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Article: Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study.

Rameshkumar, Marimuthu Ragavan / Indu, Purushothaman / Arunagirinathan, Narasingam / Venkatadri, Babu / El-Serehy, Hamed A / Ahmad, Ajaz

Saudi journal of biological sciences

2020 Volume 28, Issue 1, Page(s) 448–458

Abstract: An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent ... ...

Abstract	An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent need. In this study, flavonoid compounds were analyzed for its inhibitory potential against important protein targets of SARS-CoV-2 using computational approaches. Virtual docking was performed for screening of flavonoid compounds retrieved from PubChem against the main protease of SARS-CoV-2 using COVID-19 docking server. The cut off of dock score was set to >-9 kcal/mol and screened compounds were individually docked against main protease, RNA-dependent RNA polymerase, and spike proteins using AutoDock 4.1 software. Finally, lead flavonoid compounds were subjected to ADMET analysis. A total of 458 flavonoid compounds were virtually screened against main protease target and 36 compounds were selected based on the interaction energy value >-9 kcal/mol. Furthermore, these compounds were individually docked against protein targets and top 10 lead compounds were identified. Among the lead compounds, agathisflavone showed highest binding energy value of -8.4 kcal/mol against main protease, Albireodelphin showed highest dock score of -9.8 kcal/mol and -11.2 kcal/mol against RdRp, and spike proteins, respectively. Based on the high dock score and ADMET properties, top 5 lead molecules such as Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate were identified as potent inhibitors against main protease, RdRp, and spike protein targets of SARS-CoV-2. These all compounds are having non-carcinogenic and non-mutagenic properties. This study finding suggests that the screened compounds include Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate could be the potent inhibitors of SARS-CoV-2 targets.
Keywords	covid19
Language	English
Publishing date	2020-10-22
Publishing country	Saudi Arabia
Document type	Journal Article
ZDB-ID	2515206-3
ISSN	2213-7106 ; 1319-562X
ISSN (online)	2213-7106
ISSN	1319-562X
DOI	10.1016/j.sjbs.2020.10.028
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Article ; Online: Antiviral activity of astragaloside II, astragaloside III and astragaloside IV compounds against dengue virus: Computational docking and in vitro studies.

Indu, Purushothaman / Arunagirinathan, Narasingam / Rameshkumar, Marimuthu Ragavan / Sangeetha, Kodhandan / Divyadarshini, Angamuthu / Rajarajan, Swaminathan

Microbial pathogenesis

2020 Volume 152, Page(s) 104563

Abstract: This study was aimed to identify the phytocompounds possessing anti-dengue virus activity using in silico and in vitro approaches. A total of 7000 phytocompounds were virtually screened against protein targets (envelope, NS2b/NS3, and NS5) of dengue ... ...

Abstract	This study was aimed to identify the phytocompounds possessing anti-dengue virus activity using in silico and in vitro approaches. A total of 7000 phytocompounds were virtually screened against protein targets (envelope, NS2b/NS3, and NS5) of dengue virus using iGEMDOCK and individually docked using Maestro 10.7 module of Schrödinger software. In vitro cytotoxicity and antiviral studies were performed using vero cell line. Finally, three phytocompounds namely astragaloside II, astragaloside III, and astragaloside IV were screened based on their highest binding energy values against protein targets. Astragaloside III exhibited the highest interaction energy value of -8.718 kcal/mol and -8.447 kcal/mol against envelope, and NS2b/NS3 targets, respectively. Astragaloside IV exhibited -7.244 kcal/mol against SAM site, and -9.179 kcal/mol against RNA cap site of NS5 targets. In silico ADMET analysis revealed that astragaloside II, III, and IV were non-mutagenic and non-carcinogenic in nature and these compounds were also non-toxic to vero cells upto 1000 μg/mL. Against dengue virus serotype 3, astragaloside II exhibited substantial antiviral activity at the concentration of 1.56 μg/mL followed by astragaloside III at 6.25 μg/mL and astragaloside IV at 12.5 μg/mL. Also, against dengue serotype 1, astragaloside II showed the maximum antiviral activity at 1.56 μg/mL followed by astragaloside III and IV at 3.125 μg/mL. This study concludes that astragaloside II, III, and IV compounds had potential in vitro anti-dengue virus activity.
MeSH term(s)	Animals ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Chlorocebus aethiops ; Dengue/drug therapy ; Dengue Virus ; Molecular Docking Simulation ; Saponins ; Triterpenes ; Vero Cells ; Viral Nonstructural Proteins
Chemical Substances	Antiviral Agents ; Saponins ; Triterpenes ; Viral Nonstructural Proteins ; astragaloside II ; astragaloside A (3A592W8XKE) ; astragaloside III (WVP53009FC)
Language	English
Publishing date	2020-10-22
Publishing country	England
Document type	Journal Article
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2020.104563
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Article ; Online: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach.

