1
|
Ashique S, Mishra N, Garg A, Garg S, Farid A, Rai S, Gupta G, Dua K, Paudel KR, Taghizadeh-Hesary F. A Critical Review on the Long-Term COVID-19 Impacts on Patients With Diabetes. Am J Med 2024:S0002-9343(24)00133-5. [PMID: 38485111 DOI: 10.1016/j.amjmed.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 04/30/2024]
Abstract
BACKGROUND The world is currently grappling with the potentially life-threatening coronavirus disease 2019 (COVID-19), marking it as the most severe health crisis in the modern era. COVID-19 has led to a pandemic, with the World Health Organization (WHO) predicting that individuals with diabetes are at a higher risk of contracting the virus compared to the general population. This review aims to provide a practical summary of the long-term impacts of COVID-19 on patients with diabetes. Specifically, it focuses on the effects of SARS-CoV-2 on different types of diabetic patients, the associated mortality rate, the underlying mechanisms, related complications, and the role of vitamin D and zinc in therapeutic and preventive approaches. METHODS Relevant literature was identified through searches on PubMed, Web of Science, and Science Direct in English, up to April 2023. RESULTS COVID-19 can lead to distressing symptoms and pose a significant challenge for individuals living with diabetes. Older individuals and those with pre-existing conditions such as diabetes, coronary illness, and asthma are more susceptible to COVID-19 infection. Managing COVID-19 in individuals with diabetes presents challenges, as it not only complicates the fight against the infection but also potentially prolongs the recovery time. Moreover, the virus may thrive in individuals with high blood glucose levels. Various therapeutic approaches, including antidiabetic drugs, are available to help prevent COVID-19 in diabetic patients. CONCLUSIONS Diabetes increases the morbidity and mortality risk for patients with COVID-19. Efforts are globally underway to explore therapeutic interventions aimed at reducing the impact of diabetes on COVID-19.
Collapse
Affiliation(s)
- Sumel Ashique
- Department of Pharmaceutical Sciences, Bengal College of Pharmaceutical Sciences & Research, Durgapur, West Bengal, India
| | - Neeraj Mishra
- Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior, Madhya Pradesh, India
| | - Ashish Garg
- Drug Delivery and Nanotechnology Laboratories, Department of Pharmaceutics, Guru Ramdas Khalsa Institute of Science and Technology (Pharmacy), Kukrikheda, Barela, Jabalpur, Madhya Pradesh, India
| | - Sweta Garg
- Guru Ramdas Khalsa Institute of Science and Technology, Pharmacy, Jabalpur, Madhya Pradesh, India
| | - Arshad Farid
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Pakistan
| | - Shweta Rai
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Gyan Vihar Marg, Jagatpura, Jaipur, Rajasthan 302017, India
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, NSW, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Farzad Taghizadeh-Hesary
- ENT and Head and Neck Research Center, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
2
|
Wu W, Cheng Y, Zhou H, Sun C, Zhang S. The SARS-CoV-2 nucleocapsid protein: its role in the viral life cycle, structure and functions, and use as a potential target in the development of vaccines and diagnostics. Virol J 2023; 20:6. [PMID: 36627683 PMCID: PMC9831023 DOI: 10.1186/s12985-023-01968-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) continues to take a heavy toll on personal health, healthcare systems, and economies around the globe. Scientists are expending tremendous effort to develop diagnostic technologies for detecting positive infections within the shortest possible time, and vaccines and drugs specifically for the prevention and treatment of COVID-19 disease. At the same time, emerging novel variants have raised serious concerns about vaccine efficacy. The SARS-CoV-2 nucleocapsid (N) protein plays an important role in the coronavirus life cycle, and participates in various vital activities after virus invasion. It has attracted a large amount of attention for vaccine and drug development. Here, we summarize the latest research of the N protein, including its role in the SARS-CoV-2 life cycle, structure and function, and post-translational modifications in addition to its involvement in liquid-liquid phase separation (LLPS) and use as a basis for the development of vaccines and diagnostic techniques.
