1
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Klett T, Stahlecker J, Jaag S, Masberg B, Knappe C, Lämmerhofer M, Coles M, Stehle T, Boeckler FM. Covalent Fragments Acting as Tyrosine Mimics for Mutant p53-Y220C Rescue by Nucleophilic Aromatic Substitution. ACS Pharmacol Transl Sci 2024; 7:3984-3999. [PMID: 39698266 PMCID: PMC11651176 DOI: 10.1021/acsptsci.4c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 10/30/2024] [Accepted: 11/01/2024] [Indexed: 12/20/2024]
Abstract
The tumor suppressor p53 is frequently mutated in human cancers. The Y220C mutant is the ninth most common p53 cancer mutant and is classified as a structural mutant, as it leads to strong thermal destabilization and degradation by creating a solvent-accessible hydrophobic cleft. To identify small molecules that thermally stabilize p53, we employed DSF to screen SNAr-type electrophiles from our covalent fragment library (CovLib) for binding to different structural (Y220C, R282W) and DNA contact (R273H) mutants of p53. The reactive fragments SN001, SN006, and SN007 were detected to specifically stabilize Y220C, indicating the arylation of Cys220 in the mutational cleft, as confirmed by X-ray crystallography. The fragments occupy the central cavity and mimic the ring system of the WT tyrosine lost by the mutation. Surpassing previously reported noncovalent ligands, SN001 stabilized T-p53C-Y220C concentration-dependently up to 4.45 °C and, due to its small size, represents a promising starting point for optimization.
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Affiliation(s)
- Theresa Klett
- Lab
for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität
Tübingen, 72076 Tübingen, Germany
| | - Jason Stahlecker
- Lab
for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität
Tübingen, 72076 Tübingen, Germany
| | - Simon Jaag
- Pharmaceutical
(Bio-)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Benedikt Masberg
- Pharmaceutical
(Bio-)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Cornelius Knappe
- Pharmaceutical
(Bio-)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Pharmaceutical
(Bio-)Analysis, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Murray Coles
- Department
of Protein Evolution, Max-Planck-Institute
for Biology, 72076 Tübingen, Germany
| | - Thilo Stehle
- Interfaculty
Institute of Biochemistry, Eberhard Karls
Universität Tübingen, 72076 Tübingen, Germany
| | - Frank M. Boeckler
- Lab
for Molecular Design & Pharm. Biophysics, Institute of Pharmaceutical
Sciences, Eberhard Karls Universität
Tübingen, 72076 Tübingen, Germany
- Interfaculty
Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
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2
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Gai C, Zhang Y, Zhang S, Hu X, Song YQ, Zhuang X, Chai X, Zou Y, Ge GB, Zhao Q. The study of halogen effect on the reactivity of the serine-targeting covalent warheads. Front Chem 2024; 12:1504453. [PMID: 39691824 PMCID: PMC11649397 DOI: 10.3389/fchem.2024.1504453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 11/13/2024] [Indexed: 12/19/2024] Open
Abstract
Halogens favorably contributes to the drug potency and metabolic stability via electrostatic interactions. Herein, the halogen effects on the reactivity of the halogenated 2,2,2-trifluoroacetophenones as serine-targeting covalent warheads were investigated. Our results showed that introducing halogen atoms, especially Cl or Br, into the phenyl scaffold would influence the electron density around the ring, which led to different time-dependent inhibition response to the target serine hydrolase (hCES1A). Co-crystallography analysis not only verified that halogenated molecules preferred to form covalent adducts, but also provided the conformational information for the design of covalent inhibitors targeting to hCES1A protein for the treatment of drug-induced acute enteritis.
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Affiliation(s)
- Conghao Gai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China
| | - Ya Zhang
- Shanghai Frontiers Science Centre of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shihao Zhang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China
| | - Xueyan Hu
- Shanghai Frontiers Science Centre of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yun-Qing Song
- Shanghai Frontiers Science Centre of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoyu Zhuang
- Shanghai Frontiers Science Centre of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoyun Chai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China
| | - Yan Zou
- Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China
| | - Guang-Bo Ge
- Shanghai Frontiers Science Centre of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qingjie Zhao
- Organic Chemistry Group, College of Pharmacy, Naval Medical University, Shanghai, China
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3
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Ficarro SB, Marto ZH, Girardi NM, Deng D, Maisonet IJ, Adelmant G, Fleming LE, Sharafi M, Tavares I, Zhao A, Kim H, Seo HS, Dhe-Paganon S, Buhrlage SJ, Marto JA. Open-source electrophilic fragment screening platform to identify chemical starting points for UCHL1 covalent inhibitors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100198. [PMID: 39622293 DOI: 10.1016/j.slasd.2024.100198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 11/23/2024] [Accepted: 11/26/2024] [Indexed: 12/13/2024]
Abstract
Target-based screening of covalent fragment libraries with mass spectrometry has emerged as a powerful strategy to identify chemical starting points for small molecule inhibitors or find new binding pockets on proteins of interest. These libraries span diverse chemical space with a modest number of compounds. Screening covalent fragments against purified protein targets reduces the demands on the mass spectrometer with respect to absolute throughput, detection limit, and dynamic range. Given these relaxed analytical requirements, we sought to develop an open-source, medium-throughput mass spectrometry system for target-based covalent fragment screening. Our platform comprises automated, dual LC desalting columns integrated with electrospray ionization for rapid sample introduction and mass spectrometry detection. The system is operated through a simple Python graphical user interface running on commodity microcontroller boards which allow integration with diverse liquid chromatography and mass spectrometry instruments. We provide scripts for fragment pooling, construction of sample batches, along with routines for data processing and visualization. The system enables primary screening of ∼10,000 covalent fragments per day in pooled format. In a proof-of-concept study we executed primary and secondary screens to identify 27 hit fragments against UCHL1, a deubiquitinating enzyme that is emerging as a drug target of interest across multiple clinical indications. We validated and triaged these covalent compounds through a series of orthogonal biochemical and chemoproteomic assays. The most promising chloroacetamide covalent fragment inhibited UCHL1 activity in vitro (IC50 < 5 µM) and exhibited dose-dependent binding along with good selectivity against 57 cellular DUBs as quantified by activity-based protein profiling.
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Affiliation(s)
- Scott B Ficarro
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zachary H Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicholas M Girardi
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dingyu Deng
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isabella Jaen Maisonet
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Guillaume Adelmant
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura E Fleming
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mona Sharafi
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Isidoro Tavares
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew Zhao
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - HyoJeon Kim
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hyuk-Soo Seo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Chemical Biology Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Chemical Biology Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA; Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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4
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Antonini G, Bernardi A, Gillon E, Dal Corso A, Civera M, Belvisi L, Varrot A, Mazzotta S. Achieving High Affinity for a Bacterial Lectin with Reversible Covalent Ligands. J Med Chem 2024; 67:19546-19560. [PMID: 39480244 DOI: 10.1021/acs.jmedchem.4c01876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2024]
Abstract
High-affinity monovalent ligands for lectins are challenging to develop due to weak binding interactions. This study investigates the potential of rationally designed covalent ligands targeting the N-terminal domain of BC2L-C lectin from Burkholderia cenocepacia, a pathogen causing severe respiratory infections in immunocompromised patients. Antiadhesion therapy is emerging as a complementary approach against such infections, and bacterial lectins are suitable targets. The fucose-specific BC2L-C-Nt recognizes blood group oligosaccharides on host cells. Using a computational approach, we designed reversible covalent competitive ligands that include a fucoside anchor and a salicylaldehyde warhead targeting Lys108 near the fucose-binding site. Several candidates were synthesized and tested using competition experiments. The most effective ligand improved the IC50 of methyl-fucoside by 2 orders of magnitude, matching the affinity of the native H-type 1 trisaccharide. Control experiments confirmed the importance of both fucose anchor and salicylaldehyde moiety in the ligand's affinity. Mass analysis confirmed the covalent interaction with Lys108.
