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Cheng W, Xu Y, Jiang H, Li J, Hou Z, Meng H, Wang W, Chai C, Jiang J. SARS-CoV-2 Infection, Hospitalization, and Associated Factors Among People Living With HIV in Southeastern China From December 2022 to February 2023: Cross-Sectional Survey. JMIR Public Health Surveill 2024; 10:e51449. [PMID: 38630534 PMCID: PMC11025603 DOI: 10.2196/51449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/07/2024] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Limited studies have explored the impact of the Omicron variant on SARS-CoV-2 infection, hospitalization, and associated factors among people living with HIV, particularly in China. The adjustment of preventive policies since December 2022 in China presents an opportunity to evaluate the real-world factors influencing SARS-CoV-2 infection and related hospitalization among people living with HIV. OBJECTIVE This study aimed to investigate SARS-CoV-2 infection, hospitalization rates, and associated factors among people living with HIV following the adjustment of preventive policies from December 2022 to February 2023 in southeastern China. METHODS A cross-sectional telephone or web-based survey was conducted among people living with HIV in 5 cities in southeastern China from December 2022 to February 2023. Demographic information, SARS-CoV-2 infection and related hospitalization, and HIV-specific characteristics were collected from existing databases and special investigations. Multivariate logistic regression analyses were conducted to determine the associated factors for infection and hospitalization rates of SARS-CoV-2. Additionally, subgroup analyses were conducted for the association between vaccination and infection across different vaccination statuses and time since the last vaccination. RESULTS Among people living with HIV with a COVID-19 testing history, the SARS-CoV-2 infection rate was 67.13% (95% CI 65.81%-68.13%), whereas the hospitalization rate was 0.71% (95% CI 0.46%-0.97%). Factors such as age, latest CD4 cell count, latest HIV viral load, and transmission route were found to be associated with SARS-CoV-2 infection, while age, cancer, latest CD4 cell count, and latest HIV viral load were associated with SARS-CoV-2 hospitalization. In terms of SARS-CoV-2 vaccination, compared to unvaccinated people living with HIV, there was a lower infection rate among those who had been vaccinated for <3 months in the booster vaccination group (adjusted odds ratio [aOR] 0.72, 95% CI 0.53-0.98; P=.04); and there was also a lower risk of hospitalization among people living with HIV who had received vaccination in the past 6-12 months (aOR 0.33, 95% CI 0.14-0.81; P=.02) and more than 12 months ago (aOR 0.22, 95% CI 0.07-0.72; P=.01). CONCLUSIONS After the ease of prevention and control measures in China, we observed a high SARS-CoV-2 infection rate but a low hospitalization rate. General risk factors, such as higher age and vaccination status, and HIV-related parameters, such as the latest CD4 cell count and HIV viral load, were associated with SARS-CoV-2 infection and hospitalization. A booster vaccination campaign for booster doses should be considered among people living with HIV in confronting possible COVID-19 epidemic emergencies in the near future.
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Affiliation(s)
- Wei Cheng
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yun Xu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Haibo Jiang
- Ningbo Center for Disease Control and Prevention, Ningbo, China
| | - Jun Li
- Wenzhou Center for Disease Control and Prevention, Wenzhou, China
| | - Zhigang Hou
- Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Haibin Meng
- Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Wei Wang
- Quzhou Center for Disease Control and Prevention, Quzhou, China
| | - Chengliang Chai
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
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Marzi Khosrowshahi E, Hassanpour Sabet R, Afshar Mogaddam MR, Khoubnasabjafari M, Jouyban-Gharamaleki V, Rayatpisheh M, Anushiravani A, Ghanbari R, Jouyban A. Carbonized aerogel/ZnO-based dispersive solid phase extraction of daclatasvir and sofosbuvir from biological samples prior to liquid chromatography-tandem mass spectrometry. J Pharm Biomed Anal 2024; 238:115841. [PMID: 37995479 DOI: 10.1016/j.jpba.2023.115841] [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: 07/25/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
Daclatasvir and sofosbuvir are antiviral medications utilized in the treatment of chronic hepatitis C virus (HCV) infection. Due to their low therapeutic index, careful monitoring is necessary to ensure that the optimal dose is administered. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) is an exceptionally sensitive and specific technique for quantifying these drugs within biological matrices. In this study, we developed a novel dispersive solid-phase extraction method employing a carbonized bio aerogel composite with ZnO for efficient extraction of daclatasvir and sofosbuvir from exhaled breath condensate, urine, and plasma samples. The extracted analytes were subsequently subjected to analysis using HPLC-MS/MS. Optimal parameters including pH adjustment, sorbent quantity variation, and elution solvent selection were fine-tuned to achieve maximum recovery efficiency while ensuring selectivity enhancements. The developed method demonstrated broad linearity ranging between 1.2 and 200 ng/mL along with good precision (relative standard deviations ≤6.2 %) and an acceptable coefficient of determination (r2 ≥0.994). These findings establish our proposed method as suitable for reliable drug quantification in clinical samples.
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Affiliation(s)
| | - Roghayeh Hassanpour Sabet
- Food and Drug Safety Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Neuroscience Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Maryam Khoubnasabjafari
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Anesthesiology and Intensive Care, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Jouyban-Gharamaleki
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Rayatpisheh
- Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Anushiravani
- Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Ghanbari
- Gene Therapy Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Pharmacy, Near East University, PO BOX: 99138 Nicosia, North Cyprus, Mersin 10, Turkey.
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Velásquez PA, Hernandez JC, Galeano E, Hincapié-García J, Rugeles MT, Zapata-Builes W. Effectiveness of Drug Repurposing and Natural Products Against SARS-CoV-2: A Comprehensive Review. Clin Pharmacol 2024; 16:1-25. [PMID: 38197085 PMCID: PMC10773251 DOI: 10.2147/cpaa.s429064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024] Open
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a betacoronavirus responsible for the COVID-19 pandemic, causing respiratory disorders, and even death in some individuals, if not appropriately treated in time. To face the pandemic, preventive measures have been taken against contagions and the application of vaccines to prevent severe disease and death cases. For the COVID-19 treatment, antiviral, antiparasitic, anticoagulant and other drugs have been reused due to limited specific medicaments for the disease. Drug repurposing is an emerging strategy with therapies that have already tested safe in humans. One promising alternative for systematic experimental screening of a vast pool of compounds is computational drug repurposing (in silico assay). Using these tools, new uses for approved drugs such as chloroquine, hydroxychloroquine, ivermectin, zidovudine, ribavirin, lamivudine, remdesivir, lopinavir and tenofovir/emtricitabine have been conducted, showing effectiveness in vitro and in silico against SARS-CoV-2 and some of these, also in clinical trials. Additionally, therapeutic options have been sought in natural products (terpenoids, alkaloids, saponins and phenolics) with promising in vitro and in silico results for use in COVID-19 disease. Among these, the most studied are resveratrol, quercetin, hesperidin, curcumin, myricetin and betulinic acid, which were proposed as SARS-CoV-2 inhibitors. Among the drugs reused to control the SARS-CoV2, better results have been observed for remdesivir in hospitalized patients and outpatients. Regarding natural products, resveratrol, curcumin, and quercetin have demonstrated in vitro antiviral activity against SARS-CoV-2 and in vivo, a nebulized formulation has demonstrated to alleviate the respiratory symptoms of COVID-19. This review shows the evidence of drug repurposing efficacy and the potential use of natural products as a treatment for COVID-19. For this, a search was carried out in PubMed, SciELO and ScienceDirect databases for articles about drugs approved or under study and natural compounds recognized for their antiviral activity against SARS-CoV-2.
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Affiliation(s)
- Paula Andrea Velásquez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Juan C Hernandez
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Elkin Galeano
- Grupo Productos Naturales Marinos, Departamento de Farmacia, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jaime Hincapié-García
- Grupo de investigación, Promoción y prevención farmacéutica, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia UdeA, Medellín, Colombia
| | - María Teresa Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wildeman Zapata-Builes
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
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Tucci AR, da Rosa RM, Rosa AS, Augusto Chaves O, Ferreira VNS, Oliveira TKF, Coutinho Souza DD, Borba NRR, Dornelles L, Rocha NS, Mayer JCP, da Rocha JBT, Rodrigues OED, Miranda MD. Antiviral Effect of 5'-Arylchalcogeno-3-aminothymidine Derivatives in SARS-CoV-2 Infection. Molecules 2023; 28:6696. [PMID: 37764472 PMCID: PMC10537738 DOI: 10.3390/molecules28186696] [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: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The understanding that zidovudine (ZDV or azidothymidine, AZT) inhibits the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and that chalcogen atoms can increase the bioactivity and reduce the toxicity of AZT has directed our search for the discovery of novel potential anti-coronavirus compounds. Here, the antiviral activity of selenium and tellurium containing AZT derivatives in human type II pneumocytes cell model (Calu-3) and monkey kidney cells (Vero E6) infected with SARS-CoV-2, and their toxic effects on these cells, was evaluated. Cell viability analysis revealed that organoselenium (R3a-R3e) showed lower cytotoxicity than organotellurium (R3f, R3n-R3q), with CC50 ≥ 100 µM. The R3b and R3e were particularly noteworthy for inhibiting viral replication in both cell models and showed better selectivity index. In Vero E6, the EC50 values for R3b and R3e were 2.97 ± 0.62 µM and 1.99 ± 0.42 µM, respectively, while in Calu-3, concentrations of 3.82 ± 1.42 µM and 1.92 ± 0.43 µM (24 h treatment) and 1.33 ± 0.35 µM and 2.31 ± 0.54 µM (48 h) were observed, respectively. The molecular docking calculations were carried out to main protease (Mpro), papain-like protease (PLpro), and RdRp following non-competitive, competitive, and allosteric inhibitory approaches. The in silico results suggested that the organoselenium is a potential non-competitive inhibitor of RdRp, interacting in the allosteric cavity located in the palm region. Overall, the cell-based results indicated that the chalcogen-zidovudine derivatives were more potent than AZT in inhibiting SARS-CoV-2 replication and that the compounds R3b and R3e play an important inhibitory role, expanding the knowledge about the promising therapeutic capacity of organoselenium against COVID-19.
