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Article ; Online: Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease.

Marinho, Emanuelle Machado / Batista de Andrade Neto, João / Silva, Jacilene / Rocha da Silva, Cecília / Cavalcanti, Bruno Coelho / Marinho, Emmanuel Silva / Nobre Júnior, Hélio Vitoriano

Microbial pathogenesis

2020 Volume 148, Page(s) 104365

Abstract: ... Quinacrine and Ruxolitinib) in docking models from the SARS-CoV-2 main protease (M-pro) protein. The results ... 2 main protease. Therefore, this study allows proposing the use of baricitinib and quinacrine ... Coronavirus (COVID-19) is an enveloped RNA virus that is diversely found in humans and that has now ...

Abstract	Coronavirus (COVID-19) is an enveloped RNA virus that is diversely found in humans and that has now been declared a global pandemic by the World Health Organization. Thus, there is an urgent need to develop effective therapies and vaccines against this disease. In this context, this study aimed to evaluate in silico the molecular interactions of drugs with therapeutic indications for treatment of COVID-19 (Azithromycin, Baricitinib and Hydroxychloroquine) and drugs with similar structures (Chloroquine, Quinacrine and Ruxolitinib) in docking models from the SARS-CoV-2 main protease (M-pro) protein. The results showed that all inhibitors bound to the same enzyme site, more specifically in domain III of the SARS-CoV-2 main protease. Therefore, this study allows proposing the use of baricitinib and quinacrine, in combination with azithromycin; however, these computer simulations are just an initial step for conceiving new projects for the development of antiviral molecules.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Binding Sites/drug effects ; COVID-19/virology ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Cysteine Endopeptidases/chemistry ; Cysteine Proteinase Inhibitors/chemistry ; Cysteine Proteinase Inhibitors/pharmacology ; Drug Discovery/methods ; Drug Evaluation, Preclinical/methods ; Humans ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Cysteine Proteinase Inhibitors ; Protease Inhibitors ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-06-30
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.2020.104365
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Article ; Online: Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease

Marinho, Emanuelle Machado / Batista de Andrade Neto, João / Silva, Jacilene / Rocha da Silva, Cecília / Cavalcanti, Bruno Coelho / Marinho, Emmanuel Silva / Nobre Júnior, Hélio Vitoriano

Microbial Pathogenesis

2020 Volume 148, Page(s) 104365

Keywords	Microbiology ; Infectious Diseases ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	632772-2
ISSN	1096-1208 ; 0882-4010
ISSN (online)	1096-1208
ISSN	0882-4010
DOI	10.1016/j.micpath.2020.104365
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease

Marinho, Emanuelle Machado / Batista de Andrade Neto, João / Silva, Jacilene / Rocha da Silva, Cecília / Cavalcanti, Bruno Coelho / Marinho, Emmanuel Silva / Nobre Júnior, Hélio Vitoriano

Microb Pathog

Abstract	Coronavirus (COVID-19) is an enveloped RNA virus that is diversely found in humans and that has now been declared a global pandemic by the World Health Organization. Thus, there is an urgent need to develop effective therapies and vaccines against this disease. In this context, this study aimed to evaluate in silico the molecular interactions of drugs with therapeutic indications for treatment of COVID-19 (Azithromycin, Baricitinib and Hydroxychloroquine) and drugs with similar structures (Chloroquine, Quinacrine and Ruxolitinib) in docking models from the SARS-CoV-2 main protease (M-pro) protein. The results showed that all inhibitors bound to the same enzyme site, more specifically in domain III of the SARS-CoV-2 main protease. Therefore, this study allows proposing the use of baricitinib and quinacrine, in combination with azithromycin; however, these computer simulations are just an initial step for conceiving new projects for the development of antiviral molecules.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #632625
Database	COVID19

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Article ; Online: Pharmacophore based virtual screening for natural product database revealed possible inhibitors for SARS-COV-2 main protease.

El-Ashrey, Mohamed K / Bakr, Riham O / Fayed, Marwa A A / Refaey, Rana H / Nissan, Yassin M

Virology

2022 Volume 570, Page(s) 18–28

Abstract: ... candidates from natural origin to overcome COVID-19 pandemic. A virtual screening of the natural compounds ... 2 main protease inhibitors. ... database (47,645 compounds) using structure-based pharmacophore model and molecular docking simulations ...