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Affiliation(s)
- Giulia Antonini
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Anna Bernardi
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Emilie Gillon
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
| | - Alberto Dal Corso
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Monica Civera
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Laura Belvisi
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
| | | | - Sarah Mazzotta
- Dipartimento di Chimica, Università degli Studi di Milano, 20133 Milano, Italy
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5
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Sharma R, Oyagawa CRM, Abbasi H, Dragunow M, Conole D. Phenotypic approaches for CNS drugs. Trends Pharmacol Sci 2024; 45:997-1017. [PMID: 39438155 DOI: 10.1016/j.tips.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/09/2024] [Accepted: 09/19/2024] [Indexed: 10/25/2024]
Abstract
Central nervous system (CNS) drug development is plagued by high clinical failure rate. Phenotypic assays promote clinical translation of drugs by reducing complex brain diseases to measurable, clinically valid phenotypes. We critique recent platforms integrating patient-derived brain cells, which most accurately recapitulate CNS disease phenotypes, with higher throughput models, including immortalized cells, to balance validity and scalability. These platforms were screened with conventional commercial chemogenomic compound libraries. We explore emerging library curation strategies to improve hit rate and quality, and screening novel fragment libraries as alternatives, for more tractable drug target deconvolution. The clinically relevant models used in these platforms could harbor important, unidentified drug targets, so we review evolving agnostic target deconvolution approaches, including chemical proteomics and artificial intelligence (AI), which aid in phenotypic screening hit mechanism elucidation, thereby facilitating rational hit-to-drug optimization.
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Affiliation(s)
- Raahul Sharma
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland 1023, New Zealand; Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland 1023, New Zealand
| | - Caitlin R M Oyagawa
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland 1023, New Zealand
| | - Hamid Abbasi
- Auckland Bioengineering Institute, The University of Auckland, 70 Symonds Street, Auckland, 1010, New Zealand
| | - Michael Dragunow
- Centre for Brain Research, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland 1023, New Zealand.
| | - Daniel Conole
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, University of Auckland, 85 Park Road, Grafton, Auckland 1023, New Zealand.
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6
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Liu Y, Yu Z, Li P, Yang T, Ding K, Zhang ZM, Tan Y, Li Z. Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles. J Am Chem Soc 2024. [PMID: 39018468 DOI: 10.1021/jacs.4c04695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhongtang Yu
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Peishan Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tao Yang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ke Ding
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhi-Min Zhang
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yi Tan
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Zhengqiu Li
- State Key Laboratory of Bioactive Molecules and Druggability Assessment, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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7
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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8
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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9
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Danilack AD, Dickson CJ, Soylu C, Fortunato M, Rodde S, Munkler H, Hornak V, Duca JS. Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design. J Comput Aided Mol Des 2024; 38:21. [PMID: 38693331 DOI: 10.1007/s10822-024-00560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/03/2024]
Abstract
Covalent inhibition offers many advantages over non-covalent inhibition, but covalent warhead reactivity must be carefully balanced to maintain potency while avoiding unwanted side effects. While warhead reactivities are commonly measured with assays, a computational model to predict warhead reactivities could be useful for several aspects of the covalent inhibitor design process. Studies have shown correlations between covalent warhead reactivities and quantum mechanic (QM) properties that describe important aspects of the covalent reaction mechanism. However, the models from these studies are often linear regression equations and can have limitations associated with their usage. Applications of machine learning (ML) models to predict covalent warhead reactivities with QM descriptors are not extensively seen in the literature. This study uses QM descriptors, calculated at different levels of theory, to train ML models to predict reactivities of covalent acrylamide warheads. The QM/ML models are compared with linear regression models built upon the same QM descriptors and with ML models trained on structure-based features like Morgan fingerprints and RDKit descriptors. Experiments show that the QM/ML models outperform the linear regression models and the structure-based ML models, and literature test sets demonstrate the power of the QM/ML models to predict reactivities of unseen acrylamide warhead scaffolds. Ultimately, these QM/ML models are effective, computationally feasible tools that can expedite the design of new covalent inhibitors.
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Affiliation(s)
- Aaron D Danilack
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA.
| | - Callum J Dickson
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Cihan Soylu
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Mike Fortunato
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Stephane Rodde
- Biomedical Research, Novartis, Novartis Campus, 4056, Basel, Switzerland
| | - Hagen Munkler
- Technical Research & Development, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Viktor Hornak
- Merck Research Laboratories, 33 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Jose S Duca
- Biomedical Research, Novartis, 181 Massachusetts Avenue, Cambridge, MA, 02139, USA
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10
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Lithgo RM, Tomlinson CWE, Fairhead M, Winokan M, Thompson W, Wild C, Aschenbrenner JC, Balcomb BH, Marples PG, Chandran AV, Golding M, Koekemoer L, Williams EP, Wang S, Ni X, MacLean E, Giroud C, Godoy AS, Xavier MA, Walsh M, Fearon D, von Delft F. Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591684. [PMID: 38746446 PMCID: PMC11092469 DOI: 10.1101/2024.04.29.591684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Enteroviruses are the causative agents of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher order complications in a large-scale outbreak. The 2A protease of these viruses is responsible for the self-cleavage of the poly protein, allowing for correct folding and assembly of capsid proteins in the final stages of viral replication. These 2A proteases are highly conserved between Enterovirus species, such as Enterovirus A71 and Coxsackievirus A16 . Inhibition of the 2A protease deranges capsid folding and assembly, preventing formation of mature virions in host cells and making the protease a valuable target for antiviral activity. Herein, we describe a crystallographic fragment screening campaign that identified 75 fragments which bind to the 2A protease including 38 unique compounds shown to bind within the active site. These fragments reveal a path for the development of non-peptidomimetic inhibitors of the 2A protease with broad-spectrum anti-enteroviral activity.
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11
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Lucas SCC, Blackwell JH, Hewitt SH, Semple H, Whitehurst BC, Xu H. Covalent hits and where to find them. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100142. [PMID: 38278484 DOI: 10.1016/j.slasd.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK.
| | | | - Sarah H Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | | | - Hua Xu
- Mechanistic and structural Biology, Discovery Sciences, AstraZeneca R&D, Waltham, USA
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12
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Xu X, Han W, Ning X, Zang C, Xu C, Zeng C, Pu C, Zhang Y, Chen Y, Liu H. Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein-Ligand Interactions. J Chem Inf Model 2024; 64:1543-1559. [PMID: 38381562 DOI: 10.1021/acs.jcim.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Noncovalent interactions between small-molecule drugs and protein targets assume a pivotal role in drug design. Moreover, the design of covalent inhibitors, forming covalent bonds with amino acid residues, requires rational reactivity for their covalent warheads, presenting a key challenge as well. Understanding the intricacies of these interactions provides a more comprehensive understanding of molecular binding mechanisms, thereby guiding the rational design of potent inhibitors. In this study, we adopted the fragment-based drug design approach, introducing a novel methodology to extract noncovalent and covalent fragments according to distinct three-dimensional (3D) interaction modes from noncovalent and covalent compound libraries. Additionally, we systematically replaced existing ligands with rational fragment substitutions, based on the spatial orientation of fragments in 3D space. Furthermore, we adopted a molecular generation approach to create innovative covalent inhibitors. This process resulted in the recombination of a noncovalent compound library and several covalent compound libraries, constructed by two commonly encountered covalent amino acids: cysteine and serine. We utilized noncovalent ligands in KLIFS and covalent ligands in CovBinderInPDB as examples to recombine noncovalent and covalent libraries. These recombined compound libraries cover a substantial portion of the chemical space present in the original compound libraries and exhibit superior performance in terms of molecular scaffold diversity compared to the original compound libraries and other 11 commercial libraries. We also recombined BTK-focused libraries, and 23 compounds within our libraries have been validated by former researchers to possess potential biological activity. The establishment of these compound libraries provides valuable resources for virtual screening of covalent and noncovalent drugs targeting similar molecular targets.