Collapse
Affiliation(s)
- Wenbing Wu
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Ying Cheng
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Hong Zhou
- grid.410578.f0000 0001 1114 4286Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000 China
| | - Changzhen Sun
- grid.410578.f0000 0001 1114 4286Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000 China
| | - Shujun Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, 646000, China.
| |
Collapse
|
3
|
Pohler A, Abdelfatah S, Riedl M, Meesters C, Hildebrandt A, Efferth T. Potential Coronaviral Inhibitors of the Nucleocapsid Protein Identified In Silico and In Vitro from a Large Natural Product Library. Pharmaceuticals (Basel) 2022; 15:ph15091046. [PMID: 36145267 PMCID: PMC9503946 DOI: 10.3390/ph15091046] [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] [Received: 07/06/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
The nucleocapsid protein (NP) is one of the main proteins out of four structural proteins of coronaviruses including the severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, discovered in 2019. NP packages the viral RNA during virus assembly and is, therefore, indispensable for virus reproduction. NP consists of two domains, i.e., the N- and C-terminal domains. RNA-binding is mainly performed by a binding pocket within the N-terminal domain (NTD). NP represents an important target for drug discovery to treat COVID-19. In this project, we used the Vina LC virtual drug screening software and a ZINC-based database with 210,541 natural and naturally derived compounds that specifically target the binding pocket of NTD of NP. Our aim was to identify coronaviral inhibitors that target NP not only of SARS-CoV-2 but also of other diverse human pathogenic coronaviruses. Virtual drug screening and molecular docking procedures resulted in 73 candidate compounds with a binding affinity below −9 kcal/mol with NP NTD of SARS-CoV-1, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-NL63, HoC-229E, and HCoV-HKU1. The top five compounds that met the applied drug-likeness criteria were then tested for their binding in vitro to the NTD of the full-length recombinant NP proteins using microscale thermophoresis. Compounds (1), (2), and (4), which belong to the same scaffold family of 4-oxo-substituted-6-[2-(4a-hydroxy-decahydroisoquinolin-2-yl)2H-chromen-2-ones and which are derivates of coumarin, were bound with good affinity to NP. Compounds (1) and (4) were bound to the full-length NP of SARS-CoV-2 (aa 1–419) with Kd values of 0.798 (±0.02) µM and 8.07 (±0.36) µM, respectively. Then, these coumarin derivatives were tested with the SARS-CoV-2 NP NTD (aa 48–174). Compounds (1) and (4) revealed Kd-values of 0.95 (±0.32) µM and 7.77 (±6.39) µM, respectively. Compounds (1) and (4) caused low toxicity in human A549 and MRC-5 cell lines. These compounds may represent possible drug candidates, which need further optimization to be used against COVID-19 and other coronaviral infections.
Collapse
Affiliation(s)
- Alexandra Pohler
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Sara Abdelfatah
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Max Riedl
- High Performance Computing Group, University of Mainz, 55131 Mainz, Germany
| | - Christian Meesters
- High Performance Computing Group, University of Mainz, 55131 Mainz, Germany
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
- Correspondence: ; Tel.: +49-6131-3925751; Fax: +49-6131-3923752
| |
Collapse
|
4
|
Calvo-Alvarez E, Dolci M, Perego F, Signorini L, Parapini S, D’Alessandro S, Denti L, Basilico N, Taramelli D, Ferrante P, Delbue S. Antiparasitic Drugs against SARS-CoV-2: A Comprehensive Literature Survey. Microorganisms 2022; 10:microorganisms10071284. [PMID: 35889004 PMCID: PMC9320270 DOI: 10.3390/microorganisms10071284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023] Open
Abstract
More than two years have passed since the viral outbreak that led to the novel infectious respiratory disease COVID-19, caused by the SARS-CoV-2 coronavirus. Since then, the urgency for effective treatments resulted in unprecedented efforts to develop new vaccines and to accelerate the drug discovery pipeline, mainly through the repurposing of well-known compounds with broad antiviral effects. In particular, antiparasitic drugs historically used against human infections due to protozoa or helminth parasites have entered the main stage as a miracle cure in the fight against SARS-CoV-2. Despite having demonstrated promising anti-SARS-CoV-2 activities in vitro, conflicting results have made their translation into clinical practice more difficult than expected. Since many studies involving antiparasitic drugs are currently under investigation, the window of opportunity might be not closed yet. Here, we will review the (controversial) journey of these old antiparasitic drugs to combat the human infection caused by the novel coronavirus SARS-CoV-2.
