In silico investigation of hepatitis c virus: a novel perspective into targeted viral inhibition of NS3 helicase, NS 3/4a protease and NS5b RNA dependent RNA polymerase.

Doctoral Degrees (Pharmaceutical Sciences). University of KwaZulu-Natal. Westville, 2019.Hepatitis C Virus (HCV) is an escalating global healthcare and economic burden that requires extensive intervention to alleviate its control. Over the years, drug design efforts have produced many anti-HCV drugs; however, due to drug resistance brought on by numerous genetic variations of the virus and lack of specificity and stability, current drugs are rendered ineffective. The situation has been further intensified by the absence of a viable vaccine. For these reasons, continuous HCV research is imperative for the design and development of promising inhibitors that address the challenges faced by present antiviral therapies. Moreover, exposure of previously neglected viral protein targets can offer another potentially valuable therapeutic route in drug design research. Structure-based drug design approaches accentuate the development of small inhibitor molecules that interact with therapeutic targets through non-covalent interactions. The unexpected discovery of covalent inhibitors and their distinctive nature of instigating complete and irreversible inhibition of targets have shifted attention away from the use of non-covalent drugs in antiviral treatment. This has led to significant progress in understanding covalent inhibition regarding their underlying mechanism of action and in the design of novel covalent inhibitors that work against biological targets. However, due to difficulties arising in its application and resultant safety, the pharmaceutical industry were reluctant to pursue this strategy. With the use of rational drug design, a novel strategy was then proposed known as selective covalent inhibition. Due to the lack of competent protocols and information, little is known regarding selective covalent inhibition This study investigates three biological HCV targets, NS3 protease, RNA helicase and NS5B RNAdependent RNA polymerase. With constantly evolving viruses like HCV, computational methods including molecular modelling and docking, virtual screening and molecular dynamic simulations have allowed chemists to screen millions of compounds to filter out potential lead drugs. These in silico approaches have allowed Computer-Aided Drug Design as a cost-effective strategy to accelerate the process of drug discovery. The above techniques, with numerous other computational tools were employed in this study to fill the gap in HCV drug research by providing insights into the structural and dynamic changes that describe the mechanism of selective covalent inhibition and pharmacophoric features that lead to unearthing of potential small inhibitor molecules against Hepatitis C. v The first study (Chapter 4) provides a comprehensive review on HCV NS3/4A protein, current therapies and covalent inhibition as well as introduces a technical guideline that provides a systematic approach for the design and development of potent, selective HCV inhibitors. The second study (Chapter 5) provides a comprehensive understanding concerning the implications of selective covalent inhibition on the activity of HCV NS5B RNA-dependent RNA polymerase, with respect to key components required for viral replication, when bound to a target-specific small inhibitor molecule. The third study (Chapter 6) is preliminary investigation that uses Pharmacophore-based virtual screening as an efficient tool for the discovery of improved potential HCV NS3 helicase inhibitors. The pharmacophoric features were created based on the highly contributing amino acid residues that bind with highest affinity to the weak inhibitor, quercetin. These residues were identified based on free energy footprints obtained from molecular dynamic and thermodynamic calculations. Post molecular dynamic analysis and appropriate drug-likeness properties of the three top-hit compounds revealed that ZINC02495613 could be a more effective potential HCV helicase inhibitor; however, further validation steps are still required. This study offers a comprehensive in silico perspective to fill the gap in rational drug design research against HCV, thus providing an insight into the mechanism of selective covalent inhibition, uncovering a previously neglected viral target and identifying possible antiviral drugs. To this end, the work presented in this report is considered a fundamental platform to advance research toward the design and development of novel and selective anti-HCV drugs

Moringa oleifera crude aqueous leaf extract induces apoptosis in human hepatocellular carcinoma cells via the upregulation of NF-kB and IL-6/STAT3 pathway.

