Research Projects

The growing threat of antimicrobial resistance (AMR) necessitates novel therapeutic strategies that go beyond traditional bactericidal approaches. This project is built on the rationale that targeting bacterial virulence mechanisms, specifically biofilm-associated proteins, can disrupt infection without imposing selective pressure for resistance. Biofilms are complex microbial communities that enhance bacterial survival and drug tolerance through matrix-forming proteins, many of which are intrinsically disordered or amyloidogenic. These proteins remain underexplored in drug discovery and represent attractive targets for anti-virulence therapy. The central hypothesis is that aggregation-prone and structurally flexible regions in biofilm-associated proteins contain transient, cryptic binding pockets that can be therapeutically exploited. These pockets are often hidden in static protein structures but can be uncovered using SWISH-X, an advanced molecular dynamics protocol that employs Hamiltonian replica exchange with hydrophobic co-solvents to expose otherwise inaccessible binding sites. The project aims to 1. Identify key biofilm-forming virulence proteins such as CsgA, TasA, FapC, MTP, and P1 2. Detect cryptic pockets near functional domains using SWISH-X simulations 3. Screen natural compound libraries against these pockets 4. Validate protein–ligand interactions and induced conformational effects via molecular dynamics simulations 5. Experimentally assess biofilm disruption by selected compounds using in vitro assays Main experiments will include: Computational modelling of full-length virulence proteins, enhanced cryptic site detection through SWISH-X, Structure-based virtual screening using natural product libraries (ZINC15-NP, NPASS, AyurvedaDB), and dynamic stability assessment through molecular dynamics simulations. Experimental validation will involve standard biofilm inhibition assays such as crystal violet staining and Congo red binding, immunochemical quantification using ELISA and SPR, and structural analysis through SEM and AFM imaging. This will be the first study to apply the SWISH-X method to biofilm-associated virulence proteins, introducing a transformative approach to uncovering novel druggable sites in proteins previously considered undruggable. By integrating advanced simulations with natural compound screening and thorough experimental validation, the study will establish a scalable pipeline for identifying cryptic-site modulators that interfere with biofilm integrity. If successful, the project will yield a set of promising natural small molecules capable of disrupting biofilm architecture with minimal toxicity. It will also advance our understanding of structural dynamics in virulence proteins and contribute to the development of next-generation anti-virulence therapies. The outcomes will directly support national and global efforts to combat AMR by offering a resistance-evading alternative to conventional antibiotics.