रिसर्च धारा वेबसाइट

Dr. Uddipan Das

Photograph

Current Designation & Contact Details

Scientist-I

Department of Biophysics, Near Lecture Theater-2, PC Block, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029

Phone (office): +91-11-26594259, Ext: 4259

Email: यह ईमेल पता spambots से संरक्षित किया जा रहा है. आप जावास्क्रिप्ट यह देखने के सक्षम होना चाहिए.

Recent Employment Details (Past few years)

1. 2016 - present: Scientist-I (Department of Biophysics, All India Institute of Medical Sciences, New Delhi)

2. 2014-2016: Senior Resident/Demonstrator (Department of Biophysics, All India Institute of Medical Sciences, New Delhi)

Brief Research Area

Structural biology: We are interested in understanding the intricate structure and function of Membrane proteins and Macromolecular complexes. To accomplish this, we are harnessing the power of Cryo-Electron microscopy and X-ray crystallography along with other biophysical and biochemical methods in order to understand the structure function relationships.

Awards & Honours

1. Visiting scientist at the University of Stanford, Cryo-EM center, California 2022-2023.

2. SERB international research experience award (Government of India) 2022.

3. Visiting scholar at European Molecular biology Laboratory, Hamburg, Germany, 2013.

4. European Molecular Biology Organization (EMBO) Fellowship 2013.

5. Indian Council of Medical Research Junior research fellowship 2009.

6. Department of Biotechnology Junior research fellowship 2009.

7. Graduate Aptitude Rest in Engineering (Life Sciences), 2009

8. Centre of Scientific and Industrial Research NET 2009.

Selected Publications/Patents (Last 5 years)

Google Scholar Link: https://scholar.google.com/citations?user=_YQkkBcAAAAJ&hl=en

1. Singh M, Haque MA, Tikhomirov A, Shchekotikhin, A, Das U, Kaur, P (2022). Computational and biophysical characterization of heterocyclic derivatives of anthraquinone against Human Aurora Kinase A. ACS Omega (accepted)

2. Sharma P, Kumar M, Tripathi MK, Gupta D, Vishwakarma P, Das U & Kaur P (2022) Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern. Comput Biol Med 150, 106129.

3. Sharma D, Singh M, Kaur P & Das U* (2022) Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis , provides insights into its trehalose specificity. Acta Crystallogr Sect D Struct Biol 78, 835–845.

4. Gupta D, Kumar M, Singh M, Salman M, Das U & Kaur P (2022) Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins. J Cell Biochem 123, 719–735.

5. Singh M, Malhotra L, Haque MA, Kumar M, Tikhomirov A, Litvinova V, Korolev AM, Ethayathulla AS, Das U, Shchekotikhin AE & Kaur P (2021) Heteroarene-fused anthraquinone derivatives as potential modulators for human aurora kinase B. Biochimie 182, 152–165.

6. Sabharwal N, Varshney K, Rath PP, Gourinath S & Das U* (2020) Biochemical and biophysical characterization of nucleotide binding domain of Trehalose transporter from Mycobacterium tuberculosis. Int J Biol Macromol 152, 109–116.

7. Das U*, Singh E, Dharavath S, Tiruttani Subhramanyam UK, Pal RK, Vijayan R, Menon S, Kumar S, Gourinath S & Srinivasan A (2019) Structural insights into the substrate binding mechanism of novel ArgA from Mycobacterium tuberculosis. Int J Biol Macromol 125, 970–978.

8. Gupta AK, Pokhriyal R, Das U, Khan MI, Kumar DR, Gupta R, Chadda RK, Ramachandran R, Goyal V, Tripathi M & Hariprasad G (2019) Evaluation of α-synuclein and apolipoprotein e as potential biomarkers in cerebrospinal fluid to monitor pharmacotherapeutic efficacy in dopamine dictated disease states of parkinson’s diseaseand schizophrenia. Neuropsychiatr Dis Treat 15, 2073–2085.

9. Das U, Pogenberg V, Subhramanyam UKT, Wilmanns M, Gourinath S & Srinivasan A (2014) Crystal structure of the VapBc-15 complex from mycobacterium tuberculosis reveals a two-metal ion dependent pin-domain ribonuclease and a variable mode of toxin-antitoxin assembly. J Struct Biol 188, 249–258.