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Affiliation(s)
- Xiaohe Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Weijie Han
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Xiangzhen Ning
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chengdong Zang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chengcheng Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chen Zeng
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chengtao Pu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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13
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Keeley A, Kopranovic A, Di Lorenzo V, Ábrányi-Balogh P, Jänsch N, Lai LN, Petri L, Orgován Z, Pölöske D, Orlova A, Németh A, Desczyk C, Imre T, Bajusz D, Moriggl R, Meyer-Almes FJ, Keserü GM. Electrophilic MiniFrags Revealed Unprecedented Binding Sites for Covalent HDAC8 Inhibitors. J Med Chem 2024; 67:572-585. [PMID: 38113354 PMCID: PMC10788917 DOI: 10.1021/acs.jmedchem.3c01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Screening of ultra-low-molecular weight ligands (MiniFrags) successfully identified viable chemical starting points for a variety of drug targets. Here we report the electrophilic analogues of MiniFrags that allow the mapping of potential binding sites for covalent inhibitors by biochemical screening and mass spectrometry. Small electrophilic heterocycles and their N-quaternized analogues were first characterized in the glutathione assay to analyze their electrophilic reactivity. Next, the library was used for systematic mapping of potential covalent binding sites available in human histone deacetylase 8 (HDAC8). The covalent labeling of HDAC8 cysteines has been proven by tandem mass spectrometry measurements, and the observations were explained by mutating HDAC8 cysteines. As a result, screening of electrophilic MiniFrags identified three potential binding sites suitable for the development of allosteric covalent HDAC8 inhibitors. One of the hit fragments was merged with a known HDAC8 inhibitor fragment using different linkers, and the linker length was optimized to result in a lead-like covalent inhibitor.
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Affiliation(s)
- Aaron
B. Keeley
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Aleksandra Kopranovic
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Vincenzo Di Lorenzo
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Niklas Jänsch
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Linh N. Lai
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - László Petri
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Orgován
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Daniel Pölöske
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna Orlova
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - András
György Németh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Charlotte Desczyk
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Tímea Imre
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- MS
Metabolomics
Research Group, Research Centre for Natural
Sciences, Magyar tudósok
krt 2, H-1117 Budapest, Hungary
| | - Dávid Bajusz
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Richard Moriggl
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Franz-Josef Meyer-Almes
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - György M. Keserü
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
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14
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Mehta NV, Degani MS. The expanding repertoire of covalent warheads for drug discovery. Drug Discov Today 2023; 28:103799. [PMID: 37839776 DOI: 10.1016/j.drudis.2023.103799] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
The reactive functionalities of drugs that engage in covalent interactions with the enzyme/receptor residue in either a reversible or an irreversible manner are called 'warheads'. Covalent warheads that were previously neglected because of safety concerns have recently gained center stage as a result of their various advantages over noncovalent drugs, including increased selectivity, increased residence time, and higher potency. With the approval of several covalent inhibitors over the past decade, research in this area has accelerated. Various strategies are being continuously developed to tune the characteristics of warheads to improve their potency and mitigate toxicity. Here, we review research progress in warhead discovery over the past 5 years to provide valuable insights for future drug discovery.
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Affiliation(s)
- Namrashee V Mehta
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
| | - Mariam S Degani
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Nathalal Parekh Marg, Matunga, Mumbai 400019, Maharashtra, India.
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15
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Hocking B, Armstrong A, Mann DJ. Covalent fragment libraries in drug discovery-Design, synthesis, and screening methods. PROGRESS IN MEDICINAL CHEMISTRY 2023; 62:105-146. [PMID: 37981350 DOI: 10.1016/bs.pmch.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
As the development of drugs with a covalent mode of action is becoming increasingly popular, well-validated covalent fragment-based drug discovery (FBDD) methods have been comparatively slow to keep up with the demand. In this chapter the principles of covalent fragment reactivity, library design, synthesis, and screening methods are explored in depth, focussing on literature examples with direct applications to practical covalent fragment library design and screening. Further, questions about the future of the field are explored and potential useful advances are proposed.
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Affiliation(s)
- Brad Hocking
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alan Armstrong
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
| | - David J Mann
- Department of Life Sciences, Imperial College London, London, United Kingdom.
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16
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Stuart DD, Guzman-Perez A, Brooijmans N, Jackson EL, Kryukov GV, Friedman AA, Hoos A. Precision Oncology Comes of Age: Designing Best-in-Class Small Molecules by Integrating Two Decades of Advances in Chemistry, Target Biology, and Data Science. Cancer Discov 2023; 13:2131-2149. [PMID: 37712571 PMCID: PMC10551669 DOI: 10.1158/2159-8290.cd-23-0280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/27/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Small-molecule drugs have enabled the practice of precision oncology for genetically defined patient populations since the first approval of imatinib in 2001. Scientific and technology advances over this 20-year period have driven the evolution of cancer biology, medicinal chemistry, and data science. Collectively, these advances provide tools to more consistently design best-in-class small-molecule drugs against known, previously undruggable, and novel cancer targets. The integration of these tools and their customization in the hands of skilled drug hunters will be necessary to enable the discovery of transformational therapies for patients across a wider spectrum of cancers. SIGNIFICANCE Target-centric small-molecule drug discovery necessitates the consideration of multiple approaches to identify chemical matter that can be optimized into drug candidates. To do this successfully and consistently, drug hunters require a comprehensive toolbox to avoid following the "law of instrument" or Maslow's hammer concept where only one tool is applied regardless of the requirements of the task. Combining our ever-increasing understanding of cancer and cancer targets with the technological advances in drug discovery described below will accelerate the next generation of small-molecule drugs in oncology.
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Affiliation(s)
| | | | | | | | | | | | - Axel Hoos
- Scorpion Therapeutics, Boston, Massachusetts
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17
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Takács G, Havasi D, Sándor M, Dohánics Z, Balogh GT, Kiss R. DIY Virtual Chemical Libraries - Novel Starting Points for Drug Discovery. ACS Med Chem Lett 2023; 14:1188-1197. [PMID: 37736187 PMCID: PMC10510501 DOI: 10.1021/acsmedchemlett.3c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
The advancement of in silico technologies such as library enumeration and synthetic feasibility prediction has made drug discovery pipelines rely more and more on virtual libraries, which provide a significantly larger pool of compounds than in-stock supplier catalogs. Virtual libraries from external sources, however, may be associated with long delivery time and high cost. In this study, we present a Do-It-Yourself (DIY) combinatorial chemistry library containing over 14 million almost completely novel products built from 1000 low-cost building blocks based on robust reactions frequently applied at medicinal chemistry laboratories. The applicability of the DIY library for various drug discovery approaches is demonstrated by extensive physicochemical property, structural diversity profiling, and the generation of focused libraries. We found that internally built DIY chemical libraries present a viable alternative of external virtual catalogs by providing access to a large number of low-cost and quickly accessible potential chemical starting points for drug discovery.
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Affiliation(s)
- Gergely Takács
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Dávid Havasi
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Márk Sándor
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - Zsolt Dohánics
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
| | - György T. Balogh
- Department
of Chemical and Environmental Process Engineering, Faculty of Chemical
Technology and Biotechnology, Budapest University
of Technology and Economics, Műegyetem rakpart 3, Budapest 1111, Hungary
- Department
of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Semmelweis University, Hőgyes Endre utca 7-9, Budapest 1092, Hungary
| | - Róbert Kiss
- Mcule.com
Kft, Bartók Béla
út 105-113, Budapest 1115, Hungary
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18
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Alves ETM, Pernichelle FG, Nascimento LA, Ferreira GM, Ferreira EI. Covalent Inhibitors for Neglected Diseases: An Exploration of Novel Therapeutic Options. Pharmaceuticals (Basel) 2023; 16:1028. [PMID: 37513939 PMCID: PMC10385647 DOI: 10.3390/ph16071028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Neglected diseases, primarily found in tropical regions of the world, present a significant challenge for impoverished populations. Currently, there are 20 diseases considered neglected, which greatly impact the health of affected populations and result in difficult-to-control social and economic consequences. Unfortunately, for the majority of these diseases, there are few or no drugs available for patient treatment, and the few drugs that do exist often lack adequate safety and efficacy. As a result, there is a pressing need to discover and design new drugs to address these neglected diseases. This requires the identification of different targets and interactions to be studied. In recent years, there has been a growing focus on studying enzyme covalent inhibitors as a potential treatment for neglected diseases. In this review, we will explore examples of how these inhibitors have been used to target Human African Trypanosomiasis, Chagas disease, and Malaria, highlighting some of the most promising results so far. Ultimately, this review aims to inspire medicinal chemists to pursue the development of new drug candidates for these neglected diseases, and to encourage greater investment in research in this area.
