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Giraud F, Pereira E, Anizon F, Moreau P. Recent Advances in Pain Management: Relevant Protein Kinases and Their Inhibitors. Molecules 2021; 26:molecules26092696. [PMID: 34064521 PMCID: PMC8124620 DOI: 10.3390/molecules26092696] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
The purpose of this review is to underline the protein kinases that have been established, either in fundamental approach or clinical trials, as potential biological targets in pain management. Protein kinases are presented according to their group in the human kinome: TK (Trk, RET, EGFR, JAK, VEGFR, SFK, BCR-Abl), CMGC (p38 MAPK, MEK, ERK, JNK, ASK1, CDK, CLK2, DYRK1A, GSK3, CK2), AGC (PKA, PKB, PKC, PKMζ, PKG, ROCK), CAMK, CK1 and atypical/other protein kinases (IKK, mTOR). Examples of small molecule inhibitors of these biological targets, demonstrating an analgesic effect, are described. Altogether, this review demonstrates the fundamental role that protein kinase inhibitors could play in the development of new pain treatments.
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Park H, Jung HY, Mah S, Kim K, Hong S. Kinase and GPCR polypharmacological approach for the identification of efficient anticancer medicines. Org Biomol Chem 2020; 18:8402-8413. [PMID: 33112339 DOI: 10.1039/d0ob01917h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Discovery of an anticancer medicine using a single target protein has often been unsuccessful due to the complexity of pathogenic mechanisms as well as the presence of redundant signaling pathways. In this work, we attempted to find promising anticancer drug candidates by simultaneously targeting casein kinase 1 delta (CK1δ) and muscarinic acetylcholine receptor M3 (M3R). Through the structure-based virtual screening and de novo design with the modified potential function for protein-ligand binding, a series of benzo[4,5]imidazo[1,2-a][1,3,5]triazine-2-amine (BITA) derivatives were identified as CK1δ inhibitors and also as M3R antagonists. The biochemical potencies of these bifunctional molecules reached the nanomolar and low-micromolar levels with respect to CK1δ and M3R, respectively. A common interaction feature in the calculated CK1δ-inhibitor and M3R-antagonist complexes is that the BITA moiety is well-stabilized in the orthosteric site of M3R and the hinge region of CK1δ through the establishment of the three hydrogen bonds and the hydrophobic contacts in the vicinity. The computational and experimental results found in this work exemplify the efficiency of kinase and GPCR polypharmacology in developing anticancer medicines.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology & Institute of Anticancer Medicine Development, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Republic of Korea.
| | - Hoi-Yun Jung
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Shinmee Mah
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Kewon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Sungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. and Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
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3
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Quinazoline-directed selective ortho-iodination for the synthesis of 2-(2-iodoaryl)-4-arylquinazolines. J Organomet Chem 2017. [DOI: 10.1016/j.jorganchem.2017.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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4
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Kim D, Park JY, Kim JH. Docking-based In SilicoScreening for Identification of Micromolar Inhibitors of Tropomyosin-related Kinase A from Natural Origin. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Daehyun Kim
- Department of Chemistry; Chung-Ang University; Seoul 06974 Korea
| | - Jung Youl Park
- Industry-Academic Cooperation Foundation; Hanbat National University; Daejeon 34158 Korea
| | - Ji-Hyun Kim
- National CRI-Center for Chemical Dynamics in Living Cells; Chung-Ang University; Seoul 06974 Korea
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Alam MS, Choi SU, Lee DU. Synthesis, anticancer, and docking studies of salicyl-hydrazone analogues: A novel series of small potent tropomyosin receptor kinase A inhibitors. Bioorg Med Chem 2016; 25:389-396. [PMID: 27856237 DOI: 10.1016/j.bmc.2016.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 11/01/2016] [Accepted: 11/02/2016] [Indexed: 01/22/2023]
Abstract
A series of novel salicyl-hydrazone analogues were synthesized and evaluated for their in vitro cytotoxic activities in five human cancer cell lines, namely, lung cancer (A549), ovarian cancer (SK-OV-3), skin cancer (SK-MEL-2), colon cancer (HCT15) and pancreatic cancer (MIA-PaCa-2) cells, and for their in vitro tropomyosin receptor kinase A (TrkA) inhibitory activities. Each of the compounds showed significant cytotoxicity against all cancer cells. Compound 3i was found to be most potent against all cancer cell lines with IC50 values of 2.46 (A549), 0.87 (SK-OV-3), 1.43 (SK-MEL-2), 0.89 (HCT15), and 0.48μM (MIA-PaCa-2), followed by compound 3l. Cytotoxicity of 3i was similar to that of doxorubicin (0.87μM) against HCT15 cells. Compounds 3i and 3l also showed highest TrkA inhibitory activities with IC50 values of 0.231 and 0.380μM, respectively. A SAR study of the series revealed that compounds with hydroxyl groups showed better cytotoxicity and TrkA inhibitory potency (in the following order 2,4-OH>2,3,4-OH>3,4-OH>4-OH) than compounds possessing electron donating or withdrawing groups on the benzylidenephenyl ring. Docking studies of compounds 3i and 3l conducted on the crystal structure of TrkA receptor (a promising target for anticancer agents) showed both had a high docking score and similar order of experimental TrkA inhibitory activities. The formation of several hydrogen bonds involving N and O containing moieties contributed most significantly to ligand binding and stabilization at the active site of the receptor. In addition, ligand-receptor complexes were further stabilized by π-cation, π-anion, amide-π stacked, and van der Waal's interactions. Conformational analyses showed ligand molecules adopted similar conformations at the receptor active site during interactions, but that the low energy optimized conformations of compounds 3i and 3l differed.
