1
|
Xiu X, Li M, Hu D, Jia H, Wang H, Liu Y, Zhao X, Li Z, Liu Y, Yang H, Cheng M. Potential oral VEGFR2 inhibitors: Treatment of wet age-related macular degeneration. Bioorg Chem 2024; 144:107110. [PMID: 38224636 DOI: 10.1016/j.bioorg.2024.107110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/08/2023] [Accepted: 01/07/2024] [Indexed: 01/17/2024]
Abstract
Wet age-related macular degeneration (w-AMD) is one of the leading causes of vision loss in industrialized countries. A large body of evidence suggests that inhibitors targeting VEGFR2 may be effective in the treatment of w-AMD. The identification of an oral VEGFR2 inhibitor for the treatment of w-AMD provides an opportunity for a route of administration other than intravitreal injection. While screening potent VEGFR2 inhibitors at the enzyme and cellular levels, ensuring the safety of the compounds was our primary strategy for screening optimal compounds. Finally, compound 16 was identified, exhibiting enhanced inhibition of VEGFR2 enzyme and proliferation of BaF3-TEL-VEGFR2 cells compared to Vorolanib. Compound 16 had a weak inhibitory effect on human Ether-a-go-go-related gene (hERG) channel currents, showing a cardiac safety profile similar to Vorolanib. Compound 16 showed no significant toxicity to human liver cell LX-2, indicating a liver safety profile similar to Vorolanib. The water solubility of compound 16 was found to be higher than that of Vorolanib when tested at pH = 7.4. In addition, compound 16 was found to inhibit VEGFR2 phosphorylation in human umbilical vein endothelial cells (HUVECs) in a dose-dependent manner by WB assay. Furthermore, the in vitro preliminary evaluation of the drug-like properties of compound 16 showed remarkable plasma stability and moderate liver microsomal stability. Based on in vivo pharmacokinetic studies in ICR mice, compound 16 exhibited acceptable oral bioavailability (F = 20.2 %). Overall, these findings provide evidence that compound 16 is a leading potential oral drug candidate for w-AMD.
Collapse
Affiliation(s)
- Xiaomeng Xiu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Mengzhen Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Dexiang Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Hongwei Jia
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Yaoyang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Xueqi Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Zhenli Li
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Yang Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China
| | - Huali Yang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China.
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Liaoning Shenyang 110016, China.
| |
Collapse
|
2
|
Xiaolin X, Xiaozhi L, Guoping H, Hongwei L, Jinkuo G, Xiyun B, Zhen T, Xiaofang M, Yanxia L, Na X, Chunyan Z, Rui G, Kuan W, Cheng Z, Cuancuan W, Mingyong L, Xinping D. Overfit deep neural network for predicting drug-target interactions. iScience 2023; 26:107646. [PMID: 37680476 PMCID: PMC10480310 DOI: 10.1016/j.isci.2023.107646] [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: 02/12/2022] [Revised: 06/28/2023] [Accepted: 08/11/2023] [Indexed: 09/09/2023] Open
Abstract
Drug-target interactions (DTIs) prediction is an important step in drug discovery. As traditional biological experiments or high-throughput screening are high cost and time-consuming, many deep learning models have been developed. Overfitting must be avoided when training deep learning models. We propose a simple framework, called OverfitDTI, for DTI prediction. In OverfitDTI, a deep neural network (DNN) model is overfit to sufficiently learn the features of the chemical space of drugs and the biological space of targets. The weights of trained DNN model form an implicit representation of the nonlinear relationship between drugs and targets. Performance of OverfitDTI on three public datasets showed that the overfit DNN models fit the nonlinear relationship with high accuracy. We identified fifteen compounds that interacted with TEK, a receptor tyrosine kinase contributing to vascular homeostasis, and the predicted AT9283 and dorsomorphin were experimentally demonstrated as inhibitors of TEK in human umbilical vein endothelial cells (HUVECs).
Collapse
Affiliation(s)
- Xiao Xiaolin
- Department of Cardiology, Tianjin Fifth Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - Liu Xiaozhi
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - He Guoping
- Geriatrics Department, Traditional Chinese Medicine Hospital of Binhai New Area, Tianjin, China
| | - Liu Hongwei
- School of Clinical Medicine, North China University of Science and Technology, Tangshan, Hebei, China
- Department of Anesthesiology, Tangshan Maternal and Child Health Hospital, Tangshan, Hebei, China
| | - Guo Jinkuo
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Bian Xiyun
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - Tian Zhen
- Deepwater Technology Research Institute, China National Offshore Oil Corporation, Tianjin, China
| | - Ma Xiaofang
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - Li Yanxia
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - Xue Na
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - Zhang Chunyan
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Central Laboratory, Tianjin Fifth Central Hospital, Tianjin, China
| | - Gao Rui
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
| | - Wang Kuan
- Department of Cardiology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Zhang Cheng
- Department of Cardiology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Wang Cuancuan
- Department of Cardiology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Liu Mingyong
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- Department of Urology, Tianjin Fifth Central Hospital, Tianjin, China
| | - Du Xinping
- Department of Cardiology, Tianjin Fifth Central Hospital, Tianjin, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Premature Infants, Tianjin Fifth Central Hospital, Tianjin, China
- College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| |
Collapse
|
3
|
Nojima Y, Aoki M, Re S, Hirano H, Abe Y, Narumi R, Muraoka S, Shoji H, Honda K, Tomonaga T, Mizuguchi K, Boku N, Adachi J. Integration of pharmacoproteomic and computational approaches reveals the cellular signal transduction pathways affected by apatinib in gastric cancer cell lines. Comput Struct Biotechnol J 2023; 21:2172-2187. [PMID: 37013003 PMCID: PMC10066531 DOI: 10.1016/j.csbj.2023.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Apatinib is known to be a highly selective vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor with anti-angiogenic and anti-tumor properties. In a phase III study, the objective response rate to apatinib was low. It remains unclear why the effectivity of apatinib varies among patients and what type of patients are candidates for the treatment. In this study, we investigated the anti-tumor efficacy of apatinib against 13 gastric cancer cell lines and found that it differed depending on the cell line. Using integrated wet and dry approaches, we showed that apatinib was a multi-kinase inhibitor of c-Kit, RAF1, VEGFR1, VEGFR2, and VEGFR3, predominantly inhibiting c-Kit. Notably, KATO-III, which was the most apatinib-sensitive among the gastric cancer cell lines investigated, was the only cell line expressing c-Kit, RAF1, VEGFR1, and VEGFR3 but not VEGFR2. Furthermore, we identified SNW1 as a molecule affected by apatinib that plays an important role in cell survival. Finally, we identified the molecular network related to SNW1 that was affected by treatment with apatinib. These results suggest that the mechanism of action of apatinib in KATO-III cells is independent of VEGFR2 and that the differential efficacy of apatinib was due to differences in expression patterns of receptor tyrosine kinases. Furthermore, our results suggest that the differential efficacy of apatinib in gastric cell lines may be attributed to SNW1 phosphorylation levels at a steady state. These findings contribute to a deeper understanding of the mechanism of action of apatinib in gastric cancer cells.
Collapse
Affiliation(s)
- Yosui Nojima
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Center for Mathematical Modeling and Data Science, Osaka University, Osaka 560–8531, Japan
| | - Masahiko Aoki
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Early Clinical Development, Graduate School of Medicine, Kyoto University Hospital, Kyoto 606–8507, Japan
| | - Suyong Re
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Yuichi Abe
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya 464–8681, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Satoshi Muraoka
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
| | - Hirokazu Shoji
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
| | - Kazufumi Honda
- Department of Biomarkers for Early Detection of Cancer, National Cancer Center Research Institute, Tokyo 104–0045, Japan
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Bunkyo-ku, Tokyo 113–8602, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Proteobiologics Co., Ltd., Osaka 567–0085, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Institute for Protein Research, Osaka University, Osaka 565–0871, Japan
| | - Narikazu Boku
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104–0045, Japan
- Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, Tokyo 108–8639, Japan
- Correspondence to: Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, 4–6-1 Minato-ku, Shiroganedai, Tokyo 108–8639, Japan.
