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Pusztaszeri MP, Maleki Z. The diagnostic challenges of medullary thyroid carcinoma: A practical guide for cytopathologists. Cancer Cytopathol 2025; 133:e70023. [PMID: 40424173 PMCID: PMC12110738 DOI: 10.1002/cncy.70023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 05/01/2025] [Accepted: 05/01/2025] [Indexed: 05/29/2025]
Abstract
Medullary thyroid carcinoma (MTC) is a rare but potentially aggressive neuroendocrine tumor arising from the thyroid C cells (parafollicular cells) that produce calcitonin, representing 1%-3% of thyroid malignancies but contributing to up to 15% of thyroid cancer-related deaths. Early detection is critical for improving survival and outcomes because its tumor origin, treatment, and prognosis differ completely from papillary thyroid carcinoma. However, the low incidence of MTC and its variable cytomorphology can pose significant diagnostic challenges for cytopathologists. Referred to as the great mimicker, MTC can resemble various primary and metastatic tumors, complicating its identification, particularly in fine-needle aspiration (FNA) biopsies. Reported FNA sensitivity for a specific MTC diagnosis varies widely from 12.5% to 88.2%, with a 2014 meta-analysis estimating an overall sensitivity of 56.5% when including suspicious lesions. False-negative FNA results, often caused by misinterpretation of cytologic features or inadequate specimen quality, can lead to delayed or suboptimal treatment. Pathologists must be familiar with MTC's diverse cytopathologic presentation and maintain a low threshold for additional diagnostic tests to ensure an accurate preoperative diagnosis. This review article provides practical guidance on diagnosing MTC, emphasizing cytologic features, ancillary studies, mimickers, and common diagnostic pitfalls, serving as a valuable resource for cytopathologists, general pathologists, and trainees to improve diagnostic accuracy and patient care.
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Affiliation(s)
| | - Zahra Maleki
- Department of PathologyJohns Hopkins HospitalBaltimoreMarylandUSA
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2
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O'Boyle B, Yeung W, Lu JD, Katiyar S, Yaron-Barir TM, Johnson JL, Cantley LC, Kannan N. An atlas of bacterial serine-threonine kinases reveals functional diversity and key distinctions from eukaryotic kinases. Sci Signal 2025; 18:eadt8686. [PMID: 40327749 DOI: 10.1126/scisignal.adt8686] [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: 11/01/2024] [Accepted: 04/11/2025] [Indexed: 05/08/2025]
Abstract
Bacterial serine-threonine kinases (STKs) regulate diverse cellular processes associated with cell growth, virulence, and pathogenicity and are evolutionarily related to the druggable eukaryotic STKs. A deeper understanding of how bacterial STKs differ from their eukaryotic counterparts and how they have evolved to regulate diverse bacterial signaling functions is crucial for advancing the discovery and development of new antibiotic therapies. Here, we classified more than 300,000 bacterial STK sequences from the NCBI RefSeq nonredundant and UniProt protein databases into 35 canonical and seven pseudokinase families on the basis of the patterns of evolutionary constraints in the conserved catalytic domain and flanking regulatory domains. Through statistical comparisons, we identified features distinguishing bacterial STKs from eukaryotic STKs, including an arginine residue in a regulatory helix (C helix) that dynamically couples the ATP- and substrate-binding lobes of the kinase domain. Biochemical and peptide library screens demonstrated that evolutionarily constrained residues contributed to substrate specificity and kinase activation in the Mycobacterium tuberculosis kinase PknB. Together, these findings open previously unidentified avenues for investigating bacterial STK functions in cellular signaling and for developing selective bacterial STK inhibitors.
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Affiliation(s)
- Brady O'Boyle
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Jason D Lu
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Samiksha Katiyar
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Natarajan Kannan
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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3
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Yu H, Duan H, He R, Tian Y, Jiang J, Xiao F, Liu Q, Liu J, Li H, Yu X. Integrated transcriptomics profile reveals the role of Gal-1 and miR-21 in intrahepatic cholangiocarcinoma progression. Biochim Biophys Acta Mol Basis Dis 2025; 1871:167882. [PMID: 40318846 DOI: 10.1016/j.bbadis.2025.167882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 04/08/2025] [Accepted: 04/30/2025] [Indexed: 05/07/2025]
Abstract
Intrahepatic cholangiocarcinoma (ICC) is a highly invasive liver tumor with a poor prognosis, arises from the intrahepatic bile ducts. It is the second most common type of liver cancer. Understanding the mechanisms driving ICC progression is crucial for identification of biomarkers and therapeutic targets. Galectin-1 (Gal-1), encoded by the LGALS1 gene, is known to be upregulated in various malignancies and plays a significant role in cancer progression. However, its underlying mechanisms in ICC have yet to be fully elucidated. The study employed RNA-seq analysis, western blot, cell migration, colony forming, EdU assay, qRT-PCR, luciferase assay and mIHC to investigate the expression pattern of Gal-1 in ICC and its role in the progression of the disease. Our findings revealed a significant upregulation of Gal-1 in ICC tissues. Notably, downregulation of Gal-1inhibited ICC cell proliferation and migration. Further, Gal-1 appears to promote ICC progression through miR-21/STAT3-related pathways, playing a critical role to the tumor microenvironment. These results suggest that Gal-1 may serve as a promising molecular diagnostic marker and therapeutic target for ICC.
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Affiliation(s)
- Huasong Yu
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Huahong Duan
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Ruiqi He
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Yu Tian
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Jiayang Jiang
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Fen Xiao
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Qiao Liu
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Jie Liu
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China
| | - Hao Li
- Biliary Tract Surgery Laboratory, Department of Hepatobiliary Surgery, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, China; Hunan Research Center of Biliary Disease, the First Affiliated Hospital of Hunan Normal University, Changsha, China; Key Laboratory of Biliary Disease Prevention and treatment, the First Affiliated Hospital of Hunan Normal University, Changsha, China; Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China.
| | - Xing Yu
- Department of Basic Medical Sciences, School of Medicine, Hunan Normal University, Changsha, China; Key Laboratory of Model Animals and Stem Cell Biology of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Research Center of Reproduction and Translational Medicine of Hunan Province, School of Medicine, Hunan Normal University, Changsha, China; Hunan Provincial Key Laboratory of Regional Hereditary Birth Defects Prevention and Control, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China.
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4
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Shahwan M, Yadav DK, Khan MS, Choudhury A, Shamsi A, Hassan MI, Anwar S. Mechanistic insights into the inhibition of microtubule affinity-regulating kinase 4 by Syringic acid: A computational and experimental study. Int J Biol Macromol 2025; 309:142812. [PMID: 40216145 DOI: 10.1016/j.ijbiomac.2025.142812] [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: 02/15/2025] [Revised: 03/20/2025] [Accepted: 04/02/2025] [Indexed: 04/19/2025]
Abstract
Microtubule affinity regulating kinase 4 (MARK4) is a vital protein kinase that serves as a dual target in cancer and neurodegenerative diseases. It is implicated in the development of tauopathies and also linked to the pathogenesis of several cancer types, implying its importance. Syringic acid is a naturally occurring phenolic molecule that has shown significant efficacies in cancer and neurodegenerative diseases by modulating several key pathways. Thus, the present study aims to investigate the inhibitory potential of syringic acid against the protein kinase MARK4, employing a combination of experimental and computational approaches. Molecular docking revealed the binding of syringic acid in the MARK4's binding pocket, interacting with key functional residues of the protein kinase. Molecular dynamic simulation (MD) studies demonstrated the conformational dynamics and structural stability of MARK4 upon the binding of syringic acid. In silico findings were further complemented by experimental assays. Enzyme inhibition assay showed that syringic acid effectively inhibits MARK4 with an IC50 value of 4.32 μM. Fluorescence binding assays revealed a strong binding affinity (K = 2.8 × 106 M-1). The findings of our study establish syringic acid as a potent MARK4 inhibitor, providing a perfect platform for its use in tackling MARK4-associated diseases.
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Affiliation(s)
- Moyad Shahwan
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, United Arab Emirates; Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates
| | - Dharmendra Kumar Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, Incheon, Republic of Korea.
| | | | - Arunabh Choudhury
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
| | - Anas Shamsi
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
| | - Saleha Anwar
- Center for Medical and Bio-Allied Health Sciences Research, Ajman University, United Arab Emirates; Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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5
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: A 2025 update. Pharmacol Res 2025; 216:107723. [PMID: 40252783 DOI: 10.1016/j.phrs.2025.107723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2025] [Revised: 03/31/2025] [Accepted: 03/31/2025] [Indexed: 04/21/2025]
Abstract
Because of the deregulation of protein kinase action in many inflammatory diseases and cancer, the protein kinase family has become one of the most significant drug targets in the 21st century. There are 85 FDA-approved protein kinase antagonists that target about two dozen different enzymes and four of these drugs were approved in 2024 and a fifth was approved in 2025. Of these drugs, five target dual specificity protein kinases (MEK1/2), fourteen inhibit protein-serine/threonine protein kinases, twenty-one block nonreceptor protein-tyrosine kinases, and 45 target receptor protein-tyrosine kinases. The data indicate that 75 of these drugs are prescribed for the treatment of neoplasms. Seven drugs (abrocitinib, baricitinib, deucravacitinib, deuruxolitinib, ritlecitinib, tofacitinib, upadacitinib) are prescribed for the management of inflammatory diseases (atopic dermatitis, rheumatoid arthritis, psoriasis, alopecia areata, and ulcerative colitis). Of the 85 FDA-approved agents, about two dozen are used in the treatment of multiple diseases. The following four drugs received FDA approval in 2024 - deuruxolitinib (alopecia areata), ensartinib and lazertinib (non-small cell lung cancer), and tovorafenib (pediatric glioma) while mirdametinib was approved in 2025 for the treatment of type I neurofibromatosis (von Recklinghausen disease). Apart from netarsudil, temsirolimus, and trilaciclib, the approved protein kinase blockers are orally bioavailable. This article summarizes the physicochemical properties of all 85 FDA-approved small molecule protein kinase inhibitors including the molecular weight, number of hydrogen bond donors/acceptors, ligand efficiency, lipophilic efficiency, polar surface area, and solubility. A total of 39 of the 85 FDA-approved drugs have a least one Lipinski rule of 5 violation.
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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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6
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Gutierrez C, Rajendram P, Idowu O. Novel Cancer Therapeutics: Perioperative Implications and Challenges. Anesth Analg 2025; 140:753-766. [PMID: 39453847 DOI: 10.1213/ane.0000000000007210] [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: 10/27/2024]
Abstract
Since the introduction of immunotherapy and targeted therapies, patients not only have adequate tumoral response to these treatments, but their quality of life has improved due to milder toxicities. However, due to their wide mechanisms of action, the toxicity profile for these therapies is broad, can have an insidious onset, and their recognition can be challenging. Rarely, some of these toxicities can cause significant morbidity if not diagnosed early and lead to intensive care unit (ICU) admission and death. Anesthesiologists are likely to encounter not only a wide spectrum of these toxicities but also a wide range of severity. In some cases, they could be the first to make the diagnosis and therefore need to be prepared to rapidly assess, establish differentials, perform a diagnostic workup, and evaluate the impact the toxicity could have on the patients' care during the perioperative period. In this article, we set to review toxicities of novel cancer therapies such as checkpoint inhibitors and targeted therapies, that could present in the perioperative setting. This article will help as a guide for anesthesiologists to recognize their clinical presentation, the approach to their diagnosis, and their impact on patient care.