Abstract	The challenge continues globally triggered by the absence of an approved antiviral drug against COVID-19 virus infection necessitating global concerted efforts of scientists. Nature still provides a renewable source for drugs used to solve many health problems. The aim of this work is to provide new candidates from natural origin to overcome COVID-19 pandemic. A virtual screening of the natural compounds database (47,645 compounds) using structure-based pharmacophore model and molecular docking simulations reported eight hits from natural origin against SARS-CoV-2 main proteinase (Mpro) enzyme. The successful candidates were of terpenoidal nature including taxusabietane, Isoadenolin A & C, Xerophilusin B, Excisanin H, Macrocalin B and ponicidin, phytoconstituents isolated from family Lamiaceae and sharing a common ent-kaurane nucleus, were found to be the most successful candidates. This study suggested that the diterpene nucleus has a clear positive contribution which can represent a new opportunity in the development of SARS-CoV-2 main protease inhibitors.
MeSH term(s)	Antiviral Agents/pharmacology ; Biological Products/pharmacology ; Coronavirus 3C Proteases ; Humans ; Molecular Docking Simulation ; Pandemics ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; SARS-CoV-2 ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; Biological Products ; Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-) ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2022-03-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2022.03.003
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Article: Pharmacophore based virtual screening for natural product database revealed possible inhibitors for SARS-COV-2 main protease

El-Ashrey, Mohamed K. / Bakr, Riham O. / Fayed, Marwa A.A. / Refaey, Rana H. / Nissan, Yassin M.

Virology. 2022 May, v. 570

2022

Abstract	The challenge continues globally triggered by the absence of an approved antiviral drug against COVID-19 virus infection necessitating global concerted efforts of scientists. Nature still provides a renewable source for drugs used to solve many health problems. The aim of this work is to provide new candidates from natural origin to overcome COVID-19 pandemic. A virtual screening of the natural compounds database (47,645 compounds) using structure-based pharmacophore model and molecular docking simulations reported eight hits from natural origin against SARS-CoV-2 main proteinase (Mpro) enzyme. The successful candidates were of terpenoidal nature including taxusabietane, Isoadenolin A & C, Xerophilusin B, Excisanin H, Macrocalin B and ponicidin, phytoconstituents isolated from family Lamiaceae and sharing a common ent-kaurane nucleus, were found to be the most successful candidates. This study suggested that the diterpene nucleus has a clear positive contribution which can represent a new opportunity in the development of SARS-CoV-2 main protease inhibitors.
Keywords	COVID-19 infection ; Lamiaceae ; Severe acute respiratory syndrome coronavirus 2 ; antiviral agents ; chemical constituents of plants ; databases ; diterpenoids ; models ; pharmacology ; proteinases ; virology
Language	English
Dates of publication	2022-05
Size	p. 18-28.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2022.03.003
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Structure-Based Virtual Screening and Biochemical Validation to Discover a Potential Inhibitor of the SARS-CoV-2 Main Protease.

Gupta, Akshita / Rani, Chitra / Pant, Pradeep / Vijayan, Viswanathan / Vikram, Naval / Kaur, Punit / Singh, Tej Pal / Sharma, Sujata / Sharma, Pradeep

ACS omega

2020 Volume 5, Issue 51, Page(s) 33151–33161

Abstract: ... against this novel virus using already-approved drugs. The main protease (Mpro) of this virus plays ... approved drugs from the Drug Bank to find a possible inhibitor against Mpro using computational methods and ... further validating them with biochemical studies. The docking and molecular dynamics study revealed ...

Abstract	The recent pandemic caused by SARS-CoV-2 has led the world to a standstill, causing a medical and economic crisis worldwide. This crisis has triggered an urgent need to discover a possible treatment strategy against this novel virus using already-approved drugs. The main protease (Mpro) of this virus plays a critical role in cleaving the translated polypeptides that makes it a potential drug target against COVID-19. Taking advantage of the recently discovered three-dimensional structure of Mpro, we screened approved drugs from the Drug Bank to find a possible inhibitor against Mpro using computational methods and further validating them with biochemical studies. The docking and molecular dynamics study revealed that DB04983 (denufosol) showed the best glide docking score, -11.884 kcal/mol, and MM-PBSA binding free energy, -10.96 kcal/mol. Cobicistat, cangrelor (previous computational studies in our lab), and denufosol (current study) were tested for the in vitro inhibitory effects on Mpro. The IC
Language	English
Publishing date	2020-12-17
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.0c04808
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Article ; Online: The virtual screening application for searching potential antiviral agents to treat COVID-19 disease

Volodymyr V. Ivanov / Veronika R. Karpina / Svitlana S. Kovalenko / Ihor E. Kuznetsov / Thierry Langer / Louis J.R.M. Maes / Serhii M. Kovalenko / Larysa V. Evseeva

Журнал органічної та фармацевтичної хімії, Vol 18, Iss 2, Pp 3-

2020 Volume 15

Abstract: ... the coronavirus main protease using computer simulation tools. Results and discussion. COVID-19 coronavirus has ... structure of the virus main protease Mpro in the complex with various inhibitors (Protein Data Bank http://www.rcsb.org ... pdb, the structure code – 6LU7) the virtual screening and molecular docking of 100 known ...

