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Yang W, Wang Y, Han D, Tang W, Sun L. Recent advances in application of computer-aided drug design in anti-COVID-19 Virials Drug Discovery. Biomed Pharmacother 2024; 173:116423. [PMID: 38493593 DOI: 10.1016/j.biopha.2024.116423] [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: 12/08/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a global pandemic epidemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), which poses a serious threat to human health worldwide and results in significant economic losses. With the continuous emergence of new virus strains, small molecule drugs remain the most effective treatment for COVID-19. The traditional drug development process usually requires several years; however, the development of computer-aided drug design (CADD) offers the opportunity to develop innovative drugs quickly and efficiently. The literature review describes the general process of CADD, the viral proteins that play essential roles in the life cycle of SARS-CoV-2 and can serve as therapeutic targets, and examples of drug screening of viral target proteins by applying CADD methods. Finally, the potential of CADD in COVID-19 therapy, the deficiency, and the possible future development direction are discussed.
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Affiliation(s)
- Weiying Yang
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China
| | - Ye Wang
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Dongfeng Han
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China
| | - Wenjing Tang
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China
| | - Lichao Sun
- Department of Emergency Medicine, First Hospital of Jilin University, Changchun 130021, China.
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2
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Thi HV, Hoang TN, Le NQK, Chu DT. Application of data science and bioinformatics in RNA therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:83-97. [PMID: 38360007 DOI: 10.1016/bs.pmbts.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Nowadays, information technology (IT) has been holding a significant role in daily life worldwide. The trajectory of data science and bioinformatics promises pioneering personalized therapies, reshaping medical landscapes and patient care. For RNA therapy to reach more patients, a comprehensive understanding of the application of data science and bioinformatics to this therapy is essential. Thus, this chapter has summarized the application of data science and bioinformatics in RNA therapeutics. Data science applications in RNA therapy, such as data integration and analytics, machine learning, and drug development, have been discussed. In addition, aspects of bioinformatics such as RNA design and evaluation, drug delivery system simulation, and databases for personalized medicine have also been covered in this chapter. These insights have shed light on existing evidence and opened potential future directions. From there, scientists can elevate RNA-based therapeutics into an era of tailored treatments and revolutionary healthcare.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thanh-Nhat Hoang
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; AIBioMed Research Group, Taipei Medical University, Taipei, Taiwan
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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3
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Carter C, Airas J, Gladden H, Miller BR, Parish CA. Exploring the disruption of SARS-CoV-2 RBD binding to hACE2. Front Chem 2023; 11:1276760. [PMID: 37954960 PMCID: PMC10635427 DOI: 10.3389/fchem.2023.1276760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
The COVID-19 pandemic was declared due to the spread of the novel coronavirus, SARS-CoV-2. Viral infection is caused by the interaction between the SARS-CoV-2 receptor binding domain (RBD) and the human ACE2 receptor (hACE2). Previous computational studies have identified repurposed small molecules that target the RBD, but very few have screened drugs in the RBD-hACE2 interface. When studies focus solely on the binding affinity between the drug and the RBD, they ignore the effect of hACE2, resulting in an incomplete analysis. We screened ACE inhibitors and previously identified SARS-CoV-2 inhibitors for binding to the RBD-hACE2 interface, and then conducted 500 ns of unrestrained molecular dynamics (MD) simulations of fosinopril, fosinoprilat, lisinopril, emodin, diquafosol, and physcion bound to the interface to assess the binding characteristics of these ligands. Based on MM-GBSA analysis, all six ligands bind favorably in the interface and inhibit the RBD-hACE2 interaction. However, when we repeat our simulation by first binding the drug to the RBD before interacting with hACE2, we find that fosinopril, fosinoprilat, and lisinopril result in a strongly interacting trimeric complex (RBD-drug-hACE2). Hydrogen bonding and pairwise decomposition analyses further suggest that fosinopril is the best RBD inhibitor. However, when lisinopril is bound, it stabilizes the trimeric complex and, therefore, is not an ideal potential drug candidate. Overall, these results reveal important atomistic interactions critical to the binding of the RBD to hACE2 and highlight the significance of including all protein partners in the evaluation of a potential drug candidate.
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Affiliation(s)
- Camryn Carter
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, United States
| | - Justin Airas
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, United States
| | - Haley Gladden
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, United States
| | - Bill R Miller
- Department of Chemistry, Truman State University, Kirksville, MO, United States
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, United States
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Wang Y, Qin P, Zhao C, Li Y, Li S, Fan F, Li D, Huang H, Duan H, Yang X, Du W, Li Y. Evaluating anti-viral effect of Ivermectin on porcine epidemic diarrhea virus and analyzing the related genes and signaling pathway by RNA-seq in vitro. Virology 2023; 587:109877. [PMID: 37688922 DOI: 10.1016/j.virol.2023.109877] [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: 07/01/2023] [Revised: 08/28/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) has catastrophic impacts on the global pig industry. However, there remains no effective drugs for PEDV infection. Ivermectin is an FDA-approved anthelmintic drug used to treat worm infections. In this study, we reported the broad-spectrum antiviral activity of Ivermectin in vitro. Ivermectin can inhibit PEDV infections of different genotypes. Avermectin derivatives can also inhibit PEDV infections. A time of addition assay showed that Ivermectin exhibited potent anti-PEDV activity when added simultaneously with or post virus infection. Furthermore, Ivermectin significantly inhibited the late stage of viral infection by affecting viral release. RNA sequencing indicates Ivermectin induces cell cycle arrest, which may be related to its ability to inhibit viral release. Interestingly, when combined with Niclosamide, Ivermectin demonstrated an enhanced anti-PEDV effect. These findings highlight Ivermectin as a novel antiviral agent with potential for the development of drugs against PEDV infection.
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Affiliation(s)
- Yue Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Panpan Qin
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Chenxu Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Yaqin Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Shuai Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Fangfang Fan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Dongliang Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Huimin Huang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, 6 Long-zi-hu Street, Zhengzhou, 450046, China.
| | - Hong Duan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Xia Yang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Wenjuan Du
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584, CL, the Netherlands.
| | - Yongtao Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China; Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Henan Agricultural University, Zhengzhou, 450046, China; Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584, CL, the Netherlands.
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5
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Breitinger U, Sedky CA, Sticht H, Breitinger HG. Patch-clamp studies and cell viability assays suggest a distinct site for viroporin inhibitors on the E protein of SARS-CoV-2. Virol J 2023; 20:142. [PMID: 37422646 PMCID: PMC10329798 DOI: 10.1186/s12985-023-02095-y] [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: 07/30/2022] [Accepted: 06/08/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND SARS-CoV-2 has caused a worldwide pandemic since December 2019 and the search for pharmaceutical targets against COVID-19 remains an important challenge. Here, we studied the envelope protein E of SARS-CoV and SARS-CoV-2, a highly conserved 75-76 amino acid viroporin that is crucial for virus assembly and release. E protein channels were recombinantly expressed in HEK293 cells, a membrane-directing signal peptide ensured transfer to the plasma membrane. METHODS Viroporin channel activity of both E proteins was investigated using patch-clamp electrophysiology in combination with a cell viability assay. We verified inhibition by classical viroporin inhibitors amantadine, rimantadine and 5-(N,N-hexamethylene)-amiloride, and tested four ivermectin derivatives. RESULTS Classical inhibitors showed potent activity in patch-clamp recordings and viability assays. In contrast, ivermectin and milbemycin inhibited the E channel in patch-clamp recordings but displayed only moderate activity on the E protein in the cell viability assay, which is also sensitive to general cytotoxic activity of the tested compounds. Nemadectin and ivermectin aglycon were inactive. All ivermectin derivatives were cytotoxic at concentrations > 5 µM, i.e. below the level required for E protein inhibition. CONCLUSIONS This study demonstrates direct inhibition of the SARS-CoV-2 E protein by classical viroporin inhibitors. Ivermectin and milbemycin inhibit the E protein channel but their cytotoxicity argues against clinical application.
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Affiliation(s)
- Ulrike Breitinger
- Department of Biochemistry, German University in Cairo, Main Entrance of Al Tagamoa Al Khames, New Cairo, 11835, Egypt.
| | - Christine Adel Sedky
- Department of Biochemistry, German University in Cairo, Main Entrance of Al Tagamoa Al Khames, New Cairo, 11835, Egypt
| | - Heinrich Sticht
- Division of Bioinformatics, Institute for Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hans-Georg Breitinger
- Department of Biochemistry, German University in Cairo, Main Entrance of Al Tagamoa Al Khames, New Cairo, 11835, Egypt
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6
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [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: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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7
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Aziz S, Waqas M, Mohanta TK, Halim SA, Iqbal A, Ali A, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. Identifying non-nucleoside inhibitors of RNA-dependent RNA-polymerase of SARS-CoV-2 through per-residue energy decomposition-based pharmacophore modeling, molecular docking, and molecular dynamics simulation. J Infect Public Health 2023; 16:501-519. [PMID: 36801630 PMCID: PMC9927802 DOI: 10.1016/j.jiph.2023.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND AND OBJECTIVE The current coronavirus disease-2019 (COVID-19) pandemic has triggered a worldwide health and economic crisis. The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes the disease and completes its life cycle using the RNA-dependent RNA-polymerase (RdRp) enzyme, a prominent target for antivirals. In this study, we have computationally screened ∼690 million compounds from the ZINC20 database and 11,698 small molecule inhibitors from DrugBank to find existing and novel non-nucleoside inhibitors for SARS-CoV-2 RdRp. METHODS Herein, a combination of the structure-based pharmacophore modeling and hybrid virtual screening methods, including per-residue energy decomposition-based pharmacophore screening, molecular docking, pharmacokinetics, and toxicity evaluation were employed to retrieve novel as well as existing RdRp non-nucleoside inhibitors from large chemical databases. Besides, molecular dynamics simulation and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) method were used to investigate the binding stability and calculate the binding free energy of RdRp-inhibitor complexes. RESULTS Based on docking scores and significant binding interactions with crucial residues (Lys553, Arg557, Lys623, Cys815, and Ser816) in the RNA binding site of RdRp, three existing drugs, ZINC285540154, ZINC98208626, ZINC28467879, and five compounds from ZINC20 (ZINC739681614, ZINC1166211307, ZINC611516532, ZINC1602963057, and ZINC1398350200) were selected, and the conformational stability of RdRp due to their binding was confirmed through molecular dynamics simulation. The free energy calculations revealed these compounds possess strong binding affinities for RdRp. In addition, these novel inhibitors exhibited drug-like features, good absorption, distribution, metabolism, and excretion profile and were found to be non-toxic. CONCLUSION The compounds identified in the study by multifold computational strategy can be validated in vitro as potential non-nucleoside inhibitors of SARS-CoV-2 RdRp and holds promise for the discovery of novel drugs against COVID-19 in future.
