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Shailly Tomar
Research Interests

Educational Details
Professional Background


Honours and Awards

Teaching Engagements
Teaching Engagements

Associate Scholars

Administrative Positions
Research Interests
Antiviral research , discovery of structure-based antivirals against RNA viruses (Chikungunya, Dengue and SARS), Chimeric virus-like particles (VLPs) for vaccine therapy and virus diagnostics, Virus-host protein-protein interactions involving host pathways and evasion of innate immune responses, Structure-based engineering of antibodies, nanobodies, antiviral peptides and antiviral proteins, Integration of traditional medicinal knowledge with modern scientific approaches to validate antiviral and antimicrobial potential of ayurvedic medicinal plants and practices
Educational Details
Delhi University, Delhi
B. Sc. (Hons), Botany
All India Institute of Medical Sciences, New Delhi
M.Sc., Biophysics
Purdue University USA
Ph.D., Virology
Professional Background
17 Dec 2019 - Present
Indian Institute of Technology Rorokee
Associate Professor
17 Apr 2014 - 17 Dec 2019
IIT Roorkee
Assistant Professor
22 Feb 2011 - 03 Apr 2014
Indian Institute of Technology Roorkee
Assistant Professor (On Contract)
06 Jan 2010 - 21 Feb 2011
Indian Institute of Technology Roorkee
07 Feb 2007 - 05 Jan 2010
Department of Biotechnology IIT Roorkee
Young Scientist DST
01 Jan 2006 - 01 Jan 2007
Department of Biotechnology, IIT, Roorkee
Developing a phage-based strategy against antimicrobial resistance (AMR) bacteria using the Ganga water 18 Oct 2023 Phage-based strategy THDC India Limited 166 lakhs
Molecular studies of antiviral molecules in Gau mutra distillate and dung extract against Chikungunya and Dengue 30 Dec 2021 Identification of therapeutics from Ayurveda and medicinal plants Identification of therapeutics from Ayurveda and medicinal plants 58.63 lacs MINISTRY OF AYUSH Dr. Arvind Agarwal (CO-PI), Dr. Debabrata Sircar (Co-PI),
Computer-aided structure-based molecular engineering of nanobodies against SARS-CoV-2 Spike protein 27 Apr 2022 Protein engineering Protein engineering 30 lacs ICMR
Antivirals against Chikungunya virus targeting RNA viral capping machinery 25 Jan 2021 Discovery of antivirals Discovery of antivirals against viral replication enzymes 28.25 lacs ICMR
Development of novel purine nucleoside-quinoline conjugates as effective inhibitors for Chikungunya and Dengue viruses 01 Mar 2024 Antiviral drug discovery Officer PI 50 lacs SERB
Development of therapeutic monoclonal antibodies against Chikungunya virus 01 Apr 2024 Discovery of antivirals 20 Lacs DST (Indo- Argentina)
Protein nanoparticles based development of universal Influenza vaccine 18 Dec 2020 Vaccines Vaccines 12 lacs SERB-CRG
Discovery of structure-based antivirals against SARS-CoV2 targeting key viral genome replication enzymes 21 May 2020 Discovery of antivirals Discovery of antivirals against SARS-CoV-2 60.21 LACS DST-SERB Prof. Pravindra Kumar and Dr. Gaurav Kumar Sharma
Targeting alphavirus host protein interactions to develop antiviral therapies 01 Jan 2019 drug discovery Discovery of antivirals 60 lacs Sweden Research Council (SRC) Prof. Gerald Mclnerney, Karolinska Institutet
Development of molecular diagnostic method for early detection of Chikungunya using fluorescent virus-like nanoparticles 28 Mar 2018 Therapeutics against RNA viruses Therapeutics against RNA viruses 20 lacs DBT
Molecular and structural analysis of Chikungunya Capsid Protease for antiviral drug Discovery 01 Jan 2018 Drug discovery Drug discovery 17 Lacs DST SERB Prof. P. Kumar
Probing intermolecular contacts between capsid protein and envelope proteins of Chikungunya Virus 01 Jan 2017 protein-protein interaction studies and drug discovery Drug repurposing and discovery of antivirals against RNA viruses, protein-protein interaction studies and drug discovery 49.08 lacs ICMR
Identification and validation of small molecules targeting drugable pocket on alphavirus capsid 01 Jan 2016 Drug discovery Drug repurposing and discovery of antivirals against RNA viruses 9.35 lacs DRDE
In silico development of anti-amoebic molecules based on the structure of E. histolytica ODC 01 Jan 2015 Structural biology Structural biology 49.92 ICMR
Structural functional characterization of Chikungunya virus nsP2 protease and inhibitor screening 01 Jan 2015 Drug discovery Drug design and discovery of antivirals 50 lacs DBT
Structure activity relationship studies of protein glutamate-O-methylase 01 Dec 2015 Structural biology and biophysical characterization Structural biology and biophysical characterization 18.36 lacs UCB
Development of engineered microalgae for enhanced lipid accumulation. 08 May 2014 bioengineering 72 lacs DBT
Structural analysis of chitinase from Tamarindus indica 01 Jan 2013 Therapeutics from medicinal plant extract Therapeutics from medicinal plant extract 37.34 lacs DST
Structural and functional analysis of globulin from the seeds of Holarrhena Wrightia tinctoria, a medicinal plant. 02 May 2013 Structural and functional studies 30 lacs DBT
Structural studies of chorismate synthase 01 May 2013 Structural biology 23 Lacs CSIR
Three Dimensional Analysis of Alphavirus Capsid Protease 01 Jan 2011 Structural biology and discovery of antivirals Structural biology and discovery of antivirals 38 lacs DRDO
Structural analysis of DAHP synthase from Arabidopsis thaliana 04 May 2010 Structural biology 30 lacs DST
Targeting viral protease of emerging and neglected RNA alphaviruses. 01 Jan 2010 Discovery of antivirals against RNA viruses Discovery of antivirals against RNA viruses 3 lacs SRIC-MHRD
Structural studies of tamarind proteinase inhibitor (TPI) and its complex with trypsin. 01 Jan 2009 Identification of therapeutics from medicinal plants Identification of therapeutics from medicinal plants 15.76 lacs CSIR
Structural Characterization Of DAHP Synthase For Designing Rational Inhibitors As Antibacterial Drug. 01 May 2008 Drug designing 10 Lacs MHRD-IITR
Heterologous production and molecular characterization of alphavirus replication proteins 01 Jan 2008 Biophysical characterization studies Protein characterization studies 3 Lacs SRIC-IITR None
Structural studies of biphenyl dehydrogenase from Comamonas testosteroni strain B-356 01 Apr 2008 Structural biology 10.7 lacs CSIR
Structure-function analysis of alphavirus capping enzyme, NSP1. 01 Jan 2007 Drug discovery Drug discovery and protein characterization studies 8.22 Lacs DST None