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Affiliation(s)
- Erick Tavares Marcelino Alves
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Filipe Gomes Pernichelle
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Lucas Adriano Nascimento
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, Butantã, São Paulo 05508-000, Brazil
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19
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Martin MP, Endicott JA, Noble MEM, Tatum NJ. Crystallographic fragment screening in academic cancer drug discovery. Methods Enzymol 2023; 690:211-234. [PMID: 37858530 DOI: 10.1016/bs.mie.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) has brought several drugs to the clinic, notably to target proteins once considered to be challenging, or even undruggable. Screening in FBDD relies upon observing and/or measuring weak (millimolar-scale) binding events using biophysical techniques or crystallographic fragment screening. This latter structural approach provides no information about binding affinity but can reveal binding mode and atomic detail on protein-fragment interactions to accelerate hit-to-lead development. In recent years, high-throughput platforms have been developed at synchrotron facilities to screen thousands of fragment-soaked crystals. However, using accessible manual techniques it is possible to run informative, smaller-scale screens within an academic lab setting. This chapter describes general protocols for home laboratory-scale fragment screening, from fragment soaking through to structure solution and, where appropriate, signposts to background, protocols or alternatives elsewhere.
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Affiliation(s)
- Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Jane A Endicott
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Natalie J Tatum
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom.
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20
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Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov 2023; 18:1221-1230. [PMID: 37592849 PMCID: PMC10620067 DOI: 10.1080/17460441.2023.2246881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
INTRODUCTION Macromolecular X-ray crystallography and cryo-EM are currently the primary techniques used to determine the three-dimensional structures of proteins, nucleic acids, and viruses. Structural information has been critical to drug discovery and structural bioinformatics. The integration of artificial intelligence (AI) into X-ray crystallography has shown great promise in automating and accelerating the analysis of complex structural data, further improving the efficiency and accuracy of structure determination. AREAS COVERED This review explores the relationship between X-ray crystallography and other modern structural determination methods. It examines the integration of data acquired from diverse biochemical and biophysical techniques with those derived from structural biology. Additionally, the paper offers insights into the influence of AI on X-ray crystallography, emphasizing how integrating AI with experimental approaches can revolutionize our comprehension of biological processes and interactions. EXPERT OPINION Investing in science is crucially emphasized due to its significant role in drug discovery and advancements in healthcare. X-ray crystallography remains an essential source of structural biology data for drug discovery. Recent advances in biochemical, spectroscopic, and bioinformatic methods, along with the integration of AI techniques, hold the potential to revolutionize drug discovery when effectively combined with robust data management practices.
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Affiliation(s)
- Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Szczygiel
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Michal Gucwa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Krakow, Poland
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908
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21
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Mahía A, Kiib AE, Nisavic M, Svenningsen EB, Palmfeldt J, Poulsen TB. α-Lactam Electrophiles for Covalent Chemical Biology. Angew Chem Int Ed Engl 2023; 62:e202304142. [PMID: 37114559 DOI: 10.1002/anie.202304142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 04/29/2023]
Abstract
Electrophilic groups are one of the key pillars of contemporary chemical biology and medicinal chemistry. For instance, 3-membered N-heterocyclic compounds-such as aziridines, azirines, and oxaziridines-possess unique electronic and structural properties which underlie their potential and applicability as covalent tools. The α-lactams are also members of this group of compounds, however, their utility within the field remains unexplored. Here, we demonstrate an α-lactam reagent (AM2) that is tolerant to aqueous buffers while being reactive towards biologically relevant nucleophiles. Interestingly, carboxylesterases 1 and 2 (CES1/2), both serine hydrolases with key roles in endo- and xenobiotic metabolism, were found as primary covalent targets for AM2 in HepG2 liver cancer cells. All in all, this study constitutes the starting point for the further development and exploration of α-lactam-based electrophilic probes in covalent chemical biology.
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Affiliation(s)
- Alejandro Mahía
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Anders E Kiib
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Marija Nisavic
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Department of Clinical Medicine-Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Esben B Svenningsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine-Research Unit for Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
| | - Thomas B Poulsen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
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22
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein-Drug Adducts. Pharmaceuticals (Basel) 2023; 16:547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein-drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein-drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; (E.M.)
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23
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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24
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Wang ZZ, Shi XX, Huang GY, Hao GF, Yang GF. Fragment-based drug discovery supports drugging 'undruggable' protein-protein interactions. Trends Biochem Sci 2023; 48:539-552. [PMID: 36841635 DOI: 10.1016/j.tibs.2023.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Protein-protein interactions (PPIs) have important roles in various cellular processes, but are commonly described as 'undruggable' therapeutic targets due to their large, flat, featureless interfaces. Fragment-based drug discovery (FBDD) has achieved great success in modulating PPIs, with more than ten compounds in clinical trials. Here, we highlight the progress of FBDD in modulating PPIs for therapeutic development. Targeting hot spots that have essential roles in both fragment binding and PPIs provides a shortcut for the development of PPI modulators via FBDD. We highlight successful cases of cracking the 'undruggable' problems of PPIs using fragment-based approaches. We also introduce new technologies and future trends. Thus, we hope that this review will provide useful guidance for drug discovery targeting PPIs.
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Affiliation(s)
- Zhi-Zheng Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Xing-Xing Shi
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Guang-Yi Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China.
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China.
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25
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Hope I, Endicott JA, Watt JE. Emerging approaches to CDK inhibitor development, a structural perspective. RSC Chem Biol 2023; 4:146-164. [PMID: 36794018 PMCID: PMC9906319 DOI: 10.1039/d2cb00201a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant activity of the cyclin-dependent kinase family is frequently noted in a number of diseases identifying them as potential targets for drug development. However, current CDK inhibitors lack specificity owing to the high sequence and structural conservation of the ATP binding cleft across family members, highlighting the necessity of finding novel modes of CDK inhibition. The wealth of structural information regarding CDK assemblies and inhibitor complexes derived from X-ray crystallographic studies has been recently complemented through the use of cryo-electron microscopy. These recent advances have provided insights into the functional roles and regulatory mechanisms of CDKs and their interaction partners. This review explores the conformational malleability of the CDK subunit, the importance of SLiM recognition sites in CDK complexes, the progress made in chemically induced CDK degradation and how these studies can contribute to CDK inhibitor design. Additionally, fragment-based drug discovery can be utilised to identify small molecules that bind to allosteric sites on the CDK surface employing interactions which mimic those of native protein-protein interactions. These recent structural advances in CDK inhibitor mechanisms and in chemical probes which do not occupy the orthosteric ATP binding site can provide important insights for targeted CDK therapies.
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Affiliation(s)
- Ian Hope
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jane A Endicott
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Jessica E Watt
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Paul O'Gorman Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
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26
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Hermann MR, Tautermann CS, Sieger P, Grundl MA, Weber A. BIreactive: Expanding the Scope of Reactivity Predictions to Propynamides. Pharmaceuticals (Basel) 2023; 16:ph16010116. [PMID: 36678612 PMCID: PMC9866037 DOI: 10.3390/ph16010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/22/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
We present the first comprehensive study on the prediction of reactivity for propynamides. Covalent inhibitors like propynamides often show improved potency, selectivity, and unique pharmacologic properties compared to their non-covalent counterparts. In order to achieve this, it is essential to tune the reactivity of the warhead. This study shows how three different in silico methods can predict the in vitro properties of propynamides, a covalent warhead class integrated into approved drugs on the market. Whereas the electrophilicity index is only applicable to individual subclasses of substitutions, adduct formation and transition state energies have a good predictability for the in vitro reactivity with glutathione (GSH). In summary, the reported methods are well suited to estimate the reactivity of propynamides. With this knowledge, the fine tuning of the reactivity is possible which leads to a speed up of the design process of covalent drugs.
