1
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Kollár L, Grabrijan K, Hrast Rambaher M, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents. J Enzyme Inhib Med Chem 2024; 39:2305833. [PMID: 38410950 PMCID: PMC10901194 DOI: 10.1080/14756366.2024.2305833] [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: 08/29/2023] [Accepted: 01/08/2024] [Indexed: 02/28/2024] Open
Abstract
Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure-activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N-B bond is a new strategy for PBP1b inhibition.
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Affiliation(s)
- Levente Kollár
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
| | | | | | | | - Tímea Imre
- MS Metabolomics Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary
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2
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Cui XY, Li Z, Kong Z, Liu Y, Meng H, Wen Z, Wang C, Chen J, Xu M, Li Y, Gao J, Zhu W, Hao Z, Huo L, Liu S, Yang Z, Liu Z. Covalent targeted radioligands potentiate radionuclide therapy. Nature 2024; 630:206-213. [PMID: 38778111 DOI: 10.1038/s41586-024-07461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Targeted radionuclide therapy, in which radiopharmaceuticals deliver potent radionuclides to tumours for localized irradiation, has addressed unmet clinical needs and improved outcomes for patients with cancer1-4. A therapeutic radiopharmaceutical must achieve both sustainable tumour targeting and fast clearance from healthy tissue, which remains a major challenge5,6. A targeted ligation strategy that selectively fixes the radiopharmaceutical to the target protein in the tumour would be an ideal solution. Here we installed a sulfur (VI) fluoride exchange (SuFEx) chemistry-based linker on radiopharmaceuticals to prevent excessively fast tumour clearance. When the engineered radiopharmaceutical binds to the tumour-specific protein, the system undergoes a binding-to-ligation transition and readily conjugates to the tyrosine residues through the 'click' SuFEx reaction. The application of this strategy to a fibroblast activation protein (FAP) inhibitor (FAPI) triggered more than 80% covalent binding to the protein and almost no dissociation for six days. In mice, SuFEx-engineered FAPI showed 257% greater tumour uptake than did the original FAPI, and increased tumour retention by 13-fold. The uptake in healthy tissues was rapidly cleared. In a pilot imaging study, this strategy identified more tumour lesions in patients with cancer than did other methods. SuFEx-engineered FAPI also successfully achieved targeted β- and α-radionuclide therapy, causing nearly complete tumour regression in mice. Another SuFEx-engineered radioligand that targets prostate-specific membrane antigen (PSMA) also showed enhanced therapeutic efficacy. Considering the broad scope of proteins that can potentially be ligated to SuFEx warheads, it might be possible to adapt this strategy to other cancer targets.
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Affiliation(s)
- Xi-Yang Cui
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Zhu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Ziren Kong
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Yu Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Hao Meng
- Changping Laboratory, Beijing, P. R. China
| | - Zihao Wen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Changlun Wang
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Junyi Chen
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Mengxin Xu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
- Changping Laboratory, Beijing, P. R. China
| | - Yiyan Li
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Jingyue Gao
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wenjia Zhu
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhixin Hao
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Li Huo
- Department of Nuclear Medicine, Beijing Key Laboratory of Molecular Targeted Diagnosis and Therapy in Nuclear Medicine and State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Shaoyan Liu
- Department of Head and Neck Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Zhi Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China
| | - Zhibo Liu
- Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Peking University Cancer Hospital and Institute, Beijing, P. R. China.
- Peking University-Tsinghua University Center for Life Sciences, Peking University, Beijing, P. R. China.
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3
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Wang L, Liang Y, Luo P, Huang M, Wan Y. Novel partially reversible NDM-1 inhibitors based on the naturally occurring houttuynin. Bioorg Chem 2024; 147:107328. [PMID: 38583248 DOI: 10.1016/j.bioorg.2024.107328] [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: 02/21/2024] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/09/2024]
Abstract
Discovering novel NDM-1 inhibitors is an urgent task for treatment of 'superbug' infectious diseases. In this study, we found that naturally occurring houttuynin and its sulfonate derivatives might be effective NDM-1 inhibitors with novel mechanism, i.e. the attribute of partially covalent inhibition of sulfonate derivatives of houttuynin against NDM-1. Primary structure-activity relationship study showed that both the long aliphatic side chain and the warhead of aldehyde group are vital for the efficiency against NDM-1. The homologs with longer chains (SNH-2 to SNH-5) displayed stronger inhibitory activities with IC50 range of 1.1-1.5 μM, while the shorter chain the weaker inhibition. Further synergistic experiments in cell level confirmed that all these 4 compounds (at 32 μg/mL) recovered the antibacterial activity of meropenem (MER) against E. coli BL21/pET15b-blaNDM-1.
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Affiliation(s)
- Lifang Wang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
| | - Yaowen Liang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
| | - Pan Luo
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
| | - Manna Huang
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China.
| | - Yiqian Wan
- School of Chemical Engineering and Technology, Guangdong Engineering Technology Research Center for Platform Chemicals from Marine Biomass and Their Functionalization, Sun Yat-sen University, Zhuhai 519082, PR China
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4
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Himmelbauer M, Bajrami B, Basile R, Capacci A, Chen T, Choi CK, Gilfillan R, Gonzalez-Lopez de Turiso F, Gu C, Hoemberger M, Johnson DS, Jones JH, Kadakia E, Kirkland M, Lin EY, Liu Y, Ma B, Magee T, Mantena S, Marx IE, Metrick CM, Mingueneau M, Murugan P, Muste CA, Nadella P, Nevalainen M, Parker Harp CR, Pattaropong V, Pietrasiewicz A, Prince RJ, Purgett TJ, Santoro JC, Schulz J, Sciabola S, Tang H, Vandeveer HG, Wang T, Yousaf Z, Helal CJ, Hopkins BT. Discovery and Preclinical Characterization of BIIB129, a Covalent, Selective, and Brain-Penetrant BTK Inhibitor for the Treatment of Multiple Sclerosis. J Med Chem 2024; 67:8122-8140. [PMID: 38712838 PMCID: PMC11129193 DOI: 10.1021/acs.jmedchem.4c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 05/08/2024]
Abstract
Multiple sclerosis (MS) is a chronic disease with an underlying pathology characterized by inflammation-driven neuronal loss, axonal injury, and demyelination. Bruton's tyrosine kinase (BTK), a nonreceptor tyrosine kinase and member of the TEC family of kinases, is involved in the regulation, migration, and functional activation of B cells and myeloid cells in the periphery and the central nervous system (CNS), cell types which are deemed central to the pathology contributing to disease progression in MS patients. Herein, we describe the discovery of BIIB129 (25), a structurally distinct and brain-penetrant targeted covalent inhibitor (TCI) of BTK with an unprecedented binding mode responsible for its high kinome selectivity. BIIB129 (25) demonstrated efficacy in disease-relevant preclinical in vivo models of B cell proliferation in the CNS, exhibits a favorable safety profile suitable for clinical development as an immunomodulating therapy for MS, and has a low projected total human daily dose.
