List of Publications:

1.          Dhaka P, Mahto JK, Singh A, Kumar P, Tomar S*. Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid. Journal of Structural Biology. 2025 Mar 18:108197. DOI- 10.1016/j.jsb.2025.108197

2.     Bhutkar M, Kumar A, Rani R, Singh V, Saha A, Pathak A, Kothiala A, Mahajan S, Waghmode B, Verma S, Kumar R, Mudgal R, Sircar D, Kumar P, Tomar S*. Structure‐based identification of herbacetin and caffeic acid phenethyl ester as inhibitors of S‐adenosylmethionine‐dependent viral methyltransferase. FEBS letters. 2025 May 14. DOI- 10.1002/1873-3468.70054

3.          Das M, Kumar V, Madhukalya R, Saroj A, Rout A, Upadhyay A, Naidu G, Poluri KM, Tomar S, Kumar D, Kumar R. Purification, refolding, and pH-dependent stability evaluation of Zika virus EDIII protein. International Microbiology. 2025 Jun 6:1-0. DOI - 10.1007/s10123-025-00679-y

4.   Mahajan S, Kumar R, Singh A, Dhaka P, Pareek A, Kumar P, Tomar S*. Targeting the host protein G3BP1 for the discovery of novel antiviral inhibitors against Chikungunya virus. Virology. 2025 Apr 22:110551. DOI- 10.1016/j.virol.2025.110551

5.          Nehul S, Rani R, Walia P, Panda PK, Singh S, Chattopadhyay S, Kumar P, Tomar S.* Repurposing efavirenz, the HIV antiretroviral drug for Chikungunya virus infection. ACS Infectious Diseases. 2023 Sep 29. DOI - 10.1021/acsinfecdis.4c00992

6.          Singh A, Jangid K, Nehul S, Dhaka P, Rani R, Pareek A, Sharma GK, Kumar P, Tomar S.* Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2. Biochemistry. 2024 Oct 7. DOI- 10.1021/acs.biochem.4c00535

7.          Handa T, Saha A, Narayanan A, Ronzier E, Kumar P, Singla J, Tomar S. Structural Virology: The Key Determinants in Development of Antiviral Therapeutics. Viruses. 2025 Mar 14;17(3):417. DOI- 10.3390/v17030417

8.          Dhaka P, Singh A, Nehul S, Choudhary S, Panda PK, Sharma GK, Kumar P, Tomar S.* Disruption of Molecular Interactions between the G3BP1 Stress Granule Host Protein and the Nucleocapsid (NTD-N) Protein Impedes SARS-CoV-2 Virus Replication. Biochemistry. 2025. DOI- 10.1021/acs.biochem.4c00536

9.          Verma S, Choudhary S, Amith Kumar K, Mahto JK, Vamsi K AK, Mishra I, Prakash VB, Sircar D, Tomar S, Kumar Sharma A, Singla J, Kumar P. Mechanistic and structural insights into EstS1 esterase: A potent broad-spectrum phthalate diester degrading enzyme. Structure. 2025 Feb 6;33(2):247-261.e3. DOI: 10.1016/j.str.2024.11.006. Epub 2024 Dec 5. PMID: 39642872.

10.   Saha A, Choudhary S, Walia P, Kumar P, Tomar S. Transformative Approaches in SARS-CoV-2 Management: Vaccines, Therapeutics and Future Direction. Virology. 2025 Jan 10:110394. https://doi.org/10.1016/j.virol.2025.110394

11.          Mallick D, Tyagi V, Saroj A, Bhutkar M, Kumar V, Das M, Madhukalya R, Choudhary S, Gupta R, Singh V, Kumar D, Tomar S, Kumar R.* 2024 Optimized high-yield expression of envelope glycoprotein domain III from dengue virus serotypes 1 to 4. Biochimie. 2024 Dec 11. DOI- 10.1016/j.biochi.2024.12.003 

12.          Das M, Kumar V, Madhukalya R, Gupta R, Agarwal V, Choudhary S, Bhutkar M, Tomar S, Kumar D, Kumar R.* 2024 Purification and characterization of kyasanur forest disease virus EDIII domain of major envelope glycoprotein. Journal of Virological Methods. 2025 Apr 1;333:115089. DOI- 10.1016/j.jviromet.2024.115089 