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Affiliation(s)
- Amanda Resende Tucci
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Raquel Mello da Rosa
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Alice Santos Rosa
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Otávio Augusto Chaves
- CQC-IMS, Departamento de Química, Universidade de Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Laboratório de Imunofarmacologia, Centro de Pesquisa, Inovação e Vigilância em COVID-19 e Emergências Sanitárias (CPIV), Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro 21040-900, RJ, Brazil
| | - Vivian Neuza Santos Ferreira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Thamara Kelcya Fonseca Oliveira
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Daniel Dias Coutinho Souza
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
| | - Nathalia Roberto Resende Borba
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
| | - Luciano Dornelles
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Nayra Salazar Rocha
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João Candido Pilar Mayer
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - João B. Teixeira da Rocha
- Programa de Pós-Graduação em Bioquímica Toxicológica, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil;
| | - Oscar Endrigo D. Rodrigues
- LabSelen-NanoBio—Departamento de Química, Universidade Federal de Santa Maria, Santa Maria 97105-900, RS, Brazil; (R.M.d.R.); (L.D.); (N.S.R.); (J.C.P.M.)
| | - Milene Dias Miranda
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil; (A.R.T.); (A.S.R.); (V.N.S.F.); (T.K.F.O.); (D.D.C.S.); (N.R.R.B.)
- Programa de Pós-Graduação em Biologia Celular e Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21041-250, RJ, Brazil
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Padasas BT, Españo E, Kim SH, Song Y, Lee CK, Kim JK. COVID-19 Therapeutics: An Update on Effective Treatments Against Infection With SARS-CoV-2 Variants. Immune Netw 2023; 23:e13. [PMID: 37179752 PMCID: PMC10166656 DOI: 10.4110/in.2023.23.e13] [Citation(s) in RCA: 3] [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: 12/21/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 05/15/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is one of the most consequential global health crises in over a century. Since its discovery in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to mutate into different variants and sublineages, rendering previously potent treatments and vaccines ineffective. With significant strides in clinical and pharmaceutical research, different therapeutic strategies continue to be developed. The currently available treatments can be broadly classified based on their potential targets and molecular mechanisms. Antiviral agents function by disrupting different stages of SARS-CoV-2 infection, while immune-based treatments mainly act on the human inflammatory response responsible for disease severity. In this review, we discuss some of the current treatments for COVID-19, their mode of actions, and their efficacy against variants of concern. This review highlights the need to constantly evaluate COVID-19 treatment strategies to protect high risk populations and fill in the gaps left by vaccination.
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Affiliation(s)
| | - Erica Españo
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Sang-Hyun Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
| | - Youngcheon Song
- Department of Pharmacy, Sahmyook University, Seoul 01795, Korea
| | - Chong-Kil Lee
- Department of Pharmaceutics, College of Pharmacy, Chungbuk National University, Cheongju 28644, Korea
| | - Jeong-Ki Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong 30019, Korea
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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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Espín-Sánchez D, Ramos-Aristimbay ML, Sánchez-Vaca AS, Jaramillo-Guapisaca K, Vizueta-Rubio C, Chico-Terán F, Cerda-Mejía L, García MD. Identificación de inhibidores de las enzimas RdRp y Mpro del virus SARS-CoV-2 mediante homología estructural. BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
El COVID-19 ha generado un enorme impacto en la salud pública mundial debido a las altas tasas de contagio y mortalidad asociadas al virus SARS-CoV-2 causante de la enfermedad. Hasta la fecha, la Organización Mundial de la Salud (OMS) ha aprobado el uso de 10 vacunas aparentemente seguras y eficaces. Sin embargo, todavía existen limitaciones importantes para su administración en países en vías de desarrollo y localidades remotas, y la preocupación por la aparición de variantes del virus que puedan evadir la inmunidad adquirida mediante la vacunación se mantiene latente. Además de la prevención de la infección, son necesarios agentes terapéuticos efectivos para tratar a los pacientes diagnosticados con COVID-19. Bajo este contexto, el presente estudio tuvo como objetivo realizar un cribado virtual basado en la estructura de las enzimas proteasa (Mpro) y ARN polimerasa ARN-dependiente (RdRp) del SARS-CoV-2. Para este propósito se ensayaron inhibidores de proteínas homólogas pertenecientes a diferentes virus. El alineamiento múltiple de secuencias de estas enzimas permitió reconocer la presencia de una alta conservación de estas enzimas entre especies, especialmente de las regiones que comprenden los sitios de unión a inhibidores. Por lo tanto, se deduce que es posible emplear un enfoque de redireccionamiento de los inhibidores que fueron diseñados para tratar otras enfermedades virales. Experimentos de acoplamiento molecular permitieron identificar que los inhibidores RTP (afinidad de unión = -7.3 kcal/mol) y V3D (afinidad de unión = -8.0 kcal/mol) son excelentes inhibidores de RdRp y Mpro, respectivamente. Estos resultados sugieren que dichas moléculas son virtualmente capaces de unirse e inhibir la actividad de RdRp y Mpro y por lo tanto constituyen potenciales fármacos para combatir el SARS-CoV-2.
Palabras clave: SARS-CoV-2, COVID-19, inhibidores, RdRp, Mpro.
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Affiliation(s)
- Daysi Espín-Sánchez
- Carrera de Ingeniería Bioquímica, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - María L. Ramos-Aristimbay
- Carrera de Ingeniería Bioquímica, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - Andrés S. Sánchez-Vaca
- Carrera de Ingeniería Bioquímica, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - Karen Jaramillo-Guapisaca
- Carrera de Ingeniería Bioquímica, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - Carolina Vizueta-Rubio
- Carrera de Ingeniería Bioquímica, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - Fernanda Chico-Terán
- Carrera de Biotecnología, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - Liliana Cerda-Mejía
- Carrera de Alimentos, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
| | - Mario D. García
- Carrera de Ingeniería Bioquímica, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato ; Carrera de Biotecnología, Facultad de Ciencia e Ingeniería en Alimentos y Biotecnología Universidad Técnica de Ambato
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9
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Nucleoside Analogs and Perylene Derivatives Modulate Phase Separation of SARS-CoV-2 N Protein and Genomic RNA In Vitro. Int J Mol Sci 2022; 23:ijms232315281. [PMID: 36499608 PMCID: PMC9738865 DOI: 10.3390/ijms232315281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
The life cycle of severe acute respiratory syndrome coronavirus 2 includes several steps that are supposedly mediated by liquid-liquid phase separation (LLPS) of the viral nucleocapsid protein (N) and genomic RNA. To facilitate the rational design of LLPS-targeting therapeutics, we modeled N-RNA biomolecular condensates in vitro and analyzed their sensitivity to several small-molecule antivirals. The model condensates were obtained and visualized under physiological conditions using an optimized RNA sequence enriched with N-binding motifs. The antivirals were selected based on their presumed ability to compete with RNA for specific N sites or interfere with non-specific pi-pi/cation-pi interactions. The set of antivirals included fleximers, 5'-norcarbocyclic nucleoside analogs, and perylene-harboring nucleoside analogs as well as non-nucleoside amphiphilic and hydrophobic perylene derivatives. Most of these antivirals enhanced the formation of N-RNA condensates. Hydrophobic perylene derivatives and 5'-norcarbocyclic derivatives caused up to 50-fold and 15-fold enhancement, respectively. Molecular modeling data argue that hydrophobic compounds do not hamper specific N-RNA interactions and may promote non-specific ones. These findings shed light on the determinants of potent small-molecule modulators of viral LLPS.
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10
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Sharun K, Tiwari R, Yatoo MI, Natesan S, Megawati D, Singh KP, Michalak I, Dhama K. A comprehensive review on pharmacologic agents, immunotherapies and supportive therapeutics for COVID-19. NARRA J 2022; 2:e92. [PMID: 38449903 PMCID: PMC10914132 DOI: 10.52225/narra.v2i3.92] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 03/08/2024]
Abstract
The emergence of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has affected many countries throughout the world. As urgency is a necessity, most efforts have focused on identifying small molecule drugs that can be repurposed for use as anti-SARS-CoV-2 agents. Although several drug candidates have been identified using in silico method and in vitro studies, most of these drugs require the support of in vivo data before they can be considered for clinical trials. Several drugs are considered promising therapeutic agents for COVID-19. In addition to the direct-acting antiviral drugs, supportive therapies including traditional Chinese medicine, immunotherapies, immunomodulators, and nutritional therapy could contribute a major role in treating COVID-19 patients. Some of these drugs have already been included in the treatment guidelines, recommendations, and standard operating procedures. In this article, we comprehensively review the approved and potential therapeutic drugs, immune cells-based therapies, immunomodulatory agents/drugs, herbs and plant metabolites, nutritional and dietary for COVID-19.