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Affiliation(s)
- Martin
K. Himmelbauer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bekim Bajrami
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rebecca Basile
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Andrew Capacci
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - TeYu Chen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Colin K. Choi
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rab Gilfillan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | | | - Chungang Gu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marc Hoemberger
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas S. Johnson
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J. Howard Jones
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ekta Kadakia
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Melissa Kirkland
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Edward Y. Lin
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ying Liu
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Bin Ma
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Tom Magee
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Srinivasa Mantena
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Isaac E. Marx
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Claire M. Metrick
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Mingueneau
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Cathy A. Muste
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Prasad Nadella
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marta Nevalainen
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Chelsea R. Parker Harp
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Vatee Pattaropong
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Alicia Pietrasiewicz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Robin J. Prince
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Thomas J. Purgett
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Joseph C. Santoro
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jurgen Schulz
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Simone Sciabola
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hao Tang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - H. George Vandeveer
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Ti Wang
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Zain Yousaf
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Christopher J. Helal
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brian T. Hopkins
- Biogen Research and Development, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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5
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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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6
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Patel D, Huma ZE, Duncan D. Reversible Covalent Inhibition─Desired Covalent Adduct Formation by Mass Action. ACS Chem Biol 2024; 19:824-838. [PMID: 38567529 PMCID: PMC11040609 DOI: 10.1021/acschembio.3c00805] [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: 12/30/2023] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Covalent inhibition has seen a resurgence in the last several years. Although long-plagued by concerns of off-target effects due to nonspecific reactions leading to covalent adducts, there has been success in developing covalent inhibitors, especially within the field of anticancer therapy. Covalent inhibitors can have an advantage over noncovalent inhibitors since the formation of a covalent adduct may serve as an additional mode of selectivity due to the intrinsic reactivity of the target protein that is absent in many other proteins. Unfortunately, many covalent inhibitors form irreversible adducts with off-target proteins, which can lead to considerable side-effects. By designing the inhibitor to form reversible covalent adducts, one can leverage competing on/off kinetics in complex formation by taking advantage of the law of mass action. Although covalent adducts do form with off-target proteins, the reversible nature of inhibition prevents accumulation of the off-target adduct, thus limiting side-effects. In this perspective, we outline important characteristics of reversible covalent inhibitors, including examples and a guide for inhibitor development.
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Affiliation(s)
| | | | - Dustin Duncan
- Department of Chemistry, Brock
University, St. Catharines, Ontario L2S 3A1, Canada
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7
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Lübbers J, Lessel U, Rarey M. Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. J Chem Inf Model 2024; 64:2008-2020. [PMID: 38466793 DOI: 10.1021/acs.jcim.4c00147] [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: 03/13/2024]
Abstract
Chemical fragment spaces exceed traditional virtual compound libraries by orders of magnitude, making them ideal search spaces for drug design projects. However, due to their immense size, they are not compatible with traditional analysis and search algorithms that rely on the enumeration of molecules. In this paper, we present SpaceProp2, an evolution of the SpaceProp algorithm, which enables the calculation of exact property distributions for chemical fragment spaces without enumerating them. We extend the original algorithm by the capabilities to compute distributions for the TPSA, the number of rotatable bonds, and the occurrence of user-defined molecular structures in the form of SMARTS patterns. Furthermore, SpaceProp2 produces example molecules for every property bin, enabling a detailed interpretation of the distributions. We demonstrate SpaceProp2 on six established make-on-demand chemical fragment spaces as well as BICLAIM, the in-house fragment space of Boehringer Ingelheim. The possibility to search multiple SMARTS patterns simultaneously as well as the produced example molecules offers previously impossible insights into the composition of these vast combinatorial molecule collections, making it an ideal tool for the analysis and design of chemical fragment spaces.
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Affiliation(s)
- Justin Lübbers
- ZBH - Center for Bioinformatics, Research Group for Computational Molecular Design, Universität Hamburg, Hamburg 22761, Germany
| | - Uta Lessel
- Computational Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss 88437, Germany
| | - Matthias Rarey
- ZBH - Center for Bioinformatics, Research Group for Computational Molecular Design, Universität Hamburg, Hamburg 22761, Germany
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8
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Tillmanns J, Kicuntod J, Lösing J, Marschall M. 'Getting Better'-Is It a Feasible Strategy of Broad Pan-Antiherpesviral Drug Targeting by Using the Nuclear Egress-Directed Mechanism? Int J Mol Sci 2024; 25:2823. [PMID: 38474070 DOI: 10.3390/ijms25052823] [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: 01/28/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The herpesviral nuclear egress represents an essential step of viral replication efficiency in host cells, as it defines the nucleocytoplasmic release of viral capsids. Due to the size limitation of the nuclear pores, viral nuclear capsids are unable to traverse the nuclear envelope without a destabilization of this natural host-specific barrier. To this end, herpesviruses evolved the regulatory nuclear egress complex (NEC), composed of a heterodimer unit of two conserved viral NEC proteins (core NEC) and a large-size extension of this complex including various viral and cellular NEC-associated proteins (multicomponent NEC). Notably, the NEC harbors the pronounced ability to oligomerize (core NEC hexamers and lattices), to multimerize into higher-order complexes, and, ultimately, to closely interact with the migrating nuclear capsids. Moreover, most, if not all, of these NEC proteins comprise regulatory modifications by phosphorylation, so that the responsible kinases, and additional enzymatic activities, are part of the multicomponent NEC. This sophisticated basis of NEC-specific structural and functional interactions offers a variety of different modes of antiviral interference by pharmacological or nonconventional inhibitors. Since the multifaceted combination of NEC activities represents a highly conserved key regulatory stage of herpesviral replication, it may provide a unique opportunity towards a broad, pan-antiherpesviral mechanism of drug targeting. This review presents an update on chances, challenges, and current achievements in the development of NEC-directed antiherpesviral strategies.
