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Joshi BP, Bhandare VV, Vankawala M, Patel P, Patel R, Vyas B, Krishnamurty R. Friedelin, a novel inhibitor of CYP17A1 in prostate cancer from Cassia tora. J Biomol Struct Dyn 2023; 41:9695-9720. [PMID: 36373336 DOI: 10.1080/07391102.2022.2145497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022]
Abstract
In prostate cancer (PC), drugs targeting CYP17A1 have shown great success in regulating PC progression. However, successful drug molecules show adverse side effects and therapeutic resistance in PC. Therefore, we proposed to discover the potent phytochemical-based inhibitor against CYP17A1 using virtual screening. In this study, a phytochemicals library of ∼13800 molecules was selected to screen the best possible inhibitors against CYP17A1. A molecular modelling approach investigated detailed intermolecular interactions, their structural stability, and binding affinity. Further, in vitro and in vivo studies were performed to confirm the anticancer activity of identified potential inhibitor against CYP17A1. Friedelin from Cassia tora (CT) is identified as the best possible inhibitor from the screened library. MD simulation study reveals stable binding of Friedelin to conserved binding pocket of CYP17A1 with higher binding affinity than studied control, that is, Orteronel. Friedelin was tested on hormone-sensitive (22Rv1) and insensitive (DU145) cell lines and the IC50 value was found to be 72.025 and 81.766 µg/ml, respectively. CT extract showed a 25.28% IC50 value against 22Rv1, ∼92.6% increase in late Apoptosis/Necrosis, and three folds decrease in early apoptosis in treated cells compared to untreated cells. Further, animal studies show a marked decrease in prostate weight by 39.6% and prostate index by 36.5%, along with a reduction in serum PSA level by 71.7% and testosterone level by 92.4% compared to the testosterone group, which was further validated with histopathological studies. Thus, we propose Friedelin and CT extract as potential leads, which could be taken further for drug development in PC.[Figure: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Mahima Vankawala
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Prittesh Patel
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Surat, Gujarat, India
| | - Rajesh Patel
- Bioinformatics and Supercomputer Lab., Department of Biosciences (UGC-SAP-DRS-II & DST-FIST-I), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Bhavin Vyas
- Department of Pharmacology, Maliba Pharmacy College, Uka Tarsadia University, Tarsadi, Surat, Gujarat, India
| | - Ramar Krishnamurty
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Surat, Gujarat, India
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Patil VS, Harish DR, Charla R, Vetrivel U, Jalalpure SS, Bhandare VV, Deshpande SH, Hegde HV, Roy S. Structural insights into modeling of hepatitis B virus reverse transcriptase and identification of its inhibitors from potential medicinal plants of Western Ghats: an in silico and in vitro study. J Biomol Struct Dyn 2023:1-19. [PMID: 37811543 DOI: 10.1080/07391102.2023.2264400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The present study was proposed to model full-length HBV-RT and investigate the intermolecular interactions of known inhibitor and libraries of phytocompounds to probe the potential natural leads by in silico and in vitro studies. Homology modeling of RT was performed by Phyre2 and Modeller and virtual screening of ligands implemented through POAP pipeline. Molecular dynamics (MD) simulation (100 ns) and MM-GBSA calculations were performed using Schrodinger Desmond and Prime, respectively. Phytocompounds probable host protein targets gene set pathway enrichment and network analysis were executed by KEGG database and Cytoscape software. Prioritized plant extracts/enriched fraction LC-MS analysis was performed and along with pure compound, RT inhibitory activity, time-dependent HBsAg and HBeAg secretion, and intracellular HBV DNA, and pgRNA by qRT-PCR was performed in HepG2.2.15 cell line. Among the screened chemical library of 268 phytocompounds from 18 medicinal plants, 15 molecules from Terminalia chebula (6), Bidens pilosa (5), and Centella asiatica (4)) were identified as potential inhibitors of YMDD and RT1 motif of HBV-RT. MD simulation demonstrated stable interactions of 15 phytocompounds with HBV-RT, of which 1,2,3,4,6-Pentagalloyl Glucose (PGG) was identified as lead molecule. Out of 15 compounds, 11 were predicted to modulate 39 proteins and 15 molecular pathways associated with HBV infection. TCN and TCW (500 µg/mL) showed potent RT inhibition, decreased intracellular HBV DNA, and pgRNA, and time-dependent inhibition of HBsAg and HBeAg levels compared to PGG and Tenofovir Disoproxil Fumarate. We propose that the identified lead molecules from T. chebula as promising and cost-effective moieties for the management of HBV infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vishal S Patil
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi, Karnataka, India
| | | | - Rajitha Charla
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | - Umashankar Vetrivel
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Sunil S Jalalpure
- KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi, Karnataka, India
| | - Vishwambhar Vishnu Bhandare
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra, India
| | - Sanjay H Deshpande
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Regional Centre for Biotechnology, NCR-Biotech Science Cluster, Faridabad, India
| | - Harsha V Hegde
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | - Subarna Roy
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
