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Sebastian A, Abu Rabah RR, Zaraei SO, Vunnam S, Sultan S, Anbar HS, El-Gamal R, Tarazi H, Sarg N, Alhamad DW, Al Shamma SA, Shahin AI, Omar HA, Al-Tel TH, El-Gamal MI. Design, synthesis, biological evaluation, and in silico studies of novel pyridopyridine derivatives as anticancer candidates targeting FMS kinase. Eur J Med Chem 2024; 274:116557. [PMID: 38850857 DOI: 10.1016/j.ejmech.2024.116557] [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: 04/29/2024] [Revised: 05/29/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Design and synthesis of novel 4-carboxamidopyrido[3,2-b]pyridine derivatives as novel rigid analogues of sorafenib are reported herein. The target compounds showed potent antiproliferative activities against a panel of NCI-60 cancer cell lines as well as hepatocellular carcinoma cell line. Compounds 8g and 9f were among the most promising derivatives in terms of effectiveness and safety. Therefore, they were further examined to demonstrate their ability to induce apoptosis and alter cell cycle progression in hepatocellular carcinoma cells. The most potent compounds were tested against a panel of kinases that indicated their selectivity against FMS kinase. Compounds 8g and 8h showed the most potent activities against FMS kinase with IC50 values of 21.5 and 73.9 nM, respectively. The two compounds were also tested in NanoBRET assay to investigate their ability to inhibit FMS kinase in cells (IC50 = 563 nM (8g) and 1347 nM (8h) vs. IC50 = 1654 nM for sorafenib). Furthermore, compounds 8g and 8h possess potent inhibitory activities against macrophages when investigated in bone marrow-derived macrophages (BMDM) assay (IC50 = 56 nM and 167 nM, respectively, 164 nM for sorafenib). The safety and selectivity of these compounds were confirmed when tested against normal cell lines. Their safety profile was further confirmed using hERG assay. In silico studies were carried out to investigate their binding modes in the active site of FMS kinase, and to develop a QSAR model for these new motifs.
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Affiliation(s)
- Anusha Sebastian
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Reinad R Abu Rabah
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Seyed-Omar Zaraei
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Srinivasulu Vunnam
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Shaista Sultan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hanan S Anbar
- Department of Pharmaceutical Sciences, Dubai Pharmacy College for Girls, Dubai, 19099, United Arab Emirates
| | - Randa El-Gamal
- Department of Medical Biochemistry, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Hamadeh Tarazi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Nadin Sarg
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Dima W Alhamad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Salma A Al Shamma
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Afnan I Shahin
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates
| | - Hany A Omar
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62514, Egypt
| | - Taleb H Al-Tel
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates.
| | - Mohammed I El-Gamal
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, 27272, United Arab Emirates; Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
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Wang X, Sun J, Huang H, Tang G, Chen P, Xiang M, Li L, Zhang ZM, Gao L, Yao SQ. Kinase Inhibition via Small Molecule-Induced Intramolecular Protein Cross-Linking. Angew Chem Int Ed Engl 2024; 63:e202404195. [PMID: 38695161 DOI: 10.1002/anie.202404195] [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: 02/29/2024] [Indexed: 07/02/2024]
Abstract
Remarkable progress has been made in the development of cysteine-targeted covalent inhibitors. In kinase drug discovery, covalent inhibitors capable of targeting other nucleophilic residues (i.e. lysine, or K) have emerged in recent years. Besides a highly conserved catalytic lysine, almost all human protein kinases possess an equally conserved glutamate/aspartate (e.g. E/D) that forms a K-E/D salt bridge within the enzyme's active site. Electrophilic ynamides were previously used as effective peptide coupling reagents and to develop E/D-targeting covalent protein inhibitors/probes. In the present study, we report the first ynamide-based small-molecule inhibitors capable of inducing intramolecular cross-linking of various protein kinases, leading to subsequent irreversible inhibition of kinase activity. Our strategy took advantage of the close distance between the highly conserved catalytic K and E/D residues in a targeted kinase, thus providing a conceptually general approach to achieve irreversible kinase inhibition with high specificity and desirable cellular potency. Finally, this ynamide-facilitated, ligand-induced mechanism leading to intramolecular kinase cross-linking and inhibition was unequivocally established by using recombinant ABL kinase as a representative.
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Affiliation(s)
- Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, China
| | - Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Menghua Xiang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Lin Li
- The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 West Huangpu Avenue West, Guangzhou, 510632, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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Aboul-Soud MAM, Al-Sheikh YA, Ghneim HK, Supuran CT, Carta F. Kinase inhibitors: 20 years of success and many new challenges and recent trends in their patents. Expert Opin Ther Pat 2024; 34:583-592. [PMID: 38784980 DOI: 10.1080/13543776.2024.2355247] [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: 12/22/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
INTRODUCTION Protein kinases (PKs) play key roles in cellular signaling and regulation cascades and therefore are listed among the most investigated enzymes with the intent to develop drugs that are able to modulate their catalytic features. Specifically, PKs are involved in chronic diseases of large impact in the society such as cancers and neurodegeneration. Since the approval of Fasudil for the management of cerebral vasospasm, frantic efforts are currently ongoing for the development of selective PK-modulating agents. AREAS COVERED A selection of the most relevant patents in the European Patent Office for biomedical innovation and/or industrial development covering the years 2020-2023 on PK modulators either of the antibody and small-molecule type is reported. In addition to the examined patents, we also reported the contributions claiming the use of antibody-targeted PKs for lab bench identification kits. EXPERT OPINION The field of PK modulators for biomedical purposes is particularly crowded with contributions, making it rich in valuable information for the development of potential drugs. An emerging frontier is represented by PK activators that aims to complement the use of PK inhibitors with the final intent of finely adjusting any PK-related disruption responsible for triggering any disease.
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Affiliation(s)
- Mourad A M Aboul-Soud
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Yazeed A Al-Sheikh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hazem K Ghneim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Fabrizio Carta
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche e Nutraceutiche, University of Florence, Sesto Fiorentino, Florence, Italy
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4
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Baker ZD, Rasmussen DM, Levinson NM. Exploring the conformational landscapes of protein kinases: perspectives from FRET and DEER. Biochem Soc Trans 2024; 52:1071-1083. [PMID: 38778760 DOI: 10.1042/bst20230558] [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: 02/15/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Conformational changes of catalytically-important structural elements are a key feature of the regulation mechanisms of protein kinases and are important for dictating inhibitor binding modes and affinities. The lack of widely applicable methods for tracking kinase conformational changes in solution has hindered our understanding of kinase regulation and our ability to design conformationally selective inhibitors. Here we provide an overview of two recently developed methods that detect conformational changes of the regulatory activation loop and αC-helix of kinases and that yield complementary information about allosteric mechanisms. An intramolecular Förster resonance energy transfer-based approach provides a scalable platform for detecting and classifying structural changes in high-throughput, as well as quantifying ligand binding cooperativity, shedding light on the energetics governing allostery. The pulsed electron paramagnetic resonance technique double electron-electron resonance provides lower throughput but higher resolution information on structural changes that allows for unambiguous assignment of conformational states and quantification of population shifts. Together, these methods are shedding new light on kinase regulation and drug interactions and providing new routes for the identification of novel kinase inhibitors and allosteric modulators.
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Affiliation(s)
- Zachary D Baker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Damien M Rasmussen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
| | - Nicholas M Levinson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, U.S.A
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, U.S.A
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5
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Jiang F, Zhang F, Su Y, Zhang C, Chang T. Knowledge mapping of disease-modifying therapy (DMT) in multiple sclerosis (MS): A bibliometrics analysis. Heliyon 2024; 10:e31744. [PMID: 38868066 PMCID: PMC11168326 DOI: 10.1016/j.heliyon.2024.e31744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/14/2024] Open
Abstract
Background Multiple sclerosis (MS) is a heterogeneous autoimmune disease, with a rapidly evolving body of literature on disease-modifying therapy (DMT) that urgently needs to be synthesized and regularized. Methods The original material used for the analysis was obtained from the Web of Science Core Collection (WoSCC) in the Science Citation Index Expanded Edition (SCI-E). The data material was accessed through VOSviewer, Citespace, R package "Bibliometrix", and Scimago Graphica for data analysis and visualization. Among them, the clustering algorithm based on the Largest Likelihood Ratio (LLR) and the burst citation algorithm is the key. Results As of November 6th, 2022, 4142 publications related to emerging disease-modifying therapies (e-DMT) for MS, 6521 publications related to traditional disease-modifying therapies (t-DMT) for MS, and 1793 publications in cross-cutting disease-modifying therapies (I-DMT) for MS were included in the analysis, respectively. Publications related to DMT in MS were analyzed descriptively (for three subjects: country, institution, and author) and predictively (for two subjects: keywords and references) separately according to three sections: e-DMT, t-DMT, and I-DMT. Topics that still have relevant reference output as of 2022 include the safety of Coronavirus disease 2019 (COVID-19) mRNA vaccination, therapeutic inertia (TI), cladribine tablets, autologous hematopoietic stem cell transplantation (aHSCT), progressive multiple sclerosis, and pediatric multiple sclerosis. Conclusion The future research focus for MS DMT is the combination trial or cross-trial of various treatment methods to improve the development of individualized treatment plans for MS patients. The exact contents of the research frontiers are included but not limited to ocrelizumab, fingolimod and other monoclonal antibodies, fumaric acid ester, cladribine tablet, aHSCT, and other interventions of randomized controlled trials (RCTs); the impact of mRNA COVID-19 vaccination on MS patients; TI, patient adherence, and other medical management issues; and continued exploration of biomarkers for more accurate disease classification based on the existing clinical indication classification.
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Affiliation(s)
- Fan Jiang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
- Section of Health, No. 94804 Unit of the Chinese People's Liberation Army, Shanghai, 200434, China
- Resident Standardization Training Cadet Corps, Air Force Hospital of Eastern Theater, Nanjing, 210002, China
| | - Fenghe Zhang
- Department of Neurology and Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Yue Su
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Chao Zhang
- Department of Neurology and Institute of Neuroimmunology, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
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Balusu S, De Strooper B. The necroptosis cell death pathway drives neurodegeneration in Alzheimer's disease. Acta Neuropathol 2024; 147:96. [PMID: 38852117 PMCID: PMC11162975 DOI: 10.1007/s00401-024-02747-5] [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: 04/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/10/2024]
Abstract
Although apoptosis, pyroptosis, and ferroptosis have been implicated in AD, none fully explains the extensive neuronal loss observed in AD brains. Recent evidence shows that necroptosis is abundant in AD, that necroptosis is closely linked to the appearance of Tau pathology, and that necroptosis markers accumulate in granulovacuolar neurodegeneration vesicles (GVD). We review here the neuron-specific activation of the granulovacuolar mediated neuronal-necroptosis pathway, the potential AD-relevant triggers upstream of this pathway, and the interaction of the necrosome with the endo-lysosomal pathway, possibly providing links to Tau pathology. In addition, we underscore the therapeutic potential of inhibiting necroptosis in neurodegenerative diseases such as AD, as this presents a novel avenue for drug development targeting neuronal loss to preserve cognitive abilities. Such an approach seems particularly relevant when combined with amyloid-lowering drugs.
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Affiliation(s)
- Sriram Balusu
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium.
| | - Bart De Strooper
- Laboratory for the Research of Neurodegenerative Diseases, VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, 3000, Leuven, Belgium.
