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Article ; Online: Current Drugs and their Therapeutic Targets for Hypoxia-inducible Factors in Cancer.

Joshi, Esha / Pandya, Medha / Desai, Urja

2023 Volume 24, Issue 6, Page(s) 447–464

Abstract: Hypoxia, a prevalent characteristic of both solid and liquid malignancies, is found to regulate how genes are expressed in a way that promotes cellular adaptability and survival. Metastasis is controlled by hypoxia-inducible factors (HIFs). HIFs are ... ...

Abstract	Hypoxia, a prevalent characteristic of both solid and liquid malignancies, is found to regulate how genes are expressed in a way that promotes cellular adaptability and survival. Metastasis is controlled by hypoxia-inducible factors (HIFs). HIFs are dimeric protein molecules made up of an oxygen (O
MeSH term(s)	Humans ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; Basic Helix-Loop-Helix Transcription Factors/therapeutic use ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/pathology ; Hypoxia/drug therapy ; Hypoxia/genetics ; Oxygen
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Oxygen (S88TT14065)
Language	English
Publishing date	2023-06-01
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	2045662-1
ISSN	1875-5550 ; 1389-2037
ISSN (online)	1875-5550
ISSN	1389-2037
DOI	10.2174/1389203724666230601092245
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Article ; Online: β cell acetate production and release are negligible.

Xu, Kai / Nnyamah, Chioma / Pandya, Nupur / Sweis, Nadia / Corona-Avila, Irene / Priyadarshini, Medha / Wicksteed, Barton / Layden, Brian T

Islets

2024 Volume 16, Issue 1, Page(s) 2339558

Abstract: Background: Studies suggest that short chain fatty acids (SCFAs), which are primarily produced from fermentation of fiber, regulate insulin secretion through free fatty acid receptors 2 and 3 (FFA2 and FFA3). As these are G-protein coupled receptors ( ... ...

Abstract	Background: Studies suggest that short chain fatty acids (SCFAs), which are primarily produced from fermentation of fiber, regulate insulin secretion through free fatty acid receptors 2 and 3 (FFA2 and FFA3). As these are G-protein coupled receptors (GPCRs), they have potential therapeutic value as targets for treating type 2 diabetes (T2D). The exact mechanism by which these receptors regulate insulin secretion and other aspects of pancreatic β cell function is unclear. It has been reported that glucose-dependent release of acetate from pancreatic β cells negatively regulates glucose stimulated insulin secretion. While these data raise the possibility of acetate's potential autocrine action on these receptors, these findings have not been independently confirmed, and multiple concerns exist with this observation, particularly the lack of specificity and precision of the acetate detection methodology used. Methods: Using Min6 cells and mouse islets, we assessed acetate and pyruvate production and secretion in response to different glucose concentrations, via liquid chromatography mass spectrometry. Results: Using Min6 cells and mouse islets, we showed that both intracellular pyruvate and acetate increased with high glucose conditions; however, intracellular acetate level increased only slightly and exclusively in Min6 cells but not in the islets. Further, extracellular acetate levels were not affected by the concentration of glucose in the incubation medium of either Min6 cells or islets. Conclusions: Our findings do not substantiate the glucose-dependent release of acetate from pancreatic β cells, and therefore, invalidate the possibility of an autocrine inhibitory effect on glucose stimulated insulin secretion.
MeSH term(s)	Animals ; Mice ; Insulin-Secreting Cells ; Diabetes Mellitus, Type 2 ; Acetates ; Glucose ; Pyruvic Acid
Chemical Substances	Acetates ; Glucose (IY9XDZ35W2) ; Pyruvic Acid (8558G7RUTR)
Language	English
Publishing date	2024-04-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2589489-4
ISSN	1938-2022 ; 1938-2022
ISSN (online)	1938-2022
ISSN	1938-2022
DOI	10.1080/19382014.2024.2339558
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Article ; Online: Molecular Landscape and Computational Screening of the Natural inhibitors against HPV16 E6 Oncoprotein.

Juneja, Tanzil / Pandya, Medha D / Shah, Sejal

Asian Pacific journal of cancer prevention : APJCP

2021 Volume 22, Issue 8, Page(s) 2461–2469

Abstract: Background: Human Papillomavirus (HPV) is a small, non-enveloped, icosahedral and double-stranded DNA virus with a genome of 8 kb, belonging to the papillomaviridae family. HPV has been associated with 99.7% cases of cervical squamous cell carcinoma ... ...