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Affiliation(s)
- Khan Sharun
- Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura, India
| | - Mohd I. Yatoo
- Division of Veterinary Clinical Complex, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, Alusteng Srinagar, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir, India
| | - Senthilkumar Natesan
- Department of Infectious Diseases, Indian Institute of Public Health Gandhinagar, Opp to Airforce station HQ, Gandhinagar, India
| | - Dewi Megawati
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Warmadewa University, Denpasar, Indonesia
- Department of Medical Microbiology and Immunology, University of California, Davis, California, USA
| | - Karam P. Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
| | - Izabela Michalak
- Faculty of Chemistry, Department of Advanced Material Technologies, Wrocław University of Science and Technology, Wrocław, Poland
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, India
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11
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Rani R, Long S, Pareek A, Dhaka P, Singh A, Kumar P, McInerney G, Tomar S. Multi-target direct-acting SARS-CoV-2 antivirals against the nucleotide-binding pockets of virus-specific proteins. Virology 2022; 577:1-15. [PMID: 36244310 PMCID: PMC9539459 DOI: 10.1016/j.virol.2022.08.008] [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: 06/24/2022] [Revised: 08/20/2022] [Accepted: 08/20/2022] [Indexed: 11/30/2022]
Abstract
The nucleotide-binding pockets (NBPs) in virus-specific proteins have proven to be the most successful antiviral targets for several viral diseases. Functionally important NBPs are found in various structural and non-structural proteins of SARS-CoV-2. In this study, the first successful multi-targeting attempt to identify effective antivirals has been made against NBPs in nsp12, nsp13, nsp14, nsp15, nsp16, and nucleocapsid (N) proteins of SARS-CoV-2. A structure-based drug repurposing in silico screening approach with ADME analysis identified small molecules targeting NBPs in SARS-CoV-2 proteins. Further, isothermal titration calorimetry (ITC) experiments validated the binding of top hit molecules to the purified N-protein. Importantly, cell-based antiviral assays revealed antiviral potency for INCB28060, darglitazone, and columbianadin with EC50 values 15.71 μM, 5.36 μM, and 22.52 μM, respectively. These effective antivirals targeting multiple proteins are envisioned to direct the development of antiviral therapy against SARS-CoV-2 and its emerging variants.
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Affiliation(s)
- Ruchi Rani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Siwen Long
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Akshay Pareek
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Preeti Dhaka
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ankur Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Pravindra Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Shailly Tomar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.
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12
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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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13
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Nguyenla X, Wehri E, Van Dis E, Biering SB, Yamashiro LH, Zhu C, Stroumza J, Dugast-Darzacq C, Graham TGW, Wang X, Jockusch S, Tao C, Chien M, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Russo JJ, Ju J, Näär AM, Stanley S, Schaletzky J. Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells. Sci Rep 2022; 12:18506. [PMID: 36323770 PMCID: PMC9628577 DOI: 10.1038/s41598-022-21034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/21/2022] [Indexed: 11/07/2022] Open
Abstract
SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy is only moderate, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. This identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir's apparent potency > 25-fold. We report that HCV NS5A inhibitors act on the SARS-CoV-2 exonuclease proofreader, providing a possible explanation for the synergy observed with nucleoside analog remdesivir. FDA-approved Hepatitis C therapeutics Epclusa® (velpatasvir/sofosbuvir) and Zepatier® (elbasvir/grazoprevir) could be further optimized to achieve potency and pharmacokinetic properties that support clinical evaluation in combination with remdesivir.
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Affiliation(s)
- Xammy Nguyenla
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Scott B Biering
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Livia H Yamashiro
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Chi Zhu
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Julien Stroumza
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA, 94720, USA
| | - Thomas G W Graham
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA, 94720, USA
| | - Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA
| | - Anders M Näär
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Sarah Stanley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA, 94720, USA.
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA.
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and Neglected Diseases, 344 Li Ka Shing, Berkeley, CA, 94720, USA.
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14
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Yang C, Slavětínská LP, Fleuti M, Klepetářová B, Tichý M, Gurská S, Pavliš P, Džubák P, Hajdúch M, Hocek M. Synthesis of Polycyclic Hetero-Fused 7-Deazapurine Heterocycles and Nucleosides through C-H Dibenzothiophenation and Negishi Coupling. J Am Chem Soc 2022; 144:19437-19446. [PMID: 36245092 PMCID: PMC9619403 DOI: 10.1021/jacs.2c07517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
![]()
A new approach for synthesizing polycyclic heterofused
7-deazapurine
heterocycles and the corresponding nucleosides was developed based
on C–H functionalization of diverse (hetero)aromatics with
dibenzothiophene-S-oxide followed by the Negishi
cross-cooupling with bis(4,6-dichloropyrimidin-5-yl)zinc. This cross-coupling
afforded a series of (het)aryl-pyrimidines that were converted to
fused deazapurine heterocycles through azidation and thermal cyclization.
The fused heterocycles were glycosylated to the corresponding 2′-deoxy-
and ribonucleosides, and a series of derivatives were prepared by
nucleophilic substitutions at position 4. Four series of new polycyclic
thieno-fused 7-deazapurine nucleosides were synthesized using this
strategy. Most of the deoxyribonucleosides showed good cytotoxic activity,
especially for the CCRF-CEM cell line. Phenyl- and thienyl-substituted
thieno-fused 7-deazapurine nucleosides were fluorescent, and the former
one was converted to 2′-deoxyribonucleoside triphosphate for
enzymatic synthesis of labeled oligonucleotides.
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Affiliation(s)
- Chao Yang
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Marianne Fleuti
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Tichý
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Soňa Gurská
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Petr Pavliš
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Michal Hocek
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic,E-mail:
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15
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Inhibition of Viral RNA-Dependent RNA Polymerases by Nucleoside Inhibitors: An Illustration of the Unity and Diversity of Mechanisms. Int J Mol Sci 2022; 23:ijms232012649. [PMID: 36293509 PMCID: PMC9604226 DOI: 10.3390/ijms232012649] [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: 09/25/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
RNA-dependent RNA polymerase (RdRP) is essential for the replication and expression of RNA viral genomes. This class of viruses comprise a large number of highly pathogenic agents that infect essentially all species of plants and animals including humans. Infections often lead to epidemics and pandemics that have remained largely out of control due to the lack of specific and reliable preventive and therapeutic regimens. This unmet medical need has led to the exploration of new antiviral targets, of which RdRP is a major one, due to the fact of its obligatory need in virus growth. Recent studies have demonstrated the ability of several synthetic nucleoside analogs to serve as mimics of the corresponding natural nucleosides. These mimics cause stalling/termination of RdRP, or misincorporation, preventing virus replication or promoting large-scale lethal mutations. Several such analogs have received clinical approval and are being routinely used in therapy. In parallel, the molecular structural basis of their inhibitory interactions with RdRP is being elucidated, revealing both traditional and novel mechanisms including a delayed chain termination effect. This review offers a molecular commentary on these mechanisms along with their clinical implications based on analyses of recent results, which should facilitate the rational design of structure-based antiviral drugs.
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16
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Gillis TD, Bearne SL. Effects of the 5'-Triphosphate Metabolites of Ribavirin, Sofosbuvir, Vidarabine, and Molnupiravir on CTP Synthase Catalysis and Filament Formation: Implications for Repurposing Antiviral Agents against SARS-CoV-2. ChemMedChem 2022; 17:e202200399. [PMID: 36184568 PMCID: PMC9538051 DOI: 10.1002/cmdc.202200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Indexed: 01/14/2023]
Abstract
Repurposing of antiviral drugs affords a rapid and effective strategy to develop therapies to counter pandemics such as COVID-19. SARS-CoV-2 replication is closely linked to the metabolism of cytosine-containing nucleotides, especially cytidine-5'-triphosphate (CTP), such that the integrity of the viral genome is highly sensitive to intracellular CTP levels. CTP synthase (CTPS) catalyzes the rate-limiting step for the de novo biosynthesis of CTP. Hence, it is of interest to know the effects of the 5'-triphosphate (TP) metabolites of repurposed antiviral agents on CTPS activity. Using E. coli CTPS as a model enzyme, we show that ribavirin-5'-TP is a weak allosteric activator of CTPS, while sofosbuvir-5'-TP and adenine-arabinofuranoside-5'-TP are both substrates. β-d-N4 -Hydroxycytidine-5'-TP is a weak competitive inhibitor relative to CTP, but induces filament formation by CTPS. Alternatively, sofosbuvir-5'-TP prevented CTP-induced filament formation. These results reveal the underlying potential for repurposed antivirals to affect the activity of a critical pyrimidine nucleotide biosynthetic enzyme.
