1
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Borude AS, Deshmukh SR, Tiwari SV, Kumar SH, Thopate SR. Design and synthesis of novel Thiazolo[5,4-b]pyridine derivatives as potent and selective EGFR-TK inhibitors targeting resistance Mutations in non-small cell lung cancer. Eur J Med Chem 2024; 276:116727. [PMID: 39094428 DOI: 10.1016/j.ejmech.2024.116727] [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: 06/04/2024] [Revised: 07/22/2024] [Accepted: 07/28/2024] [Indexed: 08/04/2024]
Abstract
A novel series of substituted thiazolo[5,4-b]pyridine analogues were rationally designed and synthesized via a multi-step synthetic pathway, including Suzuki cross-coupling reaction. The anticancer activity of all forty-five synthesized derivatives was evaluated against HCC827, H1975, and A549 cancer cell lines utilizing the standard MTT assay. A significant number of the thiazolo[5,4-b]pyridine derivatives exhibited potent anticancer activity. Notably, compounds 10b, 10c, 10h, 10i, and 10k emerged as the most promising anticancer agents. The lead compound, N-(3-(6-(2-aminopyrimidin-5-yl)thiazolo[5,4-b]pyridin-2-yl)-2-methylphenyl)-2,5-difluorobenzenesulfonamide (10k), displayed remarkable potency with IC50 values of 0.010 μM, 0.08 μM, and 0.82 μM against the HCC827, NCI-H1975 and A-549 cancer cell lines, respectively, which were comparable to the clinically approved drug Osimertinib. Importantly, the potent derivatives 10b, 10c, 10h, 10i, and 10k exhibited selective cytotoxicity towards cancer cells and showing no toxicity against the normal BEAS-2B cell line at concentrations exceeding 35 μM. Mechanistic studies revealed that the active compound 10k acts as an EGFR-TK autophosphorylation inhibitor in HCC827 cells. Furthermore, apoptosis assays demonstrated that compound 10k induced substantial early apoptosis (31.9 %) and late apoptosis (8.8 %) in cancer cells, in contrast to the control condition exhibiting only 2.0 % early and 1.6 % late apoptosis. Molecular docking simulations of the synthesized compounds revealed that they formed essential hinge interactions and established hydrogen bonding with Cys797, indicating potential target engagement. These findings highlight the potential of the synthesized thiazolo [(Woodburn, 1999; Zigrossi et al., 2022) 5,45,4-b]pyridine derivatives as promising anticancer agents, warranting further investigation for the development of novel targeted therapies against non-small cell lung cancer.
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Affiliation(s)
- Avinash S Borude
- Department of Chemistry, Radhabai Kale Mahila Mahavidyalay, Ahmednagar, Maharashtra, 414001, India
| | - Santosh R Deshmukh
- Department of Chemistry, Ahmednagar College, Ahmednagar, Maharashtra, 414001, India.
| | - Shailee V Tiwari
- Department of Pharmaceutical Chemistry, Shri Ramkrishna Paramhans College of Pharmacy, Hasnapur, Parbhani, Maharashtra, 431401, India
| | - S Hemant Kumar
- thinkMolecular Technologies Pvt. Ltd, Bangalore, 560102, India
| | - Shankar R Thopate
- Department of Chemistry, Radhabai Kale Mahila Mahavidyalay, Ahmednagar, Maharashtra, 414001, India.
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2
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Boonyarit B, Yamprasert N, Kaewnuratchadasorn P, Kinchagawat J, Prommin C, Rungrotmongkol T, Nutanong S. GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity. J Comput Chem 2024; 45:2001-2023. [PMID: 38713612 DOI: 10.1002/jcc.27388] [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: 01/08/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/09/2024]
Abstract
The proteins within the human epidermal growth factor receptor (EGFR) family, members of the tyrosine kinase receptor family, play a pivotal role in the molecular mechanisms driving the development of various tumors. Tyrosine kinase inhibitors, key compounds in targeted therapy, encounter challenges in cancer treatment due to emerging drug resistance mutations. Consequently, machine learning has undergone significant evolution to address the challenges of cancer drug discovery related to EGFR family proteins. However, the application of deep learning in this area is hindered by inherent difficulties associated with small-scale data, particularly the risk of overfitting. Moreover, the design of a model architecture that facilitates learning through multi-task and transfer learning, coupled with appropriate molecular representation, poses substantial challenges. In this study, we introduce GraphEGFR, a deep learning regression model designed to enhance molecular representation and model architecture for predicting the bioactivity of inhibitors against both wild-type and mutant EGFR family proteins. GraphEGFR integrates a graph attention mechanism for molecular graphs with deep and convolutional neural networks for molecular fingerprints. We observed that GraphEGFR models employing multi-task and transfer learning strategies generally achieve predictive performance comparable to existing competitive methods. The integration of molecular graphs and fingerprints adeptly captures relationships between atoms and enables both global and local pattern recognition. We further validated potential multi-targeted inhibitors for wild-type and mutant HER1 kinases, exploring key amino acid residues through molecular dynamics simulations to understand molecular interactions. This predictive model offers a robust strategy that could significantly contribute to overcoming the challenges of developing deep learning models for drug discovery with limited data and exploring new frontiers in multi-targeted kinase drug discovery for EGFR family proteins.
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Affiliation(s)
- Bundit Boonyarit
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Nattawin Yamprasert
- School of Information, Computer, and Communication Technology, Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, Thailand
| | | | - Jiramet Kinchagawat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Chanatkran Prommin
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sarana Nutanong
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
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3
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Lei S, Sun J, Xie Y, Xiao X, He X, Lin S, Zhang H, Huang Z, Wang H, Wu X, Peng H, Liu J. Diverse functions of Tribbles homolog 3 in cancers and its potential as a therapeutic target. Carcinogenesis 2024; 45:527-542. [PMID: 38902892 DOI: 10.1093/carcin/bgae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/11/2024] [Accepted: 06/20/2024] [Indexed: 06/22/2024] Open
Abstract
Currently, cancer is the second leading cause of death worldwide, and potential targeted drugs and molecular pathways for cancer development and progression have been a hot research topic worldwide. In recent years, the importance of the kinase superfamily in diseases has been well demonstrated by studies on various molecular mechanisms of kinases and the successful application of their inhibitors in diseases. Pseudokinases are members of the kinase superfamily, which have been increasingly documented to play a crucial role in cancers year after year. As a member of pseudokinases, tribbles homolog 3 (TRIB3) also exerts diverse functions in different cancers through different interacting proteins and molecular pathways, especially in tumor immunity, stemness, drug resistance, metabolism, and autophagy. In addition, peptide drugs targeting TRIB3 have high specificity in preclinical studies, which shows great promise for TRIB3 application in diseases including cancers. In this review, we dissect diverse functions played by TRIB3 in different cancers, describing the underlying mechanisms in detail. Notably, inhibitors and agonists currently available for TRIB3 are discussed, indicating the potential for TRIB3 as a therapeutic target.
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Affiliation(s)
- Shiying Lei
- The Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jiajun Sun
- The Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yifang Xie
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
| | - Xiaojuan Xiao
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
| | - Xiaofeng He
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China
| | - Sheng Lin
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China
| | - Huifang Zhang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Zineng Huang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Haiqin Wang
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
| | - Xusheng Wu
- Shenzhen Health Development Research and Data Management Center, Shenzhen 518028, China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Jing Liu
- Molecular Biology Research Center, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha 410006, China
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4
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Wang Y, Nan X, Duan Y, Wang Q, Liang Z, Yin H. FDA-approved small molecule kinase inhibitors for cancer treatment (2001-2015): Medical indication, structural optimization, and binding mode Part I. Bioorg Med Chem 2024; 111:117870. [PMID: 39128361 DOI: 10.1016/j.bmc.2024.117870] [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: 07/03/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024]
Abstract
The dysregulation of kinases has emerged as a major class of targets for anticancer drug discovery given its node roles in the etiology of tumorigenesis, progression, invasion, and metastasis of malignancies, which is validated by the FDA approval of 28 small molecule kinase inhibitor (SMKI) drugs for cancer treatment at the end of 2015. While the preclinical and clinical data of these drugs are widely presented, it is highly essential to give an updated review on the medical indications, design principles and binding modes of these anti-tumor SMKIs approved by the FDA to offer insights for the future development of SMKIs with specific efficacy and safety.
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Affiliation(s)
- Ying Wang
- Department of Electrophysiological Diagnosis, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong 723000, China
| | - Xiang Nan
- College of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China; Department of Stomatology, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Yanping Duan
- College of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Qiuxu Wang
- Department of Stomatology, Shenzhen Second People's Hospital, Shenzhen 518035, China.
| | - Zhigang Liang
- Department of Stomatology, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Hanrong Yin
- Department of Electrophysiological Diagnosis, 3201 Hospital of Xi'an Jiaotong University Health Science Center, Hanzhong 723000, China.
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5
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Ozgencil F, Gunindi HB, Eren G. Dual-targeted NAMPT inhibitors as a progressive strategy for cancer therapy. Bioorg Chem 2024; 149:107509. [PMID: 38824699 DOI: 10.1016/j.bioorg.2024.107509] [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: 03/09/2024] [Revised: 04/29/2024] [Accepted: 05/28/2024] [Indexed: 06/04/2024]
Abstract
In mammals, nicotinamide phosphoribosyltransferase (NAMPT) is a crucial enzyme in the nicotinamide adenine dinucleotide (NAD+) synthesis pathway catalyzing the condensation of nicotinamide (NAM) with 5-phosphoribosyl-1-pyrophosphate (PRPP) to produce nicotinamide mononucleotide (NMN). Given the pivotal role of NAD+ in a range of cellular functions, including DNA synthesis, redox reactions, cytokine generation, metabolism, and aging, NAMPT has become a promising target for many diseases, notably cancer. Therefore, various NAMPT inhibitors have been reported and classified as first and second-generation based on their chemical structures and design strategies, dual-targeted being one. However, most NAMPT inhibitors suffer from several limitations, such as dose-dependent toxicity and poor pharmacokinetic properties. Consequently, there is no clinically approved NAMPT inhibitor. Hence, research on discovering more effective and less toxic dual-targeted NAMPT inhibitors with desirable pharmacokinetic properties has drawn attention recently. This review summarizes the previously reported dual-targeted NAMPT inhibitors, focusing on their design strategies and advantages over the single-targeted therapies.
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Affiliation(s)
- Fikriye Ozgencil
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye
| | - Habibe Beyza Gunindi
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye
| | - Gokcen Eren
- SIRTeam Group, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Ankara, Türkiye.
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6
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Wang ZH, Zheng X, Rao GW, Zheng Q. Targeted small molecule therapy and inhibitors for lymphoma. Future Med Chem 2024:1-20. [PMID: 39016063 DOI: 10.1080/17568919.2024.2359893] [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: 10/07/2023] [Accepted: 05/21/2024] [Indexed: 07/18/2024] Open
Abstract
Lymphoma, a blood tumor, has become the ninth most common cancer in the world in 2020. Targeted inhibition is one of the important treatments for lymphoma. At present, there are many kinds of targeted drugs for the treatment of lymphoma. Studies have shown that Histone deacetylase, Bruton's tyrosine kinase and phosphoinositide 3-kinase all play an important role in the occurrence and development of tumors and become important and promising inhibitory targets. This article mainly expounds the important role of these target protein in tumors, and introduces the mechanism of action, structure-activity relationship and clinical research of listed small molecule inhibitors of these targets, hoping to provide new ideas for the treatment of lymphoma.
