Academic History: I completed my PhD in the Department of Biochemistry, UCT in 2001. My Doctoral training as a molecular cell biologist was under the supervision of Prof Lutz Thilo (an international expert in the field of cellular membrane traffic at UCT), and dealt with the identification of factors required for specific fusogenic events along the endocytic and phagocytic pathways with relevance to the pathogen Mycobacterium tuberculosis (M.tb). After completing my PhD I became interested in plant biotechnology specifically in studying drought tolerance and the generation of drought tolerant crops. I then applied to for a hotly contested international postdoctoral fellowship funded by Atlantic philanthropies foundation based in Ireland. I was successfully appointed as a Postdoctoral fellow in the Department of Molecular and Cellular Biology at the University of Cape Town in July 2001.

I generated the first Genomic library of Xerophyta Viscosa Baker that was probed for all known abiotic stress related genes to determine their sequences for further gene expression studies to determine their relevance in drought resistance. The Genomic Library served as a template for numerous other research projects. Thereafter, I constructed a full-length cDNA library from RNA extracted from dehydrated leaves of Xerophyta viscosa. Individual clones (9000) were amplified and purified and spotted onto microarray slides.

In 2003 I was awarded a postdoctoral fellowship in the lab of Prof. Malcolm Bennett in the School of Biosciences, University of Nottingham, UK. There I performed a dehydration stress analysis on Arabidopsis thaliana plants, and specific genes were identified as up or down regulated upon dehydration stress. Unfortunately this research was prematurely halted when I returned to SA in 2004. In 2015 I moved to the Plant Sciences Department at University of the Western Cape and was awarded the Innovation NRF Postdoctoral Fellowship.

In 2007 I joined the CBTBR at Stellenbosch University as the Research Manager. I started setting up my own research endeavours in tuberculosis that led to the awarding of a Research Grant under the France/SA Scientific Cooperation Agreement in collaboration with Prof. Chantal De Chastellier (International expert in macrophage/mycobacteria electron microscopy). In 2014 as co-investigator with Prof Richard Haynes we investigated artemisinin conjugates as potential antituberculosis drugs. In November 2016 I was appointed as a senior researcher heading my own research group (Host-directed Therapeutics) in the Division of Molecular Biology and Human Genetics.

Research outputs: I have published 34 articles in peer-reviewed journals in the fields of Molecular Biology and have a h-index of 21 and i10-index of 30 on Google Scholar and an h-index of 16 on Scopus. I have also published 1 book chapter. I am also listed with one of my past PhD students on a patent. I obtained a C2 Rating from the NRF in 2020. A patent application for Germany was published on the 4 August 2022 and granted on 14 November 2024.

Reviewing, Committee Membership and Mentoring: I have reviewed funding applications for the National Research Foundation (NRF), and have examined multiple PhD and MSc theses. I have Reviewed research articles for Nature Publishing Group Scientific Reports; American Chemical Society Infectious Diseases; Emerging Microbes and Infection etc. Further, I have been a Grant Selection Committee Member for Funding applications from The Association of Commonwealth Universities. I also served as a Stellenbosch University ECAD Masters, PhD and Postdoctoral program. Currently I also serve on the HREC committee of the faculty and serve on several PhD Committees.

Research highlights: In the past 7 years, the Host-directed therapeutics (HDTs) group published 27 articles in peer-reviewed journals with three broad research focus areas to expedite discovery of new treatments for tuberculosis on all fronts. My research covers i) Repurposing of existing drugs for the treatment of tuberculosis ii) Identifying novel targets in M.tuberculosis for the development of direct antituberculosis drugs and iii) Identifying novel targets in host macrophages to develop host-directed therapeutics.

The HDTs team have made meaningful contributions to the discovery of new and re-purposed drugs with antimycobacterial activity. I was first to show that sulfamethoxazole (SMX) synergises with the first-line drug rifampicin and was not antagonistic with other first-line drugs, indicating the potential use of SMX as part of the existing antitubercular regimen to treat tuberculosis and further proteomic analysis revealed that sulfamethoxazole Induces oxidative stress in M. tuberculosis. This work was published published in Tuberculosis (IF: 3.13) currently with 13 citations and JAC (IF: 5.22) currently with 34 citations.

We have also shown the antimycobacterial activity of novel compounds such as furanone derivatives, formononetin and flavones and chalcones from plants endemic to South Africa. This work was published in Bioorganic and Medicinal Chemistry Letters (IF: 2.82) currently with 36 citations in 2015 and IUBMB Life (IF: 3.89) in 2016 currently with 14 citations.

We have demonstrated that some artemisins are active against M.tb, a project in collaboration with North-West University on the MRC Flagship MalTB Redox project. In this project, Artemisinins effective against malaria disease are evaluated for their efficacy against M.tb as it was observed before that antimalarial drugs also exert some activity against M.tb bacilli. We have demonstrated that artemisinin-cholesterol do show significant effectiveness against strains of M.tb and in contrast to artemether, the conjugates display enhanced activities. This was published in ChemMedChem in 2018 (IF: 3.47) currently with 14 citations. 

In collaboration with Dr. Chibale we have also shown that reversed isoniazid agents have improved antimycobacterial activity. This data was published in Bioorganic & Medicinal Chemistry in 2018 (IF: 3.64) currently with 8 citations.