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Affiliation(s)
- Thomas D. Gillis
- Dalhousie UniversityDepartment of Biochemistry & Molecular Biology5850 College St.Tupper Medical Building, 9JB3H 4R2HalifaxCANADA
| | - Stephen L. Bearne
- Dalhousie UniversityBiochemistry & Molecular Biology5850 College StreetTupper Medical BuildingB3H 4R2HalifaxCANADA
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17
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Petushkov I, Esyunina D, Kulbachinskiy A. Effects of natural RNA modifications on the activity of SARS-CoV-2 RNA-dependent RNA polymerase. FEBS J 2022; 290:80-92. [PMID: 35916766 PMCID: PMC9538676 DOI: 10.1111/febs.16587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/17/2022] [Accepted: 08/01/2022] [Indexed: 01/18/2023]
Abstract
RNA-dependent RNA polymerase (RdRp) plays a key role in the replication of RNA viruses, including SARS-CoV-2. Processive RNA synthesis by RdRp is crucial for successful genome replication and expression, especially in the case of very long coronaviral genomes. Here, we analysed the activity of SARS-CoV-2 RdRp (the nsp12-nsp7-nsp8 complex) on synthetic primer-templates of various structures, including substrates with mismatched primers or template RNA modifications. It has been shown that RdRp cannot efficiently extend RNA primers containing mismatches and has no intrinsic RNA cleavage activity to remove the primer 3'-end, thus necessitating the action of exoribonuclease for proofreading. Similar to DNA-dependent RNA polymerases, RdRp can perform processive pyrophosphorolysis of the nascent RNA product but this reaction is also blocked in the presence of mismatches. Furthermore, we have demonstrated that several natural post-transcriptional modifications in the RNA template, which do not prevent complementary interactions (N6-methyladenosine, 5-methylcytosine, inosine and pseudouridine), do not change RdRp processivity. At the same time, certain modifications of RNA bases and ribose residues strongly block RNA synthesis, either prior to nucleotide incorporation (3-methyluridine and 1-methylguanosine) or immediately after it (2'-O-methylation). The results demonstrate that the activity of SARS-CoV-2 RdRp can be strongly inhibited by common modifications of the RNA template suggesting a way to design novel antiviral compounds.
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Affiliation(s)
- Ivan Petushkov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
| | - Daria Esyunina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”MoscowRussia
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18
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Tuberculosis and HIV responses threatened by nCOVID-19: A situation prompting an in silico investigation of reported MbtA inhibitors for combined inhibition of SARS-CoV-2 and HIV-TB co-infection. Struct Chem 2022. [DOI: 10.1007/s11224-022-02013-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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19
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Maslova AA, Matyugina EC, Shustova EY, Volok VP, Kozlovskaya LI, Kochetkov SN, Khandazhinskaya AL. New Analogues of Uridine as Possible Anti-Viral Agents Specific to SARS-CoV-2. Mol Biol 2022; 56:469-473. [PMID: 35693979 PMCID: PMC9165921 DOI: 10.1134/s0026893322030098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/23/2022]
Affiliation(s)
- A. A. Maslova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E. C. Matyugina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E. Yu. Shustova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, 108819 Moscow, Russia
| | - V. P. Volok
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, 108819 Moscow, Russia
| | - L. I. Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, 108819 Moscow, Russia
- Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - S. N. Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A. L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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20
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Efficacy and safety of the sofosbuvir/velpatasvir combination for the treatment of patients with early mild to moderate COVID-19. Sci Rep 2022; 12:5771. [PMID: 35388092 PMCID: PMC8985058 DOI: 10.1038/s41598-022-09741-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/25/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is still a health problem worldwide despite the availability of vaccines. Therefore, there is a need for effective and safe antiviral. SARS-CoV-2 and HCV necessitate RNA-dependent RNA polymerase (RdRp) for replication; therefore, it has been hypothesized that RdRp inhibitors used to treat HCV may be effective treating SARS-CoV-2. Accordingly, we evaluated the effect of the sofosbuvir/velpatasvir (SOF/VEL) combination in early SARS-CoV-2 infection. A multicenter case-control study was conducted, enrolling 120 patients with mild or moderate COVID-19, of whom 30, HCV coinfected or not, received SOF/VEL tablets (400/100 mg) once daily for 9 days within a median of 6 days from the beginning of infection and 90 controls were treated with standard care. The primary endpoint was the effect on viral clearance, and the secondary endpoint was the improvement of clinical outcomes. Nasal swabs for SARS-CoV-2 by PCR were performed every 5-7 days. Between 5-14 days after starting SOF/VEL treatment, SAS-CoV-2 clearance was observed in 83% of patients, while spontaneous clearance in the control was 13% (p < 0.001). An earlier SARS-CoV-2 clearance was observed in the SOF/VEL group than in the control group (median 14 vs 22 days, respectively, p < 0.001) also when the first positivity was considered. None of the patients in the SOF/VEL group showed disease progression, while in the control group, 24% required more intensive treatment (high flow oxygen or noninvasive/invasive ventilation), and one patient died (p < 0.01). No significant side effects were observed in the SOF/VEL group. Early SOF/VEL treatment in mild/moderate COVID-19 seems to be safe and effective for faster elimination of SARS-CoV-2 and to prevent disease progression.
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21
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Wang X, Sacramento CQ, Jockusch S, Chaves OA, Tao C, Fintelman-Rodrigues N, Chien M, Temerozo JR, Li X, Kumar S, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Bozza PT, Russo JJ, Souza TML, Ju J. Combination of antiviral drugs inhibits SARS-CoV-2 polymerase and exonuclease and demonstrates COVID-19 therapeutic potential in viral cell culture. Commun Biol 2022; 5:154. [PMID: 35194144 PMCID: PMC8863796 DOI: 10.1038/s42003-022-03101-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Carolina Q Sacramento
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Otávio Augusto Chaves
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Natalia Fintelman-Rodrigues
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jairo R Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.,National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Dinshaw J Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY, 10065, USA
| | - Patrícia T Bozza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA
| | - Thiago Moreno L Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil. .,National Institute for Science and Technology for Innovation on Diseases of Neglected Population (INCT/IDPN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil.
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA. .,Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA. .,Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA.
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22
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Li J, Boix E. Host Defence RNases as Antiviral Agents against Enveloped Single Stranded RNA Viruses. Virulence 2021; 12:444-469. [PMID: 33660566 PMCID: PMC7939569 DOI: 10.1080/21505594.2021.1871823] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023] Open
Abstract
Owing to the recent outbreak of Coronavirus Disease of 2019 (COVID-19), it is urgent to develop effective and safe drugs to treat the present pandemic and prevent other viral infections that might come in the future. Proteins from our own innate immune system can serve as ideal sources of novel drug candidates thanks to their safety and immune regulation versatility. Some host defense RNases equipped with antiviral activity have been reported over time. Here, we try to summarize the currently available information on human RNases that can target viral pathogens, with special focus on enveloped single-stranded RNA (ssRNA) viruses. Overall, host RNases can fight viruses by a combined multifaceted strategy, including the enzymatic target of the viral genome, recognition of virus unique patterns, immune modulation, control of stress granule formation, and induction of autophagy/apoptosis pathways. The review also includes a detailed description of representative enveloped ssRNA viruses and their strategies to interact with the host and evade immune recognition. For comparative purposes, we also provide an exhaustive revision of the currently approved or experimental antiviral drugs. Finally, we sum up the current perspectives of drug development to achieve successful eradication of viral infections.
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Affiliation(s)
- Jiarui Li
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
| | - Ester Boix
- Dpt. Of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma De Barcelona, Spain
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23
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Hu S, Jiang S, Qi X, Bai R, Ye XY, Xie T. Races of small molecule clinical trials for the treatment of COVID-19: An up-to-date comprehensive review. Drug Dev Res 2021; 83:16-54. [PMID: 34762760 PMCID: PMC8653368 DOI: 10.1002/ddr.21895] [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: 08/16/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022]
Abstract
The coronavirus disease‐19 (COVID‐19) pandemic has become a global threat since its first outbreak at the end of 2019. Several review articles have been published recently, focusing on the aspects of target biology, drug repurposing, and mechanisms of action (MOAs) for potential treatment. This review gathers all small molecules currently in active clinical trials, categorizes them into six sub‐classes, and summarizes their clinical progress. The aim is to provide the researchers from both pharmaceutical industries and academic institutes with the handful information and dataset to accelerate their research programs in searching effective small molecule therapy for treatment of COVID‐19.
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Affiliation(s)
- Suwen Hu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China.,Hangzhou Huadong Medicine Group, Pharmaceutical Research Institute Co. Ltd., Hangzhou, China.,Department of Chemistry and Biochemistry Los Angeles, University of California, Los Angeles, California, USA
| | - Songwei Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Xiang Qi
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Hangzhou Normal University, Hangzhou, China.,Collaborative Innovation Center of Chinese Medicines from Zhejiang Province, Hangzhou Normal Umiversity, Hangzhou, China
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24
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Mravinec M, Bajc G, Butala M. Surface plasmon resonance approach to study drug interactions with SARS-CoV-2 RNA-dependent RNA polymerase highlights treatment potential of suramin. J Virol Methods 2021; 298:114283. [PMID: 34534610 PMCID: PMC8439102 DOI: 10.1016/j.jviromet.2021.114283] [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: 05/17/2021] [Revised: 09/09/2021] [Accepted: 09/09/2021] [Indexed: 12/05/2022]
Abstract
The SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) is essential for virus replication, therefore it is a promising drug target. Here we present a surface plasmon resonance approach to study the interaction of RdRp with drugs in real time. We monitored the effect of favipiravir, ribavirin, sofosbuvir triphosphate PSI-7409 and suramin on RdRp binding to RNA immobilized on the chip. Suramin precluded interaction of RdRp with RNA and even displaced RdRp from RNA.