13.          Kumar, N.*, Singh, A., Dhaka, P., Singh, A., Agarwala, P., Sharma, K., Bhargava, A., Bhatia, S., Launey, T., Kaushik, R*. and Tomar, S. Sanyal A., 2024. A label-free gold nanoparticles functionalized peptide dendrimer biosensor for visual detection of breakthrough infections in COVID-19 vaccinated patients. Sensing and Bio-Sensing Research, p.100718. DOI - https://doi.org/10.1016/j.sbsr.2024.100718

14.          Singh V, Bhutkar M, Choudhary S, Nehul S, Kumar R, Singla J, Kumar P, Tomar S*. Structure-guided mutations in CDRs for enhancing the affinity of neutralizing SARS-CoV-2 nanobody. Biochemical and Biophysical Research Communications. 2024 Sep 26:150746. DOI - 10.1016/j.bbrc.2024.150746

15.          Singh V, Choudhary S, Bhutkar M, Nehul S, Ali S, Singla J, Kumar P, Tomar S.* Designing and bioengineering of CDRs with higher affinity against receptor-binding domain (RBD) of SARS-CoV-2 Omicron variant. International Journal of Biological Macromolecules. 2024 Dec 13:138751. DOI- 10.1016/j.ijbiomac.2024.138751 

16. Bhutkar M, Saha A, Tomar S*. Viral methyltransferase inhibitors: berbamine, venetoclax, and ponatinib as efficacious antivirals against Chikungunya virus. Archives of Biochemistry and Biophysics, p.110111. DOI- 10.1016/j.abb.2024.110111 

17.       Rode, S., Kaur, H., Rani, R., Lonare, S., Sharma, M., Tomar, S., Kumar, P., Roy, P. and Sharma, A.K.*, 2024. Deciphering the drug delivery potential of Type1 Lipid Transfer Protein from Citrus sinensis for enhancing the therapeutic efficacy of drugs. Biochemical and Biophysical Research Communications, p.150253. DOI- 10.1016/j.bbrc.2024.150253

18.          Kaushik R, Kumar N, Yadav P, Sircar S, Shete-Aich A, Singh A, Tomar S, Launey T, Malik YS*. Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity. Microorganisms. 2024 Mar 29;12(4):696. DOI -  10.3390/microorganisms12040696

19.          Gupta DN, Lonare S, Rani R, Singh A, Ghosh DK, Tomar S, Sharma AK*. Comparative Analysis of Inhibitor Binding to Peroxiredoxins from Candidatus Liberibacter asiaticus and Its Host Citrus sinensis. Applied Biochemistry and Biotechnology. 2023 Dec 29:1-20. DOI - 10.1007/s12010-023-04798-y 

20.          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/j.abb.2023.109820 

21.          Choudhary S, Nehul S, Singh A, Panda PK, Kumar P, Sharma GK, Tomar S*. Unraveling antiviral efficacy of multifunctional immunomodulatory triterpenoids against SARS‐COV‐2 targeting main protease and papain‐like protease. IUBMB life. 2024 May;76(5):228-41. DOI - 10.1002/iub.2793

22.          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

23.          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 

24.          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. DOI - 10.1016/j.ejmech.2023.115572

25.    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 

26.          Singh VA, Nehul S, Kumar CS, Banerjee M, Kumar P, Sharma G, Tomar S*. Chimeric chikungunya virus-like particles with surface exposed SARS-CoV-2 RBD elicits potent immunogenic responses in mice. bioRxiv. 2023 Jan 29:2023-01. DOI -  https://doi.org/10.1101/2023.01.29.526074 

27.          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. DOI: 10.1016/j.virol.2022.11.012 

28.          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 - https://doi.org/10.1101/2023.07.24.550324

29.          Singh V, Dhankhar P, Dalal V, Tomar S, Kumar P. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target. J Mol Graph Model. 2022 Nov;116:108262. doi: 10.1016/j.jmgm.2022.108262. Epub 2022 Jun 30. PMID: 35839717. 

