RAS Drug Discovery

Past, Present and Future

1st Edition - October 8, 2024
Imprint: Elsevier
Editors: Adrian Gill, Kevan M. Shokat
Language: English
Paperback ISBN:
9 7 8 - 0 - 4 4 3 - 2 1 8 6 1 - 3
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 1 8 6 2 - 0

KRAS Drug Discovery: Past, Present and Future is a comprehensive overview of the state-of-the-art medicinal chemistry approaches towards targeting the formerly undruggab… Read more

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KRAS Drug Discovery: Past, Present and Future is a comprehensive overview of the state-of-the-art medicinal chemistry approaches towards targeting the formerly undruggable oncogene, KRAS. It includes Seminal medicinal chemistry case histories of KRASG12C inhibitors such as Sotorosib, the first approved KRASG12C inhibitor for NSCLC, alongside the latest advances towards identification of in vivo tools and development candidates targeting KRAS G12D, KRAS G13C and other mutations. The book also provides the reader with a comprehensive overview of the in vitro assay systems, in vivo pharmacology xenograft models and chemical biology tools available to characterize small molecule inhibitors of KRAS.

Title of Book
Cover image
Title page
Table of Contents
Copyright
Contributors
Editor biographies
RAS Hall of Fame
Foreword
Preface
Personal acknowledgements
Introduction
1. Introduction to RAS biology
RAS discovery: Origins in the study of oncogenic retroviruses
NIH/3T3 focus formation assay detection of human cancer transforming genes identify RAS as the first cancer genes
Detection of activated oncogenes in human cancer cell lines and tumors
Activated human cancer cell line oncogenes are homologs of viral RAS genes
Mechanisms of activation of human cancer–associated RAS genes
RAS mutations in human cancer
KRAS structure and biochemistry
RAS in model organisms
RAS therapeutics
KRAS posttranslational processing and plasma membrane association: The first wave of antiRAS drug discovery
KRAS effectors
RAF-MEK-ERK MAPK signaling network
Other key KRAS effectors
Synthetic lethal screens
Direct targeting of RAS
RAS proteins as antigens
The future of RAS research and therapy
Glossary
2. Targeting RAS membrane association
Introduction
Membrane targeting by protein prenylation and acylation
CaaX protein prenyltransferases
Farnesyltransferase
Protein geranylgeranyltransferase type I
Development of FTIs and clinical trials
Alternative prenylation
Postprenylation processing enzymes for CaaX proteins: RCE1 and ICMT
RAS-converting enzyme 1 proteolysis
The final step in processing of the CaaX motif: ICMT-catalyzed carboxyl methylation
Conclusion
Glossary
3. Advancing KRAS drug discovery: A deep dive into biochemical, biophysical, and cellular assays for the identification and optimization of KRAS inhibitors
Introduction
Biophysical methods
Mass spectrometry (MS)
Surface plasmon resonance (SPR)
Microscale thermophoresis (MST)
Differential scanning fluorimetry (DSF)/nanoDSF
Proximity-based techniques and assays for studying KRAS in drug discovery
FRET (Förster resonance energy transfer)
NanoBRET® (Nano-luciferase-based bioluminescence resonance energy transfer)
AlphaLISA® (amplified luminescent proximity homogeneous assay)
Cell viability assays
Cell health by redox activity
Cell health by ATP and luciferase
Cell functional assays
Western blots
ELISA
Multiplexing: Flow cytometry and FACS
Immunofluorescence and fluorescence microscopy
Future perspective
Glossary
4. KRAS-driven cancer models for in vivo pharmacology and drug discovery
Introduction
Landscape of 2D and 3D preclinical models
KRAS inhibitor profiling in cell line models
Patient-derived organoid models
Mouse models in KRAS drug development
Cell-line-derived xenograft models
Patient-derived xenograft models
Syngeneic/allograft models
Genetically engineered mouse models of KRAS-mutant cancers
Mouse models of KRAS-mutant pancreatic ductal adenocarcinoma
Mouse models of KRAS-mutant colon cancer
Mouse models of KRAS-mutant lung cancer
Modeling allele-specific differences in oncogenic KRAS
Preclinical pharmacology of KRAS inhibitors in animal models of cancer
Pharmacokinetics and pharmacodynamics
Evaluating therapeutic activity and tolerability of RAS-targeted drugs in mouse models
Conclusions and perspectives
Glossary
5. The evolution of RAS structural biology: From structures to therapeutic advances
Introduction
RAS mutations in cancer and RASopathy syndromes
RAS structures in active and inactive states: Insights into switch regions
Active RAS: State 1 versus state 2 conformations
Prenylated KRAS4b–PDEδ complex: Insights into hypervariable region structure
RAS activation by GEFs
RAS inactivation by GAPs
RAS–effector interactions
RAS proteins cluster via C-terminal anchor and phospholipid interactions
Targeting KRASG12C: Discovery of the switch-II pocket
Dual inhibitors targeting active and inactive KRASG12C
Exploiting switch-II pocket for targeting non-G12C mutant of KRAS
Exploring beyond the switch-II pocket for targeting KRAS or KRASG12C
Pan-RAS and pan-KRAS Inhibitors
Targeting KRAS–membrane interface
Biologics as RAS inhibitors
Future directions and challenges ahead
Glossary
Section 1. First-generation KRAS G12C OFF inhibitors
6. Covalently targeting KRAS G12C: From inception to the first in vivo proof of concept with ARS-1620
Introduction
Starting points
Methodology advancements applied through mass spectrometry
Discovery of the quinazoline scaffold
Optimization of quinazoline scaffold leading to discovery of ARS1620
In vivo characterization of ARS-1620
A surprising role for KRAS in its covalent inactivation
Summary of ARS1620 SAR journey
Glossary
7. LUMAKRAS® (sotorasib): Novel strategies and clinical experience
Conception: Targeting KRASG12C
Starting points: Covalent screening campaigns
Series I: Covalent switch-II pocket binders result in KRASG12C functional inhibitors
Series II: Larger purpose-built covalent screening libraries and the identification of a novel cryptic pocket
