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Gheidari D, Mehrdad M, Bayat M. Synthesis, molecular docking analysis, molecular dynamic simulation, ADMET, DFT, and drug likeness studies: Novel Indeno[1,2-b]pyrrol-4(1H)-one as SARS-CoV-2 main protease inhibitors. PLoS One 2024; 19:e0299301. [PMID: 38517870 PMCID: PMC10959350 DOI: 10.1371/journal.pone.0299301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/07/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic began in 2019 as a result of the advent of a novel coronavirus, SARS-CoV-2. At present, there are a limited number of approved antiviral agents for the treatment of COVID-19. Remdesivir, Molnupiravir, and Paxlovid have been approved by the FDA to treat COVID-19 infections. Research has shown that the main protease enzyme (Mpro) of SARS-CoV-2 plays a crucial role in the enzymatic processing of viral polyproteins. This makes Mpro an interesting therapeutic target for combating infections caused by emerging coronaviruses. METHODS The pharmacological effects of pyrroles and their derivatives have a wide range of applications. In our study, we focused on synthesizing nine novel derivatives of 2-arylamino-dihydro-indeno[1,2-b] pyrrol-4(1H)-one, with a particular emphasis on their antiviral properties. Using in silico studies involving molecular docking and DFT analyses in the gas phase using the B3LYP/6-31++G(d,p) basis set, we studied these compounds with respect to their interactions with the Mpro of SARS-CoV-2. The results of the docking analysis revealed that the synthesized compounds exhibited favorable inhibitory effects. Notably, compound 5f demonstrated the highest effectiveness against the target protein. Furthermore, the pharmacokinetic and drug-like properties of the synthesized derivatives of 2-arylamino-dihydroindeno[1,2-b] pyrrol-4(1H)-one indicated their potential as promising candidates for further development as inhibitors targeting SARS-CoV-2. However, it is imperative to determine the in vitro efficacy of these compounds through comprehensive biochemical and structural analyses.
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Affiliation(s)
- Davood Gheidari
- Faculty of Science, Department of Chemistry, University of Guilan, Rasht, Iran
| | - Morteza Mehrdad
- Faculty of Science, Department of Chemistry, University of Guilan, Rasht, Iran
| | - Mohammad Bayat
- Faculty of Science, Department of Chemistry, Imam Khomeini International University, Qazvin, Iran
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2
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Huang F, Chen C. Investigation of Bucillamine as anti-COVID-19 drug: DFT study, molecular docking, molecular dynamic simulation and ADMET analysis. J Biomol Struct Dyn 2024; 42:34-42. [PMID: 36995042 DOI: 10.1080/07391102.2023.2192791] [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: 08/17/2022] [Accepted: 03/10/2023] [Indexed: 03/31/2023]
Abstract
The novel coronavirus disease-2019 (COVID-19), caused by SARS-CoV-2, is a global health pandemic beginning in early December 2019 in Wuhan, Hubei province, China. The effective drug target among coronaviruses is the SARS-CoV-2 main protease (Mpro), because of its crucial role in processing viral polyproteins translated from the viral RNA. In this study, the bioactivity of the selected thiol drug named Bucillamine (BUC) was evaluated as a potential drug for COVID-19 treatment by using computational modeling strategies. First, the molecular electrostatic potential density (ESP) calculation was performed to estimate the chemically active atoms of BUC. Additionally, BUC was docked to the Mpro (PDB: 6LU7) to evaluate the protein-ligand binding affinities. Besides, the estimated ESP results by density functional theory (DFT) were used to illustrate the molecular docking findings. Moreover, the frontier orbitals analysis was calculated to determine the charge transfer between the Mpro and BUC. Then, the stability of protein-ligand complex was subjected to the molecular dynamic simulations. Finally, an in silico study was performed to predict drug-likeness and absorption, distribution, metabolism, excretion and toxicity profiles (ADMET) of BUC. These results propose that BUC can be a potential drug candidate against the COVID-19 disease progression.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fengwen Huang
- Key Laboratory of Neuroscience, Department of Biomedical Science, City University of HongKong, Hong Kong, China
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Chen Chen
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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3
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Zhang D, Ji L, Chen X, He Y, Sun Y, Ji L, Zhang T, Shen Q, Wang X, Wang Y, Yang S, Zhang W, Zhou C. SARS-CoV-2 Nsp15 suppresses type I interferon production by inhibiting IRF3 phosphorylation and nuclear translocation. iScience 2023; 26:107705. [PMID: 37680466 PMCID: PMC10480782 DOI: 10.1016/j.isci.2023.107705] [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: 01/30/2023] [Revised: 06/23/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes 2019 coronavirus disease (COVID-19), poses a significant threat to global public health security. Like other coronaviruses, SARS-CoV-2 has developed various strategies to inhibit the production of interferon (IFN). Here, we have discovered that SARS-CoV-2 Nsp15 obviously reduces the expression of IFN-β and IFN-stimulated genes (ISG56, CXCL10), and also inhibits IRF3 phosphorylation and nuclear translocation by antagonizing the RLR-mediated antiviral signaling pathway. Mechanically, we found that the poly-U-specific endonuclease domain (EndoU) of Nsp15 directly associates with the kinase domain (KD) of TBK1 to interfere TBK1 interacting with IRF3 and the flowing TBK1-mediated IRF3 phosphorylation. Furthermore, Nsp15 also prevented nuclear translocation of phosphorylated IRF3 via binding to the nuclear import adaptor karyopherin α1 (KPNA1) and promoting it autophagy-dependent degradation. These findings collectively reveal a novel mechanism by which Nsp15 antagonizes host's innate immune response.
