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Al Khalaf R, Bernasconi A, Pinoli P. Systematic analysis of SARS-CoV-2 Omicron subvariants' impact on B and T cell epitopes. PLoS One 2024; 19:e0307873. [PMID: 39298436 PMCID: PMC11412522 DOI: 10.1371/journal.pone.0307873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/14/2024] [Indexed: 09/21/2024] Open
Abstract
INTRODUCTION Epitopes are specific structures in antigens that are recognized by the immune system. They are widely used in the context of immunology-related applications, such as vaccine development, drug design, and diagnosis / treatment / prevention of disease. The SARS-CoV-2 virus has represented the main point of interest within the viral and genomic surveillance community in the last four years. Its ability to mutate and acquire new characteristics while it reorganizes into new variants has been analyzed from many perspectives. Understanding how epitopes are impacted by mutations that accumulate on the protein level cannot be underrated. METHODS With a focus on Omicron-named SARS-CoV-2 lineages, including the last WHO-designated Variants of Interest, we propose a workflow for data retrieval, integration, and analysis pipeline for conducting a database-wide study on the impact of lineages' characterizing mutations on all T cell and B cell linear epitopes collected in the Immune Epitope Database (IEDB) for SARS-CoV-2. RESULTS Our workflow allows us to showcase novel qualitative and quantitative results on 1) coverage of viral proteins by deposited epitopes; 2) distribution of epitopes that are mutated across Omicron variants; 3) distribution of Omicron characterizing mutations across epitopes. Results are discussed based on the type of epitope, the response frequency of the assays, and the sample size. Our proposed workflow can be reproduced at any point in time, given updated variant characterizations and epitopes from IEDB, thereby guaranteeing to observe a quantitative landscape of mutations' impact on demand. CONCLUSION A big data-driven analysis such as the one provided here can inform the next genomic surveillance policies in combatting SARS-CoV-2 and future epidemic viruses.
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Affiliation(s)
- Ruba Al Khalaf
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Anna Bernasconi
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Pietro Pinoli
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
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2
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Dong Y, Wang J, Chen L, Chen H, Dang S, Li F. Aptamer-based assembly systems for SARS-CoV-2 detection and therapeutics. Chem Soc Rev 2024; 53:6830-6859. [PMID: 38829187 DOI: 10.1039/d3cs00774j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Nucleic acid aptamers are oligonucleotide chains with molecular recognition properties. Compared with antibodies, aptamers show advantages given that they are readily produced via chemical synthesis and elicit minimal immunogenicity in biomedicine applications. Notably, aptamer-encoded nucleic acid assemblies further improve the binding affinity of aptamers with the targets due to their multivalent synergistic interactions. Specially, aptamers can be engineered with special topological arrangements in nucleic acid assemblies, which demonstrate spatial and valence matching towards antigens on viruses, thus showing potential in the detection and therapeutic applications of viruses. This review presents the recent progress on the aptamers explored for SARS-CoV-2 detection and infection treatment, wherein applications of aptamer-based assembly systems are introduced in detail. Screening methods and chemical modification strategies for aptamers are comprehensively summarized, and the types of aptamers employed against different target domains of SARS-CoV-2 are illustrated. The evolution of aptamer-based assembly systems for the detection and neutralization of SARS-CoV-2, as well as the construction principle and characteristics of aptamer-based DNA assemblies are demonstrated. The typically representative works are presented to demonstrate how to assemble aptamers rationally and elaborately for specific applications in SARS-CoV-2 diagnosis and neutralization. Finally, we provide deep insights into the current challenges and future perspectives towards aptamer-based nucleic acid assemblies for virus detection and neutralization in nanomedicine.
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Affiliation(s)
- Yuhang Dong
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Jingping Wang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Ling Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Haonan Chen
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Shuangbo Dang
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
| | - Feng Li
- State Key Laboratory of Chemical Resource Engineering, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P. R. China.
