Hit confirmation and optimization of RNA Binding proteins with KH domain.

• Grant number: 23/16654-1
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: July 01, 2024
• End date: June 30, 2025
• Field of knowledge: Health Sciences - Pharmacy
• Principal Investigator: Katlin Brauer Massirer
• Grantee: Renan Vinicius de Araujo
• Supervisor: Paul Edward Brennan
• Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Institution abroad: University of Oxford, England
• Associated to the scholarship: 22/10512-8 - Fragment-based hit discovery and characterization of RNA Binding proteins with KH domain, BP.DD

Abstract

Fragment-based Hit Discovery (FBHD) is a modern and effective tool for the discovery of lead molecules, and the development of several recent FDA-approved drugs began with this method. In our group, we study RNA binding proteins containing the KH domain, which allows a protein to bind to a specific set of target mRNAs in the cell, to control processes as transport of RNAs from the nucleus to the cytoplasm and the process of RNA splicing. This class of proteins is related to diseases including cancer and neurological diseases. In this project we will study two proteins of this family: FUBP2 and NOVA1, which have similar structural features and for which small molecule inhibitors are unavailable. During the initial stage of this work, we have expressed and purified both proteins and have performed fragment screenings by weak affinity chromatography coupled to mass spectrometry (WAC-MS) on two of them. We have then derived larger molecules from the initial hits, by organic synthesis. Here we propose to employ surface plasmon resonance (SPR) and X-ray crystallography as orthogonal assays to confirm the initial ligands for the KH domain. The aim is to elucidate the binding mode and to investigate whether it is possible to find novel, common ligands for the KH-domain. From this, we expect to understand how selectivity between KH-proteins can be achieved. The initial findings will guide a new round of organic synthesis to obtain selective and specific drug-like lead candidates. The project will greatly benefit from the infrastructure of the University of Oxford, which is considered the best in the world for biochemistry.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

SILVA, SUELEN FERNANDES; KLIPPEL, ANGELICA HOLLUNDER; SIGURDARDOTTIR, SUNNIVA; MAHDIZADEH, SAYYED JALIL; TIUKOVA, IEVGENIIA; BOURGARD, CATARINA; SALAZAR-ALVAREZ, LUIS CARLOS; PRADO, HELOISA MONTEIRO DO AMARAL; DE ARAUJO, RENAN VINICIUS; COSTA, FABIO TRINDADE MARANHAO; et al. An experimental target-based platform in yeast for screening Plasmodium vivax deoxyhypusine synthase inhibitors. PLoS Neglected Tropical Diseases, v. 18, n. 12, p. 25-pg., 2024-12-01. (14/50897-0, 23/07805-6, 19/24812-0, 23/16654-1, 22/10512-8, 18/16672-1, 15/03553-6, 18/07007-4)