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Affiliation(s)
- Cristina Gutierrez
- From the Department of Critical Care Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Prabalini Rajendram
- Department of Anesthesiology and Critical Care Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olakunle Idowu
- Department of Anesthesiology and Perioperative Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
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Rangaswamy R, Hemavathy N, Subramaniyan S, Vetrivel U, Jeyakanthan J. Harnessing allosteric inhibition: prioritizing LIMK2 inhibitors for targeted cancer therapy through pharmacophore-based virtual screening and essential molecular dynamics. J Biomol Struct Dyn 2025; 43:1129-1146. [PMID: 38063080 DOI: 10.1080/07391102.2023.2291171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/21/2023] [Indexed: 01/16/2025]
Abstract
The therapeutic potential of small molecule kinase inhibitors in cancer treatment is well recognized. However, achieving selectivity remains a formidable challenge, primarily due to the structural similarity of ATP binding pockets among kinases. Allosteric inhibition, which involves targeting binding pockets beyond the ATP-binding site, provides a promising alternative to overcome this challenge. In this study, a meticulous approach was implemented to prioritize type 3 inhibitors for LIMK2, employing a range of techniques including Molecular Dynamics (MD) simulations, e-pharmacophore-guided High Throughput Virtual Screening (HTVS), MM/GBSA and ADMETox analyses, Density Functional Theory (DFT) calculations, and MM/PBSA investigations. The e-pharmacophore model identifies a hypothesis featuring five essential pharmacophoric elements (RRRAH). Through virtual screening of the ZINC compound database, we identified only five compounds that align with all four pharmacophoric features: ZINC1044382792, ZINC1433610865, ZINC1044109145, ZINC952869440, and ZINC490621334. These compounds not only exhibit higher binding affinity but also demonstrate favorable ADME/Tox profiles. Molecular dynamics simulations underscore the stability of hydrogen bond interactions with critical cryptic LIMK2 pocket residues, Asp469 and Arg474, only for two compounds: ZINC143361086 and ZINC1044382792. These compounds also exhibit superior occupancy interactions, as indicated by HOMO-LUMO analysis. Additionally, binding free energy calculations highlight the significant affinities of these two compounds when complexed with LIMK2: -83.491 ± 1.230 kJ/mol and -90.122 ± 1.248 kJ/mol for ZINC1044382792 and ZINC1433610862, respectively. Hence, this comprehensive investigation identifies ZINC1433610862 and ZINC1044382792 as prospective hits, representing promising leads for targeting LIMK2 in cancer therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Raghu Rangaswamy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Nagarajan Hemavathy
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sneha Subramaniyan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Umashankar Vetrivel
- Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Mao W, Jiang J, Xia Y, Zhang L. Analysis of postmarketing neuropsychiatric adverse events of avapritinib based on the FDA adverse event reporting system. Sci Rep 2025; 15:3108. [PMID: 39856211 PMCID: PMC11760955 DOI: 10.1038/s41598-025-86959-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Accepted: 01/15/2025] [Indexed: 01/30/2025] Open
Abstract
Neuropsychiatric adverse events (AEs) significantly impact the quality of life of patients using avapritinib. However, the majority of current data comes from pre-marketing, with limited real-world studies. Our research aimed to explore post-marketing data of avapritinib. We evaluated the signals of avapritinib-related neuropsychiatric AEs by data mining using the FDA Adverse Event Reporting System (FAERS). Reporting odds ratio (ROR) and information component (IC) were employed to quantify the signals from the first quarter of 2020 through the fourth quarter of 2023. Subsequently, stratified analyses were conducted to further explore the effect of different stratification schemes on the association between avapritinib and neuropsychiatric AEs. Finally, a combination medication analysis was conducted to explore the impact of the co-administration of neuropsychiatric AEs. A total of 2029 neuropsychiatric AEs were reported, and 49 signals were detected, of which 5 were determined to be new signals. Avapritinib was significantly associated with the occurrence of neuropsychiatric AEs (ROR: 1.52, 95% CI: 1.44-1.61; IC: 0.43, IC025: 0.35). The stratified analysis found that gender, age and eight preferred terms (PTs), including cerebral haemorrhage, may affect the severity of AEs. Combination medication analysis showed that combining avapritinib with 19 other medications, including prochlorperazine, may increase the risk of neuropsychiatric AEs. The median time-to-onset (TTO) of avapritinib-related neuropsychiatric AEs was 32 (interquartile range [IQR] 2-200) days, with about 65% of cases occurring within the first three months of treatment. An increase in the signal for neuropsychiatric AEs was identified in post-marketing studies of avapritinib. Clinicians are advised to remain vigilant for such events, particularly during the initial stages of treatment with avapritinib.
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Affiliation(s)
- Wei Mao
- Department of Pharmacy, Nanan People's Hospital of Chongqing, Chongqing, China
| | - Junyan Jiang
- Department of Gastroenterology, Nanan People's Hospital of Chongqing, Chongqing, China
| | - Yanping Xia
- Department of Pharmacy, Nanan People's Hospital of Chongqing, Chongqing, China
| | - Lin Zhang
- Department of Pharmacy, The First Affiliated Hospital of Army Medical University, Chongqing, China.
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O'Boyle B, Yeung W, Lu JD, Katiyar S, Yaron-Barir TM, Johnson JL, Cantley LC, Kannan N. Atlas of the Bacterial Serine-Threonine Kinases expands the functional diversity of the kinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.12.632604. [PMID: 39868133 PMCID: PMC11760699 DOI: 10.1101/2025.01.12.632604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Bacterial serine-threonine protein kinases (STKs) regulate diverse cellular processes associated with cell growth, virulence, and pathogenicity. They are evolutionarily related to the druggable eukaryotic STKs. However, an incomplete knowledge of how bacterial STKs differ from their eukaryotic counterparts and how they have diverged to regulate diverse bacterial signaling functions presents a bottleneck in targeting them for drug discovery efforts. Here, we classified over 300,000 bacterial STK sequences from the NCBI RefSeq non-redundant and UniProt protein databases into 35 canonical and seven non-canonical (pseudokinase) families based on the patterns of evolutionary constraints in the conserved catalytic domain and flanking regulatory domains. Through statistical comparisons, we identified distinguishing features of bacterial STKs, including a distinctive arginine residue in a regulatory helix (C-Helix) that dynamically couples ATP and substrate binding lobes of the kinase domain. Biochemical and peptide-library screens demonstrated that constrained residues contribute to substrate specificity and kinase activation in the Mycobacterium tuberculosis kinase PknB. Collectively, these findings open new avenues for investigating bacterial STK functions in cellular signaling and for the development of selective bacterial STK inhibitors.
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10
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Li X, Ruan P, Jiang G, Zhang W. Screening and in vitro Biological Evaluation of Novel Multiple Tyrosine Kinases Inhibitors as Promising Anticancer Agents. Anticancer Agents Med Chem 2025; 25:555-562. [PMID: 37016516 DOI: 10.2174/1871520623666230403104816] [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: 09/16/2022] [Revised: 02/01/2023] [Accepted: 02/24/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Tyrosine kinases have emerged as key stimulatory drivers in several cancer-related pathways. This is particularly evident in non-small cell lung cancer with regulating cell growth and apoptosis and so on. Tyrosine kinase inhibitors (TKI) are one breakthrough option that could improve the life quality of cancer patients. OBJECTIVE This study aims to find more effective tyrosine kinase inhibitors. METHODS In this study, natural products from TargetMol that may be the potential TKI for lung cancer were screened through structure-based virtual screening and experimental validation. Moreover, the binding between the hit compounds and tyrosine kinase was explored. RESULTS From the study findings, Gramicidin and Tannic acid have strong interactions with the four tyrosine kinases (ALK, TRK, MET, and ABL), and this could significantly inhibit the viability of A549 cells in a concentrationdependent manner. CONCLUSION These findings indicated that Gramicidin and Tannic acid might be potential multiple TKI and are promising anticancer agents that call for further study.
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Affiliation(s)
- Xiuying Li
- Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Pinglang Ruan
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Gang Jiang
- Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
| | - Weidong Zhang
- Pulmonary and Critical Care Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, China
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11
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Uba AI. Computer-Aided Design of VEGFR-2 Inhibitors as Anticancer Agents: A Review. J Mol Recognit 2025; 38:e3104. [PMID: 39389566 DOI: 10.1002/jmr.3104] [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: 06/21/2024] [Revised: 08/01/2024] [Accepted: 09/03/2024] [Indexed: 10/12/2024]
Abstract
Due to its intricate molecular and structural characteristics, vascular endothelial growth factor receptor 2 (VEGFR-2) is essential for the development of new blood vessels in various pathological processes and conditions, especially in cancers. VEGFR-2 inhibitors have demonstrated significant anticancer effects by blocking many signaling pathways linked to tumor growth, metastasis, and angiogenesis. Several small compounds, including the well-tolerated sunitinib and sorafenib, have been approved as VEGFR-2 inhibitors. However, the widespread side effects linked to these VEGFR-2 inhibitors-hypertension, epistaxis, proteinuria, and upper respiratory infection-motivate researchers to search for new VEGFR-2 inhibitors with better pharmacokinetic profiles. The key molecular interactions required for the interaction of the small molecules with the protein target to produce the desired pharmacological effects are identified using computer-aided drug design (CADD) methods such as pharmacophore and QSAR modeling, structure-based virtual screening, molecular docking, molecular dynamics (MD) simulation coupled with MM/PB(GB)SA, and other computational strategies. This review discusses the applications of these methods for VEGFR-2 inhibitor design. Future VEGFR-2 inhibitor designs may be influenced by this review, which focuses on the current trends of using multiple screening layers to design better inhibitors.
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Affiliation(s)
- Abdullahi Ibrahim Uba
- Department of Molecular Biology and Genetics, Istanbul AREL University, Istanbul, Turkey
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12
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Dai J, Rayana NP, Peng M, Sugali CK, Harvey DH, Dhamodaran K, Yu E, Dalloul JM, Liu S, Mao W. Inhibition of pterygium cell fibrosis by the Rho kinase inhibitor. Sci Rep 2024; 14:30930. [PMID: 39730553 DOI: 10.1038/s41598-024-81659-6] [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: 04/14/2024] [Accepted: 11/28/2024] [Indexed: 12/29/2024] Open
Abstract
Pterygium is an ocular disease in which the conjunctival tissue invades the cornea. When the pterygium tissue reaches the pupillary region, the visual function of the patient is affected. Currently, surgical removal is the only effective treatment. However, the recurrence rate of pterygium after surgery can be high. Pterygium is also a health disparity issue since it is more prevalent in the Hispanic and Latino American population. In this study, we determined if the Rho kinase inhibitor can be used to prevent pterygium recurrence since its anti-fibrosis effects have been reported in other cell and tissue types. We cultured primary pterygium cells from pterygium tissues from Hispanic and Latino American, African American, Caucasian, and Asian donors, and used those cells for viability assays, scratch assays, migration assays, and immunostaining of F-actin, fibronectin, collagen I and α smooth muscle actin. We found that the Rho kinase inhibitor Y27632 decreased cell viability, wound healing, cell migration, as well as the expression of extracellular matrix and myofibroblast markers in cultured pterygium cells. We believe that Rho kinase inhibitors are a potential post-surgical treatment to prevent pterygium recurrence.
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Affiliation(s)
- Jiannong Dai
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Naga Pradeep Rayana
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Michael Peng
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Chenna Kesavulu Sugali
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Devon H Harvey
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Kamesh Dhamodaran
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Eric Yu
- Fulton Science Academy Private School, Alpharetta, GA, USA
| | - Joseph M Dalloul
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Shaohui Liu
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA
| | - Weiming Mao
- Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, RM305v, 1160 W. Michigan St., Indianapolis, IN, 46202, USA.
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, USA.
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, USA.
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, USA.
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, USA.
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13
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Rodrigues FAP, Oliveira CS, Sá SC, Tavaria FK, Lee SJ, Oliveira AL, Costa JB. Molecules in Motion: Unravelling the Dynamics of Vascularization Control in Tissue Engineering. Macromol Biosci 2024; 24:e2400139. [PMID: 39422632 DOI: 10.1002/mabi.202400139] [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: 03/25/2024] [Revised: 08/14/2024] [Indexed: 10/19/2024]
Abstract
Significant progress has been made in tissue engineering (TE), aiming at providing personalized solutions and overcoming the current limitations of traditional tissue and organ transplantation. 3D bioprinting has emerged as a transformative technology in the field, able to mimic key properties of the natural architecture of the native tissues. However, most successes in the area are still limited to avascular or thin tissues due to the difficulties in controlling the vascularization of the engineered tissues. To address this issue, several molecules, biomaterials, and cells with pro- and anti-angiogenic potential have been intensively investigated. Furthermore, different bioreactors capable to provide a dynamic environment for in vitro vascularization control have been also explored. The present review summarizes the main molecules and TE strategies used to promote and inhibit vascularization in TE, as well as the techniques used to deliver them. Additionally, it also discusses the current challenges in 3D bioprinting and in tissue maturation to control in vitro/in vivo vascularization. Currently, this field of investigation is of utmost importance and may open doors for the design and development of more precise and controlled vascularization strategies in TE.