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Liu B, Liu H, Han P, Wang X, Wang C, Yan X, Lei W, Xu K, Zhou J, Qi J, Fan R, Wu G, Tian WX, Gao GF, Wang Q. Enhanced potency of an IgM-like nanobody targeting conserved epitope in SARS-CoV-2 spike N-terminal domain. Signal Transduct Target Ther 2024; 9:131. [PMID: 38740785 PMCID: PMC11091055 DOI: 10.1038/s41392-024-01847-8] [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: 08/04/2023] [Revised: 03/25/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Almost all the neutralizing antibodies targeting the receptor-binding domain (RBD) of spike (S) protein show weakened or lost efficacy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged or emerging variants, such as Omicron and its sub-variants. This suggests that highly conserved epitopes are crucial for the development of neutralizing antibodies. Here, we present one nanobody, N235, displaying broad neutralization against the SARS-CoV-2 prototype and multiple variants, including the newly emerged Omicron and its sub-variants. Cryo-electron microscopy demonstrates N235 binds a novel, conserved, cryptic epitope in the N-terminal domain (NTD) of the S protein, which interferes with the RBD in the neighboring S protein. The neutralization mechanism interpreted via flow cytometry and Western blot shows that N235 appears to induce the S1 subunit shedding from the trimeric S complex. Furthermore, a nano-IgM construct (MN235), engineered by fusing N235 with the human IgM Fc region, displays prevention via inducing S1 shedding and cross-linking virus particles. Compared to N235, MN235 exhibits varied enhancement in neutralization against pseudotyped and authentic viruses in vitro. The intranasal administration of MN235 in low doses can effectively prevent the infection of Omicron sub-variant BA.1 and XBB in vivo, suggesting that it can be developed as a promising prophylactic antibody to cope with the ongoing and future infection.
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Affiliation(s)
- Bo Liu
- College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
| | - Honghui Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
| | - Xiaoyun Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
| | - Chunmei Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
- School of Life Sciences, Yunnan University, 650504, Kunming, Yunnan Province, China
| | - Xinxin Yan
- College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
| | - Wenwen Lei
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China
| | - Ke Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China
| | - Jianjie Zhou
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, 101408, Beijing, China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China
| | - Guizhen Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), 102206, Beijing, China.
| | - Wen-Xia Tian
- College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China.
| | - George F Gao
- College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China.
| | - Qihui Wang
- College of Veterinary Medicine, Shanxi Agricultural University, 030801, Jinzhong, China.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), 100101, Beijing, China.
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4
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Wang Y, Wang T, Li S, He X, Li M, Wang Z, Zheng N, Shao B, Liu TY. Enhancing geometric representations for molecules with equivariant vector-scalar interactive message passing. Nat Commun 2024; 15:313. [PMID: 38182565 PMCID: PMC10770089 DOI: 10.1038/s41467-023-43720-2] [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: 05/04/2023] [Accepted: 11/16/2023] [Indexed: 01/07/2024] Open
Abstract
Geometric deep learning has been revolutionizing the molecular modeling field. Despite the state-of-the-art neural network models are approaching ab initio accuracy for molecular property prediction, their applications, such as drug discovery and molecular dynamics (MD) simulation, have been hindered by insufficient utilization of geometric information and high computational costs. Here we propose an equivariant geometry-enhanced graph neural network called ViSNet, which elegantly extracts geometric features and efficiently models molecular structures with low computational costs. Our proposed ViSNet outperforms state-of-the-art approaches on multiple MD benchmarks, including MD17, revised MD17 and MD22, and achieves excellent chemical property prediction on QM9 and Molecule3D datasets. Furthermore, through a series of simulations and case studies, ViSNet can efficiently explore the conformational space and provide reasonable interpretability to map geometric representations to molecular structures.
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Affiliation(s)
- Yusong Wang
- Microsoft Research AI4Science, 100080, Beijing, China
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Tong Wang
- Microsoft Research AI4Science, 100080, Beijing, China.
| | - Shaoning Li
- Microsoft Research AI4Science, 100080, Beijing, China
| | - Xinheng He
- Microsoft Research AI4Science, 100080, Beijing, China
- The CAS Key Laboratory of Receptor Research and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Mingyu Li
- Microsoft Research AI4Science, 100080, Beijing, China
- Medicinal Chemistry and Bioinformatics Center, School of Medicine, Shanghai Jiaotong University, Shanghai, 200025, China
| | - Zun Wang
- Microsoft Research AI4Science, 100080, Beijing, China
| | - Nanning Zheng
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, 710049, Xi'an, China
| | - Bin Shao
- Microsoft Research AI4Science, 100080, Beijing, China.
