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National Institute of Virology, Pune

Research Projects
1. Project ID: Example: BDM1002
< 50 lacs < 3 crore > 3 crore

Broad Subjects:

Epidemiology Diagnostics

Basic Research Vaccinology

2. Title of the Project: Structural modeling of Influenza A Virus proteins: Correlates to pathogenecity and

identification of novel drug targets

3. Investigator: Dr Sarah Cherian, Scientist D

4. Co-investigators: Dr. Pratip Shil, Scientist B

5. Introduction/Rationale:
Influenza A viruses are pathogens that cause significant morbidity and mortality in humans and a variety
of animal species. These viruses possess a segmented negative-sense RNA genome and the virulence of
individual virus strains is based on a complex co-action of determinants, including the viral haemagglutinin (HA),
the RNA-dependent RNA polymerase (RdRP) and the nonstructural protein (NS1). The general rapid
appearance of strains resistant to known neuraminidase (NA) and matrix (M2) protein inhibitors, Oseltamivir and
Amantadine respectively, necessitates the development of newer antivirals.
The RdRP is a heterotrimeric complex (of PA, PB1 and PB2) with multiple enzymatic activities for
catalyzing viral RNA transcription and replication. PB1 represents the central catalytic subunit of the polymerase
complex, PB2 is responsible for recognition and binding of the cap structures of host mRNAs which are used for
priming viral transcription while PA combines essential activities required for genome replication and protein
processing. The RNA segment for PB1 also encodes a small 87-residue nonstructural protein, PB1-F2, which
has apoptotic functions. The critical role of the polymerase complex in the influenza virus life cycle and high
sequence conservation suggest it should be a major target for therapeutic intervention. However, until very
recently, functional studies and drug discovery targeting the influenza polymerase have been hampered by the
lack of three-dimensional structural information. The interactions between the domains of the monomeric units of
the RdRP complex still needs to be understood, that would further help in the design and development of
antivirals. The NS1 protein which is involved in the regulation of the innate immune response is another
attractive antiviral target that needs to be explored.

6. Objectives:
(i) Determine the structure of the PB1-PB2-PA hetero-trimer using available crystallographic
structures of the individual proteins/ hetero-dimers using protein-protein docking studies
(ii) Mapping of critical mutations on to all the homology modeled protein structures to understand
correlates with pathogenecity.
(iii) Study the intermolecular interactions in the polymerase heterotrimeric compex and identify drug
binding pockets in the RdRP complex as well as NS1 protein
(iv) Identify antiviral drug candidates using combinatorial libraries of small compounds
7. Work Plan

Homology modeled structures of HA, NA, NS1, PB1-F2 would be used to map the critical marker mutations
and also those unique to Indian isolates and correlate with pathogencity. Protein-protein docking studies
along with molecular dynamics simulation will be used to model the hetero-trimeric polymerase complexes.
Softwares such as Discovery studio, FTDock, HEX etc would be applied for this. The potential of the
polymerase complex and the NS1 protein as therapeutic targets would be further investigated. Potential
drug binding sites will be identified based on physico-chemical parameters, the ADME-TOX properties and
status of the sites in terms of selection pressure. Candidate drugs would be explored by screening small
compound libraries and drug docking studies using tools such as GOLD, Glide, FlexX, Argon lab etc.

8. Expected outcome:
(i) Determination of the molecular markers of pathogenecity and understanding the structural basis for

(ii) Identification of novel targets for drug design as well as drug candidates

9. Duration of the project: 3 years

10. Staff: A PhD student (UGC fellowship) will work on the said project (No additional staff to be appointed).

11. Budget:

Sr.No. I Year II Year III Year

1 Salaries NIL NIL NIL
(to Additional Staff)
2 Contingency Software- FlexX ( Prediction of NIL NIL
(Chemicals, protein-ligand interaction)
Reagents, etc.) BiosolveIT GmbH, Germany
INR 5,00,000/- *
3 Equipment Workstation(Core 2 Duo NIL NIL
Processor, 4 GB RAM, 300
GB HDD) INR 1,50,000/-
Total INR 6,50,000/- NIL NIL

* Perpetual Academic License