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Patil PP, Kumar P, Khanal P, Patil VS, Darasaguppe HR, Bhandare VV, Bhatkande A, Shukla S, Joshi RK, Patil BM, Roy S. Computational and experimental pharmacology to decode the efficacy of Theobroma cacao L. against doxorubicin-induced organ toxicity in EAC-mediated solid tumor-induced mice. Front Pharmacol 2023; 14:1174867. [PMID: 37324470 PMCID: PMC10264642 DOI: 10.3389/fphar.2023.1174867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023] Open
Abstract
Background and objective: Doxorubicin is extensively utilized chemotherapeutic drug, and it causes damage to the heart, liver, and kidneys through oxidative stress. Theobroma cacao L (cocoa) is reported to possess protective effects against several chemical-induced organ damages and also acts as an anticancer agent. The study aimed to determine whether the administration of cocoa bean extract reduces doxorubicin-induced organ damage in mice with Ehrlich ascites carcinoma (EAC) without compromising doxorubicin efficacy. Methodology: Multiple in vitro methods such as cell proliferation, colony formation, chemo-sensitivity, and scratch assay were carried out on cancer as well as normal cell lines to document the effect of cocoa extract (COE) on cellular physiology, followed by in vivo mouse survival analysis, and the organ-protective effect of COE on DOX-treated animals with EAC-induced solid tumors was then investigated. In silico studies were conducted on cocoa compounds with lipoxygenase and xanthine oxidase to provide possible molecular explanations for the experimental observations. Results: In vitro studies revealed potent selective cytotoxicity of COE on cancer cells compared to normal. Interestingly, COE enhanced DOX potency when used in combination. The in vivo results revealed reduction in EAC and DOX-induced toxicities in mice treated with COE, which also improved the mouse survival time; percentage of lifespan; antioxidant defense system; renal, hepatic, and cardiac function biomarkers; and also oxidative stress markers. COE reduced DOX-induced histopathological alterations. Through molecular docking and MD simulations, we observed chlorogenic acid and 8'8 methylenebiscatechin, present in cocoa, to have the highest binding affinity with lipoxygenase and xanthine oxidase, which lends support to their potential in ameliorating oxidative stress. Conclusion: The COE reduced DOX-induced organ damage in the EAC-induced tumor model and exhibited powerful anticancer and antioxidant effects. Therefore, COE might be useful as an adjuvant nutritional supplement in cancer therapy.
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Affiliation(s)
- Priyanka P. Patil
- Indian Council of Medical Research- National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, Karnataka, India
| | - Pranjal Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, Karnataka, India
| | - Vishal S. Patil
- Indian Council of Medical Research- National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Department of Pharmacology and Toxicology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, Karnataka, India
| | - Harish R. Darasaguppe
- Indian Council of Medical Research- National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | | | - Arati Bhatkande
- Indian Council of Medical Research- National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Rajesh K. Joshi
- Indian Council of Medical Research- National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | | | - Subarna Roy
- Indian Council of Medical Research- National Institute of Traditional Medicine, Belagavi, Karnataka, India
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Dodamani MH, Lila AR, Memon SS, Sarathi V, Arya S, Rane A, Sehemby MK, Garg R, Bhandare VV, Karlekar M, Patil VA, Kunwar A, Bandgar TR. Genotypic Spectrum and its Correlation with Alopecia and Clinical Response in Hereditary Vitamin D Resistant Rickets: Our Experience and Systematic Review. Calcif Tissue Int 2023; 112:483-492. [PMID: 36705686 DOI: 10.1007/s00223-023-01061-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
Alopecia in hereditary vitamin D resistant rickets (HVDRR) has some correlation with severe rickets and poor overall response. However, these observations are based on small series. Hence, we aim to assess the genotypic spectrum of HVDRR and its correlation with alopecia and clinical response. Seven genetically-proven HVDDR patients from five unrelated families and 119 probands from systematic review were analysed retrospectively for phenotypic and genotypic data and overall response to therapy. In our cohort mean age at rickets onset was 12 (± 3.4) months. Alopecia was present in all patients but one. All patients had poor overall response to oral high-dose calcium and calcitriol and most required intravenous calcium. Genetic analyses revealed four novel variants. On systematic review, alopecia was present in majority (81.5%) and preceded the onset of rickets. Patients with alopecia had higher serum calcium (7.6 vs.6.9 mg/dl, p = 0.008), lower 1, 25(OH)2 D (200 vs.320 pg/ml, p = 0.03) and similar overall response to oral therapy (28.7% vs. 35.3%, p = 0.56). Alopecia was present in 51.4% of non-truncating (NT) ligand-binding domain (LBD) variants, whereas it was universal in truncating LBD and all DNA binding-domain (DBD) variants. Overall response to oral therapy was highest in LBD-NT (46.4%) as compared to 7.6% in LBD-truncating and 19% in DBD-NT variants. Among LBD-NT variants, those affecting RXR heterodimerization, but not those affecting ligand affinity, were associated with alopecia. Both alopecia and overall response have genotypic correlation. Age at diagnosis and overall response to oral therapy were similar between patients with and without alopecia in genetically proven HVDRR.