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Affiliation(s)
- Zhong-Hui Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Xiang Zheng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Guo-Wu Rao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Quan Zheng
- Core Facility,The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou 324000, P. R. China
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7
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Ewes WA, Tawfik SS, Almatary AM, Ahmad Bhat M, El-Shafey HW, Mohamed AAB, Haikal A, El-Magd MA, Elgazar AA, Balaha M, Hamdi A. Identification of Benzothiazoles Bearing 1,3,4-Thiadiazole as Antiproliferative Hybrids Targeting VEGFR-2 and BRAF Kinase: Design, Synthesis, BIO Evaluation and In Silico Study. Molecules 2024; 29:3186. [PMID: 38999138 PMCID: PMC11243196 DOI: 10.3390/molecules29133186] [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: 06/07/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
Cancer remains a leading cause of death worldwide, often resulting from uncontrolled growth in various organs. Protein kinase inhibitors represent an important class of targeted cancer therapies. Recently, the kinases BRAF and VEGFR-2 have shown synergistic effects on tumor progression. Seeking to develop dual BRAF/VEGFR-2 inhibitors, we synthesized 18 amino-benzothiazole derivatives with structural similarities to reported dual inhibitors. Four compounds-4a, 4f, 4l, and 4r-demonstrated remarkable cytotoxicity, with IC50 values ranging from 3.58 to 15.36 μM, against three cancer cell lines. Furthermore, these compounds showed IC50 values of 38.77-66.22 μM in the case of a normal cell line, which was significantly safer than the reference, sorafenib. Subsequent investigation revealed that compound 4f exhibited the capacity to inhibit the BRAF and VEGFR-2 enzymes, with IC50 values similar to sorafenib (0.071 and 0.194 μM, respectively). Moreover, compound 4f caused G2-M- and S-phase cycle arrest. Molecular modeling demonstrated binding patterns compatible with inhibition for both targets, where 4f exerted the critical interactions in the BRAF site and interacted in the VEGFR-2 site in a manner akin to sorafenib, demonstrating affinity similar to dabrafenib.
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Affiliation(s)
- Wafaa A Ewes
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Samar S Tawfik
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Aya M Almatary
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Hamed W El-Shafey
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Ahmed A B Mohamed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abdullah Haikal
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohammed A El-Magd
- Department of Anatomy, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Abdullah A Elgazar
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Marwa Balaha
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Via dei Vestini, 31, 66100 Chieti, Italy
| | - Abdelrahman Hamdi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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8
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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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9
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Zhou J, Xia M, Huang Z, Qiao H, Yang G, Qian Y, Li P, Zhang Z, Gao X, Jiang L, Wang J, Li W, Fang P. Structure-guided conversion from an anaplastic lymphoma kinase inhibitor into Plasmodium lysyl-tRNA synthetase selective inhibitors. Commun Biol 2024; 7:742. [PMID: 38890421 PMCID: PMC11189516 DOI: 10.1038/s42003-024-06455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) play a central role in the translation of genetic code, serving as attractive drug targets. Within this family, the lysyl-tRNA synthetase (LysRS) constitutes a promising antimalarial target. ASP3026, an anaplastic lymphoma kinase (ALK) inhibitor was recently identified as a novel Plasmodium falciparum LysRS (PfLysRS) inhibitor. Here, based on cocrystal structures and biochemical experiments, we developed a series of ASP3026 analogues to improve the selectivity and potency of LysRS inhibition. The leading compound 36 showed a dissociation constant of 15.9 nM with PfLysRS. The inhibitory efficacy on PfLysRS and parasites has been enhanced. Covalent attachment of L-lysine to compound 36 resulted in compound 36K3, which exhibited further increased inhibitory activity against PfLysRS but significantly decreased activity against ALK. However, its inhibitory activity against parasites did not improve, suggesting potential future optimization directions. This study presents a new example of derivatization of kinase inhibitors repurposed to inhibit aaRS.
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Affiliation(s)
- Jintong Zhou
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Mingyu Xia
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zhenghui Huang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Hang Qiao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Guang Yang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Yunan Qian
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Peifeng Li
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Zhaolun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Xinai Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Lubin Jiang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Jing Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Pengfei Fang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.
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10
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Yuan Y, Tang X, Li H, Lang X, Li C, Song Y, Sun S, Yang Y, Zhou Z. KLSD: a kinase database focused on ligand similarity and diversity. Front Pharmacol 2024; 15:1400136. [PMID: 38957398 PMCID: PMC11217335 DOI: 10.3389/fphar.2024.1400136] [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: 03/14/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024] Open
Abstract
Due to the similarity and diversity among kinases, small molecule kinase inhibitors (SMKIs) often display multi-target effects or selectivity, which have a strong correlation with the efficacy and safety of these inhibitors. However, due to the limited number of well-known popular databases and their restricted data mining capabilities, along with the significant scarcity of databases focusing on the pharmacological similarity and diversity of SMIKIs, researchers find it challenging to quickly access relevant information. The KLIFS database is representative of specialized application databases in the field, focusing on kinase structure and co-crystallised kinase-ligand interactions, whereas the KLSD database in this paper emphasizes the analysis of SMKIs among all reported kinase targets. To solve the current problem of the lack of professional application databases in kinase research and to provide centralized, standardized, reliable and efficient data resources for kinase researchers, this paper proposes a research program based on the ChEMBL database. It focuses on kinase ligands activities comparisons. This scheme extracts kinase data and standardizes and normalizes them, then performs kinase target difference analysis to achieve kinase activity threshold judgement. It then constructs a specialized and personalized kinase database platform, adopts the front-end and back-end separation technology of SpringBoot architecture, constructs an extensible WEB application, handles the storage, retrieval and analysis of the data, ultimately realizing data visualization and interaction. This study aims to develop a kinase database platform to collect, organize, and provide standardized data related to kinases. By offering essential resources and tools, it supports kinase research and drug development, thereby advancing scientific research and innovation in kinase-related fields. It is freely accessible at: http://ai.njucm.edu.cn:8080.
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Affiliation(s)
- Yuqian Yuan
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaozhu Tang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongyan Li
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xufeng Lang
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Can Li
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yihua Song
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shanliang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ye Yang
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zuojian Zhou
- School of Artificial Intelligence and Information Technology, Nanjing University of Chinese Medicine, Nanjing, China
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11
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Mulder IA, Abbinanti M, Woller SA, Ruschel J, Coutinho JM, de Vries HE, van Bavel E, Rosen K, McKerracher L, Ayata C. The novel ROCK2 selective inhibitor NRL-1049 preserves the blood-brain barrier after acute injury. J Cereb Blood Flow Metab 2024:271678X241238845. [PMID: 38833563 DOI: 10.1177/0271678x241238845] [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] [Indexed: 06/06/2024]
Abstract
Endothelial blood-brain barrier (BBB) dysfunction is critical in the pathophysiology of brain injury. Rho-associated protein kinase (ROCK) activation disrupts BBB integrity in the injured brain. We aimed to test the efficacy of a novel ROCK2 inhibitor in preserving the BBB after acute brain injury. We characterized the molecular structure and pharmacodynamic and pharmacokinetic properties of a novel selective ROCK2 inhibitor, NRL-1049, and its first metabolite, 1-hydroxy-NRL-1049 (referred to as NRL-2017 hereon) and tested the efficacy of NRL-1049 on the BBB integrity in rodent models of acute brain injury. Our data show that NRL-1049 and NRL-2017 both inhibit ROCK activity and are 44-fold and 17-fold more selective towards ROCK2 than ROCK1, respectively. When tested in a mouse model of cortical cryoinjury, NRL-1049 significantly attenuated the increase in water content. Interestingly, 60% of the mice in the vehicle arm developed seizures within 2 hours after cryoinjury versus none in the NRL-1049 arm. In spontaneously hypertensive rats, NRL-1049 attenuated the dramatic surge in Evans Blue extravasation compared with the vehicle arm after transient middle cerebral artery occlusion. Hemorrhagic transformation was also reduced. We show that NRL-1049, a selective ROCK2 inhibitor, is a promising drug candidate to preserve the BBB after brain injury.
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Affiliation(s)
- Inge A Mulder
- Neurovascular Research Unit, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedical Engineering and Physics, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
- Amsterdam Neurosciences, Neurovascular Disorders, Amsterdam, the Netherlands
| | | | | | | | - Jonathan M Coutinho
- Amsterdam Neurosciences, Neurovascular Disorders, Amsterdam, the Netherlands
- Department of Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
| | - Helga E de Vries
- Amsterdam Neurosciences, Neurovascular Disorders, Amsterdam, the Netherlands
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | - Ed van Bavel
- Department of Biomedical Engineering and Physics, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
- Amsterdam Neurosciences, Neurovascular Disorders, Amsterdam, the Netherlands
| | | | - Lisa McKerracher
- BioAxone BioSciences Inc, Boston, MA, USA
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Cenk Ayata
- Neurovascular Research Unit, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Stroke Service, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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12
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Basciu A, Athar M, Kurt H, Neville C, Malloci G, Muredda FC, Bosin A, Ruggerone P, Bonvin AMJJ, Vargiu AV. Predicting binding events in very flexible, allosteric, multi-domain proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597018. [PMID: 38895346 PMCID: PMC11185556 DOI: 10.1101/2024.06.02.597018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Knowledge of the structures formed by proteins and small ligands is of fundamental importance for understanding molecular principles of chemotherapy and for designing new and more effective drugs. Due to the still high costs and to the several limitations of experimental techniques, it is most often desirable to predict these ligand-protein complexes in silico, particularly when screening for new putative drugs from databases of millions of compounds. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology aimed at generating bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites. Validation was performed on the enzyme adenylate kinase (ADK), a paradigmatic example of proteins that undergo very large conformational changes upon ligand binding. By only exploiting the unbound structure and the putative binding sites of the protein, we generated a significant fraction of bound-like structures, which employed in ensemble-docking calculations allowed to find native-like poses of substrates, inhibitors, and catalytically incompetent binders. Our protocol provides a general framework for the generation of bound-like conformations of flexible proteins that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening for difficult targets, prediction of the impact of amino acid mutations on structure and dynamics, and protein engineering.
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Affiliation(s)
- Andrea Basciu
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Mohd Athar
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Han Kurt
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Christine Neville
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Giuliano Malloci
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Fabrizio C. Muredda
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Andrea Bosin
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
| | - Alexandre M. J. J. Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Attilio V. Vargiu
- Physics Department, University of Cagliari, Cittadella Universitaria, I-09042 Monserrato (CA), Italy
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13
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Halimi G, Osmaniye D, Özkay Y, Kaplancıklı ZA. Development and assessment of novel pyrazole-thiadiazol hybrid derivatives as VEGFR-2 inhibitors: design, synthesis, anticancer activity evaluation, molecular docking, and molecular dynamics simulation. Z NATURFORSCH C 2024; 0:znc-2024-0067. [PMID: 38818683 DOI: 10.1515/znc-2024-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
Cancer remains a significant health challenge globally, requiring the development of targeted chemotherapeutics capable of specifically inhibiting cancer cell growth. Angiogenesis is one of the key features of tumor growth and metastasis and is, therefore, an important target for the treatment of many tumors. The vascular endothelial growth factor (VEGF) signaling pathway has proven to be a promising lead in anticancer therapy due to the central role it plays in tumor angiogenesis. Vascular endothelial growth factor receptor-2 (VEGFR-2) is a key mediator in the signaling pathway regulating angiogenesis. Targeting VEGFR-2 may disrupt angiogenesis, leading to a reduction in tumor blood supply and tumor progression. The design, synthesis, and assessment of novel VEGFR-2 inhibitor derivatives are the focus of this study, with particular emphasis on incorporating the pyrazole-thiadiazol pharmacophore into the molecular structure. Taking advantage of the pharmacophoric properties of pyrazole and 1,3,4-thiadiazol, compounds with different substituents in the main structure were designed and synthesized. The compounds were also evaluated for antiproliferative activity against cancer cell lines. Compound 4e demonstrated the highest activity among all compounds, with an IC50 of 9.673 ± 0.399 μM against HT-29 cells and 23.081 ± 0.400 μM against NIH3T3 cells. To further support the inhibitory activity of compound 4e, an in silico study was performed. Compound 4e demonstrated strong binding to the active site of VEGFR-2 in molecular docking studies, forming hydrogen bonds with key amino acid residues. The stability of the compound in the enzyme's active site was demonstrated through molecular dynamics simulations.
