Keystone Symposia “Malaria: Confronting Challenges from Drug Discovery to Treatment” – 2022: Day 1

MESA Correspondents bring you cutting-edge coverage from the Keystone Symposia 2022 “Malaria: Confronting Challenges from Drug Discovery to Treatment”

Day 1: Monday, 11th April 2022

Welcome & Keynote Address

David A. Fidock from Columbia University Medical Center, USA, opened the Malaria Keystone Symposia 2022 by expressing his pleasure to take part in the conference. He warmly welcomed 145 people attending in person, 60 attendees participating virtually and around 70 speakers. Furthermore, he thanked the co-organizers of the conference including Elizabeth A. Ashley (Lao-Oxford-Mahosot Hospital – Wellcome Trust Research Unit, Lao) and Kelly Chibale (University of Cape Town, South Africa) for putting together all the hard work. Finally, he introduced the keynote speaker Arjen M. Dondorp.

Arjen M. Dondorp (University of Oxford, Thailand) summarized the evolution over the last decade of artemisinin and Artemisinin Combination Therapy (ACT) partner drug resistance in P. falciparum in the Greater Mekong Subregion of SE Asia, and the components of the highly successful malaria elimination program in the GMS, which was initiated 10 years ago to contain the resistance problem. The experience from the GMS was discussed in the context of the recent independent emergence and spread of artemisinin resistance in Rwanda and Uganda. Artemisinin partial resistance contributes to decreased ACT efficacy, but also facilitates the selection of ACT partner drug resistance, which has caused high treatment failure of a number of ACTs in the GMS. Artemisinin resistance is mainly confined to the ring stage asexual parasite, although also schizont stage parasites show decreased susceptibility. In addition, artemisinin resistant infections show higher gametocyte carriage and reduced artemisinin sensitivity of male gametocytes, contributing to increased transmissibility. In the GMS, a successful malaria elimination program was initiated 10 years ago to contain the resistance problem. Its cornerstone is a well-organized network of village malaria workers for early diagnosis and treatment of malaria, supplemented with additional interventions such as mass drug administration in target populations. Epidemiological surveillance is another important component of the program, including genetic surveillance. Single gametocytocidal low-dose of primaquine reduces transmission of drug resistant parasites, and is also safe to use in African children, independent of the G6PD status of the patient. New drugs will be needed to treat multidrug resistant falciparum malaria, but these are not expected to come to the market within 5 years. An important approach using existing drugs are Triple ACTs, combining the artemisinin component with two well-matched partner drugs. In clinical trials these have shown to be safe, well-tolerated and efficacious also against drug resistant parasites. The artemether-lumefantrine-amodiaquine combination is now being developed as a fixed dose combination, which could also be important for Africa to, in addition to improved antimalarial stewardship, delay the further spread of artemisinin resistance and protect the current ACTs.

Session 1: Innovations in Antimalarial Drug Discoveries

Elizabeth A. Winzeler (University of California, USA) began the talk by giving an introduction to the evolution of antimalarial drug discovery which includes pharmacophore-based discovery, phenotypic screening, and structure-guided drug design. The structure-guided drug discovery is more sophisticated and efficient, compared to the previous strategies. She further highlighted that combining reverse chemical genetic methods with chemical screening can yield highly validated targets such as lysyl-tRNA synthetase. She introduced the Malaria Drug Accelerator (MalDA) consortium  that  collaborates with international groups to build up a pipeline for structure-guided drug discovery. MalDA also uses in vitro evolution and whole-genome analysis or IVIEWGA to discover clinically-relevant resistance genes. Recently, the MalDA website has been updated with a resistance database, which is useful for predicting association between phenotype and observed mutations. Winzeler also proposed the use of other species, such as yeast (Saccharomyces cerevisiae), as a model for identifying the targets of  antimalarial compounds. For future work, it is important to understand how drug resistance in the malaria parasites arise and how to prevent it.

Jacquin Niles (Massachusetts Institute of Technology, USA) shared that his laboratory is interested in establishing genetic technologies for drug discovery and target validation. Currently, there are relatively few compounds with novel mechanisms of action in the development pipeline. He described the use of conditional gene expression perturbation approaches for target validation and inhibitor discovery. In this approach, the target gene is modified using CRISPR-Cas9 genome editing to generate parasite lines that enable tunable expression of essential proteins of interest. When expression of a protein of interest decreases, this can lead to hypersensitivity to compounds targeting the protein. A rapid phenotypic screening is invented and tested with aminoacyl-tRNA synthetases (aaRSs), important enzymes in protein translation. This lead to discovery of several compounds that hit aaRSs. Niles proposes that the future work is to use his strategy to validate the biological function of genes and to discover potential antimalarials.

Susan Willye (University of Dundee, UK) started her talk by highlighting some factors hampering drug discovery programs required to combat parasitic disease such as few robustly validated drug targets within the pathogens that cause these infections thus leaving our drug discovery programs relying heavily upon phenotypic screening. She then presented target deconvolution studies as a solution to address those challenges. She presented a matrix of new methodologies in use in her lab,  including high throughput genetics, cell biology, biochemical assays, and chemical proteomics that increases the chances to understand the mode of action of compounds and identify molecular targets. She emphasized using multiple methodologies in  concert for identifying and validating molecular targets. Wylie’s team is currently in building a toolkit to support identification of molecular targets of antimalarial drugs which includes a genome-wide cosmid-based overexpression library in P. knowlesi, high throughput in vitro translation assays for P. falciparum and adapted chemical proteomic strategies for P. falciparum. Their mode of action studies currently use various strategies including chemical proteomics strategies, chemical pulldown, and thermal proteome profiling (TPP), thus providing critical information to drug-discovery programmes.

