4.6 Review

Recent Advances in Covalent Drug Discovery

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Article Pharmacology & Pharmacy

Adagrasib: First Approval

Sohita Dhillon

Summary: Adagrasib is an orally available small molecule inhibitor being developed by Mirati Therapeutics for the treatment of solid tumors with KRAS G12C mutation. It covalently binds to the mutant cysteine and locks the mutant KRAS protein in its inactive state, inhibiting downstream signaling. In December 2022, it received accelerated approval in the USA for KRAS G12C-mutated NSCLC. It is currently under regulatory review in the EU and in development for CRC.
Article Oncology

First-in-Human Phase I/IB Dose-Finding Study of Adagrasib (MRTX849) in Patients With Advanced KRASG12C Solid Tumors (KRYSTAL-1)

Sai-Hong Ignatius Ou et al.

Summary: This study reported the results of a clinical trial using adagrasib to treat non-small-cell lung cancer, colorectal cancer, and other solid tumors with the KRAS(G12C) mutation. The recommended phase II dose was identified as 600 mg twice a day, and it demonstrated good tolerability and antitumor activity.

JOURNAL OF CLINICAL ONCOLOGY (2022)

Review Chemistry, Multidisciplinary

An outlook on suicide enzyme inhibition and drug design

Mina Hajizadeh et al.

Summary: This review investigates the importance of suicide enzyme inhibition in drug design, treatment, and industrial applications. The development of biomimetic artificial enzymes to prevent inhibition and the classification of suicide enzyme inactivation classes based on target enzyme groups were highlighted as key points to address severe diseases.

JOURNAL OF THE IRANIAN CHEMICAL SOCIETY (2022)

Review Oncology

Targeting KRAS G12C with Covalent Inhibitors

Jonathan M. L. Ostrem et al.

Summary: Efforts to target the mutant cysteine of KRAS G12C have shown promising results, with some molecules already in clinical trials.

ANNUAL REVIEW OF CANCER BIOLOGY (2022)

Article Chemistry, Medicinal

Main protease mutants of SARS-CoV-2 variants remain susceptible to nirmatrelvir

Sven Ullrich et al.

Summary: The COVID-19 pandemic continues to pose a threat to public health, with emerging variants of SARS-CoV-2 potentially impacting the effectiveness of available vaccines. However, research suggests that the specific M-pro inhibitor nirmatrelvir remains effective against these variants.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2022)

Article Pharmacology & Pharmacy

Nirmatrelvir Plus Ritonavir: First Approval

Yvette N. Lamb

Summary: Nirmatrelvir plus ritonavir is a medication developed for the treatment and post-exposure prophylaxis of COVID-19. It received authorization in the UK and EU for use in adults at high risk for severe COVID-19. Nirmatrelvir is an inhibitor of SARS-CoV-2 main protease, while ritonavir is a protease inhibitor and CYP3A inhibitor.
Article Chemistry, Medicinal

Emerging Approaches to Overcome Acquired Drug Resistance Obstacles to Osimertinib in Non-Small-Cell Lung Cancer

Matin Shaikh et al.

Summary: Osimertinib, a pyrimidine core-containing compound, is the only third-generation EGFR-TKI approved to target T790M resistance, but the C797S mutation may hamper its efficacy. Further research on overcoming resistance mechanisms is needed for effective treatment of NSCLC patients.

JOURNAL OF MEDICINAL CHEMISTRY (2022)

Article Chemistry, Medicinal

The Ascension of Targeted Covalent Inhibitors

Juswinder Singh

Summary: Covalent drugs have had a significant impact on human health, but they were previously avoided by the pharmaceutical industry due to concerns about potential toxicity. However, there has been a resurgence in interest with the clinical success of targeted covalent inhibitors (TCIs) and the approval of eight drugs in the past decade. The ability to create unique drugs through the covalent mechanism of action has led to clinically decisive target product profiles. TCIs have revolutionized the treatment approach for non-small-cell lung cancer and chronic lymphocytic leukemia. This Perspective article highlights the clinical and financial success of this drug class and provides early insights into toxicity, a previously hindering factor in the field.