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Affiliation(s)
- Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25000, Pakistan; Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan.
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P. O. Box 2404, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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Bekheit MS, Panda SS, Girgis AS. Potential RNA-dependent RNA polymerase (RdRp) inhibitors as prospective drug candidates for SARS-CoV-2. Eur J Med Chem 2023; 252:115292. [PMID: 36965227 PMCID: PMC10023213 DOI: 10.1016/j.ejmech.2023.115292] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
The SARS-CoV-2 pandemic is considered as one of the most disastrous pandemics for human health and the world economy. RNA-dependent RNA polymerase (RdRp) is one of the key enzymes that control viral replication. RdRp is an attractive and promising therapeutic target for the treatment of SARS-CoV-2 disease. It has attracted much interest of medicinal chemists, especially after the approval of Remdesivir. This study highlights the most promising SARS-CoV-2 RdRp repurposed drugs in addition to natural and synthetic agents. Although many in silico predicted agents have been developed, the lack of in vitro and in vivo experimental data has hindered their application in drug discovery programs.
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Affiliation(s)
- Mohamed S Bekheit
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Siva S Panda
- Department of Chemistry and Physics, Augusta University, Augusta, GA, 30912, USA.
| | - Adel S Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza, 12622, Egypt.
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10
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Zamzami MA. Molecular docking, molecular dynamics simulation and MM-GBSA studies of the activity of glycyrrhizin relevant substructures on SARS-CoV-2 RNA-dependent-RNA polymerase. J Biomol Struct Dyn 2023; 41:1846-1858. [PMID: 35037842 DOI: 10.1080/07391102.2021.2025147] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
SARS-CoV-2 is the causative agent of Coronavirus Disease (COVID-19), which is a life-threatening disease. The World Health Organization has classified COVID-19 as a severe worldwide public health pandemic due to its high death rate, quick transmission, and lack of medicines. To counteract the recurrence of the severe acute respiratory syndrome, active antiviral medications are urgently required. Glycyrrhizin was documented with activity on different viral proteins, including SARS-CoV-2; in this study, the activity of glycyrrhizin and its substructures (604 molecules) were screened on SARS-CoV-2 RNA-dependent-RNA polymerase using molecular docking, molecular dynamic (MD) simulation, and MM/GBSA. Sixteen molecules exhibited docking energy higher than -7 kcal/mol; four compounds (10772603, 101088272, 154730753 and glycyrrhizin) showed the highest binding energy, and good stability during MD simulation. The glycyrrhizin compound exhibited favorable docking energy (-7.9 kcal/mol), and it was the most stable complex during MD simulation. The predicted binding free energy of the glycyrrhizin complex was -57 ± 8 kcal/mol. These findings suggest that this molecule, after more validation, could become a good candidate for developing and manufacturing an anti-SARS-CoV-2 medication.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Kapoor S, Singh A, Gupta V. In silico evaluation of potential intervention against SARS-CoV-2 RNA-dependent RNA polymerase. PHYSICS AND CHEMISTRY OF THE EARTH (2002) 2023; 129:103350. [PMID: 36536697 PMCID: PMC9750507 DOI: 10.1016/j.pce.2022.103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 09/17/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Background With few available effective interventions, emergence of novel mutants responding poorly to existing vaccines and ever swelling newer waves of infection, SARS-CoV-2 is posing difficult challenges to mankind. This mandates development of newer and effective therapeutics to prevent loss of life and contain the spread of this deadly virus. Nsp12 or RNA-dependent RNA polymerase (RdRp) is a suitable druggable target as it plays a central role in viral replication. Methodology Catalytically important conserved amino acid residues of RdRp were delineated through a comprehensive literature search and multiple sequence alignments. PDB ID 7BV2 was used to create binding pockets using SeeSAR and to generate docked poses of the FDA approved drugs on the receptor and estimating their binding affinity and other properties. Result In silico approach used in this study assisted in prediction of several potential RdRp inhibitors; and re-validation of the already reported ones. Five molecules namely Inosine, Ribavirin, 2-Deoxy-2-Fluoro-D-glucose, Guaifenesin, and Lamivudine were shortlisted which exhibited reasonable binding affinities, with neither torsional nor intermolecular or intramolecular clashes. Conclusion This study aimed to widen the prospect of interventions against the SARS-CoV-2 RdRp. Our results also re-validate already reported molecules like 2-Deoxy-D-glucose as a similar molecule 2-deoxy-2-fluoro-D-glucose is picked up in this study. Additionally, ribavirin and lamivudine, already known antivirals with polymerase inhibition activity are also picked up as the top leads. Selected potent inhibitors of RdRp hold promise to cater for any future coronavirus-outbreak subject to in vitro and in vivo validations.
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Affiliation(s)
- Shreya Kapoor
- Department of Microbiology, Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi, 110021, India
- Delhi Technological University, New Delhi, India
| | - Anurag Singh
- Department of Microbiology, Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi, 110021, India
- ICMR-National Institute of Virology, Pune, Maharashtra, 411021, India
| | - Vandana Gupta
- Department of Microbiology, Ram Lal Anand College, University of Delhi, Benito Juarez Road, New Delhi, 110021, India
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12
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Qayed WS, Hassan MA, Abouwarda AM, Ibrahim YM, Aboul-Fadl T. Computational Design of Azine-Linked Hybrids of 2-Indolinone-Thiazolodine Scaffold as Novel and Promising Quorum Sensing Inhibitors. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2165511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Wesam S. Qayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assuit, Egypt
| | - Mostafa A. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assuit, Egypt
| | - Ahmed Megahed Abouwarda
- Department of Microbiology, General Division of Basic Medical Sciences, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Yasser Musa Ibrahim
- Department of Microbiology, General Division of Basic Medical Sciences, Egyptian Drug Authority (EDA), Formerly National Organization for Drug Control and Research (NODCAR), Giza, Egypt
| | - Tarek Aboul-Fadl
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assuit, Egypt
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13
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Shahabadi N, Zendehcheshm S, Mahdavi M, Khademi F. Repurposing FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, and remdesivir as potential inhibitors against RNA dependent RNA polymerase of SARS-CoV-2: A comparative in silico perspective. INFORMATICS IN MEDICINE UNLOCKED 2023; 36:101147. [PMID: 36510496 PMCID: PMC9729590 DOI: 10.1016/j.imu.2022.101147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/19/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Vaccines are undoubtedly the most effective means of combating viral diseases like COVID-19. However, there are risks associated with vaccination, such as incomplete viral deactivation or potential adverse effects in humans. However, designing and developing a panel of new drug molecules is always encouraged. In an emergency, drug repurposing research is one of the most potent and rapid options. RdRp (RNA-dependent RNA polymerase) has been discovered to play a pivotal role in viral replication. In this study, FDA-approved drugs bexarotene, diiodohydroxyquinoline, abiraterone, cetilistat, and remdesivir were repurposed against the RdRp by molecular modeling, docking, and dynamic simulation. Furthermore, to validate the potency of these drugs, we compared them to the antiviral remdesivir, which inhibits RdRp. Our finding indicated that the selected drugs have a high potential to be developed as RdRp inhibitors and, with further validation studies, could serve as potential drugs for the treatment of COVID-19.
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Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran,Corresponding author. Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Saba Zendehcheshm
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Mahdavi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Fatemeh Khademi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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14
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Pyasi S, Jonniya NA, Sk MF, Nayak D, Kar P. Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of bovine ephemeral fever virus (BEFV): an in- silico study. J Biomol Struct Dyn 2022; 40:10403-10421. [PMID: 34238122 DOI: 10.1080/07391102.2021.1946714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bovine ephemeral fever virus (BEFV) is an enzootic agent that affects millions of bovines and causes major economic losses. Though the virus is seasonally reported with a very high morbidity rate (80-100%) from African, Australian, and Asiatic continents, it remains a neglected pathogen in many of its endemic areas, with no proper therapeutic drugs or vaccines presently available for treatment. The RNA-dependent RNA polymerase (RdRp) catalyzes the viral RNA synthesis and is an appropriate candidate for antiviral drug developments. We utilized integrated computational tools to build the 3D model of BEFV-RdRp and then predicted its probable active binding sites. The virtual screening and optimization against these active sites, using several small-molecule inhibitors from a different category of Life Chemical database and FDA-approved drugs from the ZINC database, was performed. We found nine molecules that have docking scores varying between -6.84 to -10.43 kcal/mol. Furthermore, these complexes were analyzed for their conformational dynamics and thermodynamic stability using molecular dynamics simulations in conjunction with the molecular mechanics generalized Born surface area (MM-GBSA) scheme. The binding free energy calculations depict that the electrostatic interactions play a dominant role in the RdRp-inhibitor binding. The hot spot residues, such as Arg565, Asp631, Glu633, Asp740, and Glu707, were found to control the RdRp-inhibitor interaction. The ADMET analysis strongly suggests favorable pharmacokinetics of these compounds that may prove useful for treating the BEFV ailment. Overall, we anticipate that these findings would help explore and develop a wide range of anti-BEFV therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Pyasi
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Debasis Nayak
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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15
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Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations. Sci Rep 2022; 12:19986. [PMID: 36411383 PMCID: PMC9676757 DOI: 10.1038/s41598-022-24695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.