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27
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Gai C, Harnor SJ, Zhang S, Cano C, Zhuang C, Zhao Q. Advanced approaches of developing targeted covalent drugs. RSC Med Chem 2022; 13:1460-1475. [PMID: 36561076 PMCID: PMC9749957 DOI: 10.1039/d2md00216g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
In recent years, the development of targeted covalent inhibitors has gained popularity around the world. Specific groups (electrophilic warheads) form irreversible bonds with the side chain of nucleophilic amino acid residues, thus changing the function of biological targets such as proteins. Since the first targeted covalent inhibitor was disclosed in the 1990s, great efforts have been made to develop covalent ligands from known reversible leads or drugs by addition of tolerated electrophilic warheads. However, high reactivity and "off-target" toxicity remain challenging issues. This review covers the concept of targeted covalent inhibition to diseases, discusses traditional and interdisciplinary strategies of cysteine-focused covalent drug discovery, and exhibits newly disclosed electrophilic warheads majorly targeting the cysteine residue. Successful applications to address the challenges of designing effective covalent drugs are also introduced.
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Affiliation(s)
- Conghao Gai
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Suzannah J Harnor
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Shihao Zhang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Céline Cano
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, School of Natural and Environmental Sciences, Bedson Building, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Chunlin Zhuang
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
| | - Qingjie Zhao
- Organic Chemistry Group, College of Pharmacy, Naval Medical University Shanghai 200433 P. R. China
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28
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Abstract
Covalent inhibition has emerged as a promising orthogonal approach for drug discovery, despite the significant challenge in achieving target specificity. To facilitate the structure-based rational design of target-specific covalent modulators, we developed an integrated computational protocol to curate covalent binders from the RCSB Protein Data Bank (PDB). Starting from the macromolecular crystallographic information files (mmCIF) in the PDB archive, covalent bond records, which indicate the side chain modification of amino acid residue by a covalent binder, were collected and cleaned. Then, residue-binder adducts, which are products of chemical reactions between targeted residues and covalent binders, were recovered with the help of the Chemical Component Dictionary in PDB. Finally, several strategies were employed to curate the pre-reaction forms of covalent binders from the adducts. Our curated CovBinderInPDB database contains 7375 covalent modifications in which 2189 unique covalent binders target nine types of amino acid residues (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, and Tyr) from 3555 complex structures of 1170 unique protein chains. This database would set a solid foundation for developing and benchmarking computational strategies for covalent modulator design and is freely accessible at https://yzhang.hpc.nyu.edu/CovBinderInPDB.
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Affiliation(s)
- Xiao-Kang Guo
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States, Simons Center for Computational Physical Chemistry, New York University, New York, New York 10003, United States, NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China,
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29
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McAulay K, Bilsland A, Bon M. Reactivity of Covalent Fragments and Their Role in Fragment Based Drug Discovery. Pharmaceuticals (Basel) 2022; 15:1366. [PMID: 36355538 PMCID: PMC9694498 DOI: 10.3390/ph15111366] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 09/27/2023] Open
Abstract
Fragment based drug discovery has long been used for the identification of new ligands and interest in targeted covalent inhibitors has continued to grow in recent years, with high profile drugs such as osimertinib and sotorasib gaining FDA approval. It is therefore unsurprising that covalent fragment-based approaches have become popular and have recently led to the identification of novel targets and binding sites, as well as ligands for targets previously thought to be 'undruggable'. Understanding the properties of such covalent fragments is important, and characterizing and/or predicting reactivity can be highly useful. This review aims to discuss the requirements for an electrophilic fragment library and the importance of differing warhead reactivity. Successful case studies from the world of drug discovery are then be examined.
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Affiliation(s)
- Kirsten McAulay
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Centre for Targeted Protein Degradation, University of Dundee, Nethergate, Dundee DD1 4HN, UK
| | - Alan Bilsland
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Marta Bon
- Cancer Research Horizons—Therapeutic Innovation, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
- Exscientia, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, UK
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30
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Bon M, Bilsland A, Bower J, McAulay K. Fragment-based drug discovery-the importance of high-quality molecule libraries. Mol Oncol 2022; 16:3761-3777. [PMID: 35749608 PMCID: PMC9627785 DOI: 10.1002/1878-0261.13277] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets. Since the number of possible molecules increases exponentially with molecular size, small fragment libraries allow for a proportionately greater coverage of their respective 'chemical space' compared with larger HTS libraries comprising larger molecules. However, good library design is essential to ensure optimal chemical and pharmacophore diversity, molecular complexity, and physicochemical characteristics. In this review, we describe our views on fragment library design, and on what constitutes a good fragment from a medicinal and computational chemistry perspective. We highlight emerging chemical and computational technologies in FBDD and discuss strategies for optimising fragment hits. The impact of novel FBDD approaches is already being felt, with the recent approval of the covalent KRASG12C inhibitor sotorasib highlighting the utility of FBDD against targets that were long considered undruggable.
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Affiliation(s)
- Marta Bon
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Alan Bilsland
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Justin Bower
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Kirsten McAulay
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
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31
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Kennedy C, McPhie K, Rittinger K. Targeting the ubiquitin system by fragment-based drug discovery. Front Mol Biosci 2022; 9:1019636. [PMID: 36275626 PMCID: PMC9580268 DOI: 10.3389/fmolb.2022.1019636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/05/2022] [Indexed: 11/22/2022] Open
Abstract
The ubiquitin system contains a wealth of potential drug targets for many diseases and conditions, including neurodegenerative, immune, metabolic and developmental diseases, as well as multiple cancers. Despite years of research, relatively few clinical inhibitors or specific chemical probes for proteins within the ubiquitin system exist, with many interesting target proteins yet to be explored. Fragment-based drug discovery (FBDD) offers efficient and broad coverage of chemical space with small libraries, using covalent and non-covalent approaches. Coupled with advances in structural biology and proteomics, FBDD now provides a thorough screening platform for inhibitor discovery within the ubiquitin system. In this mini review, we summarise the current scope of FBDD and how it has been applied to ubiquitin-activating (E1), ubiquitin-conjugating (E2), ubiquitin ligase (E3) and deubiquitinating (DUB) enzymes. We also discuss the newest frontiers of FBDD and how they could be applied to enable inhibitor and novel chemical probe discovery and provide functional insight into the ubiquitin system.
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Affiliation(s)
| | | | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, United Kingdom
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32
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St. Denis JD, Chessari G, Cleasby A, Cons BD, Cowan S, Dalton SE, East C, Murray CW, O’Reilly M, Peakman T, Rapti M, Stow JL. X-ray Screening of an Electrophilic Fragment Library and Application toward the Development of a Novel ERK 1/2 Covalent Inhibitor. J Med Chem 2022; 65:12319-12333. [DOI: 10.1021/acs.jmedchem.2c01044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jeffrey D. St. Denis
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Anne Cleasby
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Benjamin D. Cons
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Suzanna Cowan
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Samuel E. Dalton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Charlotte East
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Marc O’Reilly
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Torren Peakman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Magdalini Rapti
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
| | - Jessie L. Stow
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, United Kingdom
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33
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Sun H, Xi M, Jin Q, Zhu Z, Zhang Y, Jia G, Zhu G, Sun M, Zhang H, Ren X, Zhang Y, Xu Z, Huang H, Shen J, Li B, Ge G, Chen K, Zhu W. Chemo- and Site-Selective Lysine Modification of Peptides and Proteins under Native Conditions Using the Water-Soluble Zolinium. J Med Chem 2022; 65:11840-11853. [DOI: 10.1021/acs.jmedchem.2c00937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haiguo Sun
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Mengyu Xi
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qiang Jin
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yani Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guihua Jia
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Guanghao Zhu
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Mengru Sun
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Hongwei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Xuelian Ren
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yong Zhang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - He Huang
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Jingshan Shen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Bo Li
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, No. 38 Xue Yuan Road, Haidian District, Beijing 100191, China
| | - Guangbo Ge
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Kaixian Chen
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- Shanghai Frontiers Science Center of TCM Chemical Biology; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
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34
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Wen W, Cao H, Xu Y, Ren Y, Rao L, Shao X, Chen H, Wu L, Liu J, Su C, Peng C, Huang Y, Wan J. N-Acylamino Saccharin as an Emerging Cysteine-Directed Covalent Warhead and Its Application in the Identification of Novel FBPase Inhibitors toward Glucose Reduction. J Med Chem 2022; 65:9126-9143. [PMID: 35786925 DOI: 10.1021/acs.jmedchem.2c00336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With a resurgence of covalent drugs, there is an urgent need for the identification of new moieties capable of cysteine bond formation. Herein, we report on the N-acylamino saccharin moieties capable of novel covalent reactions with cysteine. Their utility as alternative electrophilic warheads was demonstrated through the covalent modification of fructose-1,6-bisphosphatase (FBPase), a promising target associated with cancer and type 2 diabetes. The cocrystal structure of title compound W8 bound with FBPase unexpectedly revealed that the N-acylamino saccharin moiety worked as an electrophile warhead that covalently modified the noncatalytic C128 site in FBPase while releasing saccharin, suggesting a previously undiscovered covalent reaction mechanism of saccharin derivatives with cysteine. Treatment of title compound W8 displayed potent inhibition of glucose production in vitro and in vivo. This newly discovered reactive warhead supplements the current repertoire of cysteine covalent modifiers while avoiding some of the limitations generally associated with established moieties.