Collapse
Affiliation(s)
- Estefanía Calvo-Alvarez
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
- Correspondence:
| | - Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Federica Perego
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Silvia Parapini
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Sarah D’Alessandro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (D.T.)
| | - Luca Denti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Donatella Taramelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (D.T.)
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| |
Collapse
|
5
|
Khelfaoui H, Harkati D, Saleh BA. Molecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2. J Biomol Struct Dyn 2021; 39:7246-7262. [PMID: 32752951 PMCID: PMC7484571 DOI: 10.1080/07391102.2020.1803967] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023]
Abstract
The recent new contagion coronavirus 2019 (COVID-19) disease is a new generation of severe acute respiratory syndrome coronavirus-2 SARS-CoV-2 which infected millions confirmed cases and hundreds of thousands death cases around the world so far. Molecular docking combined with molecular dynamics is one of the most important tools of drug discovery and drug design, which it used to examine the type of binding between the ligand and its protein enzyme. Global reactivity has important properties, which enable chemists to understand the chemical reactivity and kinetic stability of compounds. In this study, molecular docking and reactivity were applied for eighteen drugs, which are similar in structure to chloroquine and hydroxychloroquine, the potential inhibitors to angiotensin-converting enzyme (ACE2). Those drugs were selected from DrugBank. The reactivity, molecular docking and molecular dynamics were performed for two receptors ACE2 and [SARS-CoV-2/ACE2] complex receptor in two active sites to find a ligand, which may inhibit COVID-19. The results obtained from this study showed that Ramipril, Delapril and Lisinopril could bind with ACE2 receptor and [SARS-CoV-2/ACE2] complex better than chloroquine and hydroxychloroquine. This new understanding should help to improve predictions of the impact of such alternatives on COVID-19.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Hadjer Khelfaoui
- Group of Computational Pharmaceutical
Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter
Sciences, University of Biskra, Biskra,
Algeria
| | - Dalal Harkati
- Group of Computational Pharmaceutical
Chemistry, LMCE Laboratory, Faculty of Exact and Natural Sciences, Department of Matter
Sciences, University of Biskra, Biskra,
Algeria
| | - Basil A. Saleh
- Department of Chemistry, College of Science,
University of Basrah, Basrah, Iraq
| |
Collapse
|
6
|
SARS-CoV-2 spike protein dictates syncytium-mediated lymphocyte elimination. Cell Death Differ 2021; 28:2765-2777. [PMID: 33879858 PMCID: PMC8056997 DOI: 10.1038/s41418-021-00782-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is highly contagious and causes lymphocytopenia, but the underlying mechanisms are poorly understood. We demonstrate here that heterotypic cell-in-cell structures with lymphocytes inside multinucleate syncytia are prevalent in the lung tissues of coronavirus disease 2019 (COVID-19) patients. These unique cellular structures are a direct result of SARS-CoV-2 infection, as the expression of the SARS-CoV-2 spike glycoprotein is sufficient to induce a rapid (~45.1 nm/s) membrane fusion to produce syncytium, which could readily internalize multiple lines of lymphocytes to form typical cell-in-cell structures, remarkably leading to the death of internalized cells. This membrane fusion is dictated by a bi-arginine motif within the polybasic S1/S2 cleavage site, which is frequently present in the surface glycoprotein of most highly contagious viruses. Moreover, candidate anti-viral drugs could efficiently inhibit spike glycoprotein processing, membrane fusion, and cell-in-cell formation. Together, we delineate a molecular and cellular rationale for SARS-CoV-2 pathogenesis and identify novel targets for COVID-19 therapy.
Collapse
|
7
|
Kumavath R, Barh D, Andrade BS, Imchen M, Aburjaile FF, Ch A, Rodrigues DLN, Tiwari S, Alzahrani KJ, Góes-Neto A, Weener ME, Ghosh P, Azevedo V. The Spike of SARS-CoV-2: Uniqueness and Applications. Front Immunol 2021; 12:663912. [PMID: 34305894 PMCID: PMC8297464 DOI: 10.3389/fimmu.2021.663912] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point-of-care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.
