primary protease. This research offers novel insights into exploring COVID-19 susceptibility and enhancing survival in cervical cancer patients.
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Affiliation(s)
- Man Chu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Huihui Ji
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Kehan Li
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hejing Liu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Mengjia Peng
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhiwei Wang
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Xueqiong Zhu
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China.
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Gromowski GD, Cincotta CM, Mayer S, King J, Swafford I, McCracken MK, Coleman D, Enoch J, Storme C, Darden J, Peel S, Epperson D, McKee K, Currier JR, Okulicz J, Paquin-Proulx D, Cowden J, Peachman K. Humoral immune responses associated with control of SARS-CoV-2 breakthrough infections in a vaccinated US military population. EBioMedicine 2023; 94:104683. [PMID: 37413891 PMCID: PMC10345251 DOI: 10.1016/j.ebiom.2023.104683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND COVID-19 vaccines have been critical for protection against severe disease following infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) but gaps remain in our understanding of the immune responses that contribute to controlling subclinical and mild infections. METHODS Vaccinated, active-duty US military service members were enrolled in a non-interventional, minimal-risk, observational study starting in May, 2021. Clinical data, serum, and saliva samples were collected from study participants and were used to characterise the humoral immune responses to vaccination and to assess its impact on clinical and subclinical infections, as well as virologic outcomes of breakthrough infections (BTI) including viral load and infection duration. FINDINGS The majority of VIRAMP participants had received the Pfizer COVID-19 vaccine and by January, 2022, N = 149 had a BTI. The median BTI duration (PCR+ days) was 4 days and the interquartile range was 1-8 days. Participants that were nucleocapsid seropositive prior to their BTI had significantly higher levels of binding and functional antibodies to the spike protein, shorter median duration of infections, and lower median peak viral loads compared to seronegative participants. Furthermore, levels of neutralising antibody, ACE2 blocking activity, and spike-specific IgA measured prior to BTI also correlated with the duration of infection. INTERPRETATION We extended previous findings and demonstrate that a subset of vaccine-induced humoral immune responses, along with nucleocapsid serostatus are associated with control of SARS-CoV-2 breakthrough infections in the upper airways. FUNDING This work was funded by the DoD Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND) in collaboration with the Defense Health Agency (DHA) COVID-19 funding initiative for the VIRAMP study.
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Affiliation(s)
- Gregory D Gromowski
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Camila Macedo Cincotta
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Sandra Mayer
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jocelyn King
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Isabella Swafford
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Michael K McCracken
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Dante Coleman
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jennifer Enoch
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Casey Storme
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Janice Darden
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sheila Peel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane Epperson
- Booz Allen Hamilton, McLean, VA, USA; Enabling Biotechnologies, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense, Frederick, MD, USA
| | | | - Jeffrey R Currier
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason Okulicz
- Department of Infectious Disease, Brooke Army Medical Center, San Antonio, TX, USA
| | - Dominic Paquin-Proulx
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jessica Cowden
- Enabling Biotechnologies, Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense, Frederick, MD, USA; Department of Retrovirology, U.S. Army Medical Directorate-Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand.
| | - Kristina Peachman
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Pandit R, Matthews QL. A SARS-CoV-2: Companion Animal Transmission and Variants Classification. Pathogens 2023; 12:775. [PMID: 37375465 DOI: 10.3390/pathogens12060775] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous emergence of novel viruses and their diseases are a threat to global public health as there have been three outbreaks of coronaviruses that are highly pathogenic to humans in the span of the last two decades, severe acute respiratory syndrome (SARS)-CoV in 2002, Middle East respiratory syndrome (MERS)-CoV in 2012, and novel SARS-CoV-2 which emerged in 2019. The unprecedented spread of SARS-CoV-2 worldwide has given rise to multiple SARS-CoV-2 variants that have either altered transmissibility, infectivity, or immune escaping ability, causing diseases in a broad range of animals including human and non-human hosts such as companion, farm, zoo, or wild animals. In this review, we have discussed the recent SARS-CoV-2 outbreak, potential animal reservoirs, and natural infections in companion and farm animals, with a particular focus on SARS-CoV-2 variants. The expeditious development of COVID-19 vaccines and the advancements in antiviral therapeutics have contained the COVID-19 pandemic to some extent; however, extensive research and surveillance concerning viral epidemiology, animal transmission, variants, or seroprevalence in diverse hosts are essential for the future eradication of COVID-19.