10. Das U, Kumar N, Gourinath S & Srinivasan A (2013) Preliminary crystallographic analysis of recombinant VapBC-15 toxin-antitoxin complex from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 69, 1242–1245.

Dr. Manoj Kumar

Photograph

Current Designation & Contact Details

Scientist II

Room No. 1008, Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India

Tel: +91-11-26594816

Email: यह ईमेल पता spambots से संरक्षित किया जा रहा है. आप जावास्क्रिप्ट यह देखने के सक्षम होना चाहिए. ; यह ईमेल पता spambots से संरक्षित किया जा रहा है. आप जावास्क्रिप्ट यह देखने के सक्षम होना चाहिए.

Recent Employment Details (Past few years)

1. Scientist II, Department of Biophysics, AIIMS, New Delhi 2016 – till date

2. Senior Demonstrator, Department of Biophysics, AIIMS, New Delhi 2012-2015

Brief Research Area

I am working in the area of drug discovery for tuberculosis using rational drug design approach. My goal is to design lead molecules for treatment of drug-resistant tuberculosis. I am also working on design of lead molecules for development of drugs to shorten the treatment duration.

Selected Publications/Patents (Last 5 years)

Google Scholar link: https://scholar.google.com/citations?user=wezA8UgAAAAJ&hl=en

1. Naz F, Kumar M, Koley T, Sharma P, Haque MA, Kapil A, Kumar M, Kaur P, Ethayathulla AS. Screening of plant-based natural compounds as an inhibitor of FtsZ from Salmonella Typhi using the computational, biochemical and in vitro cell-based studies. Int J Biol Macromol. 2022 Aug 3; 219: 428-437 doi: 10.1016/j.ijbiomac.2022.07.241

2. Gupta V, Somarajan BI, Gupta S, Mahalingam K, Kumar M, Singh A. Association of EFEMP1 with juvenile-onset open angle glaucoma in a patient with concomitant COL11A1-related Stickler syndrome. Ophthalmic Genet. 2022 Aug 10:1-5. doi: 10.1080/13816810.2022.2109682.

3. Koley T, Goswami A, Kumar M, Upadhyay N, Hariprasad G. Comparative Structural Analysis of Human ACE2 Receptor with Spike Protein of SARS-CoV-2 Variants: Implications to Understand Infectivity of the Virus. Adv Appl Bioinform Chem. 2022 Jun 16;15: 21-27. doi: 10.2147/AABC.S360787.

4. Kulandaisamy R, Kushwaha T, Dalal A, Kumar V, Singh D, Baswal K, Sharma P, Praneeth K, Jorwal P, Kayampeta SR, Sharma T, Maddur S, Kumar M, Kumar S, Polamarasetty A, Singh A, Sehgal D, Gholap SL, Appaiahgari MB, Katika MR, Inampudi KK. Repurposing of FDA Approved Drugs Against SARS-CoV-2 Papain-Like Protease: Computational, Biochemical, and in vitro Studies. Front Microbiol. 2022 May 10; 13: 877813. doi: 10.3389/fmicb.2022.877813.

5. Koley T, Chowdhury SR, Kushwaha T, Kumar M, Inampudi KK, Kaur P, Singh TP, Viadiu H, Ethayathulla AS. Deciphering the mechanism of p73 recognition of p53 response elements using the crystal structure of p73-DNA complexes and computational studies. Int J BiolMacromol. 2022 May 1; 206:40-50.doi: 10.1016/j.ijbiomac.2022.02.108.

6. Anand V, Aggarwa B, Jauhari P, Kumar M, Gupta N, Kumar A, Gulati S, Kabra M. STAMBP gene mutation causing microcephaly-capillary malformation syndrome: a recognizable developmental and epileptic encephalopathy. Epileptic Disord. 2022 Jun 1;24(3):602-605. English. doi: 10.1684/epd.2021.1411.