Collapse
Affiliation(s)
- Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Flavia Figueira Aburjaile
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Athira Ch
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Diego Lucas Neres Rodrigues
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
8
|
Das S, Ramachandran AK, Birangal SR, Akbar S, Ahmed B, Joseph A. The controversial therapeutic journey of chloroquine and hydroxychloroquine in the battle against SARS-CoV-2: A comprehensive review. MEDICINE IN DRUG DISCOVERY 2021; 10:100085. [PMID: 33846702 PMCID: PMC8026171 DOI: 10.1016/j.medidd.2021.100085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/09/2021] [Accepted: 02/20/2021] [Indexed: 12/24/2022] Open
Abstract
Recently, the pandemic outbreak of a novel coronavirus, officially termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), indicated by a pulmonary infection in humans, has become one of the most significant challenges for public health. In the current fight against coronavirus disease-2019, the medical and health authorities across the world focused on quick diagnosis and isolation of patients; meanwhile, researchers worldwide are exploring the possibility of developing vaccines and novel therapeutic options to combat this deadly disease. Recently, based on various small clinical observations, uncontrolled case studies and previously reported antiviral activity against SARS-CoV-1 chloroquine (CQ) and hydroxychloroquine (HCQ) have attracted exceptional consideration as possible therapeutic agents against SARS-CoV-2. However, there are reports on little to no effect of CQ or HCQ against SARS-CoV-2, and many reports have raised concerns about their cardiac toxicity. Here, in this review, we examine the chemistry, molecular mechanism, and pharmacology, including the current scenario and future prospects of CQ or HCQ in the treatment of SARS-CoV-2.
Collapse
Affiliation(s)
- Subham Das
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
- Manipal McGill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anu Kunnath Ramachandran
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sumit Raosaheb Birangal
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Saleem Akbar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Bahar Ahmed
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India
| | - Alex Joseph
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| |
Collapse
|
9
|
Matsuo T. Viewing SARS-CoV-2 Nucleocapsid Protein in Terms of Molecular Flexibility. BIOLOGY 2021; 10:454. [PMID: 34064163 PMCID: PMC8224284 DOI: 10.3390/biology10060454] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022]
Abstract
The latest coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19) pneumonia leading to the pandemic, contains 29 proteins. Among them, nucleocapsid protein (NCoV2) is one of the abundant proteins and shows multiple functions including packaging the RNA genome during the infection cycle. It has also emerged as a potential drug target. In this review, the current status of the research of NCoV2 is described in terms of molecular structure and dynamics. NCoV2 consists of two domains, i.e., the N-terminal domain (NTD) and the C-terminal domain (CTD) with a disordered region between them. Recent simulation studies have identified several potential drugs that can bind to NTD or CTD with high affinity. Moreover, it was shown that the degree of flexibility in the disordered region has a large effect on drug binding rate, suggesting the importance of molecular flexibility for the NCoV2 function. Molecular flexibility has also been shown to be integral to the formation of droplets, where NCoV2, RNA and/or other viral proteins gather through liquid-liquid phase separation and considered important for viral replication. Finally, as one of the future research directions, a strategy for obtaining the structural and dynamical information on the proteins contained in droplets is presented.
