Size does not matter: a molecular insight into the biological activity of chemical fragments utilizing computational approaches.

Masters Degree. University of KwaZulu-Natal, Durban.Insight into the functional and physiological state of a drug target is of essential importance in the drug discovery process, with the lack of emerging (3D) drug targets we propose the integration of homology modeling which may aid in the accurate yet efficient construction of 3D protein structures. In this study we present the applications of homology modeling in drug discovery, a conclusive route map and detailed technical guideline that can be utilised to obtain the most accurate model. Even with the presence of available drug targets and substantial advancements being made in the field of drug discovery, the prevalence of incurable diseases still remains at an all-time high. In this study we explore the biological activity of chemically derived fragments from natural products utilising a range of computational approaches and implement its use in a new route towards innovative drug discovery. A potential avenue referred to as the reduce to maximum concept recently proposed by organic chemists, entails reducing the size of a chemical compound to obtain a structural analogs with retained or enhanced biological activity, better synthetic approachability and reduced toxicity. Displaying that size may not in fact matter. Molecular dynamic simulations along with toxicity profiling were comparatively performed, on natural compound Anguinomycin D and its derived analog SB 640 each in complex with the CRM1 protein which plays an avid role in cancer pathogenesis. Each system was post-dynamically studied to comprehend structural dynamics adopted by the parent compound to that exhibited by the analog. Although being reduced by 60% the analog SB 640 displayed an overall exhibition of attractive pharmacophore properties which include minimal reduction in binding affinity, enhanced synthetic approachability and reduced toxicity in comparison to the parent compound. Potent inhibitor of CRM1, Leptomycin B (LMB) displayed substantial inhibition of the CRM1 export protein by binding to four of the PKIαNES residues (ϕ0, ϕ1, ϕ2, ϕ3, and ϕ4) present within the hydrophobic binding groove of CRM1. Although being drastically reduced in size and lacking the presence of the polyketide chain present in the parent compound Anguinomycin D and LMB the analog SB 640 displaced three of these essential NES residues. The potential therapeutic activity of the structural analog remains undeniable, however the application of this approach in drug design still remains ambiguous as to which chemical fragments must be retained or truncated to ensure retention or enhanced pharmacophore properties. In this study we aimed to the use of thermodynamic calculations, which was accomplished by incorporating a MM/GBSA per-residue energy contribution footprint from molecular dynamics simulation. The proposed approach was generated for each system. Anguinomycin D and analog SB 640 each in complex with CRM1 protein, each system formed interactions with the conserved active site residues Leu 536, Thr 575, Val 576 and Lys 579. These residues were highlighted as the most energetically favourable amino acid residues contributing substantially to the total binding free energy. Thus implying a conserved selectivity and binding mode adopted by both compounds despite the omission of the prominent polyketide chain in the analog SB 640, present in the parent compound. A strategic computational approach presented in this study could serve as a beneficial tool to enhance novel drug discovery. This entire work provides an invaluable contribution to the understanding of the phenomena underlying the reduction in the size of a chemical compound to obtain the most beneficial pharmacokinetic properties and could largely contribute to the design of potent analog inhibitors for a range of drug targets implicated in the orchestration of diseases

Structural and functional characterization of the egress and invasion machinery of the Malaria parasite: proposing a new way forward in Malaria therapeutics from an atomistic perspective.

Doctoral Degree. University of KwaZulu-Natal, Durban.ABSTRACT The past decade has witnessed numerous efforts to control the invasive tactics of the malarial parasite, including focused research towards selective malarial inhibitors of Plasmodium falciparum, the most lethal strain of the Plasmodium species. The recent discovery of the key mediators of egress and erythrocyte invasion of the malaria parasite has opened a new avenue that may be harnessed for the development of effective therapeutics that may permanently eradicate the malaria virus. These new parasitic targets of P. falciparum are PIX and PX and have gained considerable attention in drug discovery pipelines however, the absence of crystal structures of these enzymes evidenced a lack in structural information, as there is currently little known regarding the structural dynamics, active site domains and the mechanism of inhibition of these enzymes. This has therefore led to the modeling of the 3D protein structure of each enzyme to gain a fundamental understanding regarding the structural and functional characteristics that may be visualized from an atomistic perspective. The emergence of new drug targets has led to the integral use of computational techniques including molecular modeling, molecular docking, virtual screening protocols and molecular dynamic simulations which allow chemists to evaluate and assess millions of compounds and thus funnel out potential lead drugs. These in silico techniques further justify the current use of Computer-Aided Drug Design as a cost-effective approach to fast track the drug discovery process. The above-mentioned techniques, amongst a vast range of other computational tools were integrated in this study to provide insight into conformational changes that elucidate potential inhibitory mechanisms, identification of the active site cleft, characterization and pharmacophoric features leading to novel small molecule inhibitors. This study focused on analysing the flap dynamics specific to the aspartic protease family of enzymes using a defined set of parameters to map out the binding domain for the design of potential antimalarial drugs. To gain a molecular perspective of the conformational binding of two proposed experimental drugs which showed substantial inhibitory activity against PIX and PX molecular dynamic simulations were performed and further evaluated employing in silico thermodynamic analysis to provide insight into the proposed binding of mode of each inhibitor, highlighting the key moieties required for binding. A pharmacophoric model was also generated using in silico tools to screen for tailored inhibitors specific to PIX. The aim of this study was to generate fundamental insight into the structural and functional characterization of two prominent targets that play an indispensable role in survival of the malaria virus. The implementation of the information extracted from this study, may provide a structural outline for molecular biologists, and pharmaceutical scientists to aid in the design of novel antimalarial therapeutics

Does Size Really Matter? Probing the Efficacy of Structural Reduction in the Optimization of Bioderived Compounds – A Computational “Proof-of-Concept”

Over the years, numerous synthetic approaches have been utilized in drug design to improve the pharmacological properties of naturally derived compounds and most importantly, minimize toxic effects associated with their transition to drugs. The reduction of complex bioderived compounds to simpler bioactive fragments has been identified as a viable strategy to develop lead compounds with improved activities and minimal toxicities. Although this ‘reductive’ strategy has been widely exemplified, underlying biological events remain unresolved, hence the unanswered question remains how does the fragmentation of a natural compound improve its bioactivity and reduce toxicities? Herein, using a combinatorial approach, we initialize a computational “proof-of- concept” to expound the differential pharmacological and antagonistic activities of a natural compound, Anguinomycin D, and its synthetic fragment, SB640 towards Exportin Chromosome Region Maintenance 1 (CRM1). Interestingly, our findings revealed that in comparison with the parent compound, SB640 exhibited improved pharmacological attributes, while toxicities and off-target activities were relatively minimal. Moreover, we observed that the reduced size of SB640 allowed ‘deep access’ at the Nuclear Export Signals (NES) binding groove of CRM1, which favored optimal and proximal positioning towards crucial residues while the presence of the long polyketide tail in Anguinomycin D constrained its burial at the hydrophobic groove. Furthermore, with regards to their antagonistic functions, structural inactivation (rigidity) was more pronounced in CRM1 when bound by SB640 as compared to Anguinomycin D. These findings provide essential insights that portray synthetic fragmentation of natural compounds as a feasible approach towards the discovery of potential leads in disease treatment. Keywords: Chromosome region maintenance 1, Anguinomycin D, SB640, Structural reduction, NES-binding groove, Polyketide tai