Advances in antiviral research
Year: 2024 , ISBN: 978-981-99-9194-5
Naveen Kumar, Yashpal Singh Malik, Shailly Tomar, Sayeh Ezzikouri | Springer Singapore
Contribution: Editor , Pages: 453 ,
Environmental Pollution: Biodegradation and Bioremediation
Year: 2017 , ISBN: 978-1626991026
Bhola R Gurjar, Shailly Tomar, and Pravindra Kumar | Bio-Green
Pages: 300 , Volumes: 1

1. Singh V, Bhutkar M, Choudhary S., Nehul S., Kumar R, Singla J., Kumar P., Tomar S*. 2024 Enhancing affinity of neutralizing SARS-CoV-2 nanobody through facile structure-guided mutations in CDRsdoi: in preprint)

2. Nehul, S., Rani, R., Panda, P. K., Kumar, P., Tomar, S*. (2024). Repurposing efavirenz, the HIV antiretroviral drug for Chikungunya virus infection. (Article in preprint)

3. Singh VA, Nehul S, Kumar CS, Banerjee M, Kumar P, Sharma G, Tomar S*. 2023 Chimeric chikungunya virus-like particles with surface exposed SARS-CoV-2 RBD elicits potent immunogenic responses in mice. bioRxiv. Jan 29:2023-01. (Article in preprint)

4. Rani, R., Nehul, S., Choudhary, S., Upadhyay, A., Sharma, G.K., Kumar, P. and Tomar, S*., 2023. Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS- CoV-2. bioRxiv, pp.2023-07. DOI:10.1101/2023.07.24.550324 (Article in preprint)

5. Bhutkar, M., Rani, R., Kothiala, A., Mahajan, S., Waghmode, B., Kumar, R., Singh, V., Sircar, D., Kumar, P. and Tomar, S*. 2022. Elucidation of the antiviral mechanism of natural therapeutic molecules Herbacetin and Caffeic acid phenethyl ester against Chikungunya and Dengue virus. bioRxiv. doi:

6. Mahajan, S., Kumar, R., Singh, A., Pareek, A., Long, S., McInerney, G., Tomar, S*., 2022. Targeting host protein G3BP1 for the discovery of novel antiviral inhibitors against the Chikungunya virus.bioRxiv. doi:

7. Choudhary, S., Nehul, S., Kumar, K.A., Sharma, S., Rani, R., Saha, A., Sharma, G.K., Tomar, S*. and Kumar, P., 2022. Crystal structure and activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease revealed new allosteric sites for antiviral therapies. bioRxiv. doi:

8. Singh, V.A., Kumar, C.S., Khare, B., Kuhn, R.J., Banerjee, M. and Tomar, S*., 2023. Surface decorated reporter-tagged chikungunya virus-like       particles for clinical diagnostics and identification of virus entry inhibitors. Virology, 578, pp.92-102

9. Bhatia, P., Singh, V.A., Rani, R., Nath, M. and Tomar, S*., 2023. Cellular uptake of metal oxide-based nanocomposites and targeting of chikungunya virus replication protein nsP3. Journal of Trace Elements in Medicine and Biology, p.127176, DOI: 10.1016/j.jtemb.2023.127176

10. de Souza, B.G., Choudhary, S., Vilela, G.G., Passos, G.F.S., Costa, C.A.C.B., de Freitas, J.D., Coelho, G.L., de Andrade Brandão, J., Anderson, L., Bassi, Ê.J. and de Araújo-Júnior, J.X., Tomar, S., Silva Junior., EF., 2023. Design, synthesis, antiviral evaluation, and In silico studies of acrylamides targeting nsP2 from Chikungunya virus. European Journal of Medicinal Chemistry, p.115572.

11. Lonare, S., Sharma, M., Dalal, V., Gubyad, M., Kumar, P., Gupta, D.N., Pareek, A., Tomar, S., Ghosh, D.K., Kumar, P. and Sharma, A.K., 2023. Identification and evaluation of potential inhibitor molecules against TcyA from Candidatus Liberibacter asiaticus. Journal of Structural Biology, 215(3), p.107992. DOI: 10.1016/j.jsb.2023.107992

12. Neetu, N., Mahto, J.K., Sharma, M., Katiki, M., Dhaka, P., Roy, P., Tomar, S., Narayan, A., Yernool, D. and Kumar, P., 2023. Sulisobenzone is a potent inhibitor of the global transcription factor Cra. Journal of Structural Biology, 215(4), p.108034. DOI: 10.1016/j.jsb.2023.108034

13. Choudhary S, Nehul S, Singh A, Panda PK, Kumar P, Sharma GK, Tomar S*. 2023 Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS‐COV‐2 targeting main protease and papain‐like protease. IUBMB lifeDOI: 10.1002/iub.2793

14. Dhaka, P., Singh, A., Choudhary, S., Peddinti, R.K., Kumar, P., Sharma, G.K. and Tomar, S*., 2023. Mechanistic and thermodynamic characterization of antiviral inhibitors targeting nucleocapsid N-terminal domain of SARS-CoV-2. Archives of Biochemistry and Biophysics, p.109820.  DOI: 10.1016/

