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Dr. J. Muthukumaran

Assistant Professor, Biotechnology

j.muthukumaran@sharda.ac.in

About

I did my PhD Bioinformatics in Pondicherry Central University, Pondicherry, India in the year of 2013. After this, I moved to Portugal for my Postdoctoral Research (2013 to 2019). Being the deep interest in computational Biology, I involve various research areas mainly (a) Structure-Based Drug Designing and Discovery, (b) Understanding the Bio-molecular interactions, (c) SNP data analysis, (d) Structural and Functional annotations of hypothetical proteins and (e) Software and Database development. I had nearly 5 years teaching and 13 years of research experiences. I have published 59 international research articles in various reputed journals and 2 book chapters in Springer Publishers.

Experience
  • Teaching: 4.5 Years
  • Research: 12 Years
Qualification
  • MSc.
  • MPhil.
  • Ph.D
Award & Recognition

  • JRF (Ministry of Electronics and Information Technology, New Delhi, India) Host Institute: Centre for Bioinformatics, Pondicherry University, Puducherry, India
  • SRF (Council of Scientific and Industrial Research, New Delhi, India) Host Institute: Centre for Bioinformatics, Pondicherry University, Puducherry, India
  • PDF (Foundation for Science and Technology, Portugal) Host Institute: Macromolecular Crystallography, Department of Chemistry, New University of Lisbon, Portugal.

Research

Book Chapters:

61. Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha, Muthukumaran. J, Amit Kumar Singh. (2021) Ligand-Based Approaches for the Development of Drugs Against SARS-CoV-2. In: .Methods in Pharmacology and Toxicology. Springer, New York, NY. https://doi.org/10.1007/7653_2020_65

60. Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha, Muthukumaran. J, Amit Kumar Singh. (2021) Computational Drug Repurposing for the Development of Drugs Against Coronaviruses. In:.Methods in Pharmacology and Toxicology. Springer, New York, NY. https://doi.org/10.1007/7653_2020_68

59. Ali, M. S., Muthukumaran, J., Jain, M., Al-Sanea, A. S. S., & Al-Lohedan, H. A. (2021). Experimental and in silico investigation on the interaction of indomethacin with bovine serum albumin: Effect of sodium dodecyl sulfate surfactant monomers on the binding. Journal of Molecular Liquids, 116858.

58. Ali MS, Muthukumaran J, Jain M, Al-Lohedan HA, Farah MA, Alsowilem OI. Experimental and computational investigation on the binding of anticancer drug gemcitabine with bovine serum albumin. J Biomol Struct Dyn. 2021 May 17:1- 14. doi: 10.1080/07391102.2021.1924270. Epub ahead of print. PMID: 33998966.

57. Muthukumaran J, Ali MS, Jain M, Santos-Silva T, Al-Lohedan HA, Al-Shuail NS. (2021). Molecular interactions of cefoperazone with bovine serum albumin: Extensive experimental and computational investigations. Journal of Molecular Liquids, 116354.

56.Jha RK, Khan RJ, Amera GM, Singh E, Pathak A, Jain M, Muthukumaran J, Singh AK. Identification of promising molecules against MurD ligase from Acinetobacter baumannii: insights from comparative protein modelling, virtual screening, molecular dynamics simulations and MM/PBSA analysis. J Mol Model. 2020 Oct 17;26(11):304. doi: 10.1007/s00894-020- 04557-4. PMID: 33068184.

55. Singh E, Khan RJ, Jha RK, Amera GM, Jain M, Singh RP, Muthukumaran J, Singh AK. A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods. J Genet Eng Biotechnol. 2020 Nov 3;18(1):69. doi: 10.1186/s43141-020-00085-z.PMID: 33141358; PMCID: PMC7607901. (Review Paper)

54. V. Sachithanandam, P. Lalitha, A. Parthiban, Muthukumaran J, Monika Jain, Ranjita Misra, T. Mageswaran, R. Sridhar, R. Purvaja, R. Ramesh, A comprehensive in silico and in vitro studies on Quinizarin: a promising phytochemical derived from Rhizophora mucronate. J Biomol Struct Dyn. 2021 Mar 8:1-12

53.          Rao, H. Surya Prakash, E. Poonguzhali, and Muthukumaran J. "Synthesis and conformational studies on 1-aryl-cis-2, 6-diphenylpiperidines." Journal of Molecular Structure (2021): 130065.

