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Munikumar M, Pradeepkiran JA, Kumar MK, Banapuram S, Bhat Edurkala A. Comprehensive structural and functional analysis of hVEGFR1: Insights into phosphorylation, molecular interactions, and potential inhibitors through docking and dynamics simulations. Cancer Treat Res Commun 2024; 39:100795. [PMID: 38428067 DOI: 10.1016/j.ctarc.2024.100795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/10/2023] [Accepted: 11/25/2023] [Indexed: 03/03/2024]
Abstract
Vascular Endothelial Growth Factor Receptor 1 (VEGFR1), is an enzyme with tyrosine kinase activity that plays a pivotal role in angiogenesis, the process of new blood vessel formation. This receptor is of significant clinical importance as it is implicated in various cancers, particularly non-small cell lung cancer (NSCLC), where its dysregulation leads to uncontrolled cell growth through ligand-induced phosphorylation. While commercially available drugs target VEGFR1, their prolonged use often leads to drug resistance and the emergence of mutations in cancer patients. To address these challenges, researchers have identified the human tyrosine kinase (hTK) domain of VEGFR1 as a potential therapeutic marker for lung malignancies. The 3D crystal structure of the hTK domain, obtained from Protein Data Bank (PDB ID: 3HNG), has provided vital structural insights of hVEGFR1. This study has revealed variations within the hVEGFR1 tyrosine kinase domain, distinguishing between regions associated with phosphorylase kinase and transferase activities. We identified numerous potential phosphorylation sites within the TK domain, shedding light on the protein's regulation and signaling possible. Detailed molecular interaction analyses have elucidated the binding forces between lead molecules and hVEGFR1, including hydrogen bonds, electrostatic, hydrophobic, and π-sigma interactions. The stability observed during molecular dynamics simulations further underscores the biological relevance of these interactions. Furthermore, docked complexes has highlighted localized structural fluctuations, offering insight into potential allosteric effects and dynamic conformational changes induced by lead molecules. These findings not only provide a comprehensive characterization of hVEGFR1 but also pave the way for the development of targeted therapies. Eventually, this study has the potential in identifying drug to combat diseases associated with hVEGFR1 dysregulation, including cancer and angiogenesis-related disorders, contributing to effective treatment strategies.
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Affiliation(s)
- Manne Munikumar
- Clinical Division, ICMR-National Institute of Nutrition, Jamai-Osmania (Post), Hyderabad, 500007, Telangana, India
| | | | | | - Swathi Banapuram
- Clinical Division & Animal Facility, ICMR-National Institute of Nutrition, Hyderabad, 500007, India
| | - Akshatha Bhat Edurkala
- Clinical Division & Animal Facility, ICMR-National Institute of Nutrition, Hyderabad, 500007, India
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Ungarala R, Munikumar M, Sinha SN, Kumar D, Sunder RS, Challa S. Assessment of Antioxidant, Immunomodulatory Activity of Oxidised Epigallocatechin-3-Gallate (Green Tea Polyphenol) and Its Action on the Main Protease of SARS-CoV-2—An In Vitro and In Silico Approach. Antioxidants (Basel) 2022; 11:antiox11020294. [PMID: 35204178 PMCID: PMC8868081 DOI: 10.3390/antiox11020294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Abstract
Owing to the instability of Epigallocatechin Gallate (EGCG), it may undergo auto-oxidation and form oxidised products or dimers. In the present study, we aimed to evaluate the therapeutic effects, including antioxidation and immunomodulatory action, of the Oxidised Epigallocatechin Gallate (O-EGCG) as compared to native EGCG and the action of these compounds on main protease (Mpro) docking against SARS-CoV-2. HCT-116 (Human Colon Cancer) cell lines were used to estimate the total antioxidant capacity and lipid peroxidation levels and pro-inflammatory markers (human IL-6, IL-1β, TNF-α). Further, molecular docking analysis was performed by AutoDock and visualised in Discovery studio. Improved antioxidant capacity of O-EGCG was observed, and there was a significant decrease in the inflammatory markers (IL-1β, IL-6, and TNF-α) when O-EGCG was applied as compared to EGCG. The O-EGCG was shown to be strongly associated with the highest docking score and active site residues of IL-1, IL-6, and TNF- α, as well as the Mpro of SARS-CoV-2, according to in silico approach. The in vitro and in silico analyses indicate an improved therapeutic action of the oxidised form of EGCG. The effective inhibitory action of O-EGCG against SARS-CoV-2 suggests further exploration of the compound against COVID-19 and its efficacy. However, in vivo studies and understanding of the mechanism of action of O-EGCG may yield a better opinion on the use of O-EGCG and future human clinical trials.