15. Gupta, D.N., Lonare, S., Rani, R., Singh, A., Ghosh, D.K., Tomar, S., and Sharma, A.K., 2023. Comparative Analysis of Inhibitor Binding to Peroxiredoxins from Candidatus Liberibacter asiaticus and Its Host Citrus sinensisApplied Biochemistry and Biotechnology. DOI: 10.1007/s12010-023-04798-y

16. Pareek, A., Kumar, R., Mudgal, R., Neetu, N., Sharma, M., Kumar, P. and Tomar, S.* (2022), Alphavirus antivirals targeting RNA-dependent RNA polymerase domain of nsP4 divulged using surface plasmon resonance. The FEBS Journal

17. Dubey, A., Choudhary, S., Kumar, P. Tomar S*. Emerging SARS-CoV-2 Variants: Genetic Variability and Clinical Implications. Current Microbiology 79, 20 (2022).

18. Gupta, D.N., Rani, R., Kokane, A.D., Ghosh, D.K., Tomar, S. and Sharma, A.K., 2022. Characterization of a cytoplasmic 2-Cys peroxiredoxin from Citrus sinensis and its potential role in protection from oxidative damage and wound healing. International Journal of Biological Macromolecules, 209, pp.1088-1099.

19. Bhutkar, M., Singh, V., Dhaka, P., and Tomar S*. Virus-host protein-protein interactions as molecular drug targets for arboviral infections. Frontiers in Virology, p.70, (2022).

20. Rani, R., Long, S., Pareek, A., Dhaka, P., Singh, A., Kumar, P., McInerney, G. and Tomar, S*., 2022. Multi-target direct-acting SARS-CoV-2 antivirals against the nucleotide-binding pockets of virus-specific proteins. Virology, 577, pp.1-15.Doi:

21. Kumar, K.A., Sharma, M., Dalal, V., Singh, V., Tomar, S. and Kumar, P., 2021. Multifunctional Inhibitors of SARS CoV2 by MM/PBSA, Essential dynamics, and Molecular dynamic investigations. Journal of Molecular Graphics and Modelling, p.107969.

22. Choudhary, S., Neetu., Singh, VA., Kumar, P., Chaudhary, M., Tomar, S*., 2021. Chikungunya virus titration, detection and diagnosis using N-Acetylglucosamine (GlcNAc) specific lectin based virus capture assay. Virus Research. p.198493. 

23. Kumar, R., Nehul, S., Singh, A. and Tomar, S*., 2021. Identification and evaluation of antiviral potential of thymoquinone, a natural compound targeting Chikungunya virus capsid protein. Virology. 561:36-46. doi: 10.1016/j.virol.2021.05.013

24. Malik, Y.S., Ansari, M.I., Kattoor, J.J., Kaushik, R., Sircar, S., Subbaiyan, A., Tiwari, R., Dhama, K., Ghosh, S., Tomar, S. and Zhang, K.Y., 2021. Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. Briefings in bioinformatics22(2), pp.1006-1022

25. Sharma, M., Mahto, J.K., Dhaka, P., Neetu, N., Tomar, S. and Kumar, P., 2021. MD simulation and MM/PBSA identifies phytochemicals as bifunctional inhibitors of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, pp.1-14.

26. Mahajan, S., Choudhary, S., Kumar, P. and Tomar, S., 2021. Antiviral strategies targeting host factors and mechanisms obliging+ ssRNA viral pathogens. Bioorganic & Medicinal Chemistry46, p.116356

27. Savita, B.K., Dalal, V., Choudhary, S., Gupta, D.N., Das, N., Tomar, S., Kumar, P., Roy, P. and Sharma, A.K., 2021. Characterization of recombinant pumpkin 2S albumin and mutation studies to unravel potential DNA/RNA binding site. Biochemical and Biophysical Research Communications580, pp.28-34. 

28. Neetu, N., Katiki, M., Mahto, J.K., Sharma, M., Narayanan, A., Maity, S., Tomar, S., Ambatipudi, K., Sharma, A.K., Yernool, D. and Kumar, P., 2021. Deciphering the enigma of missing DNA binding domain of LacI family transcription factors. Archives of Biochemistry and Biophysics, p.109060.

29. Mahto, J.K., Neetu, N., Waghmode, B., Kuatsjah, E., Sharma, M., Sircar, D., Sharma, A.K., Tomar, S., Eltis, L.D. and Kumar, P., 2021. Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni. Journal of Biological Chemistry, p.101416. DOI: 

30. Mudgal, R., Bharadwaj, C., Dubey, A., Choudhary, S., Nagarajan, P., Aggarwal, M., Ratra, Y., Basak, S. and Tomar, S.*, 2021. Selective estrogen receptor modulators limit alphavirus infection by targeting the viral capping enzyme nsP1. Antimicrobial Agents and Chemotherapy, pp.AAC-01943.DOI:

31. Neetu, N., Katiki, M., Dev, A., Gaur, S., Tomar, S. and Kumar, P., 2020. Structural and biochemical analyses reveal that chlorogenic acid inhibits the shikimate pathway. Journal of Bacteriology202(18), pp.e00248-20.Doi: 10.1128/JB.00248-20

32. Mudgal, R., Mahajan, S. and Tomar, S*., 2020. Inhibition of Chikungunya virus by an adenosine analog targeting the SAM‐dependent nsP1 methyltransferase. FEBS letters594(4), pp.678-694.

33. Choudhary, S., Kumar, R., Dalal, U., Tomar, S*. and Reddy, S.N., 2020. Green synthesis of nanometal impregnated biomass–antiviral potential. Materials Science and Engineering: C, 112, page no.110934

34. Fatma, B., Kumar, R., Singh, V.A., Nehul, S., Sharma, R., Kesari, P., Kuhn, R.J. and Tomar, S*., 2020. Alphavirus capsid protease inhibitors as potential antiviral agents for Chikungunya infection. Antiviral Research, 179, page no.104808.

