24 results on '"Selvaa Kumar, C."'
Search Results
2. Comparative docking studies to understand the binding affinity of nicotine with soluble ACE2 (sACE2)-SARS-CoV-2 complex over sACE2
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Selvaa Kumar C., Senthil Arun Kumar, and Haiyan Wei
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Nicotine ,Soluble ACE2 ,Neuronal nicotinic acetylcholine receptor ,SARS-CoV-2 ,sACE2-INS1 complex ,Smokers ,Toxicology. Poisons ,RA1190-1270 - Abstract
The study aimed to validate the proficiency of nicotine binding with the soluble angiotensin-converting enzyme II receptor (sACE2) with or without SARS-CoV-2 in the context of its binding affinity. Modelled human sACE2 and the spike (S1) protein of Indian SARS-CoV-2 (INS1) docked with each other. On the other hand, nicotine docked with sACE2 in the presence or absence of SARS-CoV-2. Nicotine established a stable interaction with negatively charged Asp368 of sACE2, which in turn binds with amino acids like Thr362, Lys363, Thr365, Thr371, and Ala372. In the presence of nicotine, INS1 and sACE2 showed a reduced binding affinity score of -12.6 kcal/mol (Vs -15.7 kcal/mol without nicotine), and a lowered interface area of 1933.6 Å2 (Vs 2057.3Å2 without nicotine). The neuronal nicotinic acetylcholine receptor (nN-AChR) and angiotensin-converting enzyme 2 (ACE2) receptor showed 19.85% sequence identity among themselves. Following these receptors possessed conserved Trp302 and Cys344 amino acids between them for nicotine binding. However, nicotine showed a higher binding affinity score of -6.33 kcal/mol for the sACE2-INS1 complex than the sACE2 alone with -5.24 kcal/mol. A lowered inhibitory constant value of 22.95μM recorded while nicotine interacted with the sACE2-INS1 complex over the sACE2 alone with 151.69 μM. In summary, nicotine showed a profound binding affinity for the sACE2-INS1 complex than the sACE2 alone paving for the clinical trials to validate its therapeutic efficacy as a bitter compound against the SARS-CoV-2 virulence.
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- 2020
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3. Computational and biological approach for studying structure-function of inhibin chimeric peptide antibodies in Clarias batrachus
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Ahmad, Irshad, Bhat, Irfan Ahmad, Jagtap, Dhanashree D., Balasinor, Nafisa H., Selvaa Kumar, C., Chanu, T.I., Rani, Babitha, Dar, Showkat Ahmad, Leya, Tasok, Gora, Adnan Hussain, and Saharan, Neelam
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- 2019
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4. Insights into the flexibility of the T3 loop and GTPase activating protein (GAP) domain of dimeric α and β tubulins from a molecular dynamics perspective.
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Selvaa Kumar C, Nikhil Gadewal, Rajan kumar Choudhary, and Debjani Dasgupta
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- 2019
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5. A novel missense COL10A1 mutation: c.2020G>A; p. Gly674Arg linked with the bowed legs stature in the Schmid metaphyseal chondrodysplasia-affected Chinese lineage
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Qiong Chen, Sheng-Nan Wu, Yong-Xing Chen, Selvaa Kumar C., Lu Zhang, Hai-Yan Wei, and Senthil Arun Kumar
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Schmid metaphyseal chondrodysplasia ,COL10A1 mutation ,Mutant α1(X) chain ,Bowed legs ,Ulna bone ,Early diagnosis ,Diseases of the musculoskeletal system ,RC925-935 - Abstract
To evaluate the clinical-phenotypic characteristics of Schmid metaphyseal chondrodysplasia (SMCD) inflicted by a novel missense mutation of COL10A1 gene: c.2020G > A; p.Gly674Arg.A female child aged about 3 yrs. and 8 months was subjected to Radiograph test to validate the symptoms of SMCD. The polymorphism analysis by the next-generation sequencing (NGS) was performed using the peripheral blood DNA samples of the patient and other family inmates, including, the younger male sibling. The effect of the mutation on the non-collagenous carboxyl-terminal (NC1) domain of collagen X was studied using the SWISS-MODEL online server for trimer modelling; PROSA and PROCHECK-Ramachandran plot for structural validation; Mean Square Plot (RMSF) for structural rigidity.Radiograph examination of lower limbs confirmed the bowed legs in both the patient and her younger brother (study groups). The inheritance of the novel missense mutation of COL10A1: c.2020G > A; p.Gly674Arg (at chromosome-6q22.1) was confirmed in the study groups from the SMCD-affected mother. The extended interactions of the mutant-Arg674 with the Ser552 and Phe589 (β strand B) in the NC1 domain of α1(X) chain monomer is more likely to intervene its trimer formation by weakening the structural rigidity of the crucial strand H compared to its wild type. This plausibly deters the collagen X synthesis inflicting the bowed legs with the altered distal ulna bone morphology in the study groups.The inheritance of COL10A1 mutation: c.2020G > A; p.Gly674Arg has inflicted the SMCD with the characteristic bowed legs in the study groups. Radiograph and NGS could be a valid diagnostic module to initiate the treatment of SMCD.
