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Article ; Online: Pinpointing top inhibitors for GSK3β from pool of indirubin derivatives using rigorous computational workflow and their validation using molecular dynamics (MD) simulations.

Pandya, Vamangi / Rao, Priyashi / Prajapati, Jignesh / Rawal, Rakesh M / Goswami, Dweipayan

2024 Volume 14, Issue 1, Page(s) 49

Abstract: Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, ... ...

Abstract	Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, there remains an unmet need for a rigorous, systematic analysis probing the theoretical inhibition dynamics of a comprehensive library of indirubin derivatives against GSK3β using advanced computational methodologies. Addressing this gap, this study embarked on an ambitious endeavor, leveraging indirubin-a renowned scaffold-as a template to curate a vast library of 1000 indirubin derivatives from PubChem. These were enriched with varied substitutions and modifications, identified via a structure similarity search with a Tanimoto similarity threshold of 85%. Harnessing a robust virtual screening workflow, we meticulously identified the top 10 contenders based on XP docking scores. Delving deeper, we gauged the binding free energy differentials (ΔGBind) of these hits, spotlighting the top three compounds that showcased unparalleled binding prowess. A comparative pharmacophore feature mapping with the reference inhibitor OH8, co-crystallized with GSK3β (PDB ID: 6Y9R), was undertaken. The binding dynamics of these elite compounds were further corroborated with 100 ns molecular dynamics simulations, underlining their stable and potent interactions with GSK3β. Remarkably, our findings unveil that these indirubin derivatives not only match but, in certain scenarios, surpass the binding affinity and specificity of OH8. By bridging this research chasm, our study amplifies the therapeutic promise of indirubin derivatives, positioning them as frontrunners in the quest for groundbreaking GSK3β inhibitors, potentially revolutionizing treatments for a myriad of ailments.
MeSH term(s)	Molecular Dynamics Simulation ; Glycogen Synthase Kinase 3 beta ; Workflow ; Indoles/pharmacology ; Molecular Docking Simulation
Chemical Substances	Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; indirubin (V86L8P74GI) ; Indoles
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50992-7
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Article: Patterns of concomitant use of

Galib, R / Dang, Poonam / Kumar, Vijay / Rana, Rakesh / Yadav, Pramod / Prajapati, P K

Ayu

2021 Volume 41, Issue 2, Page(s) 72–78

Abstract: Background: Majority of the population relies on traditional medicines for many of their health related problems. Particularly individuals with chronic illness like diabetes mellitus (DM) are more likely to simultaneously use herbal medicines. Many of ... ...

Abstract	Background: Majority of the population relies on traditional medicines for many of their health related problems. Particularly individuals with chronic illness like diabetes mellitus (DM) are more likely to simultaneously use herbal medicines. Many of such users believe that traditional medicines are natural and therefore safe, but this is a dangerous over simplification. Some herbal medicines may be associated with adverse effects, which include interactions with prescribed drugs. Information on such concomitant use of anti-diabetic drugs along with Aims and objectives: To survey the patterns of concomitant use of Ayurveda and conventional anti-diabetic drugs by diabetic patients attending an out-patient department of a tertiary care teaching hospital in New Delhi, India through a validated questionnaire. Materials and methods: This is a questionnaire-based survey, carried out after the approval of the Institutional Ethics Committee, subsequently registered at CTRI. A questionnaire to assess the pattern of concomitant use was developed; content was validated and pre-tested by a pilot study in 40 patients, further refined and used in the survey. The data was analyzed to evaluate the patterns of concomitant use of Ayurvedic and conventional anti-diabetic drugs. Results: About 95.9% of diabetic patients were taking herbo-mineral formulations concomitantly with conventional anti-diabetic drugs. Although 45.3% of diabetics were using Ayurveda interventions under the supervision of qualified AYUSH physicians, remaining involved in procuring the drugs over the counter (OTC) or from the local vendors. In majority of these instances, the use of Conclusion: The observations reveal that a majority of the diabetics (95.9%) were taking one or the other form of herbal preparations along with their conventional anti-diabetic drugs and about 44% among them were using these concomitantly. Thus, generating awareness on good practices of drug use seems to be essential.
Language	English
Publishing date	2021-10-23
Publishing country	India
Document type	Journal Article
ISSN	0974-8520
ISSN	0974-8520
DOI	10.4103/ayu.AYU_81_20
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Article ; Online: Unravelling the antifungal mode of action of curcumin by potential inhibition of CYP51B: A computational study validated in vitro on mucormycosis agent, Rhizopus oryzae.

