Dr.(Mrs.) Shailly Tomar - Department of Biosciences and Bioengineering,Indian Institute of Technology Roorkee
Dr.(Mrs.) Shailly Tomar
Shailly Tomar Professor shailly.tomar@bt.iitr.ac.in 01332-285849
Areas of Interest
  • Antiviral research , Discovery of structure based antivirals against RNA arboviruses (Chikungunya), Molecular and Structural Virology, Structural studies (X-ray and Cryo Electron microscopy (CryoEM) of pathogenic virus/viral proteins , Molecular diagnostics , Molecular diagnosis of infectious viral diseases epidemic in India and Indian subcontinent , Systems Virology:, Alphaviruses and Flaviviruses
Professional Background
2006-01-011 year Young Scientist DSTDepartment of Biotechnology, IIT, Roorkee
2007-01-013 years LecturerDepartment of Biotechnology IIT Roorkee
2010-01-01OngoingAssistant ProfessorDepartment of Biotechnology IIT Roorkee
2020-08-04OngoingAssociate ProfessorIIT Roorkee
2019-01-01OngoingProfessorIndian Institute of Technology Rorokee
Multiple Posts
2013-01-01OngoingMember Management CommitteeAarohi, Child Care Center
2013-01-013 years Faculty coordinatorAarohi, Child Care Center
2010-01-01WardenSarojini Bhawan
2007-01-011 year WardenSarojini Bhawan
Honors and Awards
Institute Research Fellowship for Outstanding Young Faculty IIT Roorkee2018
DST young scientist IIT Roorkee2006
Educational Details
B. Sc. (Hons)Botany Delhi University, Delhi1999
M.Sc.BiophysicsAll India Institute of Medical Sciences, New Delhi2001
Ph.D.VirologyPurdue University2006
Sponsored Research Projects
TopicFunding AgencyStart DatePeriod
Structure function studies of alphavirus nonstructural protein, NSP1DST2010-0110 years 7 months
Heterologous production and molecular characterization of alphavirus replication proteinsSRIC-IITR2011-019 years 7 months
Structural studies of tamarind proteinase inhibitor (TPI) and its complex with trypsin.CSIR2012-018 years 7 months
Targeting viral protease of emerging and neglected RNA alphaviruses.SRIC-MHRD2014-01Ongoing
Three Dimensional Analysis of Alphavirus Capsid ProteaseDRDO2014-01Ongoing
Structural analysis of chitinase from Tamarindus indica DST2017-01Ongoing
In silico development of anti-amoebic molecules based on the structure of E. histolytica ODCICMR2017-01Ongoing
Structural functional characterization of Chikungunya virus nsP2 protease and inhibitor screeningDBT2018-01Ongoing
Structure activity relationship studies of protein glutamate-O-methylase UCB2018-01Ongoing
Identification and validation of small molecules targeting drugable pocket on alphavirus capsidDRDE2018-01Ongoing
Probing intermolecular contacts between capsid protein and envelope proteins of Chikungunya VirusICMR2018-01Ongoing
Molecular diagnostic method for early detection of Chikungunya using fluorescent virus-like nanopartDBT2018-01Ongoing
2. Molecular and structural analysis of Chikungunya Capsid Protease for antiviral drug DiscoveryDST SERB2018-01Ongoing
Targeting alphavirus host protein interactions to develop antiviral therapiesSweden Research Council (SRC) 2019-01Ongoing
  • American Society for Virology (ASV), Member
  • Indian crystallography society (ICA), Member
  • Indian Biophysical Society (IBS), Member
  • Indian Virology Society (IVS), Member
Teaching Engagements
TitleCourse CodeClass NameSemester
Biphysical TechniquesBTN 611MSc II yearAutumn
Molecular separation techniquesIBT 301BTech institute electiveSpring
Genetics and Molecular BiologyBTN 201BTechSpring
Biophysics and Biochemistry BT 213BTech II nd yearAutumn
Molecular separation TechniquesIBT 01BTechAutumn
Separation and Analysis of BiomoleculesBTN 348BTech III yr Dept. ElectiveSpring
Research Scholar Groups
Scholar NameInterest
Rajat MudgalStudies of substrate-based inhibitors targeting non-structural proteins of alphaviruses
Harvijay SinghStudies on alpahvirus cysteine protease for antiviral drug discovery