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Affiliation(s)
- Gresa Halimi
- Department of Pharmaceutical Chemistry, 52944 Faculty of Pharmacy, Anadolu University , 26470 Eskişehir, Türkiye
- 52944 Institute of Graduate Education, Anadolu University , 26470 Eskişehir, Türkiye
| | - Derya Osmaniye
- Department of Pharmaceutical Chemistry, 52944 Faculty of Pharmacy, Anadolu University , 26470 Eskişehir, Türkiye
- 52944 Central Analysis Laboratory, Faculty of Pharmacy, Anadolu University , 26470 Eskişehir, Türkiye
| | - Yusuf Özkay
- Department of Pharmaceutical Chemistry, 52944 Faculty of Pharmacy, Anadolu University , 26470 Eskişehir, Türkiye
- 52944 Central Analysis Laboratory, Faculty of Pharmacy, Anadolu University , 26470 Eskişehir, Türkiye
| | - Zafer Asım Kaplancıklı
- Department of Pharmaceutical Chemistry, 52944 Faculty of Pharmacy, Anadolu University , 26470 Eskişehir, Türkiye
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14
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Halder P, Rai A, Talukdar V, Das P, Lakkaniga NR. Pyrazolopyridine-based kinase inhibitors for anti-cancer targeted therapy. RSC Med Chem 2024; 15:1452-1470. [PMID: 38784451 PMCID: PMC11110789 DOI: 10.1039/d4md00003j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/24/2024] [Indexed: 05/25/2024] Open
Abstract
The need for effective cancer treatments continues to be a challenge for the biomedical research community. In this case, the advent of targeted therapy has significantly improved therapeutic outcomes. Drug discovery and development efforts targeting kinases have resulted in the approval of several small-molecule anti-cancer drugs based on ATP-mimicking heterocyclic cores. Pyrazolopyridines are a group of privileged heterocyclic cores in kinase drug discovery, which are present in several inhibitors that have been developed against various cancers. Notably, selpercatinib, glumetinib, camonsertib and olverembatinib have either received approval or are in late-phase clinical studies. This review presents the success stories employing pyrazolopyridine scaffolds as hinge-binding cores to address various challenges in kinase-targeted drug discovery research.
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Affiliation(s)
- Pallabi Halder
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Anubhav Rai
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Vishal Talukdar
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Naga Rajiv Lakkaniga
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (Indian School of Mines) Dhanbad India
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15
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Budipramana K, Sangande F. Structural and molecular insights from dual inhibitors of EGFR and VEGFR2 as a strategy to improve the efficacy of cancer therapy. Chem Biol Drug Des 2024; 103:e14534. [PMID: 38697951 DOI: 10.1111/cbdd.14534] [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: 11/21/2023] [Revised: 03/29/2024] [Accepted: 04/19/2024] [Indexed: 05/05/2024]
Abstract
Epidermal growth factor receptor (EGFR) and vascular endothelial growth factor 2 (VEGFR2) are known as valid targets for cancer therapy. Overexpression of EGFR induces uncontrolled cell proliferation and VEGF expression triggering angiogenesis via VEGFR2 signaling. On the other hand, VEGF expression independent of EGFR signaling is already known as one of the mechanisms of resistance to anti-EGFR therapy. Therefore, drugs that act as dual inhibitors of EGFR and VEGFR2 can be a solution to the problem of drug resistance and increase the effectiveness of therapy. In this review, we summarize the relationship between EGFR and VEGFR2 signal transduction in promoting cancer growth and how their kinase domain structures can affect the selectivity of an inhibitor as the basis for designing dual inhibitors. In addition, several recent studies on the development of dual EGFR and VEGFR2 inhibitors involving docking simulations were highlighted in this paper to provide some references such as pharmacophore features of inhibitors and key residues for further research, especially in computer-aided drug design.
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Affiliation(s)
- Krisyanti Budipramana
- Department of Pharmaceutical Biology, Faculty of Pharmacy, University of Surabaya, Surabaya, Indonesia
| | - Frangky Sangande
- Research Center for Pharmaceutical Ingredient and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong Science Center, Bogor, Indonesia
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16
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Grogan L, Shapiro P. Progress in the development of ERK1/2 inhibitors for treating cancer and other diseases. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2024; 100:181-207. [PMID: 39034052 DOI: 10.1016/bs.apha.2024.04.001] [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: 07/23/2024]
Abstract
The extracellular signal-regulated kinases-1 and 2 (ERK1/2) are ubiquitous regulators of many cellular functions, including proliferation, differentiation, migration, and cell death. ERK1/2 regulate cell functions by phosphorylating a diverse collection of protein substrates consisting of other kinases, transcription factors, structural proteins, and other regulatory proteins. ERK1/2 regulation of cell functions is tightly regulated through the balance between activating phosphorylation by upstream kinases and inactivating dephosphorylation by phosphatases. Disruption of homeostatic ERK1/2 regulation caused by elevated extracellular signals or mutations in upstream regulatory proteins leads to the constitutive activation of ERK1/2 signaling and uncontrolled cell proliferation observed in many types of cancer. Many inhibitors of upstream kinase regulators of ERK1/2 have been developed and are part of targeted therapeutic options to treat a variety of cancers. However, the efficacy of these drugs in providing sustained patient responses is limited by the development of acquired resistance often involving re-activation of ERK1/2. As such, recent drug discovery efforts have focused on the direct targeting of ERK1/2. Several ATP competitive ERK1/2 inhibitors have been identified and are being tested in cancer clinical trials. One drug, Ulixertinib (BVD-523), has received FDA approval for use in the Expanded Access Program for patients with no other therapeutic options. This review provides an update on ERK1/2 inhibitors in clinical trials, their successes and limitations, and new academic drug discovery efforts to modulate ERK1/2 signaling for treating cancer and other diseases.
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Affiliation(s)
- Lena Grogan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States
| | - Paul Shapiro
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, United States.
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17
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Zhang H, Xu D, Huang H, Jiang H, Hu L, Liu L, Sun G, Gao J, Li Y, Xia C, Chen S, Zhou H, Kong X, Wang M, Luo C. Discovery of a Covalent Inhibitor Selectively Targeting the Autophosphorylation Site of c-Src Kinase. ACS Chem Biol 2024; 19:999-1010. [PMID: 38513196 DOI: 10.1021/acschembio.4c00048] [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: 03/23/2024]
Abstract
Nonreceptor tyrosine kinase c-Src plays a crucial role in cell signaling and contributes to tumor progression. However, the development of selective c-Src inhibitors turns out to be challenging. In our previous study, we performed posttranslational modification-inspired drug design (PTMI-DD) to provide a plausible way for designing selective kinase inhibitors. In this study, after identifying a unique pocket comprising a less conserved cysteine and an autophosphorylation site in c-Src as well as a promiscuous covalent inhibitor, chemical optimization was performed to obtain (R)-LW-Srci-8 with nearly 75-fold improved potency (IC50 = 35.83 ± 7.21 nM). Crystallographic studies revealed the critical C-F···C═O interactions that may contribute to tight binding. The kinact and Ki values validated the improved binding affinity and decreased warhead reactivity of (R)-LW-Srci-8 for c-Src. Notably, in vitro tyrosine kinase profiling and cellular activity-based protein profiling (ABPP) cooperatively indicated a specific inhibition of c-Src by (R)-LW-Srci-8. Intriguingly, (R)-LW-Srci-8 preferentially binds to inactive c-Src with unphosphorylated Y419 both in vitro and in cells, subsequently disrupting the autophosphorylation. Collectively, our study demonstrated the feasibility of developing selective kinase inhibitors by cotargeting a nucleophilic residue and a posttranslational modification site and providing a chemical probe for c-Src functional studies.
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Affiliation(s)
- Huimin Zhang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Dounan Xu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai 200444, China
| | - Hongchan Huang
- Center for Chemical Biology and Drug Discovery, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hao Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Linghao Hu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
| | - Liping Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Ge Sun
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jing Gao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Yuanqing Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Cuicui Xia
- Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Shijie Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Hu Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Xiangqian Kong
- Center for Chemical Biology and Drug Discovery, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528437, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
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18
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Du M, Xie X, Luo J, Li J. Meta-learning-based Inductive logistic matrix completion for prediction of kinase inhibitors. J Cheminform 2024; 16:44. [PMID: 38627866 PMCID: PMC11301988 DOI: 10.1186/s13321-024-00838-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/31/2024] [Indexed: 08/09/2024] Open
Abstract
Protein kinases become an important source of potential drug targets. Developing new, efficient, and safe small-molecule kinase inhibitors has become an important topic in the field of drug research and development. In contrast with traditional wet experiments which are time-consuming and expensive, machine learning-based approaches for predicting small molecule inhibitors for protein kinases are time-saving and cost-effective, which are highly desired for us. However, the issue of sample scarcity (known active and inactive compounds are usually limited for most kinases) poses a challenge to the research and development of machine learning-based kinase inhibitors' active prediction methods. To alleviate the data scarcity problem in the prediction of kinase inhibitors, in this study, we present a novel Meta-learning-based inductive logistic matrix completion method for the Prediction of Kinase Inhibitors (MetaILMC). MetaILMC adopts a meta-learning framework to learn a well-generalized model from tasks with sufficient samples, which can fast adapt to new tasks with limited samples. As MetaILMC allows the effective transfer of the prior knowledge learned from kinases with sufficient samples to kinases with a small number of samples, the proposed model can produce accurate predictions for kinases with limited data. Experimental results show that MetaILMC has excellent performance for prediction tasks of kinases with few-shot samples and is significantly superior to the state-of-the-art multi-task learning in terms of AUC, AUPR, etc., various performance metrics. Case studies also provided for two drugs to predict Kinase Inhibitory scores, further validating the proposed method's effectiveness and feasibility. SCIENTIFIC CONTRIBUTION: Considering the potential correlation between activity prediction tasks for different kinases, we propose a novel meta learning algorithm MetaILMC, which learns a prior of strong generalization capacity during meta-training from the tasks with sufficient training samples, such that it can be easily and quickly adapted to the new tasks of the kinase with scarce data during meta-testing. Thus, MetaILMC can effectively alleviate the data scarcity problem in the prediction of kinase inhibitors.
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Affiliation(s)
- Ming Du
- School of Software, Yunnan University, Kunming, 650091, China
| | - XingRan Xie
- School of Software, Yunnan University, Kunming, 650091, China
| | - Jing Luo
- State Key Laboratory for Conservation and Utilization of Bio-Resource, School of Ecology and Environment and School of Life Sciences, Yunnan University, Kunming, 650091, Yunnan, China
| | - Jin Li
- School of Software, Yunnan University, Kunming, 650091, China.
- The Key Laboratory of Software Engineering of Yunnan Province, Kunming, 650091, China.
- The Cloud Computing Engineering Research Center of Yunnan Province, Kunming, 650091, China.
