PI: Ra’ed S. A. Khashan, PhD, RPh
Education
Ph.D., Pharmaceutical Sciences (Medicinal Chemistry). 8/2003 – 8/2007
University of North Carolina at Chapel Hill – Division of Medicinal Chemistry – School of Pharmacy. Dissertation: “Development & Application of Ligand/Structure-based Computational Drug Discovery Tools Based on Frequent Subgraph Mining of Chemical Structures”.
Advisor: Prof. Alexander Tropsha. Director, Laboratory for Molecular Modeling.
M.S., Pharmaceutical Sciences (Physical Pharmacy). 8/2000 – 8/2003
University of Texas at Austin – Division of Pharmaceutics – College of Pharmacy.
Thesis: “Refinement and Validation of BCUT Descriptors for Computer Assisted Drug Discovery”.
Advisor: Prof. Robert S. Pearlman. Director, Laboratory for Development of Computer Aided Drug Discovery Software.
Bachelor of Pharmacy, on ‘Honor List’. 8/1994 – 1/1999
Jordan University of Science & Technology (JUST) – Faculty of Pharmacy, Irbid, JORDAN.
B.S., Computer Science (Minor in Chemistry), on ‘Honor List’. 8/1997 – 8/2000
Yarmouk University – Faculty of Science, Irbid, JORDAN.
Professional Experience
Associate Professor, Long Island University – Brooklyn. 8/2022 – Present
- Molecular and Structural Mechanism of DNA Targeting by a Transposon-encoded Type I-F CRISPR/Cas System.
- Implications of Molecular and Structural Mechanism of Insulin Receptor on Receptor Activation and Drug Design.
- Using AI Strategies to Support Fragment-based De Novo Drug Design (FragDeNovo) using Pocket Similarity Search of Native Protein-Ligand Complexes.
Assistant/Associate Professor, USciences – Philadelphia. 1/2018 – 8/2022
- Molecular and Structural Mechanism of DNA Targeting by a Transposon-encoded Type I-F CRISPR/Cas System.
- Implications of Molecular and Structural Mechanism of Insulin Receptor on Receptor Activation and Drug Design.
- Applying data mining and machine learning tools to develop an ANN-based multi-body interaction docking scoring function (MBI-score) based on utilizing frequent geometric and chemical patterns of interfacial atoms in native protein-ligand complexes.
Assistant Professor (Founding Faculty), UT – Tyler. 10/2014 – 12/2017
- Develop (SCORPIONS), a method for scoring computationally generated protein folds using frequent geometric motifs of internal residues found in native proteins.
- Develop a way to classify protein families/functions (based on Gene Ontology Consortium Method) using frequent geometric patterns interactions at the surface of proteins’ tertiary.
Visiting Scholar, University of North Carolina – Chapel Hill. Summer 2016
PI: Max Berkowitz
- Understanding the mechanism of how the C1 domain of CalDAG-GEFI activates the platelet-activating protein, Rap1b using Large Scale MD.
Research Fellow, CCIB, Rutgers University – Camden. 7/2014 – 10/2014
PI: Grace Brannigan.
- Estimating Binding Affinities of GABAa Neuromodulators: Using Free Energy Methods with Large Scale MD Simulations.
Assistant Professor, King Faisal University, KSA. 5/2012 – 6/2014
- Perform pocket similarity search (using graph representation of protein-ligand interfacial atoms) to generate a virtual library of fragments (FragVLib), and apply virtual screening (FragVScreen) to identify lead molecules.
- Identify Structure-Based Bioisosteres (ChemIsosteres) by mining a graph representation of protein-ligand interfacial atoms to be used for drug design and lead molecules.
- Collaborate with Dr. Ingo Muegge (at BI Pharma) to advance his famous PMF score to account for multi-body interactions.
Research Fellow, BRITE, North Carolina Central University. 1/2008 – 11/2011
Advisor: Weifan Zheng.
- Developed a novel multi-body interaction (MBI) statistical pose-scoring function for docked protein-ligand complexes using frequent geometric and chemical patterns of interfacial atoms in native protein-ligand complexes.
- Developed ‘SPIDER’, which applies Subgraph Mining technique to derive interaction patterns at protein-protein interfaces & use them to score-rank computationally generated decoys to identify nearest-native poses.
Research Assistant, University of North Carolina – Chapel Hill. 8/2003 – 8/2007
Advisor: Alexander Tropsha.
- Development of docking protocols and scoring functions using frequent geometric and chemical patterns of inter-atomic interactions at the interface of protein-ligand complexes.
- Generated QSAR/QSPR fragment-based chemical descriptors using frequent sub-graph mining, and evaluated them using QSAR modeling techniques such as k-nearest neighbor (kNN), and support vector machine (SVM).
- Designed topological (2D) Pharmacophore models using frequent sub-structure mining, and evaluated them using a classification-based association (CBA) technique.
Research Assistant Internship, Inspire Pharmaceuticals Inc., Durham, NC. Fall 2003
Supervisor: Robert Plourde.
- Development of validated QSAR models of P2Y12 receptor antagonists and their application to database mining.
Research Assistant, UT-Austin. 8/2000 – 8/2003
Advisor: Robert Pearlman.
- Refined and validated molecular descriptors (BCUT) to aid in diversity analysis for designing chemical libraries.
- Improved a program (GSSI) that calculates the free energy of desolvation by adding a hydrogen-bond component.
- Developed ProtoPlex: User-control over tautomeric & protonation states of molecules.
- Designed the graphical user interface for StereoPlex, which is a stereoisomer generator machine.
