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DR. RAMANDEEP SINGH, Ph.D.  

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.

  1. Sharma, A., Chattopadhyay, G., Chopra, P., Bhasin, M., Thakur, C., Agarwal, S., Ahmad, S., Chandra, N., Vardarajan, R. and Singh, R.  VapC21 toxin contributes to drug tolerance and interacts with non-cognate VapB32 antitoxin in Mycobacterium tuberculosis. Frontiers in Microbiology 11:2037, 2020, 1-15. 
  2. Singh, P., Khurana, H., Yadav, S.P., Dhiman, K., SIngh, P., Ashish, Singh, R. and Sharma, D. Biochemical characterization of ClpB protein from Mycobacterium tuberculosis and identification of its small molecule inhibitors. International Journal of Biological Macromolecules 165 (Pt A), 2020, 375-387. 
  3. Meena, C.L, Singh, P., Shaliwal, R.P., Kumar, V., Tiwari A.K., Asthana, S., Singh, R.* and Mahajan, D*. Synthesis and evaluation of thiophene based small molecules as potent inhibitors of Mycobacterium tuberculosis. European Journal of Medicinal Chemistry, 208, 2020. 
  4. Agarwal, S., Sharma, A., Bouzeyen, R., Deep, A., Sharma, H., Mangalaparthu, K., Datta, K.K., Kidwai, S., Gowda, H., Varadarajan, R., Sharma, R.D., Thakur, K.G.  and Singh RVapBC22 toxin-antitoxin system from Mycobacterium tuberculosis is required for pathogenesis and modulation of host immune response. Science Advances 2020, 1-15.
  5. Arora, G., Gagandeep, Behura, A. Gosain, T.P., Shaliwal, R.P., Kidwai S., Singh P., Kandi S.K., Dhiman R., Rawat, D.S. and Singh, R. NSC 18725, a pyrazole derivative inhibits growth of intracellular Mycobacterium tuberculosis by induction of autophagy. Frontiers in Microbiology 10, 2020, 1-13. 
  6. Bouzeyen, R., Haoues, M., Barbouche, M.R., Singh, R and Essafi, M. FOXO3 transcription factor regulated IL-10 expression in mycobacteria-infected macrophages, tuning their polarization and the subsequent adaptive immune response. Frontiers in Immunology 10, 2020.
  7. Pierson, E., Haufroid, M., Gosian, T.P., Chopra, P., Singh, R. and Wouter, J. Identification and repurposing of trisubstituted harmine derivatives as novel inhibitors of Mycobacterium tuberculosis phosphoserine phosphatase. Molecules 25(2), 2020, 1-13.
  8. Maurya SS, Gosain TP, Kidwai S, Singh R and Rawat DS. Synthesis of 1,3,4-oxadiazole and imidazo [1,2-1] pyridine based molecular hybrids and their in vitro antituberculosis and cytotoxicity studies. Indian Journal of Chemistry, 2019, 58B: 1005-1018. 
  9. Tandon, H., Sharma, A., Wadhwa, S., Varadarajan, R., Singh, R., Srinivasan, N., and Sandhya, S. Bioinformatic and mutational studies of related toxin-antitoxin pairs in M. tuberculosis predict and identify key functional residues. J Biol Chem 2019
  10. Kidwai, S., Bouzeyen, R., Chakraborti, S., Khare, N., Das, S., Priya Gosain, T., Behura, A., Meena, C. L., Dhiman, R., Essafi, M., Bajaj, A., Saini, D. K., Srinivasan, N., Mahajan, D., and Singh, R. NU-6027 Inhibits Growth of Mycobacterium tuberculosis by Targeting Protein Kinase D and Protein Kinase G. Antimicrob Agents Chemother 63, 2019
  11. Banerjee, S. K., Lata, S., Sharma, A. K., Bagchi, S., Kumar, M., Sahu, S. K., Sarkar, D., Gupta, P., Jana, K., Gupta, U. D., Singh, R., Saha, S., Basu, J., and Kundu, M. The sensor kinase MtrB of  Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection. J Biol Chem 2019
  12. Behura, A., Mishra, A., Chugh, S., Mawatwal, S., Kumar, A., Manna, D., Mishra, A., Singh, R., and Dhiman, R. ESAT-6 modulates Calcimycin-induced autophagy through microRNA-30a in mycobacteria infected macrophages. J Infect 79, 2019; 139-152
  13. Gupta, A., Das, P. N., Bouzeyen, R., Karmakar, S. P., Singh, R., Bairagi, N., and Chatterjee, S. (2019) Restoration of cytosolic calcium inhibits Mycobacterium tuberculosis intracellular growth: Theoretical evidence and experimental observation. J Theor Biol 472, 2019; 110-123
  14. Sitwala, N. D., Vyas, V. K., Gedia, P., Patel, K., Bouzeyen, R., Kidwai, S., Singh, R., and Ghate, M. D. 3D QSAR-based design and liquid phase combinatorial synthesis of 1,2-disubstituted benzimidazole-5-carboxylic acid and 3-substituted-5H-benzimidazo[1,2-d][1,4]benzodiazepin-6(7H)-one derivatives as anti-mycobacterial agents. Medchemcomm 10, 2019; 817-827
  15. Tandon H, Sharma A, Sandhya S, Srinivasan N and Singh RMycobacterium tuberculosis Rv0366c-Rv0367c encodes a non-canonical PezAT-like toxin-antitoxin pair. Scientific Reports 2019; 9: 1-19.
  16. Arora G, Chaudhary D, Kidwai S, Sharma D and Singh RCitE enzymes are essential to establish Mycobacterium tuberculosis infection in macrophages and guinea pigs. Frontiers in Cellular and Infection Microbiology 2018; 8:1-15.