Series III: Mitigating metabolic liabilities and optimizing potency
Lead optimization: Cryptic pockets, atropisomerism, and pharmaceutical properties
Translational science: Pharmacology and proof-of-concept
Clinical development: Monotherapy efficacy and diverse tumor settings
Clinical development: Resistance and combination therapy
Glossary
8. Discovery and development of Krazati (adagrasib/MRTX849), a potent, selective, orally bioavailable, covalent KRASG12C(OFF) inhibitor
Introduction—targeting KRASG12C
Discovery of Krazati (adagrasib/MRTX849)
Medicinal chemistry lead optimization
In vitro characterization
DMPK characterization
In vivo characterization—translational science and pharmacology
Preclinical in vitro and in vivo combination studies
Clinical development: Single agent therapy, emergence of resistance, and combination therapy
Conclusion
Glossary
9. Discovery of JDQ443 (opnurasib): A structurally diverse KRASG12C inhibitor
Introduction
Identification and optimization of the pyrazole chemotype
Lead optimization leading to the discovery of JDQ443
Glossary
10. KRAS degraders
Introduction
PROTACs
Molecular glues
Is KRAS a good target for protein degradation?
Potential advantages of KRAS degradation over inhibition
Evidence of KRAS endogenous degradation
Interaction between Wnt/β-catenin and RAS–ERK pathways
Interplay between NEDD4-1 RAS and PTEN
LTZR1 is a regulator of RAS ubiquitination and signaling
Current strategies for degrading KRAS
KRASG12C covalent heterobifunctional degraders
Combination of ARS1620 and CRBN E3 recruiting
Combination of MRTX849 and VHL E3 recruiting
KRAS G12D and pan-KRAS heterobifunctional degraders
BioPROTACs
Conclusion and perspectives
Glossary
Section 2. Second-generation G12C inhibitors and new modalities
11. Discovery of RMC-6291, a potent, orally bioavailable, covalent RAS(ON) G12C selective inhibitor
Introduction
Tri-complex technology and mechanism of action of RMC-6291
Discovery of early chemical matter
Lead optimization
RMC-6291 development candidate profile
RMC-6291 preclinical activity
Advantages of a RAS(ON) inhibitor: Rapid target engagement and insensitivity to adaptive resistance
RMC-6291: Superior response rates and durability in mouse clinical trial with 25 KRASG12C NSCLC models
RMC-6291 drives deep and durable tumor regressions in NSCLC brain metastasis model
Conclusion
Glossary
Section 3. Beyond KRAS G12C
12. The emergence of pan-KRAS drugs
KRAS introduction and the need for pan-KRAS inhibition
KRAS mutations in cancer
The rationale for pan-KRAS drugs
The structural challenge of pan inhibition
Definition of a pan-KRAS drug
Targeting the three pockets on KRAS
Which state to target—ON or OFF?
Which pocket to choose?
Which conformation?
KRAS chemical matter
Starting with KRASG12C
KRASG12D inhibitors
Pan-RAS inhibition
The first pan-KRAS inhibitor
Fragment first approach
Growing through the Glu-His-Tyr lid to G12C
In vitro pan-KRAS inhibitor BI-2865
Selectivity against NRAS and HRAS
Pan KRAS selectivity
In vivo pan-KRAS inhibitor BI-2493
Pan-KRAS inhibitor BI-3706674
pan-KRAS degraders
KRAS PROTAC introduction
VHL-based pan-KRAS PROTACs
Degradation versus inhibition
In vivo efficacy
Future of the field
Glossary
13. Development of RMC-6236, a potent and orally bioavailable RAS(ON) multi-selective tri-complex inhibitor for the treatment of RAS-addicted cancers by targeting multiple RAS variants
Introduction
Tri-complex technology and mechanism of action of RMC-6236
Discovery of initial chemical matter
Lead optimization
RMC-6236 development candidate profile
RMC-6236 inhibits mutant and wild-type K, N, and HRAS
RMC-6236 preclinical activity
Conclusion
Glossary
14. LUNA18, a macrocyclic orally bioavailable peptide pan-RAS inhibitor, discovered from a beyond rule of 5 drug discovery platform
Background and introduction
bRo5 peptide library construction and RAS screening activities
Hit to orally bioavailable cyclic peptide (LUNA18)
Conclusions
Glossary
15. Covalent inhibitors of K-Ras G12S, G12R, and G12D
Introduction to covalent targeting of K-Ras—lessons from K-Ras (G12C)
Challenges in covalent targeting beyond cysteine
Cracking the noncysteine code (K-Ras (G12S))
Arginine covalency and particular challenges of the GTP-state preference of K-Ras (G12R)
Overcoming the weak nucleophilicity of aspartate to target the most frequent allele, K-Ras (G12D)
Challenges and opportunities in covalent targeting beyond cysteine
Glossary
16. Discovery and development of MRTX1133, a potent, selective, noncovalent inhibitor of KRASG12D
Conclusion
Glossary
17. KRAS combination strategies: How well aligned is clinical and preclinical research?
Introduction
Preclinical insights
Resistance to KRAS inhibitors
Preclinical evaluation of combination therapies
Clinical insights
Contrasts with preclinical investigation
Resistance to KRASG12C inhibitors in the clinic
How are KRASG12C inhibitor combinations performing in the clinic?
Sotorasib combinations
Adragrasib combinations
Combinations in other KRASG12C inhibitors
Research in progress
RAS isoforms
MYC
Microtubule function
Aurora kinase A
Drug and xenobiotic metabolizing enzymes
Future clinical and translational priorities
Toxicity: Innovative ways to progress with combination strategies
Efficacy: Prioritizing clinical approaches to a multitude of RAS inhibitors
Glossary
18. Immune-oncology potential of KRAS inhibitors
Introduction
Oncogenic KRAS signaling drives immune evasion
Oncogenic KRAS inhibition reverses immune evasion
Clinical translation
Future directions
Glossary
19. The RAS competitive landscape
RAS competitive landscape introduction
Biopharma industry competition
Approaches to drugging RAS—a plethora of modalities
The competitive landscape by RAS mutation type
KRASG12C competitive landscape
KRASG12D competitive landscape
KRASG12V competitive landscape
Other mutant-selective RAS programs
Spectrum-selective RAS inhibitor competitive landscape
The SOS1 and SHP2 competitive landscape
Glossary
20. Conclusions: the future of RAS drug discovery
Index