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- 2020
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6. Evaluation of the antiglycating potential of thymoquinone and its interaction with BSA.
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Kumar, Dinesh, Desa, Amisha, Chougle, Sana, Bhatkalkar, Shruti G., Sachar, Shilpee, Selvaa Kumar, C., and Ali, Ahmad
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- 2022
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7. Insights into the flexibility of the T3 loop and GTPase activating protein (GAP) domain of dimeric α and β tubulins from a molecular dynamics perspective
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Debjani Dasgupta, Rajan Kumar Choudhary, Selvaa Kumar C, and Nikhil Gadewal
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0301 basic medicine ,GTP' ,GTPase-activating protein ,Protein Conformation ,Protein subunit ,Dimer ,Glycine ,Sequence alignment ,GTPase ,Molecular Dynamics Simulation ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Protein Domains ,Tubulin ,Structural Biology ,Animals ,Protein Isoforms ,Amino Acid Sequence ,Pliability ,Structural rigidity ,Binding Sites ,biology ,Organic Chemistry ,Computational Mathematics ,030104 developmental biology ,chemistry ,030220 oncology & carcinogenesis ,Mutation ,Biophysics ,biology.protein ,Anisotropy ,Cattle ,Protein Multimerization ,Sequence Alignment ,Protein Binding - Abstract
Tubulin protein is the fundamental unit of microtubules, and comprises of α and β subunits arranged in an alternate manner forming protofilaments. These longitudinal protofilaments are made up of intra- (α-β) and inter-dimer (β-α) interactions. Literature review confirms that GTP hydrolysis results in considerable structural rearrangement within GTP binding site of β-α dimer interface after the release of γ phosphate. In addition to this, the intra-dimer interface exhibits structural rigidity which needs further investigation. In this study, we explored the reasons for the flexibility and the rigidity of the β-α dimer and the α-β dimer respectively through molecular simulation and Anisotropic Normal Mode based analysis. As per the sequence alignment report, two glycine residues (Gly96 and Gly98) were observed in the T3 loop of the β subunit which get substituted by Asp98 and Ala100 in the T3 loop of the α subunit. The higher mobility of glycine residues contributes to the flexibility of the T3 loop of inter-dimer when they come in direct contact with the GTPase Activating Protein (GAP) domain of the subunit. This was confirmed through RMSD, RMSF and Radius of Gyration based studies. Conversely, the intra-dimer exhibited a lower mobility in the absence of glycine residues. As per ANM based analysis, positive domain correlations were observed between T3 loop and GAP domain of intra- and inter- dimeric contact regions. However, these correlation motions were higher in the intra-dimer as compared to the inter-dimer interface. Thus on the basis of our findings, we hypothesize that the higher flexibility of T3 loop and the GAP domain of the inter-dimer is required for structural rearrangement and protofilament stability during hydrolysis. Furthermore, the slightly rigid nature of the T3 loop and the GAP domain of the intra-dimer assists in enhancing the monomer-monomer interaction through the higher positive domain correlation.