JOURNAL OF MEDICINAL CHEMISTRY (2022)

Article Oncology

Phase I Study of JNJ-74699157 in Patients with Advanced Solid Tumors Harboring the KRAS G12C Mutation

Judy Wang et al.

Summary: This study investigated the use of the oral inhibitor JNJ-74699157, targeting the KRAS G12C mutation, in advanced cancer patients. Dose escalation led to dose-limiting toxicities of increased blood CPK and no significant clinical benefit was observed. Further enrollment was stopped due to these findings.

ONCOLOGIST (2022)

Article Multidisciplinary Sciences

Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease

Daniel W. Kneller et al.

Summary: The study designed three covalent hybrid inhibitors that showed comparable antiviral activity to a known drug in vitro. The binding mechanism of these inhibitors to the viral main protease was also analyzed, providing important atomic and thermodynamic details.

NATURE COMMUNICATIONS (2022)

Article Multidisciplinary Sciences

Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19

Hengrui Liu et al.

Summary: The authors have described small molecule inhibitors of the SARS-CoV-2 3CL protease for potential treatment of COVID-19. These inhibitors have shown promising antiviral activity and could serve as valuable tools in controlling the ongoing pandemic.

NATURE COMMUNICATIONS (2022)

Editorial Material Chemistry, Multidisciplinary

The Path to Paxlovid

Bethany Halford

ACS CENTRAL SCIENCE (2022)

Article Chemistry, Medicinal

Discovery of novel SARS-CoV-2 3CL protease covalent inhibitors using deep learning-based screen

Liying Wang et al.

Summary: A deep learning-based stepwise strategy was developed to selectively screen for highly active covalent inhibitors of SARS-CoV-2 3CL protease, providing new possibilities for drug development against COVID-19.

EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY (2022)

Article Chemistry, Medicinal

Small-Molecule Thioesters as SARS-CoV-2 Main Protease Inhibitors: Enzyme Inhibition, Structure-Activity Relationships, Antiviral Activity, and X-ray Structure Determination

Thanigaimalai Pillaiyar et al.

Summary: This study reports the design and synthesis of novel small-molecule thioesters as inhibitors of SARS-CoV-2 main protease (Mpro). The compounds showed excellent inhibition of SARS-CoV-2 Mpro and displayed antiviral activity without toxicity in host cells. Co-crystallization experiments confirmed the binding of the compounds to the catalytic Cys145 residue of the protease. Additionally, the inhibitors also showed potential in inhibiting the Mpro of other beta-coronaviruses, suggesting a broader application in treating coronaviral infections.

JOURNAL OF MEDICINAL CHEMISTRY (2022)

Review Chemistry, Medicinal

Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery

Kirsten McAulay et al.

Summary: Fragment-based drug discovery plays a crucial role in identifying new ligands, and there is increasing interest in targeted covalent inhibitors. Covalent fragment-based approaches have led to the discovery of novel targets and binding sites, including previously considered "undruggable" targets. Understanding the properties and reactivity of these covalent fragments is important in drug discovery.

PHARMACEUTICALS (2022)

Article Chemistry, Multidisciplinary

Targeted Protein Degradation by Electrophilic PROTACs that Stereoselectively and Site-Specifically Engage DCAF1

Yongfeng Tao et al.

Summary: This study reports the discovery of azetidine acrylamides that react stereoselectively and site-specifically with a cysteine in the E3 ligase substrate receptor DCAF1. These findings have the potential to develop electrophilic proteolysis-targeting chimeras (PROTACs) for targeted protein degradation and uncover ligandable sites on E3 ligases that support this process.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

Review Chemistry, Medicinal

The history, mechanism, and perspectives of nirmatrelvir (PF-07321332): an orally bioavailable main protease inhibitor used in combination with ritonavir to reduce COVID-19-related hospitalizations

Ryan P. Joyce et al.