| | - Tie-Yan Liu
- Microsoft Research AI4Science, 100080, Beijing, China
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5
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de Souza AS, Amorim VMDF, de Souza RF, Guzzo CR. Molecular dynamics simulations of the spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility. J Biomol Struct Dyn 2023; 41:9326-9343. [PMID: 36345794 DOI: 10.1080/07391102.2022.2142296] [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: 04/01/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is currently the most prevalent SARS-CoV-2 variant worldwide. Herein, we calculated molecular dynamics simulations of the trimeric spikeWT and SpikeBA.1 for 300 ns. Our results show that SpikeBA.1 has more conformational flexibility than SpikeWT. Our principal component analysis (PCA) allowed us to observe a broader spectrum of different conformations for SpikeBA.1, mainly at N-terminal domain (NTD) and receptor-binding domain (RBD). Such increased flexibility could contribute to decreased neutralizing antibody recognition of this variant. Our molecular dynamics data show that the RBDBA.1 easily visits an up-conformational state and the prevalent D614G mutation is pivotal to explain molecular dynamics results for this variant because to lost hydrogen bonding interactions between the residue pairs K854SC/D614SC, Y837MC/D614MC, K835SC/D614SC, T859SC/D614SC. In addition, SpikeBA.1 residues near the furin cleavage site are more flexible than in SpikeWT, probably due to P681H and D614G substitutions. Finally, dynamical cross-correlation matrix (DCCM) analysis reveals that D614G and P681H may allosterically affect the cleavage site S1/S2. Conversely, S2' site may be influenced by residues located between NTD and RBD of a neighboring protomer of the SpikeWT. Such communication may be lost in SpikeBA.1, explaining the changes of the cell tropism in the viral infection. In addition, the movements of the NTDWT and NTDBA.1 may modulate the RBD conformation through allosteric effects. Taken together, our results explain how the structural aspects may explain the observed gains in infectivity, immune system evasion and transmissibility of the Omicron variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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6
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Liu Y, Ye Q. The Key Site Variation and Immune Challenges in SARS-CoV-2 Evolution. Vaccines (Basel) 2023; 11:1472. [PMID: 37766148 PMCID: PMC10537874 DOI: 10.3390/vaccines11091472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a worldwide public health and economic threat, and virus variation amplifies the difficulty in epidemic prevention and control. The structure of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been studied extensively and is now well defined. The S protein is the most distinguishing feature in terms of infection and immunity, mediating virus entrance and inducing neutralizing antibodies. The S protein and its essential components are also the most promising target to develop vaccines and antibody-based drugs. Therefore, the key site mutation in the S gene is of high interest. Among them, RBD, NTD, and furin cleavage sites are the most mutable regions with the most mutation sites and the most serious consequences for SARS-CoV-2 biological characteristics, including infectivity, pathogenicity, natural immunity, vaccine efficacy, and antibody therapeutics. We are also aware that this outbreak may not be the last. Therefore, in this narrative review, we summarized viral variation and prevalence condition, discussed specific amino acid replacement and associated immune challenges and attempted to sum up some prevention and control strategies by reviewing the literature on previously published research about SARS-CoV-2 variation to assist in clarifying the mutation pathway and consequences of SARS-CoV-2 for developing countermeasures against such viruses as soon as possible.
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Affiliation(s)
| | - Qing Ye
- Department of ‘A’, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China;
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7
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Ren Z, Shen C, Peng J. Status and Developing Strategies for Neutralizing Monoclonal Antibody Therapy in the Omicron Era of COVID-19. Viruses 2023; 15:1297. [PMID: 37376597 DOI: 10.3390/v15061297] [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: 05/03/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The monoclonal antibody (mAb)-based treatment is a highly valued therapy against COVID-19, especially for individuals who may not have strong immune responses to the vaccine. However, with the arrival of the Omicron variant and its evolving subvariants, along with the occurrence of remarkable resistance of these SARS-CoV-2 variants to the neutralizing antibodies, mAbs are facing tough challenges. Future strategies for developing mAbs with improved resistance to viral evasion will involve optimizing the targeting epitopes on SARS-CoV-2, enhancing the affinity and potency of mAbs, exploring the use of non-neutralizing antibodies that bind to conserved epitopes on the S protein, as well as optimizing immunization regimens. These approaches can improve the viability of mAb therapy in the fight against the evolving threat of the coronavirus.