Ramanjit KaurIdentification and characterization of antiviral molecules against alphaviruses
Anjali MalikStructural and functional characterization of arginase enzyme from Entamoeba histolytica
Benazir FatmaStudies of alphavirus capsid and its inhibitors
Vedita Anand SinghThe plus-strand arbovirus replication inhibition studies
Akshay PareekMolecular studies of alphavirus polymerase
Supreeti MahajanIdentification and screening of inhibitors against flaviviruses
Ruchi RaniStudies of flavivirus NS5 protein and its inhibition
Sanketkumar Vishnu NehulDevelopment of a method for identification and quantification of virus particles
PHDs Supervised
TopicScholar NameStatus of PHDRegistration Date
Studies of therapeutic protein target: Ornithine decarboxylase from Entamoeba histolyticaPreeti O2007-01
Studies of shikimate pathway enzymesSatya TapasO2007-01
Structural studies of macromoleculesShikha NarangO2009-01
Structural studies of enzymes involved in bioremediation.Sonali Dhindwal O2020-08
Molecular characterization of Aura virus capsid proteinMegha AggarwalO2020-08
Functional characterization of alphaviral proteins involved in replicationManju NarwalO2011-01
Biochemical and structural studies on CheR methyltransferase from Bacillus subtilisMonu BatraO2011-01
Structural and functional studies of Chikungunya virus capsid proteinRajesh SharmaO2012-01
Visits to outside institutions
Institute VisitedPurpose of VisitDate
University of Wisconsin Madison, WI USA The 36th Annual meeting of the American Society of Virology; Jun 24-28, 20172020-08-04
Purdue UniversityVisiting Scientist, Purdue University, USA May-Jun, 2019 OVDF DST-SERB project (2019-2020)2019-01-01
Karolinska Institute, Stockholm, Sweden Visiting Scientist, Karolinska Institute, Sweden Research Council (SRC) Networking Grant; 2nd Sep - 9th Sep 20192019-01-01
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, 20192019-01-01
The European Synchrotron Radiation Facility, GrenobleResearch Experiments (X-ray data collection) 2nd-4th Dec 20172020-08-04
Department of Microbiology and Immunology Georgetown University Medical Center, Washington DC USAInvited Talk and Research collaboration, July 7th, 20172017-01-01
The Purdue Institute of Inflammation, Immunology and Infectious Disease Visiting scientist, 23 May to 29th May, 20172017-01-01
Daytona Beach, Florida, USA;Clinical Virology Conference, Daytona Beach Florida, USA. May 19-22,20162020-08-04
Dept of Biological Sciences, Purdue University, West Lafayette –IN -USAVisiting Scientist, May 15- June 15th, 20162016-01-01
Dept of Biological Sciences, Purdue University, West Lafayette –IN -USAVisiting Scientist, 7th Jun to 14th Jun 2014. 2014-01-01
Boston, MA, USA,Fourteenth Annual Structure-Based Drug Design Conference; May 21-22 2014,2014-01-01
Dept of Biological Sciences, Purdue University, West Lafayette –IN -USAVisiting Fellow, 14 to 21 July 20122020-08-04
University of Wisconsin, Madison, WIThe Annual meeting of the American Society of Virology; July 21-25, 20122012-01-01
University of Wisconsin Madison, WI USA The Annual meeting of the American Society of Virology; July 15-19, 20062020-08-04
McGill University, Montreal, CanadaThe Annual meeting of the American Society of Virology; July 10-14, 20042020-08-04
National International Collaboration
Alphaviruses, Chikungunya Virus, Dengue Virus, Antiviral drug discovery Prof. R. J. Kuhn, Department of Biological Sciences, Purdue University
Polyamine biosynthesis pathway enzymes of E. histolytica. Dr. Serge Ankri, The Ruth and Bruce Rappaport Faculty of Medicine, Israel
Targeting host factor to treat alphaviral infections Prof. Gerald McInerney, Karolinska Institutet in Stockholm Sweden
Refereed Journal Papers
  1. 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: Biol. Crystal.  57:1669-70


