Abdolkarim Farrokhzadeh

WORK HISTORY

ABOUT ABDOLKARIM FARROKHZADEH

Research Interests: Computer-aided drug design and discovery, Computational (bio)chemistry and molecular modelling, Hit-to-lead and lead optimization, Synthesis and characterization of small molecule inhibitors, Protein purification and binding affinity assays between small molecule inhibitors and proteins, Quantum mechanics calculations in organic chemistry. Experimental Skills: Synthesis of small molecule inhibitors and their characterization methods including Nuclear magnetic resonance (NMR, types of nucleus and at various temperatures), Fourier-transform infrared (FT-IR), Ultraviolet–visible (UV-Vis), High-resolution mass spectrometry (HRMS), Elemental analysis (CHNS). Membrane protein purification via affinity chromatography and size exclusion chromatography (SEC). Experimental binding affinity assays between small molecule inhibitors and proteins using techniques such as SPR, MST, and Tycho™ NT.6. Computational Skills: Compound library profiling and filtering. High-throughput virtual screening via molecular docking, including rigid docking, induced-fit docking, and covalent docking. Active-Learning Glide: This method combines Glide\'s high-performance ligand-receptor docking with Schrödinger’s state-of-the-art deep learning to efficiently screen ultra-large compound libraries. Active Learning Glide leverages docking scores for a sufficient number of ligands to train a Machine Learning (ML) model that predicts docking scores for new ligands without docking them. This method, approximately faster than Glide docking, enables the efficient screening of ultra-large libraries (over 1 billion ligands) in a reasonable time frame. High-throughput virtual screening via GPU Shape-based screening. High-throughput virtual screening via pharmacophore modeling. De Novo Design (Fragment-based drug desing). Bioisosteric replacement. Forming protein-ligand interactions with Ligand Designer. Covalent and non-covalent molecular dynamics simulations (GROMACS and AMBER) and free energy calculations (MM/GBSA, MM/PBSA) Free energy calculations for drug design with FEP+ using Schrödinger Suite software. Quantum mechanics calculations in organic chemistry, including energy calculations and structure optimization, basis set superposition error (BSSE) calculations, energy calculations of frontier orbitals (HOMO and LUMO), spectroscopy calculations (IR, Raman, UV-Vis, and NMR), AIM, NBO, and ESP analyses, and transition state calculations using QST2 and QST3 methods.