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Affiliation(s)
- Julia Tillmanns
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Josephine Lösing
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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9
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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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10
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Zhao Y, Duan K, Fan Y, Li S, Huang L, Tu Z, Sun H, Cook GM, Yang J, Sun P, Tan Y, Ding K, Li Z. Catalyst-free late-stage functionalization to assemble α-acyloxyenamide electrophiles for selectively profiling conserved lysine residues. Commun Chem 2024; 7:31. [PMID: 38355988 PMCID: PMC10866925 DOI: 10.1038/s42004-024-01107-4] [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: 11/19/2023] [Accepted: 01/15/2024] [Indexed: 02/16/2024] Open
Abstract
Covalent probes coupled with chemical proteomics represent a powerful method for investigating small molecule and protein interactions. However, the creation of a reactive warhead within various ligands to form covalent probes has been a major obstacle. Herein, we report a convenient and robust process to assemble a unique electrophile, an α-acyloxyenamide, through a one-step late-stage coupling reaction. This procedure demonstrates remarkable tolerance towards other functional groups and facilitates ligand-directed labeling in proteins of interest. The reactive group has been successfully incorporated into a clinical drug targeting the EGFR L858R mutant, erlotinib, and a pan-kinase inhibitor. The resulting probes have been shown to be able to covalently engage a lysine residue proximal to the ATP-binding pocket of the EGFR L858R mutant. A series of active sites, and Mg2+, ATP-binding sites of kinases, such as K33 of CDK1, CDK2, CDK5 were detected. This is the first report of engaging these conserved catalytic lysine residues in kinases with covalent inhibition. Further application of this methodology to natural products has demonstrated its success in profiling ligandable conserved lysine residues in whole proteome. These findings offer insights for the development of new targeted covalent inhibitors (TCIs).
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Affiliation(s)
- Yuanyuan Zhao
- 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), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Kang Duan
- 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), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Youlong Fan
- 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), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shengrong Li
- Guangdong Second Provincial General Hospital, Postdoctoral Station of Traditional Chinese Medicine, Jinan University, Guangzhou, 510632, China
| | - Liyan Huang
- 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), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Zhengchao Tu
- 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), School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 TatChee Avenue, Kowloon, Hong Kong, 999077, China
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9054, New Zealand
| | - Jing Yang
- Guangzhou National Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, China
| | - Pinghua Sun
- 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), 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), 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), 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), School of Pharmacy, 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.
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11
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Guo F, Qin S, Liu Z, Chen PR, Fan X. Decaging-to-labeling: Development and investigation of quinone methide warhead for protein labeling. Bioorg Chem 2024; 143:107088. [PMID: 38194902 DOI: 10.1016/j.bioorg.2023.107088] [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: 10/31/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
Biomolecule labeling in living systems is crucial for understanding biological processes and discovering therapeutic targets. A variety of labeling warheads have been developed for multiple biological applications, including proteomics, bioimaging, sequencing, and drug development. Quinone methides (QMs), a class of highly reactive Michael receptors, have recently emerged as prominent warheads for on-demand biomolecule labeling. Their highly flexible functionality and tunability allow for diverse biological applications, but remain poorly explored at present. In this regard, we designed, synthesized, and evaluated a series of new QM probes with a trifluoromethyl group at the benzyl position and substituents on the aromatic ring to manipulate their chemical properties for biomolecule labeling. The engineered QM warhead efficiently labeled proteins both in vitro and under living cell conditions, with significantly enhanced activity compared to previous QM warheads. We further analyzed the labeling efficacy with the assistance of density functional theory (DFT) calculations, which revealed that the QM generation process, rather than the reactivity of QM, contributes more predominantly to the labeling efficacy. Noteworthy, twelve nucleophilic residues on the BSA were labeled by the probe, including Cys, Asp, Glu, His, Lys, Asn, Gln, Arg, Ser, Thr, Trp and Tyr. Given their high efficiency and tunability, these new QM warheads may hold great promise for a broad range of applications, especially spatiotemporal proteomic profiling for in-depth biological studies.
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Affiliation(s)
- Fuhu Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shengnan Qin
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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12
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Yu D, Wagner S, Schütz M, Jeon Y, Seo M, Kim J, Brückner N, Kicuntod J, Tillmanns J, Wangen C, Hahn F, Kaufer BB, Neipel F, Eickhoff J, Klebl B, Nam K, Marschall M. An Antiherpesviral Host-Directed Strategy Based on CDK7 Covalently Binding Drugs: Target-Selective, Picomolar-Dose, Cross-Virus Reactivity. Pharmaceutics 2024; 16:158. [PMID: 38399219 PMCID: PMC10892818 DOI: 10.3390/pharmaceutics16020158] [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: 12/19/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
The repertoire of currently available antiviral drugs spans therapeutic applications against a number of important human pathogens distributed worldwide. These include cases of the pandemic severe acute respiratory coronavirus type 2 (SARS-CoV-2 or COVID-19), human immunodeficiency virus type 1 (HIV-1 or AIDS), and the pregnancy- and posttransplant-relevant human cytomegalovirus (HCMV). In almost all cases, approved therapies are based on direct-acting antivirals (DAAs), but their benefit, particularly in long-term applications, is often limited by the induction of viral drug resistance or side effects. These issues might be addressed by the additional use of host-directed antivirals (HDAs). As a strong input from long-term experiences with cancer therapies, host protein kinases may serve as HDA targets of mechanistically new antiviral drugs. The study demonstrates such a novel antiviral strategy by targeting the major virus-supportive host kinase CDK7. Importantly, this strategy focuses on highly selective, 3D structure-derived CDK7 inhibitors carrying a warhead moiety that mediates covalent target binding. In summary, the main experimental findings of this study are as follows: (1) the in vitro verification of CDK7 inhibition and selectivity that confirms the warhead covalent-binding principle (by CDK-specific kinase assays), (2) the highly pronounced antiviral efficacies of the hit compounds (in cultured cell-based infection models) with half-maximal effective concentrations that reach down to picomolar levels, (3) a particularly strong potency of compounds against strains and reporter-expressing recombinants of HCMV (using infection assays in primary human fibroblasts), (4) additional activity against further herpesviruses such as animal CMVs and VZV, (5) unique mechanistic properties that include an immediate block of HCMV replication directed early (determined by Western blot detection of viral marker proteins), (6) a substantial drug synergism in combination with MBV (measured by a Loewe additivity fixed-dose assay), and (7) a strong sensitivity of clinically relevant HCMV mutants carrying MBV or ganciclovir resistance markers. Combined, the data highlight the huge developmental potential of this host-directed antiviral targeting concept utilizing covalently binding CDK7 inhibitors.