35. Rani R, Singh A, Pareek A, Tomar S*. 2020: In Silico Guided Drug Repurposing to Combat SARS-CoV-2 by Targeting Mpro, the Key Virus Specific Protease. Chemrxiv (Article in Preprint).doi:10.26434/chemrxiv.12030345.v1

36. Choudhary, S., Malik, Y.S. and Tomar, S*., 2020. Identification of SARS-CoV-2 cell entry inhibitors by drug repurposing using in silico structure-based virtual screening approach. Frontiers in Immunology11, page no.1664.

37. Dhankhar, P., Dalal, V., Singh, V., Tomar, S*. & Kumar, P., 2020. Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2. Journal of Biomolecular Structure and Dynamics, pp.1-16.

38. Mudgal R, Nehul S, Tomar S* (2020) Prospects for mucosal vaccine: shutting the door on SARS-CoV-2.Human Vaccines & Immunotherapeutics.Dec 1;16(12):2921-2931. Epub 2020 Sep 15. doi: 10.1080/21645515.2020.1805992.

39. Dhankhar P, Dalal V, Mahto JK, Gurjar BR, Tomar S, Sharma AK, Kumar P. Characterization of dye-decolorizing peroxidase from Bacillus subtilis. Archives of Biochemistry and Biophysics. 2020 Oct 30;693:108590. Epub 2020 Sep 21. doi: 10.1016/

40. Bais S., Ratra Y., Khan N., Pandey R., Kushawaha P.,Tomar S., Medigeshi G., Singh A.,   Basak S*. (2019)  Cytopathic RNA viruses require pro-survival RelA NF-kB function for their propagation. Journal of Virology. 93(14), pp.e00081-19. doi: 10.1128/JVI.00081-19

41. Chandra R, Singh V, Tomar S*, Nath M*. Multi-core-shell composite SnO2NPs@ZIF-8: potential antiviral agent and effective photocatalyst for waste-water treatment. (2019) Environmental Science and Pollution Research Int. 26(23):23346-23358. doi: 10.1007/s11356-019-05646-5

42. Kaur R., Neetu N., Mudgal R., Jose J., Kumar P., Tomar S. (2018). Glycan-dependent chikungunya viral infection divulged by antiviral activity of NAG specific chi-like lectin. Virology 526:91-98 doi:10.1016/j.virol.2018.10.009 

43. Malik A., Dalal V., Ankri S. and Tomar S*. 2019 Structural insights into the arginase enzyme of E. histolytica and identification of novel non-amino acid based inhibitors by structure-based drug repositioning approach. The FEBS journal 286(20):4135-4155. doi: 10.1111/febs.14960

44. Dalal V, Kumar P, Rakhaminov G, Qamar A, Fan X, Hunter H, Tomar S, Golemi-Kotra D, Kumar P. 2019 Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus. Journal of Molecular Biology. ;431(17):3107-3123. doi:10.1016/j.jmb.2019.06.019.  

45. Puranik N, Rani R., Singh V., Tomar S. *, Putambkar H.M. and Srivastava P*. (2019) Evaluation of the antiviral potential of halogenated dihydrorugosaflavonoids and molecular modelling with nsP3 protein of Chikungunya virus (CHIKV). ACS Omega.  4, (23), 20335–20345

46. Sharma A., Kumar V., Chatrath A., Dev A., Prasad R., Sharma, A. K., Tomar S., Kumar P. (2018). In vitro metal catalyzed oxidative stress in DAH7PS: Methionine modification leads to structure destabilization and induce amorphous aggregation. International Journal of Biological Macromolecules 106:1089-1106.DOI: 10.1016/j.ijbiomac.2017.08.105

47. Sharma R., Kesari P., Kumar P., Tomar S*. (2018) Structure-function insights into chikungunya virus capsid protein: Small molecules targeting capsid hydrophobic pocket. Virology.  515:223-234. DOI: 10.1016/j.virol.2017.12.020

48. Singh H., Mudgal R., Narwal M., Kaur R., Singh V. A., Malik A., Chaudhary M., Tomar S*. (2018) Chikungunya virus inhibition by peptidomimetic inhibitors targeting virus-specific cysteine protease. Biochimie. 149:51-61. DOI: 10.1016/j.biochi.2018.04.004

49. Malik A., Singh H., Pareek A., Tomar S*. (2018) Biochemical and biophysical insights into the metal binding spectrum and bioactivity of arginase of Entamoeba histolytica. Metallomics. 25;10(4):623-638.  DOI: 10.1039/c8mt00002f

50. Narwal  M., Singh H., Pratap S., Malik A., Kuhn R. J., Kumar P., Tomar S*. (2018) Crystal structure of chikungunya virus nsP2 cysteine protease reveals a putative flexible loop blocking its active site. International Journal of Biological Macromolecules. 116:451- 62. DOI: 10.1016/j.ijbiomac.2018.05.007

51. Kaur R., Mudgal R., Narwal M., Tomar S*. (2018) Development of an ELISA assay for screening inhibitors against divalent metal ion dependent alphavirus capping enzyme. Virus Research. pii: S0168-1702(18)30028-5. DOI: 10.1016/j.virusres.2018.06.013

52. Saha  A.,  Acharya B. N., Priya R., Tripathi N. K., Shrivastava A., Rao M. K., Kesari P., Narwal  M., Tomar S., Bhagyawant S. S., Parida M., Dash P. K. (2018) Development of nsP2 protease based cell free high throughput screening assay for evaluation of inhibitors against emerging Chikungunya virus. Scientific Reports. 8:10831.DOI: 10.1038/s41598-018-29024-2

53. Aggarwal M., Kaur R., Saha A., Mudgal R., Yadav R., Dash P. K., Parida M., Kumar P., Tomar S. (2017). Evaluation of antiviral activity of piperazine against Chikungunya virus targeting hydrophobic pocket of alphavirus capsid protein. Antiviral Research. 146 (102-111). DOI: 10.1016/j.antiviral.2017.08.015