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16
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Gangadharan S, Ambrose JM, Rajajagadeesan A, Kullappan M, Patil S, Gandhamaneni SH, Veeraraghavan VP, Nakkella AK, Agarwal A, Jayaraman S, Surapaneni KM. Repurposing of potential antiviral drugs against RNA-dependent RNA polymerase of SARS-CoV-2 by computational approach. J Infect Public Health 2022; 15:1180-1191. [PMID: 36240528 PMCID: PMC9514006 DOI: 10.1016/j.jiph.2022.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/18/2023] Open
Abstract
The high incidences of COVID-19 cases are believed to be associated with high transmissibility rates, which emphasizes the need for the discovery of evidence-based antiviral therapies for curing the disease. The rationale of repurposing existing classes of antiviral small molecule therapeutics against SARS-CoV-2 infection has been expected to accelerate the tedious and expensive drug development process. While Remdesivir has been recently approved to be the first treatment option for specific groups of COVID-19 patients, combinatory therapy with potential antiviral drugs may be necessary to enhance the efficacy in different populations. Hence, a comprehensive list of investigational antimicrobial drug compounds such as Favipiravir, Fidaxomicin, Galidesivir, GC376, Ribavirin, Rifabutin, and Umifenovir were computationally evaluated in this study. We performed in silico docking and molecular dynamics simulation on the selected small molecules against RNA-dependent RNA polymerase, which is one of the key target proteins of SARS-CoV-2, using AutoDock and GROMACS. Interestingly, our results revealed that the macrocyclic antibiotic, Fidaxomicin, possesses the highest binding affinity with the lowest energy value of -8.97 kcal/mol binding to the same active sites of RdRp. GC376, Rifabutin, Umifenovir and Remdesivir were identified as the next best compounds. Therefore, the above-mentioned compounds could be considered good leads for further preclinical and clinical experimentations as potentially efficient antiviral inhibitors for combination therapies against SARS-CoV-2.
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Affiliation(s)
- Sivakumar Gangadharan
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
| | - Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Anusha Rajajagadeesan
- Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UTAH-84095, USA; Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Sri Harshini Gandhamaneni
- Department of General Medicine, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Aruna Kumari Nakkella
- Department of Engineering Chemistry, Dr B R Ambedkar University, Etcherla, Srikakulam 532410, Andhra Pradesh, India.
| | - Alok Agarwal
- Department of Chemistry, Chinmaya Degree College, BHEL, Haridwar 249403, Uttarakhand, India.
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Molecular Virology, Research, Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
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17
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Engin AB, Engin ED, Engin A. Can iron, zinc, copper and selenium status be a prognostic determinant in COVID-19 patients? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2022; 95:103937. [PMID: 35882309 PMCID: PMC9307469 DOI: 10.1016/j.etap.2022.103937] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 05/14/2023]
Abstract
In severe COVID-19, the levels of iron (Fe), copper (Cu), zinc (Zn) and selenium (Se), do not only regulate host immune responses, but modify the viral genome, as well. While low serum Fe concentration is an independent risk factor for the increased death rate, Zn controls oxidative stress, synthesis of inflammatory cytokines and viral replication. Therefore, Zn deficiency associates with a worse prognosis. Although Cu exposure inactivates the viral genome and exhibits spike protein dispersal, increase in Cu/Zn due to high serum Cu levels, are correlated with enhanced risk of infections. Se levels are significantly higher in surviving COVID-19 patients. Meanwhile, both Zn and Se suppress the replication of SARS-CoV-2. Since the balance between the deficiency and oversupply of these metals due to a reciprocal relationship, has decisive effect on the prognosis of the SARS-CoV-2 infection, monitoring their concentrations may facilitate improved outcomes for patients suffering from COVID-19.
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Affiliation(s)
- Ayse Basak Engin
- Gazi University, Faculty of Pharmacy, Department of Toxicology, Ankara, Turkey.
| | - Evren Doruk Engin
- Ankara University, Biotechnology Institute, Gumusdere Campus, Kecioren, Ankara, Turkey
| | - Atilla Engin
- Gazi University, Faculty of Medicine, Department of General Surgery, Ankara, Turkey
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18
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Qayed WS, Ferreira RS, Silva JRA. In Silico Study towards Repositioning of FDA-Approved Drug Candidates for Anticoronaviral Therapy: Molecular Docking, Molecular Dynamics and Binding Free Energy Calculations. Molecules 2022; 27:molecules27185988. [PMID: 36144718 PMCID: PMC9505381 DOI: 10.3390/molecules27185988] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 01/18/2023] Open
Abstract
The SARS-CoV-2 targets were evaluated for a set of FDA-approved drugs using a combination of drug repositioning and rigorous computational modeling methodologies such as molecular docking and molecular dynamics (MD) simulations followed by binding free energy calculations. Six FDA-approved drugs including, Ouabain, Digitoxin, Digoxin, Proscillaridin, Salinomycin and Niclosamide with promising anti-SARS-CoV-2 activity were screened in silico against four SARS-CoV-2 proteins—papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), SARS-CoV-2 main protease (Mpro), and adaptor-associated kinase 1 (AAK1)—in an attempt to define their promising targets. The applied computational techniques suggest that all the tested drugs exhibited excellent binding patterns with higher scores and stable complexes compared to the native protein cocrystallized inhibitors. Ouabain was suggested to act as a dual inhibitor for both PLpro and Mpro enzymes, while Digitoxin bonded perfectly to RdRp. In addition, Salinomycin targeted PLpro. Particularly, Niclosamide was found to target AAK1 with greater affinity compared to the reference drug. Our study provides comprehensive molecular-level insights for identifying or designing novel anti-COVID-19 drugs.
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Affiliation(s)
- Wesam S. Qayed
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
- Correspondence: (W.S.Q.); (J.R.A.S.)
| | - Rafaela S. Ferreira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém 66075-110, Brazil
- Correspondence: (W.S.Q.); (J.R.A.S.)
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19
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Abdizadeh R, Hadizadeh F, Abdizadeh T. Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies. J Biomol Struct Dyn 2022:1-31. [PMID: 35848354 DOI: 10.1080/07391102.2022.2098821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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20
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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21
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Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides. Virus Res 2022; 315:198769. [PMID: 35430319 PMCID: PMC9008983 DOI: 10.1016/j.virusres.2022.198769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/17/2023]
Abstract
At the end of 2019, in China, clinical signs and symptoms of unknown etiology have been reported in several patients whose sample sequencing revealed pneumonia caused by the SARS-CoV-2 virus. COVID-19 is a disease triggered by this virus, and in 2020, the World Health Organization declared it a pandemic. Since then, efforts have been made to find effective therapeutic agents against this disease. Identifying novel natural antiviral drugs can be an alternative to treatment. For this reason, antimicrobial peptides secreted by anurans' skin have gained attention for showing a promissory antiviral effect. Hence, this review aimed to elucidate how and which peptides secreted by anurans' skin can be considered therapeutic agents to treat or prevent human viral infectious diseases. Through a literature review, we attempted to identify potential antiviral frogs' peptides to combat COVID-19. As a result, the Magainin-1 and -2 peptides, from the Magainin family, the Dermaseptin-S9, from the Dermaseptin family, and Caerin 1.6 and 1.10, from the Caerin family, are molecules that already showed antiviral effects against SARS-CoV-2 in silico. In addition to these peptides, this review suggests that future studies should use other families that already have antiviral action against other viruses, such as Brevinins, Maculatins, Esculentins, Temporins, and Urumins. To apply these peptides as therapeutic agents, experimental studies with peptides already tested in silico and new studies with other families not tested yet should be considered.
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22
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Wang B, Svetlov D, Bartikofsky D, Wobus CE, Artsimovitch I. Going Retro, Going Viral: Experiences and Lessons in Drug Discovery from COVID-19. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123815. [PMID: 35744940 PMCID: PMC9228142 DOI: 10.3390/molecules27123815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 12/15/2022]
Abstract
The severity of the COVID-19 pandemic and the pace of its global spread have motivated researchers to opt for repurposing existing drugs against SARS-CoV-2 rather than discover or develop novel ones. For reasons of speed, throughput, and cost-effectiveness, virtual screening campaigns, relying heavily on in silico docking, have dominated published reports. A particular focus as a drug target has been the principal active site (i.e., RNA synthesis) of RNA-dependent RNA polymerase (RdRp), despite the existence of a second, and also indispensable, active site in the same enzyme. Here we report the results of our experimental interrogation of several small-molecule inhibitors, including natural products proposed to be effective by in silico studies. Notably, we find that two antibiotics in clinical use, fidaxomicin and rifabutin, inhibit RNA synthesis by SARS-CoV-2 RdRp in vitro and inhibit viral replication in cell culture. However, our mutagenesis studies contradict the binding sites predicted computationally. We discuss the implications of these and other findings for computational studies predicting the binding of ligands to large and flexible protein complexes and therefore for drug discovery or repurposing efforts utilizing such studies. Finally, we suggest several improvements on such efforts ongoing against SARS-CoV-2 and future pathogens as they arise.