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Affiliation(s)
- Mohammad Sayed Alam
- Division of Bioscience, Dongguk University, Gyeongju 780-714, Republic of Korea; Department of Chemistry, Jagannath University, Dhaka 1100, Bangladesh
| | - Sang-Un Choi
- Center for Drug Discovery Technology, Korea Research Institute of Chemical Technology, 141 Gajeongro, Daejeon 34114, Republic of Korea
| | - Dong-Ung Lee
- Division of Bioscience, Dongguk University, Gyeongju 780-714, Republic of Korea.
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6
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Xu D, Meroueh SO. Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries. J Chem Inf Model 2016; 56:1139-51. [PMID: 27154487 DOI: 10.1021/acs.jcim.5b00709] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Virtual screening consists of docking libraries of small molecules to a target protein followed by rank-ordering of the resulting structures using scoring functions. The ability of scoring methods to distinguish between actives and inactives depends on several factors that include the accuracy of the binding pose during the docking step and the quality of the three-dimensional structure of the target. Here, we build on our previous work to introduce a new scoring approach (SVMGen) that uses machine learning trained with features from statistical pair potentials obtained from three-dimensional crystal structures. We use SVMGen and GlideScore to explore how enrichment or rank-ordering is affected by binding pose accuracy. To that end, we create a validation set that consists strictly of proteins whose crystal structure was solved in complex with their inhibitors. For the rank-ordering studies, we use crystal structures from PDBbind along with corresponding binding affinity data provided in the database. In addition to binding pose, we investigate the effect of using modeled structures for the target on the enrichment performance of SVMGen and GlideScore. To accomplish this, we generated homology models for protein kinases in DUD-E for which crystal structures are available to enable comparison of enrichment between modeled and crystal structure. We also generate homology models for kinases in SARfari for which there are many known small-molecule inhibitors but no known crystal structure. These models are used to assess the ability of SVMGen and GlideScore to distinguish between actives and decoys. We focus our work on protein kinases considering the wealth of structural and binding affinity data that exists for this family of proteins.
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Affiliation(s)
- David Xu
- Department of BioHealth Informatics, Indiana University School of Informatics and Computing , Indianapolis, Indiana 46202, United States
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Jeong Y, Lim SM, Hong S. Discovery of wrightiadione as a novel template for the TrkA kinase inhibitors. Bioorg Med Chem Lett 2015; 25:5186-9. [PMID: 26442778 DOI: 10.1016/j.bmcl.2015.09.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 11/19/2022]
Abstract
Enzymatic kinase assays and docking simulation studies have shown that the natural product wrightiadione displays inhibitory activity toward TrkA and PLK3. In this study, the template of wrightiadione served as a starting point for Trk inhibitor development campaigns. Molecular simulation provided structural insights for the design of derivatives that were efficiently generated by our recently developed 3-step tandem synthetic approach, resulting in the discovery of compound 2h with biochemical potency at the single-digit micromolar level.