  17. Deep, A., Tiwari P., Agarwal, S., Kaundal, S., Kidwai, S., Singh R*;, and Thakur, K. G.* Structural, fnctional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin-antitoxin system: targeting a tRNAase to tackle mycobacterial adaptation. Nucleic acids Research 2018; 21: 11639-11655 *co-corresponding author.
  18. Dhiman, R., and Singh, R. Recent advances for identification of new scaffolds and drug targets for Mycobacterium tuberculosisIUBMB life 2018; 70: 905-916.
  19. Mawatwal, S., Behura A., Mishra A., Singh R., and Dhiman R. Calcimycin induced IL-12 production inhibits intracellular mycobacterial growth by enhancing autophagy. Cytokine 2018; 111: 1-12.
  20. Jha, B., Kumar, D., Sharma, A., Dwivedy, A., Singh, R., and Biswal, B.K. Identification and structural characterization of a histidinol phosphate phosphatase from Mycobacterium tuberculosisThe Journal of biological chemistry 2018; 293 (26), 10102-10118.
  21. Negi B, Poonan P, Ansari MF, et al. Synthesis, antiamoebic activity and docking studies of metronidazole-triazole-styryl hybrids. European journal of medicinal chemistry 2018; 150: 633-41.
  22. Agarwal S, Tiwari P, Deep A, Kidwai S, Gupta S, Thakur KG and Singh R. System wide analysis reveals differential regulation and in vivo essentiality of VapBC TA systems from Mycobacterium tuberculosisThe Journal of Infectious Diseases 2018; 217 (11), 1809-1820.
  23. 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; 2017; 284: 4066-4082.
  24. 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 2017; 1861 (12), 3190-3200.
  25. 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 tuberculosisAntimicrobial Agents and Chemotherapy 2017; 61 (11), 1-18.
  26. 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 tuberculosisScientific Reports; June 2016; 6:26900.
  27. 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.
  28. 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. 
  29. 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 Lett2015; Sept 1: 25 (17); 365-73. 
  30. Tiwari P, Arora G, Singh M, Kidwai S, Narayan O and Singh R*. MazF ribonucleases promote Mycobacterium tuberculosis drug tolerance and virulence in guinea pigs. Nature Communications Jan 22; 6:6059 doi 10.1038/ncomms 7059. 
  31. Kumar D, Khare G, Beena, Kidwai S, Tyagi AK, Singh R and Rawat DS. Novel isoniazid-amidoether derivatives: synthesis, characterization and antimycobacterial activity evaluation. Med Chem CommDOI:10.10392015 (6) 131-137. 
  32. 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. * co-corresponding author 2014 (5) 131-137. 
  33. Lakshinarayana SB, Boshoff HI, Cherian J, Ravindran S, GohA, Jiricek J, Nanjudappa M, Nayyar A, Gurumurthy M, Singh R, Dick T, Blasco F, Barry CE, Ho PC and Manjunatha UM. Pharmacokinetics-pharmacodynamics analysis of bicyclic -4-nitroimidazoles analogs in murine model of tuberculosis. pLOS One2014 Aug 20; 9(8) e105222. 
  34. 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 Sep 5 2014; 289(36): 25149-25165. 
  35. 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 vivoJ Bacteriol July 2014 (196)2646-2657. 
  36. 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 ChemJune 2014, (81) 301 – 313. 
  37. 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. 
  38. 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. 
  39. Singh R, Singh M, Arora G, Kumar S, Tiwari P, Kidwai S. Polyphosphate deficiency in mycobacterium tuberculosis is associated with enhanced drug susceptibility and impaired growth in guinea pigs. J Bacteriol May 2013 195 2839 – 51.
  40. Beena, Joshi S, Kumar N, Kidwai S, Singh R, Rawat DS. Synthesis and antitubercular activity evaluation of novel unsymmetrical cyclohexane-1,2-diamine derivatives. Arch Phar Nov 2012 345 (11) 896-901. 
  41. 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, Oct 2011.
  42. 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. 
  43. 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. 
  44. Singh RManjunatha 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 tuberculosisby Intracellular NO Release. Science Nov 28 2008, 322 (5906); 1392 - 1395. 
  45. 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. 
  46. 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. Impact factor: 5.48
  47. 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 20083(12) e3869. Impact factor: 3.53
  48. 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.
  49. Singh RSingh A and Tyagi AK. Deciphering the genes associated with pathogenesis of Mycobacterium tuberculosisTuberculosis Sep – Nov 2005, 85 (5-6) 325 – 335.
  50. 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 ImmunologyMay 2005, 61(5) 210-217.
  51. 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.
  52. 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.
  53. 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.