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19
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Zhang X, Duan X, Liu X. The role of kinases in peripheral nerve regeneration: mechanisms and implications. Front Neurol 2024; 15:1340845. [PMID: 38689881 PMCID: PMC11058862 DOI: 10.3389/fneur.2024.1340845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Peripheral nerve injury disease is a prevalent traumatic condition in current medical practice. Despite the present treatment approaches, encompassing surgical sutures, autologous nerve or allograft nerve transplantation, tissue engineering techniques, and others, an effective clinical treatment method still needs to be discovered. Exploring novel treatment methods to improve peripheral nerve regeneration requires more effort in investigating the cellular and molecular mechanisms involved. Many factors are associated with the regeneration of injured peripheral nerves, including the cross-sectional area of the injured nerve, the length of the nerve gap defect, and various cellular and molecular factors such as Schwann cells, inflammation factors, kinases, and growth factors. As crucial mediators of cellular communication, kinases exert regulatory control over numerous signaling cascades, thereby participating in various vital biological processes, including peripheral nerve regeneration after nerve injury. In this review, we examined diverse kinase classifications, distinct nerve injury types, and the intricate mechanisms involved in peripheral nerve regeneration. Then we stressed the significance of kinases in regulating autophagy, inflammatory response, apoptosis, cell cycle, oxidative processes, and other aspects in establishing conductive microenvironments for nerve tissue regeneration. Finally, we briefly discussed the functional roles of kinases in different types of cells involved in peripheral nerve regeneration.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, School of Life Science, Nantong Laboratory of Development and Diseases, Medical College, Clinical Medical Research Center, Affiliated Wuxi Clinical College of Nantong University, Nantong University, Nantong, China
- Clinical Medical Research Center, Wuxi No. 2 People's Hospital, Jiangnan University Medical Center, Wuxi, China
| | - Xuchu Duan
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, School of Life Science, Nantong Laboratory of Development and Diseases, Medical College, Clinical Medical Research Center, Affiliated Wuxi Clinical College of Nantong University, Nantong University, Nantong, China
| | - Xiaoyu Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, School of Life Science, Nantong Laboratory of Development and Diseases, Medical College, Clinical Medical Research Center, Affiliated Wuxi Clinical College of Nantong University, Nantong University, Nantong, China
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20
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Helmy SWA, Abdel-Aziz AK, Dokla EME, Ahmed TE, Hatem Y, Abdel Rahman EA, Sharaky M, Shahin MI, Elrazaz EZ, Serya RAT, Henary M, Ali SS, Abou El Ella DA. Novel sulfonamide-indolinone hybrids targeting mitochondrial respiration of breast cancer cells. Eur J Med Chem 2024; 268:116255. [PMID: 38401190 DOI: 10.1016/j.ejmech.2024.116255] [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: 01/14/2024] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Breast cancer (BC) still poses a threat worldwide which demands continuous efforts to present safer and efficacious treatment options via targeted therapy. Beside kinases' aberrations as Aurora B kinase which controls cell division, BC adopts distinct metabolic profiles to meet its high energy demands. Accordingly, targeting both aurora B kinase and/or metabolic vulnerability presents a promising approach to tackle BC. Based on a previously reported indolinone-based Aurora B kinase inhibitor (III), and guided by structural modification and SAR investigation, we initially synthesized 11 sulfonamide-indolinone hybrids (5a-k), which showed differential antiproliferative activities against the NCI-60 cell line panel with BC cells displaying preferential sensitivity. Nonetheless, modest activity against Aurora B kinase (18-49% inhibition) was noted at 100 nM. Screening of a representative derivative (5d) against 17 kinases, which are overexpressed in BC, failed to show significant activity at 1 μM concentration, suggesting that kinase inhibitory activity only played a partial role in targeting BC. Bioinformatic analyses of genome-wide transcriptomics (RNA-sequencing), metabolomics, and CRISPR loss-of-function screens datasets suggested that indolinone-completely responsive BC cell lines (MCF7, MDA-MB-468, and T-47D) were more dependent on mitochondrial oxidative phosphorylation (OXPHOS) compared to partially responsive BC cell lines (MDA-MB-231, BT-549, and HS 578 T). An optimized derivative, TC11, obtained by molecular hybridization of 5d with sunitinib polar tail, manifested superior antiproliferative activity and was used for further investigations. Indeed, TC11 significantly reduced/impaired the mitochondrial respiration, as well as mitochondria-dependent ROS production of MCF7 cells. Furthermore, TC11 induced G0/G1 cell cycle arrest and apoptosis of MCF7 BC cells. Notably, anticancer doses of TC11 did not elicit cytotoxic effects on normal cardiomyoblasts and hepatocytes. Altogether, these findings emphasize the therapeutic potential of targeting the metabolic vulnerability of OXPHOS-dependent BC cells using TC11 and its related sulfonamide-indolinone hybrids. Further investigation is warranted to identify their precise/exact molecular target.
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Affiliation(s)
- Sama W A Helmy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Amal Kamal Abdel-Aziz
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt; Smart Health Initiative, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Eman M E Dokla
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt.
| | - Tarek E Ahmed
- Department of Chemistry and Center of Diagnostics and Therapeutics, Georgia State University, 100 Piedmont Avenue SE, Atlanta, GA, 30303, USA
| | - Yasmin Hatem
- Research Department, 57357 Children's Cancer Hospital Egypt, Cairo, 4260102, Egypt
| | - Engy A Abdel Rahman
- Research Department, 57357 Children's Cancer Hospital Egypt, Cairo, 4260102, Egypt; Department of Pharmacology, Faculty of Medicine, Assiut University, Assiut, 71515, Egypt
| | - Marwa Sharaky
- Cancer Biology Department, Pharmacology Unit, National Cancer Institute (NCI), Cairo University, Cairo, 11796, Egypt
| | - Mai I Shahin
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Eman Z Elrazaz
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Rabah A T Serya
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt
| | - Maged Henary
- Department of Chemistry and Center of Diagnostics and Therapeutics, Georgia State University, 100 Piedmont Avenue SE, Atlanta, GA, 30303, USA
| | - Sameh S Ali
- Research Department, 57357 Children's Cancer Hospital Egypt, Cairo, 4260102, Egypt
| | - Dalal A Abou El Ella
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, Cairo, 11566, Egypt.
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21
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Tomović Pavlović K, Kocić G, Šmelcerović A. Myt1 kinase inhibitors - Insight into structural features, offering potential frameworks. Chem Biol Interact 2024; 391:110901. [PMID: 38331334 DOI: 10.1016/j.cbi.2024.110901] [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: 11/27/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
The cell cycle includes two checkpoint arrests allowing to repair of damaged DNA. Many cancer cell lines exhibit weak G1 checkpoint mechanisms relying significantly more on the G2 checkpoint than do healthy cells. Inhibition of Myt1 kinase (PKMYT1), a forgotten member of the Wee family, cyclin-dependent kinase 1 (Cdk1) inhibitory kinase, target for G2 checkpoint abrogation, whose inhibition forces cells into premature unchecked mitosis resulting in cell death, is a promising concept for anticancer therapy. There are not many inhibitors of this emerging, potentially clinically important kinase. Herein, the valuable insight into structural features and binding mechanisms of diaminopyrimidines, aminoquinolines, quinazolines, pyrido[2,3-d]pyrimidines, pyrazolo[3,4-d]pyrimidines, and pyrrolo[2,3-b]quinoxalines, as well as finally made a general scheme of fragmented structures of Myt1 inhibitors with the enzyme, offer potential frameworks useful for future directions, for further chemical optimizations, in the discovery and the design of novel effective structures, potential therapeutics.
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Affiliation(s)
- Katarina Tomović Pavlović
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia.
| | - Gordana Kocić
- Department of Biochemistry, Faculty of Medicine, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia
| | - Andrija Šmelcerović
- Department of Chemistry, Faculty of Medicine, University of Niš, Bulevar Dr Zorana Đinđića 81, 18000, Niš, Serbia.
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22
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Șandor A, Fizeșan I, Ionuț I, Marc G, Moldovan C, Oniga I, Pîrnău A, Vlase L, Petru AE, Macasoi I, Oniga O. Discovery of A Novel Series of Quinazoline-Thiazole Hybrids as Potential Antiproliferative and Anti-Angiogenic Agents. Biomolecules 2024; 14:218. [PMID: 38397456 PMCID: PMC10886515 DOI: 10.3390/biom14020218] [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: 01/31/2024] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Considering the pivotal role of angiogenesis in solid tumor progression, we developed a novel series of quinazoline-thiazole hybrids (SA01-SA07) as antiproliferative and anti-angiogenic agents. Four out of the seven compounds displayed superior antiproliferative activity (IC50 =1.83-4.24 µM) on HepG2 cells compared to sorafenib (IC50 = 6.28 µM). The affinity towards the VEGFR2 kinase domain was assessed through in silico prediction by molecular docking, molecular dynamics studies, and MM-PBSA. The series displayed a high degree of similarity to sorafenib regarding the binding pose within the active site of VEGFR2, with a different orientation of the 4-substituted-thiazole moieties in the allosteric pocket. Molecular dynamics and MM-PBSA evaluations identified SA05 as the hybrid forming the most stable complex with VEGFR2 compared to sorafenib. The impact of the compounds on vascular cell proliferation was assessed on EA.hy926 cells. Six compounds (SA01-SA05, SA07) displayed superior anti-proliferative activity (IC50 = 0.79-5.85 µM) compared to sorafenib (IC50 = 6.62 µM). The toxicity was evaluated on BJ cells. Further studies of the anti-angiogenic effect of the most promising compounds, SA04 and SA05, through the assessment of impact on EA.hy296 motility using a wound healing assay and in ovo potential in a CAM assay compared to sorafenib, led to the confirmation of the anti-angiogenic potential.
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Affiliation(s)
- Alexandru Șandor
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Ionel Fizeșan
- Department of Toxicology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Ioana Ionuț
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Gabriel Marc
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Cristina Moldovan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
| | - Ilioara Oniga
- Department of Pharmacognosy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 12 Ion Creangă Street, 400010 Cluj-Napoca, Romania;
| | - Adrian Pîrnău
- National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donath Street, 400293 Cluj-Napoca, Romania;
| | - Laurian Vlase
- Department of Pharmaceutical Technology and Biopharmaceutics, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babeș, Street, 400012 Cluj-Napoca, Romania;
| | - Andreea-Elena Petru
- Department of Toxicology, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 8 Victor Babeș Street, 400012 Cluj-Napoca, Romania;
| | - Ioana Macasoi
- Department of Toxicology, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babes” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, “Iuliu Hațieganu” University of Medicine and Pharmacy, 41 Victor Babes, Street, 400010 Cluj-Napoca, Romania; (A.Ș.); (I.I.); (G.M.); (C.M.); (O.O.)
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23
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Roskoski R. Properties of FDA-approved small molecule protein kinase inhibitors: A 2024 update. Pharmacol Res 2024; 200:107059. [PMID: 38216005 DOI: 10.1016/j.phrs.2024.107059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
Owing to the dysregulation of protein kinase activity in many diseases including cancer, this enzyme family has become one of the most important drug targets in the 21st century. There are 80 FDA-approved therapeutic agents that target about two dozen different protein kinases and seven of these drugs were approved in 2023. Of the approved drugs, thirteen target protein-serine/threonine protein kinases, four are directed against dual specificity protein kinases (MEK1/2), twenty block nonreceptor protein-tyrosine kinases, and 43 inhibit receptor protein-tyrosine kinases. The data indicate that 69 of these drugs are prescribed for the treatment of neoplasms. Six drugs (abrocitinib, baricitinib, deucravacitinib, ritlecitinib, tofacitinib, upadacitinib) are used for the treatment of inflammatory diseases (atopic dermatitis, rheumatoid arthritis, psoriasis, alopecia areata, and ulcerative colitis). Of the 80 approved drugs, nearly two dozen are used in the treatment of multiple diseases. The following seven drugs received FDA approval in 2023: capivasertib (HER2-positive breast cancer), fruquintinib (metastatic colorectal cancer), momelotinib (myelofibrosis), pirtobrutinib (mantle cell lymphoma, chronic lymphocytic leukemia, small lymphocytic lymphoma), quizartinib (Flt3-mutant acute myelogenous leukemia), repotrectinib (ROS1-positive lung cancer), and ritlecitinib (alopecia areata). All of the FDA-approved drugs are orally effective with the exception of netarsudil, temsirolimus, and trilaciclib. This review summarizes the physicochemical properties of all 80 FDA-approved small molecule protein kinase inhibitors including the molecular weight, number of hydrogen bond donors/acceptors, polar surface area, potency, solubility, lipophilic efficiency, and ligand efficiency.
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Affiliation(s)
- Robert Roskoski
- Blue Ridge Institute for Medical Research, 221 Haywood Knolls Drive, Hendersonville, NC 28791, United States.
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24
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Mugiya T, Mothibe M, Khathi A, Ngubane P, Sibiya N. Glycaemic abnormalities induced by small molecule tryosine kinase inhibitors: a review. Front Pharmacol 2024; 15:1355171. [PMID: 38362147 PMCID: PMC10867135 DOI: 10.3389/fphar.2024.1355171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024] Open
Abstract
In light of the expected increase in the prevalence of diabetes mellitus due to an aging population, sedentary lifestyles, an increase in obesity, and unhealthy diets, there is a need to identify potential pharmacological agents that can heighten the risk of developing diabetes. Similarly, it is equally important to also identify those agents that show blood glucose-lowering properties. Amongst these agents are tyrosine kinase inhibitors used to treat certain types of cancers. Over the last two decades, there has been an increase in the use of targeted chemotherapy for cancers such as renal cell carcinoma, chronic leukaemia, and gastrointestinal stromal tumours. Small molecule tyrosine kinase inhibitors have been at the forefront of targeted chemotherapy. Studies have shown that small molecule tyrosine kinase inhibitors can alter glycaemic control and glucose metabolism, with some demonstrating hypoglycaemic activities whilst others showing hyperglycaemic properties. The mechanism by which small molecule tyrosine kinase inhibitors cause glycaemic dysregulation is not well understood, therefore, the clinical significance of these chemotherapeutic agents on glucose handling is also poorly documented. In this review, the effort is directed at mapping mechanistic insights into the effect of various small molecule tyrosine kinase inhibitors on glycaemic dysregulation envisaged to provide a deeper understanding of these chemotherapeutic agents on glucose metabolism. Small molecule tyrosine kinase inhibitors may elicit these observed glycaemic effects through preservation of β-cell function, improving insulin sensitivity and insulin secretion. These compounds bind to a spectrum of receptors and proteins implicated in glucose regulation for example, non-receptor tyrosine kinase SRC and ABL. Then receptor tyrosine kinase EGFR, PDGFR, and FGFR.