52. Uppugunduri CRS, Muthukumaran J, Robin S, Santos-Silva T, Ansari M. In silico and in vitro investigations on the protein-protein interactions of glutathione S-transferases with mitogen-activated protein kinase 8 and apoptosis signal-regulating kinase 1. J Biomol Struct Dyn. 2020 Sep 30:1-11.

51. Sachithanandam V, Parthiban A, Lalitha P, Muthukumaran J, Jain M, Elumalai D, Jayabal K, Sridhar R, Ramachandran P, Ramachandran R. Biological evaluation of gallic acid and quercetin derived from Ceriops tagal: insights from extensive in vitro and in silico studies. J Biomol Struct Dyn. 2020 Sep 30:1-13.

50. Khan RJ, Jha RK, Singh E, Jain M, Amera GM, Singh RP, Muthukumaran J, Singh AK. Identification of promising antiviral drug candidates against non-structural protein 15 (NSP15) from SARS-CoV-2: an in silico assisted drug-repurposing study. J Biomol Struct Dyn. 2020 Sep 4:1-11.

49. Rao, H.S.P., Gunasundari, R. & Muthukumaran J. (2020). Crystal structure analysis of ethyl 6-(4- methoxyphenyl)-1-methyl-4-methylsulfanyl-3-phenyl-1H-pyrazolopyridine-5-carboxylate, Acta Cryst. E76: 1209-1212

48. Khan RJ, Jha RK, Amera GM, Muthukumaran J, Singh RP, Singh AK. A comprehensive in silico study towards understanding the inhibitory mechanism of Lactoperoxidase by Dapsone and Propofol. Curr Comput Aided Drug Des. 2020 Jun 27.

47. Amera, GM., Khan,RJ., Jha, KR, Pathak, A., Muthukumaran J and Singh, AK, (2020). Structure based drug designing and discovery of promising lead molecules against UDP-N-acetylenolpyruvoylglucosamine reductase (MurB): a potential drug target in multi-drug resistant Acinetobacter baumannii. J Mol Graph Model. 100:107675

46. Amera, GM., Khan,RJ., Jha, KR, Pathak, A., Muthukumaran J and Singh, AK, (2020). Prioritization of Mur Family Drug Targets against A. baumannii and identification of their homologous proteins through Molecular Phylogeny, Primary Sequence and Structural Analysis. J Genet Eng Biotechnol. 18(1):33.

45. Jain M, Muthukumaran J, Singh AK. Comparative structural and functional analysis of STL and SLL, chitin-binding lectins from Solanum spp . J Biomol Struct Dyn. 2020;1-16.

44. Mohd. Sajid Ali, Muthukumaran J and Hamad A. Al-Lohedan. (2020) Molecular interactions of ceftazidime with bovine serum albumin: Spectroscopic, molecular docking, and DFT analyses, J. Mol. Liq, 313:113490

43. Khan RJ, Jha RK, Amera GM, Jain M, Singh E, Pathak A, Singh RP, Muthukumaran J and Singh AK. (2020) Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2'-O-ribose methyltransferase . J. Biomol. Struct. Dyn. 2020; 1–14.

42. Amera, GM., Khan,RJ., Jha, KR, Pathak, A., Muthukumaran J and Singh, AK (2020). Computer Aided Ligand Based Screening for Identification of Promising Molecules against Enzymes Involved in Peptidoglycan Biosynthetic Pathway from Acinetobacter baumannii. Microb. Pathog. 147:104205

41. Jain, M., Muthukumaran J and Singh AK (2020).Structural and Functional characterization of Chitin binding Lectin from Datura stramonium: Insights from Phylogenetic analysis, Protein structure prediction, Molecular docking and Molecular dynamics simulation. J. Biomol. Struct. Dyn.1-33

40. Rao, H.S.P., Gunasundari, R. & Muthukumaran J. (2020). Crystal structure analysis of ethyl 3-(4- chloro- phen-yl)-1,6-dimethyl-4-methyl-sulfanyl-1H-pyrazolopyridine-5-carboxyl-ate, Acta Cryst. (2020). E76, 443-445

39. Amera, GM., Khan,RJ.,Pathak, A., Jha, RK., Muthukumaran J and Singh, AK (2019). Screening of Promising Molecules against MurG as Drug Target in Multi-Drug-Resistant- Acinetobacter baumannii - Insights from Comparative Protein Modeling, Molecular Docking and Molecular Dynamics Simulation. J. Biomol. Struct. & Dyn. 1-37.

