K KYEREMEH, Ghana - Development of Novel Therapeutics for Parasite Infections and Cancer by Multi-step Microbial Biodiscovery Processes and iChip

This project seeks to exploit the huge microbial biodiversity of sub-Saharan Africa to create a large library of biosynthetically talented microbes and a pipeline of novel chemical structures that can be used for the development of drugs for infections, cancer and parasitic diseases that are largely endemic to sub-Saharan Africa. The project will take advantage of different well established bioassays in the laboratories of this team to screen the microbial chemical diversity of sub-Saharan microbes. What is most important, is the already well-established ability of members of our team to perform to a very high standard certain functions including: isolation and purification of a large number of free-living microbes from soils, plants, fishes, crabs and carnivorous molluscs; chemical profiling to determine molecules that are produced by these microbes; isolation and characterization of molecules; exploitation of whole microbial genome sequences for biosynthetic gene clusters, bioinformatics, knockout and heterologous expression of silent genes for the production of novel metabolites. The requirement of selective and potent activity is very important in this research and hence low levels of novel microbial chemical structures must be able to kill parasites or bacteria without having an effect on normal human cells. The biological activity profiles of all the molecules obtained in the project will be evaluated into detail giving the possibility for the discovery of new anticancer agents.
We will assemble a total of 300 novel West African microbial strains, isolate, characterize and determine the antibiotic, antiparasitic and anticancer properties of the molecules they express under normal laboratory culture conditions. Most importantly, we will find ways to induce these microbes to express some of the molecules that are not easily produced under normal laboratory conditions by growing them in many customized media and culture conditions, co-culture with co-associating fungi, and presence of chemical cues like nitric oxide known to activate transcription of silent biosynthetic gene clusters. Furthermore, we will use bioinformatics to identify silent gene clusters that encode for potent antibiotic, antiparasitic and anticancer molecules, knockout and heterologously express these genes in easy-to-grow bacteria that allows the production of compounds in sufficient quantities. This project will build on the chemical structures obtained to create a series of derivatives and analogues that are equally active but have different and more improved characteristics as drugs. This will facilitate the identification of a "lead" molecule with potent activity, low toxicity, the ability to be administered safely and ready for testing in animal modules.

Detailed chemical profiling of 150 pre-isolated strains with HRESI-LC-MS of miniaturized crude microbial extracts will be conducted. Using compound molecular ions, fragmentation patterns and UV in combination with different databases new and novel metabolites will be identified to justify the inclusion of each microbe in this project. High-throughput microbial cultivation in situ with the isolation chip (iChip) for additional 150 strains to be isolated and their chemical profile investigated as stated previously. Crude extracts from each microbe will be evaluated in all relevant bioassays under this project. Interesting chemical profile and bioactivity will be characteristic of prioritized strains that will be large scale fermented followed by purification of compounds. Structure determination of the compounds will be achieved through spectroscopy and spectrometry. Test pure compounds in assays and whole genome sequence the source microbes with priority for novel backbones. Prioritized strains cultured in several customized media and culture conditions, co-culture with co-associating fungi, and presence of chemical cues known to activate transcription of silent genes. Already established chemical profile will enable identification of differences in metabolite production in new cultures. Evaluate new extracts to identify novel metabolites which will be isolated and submitted for bioactivity tests. Identify gene clusters responsible for the production of novel metabolites and confirm with knock-out and heterologous expression. Identify silent gene clusters encoding for molecules with antibiotic, antiparasitic and anticancer properties by identification of enzymes in the genomes or the presence of certain well known molecular markers. Followed by genetic manipulation to activate/express endogenous genes or their (re)construction in a form which is suitable for expression and production of compounds in sufficient quantities for structure-activity studies and MOA.

The greatest threat to global health and well-being (Sustainable Development Goal 3) is indeed the development of resistant by various pathogens to currently available drugs. This phenomenon is duly set to unwind every progress achieved so far in medicine. The threat of resistant pathogens is particularly common amongst antibiotics and rightfully so, however, the phenomenon is more serious especially with diseases that currently have a very narrow spectrum of treatment drugs like the neglected tropical diseases (NTD) such as schistosomiasis, trypanosomiasis and leishmaniasis. Sub-Saharan Africa (SSA) records the highest incidence of such diseases and the narrow spectrum of treatments coupled with the development of resistance creates a huge public health issue. The change of life style in SSA has led to an increasing incidence of several non-communicable diseases especially liver, breast and cervical cancer. Hence, the region represents the highest disease burden in Africa and the world. Consequently, the most prudent way to overcome the current burden of disease is to develop a huge pipeline of compounds with novel and sophisticated structures that would provide a platform for the development of new drugs until such a time when the development of resistance is curtailed.
This research is intended to discover new leads for future development of new drugs for microbial, parasitic infections and cancer by taking advantage of the huge microbial biodiversity of SSA and the growing scientific expertise in drug discovery sciences in the region. Previous microbial natural product screening efforts in Ghana have been very successful and we intend to pursue this further in our current proposal.
The significant long term beneficiaries of the project will be the poor, low income people of SSA who have lived with this heavy disease burden for many decades. However, Africa and the rest of the world will also benefit and the health professionals in the health sector who depend on the availability of effective drugs to treat and manage vulnerable patients will also see a transformation of their duties. The journey from lead to drug is a long one but, the current need for new antibiotics and antiparasitics is urgent and we believe the quantum of our discoveries will provide the driving force and generate the necessary interests to propel us to the clinical development stages. The scientific community will also benefit from the knowledge gathered from previously un- or underexplored and uncultivable microorganisms, their biology and chemistry. Undoubtedly, plants and microbes have a huge contribution to current medical practice by virtue of the discovery of artemisinins and avermectins. Discovery of taxol from a plant and subsequent identification in extracts of endophytic fungi shows the potential of nature to yield results with persistent screening efforts. A study of several whole microbial sequenced genomes shows that, only a small fraction of molecules that microbes are capable of producing have so far been characterized. Also, it is a well-known fact that, only about 0.5% of these microbes are currently cultivable under laboratory growth conditions. Hence, a majority of these potent bioactive compounds are still waiting for their discovery to completely revolutionize medicine. Our stepwise approach to discovery in this project is designed to leave no stones unturned to provide leads that are potent, drug-like, selective and highly attractive for further development into drugs. The current perceived relevance of whole microbial genome sequencing to facilitate identification of novel structures will be taken into great account for this project in addition to detailed bioassay, metabolic profiling and heterologous expression studies. This project will also facilitate the complete training of a cohort of young individuals who will take up the task of unlocking the full potential of their own SSA microbial resources.