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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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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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3
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Ravish A, Narasimhachar BC, Xi Z, Vishwanath D, Mohan A, Gaonkar SL, Chandrashekara PG, Ahn KS, Pandey V, Lobie PE, Basappa B. Development of Piperazine- and Oxazine-Linked Pyrimidines as p65 Subunit Binders of NF-κB in Human Breast Cancer Cells. Biomedicines 2023; 11:2716. [PMID: 37893090 PMCID: PMC10604619 DOI: 10.3390/biomedicines11102716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/01/2023] [Accepted: 09/12/2023] [Indexed: 10/29/2023] Open
Abstract
Nuclear factor kappa B (NF-κB) is a potential therapeutic target in breast cancer. In the current study, a new class of oxazine- and piperazine-linked pyrimidines was developed as inhibitors of NF-κB, overcoming the complexity of the oxazine structure found in nature and enabling synthesis under laboratory conditions. Among the series of synthesized and tested oxazine-pyrimidine and piperazine-pyrimidine derivatives, compounds 3a and 5b inhibited breast cancer cell (MCF-7) viability with an IC50 value of 9.17 and 6.29 µM, respectively. In silico docking studies showed that the pyrimidine ring of 3a and the 4-methoxybenzyl thiol group of 5b could strongly bind the p65 subunit of NF-κB, with the binding energies -9.32 and -7.32 kcal mol-1. Furthermore, compounds 3a and 5b inhibited NF-κB in MCF-7 breast cancer cells. In conclusion, we herein report newer structures that target NF-κB in BC cells.
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Affiliation(s)
- Akshay Ravish
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Mysore 570006, Karnataka, India; (A.R.); (D.V.); (A.M.)
| | - Bhanuprakash C. Narasimhachar
- Department of Chemistry, Yuvaraja’s College, University of Mysore, Mysuru 570005, Karnataka, India; (B.C.N.); (P.G.C.)
| | - Zhang Xi
- Shenzhen Bay Laboratory, Shenzhen 518055, China;
| | - Divakar Vishwanath
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Mysore 570006, Karnataka, India; (A.R.); (D.V.); (A.M.)
| | - Arunkumar Mohan
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Mysore 570006, Karnataka, India; (A.R.); (D.V.); (A.M.)
| | - Santosh L. Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India;
| | | | - Kwang Seok Ahn
- Department of Science in Korean Medicine, Kyung Hee University, 24 Kyungheedaero, Dongdaemungu, Seoul 02447, Republic of Korea;
| | - Vijay Pandey
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Peter E. Lobie
- Shenzhen Bay Laboratory, Shenzhen 518055, China;
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Basappa Basappa
- Laboratory of Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Mysore 570006, Karnataka, India; (A.R.); (D.V.); (A.M.)
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Ravindra MP, Lee M, Dimova S, Steven CF, Bluntzer MTJ, Brunton VG, Hulme AN. Stretching the Bisalkyne Raman Spectral Palette Reveals a New Electrophilic Covalent Motif. Chemistry 2023; 29:e202300953. [PMID: 37014262 PMCID: PMC10946950 DOI: 10.1002/chem.202300953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/05/2023]
Abstract
Small heteroaryl-diyne (Het-DY) tags with distinct vibrational frequencies, and physiologically relevant cLog P were designed for multiplexed bioorthogonal Raman imaging. Pd-Cu catalyzed coupling, combined with the use of Lei ligand, was shown to improve overall yields of the desired heterocoupled Het-DY tags, minimizing the production of homocoupled side-products. Spectral data were in agreement with the trends predicted by DFT calculations and systematic introduction of electron- rich/poor rings stretched the frequency limit of aryl-capped diynes (2209-2243 cm-1 ). The improved Log P of these Het-DY tags was evident from their diffuse distribution in cellular uptake studies and functionalizing tags with organelle markers allowed the acquisition of location-specific biological images. LC-MS- and NMR-based assays showed that some heteroaryl-capped internal alkynes are potential nucleophile traps with structure-dependent reactivity. These biocompatible Het-DY tags, equipped with covalent reactivity, open up new avenues for Raman bioorthogonal imaging.