- UK Dementia Research Institute at UCL, London, WC1E 6BT, UK.
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7
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Gilmer TM, Lai CH, Guo K, Deland K, Ashcraft KA, Stewart AE, Wang Y, Fu J, Wood KC, Kirsch DG, Kastan MB. A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors. Mol Cancer Ther 2024; 23:751-765. [PMID: 38588408 DOI: 10.1158/1535-7163.mct-23-0890] [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: 12/15/2023] [Revised: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
A majority of patients with cancer receive radiotherapy as part of their treatment regimens whether using external beam therapy or locally-delivered radioisotopes. While often effective, some tumors are inadequately controlled with radiation and radiotherapy has significant short-term and long-term toxicities for cancer survivors. Insights into molecular mechanisms involved in cellular responses to DNA breaks introduced by radiation or other cancer therapies have been gained in recent years and approaches to manipulate these responses to enhance tumor cell killing or reduce normal tissue toxicity are of great interest. Here, we report the identification and initial characterization of XRD-0394, a potent and specific dual inhibitor of two DNA damage response kinases, ATM and DNA-PKcs. This orally bioavailable molecule demonstrates significantly enhanced tumor cell kill in the setting of therapeutic ionizing irradiation in vitro and in vivo. XRD-0394 also potentiates the effectiveness of topoisomerase I inhibitors in vitro. In addition, in cells lacking BRCA1/2 XRD-0394 shows single-agent activity and synergy in combination with PARP inhibitors. A phase Ia clinical trial (NCT05002140) with XRD-0394 in combination with radiotherapy has completed. These results provide a rationale for future clinical trials with XRD-0394 in combination with radiotherapy, PARP inhibitors, and targeted delivery of topoisomerase I inhibitors.
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Affiliation(s)
| | - Chun-Hsiang Lai
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Kexiao Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Katherine Deland
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | - Kathleen A Ashcraft
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | - Amy E Stewart
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | | | | | - Kris C Wood
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
- Department of Radiation Oncology, Duke University School of Medicine, Durham, North Carolina
| | - Michael B Kastan
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
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8
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Wirth D, Özdemir E, Wimley WC, Pasquale EB, Hristova K. Transmembrane helix interactions regulate oligomerization of the receptor tyrosine kinase EphA2. J Biol Chem 2024:107441. [PMID: 38838777 DOI: 10.1016/j.jbc.2024.107441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024] Open
Abstract
The transmembrane helices of receptor tyrosine kinases (RTKs) have been proposed to switch between two different dimeric conformations, one associated with the inactive RTK and the other with the active RTK. Furthermore, recent work has demonstrated that some full-length RTKs associate into oligomers that are larger than dimers, raising questions about the roles of the TM helices in the assembly and function of these oligomers. Here we probe the roles of the TM helices in the stability of EphA2 RTK oligomers in the plasma membrane. We employ mutagenesis to evaluate the relevance of a published NMR dimeric structure of the isolated EphA2 TM helix in the context of the full-length EphA2 in the plasma membrane. We use two fluorescence methods, Förster Resonance Energy Transfer and Fluorescence Intensity Fluctuations spectrometry, which yield complementary information about the EphA2 oligomerization process. These studies reveal that the TM helix mutations affect the stability, structure, and size of EphA2 oligomers. However, the effects are multifaceted, and point to a more complex role of the TM helix than the one expected from the "TM dimer switch" model.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
| | - Ece Özdemir
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218
| | - William C Wimley
- Tulane University School of Medicine, Department of Biochemistry and Molecular Biology, New Orleans, LA
| | - Elena B Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Road, La Jolla, CA 92037
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218;.
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9
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Huang C, Hsu C, Chao M, Hsu K, Lin TE, Yen S, Tu H, Pan S. In silico identification of a novel Cdc2-like kinase 2 (CLK2) inhibitor in triple negative breast cancer. Protein Sci 2024; 33:e5004. [PMID: 38723164 PMCID: PMC11081522 DOI: 10.1002/pro.5004] [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: 01/02/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 05/13/2024]
Abstract
Dysregulation of RNA splicing processes is intricately linked to tumorigenesis in various cancers, especially breast cancer. Cdc2-like kinase 2 (CLK2), an oncogenic RNA-splicing kinase pivotal in breast cancer, plays a significant role, particularly in the context of triple-negative breast cancer (TNBC), a subtype marked by substantial medical challenges due to its low survival rates. In this study, we employed a structure-based virtual screening (SBVS) method to identify potential CLK2 inhibitors with novel chemical structures for treating TNBC. Compound 670551 emerged as a novel CLK2 inhibitor with a 50% inhibitory concentration (IC50) value of 619.7 nM. Importantly, Compound 670551 exhibited high selectivity for CLK2 over other protein kinases. Functionally, this compound significantly reduced the survival and proliferation of TNBC cells. Results from a cell-based assay demonstrated that this inhibitor led to a decrease in RNA splicing proteins, such as SRSF4 and SRSF6, resulting in cell apoptosis. In summary, we identified a novel CLK2 inhibitor as a promising potential treatment for TNBC therapy.
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Affiliation(s)
- Cheng‐Chiao Huang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Division of General Surgery, Department of SurgeryTaipei Medical University HospitalTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Chia‐Ming Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Min‐Wu Chao
- School of Medicine, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
- Institute of Biopharmaceutical Sciences, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
- The Doctoral Program of Clinical and Experimental Medicine, College of Medicine, National Sun Yat‐sen UniversityKaohsiungTaiwan
| | - Kai‐Cheng Hsu
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- Ph.D. Program in Drug Discovery and Development IndustryCollege of Pharmacy, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Drug Discovery, Taipei Medical UniversityTaipeiTaiwan
| | - Tony Eight Lin
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shih‐Chung Yen
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen)ShenzhenGuangdongChina
| | - Huang‐Ju Tu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shiow‐Lin Pan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipeiTaiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- Ph.D. Program in Drug Discovery and Development IndustryCollege of Pharmacy, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Drug Discovery, Taipei Medical UniversityTaipeiTaiwan
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10
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Yang M, Xiang H, Luo G. Targeting focal adhesion kinase (FAK) for cancer therapy: FAK inhibitors, FAK-based dual-target inhibitors and PROTAC degraders. Biochem Pharmacol 2024; 224:116246. [PMID: 38685282 DOI: 10.1016/j.bcp.2024.116246] [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: 02/19/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Focal adhesion kinase (FAK), a non-receptor tyrosine kinase, plays an essential role in regulating cell proliferation, migration and invasion through both kinase-dependent enzymatic function and kinase-independent scaffolding function. The overexpression and activation of FAK is commonly observed in various cancers and some drug-resistant settings. Therefore, targeted disruption of FAK has been identified as an attractive strategy for cancer treatment. To date, numerous structurally diverse inhibitors targeting distinct domains of FAK have been developed, encompassing kinase domain inhibitors, FERM domain inhibitors, and FAT domain inhibitors, with several FAK inhibitors advanced to clinical trials. Moreover, given the critical role of FAK scaffolding function in signal transduction, FAK-targeted PROTACs have also been developed. Although no current FAK-targeted therapeutics have been approved for the market, the combination of FAK inhibitors with other anticancer drugs has shown considerable promise in the clinic. This review provides an overview of current drug discovery strategies targeting FAK, including the development of FAK inhibitors, FAK-based dual-target inhibitors and proteolysis-targeting chimeras (PROTACs) in both literature and patent applications. Accordingly, their design and optimization process, mechanisms of action and biological activities are discussed to offer insights into future directions of FAK-targeting drug discovery in cancer therapy.
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Affiliation(s)
- Ming Yang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Hua Xiang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
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11
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Lin TE, Yen D, HuangFu W, Wu Y, Hsu J, Yen S, Sung T, Hsieh J, Pan S, Yang C, Huang W, Hsu K. An ensemble machine learning model generates a focused screening library for the identification of CDK8 inhibitors. Protein Sci 2024; 33:e5007. [PMID: 38723187 PMCID: PMC11081523 DOI: 10.1002/pro.5007] [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: 02/07/2024] [Revised: 03/26/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024]
Abstract
The identification of an effective inhibitor is an important starting step in drug development. Unfortunately, many issues such as the characterization of protein binding sites, the screening library, materials for assays, etc., make drug screening a difficult proposition. As the size of screening libraries increases, more resources will be inefficiently consumed. Thus, new strategies are needed to preprocess and focus a screening library towards a targeted protein. Herein, we report an ensemble machine learning (ML) model to generate a CDK8-focused screening library. The ensemble model consists of six different algorithms optimized for CDK8 inhibitor classification. The models were trained using a CDK8-specific fragment library along with molecules containing CDK8 activity. The optimized ensemble model processed a commercial library containing 1.6 million molecules. This resulted in a CDK8-focused screening library containing 1,672 molecules, a reduction of more than 99.90%. The CDK8-focused library was then subjected to molecular docking, and 25 candidate compounds were selected. Enzymatic assays confirmed six CDK8 inhibitors, with one compound producing an IC50 value of ≤100 nM. Analysis of the ensemble ML model reveals the role of the CDK8 fragment library during training. Structural analysis of molecules reveals the hit compounds to be structurally novel CDK8 inhibitors. Together, the results highlight a pipeline for curating a focused library for a specific protein target, such as CDK8.
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Affiliation(s)
- Tony Eight Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
- Ph.D. Program for Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Dyan Yen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
| | - Wei‐Chun HuangFu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
- Ph.D. Program for Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational MedicineTaipei Medical UniversityTaipeiTaiwan
| | - Yi‐Wen Wu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
| | - Jui‐Yi Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
- Ph.D. Program for Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
| | - Shih‐Chung Yen
- Warshel Institute for Computational BiologyThe Chinese University of Hong Kong (Shenzhen)ShenzhenGuangdongPeople's Republic of China
| | - Tzu‐Ying Sung
- Biomedical Translation Research Center, Academia SinicaTaipeiTaiwan
| | - Jui‐Hua Hsieh
- Division of Translational ToxicologyNational Institute of Environmental Health Sciences, National Institutes of HealthDurhamNorth CarolinaUSA
| | - Shiow‐Lin Pan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
- Ph.D. Program for Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational MedicineTaipei Medical UniversityTaipeiTaiwan
| | - Chia‐Ron Yang
- School of Pharmacy, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Wei‐Jan Huang
- Graduate Institute of Pharmacognosy, College of PharmacyTaipei Medical UniversityTaipeiTaiwan
| | - Kai‐Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and TechnologyTaipei Medical UniversityTaipeiTaiwan
- Ph.D. Program for Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- TMU Research Center of Cancer Translational MedicineTaipei Medical UniversityTaipeiTaiwan
- Cancer Center, Wan Fang HospitalTaipei Medical UniversityTaipeiTaiwan
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12
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Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
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Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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13
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O'Donoghue L, Smolenski A. Roles of G proteins and their GTPase-activating proteins in platelets. Biosci Rep 2024; 44:BSR20231420. [PMID: 38808367 PMCID: PMC11139668 DOI: 10.1042/bsr20231420] [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: 11/17/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Platelets are small anucleate blood cells supporting vascular function. They circulate in a quiescent state monitoring the vasculature for injuries. Platelets adhere to injury sites and can be rapidly activated to secrete granules and to form platelet/platelet aggregates. These responses are controlled by signalling networks that include G proteins and their regulatory guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Recent proteomics studies have revealed the complete spectrum of G proteins, GEFs, and GAPs present in platelets. Some of these proteins are specific for platelets and very few have been characterised in detail. GEFs and GAPs play a major role in setting local levels of active GTP-bound G proteins in response to activating and inhibitory signals encountered by platelets. Thus, GEFs and GAPs are highly regulated themselves and appear to integrate G protein regulation with other cellular processes. This review focuses on GAPs of small G proteins of the Arf, Rab, Ras, and Rho families, as well as of heterotrimeric G proteins found in platelets.