  1. 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 resolution. J. Mol. Biol. 341(3):829-37.



  1. Tomar S., Hardy R. W., Smith J. L.,  Kuhn R. J. (2006). Catalytic core of alphavirus nonstructural protein, nsP4 possesses terminal adenylyl transferase activity. J. Virol. 80(20): 9962-9.  


  2. 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.
  3. 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 Crystall. Sec. F 65, 343-345.
  1. 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 Crystall. Sec. F 65: 1179-1181.
  3. Tapas S., Patel G. K., Dhindwal S., Tomar S. (2010) In silico sequence analysis and homology modeling of DAHP synthase from Pseudomonas fragi. J. Mol.Model.17(CCP4), 621-31. 
  4. 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 Crystall.Sec. F 66, 1517-1520.
  5. 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.


  2. 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 Crystallogr Sect F Struct Biol Cryst Commun. 1;67 (Pt 11):1394-8.
  3. 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. Prot. Exp. and Purif. 79(2):277-84.
  4. 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. J. Biol. Chem. 286(42):37011-22.


  2. 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.
  3. 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.
  4. 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 J. Dec;279(24):4547-64.
  5. 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 Negl. Trop. Dis. 6(2):e1559.


  2. 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.
  3. 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 Pept. Lett. 20(5):499-509.
  4. 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.


  2. 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. J. Virol., 88(21):12242-53.


  2. 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. Sci. Rep. 5:14753.
  3. 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. Inter J. Biol. Macromol. 77:168-80
  4. 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.
  5. 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 Crystallogr. D Biol. Crystallogr. 71(Pt 2):239-55.


  2. Dhindwal S., Kesari P., Singh H., Kumar P.,  Tomar S. (2016) Conformer and Pharmacophore Based Identification of Peptidomimetic Inhibitors of Chikungunya Virus nsP2 Protease. J. of Biomol. Stru. & Dyn 2:1-18.
  3. 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.
  4. 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. J Struct Biol. 196(3):364-374.


  2. 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 Res. 146 (102-111)
  3. 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. Sci Rep.  25;7(1):6364.
  4. 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. Sci Rep.  5;7(1):4705.
  5. 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.
  6. 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. Prot. pept. lett.1;24(3):267-77.


  2. 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. Int. J. Biol. Macromol. 106:1089-1106.
  3. 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.  
  4. 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. 
  5. 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. 
  6. 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. Int J Biol Macromol. 116:451-462. 
  7. 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 Res. pii: S0168-1702(18)30028-5. 
  8.  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. Sci.Rep. 8:10831.
  9. 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 (In press).                         


Patent and Patent applications


  1. Tomar S., Kumar P., Kaur R.  A highly sensitive nsP1 enzyme assay and kit for determining inhibitors of alphavirus/chikungunya virus. Indian patent, Application no. 201711039736 on 8th November  2017
  2. Tomar S., Kumar P., Kaur R.  A highly sensitive nsP1 enzyme assay and kit for determining inhibitors of alphavirus/chikungunya virus. International patent with PCT, Application no. PCT/IB2018/051760 on 16th March 2018.
  3. Tomar S., Kumar P., Kaur R., Chaudhary N., Singh V. A. An antiviral composition of tamarind chi-like lectin and uses thereof. Indian patent, Application no. 201811019298 on 23rd May 2018.
  4. Tomar S., Kumar P.,  Singh H., Mudgal R. Chikungunya Virus Protease Inhibitors and uses thereof. Indian patent, Application no. 201811022065 on 13th June 2018.


Book Chapters


  1. Kesari P., Neetu, Tomar S., Kumar P. ( 2017) Polychlorinated Biphenyls Bioremediation. In: Environmental Pollution: Biodegradation and Bioremediation. Series   Studiumpress  LLC USA., pp. 258-280
  2. 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
  3. 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
  4. Tomar S. Kaur R., Singh V. A. (2018) 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. Academic Press, Elsevier  
  5. Tomar S. Mudgal R., Pareek A. (2018) Chapter 3: RNA Dependent RNA Polymerase: A potential alphavirus antiviral target. In: Gupta, S.P. (Ed.), Viral Polymerases: Structures, Functions, and Roles in Antiviral Drug.  Academic Press Elsevier  










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