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Affiliation(s)
- Wuqiang Wen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Hongxuan Cao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yixiang Xu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yanliang Ren
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Li Rao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Xubo Shao
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Han Chen
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Lixia Wu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Jiaqi Liu
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Chen Su
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China
| | - Yunyuan Huang
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Jian Wan
- Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China
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35
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Willis N, Mahy W, Sipthorp J, Zhao Y, Woodward HL, Atkinson BN, Bayle ED, Svensson F, Frew S, Jeganathan F, Monaghan A, Benvegnù S, Jolly S, Vecchia L, Ruza RR, Kjær S, Howell S, Snijders AP, Bictash M, Salinas PC, Vincent JP, Jones EY, Whiting P, Fish PV. Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit. J Med Chem 2022; 65:7212-7230. [PMID: 35536179 PMCID: PMC9150124 DOI: 10.1021/acs.jmedchem.2c00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 12/26/2022]
Abstract
Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.
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Affiliation(s)
- Nicky
J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - William Mahy
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - James Sipthorp
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Yuguang Zhao
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Elliott D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Sarah Frew
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Fiona Jeganathan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Amy Monaghan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefano Benvegnù
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Sarah Jolly
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Luca Vecchia
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Reinis R. Ruza
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Svend Kjær
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Steven Howell
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | | | - Magda Bictash
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Patricia C. Salinas
- Department
of Cell and Developmental Biology, Laboratory for Molecular and Cellular
Biology, University College London, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - E. Yvonne Jones
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
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36
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Ge R, Shen Z, Yin J, Chen W, Zhang Q, An Y, Tang D, Satz AL, Su W, Kuai L. Discovery of SARS-CoV-2 main protease covalent inhibitors from a DNA-encoded library selection. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:79-85. [PMID: 35063690 PMCID: PMC8767972 DOI: 10.1016/j.slasd.2022.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent inhibitors targeting the main protease (Mpro, or 3CLpro) of SARS-CoV-2 have shown promise in preclinical investigations. Herein, we report the discovery of two new series of molecules that irreversibly bind to SARS-CoV-2 Mpro. These acrylamide containing molecules were discovered using our covalent DNA-encoded library (DEL) screening platform. Following selection against SARS-CoV-2 Mpro, off-DNA compounds were synthesized and investigated to determine their inhibitory effects, the nature of their binding, and to generate preliminary structure-activity relationships. LC-MS analysis indicates a 1:1 (covalent) binding stoichiometry between our hit molecules and SARS-CoV-2 Mpro. Fluorescent staining assay for covalent binding in the presence of cell lysate suggests reasonable selectivity for SARS-CoV-2 Mpro. And lastly, inhibition of enzymatic activity was also observed against a panel of 3CLpro enzymes from different coronavirus strains, with IC50 values ranging from inactive to single digit micromolar. Our results indicate that DEL selection is a useful approach for identifying covalent inhibitors of cysteine proteases.
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Affiliation(s)
- Rui Ge
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Zuyuan Shen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Jian Yin
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Wenhua Chen
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Qi Zhang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Yulong An
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | - Dewei Tang
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China
| | | | - Wenji Su
- WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.
| | - Letian Kuai
- WuXi AppTec(,) 55 Cambridge Parkway, 8th Floor(,) Cambridge, MA 02142, USA.
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37
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Rothweiler EM, Brennan PE, Huber KVM. Covalent fragment-based ligand screening approaches for identification of novel ubiquitin proteasome system modulators. Biol Chem 2022; 403:391-402. [PMID: 35191283 DOI: 10.1515/hsz-2021-0396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022]
Abstract
Ubiquitination is a key regulatory mechanism vital for maintenance of cellular homeostasis. Protein degradation is induced by E3 ligases via attachment of ubiquitin chains to substrates. Pharmacological exploitation of this phenomenon via targeted protein degradation (TPD) can be achieved with molecular glues or bifunctional molecules facilitating the formation of ternary complexes between an E3 ligase and a given protein of interest (POI), resulting in ubiquitination of the substrate and subsequent proteolysis by the proteasome. Recently, the development of novel covalent fragment screening approaches has enabled the identification of first-in-class ligands for E3 ligases and deubiquitinases revealing so far unexplored binding sites which highlights the potential of these methods to uncover and expand druggable space for new target classes.
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Affiliation(s)
- Elisabeth M Rothweiler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
| | - Paul E Brennan
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Nuffield Department of Medicine, Centre for Medicines Discovery, Oxford OX3 7FZ, UK.,Nuffield Department of Medicine, Target Discovery Institute, Oxford OX3 7FZ, UK
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38
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de Esch IJP, Erlanson DA, Jahnke W, Johnson CN, Walsh L. Fragment-to-Lead Medicinal Chemistry Publications in 2020. J Med Chem 2022; 65:84-99. [PMID: 34928151 PMCID: PMC8762670 DOI: 10.1021/acs.jmedchem.1c01803] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 12/28/2022]
Abstract
Fragment-based drug discovery (FBDD) continues to evolve and make an impact in the pharmaceutical sciences. We summarize successful fragment-to-lead studies that were published in 2020. Having systematically analyzed annual scientific outputs since 2015, we discuss trends and best practices in terms of fragment libraries, target proteins, screening technologies, hit-optimization strategies, and the properties of hit fragments and the leads resulting from them. As well as the tabulated Fragment-to-Lead (F2L) programs, our 2020 literature review identifies several trends and innovations that promise to further increase the success of FBDD. These include developing structurally novel screening fragments, improving fragment-screening technologies, using new computer-aided design and virtual screening approaches, and combining FBDD with other innovative drug-discovery technologies.
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Affiliation(s)
- Iwan J. P. de Esch
- Division
of Medicinal Chemistry, Amsterdam Institute of Molecular and Life
Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Daniel A. Erlanson
- Frontier
Medicines, 151 Oyster
Point Blvd., South San Francisco, California 94080, United States
| | - Wolfgang Jahnke
- Novartis
Institutes for Biomedical Research, Chemical
Biology and Therapeutics, 4002 Basel, Switzerland
| | - Christopher N. Johnson
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Louise Walsh
- Astex
Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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39
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Petri L, Ábrányi-Balogh P, Vagrys D, Imre T, Varró N, Mándity I, Rácz A, Wittner L, Tóth K, Tóth EZ, Juhász T, Davis B, Keserű GM. A covalent strategy to target intrinsically disordered proteins:Discovery of novel tau aggregation inhibitors. Eur J Med Chem 2022; 231:114163. [DOI: 10.1016/j.ejmech.2022.114163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/26/2022] [Indexed: 12/28/2022]
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40
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Zheng Y, Wágner G, Hauwert N, Ma X, Vischer HF, Leurs R. New Chemical Biology Tools for the Histamine Receptor Family. Curr Top Behav Neurosci 2022; 59:3-28. [PMID: 35851442 DOI: 10.1007/7854_2022_360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The histamine research community has in the last decade been very active and generated a number of exciting new chemical biology tools for the study of histamine receptors, their ligands, and their pharmacology. In this paper we describe the development of histamine receptor structural biology, the use of receptor conformational biosensors, and the development of new ligands for covalent or fluorescent labeling or for photopharmacological approaches (photocaging and photoswitching). These new tools allow new approaches to study histamine receptors and hopefully will lead to better insights in the molecular aspects of histamine receptors and their ligands.