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Affiliation(s)
- Lorna O'Donoghue
- UCD School of Medicine, University College Dublin, UCD Conway Institute, Belfield, Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green 123, Dublin 2, Ireland
| | - Albert Smolenski
- UCD School of Medicine, University College Dublin, UCD Conway Institute, Belfield, Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, 123 St. Stephen’s Green 123, Dublin 2, Ireland
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14
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Ku AF, Sharma KL, Ta HM, Sutton CM, Bohren KM, Wang Y, Chamakuri S, Chen R, Hakenjos JM, Jimmidi R, Kent K, Li F, Li JY, Ma L, Madasu C, Palaniappan M, Palmer SS, Qin X, Robers MB, Sankaran B, Tan Z, Vasquez YM, Wang J, Wilkinson J, Yu Z, Ye Q, Young DW, Teng M, Kim C, Matzuk MM. Reversible male contraception by targeted inhibition of serine/threonine kinase 33. Science 2024; 384:885-890. [PMID: 38781365 DOI: 10.1126/science.adl2688] [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: 10/09/2023] [Accepted: 04/03/2024] [Indexed: 05/25/2024]
Abstract
Men or mice with homozygous serine/threonine kinase 33 (STK33) mutations are sterile owing to defective sperm morphology and motility. To chemically evaluate STK33 for male contraception with STK33-specific inhibitors, we screened our multibillion-compound collection of DNA-encoded chemical libraries, uncovered potent STK33-specific inhibitors, determined the STK33 kinase domain structure bound with a truncated hit CDD-2211, and generated an optimized hit CDD-2807 that demonstrates nanomolar cellular potency (half-maximal inhibitory concentration = 9.2 nanomolar) and favorable metabolic stability. In mice, CDD-2807 exhibited no toxicity, efficiently crossed the blood-testis barrier, did not accumulate in brain, and induced a reversible contraceptive effect that phenocopied genetic STK33 perturbations without altering testis size. Thus, STK33 is a chemically validated, nonhormonal contraceptive target, and CDD-2807 is an effective tool compound.
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Affiliation(s)
- Angela F Ku
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kiran L Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hai Minh Ta
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Courtney M Sutton
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kurt M Bohren
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruihong Chen
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - John M Hakenjos
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ravikumar Jimmidi
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Katarzyna Kent
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian-Yuan Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lang Ma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chandrashekhar Madasu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen S Palmer
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yasmin M Vasquez
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Zhifeng Yu
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiuji Ye
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Damian W Young
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Choel Kim
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin M Matzuk
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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15
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Zavvarian MM, Modi AD, Sadat S, Hong J, Fehlings MG. Translational Relevance of Secondary Intracellular Signaling Cascades Following Traumatic Spinal Cord Injury. Int J Mol Sci 2024; 25:5708. [PMID: 38891894 PMCID: PMC11172219 DOI: 10.3390/ijms25115708] [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: 04/09/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
Traumatic spinal cord injury (SCI) is a life-threatening and life-altering condition that results in debilitating sensorimotor and autonomic impairments. Despite significant advances in the clinical management of traumatic SCI, many patients continue to suffer due to a lack of effective therapies. The initial mechanical injury to the spinal cord results in a series of secondary molecular processes and intracellular signaling cascades in immune, vascular, glial, and neuronal cell populations, which further damage the injured spinal cord. These intracellular cascades present promising translationally relevant targets for therapeutic intervention due to their high ubiquity and conservation across eukaryotic evolution. To date, many therapeutics have shown either direct or indirect involvement of these pathways in improving recovery after SCI. However, the complex, multifaceted, and heterogeneous nature of traumatic SCI requires better elucidation of the underlying secondary intracellular signaling cascades to minimize off-target effects and maximize effectiveness. Recent advances in transcriptional and molecular neuroscience provide a closer characterization of these pathways in the injured spinal cord. This narrative review article aims to survey the MAPK, PI3K-AKT-mTOR, Rho-ROCK, NF-κB, and JAK-STAT signaling cascades, in addition to providing a comprehensive overview of the involvement and therapeutic potential of these secondary intracellular pathways following traumatic SCI.
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Affiliation(s)
- Mohammad-Masoud Zavvarian
- Division of Genetics and Development, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada; (M.-M.Z.); (A.D.M.); (S.S.); (J.H.)
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Akshat D. Modi
- Division of Genetics and Development, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada; (M.-M.Z.); (A.D.M.); (S.S.); (J.H.)
- Department of Biological Sciences, University of Toronto, Scarborough, ON M1C 1A4, Canada
- Department of Human Biology, University of Toronto, Toronto, ON M5S 3J6, Canada
| | - Sarah Sadat
- Division of Genetics and Development, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada; (M.-M.Z.); (A.D.M.); (S.S.); (J.H.)
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - James Hong
- Division of Genetics and Development, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada; (M.-M.Z.); (A.D.M.); (S.S.); (J.H.)
| | - Michael G. Fehlings
- Division of Genetics and Development, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada; (M.-M.Z.); (A.D.M.); (S.S.); (J.H.)
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON M5T 1P5, Canada
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16
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Halder P, Rai A, Talukdar V, Das P, Lakkaniga NR. Pyrazolopyridine-based kinase inhibitors for anti-cancer targeted therapy. RSC Med Chem 2024; 15:1452-1470. [PMID: 38784451 PMCID: PMC11110789 DOI: 10.1039/d4md00003j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/24/2024] [Indexed: 05/25/2024] Open
Abstract
The need for effective cancer treatments continues to be a challenge for the biomedical research community. In this case, the advent of targeted therapy has significantly improved therapeutic outcomes. Drug discovery and development efforts targeting kinases have resulted in the approval of several small-molecule anti-cancer drugs based on ATP-mimicking heterocyclic cores. Pyrazolopyridines are a group of privileged heterocyclic cores in kinase drug discovery, which are present in several inhibitors that have been developed against various cancers. Notably, selpercatinib, glumetinib, camonsertib and olverembatinib have either received approval or are in late-phase clinical studies. This review presents the success stories employing pyrazolopyridine scaffolds as hinge-binding cores to address various challenges in kinase-targeted drug discovery research.
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Affiliation(s)
- Pallabi Halder
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Anubhav Rai
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Vishal Talukdar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
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17
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Yang Y, Mou Y, Wan LX, Zhu S, Wang G, Gao H, Liu B. Rethinking therapeutic strategies of dual-target drugs: An update on pharmacological small-molecule compounds in cancer. Med Res Rev 2024. [PMID: 38769656 DOI: 10.1002/med.22057] [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: 02/15/2022] [Revised: 06/06/2023] [Accepted: 05/09/2024] [Indexed: 05/22/2024]
Abstract
Oncogenes and tumor suppressors are well-known to orchestrate several signaling cascades, regulate extracellular and intracellular stimuli, and ultimately control the fate of cancer cells. Accumulating evidence has recently revealed that perturbation of these key modulators by mutations or abnormal protein expressions are closely associated with drug resistance in cancer therapy; however, the inherent drug resistance or compensatory mechanism remains to be clarified for targeted drug discovery. Thus, dual-target drug development has been widely reported to be a promising therapeutic strategy for improving drug efficiency or overcoming resistance mechanisms. In this review, we provide an overview of the therapeutic strategies of dual-target drugs, especially focusing on pharmacological small-molecule compounds in cancer, including small molecules targeting mutation resistance, compensatory mechanisms, synthetic lethality, synergistic effects, and other new emerging strategies. Together, these therapeutic strategies of dual-target drugs would shed light on discovering more novel candidate small-molecule drugs for the future cancer treatment.
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Affiliation(s)
- Yiren Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Yi Mou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Lin-Xi Wan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Shiou Zhu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
| | - Huiyuan Gao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Bo Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, and Department of Gastroenterology and Hepatology, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, China
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18
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Gach-Janczak K, Drogosz-Stachowicz J, Janecka A, Wtorek K, Mirowski M. Historical Perspective and Current Trends in Anticancer Drug Development. Cancers (Basel) 2024; 16:1878. [PMID: 38791957 PMCID: PMC11120596 DOI: 10.3390/cancers16101878] [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: 04/16/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Cancer is considered one of the leading causes of death in the 21st century. The intensive search for new anticancer drugs has been actively pursued by chemists and pharmacologists for decades, focusing either on the isolation of compounds with cytotoxic properties from plants or on screening thousands of synthetic molecules. Compounds that could potentially become candidates for new anticancer drugs must have the ability to inhibit proliferation and/or induce apoptosis in cancer cells without causing too much damage to normal cells. Some anticancer compounds were discovered by accident, others as a result of long-term research. In this review, we have presented a brief history of the development of the most important groups of anticancer drugs, pointing to the fact that they all have many side effects.
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Affiliation(s)
- Katarzyna Gach-Janczak
- Department of Biomolecular Chemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (K.G.-J.); (A.J.); (K.W.)
| | | | - Anna Janecka
- Department of Biomolecular Chemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (K.G.-J.); (A.J.); (K.W.)
| | - Karol Wtorek
- Department of Biomolecular Chemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland; (K.G.-J.); (A.J.); (K.W.)
| | - Marek Mirowski
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, Muszynskiego 1, 90-151 Lodz, Poland
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19
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Gulia S, Chandra P, Das A. Combating anoikis resistance: bioactive compounds transforming prostate cancer therapy. Anticancer Drugs 2024:00001813-990000000-00286. [PMID: 38743565 DOI: 10.1097/cad.0000000000001616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The study aims to discuss the challenges associated with treating prostate cancer (PCa), which is known for its complexity and drug resistance. It attempts to find differentially expressed genes (DEGs), such as those linked to anoikis resistance and circulating tumor cells, in PCa samples. This study involves analyzing the functional roles of these DEGs using gene enrichment analysis, and then screening of 102 bioactive compounds to identify a combination that can control the expression of the identified DEGs. In this study, 53 DEGs were identified from PCa samples including anoikis-resistant PCa cells and circulating tumor cells in PCa. Gene enrichment analysis with regards to functional enrichment of DEGs was performed. An inclusive screening process was carried out among 102 bioactive compounds to identify a combination capable of affecting and regulating the expression of selected DEGs. Eventually, gastrodin, nitidine chloride, chenodeoxycholic acid, and bilobalide were selected, as their combination demonstrated ability to modulate expression of 50 out of the 53 genes targeted. The subsequent analysis focused on investigating the biological pathways and processes influenced by this combination. The findings revealed a multifaceted and multidimensional approach to tumor regression. The combination of bioactive compounds exhibited effects on various genes including those related to production of inflammatory cytokines, cell proliferation, autophagy, apoptosis, angiogenesis, and metastasis. The current study has made a valuable contribution to the development of a combination of bioactive natural compounds that can significantly impede the development of treatment resistance in prostate tumor while countering the tumors' evasion of the immune system. The implications of this study are highly significant as it suggests the creation of an enhanced immunotherapeutic, natural therapeutic concoction with combinatorial potential.