Abstract	Background: Human Papillomavirus (HPV) is a small, non-enveloped, icosahedral and double-stranded DNA virus with a genome of 8 kb, belonging to the papillomaviridae family. HPV has been associated with 99.7% cases of cervical squamous cell carcinoma worldwide. The HPV E6 protein is known as a potent oncogene and is closely allied with the events that result in the malignant transformation of virally infected cells. Objective: The present study aims to target plant derived anticancer molecules for HPV driven cancer using a computational approach. Methods: In this study, E6 oncoprotein was targeted by 101 plant-derived nutraceuticals using the molecular docking method. The multiple sequence analysis and phylogenetic analysis of low risk and high risk 28 HPV E6 proteins were performed. Results: Withanolide D, Ginkgetin, Theaflavin, Hesperidin, and Quercetin-3-gluconide were identified as the potential inhibitors of HPV 16 E6 protein. The zinc finger domain was identified on all variants of HPV E6 oncoprotein while high-risk HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV58, HPV68 and HPV73: probable risk HPV53 and low-risk HPV43 and HPV70 contain PDZ domain. Conclusion: The current study using bioinformatics analysis approaches reveals a promising platform for developing anti-cancerous competitive inhibitors targeting HPV. .
MeSH term(s)	Antineoplastic Agents/isolation & purification ; Antineoplastic Agents/pharmacology ; Computational Biology/methods ; DNA-Binding Proteins/antagonists & inhibitors ; Dietary Supplements/analysis ; High-Throughput Screening Assays/methods ; Humans ; Molecular Docking Simulation ; Oncogene Proteins, Viral/antagonists & inhibitors ; Phylogeny ; Phytochemicals/isolation & purification ; Phytochemicals/pharmacology
Chemical Substances	Antineoplastic Agents ; DNA-Binding Proteins ; E6 protein, Human papillomavirus type 18 ; Oncogene Proteins, Viral ; Phytochemicals
Language	English
Publishing date	2021-08-01
Publishing country	Thailand
Document type	Journal Article
ZDB-ID	2218955-5
ISSN	2476-762X ; 1513-7368
ISSN (online)	2476-762X
ISSN	1513-7368
DOI	10.31557/APJCP.2021.22.8.2461
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Article ; Online: Artificial Neural Network-Based Study Predicts GS-441524 as a Potential Inhibitor of SARS-CoV-2 Activator Protein Furin: a Polypharmacology Approach.

Dhanalakshmi, M / Das, Kajari / Pandya, Medha / Shah, Sejal / Gadnayak, Ayushman / Dave, Sushma / Das, Jayashankar

Applied biochemistry and biotechnology

2022 Volume 194, Issue 10, Page(s) 4511–4529

Abstract: Furin, a pro-protein convertase, plays a significant role as a biological scissor in bacterial, viral, and even mammalian substrates which in turn decides the fate of many viral and bacterial infections along with the numerous ailments caused by cancer, ... ...

Abstract	Furin, a pro-protein convertase, plays a significant role as a biological scissor in bacterial, viral, and even mammalian substrates which in turn decides the fate of many viral and bacterial infections along with the numerous ailments caused by cancer, diabetes, inflammations, and neurological disorders. In the wake of the current pandemic caused by the virus SARS-CoV-2, furin has become the center of attraction for researchers as the spike protein contains a polybasic furin cleavage site. In the present work, we have searched for novel inhibitors against this interesting human target from FDA-approved antiviral. To enhance the selection of new inhibitors, we employed Kohonen's artificial neural network-based self-organizing maps for ligand-based virtual screening. Promising results were obtained which can help in drug repurposing and network pharmacology studies can address the errors generated due to promiscuity/polypharmacology. We found 15 existing FDA antiviral drugs having the potential to inhibit furin. Among these, six compounds have targets on important human proteins (LDLR, FCGR1A, PCK1, TLR7, DNA, and PNP). The role of these 15 drugs inhibiting furin can be established by studying further on patients infected with number of viruses including SARS-CoV-2. Here we propose two promising candidate FDA drugs GS-441524 and Grazoprevir (MK-5172) for repurposing as inhibitors of furin. The best results were observed with GS-441524.
MeSH term(s)	Adenosine/analogs & derivatives ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Furin/genetics ; Humans ; Ligands ; Neural Networks, Computer ; Polypharmacology ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Toll-Like Receptor 7
Chemical Substances	Antiviral Agents ; Ligands ; Spike Glycoprotein, Coronavirus ; Toll-Like Receptor 7 ; spike protein, SARS-CoV-2 ; GS-441524 (1BQK176DT6) ; Furin (EC 3.4.21.75) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2022-05-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	392344-7
ISSN	1559-0291 ; 0273-2289
ISSN (online)	1559-0291
ISSN	0273-2289
DOI	10.1007/s12010-022-03928-2
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Article ; Online: Intestinal FFA2 promotes obesity by altering food intake in Western diet-fed mice.

