Converting natural product leads into structure- and ligand-based drug discovery campaigns against leishmaniasis and Chagas' disease

The neglected parasitic diseases, visceral leishmaniasis (VL), and Chagas' disease (CD), together cause an estimated 50,000 deaths annually world-wide. Most of the people affected by these terrible diseases are amongst the poorest members of society and often live in remote rural areas. Despite this death toll, the current treatments available are inadequate for many reasons. These problems include side effects, compounds not working very effectively, resistance to current drugs and the requirement for intravenous administration or repeated injections which are not suitable for the rural environments where these diseases are typically found. Consequently, the development of new, effective and safe oral drugs provides an opportunity to save many lives and improve the quality of life for whole regions of the developing world, through the reduction of the morbidity, mortality and the economic consequences of these diseases. Unfortunately there are very few compounds being developed for VL and CD.

In this proposal we aim to identify potential new targets for drug discovery programmes. These are typically enzymes, which are vital to the life of the parasites that cause the diseases. We aim to identify these start points by testing natural products against the parasites. For those natural products that kill the parasites, we will then find out how the compounds are killing the parasites. Natural products are chemical compounds that are found from natural sources, such as plants and bacteria. They often have unique chemical structures, that have not been made before by humans and are difficult to make synthetically. Therefore they provide good tools to identify potential drug targets that often would not be found by other means. Once we have identified the molecular target (enzymes) we can then carry out a drug discovery programme, either by using these natural products as starting points or using conventional drug discovery approaches to find inhibitors of the enzyme and then optimise them into potential drugs.

An established, fully integrated team comprised of the University of Dundee and University of São Paulo, São Carlos brings together the broad range of expertise required to discover these much needed drugs. The team combines natural product expertise, world renowned parasitology, expertise in identifying the modes of action of compounds in these parasites, extensive experience developing molecules that can kill the parasites, and the substantial expertise and infrastructure required to develop drug candidates suitable for progress toward clinical trials.

The development of new drugs for the treatment of kinetoplastid diseases is hampered by a lack of validated drug targets, and insufficient understanding of basic parasite biology. Here, we intend to leverage the more diverse chemistry available in natural product (NP) compounds active against Leishmania donovani and/or Trypanosoma cruzi to elucidate the MoA and enable initiation of novel structure based small molecule drug discovery programmes. Our approach to defining MoA utilizes a combination of established and novel techniques. These include:
1. High-throughput genetics: We will utilise our genome-wide RNAi library (RITseq) in T. brucei alongside our genome-scale overexpression libraries in T. brucei, L. donovani and T. cruzi. These global knock-down and overexpression methodologies enable us to rapidly assess virtually every gene in the parasite genome for their potential role(s) in resistance to the compounds we are screening. Specifically, we will identify genes, that when their levels are modulated (up or down), can confer compound resistance. We will also generate cell-lines that are resistant to our NPs in vitro. The resulting drug-resistant clones will be assessed by whole-genome sequencing to identify genomic changes responsible for resistance.
2. Cellular: We have developed a number of genetically modified parasite cell lines that enable us to report on specific cell and organellar functions (proteasome, glycosome) affected by our NPs. We also use a number of established reagents, e.g. MitoTracker, redox-active reporters. In a broad sense, these cell-based approaches provide an early and broad indication of the potential MoA our NPs.
3. Chemical proteomics: Our sophisticated mass spectrometry-based quantitative proteomics techniques allow us to directly identify proteins that selectively bind to bioactive compounds. Specific approaches that will be utilized include thermal shift proteomics (CETSA) and SILAC-facilitated pulldowns.

Societal Impact:
The World Health Organization (WHO) has produced overwhelming evidence to show that the burden caused by many of the 17 neglected tropical diseases that affect more than 1 billion people worldwide can be effectively controlled and, in many cases, eliminated or even eradicated. This project aims to lift one of the barriers to effective drug discovery for visceral leishmaniasis (VL) and Chagas' disease (CD) through identification of well validated targets and thus help find new and more effective therapies to treat 2 of these 17 diseases; VL and CD that affect millions of people worldwide and cause an estimated 50,000 deaths annually. New treatments for either of these diseases would have a major impact on the health of millions of people.

Economic Impact:
The impact of neglected diseases, such as VL and CD, is also an economic one, impacting on the economic development of countries. This is due to loss of earnings and productivity due to ill-health. Unfortunately, the people affected by such diseases often cannot afford medicines to treat these diseases. Therefore it is important that the cost of goods for new drugs for these diseases is as low as possible. There is little or no commercial motivation or opportunity for profitability associated with the research and development for improved drug therapies for these diseases. Therefore, new affordable drugs to treat these diseases will have a huge impact on the economic prosperity of disease endemic areas, positively benefiting many millions of people.

Scientific Impact:
This UK-Brazil partnership will expand and enhance the scientific knowledge on the effective drug development opportunities for these neglected parasitic diseases. It aims to deliver new drug targets and novel compounds effective in the treatment of VL and/ or CD. Treatment of these diseases is dependent on very few, poorly tolerated drugs. Resistance is a real concern as is poor efficacy with current treatment options, particularly for chronic CD.

The data and knowledge that are generated during this project will also be important to un-ravel the basic biology of these parasites. New understanding of pathways and identification of potential new drug targets will arise from investigative mode of action work in this project. This knowledge will be made available to the wider community through publication and presentation at key meetings.

This project forms a powerful platform to drive translational research between the UK and Brazil, fueling the drug discovery pipeline against an important public health threat in Brazil. The partners will benefit from important transfer of technology and expertise in various aspects of kinetoplastid drug discovery. Building a strong working relationship between the two centres in the UK and Brazil through this project will, going forward, further benefit the two centres through future exchange of students and additional project development.