HIV protease is an essential target in the treatment of AIDS. It is a homodimeric protein that catalyzes the proteolysis of larger HIV polyproteins into smaller functional proteins. Our objective is to understand the structure and dynamics of HIV protease. Our goal is to investigate its structure and dynamics, focusing on flap dynamics, mutation effects, electrostatic influences at the active site, and dimerization mechanisms. For this purpose we utilize advanced md techniques and tools like umbrella sampling, ABMD, GAMD and Markov State Modelling. 

Choleteryl ester transfer protein (CETP) has come out to be an emerging protein target in the cardiovascular disease treatment. Inhibition of its neutral lipid transfer activity increases the high density lipoprotein cholesterol concentration. Keeping this in mind, our group is studying the lipid transfer through CETP by using advanced molecular dynamic simulations. Besides, efforts have been made to design some new small molecule inhibitors of CETP by structure-based drug design and machine learning approaches.

During viral entry, the MHC complex presents antigens on the cell surface, where they are recognized by TCRs, triggering an immune response. However, the mechanism of T-cell activation via pMHC-TCR binding remains unclear. In this study, we aim to identify the conformational changes in TCR that drive immunogenicity and develop models to screen viable viral epitopes using multi-scale Molecular Dynamics (MD) simulations and Machine Learning. By analyzing structural dynamics and interaction patterns, we seek to uncover key determinants of antigen recognition. Our findings will contribute to the rational design of vaccines and immunotherapies targeting viral infections.

Proteins fold into specific 3D shapes to achieve their lowest energy state. Understanding this folding process is crucial for designing targeted medicines for diseases like cancer or Alzheimer's. Given the vast number of possible folded structures, quantum computation with its advantage of dealing with superposition of these many possible states. We are developing a quantum algorithm to efficiently explore these possibilities and identify the optimal low-energy state.

Active pharmaceutical ingredients (APIs) are essential for treating diseases, but many drugs have low solubility despite high permeability, limiting their effectiveness and delivery options. To address this, we have developed reformulated API (rAPI) technology, which complexes APIs with novel ionic liquids molecules to significantly improve the solubility of representative APIs. The synthesized rAPIs will undergo thorough characterization and be tested for solubility and efficacy in both in vitro and in vivo studies.

Traditionally, nucleic acids are stored under refrigeration, which limits accessibility and consumes resources. We explore how IL-water binary mixtures can be used to store nucleic acids at room temperature. We show that DNA stored in IL-water mixtures remains intact over 36-month time-point, unlike DNA in water or buffer, which degrades. Additionaly, we use atomistic molecular dynamics simulations to understand how ILs bind to and stabilize DNA. We are now exploring these methods to stabilize RNA as well.

Our research centers on Bio-ionic liquids (Bio-ILs) based polymers, which integrate advanced materials to address biomedical challenges. Bio-ILs are ionic liquids with biologically derived ions, offering biocompatibility and environmental benefits. They combine the stability and tunable properties of traditional ionic liquids with biological functionalities, making them ideal for applications such as tissue engineering scaffolds and antimicrobial coatings for medical devices and implants.