7. Koley T, Kumar M, Goswami A, Ethayathulla AS, Hariprasad G. Structural modeling of Omicron spike protein and its complex with human ACE-2 receptor: Molecular basis for high transmissibility of the virus. Biochem Biophys Res Commun. 2022 Feb 12; 592: 51-53. doi: 10.1016/j.bbrc.2021.12.082.

8. Kumar A, Sharma R, Faruq M, Kumar M, Sharma S, Werner R, Hiort O, Vandana J. Clinical, Biochemical, and Molecular Characterization of Indian Children with Clinically Suspected Androgen Insensitivity Syndrome. Sex Dev. 2021 Oct 22:1-12. doi: 10.1159/000519047.

9. Mishra P, Tandon G, Kumar M, Paital B, Swain SS, Kumar S, Samanta L. Promoter sequence interaction and structure based multi-targeted (redox regulatory genes) molecular docking analysis of vitamin E and curcumin in T4 induced oxidative stress model using H9C2 cardiac cell line. J BiomolStructDyn. 2021 Aug 31:1-20. doi: 10.1080/07391102.2021.1970624.

10. Sharma S, Kumar R, Jain A, Kumar M, Gauttam R, Banerjee R, Mukhopadhyay J, Tyagi JS. Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli. Biochem J. 2021 Aug 27;478(16):3079-3098. doi: 10.1042/BCJ20210268.

11. Garg S, Khan SI, Malhotra RK, Sharma MK, Kumar M, Kaur P, Nag TC, Ray R, Bhatia J, Arya DS. Cardioprotective effects of azilsartan compared with that of telmisartan on an in vivo model of myocardial ischemia-reperfusion injury. J BiochemMolToxicol. 2021 Jul;35(7):e22785. doi: 10.1002/jbt.22785.

12. Koley T, Madaan S, Chowdhury SR, Kumar M, Kaur P, Singh TP, Ethayathulla AS. Structural analysis of COVID-19 spike protein in recognizing the ACE2 receptor of different mammalian species and its susceptibility to viral infection. 3Biotech. 2021 Feb;11(2):109. doi: 10.1007/s13205-020-02599-2.

13. Malhotra L, Goyal HKV, Jhuria S, Dev K, Kumar S, Kumar M, Kaur P, Ethayathulla AS. Curcumin rescue p53Y220C in BxPC-3 pancreatic adenocarcinomas cell line: Evidence-based on computational, biophysical, and in vivo studies. BiochimBiophysActa Gen Subj. 2021 Feb;1865(2):129807. doi: 10.1016/j.bbagen.2020.129807.

14. Kumar S, Tyagi YK, Kumar M, Kumar S. Synthesis of novel 4-methylthiocoumarin and comparison with conventional coumarin derivative as a multi-target-directed ligand in Alzheimer's disease. 3 Biotech. 2020 Dec;10(12):509. doi: 10.1007/s13205-020-02481-1.

15. Tripathi A, Kumar B, Kumar M, Kaur P, Sagi SSK. Quercetin Prophylaxis: A Novel Approach to Prevent Hypoxia-Mediated Increase in Oxidative Stress, Pde-5 Activity and Transvascular Leakage in the Lungs of Rats. HSOA J Pulmo Med Respir Res. 2020 6: 041 doi:10.24966/PMRR-0177/100041

16. Garg S, Khan SI, Malhotra RK, Sharma MK, Kumar M, Kaur P, Nag TC, RumaRay, Bhatia J, Arya DS. The molecular mechanism involved in cardioprotection by the dietary flavonoid fisetin as an agonist of PPAR-γ in a murine model of myocardial infarction. Arch BiochemBiophys. 2020 Nov 15; 694:108572. doi: 10.1016/j.abb.2020.108572.

17. Sharma P, Kumar M, Dahiya S, Sood S, Das BK, Kaur P, Kapil A. Structure based drug discovery and in vitro activity testing for DNA gyrase inhibitors of Salmonella entericaserovarTyphi. Bioorg Chem. 2020 Nov;104: 104244. doi: 10.1016/j.bioorg.2020.104244.

18. Kumar S, Kumar M, Tyagi YK, Kumar S. Inhibition of Amyloid Fibrillation of HEWL by 4-Methylcoumarin and 4-Methylthiocoumarin Derivatives. Curr Pharm Biotechnol. 2021;22 (2):232-244. doi: 10.2174/1389201021666200915112849.

