Biology subjects

Kumalo, H. M.

Publications and source records attributed to Kumalo, H. M..

6 recordsLinked to original sources

bioRxiv2026

Drug Repurposing: A Potential Therapeutic Strategy for the Treatment of Chikugunya Virus

Chikungunya virus (CHIKV) infection is one of the major public health concerns in several countries around the world. CHIKV non-structural protein 2 (nsP2) is a promising drug design target due to the enzymes multifunctional properties that facilities viral replication and propagation. To date, there is an evident lack of preventative and therapeutic developments that can be used against CHIKV. Drug repurposing is a time saving and cost-effective method used for the development of new drugs. In this study, drug repurposing was implemented with the use of HIV/HCV protease inhibitors to inhibit the active site of nsP2. Molecular dynamics simulations and analysis revealed the stability of two drugs, Indinavir and Paritaprevir. Indinavir forms a hydrogen bond with a major residue, which closes the flexible loop, situated in close proximity to the active site. This conformational shift in the orientation of the enzyme prevents accessibility to the active site thus disrupting the nsP2 protein from functioning effectively in viral replication. In conclusion, the findings of this study identified Indinavir was identified as a promising CHIKV nsP2 inhibitor. This study will provide the basis to further facilitate the drug repurposing strategy as an alternative approach for drug design of CHIKV inhibitors as well as other viral families.

bioinformatics↗

bioRxiv2022

Molecular Dynamic Investigation of H5N1 Influenza Virus Dual H274Y-I222K Mutation Resistance to Peramivir

In light of the rapid rise of an influenza pandemic, the constant genetic mutations of H5N1 influenza viruses pose a threat. Mutations at the sialic site are often responsible for multiple drug resistance. To design effective new inhibitors, it is necessary to undertake research into the mechanism of resistance of influenza viruses and their rapid mutations. The molecular dynamic simulation technique has been an instrumental tool in understanding how proteins function from an atomic perspective. A thorough investigation has not been conducted using molecular dynamics to examine the impact of these mutations (I222K, H274Y, and H274Y-I222K) on Peramivir. This study investigates the effects of I222K, H274Y, H274Y-I222K substitution on the neuraminidase-Peramivir complex and identifies responsible residues for complex conformations. The mutations caused distorted Peramivir orientation in the enzyme active site, which affected the inhibitors binding. In the presence of various mutations, interaction between protein and ligand became less thermodynamically favorable. We observed the following trend in binding free energy difference: WT<I222<H274Y<H274Y-I222K. As a result of the thermodynamic instability of the mutant complexes, Peramivirs potency is reduced due to impaired binding interactions. Wild type complex displays thermodynamic stability and strong protein-ligand interactions due to their high total energy contributions and low residue flexibility. Based on the energy decomposition analysis, Arg117, Arg224, and Arg292 contributed the largest residual energy for the binding of Peramivir to wild type and mutants. These residues are thought to play a key role in the formation of the binding pocket between Peramivir and neuraminidase. This study provides a basis for investigating the effects of other mutations on Peramivirs efficacy against the H5N1 virus.

bioinformatics↗

bioRxiv2022

A molecular dynamic investigation of Human Rhinovirus 3C Protease Drug Target: Insights towards the design of potential Inhibitors

The 3C protease is distinguished from most proteases due to the presence of cysteine nucleophile that plays an essential role in viral replication. This peculiar structure encompassed with its role in viral replication has promoted 3C protease as an interesting target for therapeutic agents in the treatment of diseases caused by human rhinovirus (HRV). Herein we present a comprehensive molecular dynamics study of the comparison of two potent inhibitors, sg85 and rupintrivir complexed with HRV-3C protease. The binding free energy studies revealed a higher binding affinity for sg85 -58.853 kcal/mol than for rupintrivir -54.0873 kcal/mol and this was found to be in correlation with the experimental data. The energy decomposition analysis showed that, residues Leu 127, Thr 142, Ser 144, Gly 145, Tyr 146, Cys 147, His 161, Val 162, Gly 163, Gly 164, Asn 165, Phe 170 largely contributed to the binding of sg85, whereas His 40, Leu 127 and Gly 163 impacted the binding of rupintrivir. It further showed that His 40, Glu 71, Leu 127, Cys 147 Gly 163 and Gyl 164 are crucial residues that play a key role in ligand-enzyme binding; amongst these residues are residues of the conserved active site (His 40, Glu 71 and Cys 147). These findings provide a comprehensive understanding of the dynamics and structural features and will serve as guidance in the design and development of potent novel inhibitors of HRV. Graphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioinformatics↗

bioRxiv2022

Molecular mechanisms underlying Warburgia salutaris effects on oxidative stress and apoptotic parameters in Human Hepatoma Cells