54. Pratap S., Dev A., Kumar V., Yadav R., Narwal M., Tomar S., Kumar P. (2017) Structure of Chorismate Mutase-like Domain of DAHPS from Bacillus subtilis Complexed with Novel Inhibitor Reveals Conformational Plasticity of Active Site. Scientific Reports.  25;7(1):6364.DOI: 10.1038/s41598-017-06578-1

55. Kumar P., Kesari P., Dhindwal S., Choudhary A. K., Katiki M., Neetu, Verma A., Ambatipudi K., Tomar S., Sharma A. K., Mishra G., Kumar P. (2017) A novel function for globulin in sequestering plant hormone: Crystal structure of Wrightia tinctoria 11S globulin in complex with auxin. Scientific Reports.  5;7(1):4705. DOI: 10.1038/s41598-017-04518-7

56. Sharma A., Kumar P., Kesari P., Katiki M., Mishra M., Singh P. K., Gurjar B. R., Sharma A. K., Tomar S., Kumar P. (2017) Purification and Characterization of 2S Albumin from Seeds of Wrightia tinctoria Exhibiting Antibacterial and DNase Activity. Protein and Peptide Letters. 1;24(4):368-78. DOI: 10.2174/0929866524666170126144936

57. Kesari P., Sharma A., Katiki M. Kumar P., Gurjar B. R., Tomar S., Sharma A. K., Kumar P. (2017) Structural, Functional and Evolutionary Aspects of Seed Globulins. Protein peptide letters 1;24(3):267-77. DOI: 10.2174/0929866523666161220112641

58. Dhindwal S., Kesari P., Singh H., Kumar P.,  Tomar S. (2016) Conformer and Pharmacophore Based Identification of Peptidomimetic Inhibitors of Chikungunya Virus nsP2 Protease. Journal of Biomolecular Structure and Dynamics 2:1-18. DOI: 10.1080/07391102.2016.1261046

59. Sharma R., Fatma B., Saha A., Bajpai S., Sistla S., Dash P. K., Parida M., Kumar P., Tomar S. (2016) Inhibition of chikungunya virus by picolinate that targets viral capsid protein, Virology, 265–276. DOI: 10.1016/j.virol.2016.08.029

60. Batra M., Sharma R., Malik A., Dhindwal S., Kumar P., Tomar S. (2016) Crystal structure of pentapeptide-independent chemotaxis receptor methyltransferase (CheR) reveals idiosyncratic structural determinants for receptor recognition. Journal of Structural Biology 196(3):364-374DOI: 10.1016/j.jsb.2016.08.005

61. Aggarwal M., Sharma R., Kumar P., Parida M., Tomar S. (2015) Kinetic characterization of trans-proteolytic activity of Chikungunya virus capsid protease and development of a FRET-based HTS assay. Scientific. Reports. 5:14753.

62. Batra M., Sharma R., Chandra V., Aggarwal M., Agarwal U., Gupta P, Singh R. P., Tomar S. (2015)  In silico and proteomic analysis of protein methyltransferase CheR from Bacillus subtilis. International Journal of Biological Macromolecules. 77:168-80. DOI: 10.1016/j.ijbiomac.2015.03.023

63. Kesari P., Patil D. N., Kumar P., Tomar S.,  Sharma A. K., Kumar P. (2015)  Structural and functional evolution of chitinase-like-proteins from plants. Proteomics 15(10):1693-705. DOI: 10.1002/pmic.201400421

64. Dhindwal S., Priyadarshini P., Patil D. N., Tapas S., Kumar P., Tomar S., Kumar P. (2015) Ligand-bound structures of 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase from Moraxella catarrhalis reveal a water channel connecting to the active site for the second step of catalysis. Acta Crystallographica Section D 71(Pt 2):239-55. DOI: 10.1107/S1399004714025218

65. Aggarwal M., Dhindhwal S., Kumar P., Kuhn R. J., Tomar S. (2014) Trans-protease activity and structural insights into the active form of the alphavirus capsid protease. Journal of Virology., 88(21):12242-53. DOI: 10.1128/JVI.01692-14

66. Patil D. N., Datta M., Dev A., Dhindwal S., Singh N., Dasauni P., Kundu S., Sharma A. K., Tomar S., Kumar P. (2013) Structural investigation of a novel N-acetyl glucosamine binding chi-lectin which reveals evolutionary relationship with class III chitinases. PLoS One. 8 (5):e63779. doi: 10.1371/journal.pone.0063779.

67. Kumar P., Patil D. N., Chaudhary A., Tomar S., Yernool D., Singh N., Dasauni P., Kundu S., Kumar P.  (2013) Purification and Biophysical Characterization of an 11S Globulin from Wrightia tinctoria exhibiting Hemagglutinating Activity. Protein Peptide Letters 20(5):499-509.DOI: 10.2174/0929866511320050002

68. Preeti; Tapas S., Kumar P., Madhubala R., Tomar S. (2013) Structural Insight into DFMO Resistant Ornithine Decarboxylase from Entamoeba histolytica: An Inkling to Adaptive Evolution. PLoS ONE 8(1):e53397:10.1371/journal.pone.0053397. Epub 2013 Jan 11. DOI: 10.1371/journal.pone.0053397

69. Aggarwal M., Tapas S., Preeti, Siwach A., Kumar P., Kuhn R. J., Tomar S. (2012) Crystal structure of Aura virus capsid protease and its complex with dioxane: new insights into capsid-glycoprotein molecular contacts.  PLoS ONE 7(12):e51288.

70. Pratap S., Narwal  M., Dev A., Dhindwal S., Tomar S., Kumar P. (2012) Crimean-Congo Hemorrhagic Fever Virus: Strategies to Combat with an Emerging Threat to Human. Current Bioinformatics, 7(4), 467-477.