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Affiliation(s)
- Bing Wang
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | | | - Dylan Bartikofsky
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; (D.B.); (C.E.W.)
| | - Christiane E. Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; (D.B.); (C.E.W.)
| | - Irina Artsimovitch
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
- Correspondence:
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23
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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Delandre O, Gendrot M, Jardot P, Le Bideau M, Boxberger M, Boschi C, Fonta I, Mosnier J, Hutter S, Levasseur A, La Scola B, Pradines B. Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants. Pharmaceuticals (Basel) 2022; 15:445. [PMID: 35455442 PMCID: PMC9024598 DOI: 10.3390/ph15040445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
Over the past two years, several variants of SARS-CoV-2 have emerged and spread all over the world. However, infectivity, clinical severity, re-infection, virulence, transmissibility, vaccine responses and escape, and epidemiological aspects have differed between SARS-CoV-2 variants. Currently, very few treatments are recommended against SARS-CoV-2. Identification of effective drugs among repurposing FDA-approved drugs is a rapid, efficient and low-cost strategy against SARS-CoV-2. One of those drugs is ivermectin. Ivermectin is an antihelminthic agent that previously showed in vitro effects against a SARS-CoV-2 isolate (Australia/VI01/2020 isolate) with an IC50 of around 2 µM. We evaluated the in vitro activity of ivermectin on Vero E6 cells infected with 30 clinically isolated SARS-CoV-2 strains belonging to 14 different variants, and particularly 17 strains belonging to six variants of concern (VOC) (variants related to Wuhan, alpha, beta, gamma, delta and omicron). The in vitro activity of ivermectin was compared to those of chloroquine and remdesivir. Unlike chloroquine (EC50 from 4.3 ± 2.5 to 29.3 ± 5.2 µM) or remdesivir (EC50 from 0.4 ± 0.3 to 25.2 ± 9.4 µM), ivermectin showed a relatively homogeneous in vitro activity against SARS-CoV-2 regardless of the strains or variants (EC50 from 5.1 ± 0.5 to 6.7 ± 0.4 µM), except for one omicron strain (EC50 = 1.3 ± 0.5 µM). Ivermectin (No. EC50 = 219, mean EC50 = 5.7 ± 1.0 µM) was, overall, more potent in vitro than chloroquine (No. EC50 = 214, mean EC50 = 16.1 ± 9.0 µM) (p = 1.3 × 10-34) and remdesivir (No. EC50 = 201, mean EC50 = 11.9 ± 10.0 µM) (p = 1.6 × 10-13). These results should be interpreted with caution regarding the potential use of ivermectin in SARS-CoV-2-infected patients: it is difficult to translate in vitro study results into actual clinical treatment in patients.
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Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Priscilla Jardot
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Marion Le Bideau
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Manon Boxberger
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Sébastien Hutter
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Anthony Levasseur
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
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Panayiotakopoulos GD, Papadimitriou DT. Rifampicin for COVID-19. World J Virol 2022; 11:90-97. [PMID: 35433334 PMCID: PMC8966591 DOI: 10.5501/wjv.v11.i2.90] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 11/29/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
Vaccinations for coronavirus disease-2019 (COVID-19) have begun more than a year before, yet without specific treatments available. Rifampicin, critically important for human medicine (World Health Organization’s list of essential medicines), may prove pharmacologically effective for treatment and chemoprophylaxis of healthcare personnel and those at higher risk. It has been known since 1969 that rifampicin has a direct selective antiviral effect on viruses which have their own RNA polymerase (severe acute respiratory syndrome coronavirus 2), like the main mechanism of action of remdesivir. This involves inhibition of late viral protein synthesis, the virion assembly, and the viral polymerase itself. This antiviral effect is dependent on the administration route, with local application resulting in higher drug concentrations at the site of viral replication. This would suggest also trying lung administration of rifampicin by nebulization to increase the drug’s concentration at infection sites while minimizing systemic side effects. Recent in silico studies with a computer-aided approach, found rifampicin among the most promising existing drugs that could be repurposed for the treatment of COVID-19.
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Affiliation(s)
- George D Panayiotakopoulos
- Department of Clinical Pharmacology, University of Patras Medical School, Rion 26504, Greece
- The National Public Health Organization of Greece, Athens 15123, Greece
| | - Dimitrios T Papadimitriou
- Department of Pediatric, Adolescent Endocrinology & Diabetes, Athens Medical Center, Marousi 15125, Greece
- Endocrine Unit, Aretaieion University Hospital, Athens 11528, Greece
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Acute Cerebellar Inflammation and Related Ataxia: Mechanisms and Pathophysiology. Brain Sci 2022; 12:brainsci12030367. [PMID: 35326323 PMCID: PMC8946185 DOI: 10.3390/brainsci12030367] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/11/2022] Open
Abstract
The cerebellum governs motor coordination and motor learning. Infection with external microorganisms, such as viruses, bacteria, and fungi, induces the release and production of inflammatory mediators, which drive acute cerebellar inflammation. The clinical observation of acute cerebellitis is associated with the emergence of cerebellar ataxia. In our animal model of the acute inflammation of the cerebellar cortex, animals did not show any ataxia but hyperexcitability in the cerebellar cortex and depression-like behaviors. In contrast, animal models with neurodegeneration of the cerebellar Purkinje cells and hypoexcitability of the neurons show cerebellar ataxia. The suppression of the Ca2+-activated K+ channels in vivo is associated with a type of ataxia. Therefore, there is a gap in our interpretation between the very early phase of cerebellar inflammation and the emergence of cerebellar ataxia. In this review, we discuss the hypothesized scenario concerning the emergence of cerebellar ataxia. First, compared with genetically induced cerebellar ataxias, we introduce infection and inflammation in the cerebellum via aberrant immunity and glial responses. Especially, we focus on infections with cytomegalovirus, influenza virus, dengue virus, and SARS-CoV-2, potential relevance to mitochondrial DNA, and autoimmunity in infection. Second, we review neurophysiological modulation (intrinsic excitability, excitatory, and inhibitory synaptic transmission) by inflammatory mediators and aberrant immunity. Next, we discuss the cerebellar circuit dysfunction (presumably, via maintaining the homeostatic property). Lastly, we propose the mechanism of the cerebellar ataxia and possible treatments for the ataxia in the cerebellar inflammation.
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Sencanski M, Perovic V, Milicevic J, Todorovic T, Prodanovic R, Veljkovic V, Paessler S, Glisic S. Identification of SARS-CoV-2 Papain-like Protease (PLpro) Inhibitors Using Combined Computational Approach. ChemistryOpen 2022; 11:e202100248. [PMID: 35103413 PMCID: PMC8805381 DOI: 10.1002/open.202100248] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/13/2022] [Indexed: 11/25/2022] Open
Abstract
In the current pandemic, finding an effective drug to prevent or treat the infection is the highest priority. A rapid and safe approach to counteract COVID-19 is in silico drug repurposing. The SARS-CoV-2 PLpro promotes viral replication and modulates the host immune system, resulting in inhibition of the host antiviral innate immune response, and therefore is an attractive drug target. In this study, we used a combined in silico virtual screening for candidates for SARS-CoV-2 PLpro protease inhibitors. We used the Informational spectrum method applied for Small Molecules for searching the Drugbank database followed by molecular docking. After in silico screening of drug space, we identified 44 drugs as potential SARS-CoV-2 PLpro inhibitors that we propose for further experimental testing.
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Affiliation(s)
- Milan Sencanski
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
| | - Vladimir Perovic
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
| | - Jelena Milicevic
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
| | - Tamara Todorovic
- Faculty of ChemistryUniversity of BelgradeStudentski Trg 12–1611000BelgradeSerbia
| | - Radivoje Prodanovic
- Faculty of ChemistryUniversity of BelgradeStudentski Trg 12–1611000BelgradeSerbia
| | | | - Slobodan Paessler
- Department of PathologyUniversity of Texas Medical BranchGalvestonTX 77550USA
- Institute for Human Infections and ImmunityUniversity of Texas Medical BranchGalvestonTX 77555USA
| | - Sanja Glisic
- National Institute of the Republic of SerbiaUniversity of BelgradeMike Petrovica Alasa 12–1411000BelgradeSerbia
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28
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Kamel NA, Ismail NSM, Yahia IS, Aboshanab KM. Potential Role of Colchicine in Combating COVID-19 Cytokine Storm and Its Ability to Inhibit Protease Enzyme of SARS-CoV-2 as Conferred by Molecular Docking Analysis. Medicina (B Aires) 2021; 58:medicina58010020. [PMID: 35056328 PMCID: PMC8781828 DOI: 10.3390/medicina58010020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/03/2022] Open
Abstract
Despite the advance in the management of Coronavirus disease 2019 (COVID-19), the global pandemic is still ongoing with a massive health crisis. COVID-19 manifestations may range from mild symptoms to severe life threatening ones. The hallmark of the disease severity is related to the overproduction of pro-inflammatory cytokines manifested as a cytokine storm. Based on its anti-inflammatory activity through interfering with several pro and anti-inflammatory pathways, colchicine had been proposed to reduce the cytokine storm and subsequently improve clinical outcomes. Molecular docking analysis of colchicine against RNA-dependent RNA polymerase (RdRp) and protease enzymes of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) revealed that colchicine provided a grid-based molecular docking method, C-DOCKER interaction energy 64.26 and 47.53 (Kcal/mol) with protease and RdRp, respectively. This finding indicated higher binding stability for colchicine–protease complexes than the colchicine–RdRp complex with the involvement of seven hydrogen bonds, six hydrogen acceptors with Asn142, Gly143, Ser144, and Glu166 and one hydrogen-bond donors with Cys145 of the protease enzyme. This is in addition to three hydrophobic interactions with His172, Glu166, and Arg188. A good alignment with the reference compound, Boceprevir, indicated high probability of binding to the protease enzyme of SARS-CoV-2. In conclusion, colchicine can ameliorate the destructive effect of the COVID-19 cytokine storm with a strong evidence of antiviral activity by inhibiting the protease enzyme of SARS-CoV-2.