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Affiliation(s)
- Zuning Ren
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Chenguang Shen
- BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jie Peng
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
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Abduljalil JM, Elghareib AM, Samir A, Ezat AA, Elfiky AA. How helpful were molecular dynamics simulations in shaping our understanding of SARS-CoV-2 spike protein dynamics? Int J Biol Macromol 2023:125153. [PMID: 37268078 DOI: 10.1016/j.ijbiomac.2023.125153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
Abstract
The SARS-CoV-2 spike protein (S) represents an important viral component that is required for successful viral infection in humans owing to its essential role in recognition of and entry to host cells. The spike is also an appealing target for drug designers who develop vaccines and antivirals. This article is important as it summarizes how molecular simulations successfully shaped our understanding of spike conformational behavior and its role in viral infection. MD simulations found that the higher affinity of SARS-CoV-2-S to ACE2 is linked to its unique residues that add extra electrostatic and van der Waal interactions in comparison to the SARS-CoV S. This illustrates the spread potential of the pandemic SARS-CoV-2 relative to the epidemic SARS-CoV. Different mutations at the S-ACE2 interface, which is believed to increase the transmission of the new variants, affected the behavior and binding interactions in different simulations. The contributions of glycans to the opening of S were revealed via simulations. The immune evasion of S was linked to the spatial distribution of glycans. This help the virus to escape the immune system recognition. This article is important as it summarizes how molecular simulations successfully shaped our understanding of spike conformational behavior and its role in viral infection. This will pave the way to us preparing for the next pandemic as the computational tools are tailored to help fight new challenges.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen; Department of Botany and Microbiology, College of Science, Cairo University, Giza, Egypt
| | - Ahmed M Elghareib
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Ahmed Samir
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Ahmed A Ezat
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Abdo A Elfiky
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt.
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9
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Avelar M, Pedraza-González L, Sinicropi A, Flores-Morales V. Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach. Molecules 2023; 28:molecules28052333. [PMID: 36903578 PMCID: PMC10005606 DOI: 10.3390/molecules28052333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
The appearance of a new coronavirus, SARS-CoV-2, in 2019 kicked off an international public health emergency. Although rapid progress in vaccination has reduced the number of deaths, the development of alternative treatments to overcome the disease is still necessary. It is known that the infection begins with the interaction of the spike glycoprotein (at the virus surface) and the angiotensin-converting enzyme 2 cell receptor (ACE2). Therefore, a straightforward solution for promoting virus inhibition seems to be the search for molecules capable of abolishing such attachment. In this work, we tested 18 triterpene derivatives as potential inhibitors of SARS-CoV-2 against the receptor-binding domain (RBD) of the spike protein by means of molecular docking and molecular dynamics simulations, modeling the RBD S1 subunit from the X-ray structure of the RBD-ACE2 complex (PDB ID: 6M0J). Molecular docking revealed that at least three triterpene derivatives of each type (i.e., oleanolic, moronic and ursolic) present similar interaction energies as the reference molecule, i.e., glycyrrhizic acid. Molecular dynamics suggest that two compounds from oleanolic and ursolic acid, OA5 and UA2, can induce conformational changes capable of disrupting the RBD-ACE2 interaction. Finally, physicochemical and pharmacokinetic properties simulations revealed favorable biological activity as antivirals.
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Affiliation(s)
- Mayra Avelar
- Laboratorio de Síntesis Asimétrica y Bio-Quimioinformática (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico
- Correspondence: (M.A.); (V.F.-M.)
| | - Laura Pedraza-González
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124 Pisa, Italy
| | - Adalgisa Sinicropi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
- Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy
- CSGI, Consorzio per lo Sviluppo dei Sistemi a Grande Interfase, 50019 Sesto Fiorentino, Italy
| | - Virginia Flores-Morales
- Laboratorio de Síntesis Asimétrica y Bio-Quimioinformática (LSAyB), Ingeniería Química (UACQ), Universidad Autónoma de Zacatecas, Campus XXI Km 6 Carr. Zac-Gdl, Zacatecas 98160, Mexico
- Correspondence: (M.A.); (V.F.-M.)