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- 2019
8. A founder variant in the South Asian population leads to a high prevalence ofFANCLFanconi anemia cases in India
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Frank X. Donovan, Kenichi Yoshida, Minoru Takata, Agata Smogorzewska, Babu Rao Vundinti, Avani Solanki, Akifumi Takaori-Kondo, Niranjan Chavan, Yusuke Okuno, Selvaa Kumar C, Minako Mori, Settara C. Chandrasekharappa, Seiji Kojima, Merin George, Hiromasa Yabe, Seishi Ogawa, Sheila Mohan, Arleen D. Auerbach, Aruna Rajendran, Miharu Yabe, Hideki Muramastsu, Ramanagouda Ramanagoudr-Bhojappa, and Akira Shimamoto
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Male ,Asia ,Genotype ,Fanconi Anemia Complementation Group L Protein ,India ,Biology ,Article ,Consanguinity ,03 medical and health sciences ,Fanconi anemia ,Prevalence ,Genetics ,medicine ,Humans ,FANCL ,Gene ,Alleles ,Genetics (clinical) ,030304 developmental biology ,Chromosome Aberrations ,0303 health sciences ,030305 genetics & heredity ,Bone marrow failure ,Genetic disorder ,Genetic Variation ,Cancer ,DNA Repair Pathway ,medicine.disease ,Founder Effect ,Fanconi Anemia ,Mutation ,Female ,Founder effect - Abstract
Fanconi anemia (FA) is a rare genetic disorder characterized by bone marrow failure, predisposition to cancer, and congenital abnormalities. FA is caused by pathogenic variants in any of 22 genes involved in the DNA repair pathway responsible for removing interstrand crosslinks. FANCL, an E3 ubiquitin ligase, is an integral component of the pathway, but patients affected by disease-causing FANCL variants are rare, with only nine cases reported worldwide. We report here a FANCL founder variant, anticipated to be synonymous, c.1092G>A;p.K364=, but demonstrated to induce aberrant splicing, c.1021_1092del;p.W341_K364del, that accounts for the onset of FA in thirteen cases from South Asia, twelve from India and one from Pakistan. We comprehensively illustrate the pathogenic nature of the variant, provide evidence for a founder effect, and propose including this variant in genetic screening of suspected FA patients in India and Pakistan, as well as those with ancestry from these regions of South Asia.
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- 2019
9. Evaluation of the antiglycating potential of thymoquinone and its interaction with BSA
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Kumar, Dinesh, primary, Desa, Amisha, additional, Chougle, Sana, additional, Bhatkalkar, Shruti G., additional, Sachar, Shilpee, additional, Selvaa Kumar, C., additional, and Ali, Ahmad, additional
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- 2021
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10. A novel stop-loss DAX1 variant affecting its protein-interaction with SF1 precedes the adrenal hypoplasia congenital with rare spontaneous precocious puberty and elevated hypothalamic-pituitary-gonadal/adrenal axis responses
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Qiong Chen, Haiyan Wei, Linghua Shen, Selvaa Kumar C, Yongxing Chen, Haihua Yang, and Senthil Arun Kumar
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0301 basic medicine ,Male ,medicine.medical_specialty ,Hypothalamo-Hypophyseal System ,Adolescent ,Secondary sex characteristic ,Puberty, Precocious ,Adrenocorticotropic hormone ,030105 genetics & heredity ,Steroidogenic Factor 1 ,Primary Adrenal Insufficiency ,03 medical and health sciences ,Blood serum ,Adrenocorticotropic Hormone ,Loss of Function Mutation ,Internal medicine ,Genetics ,medicine ,Precocious puberty ,Humans ,Genetics (clinical) ,Binding Sites ,business.industry ,DAX-1 Orphan Nuclear Receptor ,Adrenal hypoplasia ,Bone age ,General Medicine ,medicine.disease ,030104 developmental biology ,Endocrinology ,Codon, Nonsense ,Hypoadrenocorticism, Familial ,DAX1 ,Follicle Stimulating Hormone ,business ,Protein Binding - Abstract