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Affiliation(s)
- Yujeong Jeong
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea; Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sang Min Lim
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalization, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea; Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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8
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Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
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Puig de la Bellacasa R, Karachaliou N, Estrada-Tejedor R, Teixidó J, Costa C, Borrell JI. ALK and ROS1 as a joint target for the treatment of lung cancer: a review. Transl Lung Cancer Res 2015; 2:72-86. [PMID: 25806218 DOI: 10.3978/j.issn.2218-6751.2013.03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/25/2013] [Indexed: 12/14/2022]
Abstract
Rearrangements of the anaplastic lymphoma kinase (ALK) have been described in multiple malignancies, including non-small cell lung cancer (NSCLC). ALK fusions have gain of function properties while activating mutations in wild-type ALK can also occur within the tyrosine kinase domain. ALK rearrangements define a new molecular subtype of NSCLC that is exquisitely sensitive to ALK inhibition. Crizotinib, an orally available small molecule ATP-mimetic compound which was originally designed as a MET inhibitor, was recognized to have "off-target" anti-ALK activity and has been approved in the USA for the treatment of patients with ALK-positive NSCLC. Chromosomal rearrangements involving the ROS1 receptor tyrosine kinase have also been recently described in NSCLC, while crizotinib is currently under clinical trial in this molecular subset of NSCLC patients. The basic approaches of any computer aided drug design work in terms of structure and ligand based drug design. Details of each of these approaches should be covered with an emphasis on utilizing both in order to develop multi-targeted small-molecule kinase inhibitors. Such multi-targeted tyrosine kinase inhibitors can have antiproliferative activity against both ROS1and ALK rearranged NSCLC. Herein, we highlight the importance of targeting these proteins and the advances in optimizing more potent and selective ALK and ROS1 kinase inhibitors.
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Affiliation(s)
- Raimon Puig de la Bellacasa
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Niki Karachaliou
- Breakthrough Cancer Research Unit, Pangaea Biotech S.L, Barcelona, Spain
| | - Roger Estrada-Tejedor
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
| | - Carlota Costa
- Breakthrough Cancer Research Unit, Pangaea Biotech S.L, Barcelona, Spain
| | - José I Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, E-08017 Barcelona, Spain
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Shin Y, Yoo C, Moon Y, Lee Y, Hong S. Efficient Synthesis of Frutinone A and Its Derivatives through Palladium-Catalyzed CH Activation/Carbonylation. Chem Asian J 2014; 10:878-81. [DOI: 10.1002/asia.201402876] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Indexed: 12/14/2022]
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11
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Wei N, Chu E, Wipf P, Schmitz JC. Protein kinase d as a potential chemotherapeutic target for colorectal cancer. Mol Cancer Ther 2014; 13:1130-41. [PMID: 24634417 DOI: 10.1158/1535-7163.mct-13-0880] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein kinase D (PKD) signaling plays a critical role in the regulation of DNA synthesis, proliferation, cell survival, adhesion, invasion/migration, motility, and angiogenesis. To date, relatively little is known about the potential role of PKD in the development and/or progression of human colorectal cancer. We evaluated the expression of different PKD isoforms in colorectal cancer and investigated the antitumor activity of PKD inhibitors against human colorectal cancer. PKD2 was the dominant isoform expressed in human colon cancer cells. PKD3 expression was also observed but PKD1 expression, at both the RNA and protein levels, was not detected. Suppression of PKD using the small molecule inhibitors CRT0066101 and kb-NB142-70 resulted in low micromolar in vitro antiproliferative activity against multiple human colorectal cancer cell lines. Drug treatment was associated with dose-dependent suppression of PKD2 activation. Incubation with CRT0066101 resulted in G(2)-M phase arrest and induction of apoptosis in human colorectal cancer cells. Further studies showed that CRT0066101 treatment gave rise to a dose-dependent increase in expression of cleaved PARP and activated caspase-3, in addition to inhibition of AKT and ERK signaling, and suppression of NF-κB activity. Transfection of PKD2-targeted siRNAs resulted in similar effects on downstream pathways as observed with small molecule inhibitors. Daily administration of CRT0066101 resulted in significant inhibition of tumor growth in HCT116 xenograft nude mice. Taken together, our studies show that PKD plays a significant role in mediating growth signaling in colorectal cancer and may represent a novel chemotherapeutic target for the treatment of colorectal cancer.
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Affiliation(s)
- Ning Wei
- Authors' Affiliations: Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine; Cancer Therapeutics Program, University of Pittsburgh Cancer Institute; and Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
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12
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Park H, Choe H, Hong S. Virtual screening and biochemical evaluation to identify new inhibitors of mammalian target of rapamycin (mTOR). Bioorg Med Chem Lett 2013; 24:835-8. [PMID: 24393580 DOI: 10.1016/j.bmcl.2013.12.081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 11/30/2022]
Abstract
Mammalian target of rapamycin (mTOR) is a promising target for the development of anticancer medicines. Here, we report the first example for a successful application of the structure-based virtual screening to identify new mTOR inhibitors. Using the scoring function improved by implementing the ligand solvation effects on protein-ligand association, six novel mTOR inhibitors are found with IC50 values ranging from 8 to 60 μM. Because these new inhibitors are also computationally screened for having desirable physicochemical properties as a drug candidate, they deserve consideration for further development by structure-activity relationship studies to optimize the inhibitory and anticancer activities. Structural features relevant to the stabilization of the inhibitors in the ATP-binding site of mTOR are addressed in detail.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-Dong, Kwangjin-Ku, Seoul 143-747, Republic of Korea.