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Affiliation(s)
- Francisco A P Rodrigues
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto, 4169-005, Portugal
| | - Cláudia S Oliveira
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto, 4169-005, Portugal
| | - Simone C Sá
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto, 4169-005, Portugal
| | - Freni K Tavaria
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto, 4169-005, Portugal
| | - Sang Jin Lee
- Wake Forest Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Ana L Oliveira
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto, 4169-005, Portugal
| | - João B Costa
- CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto, 4169-005, Portugal
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14
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Zolotareva K, Dotsenko PA, Podkolodnyy N, Ivanov R, Makarova AL, Chadaeva I, Bogomolov A, Demenkov PS, Ivanisenko V, Oshchepkov D, Ponomarenko M. Candidate SNP Markers Significantly Altering the Affinity of the TATA-Binding Protein for the Promoters of Human Genes Associated with Primary Open-Angle Glaucoma. Int J Mol Sci 2024; 25:12802. [PMID: 39684516 DOI: 10.3390/ijms252312802] [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: 09/30/2024] [Revised: 11/20/2024] [Accepted: 11/25/2024] [Indexed: 12/18/2024] Open
Abstract
Primary open-angle glaucoma (POAG) is the most common form of glaucoma. This condition leads to optic nerve degeneration and eventually to blindness. Tobacco smoking, alcohol consumption, fast-food diets, obesity, heavy weight lifting, high-intensity physical exercises, and many other bad habits are lifestyle-related risk factors for POAG. By contrast, moderate-intensity aerobic exercise and the Mediterranean diet can alleviate POAG. In this work, we for the first time estimated the phylostratigraphic age indices (PAIs) of all 153 POAG-related human genes in the NCBI Gene Database. This allowed us to separate them into two groups: POAG-related genes that appeared before and after the phylum Chordata, that is, ophthalmologically speaking, before and after the camera-type eye evolved. Next, in the POAG-related genes' promoters, we in silico predicted all 3835 candidate SNP markers that significantly change the TATA-binding protein (TBP) affinity for these promoters and, through this molecular mechanism, the expression levels of these genes. Finally, we verified our results against five independent web services-PANTHER, DAVID, STRING, MetaScape, and GeneMANIA-as well as the ClinVar database. It was concluded that POAG is likely to be a symptom of the human self-domestication syndrome, a downside of being civilized.
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Affiliation(s)
- Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
| | - Polina A Dotsenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nikolay Podkolodnyy
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Institute of Computational Mathematics and Mathematical Geophysics, SB RAS, Novosibirsk 630090, Russia
| | - Roman Ivanov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
| | - Aelita-Luiza Makarova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel S Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
| | - Vladimir Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences (ICG SB RAS), Novosibirsk 630090, Russia
- Kurchatov Genome Center at the ICG SB RAS, Novosibirsk 630090, Russia
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15
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Zhu Z, Chen C, Gu J, Wang Y, Ning W. Simultaneous Administration of Pemigatinib and Anlotinib Synergistically Induced Clinical Remission in a Case of Advanced Lung Adenocarcinoma Harboring FGFR2 Rearrangement. Am J Ther 2024; 31:724-725. [PMID: 39792501 DOI: 10.1097/mjt.0000000000001648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2025]
Affiliation(s)
- Ziwen Zhu
- Respiratory Department, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Chen
- Respiratory Department, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jing Gu
- Respiratory Department, The Third Hospital of Kunshan City, Kunshan, China
| | - Yang Wang
- Respiratory Department, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Weiwei Ning
- Respiratory Department, The First Affiliated Hospital of Soochow University, Suzhou, China
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16
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Zhu Z, Zhou S, Li S, Gong S, Zhang Q. Neutrophil extracellular traps in wound healing. Trends Pharmacol Sci 2024; 45:1033-1045. [PMID: 39419742 DOI: 10.1016/j.tips.2024.09.007] [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: 07/19/2024] [Revised: 09/22/2024] [Accepted: 09/23/2024] [Indexed: 10/19/2024]
Abstract
Wound healing is a complex and orchestrated process that involves hemostasis, inflammation, proliferation, and tissue remodeling. Neutrophil extracellular traps (NETs) are intricate web-like structures released by neutrophils, comprising decondensed chromatin, myeloperoxidase (MPO), and neutrophil elastase (NE), which play vital roles in regulating neutrophil-mediated immune regulation. While NETs contribute to wound healing, excessive activation induced by dysregulated inflammation can hinder the healing process. Understanding the pivotal role of NETs in wound healing and tissue remodeling, as well as their intricate interactions within the wound microenvironment, presents opportunities for innovative wound healing strategies. In this review we discuss the process of NET formation, explore the interactions between NETs and skin cells, and examine therapeutic strategies targeting NETs and drug delivery platforms to accelerate wound healing. Additionally, we discuss current clinical investigations and research challenges towards advancing wound care practices.
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Affiliation(s)
- Zhanyong Zhu
- Department of Plastic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Shengzhi Zhou
- Department of Plastic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Sicheng Li
- Department of Plastic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei Province, China
| | - Song Gong
- Division of Endocrinology, Tongji Hospital, Huazhong University of Science and Technology, Jiefang Road 1095, Wuhan 430030, Hubei Province, People's Republic of China.
| | - Qi Zhang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Xianning Medical College, Hubei University of Science and Technology, Xianning 437000, Hubei, China.
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17
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Ganai AM, Vrettos EI, Kyrkou SG, Zoi V, Khan Pathan T, Karpoormath R, Bouziotis P, Alexiou GA, Kastis GA, Protonotarios NE, Tzakos AG. Design Principles and Applications of Fluorescent Kinase Inhibitors for Simultaneous Cancer Bioimaging and Therapy. Cancers (Basel) 2024; 16:3667. [PMID: 39518106 PMCID: PMC11545566 DOI: 10.3390/cancers16213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Revised: 10/12/2024] [Accepted: 10/17/2024] [Indexed: 11/16/2024] Open
Abstract
Kinase inhibitors are potent therapeutic agents in cancer treatment, but their effectiveness is frequently restricted by the inability to image the tumor microenvironment. To address this constraint, kinase inhibitor-fluorophore conjugates have emerged as promising theranostic agents, allowing for simultaneous cancer diagnosis and treatment. These conjugates are gaining attention for their ability to visualize malignant tissues and concurrently enhance therapeutic interventions. This review explores the design principles governing the development of multimodal inhibitors, highlighting their potential as platforms for kinase tracking and inhibition via bioimaging. The structural aspects of constructing such theranostic agents are critically analyzed. This work could shed light on this intriguing field and provide adequate impetus for developing novel theranostic compounds based on small molecule inhibitors and fluorophores.
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Affiliation(s)
- Ab Majeed Ganai
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; (A.M.G.); (E.I.V.); (S.G.K.); (T.K.P.)
| | - Eirinaios I. Vrettos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; (A.M.G.); (E.I.V.); (S.G.K.); (T.K.P.)
| | - Stavroula G. Kyrkou
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; (A.M.G.); (E.I.V.); (S.G.K.); (T.K.P.)
| | - Vasiliki Zoi
- Neurosurgical Institute, University of Ioannina, 45110 Ioannina, Greece; (V.Z.); (G.A.A.)
| | - Tabasum Khan Pathan
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; (A.M.G.); (E.I.V.); (S.G.K.); (T.K.P.)
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban 4000, South Africa;
| | - Rajshekhar Karpoormath
- Department of Pharmaceutical Chemistry, Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal (Westville), Durban 4000, South Africa;
| | - Penelope Bouziotis
- Institute of Nuclear and Radiological Science and Technology, Energy and Safety (INRASTES), National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (P.B.); (G.A.K.); (N.E.P.)
| | - George A. Alexiou
- Neurosurgical Institute, University of Ioannina, 45110 Ioannina, Greece; (V.Z.); (G.A.A.)
| | - George A. Kastis
- Institute of Nuclear and Radiological Science and Technology, Energy and Safety (INRASTES), National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (P.B.); (G.A.K.); (N.E.P.)
- Mathematics Research Center, Academy of Athens, 11527 Athens, Greece
| | - Nicholas E. Protonotarios
- Institute of Nuclear and Radiological Science and Technology, Energy and Safety (INRASTES), National Center for Scientific Research “Demokritos”, 15310 Athens, Greece; (P.B.); (G.A.K.); (N.E.P.)
- Mathematics Research Center, Academy of Athens, 11527 Athens, Greece
| | - Andreas G. Tzakos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece; (A.M.G.); (E.I.V.); (S.G.K.); (T.K.P.)
- Institute of Materials Science and Computing, University Research Center of Ioannina (URCI), Ioannina 45110, Greece
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18
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Ma W, Hu J, Chen Z, Ai Y, Zhang Y, Dong K, Meng X, Liu L. The Development and Application of KinomePro-DL: A Deep Learning Based Online Small Molecule Kinome Selectivity Profiling Prediction Platform. J Chem Inf Model 2024; 64:7273-7290. [PMID: 39320984 DOI: 10.1021/acs.jcim.4c00595] [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: 09/27/2024]
Abstract
Characterizing the kinome selectivity profiles of kinase inhibitors is essential in the early stages of novel small-molecule drug discovery. This characterization is critical for interpreting potential adverse events caused by off-target polypharmacology effects and provides unique pharmacological insights for drug repurposing development of existing kinase inhibitor drugs. However, experimental profiling of whole kinome selectivity is still time-consuming and resource-demanding. Here, we report a deep learning classification model using an in-house built data set of inhibitors against 191 well-representative kinases constructed based on a novel strategy by systematically cleaning and integrating six public data sets. This model, a multitask deep neural network, predicts the kinome selectivity profiles of compounds with novel structures. The model demonstrates excellent predictive performance, with auROC, prc-AUC, Accuracy, and Binary_cross_entropy of 0.95, 0.92, 0.90, and 0.37, respectively. It also performs well in a priori testing for inhibitors targeting different categories of proteins from internal compound collections, significantly improving over similar models on data sets from practical application scenarios. Integrated to subsequent machine learning-enhanced virtual screening workflow, novel CDK2 kinase inhibitors with potent kinase inhibitory activity and excellent kinome selectivity profiles are successfully identified. Additionally, we developed a free online web server, KinomePro-DL, to predict the kinome selectivity profiles and kinome-wide polypharmacology effects of small molecules (available on kinomepro-dl.pharmablock.com). Uniquely, our model allows users to quickly fine-tune it with their own training data sets, enhancing both prediction accuracy and robustness.
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Affiliation(s)
- Wei Ma
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Jiaqi Hu
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Zhuangzhi Chen
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Yaoqin Ai
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Yihang Zhang
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Keke Dong
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Xiangfei Meng
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
| | - Liu Liu
- Drug Research Business Unit, PharmaBlock Sciences (Nanjing), Inc., 81 Huasheng Road, Jiangbei New Area, Nanjing, Jiangsu 210032, China
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Rocha KML, Nascimento ÉCM, de Jesus RCC, Martins JBL. In Silico Molecular Modeling of Four New Afatinib Derived Molecules Targeting the Inhibition of the Mutated Form of BCR-ABL T315I. Molecules 2024; 29:4254. [PMID: 39275102 PMCID: PMC11397288 DOI: 10.3390/molecules29174254] [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: 06/12/2024] [Revised: 08/18/2024] [Accepted: 08/19/2024] [Indexed: 09/16/2024] Open
Abstract
Four afatinib derivatives were designed and modeled. These derivatives were compared to the known tyrosine-kinase inhibitors in treating Chronic Myeloid Leukemia, i.e., imatinib and ponatinib. The molecules were evaluated through computational methods, including docking studies, the non-covalent interaction index, Electron Localization and Fukui Functions, in silico ADMET analysis, QTAIM, and Heat Map analysis. The AFA(IV) candidate significantly increases the score value compared to afatinib. Furthermore, AFA(IV) was shown to be relatively similar to the ponatinib profile when evaluating a range of molecular descriptors. The addition of a methylpiperazine ring seems to be well distributed in the structure of afatinib when targeting the BCR-ABL enzyme, providing an important hydrogen bond interaction with the Asp381 residue of the DFG-switch of BCR-ABL active site residue and the AFA(IV) new chemical entities. Finally, in silico toxicity predictions show a favorable index, with some molecules presenting the loss of the irritant properties associated with afatinib in theoretical predictions.
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MESH Headings
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/chemistry
- Afatinib/chemistry
- Afatinib/pharmacology
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Molecular Docking Simulation
- Humans
- Models, Molecular
- Computer Simulation
- Mutation
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Hydrogen Bonding
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Imidazoles/chemistry
- Imidazoles/pharmacology
- Pyridazines
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Affiliation(s)
- Kelvyn M. L. Rocha
- Department of Pharmacy, Faculty of Health Sciences, University of Brasília, Brasília 70910-900, DF, Brazil; (K.M.L.R.); (É.C.M.N.); (R.C.C.d.J.)
| | - Érica C. M. Nascimento
- Department of Pharmacy, Faculty of Health Sciences, University of Brasília, Brasília 70910-900, DF, Brazil; (K.M.L.R.); (É.C.M.N.); (R.C.C.d.J.)