Indu, Purushothaman / Rameshkumar, Marimuthu Ragavan / Arunagirinathan, Narasingam / Al-Dhabi, Naif Abdullah / Valan Arasu, Mariadhas / Ignacimuthu, Savarimuthu

Journal of infection and public health

2020 Volume 13, Issue 12, Page(s) 1856–1861

Abstract: Background: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to ... ...

Abstract	Background: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to find out the drugs for COVID-19 treatment from existing FDA approved antiviral drugs. In this study, FDA approved small molecule antiviral drugs were repurposed against the major viral proteins of SARS-CoV-2. Methods: The 3D structures of FDA approved small molecule antiviral drugs were retrieved from PubChem. Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. Furthermore, lead molecules were individually docked against protein targets using AutoDock 4.0.1 software and their drug-likeness and ADMET properties were evaluated. Results: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥-8 kcal/mol. Similarly Indinavir showed the highest binding energy of -11.5 kcal/mol against the target protein RdRp and Dolutegravir, Elbasvir, Tipranavir, Taltegravir, Grazoprevir, Daclatasvir, Glecaprevir, Ledipasvir, Pibrentasvir and Velpatasvir showed a binding energy value in range from -8 to -11.2 kcal/mol. The antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine also exhibited good bioavailability and drug-likeness properties. Conclusion: This study suggests that the screened small molecule antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine could serve as potential drugs for the treatment of COVID-19 with further validation studies.
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Coronavirus Protease Inhibitors/pharmacology ; Drug Repositioning ; Heterocyclic Compounds, 3-Ring/pharmacology ; Humans ; Indinavir/pharmacology ; Molecular Docking Simulation ; Nitriles/pharmacology ; Oxazines/pharmacology ; Piperazines/pharmacology ; Pyridines/pharmacology ; Pyridones/pharmacology ; Pyrimidines/pharmacology ; Pyrones/pharmacology ; RNA-Dependent RNA Polymerase/antagonists & inhibitors ; Raltegravir Potassium/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Sulfonamides/pharmacology
Chemical Substances	Antiviral Agents ; Coronavirus Protease Inhibitors ; Heterocyclic Compounds, 3-Ring ; Nitriles ; Oxazines ; Piperazines ; Pyridines ; Pyridones ; Pyrimidines ; Pyrones ; Sulfonamides ; etravirine (0C50HW4FO1) ; Raltegravir Potassium (43Y000U234) ; Indinavir (5W6YA9PKKH) ; dolutegravir (DKO1W9H7M1) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; tipranavir (ZZT404XD09)
Keywords	covid19
Language	English
Publishing date	2020-10-26
Publishing country	England
Document type	Journal Article
ISSN	1876-035X
ISSN (online)	1876-035X
DOI	10.1016/j.jiph.2020.10.015
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Article: Do the clonally different

Rameshkumar, Marimuthu Ragavan / Arunagirinathan, Narasingam / Swathirajan, Chinnambedu Ravichandran / Vignesh, Ramachandran / Balakrishnan, Pachamuthu / Solomon, Sunil Suhas

The Indian journal of medical research

2018 Volume 148, Issue 3, Page(s) 341–344

MeSH term(s)	Adult ; Anti-Bacterial Agents/classification ; Anti-Bacterial Agents/therapeutic use ; Drug Resistance, Bacterial/drug effects ; Drug Resistance, Bacterial/genetics ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Escherichia coli/isolation & purification ; Escherichia coli Infections/complications ; Escherichia coli Infections/drug therapy ; Escherichia coli Infections/epidemiology ; Escherichia coli Infections/microbiology ; HIV Seropositivity/complications ; HIV Seropositivity/diagnosis ; HIV Seropositivity/epidemiology ; Humans ; India/epidemiology ; Male ; Microbial Sensitivity Tests/methods ; Patient Selection
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2018-11-13
Publishing country	India
Document type	Letter
ZDB-ID	390883-5
ISSN	0971-5916 ; 0019-5340
ISSN	0971-5916 ; 0019-5340
DOI	10.4103/ijmr.IJMR_730_17
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Article ; Online: Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins