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Affiliation(s)
- Shweta Gulia
- Department of Biotechnology, Delhi technological university, Delhi, India
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20
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Musumeci F, Schenone S. Unlocking Potential and Limits of Kinase Inhibitors: The Highway to Enhanced Cancer Targeted Therapy. Pharmaceutics 2024; 16:625. [PMID: 38794286 PMCID: PMC11124881 DOI: 10.3390/pharmaceutics16050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 04/29/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Kinases are a family of enzymes comprising over five hundred members, which, when overexpressed or hyperactivated, are implicated in the pathogenesis of numerous hematological and solid cancers [...].
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Affiliation(s)
- Francesca Musumeci
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132 Genoa, Italy;
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21
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Xerxa E, Bajorath J. Data-oriented protein kinase drug discovery. Eur J Med Chem 2024; 271:116413. [PMID: 38636127 DOI: 10.1016/j.ejmech.2024.116413] [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: 02/29/2024] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/20/2024]
Abstract
The continued growth of data from biological screening and medicinal chemistry provides opportunities for data-driven experimental design and decision making in early-phase drug discovery. Approaches adopted from data science help to integrate internal and public domain data and extract knowledge from historical in-house data. Protein kinase (PK) drug discovery is an exemplary area where large amounts of data are accumulating, providing a valuable knowledge base for discovery projects. Herein, the evolution of PK drug discovery and development of small molecular PK inhibitors (PKIs) is reviewed, highlighting milestone developments in the field and discussing exemplary studies providing a basis for increasing data orientation of PK discovery efforts.
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Affiliation(s)
- Elena Xerxa
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Lamarr Institute for Machine Learning and Artificial Intelligence, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, D-53115, Bonn, Germany.
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22
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Shi Y, Wu C, Shi J, Gao T, Ma H, Li L, Zhao Y. Protein phosphorylation and kinases: Potential therapeutic targets in necroptosis. Eur J Pharmacol 2024; 970:176508. [PMID: 38493913 DOI: 10.1016/j.ejphar.2024.176508] [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: 11/10/2023] [Revised: 03/05/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Necroptosis is a pivotal contributor to the pathogenesis of various human diseases, including those affecting the nervous system, cardiovascular system, pulmonary system, and kidneys. Extensive investigations have elucidated the mechanisms and physiological ramifications of necroptosis. Among these, protein phosphorylation emerges as a paramount regulatory process, facilitating the activation or inhibition of specific proteins through the addition of phosphate groups to their corresponding amino acid residues. Currently, the targeting of kinases has gained recognition as a firmly established and efficacious therapeutic approach for diverse diseases, notably cancer. In this comprehensive review, we elucidate the intricate role of phosphorylation in governing key molecular players in the necroptotic pathway. Moreover, we provide an in-depth analysis of recent advancements in the development of kinase inhibitors aimed at modulating necroptosis. Lastly, we deliberate on the prospects and challenges associated with the utilization of kinase inhibitors to modulate necroptotic processes.
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Affiliation(s)
- Yihui Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengkun Wu
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Jiayi Shi
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Taotao Gao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Huabin Ma
- Central Laboratory, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Long Li
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang, 315211, China
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23
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Montero V, Montana M, Carré M, Vanelle P. Quinoxaline derivatives: Recent discoveries and development strategies towards anticancer agents. Eur J Med Chem 2024; 271:116360. [PMID: 38614060 DOI: 10.1016/j.ejmech.2024.116360] [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: 12/20/2023] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Cancer is a leading cause of death and a major health problem worldwide. While many effective anticancer agents are available, most drugs currently on the market are not specific, raising issues like the common side effects of chemotherapy. However, recent research hold promises for the development of more efficient and safer anticancer drugs. Quinoxaline and its derivatives are becoming recognized as a novel class of chemotherapeutic agents with activity against different tumors. The present review compiles and discusses studies concerning the therapeutic potential of the anticancer activity of quinoxaline derivatives, covering articles published between January 2018 and January 2023.
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Affiliation(s)
- Vincent Montero
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, CEDEX 05, 13385, Marseille, France; AP-HM, Service de Pharmacologie Clinique et Pharmacovigilance, Hôpital de la Timone, Marseille CEDEX 05, 13385, France.
| | - Marc Montana
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, CEDEX 05, 13385, Marseille, France; AP-HM, Oncopharma, Hôpital Nord, Marseille, France
| | - Manon Carré
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm UMR1068, CNRS UMR7258, Aix-Marseille Université UM105, Institut Paoli Calmettes - Faculté de Pharmacie, Marseille, France
| | - Patrice Vanelle
- Aix Marseille Univ, CNRS, ICR UMR 7273, Equipe Pharmaco-Chimie Radicalaire, Faculté de Pharmacie, CEDEX 05, 13385, Marseille, France; AP-HM, Service Central de la Qualité et de l'Information Pharmaceutiques, Hôpital Conception, Marseille, 13005, France
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24
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Hussain S, Mursal M, Verma G, Hasan SM, Khan MF. Targeting oncogenic kinases: Insights on FDA approved tyrosine kinase inhibitors. Eur J Pharmacol 2024; 970:176484. [PMID: 38467235 DOI: 10.1016/j.ejphar.2024.176484] [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: 09/24/2023] [Revised: 03/01/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
Protein kinases play pivotal roles in various biological functions, influencing cell differentiation, promoting survival, and regulating the cell cycle. The disruption of protein kinase activity is intricately linked to pathways in tumor development. This manuscript explores the transformative impact of protein kinase inhibitors on cancer therapy, particularly their efficacy in cases driven by targeted mutations. Focusing on key tyrosine kinase inhibitors (TKIs) like Bcr-Abl, Epidermal Growth Factor Receptor (EGFR), and Vascular Endothelial Growth Factor Receptor (VEGFR), it targets critical kinase families in cancer progression. Clinical trial details of these TKIs offer insights into their therapeutic potentials. Learning from FDA-approved kinase inhibitors, the review dissects trends in kinase drug development since imatinib's paradigm-shifting approval in 2001. TKIs have evolved into pivotal drugs, extending beyond oncology. Ongoing clinical trials explore novel kinase targets, revealing the vast potential within the human kinome. The manuscript provides a detailed analysis of advancements until 2022, discussing the roles of specific oncogenic protein kinases in cancer development and carcinogenesis. Our exploration on PubMed for relevant and significant TKIs undergoing pre-FDA approval phase III clinical trials enriches the discussion with valuable findings. While kinase inhibitors exhibit lower toxicity than traditional chemotherapy in cancer treatment, challenges like resistance and side effects emphasize the necessity of understanding resistance mechanisms, prompting the development of novel inhibitors like osimertinib targeting specific mutant proteins. The review advocates thorough research on effective combination therapies, highlighting the future development of more selective RTKIs to optimize patient-specific cancer treatment and reduce adverse events.
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Affiliation(s)
- Sahil Hussain
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India
| | - Mohd Mursal
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India
| | - Garima Verma
- RWE Specialist, HealthPlix Technologies, Bengaluru, Karnataka 560103, India
| | - Syed Misbahul Hasan
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India
| | - Mohemmed Faraz Khan
- Faculty of Pharmacy, Integral University, Kursi Road, Lucknow, 226026, India.
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25
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Shah Zaib Saleem R, Schwalm MP, Knapp S. Expanding the ligand spaces for E3 ligases for the design of protein degraders. Bioorg Med Chem 2024; 105:117718. [PMID: 38621319 DOI: 10.1016/j.bmc.2024.117718] [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: 01/24/2024] [Revised: 03/26/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Targeted protein degradation (TPD) has recently emerged as an exciting new drug modality. However, the strategy of developing small molecule-based protein degraders has evolved over the past two decades and has now established molecular tags that are already in clinical use, as well as chimeric molecules, PROteolysis TArgeting Chimeras (PROTACs), based mainly on ligand systems developed for the two E3 ligases CRBN and VHL. The large size of the human E3 ligase family suggests that PROTACs can be developed by targeting a large diversity of E3 ligases, some of which have restricted expression patterns with the potential to design disease- or tissue-specific degraders. Indeed, many new E3 ligands have been published recently, confirming the druggability of E3 ligases. This review summarises recent data on E3 ligases and highlights the challenges in developing these molecules into efficient PROTACs rivalling the established degrader systems.
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Affiliation(s)
- Rahman Shah Zaib Saleem
- Department of Chemistry & Chemical Engineering, SBA School of Sciences & Engineering, LUMS, Pakistan
| | - Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, Frankfurt, Germany.
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26
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Smith-Byrne K, Hedman Å, Dimitriou M, Desai T, Sokolov AV, Schioth HB, Koprulu M, Pietzner M, Langenberg C, Atkins J, Penha RC, McKay J, Brennan P, Zhou S, Richards BJ, Yarmolinsky J, Martin RM, Borlido J, Mu XJ, Butterworth A, Shen X, Wilson J, Assimes TL, Hung RJ, Amos C, Purdue M, Rothman N, Chanock S, Travis RC, Johansson M, Mälarstig A. Identifying therapeutic targets for cancer among 2074 circulating proteins and risk of nine cancers. Nat Commun 2024; 15:3621. [PMID: 38684708 PMCID: PMC11059161 DOI: 10.1038/s41467-024-46834-3] [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: 05/12/2023] [Accepted: 03/05/2024] [Indexed: 05/02/2024] Open
Abstract
Circulating proteins can reveal key pathways to cancer and identify therapeutic targets for cancer prevention. We investigate 2,074 circulating proteins and risk of nine common cancers (bladder, breast, endometrium, head and neck, lung, ovary, pancreas, kidney, and malignant non-melanoma) using cis protein Mendelian randomisation and colocalization. We conduct additional analyses to identify adverse side-effects of altering risk proteins and map cancer risk proteins to drug targets. Here we find 40 proteins associated with common cancers, such as PLAUR and risk of breast cancer [odds ratio per standard deviation increment: 2.27, 1.88-2.74], and with high-mortality cancers, such as CTRB1 and pancreatic cancer [0.79, 0.73-0.85]. We also identify potential adverse effects of protein-altering interventions to reduce cancer risk, such as hypertension. Additionally, we report 18 proteins associated with cancer risk that map to existing drugs and 15 that are not currently under clinical investigation. In sum, we identify protein-cancer links that improve our understanding of cancer aetiology. We also demonstrate that the wider consequence of any protein-altering intervention on well-being and morbidity is required to interpret any utility of proteins as potential future targets for therapeutic prevention.
