Bioassay-guided and computer-aided investigation of marine-derived kinase inhibitors: applications to control neurodegenerative disorders

Plisson, Fabien Gerard Christian (2012). Bioassay-guided and computer-aided investigation of marine-derived kinase inhibitors: applications to control neurodegenerative disorders PhD Thesis, Institute for Molecular Bioscience, The University of Queensland.

       
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Author Plisson, Fabien Gerard Christian
Thesis Title Bioassay-guided and computer-aided investigation of marine-derived kinase inhibitors: applications to control neurodegenerative disorders
School, Centre or Institute Institute for Molecular Bioscience
Institution The University of Queensland
Publication date 2012
Thesis type PhD Thesis
Supervisor Robert J. Capon
Total pages 394
Total colour pages 174
Total black and white pages 220
Language eng
Subjects 0305 Organic Chemistry
0304 Medicinal and Biomolecular Chemistry
Formatted abstract Protein kinases are implicated in many cellular processes, orchestrating propagation and amplification of chemical stimuli into physiological responses such as growth, differentiation, osmoregulation, proliferation, apoptosis. Deregulation of kinase activity, caused in part by genetic alterations, has since been linked to various human diseases such as vascular disorders,inflammatory diseases, cancers and neurodegenerative disorders. In total, about 40 protein kinasesare involved in preclinical and clinical trials for multiple treatments making them the second most important group of drug targets after G-protein-coupled receptors. The last 20 years have seen the emergence of protein kinase inhibitors in pharmaceutical drug pipeline. As of today, the American Food and Drug Administration has validated about 22 kinase drugs (16 small molecules and 6 monoclonal antibodies) mainly for the treatment of cancers with the latest example of INLYTATM  for chronic myelogenous leukemia. Following this success, it is clearly urgent to address such agents to many other indications like neurodegenerative disorders in order to diversify the current therapies in use. Most current kinase drugs have demonstrated poor properties to pass the bloodbrain barrier impulsing the search for new chemical entities, including from natural ecosystems.

The historical inter-dependency between healthcare and natural products started when humankind recognized plants and animals as valuable sources for treatments, the so-called traditional medicines. It is only in the mid-1960s with the advent of SCUBA diving that ocean floor could be systematically explored for drug candidates such as kinase inhibitors. One of early inputs of marine biodiscovery to kinase drug discovery was marked by the discovery of bryostatin 1, a bryozoan macrolide and the first marine-derived PKC modulator inhibiting the allosteric binding site for endogenous messengers and the induced tumor. Despite a lot of despair in phase II trials for various tumours, bryostatin 1 now appears promising in enhancing memory in animal models and is currently in Phase II for the treatment of Alzheimer's disease at the Blanchette Rockefeller Neurosciences Institute. This PhD thesis follows the steps of bryostatin 1 using Australia's rich marine biodiversity and an industry partner Noscira S.A. (Spain) to reveal unprecedented natural products potentially bioactive against therapeutically relevant kinases.

Chapter 1 covers the current status of kinase drug discovery and the 25-year-old story in marine bioprospecting for novel chemical entities inhibiting kinases, marine-derived kinase inhibitors. This chapter describes several issues and challenges faced in both research fields.

Chapters 2 to 4 present the isolation and identification of known and new chemical entities from three Australian marine specimens; two tunicates Didemnum spp. and one sponge Callyspongia sp. following traditional bioassay-guided fractionations. Each chapter depicts a class of natural products; the Lamellarins (Chapter 2), the Ningalins (Chapter 3) and the Pyrrolo-aminoimidazoles (Chapter 4). All three classes exhibit kinase inhibitory properties supported by in vitro kinase assay results and molecular modelling techniques permitting structure-activity relationship studies. Biological portfolios of these NP classes were further extended to other in-house biodiscovery programs for new P-glycoprotein inhibitors and antimicrobial agents.

Chapter 5 explores the use of in silico tools to marine biodiscovery with the development of a statistical model to predict blood-brain barrier (BBB) permeation through physicochemical properties of over 300 CNS-penetrant small molecules. The model challenges the marine-derived kinase inhibitors and current kinase inhibitor drugs revealing potential lead/hit compounds for BBB permeation. The chapter also details the implementation of virtual screening technique to speed up the search for new marine-derived kinase inhibitors, on Prof. Capon's unique Pure Compound Library (>1500 metabolites) and leading the discovery of new potent and selective CDK5 inhibitors, the Trachycladindoles.
Keyword Natural product chemistry
Drug discovery
Kinase inhibitors
Neurodegenerative disorders
Blood brain barrier
Molecular modeling
Chemometrics
Computer assisted

 
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Created: Wed, 26 Sep 2012, 10:40:29 EST by Fabien Plisson on behalf of Scholarly Publishing and Digitisation Service