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Bioinformatics/ BIF Centre

 

JAMIA HAMDARD

Hamdard Nagar, Delhi 110062

 

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Centre name

Bioinformatics Infrastructure Facility/ BIF Centre
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Year of establishment

2008 (Established under the Bioinformatics Systems Network, BTISNet, scheme of DBT, Ministry of Science & Technology)
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Funding

DBT (2008 – 2020, March 31)

Jamia Hamdard (April 1, 2020 onwards)
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Coordinators

Prof. Shakir Ali, Professor of Biochemistry, SCLS

Dr. Mymoona Akhtar, Associate Professor, SPER
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Status

A central facility of Jamia Hamdard
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Mandate

To expose students and researchers to the use of computational powers of the machines and bioinformatics in solving biological problems
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Focus

Theoretical & Computational Biology, experimental validation and capacity building – Drug discovery, Drug repurposing, ePharmacophore modelling, Systems and Network Biology and Medicine, Comparative Genomics, Disease gene mapping, Structural Biology, In silico drug design and vaccine design, Molecular medicine, Metabolic pathway studies, Biological evolution, Modelling biological systems, Data mining and analysis of large scale data, Biophysics, Complex systems, Big data analysis, Machine Learning applications for biological and medical and analysis, Pattern recognition, Data Science, Artificial intelligence, Engineering biological pathways, Study of dynamical patterns, Dynamical network theory, Electronic representation of biological modules, Modelling disease dynamics and epidemic - Modelling and analysis of disease spreading models, namely, SI, SIR, SEIR, etc. Capacity building.
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Key objectives

 

1)  Developing computational and statistical methods to integrate the genotype-phenotype, protein-protein interactions and single cell transcriptomics datasets and pathways to systems level understanding of disease mechanisms, which could ultimately translate into precise identification of potential targets.

2)  Integration of existing genomic and pharmacogenomic to identify drug mechanisms and new uses of existing drugs.

3)  Developing deep learning based chemical informatics methods for QSAR models, virtual screening and molecular modelling and docking studies.

4)  Development of analysis and visualization tools for scientific community through R-cloud and web servers.

5)   Infrastructure and technical skill development.
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Infrastructure

Hardware: Database/Application server and a medium end (Proxy & File) server; Desktops/OS (11), Optiplex (2) Workstations (4)

 

Software (licenced): SYBYL-X suite (3D-QSAR modules—CoMFA, CoMSIA for H-bonding properties and scoring combinatorial libraries, and Topomer CoMFA for Homology modelling and docking); GOLD for virtual screening, lead optimization and correct binding mode identification of active molecules; RECORE for Scaffold hopping based on small molecule crystal structure conformations; Schrodinger package—Glide (Ligand-receptor docking), Canvas (Cheminformatics computing environment), ConfGen (Bioactive conformational searching), CovDock (Pose prediction and scoring of covalently bound ligands), Epik (pKa prediction), Phase (Pharmacophore modeling solution for ligand- and structure-based drug design), SiteMap (Binding site identification), BioLuminate (Modeling solution for biologics), Prime (Protein structure prediction), Desmond (High-performance MD simulations) and FEP+ (High-performance free energy calculations)
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Programs of study (supported by the centre)

The centre gets enrolled PhD and more recently MSc students. PhD students working at the centre are registered in the School of Interdisciplinary Sciences & Technology, while the MSc students are affiliated with the Department of Computer Science, School of Engineering Science & Technology.

More than a dozen students working at the BIF Centre have been awarded PhD in Bioinformatics
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Training

The centre offers support and training to students and staff of Jamia Hamdard and also other institutions and conducts workshops, seminars and conferences in the area of bioinformatics research.
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Research

The centre has conducted research and, supported by the experimental validation, has published numerous papers.
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Publications

(1)     Mangangcha IR, Brojen Singh RK, Lebeche D, Ali S (2021). Xanthone glucoside 2-β-D-glucopyranosyl-1,3,6,7-tetrahydroxy-9H-xanthen-9-one binds to the ATP-binding pocket of glycogen synthase kinase 3β and inhibits its activity: implications in prostate cancer and associated cardiovascular disease risk. J Biomol Struct Dyn. PMID: 33769184, doi: 10.1080/07391102.2021.1902857. 

