mpapadourakis
I hold a Pharmacy degree from the University of Athens, graduating with an average grade of 8.72/10.00 and receiving a fellowship for academic excellence. As a trained pharmacist, my ultimate goal has always been to contribute to the treatment of human diseases through the discovery of novel therapeutic small molecules. To pursue this ambition, I completed a PhD in drug design under the supervision of Prof. J. Michel at the University of Edinburgh. My research focused on developing a new alchemical free energy (AFE)-based protocol to calculate binding free energies of protein-ligand complexes. The initial implementation of this protocol was among the most accurate in the SAMPL6 challenge. I further demonstrated its applicability by designing two pharmacologically relevant molecular series: selective CypD inhibitors and disruptors of the MDM2-p53 interaction.
During my PhD, I was awarded an HPC Europa3 fellowship to collaborate with Dr. Z. Cournia’s group at BRFAA, where I explored AFE protocols for designing inhibitors of intrinsically disordered proteins. After completing my PhD, I received a Bodossaki scholarship to join the Cournia lab as a postdoctoral researcher. My current work involves developing candidate drugs for cancer-related proteins using molecular dynamics (MD) simulations and AFE calculations. This includes creating a webserver that automates AFE/MD simulation setups compatible with NAMD’s dual-topology procedure and the OPLS-AA force field. I validated this tool by investigating the binding affinity of BMAA and its carbamate adducts to glutamate receptors in competition with the endogenous ligand.
Beyond academia, I have gained significant professional experience. As a senior R&D scientist at Cloudpharm, I applied my computer-aided drug design expertise to discover bioactive compounds and developed machine learning tools for predicting “green-by-design” pharmaceuticals as part of the ENVIROMED project.
Since 2023, I have been serving as an Adjunct Instructor in the Department of Nursing at the Hellenic Mediterranean University, teaching the course “Basic Principles of Pharmacology in Nursing” while continuing my postdoctoral research in the computational discovery of small-molecule inhibitors targeting Glutamate receptors.
Specialties: Computer-aided drug design, free energy calculations, molecular dynamics simulations, ligand- and structure-based drug design, Python programming.