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Affiliation(s)
- Rachana Pandit
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
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Harne R, Williams B, Abdelaal HFM, Baldwin SL, Coler RN. SARS-CoV-2 infection and immune responses. AIMS Microbiol 2023; 9:245-276. [PMID: 37091818 PMCID: PMC10113164 DOI: 10.3934/microbiol.2023015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/03/2023] Open
Abstract
The recent pandemic caused by the SARS-CoV-2 virus continues to be an enormous global challenge faced by the healthcare sector. Availability of new vaccines and drugs targeting SARS-CoV-2 and sequelae of COVID-19 has given the world hope in ending the pandemic. However, the emergence of mutations in the SARS-CoV-2 viral genome every couple of months in different parts of world is a persistent danger to public health. Currently there is no single treatment to eradicate the risk of COVID-19. The widespread transmission of SARS-CoV-2 due to the Omicron variant necessitates continued work on the development and implementation of effective vaccines. Moreover, there is evidence that mutations in the receptor domain of the SARS-CoV-2 spike glycoprotein led to the decrease in current vaccine efficacy by escaping antibody recognition. Therefore, it is essential to actively identify the mechanisms by which SARS-CoV-2 evades the host immune system, study the long-lasting effects of COVID-19 and develop therapeutics targeting SARS-CoV-2 infections in humans and preclinical models. In this review, we describe the pathogenic mechanisms of SARS-CoV-2 infection as well as the innate and adaptive host immune responses to infection. We address the ongoing need to develop effective vaccines that provide protection against different variants of SARS-CoV-2, as well as validated endpoint assays to evaluate the immunogenicity of vaccines in the pipeline, medications, anti-viral drug therapies and public health measures, that will be required to successfully end the COVID-19 pandemic.
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Affiliation(s)
- Rakhi Harne
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Brittany Williams
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Hazem F. M. Abdelaal
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Susan L. Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
| | - Rhea N. Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
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Dong J, Varbanov M, Philippot S, Vreken F, Zeng WB, Blay V. Ligand-based discovery of coronavirus main protease inhibitors using MACAW molecular embeddings. J Enzyme Inhib Med Chem 2023; 38:24-35. [PMID: 36305272 PMCID: PMC9621234 DOI: 10.1080/14756366.2022.2132486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ligand-based drug design methods are thought to require large experimental datasets to become useful for virtual screening. In this work, we propose a computational strategy to design novel inhibitors of coronavirus main protease, Mpro. The pipeline integrates publicly available screening and binding affinity data in a two-stage machine-learning model using the recent MACAW embeddings. Once trained, the model can be deployed to rapidly screen large libraries of molecules in silico. Several hundred thousand compounds were virtually screened and 10 of them were selected for experimental testing. From these 10 compounds, 8 showed a clear inhibitory effect on recombinant Mpro, with half-maximal inhibitory concentration values (IC50) in the range 0.18–18.82 μM. Cellular assays were also conducted to evaluate cytotoxic, haemolytic, and antiviral properties. A promising lead compound against coronavirus Mpro was identified with dose-dependent inhibition of virus infectivity and minimal toxicity on human MRC-5 cells.
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Affiliation(s)
- Jie Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, P. R. China
| | - Mihayl Varbanov
- Université de Lorraine, CNRS, Nancy, France
- Laboratoire de Virologie, CHRU de Nancy Brabois, Vandoeuvre-lès-Nancy, France
| | | | | | - Wen-bin Zeng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, P. R. China
| | - Vincent Blay
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, USA
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