38. Muthukumaran J, Coelho C, Santos‐Silva T, João Romão M. Systematic exploration of predicted destabilizing nonsynonymous single nucleotide polymorphisms (nsSNPs) of human aldehyde oxidase: A Bio‐ informatics study. Pharmacol Res Perspect. 2019;e00538.

37. Muthukumaran J, Ramos J, Freire F, Paquete-Ferreira J, Otrelo-Cardoso AR, Svergun D, Panjkovich A, Santos-Silva T (2019) Shedding Light on the Interaction of Human Anti-Apoptotic Bcl-2 Protein with Ligands through Biophysical and in Silico Studies. Int J Mol Sci 20, 860.

36. Alves-Barroco C, Roma-Rodrigues C, Balasubramanian N, Guimarães MA, Ferreira-Carvalho BT, Muthukumaran J, Nunes D, Fortunato E, Martins R, Santos-Silva T, Figueiredo AMS, Fernandes AR, Santos- Sanches I (2019)Biofilm development and computational screening for new putative inhibitors of a homolog of the regulatory protein BrpA in Streptococcus dysgalactiae subsp. dysgalactiae. Int. J Med Microbiol 309(3-4):169-18

35. Patricia Huezo-Diaz, Chakradhara Rao Uppugunduri S, Muthukumaran J, Mohamed Aziz Rezgui, Christina Peters, Peter Bader, Michel Duval, Henrique Bittencourt, Maja Krajinovic and Marc Ansari (2018) Association of CTH Variant with Sinusoidal Obstruction Syndrome in Children Receiving Intravenous Busulfan and Cyclophosphamide before Hematopoietic Stem Cell Transplantation, The Pharmacogenomics Journal 18, 64–69

34. Parthiban, A., Kumaravel, M., Muthukumaran J., Rukkumani, R., Krishna, R., Rao, H.S.P. (2016) Synthesis, in vitro and in silico anti-proliferative activity of 4-aryl-4H-chromene derivatives. Med Chem Res 25 (7): 1308–1315

33. Kodidela S, Pradhan SC, Muthukumaran J, Dubashi B, Santos-Silva T, et al. (2016) Genotype Distribution of Dihydrofolatereductase Variants and their Role in Disease Susceptibility to Acute Lymphoblastic Leukemia in Indian Population: An Experimental and Computational Analysis. J Leuk 4:209.

32. Martins M, Baptista PV, Mendo AS, Correia C, Videira P, Rodrigues AS, Muthukumaran J, Santos-Silva T, Silva A, Guedes da Silva MF, Gigante J, Duarte A, Gajewska M, Fernandes AR (2016) In vitro and in vivo biological characterization of the anti-proliferative potential of a cyclic trinuclear organotin(iv) complex. Mol Biosyst. 12(3):1015-23.

31. Parthiban A, Muthukumaran J, Manhas A, Srivastava K, Krishna R, Rao HS (2015) Synthesis, in vitro and in silico antimalarial activity of 7-chloroquinoline and 4H-chromene conjugates. Bioorg Med Chem Lett. 25(20):4657- 63

30. J. Senthil Kumaran, Muthukumaran J, N. Jayachandramani and S. Mahalakshmia, Synthesis, characterization, in silico DNA studies and antibacterial evaluation of transition metal complexes of thiazole based pyrazolone Schiff base, Journal of Chemical and Pharmaceutical Research, 2015, 7(4):1397-1409

29. Parthiban, A., Kumaravel, M., Muthukumaran J, Rukkumani, R., Krishna, R., Rao, H.S.P. (2015) Design, synthesis, in vitro and in silico anti-cancer activity of 4H-chromenes with C4-active methine groups, Med Chem Res 24 (3): 1226-1240.

