Investment

Details

Neglected Tropical Diseases Drug Discovery Booster II
Project Completed
Please click to see the final report.
  • RFP Year
    2016
  • Awarded Amount
    $549,447
  • Disease
    NTD (Chagas disease / Leishmaniasis)
  • Intervention
    Drug
  • Development Stage
    Lead Identification
  • Collaboration Partners
    Eisai Co., Ltd., SHIONOGI & CO., LTD., Takeda Pharmaceutical Company Limited, Drugs for Neglected Diseases initiative
  • Past Project

Introduction and Background of the Project

This is a continuation project of 'Neglected Tropical Diseases Drug Discovery Booster' invested in 2014.

 

 

Introduction

The NTD Drug Discovery Booster (Booster) project was launched in 2015 as an experiment aimed at speeding up the process and cutting the cost of finding new treatments for two diseases that put 350 million people at risk in 98 endemic countries affected with the Leishmania parasites and 100 million people at risk mainly in the Americas affected with the Trypanosoma cruzi parasites. The Booster Consortium led by DNDi entails exploring simultaneously high quality libraries to identify, in a speedy and effective way, hit series to optimize. The Consortium intends to continue the work of the Booster, feeding the mechanism with newly identified hit compounds from various hit finding exercises such as high throughput screening. The Consortium currently consists of three Japanese pharmaceutical partners (Eisai Co. Ltd, Shionogi & Co., Takeda Pharmaceutical Company Limited.) funded by GHIT Fund and AstraZeneca plc. and Celgene Corporation. Institut Pasteur Korea is also an important partner who is screening all the compounds.

 

Project objective

The Booster II has the following two objectives;

Objective 1: Delivering novel chemical series for leishmaniasis & Chagas disease

The Booster II consortium will rapidly expand at least five promising hits/hit series against Leishmania donovani and T. cruzi, the causative agents of leishmaniasis and Chagas disease, respectively. This will provide series with well-developed structure activity relationships (SAR) ready for immediate in vivo proof of concept studies or, where necessary, focused medicinal chemistry optimization to provide improved tools ready for in vivo studies.

 

Objective 2: Complete lead evaluation from previous Booster project (Booster I)

Hit series previously identified by the Booster I (4-5 series) will complete their investigation towards in vivo proof of concept studies, leading to at least one series entering into lead optimization.

 

Project design

Over the next year, the Booster Consortium will run at least 10 iterations of the booster. A single booster iteration consists of a virtual screen (in silico) at each partner company, followed by experimental testing against parasite(s) of interest. The starting points for these iterations will come from two sources:

l  At least five new seed compounds for L. donovani or T. cruzi (with 1-2 screening iterations each).

l  Molecules identified as “improved hits” during previous iterations from the Booster I (e.g. continuation of the booster process from years 1 & 2)

 

Expected output is 1-2 hit series per parasite showing encouraging in vivo activity (inclusive of any historic hit series progressed into lead optimization from Booster I).

How can your partnership (project) address global health challenges?

The Booster consortium offers a more effective discovery approach to contribute to a potential successful new treatment for leishmaniasis or Chagas disease.

For visceral leishmaniasis, existing drugs produce variable efficacy and serious toxicities; only one is administered orally and the rest are given by painful intra-venous/intra-muscular injections. In addition, there is a dichotomy of efficacy in drug action in visceral leishmaniasis-endemic regions of the world. To date, the medical needs in visceral leishmaniasis are moderately to well-met in South Asia. However, in East Africa and Latin America the efficacy and tolerability of current visceral leishmaniasis therapies remain a challenging area for improvement. Ideally, what is needed in the treatment of visceral leishmaniasis is a simple oral combination therapy that would prove advantageous/effective in maintaining or improving efficacy, improving tolerability and preventing or delaying the emergence of resistance. Furthermore, a treatment adapted to field conditions, with shorter duration and which could be used pan-geographically, would be optimal.

In the case of Chagas disease there are even fewer treatment options than for visceral leishmaniasis. Monotherapy with nifurtimox or benznidazole (both from the same nitroheterocycle class) remain the only recognized treatments, but these require long treatment courses, produce variable efficacy, and cause serious side effects resulting in 20-30% discontinuations of treatment. Therefore, it is crucial that new classes of effective, well-tolerated, orally-acting and short-course treatments are progressed into the clinic to provide improved options for patients. New classes of drugs for Chagas disease are also essential to enable development of combination therapies to combat the risk of development of resistance to monotherapies.

What sort of innovation are you bringing in your project?