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Affiliation(s)
- Noha A. Kamel
- Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo 19648, Egypt;
| | - Nasser S. M. Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt (FUE), Cairo 11835, Egypt;
| | - Ibrahim S. Yahia
- Laboratory of Nano-Smart Materials for Science and Technology (LNSMST), Department of Physics, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia;
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Nanoscience Laboratory for Environmental and Biomedical Applications (NLEBA), Semiconductor Laboratory, Department of Physics, Faculty of Education, Ain Shams University (ASU), Roxy, Cairo 11757, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology & Immunology, Faculty of Pharmacy, Ain Shams University (ASU), Abbassia, Cairo 11566, Egypt
- Correspondence: ; Tel.: +20-1-0075-82620; Fax: +20-2-2405110
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29
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Wang Y, Li P, Rajpoot S, Saqib U, Yu P, Li Y, Li Y, Ma Z, Baig MS, Pan Q. Comparative assessment of favipiravir and remdesivir against human coronavirus NL63 in molecular docking and cell culture models. Sci Rep 2021; 11:23465. [PMID: 34873274 PMCID: PMC8648821 DOI: 10.1038/s41598-021-02972-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 02/06/2023] Open
Abstract
Human coronavirus NL63 (HCoV-NL63) mainly affects young children and immunocompromised patients, causing morbidity and mortality in a subset of patients. Since no specific treatment is available, this study aims to explore the anti-SARS-CoV-2 agents including favipiravir and remdesivir for treating HCoV-NL63 infection. We first successfully modelled the 3D structure of HCoV-NL63 RNA-dependent RNA polymerase (RdRp) based on the experimentally solved SARS-CoV-2 RdRp structure. Molecular docking indicated that favipiravir has similar binding affinities to SARS-CoV-2 and HCoV-NL63 RdRp with LibDock scores of 75 and 74, respectively. The LibDock scores of remdesivir to SARS-CoV-2 and HCoV-NL63 were 135 and 151, suggesting that remdesivir may have a higher affinity to HCoV-NL63 compared to SARS-CoV-2 RdRp. In cell culture models infected with HCoV-NL63, both favipiravir and remdesivir significantly inhibited viral replication and production of infectious viruses. Overall, remdesivir compared to favipiravir is more potent in inhibiting HCoV-NL63 in cell culture. Importantly, there is no evidence of resistance development upon long-term exposure to remdesivir. Furthermore, combining favipiravir or remdesivir with the clinically used antiviral cytokine interferon-alpha resulted in synergistic effects. These findings provided a proof-of-concept that anti-SARS-CoV-2 drugs, in particular remdesivir, have the potential to be repurposed for treating HCoV-NL63 infection.
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Affiliation(s)
- Yining Wang
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1005, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Pengfei Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1005, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Sajjan Rajpoot
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552, MP, India
| | - Uzma Saqib
- Department of Chemistry, Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552, MP, India
| | - Peifa Yu
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1005, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Yunlong Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1005, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Yang Li
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1005, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Zhongren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Mirza S Baig
- Department of Biosciences and Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Simrol, Indore, 453552, MP, India.
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room Na-1005, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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30
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Svetlov D, Artsimovitch I. Reductionism Ad Absurdum: The Misadventures of Structural Biology in the Time of Coronavirus. ACS Infect Dis 2021; 7:2948-2952. [PMID: 34613689 PMCID: PMC8507565 DOI: 10.1021/acsinfecdis.1c00492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 01/18/2023]
Abstract
The tragic consequences of the COVID-19 pandemic have led to admirable responses by the global scientific community, including a profound acceleration in the pace of research and exchange of findings. However, this has had considerable costs of its own, as erroneous conclusions have propagated faster than researchers have been able to detect and correct them. We illustrate the specific misunderstandings that have resulted from reductionist approaches to the study of SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which are but one instance of a regrettably growing trend in structural biology. Far from merely being cautionary tales about the conduct of scientific research, these errors have had significant practical impact, by hampering a correct understanding of RdRp structure and mechanism, its inhibition by nucleoside analogues such as remdesivir, and the discovery and characterization of such analogues. After correcting these misunderstandings, we close with several recommendations for a broader correction of the course of scientific research.
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Affiliation(s)
- Dmitri Svetlov
- Svetlov Scientific
Software, Pasadena, California 91106, United States
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA
Biology, The Ohio State University, Columbus, Ohio 43210,
United States
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31
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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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Sumon TA, Hussain MA, Hasan M, Rashid A, Abualreesh MH, Jang WJ, Sharifuzzaman SM, Brown CL, Lee EW, Hasan MT. Antiviral peptides from aquatic organisms: Functionality and potential inhibitory effect on SARS-CoV-2. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 541:736783. [PMID: 33883784 PMCID: PMC8049179 DOI: 10.1016/j.aquaculture.2021.736783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/26/2021] [Accepted: 04/14/2021] [Indexed: 05/06/2023]
Abstract
Several antiviral peptides (AVPs) from aquatic organisms have been effective in interfering with the actions of infectious viruses, such as Human Immunodeficiency Virus-1 and Herpes Simplex Virus-1 and 2. AVPs are able to block viral attachment or entry into host cells, inhibit internal fusion or replication events by suppressing viral gene transcription, and prevent viral infections by modulating host immunity. Therefore, as promising therapeutics, the potential of aquatic AVPs for use against the COVID-19 pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is considered. At present no therapeutic drugs are yet available. A total of 32 AVPs derived from fish and shellfish species are discussed in this review paper with notes on their properties and mechanisms of action in the inhibition of viral diseases both in humans and animals, emphasizing on SARS-CoV-2. The molecular structure of novel SARS-CoV-2 with its entry mechanisms, clinical signs and symptoms are also discussed. In spite of only a few study of these AVPs against SARS-CoV-2, aquatic AVPs properties and infection pathways (entry, replication and particle release) into coronaviruses are linked in this paper to postulate an analysis of their potential but unconfirmed actions to impair SARS-CoV-2 infection in humans.
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Affiliation(s)
- Tofael Ahmed Sumon
- Department of Fish Health Management, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Ashraf Hussain
- Department of Fisheries Technology and Quality Control, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Aminur Rashid
- Department of Aquaculture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Muyassar Hamid Abualreesh
- Department of Marine Biology, Faculty of Marine Science, King Abdulaziz University, P.O. Box 80207, Jeddah 21589, Saudi Arabia
| | - Won Je Jang
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan 47340, Republic of Korea
| | - S M Sharifuzzaman
- Institute of Marine Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Christopher Lyon Brown
- FAO World Fisheries University Pilot Programme, Pukyong National University, Busan, South Korea
| | - Eun-Woo Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan 47340, Republic of Korea
| | - Md Tawheed Hasan
- Department of Aquaculture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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Rehman MFU, Akhter S, Batool AI, Selamoglu Z, Sevindik M, Eman R, Mustaqeem M, Akram MS, Kanwal F, Lu C, Aslam M. Effectiveness of Natural Antioxidants against SARS-CoV-2? Insights from the In-Silico World. Antibiotics (Basel) 2021; 10:1011. [PMID: 34439061 PMCID: PMC8388999 DOI: 10.3390/antibiotics10081011] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 01/08/2023] Open
Abstract
The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 protein targets include Main protease (MPro), Papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), Spike glycoprotein (S), Helicase (Nsp13), and E-Channel protein. Phytochemicals were evaluated by molecular docking, and MD simulations were performed using the YASARA structure using a modified genetic algorithm and AMBER03 force field. Binding energies and dissociation constants allowed the identification of potentially active compounds. Ligand-protein interactions provide an insight into the mechanism and potential of identified compounds. Glycyrrhizin and its metabolite 18-β-glycyrrhetinic acid have shown a strong binding affinity for MPro, helicase, RdRp, spike, and E-channel proteins, while a flavonoid Baicalin also strongly binds against PLpro and RdRp. The use of identified phytochemicals may help to speed up the drug development and provide natural protection against SARS-CoV-2.