28. Parthiban, A., Muthukumaran J, Moushumi Priya, A., Jayachandran, S., Krishna, R., Rao, H.S.P. (2014). Design, synthesis, molecular docking and biological evaluation of N-methyl-3-nitro-4-(nitromethyl)-4H- chromen-2- amine derivatives as potential anticancer agents. Med Chem Res, 23 (2): 642-659

27. Surekha Kanagarajan, Nachiappan Mutharasappan, Prabhu Dhamodharan, Muthukumaran J, Krishna Ramadas, Jeyakanthan Jeyaraman (2014) Exploring the structural features of Aspartate Trans Carbamoylase (TtATCase) from Thermus thermophilus HB8 through in silico approaches: A potential drug target for inborn error of pyrimidine metabolism, J Biomol Struct Dyn, 32(4):591-601

26. J. Senthil Kumaran, S. Priya, Muthukumaran J, N. Jayachandramani and S. Mahalakshmia, Synthesis, characterization and biological studies of Cu(II), Co(II), Ni(II) and Zn(II) complexes of tetradentate Schiff base ligand, Journal of Chemical and Pharmaceutical Research, 2013, 5(7):56-69

25. Manivel Panneerselvam, Kannan Muthu, Muthukumaran J, Upasana Sridharan, Pranitha Jenardhanan and Krishna Ramadas (2013), Molecular Dynamic Simulations of Tubulin-Human Gamma Synuclein Complex: Structural Insight into the regulatory mechanism involved in inducing resistance against Taxol, Molecular BioSystems ,9, 1470-1488

24. Muthukumaran J, A. Parthiban, H. Surya Prakash Rao & R. Krishna (2012), 6-Ethyl-N-methyl-3-nitro- 4-nitromethyl-4H-chromen-2-amine, Acta Cryst. E68:o180-o181

23. M. Kannan, P. Manivel , K. Geetha, Muthukumaran J, H. Surya Prakash Rao & R. Krishna (2012), Synthesis and in silico evaluation of 1N-methyl-1S-methyl-2-nitroethylene (NMSM) derivatives against Alzheimer disease: to understand their interacting mechanism with Acetylcholinesterase, J Chem Biol, 5: 151-166

22. Kannan Muthu, Manivel Panneerselvam, Muthukumaran J, Nishith Saurav Topno, Arindam Atanu Das & Ramadas Krishna (2012), Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies, J Mol Model, 18: 4865-4884

21. P. Manivel, Muthukumaran J, M. Kannan & R. Krishna (2011), Insight into residues involved in the structure and function of the breast cancer associated protein human gamma synuclein, J Mol Model, 17:251-263

20. Muthukumaran J, A. Parthiban, H. Surya Prakash Rao & R. Krishna (2011), An X-ray crystallographic study of N-methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, J Chem Crystallogr, 41:1927–1934

19. Muthukumaran J, A.Parthiban, P.Manivel, H.Surya Prakash Rao & R.Krishna (2011), 4--N-methyl-3-nitro-4H-chromen-2-amine, Acta Cryst. E67: o1395-o1396

18. Muthukumaran J, Karthikeyan S, Satheesh G, Manimaran, B & Krishna R (2011), Butane-1,4-diyl bis(pyridine-4-carboxylate), Acta Cryst. E67: o1803

17. Muthukumaran J, Nishandhini M, Chitra S, Muthusubramanian S, Manisankar P, Bhattacharya S, Krishna  R. & Jeyakanthan, J (2011), 4-{(4-Chlorophenyl)methyl}- 4,5,6,7- tetrahydro-1,2,3-benzoselenadiazole, Acta Cryst. E67: o1421-o1422

16. Muthukumaran J, Nachiappan M, Chitra S, Muthusubramanian S, Manisankar P, Bhattacharya S, Krishna R. & Jeyakanthan, J (2011), 1-(2-Naphthyl)-3-phenyl-3-(4,5,6,7-tetrahydro-1,2,3-benzoselenadiazol-4- yl)propan-1- one, Acta Cryst. E67: o2010-o2011

