The protozoan parasite Trypanosoma cruzi causes Chagas disease, which is among the deadliest parasitic infections in Latin America. Current therapies are toxic and lack efficacy against the chronic stage of infection; thus, new drugs are urgently needed. Here, we describe a previously unidentified series of quinazoline compounds with potential against Trypanosoma cruzi and the related trypanosomatid parasites Trypanosoma brucei and Leishmania donovani. We demonstrated partial efficacy of a lead quinazoline compound in a mouse model of acute Chagas disease. Mechanism of action studies using several orthogonal approaches showed that this quinazoline compound series targeted the ATP-binding pocket of T. cruzi lysyl-tRNA synthetase 1 (KRS1). A high-resolution crystal structure of KRS1 bound to the drug indicated binding interactions that led to KRS1 inhibition. Our study identified KRS1 as a druggable target for treating T. cruzi infection in a mouse model. This quinazoline series shows potential for treating Chagas disease but will require further development to become a future treatment for this neglected disease.

Neglected tropical diseases (NTDs) make up a diverse group of debilitating illnesses disproportionately affecting impoverished communities in tropical and subtropical regions. Despite their significant global health burden, they are often overshadowed by more prominent diseases, resulting in a critical lack of investment in the research and development of new treatments. A renewed focus on NTDs is, therefore, urgently needed, particularly in terms of novel therapeutic strategies. The Open Synthesis Network, launched by DNDi and partner institutions in 2016, is an innovation powerhouse that taps into the potential of students to help drive the discovery of new drugs for patients living with NTDs. We present the results of student-led work into the development of a series of aminopyrazoles for Chagas disease, a multisystemic disease caused by the Trypanosoma cruzi parasite. Seventy-four compounds were synthesized by undergraduate and postgraduate students from six universities from Brazil, Ghana, Germany, USA, and UK, illustrating that open innovation and collaboration for education can drive drug discovery forward. Early evaluation of the structure-activity relationships identified a range of potent hit compounds with selectivity for T. cruzi and no observable cytotoxicity.

The fenarimol analogue EPL-BS1246 was previously discovered to be potent against Madurella mycetomatis, the causative agent of the neglected tropical disease mycetoma. Further evaluation of a small set of fenarimol analogues in vivo revealed a correlation between efficacy and the lipophilicity (log D) of the analogues. To explore both this correlation and the series structure-activity relationship (SAR), we have evaluated a total of 185 fenarimol analogues derived from five different daughter chemotypes. Potent (MIC50 < 9 μM) in vitro activity was found for 22 analogues, five of which gave promising results in an in vivo larval survival assay. Again, a trend towards prolonged larval survival (better in vivo activity) was noted in analogues with log D values <2.5. Insights into the SAR could be gleaned that suggested optimal substituents for the rings forming the fenarimol core.

The synthesis of a biologically relevant 2-amino-N3-alkylamido 4-quinazolinone has been accomplished in four steps from commercially available materials using design principles from both modular and divergent synthesis. N3-Alkylation of 2-chloro-4(3H)-quinazolinone using methyl bromoacetate, followed by C2-amination produced a suitable scaffold for introducing molecular diversity. Optimization of alkylation conditions afforded full regioselectivity, enabling exclusive access to the N-alkylated isomer. Subsequent C2-amination using piperidine, pyrrolidine, or diethylamine, followed by amide bond formation using variously substituted phenethylamines, generated fifteen unique 4-quinazolinones bearing C2-amino and N3-alkylamido substituents. These efforts highlight the reciprocal influence of C2 and N3 substitution on functionalization at either position, establish an effective synthetic pathway toward 2,N3-disubstituted 4-quinazolinones, and enable preliminary bioactivity studies while providing an experiential learning opportunity for undergraduate student researchers.

Antimicrobial resistance (AMR) is widely acknowledged as one of the most serious public health threats facing the world, yet the private sector finds it challenging to generate much-needed medicines. As an alternative discovery approach, a small array of diarylimidazoles was screened against the ESKAPE pathogens (https://en.wikipedia.org/wiki/ESKAPE) and the results made publicly available through the Open Source Antibiotics (OSA) consortium (https://github.com/opensourceantibiotics). Of the 18 compounds tested (at 32 μg/mL), 15 showed >90% growth inhibition activity against MRSA alone. In the subsequent hit-to-lead optimization of this chemotype, 147 new heterocyclic compounds containing the diarylimidazole and other core motifs were synthesized, tested against MRSA and structure-activity relationships identified. While potent, these compounds have moderate to high intrinsic clearance and some associated toxicity. The best overall balance of parameters was found with OSA_975, a compound with good potency, solubility and reduced intrinsic clearance in rat hepatocytes. We have progressed towards the knowledge of the molecular target of these phenotypically active compounds, with proteomic techniques suggesting TGFRB1 is potentially involved in the mechanism of action. Further development of these compounds towards antimicrobial medicines is available to anyone under the licensing terms of the project.