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567–0085, Japan
- Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567–0085, Japan
- Correspondence to: Laboratory of Proteomics for Drug Discovery, National Institute of Biomedical Innovation, Health and Nutrition, 7–6-8 Saito-asagi, Ibaraki, Osaka 567–0085, Japan.
| |
Collapse
|
4
|
Llorens de los Ríos MC, Lanza PA, Barbieri CL, González ML, Chabán MF, Soria G, Vera DMA, Carpinella MC, Joray MB. The thiophene α-terthienylmethanol isolated from Tagetes minuta inhibits angiogenesis by targeting protein kinase C isozymes α and β2. Front Pharmacol 2022; 13:1007790. [PMID: 36313304 PMCID: PMC9597362 DOI: 10.3389/fphar.2022.1007790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/30/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Tumor angiogenesis is considered as a crucial pathologic feature of cancer with a key role in multidrug resistance (MDR). Adverse effects of the currently available drugs and the development of resistance to these remain as the hardest obstacles to defeat. Objetive: This work explores flora from Argentina as a source of new chemical entities with antiangiogenic activity. Methods: Tube formation assay using bovine aortic endothelial cells (BAECs) was the experiment of choice to assess antiangiogenic activity. The effect of the pure compound in cell invasiveness was investigated through the trans-well migration assay. The inhibitory effect of the pure compound on VEGFR-2 and PKC isozymes α and β2 activation was studied by molecular and massive dynamic simulations. Cytotoxicity on peripheral blood mononuclear cells and erythrocyte cells was evaluated by means of MTT and hemolysis assay, respectively. In silico prediction of pharmacological properties (ADME) and evaluation of drug-likeness features were performed using the SwissADME online tool. Results: Among the plants screened, T. minuta, showed an outstanding effect with an IC50 of 33.6 ± 3.4 μg/ml. Bio-guided isolation yielded the terthiophene α-terthienylmethanol as its active metabolite. This compound inhibited VEGF-induced tube formation with an IC50 of 2.7 ± 0.4 μM and significantly impaired the invasiveness of bovine aortic endothelial cells (BAECs) as well as of the highly aggressive breast cancer cells, MDA-MB-231, when tested at 10 μM. Direct VEGFR-2 and PKC inhibition were both explored by means of massive molecular dynamics simulations. The results obtained validated the inhibitory effect on protein kinase C (PKC) isozymes α and β2 as the main mechanism underlying its antiangiogenic activity. α-terthienylmethanol showed no evidence of toxicity against peripheral blood mononuclear and erythrocyte cells. Conclusion: These findings support this thiophene as a promising antiangiogenic phytochemical to fight against several types of cancer mainly those with MDR phenotype.
Collapse
Affiliation(s)
| | - Priscila A. Lanza
- Department of Chemistry and Biochemistry, QUIAMM–INBIOTEC–CONICET, College of Exact and Natural Sciences, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Cecilia L. Barbieri
- Department of Chemistry and Biochemistry, QUIAMM–INBIOTEC–CONICET, College of Exact and Natural Sciences, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - María L. González
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, School of Chemistry, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Macarena Funes Chabán
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, School of Chemistry, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Gastón Soria
- CIBICI CONICET and Department of Clinical Biochemistry, Faculty of Chemical Science, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - D. Mariano A. Vera
- Department of Chemistry and Biochemistry, QUIAMM–INBIOTEC–CONICET, College of Exact and Natural Sciences, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
- *Correspondence: D. Mariano A. Vera, ; María C. Carpinella, ; Mariana B. Joray,
| | - María C. Carpinella
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, School of Chemistry, Universidad Católica de Córdoba, Córdoba, Argentina
- *Correspondence: D. Mariano A. Vera, ; María C. Carpinella, ; Mariana B. Joray,
| | - Mariana B. Joray
- Fine Chemical and Natural Products Laboratory, IRNASUS CONICET-UCC, School of Chemistry, Universidad Católica de Córdoba, Córdoba, Argentina
- *Correspondence: D. Mariano A. Vera, ; María C. Carpinella, ; Mariana B. Joray,
| |
Collapse
|
5
|
Abudayah A, Daoud S, Al-Sha'er M, Taha M. Pharmacophore Modeling of Targets Infested with Activity Cliffs via Molecular Dynamics Simulation Coupled with QSAR and Comparison with other Pharmacophore Generation Methods: KDR as Case Study. Mol Inform 2022; 41:e2200049. [PMID: 35973966 DOI: 10.1002/minf.202200049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Activity cliffs (ACs) are defined as pairs of structurally similar compounds with large difference in their potencies against certain biotarget. We recently proposed that potent AC members induce significant entropically-driven conformational modifications of the target that unveil additional binding interactions, while their weakly-potent counterparts are enthalpically-driven binders with little influence on the protein target. We herein propose to extract pharmacophores for ACs-infested target(s) from molecular dynamics (MD) frames of purely "enthalpic" potent binder(s) complexed within the particular target. Genetic function algorithm/machine learning (GFA/ML) can then be employed to search for the best possible combination of MD pharmacophore(s) capable of explaining bioactivity variations within a list of inhibitors. We compared the performance of this approach with established ligand-based and structure-based methods. Kinase inserts domain receptor (KDR) was used as a case study. KDR plays a crucial role in angiogenic signaling and its inhibitors have been approved in cancer treatment. Interestingly, GFA/ML selected, MD-based, pharmacophores were of comparable performances to ligand-based and structure-based pharmacophores. The resulting pharmacophores and QSAR models were used to capture hits from the national cancer institute list of compounds. The most active hit showed anti-KDR IC50 of 2.76 µM.
Collapse
Affiliation(s)
| | | | | | - Mutasem Taha
- Faculty of pharmacy,University of jordan, JORDAN
| |
Collapse
|
6
|
Wang R, Hu X, Wang J, Zhou L, Hong Y, Zhang Y, Xiong F, Zhang X, Ye WC, Wang H. Proanthocyanidin A1 promotes the production of platelets to ameliorate chemotherapy-induced thrombocytopenia through activating JAK2/STAT3 pathway. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 95:153880. [PMID: 34906892 DOI: 10.1016/j.phymed.2021.153880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 11/22/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Chemotherapy-induced thrombocytopenia (CIT) is a severe adverse drug reaction, and the main reason for CIT is the destruction of megakaryocytes (MKs, precursor cells of platelet) in bone marrow by chemotherapy. Peanut skin, the seed coat of Arachis hypogaea L., is a traditional Chinese medicine commonly used to treat thrombocytopenia. However, its active compounds and the mechanisms remain unclear. PURPOSE This study aims to clarify the active compounds of peanut skin to exhibit thrombogenic effects against CIT and their underlying mechanisms in vitro and in vivo. STUDY DESIGN The bioassay-guided isolation based on the proliferation of MKs was used to explore the possible platelet-enhancing ingredients in peanut skin. HSCCC technique coupled with preparative HPLC was used to separate the active compounds. Dami cells and carboplatin-treated mice model were used to evaluate the thrombogenic effects of PS-1. Network pharmacology, molecular docking, dynamics simulation studies, kinase activity, surface plasmon resonance (SPR), cellular thermal shift assay (CETSA), isothermal dose-response fingerprint (ITDRFCETSA) and western blot analysis were performed to investigate the mechanisms of PS-1. RESULTS Proanthocyanidin A1 (PS-1) and its stereoisomers (PS-2-4) were demonstrated to promote the proliferation of MKs (Dami cells), especially PS-1 (EC50 = 8.58 μM). Further studies demonstrated that PS-1 could induce the differentiation of Dami cells in dose/time-dependent manner. Biological target analysis showed that PS-1 directly bound to JAK2 (KD = 2.06 μM) to exert potent activating effect (EC50 = 0.66 μM). Oral administration of PS-1 (25 or 50 mg/kg) significantly improved CIT, but this effect was confirmed to be inhibited by JAK2 inhibitor AG490, indicating that PS-1 exerted its efficacy through JAK2 in vivo. CONCLUSION Proanthocyanins (PS-1-4) derived from peanut skin were first clarified as platelet-enhancing ingredients to improve CIT. The underlying mechanism of PS-1 was proved to promote the proliferation and differentiation of MKs via JAK2/STAT3 pathway both in vitro and in vivo.