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Affiliation(s)
- Manjunath Havalappa Dodamani
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Anurag Ranjan Lila
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Saba Samad Memon
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India.
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, Karnataka, India
| | - Sneha Arya
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Ankita Rane
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Manjeet Kaur Sehemby
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Robin Garg
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | | | - Manjiri Karlekar
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Virendra A Patil
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Tushar R Bandgar
- Department of Endocrinology, Seth G.S Medical College & KEM Hospital, Parel, Mumbai, Maharashtra, 4000012, India
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Joshi BP, Bhandare VV, Patel P, Sharma A, Patel R, Krishnamurthy R. Molecular modelling studies and identification of novel phytochemical inhibitor of DLL3. J Biomol Struct Dyn 2022; 41:3089-3109. [PMID: 35220906 DOI: 10.1080/07391102.2022.2045224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Prostate cancer has been recently considered the most diagnosed cancer in male. DLL3 is overexpressed in CRPC-NE but not in localised prostate cancer or BPH. There are no effective treatments for neuroendocrine differentiated prostate cancer due to a lack of understanding of DLL3 structure and function. The structure of DLL3 is not yet determined using any experimental techniques. Hence, the structure-based drug discovery approach against prostate cancer has not shown great success. In present study, molecular modelling techniques were employed to generate three-dimensional structure of DLL3 and performed its thorough structural analysis. Further, all-atom molecular dynamics simulation was performed to obtain energetically favourable conformation. Further, we used a virtual screening using a library of >13800 phytochemicals from the IMPPAT database and other literature to select the best possible phytochemical inhibitor for DLL3 and identified the top five compounds. Relative binding affinity was calculated using the MM-PBSA approach. ADMET properties of the screened compounds reveal the toxic effect of Gnemonol C. We believe these studied physicochemical properties, functional domain identification, and binding site identification would be very useful to gain more structural and functional insights of DLL3; also, it can be used to infer their pharmacodynamics properties of DLL3 which was recently reported as an important prostate cancer target. The current study also proposes that Ergosterol Peroxide, Dioslupecin A, Mulberrofuran K, and Caracurine V have strong affinities and could serve as plausible inhibitors against DLL3. We believe this study would further help develop better drug candidates against neuroendocrine prostate cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Prittesh Patel
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Gujarat, India
| | - Abhishek Sharma
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Gujarat, India
| | - Rajesh Patel
- Bioinformatics and Supercomputer Lab., Department of Biosciences (UGC-SAP-DRS-II & DST-FIST-I), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Ramar Krishnamurthy
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Tarsadi, Gujarat, India
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Maheshwari M, Arya S, Lila AR, Sarathi V, Barnabas R, Rai K, Bhandare VV, Memon SS, Karlekar MP, Patil V, Shah NS, Kunwar A, Bandgar T. 17α-hydroxylase/17,20-lyase deficiency in 46, XY: our experience and review of literature. J Endocr Soc 2022; 6:bvac011. [PMID: 35178494 PMCID: PMC8845120 DOI: 10.1210/jendso/bvac011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Indexed: 11/19/2022] Open
Abstract