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10
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Santos FRDS, de Azevedo MSP, Bielavsky M, da Costa HHM, Ribeiro DG, Nascimento GGD, Marcondes GMP, de Castro BP, de Lima Neto DF, Prudencio CR. Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates. J Biomol Struct Dyn 2022; 40:13184-13189. [PMID: 34633892 DOI: 10.1080/07391102.2021.1982775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spike (S) protein has been recognized as a promising molecular target for diagnostic, vaccines and antiviral drugs development for COVID-19. In this study, we analyzed the most predominant mutations in the S protein of Brazilian isolates and predicted the effect of these amino acid alterations to protein conformation. A total of 25,924 sequences were obtained from GISAID for five regions of Brazilian territory (Midwest, North, Northeast, South, and Southeast), according to exclusion criteria. Most of the SARS-CoV-2 isolates belongs to the G clade and showed a large occurrence of D614G, N501Y and L18F substitutions. Prediction effects of these amino acid substitutions on the structure dynamics of the spike protein indicated a positive ΔΔG values and negative ΔΔSVib in most cases which is associated to structural stabilization and flexibility reduction of the S protein. Mutations E484K, N501Y and K417N belong to several SARS-CoV-2 variants of concern such as Alpha, Beta, Gamma and Delta, and showed high incidence among Brazilian isolates. These mutations have been described to increase RBD affinity to ACE-2 host and abolishment of RBD affinity to potent neutralizing ant-RBD. The increase in rates of infection and reinfection requires continuous genomic surveillance studies in order to characterize emerging mutations and monitor vaccine efficacy, and thus consideration structural data and dynamics in the observed phenotypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Monica Bielavsky
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | - Daniela Gomes Ribeiro
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | | | | | - Daniel Ferreira de Lima Neto
- Coordenação-Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil.,Laboratório de Termodinâmica de Proteínas, Departamento de Bioquímica, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carlos Roberto Prudencio
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
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11
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Yan ZS, Li XL, Ma YQ, Ding HM. Effect of the Graphene Nanosheet on Functions of the Spike Protein in Open and Closed States: Comparison between SARS-CoV-2 Wild Type and the Omicron Variant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13972-13982. [PMID: 36318181 PMCID: PMC9662070 DOI: 10.1021/acs.langmuir.2c02316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/05/2022] [Indexed: 05/24/2023]
Abstract
The spread of coronavirus disease 2019 caused by SARS-CoV-2 and its variants has become a global health crisis. Although there were many attempts to use nanomaterials-based devices to fight against SARS-CoV-2, it still remains elusive as to how the nanomaterials interact with SARS-CoV-2 and affect its biofunctions. Here, taking the graphene nanosheet (GN) as the model nanomaterial, we investigate its interaction with the spike protein in both WT and Omicron by molecular simulations. In the closed state, the GN can insert into the region between the receptor binding domain (RBD) and the N-terminal domain (NTD) in both wild type (WT) and Omicron, which keeps the RBD in the down conformation. In the open state, the GN can hamper the binding of up RBD to ACE2 in WT, but it has little impact on up RBD and, even worse, stimulates the down-to-up transition of down RBDs in Omicron. Moreover, the GN can insert in the vicinity of the fusion peptide in both WT and Omicron and prevents the detachment of S1 from the whole spike protein. The present study reveals the effect of the SARS-CoV-2 variant on the nanomaterial-spike protein interaction, which informs prospective efforts to design functional nanomaterials against SARS-CoV-2.