- Computational Chemistry Laboratory, Institute of Chemistry, University of Brasília, Brasília 70910-900, DF, Brazil
| | - Rafael C. C. de Jesus
- Department of Pharmacy, Faculty of Health Sciences, University of Brasília, Brasília 70910-900, DF, Brazil; (K.M.L.R.); (É.C.M.N.); (R.C.C.d.J.)
| | - João B. L. Martins
- Department of Pharmacy, Faculty of Health Sciences, University of Brasília, Brasília 70910-900, DF, Brazil; (K.M.L.R.); (É.C.M.N.); (R.C.C.d.J.)
- Computational Chemistry Laboratory, Institute of Chemistry, University of Brasília, Brasília 70910-900, DF, Brazil
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20
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Hoosemans L, Vooijs M, Hoeben A. Opportunities and Challenges of Small Molecule Inhibitors in Glioblastoma Treatment: Lessons Learned from Clinical Trials. Cancers (Basel) 2024; 16:3021. [PMID: 39272879 PMCID: PMC11393907 DOI: 10.3390/cancers16173021] [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: 07/25/2024] [Revised: 08/26/2024] [Accepted: 08/29/2024] [Indexed: 09/15/2024] Open
Abstract
Glioblastoma (GBM) is the most prevalent central nervous system tumour (CNS). Patients with GBM have a dismal prognosis of 15 months, despite an intensive treatment schedule consisting of surgery, chemoradiation and concurrent chemotherapy. In the last decades, many trials have been performed investigating small molecule inhibitors, which target specific genes involved in tumorigenesis. So far, these trials have been unsuccessful, and standard of care for GBM patients has remained the same since 2005. This review gives an overview of trials investigating small molecule inhibitors on their own, combined with chemotherapy or other small molecule inhibitors. We discuss possible resistance mechanisms in GBM, focussing on intra- and intertumoral heterogeneity, bypass mechanisms and the influence of the tumour microenvironment. Moreover, we emphasise how combining inhibitors can help overcome these resistance mechanisms. We also address strategies for improving trial outcomes through modifications to their design. In summary, this review aims to elucidate different resistance mechanisms against small molecule inhibitors, highlighting their significance in the search for novel therapeutic combinations to improve the overall survival of GBM patients.
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Affiliation(s)
- Linde Hoosemans
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, 6229 HX Maastricht, The Netherlands
| | - Marc Vooijs
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Reproduction, Maastricht University Medical Center+, 6229 HX Maastricht, The Netherlands
| | - Ann Hoeben
- Department of Medical Oncology, GROW School for Oncology and Reproduction, Maastricht University Medical Center+, 6229 HX Maastricht, The Netherlands
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21
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Silva-Carvalho AÉ, Bispo ECI, da Silva IGM, Correa JR, Carvalho JL, Gelfuso GM, Saldanha-Araujo F. Characterization of ibrutinib's effects on the morphology, proliferation, phenotype, viability, and anti-inflammatory potential of adipose-derived mesenchymal stromal cells. Sci Rep 2024; 14:19906. [PMID: 39191849 DOI: 10.1038/s41598-024-71054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 08/23/2024] [Indexed: 08/29/2024] Open
Abstract
Ibrutinib (IB) is a tyrosine kinase inhibitor (TKI) that has immunomodulatory action and can be used as second-line therapy for steroid-refractory or steroid-resistant chronic Graft versus Host Disease (cGVHD). Mesenchymal stromal cells (MSCs) are distributed throughout the body and their infusion has also been explored as a second-line therapeutic alternative for the treatment of cGVHD. Considering the currently unknown effects of IB on endogenous MSCs, as well as the possible combined use of IB and MSCs for cGVHD, we investigated whether adipose tissue-derived MSCs present IB-targets, as well as the consequences of treating MSCs with this drug, regarding cell viability, proliferation, phenotype, and anti-inflammatory potential. Interestingly, we show for the first time that MSCs express several IB target genes. Also of note, the treatment of such cells with this TKI elevated the levels of CD90 and CD105 surface proteins, as well as VCAM-1. Furthermore, IB-treated MSCs presented increased mRNA expression of the anti-inflammatory genes PD-L1, TSG-6, and IL-10. However, continued exposure to IB, even at low doses, compromised the viability of MSCs. These data indicate that the use of IB can stimulate an anti-inflammatory profile in MSCs, but also that a continued exposure to IB can compromise MSC viability over time.
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Affiliation(s)
- Amandda Évelin Silva-Carvalho
- Laboratório de Hematologia E Células-Tronco, Departamento de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brasil
- Laboratório de Farmacologia Molecular, Universidade de Brasília, Brasília, Brasil
| | - Elizabete Cristina Iseke Bispo
- Laboratório de Hematologia E Células-Tronco, Departamento de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brasil
| | | | - José Raimundo Correa
- Laboratório de Microscopia E Microanálises, Universidade de Brasília, Brasília, Brasil
| | - Juliana Lott Carvalho
- Laboratório Multidisciplinar de Biociências, Universidade de Brasília, Brasília, Brasil
| | | | - Felipe Saldanha-Araujo
- Laboratório de Hematologia E Células-Tronco, Departamento de Ciências da Saúde, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brasil.
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22
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Alsfouk A. Pyrazine-based small molecule kinase inhibitors: clinical applications and patent review (2019-2023). Future Med Chem 2024; 16:1899-1921. [PMID: 39189138 PMCID: PMC11485930 DOI: 10.1080/17568919.2024.2385293] [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: 01/20/2024] [Accepted: 07/17/2024] [Indexed: 08/28/2024] Open
Abstract
Protein kinases play a key role in cellular signaling pathways including proliferation, apoptosis, inflammation and immune regulation. Therefore, targeting kinases with small molecules has emerged as a therapeutic potential in cancers and other diseases including inflammatory and autoimmune disorders. The main chemical motifs of the available small molecule kinase inhibitors are heterocyclic, nitrogen-containing and six-membered rings including pyrazine. Several potent and selective pyrazine-based kinase inhibitors have been developed and progressed into clinical trials. The data of clinical application of kinase inhibitors demonstrate good clinical activity with manageable toxicity in several relapse-resistant malignancies and severe to moderate immunological disorders. All pyrazine-based kinase inhibitors are orally active. This paper reviews the most recent kinase literature (2019-2023) related to pyrazine-based small molecule inhibitors. This review includes the FDA (Food and Drug Administration)-approved and patent agents along with their targeted kinase, scaffold, potency, selectivity profile, assignee and biological results in clinical and preclinical studies.
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Affiliation(s)
- Aisha Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
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23
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Li Y, Qu J, Jiang L, Peng X, Wu K, Chen M, Peng Y, Cao X. Application and challenges of nitrogen heterocycles in PROTAC linker. Eur J Med Chem 2024; 273:116520. [PMID: 38788299 DOI: 10.1016/j.ejmech.2024.116520] [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: 02/28/2024] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
The absence of effective active pockets makes traditional molecularly targeted drug strategies ineffective against 80 % of human disease-related proteins. The PROTAC technology effectively makes up for the deficiency of traditional molecular targeted drugs, which produces drug activity by degrading rather than inhibiting the target protein. The degradation of PROTAC is not only affected by POI ligand and E3 ligand, but by the selection of suitable linker which can play an important role in the efficiency and selectivity of the degradation. In the early exploring stage of the PROTAC, flexible chains were priorly applied as the linker of PROTAC. Although PROTAC with flexible chains as linkers sometimes perform well in vitro bioactivity evaluations, the introduction of lipophilic flexible chains reduces the hydrophilicity of these molecules, resulting in generally poor pharmacokinetic characteristics and pharmacological activities in vivo. In addition, recent reports have also shown that some PROTAC with flexible chains have some risks to causing hemolysis in vivo. Therefore, PROTAC with flexible chains show less druggability and large difficulty to entering the clinical trial stage. On the other hand, the application of nitrogen heterocycles in the design of PROTAC linkers has been widely reported in recent years. More and more reports have shown that the introduction of nitrogen heterocycles in the linker not only can effectively improves the metabolism of PROTAC in vivo, but also can enhance the degradation efficiency and selectivity of PROTAC. These PROTAC with nitrogen heterocycle linkers have attracted much attention of pharmaceutical chemists. The introduction of nitrogen heterocycles in the linker deserves priority consideration in the primary design of the PROTAC based on various druggabilities including pharmacokinetic characteristics and pharmacological activity. In this work, we summarized the optimization process and progress of nitrogen heterocyclic rings as the PROTAC linker in recent years. However, there were still limited understanding of how to discover, design and optimize PROTAC. For example, the selection of the types of nitrogen heterocycles and the optimization sites of this linker are challenges for researchers, choosing between four to six-membered nitrogen heterocycles, selecting from saturated to unsaturated ones, and even optimizing the length and extension angle of the linker. There is a truly need for theoretical explanation and elucidation of the PROTAC to guide the developing of more effective and valuable PROTAC.
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Affiliation(s)
- Yang Li
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Junfeng Qu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lizhi Jiang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Kaiyue Wu
- Department of Pharmacy, Ezhou Central Hospital, Ezhou, Hubei, China
| | - Miaojia Chen
- Department of Pharmacy, The First People's Hospital, Pingjiang, Yueyang, Hunan, China
| | - Yuanyuan Peng
- School of Electrical and Automation Engineering, East China Jiaotong University, Nanchang, 330000, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China.
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24
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Allawi MM, Razzak Mahmood AA, Tahtamouni LH, Saleh AM, Kanaan SI, Saleh KM, AlSakhen MF, Himsawi N, Yasin SR. Anti-proliferation evaluation of new derivatives of indole-6-carboxylate ester as receptor tyrosine kinase inhibitors. Future Med Chem 2024; 16:1313-1331. [PMID: 39109434 PMCID: PMC11318749 DOI: 10.1080/17568919.2024.2347084] [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: 01/27/2024] [Accepted: 04/10/2024] [Indexed: 08/10/2024] Open
Abstract
Aim: The main goal was to create two new groups of indole derivatives, hydrazine-1-carbothioamide (4a and 4b) and oxadiazole (5, and 6a-e) that target EGFR (4a, 4b, 5) or VEGFR-2 (6a-e). Materials & methods: The new derivatives were characterized using various spectroscopic techniques. Docking studies were used to investigate the binding patterns to EGFR/VEGFR-2, and the anti-proliferative properties were tested in vitro. Results: Compounds 4a (targeting EGFR) and 6c (targeting VEGFR-2) were the most effective cytotoxic agents, arresting cancer cells in the G2/M phase and inducing the extrinsic apoptosis pathway. Conclusion: The results of this study show that compounds 4a and 6c are promising cytotoxic compounds that inhibit the tyrosine kinase activity of EGFR and VEGFR-2, respectively.
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Affiliation(s)
- Mustafa M Allawi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Uruk university, Baghdad, Iraq
| | - Ammar A Razzak Mahmood
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Baghdad, Bab-Al-Mouadam, 10001, Baghdad, Iraq
| | - Lubna H Tahtamouni
- Department of Biology & Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
- Department of Biochemistry & Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Abdulrahman M Saleh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11884, Egypt
- Aweash El-Hagar Family Medicine Center, Epidemiological Surveillance Unit, MOHP, Mansoura, 35711, Egypt
| | - Sana I Kanaan
- Department of Biology & Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Khaled M Saleh
- Department of Biology & Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Mai F AlSakhen
- Department of Biology & Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Nisreen Himsawi
- Department of Microbiology, Pathology & Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Salem R Yasin
- Department of Biology & Biotechnology, Faculty of Science, The Hashemite University, Zarqa, Jordan
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25
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Royet C, Diot S, Onofre M, Lecki L, Pastore M, Reynes C, Lorcy F, Lacheretzszablewski V, Serre I, Morris MC. Multiplexed Profiling of CDK Kinase Activities in Tumor Biopsies with Fluorescent Peptide Biosensors. ACS Sens 2024; 9:2964-2978. [PMID: 38863434 DOI: 10.1021/acssensors.4c00139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Detection of disease biomarkers constitutes a major challenge for the development of personalized and predictive diagnostics as well as companion assays. Protein kinases (PKs) involved in the coordination of cell cycle progression and proliferation that are hyperactivated in human cancers constitute attractive pharmacological targets and relevant biomarkers. Although it is relatively straightforward to assess the relative abundance of PKs in a biological sample, there is not always a direct correlation with enzymatic activity, which is regulated by several posttranslational mechanisms. Studies of relative abundance therefore convey limited information, and the lack of selective, sensitive, and standardized tools together with the inherent complexity of biological samples makes it difficult to quantify PK activities in physio-pathological tissues. To address this challenge, we have developed a toolbox of fluorescent biosensors that report on CDK activities in a sensitive, selective, dose-dependent, and quantitative fashion, which we have implemented to profile CDK activity signatures in cancer cell lines and biopsies from human tumors. In this study, we report on a standardized and calibrated biosensing approach to quantify CDK1,2,4, and 6 activities simultaneously through a combination of four different biosensors in a panel of 40 lung adenocarcinoma and 40 follicular lymphoma samples. CDK activity profiling highlighted two major patterns which were further correlated with age, sex of patients, tumor size, grade, and genetic and immunohistochemical features of the biopsies. Multiplex CDKACT biosensing technology provides new and complementary information relative to current genetic and immunohistochemical characterization of tumor biopsies, which will be useful for diagnostic purposes, potentially guiding therapeutic decision. These fluorescent peptide biosensors offer promise for personalized diagnostics based on kinase activity profiling.