The case study unveils the likely mechanism of a novel stop-loss DAX1 variant preceding the prolonged precocious puberty in the adrenal hypoplasia congenital (AHC) boy. A boy aged five years and nine months initially examined for the primary adrenal insufficiency symptoms. Next-generation sequencing confirmed the X-linked inheritance of a novel stop-loss DAX1 variant: c.1411T>C/p.Ter471Gln associated with AHC in the patient. The patient was subjected to a brief clinical follow-up from 11 to 15.1 years of age. The effect of the mutant-DAX1 variant (p.Ter471Gln) on DAX1-steroidogenic factor 1 (SF1) (protein-protein) interaction was studied by protein-protein docking using the ClusPro-online tool. At 5.9 yrs of age, the patient exhibited precocious puberty with the secondary sexual characteristics of Tanner 2 stage (of 9–14 yrs of age). The patient showed primary adrenal insufficiency with diminished cortisol concentrations at blood serum (25 ng/ml) and urine (3.55 μg/24 h) levels. Upon steroidal exposure, the patient showed normalized serum cortisol levels of 45–61 ng/ml. However, the precocious puberty got prolonged with the increased penis length of 8.5 cm and the bone age of 18 yrs old during the follow-up. The patient showed increased basal serum adrenocorticotropic hormone (110->2000 pg/ml) and follicle-stimulating hormone (18.4–22.3 mIU/ml) concentrations. Following an elevated hypothalamic-pituitary-gonadal axis activity witnessed upon gonarellin stimulation. Protein-protein docking confirmed a weaker interaction between the mutant-DAX1 (p.Ter471Gln) protein and the wild-SF1 protein. Overall, we hypothesize the weakened mutant-DAX1-SF1 (protein-protein) interaction could govern the prolonged precocious puberty augmented with the elevated hypothalamic-pituitary-gonadal/adrenal axis responses via SF1-induced neuronal nitric oxide synthetase activation in the patient.
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- 2020
11. Bioinformatics Based Understanding of Effect of Mutations in the Human β Tubulin Outside Drug Binding Sites and its Significance in Drug Resistance
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Nikhil Gadewal, Selvaa Kumar C, and Debjani Dasgupta
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Drug ,biology ,Chemistry ,media_common.quotation_subject ,Biomedical Engineering ,Health Informatics ,Drug resistance ,Vinblastine ,Tubulin ,Biochemistry ,Computer Science (miscellaneous) ,medicine ,biology.protein ,Binding site ,medicine.drug ,media_common - Abstract
Background: Human β tubulin displays resistance to drugs like Taxol and Vinblastine due to amino acids substitutions within and outside the drug binding site. Objective: This study focuses on the effect of amino acid substitutions outside the drug binding site on drug resistance. Amino acid substitution like R306C (mut2) is associated with Taxol resistance and D197N (mut1) and K350N (mut3) are associated with Vinblastine resistance. However, the mechanism of resistance has not been understood yet. This study has attempted to investigate the mechanism of resistance. Methods: SWISSMODEL server was used to model the wild and the mutant β subunits which were later considered for protein-protein and protein-ligand docking using HADDOCK and AutoDock 1.5.6 software respectively. Dimer mutants were generated using Swisspdbviewer. POCASA 1.1 server was used to calculate the overall effect of substitution on pocket volume and the effect of substitution on domain mobility was explored using GROMACS software. Results: From sequence perspective, amino acid replacement in all three positions viz. D197N (mut1), R306C (mut2) and K350N (mut3) were found to have a deleterious effect on the stability of the protein. This study was further confirmed through structural analysis. Change in hydrogen bonding pattern was observed within the site of substitution in modeled mut1 and mut3 which is known to be specifically involved in Vinblastine interaction. In mut2 associated with Taxol binding, the hydrogen bonding pattern remained unaltered. All three mutants showed better protein-protein (β-β) interactions compared to the wild-type. Pocket size analysis in β subunit revealed that Taxol binding site increased in size after substitution in mut2 compared to the wild-type. However, the size of the Vinblastine binding site in the dimer interface remained the same before and after the substitution in wild and the mutants. Wild-type (β monomer and αβ dimer) associated with Taxol and Vinblastine, respectively showed better drug interaction compared to their mutants. Conclusion: This study throws light on the mechanism of drug resistance due to amino acid substitutions outside the drug binding site. It was found that amino acid substitution outside the drug site enhanced protein-protein interaction between the β-β subunits.