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Affiliation(s)
- Ramakrishna Ungarala
- Food Safety Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India; (R.U.); (D.K.)
| | - Manne Munikumar
- Clinical Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India;
| | - Sukesh Narayan Sinha
- Food Safety Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India; (R.U.); (D.K.)
- Correspondence: ; Tel.: +91-7032426802
| | - Dileshwar Kumar
- Food Safety Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India; (R.U.); (D.K.)
| | - R. Shyam Sunder
- University College of Technology, Osmania University, Tarnaka, Hyderabad, Telangana 500007, India;
| | - Suresh Challa
- Cell Biology Division, ICMR- National Institute of Nutrition, Tarnaka, Hyderabad, Telangana 500007, India;
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Pradeepkiran JA, Munikumar M, Reddy AP, Reddy PH. Protective effects of a small molecule inhibitor ligand against hyperphosphorylated tau-induced mitochondrial and synaptic toxicities in Alzheimer disease. Hum Mol Genet 2021; 31:244-261. [PMID: 34432046 DOI: 10.1093/hmg/ddab244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022] Open
Abstract
The purpose of our study is to understand the protective effects of small molecule ligands for phosphorylated tau (p-tau) in Alzheimer's disease (ad) progression. Many reports show evidence that p-tau is reported to be an important contributor to the formation of paired helical filaments (PHFs) and neurofibrillary tangles (NFTs) in ad neurons. In ad, glycogen synthase kinase-3 beta (GSK3β), cyclin-dependent kinase- 5 (CDK5) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A), are the three important kinases responsible for tau hyperphosphorylation. Currently, there are no drugs and/or small molecules that reduce the toxicity of p-tau in ad. In the present study, we rationally selected and validated small molecule ligands that binds to the phosphorylated tau at SER23 (Ser 285). We also assessed the molecular dynamics and validated molecular docking sites for the three best ligands. Based on the best docking scores -8.09, -7.9 and - 7.8 kcal/mol, we found that ligand 1 binds to key hyperphosphorylation residues of p-tau that inhibit abnormal PHF-tau, DYRK1A, and GKS3β that reduce p-tau levels in ad. Using biochemical, molecular, immunoblotting, immunofluorescence, and transmission electron microscopy analyses, we studied the ligand 1 inhibition as well as mitochondrial and synaptic protective effects in immortalized primary hippocampal neuronal (HT22) cells. We found interactions between NAT10-262501 (ligand 1) and p-tau at key phosphorylation sites and these ligand-based inhibitions decreased PHF-tau, DYRK1A and GSK3β levels. We also found increased mitochondrial biogenesis, mitochondrial fusion and synaptic activities and reduced mitochondrial fission in ligand 1-treated mutant tau HT22 cells. Based on these results, we cautiously conclude that p-tau NAT10-262501 (ligand 1) reduces hyperphosphorylation of tau based GKS3β and CDK5 kinase regulation in ad, and aids in the maintenance of neuronal structure, mitochondrial dynamics, and biogenesis with a possible therapeutic drug target for ad.
