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Article ; Online: Editorial: ESKAPE biofilm: challenges and solutions.

Tiwari, Vishvanath

Frontiers in cellular and infection microbiology

2023 Volume 13, Page(s) 1253439

Language	English
Publishing date	2023-08-01
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2619676-1
ISSN	2235-2988 ; 2235-2988
ISSN (online)	2235-2988
ISSN	2235-2988
DOI	10.3389/fcimb.2023.1253439
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Article ; Online: Pharmacophore screening, denovo designing, retrosynthetic analysis, and combinatorial synthesis of a novel lead VTRA1.1 against RecA protein of Acinetobacter baumannii.

Tiwari, Vishvanath

Chemical biology & drug design

2022 Volume 99, Issue 6, Page(s) 839–856

Abstract: Antibiotics and disinfectants resistance is acquired by activating RecA-mediated DNA repair, which maintains ROS-dependent DNA damage caused by the antimicrobial molecules. To increase the efficacy of different antimicrobials, an inhibitor can be ... ...

Abstract	Antibiotics and disinfectants resistance is acquired by activating RecA-mediated DNA repair, which maintains ROS-dependent DNA damage caused by the antimicrobial molecules. To increase the efficacy of different antimicrobials, an inhibitor can be developed against RecA protein. The present study aims to design a denovo inhibitor against RecA protein of Acinetobacter baumannii. Pharmacophore-based screening, molecular mechanics, molecular dynamics simulation (MDS), retrosynthetic analysis, and combinatorial synthesis were used to design lead VTRA1.1 against RecA of A. baumannii. Pharmacophore models (structure-based and ligand-based) were created, and a phase library of FDA-approved drugs was prepared. Screening of the phase library against these pharmacophore models selected thirteen lead molecules. These filtered leads were used for the denovo fragment-based design, which produced 253 combinations. These designed molecules were further analyzed for its interaction with active site of RecA that selected a hybrid VTRA1. Further, retrosynthetic analysis and combinatorial synthesis produced 1000 analogs of VTRA1 by more than 100 modifications. These analogs were used for XP docking, binding free energy calculation, and MDS analysis which finally select lead VTRA1.1 against RecA protein. Further, mutations at the interacting residues of RecA with VTRA1.1, alter the unfolding rate of RecA, which suggests the binding of VTRA1.1 to these residues may alter the stability of RecA. It is also found that VTRA1.1 had reduced interaction of RecA with LexA and ssDNA polydT, showing the lead's efficacy in controlling the SOS response. Further, it was also observed that VTRA1.1 does not contain any predicted human off-targets and no cytotoxicity to cell lines. As functional RecA is involved in antimicrobial resistance, denovo designed lead VTRA1.1 against RecA may be further developed as a significant combination for therapeutic uses against A. baumannii.
MeSH term(s)	Acinetobacter baumannii/metabolism ; Anti-Bacterial Agents/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; DNA Repair ; Humans ; Molecular Dynamics Simulation ; Rec A Recombinases/chemistry ; Rec A Recombinases/genetics ; Rec A Recombinases/metabolism
Chemical Substances	Anti-Bacterial Agents ; Bacterial Proteins ; Rec A Recombinases (EC 2.7.7.-)
Language	English
Publishing date	2022-03-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/cbdd.14037
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Article ; Online: Denovo designing, retro-combinatorial synthesis, and molecular dynamics analysis identify novel antiviral VTRM1.1 against RNA-dependent RNA polymerase of SARS CoV2 virus.

Tiwari, Vishvanath

International journal of biological macromolecules

2021 Volume 171, Page(s) 358–365

Abstract: A novel coronavirus disease (COVID-19) caused by SARS-CoV2 has now spread globally. Replication/transcription machinery of this virus consists of RNA-dependent RNA polymerase (nsp12 or RdRp) and its two cofactors nsp7 and nsp8 proteins. Hence, RdRp has ... ...