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Affiliation(s)
- Chloé Royet
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Sébastien Diot
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Mélanie Onofre
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Lennard Lecki
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Manuela Pastore
- StatABio Facility─Biocampus, UAR 3426 CNRS─US 09 INSERM, Montpellier University, 141 rue de la Cardonille, 34094 Montpellier Cedex 05, France
| | - Christelle Reynes
- StatABio Facility─Biocampus, UAR 3426 CNRS─US 09 INSERM, Montpellier University, 141 rue de la Cardonille, 34094 Montpellier Cedex 05, France
| | - Frederique Lorcy
- University Hospital Centre Montpellier, 80 Av. Augustin Fliche, 34295 Montpellier, France
| | | | - Isabelle Serre
- University Hospital Centre Montpellier, 80 Av. Augustin Fliche, 34295 Montpellier, France
| | - May C Morris
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
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26
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Sayyah E, Oktay L, Tunc H, Durdagi S. Developing Dynamic Structure-Based Pharmacophore and ML-Trained QSAR Models for the Discovery of Novel Resistance-Free RET Tyrosine Kinase Inhibitors Through Extensive MD Trajectories and NRI Analysis. ChemMedChem 2024; 19:e202300644. [PMID: 38523069 DOI: 10.1002/cmdc.202300644] [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: 11/19/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024]
Abstract
Activation of RET tyrosine kinase plays a critical role in the pathogenesis of various cancers, including non-small cell lung cancer, papillary thyroid cancers, multiple endocrine neoplasia type 2A and 2B (MEN2A, MEN2B), and familial medullary thyroid cancer. Gene fusions and point mutations in the RET proto-oncogene result in constitutive activation of RET signaling pathways. Consequently, developing effective inhibitors to target RET is of utmost importance. Small molecules have shown promise as inhibitors by binding to the kinase domain of RET and blocking its enzymatic activity. However, the emergence of resistance due to single amino acid changes poses a significant challenge. In this study, a structure-based dynamic pharmacophore-driven approach using E-pharmacophore modeling from molecular dynamics trajectories is proposed to select low-energy favorable hypotheses, and ML-trained QSAR models to predict pIC50 values of compounds. For this aim, extensive small molecule libraries were screened using developed ligand-based models, and potent compounds that are capable of inhibiting RET activation were proposed.
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Affiliation(s)
- Ehsan Sayyah
- Computational Biology and Molecular Simulations Lab, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey
- Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey
| | - Lalehan Oktay
- Computational Biology and Molecular Simulations Lab, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey
- Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey
| | - Huseyin Tunc
- Department of Biostatistics and Medical Informatics, School of Medicine, Bahçeşehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Lab, Department of Biophysics, School of Medicine, Bahçeşehir University, Istanbul, Turkey
- Computational Drug Design Center (HITMER), Bahçeşehir University, Istanbul, Turkey
- Molecular Therapy Lab, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul, Turkey
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27
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Gentile G, Poggio T, Catalano A, Voutilainen M, Lahnalampi M, Andrade-Martinez M, Ma T, Sankowski R, Goncharenko L, Tholen S, Han K, Morgens DW, Prinz M, Lübbert M, Engel S, Hartmann TN, Cario G, Schrappe M, Lenk L, Stanulla M, Duyster J, Bronsert P, Bassik MC, Cleary ML, Schilling O, Heinäniemi M, Duque-Afonso J. Development of combination therapies with BTK inhibitors and dasatinib to treat CNS-infiltrating E2A-PBX1+/preBCR+ ALL. Blood Adv 2024; 8:2846-2860. [PMID: 38598725 PMCID: PMC11176965 DOI: 10.1182/bloodadvances.2023011582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 04/12/2024] Open
Abstract
ABSTRACT The t(1;19) translocation, encoding the oncogenic fusion protein E2A (TCF3)-PBX1, is involved in acute lymphoblastic leukemia (ALL) and associated with a pre-B-cell receptor (preBCR+) phenotype. Relapse in patients with E2A-PBX1+ ALL frequently occurs in the central nervous system (CNS). Therefore, there is a medical need for the identification of CNS active regimens for the treatment of E2A-PBX1+/preBCR+ ALL. Using unbiased short hairpin RNA (shRNA) library screening approaches, we identified Bruton tyrosine kinase (BTK) as a key gene involved in both proliferation and dasatinib sensitivity of E2A-PBX1+/preBCR+ ALL. Depletion of BTK by shRNAs resulted in decreased proliferation of dasatinib-treated E2A-PBX1+/preBCR+ cells compared with control-transduced cells. Moreover, the combination of dasatinib with BTK inhibitors (BTKi; ibrutinib, acalabrutinib, or zanubrutinib) significantly decreased E2A-PBX1+/preBCR+ human and murine cell proliferation, reduced phospholipase C gamma 2 (PLCG2) and BTK phosphorylation and total protein levels and increased disease-free survival of mice in secondary transplantation assays, particularly reducing CNS-leukemic infiltration. Hence, dasatinib with ibrutinib reduced pPLCG2 and pBTK in primary ALL patient samples, including E2A-PBX1+ ALLs. In summary, genetic depletion and pharmacological inhibition of BTK increase dasatinib effects in human and mouse with E2A-PBX1+/preBCR+ ALL across most of performed assays, with the combination of dasatinib and BTKi proving effective in reducing CNS infiltration of E2A-PBX1+/preBCR+ ALL cells in vivo.
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Affiliation(s)
- Gaia Gentile
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Teresa Poggio
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Antonella Catalano
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Minna Voutilainen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Marta Andrade-Martinez
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tobias Ma
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Roman Sankowski
- Department of Neuropathology, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lina Goncharenko
- Institute for Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Proteomics Platform – Core Facility, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefan Tholen
- Institute of Surgical Pathology, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Proteomics Platform – Core Facility, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kyuho Han
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - David W. Morgens
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Marco Prinz
- Department of Neuropathology, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signaling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sophia Engel
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tanja Nicole Hartmann
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Gunnar Cario
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Martin Schrappe
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lennart Lenk
- Department of Pediatrics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Martin Stanulla
- Department of Pediatrics, University Medical Center Hannover, Hannover, Germany
| | - Justus Duyster
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute of Surgical Pathology, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael C. Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Michael L. Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Oliver Schilling
- Institute for Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Proteomics Platform – Core Facility, University of Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jesús Duque-Afonso
- Department of Hematology and Oncology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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28
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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 PMCID: PMC11842024 DOI: 10.1126/science.adl2688] [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: 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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Li J, Gong C, Zhou H, Liu J, Xia X, Ha W, Jiang Y, Liu Q, Xiong H. Kinase Inhibitors and Kinase-Targeted Cancer Therapies: Recent Advances and Future Perspectives. Int J Mol Sci 2024; 25:5489. [PMID: 38791529 PMCID: PMC11122109 DOI: 10.3390/ijms25105489] [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: 04/16/2024] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Over 120 small-molecule kinase inhibitors (SMKIs) have been approved worldwide for treating various diseases, with nearly 70 FDA approvals specifically for cancer treatment, focusing on targets like the epidermal growth factor receptor (EGFR) family. Kinase-targeted strategies encompass monoclonal antibodies and their derivatives, such as nanobodies and peptides, along with innovative approaches like the use of kinase degraders and protein kinase interaction inhibitors, which have recently demonstrated clinical progress and potential in overcoming resistance. Nevertheless, kinase-targeted strategies encounter significant hurdles, including drug resistance, which greatly impacts the clinical benefits for cancer patients, as well as concerning toxicity when combined with immunotherapy, which restricts the full utilization of current treatment modalities. Despite these challenges, the development of kinase inhibitors remains highly promising. The extensively studied tyrosine kinase family has 70% of its targets in various stages of development, while 30% of the kinase family remains inadequately explored. Computational technologies play a vital role in accelerating the development of novel kinase inhibitors and repurposing existing drugs. Recent FDA-approved SMKIs underscore the importance of blood-brain barrier permeability for long-term patient benefits. This review provides a comprehensive summary of recent FDA-approved SMKIs based on their mechanisms of action and targets. We summarize the latest developments in potential new targets and explore emerging kinase inhibition strategies from a clinical perspective. Lastly, we outline current obstacles and future prospects in kinase inhibition.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (J.L.)
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Roskoski R. Combination immune checkpoint and targeted protein kinase inhibitors for the treatment of renal cell carcinomas. Pharmacol Res 2024; 203:107181. [PMID: 38614375 DOI: 10.1016/j.phrs.2024.107181] [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: 04/08/2024] [Accepted: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Kidney cancers comprise about 3% of all new malignancies in the United States. Renal cell carcinomas (RCCs) are the most common type of renal malignancy making up about 85% of kidney cancer cases. Signs and symptoms of renal cell carcinomas can result from local tumor growth, paraneoplastic syndromes, or distant metastases. The classic triad of presentation with flank pain, hematuria, and a palpable abdominal mass occurs in fewer than 10% of patients. Most diagnoses result from incidental imaging findings (ultrasonography or abdominal CT imaging) performed for another reason. Localized disease is treated by partial nephrectomy, total nephrectomy, or ablation (tumor destruction with heat or cold). When the tumors have metastasized, systemic therapy with protein-tyrosine kinase antagonists including sorafenib, sunitinib, pazopanib, and tivozanib that target vascular endothelial, platelet-derived, fibroblast, hepatocyte, and stem cell factor growth factor receptors (VEGFR, PDGFR, FGFR, MET, and Kit) were prescribed after 2005. The monoclonal antibody immune checkpoint inhibitor nivolumab (targeting programed cell death protein 1, PD1) was approved for the treatment of RCCs in 2015. It is usually used now in combination with ipilimumab (targeting CTLA-4) or cabozantinib (a multikinase blocker). Other combination therapies include pembrolizumab (targeting PD1) and axitinib (a VEGFR and PDGFR blocker) or lenvatinib (a multikinase inhibitor). Since the KEYNOTE-426 clinical trial, the use of immune checkpoint inhibitors in combination with protein-tyrosine kinase inhibitors is now the standard of care for most patients with metastatic renal cell carcinomas and monotherapies are used only in those individuals who cannot receive or tolerate immune checkpoint inhibitors.
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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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31
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Zhu N, Chen S, Jin Y, Wang M, Fang L, Xue L, Hua D, Zhang Z, Jia M, Hao M, Zhang C. Enhancing Glioblastoma Immunotherapy with Integrated Chimeric Antigen Receptor T Cells through the Re-Education of Tumor-Associated Microglia and Macrophages. ACS NANO 2024; 18:11165-11182. [PMID: 38626338 DOI: 10.1021/acsnano.4c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Glioblastoma (GBM) is an aggressive brain cancer that is highly resistant to treatment including chimeric antigen receptor (CAR)-T cells. Tumor-associated microglia and macrophages (TAMs) are major contributors to the immunosuppressive GBM microenvironment, which promotes tumor progression and treatment resistance. Hence, the modulation of TAMs is a promising strategy for improving the immunotherapeutic efficacy of CAR-T cells against GBM. Molecularly targeting drug pexidartinib (PLX) has been reported to re-educate TAMs toward the antitumorigenic M1-like phenotype. Here, we developed a cell-drug integrated technology to reversibly conjugate PLX-containing liposomes (PLX-Lip) to CAR-T cells and establish tumor-responsive integrated CAR-T cells (PLX-Lip/AZO-T cells) as a combination therapy for GBM. We used a mouse model of GBM to show that PLX-Lip was stably maintained on the surface of PLX-Lip/AZO-T cells in circulation and these cells could transmigrate across the blood-brain barrier and deposit PLX-Lip at the tumor site. The uptake of PLX-Lip by TAMs effectively re-educated them into the M1-like phenotype, which in turn boosted the antitumor function of CAR-T cells. GBM tumor growth was completely eradicated in 60% of the mice after receiving PLX-Lip/AZO-T cells and extended their overall survival time beyond 50 days; in comparison, the median survival time of mice in other treatment groups did not exceed 35 days. Overall, we demonstrated the successful fusion of CAR-T cells and small-molecule drugs with the cell-drug integrated technology. These integrated CAR-T cells provided a superior combination strategy for GBM treatment and presented a reference for the construction of integrated cell-based drugs.
