People : Scientific : Faculty & Scientists

DR. RAMANDEEP SINGH, Ph.D. 

Associate Professor
+91-129-2876305  (+91-129-2876305)
ramandeep [at] thsti [dot] res [dot] in
Postdoctoral Fellowship, National Institute of Allergy and Infectious Diseases, National Institutes of Health, USA
Ph. D. (Biochemistry),Department of Biochemistry, University of Delhi South Campus, New Delhi
M.Sc. (Biochemistry), Department of Biochemistry, University of Delhi South Campus, New Delhi
B. Sc. (Biochemistry), Department of Biochemistry, University of Delhi South Campus, New Delhi

Present Research Interest

Tuberculosis kills an annual 2 million people globally and an estimated one-third of world population is infected with latent tuberculosis. The global TB situation has worsened due to the emergence of Multi- and extensively drug resistant strains of M. tuberculosis (Mtb), failure of the BCG vaccine and synergy with AIDS. Eradication of this dreaded disease requires new strategies aimed at targeting non-replicating bacteria that characterize the latent disease as well as development of new vaccines against Mtb. Another problem that faces TB community is the emergence of MDR-TB as well as XDR-TB so we are in need of new drugs that can target these drug resistant bacilli and shorten the time of current chemotherapy. However the physiology of non-replicating bacteria and the metabolic processes that characterize these non-replicating bacteria are poorly understood. The initial focus of the lab to understand/ validate such metabolic pathways that enable mycobacteria to survive in stressful conditions as summarized below.

1. Characterization of MazF toxins of Mycobacterium tuberculosis: Toxin-antitoxin (TA) modules are one such family of proteins considered to play an important role in persistence/ latency of bacteria. There are 9 families of TA modules for e.g. MazEF, RelBE, VapBC etc. TB has 9 homologs of MazF toxins, these toxins as the name suggests inhibits bacterial metabolism by degradation of mRNA. This project would try to understand how these toxins are activated during disease relevant stress conditions by RT-PCR analysis. The project would involve making gene specific mutants, and the survival of various mutants strains would be evaluated in invitro persistence model and guinea pig pulmonary model of infection. Since there might be a factor of redundancy we would need to make a mutant strain of Mtb devoid of multiple MazF toxins. We would also try to identify what intracellular messengers act as regulators for activation of these toxins in Mtb.

2. Identification and characterization of Biochemical pathways involved in regeneration of reduced co-factors in low-oxygen conditions: During infection process persistent bacteria experience diverse and hostile environments intracellularly and must adapt to nutrient-deprived, hypoxic conditions in the granuloma. There is a school of thought that under hypoxic conditions there is a metabolic switch from aerobic metabolism to anaerobic respiration which would restore the pool of reduced co-factors such as NADH, FADH2 important for various essential metabolic pathways. The genome of Mtb has certain such biochemically uncharacterized enzymes that might enable the bacteria to survive under oxygen-depleted conditions by restoring reduced co-factor pool in the cell. This project would involve validation of enzyme functions bio-chemically and generation of gene-specific mutants. The survival of the mutant strains would be evaluated under stress conditions such as hypoxia, non-replicative persistence as well as in murine/guinea pig model of infection.

3. Identification of novel drug targets for M. tuberculosis. We are currently working on developing and establishing in vitro assays and screen inhibitor libraries for activity against M. tuberculosis.