Leishmaniasis is a collection of diseases caused by more than 20 Leishmania parasite species that manifest as either visceral, cutaneous, or mucocutaneous leishmaniasis. Despite the significant mortality and morbidity associated with leishmaniasis, it remains a neglected tropical disease. Existing treatments have variable efficacy, significant toxicity, rising resistance, and limited oral bioavailability, which necessitates the development of novel and affordable therapeutics. Here, we report on the continued optimization of a series of imidazopyridines for visceral leishmaniasis and a scaffold hop to a series of substituted 2-(pyridin-2-yl)-6,7-dihydro-5H-pyrrolo[1,2-a]imidazoles with improved absorption, distribution, metabolism, and elimination properties.

Probing multiple proprietary pharmaceutical libraries in parallel via virtual screening allowed rapid expansion of the structure–activity relationship (SAR) around hit compounds with moderate efficacy against Trypanosoma cruzi, the causative agent of Chagas Disease. A potency-improving scaffold hop, followed by elaboration of the SAR via design guided by the output of the phenotypic virtual screening efforts, identified two promising hit compounds 54 and 85, which were profiled further in pharmacokinetic studies and in an in vivo model of T. cruzi infection. Compound 85 demonstrated clear reduction of parasitemia in the in vivo setting, confirming the interest in this series of 2-(pyridin-2-yl)quinazolines as potential anti-trypanosome treatments.

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome.

Computational approaches in drug discovery and development hold great promise, with artificial intelligence methods undergoing widespread contemporary use, but the experimental validation of these new approaches is frequently inadequate. We are initiating Critical Assessment of Computational Hit-finding Experiments (CACHE) as a public benchmarking project that aims to accelerate the development of small molecule hit-finding algorithms by competitive assessment. Compounds will be identified by participants using a wide range of computational methods for dozens of protein targets selected for different types of prediction scenarios, as well as for their potential biological or pharmaceutical relevance. Community-generated predictions will be tested centrally and rigorously in an experimental hub(s), and all data, including the chemical structures of experimentally tested compounds, will be made publicly available without restrictions. The ability of a range of computational approaches to find novel compounds will be evaluated, compared, and published. The overarching goal of CACHE is to accelerate the development of computational chemistry methods by providing rapid and unbiased feedback to those developing methods, with an ancillary and valuable benefit of identifying new compound-protein binding pairs for biologically interesting targets. The initiative builds on the power of crowd sourcing and expands the open science paradigm for drug discovery.

An undergraduate laboratory was developed as part of the Drugs for Neglected Diseases initiative's Open Synthesis Network. This activity aimed to develop new compounds efficacious against visceral leishmaniasis. Students successfully synthesized, purified, and characterized ten different benzoxazole amides that were sent for biological testing against several protozoan parasites. Although all the benzoxazole amides had poor activity against L. donovani, several (2, 4, and 9) showed moderate activity against T. cruzi, T. b. rhodesiense, and T. b. brucei paired with low cell cytotoxicity. This drug discovery laboratory activity made a measurable contribution to neglected tropical disease research and was an engaging and research-orientated experience for undergraduate students. Implementation of drug discovery laboratories across a range of student levels and backgrounds is highly achievable using existing laboratory equipment and a short investment in activity preparation and can be a sustainable course component.