We examined the effects the anti-cancer agent elesclomol on M.tb. since the innate immune system employs copper to eliminate bacterial infection and that resistance to copper enhances the virulence of M.tb. As a bis-thionohydrazide, elesclomol chelates with copper to form a copper complex in situ that via redox cycling of the metal ion greatly enhances oxidative stress in tumour cells. We demonstrated that elesclomol is relatively potent against M.tb H37Rv and against multidrug resistant clinical isolates of M.tb, displays additive interactions with known tuberculosis drugs such as isoniazid and ethambutol, and a synergistic interaction with rifampicin. Controlled supplementation of elesclomol with copper in culture medium increased M.tb sensitivity by >65 fold. Overall, the activities of elesclomol in principle indicate the possibility of repurposing elesclomol or designing new thionohydrazides as potential antituberculosis drugs. This work was published in IUBMB Life in 2019 (IF: 3.89) currently with 19 citations.

We also investigated unique metabolic pathways in M.tb through state-of-the-art proteomic and metabolomic analyses and generating specific M.tb mutants to evaluate potential targets for drug intervention. Enzymes of the mycothiol and ergothioneine biosynthetic pathways are targets of choice not only because they are unique to mycobacteria but also because it protects mycobacteria against reactive oxygen species. The ergothioneine deficient M.smegmatis single mutant (^egtD) and mycothiol deficient single mutant (^mshA) were slightly sensitive to oxidative stress conditions generated by cumene hydroperoxide relativel to the wild type, while the double mutant (^mshA/egtD) was significantly affected. As opposed to mycothiol, we demonstrated that ergothioneine is secreted. This work was published in Antimicrobial Agents Chemotherapy in 2013 (IF: 5.19) currently with 70 citations.

M.tb mutants have been generated and we determined that the ERG-deficient egtB mutant which accumulated gamma-glutamylcysteine (GGC) was more resistant to oxidative and nitrosative stress than the ERG-deficient, GGC-deficient egtA mutant. This implicates GGC in the detoxification of reactive oxygen and nitrogen species in M.tb, and compensatory anti-oxidative role of ergothioneine, mycothiol and GGC in mycobacteria. Further we screened a library of compounds for blocking activity towards the enzymes of the ergothioneine pathway. This work was published in Antimicrobial Agents Chemotherapy in 2018 (IF: 5.19) currently with 13 citations and Biochemical Biophysical Research Communications in 2018 (IF; 3.57) currently with 29 citations.

We expanded our scope to research the host-response. We set out to identify factors involved in the survival of mycobacteria in mouse and human macrophages employing transcriptomics and proteomics, and then investigating these targets in infection models with the long-term aim of developing novel host-directed therapeutics for tuberculosis. In the past, researchers have carried out numerous investigations on macrophages infected with mycobacterial strains that have been cultured in the presence of detergents such as Tween-80. In 2016, my team was one of the first research groups to employ mycobacteria uniquely cultured and filtered in the absence of detergent to perform a global RNA-seq gene expression analysis on mouse bone marrow-derived macrophages. This revealed a robust response when detergent-free mycobacteria were used as compared to mycobacteria cultured in the presence of Tween-80. This work was published in PLoS One in 2016 (IF: 3,24) currently with 34 citations.

In an attempt to better understand the underlying mechanism of detergent alterations, we investigated the effect of Tween 80 on the metabolomes of the M.tb lab strain (H37Rv) and multidrug-resistant clinical strain (R179), using GC-GCxTOF-MS metabolomics. The metabolite markers identified indicated Tween 80-induced disparities in the central carbon metabolism of both strains, with an upregulation in the glyoxylate cycle, glucogenogenesis and the pentose phosphate pathway. The results also signified an increased production of mycobacterial biosynthetic precursors such as triacylglycerols, proteinogenic amino acids and nucleotide precursors, in the presence of the detergent. Collectively, these metabolome variations mimic the phenotypic changes observed when M.tb is grown in vivo, in a lipid rich environment. This study is the first to identify specific metabolome variations related to the addition of Tween 80 to the growth media during M.tb culturing. This work was published in J. Microbiol. Methods in 2019 (IF: 2.28) currently with 9 citations. We further showed that the macrophage response to hypo- and hyper-virulent clinical mycobacterial strains differed dramatically and identified host candidate genes potentially related to hypervirulence, This work was published in Virulence in 2017 (IF: 5.54) currently with 22 citations.

We then followed up these high throughput assays and investigated the role of top differentially expressed genes in the killing of mycobacteria in macrophages. We employed siRNA knock down and vector based induced expression of these genes to demonstrate their individual contribution. We demonstrated that OAS1, OAS2, OAS3 and OASL are involved in the killing of mycobacteria in THP-1 macrophages. This work was published in International Journal of Infectious Diseases in 2019 (IF: 3.62) currently with 31 citations, Molecular Immunology in 2019 (IF: 4.41) currently with 10 citations and Frontiers in Cellular and Infection Microbiology (IF: 4.30) currently with 33 citations.

Further, we conducted a global transcriptomic analysis of human blood monocyte derived macrophages infected with pathogenic and non-pathogenic mycobacteria. Differentially expressed genes were validated through qPCR and Western blots. Vector-based overexpression of the genes IFIT1, IFIT2 and IFIT3 resulted in increased killing of M.tb identifying them as targets for the development of host-directed therapeutics for the treatment of tuberculosis, published in Virulence in 2020 (IF: 4.77) with 8 Citations; and in Frontiers in Cellular and Infection Microbiology (IF:4.30) and Journal of Interferon & Cytokine Research (IF:3.70). An International patent application number PCT/IB2020/059466 in the name of Stellenbosch University entitled “IFIT Polypeptides and Uses for Treating Tuberculosis Infection” has been published on 15 April 2021 by the International Bureau of WIPO with Publication number WO 2021/070107 A1”. Inventors: Bienyameen Baker, Abhilasha Mishra. The National Phase applications In South Africa, USA and Germany was initiated on 13 April 2022. The patent application for Germany was published on the 4 August 2022 and granted on 14 November 2024.