  • Kidwai S, Park CY, Mawatwal S, Tiwari P, Jung MG, Gosain TP, Kumar P, Alland D, Kumar S, Bajaj A, Hwang YK, Song CS, Dhiman R, Lee IY and Singh R. The dual mechanism of action of 5-Nitro- 1,10-phenanthroline against Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy; Sept 2017.
  • Mawatwal S, Behura A, Ghosh A, Kidwai S, Mishra A, Deep A, Agarwal S, Saha S, Singh R and Dhiman R. Calcimycin mediates mycobacterial killing by inducing intracellular calcium regulated autophagy in a P2XR7 dependent manner. Biochim Biophys Acta; Sept 2017.
  • Deep A, Kaundal S, Agarwal S, Singh R and Thakur KG. Crystal structure of Mycobacterium tuberculosis VapC20 toxin, and its interaction with cognate antitoxin, VapB20 suggests a model for toxin-antitoxin assembly. FEBS Journal; October 2017.
  • Singh M, Tiwari P, Arora G, Agarwal S, Kidwai S and Singh R. Establishing Virulence associated Polyphosphate Kinase 2 as a drug target for Mycobacterium tuberculosis. Scientific Reports; June 2016; 6:26900
  • Banerjee SK, Kumar M, Alokam R, Sharma AK, Chatterjee A, Kumar R, Sahu SK, Jana K, Singh R, Yogeeswari P, Sriram D, Basu J, Kundu M. Targeting multiple response regulators of Mycobacterium tuberculosis auguments the host immune response to infection. Scientific Reports; May 2016; 6: 25851
  • Negi B, Kumar D, Kumbukgolla W, Jayaweera S, Ponnan P, Singh R, Agarwal S and Rawat DS. Antimethicillin resistant Staphylococcus aureus activity synergism with oxacillin and molecular docking studies of metronidazole-triazole derviatives. Eur J Med Chem 2016. June 10, 115: 426-37.
  • Kang YG, Park CY, Shin H, Singh R, Arora G, Yu CH and Lee IY. Synthesis and antitubercular activity of 2-nitroimidazooxazines with modification at the C-7 position as PA-824 analogs. Bio org Med Chem Lett 2015; Sept 1: 25 (17); 365-73.
  • Tiwari P, Arora G, Singh M, Kidwai S, Narayan O and Singh R*. MazF ribonucleases promoteMycobacterium tuberculosis drug tolerance and virulence in guinea pigs. Nature Communications Jan 22; 6:6059 doi 10.1038/ncomms 7059.
  • Kumar D, Khare G, Beena, Kidwai S, Tyagi AK, Singh R and Rawar D. Novel isoniazid-amidoether derivatives: synthesis, characterization and antimycobacterial activity evaluation. Med Chem Comm Manuscript accepted.
  • Bansal S, Singh M, Kidwai S, Bhargava P, Singh A, Sreekanth V, Singh R* and Bajaj A*. Bile acid amphiphiles with tunable head groups as highly selective anti-tubercular agents. Med Chem Comm. 2014 (5) 1761-1768. * Co-corresponding author
  • Arora G, Tiwari P, Mandal RS, Gupta A, Sharma D, Saha S and Singh R. High through put screen identifies small molecule inhibitors specific for Mycobacterium tuberculosis phosphoserine phosphatase. J Biol Chem July 2014 Sept (5) 289 (36) 25149-65.
  • Gupta M, Sajid A, Sharma K, Ghosh S, Arora G, Singh R, Nagaraja V, Tandon V and Singh Y. HupB, a nucleoid associated protein of Mycobacterium tuberculosis is modified by Serine/Threonine protein kinases in vivo. J of Bacteriol July 2014 (196) 2646-2657.
  • Kumar D, Beena, Khare G, Kidwai S, Tyagi AK, Singh R and Rawat DS. Synthesis of 1,2,3 triazole derivatives of isoniazid and their in vitro and in vivo anti-mycobacterial activity evaluation. Euro J Med Chem June 2014, (81) 301 – 313.
  • Chauhan P, Reddy PV, Singh R, Jaisinghani N, Gandotra S and Tyagi AK. Secretory phosphatases deficient mutant of Mycobacterium tuberculosis imparts protection at the primary site of infection in guinea pigs. pLOS One Oct 2013 8 (10): e77930.
  • Kumar N, Kapoor E, Singh R, Kidwai S, Kumbukgolla W, Bhagat S and Rawat DS. Synthesis and antibacterial/antitubercular activity evaluation of symmetrical trans-cyclohexane-1,4-diamine derivatives. Ind J Chem Nov 2013 52B 1441 – 1450.
  • Singh R, Singh M, Arora G, Kumar S, Tiwari P, and Kidwai S. Polyphosphate deficiency in Mycobacterium tuberculosis is associated with enhanced drug susceptibility and impaired growth in guinea pigs. J Bacteriol June 2013, 195 (12) 2839-51 .
  • Beena, Joshi S, Kumar N, Kidwai S, Singh R, and Rawat DS. Synthesis and antitubercular activity evaluation of novel unsymmetrical cyclohexane-1,2-diamine derivatives. Arch Pharm (Weinheim) 2012 345:896-901.