30.          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 - https://doi.org/10.1101/2022.11.11.516107  

31.          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: 10.1016/j.virol.2022.08.008 

32.          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. DOI - 10.1016/j.ijbiomac.2022.04.086

33.          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, 289(16), pp.4901-4924. DOI: 10.1111/febs.16397 

34.          Singh, V., Dhankhar, P., Dalal, V., Tomar, S., Golemi-Kotra, D. and Kumar, P.*, 2022. Drug-repurposing approach to combat Staphylococcus aureus: Biomolecular and binding interaction study. ACS omega, 7(43), pp.38448-38458. DOI - 10.1021/acsomega.2c03671  

35.          Mudgal, R., Bharadwaj, C., Dubey, A., Choudhary, S., Nagarajan, P., Aggarwal, M., Ratra, Y., Basak, S. and Tomar, S.*, 2022. Selective estrogen receptor modulators limit alphavirus infection by targeting the viral capping enzyme nsP1. Antimicrobial Agents and Chemotherapy, pp.AAC-01943. DOI -10.1128/AAC.01943-21

36.          Kumar, N., Uversky, V.N., Tomar, S., Li, K.S., Chappell, K. and Lau, S.K.*, 2022, Emerging and Re-emerging Viral Zoonoses. Frontiers in Microbiology, p.3270. DOI - 10.3389/fmicb.2022.978259

37.          Bhutkar, M., Singh, V., Dhaka, P., and Tomar S*. 2022. Virus-host protein-protein interactions as molecular drug targets for arboviral infections. Frontiers in Virology, p.70, (2022) DOI - https://doi.org/10.3389/fviro.2022.959586

38.          Dubey, A., Choudhary, S., Kumar, P. Tomar S*. 2022. Emerging SARS-CoV-2 Variants: Genetic Variability and Clinical Implications. Current Microbiology 79, 20 (2022). DOI - 10.1007/s00284-021-02724-1 

39.          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 - 10.1016/j.jbc.2021.101416 

40.          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. DOI - 10.1016/j.abb.2021.109060

41.          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 Communications, 580, pp.28-34.  DOI - 10.1016/j.bbrc.2021.09.076

42.          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. DOI - 10.1080/07391102.2021.1969285 

43.          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 bioinformatics, 22(2), pp.1006-1022 DOI - 10.1093/bib/bbaa383

44.          Kumar, K.A., Sharma, M., Dalal, V., Singh, V., Tomar, S. and Kumar, P.*, 2021. Multifunctional Inhibitors of SARS-CoV-2 by MM/PBSA, Essential dynamics, and Molecular dynamic investigations. Journal of Molecular Graphics and Modelling, p.107969 DOI -10.1016/j.jmgm.2021.107969

45.          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

46.          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 DOI -10.1016/j.virusres.2021.198493

47.          Mahajan, S., Choudhary, S., Kumar, P. and Tomar, S.*, 2021. Antiviral strategies targeting host factors and mechanisms obliging+ ssRNA viral pathogens. Bioorganic & Medicinal Chemistry, 46, p.116356. DOI - 10.1016/j.bmc.2021.116356

48.          Mudgal, R., Nehul, S. and Tomar, S.*, 2020. Prospects for mucosal vaccine: shutting the door on SARS-CoV-2. Human vaccines & immunotherapeutics, 16(12), pp.2921-2931. DOI - 10.1080/21645515.2020.1805992 

49.          Dhankhar, P., Dalal, V., Mahto, J.K., Gurjar, B.R., Tomar, S., Sharma, A.K. and Kumar, P.*, 2020. Characterization of dye-decolorizing peroxidase from Bacillus subtilis. Archives of Biochemistry and Biophysics, 693, p.108590. DOI - 10.1016/j.abb.2020.108590 

50.          Dhankhar, P., Dalal, V., Singh, V., Tomar, S. and 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, 40(9), pp.4084-4099. DOI - 10.1080/07391102.2020.1852968

51.          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 Immunology, 11, page no.1664. DOI -  10.3389/fimmu.2020.01664 

52.          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 Bacteriology, 202(18), pp.e00248-20. DOI - 10.1128/JB.00248-20

53.          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. DOI - 10.1016/j.antiviral.2020.104808

54.          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. DOI - 10.1016/j.msec.2020.110934

55.          Mudgal, R., Mahajan, S. and Tomar, S.*, 2020. Inhibition of Chikungunya virus by an adenosine analog targeting the SAM‐dependent nsP1 methyltransferase. FEBS letters, 594(4), pp.678-694. DOI - 10.1002/1873-3468.13642

56.          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. DOI - 10.1021/acsomega.9b02900