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Affiliation(s)
- Zeng-Shuai Yan
- National
Laboratory of Solid State Microstructures and Department of Physics,
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Xiao-Lei Li
- National
Laboratory of Solid State Microstructures and Department of Physics,
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National
Laboratory of Solid State Microstructures and Department of Physics,
Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hong-Ming Ding
- Center
for Soft Condensed Matter Physics and Interdisciplinary Research,
School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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12
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Characterization of SARS-CoV-2 Escape Mutants to a Pair of Neutralizing Antibodies Targeting the RBD and the NTD. Int J Mol Sci 2022; 23:ijms23158177. [PMID: 35897753 PMCID: PMC9332373 DOI: 10.3390/ijms23158177] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 01/27/2023] Open
Abstract
Mutations in the spike protein of SARS-CoV-2 can lead to evasion from neutralizing antibodies and affect the efficacy of passive and active immunization strategies. Immunization of mice harboring an entire set of human immunoglobulin variable region gene segments allowed to identify nine neutralizing monoclonal antibodies, which either belong to a cluster of clonally related RBD or NTD binding antibodies. To better understand the genetic barrier to emergence of SARS-CoV-2 variants resistant to these antibodies, escape mutants were selected in cell culture to one antibody from each cluster and a combination of the two antibodies. Three independently derived escape mutants to the RBD antibody harbored mutations in the RBD at the position T478 or S477. These mutations impaired the binding of the RBD antibodies to the spike protein and conferred resistance in a pseudotype neutralization assay. Although the binding of the NTD cluster antibodies were not affected by the RBD mutations, the RBD mutations also reduced the neutralization efficacy of the NTD cluster antibodies. The mutations found in the escape variants to the NTD antibody conferred resistance to the NTD, but not to the RBD cluster antibodies. A variant resistant to both antibodies was more difficult to select and only emerged after longer passages and higher inoculation volumes. VOC carrying the same mutations as the ones identified in the escape variants were also resistant to neutralization. This study further underlines the rapid emergence of escape mutants to neutralizing monoclonal antibodies in cell culture and indicates the need for thorough investigation of escape mutations to select the most potent combination of monoclonal antibodies for clinical use.
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13
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Chen Z, Zhang Y, Wang M, Islam MS, Liao P, Hu Y, Chen X. Humoral and Cellular Immune Responses of COVID-19 vaccines against SARS-Cov-2 Omicron variant: a systemic review. Int J Biol Sci 2022; 18:4629-4641. [PMID: 35874952 PMCID: PMC9305266 DOI: 10.7150/ijbs.73583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/21/2022] [Indexed: 12/13/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has undergone multiple mutations since its emergence, and its latest variant, Omicron (B.1.1.529), is the most contagious variant of concern (VOC) which poses a major and imminent threat to public health. Since firstly reported by World Health Organization (WHO) in November 2021, Omicron variant has been spreading rapidly and has become the dominant variant in many countries worldwide. Omicron is the most mutated variant so far, containing 60 mutations in its genome, including 37 mutations in the S-protein. Since all current COVID-19 vaccines in use were developed based on ancestral SARS-CoV-2 strains, whether they are protective against Omicron is a critical question which has been the center of study currently. In this article, we systemically reviewed the studies regarding the effectiveness of 2- or 3-dose vaccines delivered in either homologous or heterologous manner. The humoral and cellular immune responses elicited by various vaccine regimens to protect against Omicron variant are discussed. Current understanding of the molecular basis underlying immune escape of Omicron was also analyzed. These studies indicate that two doses of vaccination are insufficient to elicit neutralizing antibody responses against Omicron variant. Nevertheless, Omicron-specific humoral immune responses can be enhanced by booster dose of almost all type vaccines in certain degree, and heterologous vaccination strategy may represent a better choice than homogenous regimens. Intriguingly, results of studies indicate that all current vaccines are still able to elicit robust T cell response against Omicron. Future focus should be the development of Omicron variant vaccine, which may induce potent humoral as well as cellular immune responses simultaneously against all known variants of the SARS-CoV-2 virus.
