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Gossen KR, Zhang M, Nikolov ZL, Fernando SD, King MD. Binding behavior of receptor binding domain of the SARS-CoV-2 virus and ivermectin. Sci Rep 2024; 14:2743. [PMID: 38302638 PMCID: PMC10834942 DOI: 10.1038/s41598-024-53086-0] [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: 07/28/2023] [Accepted: 01/27/2024] [Indexed: 02/03/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), sparked an international debate on effective ways to prevent and treat the virus. Specifically, there were many varying opinions on the use of ivermectin (IVM) throughout the world, with minimal research to support either side. IVM is an FDA-approved antiparasitic drug that was discovered in the 1970s and was found to show antiviral activity. The objective of this study is to examine the binding behavior and rates of association and dissociation between SARS-CoV-2 receptor binding domain (RBD), IVM, and their combination using aminopropylsilane (APS) biosensors as surrogates for the hydrophobic interaction between the viral protein and human angiotensin-converting enzyme 2 (ACE2) receptors to determine the potential of IVM as a repurposed drug for SARS-CoV-2 prevention and treatment. The IVM, RBD, and combination binding kinetics were analyzed using biolayer interferometry (BLI) and validated with multiple in silico techniques including protein-ligand docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA), and principal component analysis (PCA). Our results suggest that with increasing IVM concentrations the association rate with the hydrophobic biosensor increases with a simultaneous decrease in dissociation. Significant kinetic changes to RBD, when combined with IVM, were found only at a concentration a thousand times the approved dosage with minimal changes found over a 35-min time period. Our study suggests that IVM is not an effective preventative or treatment method at the currently approved dosage.
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Affiliation(s)
- Kasidy R Gossen
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Meiyi Zhang
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Zivko L Nikolov
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Sandun D Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA
| | - Maria D King
- Department of Biological and Agricultural Engineering, Texas A&M University, 2117 TAMU, College Station, TX, 77843, USA.
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2
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Ismail CMKH, Abdul Hamid AA, Abdul Rashid NN, Lestari W, Mokhtar KI, Mustafa Alahmad BE, Abd Razak MRM, Ismail A. An ensemble docking-based virtual screening and molecular dynamics simulation of phytochemical compounds from Malaysian Kelulut Honey (KH) against SARS-CoV-2 target enzyme, human angiotensin-converting enzyme 2 (ACE-2). J Biomol Struct Dyn 2024:1-30. [PMID: 38279932 DOI: 10.1080/07391102.2024.2308762] [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: 08/21/2023] [Accepted: 01/17/2024] [Indexed: 01/29/2024]
Abstract
The human angiotensin-converting enzyme 2 (ACE-2) receptor is a metalloenzyme that plays an important role in regulating blood pressure by modulating angiotensin II. This receptor facilitates SARS-CoV-2 entry into human cells via receptor-mediated endocytosis, causing the global COVID-19 pandemic and a major health crisis. Kelulut honey (KH), one of Malaysian honey recently gained attention for its distinct flavour and taste while having many nutritional and medicinal properties. Recent study demonstrates the antiviral potential of KH against SARS-CoV-2 by inhibiting ACE-2 in vitro, but the bioactive compound pertaining to the ACE-2 inhibition is yet unknown. An ensemble docking-based virtual screening was employed to screen the phytochemical compounds from KH with high binding affinity against the 10 best representative structures of ACE-2 that mostly formed from MD simulation. From 110 phytochemicals previously identified in KH, 27 compounds passed the ADMET analysis and proceeded to docking. Among the docked compound, SDC and FMN consistently exhibited strong binding to ACE-2's active site (-9.719 and -9.473 kcal/mol) and allosteric site (-7.305 and -7.464 kcal/mol) as compared to potent ACE-2 inhibitor, MLN 4760. Detailed trajectory analysis of MD simulation showed stable binding interaction towards active and allosteric sites of ACE-2. KH's compounds show promise in inhibiting SARS-CoV-2 binding to ACE-2 receptors, indicating potential for preventive use or as a supplement to other COVID-19 treatments. Additional research is needed to confirm KH's antiviral effects and its role in SARS-CoV-2 therapy, including prophylaxis and adjuvant treatment with vaccination.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Che Muhammad Khairul Hisyam Ismail