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Affiliation(s)
| | - Manne Munikumar
- Clinical Division, ICMR-National Institute of Nutrition, Hyderabad, Telangana-500007, India
| | - Arubala P Reddy
- Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock TX 79409, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.,Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.,Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.,Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.,Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Manne M, Goudar G, Varikasuvu SR, Khetagoudar MC, Kanipakam H, Natarajan P, Ummiti MD, Yenagi VA, Chinthakindi S, Dharani P, Thota DSS, Patil S, Patil V. Cordifolioside: potent inhibitor against M pro of SARS-CoV-2 and immunomodulatory through human TGF-β and TNF-α. 3 Biotech 2021; 11:136. [PMID: 33643762 PMCID: PMC7898013 DOI: 10.1007/s13205-021-02685-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/08/2021] [Indexed: 12/23/2022] Open
Abstract
Therapeutic options for SARS-CoV-2 are limited merely to the symptoms or repurposed drugs and non-specific interventions to promote the human immune system. In the present study, chromatographic and in silico approaches were implemented to identify bioactive compounds which might play pivotal role as inhibitor for SARS-CoV-2 and human immunomodulator (TGF-β and TNF-α). Tinospora cordifolia (Willd.) Miers was evaluated for phenolic composition and explored for bioactive compounds by high-performance thin layer chromatography (HPTLC). Furthermore, the bioactive compounds such as cordifolioside, berberine, and magnoflorine were appraised as human immunomodulatory and potent inhibitor against Main Protease (Mpro) of SARS-CoV-2 through multiple docking strategies. Cordifolioside formed six stable H-bonds with His41, Ser144, Cys145, His163, His164, and Glu166 of Mpro of SARS-CoV-2, which displayed a significant role in the viral replication/transcription during infection acting towards the common conserved binding cleft among all strains of coronavirus. Overall, the study emphasized that the proposed cordifolioside might use for future investigations, which hold as a promising scaffold for developing anti-COVID-19 drug and reduce human cytokine storm.
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Ram TS, Munikumar M, Raju VN, Devaraj P, Boiroju NK, Hemalatha R, Prasad PVV, Gundeti M, Sisodia BS, Pawar S, Prasad GP, Chincholikar M, Goel S, Mangal A, Gaidhani S, Srikanth N, Dhiman KS. In silico evaluation of the compounds of the ayurvedic drug, AYUSH-64, for the action against the SARS-CoV-2 main protease. J Ayurveda Integr Med 2021; 13:100413. [PMID: 33654345 PMCID: PMC7906523 DOI: 10.1016/j.jaim.2021.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/12/2021] [Accepted: 02/17/2021] [Indexed: 12/19/2022] Open
Abstract
Background Outbreak of Corona Virus Disease in late 2019 (COVID-19) has become a pandemic global Public health emergency. Since there is no approved anti-viral drug or vaccine declared for the disease and investigating existing drugs against the COVID-19. Objective AYUSH-64 is an Ayurvedic formulation, developed and patented by Central Council of Research in Ayurvedic Sciences, India, has been in clinical use as anti-malarial, anti-inflammatory, anti-pyretic drug for few decades. Thus, the present study was undertaken to evaluate AYUSH-64 compounds available in this drug against Severe Acute Respiratory Syndrome-Corona Virus (SARS-CoV-2) Main Protease (Mpro; PDB ID: 6LU7) via in silico techniques. Materials and methods Different molecular docking software's of Discovery studio and Auto Dock Vina were used for drugs from selected AYUSH-64 compounds against SARS-CoV-2. We also conducted 100 ns period of molecular dynamics simulations with Desmond and further MM/GBSA for the best complex of AYUSH-64 with Mpro of SARS-CoV-2. Results Among 36 compounds of four ingredients of AYUSH-64 screened, 35 observed to exhibits good binding energies than the published positive co–crystal compound of N3 pepetide. The best affinity and interactions of Akuammicine N-Oxide (from Alstonia scholaris) towards the Mpro with binding energy (AutoDock Vina) of −8.4 kcal/mol and Discovery studio of Libdock score of 147.92 kcal/mol. Further, molecular dynamics simulations with MM-GBSA were also performed for Mpro– Akuammicine N-Oxide docked complex to identify the stability, specific interaction between the enzyme and the ligand. Akuammicine N-Oxide is strongly formed h-bonds with crucial Mpro residues, Cys145, and His164. Conclusion The results provide lead that, the presence of Mpro– Akuammicine N-Oxide with highest Mpro binding energy along with other 34 chemical compounds having similar activity as part of AYUSH-64 make it a suitable candidate for repurposing to management of COVID-19 by further validating through experimental, clinical studies. Main protease (Mpro) is a molecular drug target for the 2019-nCoV of epidemic disease of COVID-19. Docking strategies implemented to identify AUSH-64 having dual role as immunomodualtor and inhibition against Mpro of SARS-CoV-2. Molecular dynamics stability analysis revealed that 2019-nCoV Mpro – Akuammicine N-Oxide is stable. Akuammicine N-Oxide may represent potential treatment options against Mpro of 2019-nCoV.