Prajapati, Jignesh / Rao, Priyashi / Poojara, Lipi / Goswami, Dweipayan / Acharya, Dhaval / Patel, Saumya K / Rawal, Rakesh M

Archives of biochemistry and biophysics

2021 Volume 712, Page(s) 109048

Abstract: Like human, fungi too are known to share lot of structural similarities amongst their CYPs (Cytochrome P450 super family of enzymes) which allows antifungal 'azole' compounds to interact with CYPs of human. Clotrimazole, an 'azole' antifungal drug, is a ... ...

Abstract	Like human, fungi too are known to share lot of structural similarities amongst their CYPs (Cytochrome P450 super family of enzymes) which allows antifungal 'azole' compounds to interact with CYPs of human. Clotrimazole, an 'azole' antifungal drug, is a known inhibitor of fungal CYP named CYP51B. Curcumin, a phytochemical obtained from Curcuma longa has the ability to interact with several different human CYPs to induce inhibition. The sequence and the structural similarities amongst both human and fungal CYPs suggest a strong possibility for curcumin to interact with fungal CYP51B to behave like an antifungal agent. To test this hypothesis a study was designed involving mucormycosis agent, Rhizopus oryzae. The ability of curcumin to interact with fungal CYP51B was analysed computationally through molecular docking, MM-GBSA and Molecular Dynamics (MD) simulation assessment. Further, interaction profile for fungal CYP51B-curcumin was compared with human CYP3A4-curcumin, as there are published evidence describing curcumin as an inhibitor of human CYPs. Additionally, to validate in silico findings, an in vitro assay was performed to examine the antifungal potentials of curcumin on the R. oryzae. Conclusive results allow us to determine a plausible mode of action of curcumin to act as an antifungal against a mucormycosis agent.
MeSH term(s)	Amino Acid Sequence ; Antifungal Agents/metabolism ; Antifungal Agents/pharmacology ; Clotrimazole/metabolism ; Clotrimazole/pharmacology ; Curcumin/metabolism ; Curcumin/pharmacology ; Cytochrome P-450 Enzyme Inhibitors/metabolism ; Cytochrome P-450 Enzyme Inhibitors/pharmacology ; Cytochrome P-450 Enzyme System/metabolism ; Ergosterol/metabolism ; Fungal Proteins/antagonists & inhibitors ; Fungal Proteins/metabolism ; Humans ; Microbial Sensitivity Tests ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Phylogeny ; Protein Binding ; Rhizopus oryzae/drug effects
Chemical Substances	Antifungal Agents ; Cytochrome P-450 Enzyme Inhibitors ; Fungal Proteins ; Cytochrome P-450 Enzyme System (9035-51-2) ; Clotrimazole (G07GZ97H65) ; Curcumin (IT942ZTH98) ; Ergosterol (Z30RAY509F)
Language	English
Publishing date	2021-09-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2021.109048
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Article ; Online: PS-InSAR derived deformation study in the Kachchh, Western India

Rakesh K. Dumka / D. SuriBabu / Kapil Malik / Sandip Prajapati / P. Narain

Applied Computing and Geosciences, Vol 8, Iss , Pp 100041- (2020)

2020

Abstract: The accumulation of crustal strain towards the western part of India, especially in the Kachchh Rift basin, is making one of the most seismically active parts of the Indian plate. Several strong to major earthquakes, including the recent 2001 (M7.7) Bhuj ...

Abstract	The accumulation of crustal strain towards the western part of India, especially in the Kachchh Rift basin, is making one of the most seismically active parts of the Indian plate. Several strong to major earthquakes, including the recent 2001 (M7.7) Bhuj earthquake, were triggered in the Kachchh rift basin during the last two centuries. Therefore, in the present study, we have attempted to quantify crustal deformation towards the eastern part of mainland Kachchh using PSInSAR and GPS data from 2014 to 2019. The average LOS displacement of 4.3 mm/yr has been observed along the eastern segment of the Katrol Hill Fault (KHF). The deformation in this part can be correlated with the accumulation of strain along the hanging wall side of the south-dipping KHF. The accumulated strain is reflected in the form of seismic activity in this part and highlights the importance of the KHF zone for seismic hazard analysis. The PS-InSAR results are in good correlation with the GPS results of this part.
Keywords	PSInSAR ; GPS ; Deformation ; Kachchh ; Indian plate ; Geography. Anthropology. Recreation ; G ; Geology ; QE1-996.5 ; Electronic computers. Computer science ; QA75.5-76.95
Subject code	550
Language	English
Publishing date	2020-12-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article: Analytical profile of