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Affiliation(s)
- DongHoon Yu
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Martin Schütz
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Yeejin Jeon
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Mooyoung Seo
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Jaeseung Kim
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Nadine Brückner
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Jintawee Kicuntod
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Julia Tillmanns
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Christina Wangen
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7–13, 14163 Berlin, Germany
| | - Frank Neipel
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Straße 15, 44227 Dortmund, Germany
- The Norwegian College of Fishery Science UiT, Arctic University of Norway, 9037 Tromsø, Norway
| | - Kiyean Nam
- Qurient Co., Ltd., C-Dong, 242 Pangyo-ro, C801 Bundang-gu, Seongnam-si 13487, Republic of Korea
| | - Manfred Marschall
- Institute for Clinical and Molecular Virolosgy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, 91054 Erlangen, Germany
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13
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Lv Y, Li W, Liao W, Jiang H, Liu Y, Cao J, Lu W, Feng Y. Nano-Drug Delivery Systems Based on Natural Products. Int J Nanomedicine 2024; 19:541-569. [PMID: 38260243 PMCID: PMC10802180 DOI: 10.2147/ijn.s443692] [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: 10/08/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Natural products have proven to have significant curative effects and are increasingly considered as potential candidates for clinical prevention, diagnosis, and treatment. Compared with synthetic drugs, natural products not only have diverse structures but also exhibit a range of biological activities against different disease states and molecular targets, making them attractive for development in the field of medicine. Despite advancements in the use of natural products for clinical purposes, there remain obstacles that hinder their full potential. These challenges include issues such as limited solubility and stability when administered orally, as well as short durations of effectiveness. To address these concerns, nano-drug delivery systems have emerged as a promising solution to overcome the barriers faced in the clinical application of natural products. These systems offer notable advantages, such as a large specific surface area, enhanced targeting capabilities, and the ability to achieve sustained and controlled release. Extensive in vitro and in vivo studies have provided further evidence supporting the efficacy and safety of nanoparticle-based systems in delivering natural products in preclinical disease models. This review describes the limitations of natural product applications and the current status of natural products combined with nanotechnology. The latest advances in nano-drug delivery systems for delivery of natural products are considered from three aspects: connecting targeting warheads, self-assembly, and co-delivery. Finally, the challenges faced in the clinical translation of nano-drugs are discussed.
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Affiliation(s)
- Ying Lv
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Wenqing Li
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Wei Liao
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Haibo Jiang
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Yuwei Liu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Jiansheng Cao
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Wenfei Lu
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
| | - Yufei Feng
- Key Laboratory of Basic and Application Research of Beiyao (Heilongjiang University of Chinese Medicine), Ministry of Education, Harbin, 150040, People’s Republic of China
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14
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Mihalovits LM, Kollár L, Bajusz D, Knez D, Bozovičar K, Imre T, Ferenczy GG, Gobec S, Keserű GM. Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones. Chemphyschem 2024; 25:e202300596. [PMID: 37888491 DOI: 10.1002/cphc.202300596] [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] [Received: 08/21/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 10/28/2023]
Abstract
Heterocyclic thiones have recently been identified as reversible covalent warheads, consistent with their mild electrophilic nature. Little is known so far about their mechanism of action in labelling nucleophilic sidechains, especially cysteines. The vast number of tractable cysteines promotes a wide range of target proteins to examine; however, our focus was put on functional cysteines. We chose the main protease of SARS-CoV-2 harboring Cys145 at the active site that is a structurally characterized and clinically validated target of covalent inhibitors. We screened an in-house, cysteine-targeting covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole, benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were selected for further investigations with the objective of exploring the mechanism of inhibition of the thiones and using the thoroughly characterized Michael acceptors for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism of covalent cysteine labelling by thione derivatives, which was supported by QM and free energy calculations and by a wide range of experimental results. Our study shows that the molecular recognition step plays a crucial role in the overall binding of both sets of molecules.
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Affiliation(s)
- Levente M Mihalovits
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Levente Kollár
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Damijan Knez
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Krištof Bozovičar
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - Tímea Imre
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- MS Metabolomics Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - György G Ferenczy
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
| | - Stanislav Gobec
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000, Ljubljana, Slovenia
| | - György M Keserű
- Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., 1111, Budapest, Hungary
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15
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Goullieux M, Zoete V, Röhrig UF. Two-Step Covalent Docking with Attracting Cavities. J Chem Inf Model 2023; 63:7847-7859. [PMID: 38049143 PMCID: PMC10751798 DOI: 10.1021/acs.jcim.3c01055] [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: 07/12/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023]
Abstract
Due to their various advantages, interest in the development of covalent drugs has been renewed in the past few years. It is therefore important to accurately describe and predict their interactions with biological targets by computer-aided drug design tools such as docking algorithms. Here, we report a covalent docking procedure for our in-house docking code Attracting Cavities (AC), which mimics the two-step mechanism of covalent ligand binding. Ligand binding to the protein cavity is driven by nonbonded interactions, followed by the formation of a covalent bond between the ligand and the protein through a chemical reaction. To test the performance of this method, we developed a diverse, high-quality, openly accessible re-docking benchmark set of 95 covalent complexes bound by 8 chemical reactions to 5 different reactive amino acids. Combination with structures from previous studies resulted in a set of 304 complexes, on which AC obtained a success rate (rmsd ≤ 2 Å) of 78%, outperforming two state-of-the-art covalent docking codes, genetic optimization for ligand docking (GOLD (66%)) and AutoDock (AD (35%)). Using a more stringent success criterion (rmsd ≤ 1.5 Å), AC reached a success rate of 71 vs 55% for GOLD and 26% for AD. We additionally assessed the cross-docking performance of AC on a set of 76 covalent complexes of the SARS-CoV-2 main protease. On this challenging test set of mainly small and highly solvent-exposed ligands, AC yielded success rates of 58 and 28% for re-docking and cross-docking, respectively, compared to 45 and 17% for GOLD.