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Affiliation(s)
- Karl Smith-Byrne
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK.
| | - Åsa Hedman
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Marios Dimitriou
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Trishna Desai
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK
| | - Alexandr V Sokolov
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Helgi B Schioth
- Department of Surgical Sciences, Functional Pharmacology and Neuroscience, Uppsala University, Uppsala, Sweden
| | - Mine Koprulu
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare Institute, Queen Mary University of London, London, UK
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Precision Healthcare Institute, Queen Mary University of London, London, UK
| | - Joshua Atkins
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK
| | - Ricardo Cortez Penha
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - James McKay
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Sirui Zhou
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Brent J Richards
- Departments of Medicine (Endocrinology), Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal, QC, Canada
| | - James Yarmolinsky
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Hospitals Bristol and Weston NHS Foundation Trust and the University of Bristol, Bristol, UK
| | - Joana Borlido
- Cancer Immunology Discovery, Pfizer Worldwide Research and Development Medicine, Pfizer Inc, San Diego, USA
| | - Xinmeng J Mu
- Oncology Research Unit, Pfizer Worldwide Research and Development Medicine, Pfizer Inc, San Diego, USA
| | - Adam Butterworth
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Xia Shen
- Usher Institute, MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Jim Wilson
- Usher Institute, MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Themistocles L Assimes
- Division of Cardiovascular Medicine and the Cardiovascular Institute, School of Medicine, Stanford University, Stanford, USA
| | - Rayjean J Hung
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System and University of Toronto, Toronto, Canada
| | - Christopher Amos
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, USA
| | - Mark Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford, UK
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC-WHO), Lyon, France
| | - Anders Mälarstig
- External Science and Innovation, Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
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27
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Breton-Patient C, Billotte S, Duchambon P, Fontaine G, Bombard S, Piguel S. Light-Activatable Photocaged UNC2025 for Triggering TAM Kinase Inhibition in Bladder Cancer. Chembiochem 2024; 25:e202300855. [PMID: 38363151 DOI: 10.1002/cbic.202300855] [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: 12/20/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/17/2024]
Abstract
Photopharmacology is an emerging field that utilizes photo-responsive molecules to enable control over the activity of a drug using light. The aim is to limit the therapeutic action of a drug at the level of diseased tissues and organs. Considering the well-known implications of protein kinases in cancer and the therapeutic issues associated with protein kinase inhibitors, the photopharmacology is seen as an innovative and alternative solution with great potential in oncology. In this context, we developed the first photocaged TAM kinase inhibitors based on UNC2025, a first-in-class small molecule kinase inhibitor. These prodrugs showed good stability in biologically relevant buffer and rapid photorelease of the photoremovable protecting group upon UV-light irradiation (<10 min.). These light-activatable prodrugs led to a 16-fold decrease to a complete loss of kinase inhibition, depending on the protein and the position at which the coumarin-type phototrigger was introduced. The most promising candidate was the N,O-dicaged compound, showing the superiority of having two photolabile protecting groups on UNC2025 for being entirely inactive on TAM kinases. Under UV-light irradiation, the N,O-dicaged compound recovered its inhibitory potency in enzymatic assays and displayed excellent antiproliferative activity in RT112 cell lines.
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Affiliation(s)
- Chloé Breton-Patient
- Institut Curie, Université PSL CNRS UMR9187, Inserm U119, 91400, Orsay, France
- Université Paris-Saclay CNRS UMR9187, Inserm U119, 91400, Orsay, France
| | - Sébastien Billotte
- Université Paris-Saclay, Faculté de Pharmacie CNRS UMR 8076, 91400, Orsay, France
| | - Patricia Duchambon
- Institut Curie, Université PSL CNRS UMR9187, Inserm U119, 91400, Orsay, France
- Université Paris-Saclay CNRS UMR9187, Inserm U119, 91400, Orsay, France
| | - Gaëlle Fontaine
- Institut Curie, Université PSL CNRS UMR9187, Inserm U119, 91400, Orsay, France
- Université Paris-Saclay CNRS UMR9187, Inserm U119, 91400, Orsay, France
| | - Sophie Bombard
- Institut Curie, Université PSL CNRS UMR9187, Inserm U119, 91400, Orsay, France
- Université Paris-Saclay CNRS UMR9187, Inserm U119, 91400, Orsay, France
| | - Sandrine Piguel
- Université Paris-Saclay, Faculté de Pharmacie CNRS UMR 8076, 91400, Orsay, France
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28
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Liang LY, Geoghegan ND, Mlodzianoski M, Leis A, Whitehead LW, Surudoi MG, Young SN, Janes P, Shepherd D, Ghosal D, Rogers KL, Murphy JM, Lucet IS. Co-clustering of EphB6 and ephrinB1 in trans restrains cancer cell invasion. Commun Biol 2024; 7:461. [PMID: 38627519 PMCID: PMC11021433 DOI: 10.1038/s42003-024-06118-4] [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: 02/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024] Open
Abstract
EphB6 is an understudied ephrin receptor tyrosine pseudokinase that is downregulated in multiple types of metastatic cancers. Unlike its kinase-active counterparts which autophosphorylate and transmit signals upon intercellular interaction, little is known about how EphB6 functions in the absence of intrinsic kinase activity. Here, we unveil a molecular mechanism of cell-cell interaction driven by EphB6. We identify ephrinB1 as a cognate ligand of EphB6 and show that in trans interaction of EphB6 with ephrinB1 on neighboring cells leads to the formation of large co-clusters at the plasma membrane. These co-clusters exhibit a decreased propensity towards endocytosis, suggesting a unique characteristic for this type of cell-cell interaction. Using lattice light-sheet microscopy, 3D structured illumination microscopy and cryo-electron tomography techniques, we show that co-clustering of EphB6 and ephrinB1 promotes the formation of double-membrane tubular structures between cells. Importantly, we also demonstrate that these intercellular structures stabilize cell-cell adhesion, leading to a reduction in the invasive behavior of cancer cells. Our findings rationalize a role for EphB6 pseudokinase as a tumor suppressor when interacting with its ligands in trans.
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Affiliation(s)
- Lung-Yu Liang
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Niall D Geoghegan
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Michael Mlodzianoski
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Andrew Leis
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Lachlan W Whitehead
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Minglyanna G Surudoi
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Peter Janes
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, Level 5, ONJ Centre, 145 Studley Rd, Heidelberg, VIC, 3084, Australia
| | - Doulin Shepherd
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Debnath Ghosal
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Isabelle S Lucet
- Walter and Eliza Hall Institute for Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3052, Australia.
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29
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An J, Zhang X. Crbn-based molecular Glues: Breakthroughs and perspectives. Bioorg Med Chem 2024; 104:117683. [PMID: 38552596 DOI: 10.1016/j.bmc.2024.117683] [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: 12/11/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
CRBN is a substrate receptor for the Cullin Ring E3 ubiquitin ligase 4 (CRL4) complex. It has been observed that CRBN can be exploited by small molecules to facilitate the recruitment and ubiquitination of non-natural CRL4 substrates, resulting in the degradation of neosubstrate through the ubiquitin-proteasome system. This phenomenon, known as molecular glue-induced protein degradation, has emerged as an innovative therapeutic approach in contrast to traditional small-molecule drugs. One key advantage of molecular glues, in comparison to conventional small-molecule drugs adhering to Lipinski's Rule of Five, is their ability to operate without the necessity for specific binding pockets on target proteins. This unique characteristic empowers molecular glues to interact with conventionally intractable protein targets, such as transcription factors and scaffold proteins. The ability to induce the degradation of these previously elusive targets by hijacking the ubiquitin-proteasome system presents a promising avenue for the treatment of recalcitrant diseases. Nevertheless, the rational design of molecular glues remains a formidable challenge due to the limited understanding of their mechanisms and actions. This review offers an overview of recent advances and breakthroughs in the field of CRBN-based molecular glues, while also exploring the prospects for a systematic approach to designing these compounds.
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Affiliation(s)
- Juzeng An
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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30
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Chen MW, Li HW, Wang YQ, Wu B, Liu Z, Lai X, Deerberg J, Zhou YG. Iridium-Catalyzed Asymmetric Hydrogenation of Heteroaromatics with Multiple N Atoms via Substrate Activation: An Entry to 4,5,6,7-Tetrahydropyrazolo[1,5- a]pyrimidine-3-carbonitrile Core of a Potent BTK Inhibitor. J Org Chem 2024; 89:4336-4348. [PMID: 38465834 DOI: 10.1021/acs.joc.3c02396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The chiral 4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine is the key core skeleton of potent Bruton's tyrosine kinase (BTK) inhibitor Zanubrutinib, and the catalyst-controlled asymmetric hydrogenation of planar multinuclear pyrimidine heteroarenes with multiple N atoms could provide an efficient route toward its synthesis. Owing to the strong aromaticity and poisoning effect toward chiral transition metal catalyst, asymmetric hydrogenation of pyrazolo[1,5-a]pyrimidines with multiple nitrogen atoms is still a challenge for synthesizing the chiral 4,5,6,7-tetrahydropyrazolo[1,5-a]-pyrimidine. Herein, an efficient iridium-catalyzed asymmetric hydrogenation of pyrazolo[1,5-a]pyrimidines has been developed using substrate activation strategy, with up to 99% ee. The decagram scale synthesis further demonstrated the potential and promise of this procedure in the synthesis of Zanubrutinib. In addition, a mechanistic study indicated that the hydrogenation starts with 1,2-hydrogenation.
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Affiliation(s)
- Mu-Wang Chen
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Hong-Wang Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Ying-Qi Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Bo Wu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Zheng Liu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
| | - Xinzhong Lai
- Chemical Process Research and Development, Department of Chemistry, BeiGene, Ltd., No. 30 Science Park Rd, Zhong-Guan-Cun Life Science Park, Changping District, Beijing 102206, P. R. China
| | - Joerg Deerberg
- Chemical Process Research and Development, Department of Chemistry, BeiGene, Ltd., No. 30 Science Park Rd, Zhong-Guan-Cun Life Science Park, Changping District, Beijing 102206, P. R. China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, P. R. China
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Miao J, Zhang ZY. Drugging Protein Tyrosine Phosphatases through Targeted Protein Degradation. ChemMedChem 2024; 19:e202300669. [PMID: 38233347 PMCID: PMC11021144 DOI: 10.1002/cmdc.202300669] [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: 11/29/2023] [Revised: 12/22/2023] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that regulate protein tyrosine phosphorylation levels of a large variety of proteins in cells. Anomalies in protein tyrosine phosphorylation have been associated with the development of numerous human diseases, leading to a heightened interest in PTPs as promising targets for drug development. However, therapeutic targeting of PTPs has faced skepticism about their druggability. Besides the conventional small molecule inhibitors, proteolysis-targeting chimera (PROTAC) technology offers an alternative approach to target PTPs. PROTAC molecules utilize the ubiquitin-proteasome system to degrade specific proteins and have unique advantages compared with inhibitors: 1) PROTACs are highly efficient and can work at much lower concentrations than that expected based on their biophysical binding affinity; 2) PROTACs may achieve higher selectivity for the targeted protein than that dictated by their binding affinity alone; and 3) PROTACs may engage any region of the target protein in addition to the functional site. This review focuses on the latest advancement in the development of targeted PTP degraders and deliberates on the obstacles and prospective paths of harnessing this technology for therapeutic targeting of the PTPs.
