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Article ; Online: Evaluation of the inhibitory potential of Valproic acid against histone deacetylase of

Prasanna, Pragya / Joshi, Tanuja / Pant, Manish / Pundir, Hemlata / Chandra, Subhash

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 12, Page(s) 5447–5464

Abstract: Valproic acid (VA) is a proven inhibitor of human histone deacetylases (HDACs). The homogenous HDAC has been associated with all major human parasitic pathogens and hence, it has been considered an attractive drug target for anti-leishmanial therapy. To ... ...

Abstract	Valproic acid (VA) is a proven inhibitor of human histone deacetylases (HDACs). The homogenous HDAC has been associated with all major human parasitic pathogens and hence, it has been considered an attractive drug target for anti-leishmanial therapy. To assist in drug design endeavors for HDACs, an in-
MeSH term(s)	Humans ; Leishmania donovani ; Valproic Acid/pharmacology ; Histone Deacetylases ; Ligands ; Antiprotozoal Agents/pharmacology ; Antiprotozoal Agents/chemistry
Chemical Substances	Valproic Acid (614OI1Z5WI) ; Histone Deacetylases (EC 3.5.1.98) ; Ligands ; Antiprotozoal Agents
Language	English
Publishing date	2022-06-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2087103
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Article ; Online: Deep-learning based repurposing of FDA-approved drugs against

Joshi, Tanuja / Pundir, Hemlata / Chandra, Subhash

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 18, Page(s) 8420–8436

Abstract: ... Candida ... ...

Abstract	Candida albicans
MeSH term(s)	Aminopyridines ; Antifungal Agents/chemistry ; Antifungal Agents/pharmacology ; Benzodioxoles ; Candida albicans ; Candidiasis/drug therapy ; Cyclopropanes ; Deep Learning ; Drug Approval ; Drug Repositioning ; Folic Acid Antagonists/pharmacology ; Folic Acid Antagonists/therapeutic use ; Humans ; Lactams, Macrocyclic ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Proline/analogs & derivatives ; Rifampin/pharmacology ; Rifampin/therapeutic use ; Sulfonamides ; Tetrahydrofolate Dehydrogenase/metabolism ; United States ; United States Food and Drug Administration
Chemical Substances	Aminopyridines ; Antifungal Agents ; Benzodioxoles ; Cyclopropanes ; Folic Acid Antagonists ; Lactams, Macrocyclic ; Sulfonamides ; Proline (9DLQ4CIU6V) ; Tetrahydrofolate Dehydrogenase (EC 1.5.1.3) ; lumacaftor (EGP8L81APK) ; paritaprevir (OU2YM37K86) ; Rifampin (VJT6J7R4TR)
Language	English
Publishing date	2021-04-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1911851
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Article ; Online: Identification of Berbamine, Oxyacanthine and Rutin from Berberis asiatica as anti-SARS-CoV-2 compounds: An in silico study.

Joshi, Tanuja / Bhat, Sunaullah / Pundir, Hemlata / Chandra, Subhash

Journal of molecular graphics & modelling

2021 Volume 109, Page(s) 108028

Abstract: Owing to the shortage of specific medicines, the global pandemic of COVID-19 caused by SARS-CoV-2 has been the greatest challenge for the science community. Researchers from all over the world developed some drugs which failed to completely suppress the ... ...