71. Patil D. N., Chaudhary A., Sharma A. K., Tomar S., Kumar P. (2012) Structural basis for dual inhibitory role of tamarind Kunitz inhibitor (TKI) against factor Xa and trypsin. FEBS Journal. Dec;279(24):4547-64. DOI: 10.1111/febs.12042

72. Preeti, Tapas S., Kumar P., Madhubala R., Tomar S. (2012) Biochemical, mutational and in silico structural evidence for a functional dimeric form of the ornithine decarboxylase from Entamoeba histolytica. PLoS Neglected Tropical Diseases 6(2):e1559. DOI: 10.1371/journal.pntd.0001559

73. Aggarwal M., Dhindwal S., Pratap S., Kuhn R. J., Kumar P., Tomar S. (2011) Crystallization, high-resolution data collection and preliminary crystallographic analysis of Aura virus capsid protease and its complex with dioxane. Acta Crystallographica Section F 1;67 (Pt 11):1394-8. DOI: 10.1107/S174430911103404X

74. Tomar S., Narwal M., Harms E., Smith J. L., Kuhn R .J. (2011) Heterologous production, purification and characterization of enzymatically active Sindbis virus nonstructural protein nsP1. Protein Expression and Purification 79(2):277-84. DOI: 10.1016/j.pep.2011.05.022

75. Dhindwal S., Patil D. N., Mohammadi M., Sylvestre M., Tomar S., Kumar P. (2011) Biochemical studies and ligand bound of biphenyl dehydrogenase from Pandoraea pnomenusa strain B-356 reveal a basis for broad specificity of the enzyme. Journal of Biological Chemistry. 286(42):37011-22. DOI: 10.1074/jbc.M111.291013

76. Tapas S., Patel G. K., Dhindwal S., Tomar S. (2010) In silico sequence analysis and homology modeling of DAHP synthase from Pseudomonas fragi. Journal of Molecular Modeling.17(CCP4), 621-31. DOI: 10.1007/s00894-010-0764-y

77. Sakshi,  Patil D. N., Tomar S.,  Sylvestre M., Kumar P. (2010) Expression, purification, crystallization and preliminary crystallographic studies of cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase from Pandoraea pnomenusa B-356. Acta Crystallographica Section F 66, 1517-1520. doi: 10.1107/S1744309110036894

78. Datta M. and Tomar S. (2010) Molecular cloning and structural characterization of catalytic domain of class III chitinase Tamarindus indica. Int. J. Life Sci. and Tech. 3(2) 16-28.

79. Patil D. N., Preeti, Chaudhry A., Sharma A. K., Kumar P.*, Tomar S.* (2009) Purification, crystallization and preliminary crystallographic studies of a Kunitz-type proteinase inhibitor from tamarind (Tamarindus indica) seeds. Acta Crystallographica Section F. 65: 736-738. DOI: 10.1107/S1744309109023495

80. Patil D. N., Preeti, Chaudhry A., Tomar S., Sharma A. K., Kumar P. (2009) Isolation, purification, crystallization and preliminary crystallographic studies of chitinase from tamarind (Tamarindus indica) seeds. Acta Crystallographica Section F. 65, 343-345. DOI: 10.1107/S1744309109006472

81. Tomar S., Patil D. N., Datta M., Tapas S., Preeti, Sharma A. K., Tomar S.*, Kumar P.* (2009) Crystallization and preliminary X-ray diffraction analysis of the complex of Kunitz-type tamarind trypsin inhibitor and porcine pancreatic trypsin. Acta Crystallographica Section F 65: 1179-1181. doi: 10.1107/S1744309109041694

82. Tomar S., Hardy R. W., Smith J. L.,  Kuhn R. J. (2006). Catalytic core of alphavirus nonstructural protein, nsP4 possesses terminal adenylyl transferase activity. Journal of Virology 80(20): 9962-9. DOI: 10.1128/JVI.01067-06

83. Bilgrami S., Tomar S., Yadav S., Kaur P., Kumar J., Jabeen T., Sharma S., Singh T. P. (2004) Crystal structure of schistatin, disintegrin homodimer from saw-scaled viper (Echis carinatus) at 2.5 A resolutionJournal of Molecular Biology 341(3):829-37. DOI: 10.1016/j.jmb.2004.06.048

84. Tomar S., Yadav S., Chandra V., Kumar P., Singh T. P. (2001) Purification, crystallization and preliminary X-ray diffraction studies of disintegrin (schistatin) from saw-scaled viper (Echis carinatus). Acta Crystallographica Section D.  57:1669-70DOI: 10.1107/s0907444901012082


Patents granted and filed 

Patents Granted 

  1. Tomar S., Kumar P., Kaur R., Chaudhary N.,  Singh VA., An antiviral composition of tamarind chi-like lectin and uses thereof. Indian patent, Application no. 201811019298 on May 23rd 2018.Patent granted (Patent No. 413264)
  2. Tomar S., Kumar P., Kaur R., Chaudhary N.,  Singh VA., An antiviral composition of tamarind chi-like lectin and uses thereof. Indian patent, Application no. 201811019298 on May 23rd 2018  Patent granted (Patent No. 413264)
  3. Tomar S., Kumar P., Singh H., Mudgal R. Chikungunya virus protease inhibitors and uses thereof. Indian patent, Application no. 201811022065 on June 13th 2018 Patent granted (Patent No. 536426)