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Affiliation(s)
- Dianqi Zhang
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou 225300, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Department of Clinical Laboratory, The Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu 214221, China
| | - Likai Ji
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xu Chen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Department of Laboratory Medicine and Pathology, Jiangsu Provincial Corps Hospital of Chinese People’s Armed Police Force, Yangzhou, Jiangsu 225003, China
| | - Yumin He
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
- Medical Research Center, Northern Jiangsu People’s Hospital, Yangzhou, Jiangsu 225001, China
| | - Yijie Sun
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Li Ji
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Tiancheng Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Quan Shen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Xiaochun Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yan Wang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Shixing Yang
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou 225300, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Wen Zhang
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou 225300, China
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Chenglin Zhou
- Clinical Laboratory Center, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou 225300, China
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4
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Xu F, Li R, von Gromoff ED, Drepper F, Knapp B, Warscheid B, Baumeister R, Qi W. Reprogramming of the transcriptome after heat stress mediates heat hormesis in Caenorhabditis elegans. Nat Commun 2023; 14:4176. [PMID: 37443152 PMCID: PMC10345090 DOI: 10.1038/s41467-023-39882-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Transient stress experiences not only trigger acute stress responses, but can also have long-lasting effects on cellular functions. In Caenorhabditis elegans, a brief exposure to heat shock during early adulthood extends lifespan and improves stress resistance, a phenomenon known as heat hormesis. Here, we investigated the prolonged effect of hormetic heat stress on the transcriptome of worms and found that the canonical heat shock response is followed by a profound transcriptional reprogramming in the post-stress period. This reprogramming relies on the endoribonuclease ENDU-2 but not the heat shock factor 1. ENDU-2 co-localizes with chromatin and interacts with RNA polymerase II, enabling specific regulation of transcription after the stress period. Failure to activate the post-stress response does not affect the resistance of animals to heat shock but eliminates the beneficial effects of hormetic heat stress. In summary, our work discovers that the RNA-binding protein ENDU-2 mediates the long-term impacts of transient heat stress via reprogramming transcriptome after stress exposure.
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Affiliation(s)
- Fan Xu
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Ruoyao Li
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Erika D von Gromoff
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Friedel Drepper
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Bettina Knapp
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Bettina Warscheid
- Biochemistry-Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Ralf Baumeister
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Signalling Research Centers BIOSS and CIBSS, Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
- Center for Biochemistry and Molecular Cell Research (Faculty of Medicine), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany
| | - Wenjing Qi
- Bioinformatics and Molecular Genetics (Faculty of Biology), Albert-Ludwigs-University Freiburg, Freiburg, 79104, Germany.
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Chen P, Wu M, He Y, Jiang B, He ML. Metabolic alterations upon SARS-CoV-2 infection and potential therapeutic targets against coronavirus infection. Signal Transduct Target Ther 2023; 8:237. [PMID: 37286535 DOI: 10.1038/s41392-023-01510-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/18/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2 infection has become a global pandemic due to the high viral transmissibility and pathogenesis, bringing enormous burden to our society. Most patients infected by SARS-CoV-2 are asymptomatic or have mild symptoms. Although only a small proportion of patients progressed to severe COVID-19 with symptoms including acute respiratory distress syndrome (ARDS), disseminated coagulopathy, and cardiovascular disorders, severe COVID-19 is accompanied by high mortality rates with near 7 million deaths. Nowadays, effective therapeutic patterns for severe COVID-19 are still lacking. It has been extensively reported that host metabolism plays essential roles in various physiological processes during virus infection. Many viruses manipulate host metabolism to avoid immunity, facilitate their own replication, or to initiate pathological response. Targeting the interaction between SARS-CoV-2 and host metabolism holds promise for developing therapeutic strategies. In this review, we summarize and discuss recent studies dedicated to uncovering the role of host metabolism during the life cycle of SARS-CoV-2 in aspects of entry, replication, assembly, and pathogenesis with an emphasis on glucose metabolism and lipid metabolism. Microbiota and long COVID-19 are also discussed. Ultimately, we recapitulate metabolism-modulating drugs repurposed for COVID-19 including statins, ASM inhibitors, NSAIDs, Montelukast, omega-3 fatty acids, 2-DG, and metformin.
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Affiliation(s)
- Peiran Chen
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Mandi Wu
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China
| | - Yaqing He
- Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, Guangdong, China
| | - Binghua Jiang
- Cell Signaling and Proteomic Center, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, HKSAR, Hong Kong, China.