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
- Research Unit for Bioinformatics & Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
- Research Unit for Bioinformatics & Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | | | - Widya Lestari
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Khairani Idah Mokhtar
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Basma Ezzat Mustafa Alahmad
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Mohd Ridzuan Mohd Abd Razak
- Herbal Medicine Research Centre, Institute for Medical Research, National Institutes of Health, Shah Alam, Selangor, Malaysia
| | - Azlini Ismail
- Department of Fundamental Dental and Medical Sciences, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
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3
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Wu A, Shi K, Wang J, Zhang R, Wang Y. Targeting SARS-CoV-2 entry processes: The promising potential and future of host-targeted small-molecule inhibitors. Eur J Med Chem 2024; 263:115923. [PMID: 37981443 DOI: 10.1016/j.ejmech.2023.115923] [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: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/28/2023] [Indexed: 11/21/2023]
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, has had a huge impact on global health. To respond to rapidly mutating viruses and to prepare for the next pandemic, there is an urgent need to develop small molecule therapies that target critical stages of the SARS-CoV-2 life cycle. Inhibiting the entry process of the virus can effectively control viral infection and play a role in prevention and treatment. Host factors involved in this process, such as ACE2, TMPRSS2, ADAM17, furin, PIKfyve, TPC2, CTSL, AAK1, V-ATPase, HSPG, and NRP1, have been found to be potentially good targets with stability. Through further exploration of the cell entry process of SARS-CoV-2, small-molecule drugs targeting these host factors have been developed. This review focuses on the structural functions of potential host cell targets during the entry of SARS-CoV-2 into host cells. The research progress, chemical structure, structure-activity relationship, and clinical value of small-molecule inhibitors against COVID-19 are reviewed to provide a reference for the development of small-molecule drugs against COVID-19.
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Affiliation(s)
- Aijia Wu
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Kunyu Shi
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Ruofei Zhang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yuxi Wang
- Department of Pulmonary and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, National Clinical Research Center for Geriatrics, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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4
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Qin C, Xiang L, Wang YZ, Yu PF, Meng C, Li YW, Zhao HM, Hu X, Gao Y, Mo CH. Binding interaction of environmental DNA with typical emerging perfluoroalkyl acids and its impact on bioavailability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167392. [PMID: 37758138 DOI: 10.1016/j.scitotenv.2023.167392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 08/17/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
As the replacement compounds of perfluoroalkyl acids (PFAAs), emerging PFAAs generally exhibit equal or more hazardous toxicity than legacy PFAAs. Numerous DNA as environmental organic matters coexists with emerging PFAAs, but their interactions and the resulting interaction impacts on the bioavailability of emerging PFAAs remain insufficiently understood. Here, we studied the binding strength and mechanism between DNA and emerging PFAAs (perfluorobutyric acid, perfluorobutylsulfonic acid, and hexafluoropropylene oxide dimer acid) using perfluorooctanoic acid as the control, and further investigated the impacts of DNA binding on the bioavailability of the emerging PFAAs. Isothermal titration calorimetry and quantum chemical calculation found that the emerging PFAAs could bind with DNA bases (main thymine) by van der Waals force and halogen-bond, showing the binding affinities in the range of 7.87 × 104 to L/mol to 6.54 × 106 L/mol. The PFAAs-DNA binding significantly decreased the bioavailability of the PFAAs in both seedlings and plants of pakchoi (Brassica chinensis L.), with little differences in bioavailability change extent among PFAAs. The findings highlight the universality and similarity of the DNA binding effects on PFAAs bioavailability, which can be the natural detoxification mechanism for response to the PFAAs pollution.
