Reynisson, JLeung, ESarojini, VEurtivong, Chatchakorn2017-09-262017https://hdl.handle.net/2292/35779The late 20th century marked a phase shift in drug discovery and development by employing in silico tools that offer advantages for medicinal chemists to visualise molecular interactions through simulations of drug candidates and targets that coined the term 'molecular modelling'. Together with advances in development of software, increase in computational power and a wide range of well-characterised protein crystal structures available, it was possible for chemists to virtually screen for active drugs. Moreover, the accessibility of compound libraries gathered saw similarities in drugs and families of compounds that led to the growth of chemoinformatics that utilises the database information available, which can be applied to drug discovery and development projects. This thesis covers the bulk of today's drug discovery and development using in silico methods and its applicability mainly to anticancer drug candidates. Phosphatidylinositol - specific phospholipase C (PI-PLC) is a protein that mediates cell signalling pathways initiated by the binding of an extracellular source/signal to the cell surface. Previous work provided evidences linking it to cancer progression. The 1H-pyrazole and 3-amino-thieno[2,3-b]pyridine (AThPs) class of compounds were the products of a virtual screen conducted earlier that displayed anticancer activities. Similarity approaches were conducted based on the chemical scaffolds for the two classes which rapidly expanded the structure activity relationship (SAR) resulted in an additional 717 hits. These were docked into the PI-PLC binding pocket, the putative target of the compounds, to further focus the selection. Thirteen derivatives of the AThPs were identified and tested against the NCI60 panel of human tumour cell lines. The most active derivative was potent against the MDA-MB-435 melanoma cell line with 50% growth inhibition (GI50) at 30 nM. Also, it was found that a piperidine moiety is tolerated on the AThP scaffold with GI50 = 296 nM (MDA-MB-435) considerably expanding the SAR for the series. For the 1H-pyrazoles, four derivatives were identified using in silico similarity approach and an additionally ten were synthesised with various substituents on the phenyl moiety to extend the SAR but only modest anticancer activity was found. Furthermore, preliminary in silico drug design of the AThPs were conducted to selectively target the γ2-isoform showed dual o-methyl and m-chloro, and single substituted m-methoxy on the naphthalene moiety as reasonable candidates. A series of AThPs were also prepared and tested in a phenotypic sea urchin embryo assay to identify potent and specific molecules that affect tubulin dynamics. The most active compounds featured a tricyclic core ring system with a fused cycloheptyl or cyclohexyl substituent and unsubstituted or alkyl-substituted phenyl moiety tethered via a carboxamide. Low nano-molar potency was observed in the sea urchin embryos for the most active compounds and was suggestive of a microtubule-destabilising effect. The molecular modelling studies indicated that the tubulin colchicine site is inhibited, which often leads to microtubule-destabilisation in line with the sea urchin embryo results. Finally, the identified hits displayed a robust growth inhibition (GI50 of 50–250 nM) on multidrug-resistant melanoma MDA-MB-435 and breast MDA-MB-468 human cancer cell lines. This work demonstrated that for the AThPs, the most effective mechanism of action is microtubule-destabilisation initiated by binding to the colchicine pocket. The next project demonstrated the use of an in silico docking software to search for active hit compounds against a drug target. A virtual screen was conducted against phosphatidylcholine - specific phospholipase C derived from Bacillus cereus (PC-PLCBc) using the ChemBridge diversity collection of 5 × 104 entities. Literature reports have established a relationship between PC-PLC activity and cancer progression. The virtual screen was employed in conjunction with the Amplex Red biochemical assay which identified four different classes of novel PC-PLC inhibitors: N-phenylbenzenesulphonamide, 2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole, 2-morpholinobenzoic acids and benzamidobenzoic acids. The 2-morpholinobenzoic acids and 2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indoles were confirmed for their antiproliferative effects; 50% concentration inhibition (IC50) ~ 1 - 2 μM in MCF7 and MDA-MB-231 breast cancer cell lines. The N-phenylbenzenesulphonamide and benzamidobenzoic acids were shown to display more modest activities. The last project addressed the applicability of known drugs in chemoinformatics. The Gaussian function was employed to calculate an index that can predict the quality of drug candidates. 1880 known drugs were collected and analysed for their mainstream molecular descriptors: molecular weight (MW), octanol-water partition coefficient (log P), hydrogen bond acceptor (HA) and donor (HD), rotatable bond (RB) and polar surface area (PSA). The statistical distributions were fitted to Gaussian functions for each of the descriptors and normalised to 1. This gave a mathematical tool to calculate a score, or an Index, for each descriptor. Known Drug Indexes (KDI) were derived by summation and multiplication giving one number for each molecule calculated. The KDI summation gives a theoretical maximum of 6 whereas the multiplication method results in 1. Both KDIs are advantageous methods in deriving optimally balanced drug candidates based on the molecular descriptors used with methysergide, amsacrine and fluorometholone being the best clinically used drugs according to both methods.Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htmhttps://creativecommons.org/licenses/by-nc-nd/3.0/nz/ThesisCopyright: The authorhttp://purl.org/eprint/accessRights/OpenAccessQ111963335