Abstract	Owing to the shortage of specific medicines, the global pandemic of COVID-19 caused by SARS-CoV-2 has been the greatest challenge for the science community. Researchers from all over the world developed some drugs which failed to completely suppress the contiguous disease. SARS-CoV-2 main protease (Mpro), an important component in viral pathogenesis, is considered as a prospective drug target to stop SARS-CoV-2 infection. Since identification of phytochemicals with anti-Mpro activity has been carried out to develop the potential drugs against SARS-CoV-2. Therefore, the present study was conducted to screen phytochemicals of Berberis asiatica for anti-SARS-CoV-2 activity. Through text mining, thirty phytochemicals were reported from B. asiatica, of which, three phytochemicals (Berbamine, Oxyacanthine, and Rutin) show high affinity with the SARS-CoV-2 Mpro and exhibited favorable intermolecular interactions with the catalytic residues (His41 and Cys145) and other essential residues. The molecular dynamics simulation showed that Mpro-phytochemical complexes are more stable, less fluctuating, more compact, and moderately extended than the Mpro-X77 (Reference) complex. The number of H-bonds and MMPBSA results also demonstrates that Berbamine, Oxyacanthine, and Rutin are potent Mpro inhibitors having free energy of -20.79, -33.35, and -31.12 kcal mol
MeSH term(s)	Benzylisoquinolines ; Berberis ; COVID-19 ; Humans ; Isoquinolines ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors ; Rutin ; SARS-CoV-2
Chemical Substances	Benzylisoquinolines ; Isoquinolines ; Protease Inhibitors ; oxyacanthine (5BD0KNF4AT) ; Rutin (5G06TVY3R7) ; berbamine (V5KM4XJ0WM)
Language	English
Publishing date	2021-10-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2021.108028
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Article ; Online: In silico

Joshi, Tanuja / Joshi, Tushar / Sharma, Priyanka / Pundir, Hemlata / Chandra, Subhash

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 13, Page(s) 4816–4834

Abstract: Isocitrate Lyase (ICL) is a crucial enzyme involved in the Glyoxylate pathway, essential for the virulence of several fungal pathogens ... ...

Abstract	Isocitrate Lyase (ICL) is a crucial enzyme involved in the Glyoxylate pathway, essential for the virulence of several fungal pathogens including
MeSH term(s)	Fungicides, Industrial/pharmacology ; Fusarium/metabolism ; Isocitrate Lyase/metabolism ; Melia azedarach/metabolism ; Molecular Docking Simulation ; Molecular Dynamics Simulation
Chemical Substances	Fungicides, Industrial ; Isocitrate Lyase (EC 4.1.3.1)
Language	English
Publishing date	2020-06-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1780941
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Article ; Online: Identification of essential oil phytocompounds as natural inhibitors of Odorant-binding protein to prevent malaria through

Pundir, Hemlata / Pant, Manish / Joshi, Tanuja / Bhat, Sunaullah / Pathak, Ramanand / Bajpai, Atal Bihari / Chandra, Subhash / Tamta, Sushma

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 17, Page(s) 8323–8333

Abstract: Malaria predominantly affects millions annually in the African and Asian tropical and subtropical countries. With no effective vaccine, malaria prevention is exclusively dependent on preventing human-vector interaction. ...

Abstract	Malaria predominantly affects millions annually in the African and Asian tropical and subtropical countries. With no effective vaccine, malaria prevention is exclusively dependent on preventing human-vector interaction.
Language	English
Publishing date	2022-10-10
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2132419
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Article ; Online: Identification of SARS-CoV-2 RNA dependent RNA polymerase inhibitors using pharmacophore modelling, molecular docking and molecular dynamics simulation approaches.

Pundir, Hemlata / Joshi, Tanuja / Pant, Manish / Bhat, Sunaullah / Pandey, Jyoti / Chandra, Subhash / Tamta, Sushma

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 24, Page(s) 13366–13377

Abstract: The RNA-dependent RNA polymerase (RdRp) is one of the crucial enzymes in severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) catalysing the replication of RNA, therefore acts as a potential target for antiviral drug design. The fixation of a ... ...

Abstract	The RNA-dependent RNA polymerase (RdRp) is one of the crucial enzymes in severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) catalysing the replication of RNA, therefore acts as a potential target for antiviral drug design. The fixation of a ligand in the active site of RdRp may alter the SARS-CoV-2 life cycle. Present work aimed at identifying novel inhibitors of the SARS-CoV-2 RdRp enzyme by performing pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation (MDS). Initially, the pharmacophore model of SARS-CoV-2 RdRp was constructed and the resulting model was used to screen compounds from ChEMBL, ZINC and PubChem databases. During the investigation, 180 compounds were screened using the above model and subjected to molecular docking with RdRp. Two compounds viz. ChEMBL1276156 and PubChem135548348 showed a strong binding affinity with RdRp than its standard inhibitor, Remdesivir. Toxicity prediction of these two compounds reveals their non-toxic nature. These compounds were further subjected to MDS for 100 ns to check their stability after binding with RdRp. The MDS of RdRp-ChEMBL1276156 and RdRp-PubChem135548348 complexes show enhanced stability in comparison to the RdRp-Remdesivir complex. The average interaction energy calculated after 100 ns of MDS was -146.56 and -172.68 KJ mol
MeSH term(s)	Humans ; Molecular Docking Simulation ; COVID-19 ; Molecular Dynamics Simulation ; Pharmacophore ; RNA, Viral ; SARS-CoV-2 ; RNA-Dependent RNA Polymerase ; Antiviral Agents/pharmacology
Chemical Substances	RNA, Viral ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Antiviral Agents
Language	English
Publishing date	2021-10-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1987329
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Article ; Online: Molecular basis for the repurposing of histamine H2-receptor antagonist to treat COVID-19.