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Affiliation(s)
- Muhammad Fayyaz ur Rehman
- Department of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
- Institute of Chemistry, University of Sargodha, Sargodha 41600, Pakistan; (S.A.); (R.E.)
| | - Shahzaib Akhter
- Institute of Chemistry, University of Sargodha, Sargodha 41600, Pakistan; (S.A.); (R.E.)
| | - Aima Iram Batool
- Department of Zoology, University of Sargodha, Sargodha 41600, Pakistan;
| | - Zeliha Selamoglu
- Department of Medical Biology, Faculty of Medicine, Nigde Omer Halisdemir University, Nigde 51240, Turkey;
| | - Mustafa Sevindik
- Department of Food Processing, Bahçe Vocational School, Osmaniye Korkut Ata University, Osmaniye 80000, Turkey;
| | - Rida Eman
- Institute of Chemistry, University of Sargodha, Sargodha 41600, Pakistan; (S.A.); (R.E.)
| | - Muhammad Mustaqeem
- Department of Chemistry, University of Sargodha, Bhakkar Campus, Bhakkar 30000, Pakistan;
| | - Muhammad Safwan Akram
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK;
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
| | - Fariha Kanwal
- Med-X Research Institute, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 201620, China;
| | - Changrui Lu
- Department of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Mehwish Aslam
- School of Biological Sciences, University of the Punjab, Lahore 54600, Pakistan
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Bibi S, Hasan MM, Wang YB, Papadakos SP, Yu H. Cordycepin as a Promising Inhibitor of SARS-CoV-2 RNA dependent RNA polymerase (RdRp). Curr Med Chem 2021; 29:152-162. [PMID: 34420502 DOI: 10.2174/0929867328666210820114025] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND SARS-CoV-2, which emerged in Wuhan, China, is a new global threat that has killed millions of people and continues to do so. This pandemic has not only threatened human life but has also triggered economic downturns across the world. Researchers have made significant strides in discovering molecular insights into SARS-CoV-2 pathogenesis and developing vaccines, but there is still no successful cure for SARS-CoV-2 infected patients. OBJECTIVE The present study has proposed a drug-repositioning pipeline for the design and discovery of an effective fungal-derived bioactive metabolite as a drug candidate against SARS-CoV-2. METHODS Fungal derivative "Cordycepin" was selected for this study to investigate the inhibitory properties against RNA-dependent RNA polymerase (RdRp) (PDB ID: 6M71) of SARS-CoV-2. The pharmacological profile, intermolecular interactions, binding energy, and stability of the compound were determined utilizing cheminformatic approaches. Subsequently, molecular dynamic simulation was performed to better understand the binding mechanism of cordycepin to RdRp. RESULTS The pharmacological data and retrieved molecular dynamics simulations trajectories suggest excellent drug-likeliness and greater structural stability of cordycepin, while the catalytic residues (Asp760, Asp761), as well as other active site residues (Trp617, Asp618, Tyr619, Trp800, Glu811) of RdRp, showed better stability during the overall simulation span. CONCLUSION Promising results of pharmacological investigation along with molecular simulations revealed that cordycepin exhibited strong inhibitory potential against SARS-CoV-2 polymerase enzyme (RdRp). Hence, cordycepin should be highly recommended to test in a laboratory to confirm its inhibitory potential against the SARS-CoV-2 polymerase enzyme (RdRp).
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Affiliation(s)
- Shabana Bibi
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan. China
| | - Mohammad Mehedi Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Life Science, Mawlana Bhashani Science and Technology University, Tangail 1902. Bangladesh
| | - Yuan-Bing Wang
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan. China
| | - Stavros P Papadakos
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens (NKUA), Athens. Greece
| | - Hong Yu
- Yunnan Herbal Laboratory, College of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, Yunnan. China
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Abdizadeh R, Hadizadeh F, Abdizadeh T. In silico analysis and identification of antiviral coumarin derivatives against 3-chymotrypsin-like main protease of the novel coronavirus SARS-CoV-2. Mol Divers 2021; 26:1053-1076. [PMID: 34213728 PMCID: PMC8251691 DOI: 10.1007/s11030-021-10230-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
Abstract Coronavirus disease 2019 (COVID-19) is a pandemic viral disease caused by SARS-CoV-2 that generated serious damages for both the human population and the global economy. Therefore, it is currently considered as one of the most important global health problems of human societies and there is an urgent need for potent drugs or vaccines which can effectively combat this virus. The chymotrypsin-like protease (3CLpro) of SARS-CoV-2 plays a key role in the viral replication inside the host and thus is a promising drug target to design and develop effective antiviral drugs against SARS and other coronaviruses. This study evaluated some antiviral coumarin phytochemicals as potential inhibitors of coronaviruses 3CLpro by in silico approaches such as molecular docking, ADMET prediction, molecular dynamics simulation, and MM-PBSA binding energy calculation. Natural coumarin derivatives were docked to the 3CLpro of SARS-CoV-2 and for further investigation, docked to the 3CLpro of SARS-CoV and MERS-CoV. The docking scores of these natural compounds were compared with 3CLpro referenced inhibitors (ritonavir and lopinavir) and co-crystal inhibitor N3. Molecular docking studies suggested more than half of the coumarin phytochemicals had favorable interaction at the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward 3CLpro than ritonavir and lopinavir. Most antiviral phytochemicals interact strongly with one or both the catalytic dyad residues (His41 and Cys145) and the other key residues of SARS-CoV-2 main protease. Further, MD simulation and binding free energy calculations using MM-PBSA were carried out for three 3CLpro-coumarin complexes and 3CLpro-N3/lopinavir. The results confirmed that the 3CLpro-glycycoumarin, 3CLpro-oxypeucedanin hydrate, and 3CLpro-inophyllum P complexes were highly stable, experience fewer conformation fluctuations and share a similar degree of compactness. Also, the pharmacokinetics and drug-likeness studies showed good results for the selected coumarin phytochemicals.Therefore, the coumarin phytochemicals could be used as antiviral agents in the treatment of COVID-19 after further studies. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11030-021-10230-6.
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Affiliation(s)
- Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Farzin Hadizadeh
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tooba Abdizadeh
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, shahrekord, Iran.
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Zeng L, Li D, Tong W, Shi T, Ning B. Biochemical features and mutations of key proteins in SARS-CoV-2 and their impacts on RNA therapeutics. Biochem Pharmacol 2021; 189:114424. [PMID: 33482149 PMCID: PMC7816569 DOI: 10.1016/j.bcp.2021.114424] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. Three viral proteins, the spike protein (S) for attachment of virus to host cells, 3-chymotrypsin-like cysteine protease (Mpro) for digestion of viral polyproteins to functional proteins, and RNA-dependent-RNA-polymerase (RdRp) for RNA synthesis are the most critical proteins for virus infection and replication, rendering them the most important drug targets for both antibody and chemical drugs. Due to its low-fidelity polymerase, the virus is subject to frequent mutations. To date, the sequence data from tens of thousands of virus isolates have revealed hundreds of mutations. Although most mutations have a minimum consequence, a small number of non-synonymous mutations may alter the virulence and antigenicity of the mutants. To evaluate the effects of viral mutations on drug safety and efficacy, we reviewed the biochemical features of the three main proteins and their potentials as drug targets, and analyzed the mutation profiles and their impacts on RNA therapeutics. We believe that monitoring and predicting mutation-introduced protein conformational changes in the three key viral proteins and evaluating their binding affinities and enzymatic activities with the U.S. Food and Drug Administration (FDA) regulated drugs by using computational modeling and machine learning processes can provide valuable information for the consideration of drug efficacy and drug safety for drug developers and drug reviewers. Finally, we propose an interactive database for drug developers and reviewers to use in evaluating the safety and efficacy of U.S. FDA regulated drugs with regard to viral mutations.
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Affiliation(s)
- Li Zeng
- Changde Research Centre for Artificial Intelligence and Biomedicine, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan 415000, China
| | - Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, United States
| | - Weida Tong
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, United States
| | - Tieliu Shi
- Changde Research Centre for Artificial Intelligence and Biomedicine, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan 415000, China,Corresponding authors at: National Center for Toxicological Research, 3900 NCTR Road, HFT100, Jefferson, AR 72079, United States, (Baitang Ning); 3050 Dongting Avenue, Changde 415006, China, (Tieliu Shi)
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, 72079, United States,Corresponding authors at: National Center for Toxicological Research, 3900 NCTR Road, HFT100, Jefferson, AR 72079, United States, (Baitang Ning); 3050 Dongting Avenue, Changde 415006, China, (Tieliu Shi)
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Mathachan SR, Sardana K, Khurana A. Current Use of Ivermectin in Dermatology, Tropical Medicine, and COVID-19: An Update on Pharmacology, Uses, Proven and Varied Proposed Mechanistic Action. Indian Dermatol Online J 2021; 12:500-514. [PMID: 34430453 PMCID: PMC8354388 DOI: 10.4103/idoj.idoj_298_21] [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: 05/13/2021] [Accepted: 06/16/2021] [Indexed: 12/22/2022] Open
Abstract
Ivermectin is a broad-spectrum antiparasitic drug with anti-inflammatory, anti-viral, anti-bacterial, and anti-tumor effects. In this review, we discuss the history, pharmacology, multimodal actions, indications in dermatology and tropical medicine, therapeutic and prophylactic use of ivermectin in COVID-19, safety, adverse effects, special considerations, and drug interactions of ivermectin.
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Affiliation(s)
- Sinu Rose Mathachan
- Departments of Dermatology, Venereology and Leprosy, ABVIMS and Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Kabir Sardana
- Departments of Dermatology, Venereology and Leprosy, ABVIMS and Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Ananta Khurana
- Departments of Dermatology, Venereology and Leprosy, ABVIMS and Dr. Ram Manohar Lohia Hospital, New Delhi, India
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Yuce M, Cicek E, Inan T, Dag AB, Kurkcuoglu O, Sungur FA. Repurposing of FDA-approved drugs against active site and potential allosteric drug-binding sites of COVID-19 main protease. Proteins 2021; 89:1425-1441. [PMID: 34169568 PMCID: PMC8441840 DOI: 10.1002/prot.26164] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has serious negative effects on health, social life, and economics. Recently, vaccines from various companies have been urgently approved to control SARS-CoV-2 infections. However, any specific antiviral drug has not been confirmed so far for regular treatment. An important target is the main protease (Mpro ), which plays a major role in replication of the virus. In this study, Gaussian and residue network models are employed to reveal two distinct potential allosteric sites on Mpro that can be evaluated as drug targets besides the active site. Then, Food and Drug Administration (FDA)-approved drugs are docked to three distinct sites with flexible docking using AutoDock Vina to identify potential drug candidates. Fourteen best molecule hits for the active site of Mpro are determined. Six of these also exhibit high docking scores for the potential allosteric regions. Full-atom molecular dynamics simulations with MM-GBSA method indicate that compounds docked to active and potential allosteric sites form stable interactions with high binding free energy (∆Gbind ) values. ∆Gbind values reach -52.06 kcal/mol for the active site, -51.08 kcal/mol for the potential allosteric site 1, and - 42.93 kcal/mol for the potential allosteric site 2. Energy decomposition calculations per residue elucidate key binding residues stabilizing the ligands that can further serve to design pharmacophores. This systematic and efficient computational analysis successfully determines ivermectine, diosmin, and selinexor currently subjected to clinical trials, and further proposes bromocriptine, elbasvir as Mpro inhibitor candidates to be evaluated against SARS-CoV-2 infections.