Collapse
Affiliation(s)
- Rong Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Xiaolong Hu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Jingjin Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Lina Zhou
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yu Hong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yuanhao Zhang
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou 215028, People's Republic of China
| | - Fei Xiong
- State Key Laboratory of Bioelectronics, Jiangsu Laboratory for Biomaterials and Devices, Southeast University, Nanjing 210009, People's Republic of China
| | - Xiaoqi Zhang
- Institute of Traditional Chinese Medicine & Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Wen-Cai Ye
- Institute of Traditional Chinese Medicine & Natural Products, Jinan University, Guangzhou 510632, People's Republic of China
| | - Hao Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 210009, People's Republic of China.
| |
Collapse
|
7
|
Itoh Y, Kurohara T, Suzuki T. N<sup>+</sup>-C-H…O Hydrogen Bonds in Protein-Ligand Complexes and their Application to Drug Design. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Takayoshi Suzuki
- The Institute of Scientific and Industrial Research, Osaka University
| |
Collapse
|
8
|
Lu M, Qi Y, Han Y, Yi Q, Xu L, Sun W, Ni G, Ni X, Xu C. Design and development of novel thiazolidin-4-one-1,3,5-triazine derivatives as neuro-protective agent against cerebral ischemia-reperfusion injury in mice via attenuation of NF-ĸB. Chem Biol Drug Des 2020; 96:1315-1327. [PMID: 32543026 DOI: 10.1111/cbdd.13744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/21/2020] [Accepted: 06/05/2020] [Indexed: 11/26/2022]
Abstract
The present study enumerates the discovery and development of novel thiazolidin-4-one-1,3,5-triazine as neuro-protective agent against cerebral ischemia-reperfusion injury in mice. These compounds showed significant inhibition of NF-ĸB transcriptional activity in LPS-stimulated RAW264.7 cells, displaying compound 8k as most potent inhibitor among the tested derivative. The compound 8k was further studied in in vivo middle cerebral artery occlusion (MCAO) mice model for neuro-protective action. Results suggest that compound 8k causes attenuation of inflammation (TNF-α, IL-β, and IL-6), oxidative stress (SOD, GSH, and MDA), and apoptosis (Bcl-2, Bax, and cleaved caspase-3) in MCAO mice in concentration-dependent manner. Collectively, our results documented that compound 8k pre-treatment protects cerebral I/R. This novel lead scaffold may be helpful for investigation of new neuro-protective agent by inactivation of NF-ĸB.
Collapse
Affiliation(s)
- Min Lu
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yujun Qi
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yu Han
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Qiong Yi
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Lei Xu
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Wenlin Sun
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Guihua Ni
- Department of Neurology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Xiaoyu Ni
- Department of Rehabilitation Medicine, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Changsong Xu
- Department of Neurology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, Huai'an, China
| |
Collapse
|
9
|
Verma T, Sinha M, Bansal N. Heterocyclic Compounds Bearing Triazine Scaffold and Their Biological Significance: A Review. Anticancer Agents Med Chem 2020; 20:4-28. [DOI: 10.2174/1871520619666191028111351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/19/2019] [Accepted: 05/21/2019] [Indexed: 01/18/2023]
Abstract
Benzene is a six-membered hydrocarbon ring system and if three carbon-hydrogen units of benzene ring are replaced by nitrogen atoms then triazine is formed. Triazines are present in three isomeric forms 1,2,3- triazine, 1,2,4-triazine, and 1,3,5-triazine according to the position of the nitrogen atom. These are weak bases having weaker resonance energy than benzene, so nucleophilic substitution is preferred than electrophilic substitution. Triazine is an interesting class of heterocyclic compounds in medicinal chemistry. Numerous synthetic derivatives of triazine have been prepared and evaluated for a wide spectrum of biological activities in different models with desired findings such as antibacterial, antifungal, anti-cancer, antiviral, antimalarial, antiinflammatory, antiulcer, anticonvulsant, antimicrobial, insecticidal and herbicidal agents. Triazine analogs have exposed potent pharmacological activity. So, triazine nucleus may be considered as an interesting core moiety for researchers for the development of future drugs.
Collapse
Affiliation(s)
- Tarawanti Verma
- I.K. Gujral Punjab Technical University (IKGPTU), Jalandhar, Punjab, India
| | - Manish Sinha
- Laureate Institute of Pharmacy, Himachal Pradesh, India
| | - Nitin Bansal
- Department of Pharmacology, ASBASJSM College of Pharmacy, BELA, Ropar, Punjab, India
| |
Collapse
|
10
|
Abstract
Background:
This review presents the exhaustive exploration of 1,3,5-triazine scaffold
for development of analogs of anticancer drugs, over the last century. In the recent years, striazine
moiety has been one of the most studied moiety, showing broad-spectrum pharmacological
activities such as antibacterial, antifungal, analgesic, anti-HIV, antileishmanial, antitrypanosomal,
antimalarial and antiviral. Nowadays, many boffins are have become interested in novel
synthesis of s-triazine derivatives because of low cost and ease of availability.
Methods:
This scaffold has been extensively investigated mainly in the past decade. Many products
have been synthesized from different starting materials and these synthetic products possess
anticancer potential against various cell lines.
Results:
Many 1,3,5-triazine analogs exhibited significant anticancer activity in various models
and cell lines exhibiting different mechanisms. Some analogs have also shown good pharmacokinetic
parameters with less IC50 values.
Conclusion:
Various 1,3,5-triazine analogs have shown potent activities and may be regarded as
clinical candidates for future anticancer formulations. This review may be helpful to those researchers
seeking required information with regard to the drug design and medicinal properties of
1,3,5-triazine derivatives for selected targets. This review may also offer help to find and improve
clinically viable anticancer molecules.
Collapse
Affiliation(s)
- Rajeev Kumar
- Devsthali Vidyapeeth College of Pharmacy, Lalpur, Rudrapur (U.S. Nagar)-263148, Uttarakhand, India
| | - Neeraj Kumar
- Devsthali Vidyapeeth College of Pharmacy, Lalpur, Rudrapur (U.S. Nagar)-263148, Uttarakhand, India
| | | | - Anita Singh
- Department of Pharmacy, Kumaun University, Bhimtal, Nainital-263136, Uttarakhand, India
| |
Collapse
|
11
|
Malki A, Issa DA, Elbayaa RY, Ashour HM. Design and Synthesis of Novel Thioethers Derived from 1,5-Diphenyl-6- thioxo-6,7-dihydro-1H-pyrazolo[3,4-d]pyrimidin-4(5H)-ones as Antiangiogenic Agents. LETT DRUG DES DISCOV 2018. [DOI: 10.2174/1570180815666180518112321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background:
In attempts to discover new antiangiogenic entities, a novel series of
thioethers derived from 6-thioxo-6,7-dihydro-1H-pyrazolo[3,4-d]pyrimidine-4(5H)ones was considered
and designed.
</P><P>
Methods: Virtual screening was carried out through docking of the compounds into the vascular
endothelial growth factor and matrix metalloproteinase-9 binding sites. Molecular docking studies
were performed using Lamarckian Genetic Algorithm. Compounds possessing lowest ligandprotein
pairwise interaction energies were synthesized and screened for their antiproliferative activities
against five cancer cell lines namely MHCC97H (liver), MDA-MB 231 (Breast), Colo205 (Colon),
A549 (lung), A498 (kidney) and IC50 values were determined for the most potent compounds.
Additionally, they were tested for their antiangiogenic activities by testing their ability to inhibit
Human Umbilical Vein Endothelial Cell (HUVEC), cord formation and migration in response to
chemoattractant.
Results:
Three compounds 2a, 2b and 5b showed significant antiangiogenic activities. The allyl
thioether 2b was the most active with chemotaxis activity data nearly comparable to that of the positive
control, TNP-470. Additionally, 2a, 2b and 5b, contrary to TNP-470, interfered with the migration
of HUVECs in response to vascular endothelial growth factor rather than endothelial cells proliferation
or cord formation. Compounds 2a, 2b and 5b were also investigated for their inhibitory
effects on MMPs to investigate the relationship between their angiogenic activity and MMPs. Results
revealed that compound 2b was the most effective MMP-9 inhibitor in this series. Additionally,
compound 2b reduced the expression levels of VEGF and pERK1/2.