(2)     Sharma S, Srivastav S, Singh G, Singh S, Malik R, Alam MM, Shaqiquzamman M, Ali S, Akhter M. (2021) In silico strategies for probing novel DPP-IV inhibitors as anti-diabetic agents. J Biomol Struct Dyn. doi: 10.1080/07391102.2020.1751714. 

(3)     Mangangcha IR, Malik MZ, Kucuk O, Ali S, Singh RKB. (2020) Kinless hubs are potential target genes in prostate cancer network. Genomics 112(6):5227-5239. doi: 10.1016/j.ygeno.2020.09.033. PMID: 32976977 

(4)     Khan, B, Naiyer, A., Athar, F., Ali, S., Thakur, S.C. (2020) Synthesis, characterization and anti-inflammatory activity evaluation of 1,2,4-triazole and its derivatives as a potential scaffold for the synthesis of drugs against prostaglandin-endoperoxide synthase, J Biomol Struct Dyn.,doi: 10.1080/07391102.2019.1711193 

(5)     Sardar R, Katyal N, Ahamad S, Jade DD, Ali S, Gupta D (2020). In-silico profiling and structural insights into the impact of nSNPs in the P. falciparum acetyl-CoA transporter gene to understand the mechanism of drug resistance in malaria, J Biomol Struct Dyn. 1-12. doi.org/10.1080/07391102.2020.1711807 

(6)     Shinkafi, T.S., Kaushik, A., Mahmood, A., Tiwari, A.K., Alam, M.M., Akhter, M., Gupta, D., Ali, S. (2019) Computational prediction and experimental validation of the activator function of C2-β-D-glucopyranosyl-1,3,6,7-tetrahydroxyxanthone on pancreatic and hepatic hexokinase. J Biomol Struct Dyn., doi: 10.1080/07391102.2019.1650829 

(7)     Mangangcha, I.R., Malik, M.Z., Küçük, Ö., Ali, S., Singh, R.K.B. (2019) Identification of key regulators in prostate cancer from gene expression datasets of patients. Scientific Reports, 9:16420 | doi.org/10.1038/s41598-019-52896-x

(8)     Sardar, R., Kaushik, A., Pandey, R., Mohmmed, A., Ali, S., Gupta, D. (2019) ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors. Database – the Journal of Biological Database and Curation, 1-10

(9)     Shrivastava, A., Srivastava, S., Malik, R.,  Alam, M.M., Shaqiquzamman, M., Akhter, M. (2019). Identification of novel small molecule non-peptidomimetic inhibitor for prolyl oligopeptidase through in silico and in vitro approaches. J Biomol Struct Dyn. https://doi.org/10.1080/07391102.2019.1602078

(10) Sharma, S., Srivastava, S., Shrivastava, A., Malik, R., Almalki, F., Saifullah, K., Alam, M.M., Shaqiquzzaman, M., Ali, S., Akhter, M (2019) Mining of potential dipeptidyl peptidase-IV inhibitors as anti-diabetic agents using integrated in silico approaches, J Biomol Struct Dyn., DOI: 10.1080/07391102.2019.1701553

(11) Sharma, K., Tanwar, O., Deora, G.S., Ali, S., Alam, M.M., Zaman, M.S., Krishna, V.S., Sriram, D., Akhter, M. (2019) Expansion of a novel lead targeting M. tuberculosis DHFR as antitubercular agents. Bioorganic & Medicinal Chemistry, 27, 1421–1429. https://doi.org/10.1016/j.bmc.2019.02.053

(12) Sharma, K., Shrivastava, A., Tiwari, P., Sharma, S., Zaman, M.S., Akhter, M. (2019) 3D QSAR based virtual screening of Pyrido [1, 2-a] benzimidazoles as potent antimalarial agents. Lett. Drug Design Dis. 16, 301-312

(13) Sharma, K., Tanwar, O., Sharma, S., Ali, S., Alam, M.M., Zaman, M.S., Akhter, M. (2018) Structural comparison of Mtb-DHFR and h-DHFR for design, synthesis and evaluation of selective non-pteridine analogues as antitubercular agents. Bioorganic Chemistry 80, 319-333