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Affiliation(s)
- Nianci Zhu
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Sijia Chen
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Yu Jin
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Meng Wang
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Luyao Fang
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Lingjing Xue
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Dexiang Hua
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Ziyao Zhang
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Meng Jia
- School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Meixi Hao
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
| | - Can Zhang
- State Key Laboratory of Natural Medicines, Center of Advanced Pharmaceuticals and Biomaterials, China Pharmaceutical University, Nanjing 211198, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [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: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Maddeboina K, Yada B, Kumari S, McHale C, Pal D, Durden DL. Recent advances in multitarget-directed ligands via in silico drug discovery. Drug Discov Today 2024; 29:103904. [PMID: 38280625 DOI: 10.1016/j.drudis.2024.103904] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
To combat multifactorial refractory diseases, such as cancer, cardiovascular, and neurodegenerative diseases, multitarget drugs have become an emerging area of research aimed at 'synthetic lethality' (SL) relationships associated with drug-resistance mechanisms. In this review, we discuss the in silico design of dual and triple-targeted ligands, strategies by which specific 'warhead' groups are incorporated into a parent compound or scaffold with primary inhibitory activity against one target to develop one small molecule that inhibits two or three molecular targets in an effort to increase potency against multifactorial diseases. We also discuss the analytical exploration of structure-activity relationships (SARs), physicochemical properties, polypharmacology, scaffold feature extraction of US Food and Drug Administration (FDA)-approved multikinase inhibitors (MKIs), and updates regarding the clinical status of dual-targeted chemotypes.
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Affiliation(s)
- Krishnaiah Maddeboina
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA; Department of Biochemistry, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA.
| | - Bharath Yada
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Shikha Kumari
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Cody McHale
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Dhananjaya Pal
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Donald L Durden
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA; Department of Biochemistry, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA.
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Jeong E, Hong H, Lee YA, Kim KS. Potential Rheumatoid Arthritis-Associated Interstitial Lung Disease Treatment and Computational Approach for Future Drug Development. Int J Mol Sci 2024; 25:2682. [PMID: 38473928 PMCID: PMC11154459 DOI: 10.3390/ijms25052682] [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: 01/22/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by swelling in at least one joint. Owing to an overactive immune response, extra-articular manifestations are observed in certain cases, with interstitial lung disease (ILD) being the most common. Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is characterized by chronic inflammation of the interstitial space, which causes fibrosis and the scarring of lung tissue. Controlling inflammation and pulmonary fibrosis in RA-ILD is important because they are associated with high morbidity and mortality. Pirfenidone and nintedanib are specific drugs against idiopathic pulmonary fibrosis and showed efficacy against RA-ILD in several clinical trials. Immunosuppressants and disease-modifying antirheumatic drugs (DMARDs) with anti-fibrotic effects have also been used to treat RA-ILD. Immunosuppressants moderate the overexpression of cytokines and immune cells to reduce pulmonary damage and slow the progression of fibrosis. DMARDs with mild anti-fibrotic effects target specific fibrotic pathways to regulate fibrogenic cellular activity, extracellular matrix homeostasis, and oxidative stress levels. Therefore, specific medications are required to effectively treat RA-ILD. In this review, the commonly used RA-ILD treatments are discussed based on their molecular mechanisms and clinical trial results. In addition, a computational approach is proposed to develop specific drugs for RA-ILD.
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Affiliation(s)
- Eunji Jeong
- Department of Medicine, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea;
| | - Hyunseok Hong
- Yale College, Yale University, New Haven, CT 06520, USA;
- Department of Clinical Pharmacology and Therapeutics, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yeon-Ah Lee
- Division of Rheumatology, Department of Internal Medicine, Kyung Hee University Hospital, Seoul 02447, Republic of Korea;
| | - Kyoung-Soo Kim
- Department of Medicine, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea;
- Department of Clinical Pharmacology and Therapeutics, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
- East-West Bone & Joint Disease Research Institute, Kyung Hee University Hospital at Gangdong, Seoul 05278, Republic of Korea
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Mourya A, Prajapati N. Precision Deuteration in Search of Anticancer Agents: Approaches to Cancer Drug Discovery. Cancer Biother Radiopharm 2024; 39:1-18. [PMID: 37585602 DOI: 10.1089/cbr.2023.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
Cancer chemotherapy has been shifted from conventional cytotoxic drug therapy to selective and target-specific therapy after the findings about DNA changes and proteins that are responsible for cancer. A large number of newer drugs were discovered as targeted therapy for particular types of neoplastic disease. The initial discovery includes the development of the first in the category, imatinib, a Bcr-Abl tyrosine kinase inhibitor (TKI) for the treatment of chronic myelocytic leukemia in 2001. But the joy did not last for long as the drug developed a point mutation within the ABL1 kinase domain of BCR-ABL1, which subsequently led to the discovery of many other TKIs. Resistance was observed for newer TKIs a few years after their launching, but the use of TKIs in life-threatening cancer therapy is considered as far better compared with the risks of disease because of its target specificity and hence less toxicity. In search of a better anticancer agent, the physiochemical properties of the lead molecule have been modified for its efficacy toward disease and delay in the development of resistance. Deuteration in the drug molecule is one of such modifications that alter the pharmacokinetic properties, generally its metabolism, as compared with its pharmacodynamic effects. Precision deuteration in many anticancer drugs has been carried out to search for better drugs for cancer. In this review, the majority of anticancer drugs and molecules for which deuteration was applied to get better anticancer molecules were discussed. This review will provide a complete guide about the benefits of deuteration in cancer chemotherapy.
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MESH Headings
- Humans
- Drug Resistance, Neoplasm/genetics
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Imatinib Mesylate/therapeutic use
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Drug Discovery
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Affiliation(s)
- Aman Mourya
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Navnit Prajapati
- Faculty of Pharmacy, The Maharaja Sayajirao University of Baroda, Vadodara, India
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36
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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: 135] [Impact Index Per Article: 135.0] [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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Mushtaq A, Wu P, Naseer MM. Recent drug design strategies and identification of key heterocyclic scaffolds for promising anticancer targets. Pharmacol Ther 2024; 254:108579. [PMID: 38160914 DOI: 10.1016/j.pharmthera.2023.108579] [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: 10/05/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Cancer, a noncommunicable disease, is the leading cause of mortality worldwide and is anticipated to rise by 75% in the next two decades, reaching approximately 25 million cases. Traditional cancer treatments, such as radiotherapy and surgery, have shown limited success in reducing cancer incidence. As a result, the focus of cancer chemotherapy has switched to the development of novel small molecule antitumor agents as an alternate strategy for combating and managing cancer rates. Heterocyclic compounds are such agents that bind to specific residues in target proteins, inhibiting their function and potentially providing cancer treatment. This review focuses on privileged heterocyclic pharmacophores with potent activity against carbonic anhydrases and kinases, which are important anticancer targets. Evaluation of ongoing pre-clinical and clinical research of heterocyclic compounds with potential therapeutic value against a variety of malignancies as well as the provision of a concise summary of the role of heterocyclic scaffolds in various chemotherapy protocols have also been discussed. The main objective of the article is to highlight key heterocyclic scaffolds involved in recent anticancer drug design that demands further attention from the drug development community to find more effective and safer targeted small-molecule anticancer agents.
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Affiliation(s)
- Alia Mushtaq
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
| | - Muhammad Moazzam Naseer
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan; Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany.
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Zarei P, Ghasemi F. The Application of Artificial Intelligence and Drug Repositioning for the Identification of Fibroblast Growth Factor Receptor Inhibitors: A Review. Adv Biomed Res 2024; 13:9. [PMID: 38525398 PMCID: PMC10958741 DOI: 10.4103/abr.abr_170_23] [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: 05/18/2023] [Revised: 08/24/2023] [Accepted: 09/03/2023] [Indexed: 03/26/2024] Open
Abstract
Artificial intelligence talks about modeling intelligent behavior through a computer with the least human involvement. Drug repositioning techniques based on artificial intelligence accelerate the research process and decrease the cost of experimental studies. Dysregulation of fibroblast growth factor (FGF) receptors as the tyrosine kinase family of receptors plays a vital role in a wide range of malignancies. Because of their functional significance, they were considered promising drug targets for the therapy of various cancers. This review has summarized small molecules capable of inhibiting FGF receptors that progressed using artificial intelligence and repositioning drugs examined in clinical trials associated with cancer therapy. This review is based on a literature search in PubMed, Web of Science, Scopus EMBASE, and Google Scholar databases to gather the necessary information in each chapter by employing keywords like artificial intelligence, computational drug design, drug repositioning, and FGF receptor inhibitors. To achieve this goal, a spacious literature review of human studies in these fields-published over the last 20 decades-was performed. According to published reports, nonselective FGF receptor inhibitors can be used for cancer management, and multitarget kinase inhibitors are the first drug class approved due to more advanced clinical studies. For example, AZD4547 and BGJ398 are gradually entering the consumption cycle and are good options as combined treatments. Artificial intelligence and drug repositioning methods can help preselect suitable drug targets more successfully for future inhibition of carcinogenicity.
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Affiliation(s)
- Parvin Zarei
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fahimeh Ghasemi
- Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan, Iran
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Teuber A, Schulz T, Fletcher BS, Gontla R, Mühlenberg T, Zischinsky ML, Niggenaber J, Weisner J, Kleinbölting SB, Lategahn J, Sievers S, Müller MP, Bauer S, Rauh D. Avapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA. Nat Commun 2024; 15:63. [PMID: 38167404 PMCID: PMC10761696 DOI: 10.1038/s41467-023-44376-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Avapritinib is the only potent and selective inhibitor approved for the treatment of D842V-mutant gastrointestinal stromal tumors (GIST), the most common primary mutation of the platelet-derived growth factor receptor α (PDGFRA). The approval was based on the NAVIGATOR trial, which revealed overall response rates of more than 90%. Despite this transformational activity, patients eventually progress, mostly due to acquired resistance mutations or following discontinuation due to neuro-cognitive side effects. These patients have no therapeutic alternative and face a dismal prognosis. Notable, little is known about this drug's binding mode and its medicinal chemistry development, which is instrumental for the development of the next generation of drugs. Against this background, we solve the crystal structures of avapritinib in complex with wild-type and mutant PDGFRA and stem cell factor receptor (KIT), which provide evidence and understanding of inhibitor binding and lead to the identification of a sub-pocket (Gα-pocket). We utilize this information to design, synthesize and characterize avapritinib derivatives for the determination of key pharmacophoric features to overcome drug resistance and limit potential blood-brain barrier penetration.
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Grants
- BA 5214/1-2 Deutsche Forschungsgemeinschaft (German Research Foundation)
- This work was co-funded by the German Research Foundation (DFG; BA 5214/1-2 (SB) | RA 1055/3-2 (DR)), the State of North Rhine-Westphalia (NRW), the European Union (European Regional Development Fund: Investing In Your Future) (EFRE-800400), DDHD (Drug Discovery Hub Dortmund, (DR)), the German Federal Ministry of Education and Research (InCa (01ZX2201B, (DR)), the Mercator Research Center Ruhr (MERCUR), IGNITE (Ex-2021-0033, (DR and SB)) and was supported by the "Netzwerke 2021" program, an initiative of the Ministry of Culture and Science of the State of North Rhine-Westphalia (CANcer TARgeting, NW21-062C, (DR and SB)). This work was supported by the Swiss Light Source of the Paul Scherrer Institute (SLS, Villingen, Switzerland) and The European Synchrotron Radiation Facility (ESRF, Grenoble, France, proposal MX-2391, DOI: 10.15151/ESRF-ES-744176088 and DOI: 10.15151/ESRF-ES-925653639, (DR and MPM)).