Conclusion:
Our results suggest that compound 2b is considered as a promising antiangiogenic
agent by targeting VEGF and MMP-9.
Collapse
Affiliation(s)
- Ahmed Malki
- Biomedical Science Department, College of Health Sciences, Qatar University, Doha, Qatar
| | - Doaa A.E Issa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Rasha Y. Elbayaa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| | - Hayam M.A. Ashour
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt
| |
Collapse
|
12
|
Makowska A, Sączewski F, Bednarski PJ, Sączewski J, Balewski Ł. Hybrid Molecules Composed of 2,4-Diamino-1,3,5-triazines and 2-Imino-Coumarins and Coumarins. Synthesis and Cytotoxic Properties. Molecules 2018; 23:molecules23071616. [PMID: 29970833 PMCID: PMC6099606 DOI: 10.3390/molecules23071616] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/30/2018] [Accepted: 07/02/2018] [Indexed: 01/22/2023] Open
Abstract
A series of 2-imino-2H-chromen-3-yl-1,3,5-triazine compounds 5⁻12, which are namely hybrids of 2,4-diamino-1,3,5-triazines and 2-imino-coumarins, was synthesized by reacting 2-(4,6-diamine-1,3,5-triazin-2-yl)acetonitriles 1⁻4 with 2-hydroxybenzaldehydes. After this, upon heating in aqueous DMF, 2-imino-2H-chromen-3-yl-1,3,5-triazines 10 and 12 were converted into the corresponding 2H-chromen-3-yl-1,3,5-triazines 13 and 14, which are essentially hybrids of 2,4-diamino-1,3,5-triazines and coumarins. The in vitro anticancer activity of the newly prepared compounds was evaluated against five human cancer cell lines: DAN-G, A-427, LCLC-103H, SISO and RT-4. The greatest cytotoxic activity displayed 4-[7-(diethylamino)-2-imino-2H-chromen-3-yl]-6-(4-phenylpiperazin-1-yl)-1,3,5-triazin-2-amine (11, IC50 in the range of 1.51⁻2.60 μM).
Collapse
Affiliation(s)
- Anna Makowska
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland.
| | - Franciszek Sączewski
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland.
| | - Patrick J Bednarski
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, L.-F.-Jahn Str., D-17489 Greifswald, Germany.
| | - Jarosław Sączewski
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland.
| | - Łukasz Balewski
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Medical University of Gdańsk, 80-416 Gdańsk, Poland.
| |
Collapse
|
13
|
Shan Y, Wang B, Zhang J. New strategies in achieving antiangiogenic effect: Multiplex inhibitors suppressing compensatory activations of RTKs. Med Res Rev 2018; 38:1674-1705. [DOI: 10.1002/med.21517] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/19/2018] [Accepted: 05/19/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Yuanyuan Shan
- Department of Pharmacy; The First Affiliated Hospital of Xi'an Jiaotong University; Xi'an China
| | - Binghe Wang
- Department of Chemistry; Center for Diagnostics and Therapeutics; Georgia State University; Atlanta GA USA
| | - Jie Zhang
- School of Pharmacy, Health Science Center; Xi'an Jiaotong University; Xi'an China
| |
Collapse
|
14
|
Abstract
Creolimax fragrantissima is a member of the ichthyosporean clade, the earliest branching holozoan lineage. The kinome of Creolimax is markedly reduced as compared to those of metazoans. In particular, Creolimax possesses a single non-receptor tyrosine kinase: CfrSrc, the homolog of c-Src kinase. CfrSrc is an active tyrosine kinase, and it is expressed throughout the lifecycle of Creolimax. In animal cells, the regulatory mechanism for Src involves tyrosine phosphorylation at a C-terminal site by Csk kinase. The lack of Csk in Creolimax suggests that a different mode of negative regulation must exist for CfrSrc. We demonstrate that CfrPTP-3, one of the 7 tyrosine-specific phosphatases (PTPs) in Creolimax, suppresses CfrSrc activity in vitro and in vivo. Transcript levels of CfrPTP-3 and two other PTPs are significantly higher than that of CfrSrc in the motile amoeboid and sessile multinucleate stages of the Creolimax life cycle. Thus, in the context of a highly reduced kinome, a pre-existing PTP may have been co-opted for the role of Src regulation. Creolimax represents a unique model system to study the adaptation of tyrosine kinase signaling and regulatory mechanisms.
Collapse
|
15
|
Lin FY, Esposito EX, Tseng YJ. LeadOp+R: Structure-Based Lead Optimization With Synthetic Accessibility. Front Pharmacol 2018; 9:96. [PMID: 29556192 PMCID: PMC5845126 DOI: 10.3389/fphar.2018.00096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
We previously described a structure-based fragment hopping for lead optimization using a pre-docked fragment database, “LeadOp,” that conceptually replaced “bad” fragments of a ligand with “good” fragments while leaving the core of the ligand intact thus improving the compound's activity. LeadOp was proven to optimize the query molecules and systematically developed improved analogs for each of our example systems. However, even with the fragment-based design from common building blocks, it is still a challenge for synthesis. In this work, “LeadOp+R” was developed based on 198 classical chemical reactions to consider the synthetic accessibility while optimizing leads. LeadOp+R first allows user to identify a preserved space defined by the volume occupied by a fragment of the query molecule to be preserved. Then LeadOp+R searches for building blocks with the same preserved space as initial reactants and grows molecules toward the preferred receptor-ligand interactions according to reaction rules from reaction database in LeadOp+R. Multiple conformers of each intermediate product were considered and evaluated at each step. The conformer with the best group efficiency score would be selected as the initial conformer of the next building block until the program finished optimization for all selected receptor-ligand interactions. The LeadOp+R method was tested with two biomolecular systems: Tie-2 kinase and human 5-lipoxygenase. The LeadOp+R methodology was able to optimize the query molecules and systematically developed improved analogs for each of our example systems. The suggested synthetic routes for compounds proposed by LeadOp+R were the same as the published synthetic routes devised by the synthetic/organic chemists.
Collapse
Affiliation(s)
- Fang-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Yufeng J Tseng
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.,Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| |
Collapse
|
16
|
Zhang L, Shan Y, Li C, Sun Y, Su P, Wang J, Li L, Pan X, Zhang J. Discovery of novel anti-angiogenesis agents. Part 6: Multi-targeted RTK inhibitors. Eur J Med Chem 2017; 127:275-285. [DOI: 10.1016/j.ejmech.2016.12.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 01/20/2023]
|
17
|
Wang X, He Y, Ren M, Liu S, Liu H, Huang G. Pd-Catalyzed Ligand-Free Synthesis of Arylated Heteroaromatics by Coupling of N-Heteroaromatic Bromides with Iodobenzene Diacetate, Iodosobenzene, or Diphenyliodonium Salts. J Org Chem 2016; 81:7958-62. [PMID: 27458647 DOI: 10.1021/acs.joc.6b01103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An efficient method for synthesizing arylated heteroaromatics has been reported via Pd-catalyzed ligand-free cross-coupling of N-heteroaromatic bromides with iodine(III) reagents under mild conditions. Iodobenzene diacetate, iodosobenzene, and diphenyliodonium salts act as ideal arylated sources in this reaction, producing bioactive aromatic-substituted pyridines and quinolines in moderate to high yields.
Collapse
Affiliation(s)
- Xiajun Wang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
| | - Yongqin He
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
| | - Mengdan Ren
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
| | - Shengkang Liu
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
| | - He Liu
- Department of Chemistry, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Guosheng Huang
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University , Lanzhou 730000, China
| |
Collapse
|
18
|
Gao GL, Xia W, Jain P, Yu JQ. Pd(II)-Catalyzed C3-Selective Arylation of Pyridine with (Hetero)arenes. Org Lett 2016; 18:744-7. [PMID: 26835845 DOI: 10.1021/acs.orglett.5b03712] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Palladium catalyzed, nondirected C3-selective arylation of pyridines with arenes and heteroarenes in the presence of 1,10-phenanthroline as the ligand has been developed. The optimized conditions allow for a highly C3-selective arylation of pyridines, affording various 3,3'-bipyridines and 3-arylpyridines.