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Key Words
- 2019 novel coronavirus, 2019-nCOV
- AYUSH-64
- Absorption, Distribution, Metabolism, Excretion, and Toxicity, ADME/T
- COVID-19
- Coronavirus disease of 2019, COVID-19
- Coronavirus, CoV
- Dynamics simulations
- Main Protease
- Main protease, Mpro
- Middle East Respiratory Syndrome, MERS
- Molecular Docking
- Molecular Dynamics simulations, MD simulations
- Molecular Mechanics/Generalized Born Surface Area, MM/GBSA
- Number of atoms, Pressure, Temperature, NPT
- Protein Data Bank, PDB
- RNA‐dependent RNA polymerase, RdRp
- Radius of Gyration, rGyr
- Root Mean Square Deviation, RMSD
- Root Mean Square Fluctuation, RMSF
- SARS-CoV-2
- Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2
- Severe Acute Respiratory Syndrome, SARS
- Simulation Event Analysis, SEA
- Simulation Quality Analysis, SQA
- World Health Organization, WHO
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Affiliation(s)
- Thrigulla Saketh Ram
- Research Officer (Ayurveda), CCRAS-National Institute of Indian Medical Heritage, Revenue Board Colony, Gaddiannaram, Hyderabad-500036, Telangana State, India
| | - Manne Munikumar
- Scientist-C (Bioinformatics), NIN-TATA Centre for Excellence in Public Health Nutrition, ICMR-National Institute of Nutrition, Hyderabad-500007, Telangana State, India
| | - Vankudavath Naik Raju
- Scientist-C (Programmer), Nutrition Information, Communication & Health Education (NICHE), ICMR-National Institute of Nutrition, Hyderabad-500007, Telangana State, India
| | - Parasannanavar Devaraj
- Scientist-C, ICMR-National Institute of Nutrition, Hyderabad-500007, Telangana State, India
| | - Naveen Kumar Boiroju
- Scientist-C, ICMR-National Institute of Nutrition, Hyderabad-500007, Telangana State, India
| | - Rajkumar Hemalatha
- Scientist-G, Director, ICMR-National Institute of Nutrition, Hyderabad-500007, Telangana State, India
| | - P V V Prasad
- Assistant Director In-charge, CCRAS-National Institute of Indian Medical Heritage, Revenue Board Colony, Gaddiannaram, Hyderabad-500036, Telangana State, India
| | - Manohar Gundeti
- Research Officer (Ayurveda), CCRAS-Raja Ramdeo Anandilal Podar (RRAP) Central Ayurveda Research Institute for Cancer, Mumbai
| | - Brijesh S Sisodia
- Asst. Director (Biochemistry), CCRAS-Regional Ayurveda Research Institute for Drug Development, Gwalior
| | - Sharad Pawar
- Research Officer, Scientist-2 (Pharmacognosy), CCRAS-Regional Ayurveda Institute for Fundamental Research, Pune
| | - G P Prasad
- Assistant Director (Ayurveda), CCRAS-Regional Ayurveda Institute for Fundamental Research, Pune
| | - Mukesh Chincholikar
- Research Officer (Ayurveda), Central Council for Research in Ayurvedic Sciences, New Delhi
| | - Sumeet Goel
- Research Officer (Ayurveda), Central Council for Research in Ayurvedic Sciences, New Delhi
| | - Anupam Mangal
- Assistant Director (Pharmacognosy), Central Council for Research in Ayurvedic Sciences, New Delhi
| | - Sudesh Gaidhani
- Assistant Director (Pharmacology), Central Council for Research in Ayurvedic Sciences, New Delhi
| | - N Srikanth
- Deputy Director General, Central Council for Research in Ayurvedic Sciences, New Delhi
| | - K S Dhiman
- Director General, Central Council for Research in Ayurvedic Sciences, New Delhi
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Arokiaraj SR, Tajuddin NB, Muthusamy K, Jayaraj JM, Alagumuthu M. TRAF2 and NCK-Interacting Kinase Inhibitors for Colorectal Cancer: In Vitro and Theoretical Validations. ACS COMBINATORIAL SCIENCE 2020; 22:608-616. [PMID: 32960032 DOI: 10.1021/acscombsci.0c00027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
TRAF2 and NCK-interacting kinase (TNIK) is a critical factor in colorectal cancer (CRC) proliferation mediated by Wnt signaling. We attempted to identify efficient TNIK inhibitors using computational high-throughput virtual screening (HTVS) from various drug banks and databases. By performing/on performing e-pharmacophore screening and molecular docking methods, from ∼700 000 molecules, compounds LC_222150, LC_112060, and LC_64796 were identified as potential leads, through molecular dynamics (MD) simulations and density functional theory (DFT). These top 3 structures were commercially procured, and their inhibitory activity was assessed in vitro. Significant TNIK inhibition was observed, with an average IC50 of 18.33 ± 0.75 nM. In terms of anticancer activity, the observed average relative % activity (RPA) of 90.28 ± 1.04 for these compounds compared well with doxorubicin (86.75 ± 1.45) as a standard. Compounds LC_222150, LC_112060, and LC_64796, therefore, warrant further evaluation in vivo to assess their CRC therapeutic effects.