57.          Malik A., Dalal V., Ankri S. and Tomar S*. 2019 Structural insights into Entamoeba histolytica arginase and structure-based identification of novel non-amino acid based inhibitors as potential anti-amoebic molecules. The FEBS journal 286(20):4135-4155. DOI - 10.1111/febs.14960

58.          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  

59.          Bais S., Ratra Y., Khan N., Pandey R., Kushawaha P.,Tomar S., Medigeshi G., Singh A.,   Basak S*. (2019) Chandipura Virus Utilizes the Prosurvival Function of RelA NF-κB for Its Propagation. Journal of Virology. 93(14), pp.e00081-19. DOI - 10.1128/JVI.00081-19.  

60.          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

61.          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 

62.          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, 265–276. DOI - 10.1016/j.virol.2017.12.020

63.          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, 256, pp.209-218. DOI - 10.1016/j.virusres.2018.06.013

64.          Sharma A., Kumar V., Chatrath A., Dev A., Prasad R., Sharma, A.K., Tomar S. and 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

65.          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

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

67.          Narwal M., Singh H., Pratap S., Malik A., Kuhn RJ., 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 116:451-462. DOI - 10.1016/j.ijbiomac.2018.05.007 

68.          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

69.          Aggarwal M., Kaur R., Saha A., Mudgal R., Yadav R., Dash P.K., Parida M., Kumar P. and 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

70.          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 

71.          Kumar P, Kesari P, Dhindwal S, Choudhary AK, Katiki M, Neetu, Verma A, Ambatipudi K, Tomar S, Sharma AK, 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

72.          Sharma A, Kumar P, Kesari P, Katiki M, Mishra M, K Singh P, R Gurjar B, K Sharma A, 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 

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

74.          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

75.   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  Volume 498, 265–276. DOI - 10.1016/j.virol.2016.08.029

76. 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):364-374.  DOI - 10.1016/j.jsb.2016.08.005

77.           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. DOI - 10.1038/srep14753

78.          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

79. 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

80.          Dhindwal S., Priyadarshini P., Patil D.N., Tapas S., Kumar P., Tomar S and 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 Biological Crystallography 71 (Pt 2):239-55. DOI - 10.1107/S1399004714025218

81.          Aggarwal M, Dhindhwal S, Kumar P, Kuhn RJ, 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  

82.          Patil DN, Datta M, Dev A, Dhindwal S, Singh N, Dasauni P, Kundu S, Sharma AK, 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 

83.          Kumar P, Patil DN, 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  

84.          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:DOI -  10.1371/journal.pone.0053397

85.          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. DOI - 10.1371/journal.pone.0051288.

86.           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. DOI - 10.2174/157489312803900901

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

88.          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 

89.          Aggarwal M., Dhindwal S., Pratap S., Kuhn R. J., Kumar P. and 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: Structural Biology and Crystallization Communications Nov 1;67 (Pt 11):1394-8, DOI - 10.1107/S174430911103404X

90.          Tomar S, Narwal M, Harms E, Smith JL, Kuhn RJ.* 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  

91.          Dhindwal S, Patil DN, 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 

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

93.          Sakshi, Patil D.N., Tomar S., Sylvestre M. and 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

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

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

96.          Tomar S., Patil D. N., Datta M., Tapas S., Preeti, Sharma A. K., Tomar S* and 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: Structural biology communications, 65: 1179-1181. DOI - 10.1107/S1744309109041694

97.          Tomar S, Hardy R. W., Smith J. L., and 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 

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

99.   Tomar S, Yadav S., Chandra V., Kumar P., and 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: Biological Crystallography. 57:1669-70. DOI: 10.1107/s0907444901012082

Books authored 09 (Nine)

1. Sharma G, Nehul S, Choudhary S, Mahajan S. 2024. Book chapter: In vitro and in vivo evaluation tools of SARS-CoV-2 Antiviral Drugs. Springer Press.  
2. Singh A, Dhaka P, Kumar P, Tomar S, Singla J. 2024. Book chapter: Bioinformatics databases and tools available for the development of antiviral drugs. Springer press.
3. Rani R, Bhutkar M, Tomar S. 2022-2023. Chapter4: Therapeutic antiviral potential of flavanoids. Apple Academic Press(AAP)
4. 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.
5. 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; https://doi.org/10.1016/B978-0-12-815422-9.00002-4
6. 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 https://doi.org/10.1016/B978-0-12-815422-9.00003-6.
7. 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
8.  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
9. 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.  