Lednovich, Kristen R / Gough, Sophie / Priyadarshini, Medha / Pandya, Nupur / Nnyamah, Chioma / Xu, Kai / Wicksteed, Barton / Mishra, Sidharth / Jain, Shalini / Zapater, Joseph L / Cordoba-Chacon, Jose / Yadav, Hariom / Layden, Brian T

The Journal of endocrinology

2024 Volume 260, Issue 2

Abstract: Short-chain fatty acids (SCFAs) are key nutrients that play a diverse set of roles in physiological function, including regulating metabolic homeostasis. Generated through the fermentation of dietary fibers in the distal colon by the gut microbiome, ... ...

Abstract	Short-chain fatty acids (SCFAs) are key nutrients that play a diverse set of roles in physiological function, including regulating metabolic homeostasis. Generated through the fermentation of dietary fibers in the distal colon by the gut microbiome, SCFAs and their effects are partially mediated by their cognate receptors, including free fatty acid receptor 2 (FFA2). FFA2 is highly expressed in the intestinal epithelial cells, where its putative functions are controversial, with numerous in vivo studies relying on global knockout mouse models to characterize intestine-specific roles of the receptor. Here, we used the Villin-Cre mouse line to generate a novel, intestine-specific knockout mouse model for FFA2 (Vil-FFA2) to investigate receptor function within the intestine. Because dietary changes are known to affect the composition of the gut microbiome, and can thereby alter SCFA production, we performed an obesogenic challenge on male Vil-FFA2 mice and their littermate controls (FFA2-floxed, FFA2fl/fl) to identify physiological changes on a high-fat, high-sugar 'Western diet' (WD) compared to a low-fat control diet (CD). We found that the WD-fed Vil-FFA2 mice were transiently protected from the obesogenic effects of the WD and had lower fat mass and improved glucose homeostasis compared to the WD-fed FFA2fl/fl control group during the first half of the study. Additionally, major differences in respiratory exchange ratio and energy expenditure were observed in the WD-fed Vil-FFA2 mice, and food intake was found to be significantly reduced at multiple points in the study. Taken together, this study uncovers a novel role of intestinal FFA2 in mediating the development of obesity.
MeSH term(s)	Animals ; Male ; Mice ; Diet, Western/adverse effects ; Eating ; Fatty Acids, Volatile/metabolism ; Intestines/metabolism ; Mice, Inbred C57BL ; Mice, Knockout ; Obesity/genetics ; Obesity/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism
Chemical Substances	Fatty Acids, Volatile ; Ffar2 protein, mouse ; Receptors, G-Protein-Coupled
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	3028-4
ISSN	1479-6805 ; 0022-0795
ISSN (online)	1479-6805
ISSN	0022-0795
DOI	10.1530/JOE-23-0184
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Article ; Online: An inimitable proprotein convertase subtilisin kexin-9 (PCSK9) cleavage site VFAQ on Spike protein along with furin cleavage site makes SARS-CoV-2 unique

Pandya, Medha D / Shukla, Dhruvam / Shah, Sejal / Das, Kajari / Dave, Sushma / Das, Jayashankar

bioRxiv

Abstract: A novel coronavirus (2019-nCoV) or Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) that affects humans has been discovered in Wuhan, China, in 2019. Its genome has been sequenced, and the genetic data was quickly made public. We discovered ... ...

Abstract	A novel coronavirus (2019-nCoV) or Severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) that affects humans has been discovered in Wuhan, China, in 2019. Its genome has been sequenced, and the genetic data was quickly made public. We discovered a novel proprotein convertase subtilisin kexin-9 ( PCSK9) cleavage site in the Spike protein of the 2019-nCoV. The recent research also demonstrates that the previously found proprotein convertase 3 (PC3) or furin cleavage site, which was assumed to be unique, is already present in animal corona viruses. In this article, we suggest that the combination of the both proprotein convertase PC3 cleavage site and the PCSK9 site renders SARS-CoV-2 unique in terms of the pathogenicity, potential functional effects, and implications for the development of antiviral drugs.
Keywords	covid19
Language	English
Publishing date	2023-05-05
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.05.04.539453
Database	COVID19