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6
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Noor R. How do the severe acute respiratory coronavirus 2 (SARS-CoV-2) and its variants escape the host protective immunity and mediate pathogenesis? BULLETIN OF THE NATIONAL RESEARCH CENTRE 2022; 46:255. [PMID: 36254244 PMCID: PMC9556142 DOI: 10.1186/s42269-022-00945-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/06/2022] [Indexed: 05/10/2023]
Abstract
Background To protect the global population from the ongoing COVID-19 pandemic caused by the severe acute respiratory β-coronavirus 2 (SARS-CoV-2), a number of vaccines are currently being used in three dosages (i.e., along with the booster dose) to induce the immunity required to combat the SARS-CoV-2 and its variants. So far, several antivirals and the commercial vaccines have been found to evoke the required humoral and cellular immunity within a huge population around world. However, an important aspect to consider is the avoidance mechanism of the host protective immunity by SARS-CoV-2 variants. Main body of the abstract Indeed, such an immune escape strategy has been noticed previously in case of SARS-CoV-1 and the Middle East Respiratory Syndrome coronavirus (MERS-CoV). Regarding the SARS-CoV-2 variants, the most important aspect on vaccine development is to determine whether the vaccine is actually capable to elicit the immune response or not, especially the viral spike (S) protein. Short conclusion Present review thus focused on such elicitation of immunity as well as pondered to the avoidance of host immunity by the SARS-CoV-2 Wuhan strain and its variants.
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Affiliation(s)
- Rashed Noor
- Department of Life Sciences (DLS), School of Environment and Life Sciences (SELS), Independent University, Bangladesh (IUB), Plot 16, Block B, Aftabuddin Ahmed Road, Bashundhara, Dhaka 1229 Bangladesh
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7
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Ye ZW, Ong CP, Tang K, Fan Y, Luo C, Zhou R, Luo P, Cheng Y, Gray VS, Wang P, Chu H, Chan JFW, To KKW, Chen H, Chen Z, Yuen KY, Ling GS, Yuan S, Jin DY. Intranasal administration of a single dose of a candidate live attenuated vaccine derived from an NSP16-deficient SARS-CoV-2 strain confers sterilizing immunity in animals. Cell Mol Immunol 2022; 19:588-601. [PMID: 35352010 PMCID: PMC8961489 DOI: 10.1038/s41423-022-00855-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 12/17/2022] Open
Abstract
Live attenuated vaccines might elicit mucosal and sterilizing immunity against SARS-CoV-2 that the existing mRNA, adenoviral vector and inactivated vaccines fail to induce. Here, we describe a candidate live attenuated vaccine strain of SARS-CoV-2 in which the NSP16 gene, which encodes 2′-O-methyltransferase, is catalytically disrupted by a point mutation. This virus, designated d16, was severely attenuated in hamsters and transgenic mice, causing only asymptomatic and nonpathogenic infection. A single dose of d16 administered intranasally resulted in sterilizing immunity in both the upper and lower respiratory tracts of hamsters, thus preventing viral spread in a contact-based transmission model. It also robustly stimulated humoral and cell-mediated immune responses, thus conferring full protection against lethal challenge with SARS-CoV-2 in a transgenic mouse model. The neutralizing antibodies elicited by d16 effectively cross-reacted with several SARS-CoV-2 variants. Secretory immunoglobulin A was detected in the blood and nasal wash of vaccinated mice. Our work provides proof-of-principle evidence for harnessing NSP16-deficient SARS-CoV-2 for the development of live attenuated vaccines and paves the way for further preclinical studies of d16 as a prototypic vaccine strain, to which new features might be introduced to improve safety, transmissibility, immunogenicity and efficacy.
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Affiliation(s)
- Zi-Wei Ye
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Chon Phin Ong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Kaiming Tang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Yilan Fan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Cuiting Luo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Runhong Zhou
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Peng Luo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Yun Cheng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Victor Sebastien Gray
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China
| | - Pui Wang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Hin Chu
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Jasper Fuk-Woo Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Kelvin Kai-Wang To
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Honglin Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Zhiwei Chen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China
| | - Guang Sheng Ling
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.
| | - Shuofeng Yuan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, 102 Pokfulam Road, Pokfulam, Hong Kong, China.
| | - Dong-Yan Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong, China.
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Beloukas A, Rampias T. Biological and Clinical Significance of Adaptive Evolution of Coronaviruses. Life (Basel) 2021; 11:life11111129. [PMID: 34833006 PMCID: PMC8617743 DOI: 10.3390/life11111129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/21/2021] [Indexed: 12/27/2022] Open
Affiliation(s)
- Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
- Correspondence: (A.B.); (T.R.)
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, Basic Research Center, 11527 Athens, Greece
- Correspondence: (A.B.); (T.R.)
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Hijikata A, Shionyu C, Nakae S, Shionyu M, Ota M, Kanaya S, Shirai T. Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins. Biophys Physicobiol 2021; 18:226-240. [PMID: 34745807 PMCID: PMC8550875 DOI: 10.2142/biophysico.bppb-v18.025] [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: 08/06/2021] [Accepted: 09/30/2021] [Indexed: 01/31/2023] Open
Abstract
More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of in silico and in vitro screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity in vitro, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Clara Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shigehiko Kanaya
- Computational Biology Lab. Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
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