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Affiliation(s)
- Sherlin Rosita Arokiaraj
- PG and Research Deptartment of Biotechnology, Jamal Mohamed College (Autonomous), Bharathidasan University, Tiruchirappalli-620020, India
| | - Nargis Begum Tajuddin
- PG and Research Deptartment of Biotechnology, Jamal Mohamed College (Autonomous), Bharathidasan University, Tiruchirappalli-620020, India
| | | | | | - Manikandan Alagumuthu
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore-632014, India
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Naik VR, Munikumar M, Ramakrishna U, Srujana M, Goudar G, Naresh P, Kumar BN, Hemalatha R. Remdesivir (GS-5734) as a therapeutic option of 2019-nCOV main protease - in silico approach. J Biomol Struct Dyn 2020; 39:4701-4714. [PMID: 32568620 PMCID: PMC7332877 DOI: 10.1080/07391102.2020.1781694] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
2019 – Novel Coronavirus (2019-nCOV), enclosed large genome positive-sense RNA virus characterized by crown-like spikes that protrude from their surface, and have a distinctive replication strategy. The 2019-nCOV belongs to the Coronaviridae family, principally consists of virulent pathogens showing zoonotic property, has emerged as a pandemic outbreak with high mortality and high morbidity rate around the globe and no therapeutic vaccine or drugs against 2019-nCoV are discovered till now. In this study, in silico methods and algorithms were used for sequence, structure analysis and molecular docking on Mpro of 2019-nCOV. The co-crystal structure of 2019-nCOV protease, 6LU7 have ∼99% identity with SARS-CoV protease. The 6LU7 residues, Cys145 and His164 are playing a significant role in replication and are essential for the survival of 2019-nCOV. Alongside, 2019-nCOV Mpro sequence is non-homologous to human host-pathogen. Complete genome sequence analysis, structural and molecular docking results revealed that Remdesivir is having a better binding affinity with -8.2 kcal/mol than the rest of protease inhibitors, and peptide. Remdesivir is strongly forming h-bonds with crucial Mpro residues, Cys145, and His164. Further, MD simulation analysis also confirmed, that these residues are forming H-bond with Remdesivir during 100 ns simulations run and found stable (∼99%) by RMSD and RMSF. Thus, present in silico study at molecular approaches suggest that, Remdesivir is a potent therapeutic inhibitor against 2019-nCoV. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Vankudavath Raju Naik
- Extension and Training Division, ICMR-National Institute of Nutrition, Hyderabad, India
| | - Manne Munikumar
- NIN-TATA Centre for Excellence in Public Health Nutrition, ICMR-National Institute of Nutrition, Hyderabad, India
| | | | - Medithi Srujana
- Symbiosis Institue of Health Sciences, Symbiosis International (Deemed University), Pune, India
| | - Giridhar Goudar
- Food Quality Analysis and Biochemistry Division, Biochem Research and Testing Laboratory, Dharwad, India
| | - Pittla Naresh
- NIN-TATA Centre for Excellence in Public Health Nutrition, ICMR-National Institute of Nutrition, Hyderabad, India
| | | | - Rajkumar Hemalatha
- Division of Clinical Epidemiology, ICMR-National Institute of Nutrition, Hyderabad, India
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