KRAS Inhibitor That Simultaneously Inhibits Nucleotide Exchange Activity and Effector Engagement

Overview

Journal ACS Bio Med Chem Au

Publisher American Chemical Society

Specialty Biochemistry

Date 2023 Apr 27

PMID 37101428

Authors

Cynthia V Pagba

Amit K Gupta

Ali K Naji

Dharini van der Hoeven

Kelly Churion

Xiaowen Liang

Jacob Jakubec

Magnus Hook

Yan Zuo

Marisela Martinez de Kraatz

Jeffrey A Frost

Alemayehu A Gorfe

Affiliations

Soon will be listed here.

Abstract

We describe a small molecule ligand (2-hydroxy-5-{[(2-phenylcyclopropyl) carbonyl] amino} benzoic acid) as an initial lead for the development of direct inhibitors of KRAS, a notoriously difficult anticancer drug target. We show that the compound binds to KRAS near the switch regions with affinities in the low micromolar range and exerts different effects on KRAS interactions with binding partners. Specifically, impedes the interaction of KRAS with its effector Raf and reduces both intrinsic and SOS-mediated nucleotide exchange rates. Likely as a result of these effects, inhibits signal transduction through the MAPK pathway in cells expressing mutant KRAS and inhibits the growth of pancreatic and colon cancer cells harboring mutant KRAS. We thus propose compound as a useful initial lead for the development of broad-acting inhibitors that target multiple KRAS mutants and simultaneously deplete the fraction of GTP-loaded KRAS while abrogating the effector-binding ability of the already GTP-loaded fraction.

Citing Articles

New insights into protein-protein interaction modulators in drug discovery and therapeutic advance.

Nada H, Choi Y, Kim S, Jeong K, Meanwell N, Lee K Signal Transduct Target Ther. 2024; 9(1):341.

PMID: 39638817 PMC: 11621763. DOI: 10.1038/s41392-024-02036-3.

KRAS Mutation Subtypes and Their Association with Other Driver Mutations in Oncogenic Pathways.

Mondal K, Posa M, Shenoy R, Roychoudhury S Cells. 2024; 13(14.

PMID: 39056802 PMC: 11274496. DOI: 10.3390/cells13141221.

Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions.

Mahran R, Vello N, Komulainen A, Malakoutikhah M, Harma H, Kopra K Sci Rep. 2023; 13(1):20066.

PMID: 37973851 PMC: 10654576. DOI: 10.1038/s41598-023-46720-w.

CSC01 shows promise as a potential inhibitor of the oncogenic G13D mutant of KRAS: an in silico approach.

Durojaye O, Ejaz U, Uzoeto H, Fadahunsi A, Opabunmi A, Ekpo D Amino Acids. 2023; 55(12):1745-1764.

PMID: 37500789 DOI: 10.1007/s00726-023-03304-2.

RAS-targeted cancer therapy: Advances in drugging specific mutations.

Liu C, Ye D, Yang H, Chen X, Su Z, Li X MedComm (2020). 2023; 4(3):e285.

PMID: 37250144 PMC: 10225044. DOI: 10.1002/mco2.285.

References

Hocker H, Cho K, Chen C, Rambahal N, Sagineedu S, Shaari K . Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function. Proc Natl Acad Sci U S A. 2013; 110(25):10201-6. PMC: 3690838. DOI: 10.1073/pnas.1300016110. View

Kessler D, Gmachl M, Mantoulidis A, Martin L, Zoephel A, Mayer M . Drugging an undruggable pocket on KRAS. Proc Natl Acad Sci U S A. 2019; 116(32):15823-15829. PMC: 6689897. DOI: 10.1073/pnas.1904529116. View

Cruz-Migoni A, Canning P, Quevedo C, Bataille C, Bery N, Miller A . Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds. Proc Natl Acad Sci U S A. 2019; 116(7):2545-2550. PMC: 6377466. DOI: 10.1073/pnas.1811360116. View

Welsch M, Kaplan A, Chambers J, Stokes M, Bos P, Zask A . Multivalent Small-Molecule Pan-RAS Inhibitors. Cell. 2017; 168(5):878-889.e29. PMC: 5362268. DOI: 10.1016/j.cell.2017.02.006. View