(14) Kumar, G., Tanwar, O., Kumar, J., Akhter, M., Sharma, S., Pillai, C.R., Alam, M.M., Zama, M.S. (2018) Pyrazole-pyrazoline as promising novel antimalarial agents: a mechanistic study. Eur. J. Med. Chem. 149, 139-147

(15) Sharma, K., Shrivastava, A., Mehra, R.N., Deora, G.S., Alam, M.M., Zaman, M.S., Akhter, M. (2018) Synthesis of novel benzimidazole acrylonitriles for inhibition of Plasmodium falciparum growth by dual target inhibition. Arch Pharm (Weinheim) 35, 1-13

(16) Akhter, M., Tasleem, M., Alam, M.M., Ali, S. (2017) In silico approach for bioremediation of arsenic by structure prediction and docking studies of arsenite oxidase from Pseudomonas stutzeri TS44. International Biodeterioration and Biodegradation 122, 82-91

(17) Kaushik, A., Ali, S., Gupta, D. (2017) Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways. Scientific Reports 7, 40450, doi:10.1038/srep40450

(18) Pandey, A.K., Sharma, S., Pandey, M., Alam, M.M., Zaman, M.S., Akhter, M. (2016) 4,5-Dihydrooxazole-Pyrazoline hybrids: Synthesis and their evaluation as potential antimalarial agents. Eur J Med Chem 123, 476-86

(19) Sharma, S., Paliwal, S., Singh, S., Akhter, M. (2016) Molecular modeling of viral nucleocapsid protein Zn fingers modulators. Ind J Biochem Biophy 53, 24-38

(20) Sharma, S., Singh, S., Akhter, M., Paliwal, S. (2016) Similarity analysis studies on (sulfonyl) benzene derivatives as anti-HIV agents. Internat J Pharm Chem Anal 174-182

(21) Shrivastava, A, Kumar, J., Akhter, M., Alam, M.M., Zaman, M.S. (2016) In-silico assessment of various PDB entries of Pf LDH enzyme for their use in SBDD, Chemical Informatic 2, 1-9

(22) Akhter, M. (2016) Challenges in docking: mini review. JSM Chemistry 2, 1-8

(23) Yaseen, R., Pushpalatha, H., Akthar, M., Sharma, K., Shafi, S., Singh, S., Javed, K. (2016) Design and synthesis of pyridazinone-substituted benzenesulphonylurea derivatives as anti-hyperglycaemic agents and inhibitors of aldose reductase - an enzyme embroiled in diabetic complications, J Enzyme Inhib Med Chem 31(6):1415-1427

(24) Khan, M.F., Verma, G., Akhter, W., Shaquiquzzaman, M., Akhter, M., Rizvi, M.A., Alam, M.M. (2016) Pharmacophore modeling, 3D-QSAR, docking study and ADME prediction of acyl 1,3,4-thiadiazole amides and sulfonamides as antitubulin agents, Arab J Chem, http://dx.doi.org/10.1016/j.arabjc.2016.11.004

(25) Akhtar, W., Shaquiquzzaman, M., Akhter, M., Verma, G., Khan, M.F., Alam, M.M. (2016) The therapeutic journey of pyridazinone, Eur J Med Chem, 123:256-281   

(26) Khan, M.F., Alam, M.M., Verma, G., Akhtar, W., Akhter, M., Shaquiquzzaman, M. (2016) The therapeutic voyage of pyrazole and its analogs: a review, Eur J Med Chem 14:170-201

(27) Verma, G., Khan, M.F., Akhtar, W., Alam, M.M., Akhter, M., Alam, O., Hasan, S.M., Shaquiquzzaman, M. (2016) Pharmacophore modeling, 3D-QSAR, docking and ADME prediction of quinazoline based EGFR Inhibitors, Arab J Chem, doi.org/10.1016/j.arabjc.2016.09.019

(28) Chhabra, S., Shaquiquzzaman, M., Alam, M.M., Akhter, M. (2016) Oxazolones: a review of its synthesis, J Pharm Med Chem 2:109-113