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Affiliation(s)
- Mathilde Goullieux
- SIB
Swiss Institute of Bioinformatics, Molecular Modeling Group, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- SIB
Swiss Institute of Bioinformatics, Molecular Modeling Group, CH-1015 Lausanne, Switzerland
- Department
of Oncology UNIL-CHUV, Lausanne University, Ludwig Institute for Cancer Research
Lausanne Branch, CH-1066 Epalinges, Switzerland
| | - Ute F. Röhrig
- SIB
Swiss Institute of Bioinformatics, Molecular Modeling Group, CH-1015 Lausanne, Switzerland
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16
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Scott KA, Kojima H, Ropek N, Warren CD, Zhang TL, Hogg SJ, Webster C, Zhang X, Rahman J, Melillo B, Cravatt BF, Lyu J, Abdel-Wahab O, Vinogradova EV. Covalent Targeting of Splicing in T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572199. [PMID: 38187674 PMCID: PMC10769204 DOI: 10.1101/2023.12.18.572199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide chemical probe EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and availability of functional mRNA pools that can be depleted due to extensive alternative splicing. We further introduce a comprehensive list of proteins involved in splicing and leverage both cysteine- and protein-directed activity-based protein profiling (ABPP) data with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in primary human T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.
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17
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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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18
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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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19
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Csorba N, Ábrányi-Balogh P, Keserű GM. Covalent fragment approaches targeting non-cysteine residues. Trends Pharmacol Sci 2023; 44:802-816. [PMID: 37770315 DOI: 10.1016/j.tips.2023.08.014] [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: 06/10/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.
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Affiliation(s)
- Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary.
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20
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Schütz M, Wangen C, Sommerer M, Kögler M, Eickhoff J, Degenhart C, Klebl B, Naing Z, Egilmezer E, Hamilton ST, Rawlinson WD, Sticht H, Marschall M. Cytomegalovirus cyclin-dependent kinase ortholog vCDK/pUL97 undergoes regulatory interaction with human cyclin H and CDK7 to codetermine viral replication efficiency. Virus Res 2023; 335:199200. [PMID: 37591314 PMCID: PMC10445456 DOI: 10.1016/j.virusres.2023.199200] [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: 06/15/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Human cytomegalovirus (HCMV) infection is shaped by a tightly regulated interplay between viral and cellular proteins. Distinct kinase activities, such as the viral cyclin-dependent kinase ortholog (vCDK) pUL97 and cellular CDK7 are both crucial for efficient viral replication. Previously, we reported that both kinases, vCDK/pUL97 and CDK7, interact with cyclin H, thereby achieving an enhanced level of kinase activity and overall functionality in viral replication. Here we provide a variety of novel results, as generated on a methodologically extended basis, and present a concept for the codetermination of viral replication efficiency through these kinase activities: (i) cyclin H expression, in various human cell types, is substantially upregulated by strains of HCMV including the clinically relevant HCMV Merlin; (ii) vCDK/pUL97 interacts with human cyclin H in both HCMV-infected and plasmid-transfected cell systems; (iii) a doxycycline-inducible shRNA-dependent knock-down (KD) of cyclin H significantly reduces pUL97 activity (qSox in vitro kinase assay); (iv) accordingly, pUL97 in vitro kinase activity is seen significantly increased upon addition of recombinant cyclin H; (v) as a point of specific importance, human CDK7 activity shows an increase by vCDK/pUL97-mediated trans-stimulation (whereas pUL97 is not stimulated by CDK7); (vi) phosphosite-specific antibodies indicate an upregulated CDK7 phosphorylation upon HCMV infection, as mediated through a pUL97-specific modulatory effect (i.e. shown by pUL97 inhibitor treatment or pUL97-deficient viral mutant); (vii) finally, an efficient KD of cyclin H in primary fibroblasts generally results in an impaired HCMV replication efficiency as measured on protein and genomic levels. These results show evidence for the codetermination of viral replication by vCDK/pUL97, cyclin H and CDK7, thus supporting the specific importance of cyclin H as a central regulatory factor, and suggesting novel targeting options for antiviral drugs.
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Affiliation(s)
- Martin Schütz
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany.
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany
| | - Mona Sommerer
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany
| | - Melanie Kögler
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany
| | | | | | - Bert Klebl
- Lead Discovery Center GmbH, Dortmund, Germany
| | - Zin Naing
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - Ece Egilmezer
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - Stuart T Hamilton
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - William D Rawlinson
- Serology and Virology Division, NSW Health Pathology Microbiology, Prince of Wales Hospital, and Schools of Women's and Children's Health, Medicine and Biotechnology and Biomolecular Sciences, University of New South Wales, High Street, Sydney, Australia
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, FAU, Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Schlossgarten 4, Erlangen 91054, Germany.