Books edited:

1.     Book Title: Advances in antiviral research by Kumar N., Malik YS., Tomar S., Ezzikouri S. (2024) Springer Singapore.

     2.     Book Title: Environmental Pollution: Biodegradation and Bioremediation by Kumar P, Bhola R. Gujjar and Tomar S. (2017) Environmental Pollution: Monitoring and Control; Series Studium Press LLC USA

Patents granted:

1.     Tomar S., Kumar P. and Kaur R.; “A method for screening NSP1 capping enzyme inhibitors of Chikungunya” Indian patent application no. : 201711039736 (8^th Nov 2017) Patent granted (Patent No. 429557) 

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 23^rd 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 13^th 2018 Patent granted (Patent No. 536426) 

4.     Tomar S., Mudgal R, and Dubey A., An antiviral composition against alphaviruses. Indian Patent Application no 201911049130, Dated 29th Nov, 2019. Patent granted (Patent No. 522710)

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 2^nd June 2020. (Patent No. 516546)

Patents filed:

2023:

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 23^rd, 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)

2022:

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)

2021:

4. Tomar S., Khoba Prafful., Bhutkar M., A portable ultraviolet sterilization and disinfection device. Indian Patent, Provisional Application no. 202111046071 dated. 09/10/2021

2019:

5. Tomar S., Kumar P., Neetu, Singh VA. and Choudhary S. Chikungunya virus titration and detection kit. Indian patent application no.  201911035044 on 30^th Aug, 2019

2018:

6. 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 (16^th March 2018).

Invited Lectures (26)

 1.     Tomar S, Dhaka P, Nehul S, Verma S, Mahajan S, Kumar R; “Virus-host protein-protein interactions as molecular drug targets against RNA viruses”. 7th Molecular Virology Meeting at IISc Bangalore on   September 22-23, 2023.

2.     Tomar S, Choudhary S, Singh A, Dhaka P, Sharma GK, Kumar P; Structure-assisted targeting of SARS-CoV-2 proteases for discovery of antivirals, Focused Meeting on Biochemistry & Molecular Biology of RNA Viruses at RCB from 15-18^th November 2022.

3.     Tomar S., Structure-Assisted Single Molecule Multi-targeting of SARS-CoV2. DBT/Wellcome trust India alliance CBE Lecture. Organized by Guru Angad Dev Veterinary and Animal Sciences University & IIT Roorkee, 30^th September 2022.

4.     Tomar S., SARS-CoV-2 Nucleocapsid protein-A virus-specific Molecular Drug Target, VIBCON, 26^th Annual convention of  Indian Society of Veterinary Immunology and Biotechnology & International conference (virtual mode) on Transforming Livestock Economy through Innovations in Immunology and Biotechnology, Feb 4^th -5^th, 2022.

5.     Tomar S., Antiviral strategies targeting virus-specific proteins to combat alphaviruses, Indo-US symposium on Molecular Virology, held by IIT Mandi, Feb 15-17, 2022

6.     Tomar S, Kumar R, Nehul S, Fatma B; Structure-based targeting of alphavirus capsid protein for antiviral therapy, National seminar on crystallography, Dept. of Biosciences and Bioengineering, IIT Roorkee (247667), Uttarakhand India (25^th-27^th November 2021)

7.     Tomar S., Structure assisted therapeutics approaches to combat RNA viruses, International symposium on Emerging Focus on Immunology in Augmenting Animal and Human Health, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Punjab, Feb 19-20, 2021

8.     Tomar S. Structure-based discovery of antiviral molecules to combat Chikungunya virus. Indo-Italian Elettra Beamline User Meeting and Outreach Program, AIIMS New Delhi November 11-12, 2019

9.     Tomar S. Discovery of structure-based antivirals targeting Chikungunya virus proteases. Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institute, Stockholm, Sweden, 5^th Sep 2019

10.  Tomar S. Structure-based antivirals for Chikungunya. Invited speaker for a seminar at Purdue Institute of Inflammation, Immunology and Infectious Disease. Purdue University, West Lafayette, IN USA. 30^th May, 2019.

