Computer aided drug discovery tools and pipelines for molecule targeted inhibition of Topoisomerases I and II in cancer

Computer Aided Drug Discovery (CADD) is a broad field which uses scientific tools from various disparate disciplines towards drug discovery and design. The tools of CADD include receptor based methods such as docking and Molecular Dynam- ics (MD), and ligand based methods such as Quantitative Structure Activity Rela- tionship (QSAR) / Quantitative Structure Property Relationship (QSPR) approaches relying directly on the structure of small molecules. In this thesis both of these approaches to CADD have been utilized together to drug topoisomerases. There are two clinically relevant members of the Topoisomerase (TOP) protein family, TOP I and TOP II, both of which the tools of CADD were applied. For the former, sev- eral novel TOP I natural product-like inhibitors were developed and characterized with molecular dynamics simulations. This led to the in-silico based prediction of unique but strong non-covalent interactions in the binding site, as well as a rational- ization of the difference in activity between two enantiomers. For TOP II, a broader CADD campaign was initiated to screen ⇠ 12 million molecules from the ZINC Is Not Commercial (ZINC)-15 [1] database against TOP II. This was facilitated by the implementation of consensus voting protocols from various virtual screening programs [2] and compositions of machine learning techniques. With a synergy between in-silico and wet-lab components, a rational drug discovery pipeline was executed to discover and characterize a highly potent inhibitor. The identified com- pound has been shown to inhibit topoisomerase in a Kinetoplast DNA (KDNA) de- catenation assay with a nanomolar Concentration at 50% Cellular Inhibition (IC50). Furthermore, it has been demonstrated that the identified drug candidate does not act as a ”DNA poison”, as no linear Deoxyribonucleic Acid (DNA) is formed upon incubation with TOP II in a relaxation assay and no general DNA damage is observed. Finally, a mechanism of action for the lead compound is proposed, based on experimental and in-silico evidence.Science, Faculty ofGraduat