Summary: The rapid development of effective vaccines has decreased hospitalization and mortality rate. However, with the risk of mutated strains, there is an increasing demand for antivirals. Nirmatrelvir is an orally bioavailable antiviral that can be administered in outpatient settings to minimize hospitalizations and death.

MEDICINAL CHEMISTRY RESEARCH (2022)

Article Chemistry, Medicinal

Targeting SARS-CoV-2 Main Protease for Treatment of COVID-19: Covalent Inhibitors Structure-Activity Relationship Insights and Evolution Perspectives

Gabriele La Monica et al.

Summary: This perspective analyzes the current research status of covalent SARS-CoV-2 MPRO inhibitors, including different categories of drugs, their mechanisms, and the roles of pharmacophoric moieties and chiral carbons. The provided analyses of noncovalent and covalent in vitro protocols are helpful for the scientific community to discover more efficient inhibitors.

JOURNAL OF MEDICINAL CHEMISTRY (2022)

Editorial Material Biochemistry & Molecular Biology

The Rise of Molecular Glues

Stuart L. Schreiber

Summary: The 30th anniversary of the discovery of cyclosporin A and FK506 marks a milestone in understanding their role as molecular glues that induce new protein-protein interactions. The emergence of new molecular-glue probes and medications has sparked interest in this field.
Article Biochemistry & Molecular Biology

Recent progress in covalent warheads for in vivo targeting of endogenous proteins

Naoya Shindo et al.

Summary: Covalent drugs modify endogenous target proteins to exert potent and durable activity, with current focus on developing targeted covalent inhibitors (TCIs) to maximize efficacy and minimize toxicity risks. The characteristics of warheads affect the target selectivity of TCIs.

BIOORGANIC & MEDICINAL CHEMISTRY (2021)

Article Multidisciplinary Sciences

Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

Goran Kokic et al.

Summary: Remdesivir is the only FDA-approved drug for treating COVID-19 patients, working by inhibiting the RNA-dependent RNA polymerase (RdRp) of coronaviruses. It hinders RNA synthesis and impairs proofreading by the viral 3'-exonuclease, leading to a stalled replication process.

NATURE COMMUNICATIONS (2021)

Review Biochemistry & Molecular Biology

The rise of covalent proteolysis targeting chimeras

Ronen Gabizon et al.

Summary: Targeted protein degradation through PROTACs has advantages over direct protein inhibition, but faces challenges such as limited E3 ligase selection and the need for strong target binding. Covalent PROTACs have the potential to expand target and E3 ligase pools, improve complex formation kinetics, and provide additional selectivity to degraders.

CURRENT OPINION IN CHEMICAL BIOLOGY (2021)

Article Pharmacology & Pharmacy

Sotorasib: First Approval

Hannah A. Blair

Summary: Sotorasib, a RAS GTPase family inhibitor developed by Amgen, has been granted accelerated approval by the US FDA for the treatment of KRAS G12C-mutated NSCLC patients who have received prior systemic therapy. This milestone marks the first approval for sotorasib in this patient population.
Article Chemistry, Medicinal

Unraveling the Role of Linker Design in Proteolysis Targeting Chimeras

Troy A. Bemis et al.

Summary: A current bottleneck in the development of PROTACs is the empirical nature of linker length structure-activity relationships. A multi-disciplinary approach has been detailed to alleviate this bottleneck. Research has focused on synthetic approaches to increase throughput, advances in structural biology and computational chemistry for rational PROTAC design, and de novo linker design in silico.

JOURNAL OF MEDICINAL CHEMISTRY (2021)

Editorial Material Pharmacology & Pharmacy

Commentary: PROTACs make undruggable targets druggable: Challenge and opportunity

Bin Lu et al.

ACTA PHARMACEUTICA SINICA B (2021)

Review Biochemistry & Molecular Biology

The role of reversible and irreversible covalent chemistry in targeted protein degradation

Hannah Kiely-Collins et al.