Patents filed 

  1.  Kumar N., Tomar S., Saini R., Singh A., Kumar M., Bhatia S., Sanyal A., Chimeric neuraminidase tetramers as universal influenza vaccine candidates. (2023) (Indian Patent Application No. 202411006826, February 23rd, 2024)
  2. Tomar S. Kumar P., Singh VA., Nehul S.K., Sharma G. Alphavirus virus-like particles (VLP) containing immunogenic proteins of pathogens and its uses thereof. (Indian Patent Application No. 202311004737, January 24th, 2023)
  3. Tomar S., Kumar P., Singh V.A., Nanoluciferse reporter tagged virus-like particles, a method for producing the same, and applications thereof (Indian patent application, 202211066289., 18th November 2022)
  4. Tomar S., Khoba Prafful., Bhutkar M., A portable ultraviolet sterilization and disinfection device. Indian Patent, Provisional Application no. 202111046071 dated. 09/10/2021
  5. Tomar,S., Kumar, P., Sircar, D., Kumar, R., Singh, V.A. A prophylactic and therapeutic antiviral composition and method thereof. Indian Patent, Application no. 202011023131, Dated 2nd June 2020.
  6. Tomar S., Mudgal R, and Dubey A., An antiviral composition against alphaviruses. Indian Patent Application no 201911049130, Dated 29th Nov, 2019
  7. Tomar S., Kumar P., Neetu, Singh VA. and Choudhary S. Chikungunya virus titration and detection kit. Indian patent application no. 201911035044 on 30th Aug, 2019
  8. Tomar S., Kumar P. and Kaur R.; “A highly sensitive nsp1 enzyme assay and kit for determining inhibitors of alphavirus/chikungunya virus.” PCT application no. PCT/IB2018/051760 (16th March 2018).