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Affiliation(s)
- Martina Mravinec
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Gregor Bajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana 1000, Slovenia
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana 1000, Slovenia.
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25
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Singh P, Tripathi MK, Yasir M, Khare R, Shrivastava R. In silico identification of promising inhibitor against RNA-dependent RNA polymerase target of SARS-CoV-2. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2021; 10:131-140. [PMID: 34476266 PMCID: PMC8340315 DOI: 10.22099/mbrc.2021.40367.1621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The severe acute respiratory syndrome is a viral respiratory disease recognised as COVID-19, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Formerly, no precise remedies are available, and many studies regarding COVID-19 prevention and treatment are under development. Several targets for the design of drugs are identified, and studies are in headway to explore the potential target. RNA-dependent RNA polymerase (RdRp) protein identified as a promising target against SARS-CoV-2 infection for the drug design due to its significant role in viral replication. The present study focuses on identifying the binding effect of previously known RdRp inhibitors with RdRp of SARS-CoV-2 using molecular docking and molecular dynamics simulation approaches. Molecular docking and binding free energy calculations against RdRp enzyme identified suramin as a potential compound that showed the highest docking score of -7.83 Kcal/mole and binding energy of -80.83 Kcal/mole as a comparison to other compounds. Further, molecular dynamics simulation studies were moreover showed the stable binding behaviour of suramin docked complex in the protein active site. Thus, the study concludes that suramin might be helpful as a potential inhibitor against RNA-dependent RNA polymerase of SRAS-CoV-2. However, further investigation is needed to assess the possible effect of inhibitors on RdRp through in vitro and in vivo experiments.
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Affiliation(s)
- Pushpendra Singh
- State Virus Research and Diagnostic Laboratory, Department of Microbiology, All India Institute of Medical Sciences, Raipur, Chhattisgarh-492099 India.,Equally contributed, Pushpendra Singh and Manish Kumar Tripathi both are joint first author
| | - Manish Kumar Tripathi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi-110029, India.,Equally contributed, Pushpendra Singh and Manish Kumar Tripathi both are joint first author
| | - Mohammad Yasir
- Department of Nephrology, All India Institute of Medical Science Bhopal, Madhya Pradesh-462020 India
| | - Ruchi Khare
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh-462003 India
| | - Rahul Shrivastava
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, Madhya Pradesh-462003 India
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26
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García-Trejo JJ, Ortega R, Zarco-Zavala M. Putative Repurposing of Lamivudine, a Nucleoside/Nucleotide Analogue and Antiretroviral to Improve the Outcome of Cancer and COVID-19 Patients. Front Oncol 2021; 11:664794. [PMID: 34367956 PMCID: PMC8335563 DOI: 10.3389/fonc.2021.664794] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
Lamivudine, also widely known as 3TC belongs to a family of nucleotide/nucleoside analogues of cytidine or cytosine that inhibits the Reverse Transcriptase (RT) of retroviruses such as HIV. Lamivudine is currently indicated in combination with other antiretroviral agents for the treatment of HIV-1 infection or for chronic Hepatitis B (HBV) virus infection associated with evidence of hepatitis B viral replication and active liver inflammation. HBV reactivation in patients with HBV infections who receive anticancer chemotherapy can be a life-threatening complication during and after the completion of chemotherapy. Lamivudine is used, as well as other antiretrovirals, to prevent the reactivation of the Hepatitis B virus during and after chemotherapy. In addition, Lamivudine has been shown to sensitize cancer cells to chemotherapy. Lamivudine and other similar analogues also have direct positive effects in the prevention of cancer in hepatitis B or HIV positive patients, independently of chemotherapy or radiotherapy. Recently, it has been proposed that Lamivudine might be also repurposed against SARS-CoV-2 in the context of the COVID-19 pandemic. In this review we first examine recent reports on the re-usage of Lamivudine or 3TC against the SARS-CoV-2, and we present docking evidence carried out in silico suggesting that Lamivudine may bind and possibly work as an inhibitor of the SARS-CoV-2 RdRp RNA polymerase. We also evaluate and propose assessment of repurposing Lamivudine as anti-SARS-CoV-2 and anti-COVID-19 antiviral. Secondly, we summarize the published literature on the use of Lamivudine or (3TC) before or during chemotherapy to prevent reactivation of HBV, and examine reports of enhanced effectiveness of radiotherapy in combination with Lamivudine treatment against the cancerous cells or tissues. We show that the anti-cancer properties of Lamivudine are well established, whereas its putative anti-COVID effect is under investigation. The side effects of lamivudine and the appearance of resistance to 3TC are also discussed.
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Affiliation(s)
- José J García-Trejo
- Department of Biology, Laboratory of Bioenergetics, Chemistry Faculty and School, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Raquel Ortega
- Department of Biology, Laboratory of Bioenergetics, Chemistry Faculty and School, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Mariel Zarco-Zavala
- Department of Biology, Laboratory of Bioenergetics, Chemistry Faculty and School, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
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27
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Wang X, Sacramento CQ, Jockusch S, Chaves OA, Tao C, Fintelman-Rodrigues N, Chien M, Temerozo JR, Li X, Kumar S, Xie W, Patel DJ, Meyer C, Garzia A, Tuschl T, Bozza PT, Russo JJ, Souza TML, Ju J. Combination of Antiviral Drugs to Inhibit SARS-CoV-2 Polymerase and Exonuclease as Potential COVID-19 Therapeutics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.07.21.453274. [PMID: 34312622 PMCID: PMC8312893 DOI: 10.1101/2021.07.21.453274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SARS-CoV-2 has an exonuclease-based proofreader, which removes nucleotide inhibitors such as Remdesivir that are incorporated into the viral RNA during replication, reducing the efficacy of these drugs for treating COVID-19. Combinations of inhibitors of both the viral RNA-dependent RNA polymerase and the exonuclease could overcome this deficiency. Here we report the identification of hepatitis C virus NS5A inhibitors Pibrentasvir and Ombitasvir as SARS-CoV-2 exonuclease inhibitors. In the presence of Pibrentasvir, RNAs terminated with the active forms of the prodrugs Sofosbuvir, Remdesivir, Favipiravir, Molnupiravir and AT-527 were largely protected from excision by the exonuclease, while in the absence of Pibrentasvir, there was rapid excision. Due to its unique structure, Tenofovir-terminated RNA was highly resistant to exonuclease excision even in the absence of Pibrentasvir. Viral cell culture studies also demonstrate significant synergy using this combination strategy. This study supports the use of combination drugs that inhibit both the SARS-CoV-2 polymerase and exonuclease for effective COVID-19 treatment.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Carolina Q. Sacramento
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Otávio Augusto Chaves
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Natalia Fintelman-Rodrigues
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Jairo R. Temerozo
- Laboratory on Thymus Research, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Dinshaw J. Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Cindy Meyer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065
| | - Patrícia T. Bozza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - James J. Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Thiago Moreno L. Souza
- Laboratory of Immunopharmacology, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology for Innovation on Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027
- Department of Chemical Engineering, Columbia University, New York, NY 10027
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY 10032
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28
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Li X, Zhang L, Chen S, Ouyang H, Ren L. Possible Targets of Pan-Coronavirus Antiviral Strategies for Emerging or Re-Emerging Coronaviruses. Microorganisms 2021; 9:1479. [PMID: 34361915 PMCID: PMC8306356 DOI: 10.3390/microorganisms9071479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/16/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which caused Coronaviruses Disease 2019 (COVID-19) and a worldwide pandemic, is the seventh human coronavirus that has been cross-transmitted from animals to humans. It can be predicted that with continuous contact between humans and animals, more viruses will spread from animals to humans. Therefore, it is imperative to develop universal coronavirus or pan-coronavirus vaccines or drugs against the next coronavirus pandemic. However, a suitable target is critical for developing pan-coronavirus antivirals against emerging or re-emerging coronaviruses. In this review, we discuss the latest progress of possible targets of pan-coronavirus antiviral strategies for emerging or re-emerging coronaviruses, including targets for pan-coronavirus inhibitors and vaccines, which will provide prospects for the current and future research and treatment of the disease.
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Affiliation(s)
| | | | | | | | - Linzhu Ren
- Key Laboratory for Zoonoses Research, College of Animal Sciences, Ministry of Education, Jilin University, 5333 Xi’An Road, Changchun 130062, China; (X.L.); (L.Z.); (S.C.); (H.O.)
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29
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Palko N, Grishina M, Potemkin V. Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes. Molecules 2021; 26:3960. [PMID: 34203564 PMCID: PMC8272208 DOI: 10.3390/molecules26133960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.