Summary: PROTACs are an exciting technology in chemical biology and drug discovery that degrade disease-causing proteins by hijacking the endogenous ubiquitin-proteasome system. This review explores the role of reversible and irreversible covalent chemistry in targeted protein degradation, highlighting the key advantages of targeted covalent inhibitors. They enhance the selectivity of PROTACs, enable access to more of the undruggable proteome, and expand the repertoire of recruited E3 ligases.

CELL CHEMICAL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Covalent PROTACs: the best of both worlds?

Neil P. Grimster

Summary: Covalent PROTACs combine targeted covalent inhibitors (TCIs) and proteolysis targeting chimeras (PROTACs), showing potential for expanding the druggable proteome. While offering advantages, there are also disadvantages to consider.

RSC MEDICINAL CHEMISTRY (2021)

Article Chemistry, Multidisciplinary

A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins

Rodrigo A. Gama-Brambila et al.

Summary: The discovery of clustered regularly interspaced short palindromic repeats and their associated proteins has led to the development of new methods to control Cas proteins, including fusion proteins and PROTACs. Engineering Cas proteins with a pi-clamp system allows for labeling and degradation in live cells, showing a wide range of potential applications in regulating stability and activity of FCPF-tagging proteins through perfluoroaromatics-induced proximity.

JACS AU (2021)

Review Oncology

Inhibitors targeting Bruton's tyrosine kinase in cancers: drug development advances

Tingyu Wen et al.

Summary: BTK inhibitor ibrutinib has revolutionized the management of B-cell malignancies by creating a chemotherapy-free era, with sales exceeding 230 billion dollars in just 6 years and becoming one of the top five best-selling medicines globally. Numerous clinical trials of BTK inhibitors were initiated in the past decade, with around 73 trials intensively announced or updated in the most recent 3 years.

LEUKEMIA (2021)

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Amanda Davies et al.

CLINICAL NUTRITION (2020)

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FDA Approval Summary: Palbociclib for Male Patients with Metastatic Breast Cancer

Suparna Wedam et al.

CLINICAL CANCER RESEARCH (2020)

Article Multidisciplinary Sciences

CRISPR-engineered T cells in patients with refractory cancer

Edward A. Stadtmauer et al.

SCIENCE (2020)

Review Immunology

SARS-CoV-2 Vaccines: Status Report

Fatima Amanat et al.

IMMUNITY (2020)

Review Infectious Diseases

The SARS-CoV-2 outbreak: What we know

Di Wu et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

Article Multidisciplinary Sciences

The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K

Mikolaj Slabicki et al.

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Article Pharmacology & Pharmacy

Remdesivir: First Approval

Yvette N. Lamb

Article Chemistry, Medicinal

Understanding and Improving the Membrane Permeability of VH032-Based PROTACs

Victoria G. Klein et al.

ACS MEDICINAL CHEMISTRY LETTERS (2020)

Review Multidisciplinary Sciences

SARS-CoV-2 vaccines in development

Florian Krammer

NATURE (2020)

Review Biotechnology & Applied Microbiology

Amidase as a versatile tool in amide-bond cleavage: From molecular features to biotechnological applications

Zheming Wu et al.

BIOTECHNOLOGY ADVANCES (2020)

Article Biochemistry & Molecular Biology

Exploring Targeted Degradation Strategy for Oncogenic KRASG12C

Mei Zeng et al.

CELL CHEMICAL BIOLOGY (2020)

Article Chemistry, Physical

The pH dependent mechanisms of non-enzymatic peptide bond cleavage reactions

Yi Sun et al.

PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2020)

Review Chemistry, Organic

Chemical transformations of quaternary ammonium salts via C-N bond cleavage

Zhong-Xia Wang et al.

ORGANIC & BIOMOLECULAR CHEMISTRY (2020)

Article Chemistry, Multidisciplinary

Protein degradation through covalent inhibitor-based PROTACs

Gang Xue et al.