(29) Khan, M.F., Verma, G., Akhter, W., Akhter, M., Alam, M.M., Shaquiquzzaman, M. (2016) Microwave assisted aynthesis and antimalarial activity of coumarin-pyrazoline hybrids, J Pharm Med Chem, 2(2):137-40

(30) Hameed, A.D., Akhtar, M., Javed, K. (2016) Synthesis and biological evaluation of new phthalazinone derivatives as anti-inflammatory and anti-proliferative agents, Arch Pharm Chem Life Sci 349:150-159

(31) Rawat, N., Akhtar, W., Shaquiquzzaman, M., Akhter, M., Hussain, A., Alam, M.M. (2016) A review on a cystic fibrosis transmembrane conductance regulator potentiator-IVacaftor, World J Pharmacy and Pharm Sci 5:11

(32) Shaquiquzzaman, M., Verma, G., Marella, A., Akhter, M., Akhtar, W., Khan, M.F., Tasneem, S., Alam, M.M. (2015) Piperazine scaffold: a remarkable tool in generation of diverse pharmacological agents, Eur J Med Chem, 102:487-529

(33) Marella, A., Shaquiquzzaman, M., Akhter, M., Verma, G., Alam, M.M. (2015) Novel pyrazole–pyrazoline hybrids endowed with thioamide as antimalarial agents: their synthesis and 3D-QSAR studies, J Enz Inhib Med Chem 30:597-606

(34) Saha, R., Alam, M.M., Akhter, M. (2015) Novel hybrid-pyrrole derivatives: their synthesis antitubercular evaluation and docking studies, RSC Advances 5:12807-820

(35) Saha, R., Tanwar, O., Alam, M.M., Shaquiquzzaman, M., Akhter, M. (2015) Pharmacophore based virtual screening, synthesis and SAR of novel inhibitors of Mycobacterium sulfotransferase, Bioorg Med Chem Lett 25:701-707

(36) Marella, A., Akhter, M., Shaquiquzzaman, M., Tanwar, O., Verma, G., Alam, M.M. (2015) Synthesis, 3D QSAR and docking studies of pyrimidine nitrile pyrazolone: a novel class of hybrid antimalarial agents, Med Chem Res 24:1018-1037

(37) Akhter, M., Tanwar, O., Saha, R., Alam, M.M. (2015) Synthesis and antimalarial activity of quinoline substituted furanone derivatives and their identification as selective falcipain-2 inhibitors Med Chem Res 24:879-890

(38) Ali, M.R., Verma, G., Shaquiquzzaman, M., Akhter, M., Alam, M.M. (205) Synthesis and anticonvulsant activity of some newer dihydro-pyrimidine-5-carbonitrile derivatives: Part II, J Taibah Univ Med Sci 10:437-443

(39) Alam, M.A., Alam, M.M., Shaquiquzzaman, M., Khan, S.A., Akhter, M. (2015) Synthesis, in-silico studies of new substituted pyrazolone based hydrazone derivatives and their biological activities, Inter J Pharm Chem Anal 2:65-73

(40) Kumar, J., Akhtar, M., Ranjan, C., Chawla, G. (2015) Design, synthesis and neuropharmacological evaluation of thiophene incorporated isoxazole derivatives as antidepressant and antianxiety agents activities, Inter J Pharm Chem Anal 2:74-8

(41) Akhter, W., Marella, A., Zaman, M.S., Akhter, M., Alam, M.M. (2015) Microwave assisted synthesis of pyrazoline-coumarin hybrids and their in vitro antimalarial evaluation, J Pharmacy Res 9:318-322

(42) Kaushik, A., Bhatia, Y., Ali, S., Gupta, D. (2015) Gene network rewiring to study melanoma stage progression and elements essential for driving melanoma, PLoS ONE 10(11)

(43) Nargotra, A., Rukmankesh, Ali, S., Koul, S. (2014) Structural characterization of Bacillus subtilis membrane protein Bmr: an in silico approach, Curr Comput Aided Drug Des 10:226-36

(44) Akhter, M., Sharma, K., Alam, M.M., Zaman, M.S., Husain, A., Ali, S., Shah, A.K.  (2014) Structure assessment analysis of core domain of seven protein data bank entries of HIV-1 protease using different in silico techniques. Current Enzyme Inhibition 2014, 10, 98-104.