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21
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Zhang J, Gao W, Wang Y, Chang J, Yu B. Targeted covalent inhibitors for novel therapeutics. Future Med Chem 2023; 15:1739-1741. [PMID: 37791528 DOI: 10.4155/fmc-2023-0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Affiliation(s)
- Jingya Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenshuo Gao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yixia Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Junbiao Chang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang, 453007, China
| | - Bin Yu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Pingyuan Laboratory, State Key Laboratory of Antiviral Drugs, Henan Normal University, Xinxiang, 453007, China
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22
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Ngo C, Fried W, Aliyari S, Feng J, Qin C, Zhang S, Yang H, Shanaa J, Feng P, Cheng G, Chen XS, Zhang C. Alkyne as a Latent Warhead to Covalently Target SARS-CoV-2 Main Protease. J Med Chem 2023; 66:12237-12248. [PMID: 37595260 PMCID: PMC10510381 DOI: 10.1021/acs.jmedchem.3c00810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 08/20/2023]
Abstract
There is an urgent need for improved therapy to better control the ongoing COVID-19 pandemic. The main protease Mpro plays a pivotal role in SARS-CoV-2 replications, thereby representing an attractive target for antiviral development. We seek to identify novel electrophilic warheads for efficient, covalent inhibition of Mpro. By comparing the efficacy of a panel of warheads installed on a common scaffold against Mpro, we discovered that the terminal alkyne could covalently modify Mpro as a latent warhead. Our biochemical and X-ray structural analyses revealed the irreversible formation of the vinyl-sulfide linkage between the alkyne and the catalytic cysteine of Mpro. Clickable probes based on the alkyne inhibitors were developed to measure target engagement, drug residence time, and off-target effects. The best alkyne-containing inhibitors potently inhibited SARS-CoV-2 infection in cell infection models. Our findings highlight great potentials of alkyne as a latent warhead to target cystine proteases in viruses and beyond.
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Affiliation(s)
- Chau Ngo
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - William Fried
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Saba Aliyari
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Joshua Feng
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Qin
- Section
of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States
| | - Shilei Zhang
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Hanjing Yang
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Jean Shanaa
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Pinghui Feng
- Section
of Infection and Immunity, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California 90089, United States
| | - Genhong Cheng
- Department
of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Xiaojiang S. Chen
- Molecular
and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department
of Chemistry and Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
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23
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Zhou X, Ji Y, Zhou J. Multiple Strategies to Develop Small Molecular KRAS Directly Bound Inhibitors. Molecules 2023; 28:molecules28083615. [PMID: 37110848 PMCID: PMC10146153 DOI: 10.3390/molecules28083615] [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: 03/13/2023] [Revised: 04/08/2023] [Accepted: 04/17/2023] [Indexed: 04/29/2023] Open
Abstract
KRAS gene mutation is widespread in tumors and plays an important role in various malignancies. Targeting KRAS mutations is regarded as the "holy grail" of targeted cancer therapies. Recently, multiple strategies, including covalent binding strategy, targeted protein degradation strategy, targeting protein and protein interaction strategy, salt bridge strategy, and multivalent strategy, have been adopted to develop KRAS direct inhibitors for anti-cancer therapy. Various KRAS-directed inhibitors have been developed, including the FDA-approved drugs sotorasib and adagrasib, KRAS-G12D inhibitor MRTX1133, and KRAS-G12V inhibitor JAB-23000, etc. The different strategies greatly promote the development of KRAS inhibitors. Herein, the strategies are summarized, which would shed light on the drug discovery for both KRAS and other "undruggable" targets.
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Affiliation(s)
- Xile Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, China
| | - Yang Ji
- Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
| | - Jinming Zhou
- Drug Development and Innovation Center, College of Chemistry and Life Sciences, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, China
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24
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Tillmanns J, Häge S, Borst EM, Wardin J, Eickhoff J, Klebl B, Wagner S, Wangen C, Hahn F, Socher E, Marschall M. Assessment of Covalently Binding Warhead Compounds in the Validation of the Cytomegalovirus Nuclear Egress Complex as an Antiviral Target. Cells 2023; 12:cells12081162. [PMID: 37190072 DOI: 10.3390/cells12081162] [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: 01/27/2023] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Herpesviral nuclear egress is a regulated process of viral capsid nucleocytoplasmic release. Due to the large capsid size, a regular transport via the nuclear pores is unfeasible, so that a multistage-regulated export pathway through the nuclear lamina and both leaflets of the nuclear membrane has evolved. This process involves regulatory proteins, which support the local distortion of the nuclear envelope. For human cytomegalovirus (HCMV), the nuclear egress complex (NEC) is determined by the pUL50-pUL53 core that initiates multicomponent assembly with NEC-associated proteins and capsids. The transmembrane NEC protein pUL50 serves as a multi-interacting determinant that recruits regulatory proteins by direct and indirect contacts. The nucleoplasmic core NEC component pUL53 is strictly associated with pUL50 in a structurally defined hook-into-groove complex and is considered as the potential capsid-binding factor. Recently, we validated the concept of blocking the pUL50-pUL53 interaction by small molecules as well as cell-penetrating peptides or an overexpression of hook-like constructs, which can lead to a pronounced degree of antiviral activity. In this study, we extended this strategy by utilizing covalently binding warhead compounds, originally designed as binders of distinct cysteine residues in target proteins, such as regulatory kinases. Here, we addressed the possibility that warheads may likewise target viral NEC proteins, building on our previous crystallization-based structural analyses that revealed distinct cysteine residues in positions exposed from the hook-into-groove binding surface. To this end, the antiviral and NEC-binding properties of a selection of 21 warhead compounds were investigated. The combined findings are as follows: (i) warhead compounds exhibited a pronounced anti-HCMV potential in cell-culture-based infection models; (ii) computational analysis of NEC primary sequences and 3D structures revealed cysteine residues exposed to the hook-into-groove interaction surface; (iii) several of the active hit compounds exhibited NEC-blocking activity, as shown at the single-cell level by confocal imaging; (iv) the clinically approved warhead drug ibrutinib exerted a strong inhibitory impact on the pUL50-pUL53 core NEC interaction, as demonstrated by the NanoBiT assay system; and (v) the generation of recombinant HCMV ∆UL50-ΣUL53, allowing the assessment of viral replication under conditional expression of the viral core NEC proteins, was used for characterizing viral replication and a mechanistic evaluation of ibrutinib antiviral efficacy. Combined, the results point to a rate-limiting importance of the HCMV core NEC for viral replication and to the option of exploiting this determinant by the targeting of covalently NEC-binding warhead compounds.