Rameshkumar, Marimuthu Ragavan / Indu, Purushothaman / Arunagirinathan, Narasingam / Venkatadri, Babu / El-Serehy, Hamed A. / Ahmad, Ajaz

Saudi Journal of Biological Sciences ; ISSN 1319-562X

A molecular docking study

2020

Keywords	General Agricultural and Biological Sciences ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
DOI	10.1016/j.sjbs.2020.10.028
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Article ; Online: Occurrence of extended-spectrum β-lactamase, AmpC, and carbapenemase-producing genes in gram-negative bacterial isolates from human immunodeficiency virus infected patients.

Rameshkumar, Marimuthu Ragavan / Arunagirinathan, Narasingam / Senthamilselvan, Balasubramanian / Swathirajan, Chinnambedu Ravichandran / Solomon, Sunil Suhas / Vignesh, Ramachandran / Balakrishnan, Pachamuthu / Aljowaie, Reem M / Almaary, Khalid S / Chen, Tse-Wei

Journal of infection and public health

2021 Volume 14, Issue 12, Page(s) 1881–1886

Abstract: Background: Progressive decline of immune response in HIV patients makes them susceptible to frequent bacterial infections. High usage of antibiotics influences the emergence of multidrug-resistant bacteria and worsens the clinical outcomes. In this ... ...

Abstract	Background: Progressive decline of immune response in HIV patients makes them susceptible to frequent bacterial infections. High usage of antibiotics influences the emergence of multidrug-resistant bacteria and worsens the clinical outcomes. In this study, the occurrence of drug-resistant genes in Gram-negative bacterial isolates from HIV patients in South India was analyzed. Methods: A total of 173 Gram-negative bacterial (GNB) isolates from HIV patients were screened for antibiotic susceptibility profile using the Kirby-Bauer diskdiffusion method. Positivity of drug-resistant genes was analyzed using polymerase chain reaction method. Results: In this study, 72.8% of bacterial isolates were obtained from urine specimens, and Escherichia coli (47.4%) was the predominantly isolated bacterium. Overall, 87.3% and 83.2% of GNB were resistant to 3rd generation cephalosporin antibiotics such as cefotaxime and ceftazidime, respectively, 56.6% were resistant to cephamycin (cefoxitin) and 43% to carbapenem (imipenem) antibiotics. Extended-spectrum β-lactamases (ESBL) production was noted among 79.5% of GNB isolates, followed by AmpC (57.1%) and Metallo β-lactamases (37.3%). Molecular analysis revealed that ESBL genes such as blaTEM (94.1%), blaCTX-M (89.2%), and blaSHV (24.2%) were detected at higher levels among GNB isolates. Carbapenemase-producing genes such as blaOXA-48 (20%), blaOXA-23 (2.6%), and both blaOXA-23 and blaOXA-51 like genes (2.6%) and AmpC producing genes such as blaCIT (26.7%), blaDHA (3.6%), and blaACC (1.8%) were detected at low-level. Conclusions: This study concludes that ESBL producing genes are detected at high level among gram-negative bacterial isolates from HIV patients in South India.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics ; HIV ; HIV Infections/complications ; Humans ; Microbial Sensitivity Tests ; beta-Lactamases/genetics
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; beta-Lactamases (EC 3.5.2.6) ; carbapenemase (EC 3.5.2.6)
Language	English
Publishing date	2021-11-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2467587-8
ISSN	1876-035X ; 1876-0341
ISSN (online)	1876-035X
ISSN	1876-0341
DOI	10.1016/j.jiph.2021.11.008
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Article: Ertapenem for multiple β-lactamases producing Gram-negative bacteria causing urinary tract infections in HIV patients.

Kumar, Marimuthu Ragavan Ramesh / Arunagirinathan, Narasingam / Vignesh, Ramachandran / Balakrishnan, Pachamuthu / Solomon, Suniti / Sunil, Solomon S

Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences

2017 Volume 22, Page(s) 69

Language	English
Publishing date	2017-05-30
Publishing country	India
Document type	Journal Article
ZDB-ID	2513029-8
ISSN	1735-7136 ; 1735-1995
ISSN (online)	1735-7136
ISSN	1735-1995
DOI	10.4103/jrms.JRMS_884_16
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Article: Detection of