Singh, Thakur Rakesh / Fanasiya, Krishna M / Bedarkar, Prashant / Patgiri, B J / Prajapati, P K

Ayu

2018 Volume 38, Issue 3-4, Page(s) 158–164

Abstract: Background: Kukkutanda: Aims and objectives: To develop analytical profile of KTB prepared by two different methods.: Materials and methods: Two samples of KTB were prepared. Sample KTB-A was prepared by : Observations and results: 22.75% and ... ...

Abstract	Background: Kukkutanda Aims and objectives: To develop analytical profile of KTB prepared by two different methods. Materials and methods: Two samples of KTB were prepared. Sample KTB-A was prepared by Observations and results: 22.75% and 41.16% of Calcium was detected in samples KTB-A and KTB-B, respectively. 0.29% and 0.15% of magnesium was found in samples KTB-A and KTB-B respectively. Both the samples of Conclusions: Minimum four
Language	English
Publishing date	2018-09-11
Publishing country	India
Document type	Journal Article
ISSN	0974-8520
ISSN	0974-8520
DOI	10.4103/ayu.AYU_209_17
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Article: Perceiving SARS-CoV-2 Mpro and PLpro dual inhibitors from pool of recognized antiviral compounds of endophytic microbes: an in silico simulation study.

Prajapati, Jignesh / Patel, Rohit / Rao, Priyashi / Saraf, Meenu / Rawal, Rakesh / Goswami, Dweipayan

Structural chemistry

2022 Volume 33, Issue 5, Page(s) 1619–1643

Abstract: Coronavirus disease 2019 (COVID-19) persists and shook the global population where the endgame to this pandemic is brought on by developing vaccines in record-breaking time. Nevertheless, these vaccines are far from perfect where their efficiency ranges ... ...

Abstract	Coronavirus disease 2019 (COVID-19) persists and shook the global population where the endgame to this pandemic is brought on by developing vaccines in record-breaking time. Nevertheless, these vaccines are far from perfect where their efficiency ranges from 65 to 90%; therefore, vaccines are not the one only solution to overcome this situation, and apart from administration of vaccines, the scientific community is at quest for finding alternative solutions to incumber SARS-CoV-2 infection. In this study, our research group is keen on identifying a bioactive molecule that is independent in its mode of action from existing vaccines which can potentially target the SARS-CoV-2 virus replicative efficacy. Papain-like protease (PLpro) and main protease (Mpro) are the most lucrative targets of COVIDs against which the drugs can be developed, as these proteases play a vital role in the replication and development of viral particles. Researchers have modelled a compound such as GRL0617 and X77 as an inhibitor of Mpro and PLpro, respectively, but use of these compounds has several limitations on hosts like toxicity and solubility. Under the current study by deploying rigorous computational assessments, pool of microbial secondary metabolites was screened and handpicked to search a structural or functional analogue of GRL0617 and X77, with an idea to identify a compound that can serve as dual inhibitor for both PLpro and Mpro. From the manually curated database of known antiviral compounds from fungal origin, we found cytonic acids A and B to potentially serve as dual inhibitor of PLpro and Mpro.
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2018832-8
ISSN	1572-9001 ; 1040-0400
ISSN (online)	1572-9001
ISSN	1040-0400
DOI	10.1007/s11224-022-01932-0
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Article ; Online: Molecular Chaperones' Potential against Defective Proteostasis of Amyotrophic Lateral Sclerosis.

Kinger, Sumit / Dubey, Ankur Rakesh / Kumar, Prashant / Jagtap, Yuvraj Anandrao / Choudhary, Akash / Kumar, Amit / Prajapati, Vijay Kumar / Dhiman, Rohan / Mishra, Amit

Cells

2023 Volume 12, Issue 9

Abstract: Amyotrophic lateral sclerosis (ALS) is a neuronal degenerative condition identified via a build-up of mutant aberrantly folded proteins. The native folding of polypeptides is mediated by molecular chaperones, preventing their pathogenic aggregation. The ... ...