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- 2018
12. Imatinib resistance due to a novel and rare class of mutation at position S348 (1043nt C→A) of Bcr/Abl gene in a chronic myeloid leukemia patient
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Somprakash Dhangar, Selvaa Kumar C, Babu Rao Vundinti, and S Chandrakala
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03 medical and health sciences ,Cancer Research ,0302 clinical medicine ,ABL ,Oncology ,Imatinib resistance ,030220 oncology & carcinogenesis ,Mutation (genetic algorithm) ,Cancer research ,Myeloid leukemia ,Hematology ,Biology ,030215 immunology - Published
- 2018
13. Risk association of BST2 gene variants with disease progression in HIV-1 infected Indian cohort
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Gupte, Divyambari S., primary, Patil, Amol, additional, Selvaa Kumar, C., additional, Pandey, Sudhanshu, additional, Achrekar, Swati K., additional, Paranjape, Ramesh S., additional, and Jagtap, Dhanashree D., additional
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- 2020
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14. New Insights of Inhibins in Ovarian Physiology of Fish
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Ahmad, Irshad, primary, Bhat, Irfan Ahmad, additional, Jagtap, Dhanashree D., additional, Selvaa Kumar, C., additional, Ferosekhan, S., additional, and Afonso, Luis O. B., additional
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- 2020
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15. Binding behaviour of aminoglycoside drug kanamycin with calf thymus DNA: Thermodynamic, spectroscopic and molecular modelling studies
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Neelam Keswani, Aparna Panicker, and Selvaa Kumar C
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Circular dichroism ,Hydrogen bond ,Aminoglycoside ,Isothermal titration calorimetry ,Kanamycin ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,Binding constant ,010406 physical chemistry ,0104 chemical sciences ,chemistry.chemical_compound ,chemistry ,Biophysics ,medicine ,Molecule ,Physical and Theoretical Chemistry ,0210 nano-technology ,Instrumentation ,DNA ,medicine.drug - Abstract
In this work, the binding mode of antibiotic drug kanamycin with Calf thymus DNA (ctDNA) was assessed using thermodynamic, spectroscopic and molecular docking studies. Isothermal Titration Calorimetry (ITC) studies suggest that the binding is enthalpically favored with a small entropic change and a binding constant of the order of 104 mol−1 dm3, which remains almost same in the studied temperature range. Studies in the presence of osmolytes tetraethylene glycol and sucrose show no appreciable change in the binding behaviour as well as on the stability of the DNA-kanamycin complex. These finding suggests that the number of water molecule released or taken up is not significant in the binding process. Competitive fluorescence displacement assay and circular dichroism studies show that kanamycin follows groove binding mode of interaction. Molecular docking studies also supports that kanamycin prefers groove binding mode, stabilized by hydrogen bonding.
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- 2021
16. An in silico based characterization and analysis of Human matrix metalloproteinases (MMPs)
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null Pritam Kumar Panda and null Selvaa Kumar C
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Background and aims: Potentially involved proteins which are implicated as a specific target for any diseased condition mayimplicate certain unusual features in several pathological conditions. Human Matrix metalloproteinase (MMP) family ofendopeptidases is one such family responsible for many beneficial as well as several pathological critical diseases. With the adventof field of bioinformatics and computational efforts can aid researchers to comprehend their system of work. Methodology: Aninsilico characterization of the MMP family has been carried out to analyze their primary, secondary, structural and functionalperspective . The research has been focused on specific MMPs in which the further study was based on Mutational analysisconfirming the pathogenicity of MMPs in cancer metastasis. The basic approach was to screen large protein families which playsdual role during normal and diseased conditions. Results: Thus it is hypothesized that cysteine rich and highly thermostableMMPs might be key players in diseased conditions. Conclusion: It can also be concluded that the disease responsive MMPs mightbe considered as promising targets for treatment of cancer.
