Strategic Design and Development of Small Molecules and Peptides as Enzyme Inhibitors

Abstract

Chapter one introduces the emerging developments in heparanase (HPSE) drug discovery as it gained momentum in the discovery pipeline almost 30 years ago. HPSE is an underlying denominator in many pathologies, including diabetes, refractory melanoma, and cancer metastasis, which makes it a promising target in the innovative drug discovery pipeline. The pursuit of developing drugs targeting HPSE through clinical trials has been long anticipated in this drug discovery journey. In chapter one we outlined the progress of the four drug leads of oligosaccharide origin that have entered clinical trials. Cutting-edge medicinal chemistry techniques from multiple discovery campaigns are also discussed, including the use of drug repurposing, high throughput chemical screening (HTCS), and virtual screening.

Chapter two describes the structure-activity relationship (SAR) for two series of small molecules as potential inhibitors of HPSE. The initial series (Series I) was developed as part of our SAR-guided exploration surrounding the scaffold of compound BT2012, which was discovered through a HTCS campaign conducted by Beta Therapeutics, a Canberra-based biotechnology company. Additionally, we employed rational design strategies incorporating structural simplification, extensions, and bioisosteric substitutions to synthesise various derivatives. In order to gain further insight into the development of potent inhibitors, we employed the scaffold hopping approach to broaden our search within the bioactive pharmacopoeia. To this end, we identified doxazosin mesylate, which exhibited micromolar activity against HPSE and served as a valuable inspiration for the design of BT2162. A second series (Series II) of small molecules was developed to probe the bioactive scaffold of BT2162, and potentially develop other effective inhibitors in the process. These efforts gave rise to the discovery of several small molecules with sub-micromolar activity.

Chapter three features a collaborative effort to develop a series of covalent fragments and peptidomimetics with electrophilic warheads to inhibit Chikungunya non-structural polyprotein-2 protease (CHIKV nsP2 pro) activity. The biochemical FRET-based assay determined that some compounds were potential inhibitors that exhibited greater than 35% loss of nsP2 pro activity at a concentration of 1 mM. Upon further examination, it was determined that these fragments formed irreversible conjugates with CHIKV nsP2 pro, primarily through a Michael acceptor motif. LMW molecules have promising potential as inhibitors of CHIKV nsP2 pro and will contribute towards the discovery of antiviral therapies for CHIKV.

Chapter four is an overview of the trends and developments of organic synthetic, biocompatible, and bioorthogonal techniques from the literature that have been employed by medicinal chemists for peptide macrocyclisation. Chapter four sheds light on the scope and limitations of the synthetic methodologies and discusses the potential for optimizing many of these approaches to generate a diverse range of cyclic peptides in biological milieu.

Chapter five showcases a facile and biocompatible approach to prepare peptides containing a C-terminal nitrile motif, which is installed using the Dawson linker. Two general approachesfor thiazoline macrocyclisation are also explored, the initial strategy uses a neutral aqueousbuffer, and the second method takes advantage of an alkaline organic solution, offering astreamlined one-pot procedure. Furthermore, chapter five introduces the pioneering process ofoxidizing a peptide macrocycle featuring a thiazoline linkage using a metal-free strategy on apeptide model. Show more