The Booster process benefits from simultaneously searching a combined compound collection of several million high-quality, drug-like, small molecules and rapidly testing them in the same, standardized in vitro assays to develop a robust SAR for the series. The Booster collection of compounds, which each pharmaceutical company has been collecting and preparing for its own drug discovery research, clearly offers a significant advantage. The combination of different scientific approaches to the in silico screening question results in a broader and more varied screening of compounds with potential parasitic activity compared to what may be synthesized in a traditional hit to lead project. The first 18 months of the Booster consortium have successfully validated the approach, demonstrating a clear advantage of the use of collaborative in silico screening across pharmaceutical partners. In particular, the ability of the booster process to identify new areas of chemical space via a first iteration and then provide an investigation of that chemical space via subsequent second (and third) iterations has led directly to the discovery of new hit series against both parasites of interest. The Consortium intends to continue the work of the Booster, feeding the Booster mechanism with newly identified hit compounds from various hit finding exercises such as high throughput screening resulting in new hit series for entry into future lead optimization programs.

Role and Responsibility of Each Partner

Takeda, Shionogi and Eisai will perform in silico screening of their internal libraries around each seed. They will prepare plates of compounds for shipment to the DNDi screening centre for testing. The companies will also provide intellectual input on the analysis of results coming from the iterations, as well as provide any additional relevant internal information about their compounds chosen for inclusion in a hit series.

DNDi will coordinate the project, conduct the experimental screening of the compounds via one of its dedicated screening centres, and complete the computational and medicinal chemistry analysis of the screening results.

Others (including references if necessary)

The results from the Booster consortium have been presented as a poster at the EFMC ISMC meeting (Manchester, UK, Aug 2016).

Final Report

1. Project objective

The NTD Drug Discovery Booster (Booster) was launched in 2015 to speed up the process and cut the cost of finding new treatments for leishmaniasis & Chagas disease. During the Booster II time period, the Booster consortium will expand at least five promising hits for leishmaniasis & Chagas disease respectively, resulting in hit series with well-developed structure activity relationships (SAR) ready for in vivo proof of concept studies or focused medicinal chemistry optimization to provide improved tools ready for in vivo studies. The lead evaluation from previous Booster I will be completed, leading to at least one series entering into lead optimization.

 

2. Project design

Over the Booster II time period, the Booster consortium runs at least 10 iterations of the booster. A single booster iteration consists of a virtual screen (in silico) at each partner company, followed by experimental testing against parasite (s) of interest. The starting points for these iterations come from at least five new seed compounds for L. donovani or T. cruzi (with 1-2 screening iterations each) and molecules identified as “improved hits” during previous iterations from the Booster I. 1-2 hit series per parasite identified by the Booster I & II are expected to show encouraging in vivo activity.

 

3. Results, lessons learned

The Booster consortium launched total 35 iterations of the booster around 17 distinct seed compounds since 2015.

Nine seeds have successfully resulted in identification of 11 new hit series (in two cases a single seed resulted in two distinct hit series); three hit series are selective for T. cruzi, and eight hit series are active against both parasites. Five of the identified hit series are currently under further investigation, building on SAR derived from the booster process.

Four of the hit series identified a compound or compounds for use in proof of concept studies in vivo. Of the compounds tested, one series demonstrated moderate in vivo efficacy for Chagas, one series has demonstrated moderate in vivo efficacy for leishmaniasis. The results of both compounds are encouraging, but the level of efficacy displayed is not yet sufficient to move these series into lead optimization. Further optimization with all four of the series is taken over by the Booster III in order to improve the efficacy in vivo to a level sufficient for progress to lead optimization, or identify compounds which demonstrate efficacy in vivo.

 

During Booster II, we have learned that it is possible to identify compounds with in vivo POC ready profiles directly from the booster process (2 examples), however as with many other hit to lead approaches this does not necessarily guarantee efficacy in the POC model. In some instances, further SAR development is required before identifying POC molecules, and the information obtained from the booster process is essential in enabling this optimization.

The Booster also allows us to rapidly deprioritize series with minimal opportunity for advancing in favor of those with higher chance of success; such decisions can be made by analyzing the SAR and hit rate provided by the booster process to determine those hits and series readily amenable to modification and optimization.

As the Booster has matured and promising hit series have emerged, we have been delighted to receive generous in-kind support from some of the consortium members for further medicinal chemistry optimization of these series.

Finally, we have learned more about the nature of good chemical starting points (“seeds”) for the booster process, allowing us to be more judicious in selection of seeds in future versions of the Booster.