- Published
- 2015
17. Dipeptidyl peptidase IV Inhibitory activity of Terminalia arjuna attributes to its cardioprotective effects in experimental diabetes: In silico, in vitro and in vivo analyses
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Ipseeta Ray Mohanty, Ujwala Maheshwari, Selvaa Kumar C, and Manjusha K. Borde
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Male ,animal structures ,Cardiotonic Agents ,Dipeptidyl Peptidase 4 ,Myocardial Infarction ,Pharmaceutical Science ,Pharmacology ,Dipeptidyl peptidase ,Diabetes Mellitus, Experimental ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,In vivo ,Drug Discovery ,medicine ,Animals ,Humans ,Hypoglycemic Agents ,Vildagliptin ,Computer Simulation ,Gallic acid ,Rats, Wistar ,030304 developmental biology ,0303 health sciences ,Dipeptidyl-Peptidase IV Inhibitors ,biology ,Chemistry ,Plant Extracts ,Saponins ,biology.organism_classification ,Triterpenes ,Molecular Docking Simulation ,Complementary and alternative medicine ,Diabetes Mellitus, Type 2 ,Docking (molecular) ,030220 oncology & carcinogenesis ,Sitagliptin ,Terminalia ,Molecular Medicine ,Terminalia arjuna ,medicine.drug ,Ellagic acid - Abstract
Background The marketed synthetic (Dipeptidyl peptidase-IV) DPP-IV Inhibitors are expensive antidiabetic drugs and have been reported to cause unacceptable adverse effects such as pancreatitis, angioedema, thyroid and pancreatic cancers. In this scenario research to develop novel DPP-IV Inhibitors from alternative sources is the need of the hour. Hypothesis/purpose Terminalia arjuna, a medicinal herb with antidiabetic and cardioprotective activities may represent a natural DPP-IV Inhibitor, the DPP-IV Inhibitory activity of which may translate into demonstrable therapeutic benefits in setting of diabetes with cardiovascular co-morbidities. Study design The study type used for the present study was an experimental (In vitro, In vivo and In silico) design. Method The DPP-IV Inhibitory, antidiabetic and cardioprotective effects of Terminalia arjuna was evaluated in the experimental model of myocardial infarction co-existing with diabetes. To determine the active principle of Terminalia arjuna responsible for DPP-IV Inhibitory activity, the crystal structure of DPP-IV was considered as receptor which was docked against Arjunetin, Arjungenin, Arjunic acid, Arjunone, Ellagic acid, Gallic acid, Sitagliptin and Vildagliptin. The binding sites as well as affinity of various active ingredients of Terminalia arjuna for DPP- IV enzyme was elucidated using in silico studies and compared to Vildagliptin. Results Terminalia arjuna demonstrated significant DPP-IV Inhibitory, antidiabetic (significant reduction in HbA1C) and cardioprotective effects (restoration of myocardial CPK-MB) in the experimental model of myocardial infarction co-existing with diabetes. The cardioprotective efficacy correlated to its DPP-IV Inhibitory activity. The active ingredients of Terminalia arjuna (Arjunetin, Arjungenin, Arjunic Acid Arjunone, Ellagic acid and Gallic acid) demonstrated significant inhibition of DPP-IV enzyme. Arjunic acid and Arjunone prefers the active site pocket of DPP-IV enzyme. Compounds like Arjunetin and Vildagliptin prefers to bind near the interface region of the DPP-IV as their biological active forms are homodimer. Sitagliptin binds near the α/β hydrolase domain. Conclusion The DPP-IV Inhibitory activity of Terminalia arjuna was found to be comparable to Vildagliptin. The DPP-IV Inhibitory activity translated into significant cardioprotective effects in the setting of diabetes. The active ingredient of Terminalia arjuna; Arjunetin, Arjungenin, Ellagic acid and Arjunic acid showed superior DPP-IV Inhibitory activity as compared to synthetic DPP-IV inhibitors (Sitagliptin and Vildagliptin) based on results of docking studies.