Collapse
Affiliation(s)
- Tatsuhito Matsuo
- Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1106, Japan;
- Laboratoire Interdisciplinaire de Physique (LiPhy), Grenoble-Alpes University, 140 Rue de la Physique, 38402 Saint Martin d’Hères, France
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, CEDEX 9, 38042 Grenoble, France
| |
Collapse
|
10
|
Mathew SM, Benslimane F, Althani AA, Yassine HM. Identification of potential natural inhibitors of the receptor-binding domain of the SARS-CoV-2 spike protein using a computational docking approach. Qatar Med J 2021; 2021:12. [PMID: 34604010 PMCID: PMC8474837 DOI: 10.5339/qmj.2021.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/13/2021] [Indexed: 12/23/2022] Open
Abstract
Background: The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only zoonotic-origin CoV to reach the pandemic stage, to which neither an effective vaccine nor a specific therapy is available. The spike glycoprotein harbors the receptor-binding domain (RBD) that mediates the virus's entry to host cells. This study aimed to identify novel inhibitors that target the spike protein's RBD domain through computational screening of chemical and natural compounds. Method: The spike protein was modeled from the recently reported electron microscopy protein structure (PDB ID: 6VSB) and the previously described SARS-CoV protein structure (PDB ID: 6ACD and 6ACJ). Virtual lab bench CLC Drug Discovery was used to computationally screen for potential inhibitory effects of currently prescribed drugs (n = 22), natural antiviral drugs (n = 100), and natural compounds (n = 35032). Quantitative Structure-Activity Relationship (QSAR) studies were also performed to determine the leading binders known for their antiviral activity. Results: Among the drugs currently used to treat SARS-CoV2, hydroxychloroquine and favipiravir were identified as the best binders with an average of four H-bonds, with a binding affinity of - 36.66 kcal/mol and a minimum interaction energy of - 6.63 kcal/mol. In an evaluation of antiviral compounds, fosamprenavir and abacavir showed effective binding of five H-bonds, with an average binding affinity of - 18.75 kcal.mol- 1 and minimum interaction energy of - 3.57 kcal/mol. Furthermore, screening of 100 natural antiviral compounds predicted potential binding modes of glycyrrhizin, nepritin, punicalagin, epigallocatechin gallate, and theaflavin (average binding affinity of - 49.88 kcal/mol and minimum interaction energy of - 4.35 kcal/mol). Additionally, the study reports a list of 25 natural compounds that showed effective binding with an improved average binding affinity of - 51.46 kcal/mol. Conclusions: Using computational screening, we identified potential SARS-CoV-2 S glycoprotein inhibitors that bind to the RBD region. Using structure-based design and combination-based drug therapy, the identified molecules could be used to generate anti-SARS-CoV-2 drug candidates.
Collapse
Affiliation(s)
| | | | - Asmaa A Althani
- Biomedical Research Center, Qatar University, Doha, Qatar
- Department of Biomedical Sciences, College of Health Sciences-QU Health, Qatar University, Doha, Qatar E-mail:
| | | |
Collapse
|
11
|
Sarcinelli MA, Martins da Silva T, Artico Silva AD, Ferreira de Carvalho Patricio B, Mendes de Paiva FC, Santos de Lima R, Leal da Silva M, Antunes Rocha HV. The pulmonary route as a way to drug repositioning in COVID-19 therapy. J Drug Deliv Sci Technol 2021; 63:102430. [PMID: 33649708 PMCID: PMC7903910 DOI: 10.1016/j.jddst.2021.102430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/04/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
Introduction The outbreak of the disease caused by the new coronavirus (COVID-19) has been affecting society's routine and its patterns of interaction worldwide, in addition to the impact on the global economy. To date, there is still no clinically effective treatment for this comorbidity, and drug repositioning might be a good strategy considering the established clinical safety profile. In this context, since COVID-19 affects the respiratory tract, a promising approach would be the pulmonary drug delivery. Objective Identify repurposing drug candidates for the treatment of COVID-19 based on the data of ongoing clinical trials and in silico studies and also assess their potential to be applied in formulations for pulmonary administration. Method A integrative literature review was conducted between June and July 2020, by extracting the results from Clinical Trials, PubMed, Web of Science and Science Direct databases. Results By crossing the results obtained from diverse sources, 21 common drugs were found, from which only 4 drugs presented studies of pulmonary release formulations, demonstrating the need for greater investment and incentive in this field. Conclusion Even though the lung is a target that facilitates viral infection and replication, formulations for pulmonary delivery of suitable drugs are still lacking for COVID-19 treatment. However, it is indisputable that the pandemic constitutes a concrete demand, with a profound impact on public health, and that, with the appropriate investments, it will give the pharmaceutical industry an opportunity to reinforce the pulmonary delivery field.
