Selective and noncovalent targeting of RAS mutants for inhibition and degradation
Abstract
AbstractActivating mutants of RAS are commonly found in human cancers, but to date selective targeting of RAS in the clinic has been limited to KRAS(G12C) through covalent inhibitors. Here, we report a monobody, termed 12VC1, that recognizes the active state of both KRAS(G12V) and KRAS(G12C) up to 400-times more tightly than wild-type KRAS. The crystal structures reveal that 12VC1 recognizes the mutations through a shallow pocket, and 12VC1 competes against RAS-effector interaction. When expressed intracellularly, 12VC1 potently inhibits ERK activation and the proliferation of RAS-driven cancer cell lines in vitro and in mouse xenograft models. 12VC1 fused to VHL selectively degrades the KRAS mutants and provides more extended suppression of mutant RAS activity than inhibition by 12VC1 alone. These results demonstrate the feasibility of selective targeting and degradation of KRAS mutants in the active state with noncovalent reagents and provide a starting point for designing noncovalent therapeutics against oncogenic RAS mutants.
- Authors:
-
- New York Univ. (NYU), NY (United States). Perlmutter Cancer Center
- New York Univ. (NYU), NY (United States). Perlmutter Cancer Center and Grossman School of Medicine
- New York Univ. (NYU), NY (United States)
- Medical Univ. of South Carolina, Charleston, SC (United States); Ralph H. Johnson VA Medical Center, Charleston, SC (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Institutes of Health (NIH); Cancer Center Support Grant
- OSTI Identifier:
- 1806319
- Alternate Identifier(s):
- OSTI ID: 1818360
- Grant/Contract Number:
- AC02-06CH11357; R35 GM127040; R01 CA194864; R21 CA201717; R01 CA212608; P30CA016087
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 60 APPLIED LIFE SCIENCES; drug discovery; oncogenes
Citation Formats
Teng, Kai Wen, Tsai, Steven T., Hattori, Takamitsu, Fedele, Carmine, Koide, Akiko, Yang, Chao, Hou, Xuben, Zhang, Yingkai, Neel, Benjamin G., O’Bryan, John P., and Koide, Shohei. Selective and noncovalent targeting of RAS mutants for inhibition and degradation. United States: N. p., 2021.
Web. doi:10.1038/s41467-021-22969-5.
Teng, Kai Wen, Tsai, Steven T., Hattori, Takamitsu, Fedele, Carmine, Koide, Akiko, Yang, Chao, Hou, Xuben, Zhang, Yingkai, Neel, Benjamin G., O’Bryan, John P., & Koide, Shohei. Selective and noncovalent targeting of RAS mutants for inhibition and degradation. United States. https://doi.org/10.1038/s41467-021-22969-5
Teng, Kai Wen, Tsai, Steven T., Hattori, Takamitsu, Fedele, Carmine, Koide, Akiko, Yang, Chao, Hou, Xuben, Zhang, Yingkai, Neel, Benjamin G., O’Bryan, John P., and Koide, Shohei. Tue .
"Selective and noncovalent targeting of RAS mutants for inhibition and degradation". United States. https://doi.org/10.1038/s41467-021-22969-5. https://www.osti.gov/servlets/purl/1806319.
@article{osti_1806319,
title = {Selective and noncovalent targeting of RAS mutants for inhibition and degradation},
author = {Teng, Kai Wen and Tsai, Steven T. and Hattori, Takamitsu and Fedele, Carmine and Koide, Akiko and Yang, Chao and Hou, Xuben and Zhang, Yingkai and Neel, Benjamin G. and O’Bryan, John P. and Koide, Shohei},
abstractNote = {AbstractActivating mutants of RAS are commonly found in human cancers, but to date selective targeting of RAS in the clinic has been limited to KRAS(G12C) through covalent inhibitors. Here, we report a monobody, termed 12VC1, that recognizes the active state of both KRAS(G12V) and KRAS(G12C) up to 400-times more tightly than wild-type KRAS. The crystal structures reveal that 12VC1 recognizes the mutations through a shallow pocket, and 12VC1 competes against RAS-effector interaction. When expressed intracellularly, 12VC1 potently inhibits ERK activation and the proliferation of RAS-driven cancer cell lines in vitro and in mouse xenograft models. 12VC1 fused to VHL selectively degrades the KRAS mutants and provides more extended suppression of mutant RAS activity than inhibition by 12VC1 alone. These results demonstrate the feasibility of selective targeting and degradation of KRAS mutants in the active state with noncovalent reagents and provide a starting point for designing noncovalent therapeutics against oncogenic RAS mutants.},
doi = {10.1038/s41467-021-22969-5},
journal = {Nature Communications},
number = 1,
volume = 12,
place = {United States},
year = {Tue May 11 00:00:00 EDT 2021},
month = {Tue May 11 00:00:00 EDT 2021}
}
Works referenced in this record:
An affinity-directed protein missile system for targeted proteolysis
journal, October 2016
- Fulcher, Luke J.; Macartney, Thomas; Bozatzi, Polyxeni
- Open Biology, Vol. 6, Issue 10
Absolute Quantification of Endogenous Ras Isoform Abundance
journal, November 2015
- Mageean, Craig J.; Griffiths, John R.; Smith, Duncan L.