Abstract	Amyotrophic lateral sclerosis (ALS) is a neuronal degenerative condition identified via a build-up of mutant aberrantly folded proteins. The native folding of polypeptides is mediated by molecular chaperones, preventing their pathogenic aggregation. The mutant protein expression in ALS is linked with the entrapment and depletion of chaperone capacity. The lack of a thorough understanding of chaperones' involvement in ALS pathogenesis presents a significant challenge in its treatment. Here, we review how the accumulation of the ALS-linked mutant FUS, TDP-43, SOD1, and C9orf72 proteins damage cellular homeostasis mechanisms leading to neuronal loss. Further, we discuss how the HSP70 and DNAJ family co-chaperones can act as potential targets for reducing misfolded protein accumulation in ALS. Moreover, small HSPB1 and HSPB8 chaperones can facilitate neuroprotection and prevent stress-associated misfolded protein apoptosis. Designing therapeutic strategies by pharmacologically enhancing cellular chaperone capacity to reduce mutant protein proteotoxic effects on ALS pathomechanisms can be a considerable advancement. Chaperones, apart from directly interacting with misfolded proteins for protein quality control, can also filter their toxicity by initiating strong stress-response pathways, modulating transcriptional expression profiles, and promoting anti-apoptotic functions. Overall, these properties of chaperones make them an attractive target for gaining fundamental insights into misfolded protein disorders and designing more effective therapies against ALS.
MeSH term(s)	Humans ; Amyotrophic Lateral Sclerosis/metabolism ; Proteostasis ; Molecular Chaperones/metabolism ; HSP40 Heat-Shock Proteins ; Mutant Proteins/metabolism
Chemical Substances	Molecular Chaperones ; HSP40 Heat-Shock Proteins ; Mutant Proteins
Language	English
Publishing date	2023-05-02
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12091302
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Article ; Online: Formulation, optimization and evaluation of sustained release microsphere of ketoprofen.

Prajapati, Chirag V / Patel, Rakesh P / Prajapati, Bupendra G

Journal of pharmacy & bioallied sciences

2012 Volume 4, Issue Suppl 1, Page(s) S101–3

Abstract: The objective of this study is to formulate ketoprofen loaded microspheres of Acrycoat S100 by an o/w emulsion solvent evaporation method. It potently inhibits the enzyme cyclooxygenase resulting in prostaglandin synthesis inhibition. Ketoprofen causes ... ...

Abstract	The objective of this study is to formulate ketoprofen loaded microspheres of Acrycoat S100 by an o/w emulsion solvent evaporation method. It potently inhibits the enzyme cyclooxygenase resulting in prostaglandin synthesis inhibition. Ketoprofen causes an irritation in the gastrointestinal mucous membrane and possesses a bitter taste and aftertaste. The half-life in plasma is about 1-2hrs. This makes ketoprofen a very good candidate for the formulation of controlled release dosage forms. Ketoprofen microspheres help to protect the gastric mucous membrane from drug irritation and to mask its taste. The prepared microspheres were evaluated for micromeritic properties, particle size, effect of surfactant concentration, percentage yield, incorporation efficiency, drug polymer compatibility (IR and DSC study), scanning electron microscopy and in vitro drug release. The microspheres produced exhibited good encapsulation efficiencies and micromeritic properties. Encapsulation efficiency of microsphere is around 78%. The mean diameters of microspheres were found in required micrometer range. The results of optimized formulations showed a narrow size distribution and smooth surface. The DSC and the FTIR analysis showed the absence of any potent incompatibility between the drug and the polymer. In-vitro release showed 86.4% drug release after 12 hours. Results of present study suggest that Acrycoat S100 loaded microsphere of ketoprofen can be successfully designed to develop sustained drug delivery system. The solvent evaporation method is a suitable technique for the preparation of Acrycoat S100 microspheres for controlling the release of Ketoprofen for a prolonged duration.
Language	English
Publishing date	2012-08-23
Publishing country	India
Document type	Journal Article
ZDB-ID	2573569-X
ISSN	0975-7406 ; 0975-7406
ISSN (online)	0975-7406
ISSN	0975-7406
DOI	10.4103/0975-7406.94156
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Article ; Online: Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation.

Patel, Rohit / Prajapati, Jignesh / Rao, Priyashi / Rawal, Rakesh M / Saraf, Meenu / Goswami, Dweipayan

Molecular diversity

2021 Volume 26, Issue 4, Page(s) 2189–2209

Abstract: Papain-like protease (nsp-3; non-structural protein) of novel corona virus is an ideal target for developing drugs as it plays multiple important functions for viral growth and replication. For instance, role of nsp-3 has been recognized in cleavage of ... ...