Collapse
Affiliation(s)
- Michelle Alvares Sarcinelli
- Laboratório de Micro e Nanotecnologia, Instituto de Tecnologia Em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil.,Rede Rio de Inovação em Nanossistemas para a Saúde - NanoSAÚDE/ FAPERJ, Rio de Janeiro, RJ, Brazil
| | - Thalita Martins da Silva
- Laboratório de Micro e Nanotecnologia, Instituto de Tecnologia Em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil.,Rede Rio de Inovação em Nanossistemas para a Saúde - NanoSAÚDE/ FAPERJ, Rio de Janeiro, RJ, Brazil.,Programa de Pós-graduação em Pesquisa Translacional em Fármacos e Medicamentos, Instituto de Tecnologia em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil
| | - Andressa Daniele Artico Silva
- Laboratório de Micro e Nanotecnologia, Instituto de Tecnologia Em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil.,Rede Rio de Inovação em Nanossistemas para a Saúde - NanoSAÚDE/ FAPERJ, Rio de Janeiro, RJ, Brazil
| | - Beatriz Ferreira de Carvalho Patricio
- Laboratório de Micro e Nanotecnologia, Instituto de Tecnologia Em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil.,Rede Rio de Inovação em Nanossistemas para a Saúde - NanoSAÚDE/ FAPERJ, Rio de Janeiro, RJ, Brazil
| | - Flávia Costa Mendes de Paiva
- Laboratório de Micro e Nanotecnologia, Instituto de Tecnologia Em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil.,Rede Rio de Inovação em Nanossistemas para a Saúde - NanoSAÚDE/ FAPERJ, Rio de Janeiro, RJ, Brazil.,Programa de Pós-graduação em Pesquisa Translacional em Fármacos e Medicamentos, Instituto de Tecnologia em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil
| | - Raissa Santos de Lima
- Programa de Pós-Graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, 21041-361, Brazil
| | - Manuela Leal da Silva
- Programa de Pós-Graduação em Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, 21041-361, Brazil.,Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal Do Rio de Janeiro, Macaé, RJ, 27965-045, Brazil
| | - Helvécio Vinícius Antunes Rocha
- Laboratório de Micro e Nanotecnologia, Instituto de Tecnologia Em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil.,Rede Rio de Inovação em Nanossistemas para a Saúde - NanoSAÚDE/ FAPERJ, Rio de Janeiro, RJ, Brazil.,Programa de Pós-graduação em Pesquisa Translacional em Fármacos e Medicamentos, Instituto de Tecnologia em Fármacos (Farmanguinhos), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, 21040-361, Brazil
| |
Collapse
|
12
|
Stoian AP, Catrinoiu D, Rizzo M, Ceriello A. Hydroxychloroquine, COVID-19 and diabetes. Why it is a different story. Diabetes Metab Res Rev 2021; 37:e3379. [PMID: 32592507 PMCID: PMC7362015 DOI: 10.1002/dmrr.3379] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Accepted: 06/22/2020] [Indexed: 12/23/2022]
Abstract
Hydroxychloroquine has been proposed for the cure of the COVID-19 due to its anti-inflammatory and anti-viral action. People with diabetes are more prone to severe outcome if affected by COVID-19 and the use of Hydroxychloroquine might have some benefit in this setting. However, the use of Hydroxychloroquine in diabetes deserves particular attention for its documented hypoglycemic action.