Adrian Gill

Adrian has over 25 years of drug discovery and development experience in senior roles across a diverse range of disease areas in both large pharma and biotech environments and been heavily involved in the identification of multiple clinical candidates across a variety of disease areas. He is a co-inventor of RMC-4630, Revolution Medicines first development candidate selectively targeting SHP2 and RMC-5552, a bi-steric inhibitor which selectively targets mTORC1. Adrian has been instrumental in the design and development of four more recent RAS(ON) development candidates from the Revolution Medicines tri-complex inhibitor platform and is also a co-inventor of RMC-6236 (RAS MULTI inhibitor), RMC-6291(KRASG12C inhibitor), RMC-8839 (KRASG13C inhibitor) and RMC-9805(KRASG12D inhibitor). Adrian has authored over 25 publications in peer-reviewed journals, is a named inventor on over 45 issued and pending small molecule patent applications and has given multiple invited presentations at national and international conferences. Adrian received his Ph.D. in organic chemistry from the University of Sussex, U.K. and has a bachelor’s degree in applied chemistry from the University of Salford, U.K. Adrian is a member of the Royal Society of Chemistry, the SCI, the American Chemical Society and an invited member of the AACR Chemistry in Cancer Research (CICR) Steering Committee. Adrian is also a member of XPose Therapeutics and Curve Therapeutics scientific advisory boards and an honorary Prof. of Drug Discovery at the Sussex University Drug Discovery Center, UK.

Affiliations and expertise

SVP Discovery Chemistry, Revolution Medicines Inc., USA

Kevan M. Shokat

Professor Kevan is currently an Investigator of the Howard Hughes Medical Institute, Chair of the Department of Cellular and Molecular Pharmacology at UCSF and a Professor of Chemistry at UC Berkeley. He was inducted into the National Academy of Sciences (2010), the Institute of Medicine (2011), and the American Academy of Arts and Sciences (2011). His lab is most well-known for drugging the "undruggable" oncogene K-Ras (G12C) in 2013. In May of 2021 the drug sotorasib which binds to the same pocket on K-Ras (G12C) was approved for the treatment of lung cancer patients with this mutation. The field of K-Ras drug discovery is expanding quickly to hunt for drugs to target the other K-Ras mutants such as those which drive colon and pancreatic cancers which collectively represent almost 20% of all cancer patients world-wide. Kevan has been a co-founder of a number companies from their inception to public offering or acquisition and he is a co-founder of several currently private companies.

Affiliations and expertise

Department of Cellular and Molecular Pharmacology at UCSF; Professor of Chemistry at UC Berkeley; Howard Hughes Medical Institute investigator, USA

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