- PLOS ONE, Vol. 10, Issue 11
Proteolysis-Targeting Chimeras as Therapeutics and Tools for Biological Discovery
journal, April 2020
- Burslem, George M.; Crews, Craig M.
- Cell, Vol. 181, Issue 1
Allosteric modulation of a human protein kinase with monobodies
journal, June 2019
- Zorba, Adelajda; Nguyen, Vy; Koide, Akiko
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 28
A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain
journal, March 2010
- Wojcik, John; Hantschel, Oliver; Grebien, Florian
- Nature Structural & Molecular Biology, Vol. 17, Issue 4
GTP-State-Selective Cyclic Peptide Ligands of K-Ras(G12D) Block Its Interaction with Raf
journal, September 2020
- Zhang, Ziyang; Gao, Rong; Hu, Qi
- ACS Central Science, Vol. 6, Issue 10
K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions
journal, November 2013
- Ostrem, Jonathan M.; Peters, Ulf; Sos, Martin L.
- Nature, Vol. 503, Issue 7477
SAINT: probabilistic scoring of affinity purification–mass spectrometry data
journal, December 2010
- Choi, Hyungwon; Larsen, Brett; Lin, Zhen-Yuan
- Nature Methods, Vol. 8, Issue 1
Phase I/II study of COVID-19 RNA vaccine BNT162b1 in adults
journal, August 2020
- Mulligan, Mark J.; Lyke, Kirsten E.; Kitchin, Nicholas
- Nature, Vol. 586, Issue 7830
RasIns: Genetically Encoded Intrabodies of Activated Ras Proteins
journal, February 2017
- Cetin, Mehmet; Evenson, William E.; Gross, Garrett G.
- Journal of Molecular Biology, Vol. 429, Issue 4
Towards automated crystallographic structure refinement with phenix.refine
journal, March 2012
- Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel
- Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
journal, August 2013
- Salomon-Ferrer, Romelia; Götz, Andreas W.; Poole, Duncan
- Journal of Chemical Theory and Computation, Vol. 9, Issue 9
Inhibition of RAS function through targeting an allosteric regulatory site
journal, November 2016
- Spencer-Smith, Russell; Koide, Akiko; Zhou, Yong
- Nature Chemical Biology, Vol. 13, Issue 1
Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface
journal, June 2020
- Shigdel, Uddhav K.; Lee, Seung-Joo; Sowa, Mathew E.
- Proceedings of the National Academy of Sciences, Vol. 117, Issue 29
Resveratrol serves as a protein-substrate interaction stabilizer in human SIRT1 activation
journal, November 2016
- Hou, Xuben; Rooklin, David; Fang, Hao
- Scientific Reports, Vol. 6, Issue 1
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
journal, April 2012
- Götz, Andreas W.; Williamson, Mark J.; Xu, Dong
- Journal of Chemical Theory and Computation, Vol. 8, Issue 5
K-Ras Populates Conformational States Differently from Its Isoform H-Ras and Oncogenic Mutant K-RasG12D
journal, June 2018
- Parker, Jillian A.; Volmar, Alicia Y.; Pavlopoulos, Spiro
- Structure, Vol. 26, Issue 6
Cytosolic delivery of proteins by cholesterol tagging
journal, June 2020
- Tai, Wanyi; Zhao, Pengfei; Gao, Xiaohu
- Science Advances, Vol. 6, Issue 25
Targeting Endogenous K-RAS for Degradation through the Affinity-Directed Protein Missile System
journal, September 2020
- Röth, Sascha; Macartney, Thomas J.; Konopacka, Agnieszka
- Cell Chemical Biology, Vol. 27, Issue 9
Development and testing of a general amber force field
journal, January 2004
- Wang, Junmei; Wolf, Romain M.; Caldwell, James W.
- Journal of Computational Chemistry, Vol. 25, Issue 9
A Rational Approach for Creating Peptides Mimicking Antibody Binding
journal, January 2019
- Sachdeva, Sameer; Joo, Hyun; Tsai, Jerry
- Scientific Reports, Vol. 9, Issue 1
Phthalimide conjugation as a strategy for in vivo target protein degradation
journal, May 2015
- Winter, G. E.; Buckley, D. L.; Paulk, J.