Abstract	Aim. To provide a brief literature review regarding the structure of the human coronavirus SARS-CoV-2, the mechanism of its replication and the role of viral proteases in this process; to analyze the ability of the known antiviral agents and compounds synthesized de novo in order to bind and inhibit the coronavirus main protease using computer simulation tools. Results and discussion. COVID-19 coronavirus has become a worldwide challenge in recent months. Taking into account the rapid spread and severity of COVID-19 among a significant part of the population there is an urgent need to develop effective medicines and appropriate treatment protocols, which, unfortunately, are not yet available. Currently, the search for molecules with an acceptable toxicity profile that are able to inhibit and/or stop coronavirus SARS-CoV-2 replication in the human body is very relevant. In this study, the virtual screening and molecular docking of both antiviral agents known and new compounds synthesized have been performed based on the structure of the main protease Mpro of SARS-CoV-2. The regularities identified during our study can be useful for searching and developing new antiviral drugs to control COVID-19 and other coronavirus infections. The analysis of the results of calculations of physicochemical characteristics of antiviral agents, as well as the determination of their binding sites with the main viral protease Mpro gives an optimistic assessment of the possibility to develop new drugs based on the structures of the known antiviral drugs or their modified analogs. Experimental part. Based on recent studies of the crystal structure of the virus main protease Mpro in the complex with various inhibitors (Protein Data Bank http://www.rcsb.org/pdb, the structure code – 6LU7) the virtual screening and molecular docking of 100 known antiviral agents and 50 novel compounds synthesized were performed. The screening data for the in vitro antimalarial activity of the compounds synthesized were presented. The following binding ...
Keywords	coronavirus infection ; sars-cov-2 ; mpro protease ; 6lu7 ; molecular docking ; virtual screening ; antiviral activity ; оxadiazole ; quinazolin-5-ones ; triazolopyridine ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	National University of Pharmacy (Kharkiv, Ukraine)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Structure-Based Virtual Screening of a Natural Product Database to Identify Several Possible SARS-CoV-2 Main Protease Inhibitors

Ettayapuram Ramaprasad, Azhagiya Singam / La merrill, Michele / Durkin, Kathleen A. / Smith, Martyn T.

2020

Abstract: ... were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due ... known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted ... there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds ...

Abstract	A novel coronavirus (SARS-CoV-2) has been the cause of a recent pandemic of respiratory illness known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted in an enormous number of seriously ill patients requiring hospitalization. In the absence of an effective vaccine, there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds in foods and plants may be one source of anti-viral compounds. Here, natural product chemicals from the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBE<sub>DB</sub>) were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due to its importance in the replication of SARS-CoV-2. Molecular docking was used to screen the natural products against Mpro to identify potential candidates. The identified candidates were further filtered using molecular dynamics simulation investigation. Nine natural compounds were identified for experimental validation, with carlinoside and quercetin 3-o-sophoroside being the top candidates.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12143394.v1
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Structure-Based Virtual Screening of a Natural Product Database to Identify Several Possible SARS-CoV-2 Main Protease Inhibitors

Ettayapuram Ramaprasad, Azhagiya Singam / La merrill, Michele / Durkin, Kathleen A. / Smith, Martyn T.

2020

Abstract	A novel coronavirus (SARS-CoV-2) has been the cause of a recent pandemic of respiratory illness known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted in an enormous number of seriously ill patients requiring hospitalization. In the absence of an effective vaccine, there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds in foods and plants may be one source of anti-viral compounds. Here, natural product chemicals from the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBE<sub>DB</sub>) were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due to its importance in the replication of SARS-CoV-2. Molecular docking was used to screen the natural products against Mpro to identify potential candidates. The identified candidates were further filtered using molecular dynamics simulation investigation. Nine natural compounds were identified for experimental validation, with carlinoside and quercetin 3-o-sophoroside being the top candidates.
Keywords	covid19
Publisher	American Chemical Society (ACS)
Publishing country	us
Document type	Book ; Online
DOI	10.26434/chemrxiv.12143394
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Structure-Based Virtual Screening of a Natural Product Database to Identify Several Possible SARS-CoV-2 Main Protease Inhibitors

Azhagiya Singam Ettayapuram Ramaprasad / Michele La merrill / Kathleen A. Durkin / Martyn T. Smith

2020

Abstract: ... screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due ... known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted ... there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds ...

Abstract	A novel coronavirus (SARS-CoV-2) has been the cause of a recent pandemic of respiratory illness known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted in an enormous number of seriously ill patients requiring hospitalization. In the absence of an effective vaccine, there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds in foods and plants may be one source of anti-viral compounds. Here, natural product chemicals from the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBE DB ) were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due to its importance in the replication of SARS-CoV-2. Molecular docking was used to screen the natural products against Mpro to identify potential candidates. The identified candidates were further filtered using molecular dynamics simulation investigation. Nine natural compounds were identified for experimental validation, with carlinoside and quercetin 3-o-sophoroside being the top candidates.
Keywords	Computational Chemistry and Modeling ; Chemoinformatics - Computational Chemistry ; main protease ; coronavirus ; covid19
Subject code	540
Publishing date	2020-04-20T11:34:23Z
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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