Context There are more than 100 pathogenic variants in CYP17A1 that have been identified in patients with 17α-hydroxylase/17,20-lyase deficiency (17OHD). Objective We aimed to describe 46,XY patients with 17OHD from our center and review the literature. Methods We retrospectively analyzed genetically proven index cases of 17OHD from our 46,XY disorders of sex development cohort and reviewed similar cases from the literature (n = 150). Based on the phenotype, 17OHD probands were classified into combined severe deficiency (n = 128) and combined partial deficiency (n = 16). Additionally, patients with the apparent isolated 17,20-lyase deficiency (n = 7, from 6 families) were noted. Residual enzyme activities with the observed mutant enzymes were divided in 2 categories as < 1% and ≥ 1%, each for hydroxylase and lyase. Results We present 4 index cases of 46,XY 17OHD with a complete spectrum of undervirilization and 2 novel variants in CYP17A1. In the review, the combined severe deficiency was the most common form, with more frequent female sex of rearing, hypertension, hypokalemia, suppressed renin, higher plasma corticotropin, lower serum cortisol, and androgens. Immunoassay-measured serum aldosterone was frequently (68.2%) unsuppressed (>5 ng/dL). Elevated serum progesterone had high sensitivity for diagnosis of combined 17OHD, even in combined partial deficiency (83.3%). Among patients with clinical phenotype of combined severe deficiency, 11.5% had partial 17α-hydroxylase and complete 17,20-lyase deficiency (>1%/<1%) and had significantly higher serum cortisol than those with < 1%/<1% activity. Conclusion We report the first monocentric case series of Asian Indian 46,XY patients with 17OHD. We propose that a phenotype of severe undervirilization with milder cortisol deficiency may represent a distinct subtype of combined severe 17OHD with residual 17α-hydroxylase activity but severe 17,20-lyase deficiency (>1%/<1%), which needs further validation.
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Affiliation(s)
- Madhur Maheshwari
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Sneha Arya
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Anurag Ranjan Lila
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, India
| | - Rohit Barnabas
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Khushnandan Rai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | | | - Saba Samad Memon
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | | | - Virendra Patil
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Nalini S Shah
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Tushar Bandgar
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
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Patil VA, Lila AR, Shah N, Ekbote AV, Shah R, Bhandare VV, Sarathi V, Arya S, Memon SS, Kunwar A, Bandgar T. GNRH1 Variants in Congenital Hypogonadotropic Hypogonadism: Single-Center Experience and Systematic Literature Review. Neuroendocrinology 2022; 112:723-732. [PMID: 34923491 DOI: 10.1159/000521558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVE As GNRH1 genotype-phenotype correlation in CHH is not well studied, we aim to describe the GNRH1 variants in our CHH cohort and present a systematic review as well as genotype-phenotype analysis of all mutation-positive cases reported in the world literature. DESIGN This is a retrospective study of GNRH1 mutation-positive patients from a western Indian center. PRISMA guidelines-based PubMed search of the published literature of all GNRH1 mutation-positive patients was conducted. SETTING This study was conducted in an academic medical center. PATIENT(S) This study included 2 probands from our cohort and 19 probands from the world literature. MAIN OUTCOME MEASURE(S) Demographic details, clinical presentation, biochemistry, imaging, treatment details, and genotypic data were recorded. RESULT(S) Two probands in our cohort carried two novel pathogenic biallelic GNRH1 variants (p.Glu24Leu, c.238-2A>G). Both had a severe reproductive phenotype. We report successful gonadotropin therapy and fertility in 1 proband. We included 19 probands from 12 studies after the literature review. Ten CHH probands (inclusive 2 from this study) with biallelic GNRH1 variants had severe reproductive phenotype, low gonadotropin levels, low/normal prolactin, normal pituitary imaging, and no extra-reproductive phenotype. Of seven biallelic variants reported, three were frameshift, two were splice-site, and two were missense mutations. All of them were pathogenic/likely pathogenic without oligogenicity. Of seven monoallelic GNRH1 variants reported in 11 probands, 4 had nonreproductive phenotype, 3 were benign/likely benign, and 4 were oligogenic. CONCLUSION(S) GNRH1 biallelic variants lead to severe reproductive phenotype, with low gonadotropin levels without nonreproductive features or oligogenicity. However, the role of GNRH1 monoallelic variants in CHH pathophysiology for reported variants remains questionable.