Collapse
Affiliation(s)
- Anca Pantea Stoian
- Diabetes, Nutrition and Metabolic Diseases Department“Carol Davila” University of MedicineBucharestRomania
| | - Doina Catrinoiu
- Faculty of Medicine, Clinical Center of Diabetes, Nutrition and Metabolic DiseasesOvidius University of ConstantaConstantaRomania
| | - Manfredi Rizzo
- Division of Endocrinology, Diabetes and Metabolism, Department of MedicineUniversity of South CarolinaColumbiaSouth CarolinaUSA
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical SpecialtiesUniversity of PalermoPalermoItaly
| | | |
Collapse
|
13
|
Yamamoto K, Suzuki M, Yamada G, Sudo T, Nomoto H, Kinoshita N, Nakamura K, Tsujimoto Y, Kusaba Y, Morita C, Moriya A, Maeda K, Yagi S, Kimura M, Ohmagari N. Utility of the antigen test for coronavirus disease 2019: Factors influencing the prediction of the possibility of disease transmission. Int J Infect Dis 2021; 104:65-72. [PMID: 33401037 PMCID: PMC7778366 DOI: 10.1016/j.ijid.2020.12.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/23/2020] [Accepted: 12/26/2020] [Indexed: 12/18/2022] Open
Abstract
Objectives Rapid antigen testing (RAT) for coronavirus disease 2019 (COVID-19) has lower sensitivity but high accuracy during the early stage when compared to reverse transcription quantitative polymerase chain reaction (RT-qPCR). The aim of this study was to investigate the concordance between RAT and RT-qPCR results, and their prediction of disease transmission. Methods This single-center retrospective observational study of inpatients with COVID-19 was conducted from March 6 to June 14, 2020. Nasopharyngeal swabs were used to perform RAT and RT-qPCR. The primary endpoint was concordance between RAT and RT-qPCR results. The secondary endpoints were the factors causing disagreement in the results and the estimated transmissibility in RT-qPCR-positive patients with mild symptoms. Results Overall, 229 samples in viral transport medium (VTM) were obtained from 105 patients. The positive and negative concordance rates for VTM were 41% vs 99% (κ = 0.37) and 72% vs 100% (κ = 0.50) for samples collected on disease days 2–9. An increased body temperature (odds ratio 0.54) and absence of drugs with potential antiviral effect (odds ratio 0.48) yielded conflicting results. RAT was associated with the ability to end isolation (OR 0.11, 95% confidence interval 0.20–0.61). Conclusions RAT and RT-qPCR results were highly consistent for samples collected at the appropriate time and could be useful for inferring the possibility of transmissibility.
Collapse
Affiliation(s)
- Kei Yamamoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Michiyo Suzuki
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Gen Yamada
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Tsutomu Sudo
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Hidetoshi Nomoto
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Noriko Kinoshita
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Keiji Nakamura
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Yoshie Tsujimoto
- Department of Respirology, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Yusaku Kusaba
- Department of Respirology, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Chie Morita
- Department of Respirology, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Ataru Moriya
- Clinical Laboratory, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Kenji Maeda
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo, 162-0052, Japan.
| | | | - Motoi Kimura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan.
| |
Collapse
|
14
|
Tatar G, Ozyurt E, Turhan K. Computational drug repurposing study of the RNA binding domain of SARS-CoV-2 nucleocapsid protein with antiviral agents. Biotechnol Prog 2020; 37:e3110. [PMID: 33314794 PMCID: PMC7883068 DOI: 10.1002/btpr.3110] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/29/2020] [Accepted: 12/04/2020] [Indexed: 12/21/2022]
Abstract
The recent outbreak of coronavirus disease (COVID‐19) in China caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has led to worldwide human infections and deaths. The nucleocapsid (N) protein of coronaviruses (CoVs) is a multifunctional RNA binding protein necessary for viral RNA replication and transcription. Therefore, it is a potential antiviral drug target, serving multiple critical functions during the viral life cycle. This study addresses the potential to repurpose antiviral compounds approved or in development for treating human CoV induced infections against SARS‐CoV‐2 N. For this purpose, we used the docking methodology to better understand the inhibitory mechanism of this protein with the existing 34 antiviral compounds. The results of this analysis indicate that rapamycin, saracatinib, camostat, trametinib, and nafamostat were the top hit compounds with binding energy (−11.87, −10.40, −9.85, −9.45, −9.35 kcal/mol, respectively). This analysis also showed that the most common residues that interact with the compounds are Phe66, Arg68, Gly69, Tyr123, Ile131, Trp132, Val133, and Ala134. Subsequently, protein‐ligand complex stability was examined with molecular dynamics simulations for these five compounds, which showed the best binding affinity. According to the results of this study, the interaction between these compounds and crucial residues of the target protein were maintained. These results suggest that these residues are potential drug targeting sites for the SARS‐CoV‐2 N protein. This study information will contribute to the development of novel compounds for further in vitro and in vivo studies of SARS‐CoV‐2, as well as possible new drug repurposing strategies to treat COVID‐19 disease.
