Hasan, Md Nazmul
The goals for the Spring 2025 semester:
- Determining protein-protein relative binding free energies of a set of 20 PPIs with MM-PBSA and MM-GBSA method considering both enthalpy and configurational entropy.
- Implementing BFEE2 protocol (with geometric route) to determine the absolute binding free energies of the same 20 PPIs dataset.
- Large scale virtual screening of small molecule libraries and peptides for IL-13Rα1/IL-13 implicated in Atopic Dermatitis and designing of a series of lead compounds.
- Perform fragment-based drug discovery to generate a lead molecule for IL-13Rα1/IL-13.
- Applying validated methods (MM-PBSA and MM-GBSA in goal 1 and BFEE2 in goal 2) for lead optimization and perform structure-activity-relationship of the lead molecules.
Personal Statement:
I am thankful to the Milwaukee Institute for Drug Discovery for supporting my research in Spring 2025 semester. This Research Assistantship helped me to focus deeply on my research in developing computational protocol for calculating relative binding free energies of protein-protein interaction systems. I also performed large-scale virtual screening of potential small molecule inhibitors against IL-13Rα1/IL-13 complex during this period. I have presented the outcome of my research at a local ACS conference. Moreover, based on these research findings, I have submitted a first-authored research article. Alongside, this assistantship gave me the opportunity to work with an undergraduate student which accelerated the progress of the research. I really appreciate the contribution of Ashe in the research and hope to continue the work in coming semesters. Overall, it was a great experience to be an MIDD research assistant which will positively impact on my future career.
Undergraduate student: Ashe Barbian
During my time working with the Saha Group, I have gained valuable experience in computational chemistry and data-driven research. I began by completing site-specific molecular docking simulations using AutoDock Vina to help characterize potential inhibitors for a target protein, which introduced me to key concepts in structure-based drug design. To support these docking studies, I gathered chemical information through API queries to publicly accessible chemical databases, allowing me to build a data set of relevant aspects of the compounds for analysis. I then used KNIME to collate and organize the resulting datasets, enabling more efficient interpretation of docking results and identification of promising inhibitors. These experiences have strengthened my understanding of applications for cheminformatics in drug design.