15. Muthukumaran J, Nishandhini M, Chitra S, Muthusubramanian S, Manisankar P, Bhattacharya S, Krishna R. & Jeyakanthan, J (2011), 3-(4-Methylphenyl)-1-phenyl-3-(4,5,6,7-tetrahydro-1,2,3-benzoselenadiazol-4- yl)propan-1-one, Acta Cryst. E67: o1660-o1661

14. Muthukumaran J, A. Parthiban, M. Kannan, H. Surya Prakash Rao & R. Krishna (2011), 6,8-Dichloro- N-methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, Acta Cryst. E67: o898-o899

13. Muthukumaran J, A. Parthiban, P. Manivel, H. Surya Prakash Rao & R. Krishna (2011), 6-Methoxy-N- methyl-3-nitro-4-nitromethyl-4H-chromen-2-amine, Acta Cryst. E67: o1276-o1277

12. Muthukumaran J, P. Manivel, M. Kannan, J. Jeyakanthan & R. Krishna (2011), A framework for classification of antifreeze proteins in over wintering plants based on their sequence and structural features, J Bioinform Seq Anal, 3: 70-88

11. Muthukumaran J, P. Manivel, M. Kannan, J. Jeyakanthan & R. Krishna (2011), Advancement in computational analysis methods of plant antifreeze proteins (AFPs): An application towards classification and gene expression studies of leucine rich repeat (LRR) and ice-recrystallization inhibition domain (IRI) containing AFPs, J Comput Biol Bioinform Res, 3: 65-82

10. Muthukumaran J, Mannu Jayakanthan, Sanniyasi Chandrasekar and Premendu P. Mathur (2011), Bind-Predict: An algorithm for identifying zinc fingerbinding motifs in DNA sequences, J Comput Biol Bioinform Res, 3: 91-102

9. Karthikeyan S, Muthukumaran J, Krishna R. and Manimaran, B (2011), 2,2'-diphenol, Acta Cryst. E67: o1765-o1766

8. Muthukumaran J, Kannan M, Vanitha A, Manimaran B. & Krishna R (2010), Bis(-phenyltellurido- 2Te:Te)bis, Acta Cryst. E66: m558-m559

7. Vanitha A, Muthukumaran J, Krishna R & Manimaran, B (2010), Heptacarbonyl1 3C,24C-(4- phenylpyridine-1N)di--phenyltellurido-1:24Te:Te-dirhenium(I), Acta Cryst E66: m518-m5

6. Ankita Punetha, Muthukumaran J, Anmol Jaywant Hemrom, Nagarajan Arumugam, Mannu Jayakanthan and Durai Sundar (2010) Towards understanding the regulation of rubber biosynthesis: Insights into the initiator and elongator enzymes. J Bioinform Seq Anal, 2: 1-10

5. Satyanarayana CR, Devendran A, Muthukumaran J, Mannu J, Mathur PP, Gopal SD, Rajagopal K, Chandrasekaran A (2009), Influence of the genetic polymorphisms in the 5' flanking and exonic regions of CYP2C19 on proguanil oxidation. Drug Metab Pharmacokinet. 2009;24(6):537-48.

4. Jayakanthan M, Chandrasekar S, Muthukumaran J, Mathur PP (2009) Analysis of CYP3A4-HIV-1 protease drugs interactions by computational methods for Highly Active Antiretroviral Therapy in HIV/AIDS. J Mol Graph Model. 2010 Jan;28(5):455-63

3. Jayakanthan M, Muthukumaran J, Chandrasekar S, Chawla K, Punetha A, Sundar D (2009) ZifBASE: a database of zinc finger proteins and associated resources. BMC Genomics 10:421

2. Balachandran N, Kichenamourthy S, Muthukumaran J, Jayakanthan M, Chandrasekar S, Punetha A and Sundar D (2009) Diversity of true mangroves and their associates in the Pondicherry region of South India and development of a mangrove knowledgebase. J Ecol Nat Environ 1: 99-105

1. Karthick RNS, Muthukumaran J (2008) Prediction of Three Dimensional Model and Active Site Analysis of Inducible Serine Protease Inhibitor -2 (ISPI -2) in Galleria Mellonella. J Comput Sci Syst Biol 1: 119-125

Area of Interest

  • Protein Structural Biology