Rameshkumar, Marimuthu Ragavan / Arunagirinathan, Narasingam / Indu, Purushothaman / Swathirajan, Chinnambedu Ravichandran / Solomon, Sunil Suhas / Vignesh, Ramachandran / Balakrishnan, Pachamuthu

Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences

2018 Volume 23, Page(s) 112

Language	English
Publishing date	2018-12-28
Publishing country	India
Document type	Journal Article
ZDB-ID	2513029-8
ISSN	1735-7136 ; 1735-1995
ISSN (online)	1735-7136
ISSN	1735-1995
DOI	10.4103/jrms.JRMS_627_18
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Article: Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study

Ragavan Rameshkumar, Marimuthu / Indu, Purushothaman / Arunagirinathan, Narasingam / Venkatadri, Babu / El-Serehy, Hamed A / Ahmad, Ajaz

Abstract	An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent need. In this study, flavonoid compounds were analyzed for its inhibitory potential against important protein targets of SARS-CoV-2 using computational approaches. Virtual docking was performed for screening of flavonoid compounds retrieved from PubChem against the main protease of SARS-CoV-2 using COVID-19 docking server. The cut off of dock score was set to >-9kcal/mol and screened compounds were individually docked against main protease, RNA-dependent RNA polymerase, and spike proteins using AutoDock 4.1 software. Finally, lead flavonoid compounds were subjected to ADMET analysis. A total of 458 flavonoid compounds were virtually screened against main protease target and 36 compounds were selected based on the interaction energy value >-9kcal/mol. Furthermore, these compounds were individually docked against protein targets and top 10 lead compounds were identified. Among the lead compounds, agathisflavone showed highest binding energy value of -8.4 kcal/mol against main protease, Albireodelphin showed highest dock score of -9.8 kcal/mol and -11.2 kcal/mol against RdRp, and spike proteins, respectively. Based on the high dock score and ADMET properties, top 5 lead molecules such as Albireodelphin, Apigenin 7-(6''-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6''-O-malonate were identified as potent inhibitors against main protease, RdRp, and spike protein targets of SARS-CoV-2. These all compounds are having non-carcinogenic and non-mutagenic properties.This study finding suggests that the screened compounds include Albireodelphin, Apigenin 7-(6''-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6''-O-malonate could be the potent inhibitors of SARS-CoV-2 targets.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #894218
Database	COVID19

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Article: Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine against main protease and RNA-dependent RNA polymerase of SARS-CoV-2: A molecular docking and drug repurposing approach

Indu, Purushothaman / Rameshkumar, Marimuthu Ragavan / Arunagirinathan, Narasingam / Al-Dhabi, Naif Abdullah / Valan Arasu, Mariadhas / Ignacimuthu, Savarimuthu

J. infect. public health

Abstract: BACKGROUND: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to ... ...

Abstract	BACKGROUND: Outbreak of COVID-19 has been recognized as a global health concern since it causes high rates of morbidity and mortality. No specific antiviral drugs are available for the treatment of COVID-19 till date. Drug repurposing strategy helps to find out the drugs for COVID-19 treatment from existing FDA approved antiviral drugs. In this study, FDA approved small molecule antiviral drugs were repurposed against the major viral proteins of SARS-CoV-2. METHODS: The 3D structures of FDA approved small molecule antiviral drugs were retrieved from PubChem. Virtual screening was performed to find out the lead antiviral drug molecules against main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) using COVID-19 Docking Server. Furthermore, lead molecules were individually docked against protein targets using AutoDock 4.0.1 software and their drug-likeness and ADMET properties were evaluated. RESULTS: Out of 65 FDA approved small molecule antiviral drugs screened, Raltegravir showed highest interaction energy value of -9 kcal/mol against Mpro of SARS-CoV-2 and Indinavir, Tipranavir, and Pibrentasvir exhibited a binding energy value of ≥-8 kcal/mol. Similarly Indinavir showed the highest binding energy of -11.5 kcal/mol against the target protein RdRp and Dolutegravir, Elbasvir, Tipranavir, Taltegravir, Grazoprevir, Daclatasvir, Glecaprevir, Ledipasvir, Pibrentasvir and Velpatasvir showed a binding energy value in range from -8 to -11.2 kcal/mol. The antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine also exhibited good bioavailability and drug-likeness properties. CONCLUSION: This study suggests that the screened small molecule antiviral drugs Raltegravir, Indinavir, Tipranavir, Dolutegravir, and Etravirine could serve as potential drugs for the treatment of COVID-19 with further validation studies.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #894049
Database	COVID19

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