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Affiliation(s)
- Takudzwa Mugiya
- Pharmacology Division, Faculty of Pharmacy, Rhodes University, Makhanda, South Africa
| | - Mamosheledi Mothibe
- Pharmacology Division, Faculty of Pharmacy, Rhodes University, Makhanda, South Africa
| | - Andile Khathi
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Phikelelani Ngubane
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Ntethelelo Sibiya
- Pharmacology Division, Faculty of Pharmacy, Rhodes University, Makhanda, South Africa
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25
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Eissa IH, Elkady H, Rashed M, Elwan A, Hagras M, Dahab MA, Taghour MS, Ibrahim IM, Husein DZ, Elkaeed EB, Al-ghulikah HA, Metwaly AM, Mahdy HA. Discovery of new thiazolidine-2,4-dione derivatives as potential VEGFR-2 inhibitors: In vitro and in silico studies. Heliyon 2024; 10:e24005. [PMID: 38298627 PMCID: PMC10828660 DOI: 10.1016/j.heliyon.2024.e24005] [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: 10/06/2023] [Revised: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024] Open
Abstract
In this study, a series of seven novel 2,4-dioxothiazolidine derivatives with potential anticancer and VEGFR-2 inhibiting abilities were designed and synthesized as VEGFR-2 inhibitors. The synthesized compounds were tested in vitro for their potential to inhibit VEGFR-2 and the growth of HepG2 and MCF-7 cancer cell lines. Among the compounds tested, compound 22 (IC50 = 0.079 μM) demonstrated the highest anti-VEGFR-2 efficacy. Furthermore, it demonstrated significant anti-proliferative activities against HepG2 (IC50 = 2.04 ± 0.06 μM) and MCF-7 (IC50 = 1.21 ± 0.04 M). Additionally, compound 22 also increased the total apoptotic rate of the MCF-7 cancer cell lines with cell cycle arrest at S phase. As well, computational methods were applied to study the VEGFR-2-22 complex at the molecular level. Molecular docking and molecular dynamics (MD) simulations were used to investigate the complex's structural and kinetic characteristics. The DFT calculations further revealed the structural and electronic properties of compound 22. Finally, computational ADMET and toxicity tests were performed indicating the likeness of the proposed compounds to be drugs. The results suggest that compound 22 displays promise as an effective anticancer treatment and can serve as a model for future structural modifications and biological investigations in this field.
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Affiliation(s)
- Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Mahmoud Rashed
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Alaa Elwan
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Mohamed Hagras
- Department of Pharmaceutical Organic Chemistry, College of Pharmacy, Al-Azhar University, Cairo, 11884, Egypt
| | - Mohammed A. Dahab
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Mohammed S. Taghour
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Dalal Z. Husein
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja, 72511, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, 13713, Saudi Arabia
| | - Hanan A. Al-ghulikah
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
| | - Hazem A. Mahdy
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, 11884, Egypt
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26
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Chen Y, Sonawane A, Manda R, Gadi RK, Tesmer JJG, Ghosh AK. Development of a new class of potent and highly selective G protein-coupled receptor kinase 5 inhibitors and structural insight from crystal structures of inhibitor complexes. Eur J Med Chem 2024; 264:115931. [PMID: 38016297 PMCID: PMC10841647 DOI: 10.1016/j.ejmech.2023.115931] [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: 09/22/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/30/2023]
Abstract
G protein-coupled receptor kinase 5 (GRK5) is an important drug development target for heart failure, cardiac hypertrophy, and cancer. We have designed and developed a new class of highly selective, potent, and non-covalent GRK5 inhibitors. One of the inhibitors displayed GRK5 IC50 value of 10 nM and exhibited >100,000-fold selectivity over GRK2. The X-ray structure of a ketoamide-derived inhibitor-bound GRK5 showed the formation of a hemithioketal intermediate with active site Cys474 in the GRK5 active site and provided new insights into the ligand-binding site interactions responsible for high selectivity. The current studies serve as an important guide to therapeutic GRK5 inhibitor drug development.
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Affiliation(s)
- Yueyi Chen
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Amol Sonawane
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Rajesh Manda
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ranjith Kumar Gadi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - John J G Tesmer
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Arun K Ghosh
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA; Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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27
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Hussein AM, Al Bahir A, Zaki YH, Ahmed OM, Eweas AF, Elroby SA, Mohamed MA. Synthesis, in vitro antioxidant, anticancer activity and molecular docking of new thiazole derivatives. RESULTS IN CHEMISTRY 2024; 7:101508. [DOI: 10.1016/j.rechem.2024.101508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024] Open
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28
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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: 0] [Impact Index Per Article: 0] [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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29
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Abdelhamed AM, Hassan RA, Kadry HH, Helwa AA. Novel pyrazolo[3,4- d]pyrimidine derivatives: design, synthesis, anticancer evaluation, VEGFR-2 inhibition, and antiangiogenic activity. RSC Med Chem 2023; 14:2640-2657. [PMID: 38107182 PMCID: PMC10718518 DOI: 10.1039/d3md00476g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/23/2023] [Indexed: 12/19/2023] Open
Abstract
A novel series of 12 pyrazolo[3,4-d]pyrimidine derivatives were created and evaluated in vitro for their antiproliferative activity against the NCI 60 human tumor cell line panel. Compounds 12a-d displayed significant antitumor activity against MDA-MB-468 and T-47D (breast cancer cell lines), especially compound 12b, which exhibited the highest anticancer activity against MDA-MB-468 and T-47D cell lines with IC50 values of 3.343 ± 0.13 and 4.792 ± 0.21 μM, respectively compared to staurosporine with IC50 values of 6.358 ± 0.24 and 4.849 ± 0.22 μM. The most potent cytotoxic derivatives 12a-d were studied for their VEGFR-2 inhibitory activity to explore the mechanism of action of these substances. Compound 12b had potent activity against VEGFR-2 with an IC50 value of 0.063 ± 0.003 μM, compared to sunitinib with IC50 = 0.035 ± 0.012 μM. Moreover, there was an excellent reduction in HUVEC migratory potential that resulted in a significant disruption of wound healing patterns by 23% after 72 h of treatment with compound 12b. Cell cycle and apoptosis investigations showed that compound 12b could stop the cell cycle at the S phase and significantly increase total apoptosis in the MDA-MB-468 cell line by 18.98-fold compared to the control. Moreover, compound 12b increased the caspase-3 level in the MDA-MB-468 cell line by 7.32-fold as compared to the control.
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Affiliation(s)
- Ahmed M Abdelhamed
- Pharmaceutical Organic Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST) 6th of October City Egypt
| | - Rasha A Hassan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University Kasr El-Aini Street Cairo 11562 Egypt
| | - Hanan H Kadry
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University Kasr El-Aini Street Cairo 11562 Egypt
| | - Amira A Helwa
- Pharmaceutical Organic Chemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST) 6th of October City Egypt
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30
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Lien VT, Hauge E, Nuruddin S, Klaveness J, Olberg DE. Synthesis and preclinical evaluation of a selective MET kinase positron emission tomography tracer. J Labelled Comp Radiopharm 2023; 66:452-460. [PMID: 37867318 DOI: 10.1002/jlcr.4066] [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: 03/15/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023]
Abstract
The tyrosine kinase MET (hepatocyte growth factor receptor) is activated or mutated in a wide range of cancers and is often correlated with a poor prognosis. Precision medicine with positron emission tomography (PET) can potentially aid in the assessment of tumor biochemistry and heterogeneity, which can prompt the selection of the most effective therapeutic regimes. The selective MET inhibitor PF04217903 (1) formed the basis for a bioisosteric replacement, leading to the deoxyfluorinated analog [18 F]2. [18 F]2 could be synthesized with a "hydrous fluoroethylation" protocol in 6.3 ± 2.6% radiochemical yield and a molar activity of >50 GBq/μmol. In vitro autoradiography indicated that [18 F]2 selectively binds to MET in PC3 tumor tissue, and in vivo biodistribution in mice showed predominantly a hepatobiliary excretion along with a low retention of radiotracer in other organs.
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Affiliation(s)
- Vegard Torp Lien
- Department of Pharmacy, University of Oslo, Oslo, Norway
- Norwegian Medical Cyclotron Center, Oslo, Norway
| | - Emily Hauge
- Department of Pharmacy, University of Oslo, Oslo, Norway
- Norwegian Medical Cyclotron Center, Oslo, Norway
| | | | - Jo Klaveness
- Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Dag Erlend Olberg
- Department of Pharmacy, University of Oslo, Oslo, Norway
- Norwegian Medical Cyclotron Center, Oslo, Norway
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31
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Chen R, Wang Z, Sima L, Cheng H, Luo B, Wang J, Guo B, Mao S, Zhou Z, Peng J, Tang L, Liu X, Liao W. Design, synthesis and evaluation of 2, 6, 8-substituted Imidazopyridine derivatives as potent PI3K α inhibitors. J Enzyme Inhib Med Chem 2023; 38:2155638. [PMID: 36650905 PMCID: PMC9858543 DOI: 10.1080/14756366.2022.2155638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Inhibition of PI3K pathway has become a desirable strategy for cancer treatment. In this work, a series of 2, 6, 8-substituted Imidazo[1,2-a]pyridine derivatives were designed and screened for their activities against PI3Kα and a panel of PI3Kα-addicted cancer cells. Among them, compound 35 was identified as a PI3Kα inhibitor with nanomolar potency as well as acceptable antiproliferative activity. Flow cytometry analysis confirmed 35 induced cell cycle arrest and apoptosis in T47D cells. In addition, it also showed desirable in vitro ADME properties. The design, synthesis, and SAR exploration of 35 are described within.
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Affiliation(s)
- Rui Chen
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China
| | - Zhongyuan Wang
- Department of Pharmacy, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Lijie Sima
- Department of Hematology and Oncology, The Affiliated Shaoyang Hospital, Hengyang Medical School, University of South China (Shaoyang Central Hospital), China
| | - Hu Cheng
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China
| | - Bilan Luo
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China
| | - Jianta Wang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China
| | - Bing Guo
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang, China
| | - Shunyi Mao
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, China
| | - Zhixu Zhou
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, China
| | - Jingang Peng
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China
| | - Lei Tang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China
| | - Xinfu Liu
- Department of Hematology and Oncology, The Affiliated Shaoyang Hospital, Hengyang Medical School, University of South China (Shaoyang Central Hospital), China,CONTACT Xinfu Liu Department of Hematology and Oncology, The Affiliated Shaoyang Hospital, Hengyang Medical School, University of South China (Shaoyang Central Hospital), Guiyang550004, China
| | - Weike Liao
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang, China,Weike Liao Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, Guizhou Medical University, Guiyang550004, China
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32
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Rivoal M, Dubuquoy L, Millet R, Leleu-Chavain N. Receptor Interacting Ser/Thr-Protein Kinase 2 as a New Therapeutic Target. J Med Chem 2023; 66:14391-14410. [PMID: 37857324 DOI: 10.1021/acs.jmedchem.3c00593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Receptor interacting serine/threonine protein kinase 2 (RIPK2) is a downstream signaling molecule essential for the activation of several innate immune receptors, including the NOD-like receptors (NOD1 and NOD2). Recognition of pathogen-associated molecular pattern proteins by NOD1/2 leads to their interaction with RIPK2, which induces release of pro-inflammatory cytokines through the activation of NF-κB and MAPK pathways, among others. Thus, RIPK2 has emerged as a key mediator of intracellular signal transduction and represents a new potential therapeutic target for the treatment of various conditions, including inflammatory diseases and cancer. In this Perspective, first, an overview of the mechanisms that underlie RIPK2 function will be presented along with its role in several diseases. Then, the existing inhibitors that target RIPK2 and different therapeutic strategies will be reviewed, followed by a discussion on current challenges and outlook.