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Affiliation(s)
- Virendra A Patil
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Anurag Ranjan Lila
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Nalini Shah
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Alka V Ekbote
- Clinical and Molecular Genetics, Kamalnayan Bajaj Hospital, Aurangabad, India
| | - Ravikumar Shah
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | | | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bengaluru, India
| | - Sneha Arya
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Saba Samad Memon
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Tushar Bandgar
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
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Dodamani MH, Sehemby M, Memon SS, Sarathi V, Lila AR, Chapla A, Bhandare VV, Patil VA, Shah NS, Thomas N, Kunwar A, Bandgar TR. Genotype and phenotypic spectrum of vitamin D dependent rickets type 1A: our experience and systematic review. J Pediatr Endocrinol Metab 2021; 34:1505-1513. [PMID: 34492747 DOI: 10.1515/jpem-2021-0403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/26/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND Vitamin D dependent rickets type 1 (VDDR1) is a rare disease due to pathogenic variants in 1-α hydroxylase gene. We describe our experience with systematic review of world literature to describe phenotype and genotype. METHODS Seven patients from six unrelated families with genetically proven VDDR1 from our cohort and 165 probands from systematic review were analyzed retrospectively. The clinical features, biochemistry, genetics, management, and long-term outcome were retrieved. RESULTS In our cohort, the median age at presentation and diagnosis was 11(4-18) and 40(30-240) months. The delayed diagnoses were due to misdiagnoses as renal tubular acidosis and hypophosphatemic rickets. Four had hypocalcemic seizures in infancy whereas all had rickets by 2 years. All patients had biochemical response to calcitriol, however two patients diagnosed post-puberty had persistent deformity. Genetic analysis revealed two novel (p.Met260Arg, p.Arg453Leu) and a recurring variant (p.Phe443Profs*24). Systematic review showed that seizures as most common presentation in infancy, whereas delayed motor milestones and deformities after infancy. Diagnosis was delayed in 27 patients. Patients with unsatisfactory response despite compliance were >12 years at treatment initiation. Inappropriately normal 1,25(OH)2D may be present, however suppressed ratio of 1,25(OH)2 D/25(OH)D may provide a clue to diagnosis. Various region specific and hot-spot recurrent variants are described. Patients with truncating variants had higher daily calcitriol requirement and greatly suppressed ratio of 1,25(OH)2D/25(OH)D. CONCLUSION Delayed diagnosis may lead to permanent short stature and deformities. Truncating variants tend to have severe disease as compared to non-truncating variants. Diagnostic accuracy of 1,25(OH)2 D/25(OH)D ratio needs further validation.
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Affiliation(s)
| | - Manjeetkaur Sehemby
- Department of Endocrinology, Seth G.S Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Saba Samad Memon
- Department of Endocrinology, Seth G.S Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi institute of medical sciences and research centre, Bangalore, Karnataka, India
| | - Anurag R Lila
- Department of Endocrinology, Seth G.S Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Aaron Chapla
- Department of Endocrinology, Diabetes & Metabolism, Christian Medical College and Hospital, Vellore, Tamilnadu, India
| | | | - Virendra A Patil
- Department of Endocrinology, Seth G.S Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Nalini S Shah
- Department of Endocrinology, Seth G.S Medical College and KEM Hospital, Mumbai, Maharashtra, India
| | - Nihal Thomas
- Department of Endocrinology, Diabetes & Metabolism, Christian Medical College and Hospital, Vellore, Tamilnadu, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Tushar R Bandgar
- Department of Endocrinology, Seth G.S Medical College and KEM Hospital, Mumbai, Maharashtra, India
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Pandey B, Dev A, Chakravorty D, Bhandare VV, Polley S, Roy S, Basu G. Insights on the disruption of the complex between human positive coactivator 4 and p53 by small molecules. Biochem Biophys Res Commun 2021; 578:15-20. [PMID: 34534740 DOI: 10.1016/j.bbrc.2021.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 08/29/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Interaction between human positive coactivator 4 (PC4), an abundant nuclear protein, and the tumor suppressor protein p53 plays a crucial role in initiating apoptosis. In certain neurodegenerative diseases PC4 assisted-p53-dependent apoptosis may play a central role. Thus, disruption of p53-PC4 interaction may be a good drug target for certain disease pathologies. A p53-derived short peptide (AcPep) that binds the C-terminal domain of PC4 (C-PC4) is known to disrupt PC4-p53 interaction. To fully characterize its binding mode and binding site on PC4, we co-crystallized C-PC4 with the peptide and determined its structure. The crystal, despite exhibiting mass spectrometric signature of the peptide, lacked peptide electron density and showed a novel crystal lattice, when compared to C-PC4 crystals without the peptide. Using peptide-docked models of crystal lattices, corresponding to our structure and the peptide-devoid structure we show the origin of the novel crystal lattice to be dynamically bound peptide at the previously identified putative binding site. The weak binding is proposed to be due to the lack of the N-terminal domain of PC4 (N-PC4), which we experimentally show to be disordered with no effect on PC4 stability. Taking cue from the structure, virtual screening of ∼18.6 million small molecules from the ZINC15 database was performed, followed by toxicity and binding free energy filtering. The novel crystal lattice of C-PC4 in presence of the peptide, the role of the disordered N-PC4 and the high throughput identification of potent small molecules will allow a better understanding and control of p53-PC4 interaction.