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Affiliation(s)
- Merve Yuce
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Erdem Cicek
- Computational Science and Engineering Division, Informatics Institute, Istanbul Technical University, Istanbul, Turkey
| | - Tugce Inan
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Aslihan Basak Dag
- Department of Molecular Biology and Genetics, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Fethiye Aylin Sungur
- Computational Science and Engineering Division, Informatics Institute, Istanbul Technical University, Istanbul, Turkey
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Bhardwaj VK, Singh R, Sharma J, Rajendran V, Purohit R, Kumar S. Bioactive Molecules of Tea as Potential Inhibitors for RNA-Dependent RNA Polymerase of SARS-CoV-2. Front Med (Lausanne) 2021; 8:684020. [PMID: 34136511 PMCID: PMC8200525 DOI: 10.3389/fmed.2021.684020] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/16/2021] [Indexed: 01/18/2023] Open
Abstract
The coronavirus disease (COVID-19), a worldwide pandemic, is caused by the severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2). At this moment in time, there are no specific therapeutics available to combat COVID-19. Drug repurposing and identification of naturally available bioactive molecules to target SARS-CoV-2 are among the key strategies to tackle the notorious virus. The enzyme RNA-dependent RNA polymerase (RdRp) performs a pivotal role in replicating the virus. RdRp is a prime target for Remdesivir and other nucleotides analog-based antiviral drugs. In this study, we showed three bioactive molecules from tea (epicatechin-3,5-di-O-gallate, epigallocatechin-3,5-di-O-gallate, and epigallocatechin-3,4-di-O-gallate) that showed better interaction with critical residues present at the catalytic center and the NTP entry channel of RdRp than antiviral drugs Remdesivir and Favipiravir. Our computational approach to identify these molecules included molecular docking studies, followed by robust molecular dynamics simulations. All the three molecules are readily available in tea and could be made accessible along with other medications to treat COVID-19 patients. However, these results require validation by further in vitro and in vivo studies.
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Affiliation(s)
- Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Biotechnology Division, CSIR-IHBT, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Biotechnology Division, CSIR-IHBT, Palampur, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Biotechnology Division, CSIR-IHBT, Palampur, India
| | | | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, India
- Biotechnology Division, CSIR-IHBT, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-IHBT, Palampur, India
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Agrawal N, Goyal A. Potential Candidates against COVID-19 Targeting RNA-Dependent RNA Polymerase: A Comprehensive Review. Curr Pharm Biotechnol 2021; 23:396-419. [PMID: 33882805 DOI: 10.2174/1389201022666210421102513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/26/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Due to the extremely contagious nature of SARS-COV-2, it presents a significant threat to humans worldwide. A plethora of studies are going on all over the world to discover the drug to fight SARS-COV-2. One of the most promising targets is RNA-dependent RNA polymerase (RdRp), responsible for viral RNA replication in host cells. Since RdRp is a viral enzyme with no host cell homologs, it allows the development of selective SARS-COV-2 RdRp inhibitors. A variety of studies used in silico approaches for virtual screening, molecular docking, and repurposing of already existing drugs and phytochemicals against SARS-COV-2 RdRp. This review focuses on collating compounds possessing the potential to inhibit SARS-COV-2 RdRp based on in silico studies to give medicinal chemists food for thought so that the existing drugs can be repurposed for the control and treatment of ongoing COVID-19 pandemic after performing in vitro and in vivo experiments.
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Affiliation(s)
- Neetu Agrawal
- Institute of Pharmaceutical Research, GLA University, Mathura-281406 (U.P.), India
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura-281406 (U.P.), India
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Pérez-Moraga R, Forés-Martos J, Suay-García B, Duval JL, Falcó A, Climent J. A COVID-19 Drug Repurposing Strategy through Quantitative Homological Similarities Using a Topological Data Analysis-Based Framework. Pharmaceutics 2021; 13:pharmaceutics13040488. [PMID: 33918313 PMCID: PMC8066156 DOI: 10.3390/pharmaceutics13040488] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
Since its emergence in March 2020, the SARS-CoV-2 global pandemic has produced more than 116 million cases and 2.5 million deaths worldwide. Despite the enormous efforts carried out by the scientific community, no effective treatments have been developed to date. We applied a novel computational pipeline aimed to accelerate the process of identifying drug repurposing candidates which allows us to compare three-dimensional protein structures. Its use in conjunction with two in silico validation strategies (molecular docking and transcriptomic analyses) allowed us to identify a set of potential drug repurposing candidates targeting three viral proteins (3CL viral protease, NSP15 endoribonuclease, and NSP12 RNA-dependent RNA polymerase), which included rutin, dexamethasone, and vemurafenib. This is the first time that a topological data analysis (TDA)-based strategy has been used to compare a massive number of protein structures with the final objective of performing drug repurposing to treat SARS-CoV-2 infection.
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Affiliation(s)
- Raul Pérez-Moraga
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
| | - Jaume Forés-Martos
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
- Biomedical Research Networking Center of Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Beatriz Suay-García
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
| | | | - Antonio Falcó
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (A.F.); (J.C.)
| | - Joan Climent
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (A.F.); (J.C.)
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Joarder T, Khaled MN, Joarder MA. Urban educated group's perceptions of the COVID-19 pandemic management in Bangladesh: a qualitative exploration. F1000Res 2021; 10:170. [PMID: 34557291 PMCID: PMC8444153 DOI: 10.12688/f1000research.28333.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 12/03/2022] Open
Abstract
Background: Since the emergence of the COVID-19 outbreak, Government of Bangladesh (GoB) has taken various measures to restrict virus transmission and inform the people of the situation. However, the success of such measures largely depends on a positive public perception of the government's ability to act decisively and the transparency of its communication. We explored public perceptions of pandemic management efforts by the Bangladeshi health sector decision-makers in this study. Methods: As this qualitative research was conducted during the COVID-19 pandemic, data was gathered through seven online mixed-gender focus group discussions involving 50 purposively selected clinicians and non-clinicians. Results: The study participants concurred that, from the outset, decision-makers failed to engage the right kind of experts, which resulted in poor pandemic management that included imposing lockdown in periphery areas without arranging patient transport to the center, declaring certain hospitals as COVID-19 dedicated without preparing the facilities or the staff, and engaging private hospitals in care without allowing them to test the patients for COVID-19 infection. Several participants also commented on ineffective actions on behalf of the GoB, such as imposing home quarantine instead of institutional, corruption, miscommunication, and inadequate private sector regulation. The perception of the people regarding service providers is that they lacked responsiveness in providing treatment, with some doctors misleading the public by sharing misinformation. Service providers, on the other hand, observed that decision-makers failed to provide them with proper training, personal protective equipment, and workplace security, which has resulted in a high number of deaths among medical staff. Conclusions: The Bangladeshi health sector decision-makers should learn from their mistakes to prevent further unnecessary loss of life and long-term economic downturn. They should adopt a science-based response to the COVID-19 pandemic in the short term while striving to develop a more resilient health system in the long run.
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Joarder T, Khaled MN, Joarder MA. Public perceptions of the COVID-19 pandemic management in Bangladesh: a qualitative exploration. F1000Res 2021; 10:170. [PMID: 34557291 PMCID: PMC8444153 DOI: 10.12688/f1000research.28333.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/17/2021] [Indexed: 04/04/2024] Open
Abstract
Background: Since the emergence of the COVID-19 outbreak, Government of Bangladesh (GoB) has taken various measures to restrict virus transmission and inform the people of the situation. However, the success of such measures largely depends on a positive public perception of the government's ability to act decisively and the transparency of its communication. We explored public perceptions of pandemic management efforts by the Bangladeshi health sector decision-makers in this study. Methods: As this qualitative research was conducted during the COVID-19 pandemic, data was gathered through seven online mixed-gender focus group discussions involving 50 purposively selected clinicians and non-clinicians. Results: The study participants concurred that, from the outset, decision-makers failed to engage the right kind of experts, which resulted in poor pandemic management that included imposing lockdown in periphery areas without arranging patient transport to the center, declaring certain hospitals as COVID-19 dedicated without preparing the facilities or the staff, and engaging private hospitals in care without allowing them to test the patients for COVID-19 infection. Several participants also commented on ineffective actions on behalf of the GoB, such as imposing home quarantine instead of institutional, corruption, miscommunication, and inadequate private sector regulation. The perception of the people regarding service providers is that they lacked responsiveness in providing treatment, with some doctors misleading the public by sharing misinformation. Service providers, on the other hand, observed that decision-makers failed to provide them with proper training, personal protective equipment, and workplace security, which has resulted in a high number of deaths among medical staff. Conclusions: The Bangladeshi health sector decision-makers should learn from their mistakes to prevent further unnecessary loss of life and long-term economic downturn. They should adopt a science-based response to the COVID-19 pandemic in the short term while striving to develop a more resilient health system in the long run.