Abstract	A novel coronavirus disease (COVID-19) caused by SARS-CoV2 has now spread globally. Replication/transcription machinery of this virus consists of RNA-dependent RNA polymerase (nsp12 or RdRp) and its two cofactors nsp7 and nsp8 proteins. Hence, RdRp has emerged as a promising target to control COVID-19. In the present study, we are reporting a novel inhibitor VTRM1.1 against the RdRp protein of SARS CoV2. A series of antivirals were tested for binding to the catalytic residues of the active site of RdRp protein. In-silico screening, molecular mechanics, molecular dynamics simulation (MDS) analysis suggest ribavirin, and remdesivir have good interaction with the binding site of the RdRp protein as compared to other antiviral investigated. Hence, ribavirin and remdesivir were used for the denovo fragments based antiviral design. This design, along with docking and MDS analysis, identified a novel inhibitor VTRM1 that has better interaction with RdRp as compared to their parent molecules. Further, to produce a lead-like compound, retrosynthetic analysis, and combinatorial synthesis were performed, which produces 1000 analogs of VTRM1. These analogs were analysed by docking and MDS analysis that identified VTRM1.1 as a possible lead to inhibit RdRp protein. This lead has a good docking score, favourable binding energy and bind at catalytic residues of the active site of RdRp. The VTRM1.1 also interacts with RdRp in the presence of RNA primer and other cofactors. It was also seen that, VTRM1.1 do not have off-target in human. Therefore, the present study suggests a hybrid inhibitor VTRM1.1 for the RNA-dependent RNA polymerase of SARS CoV2 that may be useful to control infection caused by COVID-19.
Language	English
Publishing date	2021-01-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2020.12.223
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Article: Novel hybrid antiviral VTRRT-13V2.1 against SARS-CoV2 main protease: retro-combinatorial synthesis and molecular dynamics analysis.

Tiwari, Vishvanath

Heliyon

2020 Volume 6, Issue 10, Page(s) e05122

Abstract: The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease ( ... ...

Abstract	The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (M
Keywords	covid19
Language	English
Publishing date	2020-09-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2020.e05122
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Article ; Online: De novo

Tiwari, Vishvanath

Biology open

2020 Volume 9, Issue 10

Abstract: SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin ... ...

Abstract	SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/metabolism ; Cell Death/drug effects ; Combinatorial Chemistry Techniques ; Humans ; Molecular Docking Simulation ; Peptidyl-Dipeptidase A/chemistry ; Peptidyl-Dipeptidase A/metabolism ; Protein Binding/drug effects ; Protein Domains ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism ; Thermodynamics
Chemical Substances	Antiviral Agents ; Spike Glycoprotein, Coronavirus ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-10-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2632264-X
ISSN	2046-6390 ; 2046-6390
ISSN (online)	2046-6390
ISSN	2046-6390
DOI	10.1242/bio.054056
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Article ; Online: Molecular insight into the therapeutic potential of phytoconstituents targeting protein conformation and their expression.

Tiwari, Vishvanath

Phytomedicine : international journal of phytotherapy and phytopharmacology

2018 Volume 52, Page(s) 225–237

Abstract: Background: Native protein conformation is essential for the functional activity of the proteins and enzymes. Defects in conformation or alterations in expression of the proteins have been reported in various diseases.: Purpose: The aim of this study ...

Abstract	Background: Native protein conformation is essential for the functional activity of the proteins and enzymes. Defects in conformation or alterations in expression of the proteins have been reported in various diseases. Purpose: The aim of this study is to review the molecular insight into the therapeutic potential of phytoconstituents targeting protein conformations or expressions. Methods: Published literatures were searched in PubMed, Scopus, Web of Science; Article published till Dec 2017 were extracted. The literature was assessed from the Central University of Rajasthan, India. Present study evaluate article based on the role of active plant constituents on the conformation and expression of the different proteins. Results: Plant components play their role either at the molecular level or cellular level and exhibit antibacterial, antiviral, anti-neurodegenerative and other activities. Plant active compounds isolated from different plants may either stabilize or destabilize the conformation of proteins or alter expression level of the protein involved in these diseases, therefore, can play a significant role in preventing diseases caused by the alteration in these proteins. Conclusion: In the present article, we have reviewed the molecular mechanism of plant active compounds, their target proteins, methods of extraction and identification, and their biological significances. Therefore, a proper understanding of the effect of these herbal molecules on the concerned proteins may help to develop new herbal-based therapeutics for various diseases.
MeSH term(s)	Animals ; Humans ; Phytochemicals/pharmacology ; Phytotherapy ; Plants, Medicinal/chemistry ; Protein Conformation/drug effects
Chemical Substances	Phytochemicals
Keywords	covid19
Language	English
Publishing date	2018-09-26
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	1205240-1
ISSN	1618-095X ; 0944-7113
ISSN (online)	1618-095X
ISSN	0944-7113
DOI	10.1016/j.phymed.2018.09.214
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Article ; Online: Post-translational modification of ESKAPE pathogens as a potential target in drug discovery.

Tiwari, Vishvanath

Drug discovery today

2018 Volume 24, Issue 3, Page(s) 814–822

Abstract: ESKAPE pathogens are gaining clinical importance owing to their high pervasiveness and increasing resistance to various antimicrobials. These bacteria have several post-translational modifications (PTMs) that destabilize or divert host cell pathways. ... ...