Collapse
Affiliation(s)
- Guo-Lin Gao
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,The Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology , Harbin 150080, China
| | - Wujiong Xia
- The Academy of Fundamental and Interdisciplinary Science, Harbin Institute of Technology , Harbin 150080, China
| | - Pankaj Jain
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jin-Quan Yu
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
19
|
Development of anti-angiogenic tyrosine kinases inhibitors: molecular structures and binding modes. Cancer Chemother Pharmacol 2016; 77:905-26. [DOI: 10.1007/s00280-016-2961-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
|
20
|
Elsayed NMY, Abou El Ella DA, Serya RAT, Tolba MF, Shalaby R, Abouzid KAM. Design, synthesis and biological evaluation of indazole–pyrimidine based derivatives as anticancer agents with anti-angiogenic and antiproliferative activities. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00602c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three series of novel indazole–pyrimidine based compounds were designed, synthesized and biologically evaluated as VEGFR-2 kinase inhibitors.
Collapse
Affiliation(s)
- Nevine M. Y. Elsayed
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Dalal A. Abou El Ella
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Rabah A. T. Serya
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Mai F. Tolba
- Pharmacology and Toxicology Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Raed Shalaby
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| | - Khaled A. M. Abouzid
- Pharmaceutical Chemistry Department
- Faculty of Pharmacy
- Ain Shams University
- Abbassia
- Egypt
| |
Collapse
|
21
|
Pan P, Tian S, Sun H, Kong X, Zhou W, Li D, Li Y, Hou T. Identification and Preliminary SAR Analysis of Novel Type-I Inhibitors of TIE-2 via Structure-Based Virtual Screening and Biological Evaluation in in vitro Models. J Chem Inf Model 2015; 55:2693-704. [DOI: 10.1021/acs.jcim.5b00576] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Sheng Tian
- Institute
of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | | | - Xiaotian Kong
- Institute
of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | | | | | - Youyong Li
- Institute
of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | | |
Collapse
|
22
|
Investigation of new 2-aryl substituted Benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors targeting vascular endothelial growth factor receptor 2. Eur J Med Chem 2015; 103:29-43. [PMID: 26318056 DOI: 10.1016/j.ejmech.2015.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/28/2015] [Accepted: 08/11/2015] [Indexed: 02/06/2023]
Abstract
Vascular Endothelial Growth Factor (VEGF) pathway has emerged as one of the most important positive modulators of Angiogenesis, a central process implicated in tumour growth and metastatic dissemination. This led to the design and development of anti-VEGF monoclonal antibodies and small-molecule ATP-competitive VEGFR-inhibitors. In this study, we describe the synthesis and the biological evaluation of novel 2-aryl substituted benzothiopyrano-fused pyrimidines 1a-i, 2a-i and 3a-i. The ability of the compounds to target the VEGF pathway was determined in vitro exploiting the compounds' antiproliferative efficacy against HUVEC cells. The VEGFR-2 inhibition was confirmed by enzymatic assays on recombinant human kinase insert domain receptor (KDR), by cell-based phospho-VEGFR-2 inhibition assays, and by ex vivo rat aortic ring tests. The selectivity profile of the best performing derivatives belonging to series 2 was further explored combining modeling studies and additional assays in a panel of human cell lines and other kinases.
Collapse
|
23
|
Ragno R, Ballante F, Pirolli A, Wickersham RB, Patsilinakos A, Hesse S, Perspicace E, Kirsch G. Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches. J Comput Aided Mol Des 2015. [PMID: 26194852 DOI: 10.1007/s10822-015-9859-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors.
Collapse
Affiliation(s)
- Rino Ragno
- Rome Center for Molecular Design, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, P. le A. Moro 5, 00185, Rome, Italy,
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Geuns-Meyer S, Cee VJ, Deak HL, Du B, Hodous BL, Nguyen HN, Olivieri PR, Schenkel LB, Vaida KR, Andrews P, Bak A, Be X, Beltran PJ, Bush TL, Chaves MK, Chung G, Dai Y, Eden P, Hanestad K, Huang L, Lin MHJ, Tang J, Ziegler B, Radinsky R, Kendall R, Patel VF, Payton M. Discovery of N-(4-(3-(2-aminopyrimidin-4-yl)pyridin-2-yloxy)phenyl)-4-(4-methylthiophen-2-yl)phthalazin-1-amine (AMG 900), a highly selective, orally bioavailable inhibitor of aurora kinases with activity against multidrug-resistant cancer cell lines. J Med Chem 2015; 58:5189-207. [PMID: 25970324 DOI: 10.1021/acs.jmedchem.5b00183] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Efforts to improve upon the physical properties and metabolic stability of Aurora kinase inhibitor 14a revealed that potency against multidrug-resistant cell lines was compromised by increased polarity. Despite its high in vitro metabolic intrinsic clearance, 23r (AMG 900) showed acceptable pharmacokinetic properties and robust pharmacodynamic activity. Projecting from in vitro data to in vivo target coverage was not practical due to disjunctions between enzyme and cell data, complex and apparently contradictory indicators of binding kinetics, and unmeasurable free fraction in plasma. In contrast, it was straightforward to relate pharmacokinetics to pharmacodynamics and efficacy by following the time above a threshold concentration. On the basis of its oral route of administration, a selectivity profile that favors Aurora-driven pharmacology and its activity against multidrug-resistant cell lines, 23r was identified as a potential best-in-class Aurora kinase inhibitor. In phase 1 dose expansion studies with G-CSF support, 23r has shown promising single agent activity.
Collapse
Affiliation(s)
- Stephanie Geuns-Meyer
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Victor J Cee
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Holly L Deak
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Bingfan Du
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Brian L Hodous
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Hanh Nho Nguyen
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Philip R Olivieri
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Laurie B Schenkel
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Karina R Vaida
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Paul Andrews
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Annette Bak
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Xuhai Be
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Pedro J Beltran
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Tammy L Bush
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Mary K Chaves
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Grace Chung
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Yang Dai
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Patrick Eden
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Kelly Hanestad
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Liyue Huang
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Min-Hwa Jasmine Lin
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jin Tang
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Beth Ziegler
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Robert Radinsky
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Richard Kendall
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Vinod F Patel
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Marc Payton
- †Departments of Medicinal Chemistry, ‡Pharmaceutical Research and Development, §Pharmacokinetics and Drug Metabolism, ∥Molecular Structure, and ⊥Oncology Research, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, United States, and Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, United States
| |
Collapse
|
25
|
Pan X, Dong J, Shi Y, Shao R, Wei F, Wang J, Zhang J. Discovery of novel Bcr-Abl inhibitors with diacylated piperazine as the flexible linker. Org Biomol Chem 2015; 13:7050-66. [DOI: 10.1039/c5ob00430f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Forty-two compounds with flexible diacylated piperazine linkers were designed, synthesized and evaluated as novel Bcr-Abl inhibitors.
Collapse
Affiliation(s)
- Xiaoyan Pan
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| | - Jinyun Dong
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| | - Yaling Shi
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| | - Ruili Shao
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| | - Fen Wei
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| | - Jinfeng Wang
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| | - Jie Zhang
- School of Pharmacy
- Health Science Center
- Xi'an Jiaotong University
- Xi'an
- P.R. China
| |
Collapse
|
26
|
Horbert R, Pinchuk B, Johannes E, Schlosser J, Schmidt D, Cappel D, Totzke F, Schächtele C, Peifer C. Optimization of potent DFG-in inhibitors of platelet derived growth factor receptorβ (PDGF-Rβ) guided by water thermodynamics. J Med Chem 2014; 58:170-82. [PMID: 25007344 DOI: 10.1021/jm500373x] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In this study we report on the hit optimization of substituted 3,5-diaryl-pyrazin-2(1H)-ones toward potent and effective platelet-derived growth factor receptor (PDGF-R) β-inhibitors. Originally, the 3,5-diaryl-pyrazin-2-one core was derived from the marine sponge alkaloid family of hamacanthins. In our first series compound 2 was discovered as a promising hit showing strong activity against PDGF-Rβ in the kinase assay (IC50 = 0.5 μM). Furthermore, 2 was shown to be selective for PDGF-Rβ in a panel of 24 therapeutically relevant protein kinases. Molecular modeling studies on a PDGF-Rβ homology model using prediction of water thermodynamics suggested an optimization strategy for the 3,5-diaryl-pyrazin-2-ones as DFG-in binders by using a phenolic OH function to replace a structural water molecule in the ATP binding site. Indeed, we identified compound 38 as a highly potent inhibitor with an IC50 value of 0.02 μM in a PDGF-Rβ enzymatic assay also showing activity against PDGF-R dependent cancer cells.