(45) Tanwar, O., Tanwar, L., Shaquiquzzaman, M., Alam, M.M., Akhter, M. (2014) Structure based virtual screening of MDPI database: discovery of structurally diverse and novel DPP-IV inhibitors. Bioorg Med Chem Lett. 24(15):3447-51. doi: 10.1016/j.bmcl.2014.05.076.

(46) Tanwar, O., Deora, G.S., Tanwar, L., Kumar, G., Janardhan, S., Alam, M.M., Shaquiquzzaman, M., Akhter M. (2014) Novel hydrazine derivatives as selective DPP-IV inhibitors: findings from virtual screening and validation through molecular dynamics simulations. J Mol Model. 20(4):2118. doi: 10.1007/s00894-014-2118-27.

(47) Marella, A., Akhter, M., Shaquiquzzaman, M., Husain, A., Akhter, M., Verma, G., Alam, M.M. (2014) Synthesis and in-vitro antimalarial evaluation of pyrazoline: a new antimalarial scaffold, J Pharm Res 8:77-80

(48) Marella, A., Tanwar, O., Saha, R., Alam, M.M., Zaman, M.S., Akhter, M. (2013) 3D Quantitative structure-activity relationship for quinoline, benzimidazole and benzofuran-based analogs as phosphodiesterases IV (PDE-IV) inhibitors, Medicinal Chemistry Research 22 (11):5153-5166

(49) Tanwar, O., Marella, A., Shrivastava, S., Alam, M.M., Akhtar, M. (2013) Pharmacophore model generation and 3D-QSAR analysis of N-acyl and N-aroylpyrazolines for enzymatic and cellular B-Raf kinase inhibition, Medicinal Chemistry Research 22(5):2174-2187

(50) Tanwar, O., Saha, R., Alam, M.M., Akhtar, M. (2012) 3D-QSAR of amino-substituted pyrido[3,2β]pyrazinones as PDE-5 inhibitors, Medicinal Chemistry Research 21(2):202-211
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Connecting Science with the society – Success story

 

Connecting Science with the society – Success story

Bioremediation of arsenic

According to a report in Times of India on December 24, 2017, about 239 million peoples across 153 districts in 21 states drink arsenic-polluted water which, besides arsenicosis (arsenic poisoning)1, has also been linked to cancer in India2. UP has the largest number of people, over 70 million, expose to arsenic, while as percentage of state population Assam tops the list with over 65% of its population affected with arsenic. Utilizing the potential of microorganisms for managing arsenic contamination has been suggested to be a feasible and sustainable approach to combat arsenic contamination3.

DBT BIF Centre at Jamia Hamdard has successfully used the computational methods for bioremediation of arsenic by structure prediction and docking analysis of arsenite oxidase from Pseudomonas stutzeri TS44, suggesting TS44 arsenite oxidase a low cost and eco-friendly alternative method for bioremediation for arsenite4.

Identification of some natural activators and inhibitors of enzyme activity

The centre has reported few natural activators/ inhibitors of enzyme activity, such as hexokinase 4 (HK4) and GSK-3b, etc. HK4, for example, an isozyme of hexokinase found in pancreas, liver and neuroendocrine cells. In the pancreas, HK4 has been identified as a glucose sensor, regulating the release of insulin by the Pancreatic β cells. BIF Jamia Hamdard has identified a xanthone glucoside found in many plant species to activate HK4 function, causing insulin release and hence enhance the uptake and utilization of the glucose by the liver and other cells5.

References

 

  1. http://timesofindia.indiatimes.com/articleshow/62226542.cms?utm_source=contentofinterest&utm_medium=text&utm_campaign=cppst
  2. https://edition.cnn.com/2017/04/28/health/arsenic-water-pollution-cancer-india/index.html
  3. https://doi.org/10.3389/fenvs.2018.00024
  4. https://www.sciencedirect.com/science/article/pii/S0964830516306515
  5. https://doi.org/10.1080/07391102.2019.1650829

 

 

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