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Affiliation(s)
- Nadezhda Palko
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
| | - Vladimir Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, 454080 Chelyabinsk, Russia
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Sacramento CQ, Fintelman-Rodrigues N, Temerozo JR, Da Silva ADPD, Dias SDSG, da Silva CDS, Ferreira AC, Mattos M, Pão CRR, de Freitas CS, Soares VC, Hoelz LVB, Fernandes TVA, Branco FSC, Bastos MM, Boechat N, Saraiva FB, Ferreira MA, Jockusch S, Wang X, Tao C, Chien M, Xie W, Patel D, Garzia A, Tuschl T, Russo JJ, Rajoli RKR, Pedrosa CSG, Vitória G, Souza LRQ, Goto-Silva L, Guimarães MZ, Rehen SK, Owen A, Bozza FA, Bou-Habib DC, Ju J, Bozza PT, Souza TML. In vitro antiviral activity of the anti-HCV drugs daclatasvir and sofosbuvir against SARS-CoV-2, the aetiological agent of COVID-19. J Antimicrob Chemother 2021; 76:1874-1885. [PMID: 33880524 PMCID: PMC8083231 DOI: 10.1093/jac/dkab072] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Current approaches of drug repurposing against COVID-19 have not proven overwhelmingly successful and the SARS-CoV-2 pandemic continues to cause major global mortality. SARS-CoV-2 nsp12, its RNA polymerase, shares homology in the nucleotide uptake channel with the HCV orthologue enzyme NS5B. Besides, HCV enzyme NS5A has pleiotropic activities, such as RNA binding, that are shared with various SARS-CoV-2 proteins. Thus, anti-HCV NS5B and NS5A inhibitors, like sofosbuvir and daclatasvir, respectively, could be endowed with anti-SARS-CoV-2 activity. METHODS SARS-CoV-2-infected Vero cells, HuH-7 cells, Calu-3 cells, neural stem cells and monocytes were used to investigate the effects of daclatasvir and sofosbuvir. In silico and cell-free based assays were performed with SARS-CoV-2 RNA and nsp12 to better comprehend the mechanism of inhibition of the investigated compounds. A physiologically based pharmacokinetic model was generated to estimate daclatasvir's dose and schedule to maximize the probability of success for COVID-19. RESULTS Daclatasvir inhibited SARS-CoV-2 replication in Vero, HuH-7 and Calu-3 cells, with potencies of 0.8, 0.6 and 1.1 μM, respectively. Although less potent than daclatasvir, sofosbuvir alone and combined with daclatasvir inhibited replication in Calu-3 cells. Sofosbuvir and daclatasvir prevented virus-induced neuronal apoptosis and release of cytokine storm-related inflammatory mediators, respectively. Sofosbuvir inhibited RNA synthesis by chain termination and daclatasvir targeted the folding of secondary RNA structures in the SARS-CoV-2 genome. Concentrations required for partial daclatasvir in vitro activity are achieved in plasma at Cmax after administration of the approved dose to humans. CONCLUSIONS Daclatasvir, alone or in combination with sofosbuvir, at higher doses than used against HCV, may be further fostered as an anti-COVID-19 therapy.
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Affiliation(s)
- Carolina Q Sacramento
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Jairo R Temerozo
- Laboratório de Pesquisas sobre o Timo, IOC, Fiocruz, Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), IOC, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Aline de Paula Dias Da Silva
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Suelen da Silva Gomes Dias
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Carine Dos Santos da Silva
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - André C Ferreira
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
- Universidade Iguaçu, Nova Iguaçu, RJ, Brazil
| | - Mayara Mattos
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Camila R R Pão
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Caroline S de Freitas
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Vinicius Cardoso Soares
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | | | - Tácio Vinício Amorim Fernandes
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
- Laboratório de Macromoléculas, Diretoria de Metrologia Aplicada às Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia-INMETRO, Duque de Caxias, RJ 25250-020, Brazil
| | | | - Mônica Macedo Bastos
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Núbia Boechat
- Instituto de Tecnologia de Fármacos (Farmanguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Felipe B Saraiva
- Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Marcelo Alves Ferreira
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
- Instituto de Tecnologia em Imunobiológicos (Bio-Manguinhos), Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Steffen Jockusch
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Minchen Chien
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Wei Xie
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Dinshaw Patel
- Laboratory of Structural Biology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Aitor Garzia
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - James J Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Rajith K R Rajoli
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L7 3NY, UK
| | | | | | | | | | - Marilia Zaluar Guimarães
- Instituto D'Or de Pesquisa e Ensino, Rio de Janeiro, RJ, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Stevens K Rehen
- Instituto D'Or de Pesquisa e Ensino, Rio de Janeiro, RJ, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andrew Owen
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L7 3NY, UK
| | - Fernando A Bozza
- Instituto D'Or de Pesquisa e Ensino, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Dumith Chequer Bou-Habib
- Laboratório de Pesquisas sobre o Timo, IOC, Fiocruz, Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Neuroimmunomodulation (INCT/NIM), IOC, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA
| | - Patrícia T Bozza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
| | - Thiago Moreno L Souza
- Laboratório de Imunofarmacologia, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil
- National Institute for Science and Technology on Innovation in Diseases of Neglected Populations (INCT/IDPN), Center for Technological Development in Health (CDTS), Fiocruz, Rio de Janeiro, RJ, Brazil
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Massarvva T. Clinical outcomes of COVID-19 amongst HIV patients: a systematic literature review. Epidemiol Health 2021; 43:e2021036. [PMID: 34015893 PMCID: PMC8342867 DOI: 10.4178/epih.e2021036] [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: 04/23/2021] [Accepted: 05/17/2021] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The global pandemic coronavirus disease 2019 (COVID-19) emerged in the city of Wuhan, China around December 2019. Since then, the virus has caused severe morbidity and mortality worldwide and has put pressure on the global medical system. Still, there are limited data regarding the clinical impact of COVID-19 on people living with human immunodeficiency virus (HIV). The primary aim of this study was, therefore, to systematically review up-to-date studies reporting the clinical outcomes of COVID-19 amongst HIV patients. METHODS A thorough literature search was carried out using MEDLINE, Embase, Scopus, and the Cochrane Library Databases in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. RESULTS A total of 22 studies were identified. Amongst 730 HIV/COVID-19-coinfected patients, 79.4% were males, the median age was 51.5 years, and the number of reported patients receiving antiretroviral drugs was 708 (97.2%). Most coinfected patients had mild to moderate symptoms, including cough (37.7%), fever (37.5%), and dyspnoea (24.7%). Among pre-existing comorbidities, hypertension (26.3%) was the most prevalent in HIV/COVID-19 coinfected patients, and 87% of coinfected patients recovered. CONCLUSIONS Based on the existing data in this systematic literature review, HIV patients with pre-existing comorbidities, obesity, and older age should be considered as a high-risk group for COVID-19. Furthermore, coinfected patients appear to have marginally comparable clinical outcomes with the general population. The study's findings highlight the need for further investigation to elucidate the impact of COVID-19 infection on HIV patients.
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Affiliation(s)
- Thomas Massarvva
- Department of Primary Care and Population Health, University of Nicosia Medical School, Nicosia, Cyprus
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32
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Li Y, Zhang HX, Luo WD, Lam CWK, Wang CY, Bai LP, Wong VKW, Zhang W, Jiang ZH. Profiling Ribonucleotide and Deoxyribonucleotide Pools Perturbed by Remdesivir in Human Bronchial Epithelial Cells. Front Pharmacol 2021; 12:647280. [PMID: 33995062 PMCID: PMC8120990 DOI: 10.3389/fphar.2021.647280] [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: 12/29/2020] [Accepted: 03/23/2021] [Indexed: 11/13/2022] Open
Abstract
Remdesivir (RDV) has generated much anticipation for its moderate effect in treating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the unsatisfactory survival rates of hospitalized patients limit its application to the treatment of coronavirus disease 2019 (COVID-19). Therefore, improvement of antiviral efficacy of RDV is urgently needed. As a typical nucleotide analog, the activation of RDV to bioactive triphosphate will affect the biosynthesis of endogenous ribonucleotides (RNs) and deoxyribonucleotides (dRNs), which are essential to RNA and DNA replication in host cells. The imbalance of RN pools will inhibit virus replication as well. In order to investigate the effects of RDV on cellular nucleotide pools and on RNA transcription and DNA replication, cellular RNs and dRNs concentrations were measured by the liquid chromatography-mass spectrometry method, and the synthesis of RNA and DNA was monitored using click chemistry. The results showed that the IC50 values for BEAS-2B cells at exposure durations of 48 and 72 h were 25.3 ± 2.6 and 9.6 ± 0.7 μM, respectively. Ten (10) μM RDV caused BEAS-2B arrest at S-phase and significant suppression of RNA and DNA synthesis after treatment for 24 h. In addition, a general increase in the abundance of nucleotides and an increase of specific nucleotides more than 2 folds were observed. However, the variation of pyrimidine ribonucleotides was relatively slight or even absent, resulting in an obvious imbalance between purine and pyrimidine ribonucleotides. Interestingly, the very marked disequilibrium between cytidine triphosphate (CTP) and cytidine monophosphate might result from the inhibition of CTP synthase. Due to nucleotides which are also precursors for the synthesis of viral nucleic acids, the perturbation of nucleotide pools would block viral RNA replication. Considering the metabolic vulnerability of endogenous nucleotides, exacerbating the imbalance of nucleotide pools imparts great promise to enhance the efficacy of RDV, which possibly has special implications for treatment of COVID-19.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Hui-Xia Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Wen-Di Luo
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Christopher Wai Kei Lam
- Faculty of Medicine and State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau, China
| | - Cai-Yun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease (Macau University of Science and Technology), Taipa, Macau, China
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Modelling single-molecule kinetics of helicase translocation using high-resolution nanopore tweezers (SPRNT). Essays Biochem 2021; 65:109-127. [PMID: 33491732 DOI: 10.1042/ebc20200027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022]
Abstract
Single-molecule picometer resolution nanopore tweezers (SPRNT) is a technique for monitoring the motion of individual enzymes along a nucleic acid template at unprecedented spatiotemporal resolution. We review the development of SPRNT and the application of single-molecule kinetics theory to SPRNT data to develop a detailed model of helicase motion along a single-stranded DNA substrate. In this review, we present three examples of questions SPRNT can answer in the context of the Superfamily 2 helicase Hel308. With Hel308, SPRNT's spatiotemporal resolution enables resolution of two distinct enzymatic substates, one which is dependent upon ATP concentration and one which is ATP independent. By analyzing dwell-time distributions and helicase back-stepping, we show, in detail, how SPRNT can be used to determine the nature of these observed steps. We use dwell-time distributions to discern between three different possible models of helicase backstepping. We conclude by using SPRNT's ability to discern an enzyme's nucleotide-specific location along a DNA strand to understand the nature of sequence-specific enzyme kinetics and show that the sequence within the helicase itself affects both step dwell-time and backstepping probability while translocating on single-stranded DNA.