Jerzy Michal Dziekan (Nanyang technological University, Singapore) focused his talk on mapping the druggable landscape of malaria parasites using thermal proteome profiling. He gave an overview of  the MS-CETSA-Cellular Thermal Shift assay as a tool for antimalarial drug-target deconvolution. His work evaluated a library of antimalarial compounds to identify interactions with Plasmodium proteins. Dzieken used cellular thermal shift assays to identify compound-target interactions. He presented a wide range of new interactions between a  range  of antimalarial compounds and Plasmodium proteins,  which excitingly sets the stage for additional functional validation via orthogonal  approaches..

Alison E. Roth (Walter Reed Army Institute of Research, USA) and her lab with the aim of identifying novel antimalarial compounds measurable to tafenoquine and to accelerate drug discovery, developed P. cynomolgi assay for identifying compounds targeting hypnozoite stage of the parasites. The assay also incorporates high-throughput data pipeline for data analysis. This approach has been used to screen a large number of compound libraries. Another approach is artificial intelligence (AI) is being developed to accelerate the identification of anti-hypnozoite compounds.  Lastly, Alison pointed out that collaborations are key for success.

Session 2 : Advancing Drug Discovery Efforts

Jeremy Burrows (Medicine of Malaria Venture – MMV, Switzerland) began his talk by giving an overview of malaria case management which is dominated by artemisinin combination therapies (ACTs). ACTs are still working in Africa but there is a risk of resistance because of the spread of de novo artemisinin resistant K13 mutations. For seasonal malaria chemoprevention, sulphadoxine-pyrimethamine-amodiaquine is approved for use in 0-5 year children. Burrows described the target product profile (TPP) for new antimalarials and presented a strategy that covers case management, prophylaxis, severe malaria management, and a radical cure for relapsing P. vivax malaria. MMV and partners have developed several assays to facilitate drug discovery. Examples of these assays include liver, blood and gametocyte stages, as well as humanised mouse model for P. falciparum infections.  MMV with its partners have delivered 34 candidate drugs over the last 15 years.  The four strategies used to discover these have included inspiration from natural products, delivering back-up compounds that address liabilities of compounds in the clinical portfolio,  phenotypic screening and target based approaches. Lastly, Burrows outlined some challenges for antimalarial drug discovery, one of the most important is antimalarial resistance; a newly developed resistance risk assessment is used to aid prioritization and to influence the combination strategy.

Laura Sanz (GlaxoSmithKline – GSK, Spain) presented the approaches adopted by GSK to fight malaria disease: treatment, prevention and vector control. She focused on treatment and mentioned  antimalarial therapeutic requirements: safety, efficacity, oral administration, drug resilience against antimalarial resistance combination therapies, and the development of new regimens . She introduced a novel drug for treatment of malaria, GSK701 (MMV1582367), as a potential drug to replace artemisinin in combination therapies. This is a fast-acting antimalarial, with anticipated low propensity to select for parasite resistance. Toxicological studies have shown it is safe, and GSK701 acts through a novel antimalarial mechanism of action.

Kelly Chibale (University of CapeTown, South Africa) described how, using genomic and chemoproteomics, several chemotypes targeting P. falciparum kinases have been discovered. Even though there is concern about the toxicity of inhibitors targeting protein kinases, the phylogenetic differences between human and malarial parasite kinases suggest selectivity can be achieved. Chibale proposed a very efficient drug repurposing strategy that uses clinically characterized human kinase inhibitors for antimalarial discovery. The benefit of repurposing drugs is that these drugs have been previously studied in clinical trials in humans for safety and tolerance. However, the key challenge is to minimize off-target activity against human kinases.

Andrew B. Tobin (University of Glasgow, UK) dived into the details of protein kinases as antimalarial targets, focussing on his team’s work on kinase inhibitors. Using biochemical and genetic validation, his team identified PfCLK3 as a promising target.  A promising compound (TCMDC-135051) which inhibits PfCLK3 is currently undergoing chemical optimization. PfCLK3 is involved in RNA splicing and is therefore essential for the parasite survival in liver stage, blood stage, and gametocyte stage.

Didier Jean Leroy (Medicine of Malaria Venture – MMV, Switzerland) presented on orthology-based screening performed to obtain the MMV68853 antimalarial candidate. This is a fast killer compound which has shown efficacious exposure in humanized mice infected with P. falciparum. It is highly potent on early rings to late trophozoites, and selects for low-grade resistance via mutations in PfACG1 and PfEHD. Mutations in PfACG1 and PfEHD do not confer cross resistance with antimalarials, and PfACG1 and PfEHD are localized mainly to distinct intracellular parasite vesicles. Its target is still elusive, and the mode of action is being studied. The fast killer antimalarial candidate, MMV68853, almost as fast-acting as artemisinin, is currently in the phase I clinical trial.

This report is brought to you by the MESA Correspondents Patricia Doumbe Belisse, Nutpakal Ketprasit and Samuel Blankson. Senior editorial support has been facilitated by the Chairs and Speakers of the session.