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Affiliation(s)
| | | | | | | | | | | | - Xin Chen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau SAR 999078, China
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14
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Zahradník J, Nunvar J, Schreiber G. Perspectives: SARS-CoV-2 Spike Convergent Evolution as a Guide to Explore Adaptive Advantage. Front Cell Infect Microbiol 2022; 12:748948. [PMID: 35711666 PMCID: PMC9197234 DOI: 10.3389/fcimb.2022.748948] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 04/19/2022] [Indexed: 01/22/2023] Open
Abstract
Viruses rapidly co-evolve with their hosts. The 9 million sequenced SARS-CoV-2 genomes by March 2022 provide a detailed account of viral evolution, showing that all amino acids have been mutated many times. However, only a few became prominent in the viral population. Here, we investigated the emergence of the same mutations in unrelated parallel lineages and the extent of such convergent evolution on the molecular level in the spike (S) protein. We found that during the first phase of the pandemic (until mid 2021, before mass vaccination) 31 mutations evolved independently ≥3-times within separated lineages. These included all the key mutations in SARS-CoV-2 variants of concern (VOC) at that time, indicating their fundamental adaptive advantage. The omicron added many more mutations not frequently seen before, which can be attributed to the synergistic nature of these mutations, which is more difficult to evolve. The great majority (24/31) of S-protein mutations under convergent evolution tightly cluster in three functional domains; N-terminal domain, receptor-binding domain, and Furin cleavage site. Furthermore, among the S-protein receptor-binding motif mutations, ACE2 affinity-improving substitutions are favoured. Next, we determined the mutation space in the S protein that has been covered by SARS-CoV-2. We found that all amino acids that are reachable by single nucleotide changes have been probed multiple times in early 2021. The substitutions requiring two nucleotide changes have recently (late 2021) gained momentum and their numbers are increasing rapidly. These provide a large mutation landscape for SARS-CoV-2 future evolution, on which research should focus now.
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Affiliation(s)
- Jiri Zahradník
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jaroslav Nunvar
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czechia
- Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (BIOCEV), Vestec, Czechia
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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15
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Tang H, Zeng R, He E, Zhang I, Ding C, Zhang A. Piezo-Type Mechanosensitive Ion Channel Component 1 (Piezo1): A Promising Therapeutic Target and Its Modulators. J Med Chem 2022; 65:6441-6453. [DOI: 10.1021/acs.jmedchem.2c00085] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Hairong Tang
- Pharm-X Center, Laboratory of Medicinal Chemical Biology & Frontiers on Drug Discovery (RLMCBFDD), School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ruoqing Zeng
- Pharm-X Center, Laboratory of Medicinal Chemical Biology & Frontiers on Drug Discovery (RLMCBFDD), School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ende He
- Pharm-X Center, Laboratory of Medicinal Chemical Biology & Frontiers on Drug Discovery (RLMCBFDD), School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Chunyong Ding
- Pharm-X Center, Laboratory of Medicinal Chemical Biology & Frontiers on Drug Discovery (RLMCBFDD), School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ao Zhang
- Pharm-X Center, Laboratory of Medicinal Chemical Biology & Frontiers on Drug Discovery (RLMCBFDD), School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Lingang National Laboratory, Shanghai 200210,China
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16
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Yu W, Zhong N, Li X, Ren J, Wang Y, Li C, Yao G, Zhu R, Wang X, Jia Z, Wu C, Chen R, Zheng W, Liao H, Wu X, Yuan X. Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches. Viruses 2022; 14:v14020186. [PMID: 35215781 PMCID: PMC8875849 DOI: 10.3390/v14020186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 12/25/2022] Open
Abstract
The COVID-19 epidemic is raging around the world. Neutralizing antibodies are powerful tools for the prevention and treatment of SARS-CoV-2 infection. Antibody CR3022, a SARS-CoV neutralizing antibody, was found to cross-react with SARS-CoV-2, but its affinity was lower than that of its binding with SARS-CoV, which greatly limited the further development of CR3022 against SARS-CoV-2. Therefore, it is necessary to improve its affinity to SARS-CoV-2 in vitro. In this study, the structure-based molecular simulations were utilized to virtually mutate the possible key residues in the complementarity-determining regions (CDRs) of the CR3022 antibody. According to the criteria of mutation energy, the mutation sites that have the potential to impact the antibody affinity were then selected. Then optimized CR3022 mutants with the enhanced affinity were further identified and verified by enzyme-linked immunosorbent assay (ELISA), surface plasma resonance (SPR) and autoimmune reactivity experiments. Finally, molecular dynamics (MD) simulation and binding free energy calculation (MM/PBSA) were performed on the wild-type CR3022 and its two double-site mutants to understand in more detail the contribution of these sites to the higher affinity. It was found that the binding affinity of the CR3022 antibody could be significantly enhanced more than ten times after the introduction of the S103F/Y mutation in HCDR–3 and the S33R mutation in LCDR–1. The additional hydrogen-bonding, hydrophobic interactions, as well as salt-bridges formed between the modified double-site mutated antibody and SARS-CoV-2 RBD were identified. The computational and experimental results clearly demonstrated that the affinity of the modified antibody has been greatly enhanced. This study indicates that CR3022 as a neutralizing antibody recognizing the conserved region of RBD against SARS-CoV with cross-reactivity with SARS-CoV-2, a different member in a large family of coronaviruses, could be improved by the computational and experimental approaches which provided insights for developing antibody drugs against SARS-CoV-2.
