Plasmodium Protein Kinase Focused Antimalarials Discovery

Malaria still afflicts about half of the world population causing more than 400,000 deaths, mostly children. It is
quite alarming that the options for malaria therapy are increasingly becoming limited because of widespread
drug resistance. Furthermore, most of the antimalarials act only on the erythrocytic stages, the drugs for
prophylaxis and relapse of malaria are suboptimal. To address the fragility of malaria therapy, we propose to
discover and optimize next generation antimalarials acting on underexplored Plasmodium kinases. We will
leverage wealth of knowledge on diverse chemical scaffolds and know-how related to the drug development
and tolerability of kinase inhibitor-based therapies for various human diseases. We will focus on type II kinase
inhibitors that have been designed to overcome selectivity issues by using both the ATP-binding site as well as
the adjacent hydrophobic region created by the activation loop in the inactive conformation. To the best of our
knowledge, type II inhibitors are yet to be explored as antimalarial agents. Premise for this proposal is based
on our promising preliminary screening that has identified type II compounds with therapeutic and prophylactic
activities. The goal of this project is to test the hypothesis that we can design effective type II chemical
scaffolds that act on multiple stages of parasite development. To achieve this goal, we propose to pursue the
following: (1) Design and synthesize optimized selective antimalarial type II compounds for in vivo application;
antiplasmodial hits will be optimized to improve potency, selectivity, and pharmacological properties through
stages of iterative analog design, synthesis, and evaluation of biological and biochemical activities. (2)
Determine rate of killing, resistance profile, stage susceptibility, and efficacy of lead compounds in murine and
humanized mouse models. Furthermore, the ability of the lead compounds to inhibit liver stage infection and
gametocyte maturation will be assessed. 3) We will identify targets of antimalarial chemotypes using in vitro
evolution of resistance followed by whole genome sequencing. We will use conditional knockdown and copy
number variation of the resistance determinants for target validation. We will conduct phosphoproteomics
analysis to uncover signaling pathways modulated by the type II inhibitors under study. The research in this
endeavor will be conducted through a multidisciplinary collaboration between the laboratories of Debopam
Chakrabarti (University of Central Florida), Nathanael Gray (Stanford University), Elizabeth Winzeler
(University of California San Diego) with combined expertise in medicinal chemistry, kinase chemical biology,
malaria cell biology, anti-infective discovery, target identification, and validation. Successful completion of
these goal will lead to the discovery of novel chemical leads with therapeutic and prophylactic potential.

Grant Number: 5R01AI172066-04
NIH Institute/Center: NIH
Principal Investigator: DEBOPAM CHAKRABARTI