A Fragment-Based Strategy for K-RAS Covalent Inhibitors

基于片段的 K-RAS 共价抑制剂策略

• 批准号: 10653029
• 负责人: Samy Meroueh
• 金额: $ 45.98万
• 依托单位: INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-02 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10653029
• 关键词: Affinity; Amino Acids; Binding; Binding Sites; Biochemical; Biological; Biological Assay; Cancer cell line; Cell Proliferation; Cell Survival; Cells; Cellular biology; Clinical Trials; Codon Nucleotides; Collection; Colon Carcinoma; Colorectal; Colorectal Cancer; Communities; Computing Methodologies; Cysteine; Data; Development; Event; Fluorescence; Fluorides; GTP Binding; Goals; Guanine; Guanine Nucleotide Exchange Factors; Guanosine Triphosphate Phosphohydrolases; KRAS2 gene; Libraries; Ligands; Lung Adenocarcinoma; Lysine; Malignant Neoplasms; Malignant neoplasm of lung; Mass Spectrum Analysis; Methods; Mission; Mutate; Mutation; Non-Small-Cell Lung Carcinoma; Nucleotides; Oncogenes; Oncogenic; Pancreatic Ductal Adenocarcinoma; Pharmaceutical Preparations; Phosphorylation; Positioning Attribute; Proliferating; Proteins; Public Health; RAS driven tumor; Ras Inhibitor; Reaction; Reporting; Resolution; Roentgen Rays; Serine; Signal Transduction; Site; Solubility; Son; Structure; Testing; Therapeutic; Therapeutic Agents; Threonine; Time; Tyrosine; United States National Institutes of Health; Western Blotting; Work; X-Ray Crystallography; adduct; antagonist; cancer cell; cheminformatics; covalent bond; design; experience; inhibitor; lead optimization; liquid chromatography mass spectrometry; mortality; mutant; novel; pancreatic cancer patients; pancreatic ductal adenocarcinoma cell; reaction rate; screening; small molecule; small molecule inhibitor; structural biology; therapeutic development; three dimensional structure; tumor; tumor growth

ABSTRACT KRAS is the most frequently mutated oncogene with mutation rates of 95% in pancreatic ductal adenocarcinoma (PDAC), 45% in colorectal cancer, and 30% in lung adenocarcinomas. The most common K-RAS mutations occur at codon 12, namely G12D, G12V, G12C, and G12R. K-RAS was considered undruggable due to lack of well-defined drug-binding pockets. But a recent breakthrough was achieved with covalent inhibitors that form a bond with K-RAS G12C cysteine. Several of these compounds are in clinical trials, and one was given FastTrack status by the FDA. Unfortunately, only a small fraction of K-RAS oncogene mutants harbor the G12C mutation, and G12D, G12V and other mutations do not provide an accessible cysteine nucleophile. In recent work with the RAS GTPase Ral we showed through high-resolution structures and extensive biochemical studies that covalent bond formation with Tyr-82 created a well-defined novel binding site located between the Switch II and the Switch I/II pockets. Additional fragment screening carried out more recently identified a fragment that forms a covalent bond at K-RAS Switch II Tyr-64 to inhibit activation of the GTPase by the Son-of-Sevenless (SOS) guanine exchange factor. Here, we hypothesize that covalent bond formation with tyrosine or other amino acids on K- RAS will inhibit activation or effector binding and block K-RAS signaling in cancer cells. Our preliminary data and extensive experience in the field puts us in a strong position to accomplish our objectives. In Specific Aim 1, we employ ligand- and structure-based methods to generate fragment electrophile libraries from large commercial collections, and we follow a structure-based method to grow hit fragments into neighboring pockets to enhance their binding affinity and reaction rates. In Specific Aim 2, we will carry out well-established intact protein mass spectrometry, nucleotide exchange, and effector binding studies to screen fragment libraries for hit compounds, and to characterize small molecules that emerge from fragment growing strategies. In Specific Aim 3, we will use X-ray crystallography to solve the structure of hit fragments and derivatives that emerge from fragment growing efforts. We also carry out cell biological studies to confirm direct engagement of K-RAS, inhibition of K- RAS signaling, and inhibition of cancer cell proliferation. We expect to identify high quality fragments and small molecules that form a covalent bond at wild-type and mutant K-RAS oncogenes, inhibit K-RAS wild-type or oncogene mutant activity in cancer cell lines, and inhibit PDAC and lung adenocarcinoma cancer cell viability. These compounds will serve as starting points to pursue in lead optimization efforts towards the development of therapeutic agents for the treatment of K-RAS-driven tumors.

摘要

项目成果

The inhibition of pancreatic cancer progression by K-Ras-overexpressing mesenchymal stem cell-derived secretomes.

• DOI: 10.1038/s41598-023-41835-6
• 发表时间: 2023-09-12
• 期刊: Scientific reports
• 影响因子: 4.6

Covalent Fragment Inhibits RhoA Activation by Guanine Exchange Factors.

共价片段通过鸟嘌呤交换因子抑制 RhoA 激活。

• DOI: 10.1021/acschemneuro.3c00154
• 发表时间: 2023
• 期刊: ACS chemical neuroscience
• 影响因子: 5
• 作者: Hussain,MuhammadS;Liu,Degang;Alilain,WarrenJ;Meroueh,SamyO
• 通讯作者: Meroueh,SamyO

Crystal Packing Reveals a Potential Autoinhibited KRAS Dimer Interface and a Strategy for Small-Molecule Inhibition of RAS Signaling.

• DOI: 10.1021/acs.biochem.3c00378
• 发表时间: 2023-11
• 期刊: Biochemistry
• 影响因子: 2.9
• 作者: Robert J Brenner;Alexander D Landgraf;K. Bum-Erdene;Giovanni Gonzalez-Gutierrez;S. Meroueh