Collapse
Affiliation(s)
- Rebecca Horbert
- Institute of Pharmacy, Christian-Albrechts-University of Kiel , Gutenbergstraße 76, D-24116 Kiel, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Singla P, Luxami V, Paul K. Benzimidazole-biologically attractive scaffold for protein kinase inhibitors. RSC Adv 2014. [DOI: 10.1039/c3ra46304d] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
28
|
Hari SB, Perera BGK, Ranjitkar P, Seeliger MA, Maly DJ. Conformation-selective inhibitors reveal differences in the activation and phosphate-binding loops of the tyrosine kinases Abl and Src. ACS Chem Biol 2013; 8:2734-43. [PMID: 24106839 DOI: 10.1021/cb400663k] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases.
Collapse
Affiliation(s)
- Sanjay B. Hari
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - B. Gayani K. Perera
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Pratistha Ranjitkar
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Markus A. Seeliger
- Department
of Pharmacological Sciences, Stony Brook University Medical School, Stony
Brook, New York 11794, United States
| | - Dustin J. Maly
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
29
|
Targeting tumor micro-environment for design and development of novel anti-angiogenic agents arresting tumor growth. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2013; 113:333-54. [PMID: 24139944 DOI: 10.1016/j.pbiomolbio.2013.10.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/05/2013] [Accepted: 10/08/2013] [Indexed: 12/12/2022]
Abstract
Angiogenesis: a process of generation of new blood vessels has been proved to be necessary for sustained tumor growth and cancer progression. Inhibiting angiogenesis pathway has long been remained a significant hope for the development of novel, effective and target orientated antitumor agents arresting the tumor proliferation and metastasis. The process of neoangiogenesis as a biological process is regulated by several pro- and anti-angiogenic factors, especially vascular endothelial growth factor, fibroblast growth factor, epidermal growth factor, hypoxia inducible factor 1 and transforming growth factor. Every endothelial cell destined for vessel formation is equipped with receptors for these angiogenic peptides. Moreover, numerous other angiogenic cytokines such as platelet derived growth factor (PGDF), placenta growth factor (PGF), nerve growth factor (NGF), stem-cell factor (SCF), and interleukins-2, 4, 6 etc. These molecular players performs critical role in regulating the angiogenic switch. Couple of decade's research in molecular aspects of tumor biology has unraveled numerous structural and functional mysteries of these angiogenic peptides. In present article, a detailed update on the functional and structural peculiarities of the various angiogenic peptides is described focusing on structural opportunities made available that has potential to be used to modulate function of these angiogenic peptides in developing therapeutic agents targeting neoplastic angiogenesis. The data may be useful in the mainstream of developing novel anticancer agents targeting tumor angiogenesis. We also discuss major therapeutic agents that are currently used in angiogenesis associated therapies as well as those are subject of active research or are in clinical trials.
Collapse
|
30
|
Pinchuk B, Johannes E, Gul S, Schlosser J, Schaechtele C, Totzke F, Peifer C. Marine derived hamacanthins as lead for the development of novel PDGFRβ protein kinase inhibitors. Mar Drugs 2013; 11:3209-23. [PMID: 24065162 PMCID: PMC3806475 DOI: 10.3390/md11093209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/01/2013] [Accepted: 08/08/2013] [Indexed: 12/04/2022] Open
Abstract
In this study, we report on pyrazin-2(1H)-ones as lead for the development of potent adenosine triphosphate (ATP) competitive protein kinase inhibitors with implications as anti-cancer drugs. Initially, we identified the pyrazin-2(1H)-one scaffold from hamacanthins (deep sea marine sponge alkaloids) by Molecular Modeling studies as core binding motif in the ATP pocket of receptor tyrosine kinases (RTK), which are validated drug targets for the treatment of various neoplastic diseases. Structure-based design studies on a human RTK member PDGFR (platelet-derived growth factor receptor) suggested a straight forward lead optimization strategy. Accordingly, we focused on a Medicinal Chemistry project to develop pyrazin-2(1H)-ones as optimized PDGFR binders. In order to reveal Structure-Activity-Relationships (SAR), we established a flexible synthetic route via microwave mediated ring closure to asymmetric 3,5-substituted pyrazin-2(1H)-ones and produced a set of novel compounds. Herein, we identified highly potent PDGFR binders with IC50 values in an enzymatic assay below µM range, and possessing significant activity against PDGFR dependent cancer cells. Thus, marine hamacanthin-derived pyrazin-2(1H)-ones showing interesting properties as lead for their further development towards potent PDGFR-inhibitors.
Collapse
Affiliation(s)
- Boris Pinchuk
- Institute of Pharmacy, University of Kiel, Gutenbergstraße 76, Kiel D-24118, Germany; E-Mails: (B.P.); (E.J.); (J.S.)
- European ScreeningPort GmbH, Schnackenburgallee 114, Hamburg D-22525, Germany; E-Mail:
| | - Eugen Johannes
- Institute of Pharmacy, University of Kiel, Gutenbergstraße 76, Kiel D-24118, Germany; E-Mails: (B.P.); (E.J.); (J.S.)
| | - Sheraz Gul
- European ScreeningPort GmbH, Schnackenburgallee 114, Hamburg D-22525, Germany; E-Mail:
| | - Joachim Schlosser
- Institute of Pharmacy, University of Kiel, Gutenbergstraße 76, Kiel D-24118, Germany; E-Mails: (B.P.); (E.J.); (J.S.)
| | - Christoph Schaechtele
- ProQinase GmbH, Breisacherstraße 117, Freiburg D-79106, Germany; E-Mails: (C.S.); (F.T.)
| | - Frank Totzke
- ProQinase GmbH, Breisacherstraße 117, Freiburg D-79106, Germany; E-Mails: (C.S.); (F.T.)
| | - Christian Peifer
- Institute of Pharmacy, University of Kiel, Gutenbergstraße 76, Kiel D-24118, Germany; E-Mails: (B.P.); (E.J.); (J.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +49-431-880-1137; Fax +49-431-880-1352
| |
Collapse
|
31
|
Oguro Y, Cary DR, Miyamoto N, Tawada M, Iwata H, Miki H, Hori A, Imamura S. Design, synthesis, and evaluation of novel VEGFR2 kinase inhibitors: Discovery of [1,2,4]triazolo[1,5-a]pyridine derivatives with slow dissociation kinetics. Bioorg Med Chem 2013; 21:4714-29. [DOI: 10.1016/j.bmc.2013.04.042] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/12/2013] [Accepted: 04/13/2013] [Indexed: 01/03/2023]
|
32
|
Patel PR, Sun H, Li SQ, Shen M, Khan J, Thomas CJ, Davis MI. Identification of potent Yes1 kinase inhibitors using a library screening approach. Bioorg Med Chem Lett 2013; 23:4398-403. [PMID: 23787099 PMCID: PMC3769177 DOI: 10.1016/j.bmcl.2013.05.072] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 05/17/2013] [Accepted: 05/20/2013] [Indexed: 12/21/2022]
Abstract
Yes1 kinase has been implicated as a potential therapeutic target in a number of cancers including melanomas, breast cancers, and rhabdomyosarcomas. Described here is the development of a robust and miniaturized biochemical assay for Yes1 kinase that was applied in a high throughput screen (HTS) of kinase-focused small molecule libraries. The HTS provided 144 (17% hit rate) small molecule compounds with IC₅₀ values in the sub-micromolar range. Three of the most potent Yes1 inhibitors were then examined in a cell-based assay for inhibition of cell survival in rhabdomyosarcoma cell lines. Homology models of Yes1 were generated in active and inactive conformations, and docking of inhibitors supports binding to the active conformation (DFG-in) of Yes1. This is the first report of a large high throughput enzymatic activity screen for identification of Yes1 kinase inhibitors, thereby elucidating the polypharmacology of a variety of small molecules and clinical candidates.