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Affiliation(s)
- Bhawna Pandey
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Aditya Dev
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Debamitra Chakravorty
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | | | - Smarajit Polley
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.
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Arya S, Barnabas R, Lila AR, Sarathi V, Memon SS, Bhandare VV, Thakkar K, Patil V, Shah NS, Kunwar A, Bandgar T. Clinical, Hormonal, Genetic, and Molecular Characteristics in Androgen Insensitivity Syndrome in an Asian Indian Cohort from a Single Centre in Western India. Sex Dev 2021; 15:253-261. [PMID: 34333495 DOI: 10.1159/000517763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/09/2021] [Indexed: 11/19/2022] Open
Abstract
The study aimed to analyze clinical and hormonal phenotype,and genotype in patients with genetically proven androgen insensitivity syndrome (AIS) from Western India. Index patients with pathogenic variants in the androgen receptor (AR) gene were identified from a consecutive 46,XY DSD cohort (n = 150) evaluated with clinical exome sequencing, and their genetically-proven affected relatives were also included. In sum, 15 index cases (9 complete AIS [CAIS] and 6 partial AIS [PAIS]) were identified making AIS the second most common (10%) cause of 46,XY DSD, next to 5α-reductase 2 deficiency (n = 26; 17.3%). Most patients presented late in the postpubertal period with primary amenorrhoea in CAIS (89%) and atypical genitalia with gynecomastia in PAIS (71.4%). All CAIS were reared as females and 83.3% of PAIS as males with no gender dysphoria. Four of 6 patients with available testosterone to dihydrotestosterone ratio had a false elevation (>10). Metastatic dysgerminoma was seen in 1 patient in CAIS, while none in the PAIS group had malignancy. Fifteen different (including 6 novel) pathogenic/likely pathogenic variants in AR were found. Nonsense and frameshift variants exclusively led to CAIS phenotype, whereas missense variants led to variable phenotypes. In this largest, monocentric study from the Asian Indian subcontinent, AIS was the second most common cause of 46,XY DSD with similar phenotype but later presentation when compared to cases in the rest of the world. The study reports 6 novel pathogenic variants in AR.
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Affiliation(s)
- Sneha Arya
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Rohit Barnabas
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Anurag Ranjan Lila
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, India
| | - Saba Samad Memon
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | | | - Kunal Thakkar
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Virendra Patil
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Nalini Samir Shah
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Tushar Bandgar
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
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Karlekar MP, Sarathi V, Lila A, Rai K, Arya S, Bhandare VV, Atluri S, Patil V, Ramteke-Jadhav S, Shah NS, Kunwar A, Bandgar T. Expanding genetic spectrum and discriminatory role of steroid profiling by LC-MS/MS in 11β-hydroxylase deficiency. Clin Endocrinol (Oxf) 2021; 94:533-543. [PMID: 33275286 DOI: 10.1111/cen.14376] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To report clinical, hormonal and structural effects of CYP11B1 pathogenic variations in Indian patients with 11β-hydroxylase deficiency (11βOHD) and find hormonal criteria that accurately distinguish 11βOHD from 21α-hydroxylase deficiency (21OHD). DESIGN Retrospective record review of genetically diagnosed patients with 11βOHD. PATIENTS AND MEASUREMENTS Clinical features, hormonal parameters at diagnosis (by immunoassay) and recent follow-up of 13 genetically proven 11βOHD patients managed at our centre were retrospectively reviewed. ACTH-stimulated serum adrenal steroids (measured by LC-MS/MS) of 11βOHD were compared with those of simple virilizing and non-classic 21OHD. Structural analysis of the observed pathogenic variations was performed by computational modelling. RESULTS Nine (four females) and four (all females) patients had classic and non-classic disease, respectively. All 11βOHD patients had elevated ACTH-stimulated serum 11-deoxycortisol (26.5-342.7 nmol/L) whereas none had elevated serum 17-hydroxyprogesterone (4.2-21.2 nmol/L); both hormonal parameters distinguished 11βOHD from 21OHD with 100% accuracy. ACTH-stimulated serum cortisol, but not 11-deoxycortisol, clearly distinguished classic (<70 nmol/L) from non-classic (>160 nmol/L) disease. Thirteen (eight novel, two recurrent) pathogenic variants were observed. Only missense mutations were observed among patients with non-classic disease. Computational modelling predicted the possible affection of enzyme structure and function for all the observed missense mutations. CONCLUSIONS This first Indian study describes 13 11βOHD patients, including four with the rarer non-classic variant. A total of eight novel pathogenic variants were identified in our study, highlighting regional genetic heterogeneity. Measurement of ACTH-stimulated adrenal steroids by LC-MS/MS will help avoid the misdiagnosis of 11βOHD as 21OHD and has potential to distinguish classic from non-classic 11βOHD.
