Application and development of in silico methods in drug discovery

Abstract

Computer aided drug design has become a cost effective collection of methods for discovering and developing drug candidates. The thesis contributes to this effort by applying and evaluating different computational strategies. In this thesis I did research towards the development of a new molecular descriptor, Gibbs free energy of hydration, for drug designing. It is followed by molecular modelling in order to elucidate the biomolecular targets of thieno[2,3-b]pyridine (TPs) anti-cancer agents. Furthermore, virtual screening was employed to find hits inhibiting the enzymatic target polyphenol oxidases (PPOs). Finally, molecular modelling was employed to investigate the binding motifs of tyrosyl-DNA phosphodiesterase 1(TDP1) inhibitors. This thesis begins with the question of whether calculated hydration energy (ΔGhyd) can be used as a molecular descriptor in defining promising regions of chemical space for drug design. Calculating ΔGhyd using the Density Solvation Model (SMD) in conjunction with the Density Functional Theory (DFT) gave an excellent correlation with experimental values. Three compound collections were used: Known drugs (n = 150), drug-like compounds (n = 100) and simple organic compounds (n = 140). A relatively broad distribution was seen for the known drugs, with an average at -15.3 kcal/mol. Interestingly, much lower averages were found for the drug-like compounds (-7.5 kcal/mol) and the simple organic compounds (-3.1 kcal/mol) respectively. This trend was not observed for these collections when calculated partition coefficient (Log P) and water solubility (Log S) values were used. The considerable greater exothermic ΔGhyd average for the known drugs clearly indicates that, in order to develop a successful drug candidate, a value of ΔGhyd<-5 kcal/mol or less is preferable. The next point of investigation was to develop a panel of docking scaffolds for the known molecular targets of the anticancer agents, TPs, in order to glean insight into their mechanism of action. According to the panel, the A2A receptor showed the strongest binding, inferring it to be the most plausible target, closely followed by tubulin. To investigate whether the TPs modulate G protein-coupled receptors (GPCRs) other than A2A, a screen against 168 GPCRs was conducted. According to the results, ligand 1 (3-chloro-2-methyl - thieno[2,3-b]pyridine) modulates five receptors in the low μM region, four as an antagonist; CRL-RAMP3 (IC50--11.9 μM), NPSR1B (IC50--1.0 μM), PRLHR (IC50--9.3 μM), and CXCR4 (IC50--6.9 μM). Finally, one agonist, GPRR35, was found (EC50 of 7.5 μM). Molecular modelling showed good binding to all of the receptors investigated; however, none of these surpass the A2A receptor. Moreover, in order to improve water solubility of the TPs, a morpholine moiety was tethered to the molecular scaffold by substituting the sulphur atom with nitrogen, resulting in a 1Hpyrrolo[2,3-b]pyridine core structure. The water solubility was increased by three orders of a magnitude from 1.2 μg/mL (1 - thieno[2,3-b]pyridine) to 1.3 mg/mL (3a- pyrrolo[2,3-b]pyridine), however these ligands were only marginally active against cancer cells. Furthermore, a virtual screen was conducted against Polyphenol oxidases (PPOs), enzymes that catalyse the oxidation of phenolic compounds using natural product library. The virtual screen yielded two hits, confirmed by an NMR-based assay. Two compounds, 16 (STOCK1N-17176) and 26 (STOCK1N-18947), led to a ~40% reduction in the catalytic activity of grape PPO that do not contain a phenol or diphenol core (unlike many reported PPO inhibitors). Furthermore, in order to explore the chemical space around tropolone (a known inhibitor) for activity against PPO, close structural analogues were docked in the scaffold. It resulted in six hits and these analogues were purchased and tested. As a result, a new, more potent analogue 41 (2,3-dihydroxy-5-(1-methylethyl)-tropolone) was identified with an IC50 value of 2 ± 0.5 μM. Based on my results, the natural product library from InterBioScreen with the methods outlined here can reliably yield positive results from a virtual screen, leading to tractable compounds for further drug development. Finally, in this thesis, I investigated the potential binding motifs of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors. Molecular modelling was used to investigate the biological activity of aminoadamantanes containing monoterpene-derived fragments against TDP1. They showed plausible binding modes that can be attributed to the efficacy of the compounds.