- Published
- 2018
18. Structure modeling and dynamics driven mutation and phosphorylation analysis of Beta-amyloid peptides
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Ved Prakash, Selvaa kumar C, Ankita singh, and Sunil Kumar Singh
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Mutation ,Alzheimer׳s disease ,Amyloid ,Beta sheet ,General Medicine ,Hypothesis ,Biology ,medicine.disease_cause ,Bioinformatics ,medicine.disease ,Gromos ,Cell biology ,Aβ protein ,medicine ,Extracellular ,Phosphorylation ,Alzheimer's disease ,Amyloid-beta peptide ,UCSF Chimera ,Beta (finance) ,PPI-Pred ,Argus Lab ,Amyloid-beta precursor protein - Abstract
The most common characteristics of diverse age-related neurodegenerative diseases are aggregation and accumulation of the misfolded protein in the brain. Alzheimer׳s disease (AD) is one of these protein conformational diseases. Extracellular accumulation of amyloid β (Aβ) is one the neuropathological hallmarks of Alzheimer disease. Various studies have shown that mutation in specific hydrophobic region of Aβ protein inhibit the formation of β sheet, thus aggregation of this protein is stalled. The identification of such mutation in Aβ protein can help us in elucidating the etiology of sporadic Aβ. In our study we have selected three positions: 19ILU, 21ALA and 41ILU in Aβ protein based on their hydrophobic nature and substituted them with PRO ( βSheet breaker). The effects of the substitutions were analysed using molecular dynamics simulation studies. The results validated that the mutations in the specified regions change the hydrophobicity of the protein and the βsheet formation was declined to zero per cent.
- Published
- 2014
19. Molecular characterization of inhibin-A: Structure and expression analysis in Clarias batrachus
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Ahmad, Irshad, primary, Jagtap, Dhanashree D., additional, Selvaa Kumar, C., additional, Balasinor, Nafisa H., additional, Babitha Rani, A.M., additional, Agarwal, Deepak, additional, and Saharan, Neelam, additional
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- 2018
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20. Identification of Leads from Marine Seaweeds against Human β-tubulin
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Selvaa Kumar C, Nikhil Gadewal, and Sudheer M.M. Mohammed
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Drug Discovery ,Pharmaceutical Science ,Molecular Medicine - Published
- 2013
21. Identification of Leads from Marine Seaweeds against Human β-tubulin
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Selvaa Kumar C, Nikhil Gadewal, and Sudheer M. M. Mohammed
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biology ,Chemistry ,Stereochemistry ,Pharmaceutical Science ,macromolecular substances ,biology.organism_classification ,Anticancer drug ,Brown algae ,Tubulin ,Biochemistry ,Microtubule ,Drug Discovery ,Helix ,biology.protein ,Molecular Medicine ,Cancer cell lines ,Binding site ,Conformational isomerism - Abstract
Tubulin has received more attention as potent anticancer drug target because it is the fundamental unit of microtubules and plays an active role in cell division. The drugs against �-tubulin are mainly derived from terrestrial plants and marine resources. Of these, red and brown algae from the marine environment produce better secondary metabolites. These compounds are found to be active against cancer cell lines. Since there is no study reported till date about the activity of these compounds against human � -tubulin, we have investigated the role of 517 compounds available in the seaweed secondary metabolites database against modeled human � -tubulin. All the conformers of lead compounds (RL381, RL366, RL376 and RG012) when docked at the taxol binding site showed better interactions with the H1-S2 loop and M-loop which are actively involved in lateral interactions of tubulins and also with the helix H7 which is the connecting link between N-terminal and intermediate domain. Important residues involved in polar interaction by these lead compounds were D224, H227, R276, R282 and R359 which closely mimicked the interaction of taxol with � -tubulin. We then attempted to calibrate the available molecules based on their Lipinski rule, binding affinity and other descriptor based comparison to identify potential lead molecules which could be used as drugs against humantubulin.