Master of Science in Medical Biochemistry. University of KwaZulu-Natal, Durban 2016.Abstract available in PDF file

Long COVID: a review and proposed visualization of the complexity of long COVID

Post-Acute Sequelae of Severe Acute Respiratory Syndrome Coronavirus – 2 (SARS-CoV-2) infection, or Long COVID, is a prevailing second pandemic with nearly 100 million affected individuals globally and counting. We propose a visual description of the complexity of Long COVID and its pathogenesis that can be used by researchers, clinicians, and public health officials to guide the global effort toward an improved understanding of Long COVID and the eventual mechanism-based provision of care to afflicted patients. The proposed visualization or framework for Long COVID should be an evidence-based, dynamic, modular, and systems-level approach to the condition. Furthermore, with further research such a framework could establish the strength of the relationships between pre-existing conditions (or risk factors), biological mechanisms, and resulting clinical phenotypes and outcomes of Long COVID. Notwithstanding the significant contribution that disparities in access to care and social determinants of health have on outcomes and disease course of long COVID, our model focuses primarily on biological mechanisms. Accordingly, the proposed visualization sets out to guide scientific, clinical, and public health efforts to better understand and abrogate the health burden imposed by long COVID

Long COVID: An approach to clinical assessment and management in primary care

Long COVID is an emerging public health threat, following swiftly behind the surges of acute infection over the course of the COVID-19 pandemic. It is estimated that there are already approximately 100 million people suffering from Long COVID globally, 0.5 million of whom are South African, and for whom our incomplete understanding of the condition has forestalled appropriate diagnosis and clinical care. There are several leading postulates for the complex, multi-mechanistic pathogenesis of Long COVID. Patients with Long COVID may present with a diversity of clinical phenotypes, often with significant overlap, which may exhibit temporal heterogeneity and evolution. Post-acute care follow-up, targeted screening, diagnosis, a broad initial assessment and more directed subsequent assessments are necessary at the primary care level. Symptomatic treatment, self-management and rehabilitation are the mainstays of clinical care for Long COVID. However, evidence-based pharmacological interventions for the prevention and treatment of Long COVID are beginning to emerge. This article presents a rational approach for assessing and managing patients with Long COVID in the primary care setting

Long COVID: a review and proposed visualization of the complexity of long COVID

: Post-Acute Sequelae of Severe Acute Respiratory Syndrome Coronavirus - 2 (SARS-CoV-2) infection, or Long COVID, is a prevailing second pandemic with nearly 100 million affected individuals globally and counting. We propose a visual description of the complexity of Long COVID and its pathogenesis that can be used by researchers, clinicians, and public health officials to guide the global effort toward an improved understanding of Long COVID and the eventual mechanism-based provision of care to afflicted patients. The proposed visualization or framework for Long COVID should be an evidence-based, dynamic, modular, and systems-level approach to the condition. Furthermore, with further research such a framework could establish the strength of the relationships between pre-existing conditions (or risk factors), biological mechanisms, and resulting clinical phenotypes and outcomes of Long COVID. Notwithstanding the significant contribution that disparities in access to care and social determinants of health have on outcomes and disease course of long COVID, our model focuses primarily on biological mechanisms. Accordingly, the proposed visualization sets out to guide scientific, clinical, and public health efforts to better understand and abrogate the health burden imposed by long COVID

Understanding the Hsp90 N-Terminal Dynamics: Structural and Molecular Insights into the Therapeutic Activities of Anticancer Inhibitors Radicicol (RD) and Radicicol Derivative (NVP-YUA922)

Heat shock protein 90 (Hsp90) is a crucial component in carcinogenesis and serves as a molecular chaperone that facilitates protein maturation whilst protecting cells against temperature-induced stress. The function of Hsp90 is highly dependent on adenosine triphosphate (ATP) binding to the N-terminal domain of the protein. Thus, inhibition through displacement of ATP by means of competitive binding with a suitable organic molecule is considered an attractive topic in cancer research. Radicicol (RD) and its derivative, resorcinylic isoxazole amine NVP-AUY922 (NVP), have shown promising pharmacodynamics against Hsp90 activity. To date, the underlying binding mechanism of RD and NVP has not yet been investigated. In this study, we provide a comprehensive understanding of the binding mechanism of RD and NVP, from an atomistic perspective. Density functional theory (DFT) calculations enabled the analyses of the compounds’ electronic properties and results obtained proved to be significant in which NVP was predicted to be more favorable with solvation free energy value of −23.3 kcal/mol and highest stability energy of 75.5 kcal/mol for a major atomic delocalization. Molecular dynamic (MD) analysis revealed NVP bound to Hsp90 (NT-NVP) is more stable in comparison to RD (NT-RD). The Hsp90 protein exhibited a greater binding affinity for NT-NVP (−49.4 ± 3.9 kcal/mol) relative to NT-RD (−28.9 ± 4.5 kcal/mol). The key residues influential in this interaction are Gly 97, Asp 93 and Thr 184. These findings provide valuable insights into the Hsp90 dynamics and will serve as a guide for the design of potent novel inhibitors for cancer treatment