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Affiliation(s)
- Manasa Punaha Ravindra
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Martin Lee
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Silviya Dimova
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Craig F. Steven
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Marie T. J. Bluntzer
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Valerie G. Brunton
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Alison N. Hulme
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
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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: 13] [Impact Index Per Article: 6.5] [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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6
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Systematic Exploration of Privileged Warheads for Covalent Kinase Drug Discovery. Pharmaceuticals (Basel) 2022; 15:ph15111322. [PMID: 36355497 PMCID: PMC9695834 DOI: 10.3390/ph15111322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Kinase-targeted drug discovery for cancer therapy has advanced significantly in the last three decades. Currently, diverse kinase inhibitors or degraders have been reported, such as allosteric inhibitors, covalent inhibitors, macrocyclic inhibitors, and PROTAC degraders. Out of these, covalent kinase inhibitors (CKIs) have been attracting attention due to their enhanced selectivity and exceptionally strong affinity. Eight covalent kinase drugs have been FDA-approved thus far. Here, we review current developments in CKIs. We explore the characteristics of the CKIs: the features of nucleophilic amino acids and the preferences of electrophilic warheads. We provide systematic insights into privileged warheads for repurposing to other kinase targets. Finally, we discuss trends in CKI development across the whole proteome.
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Nangia AK, Desiraju GR. Heterosynthons, Solid Form Design and Enhanced Drug Bioavailability. Angew Chem Int Ed Engl 2022; 61:e202207484. [DOI: 10.1002/anie.202207484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Ashwini K. Nangia
- School of Chemistry University of Hyderabad Prof. C. R. Rao Road, Gachibowli, Central University P.O. Hyderabad 500 046 India
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore 560 012 India
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Nangia AK, Desiraju GR. Heterosynthons, Solid Form Design and Enhanced Drug Bioavailability. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ashwini K. Nangia
- School of Chemistry University of Hyderabad Prof. C. R. Rao Road, Gachibowli, Central University P.O. Hyderabad 500 046 India
| | - Gautam R. Desiraju
- Solid State and Structural Chemistry Unit Indian Institute of Science Bangalore 560 012 India
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Norman JP, Larson NG, Entz ED, Neufeldt SR. Unconventional Site Selectivity in Palladium-Catalyzed Cross-Couplings of Dichloroheteroarenes under Ligand-Controlled and Ligand-Free Systems. J Org Chem 2022; 87:7414-7421. [PMID: 35584051 DOI: 10.1021/acs.joc.2c00665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Halides adjacent to nitrogen are conventionally more reactive in Pd-catalyzed cross-couplings of dihalogenated N-heteroarenes. However, a very sterically hindered N-heterocyclic carbene ligand is shown to promote room-temperature cross-coupling at C4 of 2,4-dichloropyridines with high selectivity (∼10:1). This work represents the first highly selective method with a broad scope for C4-coupling of these substrates where selectivity is clearly under ligand control. Under the optimized conditions, diverse substituted 2,4-dichloropyridines and related compounds undergo cross-coupling to form C4-C(sp2) and C4-C(sp3) bonds using organoboron, -zinc, and -magnesium reagents. The synthetic utility of this method is highlighted in multistep syntheses that combine C4-selective cross-coupling with subsequent nucleophilic aromatic substitution reactions. The majority of the products herein (71%) have not been previously reported, emphasizing the ability of this methodology to open up underexplored chemical space. Remarkably, we find that ligand-free "Jeffery" conditions enhance the C4 selectivity of Suzuki coupling by an order of magnitude (>99:1). These ligand-free conditions enable the first C5-selective cross-couplings of 2,5-dichloropyridine and 2,5-dichloropyrimidine.
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Affiliation(s)
- Jacob P Norman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Nathaniel G Larson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Emily D Entz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Sharon R Neufeldt
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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