- Published
- 2012
22. HbAHP-25, an In-Silico Designed Peptide, Inhibits HIV-1 Entry by Blocking gp120 Binding to CD4 Receptor
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Selvaa kumar C, Mandar Patgaonkar, Achhelal R. Pasi, Kudumula Venkata Rami Reddy, and Tahir Bashir
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Male ,Models, Molecular ,Protein Conformation ,viruses ,HIV Core Protein p24 ,HIV Infections ,Peptide ,Plasma protein binding ,HIV Antibodies ,HIV Envelope Protein gp120 ,Epitope ,Epitopes ,Hemoglobins ,HIV Fusion Inhibitors ,Peptide sequence ,chemistry.chemical_classification ,Multidisciplinary ,biology ,Antibodies, Monoclonal ,virus diseases ,Vesicular stomatitis virus ,CD4 Antigens ,Medicine ,Female ,Antibody ,Protein Binding ,Research Article ,Adult ,Sexual transmission ,Cell Survival ,Science ,Molecular Sequence Data ,Virus ,Cell Line ,Young Adult ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Virus Internalization ,biology.organism_classification ,Virology ,Molecular biology ,Peptide Fragments ,Rats ,chemistry ,HIV-1 ,biology.protein ,Peptides - Abstract
Human Immunodeficiency Virus (HIV-1) poses a serious threat to the developing world and sexual transmission continues to be the major source of new infections. Therefore, the development of molecules, which prevent new HIV-1 infections, is highly warranted. In the present study, a panel of human hemoglobin (Hb)-α subunit derived peptides and their analogues, with an ability to bind gp120, were designed in-silico and their anti-HIV-1 activity was evaluated. Of these peptides, HbAHP-25, an analogue of Hb-α derived peptide, demonstrated significant anti-HIV-1 activity. HbAHP-25 was found to be active against CCR5-tropic HIV-1 strains (ADA5 and BaL) and CXCR4-tropic HIV-1 strains (IIIB and NL4-3). Surface plasmon resonance (SPR) and ELISA revealed direct interaction between HbAHP-25 and HIV-1 envelope protein, gp120. The peptide prevented binding of CD4 to gp120 and blocked subsequent steps leading to entry and/or fusion or both. Anti-HIV activity of HbAHP-25 appeared to be specific as it failed to inhibit the entry of HIV-1 pseudotyped virus (HIV-1 VSV). Further, HbAHP-25 was found to be non-cytotoxic to TZM-bl cells, VK2/E6E7 cells, CEM-GFP cells and PBMCs, even at higher concentrations. Moreover, HbAHP-25 retained its anti-HIV activity in presence of seminal plasma and vaginal fluid. In brief, the study identified HbAHP-25, a novel anti-HIV peptide, which directly interacts with gp120 and thus has a potential to inhibit early stages of HIV-1 infection.
- Published
- 2015
23. Seminal role of deletion of amino acid residues in H1-S2 and S-loop regions in eukaryotic β-tubulin investigated from docking and dynamics perspective
- Author
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Selvaa Kumar, C, primary, Gadewal, Nikhil, additional, and Mohammed, Sudheer MM, additional
- Published
- 2015
- Full Text
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24. Molecular docking analysis of hyperphosphorylated tau protein with compounds derived from Bacopa monnieri and Withania somnifera.
- Author
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Dixit H, Selvaa Kumar C, Dasgupta D, and Gadewal N
- Abstract
Tau protein, the major player in Alzheimer's disease forms neurofibrillary tangles in elderly people. Bramhi (Baccopa Monniera) is often used as an ayurvedic treatment for Alzheimer's disease. Therefore it is of interest to study the interaction of compounds derived from Baccopa with the Tau protein involved in tangle formation. We show that compounds such as bacopaside II, bacopaside XII, and nicotine showed optimal binding features with the R2 repeat domain of hyperphosphorylated tau protein for further consideration in the context of Alzheimer's disease (AD)., Competing Interests: There are no conflicts of interest., (© 2021 Biomedical Informatics.)
- Published
- 2021
- Full Text
- View/download PDF
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