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Affiliation(s)
- Yang Zheng
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular Life Sciences (AIMMS), Amsterdam, The Netherlands
| | - Gábor Wágner
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular Life Sciences (AIMMS), Amsterdam, The Netherlands
| | - Niels Hauwert
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular Life Sciences (AIMMS), Amsterdam, The Netherlands
| | - Xiaoyuan Ma
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular Life Sciences (AIMMS), Amsterdam, The Netherlands
| | - Henry F Vischer
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular Life Sciences (AIMMS), Amsterdam, The Netherlands
| | - Rob Leurs
- Department of Medicinal Chemistry, Faculty of Science, Amsterdam Institute of Molecular Life Sciences (AIMMS), Amsterdam, The Netherlands.
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41
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Pasqualetto G, Pileggi E, Schepelmann M, Varricchio C, Rozanowska M, Brancale A, Bassetto M. Ligand-based rational design, synthesis and evaluation of novel potential chemical chaperones for opsin. Eur J Med Chem 2021; 226:113841. [PMID: 34555613 DOI: 10.1016/j.ejmech.2021.113841] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/07/2021] [Accepted: 09/07/2021] [Indexed: 12/01/2022]
Abstract
Inherited blinding diseases retinitis pigmentosa (RP) and a subset of Leber's congenital amaurosis (LCA) are caused by the misfolding and mistrafficking of rhodopsin molecules, which aggregate and accumulate in the endoplasmic reticulum (ER), leading to photoreceptor cell death. One potential therapeutic strategy to prevent the loss of photoreceptors in these conditions is to identify opsin-binding compounds that act as chemical chaperones for opsin, aiding its proper folding and trafficking to the outer cell membrane. Aiming to identify novel compounds with such effect, a rational ligand-based approach was applied to the structure of the visual pigment chromophore, 11-cis-retinal, and its locked analogue 11-cis-6mr-retinal. Following molecular docking studies on the main chromophore binding site of rhodopsin, 49 novel compounds were synthesized according to optimized one-to seven-step synthetic routes. These agents were evaluated for their ability to compete for the chromophore binding site of opsin, and their capacity to increase the trafficking of the P23H opsin mutant from the ER to the cell membrane. Different new molecules displayed an effect in at least one assay, acting either as chemical chaperones or as stabilizers of the 9-cis-retinal-rhodopsin complex. These compounds could provide the basis to develop novel therapeutics for RP and LCA.
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Affiliation(s)
- Gaia Pasqualetto
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| | - Elisa Pileggi
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| | - Martin Schepelmann
- Institute of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, 1090, Austria; School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Carmine Varricchio
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| | - Malgorzata Rozanowska
- School of Optometry and Vision Sciences, Cardiff University, Cardiff, CF24 4HQ, UK; Cardiff Institute for Tissue Engineering and Repair (CITER), Cardiff University, Cardiff, CF10 3NB, UK
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, UK
| | - Marcella Bassetto
- Department of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea, SA2 8PP, UK.
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42
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Thomas RP, Heap RE, Zappacosta F, Grant EK, Pogány P, Besley S, Fallon DJ, Hann MM, House D, Tomkinson NCO, Bush JT. A direct-to-biology high-throughput chemistry approach to reactive fragment screening. Chem Sci 2021; 12:12098-12106. [PMID: 34667575 PMCID: PMC8457371 DOI: 10.1039/d1sc03551g] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/05/2021] [Indexed: 11/21/2022] Open
Abstract
Methods for rapid identification of chemical tools are essential for the validation of emerging targets and to provide medicinal chemistry starting points for the development of new medicines. Here, we report a screening platform that combines 'direct-to-biology' high-throughput chemistry (D2B-HTC) with photoreactive fragments. The platform enabled the rapid synthesis of >1000 PhotoAffinity Bits (HTC-PhABits) in 384-well plates in 24 h and their subsequent screening as crude reaction products with a protein target without purification. Screening the HTC-PhABit library with carbonic anhydrase I (CAI) afforded 7 hits (0.7% hit rate), which were found to covalently crosslink in the Zn2+ binding pocket. A powerful advantage of the D2B-HTC screening platform is the ability to rapidly perform iterative design-make-test cycles, accelerating the development and optimisation of chemical tools and medicinal chemistry starting points with little investment of resource.
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Affiliation(s)
- Ross P Thomas
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Department of Pure and Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Rachel E Heap
- GlaxoSmithKline South Collegeville Road Collegeville PA 19426 USA
| | | | - Emma K Grant
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Peter Pogány
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Stephen Besley
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - David J Fallon
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Michael M Hann
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - David House
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Jacob T Bush
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
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43
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Serafim RAM, Elkins JM, Zuercher WJ, Laufer SA, Gehringer M. Chemical Probes for Understudied Kinases: Challenges and Opportunities. J Med Chem 2021; 65:1132-1170. [PMID: 34477374 DOI: 10.1021/acs.jmedchem.1c00980] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over 20 years after the approval of the first-in-class protein kinase inhibitor imatinib, the biological function of a significant fraction of the human kinome remains poorly understood while most research continues to be focused on few well-validated targets. Given the strong genetic evidence for involvement of many kinases in health and disease, the understudied fraction of the kinome holds a large and unexplored potential for future therapies. Specific chemical probes are indispensable tools to interrogate biology enabling proper preclinical validation of novel kinase targets. In this Perspective, we highlight recent case studies illustrating the development of high-quality chemical probes for less-studied kinases and their application in target validation. We spotlight emerging techniques and approaches employed in the generation of chemical probes for protein kinases and beyond and discuss the associated challenges and opportunities.
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Affiliation(s)
- Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Jonathan M Elkins
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - William J Zuercher
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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44
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Silvestri IP, Colbon PJJ. The Growing Importance of Chirality in 3D Chemical Space Exploration and Modern Drug Discovery Approaches for Hit-ID: Topical Innovations. ACS Med Chem Lett 2021; 12:1220-1229. [PMID: 34413951 PMCID: PMC8366003 DOI: 10.1021/acsmedchemlett.1c00251] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/02/2021] [Indexed: 12/19/2022] Open
Abstract
Modern-day drug discovery is now blessed with a wide range of high-throughput hit identification (hit-ID) strategies that have been successfully validated in recent years, with particular success coming from high-throughput screening, fragment-based lead discovery, and DNA-encoded library screening. As screening efficiency and throughput increases, this enables the viable exploration of increasingly complex three-dimensional (3D) chemical structure space, with a realistic chance of identifying highly specific hit ligands with increased target specificity and reduced attrition rates in preclinical and clinical development. This minireview will explore the impact of an improved design of multifunctionalized, sp3-rich, stereodefined scaffolds on the (virtual) exploration of 3D chemical space and the specific requirements for different hit-ID technologies.
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Affiliation(s)
- Ilaria Proietti Silvestri
- Department of Chemistry University
of Liverpool, Liverpool ChiroChem, Ltd., Crown Street, Liverpool L69 7ZD, United
Kingdom
| | - Paul J. J. Colbon
- Department of Chemistry University
of Liverpool, Liverpool ChiroChem, Ltd., Crown Street, Liverpool L69 7ZD, United
Kingdom
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45
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Craven GB, Briggs EL, Zammit CM, McDermott A, Greed S, Affron DP, Leinfellner C, Cudmore HR, Tweedy RR, Luisi R, Bull JA, Armstrong A. Synthesis and Configurational Assignment of Vinyl Sulfoximines and Sulfonimidamides. J Org Chem 2021; 86:7403-7424. [PMID: 34003635 DOI: 10.1021/acs.joc.1c00373] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Vinyl sulfones and sulfonamides are valued for their use as electrophilic warheads in covalent protein inhibitors. Conversely, the S(VI) aza-isosteres thereof, vinyl sulfoximines and sulfonimidamides, are far less studied and have yet to be applied to the field of protein bioconjugation. Herein, we report a range of different synthetic methodologies for constructing vinyl sulfoximine and vinyl sulfonimidamide architectures that allows access to new areas of electrophilic chemical space. We demonstrate how late-stage functionalization can be applied to these motifs to incorporate alkyne tags, generating fully functionalized probes for future chemical biology applications. Finally, we establish a workflow for determining the absolute configuration of enantioenriched vinyl sulfoximines and sulfonimidamides by comparing experimentally and computationally determined electronic circular dichroism spectra, enabling access to configurationally assigned enantiomeric pairs by separation.