Collapse
Affiliation(s)
- Paresma R. Patel
- Basic Science Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, United States
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, United States
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Samuel Q. Li
- Oncogenomics Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892 United States
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Javed Khan
- Oncogenomics Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892 United States
| | - Craig J. Thomas
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, United States
| | - Mindy I. Davis
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, United States
| |
Collapse
|
33
|
Peng YH, Shiao HY, Tu CH, Liu PM, Hsu JTA, Amancha PK, Wu JS, Coumar MS, Chen CH, Wang SY, Lin WH, Sun HY, Chao YS, Lyu PC, Hsieh HP, Wu SY. Protein Kinase Inhibitor Design by Targeting the Asp-Phe-Gly (DFG) Motif: The Role of the DFG Motif in the Design of Epidermal Growth Factor Receptor Inhibitors. J Med Chem 2013; 56:3889-903. [DOI: 10.1021/jm400072p] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi-Hui Peng
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hui-Yi Shiao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Chih-Hsiang Tu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
- Institute of Bioinformatics
and Structural Biology, National Tsing Hua University, 101, Sect.
2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Pang-Min Liu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - John Tsu-An Hsu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Prashanth Kumar Amancha
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School
of Life Sciences, Pondicherry University, Kalapet, Puducherry 605014,
India
| | - Chun-Hwa Chen
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Sing-Yi Wang
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Wen-Hsing Lin
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Hsu-Yi Sun
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Yu-Sheng Chao
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Ping-Chiang Lyu
- Institute of Bioinformatics
and Structural Biology, National Tsing Hua University, 101, Sect.
2, Guangfu Road, Hsinchu 300, Taiwan, ROC
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and
Pharmaceutical Research, National Health Research Institutes, 35 Keyan
Road, Zhunan Town, Miaoli County 350, Taiwan, ROC
| |
Collapse
|
34
|
Arcari JT, Beebe JS, Berliner MA, Bernardo V, Boehm M, Borzillo GV, Clark T, Cohen BD, Connell RD, Frost HN, Gordon DA, Hungerford WM, Kakar SM, Kanter A, Keene NF, Knauth EA, LaGreca SD, Lu Y, Martinez-Alsina L, Marx MA, Morris J, Patel NC, Savage D, Soderstrom CI, Thompson C, Tkalcevic G, Tom NJ, Vajdos FF, Valentine JJ, Vincent PW, Wessel MD, Chen JM. Discovery and synthesis of novel 4-aminopyrrolopyrimidine Tie-2 kinase inhibitors for the treatment of solid tumors. Bioorg Med Chem Lett 2013; 23:3059-63. [DOI: 10.1016/j.bmcl.2013.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/25/2013] [Accepted: 03/04/2013] [Indexed: 11/26/2022]
|
35
|
Perspicace E, Jouan-Hureaux V, Ragno R, Ballante F, Sartini S, La Motta C, Da Settimo F, Chen B, Kirsch G, Schneider S, Faivre B, Hesse S. Design, synthesis and biological evaluation of new classes of thieno[3,2-d]pyrimidinone and thieno[1,2,3]triazine as inhibitor of vascular endothelial growth factor receptor-2 (VEGFR-2). Eur J Med Chem 2013; 63:765-81. [DOI: 10.1016/j.ejmech.2013.03.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 03/07/2013] [Accepted: 03/10/2013] [Indexed: 11/26/2022]
|
36
|
Backes A, Zech B, Felber B, Klebl B, Müller G. Small-molecule inhibitors binding to protein kinase. Part II: the novel pharmacophore approach of type II and type III inhibition. Expert Opin Drug Discov 2013; 3:1427-49. [PMID: 23506107 DOI: 10.1517/17460440802580106] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Protein kinases are essential enzymes propagating cellular signal transduction processes and consequently emerged as central targets for drug discovery against a wide range of diseases with a strong historical focus on oncological disorders. Several high-resolution crystal structures of various ATP-competitive inhibitors in complex with their target protein kinases have been determined and represent a wealth of detailed information about binding modes, inhibition mechanisms, and associated structure- activity relationships of target-bound small molecules. OBJECTIVE In this second part of a two-part review, we discuss the binding mode of inhibitors that target protein kinases in their inactive state. METHODS The scope of this review covers inhibitors for which crystal structures in complex with their respective kinases in the inactive state are available. RESULTS Structural parameters of both inhibitors and kinases contribute to the complexity of designing kinase inhibitors. Kinase inhibitors that target the inactive state of a kinase have become a novel rule in the design of highly active and selective compounds. The combination of high-resolution structures of ligand-enzyme complexes with especially detailed kinetic studies will in the long-term help to develop new low-molecular weight type II inhibitors.
Collapse
Affiliation(s)
- Ac Backes
- Sandoz GmbH, Biochemiestrasse 10, 6336 Langkampfen, Austria +43 5338 200 5235 ; +43 5338 200 460 ;
| | | | | | | | | |
Collapse
|
37
|
Abstract
VEGF is an important signaling protein involved in both vasculogenesis and angiogenesis. As an essential receptor protein tyrosine kinase propagating cellular signal transduction processes, VEGFR-2 is a central target for drug discovery against tumor-associated angiogenesis. Since the autophosphorylation of VEGFR-2 represents a key step in this signal pathway that contributes to angiogenesis, the discovery of small molecule inhibitors that block this reaction has attracted great interest for novel drugs research and development. Advances in the understanding of catalytic cleft and the conformational changes of DFG motif have resulted in the development of small molecule inhibitors known as type I and type II. High-resolution crystal structures of various inhibitors in complex with the receptor offer an insight into the relationship among binding modes, inhibition mechanisms, activity, selectivity and resistance. To control selectivity, improve activity and introduce intellectual property novelty, the strategies for the further development are discussed through structural and conformational analysis in this review.