- Science, Vol. 348, Issue 6241
Targeted Protein Degradation through Cytosolic Delivery of Monobody Binders Using Bacterial Toxins
journal, April 2019
- Schmit, Nadine Eliane; Neopane, Katyayanee; Hantschel, Oliver
- ACS Chemical Biology, Vol. 14, Issue 5
Engineered protein scaffolds as leads for synthetic inhibitors of protein–protein interactions
journal, June 2018
- Wuo, Michael G.; Arora, Paramjit S.
- Current Opinion in Chemical Biology, Vol. 44
Drugging the undruggable RAS: Mission Possible?
journal, October 2014
- Cox, Adrienne D.; Fesik, Stephen W.; Kimmelman, Alec C.
- Nature Reviews Drug Discovery, Vol. 13, Issue 11
A Raf-Competitive K-Ras Binder Can Fail to Functionally Antagonize Signaling
journal, May 2018
- Kauke, Monique J.; Tisdale, Alison W.; Kelly, Ryan L.
- Molecular Cancer Therapeutics, Vol. 17, Issue 8
PROTACs: great opportunities for academia and industry
journal, December 2019
- Sun, Xiuyun; Gao, Hongying; Yang, Yiqing
- Signal Transduction and Targeted Therapy, Vol. 4, Issue 1
RAS-targeted therapies: is the undruggable drugged?
journal, June 2020
- Moore, Amanda R.; Rosenberg, Scott C.; McCormick, Frank
- Nature Reviews Drug Discovery, Vol. 19, Issue 8
An engineered protein antagonist of K-Ras/B-Raf interaction
journal, July 2017
- Kauke, Monique J.; Traxlmayr, Michael W.; Parker, Jillian A.
- Scientific Reports, Vol. 7, Issue 1
A potent KRAS macromolecule degrader specifically targeting tumours with mutant KRAS
journal, June 2020
- Bery, Nicolas; Miller, Ami; Rabbitts, Terry
- Nature Communications, Vol. 11, Issue 1
Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition
journal, January 2020
- Xue, Jenny Y.; Zhao, Yulei; Aronowitz, Jordan
- Nature, Vol. 577, Issue 7790
Targeting the α4–α5 dimerization interface of K-RAS inhibits tumor formation in vivo
journal, December 2018
- Khan, Imran; Spencer-Smith, Russell; O’Bryan, John P.
- Oncogene, Vol. 38, Issue 16
Molecular Mechanism for Conformational Dynamics of Ras·GTP Elucidated from In-Situ Structural Transition in Crystal
journal, May 2016
- Matsumoto, Shigeyuki; Miyano, Nao; Baba, Seiki
- Scientific Reports, Vol. 6, Issue 1
Drugging an undruggable pocket on KRAS
journal, July 2019
- Kessler, Dirk; Gmachl, Michael; Mantoulidis, Andreas
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 32
Knockdown of Oncogenic KRAS in Non–Small Cell Lung Cancers Suppresses Tumor Growth and Sensitizes Tumor Cells to Targeted Therapy
journal, February 2011
- Sunaga, Noriaki; Shames, David S.; Girard, Luc
- Molecular Cancer Therapeutics, Vol. 10, Issue 2
The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity
journal, October 2019
- Canon, Jude; Rex, Karen; Saiki, Anne Y.
- Nature, Vol. 575, Issue 7781
Facile target validation in an animal model with intracellularly expressed monobodies
journal, July 2018
- Gupta, Ankit; Xu, Jing; Lee, Shirley
- Nature Chemical Biology, Vol. 14, Issue 9
Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor
journal, January 2018
- Janes, Matthew R.; Zhang, Jingchuan; Li, Lian-Sheng
- Cell, Vol. 172, Issue 3
Targeted Degradation of Oncogenic KRAS G12C by VHL-Recruiting PROTACs
journal, July 2020
- Bond, Michael J.; Chu, Ling; Nalawansha, Dhanusha A.
- ACS Central Science, Vol. 6, Issue 8
Design of protein function leaps by directed domain interface evolution
journal, April 2008
- Huang, J.; Koide, A.; Makabe, K.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 18
HKL -3000: the integration of data reduction and structure solution – from diffraction images to an initial model in minutes
journal, July 2006
- Minor, Wladek; Cymborowski, Marcin; Otwinowski, Zbyszek
- Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 8
Tumour suppression by the human von Hippel-Lindau gene product
journal, August 1995
- Iliopoulos, Othon; Kibel, Adam; Gray, Steven
- Nature Medicine, Vol. 1, Issue 8
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
journal, July 2015
- Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik
- Journal of Chemical Theory and Computation, Vol. 11, Issue 8
An mRNA Vaccine against SARS-CoV-2 — Preliminary Report
journal, November 2020
- Jackson, Lisa A.; Anderson, Evan J.; Rouphael, Nadine G.