19. Kumar A, Sharma R, Faruq M, Suroliya V, Kumar M, Sharma S, Werner R, Hiort O, Jain V. Spectrum of Pathogenic Variants in SRD5A2 in Indian Children with 46,XY Disorders of Sex Development and Clinically Suspected Steroid 5α-Reductase 2 Deficiency. Sex Dev. 2019;13 (5-6):228-239. doi: 10.1159/000509812.

20. Naz F, Mashkoor M, Sharma P, Haque MA, Kapil A, Kumar M, Kaur P, Abdul Samath E. Drug repurposing approach to target FtsZ cell division protein from Salmonella Typhi. Int J BiolMacromol. 2020 Sep 15; 159:1073-1083. doi: 10.1016/j.ijbiomac.2020.05.063.

21. Kulandaisamy R, Kushwaha T, Kumar V, De S, Kumar S, Upadhyay SK, Kumar M, Inampudi KK. Characterization of active/binding site residues of peptidyl-tRNA hydrolase using biophysical and computational studies. Int J BiolMacromol. 2020 Sep 15;159: 877-885. doi: 10.1016/j.ijbiomac.2020.05.133.

22. Perveen S, Gupta N, Kumar M, Kaur P, Chowdhury MR, Kabra M. Spectrum of amyloglucosidase mutations in Asian Indian patients with Glycogen storage disease type III. Am J Med Genet A. 2020 May;182(5):1190-1200. doi: 10.1002/ajmg.a.61547.

23. Tripathi A, Kumar M, Kaur P, Kumar B, Sagi SSK. Efficacy of Quercetin as a potent sensitizer of β2-AR in combating the impairment of fluid clearance in lungs of rats under hypoxia. RespirPhysiolNeurobiol. 2020 Feb;273: 103334. doi: 10.1016/j.resp.2019.103334.

24. Pandey G, Bakhshi S, Kumar M, Thakur B, Jain P, Kaur P, Chauhan SS. Prognostic and therapeutic relevance of cathepsin B in pediatric acute myeloid leukemia. Am J Cancer Res. 2019 Dec 1; 9 (12): 2634-2649.

25. Kumar A, Jain V, Chowdhury MR, Kumar M, Kaur P, Kabra M. Pathogenic/likely pathogenic variants in the SHOX, GHR and IGFALS genes among Indian children with idiopathic short stature. J PediatrEndocrinolMetab. 2020 Jan 28;33(1):79-88. doi: 10.1515/jpem-2019-0234.

26. Sudarshan S, Kumar M, Kaur P, Kumar A, G S, Sapra S, Gulati S, Gupta N, Kabra M, Roy Chowdhury M. Decoding of novel missense TSC2 gene variants using in-silico methods. BMC Med Genet. 2019 Oct 26;20(1):164. doi: 10.1186/s12881-019-0891-y.

27. Yadav P, Kumar M, Bansal R, Kaur P, Ethayathulla AS. Structure model of ferrochelatase from Salmonella Typhi elucidating metalation mechanism. Int J BiolMacromol. 2019 Apr 15;127: 585-593. doi: 10.1016/j.ijbiomac.2019.01.066.

28. Gupta N, Tewari VV, Kumar M, Langeh N, Gupta A, Mishra P, Kaur P, Ramprasad V, Murugan S, Kumar R, Jana M, Kabra M. Asparagine Synthetase deficiency-report of a novel mutation and review of literature. Metab Brain Dis. 2017 Dec;3 2(6):1889-1900. doi: 10.1007/s11011-017-0073-6.

29. Yenamandra VK, Vellarikkal SK, Kumar M, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Ray SB, Dinda AK, Kabra M, Kaur P, Sharma VK, Sethuraman G. Application of whole exome sequencing in elucidating the phenotype and genotype spectrum of junctional epidermolysis bullosa: A preliminary experience of a tertiary care centre in India. J Dermatol Sci. 2017 Apr; 86(1):30-36. doi: 10.1016/j.jdermsci.2016.12.020.