Books Authored

  1. Singh A, Dhaka P, Kumar P, Tomar S, Singla J. 2024. Book Chapter 2: Bioinformatics databases and tools available for the development of antiviral drugs. Nature Springer Singapore Press. DOI:10.1007/978-981-99-9195-2_2
  2. Rani R, Bhutkar M, Tomar S. 2023. Chapter 4: Therapeutic antiviral potential of flavonoids. Apple Academic Press (AAP)
  3. Tomar, S., Mahajan, S. and Kumar, R., 2020. Chapter 19: Advances in structure-assisted antiviral discovery for animal viral diseases. In Genomics and biotechnological advances in veterinary, poultry, and fisheries (pp. 435-468). Academic Press.
  4. Tomar S. Kaur R., Singh VA (2019) Chapter 2: Structure-Function Relationship of Negative- Stranded Viral RNA Polymerases: Prospectives for Antiviral Therapy. In: Gupta, S.P. (Ed.), Viral Polymerases: Structures, Functions, and Roles in Antiviral Drug Targets. Academic Press, Elsevier 2019, Pages 43-67;
  5. Tomar S. Mudgal R and Pareek A. (2019) Chapter 3: RNA-Dependent RNA Polymerase of Alphaviruses: A Potential Target for the Design of Drugs Against Alphaviruses In: Gupta, SP. (Ed.), Viral Polymerases: Structures, Functions, and Roles in Antiviral Drug Targets. Acad. Press Elsevier
  6. Kesari, P., Neetu, Tomar,S., Kumar, P., (2017). Polychlorinated Biphenyls Bioremediation. In: Environmental Pollution: Biodegradation and Bioremediation. Series Studium press LLC USA., pp. 258-280
  7. Tomar, S., Aggarwal, M. (2017). Structure and function of alphavirus proteases. In: Gupta, S.P. (Ed.), Viral Proteases and Their Inhibitors. Academic Press. Elsevier Inc., pp. 105-136
  8. Tomar, S., Mudgal, R., Fatima B. (2017). Flavivirus Protease: An antiviral target. In: Gupta, S.P. (Ed.), Viral Proteases and Their Inhibitors. Academic Press. Elsevier Inc., pp. 137-161.
Honors And Awards
Purdue University, USA
Visiting Scientist, OVDF DST SERB
IIT Roorkee
Institute Research Fellowship for Outstanding Young Faculty
Karolinska Institute, Stockholm, Sweden
Visiting Scientist, Karolinska Institute, Sweden Research Council (SRC) Grant
IIT Roorkee
DST young scientist
American Society for Virology (ASV)
04 Aug 2020 - Present
Indian crystallography society (ICA)
04 Aug 2020 - Present
Indian Biophysical Society (IBS)
04 Aug 2020 - Present
Indian Virology Society (IVS)
04 Aug 2020 - Present
Teaching Engagements
Teaching Engagements
Biphysical Techniques ( BTN 611 )
Molecular separation techniques ( IBT 301 )
Genetics and Molecular Biology ( BTN 201 )
Biophysics and Biochemistry ( BT 213 )
Molecular separation Techniques ( IBT 01 )
Separation and Analysis of Biomolecules ( BTN 348 )
Molecular studies of antivirals targeting RNA virus replication
14 Jul 2023 - Present
Other Supervisors: , Scholar: Priyanshu Walia
Antivirus therapeutics against RNA virus
14 Jul 2023 - Present
Other Supervisors: , Scholar: Pratibha Verma
Identification and structure determination of bacteriophages against ESKAPE pathogens
14 Jul 2023 - Present
Other Supervisors: Prof. AK Sharma, Scholar: Anuj Jangid
Development of VLP based technological platform for diagnostics and therapeutics against viral infections
10 Jul 2022 - Present
Other Supervisors: None, Scholar: Ankita Saha
Structure-based identification and designing of antivirals against RNA viruses
10 Jul 2022 - Present
Other Supervisors: None, Scholar: Tanuj Handa
Viral capsid protein-A therapeutic antiviral target
10 Jul 2018 - Present
Other Supervisors: Prof. Pravindra Kumar, Scholar: Preeti Dhaka
Structural and functional investigations of alphavirus nsp4
19 Dec 2017 - Present
Other Supervisors: None, Scholar: Ankur Singh
Biomarker studies of Dengue disease severity
30 Dec 2017 - Present
Other Supervisors: None, Scholar: Mandar Bhutkar
Structure-guided affinity maturation of nanobodies targeting spike protein of SARS-CoV-2
30 Dec 2017 - Present
Other Supervisors: Prof. Pravindra Kumar, Scholar: Vishakha Singh
Protein-protein interactions as therapeutic target in RNA viruses
06 Jul 2017 - 16 May 2024
Other Supervisors: None, Scholar: Sanket kumar Vishnu Nehul
Viral cysteine proteases of +ssRNA viruses as antiviral drug targets
30 Jul 2017 - 02 May 2024
Other Supervisors: None, Scholar: Shweta Choudhary
Identification and screening of drugs against Flaviviruses
10 Jul 2016 - 01 Mar 2023
Other Supervisors: None, Scholar: Supreeti Mahajan
Studies of potential SARS-CoV-2 antivirals against nucleotide-binding pockets of virus-specific proteins
10 Mar 2017 - 27 Apr 2023
Other Supervisors: None, Scholar: Ruchi Rani
Identification of antivirals against arboviruses
10 Jul 2016 - 01 Jun 2023
Other Supervisors: None, Scholar: Vedita Anand Singh
Mixed metal oxides/sulphides based nano composites and their applications
16 Jul 2016 - 10 Sep 2022
Other Supervisors: Prof. Mala Nath, Scholar: Pooja Bhatia
Molecular characterization of RNA dependent RNA polymerase (RdRp)
10 Jun 2016 - 10 Feb 2022
Other Supervisors: None, Scholar: Akshay Pareek
Alphavirus capsid protease and its inhibitors
10 Jul 2013 - 15 May 2019
Other Supervisors: None, Scholar: Benazir Fatma
Identification and characterization of antiviral molecules against Alphaviruses
01 Jan 2013 - 01 Jan 2018
Other Supervisors: None, Scholar: Ramanjit Kaur
Structural and functional characterization of Arginase enzyme from Entamoeba histolytica
10 Jul 2013 - 01 Jan 2019
Other Supervisors: None, Scholar: Anjali Malik
Studies of substrate-based inhibitors targeting non-structural proteins of Alphaviruses
10 Jul 2012 - 10 Sep 2018
Other Supervisors: None, Scholar: Rajat Mudgal
Studies on alpahvirus cysteine protease for antiviral drug discovery
01 Jan 2013 - 01 Sep 2018
Other Supervisors: None, Scholar: Harvijay Singh
Structural and functional studies of Chikungunya virus capsid protein
01 Jul 2012 - 10 Aug 2017
Other Supervisors: None, Scholar: Rajesh Sharma
Biochemical and structural studies on CheR methyltransferase from Bacillus subtilis
01 Jul 2011 - 06 Jul 2016
Other Supervisors: Dr. R.P. Singh, Scholar: Monu Batra
Functional characterization of alphaviral proteins involved in replication
01 Jan 2010 - 01 Jan 2015
Other Supervisors: none, Scholar: Manju Narwal
Structural studies of macromolecules
01 Jan 2009 - 10 Jun 2014
Other Supervisors: Prof. U. P. Singh, Scholar: Shikha Narang
Structural studies of enzymes involved in bioremediation.
04 Dec 2009 - 10 Jun 2014
Other Supervisors: Dr. Pravindra Kumar, Scholar: Sonali Dhindwal
Molecular characterization of Aura virus capsid protein
04 Sep 2009 - 04 Sep 2014
Other Supervisors: None, Scholar: Megha Aggarwal
Studies of therapeutic protein target: Ornithine decarboxylase from Entamoeba histolytica
01 Jan 2007 - 01 Jan 2012
Other Supervisors: None, Scholar: Preeti
Studies of shikimate pathway enzymes
01 Jan 2007 - 10 Oct 2012
Other Supervisors: None, Scholar: Satya Tapas
University of Wisconsin Madison, WI USA
The 36th Annual meeting of the American Society of Virology; Jun 24-28, 2017
Purdue University
Visiting Scientist, Purdue University, USA May-Jun, 2019 OVDF DST-SERB project (2019-2020)
Karolinska Institute, Stockholm, Sweden
Visiting Scientist, Karolinska Institute, Sweden Research Council (SRC) Networking Grant; 2nd Sep - 9th Sep 2019
University of Wisconsin, Madison
International Society for Computational Biology (IBSC) society Great Lakes Bioinformatics Conference at the University of Wisconsin at Madison, May 19 - 22, 2019
The European Synchrotron Radiation Facility, Grenoble
Research Experiments (X-ray data collection) 2nd-4th Dec 2017
Department of Microbiology and Immunology Georgetown University Medical Center, Washington DC USA
Invited Talk and Research collaboration, July 7th, 2017
The Purdue Institute of Inflammation, Immunology and Infectious Disease
Visiting scientist, 23 May to 29th May, 2017
Daytona Beach, Florida, USA;
Clinical Virology Conference, Daytona Beach Florida, USA. May 19-22,2016
Dept of Biological Sciences, Purdue University, West Lafayette –IN -USA
Visiting Scientist, May 15- June 15th, 2016
Dept of Biological Sciences, Purdue University, West Lafayette –IN -USA
Visiting Scientist, 7th Jun to 14th Jun 2014.
Boston, MA, USA,
Fourteenth Annual Structure-Based Drug Design Conference; May 21-22 2014,
Dept of Biological Sciences, Purdue University, West Lafayette –IN -USA
Visiting Fellow, 14 to 21 July 2012
University of Wisconsin, Madison, WI
The Annual meeting of the American Society of Virology; July 21-25, 2012
University of Wisconsin Madison, WI USA
The Annual meeting of the American Society of Virology; July 15-19, 2006
McGill University, Montreal, Canada
The Annual meeting of the American Society of Virology; July 10-14, 2004
Administrative Positions
Prof In Charge BSL3 virus containment facility
03 Jan 2024 - Present
Department of Biosciences and Bioengineering, IIT Roorkee
Faculty coordinator
01 Jan 2013 - 01 Jan 2016
Aarohi, Child Care Center
Member Management Committee
01 Jan 2013 - 01 Mar 2017
Aarohi, Child Care Center
01 Jan 2010 - 01 Jan 2010
Sarojini Bhawan
01 Jan 2007 - 01 Jan 2008
Sarojini Bhawan