Collapse
|
38
|
Yang J, Liu S, Zheng JF, Zhou JS. Room-Temperature Suzuki-Miyaura Coupling of Heteroaryl Chlorides and Tosylates. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200918] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
39
|
Smith AL, D’Angelo ND, Bo YY, Booker SK, Cee VJ, Herberich B, Hong FT, Jackson CLM, Lanman BA, Liu L, Nishimura N, Pettus LH, Reed AB, Tadesse S, Tamayo NA, Wurz RP, Yang K, Andrews KL, Whittington DA, McCarter JD, Miguel TS, Zalameda L, Jiang J, Subramanian R, Mullady EL, Caenepeel S, Freeman DJ, Wang L, Zhang N, Wu T, Hughes PE, Norman MH. Structure-Based Design of a Novel Series of Potent, Selective Inhibitors of the Class I Phosphatidylinositol 3-Kinases. J Med Chem 2012; 55:5188-219. [DOI: 10.1021/jm300184s] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Adrian L. Smith
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Noel D. D’Angelo
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Yunxin Y. Bo
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Shon K. Booker
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Victor J. Cee
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Brad Herberich
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Fang-Tsao Hong
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Claire L. M. Jackson
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Brian A. Lanman
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Longbin Liu
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Nobuko Nishimura
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Liping H. Pettus
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Anthony B. Reed
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Seifu Tadesse
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Nuria A. Tamayo
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Ryan P. Wurz
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Kevin Yang
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Kristin L. Andrews
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Douglas A. Whittington
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - John D. McCarter
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Tisha San Miguel
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Leeanne Zalameda
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Jian Jiang
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Raju Subramanian
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Erin L. Mullady
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Sean Caenepeel
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Daniel J. Freeman
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Ling Wang
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Nancy Zhang
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Tian Wu
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Paul E. Hughes
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| | - Mark H. Norman
- Departments
of Medicinal Chemistry, ‡Molecular Structure, ∥Pharmacokinetics and Drug Metabolism, ⊥High-Throughput
Screening/Molecular Pharmacology, #Oncology Research, and ×Pharmaceutics, Amgen Inc., One Amgen Center Drive, Thousand Oaks,
California 91320-1799, United States
- Departments
of Molecular Structure and ∇High-Throughput Screening/Molecular Pharmacology, Amgen Inc., 360 Binney Street, Cambridge,
Massachusetts 02142, United States
| |
Collapse
|
40
|
Rossi R, Bellina F, Lessi M. Selective Palladium-Catalyzed Suzuki-Miyaura Reactions of Polyhalogenated Heteroarenes. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100942] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
41
|
Fabbro D, Cowan-Jacob SW, Möbitz H, Martiny-Baron G. Targeting cancer with small-molecular-weight kinase inhibitors. Methods Mol Biol 2012; 795:1-34. [PMID: 21960212 DOI: 10.1007/978-1-61779-337-0_1] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Protein and lipid kinases fulfill essential roles in many signaling pathways that regulate normal cell functions. Deregulation of these kinase activities lead to a variety of pathologies ranging from cancer to inflammatory diseases, diabetes, infectious diseases, cardiovascular disorders, cell growth and survival. 518 protein kinases and about 20 lipid-modifying kinases are encoded by the human genome, and a much larger proportion of additional kinases are present in parasite, bacterial, fungal, and viral genomes that are susceptible to exploitation as drug targets. Since many human diseases result from overactivation of protein and lipid kinases due to mutations and/or overexpression, this enzyme class represents an important target for the pharmaceutical industry. Approximately one third of all protein targets under investigation in the pharmaceutical industry are protein or lipid kinases.The kinase inhibitors that have been launched, thus far, are mainly in oncology indications and are directed against a handful of protein and lipid kinases. With one exception, all of these registered kinase inhibitors are directed toward the ATP-site and display different selectivities, potencies, and pharmacokinetic properties. At present, about 150 kinase-targeted drugs are in clinical development and many more in various stages of preclinical development. Kinase inhibitor drugs that are in clinical trials target all stages of signal transduction from the receptor protein tyrosine kinases that initiate intracellular signaling, through second-messenger-dependent lipid and protein kinases, and protein kinases that regulate the cell cycle.This review provides an insight into protein and lipid kinase drug discovery with respect to achievements, binding modes of inhibitors, and novel avenues for the generation of second-generation kinase inhibitors to treat cancers.
Collapse
Affiliation(s)
- Doriano Fabbro
- Novartis Institutes for Biomedical Research, Expertise Platform Kinases, Basel, Switzerland.
| | | | | | | |
Collapse
|
42
|
Bonnet P, Mucs D, Bryce RA. Targeting the inactive conformation of protein kinases: computational screening based on ligand conformation. MEDCHEMCOMM 2012. [DOI: 10.1039/c1md00256b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
43
|
Sreedhar B, Yada D, Reddy PS. Nanocrystalline Titania-Supported Palladium(0) Nanoparticles for Suzuki-Miyaura Cross-Coupling of Aryl and Heteroaryl Halides. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
44
|
Shen F, Li X, Zhang X, Qin Z, Yin Q, Chen H, Zhang J. Synthesis of 1-Aryl-1H
-indazoles via a Ligand-Free Copper- Catalyzed Intramolecular Amination Reaction. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201190224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
45
|
Bamborough P, Brown MJ, Christopher JA, Chung CW, Mellor GW. Selectivity of kinase inhibitor fragments. J Med Chem 2011; 54:5131-43. [PMID: 21699136 DOI: 10.1021/jm200349b] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A kinase-focused screening set of fragments has been assembled and has proved successful for the discovery of ligand-efficient hits against many targets. Here we present some of our general conclusions from this exercise. Notably, we present the first profiling results for literature fragments that have previously been used as starting points for optimization against individual kinases. We consider the importance of screening format and the extent to which selectivity is helpful in selecting fragments for progression. Results are also outlined for fragments targeting the DFG-out conformation and for atypical kinases such as PIM1 and lipid kinases.
Collapse
Affiliation(s)
- Paul Bamborough
- GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
| | | | | | | | | |
Collapse
|
46
|
Mucs D, Bryce RA, Bonnet P. Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors. J Comput Aided Mol Des 2011; 25:569-81. [PMID: 21681554 DOI: 10.1007/s10822-011-9442-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 06/01/2011] [Indexed: 01/19/2023]
Abstract
The identification of new, potent and selective inhibitors of important protein kinase targets is a major goal of drug discovery. Here we analyze the crystal structures of 55 protein kinase complexes with Type II inhibitors and find they adopt a conserved twisted V-shape, with an angle of 121 ± 8° and twist of 78 ± 8°. The tightly conserved twist appears important in ensuring ligands curve around the protein backbone and towards the deep pocket. From this, we develop predictive pharmacophore- and shape-based screens to identify Type II inhibitors from a database which also contains Type I inhibitors as decoys. Both approaches exhibit a good level of discrimination for Type II molecules. The most effective pharmacophore model requires six features and three excluded volume regions. Shape-based screening using ROCS generally performs at least as well as pharmacophore approaches. There is only a moderate dependence of shape-based or pharmacophore-based screens on the underlying conformer generator (MOE, Macromodel, Omega and SPE), as well as on ligand linkage chemistry (amide and urea). Finally, we apply our approach to retrieval of Type II inhibitors from a modified version of the DUD database, containing over 104,000 compounds. We observe good enrichment, providing further evidence that the in silico screens developed here will constitute useful guides for identification of small molecule inhibitors targetting protein kinases in their inactive conformational state.
Collapse
Affiliation(s)
- Daniel Mucs
- School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | | | | |
Collapse
|
47
|
Backes AC, Müller G, Sennhenn PC. Design Principles of Deep Pocket-Targeting Protein Kinase Inhibitors. PROTEIN KINASES AS DRUG TARGETS 2011. [DOI: 10.1002/9783527633470.ch6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
48
|
Ishikawa M, Hashimoto Y. Improvement in aqueous solubility in small molecule drug discovery programs by disruption of molecular planarity and symmetry. J Med Chem 2011; 54:1539-54. [PMID: 21344906 DOI: 10.1021/jm101356p] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Minoru Ishikawa
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | | |
Collapse
|
49
|
Cee VJ, Schenkel LB, Hodous BL, Deak HL, Nguyen HN, Olivieri PR, Romero K, Bak A, Be X, Bellon S, Bush TL, Cheng AC, Chung G, Coats S, Eden PM, Hanestad K, Gallant PL, Gu Y, Huang X, Kendall RL, Lin MHJ, Morrison MJ, Patel VF, Radinsky R, Rose PE, Ross S, Sun JR, Tang J, Zhao H, Payton M, Geuns-Meyer SD. Discovery of a Potent, Selective, and Orally Bioavailable Pyridinyl-Pyrimidine Phthalazine Aurora Kinase Inhibitor. J Med Chem 2010; 53:6368-77. [DOI: 10.1021/jm100394y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | - Xuhai Be
- Pharmacokinetics and Drug Metabolism
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Ranjitkar P, Brock AM, Maly DJ. Affinity reagents that target a specific inactive form of protein kinases. ACTA ACUST UNITED AC 2010; 17:195-206. [PMID: 20189109 DOI: 10.1016/j.chembiol.2010.01.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/18/2010] [Accepted: 01/20/2010] [Indexed: 02/01/2023]
Abstract
A number of small-molecule inhibitors have been developed that target the catalytic domains of protein kinases that are not in an active conformation. An inactive form that has been observed in several kinases is the DFG-out conformation. This conformation is characterized by an almost 180 degrees rotation of the conserved Asp-Phe-Gly (DFG) motif in the ATP-binding cleft relative to the active form. However, the sequence and structural determinants that allow a kinase to stably adopt the DFG-out conformation are not known. Here, we characterize a series of inhibitors based on a general pharmacophore for this inactive form. We demonstrate that modified versions of these inhibitors can be used to study the thermodynamics and kinetics of ligand binding to DFG-out-adopting kinases and for enriching these kinases from complex protein mixtures.
Collapse
|