Ishola, Ahmed A / Joshi, Tanuja / Abdulai, Suliat I / Tijjani, Habibu / Pundir, Hemlata / Chandra, Subhash

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 13, Page(s) 5785–5802

Abstract: With the world threatened by a second surge in the number of Coronavirus cases, there is an urgent need for the development of effective treatment for the novel coronavirus (COVID-19). Recently, global attention has turned to preliminary reports on the ... ...

Abstract	With the world threatened by a second surge in the number of Coronavirus cases, there is an urgent need for the development of effective treatment for the novel coronavirus (COVID-19). Recently, global attention has turned to preliminary reports on the promising anti-COVID-19 effect of histamine H2-receptor antagonists (H2RAs), most especially Famotidine. Therefore, this study was designed to exploit a possible molecular basis for the efficacy of H2RAs against coronavirus. Molecular docking was performed between four H2RAs, Cimetidine, Famotidine, Nizatidine, Ranitidine, and three non-structural proteins viz. NSP3, NSP7/8 complex, and NSP9. Thereafter, a 100 ns molecular dynamics simulation was carried out with the most outstanding ligands to determine the stability. Thereafter, Famotidine and Cimetidine were subjected to gene target prediction analysis using HitPickV2 and eXpression2Kinases server to determine the possible network of genes associated with their anti-COVID activities. Results obtained from molecular docking showed the superiority of Famotidine and Cimetidine compared to other H2RAs with a higher binding affinity to all selected targets. Molecular dynamic simulation and MMPBSA results revealed that Famotidine as well as Cimetidine bind to non-structural proteins more efficiently with high stability over 100 ns. Results obtained suggest that Famotidine and Cimetidine could be a viable option to treat COVID-19 with a mechanism of action that involves the inhibition of viral replication through the inhibition of non-structural proteins. Therefore, Famotidineand Cimetidine qualify for further study as a potential treatment for COVID-19.
MeSH term(s)	Cimetidine/pharmacology ; Famotidine/pharmacology ; Histamine ; Histamine H2 Antagonists/pharmacology ; Humans ; Molecular Docking Simulation ; COVID-19 Drug Treatment
Chemical Substances	Histamine H2 Antagonists ; Famotidine (5QZO15J2Z8) ; Cimetidine (80061L1WGD) ; Histamine (820484N8I3)
Language	English
Publishing date	2021-01-25
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1873191
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Article ; Online: Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease.

Joshi, Tanuja / Joshi, Tushar / Pundir, Hemlata / Sharma, Priyanka / Mathpal, Shalini / Chandra, Subhash

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 17, Page(s) 6728–6746

Abstract: The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are ... ...

Abstract	The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are available to combat COVID-19. Therefore, the whole world is looking for new drug candidates that can treat the COVID-19. In this study, we conducted a virtual screening of natural compounds using a deep-learning method. A deep-learning algorithm was used for the predictive modeling of a CHEMBL3927 dataset of inhibitors of Main protease (Mpro). Several predictive models were developed and evaluated based on R
MeSH term(s)	COVID-19 ; Deep Learning ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Peptide Hydrolases ; Protease Inhibitors/pharmacology ; SARS-CoV-2
Chemical Substances	Protease Inhibitors ; Peptide Hydrolases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2020-08-05
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1802341
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Article ; Online: Using Chou's 5-steps rule to study pharmacophore-based virtual screening of SARS-CoV-2 Mpro inhibitors.