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Affiliation(s)
- Morgane Rivoal
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Laurent Dubuquoy
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Régis Millet
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Natascha Leleu-Chavain
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
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Fischer M, Luck M, Werle M, Vogel A, Bashawat M, Ludwig K, Scheidt HA, Müller P. The small-molecule kinase inhibitor ceritinib, unlike imatinib, causes a significant disturbance of lipid membrane integrity: A combined experimental and MD study. Chem Phys Lipids 2023; 257:105351. [PMID: 37863350 DOI: 10.1016/j.chemphyslip.2023.105351] [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: 07/11/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023]
Abstract
Ceritinib and imatinib are small-molecule protein kinase inhibitors which are applied as therapeutic agents against various diseases. The fundamentals of their clinical use, i.e. their pharmacokinetics as well as the mechanisms of the inhibition of the respective kinases, are relatively well studied. However, the interaction of the drugs with membranes, which can be a possible cause of side effects, has hardly been investigated so far. Therefore, we have characterized the interaction of both drugs with lipid membranes consisting of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) in the absence and in the presence of cholesterol. For determining the membrane impact of both drugs on a molecular level, different experimental (NMR, ESR, fluorescence) and theoretical (MD simulations) approaches were applied. The data show that ceritinib, in contrast to imatinib, interacts more effectively with membranes significantly affecting various physico-chemical membrane parameters like membrane order and transmembrane permeation of polar solutes. The pronounced membrane impact of ceritinib can be explained by a strong affinity of the drug towards POPC which competes with the POPC-cholesterol interaction by that attenuating the ordering effect of cholesterol. The data are relevant for understanding putative toxic and cytotoxic side effects of these drugs such as the triggering of cell lysis or apoptosis.
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Affiliation(s)
- Markus Fischer
- Leipzig University, Institute for Medical Physics and Biophysics, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Meike Luck
- Humboldt University Berlin, Department of Biology, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Max Werle
- Humboldt University Berlin, Department of Biology, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Alexander Vogel
- Leipzig University, Institute for Medical Physics and Biophysics, Härtelstr. 16-18, D-04107 Leipzig, Germany
| | - Mohammad Bashawat
- Humboldt University Berlin, Department of Biology, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Kai Ludwig
- Freie Universität Berlin, Research Center for Electron Microscopy and Core Facility BioSupraMol, Institute of Chemistry and Biochemistry, Fabeckstr. 36a, D-14195 Berlin, Germany
| | - Holger A Scheidt
- Leipzig University, Institute for Medical Physics and Biophysics, Härtelstr. 16-18, D-04107 Leipzig, Germany.
| | - Peter Müller
- Humboldt University Berlin, Department of Biology, Invalidenstr. 42, D-10115 Berlin, Germany.
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El-Hddad S, Sobhy M, Ayoub A, El-Adl K. In silico molecular docking, dynamics simulation and repurposing of some VEGFR-2 inhibitors based on the SARS-CoV-2-main-protease inhibitor N3. J Biomol Struct Dyn 2023; 41:9267-9281. [PMID: 36399002 DOI: 10.1080/07391102.2022.2148000] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
Abstract
The global and rapid spread of the novel human coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has brought immediate urgency to the discovery of favorable targets for COVID-19 treatment. Here, we consider drug reuse as an attractive methodology for drug discovery by reusing existing drugs to treat diseases other than their initial indications. Here, we review current information concerning the global health issue of COVID-19 including VEGFR-2 inhibitors. Besides, we describe computational approaches to be used in drug repurposing and highlight examples of in silico studies of drug development efforts against SARS-CoV-2. The present study suggests the potential anti-SARS-CoV-2 activities of 35 reported VEGFR-2 inhibitors containing the amide and urea linkers. Nineteen members revealed the best in silico results and hence, were subjected to further molecular dynamics (MD) simulation for their inhibitory activities against SARS-CoV-2 Mpro across 100 ns. Furthermore, MD simulations followed by calculations of the free energy of binding were also carried out for the most promising ligand-pocket complexes from docking studies to clarify some information on their dynamic and thermodynamic properties and approve the docking results. These results we obtained probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanadelaslam El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University, Al Bayda, Libya
| | - Mohamed Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Ahmed Ayoub
- HTuO Biosciences Inc., Vancouver, BC, Canada
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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Pratap Reddy Gajulapalli V. Development of Kinase-Centric Drugs: A Computational Perspective. ChemMedChem 2023; 18:e202200693. [PMID: 37442809 DOI: 10.1002/cmdc.202200693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023]
Abstract
Kinases are prominent drug targets in the pharmaceutical and research community due to their involvement in signal transduction, physiological responses, and upon dysregulation, in diseases such as cancer, neurological and autoimmune disorders. Several FDA-approved small-molecule drugs have been developed to combat human diseases since Gleevec was approved for the treatment of chronic myelogenous leukemia. Kinases were considered "undruggable" in the beginning. Several FDA-approved small-molecule drugs have become available in recent years. Most of these drugs target ATP-binding sites, but a few target allosteric sites. Among kinases that belong to the same family, the catalytic domain shows high structural and sequence conservation. Inhibitors of ATP-binding sites can cause off-target binding. Because members of the same family have similar sequences and structural patterns, often complex relationships between kinases and inhibitors are observed. To design and develop drugs with desired selectivity, it is essential to understand the target selectivity for kinase inhibitors. To create new inhibitors with the desired selectivity, several experimental methods have been designed to profile the kinase selectivity of small molecules. Experimental approaches are often expensive, laborious, time-consuming, and limited by the available kinases. Researchers have used computational methodologies to address these limitations in the design and development of effective therapeutics. Many computational methods have been developed over the last few decades, either to complement experimental findings or to forecast kinase inhibitor activity and selectivity. The purpose of this review is to provide insight into recent advances in theoretical/computational approaches for the design of new kinase inhibitors with the desired selectivity and optimization of existing inhibitors.
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Wang L, Yang Z, Li G, Liu Y, Ai C, Rao Y. Discovery of small molecule degraders for modulating cell cycle. Front Med 2023; 17:823-854. [PMID: 37935945 DOI: 10.1007/s11684-023-1027-5] [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: 05/17/2023] [Accepted: 08/16/2023] [Indexed: 11/09/2023]
Abstract
The cell cycle is a complex process that involves DNA replication, protein expression, and cell division. Dysregulation of the cell cycle is associated with various diseases. Cyclin-dependent kinases (CDKs) and their corresponding cyclins are major proteins that regulate the cell cycle. In contrast to inhibition, a new approach called proteolysis-targeting chimeras (PROTACs) and molecular glues can eliminate both enzymatic and scaffold functions of CDKs and cyclins, achieving targeted degradation. The field of PROTACs and molecular glues has developed rapidly in recent years. In this article, we aim to summarize the latest developments of CDKs and cyclin protein degraders. The selectivity, application, validation and the current state of each CDK degrader will be overviewed. Additionally, possible methods are discussed for the development of degraders for CDK members that still lack them. Overall, this article provides a comprehensive summary of the latest advancements in CDK and cyclin protein degraders, which will be helpful for researchers working on this topic.
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Affiliation(s)
- Liguo Wang
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Zhouli Yang
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Guangchen Li
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Yongbo Liu
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| | - Chao Ai
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, China.
| | - Yu Rao
- MOE Key Laboratory of Protein Sciences, School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China.
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Li L, Liu S, Wang B, Liu F, Xu S, Li P, Chen Y. An Updated Review on Developing Small Molecule Kinase Inhibitors Using Computer-Aided Drug Design Approaches. Int J Mol Sci 2023; 24:13953. [PMID: 37762253 PMCID: PMC10530957 DOI: 10.3390/ijms241813953] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/31/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Small molecule kinase inhibitors (SMKIs) are of heightened interest in the field of drug research and development. There are 79 (as of July 2023) small molecule kinase inhibitors that have been approved by the FDA and hundreds of kinase inhibitor candidates in clinical trials that have shed light on the treatment of some major diseases. As an important strategy in drug design, computer-aided drug design (CADD) plays an indispensable role in the discovery of SMKIs. CADD methods such as docking, molecular dynamic, quantum mechanics/molecular mechanics, pharmacophore, virtual screening, and quantitative structure-activity relationship have been applied to the design and optimization of small molecule kinase inhibitors. In this review, we provide an overview of recent advances in CADD and SMKIs and the application of CADD in the discovery of SMKIs.
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Affiliation(s)
- Linwei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Songtao Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Bi Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Fei Liu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Shu Xu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Pirui Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yu Chen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (L.L.); (S.L.); (B.W.); (F.L.); (S.X.)
- Jiangsu Province Engineering Research Center of Eco-Cultivation and High-Value Utilization of Chines Medicinal Materials, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
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38
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Le TTH, Tran LH, Nguyen MT, Pham MQ, Phung HTT. Calculation of binding affinity of JAK1 inhibitors via accurately computational estimation. J Biomol Struct Dyn 2023; 41:7224-7234. [PMID: 36069111 DOI: 10.1080/07391102.2022.2118830] [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: 01/24/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
Janus kinase 1 (JAK1) is a tyrosine kinase that is involved in the initiation of responses to a number of different cytokine receptor families. The JAK1-dependent pathway is a therapeutic target, and several JAK inhibitors have been developed thanks to intensive research. However, since the ATP binding sites of JAK family members are quite alike, JAK1 inhibitors can thus be less selective, resulting in unanticipated adverse effects. Despite this, minor variations in the ATP-binding site have been extensively used to find a variety of small compounds with different inhibitory properties. Stronger binding affinity of JAK1 inhibitors is believed to be able to reduce the negative effects, leading to better treatment results. Therefore, a thorough computational search that can effectively identify ligands with extremely high binding affinity for JAK1 to serve as promising inhibitors is required. Here, a method combining steered-molecular dynamic (SMD) simulations with a modified linear interaction energy (LIE) model has been developed to evaluate the binding affinities of known JAK1 inhibitors. The correlation coefficient between the estimated and experimental values was 0.72 and a root-mean-square error was 0.97 kcal•mol-1, revealing that the SMD/LIE method can precisely and quickly predict the binding free energies of JAK1 inhibitors. Furthermore, three marine fungus-derived compounds, namely hansforesters E, hansforesters G and tetroazolemycins B, were identified to be particularly promising JAK1 inhibitors, accordingly. These findings show that the SMD/LIE method has a lot of promise for in silico screening of possible JAK1 inhibitors from a vast number of compounds that are now accessible.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thi-Thuy-Huong Le
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Linh Hoang Tran
- Vietnam National University, Ho Chi Minh City, Vietnam
- Faculty of Civil Engineering, Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City, Vietnam
| | - Minh Tam Nguyen
- Laboratory of Theoretical and Computational Biophysics, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Minh Quan Pham
- Institute of Natural Products Chemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huong Thi Thu Phung
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
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Abdullah S, Ganguly S. An overview of imidazole and its analogues as potent anticancer agents. Future Med Chem 2023; 15:1621-1646. [PMID: 37727960 DOI: 10.4155/fmc-2023-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023] Open
Abstract
The quest for novel, physiologically active imidazoles remains an exciting topic of research among medicinal chemists. The imidazole ring is a five-membered aromatic heterocycle that is found in both natural and synthesized compounds. Multiple anticancer drug classes are currently available on the market, but concerns including toxicity, limited efficacy and solubility have lowered the overall therapeutic index. Therefore, the hunt for new potential chemotherapeutic agents persists. The development of imidazole as a reliable and safer alternative to anticancer treatment is generating much attention among experts. Tubulin or microtubule polymerization inhibition and changes in the structure and function of DNA, VEGF, topoisomerase, kinases, histone deacetylases and certain other proteins that affect gene expression are among the putative targets.