CHEMICAL COMMUNICATIONS (2020)

Review Chemistry, Medicinal

Covalent Inhibition in Drug Discovery

Avick Kumar Ghosh et al.

CHEMMEDCHEM (2019)

Article Chemistry, Physical

Covalent Inhibition Mechanism of Antidiabetic Drugs-Vildagliptin vs Saxagliptin

Yong-Heng Wang et al.

ACS CATALYSIS (2019)

Review Pharmacology & Pharmacy

Bortezomib for the Treatment of Hematologic Malignancies: 15 Years Later

Pawel Robak et al.

DRUGS IN R&D (2019)

Review Pharmacology & Pharmacy

Binding affinity in drug design: experimental and computational techniques

Visvaldas Kairys et al.

EXPERT OPINION ON DRUG DISCOVERY (2019)

Article Biochemistry & Molecular Biology

Targeting KRAS Mutant Cancers with a Covalent G12C-Specific Inhibitor

Matthew R. Janes et al.

Review Chemistry, Multidisciplinary

Structure-based design of targeted covalent inhibitors

Richard Lonsdale et al.

CHEMICAL SOCIETY REVIEWS (2018)

Review Chemistry, Medicinal

Docking of Covalent Ligands: Challenges and Approaches

Christoph Sotriffer

MOLECULAR INFORMATICS (2018)

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Acalabrutinib: First Global Approval

Anthony Markham et al.

Article Biochemical Research Methods

Identification of New ATG4B Inhibitors Based on a Novel High-Throughput Screening Platform

Danqing Xu et al.

SLAS DISCOVERY (2017)

Review Pharmacology & Pharmacy

Targeted protein degradation by PROTACs

Taavi K. Neklesa et al.

PHARMACOLOGY & THERAPEUTICS (2017)

Article Biochemistry & Molecular Biology

Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex

Teresa A. F. Cardote et al.

STRUCTURE (2017)

Review Oncology

Drugging the 'undruggable' cancer targets

Chi V. Dang et al.

NATURE REVIEWS CANCER (2017)

Article Chemistry, Medicinal

Pan Assay Interference Compounds (PAINS) and Other Promiscuous Compounds in Antifungal Research

Martin Pouliot et al.

JOURNAL OF MEDICINAL CHEMISTRY (2016)

Article Chemistry, Multidisciplinary

π-Clamp-mediated cysteine conjugation

Chi Zhang et al.

NATURE CHEMISTRY (2016)

Review Chemistry, Multidisciplinary

Targeted Covalent Inhibitors for Drug Design

Thomas A. Baillie

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Osimertinib: First Global Approval

Sarah L. Greig

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EXPERT OPINION ON DRUG DISCOVERY (2016)

Article Oncology

KRAS as a Therapeutic Target

Frank McCormick

CLINICAL CANCER RESEARCH (2015)

Review Biochemistry & Molecular Biology

Theory and Applications of Covalent Docking in Drug Discovery: Merits and Pitfalls

Hezekiel Mathambo Kumalo et al.

MOLECULES (2015)

Review Pharmacology & Pharmacy

The contributions of Sidney D. Nelson to drug metabolism research

Thomas A. Baillie

DRUG METABOLISM REVIEWS (2015)

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Mechanistic Insights into a Classic Wonder Drug-Aspirin

Jinping Lei et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)

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Ibrutinib: First Global Approval

Fiona Cameron et al.

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In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C

John C. Hunter et al.

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EUROPEAN JOURNAL OF PHARMACOLOGY (2009)

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Beyond Picomolar Affinities: Quantitative Aspects of Noncovalent and Covalent Binding of Drugs to Proteins

Adam J. T. Smith et al.

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Activity-based protein profiling: From enzyme chemistry

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EGFR mutation and resistance of non-small-cell lung cancer to gefitinib

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End points and United States food and drug administration approval of oncology drugs

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