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Affiliation(s)
- A Teuber
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - T Schulz
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - B S Fletcher
- Department of Medical Oncology and Sarcoma Center and West German Cancer Center, DKTK partner site Essen, German Cancer Consortium (DKTK), University Duisburg-Essen, Medical School, Essen, Germany
| | - R Gontla
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - T Mühlenberg
- Department of Medical Oncology and Sarcoma Center and West German Cancer Center, DKTK partner site Essen, German Cancer Consortium (DKTK), University Duisburg-Essen, Medical School, Essen, Germany
| | - M-L Zischinsky
- Lead Discovery Center GmbH, Department for in vitro ADME and PK, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - J Niggenaber
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - J Weisner
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - S B Kleinbölting
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - J Lategahn
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - S Sievers
- Compound Management and Screening Center, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - M P Müller
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany
| | - S Bauer
- Department of Medical Oncology and Sarcoma Center and West German Cancer Center, DKTK partner site Essen, German Cancer Consortium (DKTK), University Duisburg-Essen, Medical School, Essen, Germany
| | - D Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University and Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW), Otto-Hahn-Strasse 4a, 44227, Dortmund, Germany.
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40
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Du J. Study of Therapeutic Mechanisms of Bupi Yichang Formula against Colon Cancer Based on Network Pharmacology, Machine Learning, and Experimental Verification. Crit Rev Immunol 2024; 44:67-87. [PMID: 38421706 DOI: 10.1615/critrevimmunol.2023051509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Bupi Yichang formula (BPYCF) has shown the anti-cancer potential; however, its effects on colon cancer and the mechanisms remain unknown. This study intended to explore the effects of BPYC on colon cancer and its underlying mechanisms. BPYCF-related and colon cancer-related targets were acquired from public databases, followed by differentially expressed genes (DEG) identification. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using clusterProfiler. A protein-protein interaction (PPI) network was constructed using STRING database. CytoHubba and MCODE to screen the hub targets. A diagnostic model was built using random forest algorithm. Molecular docking was conducted using PyMOL and AutoDock. High-performance liquid chromatograph-mass spectrometry (HPLC-MS) analysis and in vitro validation were performed. Forty-six overlapping targets of BPYCF-related, colon cancer-related targets, and DEGs were obtained. GO and KEGG analyses showed that the targets were mainly enriched in response to lipopolysaccharide, neuronal cell body, protein serine/threonine/tyrosine, as well as C-type lectin receptor, NOD-like receptor, and TNF signaling pathways. Five targets were identified as the pivotal targets, among which, NOS3, CASP8, RIPK3, and TNFRSF10B were stably docked with the core active component, naringenin. Naringenin was also identified from the BPYCF sample through HPLC-MS analysis. In vitro experiments showed that BPYCF inhibited cell viability, reduced NOS3 expression, and elevated CASP8, RIPK3, and TNFRSF10B expression in colon cancer cells. BPYCF might treat colon cancer mainly by regulating NOS3, CASP8, RIPK3, and TN-FRSF10B. This study first revealed the therapeutic effects and mechanisms of BPYCF against colon cancer, paving the path for the development of targeted therapeutic strategies for this cancer in the clinic.
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Affiliation(s)
- Juan Du
- Beijing Friendship Hospital, Capital Medical University
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41
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Metwally K, Abo-Dya NE. Pyrrolo[2,3-D]Pyrimidines as EGFR and VEGFR Kinase Inhibitors: A Comprehensive SAR Review. Curr Med Chem 2024; 31:5918-5936. [PMID: 37581522 DOI: 10.2174/0929867331666230815115111] [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: 05/12/2023] [Revised: 06/17/2023] [Accepted: 07/25/2023] [Indexed: 08/16/2023]
Abstract
Tyrosine kinases are implicated in a wide array of cellular physiological processes, including cell signaling. The discovery of the BCR-ABL tyrosine kinase inhibitor imatinib and its FDA approval in 2001 paved the way for the development of small molecule chemical entities of diverse structural backgrounds as tyrosine kinase inhibitors for the treatment of various ailments. Two of the most prominent tyrosine kinases as drug targets are the epidermal growth factor receptor (EGFR) and the vascular endothelial growth factor receptor (VEGFR), as evidenced by the clinical success of their many inhibitors in the drug market. Among several other physiological roles, EGFR regulates epithelial tissue development and homeostasis, while VEGFR regulates tumor-induced angiogenesis. The pyrrolo[2,3-d]pyrimidine nucleus represents a deaza-isostere of adenine, the nitrogenous base of ATP. The recent introduction of many pyrrolo[2,3-d]pyrimidines to the drug market as tyrosine kinase inhibitors makes them a hot topic in the medicinal chemistry research area at the present time. This review article comprehensively sheds light on the structure-activity relationship (SAR) of pyrrolo[2,3-d]pyrimidines as EGFR and VEGFR tyrosine kinase inhibitors, aiming to provide help medicinal chemists in the design of future pyrrolopyrimidine kinase inhibitors.
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Affiliation(s)
- Kamel Metwally
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk 71491, Saudi Arabia
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Tabuk 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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Saini R, Kumari S, Singh A, Mishra A. From nature to cancer therapy: Evaluating the Streptomyces clavuligerus secondary metabolites for potential protein kinase inhibitors. J Cell Biochem 2024; 125:59-78. [PMID: 38047468 DOI: 10.1002/jcb.30501] [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: 09/13/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023]
Abstract
The study aimed to evaluate the antioxidant, protein kinase inhibitory (PKIs) potential, cytotoxicity activity of Streptomyces clavuligerus extract. DPPH assay revealed a robust free radical scavenging capacity (IC50 28.90 ± 0.24 µg/mL) of organic extract with a maximum inhibition percentage of 61 ± 1.04%. PKIs assay revealed the formation of a whitish bald zone by S. clavuligerus extracts which indicates the presence of PKIs. The cytotoxicity activity of organic fraction of extract through Sulforhodamine B assay on MCF-7, Hop-62, SiHa, and PC-3 cell lines demonstrated the lowest GI50 value against the MCF-7 cell line followed by the PC-3 cell line, showing potent growth inhibitory potential against human breast cancer and human prostate cancer cell line. HR-LCMS analysis identified multiple secondary metabolites from the organic and aqueous extracts of S. clavuligerus when incubated at 30°C under 200 rpm for 3 days. All the secondary metabolites were elucidated for their potential to inhibit RTKs by molecular docking, molecular dynamic simulation, MM/GBSA calculations, and free energy approach. It revealed the superior inhibitory potential of epirubicin (Epi) and dodecaprenyl phosphate-galacturonic acid (DPGA) against fibroblast growth factors receptor (FGFR). Epi also exhibited excellent inhibitory activity against the platelet-derived growth factor receptor (PDGFR), while DPGA effectively inhibited the vascular endothelial growth factor receptor. Additionally, the presence Epi in S. clavuligerus extract was validated through the HPLC technique. Thus, our findings highlight a superior inhibitory potential of Epi against FGFR and PDGFR RTKs than the FDA-approved drug.
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Affiliation(s)
- Ravi Saini
- Biomolecular Laboratory, School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Sonali Kumari
- Biomolecular Laboratory, School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
| | - Amit Singh
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Abha Mishra
- Biomolecular Laboratory, School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, India
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Roskoski R. Cost in the United States of FDA-approved small molecule protein kinase inhibitors used in the treatment of neoplastic and non-neoplastic diseases. Pharmacol Res 2024; 199:107036. [PMID: 38096958 DOI: 10.1016/j.phrs.2023.107036] [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: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Because genetic alterations including mutations, overexpression, translocations, and dysregulation of protein kinases are involved in the pathogenesis of many illnesses, this enzyme family is the target of many drug discovery programs worldwide. The FDA has approved 80 small molecule protein kinase inhibitors with 77 drugs orally bioavailable. The data indicate that 69 of these medicinals are approved for the management of neoplasms including solid tumors such as breast and lung cancer as well as non-solid tumors such as leukemia. Moreover, the remaining 11 drugs target non-neoplastic diseases including psoriasis, rheumatoid arthritis, and ulcerative colitis. The cost of drugs was obtained from www.pharmacychecker.com using the FDA label to determine the dosage and number of tablets required per day. This methodology excludes any private or governmental insurance coverage, which would cover the entire cost or more likely a fraction of the stated price. The average monthly cost for the treatment of neoplastic diseases was $17,900 with a price of $44,000 for futibatinib (used to treat cholangiocarcinomas with FGFR2 fusions) and minimum of $5100 for binimetinib (melanoma). The average monthly cost for the treatment of non-neoplastic diseases was $6800 with a maximum of $17,000 for belumosudil (graft vs. host disease) and a minimum of $200 for netarsudil eye drops (glaucoma). There is a negative correlation of the cost of the drugs and the incidence of the targeted disease. Many of these agents are or were designated as orphan drugs meaning that there are fewer than 200,000 potential patients in the United States.
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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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44
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Çoban G. Structure-based virtual screening and molecular dynamics simulations for detecting novel candidates for allosteric inhibition of EGFRT790M. J Biomol Struct Dyn 2024; 42:571-597. [PMID: 37029759 DOI: 10.1080/07391102.2023.2194425] [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: 11/08/2022] [Accepted: 03/17/2023] [Indexed: 04/09/2023]
Abstract
Structure-based virtual screening (SBVS) was applied to predict lead compounds for the allosteric inhibition of epidermal growth factor receptor (EGFR) by screening the library of chemical compounds prepared from the e-molecules chemical database. The library of chemical compounds consisting of 133,083 ligands was composed by evaluating the chemical and physical properties of e-molecules chemicals. The prepared library was screened by CCDC Gold software in the allosteric binding site of EGFRT790M using the library and virtual screening default parameters to filter out, respectively. The GOLD fitness scores 75 and 80 were selected as threshold values for the library and virtual screening processes, respectively. After the docking study, molecular dynamics simulations (MDS) of the top 25 compounds were built for calculating binding free energies from their MDS trajectories. MM-GBSA binding free energies for the compounds were computed from 20 ns MDS, 50 ns MDS and 200 ns MDS trajectories to filter out the candidates. Following MM-GBSA/MM-PBSA binding free energy calculations, six compounds were detected as the most promising candidates for allosteric inhibition of EGFRT790M. The dynamic behaviors of final compounds inside EGFR T790M were searched using structure stability, binding modes and energy decomposition analysis. Besides, the estimated inhibitors were exposed to docking study and MM-GBSA/MM-PBSA binding free energy calculations inside wild-type EGFR, respectively, to be determined their selectivity towards mutant form. Five of the estimated inhibitors displayed estimated selectivity towards EGFRT790M. Besides the ADMET properties of the estimated inhibitors were predicted by PreAdmet tools.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Güneş Çoban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Bornova, Izmir, Turkey
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45
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Lv X, Wang Z, Wang Z, Yin H, Xia Y, Jiang L, Liu Y. Avapritinib Carries the Risk of Drug Interaction via Inhibition of UDP-Glucuronyltransferase (UGT) 1A1. Curr Drug Metab 2024; 25:197-204. [PMID: 38803186 DOI: 10.2174/0113892002288312240521092054] [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: 11/28/2023] [Revised: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Avapritinib is the only drug for adult patients with PDGFRA exon 18 mutated unresectable or metastatic gastrointestinal stromal tumor (GIST). Although avapritinib has been approved by the FDA for four years, little is known about the risk of drug-drug interactions (DDIs) via UDP-glucuronyltransferases (UGTs) inhibition. OBJECTIVE The aim of the present study was to systematically evaluate the inhibitory effects of avapritinib against UGTs and to quantitatively estimate its potential DDIs risk in vivo. METHODS Recombinant human UGTs were employed to catalyze the glucuronidation of substrates in a range of concentrations of avapritinib. The kinetics analysis was performed to evaluate the inhibition types of avapritinib against UGTs. The quantitative prediction of DDIs was done using in vitro-in vivo extrapolation (IVIVE). RESULTS Avapritinib had a potent competitive inhibitory effect on UGT1A1. Quantitative prediction results showed that avapritinib administered at clinical doses might result in a 14.85% increase in area under the curve (AUC) of drugs primarily cleared by UGT1A1. Moreover, the Rgut value was calculated to be 18.44. CONCLUSION Avapritinib has the potential to cause intestinal DDIs via the inhibition of UGT1A1. Additional attention should be paid when avapritinib is coadministered with UGT1A1 substrates.