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Affiliation(s)
- Salik Abdullah
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Jharkhand, 835215, India
| | - Swastika Ganguly
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Jharkhand, 835215, India
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40
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Sayed MTM, Halim PA, El-Ansary AK, Hassan RA. Design, synthesis, anticancer evaluation, and in silico studies of some thieno[2,3-d]pyrimidine derivatives as EGFR inhibitors. Drug Dev Res 2023; 84:1299-1319. [PMID: 37357422 DOI: 10.1002/ddr.22088] [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: 04/08/2023] [Revised: 05/17/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
Abstract
New series of 20 thieno[2,3-d]pyrimidine derivatives have been synthesized. The National Cancer Institute evaluated all the newly synthesized compounds for their antiproliferative activity against a panel of 60 cancer cell lines. Compound 7b exhibited a remarkable antineoplastic activity at 10 µM dose and was therefore tested at five dose concentrations. The significant and broad-spectrum antineoplastic action of compound 7b was observed against 37 of the tested cancer cell lines with a dose that inhibits 50% of the growth compared to control values in the micromolar range of 1.95-9.6 µM. The dose which inhibits the growth completely in the cytostatic range of 3.99-100 µM was also observed. Compound 7b effectively inhibited epidermal growth factor receptor (EGFR) with 50% inhibition concentration value (IC50 ) = 0.096 ± 0.004 compared to erlotinib with IC50 = 0.037 ± 0.002. Moreover, compound 7b revealed a powerful downregulation effect on total EGFR concentration and its phosphorylation. In addition, compound 7b inhibited phosphatidylinositol 3-kinase, protein kinase B, and the mammalian target of rapamycin pathway phosphorylation. Furthermore, compound 7b raised total apoptosis by 21.93-fold in the ovarian cancer cell line (OVCAR-4) and caused an arrest in the cell cycle in the G1/S phase. It also raised the level of caspase-3 by 4.72-fold. Furthermore, to determine the binding manner of the most effective derivatives and validate their capacity to comply with the pharmacophoric properties necessary for EGFR inhibition, they were docked into the active site of the EGFR.
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Affiliation(s)
- Menna Tallah M Sayed
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Peter A Halim
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Afaf K El-Ansary
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Rasha A Hassan
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Medishetti R, C MR, Chatti K. Cabozantinib-induced edema in zebrafish represents an adverse effect characterized by defects in lymphatic vasculature and renal function. J Biochem Mol Toxicol 2023; 37:e23413. [PMID: 37335823 DOI: 10.1002/jbt.23413] [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: 09/30/2022] [Revised: 03/21/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Tyrosine kinase inhibitors (TKIs) are a major class of targeted cancer therapy drugs. Overcoming the limitations of approved TKIs and the development of new TKIs continues to be an important need. The adoption of higher throughput and accessible animal models to evaluate TKI adverse effects will help in this regard. We exposed zebrafish larvae to a set of 22 Food and Drug Administration-approved TKIs and assessed mortality, early developmental abnormalities, and gross morphological abnormalities posthatching. We found edema posthatching as a consistent and prominent consequence of VEGFR inhibitors, and of cabozantinib in particular. The edema occurred at concentrations that did not cause lethality or any other abnormality, and was independent of the developmental stage. Further experiments identified loss of blood and lymphatic vasculature, and suppression of renal function in larvae exposed to 10 µM cabozantinib. Molecular analysis showed downregulation of the vasculature marker genes vegfr, prox1a, sox18, and the renal function markers nephrin and podocin as the potential molecular basis for the above defects, implicating them in the mechanism of cabozantinib-induced edema. Our findings reveal edema as a previously unreported phenotypic effect of cabozantinib and identify the likely mechanistic basis. These findings also highlight the need for studies investigating edema due to vascular and renal dysfunction as a potential clinical adverse effect of cabozantinib, and possibly other VEGFR inhibitors.
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Affiliation(s)
- Raghavender Medishetti
- Center for Innovation in Molecular and Pharmaceutical Sciences, Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mallikarjuna Rao C
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Kiranam Chatti
- Center for Innovation in Molecular and Pharmaceutical Sciences, Dr. Reddy's Institute of Life Sciences, University of Hyderabad Campus, Gachibowli, Hyderabad, Telangana, India
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42
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Badawi WA, Samir M, Fathy HM, Okda TM, Noureldin MH, Atwa GMK, AboulWafa OM. Design, synthesis and molecular docking study of new pyrimidine-based hydrazones with selective anti-proliferative activity against MCF-7 and MDA-MB-231 human breast cancer cell lines. Bioorg Chem 2023; 138:106610. [PMID: 37210828 DOI: 10.1016/j.bioorg.2023.106610] [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: 03/15/2023] [Revised: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 05/23/2023]
Abstract
Efforts were directed on the design, synthesis and evaluation of the anticancer activity of some pyrimidine-based hydrazones against two breast cancer cell lines, MCF-7 and MDA-MB-231. Preliminary screening results revealed that some candidates scrutinized for their antiproliferative activities exhibited IC50 values of 0.87 μM-12.91 μM in MCF-7 and 1.75 μM-9.46 μM in MDA-MB-231 cells, indicating almost equal activities on both cell lines and better growth inhibition activities than those of the positive control 5-fluorouracil (5-FU) which displayed IC50 values of 17.02 μM and 11.73 μM respectively. Selectivity of the significantly active compounds was estimated against MCF-10A normal breast cells when compounds 7c, 8b, 9a and 10b exhibited superior activity for cancerous cells than for normal cells when compound 10b presented the best selectivity Index (SI) with respect to both MCF-7 and MDA-MB-231 cancer cells in comparison to the reference drug 5-FU. Mechanisms of their actions were explored by inspecting activation of caspase-9, annexin V staining and cell cycle analysis. It was noticed that compounds 7c, 8b, 8c 9a-c and 10b produced an increase in caspase-9 levels in MCF-7 treated cells with 10b inducing the highest elevation (27.13 ± 0.54 ng/mL) attaining 8.26-fold when compared to control MCF-7 which was higher than that of staurosporine (19.011 ± 0.40 ng/mL). The same compounds boosted caspase-9 levels in MDA-MB-231 treated cells when an increase in caspase-9 concentration reaching 20.40 ± 0.46 ng/mL (4.11-fold increase) was observed for compound 9a. We also investigated the role of these compounds for their increasing apoptosis ability against the 2 cell lines. Compounds 7c, 8b and 10b tested on MCF-7 cells displayed pre-G1 apoptosis and arrested cell cycle in particular at the S and G1 phases. Further clarification of their effects was made by modulating their related activities as inhibitors of ARO and EGFR enzymes when 8c and 9b showed 52.4% and 58.9% inhibition activity relative to letrozole respectively and 9b and 10b showed 36% and 39% inhibition activity of erlotinib. Also, the inhibition activity was verified by docking into the chosen enzymes.
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Affiliation(s)
- Waleed A Badawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Damanhour, 22511, Egypt.
| | - Mohamed Samir
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch 71524, Assiut, Egypt
| | - Hazem M Fathy
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut Branch 71524, Assiut, Egypt
| | - Tarek M Okda
- Department of Biochemistry, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt
| | - Mohamed H Noureldin
- Department of Biochemistry, Division of Clinical and Biological Sciences, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport, Alexandria P. O. Box 1029, Egypt
| | - Gamal M K Atwa
- Department of Biochemistry, Faculty of Pharmacy, Port Said University, Port Said 42515, Egypt
| | - Omaima M AboulWafa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21215, Egypt
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Takla FN, Bayoumi WA, El-Messery SM, Nasr MNA. Developing multitarget coumarin based anti-breast cancer agents: synthesis and molecular modeling study. Sci Rep 2023; 13:13370. [PMID: 37591917 PMCID: PMC10435442 DOI: 10.1038/s41598-023-40232-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
A new series of 7-substituted coumarin scaffolds containing a methyl ester moiety at the C4-position were synthesized and tested for their in vitro anti-proliferative activity against MCF-7 and MDA-MB-231 breast cancer cell lines using Doxorubicin (DOX) as reference. Compounds 2 and 8 showed noticeable selectivity against MCF-7 with IC50 = 6.0 and 5.8 µM, respectively compared to DOX with IC50 = 5.6 µM. Compounds 10, 12, and 14 exhibited considerable selectivity against Estrogen Negative cells with IC50 = 2.3, 3.5, and 1.9 µM, respectively) compared to DOX with (IC50 = 7.3 µM). The most promising compounds were tested as epidermal growth factor receptor and aromatase (ARO) enzymes inhibitors using erlotinib and exemestane (EXM) as standards, respectively. Results proved that compound 8 elicited the highest inhibitory activity (94.73% of the potency of EXM), while compounds 10 and 12 displayed 97.67% and 81.92% of the potency of Erlotinib, respectively. Further investigation showed that the promising candidates 8, 10, and 12 caused cell cycle arrest at G0-G1 and S phases and induced apoptosis. The mechanistic pathway was confirmed by elevating caspases-9 and Bax/Bcl-2 ratio. A set of in silico methods was also performed including docking, bioavailability ADMET screening and QSAR study.
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Affiliation(s)
- Fiby N Takla
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, International Coastal Road, Gamasa City, 35712, Egypt
| | - Waleed A Bayoumi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Shahenda M El-Messery
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Magda N A Nasr
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
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Singh A, Sonawane P, Kumar A, Singh H, Naumovich V, Pathak P, Grishina M, Khalilullah H, Jaremko M, Emwas AH, Verma A, Kumar P. Challenges and Opportunities in the Crusade of BRAF Inhibitors: From 2002 to 2022. ACS OMEGA 2023; 8:27819-27844. [PMID: 37576670 PMCID: PMC10413849 DOI: 10.1021/acsomega.3c00332] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 08/15/2023]
Abstract
Serine/threonine-protein kinase B-Raf (BRAF; RAF = rapidly accelerated fibrosarcoma) plays an important role in the mitogen-activated protein kinase (MAPK) signaling cascade. Somatic mutations in the BRAF gene were first discovered in 2002 by Davies et al., which was a major breakthrough in cancer research. Subsequently, three different classes of BRAF mutants have been discovered. This class includes class I monomeric mutants (BRAFV600), class II BRAF homodimer mutants (non-V600), and class III BRAF heterodimers (non-V600). Cancers caused by these include melanoma, thyroid cancer, ovarian cancer, colorectal cancer, nonsmall cell lung cancer, and others. In this study, we have highlighted the major binding pockets in BRAF protein, their active and inactive conformations with inhibitors, and BRAF dimerization and its importance in paradoxical activation and BRAF mutation. We have discussed the first-, second-, and third-generation drugs approved by the Food and Drug Administration and drugs under clinical trials with all four different binding approaches with DFG-IN/OUT and αC-IN/OUT for BRAF protein. We have investigated particular aspects and difficulties with all three generations of inhibitors. Finally, this study has also covered recent developments in synthetic BRAF inhibitors (from their discovery in 2002 to 2022), their unique properties, and importance in inhibiting BRAF mutants.
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Affiliation(s)
- Ankit
Kumar Singh
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Pankaj Sonawane
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Adarsh Kumar
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Harshwardhan Singh
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
| | - Vladislav Naumovich
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Prateek Pathak
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Maria Grishina
- Laboratory
of Computational Modeling of Drugs, Higher Medical and Biological
School, South Ural State University, Chelyabinsk 454008, Russia
| | - Habibullah Khalilullah
- Department
of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of
Pharmacy, Qassim University, Unayzah 51911, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health
Initiative and Red Sea Research Center, Division of Biological and
Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core
Laboratories, King Abdullah University of
Science and Technology, Thuwal 23955-6900, Saudi
Arabia
| | - Amita Verma
- Bioorganic
and Medicinal Chemistry Research Laboratory, Department of Pharmaceutical
Sciences, Sam Higginbottom University of
Agriculture, Technology and Sciences, Prayagraj 211007, India
| | - Pradeep Kumar
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda 151401, India
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Seif SE, Mahmoud Z, Wardakhan WW, Abdou AM, Hassan RA. Design and synthesis of novel hexahydrobenzo[4,5]thieno[2,3-d]pyrimidine derivatives as potential anticancer agents with antiangiogenic activity via VEGFR-2 inhibition, and down-regulation of PI3K/AKT/mTOR signaling pathway. Drug Dev Res 2023; 84:839-860. [PMID: 37016480 DOI: 10.1002/ddr.22058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/26/2023] [Accepted: 03/09/2023] [Indexed: 04/06/2023]
Abstract
New thieno[2,3-d]pyrimidine derivatives were designed and synthesized. The National Cancer Institute (NCI) evaluated the synthesized novel compounds against a panel of 60 tumor cell lines for their antiproliferative activity. Compounds 6b, 6f, and 6g showed potent anticancer activity at 10 µM dose, with mean GI of 20.86%, 76.41%, and 31.49%, respectively. Compound 6f was selected for five-dose concentrations evaluation. Compound 6f scored a submicromolar range of GI50 values against 10 cancer cell lines, indicating broad-spectrum and potent antiproliferative activity. Compound 6f TGI values were recorded in the cytostatic range of 4.02-95.1 µM. In comparison to sorafenib, the tested compounds 6b, 6f, and 6g inhibited VEGFR-2 with IC50 values of 0.290 ± 0.032, 0.066 ± 0.004, and 0.16 ± 0.006 µM, correspondingly. Compound 6f significantly reduced the total VEGFR-2 expression and its phosphorylation. Additionally, 6f reduced the phosphorylation of PI3K, Akt, and mTOR pathway proteins. Moreover, the migratory potential of HUVECs was significantly reduced, after 72 h of treatment with compound 6f, resulting in disrupted wound healing patterns which verified the angiogenesis suppression properties of compound 6f. Compound 6f increased the total apoptosis percentage by 21.27-fold compared to sorafenib, which caused a 24.11-fold increase in the total apoptosis percentage. This apoptotic activity was accompanied by a 7.81-fold increase in the level of apoptotic caspase-3. Furthermore, the cell cycle analysis revealed that the target derivative 6f reduced cellular proliferation and induced an arrest in HCT-15 colon cancer cell cycle at the S phase. Molecular modeling was used to determine the binding profile and affinity of derivative 6f toward the VEGFR-2 active site.