 

  1. Singh RKumar P and Tahlan T. Drugs against Mycobacterium tuberculosis. Book Chapter in Drug discovery targeting drug-resistant bacteria. Elsevier Press. 2020.

  2.  Anil K Tyagi, Ramandeep Singh and Vibha Gupta.  Role of Mycobacterial Kinases and Phosphatases in bacterial growth and pathogenesis in “The Mycobacterial Cell Envelope, an overview” edited by Dr. Mamadou Daffe and Dr. Jean Marc Reyrat, 2008.

  3. Helena I Boshoff, Ramandeep Singh and Clifton E. Barry III. Virulence and Persistence mechanisms of Mycobacterium tuberculosis, in Handbook of Tuberculosis: Molecular Biology and Biochemistry edited by Dr. Stefan H. E. Kaufmann and Dr. Eric J Rubin, 2008.

 

1. Mutants of mycobacteria and process there off (US Patent filed ).

2. Recombinant BCG- Ag85C based immunization against Mycobacterium (Indian patent filed).

3. 1. 7-substituted 2-nitro 6,7- dihydroimidazo [2,1-b][1,3] oxazine derivatives of their optical isomers, pharmaceutical composition containing the same as an active ingredient (Korean Patent filed).

4. 5-Nitro-1,10, phenanthroline derivatives and pharmaceutical composition for prevention and treatment of tuberculosis containing the same (Korean Patent No. 10-1757629).

  • 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. DEEPIKA CHOUDHARY
PROJECT ASSOCIATE-I

MS. TANNU PRIYA GOSAIN
PH.D STUDENT

MR. SAURABH CHUGH
PH.D STUDENT

MS. MANISHA SINGH
PH.D STUDENT

MR. PANKAJ CHOPRA
PROJECT ASSOCIATE-I

DR. PADAM SINGH
POST DOCTORAL FELLOW

MS. NEELAM SINGH
JUNIOR RESEARCH FELLOW

MS. MANISHA PRIYA
PH.D STUDENT

MR. ARUN SHARMA
PH.D STUDENT

DR. KAMALESH VERMA
RESEARCH ASSOCIATE

MS. PUJA DOKANIA
RESEARCH ASSISTANT