Pundir, Hemlata / Joshi, Tanuja / Joshi, Tushar / Sharma, Priyanka / Mathpal, Shalini / Chandra, Subhash / Tamta, Sushma

Molecular diversity

2020 Volume 25, Issue 3, Page(s) 1731–1744

Abstract: Recently emerged SARS-CoV-2 is the cause of the ongoing outbreak of COVID-19. It is responsible for the deaths of millions of people and has caused global economic and social disruption. The numbers of COVID-19 cases are increasing exponentially across ... ...

Abstract	Recently emerged SARS-CoV-2 is the cause of the ongoing outbreak of COVID-19. It is responsible for the deaths of millions of people and has caused global economic and social disruption. The numbers of COVID-19 cases are increasing exponentially across the world. Control of this pandemic disease is challenging because there is no effective drug or vaccine available against this virus and this situation demands an urgent need for the development of anti-SARS-CoV-2 potential medicines. In this regard, the main protease (Mpro) has emerged as an essential drug target as it plays a vital role in virus replication and transcription. In this research, we have identified two novel potent inhibitors of the Mpro (PubChem3408741 and PubChem4167619) from PubChem database by pharmacophore-based high-throughput virtual screening. The molecular docking, toxicity, and pharmacophore analysis indicate that these compounds may act as potential anti-viral candidates. The molecular dynamic simulation along with the binding free energy calculation by MMPBSA showed that these compounds bind to Mpro enzyme with high stability over 50 ns. Our results showed that two compounds: PubChem3408741 and PubChem4167619 had the binding free energy of - 94.02 kJ mol
MeSH term(s)	Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Drug Evaluation, Preclinical ; Molecular Docking Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Protease Inhibitors/pharmacology ; Protein Conformation ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Thermodynamics ; User-Computer Interface
Chemical Substances	Protease Inhibitors ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-10-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-020-10148-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 4946: Show issues

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Article ; Online: A dynamic simulation study of FDA drug from zinc database against COVID-19 main protease receptor.

Mathpal, Shalini / Joshi, Tushar / Sharma, Priyanka / Joshi, Tanuja / Pundir, Hemlata / Pande, Veena / Chandra, Subhash

Journal of biomolecular structure & dynamics

2020 Volume 40, Issue 3, Page(s) 1084–1100

Abstract: The sudden outbreak of COVID-19 has been responsible for several deaths across the globe. Due to its high contagious nature, it spreads from one human to another very quickly. Now it becomes a global public health threat with no approved treatments. In ... ...

Abstract	The sudden outbreak of COVID-19 has been responsible for several deaths across the globe. Due to its high contagious nature, it spreads from one human to another very quickly. Now it becomes a global public health threat with no approved treatments. In silico techniques can accelerate the drug development process. Our research aimed to identify the novel drugs for inhibition of Main protease (Mpro) enzyme of COVID-19 by performing in silico approach. In this context, a library consisting of 3180 FDA-approved drugs from 'the ZINC database' was used to identify novel drug candidates against 'the Mpro' of SARS-CoV-2. Initially, the top 10 drugs out of 3180 drugs were selected by molecular docking according to their binding score. Among 10 selected drugs; seven drugs that showed binding with Mpro enzyme residue Glu166 were subjected to100 ns Molecular dynamics (MD) simulation. Out of seven compounds, four namely, ZINC03831201, ZINC08101052, ZINC01482077, and ZINC03830817 were found significant based on MD simulation results. Furthermore, RMSD, RMSF, RG, SASA, PCA, MMPBSA (for last 40 ns) were calculated for the 100 ns trajectory period. Currently, the world needs potent drugs in a short period and this work suggests that these four drugs could be used as novel drugs against COVID-19 and it also provides new lead compounds for further in vitro, in vivo, and ongoing clinical studies against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	COVID-19 ; Humans ; Molecular Docking Simulation ; Peptide Hydrolases ; Pharmaceutical Preparations ; SARS-CoV-2 ; Zinc
Chemical Substances	Pharmaceutical Preparations ; Peptide Hydrolases (EC 3.4.-) ; Zinc (J41CSQ7QDS)
Keywords	covid19
Language	English
Publishing date	2020-09-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1821785
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