Hit-to-lead development of new antimalarial compounds from DDI library
Project Completed
Please click to see the final report.
  • RFP Year
  • Awarded Amount
  • Disease
  • Intervention
  • Development Stage
    Lead Identification
  • Collaboration Partners
    University of Tokyo ,  Medicines for Malaria Venture (MMV)
  • Past Project

Introduction and Background of the Project


Malaria is the disease caused by the parasite called Plasmodium and results in approximately 450 thousand deaths annually. Malaria is one of the major cause of death in Africa, particularly children under the age of five and pregnant women. There is no preventive vaccine against malaria. Furthermore, drug resistant malaria parasites continue to emerge against all clinically used antimalarial drugs. Therefore, discovery and development of new antimalarial compounds are constantly needed.


Project objective

We will generate structurally optimized lead compounds effective against malaria parasites, based on the hit compounds identified by The University of Tokyo and Medicines for Malaria Venture (MMV) in the previous screening campaign in 2018-2020, supported by GHIT Fund. In the preceding project, we identified a number of hits that kill the malaria parasites under micromolar concentrations, by phenotypic screening of 210,000 structurally defined compounds from Drug Discovery Initiative, Japan. In the present project, we will conduct structural optimization of the selected six series to develop new antimalarial leads. We aim at new compounds with a novel scaffold, mechanism of action, and improved efficacy and safely.


Project design

The University of Tokyo and MMV will work together to generate a few series of new compounds that kill malaria parasites by structural modifications of the initial hit series. The new compounds will be further tested for efficacy against both drug-sensitive and resistant malaria strains and also for in vitro safety. It will be also elucidated how the new compounds kill the parasites. Malaria parasites are transmitted between humans and mosquitoes. We will also evaluate what developmental stages of parasites the new compounds are efficacious to, e.g., parasites in the human liver, erythrocytes, mosquito gut, and the salivary gland.

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

Drug resistant malaria has already emerged in all endemic areas, which necessitates discovery and further development of new leads that have a novel mode of action and thus effective against drug resistant malaria. This project can potentially bring in new lead compounds that have novel structure and mode of action. Such compounds are expected to be further proven to be efficacious toward multiple parasite stages, safely usable for children and pregnant women, applicable for prophylactics as well as chemotherapeutics.

What sort of innovation are you bringing in your project?

This is the first project in which hit compounds originated from Japanese academia will enter the chemical optimization stage for further antimalarial development. All the previous attempts were exclusively made using compound libraries from pharmaceutical industries.

Role and Responsibility of Each Partner

The University of Tokyo, together with Nagoya Institute of Technology, leads chemical synthesis of compounds from 2-3 series identified in the previous screening campaign. The University of Tokyo, in a collaboration with Juntendo University and Ehime University, will also elucidate the mechanism of action of the new lead compounds and demonstrate what stages of the malaria parasites the new leads target. MMV will evaluate physicochemical properties, stability, safety, as well as absorption-distribution-metabolism-excretion (ADME) properties, of the new leads. MMV will also evaluate efficacy of the leads against drug resistant malaria strains to exclude compounds that have the mechanism of action that overlaps with the existing antimalarials.

Final Report

1. Project objective

We aimed to generate new antimalarial leads from seven hit series identified by phenotypic screening of 210,000 structurally defined compounds from academia (Drug Discovery Initiative, Japan). These leads should ideally have good properties that fulfill target compound profiles Medicines for Malaria Venture (MMV) defines, including in vivo potency by oral administration, no acute toxicity, balanced physicochemical properties, stability, safety, and good absorption-distribution-metabolism-excretion (ADME) properties, and good bioavailability. We also aimed to establish structural activity relationship (SAR) and elucidate mechanism of action of the leads by chemogenomic approaches.


2. Project design

The project involved The University of Tokyo (UTokyo), Nagoya Institute of Technology (NIT), and MMV. Designing and synthesis of seven hit series were conducted by MMV and NIT. Parasitological and cytotoxicity assays were conducted by UTokyo, while evaluation of physicochemical properties, cross resistance, early ADME, and in vivo pharmacokinetics were carried out by MMV. SAR was established to identify minimal effective pharmacophores, optimize the structure of all hit series, and also prioritize and triage hit series. Generation of Plasmodium falciparum resistant lines against the hit series, followed by whole genome sequencing, was conducted by UTokyo, to elucidate the mechanism of action and resistance. Target of some series was also identified by chemical approaches, conducted by UTokyo.


3. Results, lessons learned

Out of seven hit series identified from DDI library, five series (series 1-5) were mainly explored by synthesis of ~200 structurally related compounds. Series 5 was most extensively explored with >190 derivatives. Series 5 initially gave promising profiles including moderate anti-erythrocytic stage efficacy against both drug sensitive and resistant P. falciparum lines, no cytotoxicity, no cardiotoxicity (hERG), good solubility, and moderate rate of kill. Series 5 did not produce resistance in a panel of P. falciparum lines with the resistance mechanisms against existing drugs. However, due to lack of balanced membrane permeability (and oral bioavailability) and metabolic instability, no compound combines all the good drug-like properties required to meet the MMV criteria for an early lead. Six other series were also parked during investigation for several reasons: inability to separate efficacy and cytotoxicity, structural complexity (2-3 chiral centers),  metabolic instability due to peptide-like structure, cross resistance by known mechanisms, and/or promiscuous SAR. Independent resistance mechanisms against three compounds (series 3-5) were genetically identified. A new unexplored attractive target against series 4 was chemically identified, and will be further pursued. The project also promoted networking among Japanese and international academic partners and capacity building of Japanese academia in drug development.