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Affiliation(s)
- Wei Yu
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Nan Zhong
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou 510632, China
| | - Xin Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- National Engineering Research Center of Genetic Medicine, Guangzhou 510632, China
| | - Jiayi Ren
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- School of Health, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Yueming Wang
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Chengming Li
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Gui Yao
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Rui Zhu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
| | - Xiaoli Wang
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Zhenxing Jia
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Changwen Wu
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Rongfeng Chen
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Weihong Zheng
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
| | - Huaxin Liao
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
| | - Xiaomin Wu
- Anhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China; (G.Y.); (R.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
| | - Xiaohui Yuan
- Institute of Biomedicine, Jinan University, Guangzhou 510632, China; (W.Y.); (N.Z.); (X.L.); (J.R.); (Y.W.); (C.L.)
- Zhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, China; (X.W.); (Z.J.); (C.W.); (R.C.); (W.Z.)
- Correspondence: (H.L.); (X.W.); (X.Y.); Tel.: +86-756-726-3999 (X.Y.)
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17
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Aminpour M, Cannariato M, Zucco A, Di Gregorio E, Israel S, Perioli A, Tucci D, Rossi F, Pionato S, Marino S, Deriu MA, Velpula KK, Tuszynski JA. Computational Study of Potential Galectin-3 Inhibitors in the Treatment of COVID-19. Biomedicines 2021; 9:1208. [PMID: 34572394 PMCID: PMC8466820 DOI: 10.3390/biomedicines9091208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022] Open
Abstract
Galectin-3 is a carbohydrate-binding protein and the most studied member of the galectin family. It regulates several functions throughout the body, among which are inflammation and post-injury remodelling. Recent studies have highlighted the similarity between Galectin-3's carbohydrate recognition domain and the so-called "galectin fold" present on the N-terminal domain of the S1 sub-unit of the SARS-CoV-2 spike protein. Sialic acids binding to the N-terminal domain of the Spike protein are known to be crucial for viral entry into humans, and the role of Galectin-3 as a mediator of lung fibrosis has long been the object of study since its levels have been found to be abnormally high in alveolar macrophages following lung injury. In this context, the discovery of a double inhibitor may both prevent viral entry and reduce post-infection pulmonary fibrosis. In this study, we use a database of 56 compounds, among which 37 have known experimental affinity with Galectin-3. We carry out virtual screening of this database with respect to Galectin-3 and Spike protein. Several ligands are found to exhibit promising binding affinity and interaction with the Spike protein's N-terminal domain as well as with Galectin-3. This finding strongly suggests that existing Galectin-3 inhibitors possess dual-binding capabilities to disrupt Spike-ACE2 interactions. Herein we identify the most promising inhibitors of Galectin-3 and Spike proteins, of which five emerge as potential dual effective inhibitors. Our preliminary results warrant further in vitro and in vivo testing of these putative inhibitors against SARS-CoV-2 with the hope of being able to halt the spread of the virus in the future.
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Affiliation(s)
- Maral Aminpour
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB T6G 1Z2, Canada;
| | - Marco Cannariato
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Angelica Zucco
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Elisabetta Di Gregorio
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Simone Israel
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Annalisa Perioli
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Davide Tucci
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Francesca Rossi
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Sara Pionato
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Silvia Marino
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Marco A. Deriu
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
| | - Kiran K. Velpula
- Department of Cancer Biology and Pharmacology, Pediatrics and Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
| | - Jack A. Tuszynski
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy; (M.C.); (A.Z.); (E.D.G.); (S.I.); (A.P.); (D.T.); (F.R.); (S.P.); (S.M.); (M.A.D.)
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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