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Article: Artificial Neural Network-Based Study Predicts GS-441524 as a Potential Inhibitor of SARS-CoV-2 Activator Protein Furin: a Polypharmacology Approach

Dhanalakshmi, M. / Das, Kajari / Pandya, Medha / Shah, Sejal / Gadnayak, Ayushman / Dave, Sushma / Das, Jayashankar

Applied biochemistry and biotechnology. 2022 Oct., v. 194, no. 10

2022

Abstract	Furin, a pro-protein convertase, plays a significant role as a biological scissor in bacterial, viral, and even mammalian substrates which in turn decides the fate of many viral and bacterial infections along with the numerous ailments caused by cancer, diabetes, inflammations, and neurological disorders. In the wake of the current pandemic caused by the virus SARS-CoV-2, furin has become the center of attraction for researchers as the spike protein contains a polybasic furin cleavage site. In the present work, we have searched for novel inhibitors against this interesting human target from FDA-approved antiviral. To enhance the selection of new inhibitors, we employed Kohonen’s artificial neural network-based self-organizing maps for ligand-based virtual screening. Promising results were obtained which can help in drug repurposing and network pharmacology studies can address the errors generated due to promiscuity/polypharmacology. We found 15 existing FDA antiviral drugs having the potential to inhibit furin. Among these, six compounds have targets on important human proteins (LDLR, FCGR1A, PCK1, TLR7, DNA, and PNP). The role of these 15 drugs inhibiting furin can be established by studying further on patients infected with number of viruses including SARS-CoV-2. Here we propose two promising candidate FDA drugs GS-441524 and Grazoprevir (MK-5172) for repurposing as inhibitors of furin. The best results were observed with GS-441524.
Keywords	DNA ; Severe acute respiratory syndrome coronavirus 2 ; biotechnology ; diabetes ; drugs ; humans ; neural networks ; pandemic ; pharmacology ; viruses
Language	English
Dates of publication	2022-10
Size	p. 4511-4529.
Publishing place	Springer US
Document type	Article
ZDB-ID	392344-7
ISSN	0273-2289
ISSN	0273-2289
DOI	10.1007/s12010-022-03928-2
Database	NAL-Catalogue (AGRICOLA)

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Article: Unravelling Vitamin B12 as a potential inhibitor against SARS-CoV-2: A computational approach.

Pandya, Medha / Shah, Sejal / M, Dhanalakshmi / Juneja, Tanzil / Patel, Amisha / Gadnayak, Ayushman / Dave, Sushma / Das, Kajari / Das, Jayashankar

Informatics in medicine unlocked

2022 Volume 30, Page(s) 100951

Abstract: The new severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is the etiological agent of Coronavirus disease 2019 (COVID-19), which becomes an eventual pandemic outbreak. Lack of proper therapeutic management has accelerated the researchers to ... ...

Abstract	The new severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is the etiological agent of Coronavirus disease 2019 (COVID-19), which becomes an eventual pandemic outbreak. Lack of proper therapeutic management has accelerated the researchers to repurpose existing drugs with known preclinical and toxicity profiles, which can easily enter Phase 3 or 4 or can be used directly in clinical settings. Vitamins are necessary nutrients for cell growth, function, and development. Furthermore, they play an important role in pathogen defence via cell-mediated responses and boost immunity. Using a computational approach, we intend to identify the probable inhibitory effect of all vitamins on the drug targets of COVID-19. The computational analysis demonstrated that vitamin B12 resulted in depicting suitable significant binding with furin, RNA dependent RNA polymerase (RdRp), Main proteases (Mpro), ORF3a and ORF7a and Vitamin D3 with spike protein and vitamin B9 with non structural protein 3 (NSP3). A detailed examination of vitamins suggests that vitamin B12 may be the component that reduces virulence by blocking furin which is responsible for entry of virus in the host cell. Details from the Molecular Dynamics (MD) simulation study aided in determining vitamin B12 as a possible furin inhibitor.
Language	English
Publishing date	2022-04-20
Publishing country	England
Document type	Journal Article
ISSN	2352-9148
ISSN	2352-9148
DOI	10.1016/j.imu.2022.100951
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Article ; Online: Unravelling Vitamin B12 as a potential inhibitor against SARS-CoV-2

Medha Pandya / Sejal Shah / Dhanalakshmi M / Tanzil Juneja / Amisha Patel / Ayushman Gadnayak / Sushma Dave / Kajari Das / Jayashankar Das

Informatics in Medicine Unlocked, Vol 30, Iss , Pp 100951- (2022)

