Our Research Focus

At the heart of life lies the dynamic interaction between biomolecules - Proteins communicating with other proteins, DNA, RNA, or ligands; lipids forming the membranes that host and regulate these interactions. In our lab at the Centre for Bioseparation Technology (CBST), VIT Vellore, we focus on uncovering these fundamental molecular mechanisms through an integrated approach in Protein Structural Biology.

Our lab research primarily focuses on targeted drug therapy and small molecule inhibitor discovery against proteins causing antimicrobial resistance (AMR) in high priority pathogens. 

Our multifaceted approach to target AMR involves:

1) First, structural characterization and inhibitor development for clinically significant beta-lactamases prevalent in A.baumannii and P. aeruginosa, such as ADC, OXA, and PDC, respectively,

2) Second, to understand the novel antimicrobial resistance mechanism caused by vibrio antibiotic resistance (var) regulon in antimicrobial resistant Vibrio sp. and identify small drug molecule to inhibit the resistance due to var regulon (Supported by SERB SURE: SUR/2022/000594),

3) Third, understanding the molecular mechanisms in the activation of the suicidal module toxin-antitoxin system, as an antibacterial approach in the pathogenic strain like Acinetobacter sp., as a non-conventional antibacterial approach 

4) Finally, we try to structurally characterize and inhibit the theragnostic molecules in S.enterica species

Apart from AMR, we also work on protein engineering the gene editing proteins (CBEs and ABEs) to enhance their stability and minimise off-target editing.

Our Workflow

We follow a systematic pipeline to decipher the structure–function relationship of proteins:

1. Gene Cloning and Plasmid Engineering

We begin by cloning genes encoding key bacterial proteins into suitable expression plasmids using advanced molecular biology techniques.

2. Protein Expression and Purification

Recombinant proteins are expressed in bacterial systems and purified using multiple chromatographic methods, including:

         •    Affinity chromatography

         •    Ion exchange chromatography

         •    Size exclusion chromatography

Each step is optimized to ensure high purity and proper folding of the target protein.

3. Structural Elucidation

Our core strength lies in solving the 3D structures of proteins and protein-ligand complexes using:

         •    X-ray Crystallography

         •    Molecular Docking

         •    (Future scope includes Cryo-EM and NMR)

We collaborate with national and international structural biology centers to enhance our capabilities and throughput.

4. Functional and Kinetic Assays

We perform:

         •    Ligand-binding studies

         •    Enzyme kinetics

         •    Interaction analysis (e.g., protein-DNA or protein-metal interactions)

These help us correlate structure with biological function and uncover the physiological relevance of the protein.

5. In-silico protein-protein/ligand interaction studies

With regard to the inactivation of critical proteins, we work to identify novel drug inhibitor variants facilitating drug discovery. The protocol involves following work flow:

         •    Homology modeling and validation

         •    Virtual screening from chemical library

    •    Autodock using autodock vina and binding energy calculation

                •    3D-QSAR Analysis and binding energy calculation

         •    Interaction analysis (e.g., protein-DNA or protein-metal interactions)

   •    Docking validation through Molecular dynamic simulations

These help us correlate structure with biological function and uncover the physiological relevance of the protein.

Integrated Structural Biology Approach

We believe that understanding biological systems requires more than one technique. Our lab integrates:

         •    Structure determination (X-ray, ligand-protein interactions)

         •    Functional validation (Activity assays, Spectroscopy)

                •    Computational analysis (Protein modeling, molecular docking via NBIS   BeyondFold)   

This multidisciplinary approach provides a comprehensive view of how bacterial proteins contribute to virulence, stress response, and survival.

Facilities available at our centre

1. AKTA Start purification system

2. BIACORE™-3000 (GE Healthcare, USA)

3. ESI-QUAD-TOF Mass spec (Agilent Tech, USA)

4. HPLC systems (Waters, USA)

5. Ultracentrifuge (Beckman)

6. Centrifuge (eppendorf)

7. Spectrophotometer(Hitachi)

8. Thermocycler (Eppendorf)

9. Plate reader (BMG, Fluostar, Germany)

10.  GELDOC (Biorad, USA)

11.  SDS-PAGE and Western blot apparatus (Biorad)

12.  Cryostorage facility (Liquid Nitrogen)

13.  Deep freezer (-80 Heraus, Thermo; -20C Vest frost)

14.  Cold room (Blue Star)

15.  Microscope (Olympus)

16.  Sonicator

17.  Lyophilizer

18.  High-sensitivity SPR system

19. Thermo-Nano drop

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