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Affiliation(s)
- Chao Qin
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China; Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Xiang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yi-Ze Wang
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Peng-Fei Yu
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Can Meng
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yan-Wen Li
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hai-Ming Zhao
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ce-Hui Mo
- Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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Li Z, Hasson A, Daggumati L, Zhang H, Thorek DLJ. Molecular Imaging of ACE2 Expression in Infectious Disease and Cancer. Viruses 2023; 15:1982. [PMID: 37896761 PMCID: PMC10610869 DOI: 10.3390/v15101982] [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: 08/23/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Angiotensin-converting enzyme 2 (ACE2) is a cell-surface receptor that plays a critical role in the pathogenesis of SARS-CoV-2 infection. Through the use of ligands engineered for the receptor, ACE2 imaging has emerged as a valuable tool for preclinical and clinical research. These can be used to visualize the expression and distribution of ACE2 in tissues and cells. A variety of techniques including optical, magnetic resonance, and nuclear medicine contrast agents have been developed and employed in the preclinical setting. Positron-emitting radiotracers for highly sensitive and quantitative tomography have also been translated in the context of SARS-CoV-2-infected and control patients. Together this information can be used to better understand the mechanisms of SARS-CoV-2 infection, the potential roles of ACE2 in homeostasis and disease, and to identify potential therapeutic modulators in infectious disease and cancer. This review summarizes the tools and techniques to detect and delineate ACE2 in this rapidly expanding field.
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Affiliation(s)
- Zhiyao Li
- Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; (Z.L.); (A.H.); (H.Z.)
- Program in Quantitative Molecular Therapeutics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA;
| | - Abbie Hasson
- Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; (Z.L.); (A.H.); (H.Z.)
- Program in Quantitative Molecular Therapeutics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA;
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
| | - Lasya Daggumati
- Program in Quantitative Molecular Therapeutics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA;
- School of Medicine Missouri, University of Missouri-Kansas City, Kansas, MO 64108, USA
| | - Hanwen Zhang
- Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; (Z.L.); (A.H.); (H.Z.)
- Program in Quantitative Molecular Therapeutics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA;
- Siteman Cancer Center, St. Louis, MO 63110, USA
| | - Daniel L. J. Thorek
- Mallinckrodt Institute of Radiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; (Z.L.); (A.H.); (H.Z.)
- Program in Quantitative Molecular Therapeutics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA;
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
- Siteman Cancer Center, St. Louis, MO 63110, USA
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6
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Sha A, Liu Y, Hao H. Current state-of-the-art and potential future therapeutic drugs against COVID-19. Front Cell Dev Biol 2023; 11:1238027. [PMID: 37691829 PMCID: PMC10485263 DOI: 10.3389/fcell.2023.1238027] [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: 06/10/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
The novel coronavirus disease (COVID-19) continues to endanger human health, and its therapeutic drugs are under intensive research and development. Identifying the efficacy and toxicity of drugs in animal models is helpful for further screening of effective medications, which is also a prerequisite for drugs to enter clinical trials. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) invades host cells mainly by the S protein on its surface. After the SARS-CoV-2 RNA genome is injected into the cells, M protein will help assemble and release new viruses. RdRp is crucial for virus replication, assembly, and release of new virus particles. This review analyzes and discusses 26 anti-SARS-CoV-2 drugs based on their mechanism of action, effectiveness and safety in different animal models. We propose five drugs to be the most promising to enter the next stage of clinical trial research, thus providing a reference for future drug development.