Eumycetoma is a chronic subcutaneous neglected tropical disease that can be caused by more than 40 different fungal causative agents. The most common causative agents produce black grains and belong to the fungal orders Sordariales and Pleosporales. The current antifungal agents used to treat eumycetoma are itraconazole or terbinafine, however, their cure rates are low. To find novel drugs for eumycetoma, we screened 400 diverse drug-like molecules from the Pandemic Response Box against common eumycetoma causative agents as part of the Open Source Mycetoma initiative (MycetOS). 26 compounds were able to inhibit the growth of Madurella mycetomatis, Madurella pseudomycetomatis and Madurella tropicana, 26 compounds inhibited Falciformispora senegalensis and seven inhibited growth of Medicopsis romeroi in vitro. Four compounds were able to inhibit the growth of all five species of fungi tested. They are the benzimidazole carbamates fenbendazole and carbendazim, the 8-aminoquinolone derivative tafenoquine and MMV1578570. Minimal inhibitory concentrations were then determined for the compounds active against M. mycetomatis. Compounds showing potent activity in vitro were further tested in vivo. Fenbendazole, MMV1782387, ravuconazole and olorofim were able to significantly prolong Galleria mellonella larvae survival and are promising candidates to explore in mycetoma treatment and to also serve as scaffolds for medicinal chemistry optimisation in the search for novel antifungals to treat eumycetoma.

The current Covid-19 pandemic has underlined the need for amore coordinated and forward-looking investment in the search for newmedicines targeting emerging health care threats. Repositioning currentlyapproved drugs is a popular approach to any new emerging disease, but itrepresents afirst wave of response. Behind this would be a second wave of morespecifically designed therapies based on activities against specific moleculartargets or in phenotypic assays. Following the successful deployment and uptakeof previous open access compound collections, we assembled the PandemicResponse Box, a collection of 400 compounds to facilitate drug discovery inemerging infectious disease. These are based on public domain information onchemotypes currently in discovery and early development which have beenshown to have useful activities and were prioritized by medicinal chemistryexperts. They are freely available to the community as a pharmacological test setwith the understanding that data will be shared rapidly in the public domain.

The Neglected Tropical Disease (NTD) Drug Discovery Booster is a collaborative project in early small molecule drug discovery running since 2015 between Drugs for Neglected Diseases initiative (DNDi) and pharmaceutical partners across the globe, including Astellas Pharma Ltd., Eisai Co., Ltd., Shionogi & Co., Ltd. and Takeda Pharmaceutical Company Ltd. in Japan, along with AbbVie Inc., Merck KGaA, AstraZeneca plc and Celgene Corporation. The Booster engages these partners to share both their experience with in silico screening as well as their proprietary chemical libraries to further develop new starting points for NTDs such as visceral leishmaniasis and Chagas disease. This collaborative approach allows DNDi to access new chemical space and elaborate the structure activity relationships (SAR) around phenotypic screening hits against the causative parasites of these diseases (Trypanosoma cruzi, Leishmania donovani and infantum) as well as access new starting points via innovative scaffold hops proposed by the partners. Since 2015 the Booster has probed over 20 new starting point "hits" for these diseases, successfully converting over half into new series for further exploitation. These series were developed further in partnership with the booster collaborators to enable in vivo proof of concept studies, with series from the booster progressing into lead optimization. Our efforts in the NTD Discovery Booster have demonstrated clear advantages of this precompetitive sharing mechanism and the synergistic value of exploring multiple proprietary compound libraries in parallel. The most advanced of these Booster projects is projected to deliver a preclinical candidate for leishmaniasis within the next 2 years.

Aninnovative pre-competitive virtual screening collaboration was engaged tovalidate and subsequently explore an imidazo[1,2-a]pyridine screening hit forvisceral leishmaniasis. Parasitology and early ADME data is presented.

Eumycetoma is a chronic infectious disease characterized by a large subcutaneous mass, often caused by the fungus Madurella mycetomatis. A combination of surgery and prolonged medication is needed to treat this infection with a success rate of only 30%. There is, therefore, an urgent need to find more effective drugs for the treatment of this disease. In this study, we screened 800 diverse drug-like molecules and identified 215 molecules that were active in vitro. Minimal inhibitory concentrations were determined for the 13 most active compounds. One of the most potent compounds, a fenarimol analogue for which a large analogue library is available, led to the screening of an additional 35 compounds for their in vitro activity against M. mycetomatis hyphae, rendering four further hit compounds. To assess the in vivo potency of these hit compounds, a Galleria mellonella larvae model infected with M. mycetomatis was used. Several of the compounds identified in vitro demonstrated promising efficacy in vivo in terms of prolonged larval survival and/or reduced fungal burden. The results presented in this paper are the starting point of an Open Source Mycetoma (MycetOS) approach in which members of the global scientific community are invited to participate and contribute as equal partners. We hope that this initiative, coupled with the promising new hits we have reported, will lead to progress in drug discovery for this most neglected of neglected tropical diseases.