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Affiliation(s)
- Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
- Department of Chemistry, 560 Oval Drive, West Lafayette, IN 47907, USA
- Institute for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, IN 47907, USA
- Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA
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de Sena Murteira Pinheiro P, Franco LS, Montagnoli TL, Fraga CAM. Molecular hybridization: a powerful tool for multitarget drug discovery. Expert Opin Drug Discov 2024; 19:451-470. [PMID: 38456452 DOI: 10.1080/17460441.2024.2322990] [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: 10/24/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024]
Abstract
INTRODUCTION The current drug discovery paradigm of 'one drug, multiple targets' has gained attention from both the academic medicinal chemistry community and the pharmaceutical industry. This is in response to the urgent need for effective agents to treat multifactorial chronic diseases. The molecular hybridization strategy is a useful tool that has been widely explored, particularly in the last two decades, for the design of multi-target drugs. AREAS COVERED This review examines the current state of molecular hybridization in guiding the discovery of multitarget small molecules. The article discusses the design strategies and target selection for a multitarget polypharmacology approach to treat various diseases, including cancer, Alzheimer's disease, cardiac arrhythmia, endometriosis, and inflammatory diseases. EXPERT OPINION Although the examples discussed highlight the importance of molecular hybridization for the discovery of multitarget bioactive compounds, it is notorious that the literature has focused on specific classes of targets. This may be due to a deep understanding of the pharmacophore features required for target binding, making targets such as histone deacetylases and cholinesterases frequent starting points. However, it is important to encourage the scientific community to explore diverse combinations of targets using the molecular hybridization strategy.
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Affiliation(s)
- Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas Silva Franco
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tadeu Lima Montagnoli
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Alsalmi O, Mashraqi MM, Alshamrani S, Almasoudi HH, Alharthi AA, Gharib AF. Variolin B from sea sponge against lung cancer: a multitargeted molecular docking with fingerprinting and molecular dynamics simulation study. J Biomol Struct Dyn 2024; 42:3507-3519. [PMID: 37855303 DOI: 10.1080/07391102.2023.2272204] [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: 02/08/2023] [Accepted: 05/07/2023] [Indexed: 10/20/2023]
Abstract
Lung Cancer is the one that causes more fatalities in the world compared to other cancers, and its uniqueness is that it can be found in both males and females. However, recent data has shown that males are more affected due to lifestyle habits like smoking, tobacco consumption and inhaling polluted air. The World Health Organization has kept lung cancer on its priority list as it causes 1.8 million deaths worldwide each year, and the predictions show that the cases are going to increase year by year, and by 2050, there can be 3.8 million new cases and 3.2 million deaths, and the global health system is not prepared for it. Also, finding drug candidates that can help shrink cancerous cells and lead to their death is essential to reduce global mortality. The system needs drug compounds that can inhibit multiple paths together not to enter drug resistance quickly and to reduce costs. Our study identified a compound named Variolin B (DB08694) that belongs to the organic compounds class of pyrrolopyridines. The identified compound can inhibit multiple proteins, drastically reducing the global burden. Variolin B was identified as a potential candidate against lung cancer using the multisampling algorithm such as HTVS, SP, and XP, followed by MM\GBSA calculations showing the docking score of -9.245 Kcal/mol to -5.92 Kcal/mol. Also, we have validated it with ADMET predictions and molecular fingerprinting to analyse the interaction patterns. Further, the study was extended to molecular dynamics simulations for 100 ns to understand the complex stability and simulative interactions. The complex's overall molecular dynamics simulation helped us understand that the identified candidate is stable with the lowest deviation and fluctuations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ohud Alsalmi
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Afaf Awwadh Alharthi
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Amal F Gharib
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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Qi X, Li G, Liu J, Mou L, Zhang Y, Guo S, Chen X, Li W. Structural and energetic insights into the selective inhibition of PKMYT1 against WEE1. J Biomol Struct Dyn 2024; 42:3010-3018. [PMID: 37345529 DOI: 10.1080/07391102.2023.2225106] [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: 02/14/2023] [Accepted: 04/30/2023] [Indexed: 06/23/2023]
Abstract
Protein kinase, membrane-associated tyrosine/threonine 1 (PKMYT1), a member of the WEE family and responsible for the regulation of CDK1 phosphorylation, has been considered a promising therapeutic target for cancer therapy. However, the highly structural conservation of the ATP-binding sites of the WEE family poses a challenge to the design of selective inhibitors for PKMYT1. Here, molecular docking, multiple microsecond-length molecular dynamics (MD) simulations and end-point free energy calculations were performed to uncover the molecular mechanism of the binding selectivity of RP-6306 toward PKMYT1 over its highly homologous kinase WEE1. The binding specificity of RP-6306 reported in previous experimental bioassays was clarified by MD simulations and binding free energy calculations. Further, the binding free energy prediction indicated that the binding selectivity of RP-6306 largely derived from the difference in the protein-ligand electrostatic interactions. The per-residue free energy decomposition suggested that the non-conserved gatekeeper residue in the hinge domain of PKMYT1/WEE1, Thr187/Asn376, is the critical factor responsible for the binding selectivity of RP-6306 toward PKMYT1. In addition, a water-mediated hydrogen bond was formed between RP-6306 and Gly191 at the hinge domain in the PKMYT1/RP-6306 complex, which was absent in the WEE1/RP-6306 complex. This study is expected to offer useful information for the design of more potent and selective PKMYT1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xuesen Qi
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Guozhen Li
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Jiahai Liu
- Department of Gastrointestinal and Anal Diseases Surgery, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Linkai Mou
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Yusheng Zhang
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Shilin Guo
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Xiangyu Chen
- School of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
| | - Wenxing Li
- Pathology Department, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
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Krishna Rao V, Paul S, Gulkis M, Shen Z, Nair H, Singh A, Li C, Sharma AK, Çağlayan M, Das C, Das B, Kundu CN, Narayan S, Guchhait SK. Molecular editing of NSC-666719 enabling discovery of benzodithiazinedioxide-guanidines as anticancer agents. RSC Med Chem 2024; 15:937-962. [PMID: 38516586 PMCID: PMC10953490 DOI: 10.1039/d3md00648d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
DNA polymerase β (Polβ) is crucial for the base excision repair (BER) pathway of DNA damage repair and is an attractive target for suppressing tumorigenesis as well as chemotherapeutic intervention of cancer. In this study, a unique strategy of scaffold-hopping-based molecular editing of a bioactive agent NSC-666719 was investigated, which led to the development of new molecular motifs with Polβ inhibitory activity. NSC compound and its analogs (two series) were prepared, focusing on pharmacophore-based molecular diversity. Most compounds showed higher activities than the parent NSC-666719 and exhibited effects on apoptosis. The inhibitory activity of Polβ was evaluated in both in vitro reconstituted and in vivo intact cell systems. Compound 10e demonstrated significant Polβ interaction and inhibition characteristics, including direct, non-covalent, reversible, and comparable binding affinity. The investigated approach is useful, and the discovered novel analogs have a high potential for developing as anticancer therapeutics.
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Affiliation(s)
- Vajja Krishna Rao
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
| | - Subarno Paul
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Zhihang Shen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Haritha Nair
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Amandeep Singh
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Arun K Sharma
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Chinmay Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Biswajit Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Chanakya N Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Satya Narayan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Sankar K Guchhait
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
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Tang G, Wang W, Zhu C, Huang H, Chen P, Wang X, Xu M, Sun J, Zhang CJ, Xiao Q, Gao L, Zhang ZM, Yao SQ. Global Reactivity Profiling of the Catalytic Lysine in Human Kinome for Covalent Inhibitor Development. Angew Chem Int Ed Engl 2024; 63:e202316394. [PMID: 38248139 DOI: 10.1002/anie.202316394] [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: 10/30/2023] [Revised: 01/21/2024] [Accepted: 01/21/2024] [Indexed: 01/23/2024]
Abstract
Advances in targeted covalent inhibitors (TCIs) have been made by using lysine-reactive chemistries. Few aminophiles possessing balanced reactivity/stability for the development of cell-active TCIs are however available. We report herein lysine-reactive activity-based probes (ABPs; 2-14) based on the chemistry of aryl fluorosulfates (ArOSO2 F) capable of global reactivity profiling of the catalytic lysine in human kinome from mammalian cells. We concurrently developed reversible covalent ABPs (15/16) by installing salicylaldehydes (SA) onto a promiscuous kinase-binding scaffold. The stability and amine reactivity of these probes exhibited a broad range of tunability. X-ray crystallography and mass spectrometry (MS) confirmed the successful covalent engagement between ArOSO2 F on 9 and the catalytic lysine of SRC kinase. Chemoproteomic studies enabled the profiling of >300 endogenous kinases, thus providing a global landscape of ligandable catalytic lysines of the kinome. By further introducing these aminophiles into VX-680 (a noncovalent inhibitor of AURKA kinase), we generated novel lysine-reactive TCIs that exhibited excellent in vitro potency and reasonable cellular activities with prolonged residence time. Our work serves as a general guide for the development of lysine-reactive ArOSO2 F-based TCIs.
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Affiliation(s)
- Guanghui Tang
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengjun Zhu
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Huisi Huang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Peng Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Manyi Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jie Sun
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Chong-Jing Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chi-nese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, China
| | - Zhi-Min Zhang
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, Singapore, 117543, Singapore
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Zhang Y, Deng J, Tian H, Qi H, Xiong T, Lin S, Dong Y, Luo L, Wu D, Zhang K, Ji M, Du T, Sheng L, Chen X, Xu H. Design, Synthesis, and Bioevaluation of Novel Reversibly Photoswitchable PI3K Inhibitors Based on Phenylazopyridine Derivatives toward Light-Controlled Cancer Treatment. J Med Chem 2024; 67:3504-3519. [PMID: 38377311 DOI: 10.1021/acs.jmedchem.3c01864] [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: 02/22/2024]
Abstract
Photopharmacology is an emerging approach for achieving light-controlled drug activity. Herein, we design and synthesize a novel series of photoswitchable PI3K inhibitors by replacing a sulfonamide moiety with an azo group in a 4-methylquinazoline-based scaffold. Through structure-activity relationship studies, compound 6g is identified to be effectively switched between its trans- and cis-configuration under irradiation with proper wavelengths. Molecular docking studies show the cis-isomer of 6g is favorable to bind to the PI3K target, supporting compound 6g in the PSS365 (cis-isomer enriched) was more potent than that in the PSSdark (trans-isomer dominated) in PI3K enzymatic assay, cell antiproliferative assay, Western blotting analysis on PI3K downstream effectors, cell cycle analysis, colony formation assay, and wound-healing assay. Relative to the cis-isomer, the trans-isomer is more metabolically stable and shows good pharmacokinetic properties in mice. Moreover, compound 6g inhibits tumor growth in nude mice and a zebrafish HGC-27 xenograft model.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Jialing Deng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Hua Tian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Haixiang Qi
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Tianning Xiong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Songwen Lin
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Yi Dong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Lijun Luo
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Deyu Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Kehui Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Ming Ji
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Tingting Du
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Li Sheng
- Beijing Key Laboratory of Non-Clinical Drug Metabolism and PK/PD Study, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiaoguang Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Heng Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- CAMS Key Laboratory of Small Molecule Immuno-Oncology Drug Discovery, Chinese Academy of Medical Sciences, Beijing 100050, China
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Xu X, Han W, Ning X, Zang C, Xu C, Zeng C, Pu C, Zhang Y, Chen Y, Liu H. Constructing Innovative Covalent and Noncovalent Compound Libraries: Insights from 3D Protein-Ligand Interactions. J Chem Inf Model 2024; 64:1543-1559. [PMID: 38381562 DOI: 10.1021/acs.jcim.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Noncovalent interactions between small-molecule drugs and protein targets assume a pivotal role in drug design. Moreover, the design of covalent inhibitors, forming covalent bonds with amino acid residues, requires rational reactivity for their covalent warheads, presenting a key challenge as well. Understanding the intricacies of these interactions provides a more comprehensive understanding of molecular binding mechanisms, thereby guiding the rational design of potent inhibitors. In this study, we adopted the fragment-based drug design approach, introducing a novel methodology to extract noncovalent and covalent fragments according to distinct three-dimensional (3D) interaction modes from noncovalent and covalent compound libraries. Additionally, we systematically replaced existing ligands with rational fragment substitutions, based on the spatial orientation of fragments in 3D space. Furthermore, we adopted a molecular generation approach to create innovative covalent inhibitors. This process resulted in the recombination of a noncovalent compound library and several covalent compound libraries, constructed by two commonly encountered covalent amino acids: cysteine and serine. We utilized noncovalent ligands in KLIFS and covalent ligands in CovBinderInPDB as examples to recombine noncovalent and covalent libraries. These recombined compound libraries cover a substantial portion of the chemical space present in the original compound libraries and exhibit superior performance in terms of molecular scaffold diversity compared to the original compound libraries and other 11 commercial libraries. We also recombined BTK-focused libraries, and 23 compounds within our libraries have been validated by former researchers to possess potential biological activity. The establishment of these compound libraries provides valuable resources for virtual screening of covalent and noncovalent drugs targeting similar molecular targets.