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Affiliation(s)
| | - Zeinab Mahmoud
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | | | - Amr M Abdou
- Department of Microbiology and Immunology, National Research Centre, Giza, Egypt
| | - Rasha A Hassan
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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46
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Duan H, Li L, He S. Advances and Prospects in the Treatment of Pancreatic Cancer. Int J Nanomedicine 2023; 18:3973-3988. [PMID: 37489138 PMCID: PMC10363367 DOI: 10.2147/ijn.s413496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023] Open
Abstract
Pancreatic cancer is a highly malignant and incurable disease, characterized by its aggressive nature and high fatality rate. The most common type is pancreatic ductal adenocarcinoma (PDAC), which has poor prognosis and high mortality rate. Current treatments for pancreatic cancer mainly encompass surgery, chemotherapy, radiotherapy, targeted therapy, and combination regimens. However, despite efforts to improve prognosis, and the 5-year survival rate for pancreatic cancer remains very low. Therefore, it's urgent to explore novel therapeutic approaches. With the rapid development of therapeutic strategies in recent years, new ideas have been provided for treating pancreatic cancer. This review expositions the advancements in nano drug delivery system, molecular targeted drugs, and photo-thermal treatment combined with nanotechnology for pancreatic cancer. It comprehensively analyzes the prospects of combined drug delivery strategies for treating pancreatic cancer, aiming at a deeper understanding of the existing drugs and therapeutic approaches, promoting the development of new therapeutic drugs, and attempting to enhance the therapeutic effect for patients with this disease.
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Affiliation(s)
- Huaiyu Duan
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People’s Republic of China
| | - Li Li
- Department of Hepatobiliary Pancreatic Oncology, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, People’s Republic of China
| | - Shiming He
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, People’s Republic of China
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47
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Wang TW, Hsu MS, Lin YH, Chiu HY, Chao HS, Liao CY, Lu CF, Wu YT, Huang JW, Chen YM. Application of Radiomics in Prognosing Lung Cancer Treated with Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitors: A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:3542. [PMID: 37509204 PMCID: PMC10377421 DOI: 10.3390/cancers15143542] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
In the context of non-small cell lung cancer (NSCLC) patients treated with EGFR tyrosine kinase inhibitors (TKIs), this research evaluated the prognostic value of CT-based radiomics. A comprehensive systematic review and meta-analysis of studies up to April 2023, which included 3111 patients, was conducted. We utilized the Quality in Prognosis Studies (QUIPS) tool and radiomics quality scoring (RQS) system to assess the quality of the included studies. Our analysis revealed a pooled hazard ratio for progression-free survival of 2.80 (95% confidence interval: 1.87-4.19), suggesting that patients with certain radiomics features had a significantly higher risk of disease progression. Additionally, we calculated the pooled Harrell's concordance index and area under the curve (AUC) values of 0.71 and 0.73, respectively, indicating good predictive performance of radiomics. Despite these promising results, further studies with consistent and robust protocols are needed to confirm the prognostic role of radiomics in NSCLC.
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Affiliation(s)
- Ting-Wei Wang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Biophotonics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ming-Sheng Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yi-Hui Lin
- Department of Radiation Oncology, Taichung Veterans General Hospital, Taichung 407, Taiwan
| | - Hwa-Yen Chiu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Biophotonics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
| | - Heng-Sheng Chao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chien-Yi Liao
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Chia-Feng Lu
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Yu-Te Wu
- Institute of Biophotonics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Jing-Wen Huang
- Department of Radiation Oncology, Taichung Veterans General Hospital, Taichung 407, Taiwan
| | - Yuh-Min Chen
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan
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48
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Jaworski C, Iliev P, Wängler C, Wängler B, Page B, Schirrmacher R, Bailey JJ. Type I inhibitors of tropomyosin receptor kinase (Trk): a 2020-2022 patent update. Expert Opin Ther Pat 2023; 33:503-521. [PMID: 37735897 DOI: 10.1080/13543776.2023.2262136] [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: 06/28/2023] [Accepted: 09/19/2023] [Indexed: 09/23/2023]
Abstract
INTRODUCTION Trk inhibitors are significant in the realm of personalized medicine as they target specific genetic alterations, such as NTRK gene fusions, leading to improved treatment outcomes for cancer patients. By tailoring the treatment to the genetic characteristics of the tumor rather than the tumor type, Trk inhibitors offer the potential for more effective and precise therapies, resulting in enhanced response rates and prolonged survival for patients with NTRK fusion-positive cancers. AREAS COVERED Patents covering type I inhibitors targeting the Trk family are discussed, building upon our prior review series on Trk inhibitors. Relevant patents were identified through the Web of Science database, Google, and Google Patents. EXPERT OPINION The field of Trk inhibitors has evolved significantly, as reflected in the current patent literature, which emphasizes the selective structural refinement of clinical champions. Efforts now concentrate on enhancing efficacy against on-target resistance mechanisms, with modifications made to improve potency, reduce toxicity, and enhance pharmacokinetics. Combination therapies show potential to address off-target resistance mechanisms and improve treatment outcomes. Challenges remain in accurately diagnosing NTRK gene alterations and integrating screening into routine clinical practice. Trk inhibitors have surpassed their conventional role of inhibition and are now seeing new applications in radiopharmaceutical development and as molecular targeting agents.
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Affiliation(s)
- Carolin Jaworski
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
| | - Petar Iliev
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Carmen Wängler
- Biomedical Chemistry, Department of Clinical Radiology and Nuclear Medicine, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Björn Wängler
- Molecular Imaging and Radiochemistry, Department of Clinical Radiology and Nuclear Medicine, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Brent Page
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Ralf Schirrmacher
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Canada
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Mukhtar RM, Abdelmoniem N, Elrufaie HA, Edris A, Ghaboosh H, Mahgoub MA, Garelnabi EAE, Osman W, Sherif AE, Ashour A, Ghazawi KF, Samman WA, Alhaddad AA, Bafail R, Ibrahim SRM, Mohamed GA, Alzain AA. Unlocking the potential of approved drugs for the allosteric inhibition of tropomyosin-receptor kinase A using molecular docking and molecular dynamics studies. Front Chem 2023; 11:1205724. [PMID: 37351516 PMCID: PMC10282146 DOI: 10.3389/fchem.2023.1205724] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/22/2023] [Indexed: 06/24/2023] Open
Abstract
Tropomyosin-receptor kinase A (TrkA) is the primary isoform among the tropomyosin-receptor kinases that have been associated with human cancer development, contributing to approximately 7.4% of all cancer cases. TrkA represents an attractive target for cancer treatment; however, currently available TrkA inhibitors face limitations in terms of resistance development and potential toxicity. Hence, the objective of this study was to identify new allosteric-approved inhibitors of TrkA that can overcome these challenges and be employed in cancer therapy. To achieve this goal, a screening of 9,923 drugs from the ChEMBL database was conducted to assess their repurposing potential using molecular docking. The top 49 drug candidates, exhibiting the highest docking scores (-11.569 to -7.962 kcal/mol), underwent MM-GBSA calculations to evaluate their binding energies. Delanzomib and tibalosin, the top two drugs with docking scores of -10.643 and -10.184 kcal/mol, respectively, along with MM-GBSA dG bind values of -67.96 and -50.54 kcal/mol, were subjected to 200 ns molecular dynamic simulations, confirming their stable interactions with TrkA. Based on these findings, we recommend further experimental evaluation of delanzomib and tibalosin to determine their potential as allosteric inhibitors of TrkA. These drugs have the potential to provide more effective and less toxic therapeutic alternatives. The approach employed in this study, which involves repurposing drugs through molecular docking and molecular dynamics, serves as a valuable tool for identifying novel drug candidates with distinct therapeutic uses. This methodology can contribute to reducing the attrition rate and expediting the process of drug discovery.
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Affiliation(s)
- Rua M. Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Nihal Abdelmoniem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Hisham A. Elrufaie
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Alaa Edris
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Hiba Ghaboosh
- Department of Pharmaceutics, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Mohanad A. Mahgoub
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
| | - Elrashied A. E. Garelnabi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Wadah Osman
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Asmaa E. Sherif
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Kholoud F. Ghazawi
- Clinical Pharmacy Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Waad A. Samman
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Aisha A. Alhaddad
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Rawan Bafail
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | - Sabrin R. M. Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahim A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Gezira, Sudan
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50
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Ahmed M, Wuethrich A, Constantin N, Shanmugasundaram KB, Mainwaring P, Kulasinghe A, O'Leary C, O'Byrne K, Sina AAI, Carrascosa LG, Trau M. Liquid Biopsy Snapshots of Key Phosphoproteomic Pathways in Lung Cancer Patients for Diagnosis and Therapy Monitoring. Anal Chem 2023. [PMID: 37224231 DOI: 10.1021/acs.analchem.3c00519] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phosphorylation is a post-translational modification in proteins that changes protein conformation and activity for regulating signal transduction pathways. This mechanism is frequently impaired in lung cancer, resulting in permanently active constitutive phosphorylation to initiate tumor growth and/or reactivate pathways in response to therapy. We developed a multiplexed phosphoprotein analyzer chip (MPAC) that enables rapid (detection time: 5 min) and sensitive (LOD: 2 pg/μL) detection of protein phosphorylation and presents phosphoproteomic profiling of major phosphorylation pathways in lung cancer. We monitored phosphorylated receptors and downstream proteins involved in mitogen-activated protein kinase (MAPK) and PI3K/AKT/mTOR pathways in lung cancer cell line models and patient-derived extracellular vesicles (EV). Using kinase inhibitor drugs in cell line models, we found that the drug can inhibit the phosphorylation and/or activation of the kinase pathway. We then generated a phosphorylation heatmap by EV phosphoproteomic profiling of plasma samples isolated from 36 lung cancer patients and 8 noncancer individuals. The heatmap showed a clear difference between the noncancer and cancer samples and identify the specific proteins that are activated in the cancer samples. Our data also showed that MPAC could monitor immunotherapy responses by assessment of the phosphorylation states of the proteins, particularly for PD-L1. Finally, with a longitudinal study, we found that the phosphorylation levels of the proteins were indicative of a positive response to therapy. We believe that this study will lead to personalized treatment by providing a better understanding of the active and resistant pathways and will provide a tool for selecting combined and targeted therapies for precision medicine.
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Affiliation(s)
- Mostak Ahmed
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Alain Wuethrich
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Nicolas Constantin
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Karthik Balaji Shanmugasundaram
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Paul Mainwaring
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Arutha Kulasinghe
- School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Connor O'Leary
- Princess Alexandra Hospital, Woolloongabba, QLD 4102, Australia
| | - Ken O'Byrne
- School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Abu Ali Ibn Sina
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Laura G Carrascosa
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
| | - Matt Trau
- Center for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Bldg 75), Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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