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Raheem A, Liang L, Zhang G, Cui S. Modulatory Effects of Probiotics During Pathogenic Infections With Emphasis on Immune Regulation. Front Immunol 2021; 12:616713. [PMID: 33897683 PMCID: PMC8060567 DOI: 10.3389/fimmu.2021.616713] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 02/12/2021] [Indexed: 12/11/2022] Open
Abstract
In order to inhibit pathogenic complications and to enhance animal and poultry growth, antibiotics have been extensively used for many years. Antibiotics applications not only affect target pathogens but also intestinal beneficially microbes, inducing long-lasting changes in intestinal microbiota associated with diseases. The application of antibiotics also has many other side effects like, intestinal barrier dysfunction, antibiotics residues in foodstuffs, nephropathy, allergy, bone marrow toxicity, mutagenicity, reproductive disorders, hepatotoxicity carcinogenicity, and antibiotic-resistant bacteria, which greatly compromise the efficacy of antibiotics. Thus, the development of new antibiotics is necessary, while the search for antibiotic alternatives continues. Probiotics are considered the ideal antibiotic substitute; in recent years, probiotic research concerning their application during pathogenic infections in humans, aquaculture, poultry, and livestock industry, with emphasis on modulating the immune system of the host, has been attracting considerable interest. Hence, the adverse effects of antibiotics and remedial effects of probiotics during infectious diseases have become central points of focus among researchers. Probiotics are live microorganisms, and when given in adequate quantities, confer good health effects to the host through different mechanisms. Among them, the regulation of host immune response during pathogenic infections is one of the most important mechanisms. A number of studies have investigated different aspects of probiotics. In this review, we mainly summarize recent discoveries and discuss two important aspects: (1) the application of probiotics during pathogenic infections; and (2) their modulatory effects on the immune response of the host during infectious and non-infectious diseases.
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Affiliation(s)
- Abdul Raheem
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
| | - Lin Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
| | - Guangzhi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
| | - Shangjin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing, China
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Udofia IA, Gbayo KO, Oloba-Whenu OA, Ogunbayo TB, Isanbor C. In silico studies of selected multi-drug targeting against 3CLpro and nsp12 RNA-dependent RNA-polymerase proteins of SARS-CoV-2 and SARS-CoV. NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS 2021; 10:22. [PMID: 33786291 PMCID: PMC7992627 DOI: 10.1007/s13721-021-00299-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/25/2021] [Accepted: 03/12/2021] [Indexed: 12/20/2022]
Abstract
An outbreak of a cluster of viral pneumonia cases, subsequently identified as coronavirus disease 2019 (COVID-19), due to a novel SARS-CoV-2 necessitates an urgent need for a vaccine to prevent infection or an approved medication for a cure. In our in silico molecular docking study, a total of 173 compounds, including FDA-approved antiviral drugs, with good ADME descriptors, and some other nucleotide analogues were screened. The results show that these compounds demonstrate strong binding affinity for the residues at the active sites of RNA-dependent RNA-polymerase (RdRp) modelled structures and Chymotrypsin-like cysteine protease (3CLpro) of the HCoV proteins. Free energies (ΔG's) of binding for SARS-CoV-2 and SARS-CoV RdRp range from - 5.4 to - 8.8 kcal/mol and - 4.9 to - 8.7 kcal/mol, respectively. Also, SARS-CoV-2 and SARS-CoV 3CLpro gave ΔG values ranging from - 5.1 to - 8.4 kcal/mol and - 5.5 to - 8.6 kcal/mol, respectively. Interesting results are obtained for ivermectin, an antiparasitic agent with broad spectrum activity, which gave the highest binding energy value (- 8.8 kcal/mol) against the 3CLpro of SARS-CoV-2 and RdRps of both SARS-CoV and SARS-CoV-2. The reason for such high binding energy values is probably due to the presence of hydroxy, methoxy and sugar moieties in its structure. The stability of the protein-ligand complexes of polymerase inhibitors considered in this investigation, such as Sofosbuvir, Remdesivir, Tenofovir, Ribavirin, Galidesivir, 5c3, 5h1 and 7a1, show strong to moderate hydrogen bonding and hydrophobic interactions (π-π stacked, π-π T-shaped, π-sigma and π-alkyl). The stability provided from such interactions translate into greater antiviral activity or inhibitory effect of the ligands. Assessment of the average free energies of binding of the FDA approved drugs are highly comparable for conformers of a particular inhibitor, indicating similar modes of binding within the pockets. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13721-021-00299-2.
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A review on the interaction of nucleoside analogues with SARS-CoV-2 RNA dependent RNA polymerase. Int J Biol Macromol 2021; 181:605-611. [PMID: 33766591 PMCID: PMC7982646 DOI: 10.1016/j.ijbiomac.2021.03.112] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
The outbreaks of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) in 2019, have highlighted the concerns about the lack of potential vaccines or antivirals approved for inhibition of CoVs infection. SARS-CoV-2 RNA dependent RNA polymerase (RdRp) which is almost preserved across different viral species can be a potential target for development of antiviral drugs, including nucleoside analogues (NA). However, ExoN proofreading activity of CoVs leads to their protection from several NAs. Therefore, potential platforms based on the development of efficient NAs with broad-spectrum efficacy against human CoVs should be explored. This study was then aimed to present an overview on the development of NAs-based drug repurposing for targeting SARS-CoV-2 RdRp by computational analysis. Afterwards, the clinical development of some NAs including Favipiravir, Sofosbuvir, Ribavirin, Tenofovir, and Remdesivir as potential inhibitors of RdRp, were surveyed. Overall, exploring broad-spectrum NAs as promising inhibitors of RdRp may provide useful information about the identification of potential antiviral repurposed drugs against SARS-CoV-2.
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Kevadiya BD, Machhi J, Herskovitz J, Oleynikov MD, Blomberg WR, Bajwa N, Soni D, Das S, Hasan M, Patel M, Senan AM, Gorantla S, McMillan J, Edagwa B, Eisenberg R, Gurumurthy CB, Reid SPM, Punyadeera C, Chang L, Gendelman HE. Pharmacotherapeutics of SARS-CoV-2 Infections. J Neuroimmune Pharmacol 2021; 16:12-37. [PMID: 33403500 PMCID: PMC7785334 DOI: 10.1007/s11481-020-09968-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 01/31/2023]
Abstract
The COVID-19 pandemic has affected more than 38 million people world-wide by person to person transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Therapeutic and preventative strategies for SARS-CoV-2 remains a significant challenge. Within the past several months, effective treatment options have emerged and now include repurposed antivirals, corticosteroids and virus-specific antibodies. The latter has included convalescence plasma and monoclonal antibodies. Complete viral eradication will be achieved through an effective, safe and preventative vaccine. To now provide a comprehensive summary for each of the pharmacotherapeutics and preventative strategies being offered or soon to be developed for SARS-CoV-2.