This study aims to determine the molecular effects of Warburgia salutaris extract in HepG2 cells and elucidate the possible mechanisms. The MTT assay was employed to determine cell viability and the half maximal inhibitory concentration (IC50) of Warburgia salutaris-treated in HepG2 cells (0-5mg/ml). Extracellular lactate dehydrogenase and ATP were also quantified as a measure of cell viability. The production of reactive oxygen species (ROS) was assessed by quantifying lipid peroxidation and oxidative DNA damage, and reactive nitrogen species (RNS) in treated HepG2 cells. The cells response to free radicals was assessed by measuring GSH. Stress response antioxidant and apoptotic markers were detected using western blotting and /or qPCR. Cell death parameters assayed included annexin V, caspase activity and necrosis. Single-cell gel electrophoresis (SCGE) was used to visualise DNA damage in the HepG2 cells and confirmed with DNA fragmentation assay. The Hoechst assay allowed the visualisation of the nucleus to assess cell growth and apoptosis. Decreased cell viability was associated with a decreased level of ATP. The presence of oxidative stress was suggested by increased HSP70 and Nrf2 protein expression and confirmed by increase ROS, RNS, GPx and catalase; and a corresponding decrease of SOD2 and glutathione. Caspase 8 showed no significant difference between treatment concentrations, caspase 9 was decreased and caspase 3/7 increased. A reduction in p53 correlated with chromatin changes, increase in comet lengths and DNA fragmentation. NF{kappa}B protein was significantly decreased at the IC50, along with decreased cMyc protein expression. Our findings shows that Warburgia salutaris promotes apoptosis by inducing oxidative stress in HepG2 cells and may be a potential anti-cancer agent that would serve as an alternative to conventional therapeutic agents.

biochemistry↗

bioRxiv2018

In Vitro Potentiation of Carbapenems with Tannic Acid Against Carbapenemase Producing Enterobacteriaceae: Exploring Natural Products as Potential Carbapenemase Inhibitors

Resistance to antibiotics is increasing worldwide, necessitating urgent action to sustain the efficacy of existing antibiotics in clinical use. We show that tannic acid (TA) in combination with carbapenems can reduce and/or reverse the minimum inhibitory concentrations (MICs) of carbapenems to susceptible values in Enterobacteriaceae that express class A and B carbapenemases. MICs of carbapenems in the presence and absence of TA and other efflux pump inhibitors, TA-carbapenemases inhibition assays and computational studies were undertaken to determine the effect of TA on carbapenem susceptibility in Enterobacteriaceae. TA had the greatest effect on metallo-{beta}-lactamases (MBLs) followed by class A serine-{beta}-lactamases (SBLs). Antibiotic susceptibility testing showed that TA reversed the MICs of MBLs to susceptible values whilst substantially reducing the MICs of SBLs (class A). Tolerable cytotoxicity effect was observed for the concentrations tested. TA inhibited enzymes with a marked difference between {approx}50% inhibition (IC50) for NDM-1 and KPC-2. Computational studies including molecular docking, molecular dynamics simulations and binding free energy calculations showed that TA interact with both MBLs and SBLs hydrophobic sites. Moreover, TA had a stronger binding affinity for MBLs than SBLs as the MBLs, specifically VIM-1 and NDM-1, interact with a larger number of their catalytic active-site residues than that of OXA- 48 and KPC-2. These in vitro evaluations together with computational simulation explain the potentiating effect of TA toward carbapenems against carbapenem-resistance enterobacteriaceae. This study proposes TA as a promising adjuvant for MBLs and SBLs.

microbiology↗

bioRxiv2018

Evaluation of 1, 4, 7-Triazacyclononane (TACN) as a potential Metallo-B-Lactamase inhibitor in Enterobacteriaceae: Restoring the Activity of B-lactams

Metallo-{beta}-lactamase producing Enterobacteriaceae are of grave clinical concern particularly as there are no Metallo-{beta}-lactamase (MBL) inhibitors approved for clinical use. The discovery and development of MBL inhibitors to restore the efficacy of available {beta}-lactams are thus imperative. We investigated a zinc-chelating moiety, 1, 4, 7-triazacyclononane (TACN) for its inhibitory activity against clinical carbapenem-resistant Enterobacteriaceae. Minimum inhibitory concentrations (MICs), minimum bactericidal concentrations (MBCs), serum effect, fractional inhibitory concentrations index and time-kill kinetics were performed using broth microdilution techniques according to the Clinical Laboratory Standard Institute (CSLI) guidelines. Enzyme kinetic parameters and cytotoxicity effects of TACN were determined using spectrophotometric assays. The interactions of the enzyme-TACN complex were investigated by computational studies. Meropenem regained its activity against carbapenemase-producing Enterobacteriaceae, with the MIC decreasing to 0.03 mg/L in the presence of TACN. TACN-Meropenem combinations showed bactericidal effects with MIC/MBC ratio of [≤]4, and synergistic activity was observed. Human serum effects on the MICs were insignificant, and TACN was found to be non-cytotoxic at concentrations above the MIC values. Computational studies predicted that TACN inhibits MBLs by targeting their catalytic active site pockets. This was supported by its inhibition constant Ki = 0.044 {micro}M and inactivation constant kinact= 0.0406 (min-1) demonstrating that TACN inhibits MBLs efficiently and holds promise as a potential inhibitor.\n\nImportanceCarbapenem-resistant Enterobacteriaceae (CRE)-mediated infections remain a significant public health concern and have been reported as critical in the World Health Organizations Priority Pathogens List for the Research and Development of New Antibiotics. CRE produce enzymes such as Metallo-{beta}-lactamases (MBLs), which inactivate {beta}-lactam antibiotics. Combination therapies involving a {beta}-lactam antibiotic and a {beta}-lactamase inhibitor remain a major treatment option for infections caused by {beta}-lactamase-producing organisms. Currently, no MBL inhibitor-{beta}-lactam combination therapy is clinically available for MBL-positive bacterial infections. Hence, developing efficient molecules capable of inhibiting these enzymes could be a promising way to overcome this phenomenon. TACN played a significant role in the inhibitory activity of the tested molecules against CREs by potentiating the carbapenem. This study demonstrated that TACN inhibits MBLs efficiently and holds promises as a potential MBLs inhibitor to help curb the global health threat posed by MBL-producing CREs.

microbiology↗