11.  Tomar S. Structure-assisted discovery of antivirals targeting chikungunya viral protease. The national symposium on “Structure Assisted development of Novel Therapeutics” February 12-16, 2019 Organized by Regional Center for Biotechnology (RCB), Faridabad.

12.  Tomar S. Singh H. Mudgal R., Kumar P. Structure-based antivirals targeting chikungunya virus cysteine protease. The 46th National Seminar on Crystallography (NSC)  held at National Institute of Mental Health And Neuro Sciences(NIMHANS),
Bangalore – 560029, June 27^th - 29^th, 2018.  Pg 54

13.  Tomar S. (2018) “Chikungunya antiviral drug discovery” a guest lecture in the Faculty Development Program on "Biosafety and IPR issues in Bio-Pharma Research" at MIET Meerut, 21st to 25th May, 2018

14.  Tomar S. (2018) Purpose of Science. VIGYAN JYOTI - a Basic Science and Engineering Camp for High School Girls, sponsored by Department of Science and Technology (DST), Government of India held at at IIT Bombay

15.  Tomar S. Kaur R, Mudgal R, Kumar P. (2017) Proteomics and structural approaches for exploring antiviral potential of plants proteins. 3rd Plant Proteomics Workshop: Mining Proteome & Deep Proteome (by sub-cellular proteome analysis, depletion, affinity enrichment and beyond) 19th-23rd December, 2017. 

16.  Tomar S. (2017) “Three Dimensional Structure Analysis of Alpha Virus Capsid Protease.” ER&IPR Meeting at DRDO Bhawan, Rajaji Marg, New Delhi13^th Dec to 14 Dec 2017.

17.  Tomar S. Title: Structure-function analysis of chikungunya proteases and substrate structure based peptidomimetic antivirals. In the Department of Microbiology and Immunology Georgetown University Medical Center Washington DC, 6^th July2017

18.  Tomar S. “Molecular investigation of pharmacological activities of panchagavya against infectious viral diseases: Chikungunya and Dengue” presented in National Brainstroming-cum-Consultative Workshop on Scientific Validation and Research on Panchgavya (SAVROP) Unnat Bharat Abhiyan held at CRDT, IIT Delhi 18^th to 19^th Dec, 2016

19.  Tomar S. Molecular Drug Targets for Chikungunya Virus, in the Department of Molecular Biosciences Northwestern University, Chicago, USA 25^th May 2016

20.  Tomar S. Structural and functional studies of capsid protein from alphaviruses at Defence R & D Establishment (DRDE) Jhansi Road, Gwalior-474002 M.P., INDIA 18^th Aug 2015.

21.  Tomar S., Aggarwal M, Sharma R. and Kumar P. Molecular and structural strategies to combat pathogenic plus-strand RNA viruses. Current Trends in Structural Biology (CTSB) at AIIMS New Delhi 20th February 2013.

22.  Tomar S. “Alphavirus replication protein nsP1: a novel drug target” Conference on Infectious Diseases: Novel Strategies for Design & Development of Vaccines and Drugs. Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.  5-8 January 2010.

23.  Tomar S., Smith J. L., Hardy R. W., and Kuhn R. J. “A novel function of alphavirus nonstructural protein, nsP4.” at the American Society for Virology 25^th Annual Meeting held at the University of Wisconsin-Madison, USA. 2006.

24.  Tomar S., and Kuhn R. J. “Human pathogens: single-stranded, enveloped, positive sense RNA viruses.” at the 5^th Purdue Biology Graduate Student Retreat held at Lindsey Laboratory, Ross Reserve, West Lafayette, Indiana, USA. 2006.

25.  Tomar S., Hardy R. W., Smith J. L., and Kuhn R. J. “A novel function of alphavirus non-structural protein, nsP4.” at the Structural Biology Seminar Series, Department of Biology, Purdue University, Indiana USA. 2006.

26.  Tomar S., Smith J. L., and Kuhn R. J. “Expression and purification of alphavirus nsP1 and nsP4 for structural analysis” at the 23^rd annual meeting of American Society of Virology held at McGill University, Montreal, Quebec, Canada. 2004.

Editorial boards:

• Antiviral Research (2024-present)

• Virology (2024-present)

 Professional Affiliations:

• Member: American Society for Virology (ASV)
• Member American Society for Microbiology (ASM)
• Member: Indian crystallography society (ICA)