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Affiliation(s)
- Xiaohe Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Weijie Han
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Xiangzhen Ning
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chengdong Zang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chengcheng Xu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chen Zeng
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Chengtao Pu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yanmin Zhang
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Yadong Chen
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Haichun Liu
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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Schmitt L, Lechtenberg I, Drießen D, Flores-Romero H, Skowron MA, Sekeres M, Hoppe J, Krings KS, Llewellyn TR, Peter C, Stork B, Qin N, Bhatia S, Nettersheim D, Fritz G, García-Sáez AJ, Müller TJJ, Wesselborg S. Novel meriolin derivatives activate the mitochondrial apoptosis pathway in the presence of antiapoptotic Bcl-2. Cell Death Discov 2024; 10:125. [PMID: 38461295 PMCID: PMC10924942 DOI: 10.1038/s41420-024-01901-y] [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: 10/31/2023] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
Meriolin derivatives represent a new class of kinase inhibitors with a pronounced cytotoxic potential. Here, we investigated a newly synthesized meriolin derivative (termed meriolin 16) that displayed a strong apoptotic potential in Jurkat leukemia and Ramos lymphoma cells. Meriolin 16 induced apoptosis in rapid kinetics (within 2-3 h) and more potently (IC50: 50 nM) than the previously described derivatives meriolin 31 and 36 [1]. Exposure of Ramos cells to meriolin 16, 31, or 36 for 5 min was sufficient to trigger severe and irreversible cytotoxicity. Apoptosis induction by all three meriolin derivatives was independent of death receptor signaling but required caspase-9 and Apaf-1 as central mediators of the mitochondrial death pathway. Meriolin-induced mitochondrial toxicity was demonstrated by disruption of the mitochondrial membrane potential (ΔΨm), mitochondrial release of proapoptotic Smac, processing of the dynamin-like GTPase OPA1, and subsequent fragmentation of mitochondria. Remarkably, all meriolin derivatives were able to activate the mitochondrial death pathway in Jurkat cells, even in the presence of the antiapoptotic Bcl-2 protein. In addition, meriolins were capable of inducing cell death in imatinib-resistant K562 and KCL22 chronic myeloid leukemia cells as well as in cisplatin-resistant J82 urothelial carcinoma and 2102EP germ cell tumor cells. Given the frequent inactivation of the mitochondrial apoptosis pathway by tumor cells, such as through overexpression of antiapoptotic Bcl-2, meriolin derivatives emerge as promising therapeutic agents for overcoming treatment resistance.
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Affiliation(s)
- Laura Schmitt
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ilka Lechtenberg
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Drießen
- Institute of Organic Chemistry and Macromolecular Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hector Flores-Romero
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
- Ikerbasque, Basque Foundation for Science, 48013, Bilbao, Spain
- Achucarro Basque Center for Neuroscience, Leioa, Spain
| | - Margaretha A Skowron
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - Marlena Sekeres
- Institute of Toxicology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Julia Hoppe
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Karina S Krings
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Tanya R Llewellyn
- Clinic of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Christoph Peter
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Björn Stork
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Nan Qin
- Clinic of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Germany
| | - Daniel Nettersheim
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Moorenstraße 5, Düsseldorf, Germany
| | - Gerhard Fritz
- Institute of Toxicology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Ana J García-Sáez
- Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - Thomas J J Müller
- Institute of Organic Chemistry and Macromolecular Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Sebastian Wesselborg
- Institute for Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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Li X, Hou C, Yang M, Luo B, Mao N, Chen K, Chen Z, Bai Y. The effect of phosphorylation on the conformational dynamics and allostery of the association of death-associated protein kinase with calmodulin. J Biomol Struct Dyn 2024:1-9. [PMID: 38457488 DOI: 10.1080/07391102.2024.2316763] [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: 11/15/2023] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
Protein phosphorylation plays an important role in the signal transduction and is capable of regulation of cell activity. The death-associated protein kinase 1 (DAPK1), as a Ser/Thr kinase, interacts with calmodulin (CaM) to regulate apoptotic and autophagic signaling. Autophosphorylation of DAPK1 at Ser308 located at the autoregulatory domain (ARD) blocks CaM binding and inhibits kinase catalytic activity. However, the mechanism underlying the influence of Ser308 phosphorylation (pS308) on the DAPK1 activity remains unclear. Here, we performed multiple, microsecond length molecular dynamics (MD) simulations, the molecular mechanics generalized Born/surface area (MM-GBSA) binding free energy calculations, principal component analysis, and dynamic cross-correlation analysis to unravel the conformational dynamics and allostery of the DAPK1 - CaM interaction triggered by the pS308 at the ARD. MD simulations showed that pS308 affected the conformational stability of the DAPK1 - CaM complex. Further energetic and structural exploration revealed that pS308 weakened the association of the phosphorylated DAPK1 to CaM, which lowered the susceptibility of DAPK1 to be activated by CaM. This result can provide mechanistic insights into the molecular underpinning through which the DAPK1 kinase activity is modulated by the auto-phosphorylation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaolong Li
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Canglong Hou
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Mingyuan Yang
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Beier Luo
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Ningfang Mao
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Kai Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
| | - Yushu Bai
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, China
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Veth TS, Kannegieter NM, de Graaf EL, Ruijtenbeek R, Joore J, Ressa A, Altelaar M. Innovative strategies for measuring kinase activity to accelerate the next wave of novel kinase inhibitors. Drug Discov Today 2024; 29:103907. [PMID: 38301799 DOI: 10.1016/j.drudis.2024.103907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
The development of protein kinase inhibitors (PKIs) has gained significance owing to their therapeutic potential for diseases like cancer. In addition, there has been a rise in refining kinase activity assays, each possessing unique biological and analytical characteristics crucial for PKI development. However, the PKI development pipeline experiences high attrition rates and approved PKIs exhibit unexploited potential because of variable patient responses. Enhancing PKI development efficiency involves addressing challenges related to understanding the PKI mechanism of action and employing biomarkers for precision medicine. Selecting appropriate kinase activity assays for these challenges can overcome these attrition rate issues. This review delves into the current obstacles in kinase inhibitor development and elucidates kinase activity assays that can provide solutions.
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Affiliation(s)
- Tim S Veth
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | | | - Erik L de Graaf
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | | | - Jos Joore
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | - Anna Ressa
- Pepscope, Nieuwe Kanaal 7, 6709 PA Wageningen, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands; Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands.
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42
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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [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: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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Wittlinger F, Ogboo BC, Shevchenko E, Damghani T, Pham CD, Schaeffner IK, Oligny BT, Chitnis SP, Beyett TS, Rasch A, Buckley B, Urul DA, Shaurova T, May EW, Schaefer EM, Eck MJ, Hershberger PA, Poso A, Laufer SA, Heppner DE. Linking ATP and allosteric sites to achieve superadditive binding with bivalent EGFR kinase inhibitors. Commun Chem 2024; 7:38. [PMID: 38378740 PMCID: PMC10879502 DOI: 10.1038/s42004-024-01108-3] [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: 09/06/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Bivalent molecules consisting of groups connected through bridging linkers often exhibit strong target binding and unique biological effects. However, developing bivalent inhibitors with the desired activity is challenging due to the dual motif architecture of these molecules and the variability that can be introduced through differing linker structures and geometries. We report a set of alternatively linked bivalent EGFR inhibitors that simultaneously occupy the ATP substrate and allosteric pockets. Crystal structures show that initial and redesigned linkers bridging a trisubstituted imidazole ATP-site inhibitor and dibenzodiazepinone allosteric-site inhibitor proved successful in spanning these sites. The re-engineered linker yielded a compound that exhibited significantly higher potency (~60 pM) against the drug-resistant EGFR L858R/T790M and L858R/T790M/C797S, which was superadditive as compared with the parent molecules. The enhanced potency is attributed to factors stemming from the linker connection to the allosteric-site group and informs strategies to engineer linkers in bivalent agent design.
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Affiliation(s)
- Florian Wittlinger
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Blessing C Ogboo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Ekaterina Shevchenko
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
| | - Tahereh Damghani
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Calvin D Pham
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Ilse K Schaeffner
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Brandon T Oligny
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Surbhi P Chitnis
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA
| | - Tyler S Beyett
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, 5119 Rollins Research Center, 1510 Clifton Rd, Atlanta, GA, 30322, USA
| | - Alexander Rasch
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Brian Buckley
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Daniel A Urul
- AssayQuant Technologies, Inc., Marlboro, MA, 01752, USA
| | - Tatiana Shaurova
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Earl W May
- AssayQuant Technologies, Inc., Marlboro, MA, 01752, USA
| | | | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela A Hershberger
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Antti Poso
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany
- School of Pharmacy, University of Eastern Finland, 70210, Kuopio, Finland
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies" Eberhard Karls Universität Tübingen, 72076, Tübingen, Germany.
- Tübingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tübingen, Germany.
| | - David E Heppner
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
- Department of Structural Biology, University at Buffalo, The State University of New York, Buffalo, NY, 14260, USA.
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Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
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Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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Dunn TN, Cope DI, Tang S, Sirupangi T, Parks SE, Liao Z, Yuan F, Creighton CJ, Masand RP, Alpuing Radilla L, Guan X, Detti L, Monsivais D, Matzuk MM. Inhibition of CSF1R and KIT With Pexidartinib Reduces Inflammatory Signaling and Cell Viability in Endometriosis. Endocrinology 2024; 165:bqae003. [PMID: 38227801 PMCID: PMC10948355 DOI: 10.1210/endocr/bqae003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/26/2023] [Accepted: 01/14/2024] [Indexed: 01/18/2024]
Abstract
Endometriosis is a common and debilitating disease, affecting ∼170 million women worldwide. Affected patients have limited therapeutic options such as hormonal suppression or surgical excision of the lesions, though therapies are often not completely curative. Targeting receptor tyrosine kinases (RTKs) could provide a nonhormonal treatment option for endometriosis. We determined that 2 RTKs, macrophage-colony stimulating factor 1 receptor (CSF1R) and mast/stem cell growth factor receptor KIT (KIT), are overexpressed in endometriotic lesions and could be novel nonhormonal therapeutic targets for endometriosis. The kinase activity of CSF1R and KIT is suppressed by pexidartinib, a small molecule inhibitor that was recently approved by the US Food and Drug Administration. Using immunohistochemistry, we detected CSF1R and KIT in endometriotic tissues obtained from peritoneal lesions, colorectal lesions, and endometriomas. Specifically, we show that KIT is localized to the epithelium of the lesions, while CSF1R is expressed in the stroma and macrophages of the endometriotic lesions. Given the high epithelial expression of CSF1R and KIT, 12Z endometriotic epithelial cells were used to evaluate the efficacy of dual CSF1R and KIT inhibition with pexidartinib. We found that pexidartinib suppressed activation in 12Z cells of JNK, STAT3, and AKT signaling pathways, which control key proinflammatory and survival networks within the cell. Using quantitative real-time polymerase chain reaction, we determined that pexidartinib suppressed interleukin 8 (IL8) and cyclin D1 (CCND1) expression. Lastly, we demonstrated that pexidartinib decreased cell growth and viability. Overall, these results indicate that pexidartinib-mediated CSF1R and KIT inhibition reduces proinflammatory signaling and cell viability in endometriosis.