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Affiliation(s)
- Julia Tillmanns
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Sigrun Häge
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Eva Maria Borst
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
| | - Julia Wardin
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH (LDC), 44227 Dortmund, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH (LDC), 44227 Dortmund, Germany
- The Norwegian College of Fishery Science UiT, The Arctic University of Norway, 9037 Tromsø, Norway
| | - Sabrina Wagner
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Christina Wangen
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Friedrich Hahn
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Eileen Socher
- Institute of Anatomy, Functional and Clinical Anatomy, FAU, 91054 Erlangen, Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular Virology, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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25
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [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
- 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
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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26
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Fang L, Chu M, Yan C, Liu Y, Zhao Z. Palbociclib and Michael-acceptor hybrid compounds as CDK4/6 covalent inhibitors: improved potency, broad anticancer spectrum and overcoming drug resistance. Bioorg Med Chem 2023; 84:117263. [PMID: 37011445 DOI: 10.1016/j.bmc.2023.117263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/28/2023]
Abstract
To search for potent CDK4/6 covalent inhibitors, total 14 compounds have been designed and synthesized by connecting different Michael-acceptor to the piperazine moiety of palbociclib. All the compounds displayed good antiproliferative activity against human hepatoma cell (HepG2), non-small cell lung cancer (A549), and breast cancer (MDA-MB-231 and MCF-7) cell lines. In particular, compound A4 showed the highest inhibitory activity to MDA-MB-231 and MCF-7 cells with IC50 values of 0.51 μM and 0.48 μM, respectively. More importantly, A4 also showed strong inhibition against MDA-MB-231/palbociclib cells, indicating that A4 could effectively avoid the resistance of palbociclib. In the enzyme test, A4 showed selective inhibitory activity against CDK4/6, with the IC50 value of 18 nM and 13 nM, respectively. It was also found that A4 could efficiently induce apoptosis and arrest the cell cycle at G0/G1 phase. Moreover, A4 could significantly decrease the phosphorylation level of CDK4 and CDK6. HPLC and molecular modeling studies suggested that A4 could form a covalent bond with the target protein.
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Affiliation(s)
- Lei Fang
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Mengqi Chu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Changhang Yan
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yilin Liu
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Zimeng Zhao
- Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
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27
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Lv S, Xu F, Fan Y, Ding K, Li Z. Cyclopropenone, Cyclopropeniminium Ion, and Cyclopropenethione as Novel Electrophilic Warheads for Potential Target Discovery of Triple-Negative Breast Cancer. J Med Chem 2023; 66:2851-2864. [PMID: 36762554 DOI: 10.1021/acs.jmedchem.2c01889] [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: 02/11/2023]
Abstract
Because very few targets are currently available for drug development, triple-negative breast cancer (TNBC) has been defined as one of the most difficult diseases for chemotherapy. Herein, we describe a suite of novel electrophilic warheads, which we have used in chemical proteomics studies in a search for potential targets for TNBC. Binding site analysis revealed that these warheads can modify not only highly nucleophilic residues, including cysteine and lysine, but also weakly nucleophilic residues. Cys12 of Kirsten rat sarcoma (KRASG12C) was successfully labeled by cyclopropenone and the cyclopropeniminium ions. Moderate inhibitory activity against TNBC cells was achieved with these novel electrophile-based probes. Activity-based protein profiling reveals that these electrophiles can covalently label a series of essential protein targets, including ALDH2, LRPPRC, and FABP5 from MDA-MB-231 cells. Further functional validation experiments demonstrated that FABP5 might be a potential target for TNBC.
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Affiliation(s)
- Shumin Lv
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Fang Xu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Youlong Fan
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Ke Ding
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Zhengqiu Li
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development (MOE), MOE Key Laboratory of Tumor Molecular Biology, School of Pharmacy, Jinan University, Guangzhou 510632, China
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28
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bioTCIs: Middle-to-Macro Biomolecular Targeted Covalent Inhibitors Possessing Both Semi-Permanent Drug Action and Stringent Target Specificity as Potential Antibody Replacements. Int J Mol Sci 2023; 24:ijms24043525. [PMID: 36834935 PMCID: PMC9968108 DOI: 10.3390/ijms24043525] [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: 12/26/2022] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023] Open
Abstract
Monoclonal antibody therapies targeting immuno-modulatory targets such as checkpoint proteins, chemokines, and cytokines have made significant impact in several areas, including cancer, inflammatory disease, and infection. However, antibodies are complex biologics with well-known limitations, including high cost for development and production, immunogenicity, a limited shelf-life because of aggregation, denaturation, and fragmentation of the large protein. Drug modalities such as peptides and nucleic acid aptamers showing high-affinity and highly selective interaction with the target protein have been proposed alternatives to therapeutic antibodies. The fundamental limitation of short in vivo half-life has prevented the wide acceptance of these alternatives. Covalent drugs, also known as targeted covalent inhibitors (TCIs), form permanent bonds to target proteins and, in theory, eternally exert the drug action, circumventing the pharmacokinetic limitation of other antibody alternatives. The TCI drug platform, too, has been slow in gaining acceptance because of its potential prolonged side-effect from off-target covalent binding. To avoid the potential risks of irreversible adverse drug effects from off-target conjugation, the TCI modality is broadening from the conventional small molecules to larger biomolecules possessing desirable properties (e.g., hydrolysis resistance, drug-action reversal, unique pharmacokinetics, stringent target specificity, and inhibition of protein-protein interactions). Here, we review the historical development of the TCI made of bio-oligomers/polymers (i.e., peptide-, protein-, or nucleic-acid-type) obtained by rational design and combinatorial screening. The structural optimization of the reactive warheads and incorporation into the targeted biomolecules enabling a highly selective covalent interaction between the TCI and the target protein is discussed. Through this review, we hope to highlight the middle to macro-molecular TCI platform as a realistic replacement for the antibody.