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Affiliation(s)
- Xin Lv
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Zhen Wang
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Zhe Wang
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hang Yin
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Yangliu Xia
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Lili Jiang
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
| | - Yong Liu
- School of Chemical Engineering, Ocean and Life Sciences, Dalian University of Technology, Panjin, 124221, China
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Silnitsky S, Rubin SJS, Zerihun M, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part I: Protein Kinase C Activation and Its Role in Cancer and Cardiovascular Diseases. Int J Mol Sci 2023; 24:17600. [PMID: 38139428 PMCID: PMC10743896 DOI: 10.3390/ijms242417600] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Protein kinases are one of the most significant drug targets in the human proteome, historically harnessed for the treatment of cancer, cardiovascular disease, and a growing number of other conditions, including autoimmune and inflammatory processes. Since the approval of the first kinase inhibitors in the late 1990s and early 2000s, the field has grown exponentially, comprising 98 approved therapeutics to date, 37 of which were approved between 2016 and 2021. While many of these small-molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP binding pocket have been massively successful for oncological indications, their poor selectively for protein kinase isozymes have limited them due to toxicities in their application to other disease spaces. Thus, recent attention has turned to the use of alternative allosteric binding mechanisms and improved drug platforms such as modified peptides to design protein kinase modulators with enhanced selectivity and other pharmacological properties. Herein we review the role of different protein kinase C (PKC) isoforms in cancer and cardiovascular disease, with particular attention to PKC-family inhibitors. We discuss translational examples and carefully consider the advantages and limitations of each compound (Part I). We also discuss the recent advances in the field of protein kinase modulators, leverage molecular docking to model inhibitor-kinase interactions, and propose mechanisms of action that will aid in the design of next-generation protein kinase modulators (Part II).
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Affiliation(s)
- Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel; (S.S.); (M.Z.)
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He S, Silva LD, Rutter GA, Lim GE. A high-throughput screening approach to discover potential colorectal cancer chemotherapeutics: Repurposing drugs to disrupt 14-3-3 protein-BAD interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571727. [PMID: 38168191 PMCID: PMC10760183 DOI: 10.1101/2023.12.14.571727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Inducing apoptosis in different types of cancer cells is an effective therapeutic strategy. However, the success of existing chemotherapeutics can be compromised by tumor cell resistance and systemic off-target effects. Therefore, the discovery of pro-apoptotic compounds with minimal systemic side-effects is crucial. 14-3-3 proteins are molecular scaffolds that serve as important regulators of cell survival. Our previous study demonstrated that 14-3-3ζ can sequester BAD, a pro-apoptotic member of the BCL-2 protein family, in the cytoplasm and prevent its translocation to mitochondria to inhibit the induction of apoptosis. Despite being a critical mechanism of cell survival, it is unclear whether disrupting 14-3-3 protein:BAD interactions could be harnessed as a chemotherapeutic approach. Herein, we established a BRET-based high-throughput drug screening approach (Z'-score= 0.52) capable of identifying molecules that can disrupt 14-3-3ζ:BAD interactions. An FDA-approved drug library containing 1971 compounds was used for screening, and the capacity of identified hits to induce cell death was examined in NIH3T3-fibroblasts and colorectal cancer cell lines, HT-29 and Caco-2. Our in vitro results suggest that terfenadine, penfluridol, and lomitapide could be potentially repurposed for treating colorectal cancer. Moreover, our screening method demonstrates the feasibility of identifying pro-apoptotic agents that can be applied towards conditions where aberrant cell growth or function are key determinants of disease pathogenesis.
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Affiliation(s)
- Siyi He
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Luis Delgadillo Silva
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Guy A. Rutter
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Department of Diabetes, Endocrinology and Medicine, Faculty of Medicine, Imperial College, London, UK
- LKC School of Medicine, Nanyang Technological College, Singapore, Republic of Singapore
| | - Gareth E. Lim
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
- Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
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Salama EE, Youssef MF, Aboelmagd A, Boraei ATA, Nafie MS, Haukka M, Barakat A, Sarhan AAM. Discovery of Potent Indolyl-Hydrazones as Kinase Inhibitors for Breast Cancer: Synthesis, X-ray Single-Crystal Analysis, and In Vitro and In Vivo Anti-Cancer Activity Evaluation. Pharmaceuticals (Basel) 2023; 16:1724. [PMID: 38139850 PMCID: PMC10748079 DOI: 10.3390/ph16121724] [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: 11/09/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
According to data provided by the World Health Organization (WHO), a total of 2.3 million women across the globe received a diagnosis of breast cancer in the year 2020, and among these cases, 685,000 resulted in fatalities. As the incidence of breast cancer statistics continues to rise, it is imperative to explore new avenues in the ongoing battle against this disease. Therefore, a number of new indolyl-hydrazones were synthesized by reacting the ethyl 3-formyl-1H-indole-2-carboxylate 1 with thiosemicarbazide, semicarbazide.HCl, 4-nitrophenyl hydrazine, 2,4-dinitrophenyl hydrazine, and 4-amino-5-(1H-indol-2-yl)-1,2,4-triazole-3-thione to afford the new hit compounds, which were assigned chemical structures as thiosemicarbazone 3, bis(hydrazine derivative) 5, semicarbzone 6, Schiff base 8, and the corresponding hydrazones 10 and 12 by NMR, elemental analysis, and X-ray single-crystal analysis. The MTT assay was employed to investigate the compounds' cytotoxicity against breast cancer cells (MCF-7). Cytotoxicity results disclosed potent IC50 values against MCF-7, especially compounds 5, 8, and 12, with IC50 values of 2.73 ± 0.14, 4.38 ± 0.23, and 7.03 ± 0.37 μM, respectively, compared to staurosproine (IC50 = 8.32 ± 0.43 μM). Consequently, the activities of compounds 5, 8, and 12 in relation to cell migration were investigated using the wound-healing test. The findings revealed notable wound-healing efficacy, with respective percentages of wound closure measured at 48.8%, 60.7%, and 51.8%. The impact of the hit compounds on cell proliferation was assessed by examining their apoptosis-inducing properties. Intriguingly, compound 5 exhibited a significant enhancement in cell death within MCF-7 cells, registering a notable increase of 39.26% in comparison to the untreated control group, which demonstrated only 1.27% cell death. Furthermore, the mechanism of action of compound 5 was scrutinized through testing against kinase receptors. The results revealed significant kinase inhibition, particularly against PI3K-α, PI3K-β, PI3K-δ, CDK2, AKT-1, and EGFR, showcasing promising activity, compared to standard drugs targeting these receptors. In the conclusive phase, through in vivo assay, compound 5 demonstrated a substantial reduction in tumor volume, decreasing from 106 mm³ in the untreated control to 56.4 mm³. Moreover, it significantly attenuated tumor proliferation by 46.9%. In view of these findings, the identified leads exhibit promises for potential development into future medications for the treatment of breast cancer, as they effectively hinder both cell migration and proliferation.
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Affiliation(s)
- Eid E. Salama
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (M.F.Y.); (A.A.); or (A.T.A.B.); (M.S.N.)
| | - Mohamed F. Youssef
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (M.F.Y.); (A.A.); or (A.T.A.B.); (M.S.N.)
| | - Ahmed Aboelmagd
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (M.F.Y.); (A.A.); or (A.T.A.B.); (M.S.N.)
| | - Ahmed T. A. Boraei
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (M.F.Y.); (A.A.); or (A.T.A.B.); (M.S.N.)
| | - Mohamed S. Nafie
- Department of Chemistry, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt; (M.F.Y.); (A.A.); or (A.T.A.B.); (M.S.N.)
- Department of Chemistry, College of Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Matti Haukka
- Department of Chemistry, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland;
| | - Assem Barakat
- Chemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed A. M. Sarhan
- Chemistry Department, Faculty of Science, Arish University, Al-Arish 45511, Egypt; or
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Kattar SD, Gulati A, Margrey KA, Keylor MH, Ardolino M, Yan X, Johnson R, Palte RL, McMinn SE, Nogle L, Su J, Xiao D, Piesvaux J, Lee S, Hegde LG, Woodhouse JD, Faltus R, Moy LY, Xiong T, Ciaccio PJ, Pearson K, Patel M, Otte KM, Leyns CEG, Kennedy ME, Bennett DJ, DiMauro EF, Fell MJ, Fuller PH. Discovery of MK-1468: A Potent, Kinome-Selective, Brain-Penetrant Amidoisoquinoline LRRK2 Inhibitor for the Potential Treatment of Parkinson's Disease. J Med Chem 2023; 66:14912-14927. [PMID: 37861679 DOI: 10.1021/acs.jmedchem.3c01486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Genetic mutation of the leucine-rich repeat kinase 2 (LRRK2) protein has been associated with Parkinson's disease (PD), a disabling and progressive neurodegenerative disorder that is devoid of efficacious disease-modifying therapies. Herein, we describe the invention of an amidoisoquinoline (IQ)-derived LRRK2 inhibitor lead chemical series. Knowledge-, structure-, and property-based drug design in concert with rigorous application of in silico calculations and presynthesis predictions enabled the prioritization of molecules with favorable CNS "drug-like" physicochemical properties. This resulted in the discovery of compound 8, which was profiled extensively before human ether-a-go-go (hERG) ion channel inhibition halted its progression. Strategic reduction of lipophilicity and basicity resulted in attenuation of hERG ion channel inhibition while maintaining a favorable CNS efflux transporter profile. Further structure- and property-based optimizations resulted in the discovery of preclinical candidate MK-1468. This exquisitely selective LRRK2 inhibitor has a projected human dose of 48 mg BID and a preclinical safety profile that supported advancement toward GLP toxicology studies.
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Affiliation(s)
- Solomon D Kattar
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Anmol Gulati
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kaila A Margrey
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mitchell H Keylor
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Michael Ardolino
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Xin Yan
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rebecca Johnson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Rachel L Palte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Spencer E McMinn
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lisa Nogle
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jing Su
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dong Xiao
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jennifer Piesvaux
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Susi Lee
- Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Laxminarayan G Hegde
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Janice D Woodhouse
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Robert Faltus
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Lily Y Moy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Tina Xiong
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Paul J Ciaccio
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Kara Pearson
- Merck & Co., Inc., 770 Sumneytown Pike., West Point, Pennsylvania 19486, United States
| | - Mayankbhai Patel
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Karin M Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Cheryl E G Leyns
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew E Kennedy
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | | | - Erin F DiMauro
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Matthew J Fell
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Peter H Fuller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
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50
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Xiang J, Wang Y, Wang W, Yu J, Zheng L, Hong Y, Shi L, Zhang C, Chen N, Xu J, Gong X, Zhang Z, Cui H, Zhou Q, Zhang D, Liu Y, Ke Y, Shen J, Xia G, Bai X. Design, synthesis, and pharmacological evaluation of quinazoline derivatives as novel and potent pan-JAK inhibitors. Bioorg Chem 2023; 140:106765. [PMID: 37582330 DOI: 10.1016/j.bioorg.2023.106765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023]
Abstract
Janus kinases (JAKs) play a critical role in modulating the function and expression of inflammatory cytokines related to rheumatoid arthritis (RA). Herein, we report the design, synthesis, and structure-activity relationships (SARs) of a series of novel quinazoline derivatives as JAK inhibitors. Among these inhibitors, compound 11n showed high potency against JAKs (JAK1/JAK2/JAK3/TYK2, IC50 = 0.40, 0.83, 2.10, 1.95 nM), desirable metabolic characters, and excellent pharmacokinetic properties. In collagen-induced arthritis (CIA) models, compound 11n exhibited significant reduction in joint swelling with good safety, which could be served as a potential therapeutic candidate for the treatment of inflammatory diseases.
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Affiliation(s)
- Jinbao Xiang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Yuji Wang
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Wanhe Wang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Jianxin Yu
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Lianyou Zheng
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Yuan Hong
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Lingling Shi
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Chunling Zhang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Na Chen
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Jia Xu
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Xuelian Gong
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Zhuoqi Zhang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Hongming Cui
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Qian Zhou
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Dapeng Zhang
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China
| | - Yanjun Liu
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Ying Ke
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Jingkang Shen
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China
| | - Guangxin Xia
- Central Research Institute, National Key Laboratory of Innovative Immunotherapy, Shanghai Pharmaceuticals Holding Co., Ltd., Shanghai 201203, PR China.
| | - Xu Bai
- The Center for Combinatorial Chemistry and Drug Discovery of Jilin University, The School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, PR China.
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