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Affiliation(s)
- Ailong Sha
- School of Teacher Education, Chongqing Three Gorges University, Chongqing, China
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Yi Liu
- School of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, China
| | - Haiyan Hao
- School of Environmental and Chemical Engineering, Chongqing, China
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7
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Bisht D, Sajjanar BK, Saxena S, Kakodia B, Dighe V, Thakuria D, Kharayat NS, Chanu KV, Kumar S. Identification and characterization of phage display-selected peptides having affinity to Peste des petits ruminants virus. J Immunol Methods 2023; 515:113455. [PMID: 36893896 DOI: 10.1016/j.jim.2023.113455] [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: 10/13/2022] [Revised: 01/23/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023]
Abstract
Phage display is a well-established technique used for selecting novel ligands having affinity to a plethora of targets including proteins, viruses, whole bacterial and mammalian cells as well as lipid targets. In the present study, phage display technology was used to identify peptides having affinity to PPRV. The binding capacity of these peptides was characterized through various formats of ELISA using phage clones, linear and multiple antigenic peptides. The whole PPRV was used as an immobilized target in a surface biopanning process using a 12-mer phage display random peptide library. After five rounds of biopanning, forty colonies were picked and amplified followed by DNA isolation and amplification for sequencing. Sequencing suggested 12 different clones expressing different peptide sequence Phage-ELISA was performed using all 12 phage clones. Results indicated that four phage clones i.e., P4, P8, P9 and P12 had a specific binding activity to PPR virus. Linear peptides displayed by all 12 clones were synthesized using solid phase peptide synthesis and subjected to virus capture ELISA. No significant binding of the linear peptides with PPRV was evident which may be due to loss of conformation of linear peptide after coating. When the four selected phage clones displayed peptide sequences were synthesized in Multiple antigenic peptide (MAP) format and used in virus capture ELISA, the results indicated significant binding of PPRV to the MAPs. It may be due to increased avidity and/or better projection of binding residues in 4-armed MAPs as compared to linear peptides. MAP-peptides were also conjugated on gold nanoparticles (AuNPs). Visual colour change from wine red to purple was observed on addition of PPRV in MAP-conjugated AuNPs solution. This colour change may be attributable to the networking of PPRV with MAP -conjugated AuNPs resulting in aggregation of AuNPs. All these results supported the hypothesis that the phage display selected peptides were capable of binding to the PPRV. The potential of these peptides to develop novel diagnostic or therapeutic agents remains to be investigated.
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Affiliation(s)
- Deepika Bisht
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India; Division of Virology, ICAR-Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand 263138, India.
| | - B K Sajjanar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
| | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
| | - Bhuvna Kakodia
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
| | - Vikas Dighe
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
| | - Dimpal Thakuria
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India; ICAR-Directorate of Coldwater Fisheries Research, Bhimtal, Nainital, Uttarakhand 263136, India.
| | - Nitish S Kharayat
- Temperate Animal Husbandry Division, ICAR-Indian Veterinary Research Institute, Mukteswar Campus, Nainital, Uttarakhand 263138, India.
| | | | - Satish Kumar
- Division of Veterinary Biotechnology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India.
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Cournia Z, Soares TA, Wahab HA, Amaro RE. Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. J Chem Inf Model 2022; 62:6287-6291. [PMID: 36567670 DOI: 10.1021/acs.jcim.2c01543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
| | - Thereza A Soares
- Department of Chemistry, University of São Paulo, 14040-901 Ribeirão Preto, Brazil.,Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315 Oslo, Norway
| | - Habibah A Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, 3234 Urey Hall, #0340, 9500 Gilman Drive, La Jolla, 92093-0340 San Diego, California, United States
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Dutta S, Panthi B, Chandra A. All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes. J Phys Chem B 2022; 126:5375-5389. [PMID: 35833966 PMCID: PMC9328126 DOI: 10.1021/acs.jpcb.2c00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/25/2022] [Indexed: 12/18/2022]
Abstract
The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its receptor binding domain (RBD). We have investigated the molecular nature of this interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations. The present work involves generation and analysis of 2.5 μs of unbiased and 4.2 μs of biased molecular dynamics trajectories in total for five explicitly solvated RBD-ACE2 systems at full atomic level. First, we have made a comparative analysis of the details of residue-wise specific interactions of the spike protein with ACE2 for SARS-CoV-1 and SARS-CoV-2. It is found that the average numbers of both direct interprotein and water-bridged hydrogen bonds between the RBD and ACE2 are higher for SARS-CoV-2 than SARS-CoV-1. These higher hydrogen bonded interactions are further aided by enhanced nonspecific electrostatic attractions between the two protein surfaces for SARS-CoV-2. The free energy calculations reveal that there is an increase in the free energy barrier by ∼1.5 kcal/mol for the unbinding of RBD from ACE2 for SARS-CoV-2 compared to that for SARS-CoV-1. Subsequently, we considered the RBDs of three variants of SARS-CoV-2, namely N501Y, E484Q/L452R, and N440K. The free energy barrier of protein unbinding for the N501Y variant is found to be ∼4 kcal/mol higher than the wild type SARS-CoV-2 which can be attributed to additional specific interactions involving Tyr501 of RBD and Lys353 and Tyr42 of ACE2 and also enhanced nonspecific electrostatic interaction between the protein surfaces. For the other two mutant variants of E484Q/L452R and N440K, the free energy barrier for protein unbinding increases by ∼2 and ∼1 kcal/mol, respectively, compared with the wild type SARS-CoV-2, which can be attributed to an increase in the number of interprotein hydrogen bonds for the former and also to enhanced positive electrostatic potential on the RBD surfaces for both of the variants. The successive breaking of interprotein hydrogen bonds along the free energy pathway of the unbinding process is also found out for all five systems studied here.