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Affiliation(s)
- Timothy N Dunn
- Division of Reproductive Endocrinology & Infertility, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dominique I Cope
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Suni Tang
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tirupataiah Sirupangi
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sydney E Parks
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zian Liao
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fei Yuan
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine at Baylor College of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ramya P Masand
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Linda Alpuing Radilla
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiaoming Guan
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Laura Detti
- Division of Reproductive Endocrinology & Infertility, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Diana Monsivais
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Martin M Matzuk
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX 77030, USA
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van Gerwen J, Masson SWC, Cutler HB, Vegas AD, Potter M, Stöckli J, Madsen S, Nelson ME, Humphrey SJ, James DE. The genetic and dietary landscape of the muscle insulin signalling network. eLife 2024; 12:RP89212. [PMID: 38329473 PMCID: PMC10942587 DOI: 10.7554/elife.89212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
Metabolic disease is caused by a combination of genetic and environmental factors, yet few studies have examined how these factors influence signal transduction, a key mediator of metabolism. Using mass spectrometry-based phosphoproteomics, we quantified 23,126 phosphosites in skeletal muscle of five genetically distinct mouse strains in two dietary environments, with and without acute in vivo insulin stimulation. Almost half of the insulin-regulated phosphoproteome was modified by genetic background on an ordinary diet, and high-fat high-sugar feeding affected insulin signalling in a strain-dependent manner. Our data revealed coregulated subnetworks within the insulin signalling pathway, expanding our understanding of the pathway's organisation. Furthermore, associating diverse signalling responses with insulin-stimulated glucose uptake uncovered regulators of muscle insulin responsiveness, including the regulatory phosphosite S469 on Pfkfb2, a key activator of glycolysis. Finally, we confirmed the role of glycolysis in modulating insulin action in insulin resistance. Our results underscore the significance of genetics in shaping global signalling responses and their adaptability to environmental changes, emphasising the utility of studying biological diversity with phosphoproteomics to discover key regulatory mechanisms of complex traits.
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Affiliation(s)
- Julian van Gerwen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Stewart WC Masson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Harry B Cutler
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Alexis Diaz Vegas
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Meg Potter
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Jacqueline Stöckli
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Søren Madsen
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Marin E Nelson
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - Sean J Humphrey
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Sciences, University of SydneySydneyAustralia
- Faculty of Medicine and Health, University of SydneySydneyAustralia
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Zhang C, Chen Y, Li Y, Shi N, Teng Y, Li N, Tang M, Ma Z, Deng D, Chen L. Discovery of 4-amino-1,6-dihydro-7H-pyrrolo[2,3-d]pyridazin-7-one derivatives as potential receptor-interacting serine/threonine-protein kinase 1 (RIPK1) inhibitors. Eur J Med Chem 2024; 265:116076. [PMID: 38171150 DOI: 10.1016/j.ejmech.2023.116076] [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: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is an important regulatory factor in the necroptosis signaling pathway, and is considered an attractive therapeutic target for treating multiple inflammatory diseases. Herein, we describe the design, synthesis, and structure-activity relationships of 4-amino-1,6-dihydro-7H-pyrrolo [2,3-d]pyridazin-7-one derivatives as RIPK1 inhibitors. Among them, 13c showed favorable RIPK1 kinase inhibition activity with an IC50 value of 59.8 nM, and high RIPK1 binding affinity compared with other regulatory kinases of necroptosis (RIPK1 Kd = 3.5 nM, RIPK3 Kd = 1700 nM, and MLKL Kd > 30,000 nM). 13c efficiently blocked TNFα-induced necroptosis in both human and murine cells (EC50 = 1.06-4.58 nM), and inhibited TSZ-induced phosphorylation of the RIPK1/RIPK3/MLKL pathway. In liver microsomal assay studies, the clearance rate and half-life of 13c were 18.40 mL/min/g and 75.33 min, respectively. 13c displayed acceptable pharmacokinetic characteristics, with oral bioavailability of 59.55%. In TNFα-induced systemic inflammatory response syndrome, pretreatment with 13c could effectively protect mice from loss of body temperature and death. Overall, these compounds are promising candidates for future optimization studies.
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Affiliation(s)
- Chufeng Zhang
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yulian Chen
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yong Li
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China; Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Na Shi
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Yaxin Teng
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Na Li
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Minghai Tang
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Ziyan Ma
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Dexin Deng
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Lijuan Chen
- State Key Laboratory of Biotherapy and Cancer Center and Collaborative Innovation Center of Biotherapy, West China Hospital of Sichuan University, Chengdu, 610041, China; Chengdu Zenitar Biomedical Technology Co., Ltd, Chengdu, 610041, China.
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Wu YW, HuangFu WC, Lin TE, Peng CH, Tu HJ, Sung TY, Sung TY, Yen SC, Pan SL, Hsu KC. Identification of selective dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) inhibitors and their effects on tau and microtubule. Int J Biol Macromol 2024; 259:129074. [PMID: 38163507 DOI: 10.1016/j.ijbiomac.2023.129074] [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: 04/28/2023] [Revised: 11/17/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
The overexpression of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A), commonly observed in neurodegenerative diseases like Alzheimer's disease (AD) and Down syndrome (DS), can induce the formation of neurofibrillary tangles (NFTs) and amyloid plaques. Hence, designing a selective DYRK1A inhibitor would result in a promising small molecule for treating neurodegenerative diseases. Developing selective inhibitors for DYRK1A has been a difficult challenge due to the highly preserved ATP-binding site of protein kinases. In this study, we employed a structure-based virtual screening (SBVS) campaign targeting DYRK1A from a database containing 1.6 million compounds. Enzymatic assays were utilized to verify inhibitory properties, confirming that Y020-3945 and Y020-3957 showed inhibitory activity towards DYRK1A. In particular, the compounds exhibited high selectivity for DYRK1A over a panel of 120 kinases, reduced the phosphorylation of tau, and reversed the tubulin polymerization for microtubule stability. Additionally, treatment with the compounds significantly reduced the secretion of inflammatory cytokines IL-6 and TNF-α activated by DYRK1A-assisted NFTs and Aβ oligomers. These identified inhibitors possess promising therapeutic potential for conditions associated with DYRK1A in neurodegenerative diseases. The results showed that Y020-3945 and Y020-3957 demonstrated structural novelty compared to known DYRK1A inhibitors, making them a valuable addition to developing potential treatments for neurodegenerative diseases.
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Affiliation(s)
- Yi-Wen Wu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chun HuangFu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tony Eight Lin
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chao-Hsiang Peng
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Huang-Ju Tu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ting-Yi Sung
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Ying Sung
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Chung Yen
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, People's Republic of China
| | - Shiow-Lin Pan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei, Taiwan; Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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Xiao YC, Chen FE. The vinyl sulfone motif as a structural unit for novel drug design and discovery. Expert Opin Drug Discov 2024; 19:239-251. [PMID: 37978948 DOI: 10.1080/17460441.2023.2284201] [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: 09/01/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
INTRODUCTION Vinyl sulfones are a special sulfur-containing structural unit that have attracted considerable attention, owing to their important role in serving as key structural motifs of various biologically active compounds as well as serving as versatile building blocks for organic transformations. The synthetic strategy of vinyl sulfone derivatives has been substantially upgraded over the past 30 years, and the wide application of this functional group in drug design and discovery has been promoted. AREA COVERED In this review, the authors review the application of vinyl sulfones in drug discovery and select optimized compounds which might have significant impact or potential inspiration for drug design. EXPERT OPINION Vinyl sulfones have been reported to target various macromolecular targets via non-covalent or covalent interactions, including multiple kinases, tubulin, cysteine protease, transcription factor, and so on. Thus, it has been significantly applied as a privileged scaffold in the design of anticancer, anti-infective, anti-inflammatory, and neuroprotective agents. However, much work remains to be done to improve the drug-like properties, such as chemical and metabolic stability, ADME, and toxicity. Besides, the chemical space of vinyl sulfones needs to be expanded, including but not limited to the design of constrained endocyclic and exocyclic vinyl sulfones.
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Affiliation(s)
- You-Cai Xiao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Ministry of Education and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Fen-Er Chen
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Ministry of Education and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu, China
- Engineering Center of Catalysis and Synthesis for Chiral Molecules, Department of Chemistry, Fudan University, Shanghai, China
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: A 2024 update. Pharmacol Res 2024; 200:107059. [PMID: 38216005 DOI: 10.1016/j.phrs.2024.107059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Owing to the dysregulation of protein kinase activity in many diseases including cancer, this enzyme family has become one of the most important drug targets in the 21st century. There are 80 FDA-approved therapeutic agents that target about two dozen different protein kinases and seven of these drugs were approved in 2023. Of the approved drugs, thirteen target protein-serine/threonine protein kinases, four are directed against dual specificity protein kinases (MEK1/2), twenty block nonreceptor protein-tyrosine kinases, and 43 inhibit receptor protein-tyrosine kinases. The data indicate that 69 of these drugs are prescribed for the treatment of neoplasms. Six drugs (abrocitinib, baricitinib, deucravacitinib, ritlecitinib, tofacitinib, upadacitinib) are used for the treatment of inflammatory diseases (atopic dermatitis, rheumatoid arthritis, psoriasis, alopecia areata, and ulcerative colitis). Of the 80 approved drugs, nearly two dozen are used in the treatment of multiple diseases. The following seven drugs received FDA approval in 2023: capivasertib (HER2-positive breast cancer), fruquintinib (metastatic colorectal cancer), momelotinib (myelofibrosis), pirtobrutinib (mantle cell lymphoma, chronic lymphocytic leukemia, small lymphocytic lymphoma), quizartinib (Flt3-mutant acute myelogenous leukemia), repotrectinib (ROS1-positive lung cancer), and ritlecitinib (alopecia areata). All of the FDA-approved drugs are orally effective with the exception of netarsudil, temsirolimus, and trilaciclib. This review summarizes the physicochemical properties of all 80 FDA-approved small molecule protein kinase inhibitors including the molecular weight, number of hydrogen bond donors/acceptors, polar surface area, potency, solubility, lipophilic efficiency, and ligand efficiency.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 221 Haywood Knolls Drive, Hendersonville, NC 28791, United States.
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