Grant B, Lukman S, Hocker H, Sayyah J, Brown J, McCammon J . Novel allosteric sites on Ras for lead generation. PLoS One. 2011; 6(10):e25711. PMC: 3201956. DOI: 10.1371/journal.pone.0025711. View

Margarit S, Bar-Sagi D, Kuriyan J . The structural basis of the activation of Ras by Sos. Nature. 1998; 394(6691):337-43. DOI: 10.1038/28548. View

Ford B, Skowronek K, Boykevisch S, Bar-Sagi D, Nassar N . Structure of the G60A mutant of Ras: implications for the dominant negative effect. J Biol Chem. 2005; 280(27):25697-705. DOI: 10.1074/jbc.M502240200. View

Fell J, Fischer J, Baer B, Blake J, Bouhana K, Briere D . Identification of the Clinical Development Candidate , a Covalent KRAS Inhibitor for the Treatment of Cancer. J Med Chem. 2020; 63(13):6679-6693. DOI: 10.1021/acs.jmedchem.9b02052. View

Xu S, Long B, Boris G, Chen A, Ni S, Kennedy M . Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras. Acta Crystallogr D Struct Biol. 2017; 73(Pt 12):970-984. DOI: 10.1107/S2059798317015418. View

10.

McCarthy M, Pagba C, Prakash P, Naji A, van der Hoeven D, Liang H . Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding. ACS Omega. 2019; 4(2):2921-2930. PMC: 6396121. DOI: 10.1021/acsomega.8b03308. View

11.

Vetter I, Wittinghofer A . The guanine nucleotide-binding switch in three dimensions. Science. 2001; 294(5545):1299-304. DOI: 10.1126/science.1062023. View

12.

Hunter J, Manandhar A, Carrasco M, Gurbani D, Gondi S, Westover K . Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations. Mol Cancer Res. 2015; 13(9):1325-35. DOI: 10.1158/1541-7786.MCR-15-0203. View

13.

Quevedo C, Cruz-Migoni A, Bery N, Miller A, Tanaka T, Petch D . Small molecule inhibitors of RAS-effector protein interactions derived using an intracellular antibody fragment. Nat Commun. 2018; 9(1):3169. PMC: 6085350. DOI: 10.1038/s41467-018-05707-2. View

14.

Marchand J, Kaiser D, Pollard T, Higgs H . Interaction of WASP/Scar proteins with actin and vertebrate Arp2/3 complex. Nat Cell Biol. 2001; 3(1):76-82. DOI: 10.1038/35050590. View

15.

Milburn M, Tong L, Devos A, Brunger A, Yamaizumi Z, Nishimura S . Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science. 1990; 247(4945):939-45. DOI: 10.1126/science.2406906. View

16.

Ahmed D, Eide P, Eilertsen I, Danielsen S, Eknaes M, Hektoen M . Epigenetic and genetic features of 24 colon cancer cell lines. Oncogenesis. 2013; 2:e71. PMC: 3816225. DOI: 10.1038/oncsis.2013.35. View

17.

Bery N, Cruz-Migoni A, Bataille C, Quevedo C, Tulmin H, Miller A . BRET-based RAS biosensors that show a novel small molecule is an inhibitor of RAS-effector protein-protein interactions. Elife. 2018; 7. PMC: 6039175. DOI: 10.7554/eLife.37122. View

18.

Cox A, Fesik S, Kimmelman A, Luo J, Der C . Drugging the undruggable RAS: Mission possible?. Nat Rev Drug Discov. 2014; 13(11):828-51. PMC: 4355017. DOI: 10.1038/nrd4389. View

19.

Maurer T, Garrenton L, Oh A, Pitts K, Anderson D, Skelton N . Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. Proc Natl Acad Sci U S A. 2012; 109(14):5299-304. PMC: 3325706. DOI: 10.1073/pnas.1116510109. View

20.

Pollard T . A guide to simple and informative binding assays. Mol Biol Cell. 2010; 21(23):4061-7. PMC: 2993736. DOI: 10.1091/mbc.E10-08-0683. View