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Affiliation(s)
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, India
| | - Anurag Lila
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Khushnandan Rai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sneha Arya
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | | | - Sridevi Atluri
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, India
| | - Virendra Patil
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Swati Ramteke-Jadhav
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Nalini S Shah
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Tushar Bandgar
- Department of Endocrinology, Seth G S Medical College & KEM Hospital, Mumbai, India
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Arya S, Tiwari A, Lila AR, Sarathi V, Bhandare VV, Kumbhar BV, Rai K, Kunwar A, Thakkar H, Thakkar K, Memon SS, Patil V, Khadilkar K, Jadhav SS, Shah NS, Bandgar T. Homozygous p.Val89Leu plays an important pathogenic role in 5α-reductase type 2 deficiency patients with homozygous p.Arg246Gln in SRD5A2. Eur J Endocrinol 2020; 183:275-284. [PMID: 32567554 DOI: 10.1530/eje-19-1050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 06/18/2020] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To evaluate the pathogenic role of a few benign variants and hypomorphic pathogenic variants in SRD5A2. DESIGN AND METHODS We retrospectively analyzed phenotypes and genotypes in 23 Indian patients with genetically proven steroid 5α-reductase 2 (SRD5A2) deficiency. The interactions of the SRD5A2 enzymes resulting due to the most common benign variant (p.Val89Leu), the most common (hypomorphic) pathogenic variant (p.Arg246Gln) and the double variants (p.Val89Leu and p.Arg246Gln) in SRD5A2 were compared with that of the wild type (WT) enzyme by molecular dynamics (MD) simulation. RESULTS The majority (n = 19, 82.61%) of patients presented for atypical genitalia and had male gender identity (16/20). Including the two novel ones (p.Leu83Pro, p.Ala28Leufs*103), a total of nine different pathogenic variants were observed. p.Arg246Gln was the most common pathogenic variant (n = 12). Homozygous p.Arg246Gln (n = 9) variant was associated with milder undervirilization (Sinnecker score of ≤3a: 8/9 vs 6/14, P = 0.04) and had concurrent homozygous p.Val89Leu in all patients. Interestingly, asymptomatic fathers of two index patients were homozygous for p.Arg246Gln which questioned the pathogenicity of the variation as a sole factor. Unlike all symptomatic homozygous p.Arg246Gln patients who were also homozygous for p.Val89Leu, asymptomatic homozygous p.Arg246Gln fathers were heterozygous for p.Val89Leu. On MD simulation SRD5A2 p.Val89Leu-Testeosterone (T) and SRD5A2 p.Arg246Gln-T complexes, but not SRD5A2 p.Val89Leu and p.Arg246Gln-T complex, demonstrated close interaction between NADPH and T as that of SRD5A2 WT-T. CONCLUSIONS p.Arg246Gln may not be pathogenic as a sole variation even in the homozygous state; additional contribution of homozygous p.Val89Leu variant may be essential for the pathogenicity of p.Arg246Gln in SRD5A2.