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Affiliation(s)
- Saheb Dutta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Bhavana Panthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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10
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Yoshida N, Maruyama Y, Mitsutake A, Kuroda A, Fujiki R, Kanemaru K, Okamoto D, Kobryn AE, Gusarov S, Nakano H. Computational Analysis of the SARS-CoV-2 RBD-ACE2-Binding Process Based on MD and the 3D-RISM Theory. J Chem Inf Model 2022; 62:2889-2898. [PMID: 35583118 PMCID: PMC9159518 DOI: 10.1021/acs.jcim.2c00192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Indexed: 12/26/2022]
Abstract
The binding process of angiotensin-converting enzyme 2 (ACE2) to the receptor-binding domain (RBD) of the severe acute respiratory syndrome-like coronavirus 2 spike protein was investigated using molecular dynamics simulation and the three-dimensional reference interaction-site model theory. The results suggested that the protein-binding process consists of a protein-protein approaching step, followed by a local structural rearrangement step. In the approaching step, the interprotein interaction energy decreased as the proteins approached each other, whereas the solvation free energy increased. As the proteins approached, the glycan of ACE2 first established a hydrogen bond with the RBD. Thereafter, the number of interprotein hydrogen bonds increased rapidly. The solvation free energy increased because of the desolvation of the protein as it approached its partner. The spatial distribution function of the solvent revealed the presence of hydrogen bonds bridged by water molecules on the RBD-ACE2 interface. Finally, principal component analysis revealed that ACE2 showed a pronounced conformational change, whereas there was no significant change in RBD.
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Affiliation(s)
- Norio Yoshida
- Department of Chemistry, Graduate School of Science,
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka
819-0395, Japan
- Department of Complex Systems Science,
Graduate School of Informatics, Furo-cho, Chikusa-Ward, Nagoya 464-8601,
Japan
| | - Yutaka Maruyama
- Department of Physics, School of Science and Technology,
Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kanagawa,
Kawasaki 214-8571, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology,
Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kanagawa,
Kawasaki 214-8571, Japan
| | - Akiyoshi Kuroda
- RIKEN Center for Computational
Science, 7-1-26, Minatojima-Minami-Machi, Chuo-ku, Hyogo, Kobe 650-0047,
Japan
| | - Ryo Fujiki
- Department of Chemistry, Graduate School of Science,
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka
819-0395, Japan
| | - Kodai Kanemaru
- Department of Chemistry, Graduate School of Science,
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka
819-0395, Japan
| | - Daisuke Okamoto
- Department of Chemistry, Graduate School of Science,
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka
819-0395, Japan
| | - Alexander E. Kobryn
- Nanotechnology Research Centre, National
Research Council Canada, 11421 Saskatchewan Drive NW, Edmonton AB T6G 2M9,
Canada
| | - Sergey Gusarov
- Nanotechnology Research Centre, National
Research Council Canada, 11421 Saskatchewan Drive NW, Edmonton AB T6G 2M9,
Canada
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science,
Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka
819-0395, Japan
| |
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