Abstract	ESKAPE pathogens are gaining clinical importance owing to their high pervasiveness and increasing resistance to various antimicrobials. These bacteria have several post-translational modifications (PTMs) that destabilize or divert host cell pathways. Prevalent PTMs of ESKAPE pathogens include addition of chemical groups (acetylation, phosphorylation, methylation and hydroxylation) or complex molecules (AMPylation, ADP-ribosylation, glycosylation and isoprenylation), covalently linked small proteins [ubiquitylation, ubiquitin-like proteins (UBL) conjugation and small ubiquitin-like modifier (SUMO)] or modification of amino acid side-chains (eliminylation and deamidation). Therefore, the understanding of different bacterial PTMs and host proteins manipulated by these PTMs provides better insight into host-pathogen interaction and will also help to develop new antibacterial agents against ESKAPE pathogens.
MeSH term(s)	Animals ; Bacterial Physiological Phenomena ; Drug Discovery ; Drug Resistance, Bacterial ; Host-Pathogen Interactions ; Humans ; Protein Processing, Post-Translational
Language	English
Publishing date	2018-12-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1324988-5
ISSN	1878-5832 ; 1359-6446
ISSN (online)	1878-5832
ISSN	1359-6446
DOI	10.1016/j.drudis.2018.12.005
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Article: Novel hybrid antiviral VTRRT-13V2.1 against SARS-CoV2 main protease: retro-combinatorial synthesis and molecular dynamics analysis

Tiwari, Vishvanath

Heliyon. 2020 Oct., v. 6, no. 10

2020

Abstract: The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (Mᵖʳᵒ) emerged as a promising drug target because of its essential role in the ... ...

Abstract	The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (Mᵖʳᵒ) emerged as a promising drug target because of its essential role in the processing of polyproteins, which is translated from viral RNA. The present study reports a designed novel hybrid antiviral molecule (VTRRT-13.V2.1) against SARS-CoV2 main protease. A series of different combinations of hybrid antiviral were generated from nonspecific antiviral molecules currently used to control COVID-19. To enhance the specificity of the designed hybrid antiviral molecule, the core pocket region of the active site of Mᵖʳᵒ protein was targeted. In-silico screening, molecular mechanics, molecular dynamics simulation (MDS) analysis identified a hybrid VTRRT-13.V2 molecule. Retrosynthetic analysis and combinatorial synthesis generated 1000 analogs of VTRRT-13.V2 molecules. Docking, molecular mechanics, and MDS analysis selected VTRRT-13.V2.1 as a possible inhibitor for SARS-CoV2 main protease. Comparative analysis of all the results showed that VTRRT-13.V2.1 have the highest docking Glide score (-12.28 kcal/mol) and best binding energy (-52.23 kcal/mol) as compared to the other hybrid constructs such as VTRRT-13.V2 (-9.47 and -47.36 kcal/mol), VTRRT-13 (-8.9 and -47.55 kcal/mol), and current antiviral investigated. The mutational sensitivity screening showed that binding residues of Mᵖʳᵒ are not present in mutation hotspots. It was also observed that VTRRT-13.V2.1 does not have any human off-targets. SARS-CoV2 main protease is essential for the survival of this virus; hence, a designed novel hybrid antiviral molecule (VTRRT-13.V2.1) might be useful to control the infection of COVID-19 infection.
Keywords	COVID-19 infection ; RNA ; Severe acute respiratory syndrome coronavirus 2 ; active sites ; computer simulation ; drugs ; energy ; humans ; hybrids ; mechanics ; molecular dynamics ; morbidity ; mortality ; mutation ; polyproteins ; proteinases ; viruses
Language	English
Dates of publication	2020-10
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2020.e05122
Database	NAL-Catalogue (AGRICOLA)

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Article: De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2

Tiwari, Vishvanath

Abstract	SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a de novo designed novel hybrid antiviral 'VTAR-01' molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. In silico screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for de novo fragment-based antiviral design. De novo designing, docking and MDS analysis identified a 'VTAR' hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this i n s ilico designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #878889
Database	COVID19

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Book ; Online: De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2

Tiwari, Vishvanath

2020

Abstract	SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a de novo designed novel hybrid antiviral ‘VTAR-01’ molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. In silico screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for de novo fragment-based antiviral design. De novo designing, docking and MDS analysis identified a ‘VTAR’ hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this i n s ilico designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.
Keywords	RESEARCH ARTICLE ; covid19
Language	English
Publishing date	2020-10-15 00:59:38.0
Publisher	The Company of Biologists Ltd
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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