A computational approach

2022

Abstract	The new severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) is the etiological agent of Coronavirus disease 2019 (COVID-19), which becomes an eventual pandemic outbreak. Lack of proper therapeutic management has accelerated the researchers to repurpose existing drugs with known preclinical and toxicity profiles, which can easily enter Phase 3 or 4 or can be used directly in clinical settings. Vitamins are necessary nutrients for cell growth, function, and development. Furthermore, they play an important role in pathogen defence via cell-mediated responses and boost immunity. Using a computational approach, we intend to identify the probable inhibitory effect of all vitamins on the drug targets of COVID-19. The computational analysis demonstrated that vitamin B12 resulted in depicting suitable significant binding with furin, RNA dependent RNA polymerase (RdRp), Main proteases (Mpro), ORF3a and ORF7a and Vitamin D3 with spike protein and vitamin B9 with non structural protein 3 (NSP3). A detailed examination of vitamins suggests that vitamin B12 may be the component that reduces virulence by blocking furin which is responsible for entry of virus in the host cell. Details from the Molecular Dynamics (MD) simulation study aided in determining vitamin B12 as a possible furin inhibitor.
Keywords	Vitamins ; Furin ; Vitamin B12 ; SARS-CoV-2 ; Drug targets ; Covid-19 ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein.

Manjunathan, Reji / Periyaswami, Vijayalakshmi / Mitra, Kartik / Rosita, Arokiaraj Sherlin / Pandya, Medha / Selvaraj, Jayaraman / Ravi, Lokesh / Devarajan, Nalini / Doble, Mukesh

BMC bioinformatics

2022 Volume 23, Issue 1, Page(s) 180

Abstract: Background: The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMPRSS2 as a therapeutic target for ...

Abstract	Background: The Transmembrane Serine Protease 2 (TMPRSS2) of human cell plays a significant role in proteolytic cleavage of SARS-Cov-2 coronavirus spike protein and subsequent priming to the receptor ACE2. Approaching TMPRSS2 as a therapeutic target for the inhibition of SARS-Cov-2 infection is highly promising. Hence, in the present study, we docked the binding efficacy of ten naturally available phyto compounds with known anti-viral potential with TMPRSS2. The aim is to identify the best phyto compound with a high functional affinity towards the active site of the TMPRSS2 with the aid of two different docking software. Molecular Dynamic Simulations were performed to analyse the conformational space of the binding pocket of the target protein with selected molecules. Results: Docking analysis using PyRx version 0.8 along with AutoDockVina reveals that among the screened phyto compounds, Genistein shows the maximum binding affinity towards the hydrophobic substrate-binding site of TMPRSS2 with three hydrogen bonds interaction ( - 7.5 kcal/mol). On the other hand, molecular docking analysis using Schrodinger identified Quercetin as the most potent phyto compound with a maximum binding affinity towards the hydrophilic catalytic site of TMPRSS2 ( - 7.847 kcal/mol) with three hydrogen bonds interaction. The molecular dynamics simulation reveals that the Quercetin-TMPRSS complex is stable until 50 ns and forms stable interaction with the protein ( - 22.37 kcal/mol of MM-PBSA binding free energy). Genistein creates a weak interaction with the loop residues and hence has an unstable binding and exits from the binding pocket. Conclusion: The compounds, Quercetin and Genistein, can inhibit the TMPRSS2 guided priming of the spike protein. The compounds could reduce the interaction of the host cell with the type I transmembrane glycoprotein to prevent the entry of the virus. The critical finding is that compared to Genistein, Quercetin exhibits higher binding affinity with the catalytic unit of TMPRSS2 and forms a stable complex with the target. Thus, enhancing our innate immunity by consuming foods rich in Quercetin and Genistein or developing a novel drug in the combination of Quercetin and Genistein could be the brilliant choices to prevent SARS-Cov-2 infection when we consider the present chaos associated with vaccines and anti-viral medicines.
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Genistein/pharmacology ; Humans ; Molecular Docking Simulation ; Quercetin/pharmacology ; SARS-CoV-2 ; Serine Endopeptidases ; Spike Glycoprotein, Coronavirus ; Virus Internalization
Chemical Substances	Antiviral Agents ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Quercetin (9IKM0I5T1E) ; Genistein (DH2M523P0H) ; Serine Endopeptidases (EC 3.4.21.-) ; TMPRSS2 protein, human (EC 3.4.21.-)
Language	English
Publishing date	2022-05-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-022-04724-9
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