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Affiliation(s)
- Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA.
| | - Jatin Machhi
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Jonathan Herskovitz
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Maxim D Oleynikov
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Wilson R Blomberg
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Neha Bajwa
- Department of Pharmaceutical Sciences & Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda, Pb, India
| | - Dhruvkumar Soni
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Srijanee Das
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Ahmed M Senan
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 20095, China
| | - Santhi Gorantla
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - JoEllyn McMillan
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - Benson Edagwa
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | | | - Channabasavaiah B Gurumurthy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
| | - St Patrick M Reid
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Chamindie Punyadeera
- The School of Biomedical Sciences and the Institute of Health and Biomedical Innovation, Queensland University of Technology and the Translational Research Institute, Brisbane, Australia
| | - Linda Chang
- Departments of Diagnostic Radiology & Nuclear Medicine, and Neurology, School of Medicine, University of Maryland, Baltimore, MD, 21201, USA
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198-5880, USA
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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Dongol K, Neupane Y, Das Dutta H, Raj Gyawali B, Kharel B. Prevalence of Foreign Body Aspiration in Children in a Tertiary Care Hospital. JNMA J Nepal Med Assoc 2021; 59:111-115. [PMID: 34506471 PMCID: PMC8959221 DOI: 10.31729/jnma.5393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 11/11/2022] Open
Abstract
Introduction: Foreign body aspiration is a common problem in children with significant mortality and morbidity. This study aims to determine the prevalence of foreign body aspiration in children in a tertiary care hospital of Nepal. Methods: A descriptive cross-sectional study was conducted at Tribhuvan University Teaching Hospital from April 2010 to March 2016 after obtaining ethical approval from Institutional Review Committee (Reference number- 08(6-11)E277/78). All children of age up to 15 years with suspected foreign body aspiration were included. The data was collected from the medical record section and entered in Microsoft Excel. The descriptive statistical analysis was performed. Results: A total of 26,294 patients were included in the study. The prevalence of foreign body aspiration in children was found to be 98 (0.37%). On rigid bronchoscopy, 82 patients (83.6%) were confirmed to have a foreign body in the airway. The peak incidence of foreign body aspiration was seen in patients of age group one to two years. The commonest foreign body in the airway was a peanut. Conclusions: The prevalence of foreign body aspiration in children was low, which is similar to other studies. Foreign body aspiration may lead to dreadful complications. Therefore, both the clinicians and the public need to be cautious about it.
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Affiliation(s)
- Kripa Dongol
- Department of ENT, Tribhuvan University Teaching Hospital, Maharajgunj, Kathmandu, Nepal
| | - Yogesh Neupane
- Department of ENT, Tribhuvan University Teaching Hospital, Maharajgunj, Kathmandu, Nepal
| | - Heempali Das Dutta
- Department of ENT, Tribhuvan University Teaching Hospital, Maharajgunj, Kathmandu, Nepal
| | - Bigyan Raj Gyawali
- Department of ENT, Tribhuvan University Teaching Hospital, Maharajgunj, Kathmandu, Nepal
| | - Bijaya Kharel
- Department of ENT, Tribhuvan University Teaching Hospital, Maharajgunj, Kathmandu, Nepal
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Bisindolylmaleimide IX: A novel anti-SARS-CoV2 agent targeting viral main protease 3CLpro demonstrated by virtual screening pipeline and in-vitro validation assays. Methods 2021; 195:57-71. [PMID: 33453392 PMCID: PMC7807167 DOI: 10.1016/j.ymeth.2021.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/10/2021] [Indexed: 01/24/2023] Open
Abstract
SARS-CoV-2, the virus that causes COVID-19 consists of several enzymes with essential functions within its proteome. Here, we focused on repurposing approved and investigational drugs/compounds. We targeted seven proteins with enzymatic activities known to be essential at different stages of the viral cycle including PLpro, 3CLpro, RdRP, Helicase, ExoN, NendoU, and 2'-O-MT. For virtual screening, energy minimization of a crystal structure of the modeled protein was carried out using the Protein Preparation Wizard (Schrodinger LLC 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs and investigational molecules (n = 5903). The screening was performed against viral targets using three sequential docking modes (i.e., HTVS, SP, and XP). Virtual screening identified ∼290 potential inhibitors based on the criteria of energy, docking parameters, ligand, and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. The top lead from each target pool was further subjected to molecular dynamics simulation using the Desmond module. The resulting top eight hits were tested for their SARS-CoV-2 anti-viral activity in-vitro. Among these, a known inhibitor of protein kinase C isoforms, Bisindolylmaleimide IX (BIM IX), was found to be a potent inhibitor of SARS-CoV-2. Further, target validation through enzymatic assays confirmed 3CLpro to be the target. This is the first study that has showcased BIM IX as a COVID-19 inhibitor thereby validating our pipeline.
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40
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De Clercq E. Perspectives for antivirals to limit SARS-CoV-2 infection (COVID-19). MICROBIOLOGY AUSTRALIA 2021. [DOI: 10.1071/ma21013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Compared with vaccines, antivirals for curbing COVID-19 (SARS-CoV-2 infection) have been developed at a much lower pace. Favipiravir has proven efficacious (in hamsters) but only at a very high dose which may not be feasible in humans. Remdesivir is the sole antiviral approved by the US FDA, but it has not been extensively evaluated for its safety. EIDD-1931 and EIDD-2801 have not been evaluated clinically. Mpro (protease) inhibitors likewise need to be subjected to clinical efficacy and safety studies. Remdesivir is a C-nucleoside and this class of compounds should be further evaluated. Polyanionic substances interfering with virus adsorption to the host cells have not been explored. They may possibly be administered by inhalation. Corticosteroids (such as dexamethasone), while virus-stimulating rather than inhibitory, may counteract the ‘cytokine storm’. Combination of (two or more of) the compounds mentioned above may offer an increased benefit through a synergistic interaction.
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Ghanbari R, Teimoori A, Sadeghi A, Mohamadkhani A, Rezasoltani S, Asadi E, Jouyban A, Sumner SCJ. Existing antiviral options against SARS-CoV-2 replication in COVID-19 patients. Future Microbiol 2020; 15:1747-1758. [PMID: 33404263 PMCID: PMC7789744 DOI: 10.2217/fmb-2020-0120] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/18/2020] [Indexed: 02/08/2023] Open
Abstract
COVID-19 caused by SARS-CoV-2, is an international concern. This infection requires urgent efforts to develop new antiviral compounds. To date, no specific drug in controlling this disease has been identified. Developing the new treatment is usually time consuming, therefore using the repurposing broad-spectrum antiviral drugs could be an effective strategy to respond immediately. In this review, a number of broad-spectrum antivirals with potential efficacy to inhibit the virus replication via targeting the virus spike protein (S protein), RNA-dependent RNA polymerase (RdRp), 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro) that are critical in the pathogenesis and life cycle of coronavirus, have been evaluated as possible treatment options against SARS-CoV-2 in COVID-19 patients.
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Affiliation(s)
- Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Science, Tehran 1411713135, Iran
| | - Ali Teimoori
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 65178-38678, Iran
| | - Anahita Sadeghi
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Science, Tehran 1411713135, Iran
| | - Ashraf Mohamadkhani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Science, Tehran 1411713135, Iran
| | - Sama Rezasoltani
- Foodborne & Waterborne Diseases Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 1985717411, Iran
| | - Ebrahim Asadi
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada
| | - Abolghasem Jouyban
- Pharmaceutical Analysis Research Center & Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166/1573, Iran
| | - Susan CJ Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 28081, USA
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42
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Chien M, Anderson TK, Jockusch S, Tao C, Li X, Kumar S, Russo JJ, Kirchdoerfer RN, Ju J. Nucleotide Analogues as Inhibitors of SARS-CoV-2 Polymerase, a Key Drug Target for COVID-19. J Proteome Res 2020; 19:4690-4697. [PMID: 32692185 PMCID: PMC7640960 DOI: 10.1021/acs.jproteome.0c00392] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Indexed: 12/18/2022]
Abstract
SARS-CoV-2 is responsible for the current COVID-19 pandemic. On the basis of our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously demonstrated that three nucleotide analogues (the triphosphates of Sofosbuvir, Alovudine, and AZT) inhibit the SARS-CoV RNA-dependent RNA polymerase (RdRp). We also demonstrated that a library of additional nucleotide analogues terminate RNA synthesis catalyzed by the SARS-CoV-2 RdRp, a well-established drug target for COVID-19. Here, we used polymerase extension experiments to demonstrate that the active triphosphate form of Sofosbuvir (an FDA-approved hepatitis C drug) is incorporated by SARS-CoV-2 RdRp and blocks further incorporation. Using the molecular insight gained from the previous studies, we selected the active triphosphate forms of six other antiviral agents, Alovudine, Tenofovir alafenamide, AZT, Abacavir, Lamivudine, and Emtricitabine, for evaluation as inhibitors of the SARS-CoV-2 RdRp and demonstrated the ability of these viral polymerase inhibitors to be incorporated by SARS-CoV-2 RdRp, where they terminate further polymerase extension with varying efficiency. These results provide a molecular basis for inhibition of the SARS-CoV-2 RdRp by these nucleotide analogues. If sufficient efficacy of some of these FDA-approved drugs in inhibiting viral replication in cell culture is established, they may be explored as potential COVID-19 therapeutics.
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Affiliation(s)
- Minchen Chien
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Thomas K. Anderson
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Steffen Jockusch
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Chuanjuan Tao
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Xiaoxu Li
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Shiv Kumar
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - James J. Russo
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
| | - Robert N. Kirchdoerfer
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jingyue Ju
- Center
for Genome Technology and Biomolecular Engineering, Departments of Chemical
Engineering, Pharmacology, and Chemistry, Columbia University, New York, New York 10027, United States
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