Collapse
Affiliation(s)
- Gizem Tatar
- Department of Biostatistics and Medical Informatics, Karadeniz Technical University, Trabzon, Turkey
| | - Ezgi Ozyurt
- Department of Biostatistics and Medical Informatics, Karadeniz Technical University, Trabzon, Turkey
| | - Kemal Turhan
- Department of Biostatistics and Medical Informatics, Karadeniz Technical University, Trabzon, Turkey
| |
Collapse
|
15
|
Witika BA, Makoni PA, Mweetwa LL, Ntemi PV, Chikukwa MTR, Matafwali SK, Mwila C, Mudenda S, Katandula J, Walker RB. Nano-Biomimetic Drug Delivery Vehicles: Potential Approaches for COVID-19 Treatment. Molecules 2020; 25:E5952. [PMID: 33339110 PMCID: PMC7765509 DOI: 10.3390/molecules25245952] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
The current COVID-19 pandemic has tested the resolve of the global community with more than 35 million infections worldwide and numbers increasing with no cure or vaccine available to date. Nanomedicines have an advantage of providing enhanced permeability and retention and have been extensively studied as targeted drug delivery strategies for the treatment of different disease. The role of monocytes, erythrocytes, thrombocytes, and macrophages in diseases, including infectious and inflammatory diseases, cancer, and atherosclerosis, are better understood and have resulted in improved strategies for targeting and in some instances mimicking these cell types to improve therapeutic outcomes. Consequently, these primary cell types can be exploited for the purposes of serving as a "Trojan horse" for targeted delivery to identified organs and sites of inflammation. State of the art and potential utilization of nanocarriers such as nanospheres/nanocapsules, nanocrystals, liposomes, solid lipid nanoparticles/nano-structured lipid carriers, dendrimers, and nanosponges for biomimicry and/or targeted delivery of bioactives to cells are reported herein and their potential use in the treatment of COVID-19 infections discussed. Physicochemical properties, viz., hydrophilicity, particle shape, surface charge, composition, concentration, the use of different target-specific ligands on the surface of carriers, and the impact on carrier efficacy and specificity are also discussed.
Collapse
Affiliation(s)
- Bwalya A. Witika
- Department of Pharmacy, DDT College of Medicine, P.O. Box 70587, Gaborone 00000, Botswana; (B.A.W.); (L.L.M.)
- Division of Pharmaceutics, Faculty of Pharmacy, Rhodes University, Makhanda 6140, South Africa; (P.A.M.); (P.V.N.); (M.T.R.C.)
| | - Pedzisai A. Makoni
- Division of Pharmaceutics, Faculty of Pharmacy, Rhodes University, Makhanda 6140, South Africa; (P.A.M.); (P.V.N.); (M.T.R.C.)
| | - Larry L. Mweetwa
- Department of Pharmacy, DDT College of Medicine, P.O. Box 70587, Gaborone 00000, Botswana; (B.A.W.); (L.L.M.)
| | - Pascal V. Ntemi
- Division of Pharmaceutics, Faculty of Pharmacy, Rhodes University, Makhanda 6140, South Africa; (P.A.M.); (P.V.N.); (M.T.R.C.)
| | - Melissa T. R. Chikukwa
- Division of Pharmaceutics, Faculty of Pharmacy, Rhodes University, Makhanda 6140, South Africa; (P.A.M.); (P.V.N.); (M.T.R.C.)
| | - Scott K. Matafwali
- Department of Basic Sciences, School of Medicine, Copperbelt University, Ndola 10101, Zambia;
| | - Chiluba Mwila
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (C.M.); (S.M.)
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (C.M.); (S.M.)
| | - Jonathan Katandula
- Department of Biosciences and Chemistry, Faculty of Health and Wellbeing, Sheffield Hallam University, Sheffield S1 1WB, UK;
| | - Roderick B. Walker
- Division of Pharmaceutics, Faculty of Pharmacy, Rhodes University, Makhanda 6140, South Africa; (P.A.M.); (P.V.N.); (M.T.R.C.)
| |
Collapse
|
16
|
Mukherjee S, Dasgupta S, Adhikary T, Adhikari U, Panja SS. Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study. J Biomol Struct Dyn 2020; 39:7322-7334. [PMID: 32772895 PMCID: PMC7484585 DOI: 10.1080/07391102.2020.1804458] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Soumita Mukherjee
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Subrata Dasgupta
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Tapasendra Adhikary
- Department of Metallurgical & Materials Engineering, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Utpal Adhikari
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Sujit Sankar Panja
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| |
Collapse
|