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29
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Reddi RN, Rogel A, Gabizon R, Rawale DG, Harish B, Marom S, Tivon B, Arbel YS, Gurwicz N, Oren R, David K, Liu J, Duberstein S, Itkin M, Malitsky S, Barr H, Katz BZ, Herishanu Y, Shachar I, Shulman Z, London N. Sulfamate Acetamides as Self-Immolative Electrophiles for Covalent Ligand-Directed Release Chemistry. J Am Chem Soc 2023; 145:3346-3360. [PMID: 36738297 PMCID: PMC9936582 DOI: 10.1021/jacs.2c08853] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Electrophiles for covalent inhibitors that are suitable for in vivo administration are rare. While acrylamides are prevalent in FDA-approved covalent drugs, chloroacetamides are considered too reactive for such purposes. We report sulfamate-based electrophiles that maintain chloroacetamide-like geometry with tunable reactivity. In the context of the BTK inhibitor ibrutinib, sulfamate analogues showed low reactivity with comparable potency in protein labeling, in vitro, and cellular kinase activity assays and were effective in a mouse model of CLL. In a second example, we converted a chloroacetamide Pin1 inhibitor to a potent and selective sulfamate acetamide with improved buffer stability. Finally, we show that sulfamate acetamides can be used for covalent ligand-directed release (CoLDR) chemistry, both for the generation of "turn-on" probes as well as for traceless ligand-directed site-specific labeling of proteins. Taken together, this chemistry represents a promising addition to the list of electrophiles suitable for in vivo covalent targeting.
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Affiliation(s)
- Rambabu N. Reddi
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel,
| | - Adi Rogel
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ronen Gabizon
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dattatraya Gautam Rawale
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Battu Harish
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shir Marom
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Barr Tivon
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yamit Shorer Arbel
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Neta Gurwicz
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Roni Oren
- Department
of Veterinary Resources, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Keren David
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Jingjing Liu
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Shirly Duberstein
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Maxim Itkin
- Life Sciences
Core Facilities, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Life Sciences
Core Facilities, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Haim Barr
- Wohl
Institute for Drug Discovery of the Nancy and Stephen Grand Israel
National Center for Personalized Medicine, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ben-Zion Katz
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel,Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Yair Herishanu
- Sackler
Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel,Department
of Hematology, Tel Aviv Sourasky Medical
Center, Tel Aviv 6423906, Israel
| | - Idit Shachar
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Ziv Shulman
- Dept.
of Systems Immunology, The Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Nir London
- Dept.
of Chemical and Structural Biology, The
Weizmann Institute of Science, Rehovot 7610001, Israel,
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30
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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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31
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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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32
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Vandyshev DY, Shikhaliev KS, Prezent MA, Kozaderov OA, Ovchinnikov OV, Smirnov MS, Ilyinova TN, Mangusheva DA, Iminova RR, Chetti P. ANALYSIS OF THE SPECTRAL-LUMINESCENT PROPERTIES OF IMIDAZO[1,2-b]PYRIDO[4,3-e][1,2,4]TRIAZIN-6(7Н)-ONES. LUMINESCENCE 2022; 37:1689-1700. [PMID: 35863912 DOI: 10.1002/bio.4344] [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: 05/20/2022] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 11/08/2022]
Abstract
The article presents a method for the construction of a new tricyclic system of imidazo[1,2-b]pyrido[4,3-e][1,2,4]triazin-6(7Н)-ones based on subsequent reactions of the obtained 1,2-diamino-4-phenylimidazole ethyl ether of 3-methyl-6-phenylimidazo[1,2-b][1,2,4]triazin-2-carboxylic acid with dimethylformamide dimethylacetal and primary amines. The structures of the obtained compounds were confirmed using the data obtained by 1 Н and 13 С NMR, HRMS, and XRD. We analysed the dependence of the absorption and photoluminescence spectra on the structure of the compounds obtained using methods of quantum chemistry. The theoretical results were compared to the data of a real experiment. The article suggests a range of practical applications for imidazo[1,2-b]pyrido[4,3-e][1,2,4]triazin-6(7Н)-ones.
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Affiliation(s)
- Dmitriy Yu Vandyshev
- Department of Organic Chemistry. Chemical Faculty. Voronezh State University, Voronezh, Russia
| | - Khidmet S Shikhaliev
- Department of Organic Chemistry. Chemical Faculty. Voronezh State University, Voronezh, Russia
| | - Mikhail A Prezent
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Oleg A Kozaderov
- Department of Organic Chemistry. Chemical Faculty. Voronezh State University, Voronezh, Russia
| | - Oleg V Ovchinnikov
- Department of Optics and Spectroscopy. Faculty of Physics. Voronezh State University, Voronezh, Russia
| | - Mikhail S Smirnov
- Department of Optics and Spectroscopy. Faculty of Physics. Voronezh State University, Voronezh, Russia
| | - Tatiana N Ilyinova
- Department of Clinical Laboratory Diagnostics, Voronezh Medical State University, Voronezh, Russia
| | - Daria A Mangusheva
- Department of Organic Chemistry. Chemical Faculty. Voronezh State University, Voronezh, Russia
| | - Renata R Iminova
- Department of Organic Chemistry. Chemical Faculty. Voronezh State University, Voronezh, Russia
| | - Prabhakar Chetti
- National Institute of Technology Kurukshetra, Kurukshetra, India
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33
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Li L, Meyer C, Zhou ZW, Elmezayen A, Westover K. Therapeutic Targeting the Allosteric Cysteinome of RAS and Kinase Families. J Mol Biol 2022; 434:167626. [PMID: 35595166 DOI: 10.1016/j.jmb.2022.167626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/25/2022] [Accepted: 05/03/2022] [Indexed: 12/14/2022]
Abstract
Allosteric mechanisms are pervasive in nature, but human-designed allosteric perturbagens are rare. The history of KRASG12C inhibitor development suggests that covalent chemistry may be a key to expanding the armamentarium of allosteric inhibitors. In that effort, irreversible targeting of a cysteine converted a non-deal allosteric binding pocket and low affinity ligands into a tractable drugging strategy. Here we examine the feasibility of expanding this approach to other allosteric pockets of RAS and kinase family members, given that both protein families are regulators of vital cellular processes that are often dysregulated in cancer and other human diseases. Moreover, these heavily studied families are the subject of numerous drug development campaigns that have resulted, sometimes serendipitously, in the discovery of allosteric inhibitors. We consequently conducted a comprehensive search for cysteines, a commonly targeted amino acid for covalent drugs, using AlphaFold-generated structures of those families. This new analysis presents potential opportunities for allosteric targeting of validated and understudied drug targets, with an emphasis on cancer therapy.
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Affiliation(s)
- Lianbo Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Cynthia Meyer
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Ammar Elmezayen
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA
| | - Kenneth Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, 75390, USA.
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