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Affiliation(s)
- Gregory B Craven
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K.,The Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Edward L Briggs
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Charlotte M Zammit
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alexander McDermott
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Stephanie Greed
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Dominic P Affron
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Charlotte Leinfellner
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Hannah R Cudmore
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Ruth R Tweedy
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Renzo Luisi
- Department of Pharmacy-Drug Sciences, University of Bari, "A. Moro" Via E. Orabona 4, Bari 70125, Italy
| | - James A Bull
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Alan Armstrong
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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46
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Tabuchi Y, Watanabe T, Katsuki R, Ito Y, Taki M. Direct screening of a target-specific covalent binder: stringent regulation of warhead reactivity in a matchmaking environment. Chem Commun (Camb) 2021; 57:5378-5381. [PMID: 33978001 DOI: 10.1039/d1cc01773j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A peptide-type covalent binder for a target protein was obtained by direct and stringent screening of a warhead-modified peptide library on the robust T7 phage. The aryl fluorosulfate (fosylate) warhead was activated only in a matchmaking microenvironment created between the target protein and an appropriate peptide during the reactivity/affinity-based co-selection process of extended phage display.
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Affiliation(s)
- Yudai Tabuchi
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Takahito Watanabe
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Riku Katsuki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
| | - Yuji Ito
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima University, 1-21-35 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Masumi Taki
- Department of Engineering Science, Bioscience and Technology Program, The Graduate School of Informatics and Engineering, The University of Electro-Communications (UEC), 1-5-1 Chofugaoka, Chofu, Tokyo 182-8585, Japan.
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47
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Moreira-Filho JT, Silva AC, Dantas RF, Gomes BF, Souza Neto LR, Brandao-Neto J, Owens RJ, Furnham N, Neves BJ, Silva-Junior FP, Andrade CH. Schistosomiasis Drug Discovery in the Era of Automation and Artificial Intelligence. Front Immunol 2021; 12:642383. [PMID: 34135888 PMCID: PMC8203334 DOI: 10.3389/fimmu.2021.642383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Schistosomiasis is a parasitic disease caused by trematode worms of the genus Schistosoma and affects over 200 million people worldwide. The control and treatment of this neglected tropical disease is based on a single drug, praziquantel, which raises concerns about the development of drug resistance. This, and the lack of efficacy of praziquantel against juvenile worms, highlights the urgency for new antischistosomal therapies. In this review we focus on innovative approaches to the identification of antischistosomal drug candidates, including the use of automated assays, fragment-based screening, computer-aided and artificial intelligence-based computational methods. We highlight the current developments that may contribute to optimizing research outputs and lead to more effective drugs for this highly prevalent disease, in a more cost-effective drug discovery endeavor.
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Affiliation(s)
- José T. Moreira-Filho
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Arthur C. Silva
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Rafael F. Dantas
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Barbara F. Gomes
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Lauro R. Souza Neto
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Didcot, United Kingdom
- Research Complex at Harwell, Didcot, United Kingdom
| | - Raymond J. Owens
- The Rosalind Franklin Institute, Harwell, United Kingdom
- Division of Structural Biology, The Wellcome Centre for Human Genetic, University of Oxford, Oxford, United Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruno J. Neves
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
| | - Floriano P. Silva-Junior
- LaBECFar – Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carolina H. Andrade
- LabMol – Laboratory for Molecular Modeling and Drug Design, Faculdade de Farmácia, Universidade Federal de Goiás – UFG, Goiânia, Brazil
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48
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Crowley VM, Thielert M, Cravatt BF. Functionalized Scout Fragments for Site-Specific Covalent Ligand Discovery and Optimization. ACS CENTRAL SCIENCE 2021; 7:613-623. [PMID: 34056091 PMCID: PMC8155467 DOI: 10.1021/acscentsci.0c01336] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Indexed: 05/14/2023]
Abstract
Covalent ligands are a versatile class of chemical probes and drugs that can target noncanonical sites on proteins and display differentiated pharmacodynamic properties. Chemical proteomic methods have been introduced that leverage electrophilic fragments to globally profile the covalent ligandability of nucleophilic residues, such as cysteine and lysine, in native biological systems. Further optimization of these initial ligandability events without resorting to the time-consuming process of individualized protein purification and functional assay development, however, presents a persistent technical challenge. Here, we show that broadly reactive electrophilic fragments, or "scouts", can be converted into site-specific target engagement probes for screening small molecules against a wide array of proteins in convenient gel- and ELISA-based assay formats. We use these assays to expediently optimize a weak potency fragment hit into a sub-μM inhibitor that selectively engages an active-site cysteine in the retinaldehyde reductase AKR1B10. Our findings provide a road map to optimize covalent fragments into more advanced chemical probes without requiring protein purification or structural analysis.
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49
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Dahlin JL, Auld DS, Rothenaigner I, Haney S, Sexton JZ, Nissink JWM, Walsh J, Lee JA, Strelow JM, Willard FS, Ferrins L, Baell JB, Walters MA, Hua BK, Hadian K, Wagner BK. Nuisance compounds in cellular assays. Cell Chem Biol 2021; 28:356-370. [PMID: 33592188 PMCID: PMC7979533 DOI: 10.1016/j.chembiol.2021.01.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 12/17/2022]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity ("nuisance compounds") are routinely encountered in cellular assays, including phenotypic and high-content screening assays. Much is known regarding compound-dependent assay interferences in cell-free assays. However, despite the essential role of cellular assays in chemical biology and drug discovery, there is considerably less known about nuisance compounds in more complex cell-based assays. In our view, a major obstacle to realizing the full potential of chemical biology will not just be difficult-to-drug targets or even the sheer number of targets, but rather nuisance compounds, due to their ability to waste significant resources and erode scientific trust. In this review, we summarize our collective academic, government, and industry experiences regarding cellular nuisance compounds. We describe assay design strategies to mitigate the impact of nuisance compounds and suggest best practices to efficiently address these compounds in complex biological settings.
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Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA.
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA 02139, USA
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Steve Haney
- Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA
| | - Jonathan Z Sexton
- Department of Internal Medicine, Gastroenterology, Michigan Medicine at the University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jarrod Walsh
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park SK10 4TG, UK
| | | | | | | | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 211816, People's Republic of China
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN 55414, USA
| | - Bruce K Hua
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02140, USA
| | - Kamyar Hadian
- Assay Development and Screening Platform, Helmholtz Zentrum Muenchen, 85764 Neuherberg, Germany
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02140, USA
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50
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Ahn YC, May VK, Bedford GC, Tuley AA, Fast W. Discovery of 4,4'-Dipyridylsulfide Analogs as "Switchable Electrophiles" for Covalent Inhibition. ACS Chem Biol 2021; 16:264-269. [PMID: 33492128 DOI: 10.1021/acschembio.0c00890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrophilic heterocycles offer attractive features as covalent fragments for inhibitor and probe development. A focused library of heterocycles for which protonation can enhance reactivity (called "switchable electrophiles") is screened for inhibition of the proposed drug target dimethylarginine dimethylaminohydrolase (DDAH). Several novel covalent fragments are identified: 4-chloroquinoline, 4-bromopyridazine, and 4,4-dipyridylsulfide. Mechanistic studies of DDAH inactivation by 4,4-dipyridylsulfide reveal selective covalent S-pyridinylation of the active-site Cys through catalysis by a neighboring Asp residue. Inactivation (kinact/KI = 0.33 M-1 s-1) proceeds with release of 4-thiopyridone (0.78 equiv), and structure-activity relationships reveal that the leaving group pKa can be modulated to tune reactivity. The use of a "switchable electrophile" strategy helps impart selectivity, even to fragment-sized modifiers. Identification of 4,4-dipyridylsulfide analogs as inactivators offers an easily tunable covalent fragment with multiple derivatization sites on both the leaving and staying groups.
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Affiliation(s)
- Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Valerie K. May
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Guy C. Bedford
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Alfred A. Tuley
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, United States
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