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Raj V, Park JG, Cho KH, Choi P, Kim T, Ham J, Lee J. Assessment of antiviral potencies of cannabinoids against SARS-CoV-2 using computational and in vitro approaches. Int J Biol Macromol 2021; 168:474-485. [PMID: 33290767 PMCID: PMC7836687 DOI: 10.1016/j.ijbiomac.2020.12.020] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Effective treatment choices to the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are limited because of the absence of effective target-based therapeutics. The main object of the current research was to estimate the antiviral activity of cannabinoids (CBDs) against the human coronavirus SARS-CoV-2. In the presented research work, we performed in silico and in vitro experiments to aid the sighting of lead CBDs for treating the viral infections of SARS-CoV-2. Virtual screening was carried out for interactions between 32 CBDs and the SARS-CoV-2 Mpro enzyme. Afterward, in vitro antiviral activity was carried out of five CBDs molecules against SARS-CoV-2. Interestingly, among them, two CBDs molecules namely Δ9 -tetrahydrocannabinol (IC50 = 10.25 μM) and cannabidiol (IC50 = 7.91 μM) were observed to be more potent antiviral molecules against SARS-CoV-2 compared to the reference drugs lopinavir, chloroquine, and remdesivir (IC50 ranges of 8.16-13.15 μM). These molecules were found to have stable conformations with the active binding pocket of the SARS-CoV-2 Mpro by molecular dynamic simulation and density functional theory. Our findings suggest cannabidiol and Δ9 -tetrahydrocannabinol are possible drugs against human coronavirus that might be used in combination or with other drug molecules to treat COVID-19 patients.
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Affiliation(s)
- Vinit Raj
- School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jae Gyu Park
- Advanced Bio Convergence Center, Pohang Technopark Foundation, Pohang, Republic of Korea
| | - Kiu-Hyung Cho
- Gyeongbuk Institute for Bio industry, Andong, Republic of Korea
| | - Pilju Choi
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Taejung Kim
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea
| | - Jungyeob Ham
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology (UST), Seoul, Republic of Korea.
| | - Jintae Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan, Republic of Korea.
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Tian L, Qiang T, Liang C, Ren X, Jia M, Zhang J, Li J, Wan M, YuWen X, Li H, Cao W, Liu H. RNA-dependent RNA polymerase (RdRp) inhibitors: The current landscape and repurposing for the COVID-19 pandemic. Eur J Med Chem 2021; 213:113201. [PMID: 33524687 PMCID: PMC7826122 DOI: 10.1016/j.ejmech.2021.113201] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/14/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023]
Abstract
The widespread nature of several viruses is greatly credited to their rapidly altering RNA genomes that enable the infection to persist despite challenges presented by host cells. Within the RNA genome of infections is RNA-dependent RNA polymerase (RdRp), which is an essential enzyme that helps in RNA synthesis by catalysing the RNA template-dependent development of phosphodiester bonds. Therefore, RdRp is an important therapeutic target in RNA virus-caused diseases, including SARS-CoV-2. In this review, we describe the promising RdRp inhibitors that have been launched or are currently in clinical studies for the treatment of RNA virus infections. Structurally, nucleoside inhibitors (NIs) bind to the RdRp protein at the enzyme active site, and nonnucleoside inhibitors (NNIs) bind to the RdRp protein at allosteric sites. By reviewing these inhibitors, more precise guidelines for the development of more promising anti-RNA virus drugs should be set, and due to the current health emergency, they will eventually be used for COVID-19 treatment.
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Affiliation(s)
- Lei Tian
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China; Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Taotao Qiang
- College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Chengyuan Liang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China.
| | - Xiaodong Ren
- Medical College, Guizhou University, Guiyang, 550025, PR China.
| | - Minyi Jia
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Jiayun Zhang
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Jingyi Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Minge Wan
- School of Medicine and Pharmacy, Shaanxi University of Business & Commerce, Xi'an, 712046, PR China
| | - Xin YuWen
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Han Li
- Faculty of Pharmacy, Shaanxi University of Science & Technology, Xi'an, 710021, PR China
| | - Wenqiang Cao
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai, 519030, PR China.
| | - Hong Liu
- Zhuhai Jinan Selenium Source Nanotechnology Co., Ltd., Hengqin New Area, Zhuhai, 519030, PR China.
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Azim KF, Ahmed SR, Banik A, Khan MMR, Deb A, Somana SR. Screening and druggability analysis of some plant metabolites against SARS-CoV-2: An integrative computational approach. INFORMATICS IN MEDICINE UNLOCKED 2020; 20:100367. [PMID: 32537482 PMCID: PMC7280834 DOI: 10.1016/j.imu.2020.100367] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 12/16/2022] Open
Abstract
The sudden outbreak of novel coronavirus has caused a global concern due to its infection rate and mortality. Despite extensive research, there are still no specific drugs or vaccines to combat SARS-CoV-2 infection. Hence, this study was designed to evaluate some plant-based active compounds for drug candidacy against SARS-CoV-2 by using virtual screening methods and various computational analyses. A total of 27 plant metabolites were screened against SARS-CoV-2 main protease proteins (MPP), Nsp9 RNA binding protein, spike receptor binding domain, spike ecto-domain and HR2 domain using a molecular docking approach. Four metabolites, i.e., asiatic acid, avicularin, guajaverin, and withaferin showed maximum binding affinity with all key proteins in terms of lowest global binding energy. The crucial binding sites and drug surface hotspots were unravelled for each viral protein. The top candidates were further employed for ADME (absorption, distribution, metabolism, and excretion) analysis to investigate their drug profiles. Results suggest that none of the compounds render any undesirable consequences that could reduce their drug likeness properties. The analysis of toxicity pattern revealed no significant tumorigenic, mutagenic, irritating, or reproductive effects by the compounds. However, withaferin was comparatively toxic among the top four candidates with considerable cytotoxicity and immunotoxicity. Most of the target class by top drug candidates belonged to enzyme groups (e.g. oxidoreductases hydrolases, phosphatases). Moreover, results of drug similarity prediction revealed two approved structural analogs of Asiatic acid i.e. Hydrocortisone (DB00741) (previously used for SARS-CoV-1 and MERS) and Dinoprost-tromethamine (DB01160) from DrugBank. In addition, two other biologically active compounds, Mupirocin (DB00410) and Simvastatin (DB00641) could be an option for the treatment of viral infections. The study may pave the way to develop effective medications and preventive measure against SARS-CoV-2. Due to the encouraging results, we highly recommend further in vivo trials for the experimental validation of our findings.
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Affiliation(s)
- Kazi Faizul Azim
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Sheikh Rashel Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Plant and Environmental Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Anik Banik
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Md Mostafigur Rahman Khan
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Anamika Deb
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Saneya Risa Somana
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
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Ogunyemi OM, Gyebi GA, Elfiky AA, Afolabi SO, Ogunro OB, Adegunloye AP, Ibrahim IM. Alkaloids and flavonoids from African phytochemicals as potential inhibitors of SARS-Cov-2 RNA-dependent RNA polymerase: an in silico perspective. Antivir Chem Chemother 2020; 28:2040206620984076. [PMID: 33372806 PMCID: PMC7783895 DOI: 10.1177/2040206620984076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
Corona Virus Disease 2019 (COVID-19) is a pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Exploiting the potentials of phytocompounds is an integral component of the international response to this pandemic. In this study, a virtual screening through molecular docking analysis was used to screen a total of 226 bioactive compounds from African herbs and medicinal plants for direct interactions with SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). From these, 36 phytocompounds with binding affinities higher than the approved reference drugs (remdesivir and sobosivir), were further docked targeting the active sites of SARS-CoV-2, as well as SARS-CoV and HCV RdRp. A hit list of 7 compounds alongside two positive controls (remdesivir and sofosbuvir) and two negative controls (cinnamaldehyde and Thymoquinone) were further docked into the active site of 8 different conformations of SARS-CoV-2 RdRp gotten from molecular dynamics simulation (MDS) system equilibration. The top docked compounds were further subjected to predictive druglikeness and ADME/tox filtering analyses. Drugable alkaloids (10'-hydroxyusambarensine, cryptospirolepine, strychnopentamine) and flavonoids (usararotenoid A, and 12α-epi-millettosin), were reported to exhibit strong affinity binding and interactions with key amino acid residues in the catalytic site, the divalent-cation-binding site, and the NTP entry channel in the active region of the RdRp enzyme as the positive controls. These phytochemicals, in addition to other promising antivirals such as remdesivir and sofosbuvir, may be exploited towards the development of a cocktail of anti-coronavirus treatments in COVID-19. Experimental studies are recommended to validate these study.
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Affiliation(s)
- Oludare M Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit,
Department of Biochemistry, Salem University, Lokoja, Nigeria
| | - Gideon A Gyebi
- Department of Biochemistry, Bingham University, Karu,
Nigeria
| | - Abdo A Elfiky
- Faculty of Sciences, Department of Biophysics Cairo University,
Giza, Egypt
| | - Saheed O Afolabi
- Department of Pharmacology and Therapeutics, Faculty of Basic
Medical Sciences University of Ilorin, Ilorin, Nigeria
| | - Olalekan B Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan,
Nigeria
| | - Adegbenro P Adegunloye
- Department of Biochemistry, Faculty of Life Sciences, University
of Ilorin, Ilorin, Nigeria
| | - Ibrahim M Ibrahim
- Faculty of Sciences, Department of Biophysics Cairo University,
Giza, Egypt
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