- New England Journal of Medicine, Vol. 383, Issue 20
The fibronectin type III domain as a scaffold for novel binding proteins
journal, December 1998
- Koide, Akiko; Bailey, Charles W.; Huang, Xiaolin
- Journal of Molecular Biology, Vol. 284, Issue 4
NMR-based functional profiling of RASopathies and oncogenic RAS mutations
journal, March 2013
- Smith, M. J.; Neel, B. G.; Ikura, M.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 12
Features and development of Coot
journal, March 2010
- Emsley, P.; Lohkamp, B.; Scott, W. G.
- Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
Allele-specific inhibitors inactivate mutant KRAS G12C by a trapping mechanism
journal, January 2016
- Lito, P.; Solomon, M.; Li, L. -S.
- Science, Vol. 351, Issue 6273
Heterogeneous distribution of K-ras mutations in primary colon carcinomas: implications for EGFR-directed therapy
journal, May 2011
- Oltedal, Satu; Aasprong, Ole Gunnar; Møller, Jannicke H.
- International Journal of Colorectal Disease, Vol. 26, Issue 10
The Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case Study
journal, January 2018
- Burslem, George M.; Smith, Blake E.; Lai, Ashton C.
- Cell Chemical Biology, Vol. 25, Issue 1
Selective targeting of point-mutated KRAS through artificial microRNAs
journal, May 2017
- Acunzo, Mario; Romano, Giulia; Nigita, Giovanni
- Proceedings of the National Academy of Sciences, Vol. 114, Issue 21
K-Ras(G12D)-selective inhibitory peptides generated by random peptide T7 phage display technology
journal, March 2017
- Sakamoto, Kotaro; Kamada, Yusuke; Sameshima, Tomoya
- Biochemical and Biophysical Research Communications, Vol. 484, Issue 3
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
journal, July 2004
- Dolinsky, T. J.; Nielsen, J. E.; McCammon, J. A.
- Nucleic Acids Research, Vol. 32, Issue Web Server, p. W665-W667
Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains
journal, August 2013
- Sha, F.; Gencer, E. B.; Georgeon, S.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 37
AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces
journal, July 2015
- Rooklin, David; Wang, Cheng; Katigbak, Joseph
- Journal of Chemical Information and Modeling, Vol. 55, Issue 8
Exquisitely Specific anti-KRAS Biodegraders Inform on the Cellular Prevalence of Nucleotide-Loaded States
journal, December 2020
- Lim, Shuhui; Khoo, Regina; Juang, Yu-Chi
- ACS Central Science, Vol. 7, Issue 2
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD
journal, March 2015
- Fetics, Susan K.; Guterres, Hugo; Kearney, Bradley M.
- Structure, Vol. 23, Issue 3
Cerulean, Venus, and VenusY67C FRET Reference Standards
journal, December 2006
- Koushik, Srinagesh V.; Chen, Huanmian; Thaler, Christopher
- Biophysical Journal, Vol. 91, Issue 12
Teaching an Old Scaffold New Tricks: Monobodies Constructed Using Alternative Surfaces of the FN3 Scaffold
journal, January 2012
- Koide, Akiko; Wojcik, John; Gilbreth, Ryan N.
- Journal of Molecular Biology, Vol. 415, Issue 2
The Protein Data Bank
journal, May 2002
- Berman, Helen M.; Battistuz, Tammy; Bhat, T. N.
- Acta Crystallographica Section D Biological Crystallography, Vol. 58, Issue 6
RAS Proteins and Their Regulators in Human Disease
journal, June 2017
- Simanshu, Dhirendra K.; Nissley, Dwight V.; McCormick, Frank
- Cell, Vol. 170, Issue 1
The PDB_REDO server for macromolecular structure model optimization
journal, May 2014
- Joosten, Robbie P.; Long, Fei; Murshudov, Garib N.
- IUCrJ, Vol. 1, Issue 4
Phaser crystallographic software
journal, July 2007
- McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
- Journal of Applied Crystallography, Vol. 40, Issue 4
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
journal, June 2013
- Roe, Daniel R.; Cheatham, Thomas E.
- Journal of Chemical Theory and Computation, Vol. 9, Issue 7
Partial molar volumes of proteins: amino acid side-chain contributions derived from the partial molar volumes of some tripeptides over the temperature range 10–90°C
journal, November 1999
- Häckel, Marko; Hinz, Hans-Jürgen; Hedwig, Gavin R.
- Biophysical Chemistry, Vol. 82, Issue 1