  • Gurumurthy M, Mukherjee T, Dowd CS, Singh R, Niyomrattanakit P, Tay JA, Nayyar A, Lee YS, Cherian J, Boshoff HI, Dick T, Barry CE and Manjunatha UH. Substrate Specificity of the Deazaflavin Dependent Nitroreductase (Ddn) from Mycobacterium tuberculosis is responsible for the Bioreductive activation of Bicyclic Nitroimidazoles. FEBS J, 2012, Jan 279 (1); 113-25.
  • Cherian J, Choi I, Nayyar A, Manjunatha UH, Lee YS, Boshoff HI, Singh R, Ha YH, Goodwin M, Lakshminarayana SB, Niyomrattanakit P, Jiricek J, Ravindran S, Dick T, Keller TH, Dartois V and Barry CE. Structure-activity relationships of antitubercular nitroimidazoles. 3. Exploration of the linker and lipophilic tail of the ((s)-2-nitro-6,7, dihydro-5H-imidazo [2,1-b][1,3]oxazin-6-yl)-(4-trifluoromethoxybenzyle) amine (6-amino-PA-824). J Med Chem 2011, Aug 25; 54 (16) 5639-59.
  • Singh R, Barry CE 3rd and Boshoff HI. The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. J Bacteriol Mar 2010, 192 (5) 1279 – 91.
  • Singh R, Manjunatha UH, Boshoff HI, Ha YH, Niyomrattanakit P, Ledwidge R, Dowd CS, Lee IY, Kim P, Zhang L, Kang S, Keller TH, Jiricek J and Barry CE, 3rd. PA-824 Kills Nonreplicating Mycobacterium tuberculosis by Intracellular NO Release. Science Nov 28 2008, 322 (5906); 1392 - 1395.
  • Kim P, Zhang L, Manjunatha UH, Singh R, Patel S, Jiricek J, Keller TH, Boshoff HI, Barry CE 3rd and Dowd CS. Structure-activity relationships of antitubercular nitroimidazoles. I. Structural features associated with aerobic and anaerobic activity of 4- and 5-nitroimidazoles. J Med Chem Feb 11 2009 52 (5) 1317 – 1328.
  • Kim P, Kang S, Boshoff HI, Jiricek J, Collins M, Singh R, Manjunath UH, Zhang L, Goodwin M, Keller TH, Dowd CS and Barry CE 3rd. Structure-activity relationships of antitubercular nitroimidazoles II. Determinants of aerobic activity and QSAR modeling. J Med Chem Feb 11 2009 52 (5) 1329 – 1344.
  • Jain, R, Dey B, Dhar N, Rao V, Singh R, Gupta UD, Katoch VM, Ramanathan VD and Tyagi AK. Modulation of Cytokine Milieu in Lung by Recombinant BCG Over-expressing Ag85C Confers Enhanced and Long-lasting Protection against Tuberculosis. PLoS ONE Dec 4 2008, 3(12) e3869.
  • Khera A, Singh R, Shakila H, Rao V, Dhar N, Parmasivan, CN, Ramanathan, VD and Tyagi, AK Elicitation of efficient, protective immune responses by using DNA vaccines against tuberculosis. Vaccine Dec 1 2005, 23 (48-49) 5655 - 5665.
  • Singh R, Singh A and Tyagi AK. Deciphering the genes associated with pathogenesis of Mycobacterium tuberculosis. Tuberculosis Sep – Nov 2005, 85 (5-6) 325 – 335.
  • Rao V, Dhar N, Shakila H, Singh R, Khera A, Parmasivan CN, Narayanan PR, Ramanathan VD and Tyagi AK Over-expression of the 19kDa lipoprotein of Mycobacterium tuberculosis obliterates the protective efficacy of BCG by polarizing the host immune responses to the Th2 phenotype. Scandinavian Journal of Immunology May 2005, 61(5) 210-217.
  • Chopra P, Koduri H, Singh R, Koul A, Ghildiyal M, Sharma K, Tyagi AK and Singh Y. Nucleoside diphosphate kinase of Mycobacterium tuberculosis acts as GTPase activating protein for Rho-GTPases. FEBS Lett July 2004, 571 (1–3) 212–216.
  • Singh R., Rao V, Shakila H, Gupta R, Khera A, Dhar N, Singh A, Koul A, Singh Y, Naseema M, Narayanan PR, Paramasivan CN, Ramanathan VD and Tyagi AK. Disruption of mptpB impairs the ability of Mycobacterium tuberculosis to survive in guinea pigs. Mol Microbiol Nov 2003, 50 (3) 751 – 762.
  • Chopra P, Singh B, Singh R, Vohra R, Koul A, Meena LS, Koduri H, Ghildiyal M, Deol P, Das TK, Tyagi AK and Singh Y. Phosphoprotein phosphatase of Mycobacterium tuberculosis dephosphorylates serine-threonine kinases PknA and PknB. Biochem Biophys Res Commun. Nov 2003, 311(1) 112–120.
  • Fellows award for Research Excellence by the National Institutes of Health 2007
  • Ramalingaswami Fellowship from Department of Biotechnology; 2010-2015
  • National Bioscience Award for career development from Department of Biotechnology; 2015

MR. SAQIB KIDWAI
TECHNICAL OFFICER-I

MS. SAKSHI AGARWAL
PH.D STUDENT

MS. DEEPIKA CHOUDHARY
PH.D STUDENT

MS. GARIMA ARORA
ICMR SENIOR RESEARCH FELLOW

MR. RAVI P SHALIWAL
PH.D STUDENT

MS. TANNU PRIYA GOSAIN
PH.D STUDENT