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Affiliation(s)
- Sneha Arya
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Ankita Tiwari
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Anurag Ranjan Lila
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Vijaya Sarathi
- Department of Endocrinology, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, India
| | | | - Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Khushnandan Rai
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Hemangini Thakkar
- Department of Radiology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Kunal Thakkar
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Saba Samad Memon
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Virendra Patil
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Kranti Khadilkar
- Department of Endocrinology, Narayana Health City, Bangalore, India
| | - Swati S Jadhav
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Nalini S Shah
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
| | - Tushar Bandgar
- Department of Endocrinology, Seth G S Medical College and KEM Hospital, Mumbai, India
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Kumbhar BV, Bhandare VV. Exploring the interaction of Peloruside-A with drug resistant αβII and αβIII tubulin isotypes in human ovarian carcinoma using a molecular modeling approach. J Biomol Struct Dyn 2020; 39:1990-2002. [DOI: 10.1080/07391102.2020.1745689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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14
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Bhandare VV, Kumbhar BV, Kunwar A. Differential binding affinity of tau repeat region R2 with neuronal-specific β-tubulin isotypes. Sci Rep 2019; 9:10795. [PMID: 31346240 PMCID: PMC6658543 DOI: 10.1038/s41598-019-47249-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/05/2019] [Indexed: 12/14/2022] Open
Abstract
Tau is a microtubule-associated protein whose C-terminal domain consisting of four repeat regions R1, R2, R3 and R4 binds to microtubules to stabilize them. In several neurodegenerative diseases, tau detaches from microtubules to form insoluble aggregates leading to tauopathy. Microtubules are made up of αβ tubulin subunits. Seven α-tubulin and nine β-tubulin isotypes have been reported to be present in humans till date. These tubulin isotypes show residue composition variations mainly at C-terminal region and bind to motor proteins and anti-mitotic drugs differently. These tubulin isotypes show tissue specific expression as their relative proportion varies significantly in different type of cells. It is also known that tau binds differently to different cell lines and can either promote or demote microtubule polymerization. However, the relative binding affinity of tau to the different β-tubulin isotypes present in different cell lines is completely unknown. Here, we study relative binding affinity of Tau repeat region R2 to neuronal specific tubulin isotypes βI, βIIb, and βIII using molecular modelling approach. The order of binding energy of tau with tubulin is βIII > βIIb > βI. Our strategy can be potentially adapted to understand differential binding affinity of tau towards β-tubulin isotypes present in other cell lines.
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Affiliation(s)
- Vishwambhar Vishnu Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India
| | - Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, Maharashtra, India.
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Kumbhar BV, Bhandare VV, Panda D, Kunwar A. Delineating the interaction of combretastatin A-4 with αβ tubulin isotypes present in drug resistant human lung carcinoma using a molecular modeling approach. J Biomol Struct Dyn 2019; 38:426-438. [DOI: 10.1080/07391102.2019.1577174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bajarang Vasant Kumbhar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Vishwambhar Vishnu Bhandare
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ambarish Kunwar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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Bhandare VV, Ramaswamy A. The proteinopathy of D169G and K263E mutants at the RNA Recognition Motif (RRM) domain of tar DNA-binding protein (tdp43) causing neurological disorders: A computational study. J Biomol Struct Dyn 2017; 36:1075-1093. [DOI: 10.1080/07391102.2017.1310670] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Amutha Ramaswamy
- Centre for Bioinformatics, Pondicherry University, Pondicherry 605014, India
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Bhandare VV, Ramaswamy A. Identification of possible siRNA molecules for TDP43 mutants causing amyotrophic lateral sclerosis: In silico design and molecular dynamics study. Comput Biol Chem 2016; 61:97-108. [PMID: 26854610 DOI: 10.1016/j.compbiolchem.2016.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 12/29/2015] [Accepted: 01/08/2016] [Indexed: 12/12/2022]
Abstract
The DNA binding protein, TDP43 is a major protein involved in amyotrophic lateral sclerosis and other neurological disorders such as frontotemporal dementia, Alzheimer disease, etc. In the present study, we have designed possible siRNAs for the glycine rich region of tardbp mutants causing ALS disorder based on a systematic theoretical approach including (i) identification of respective codons for all mutants (reported at the protein level) based on both minimum free energy and probabilistic approaches, (ii) rational design of siRNA, (iii) secondary structure analysis for the target accessibility of siRNA, (iii) determination of the ability of siRNA to interact with mRNA and the formation/stability of duplex via molecular dynamics study for a period of 15ns and (iv) characterization of mRNA-siRNA duplex stability based on thermo-physical analysis. The stable GC-rich siRNA expressed strong binding affinity towards mRNA and forms stable duplex in A-form. The linear dependence between the thermo-physical parameters such as Tm, GC content and binding free energy revealed the ability of the identified siRNAs to interact with mRNA in comparable to that of the experimentally reported siRNAs. Hence, this present study proposes few siRNAs as the possible gene silencing agents in RNAi therapy based on the in silico approach.
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Affiliation(s)
| | - Amutha Ramaswamy
- Centre for Bioinformatics, Pondicherry University, Pondicherry 605014, India.
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