Abstract	Papain-like protease (nsp-3; non-structural protein) of novel corona virus is an ideal target for developing drugs as it plays multiple important functions for viral growth and replication. For instance, role of nsp-3 has been recognized in cleavage of viral polyprotein; furthermore, in infected host it weakens the immune system via downregulating the production of type I interferon. This downregulation is promoted by removal of ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon-responsive factor 3 (IRF3) protein. Among known inhibitors of SARS-CoV-PLpro GRL0617 is by far the most effective inhibitor. As PLpro of SARS-CoV2 is having more than 80% similarity with SARS-CoV-PLpro, GRL0617 is reported to be effective even against SARS-CoV2. Owing to this similarity, certain key amino acids remain the same/conserved in both proteins. Among conserved amino acids Tyr268 for SARS-CoV2 and Tyr269 for SARS-CoV produce important hydrophobic interactions with aromatic rings of GRL0617. Here, in this study antibacterial compounds were collected from ZINC database, and they were filtered to select compounds that are having similar structural features as GRL0617. This filtered library of compound was then docked with SARS-CoV and CoV2-PLpro. Five hits were noted that were able to interact with Tyr268 (SARS-CoV2) and Tyr269 (SARS-CoV). Further, best hit 2-(2-((benzofuran-2-carboxamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid (ZINC44459905) was studied using molecular dynamic simulation where stability of protein-ligand complex as well as stability of produced interactions was noted.
MeSH term(s)	Amino Acids ; Aniline Compounds/pharmacology ; Anti-Bacterial Agents ; Benzamides/pharmacology ; COVID-19/drug therapy ; Coronavirus Papain-Like Proteases/antagonists & inhibitors ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Naphthalenes/pharmacology ; RNA, Viral ; SARS-CoV-2/drug effects ; Ubiquitins/chemistry ; Ubiquitins/metabolism
Chemical Substances	5-amino-2-methyl-N-((R)-1-(1-naphthyl)ethyl)benzamide ; Amino Acids ; Aniline Compounds ; Anti-Bacterial Agents ; Benzamides ; Naphthalenes ; RNA, Viral ; Ubiquitins ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
Language	English
Publishing date	2021-09-30
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/s11030-021-10325-0
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Article ; Online: ZYKR1, a novel, potent, and peripherally selective kappa opioid receptor agonist reduces visceral pain and pruritus in animal models.

Jain, Mukul R / Patel, Rakesh B / Prajapati, Kanaiyalal D / Vyas, Purvi / Bandyopadhyay, Debdutta / Prajapati, Vijay / Bahekar, Rajesh / Patel, Prakash N / Kawade, Harish M / Kokare, Dadasaheb M / Pawar, Vishwanath / Desai, Ranjit

European journal of pharmacology

2022 Volume 924, Page(s) 174961

Abstract: Opioid receptor agonists are effective analgesic agents. Central activation of the mu and/or kappa opioid receptors (KOR) is associated with CNS side effects, which limits their effectiveness. Recent studies indicated that peripherally restricted, ... ...

Abstract	Opioid receptor agonists are effective analgesic agents. Central activation of the mu and/or kappa opioid receptors (KOR) is associated with CNS side effects, which limits their effectiveness. Recent studies indicated that peripherally restricted, selective KOR agonists were potent analgesics and devoid of CNS-related side effects. To confirm this hypothesis, we designed a novel, potent, and peripherally restricted KOR-selective agonist, ZYKR1. The analgesic efficacy, brain penetration and safety of ZYKR1 were assessed in pre-clinical models. ZYKR1 showed KOR agonistic activity in the cAMP assay, with an EC
MeSH term(s)	Animals ; Male ; Mice ; Rats ; Analgesics/pharmacology ; Analgesics, Opioid/pharmacology ; Analgesics, Opioid/therapeutic use ; Models, Animal ; Pruritus ; Receptors, Opioid, kappa/agonists ; Receptors, Opioid, mu/metabolism ; Visceral Pain/drug therapy
Chemical Substances	Analgesics ; Analgesics, Opioid ; Receptors, Opioid, kappa ; Receptors, Opioid, mu ; ZYKR1
Language	English
Publishing date	2022-04-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80121-5
ISSN	1879-0712 ; 0014-2999
ISSN (online)	1879-0712
ISSN	0014-2999
DOI	10.1016/j.ejphar.2022.174961
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