| | - Hyeonjeong Choe
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Sungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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Park H, Pham NC, Chun HJ, Ryu SE. Identification of Potent Leukocyte Common Antigen-Related Phosphatase Inhibitors via Structure-Based Virtual Screening. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.2006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Choe H, Kim J, Hong S. Structure-based design of flavone-based inhibitors of wild-type and T315I mutant of ABL. Bioorg Med Chem Lett 2013; 23:4324-7. [PMID: 23790540 DOI: 10.1016/j.bmcl.2013.05.095] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 05/26/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
The existence of drug resistance caused by mutations in the break-point cluster region-Abelson (BCR-ABL) tyrosine kinase domain remains a clinical challenge due to limited treatment options for effective CML therapies. Here, we report a series of flavone-based common inhibitors equipotent for the wild type and the most drug-resistant T315I mutant of BCR-ABL. The original hit 1 was extensively modified through a structure-based drug design strategy, especially by varying the C7 acetamide appendage of the scaffold to exploit extended interactions with P-loop residues. Structural features relevant to the stabilization of the newly identified inhibitors in the ATP-binding site of ABL are discussed in detail.
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Affiliation(s)
- Hyeonjeong Choe
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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Park H, Hong S, Kim J, Hong S. Discovery of Picomolar ABL Kinase Inhibitors Equipotent for Wild Type and T315I Mutant via Structure-Based de Novo Design. J Am Chem Soc 2013; 135:8227-37. [DOI: 10.1021/ja311756u] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hwangseo Park
- Department of Bioscience and
Biotechnology, Sejong University, Seoul
143-747, Korea
| | - Seunghee Hong
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea
| | - Jinhee Kim
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea
| | - Sungwoo Hong
- Department
of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Korea
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16
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Kim JY, Ryu CJ, Park H. Effects of Tropomyosin-Related Kinase A Inhibitors on the Proliferation of Human Lung Cancer Cells. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.4.1293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Hong S, Kim J, Yun SM, Lee H, Park Y, Hong SS, Hong S. Discovery of New Benzothiazole-Based Inhibitors of Breakpoint Cluster Region-Abelson Kinase Including the T315I Mutant. J Med Chem 2013; 56:3531-45. [DOI: 10.1021/jm301891t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Seunghee Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Jinhee Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Sun-Mi Yun
- Department of Biomedical Sciences,
College of Medicine, Inha University, Incheon
400-712, Korea
| | - Hyunseung Lee
- Department of Biomedical Sciences,
College of Medicine, Inha University, Incheon
400-712, Korea
| | - Yoonsu Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Soon-Sun Hong
- Department of Biomedical Sciences,
College of Medicine, Inha University, Incheon
400-712, Korea
| | - Sungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
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18
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Yuriev E, Ramsland PA. Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit 2013; 26:215-39. [PMID: 23526775 DOI: 10.1002/jmr.2266] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 01/16/2013] [Accepted: 01/19/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences; Monash University; Parkville; VIC; 3052; Australia
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19
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Park H, Park SY, Ryu SE. Homology modeling and virtual screening approaches to identify potent inhibitors of slingshot phosphatase 1. J Mol Graph Model 2013; 39:65-70. [DOI: 10.1016/j.jmgm.2012.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 10/29/2012] [Accepted: 10/30/2012] [Indexed: 01/26/2023]
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20
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Park H, Jeon JY, Ryu SE. Virtual Screening and Biochemical Evaluation of Mitogen-activated Protein Kinase Phosphatase 4 Inhibitors. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.11.3772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Park H, Park SY, Oh JJ, Ryu SE. Identification of Potent VHZ Phosphatase Inhibitors with Structure-Based Virtual Screening. ACTA ACUST UNITED AC 2012; 18:226-31. [DOI: 10.1177/1087057112463067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
VH1-like phosphatase Z (VHZ) has proved to be a promising target for the development of therapeutics for the treatment of human cancers. Here, we report the first example for a successful application of structure-based virtual screening to identify the novel small-molecule inhibitors of VHZ. These inhibitors revealed high potencies with the associated IC50 values ranging from 3 to 20 µM and were also screened for having desirable physicochemical properties as a drug candidate. Therefore, they deserve consideration for further development by structure-activity relationship studies to optimize inhibitory and anticancer activities. Structural features relevant to the stabilization of the newly identified inhibitors in the active site of VHZ are discussed in detail.
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Affiliation(s)
| | | | - Jung Jin Oh
- The Johns Hopkins University, Baltimore, MD, USA
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22
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Discovery of potent inhibitors of receptor protein tyrosine phosphatase sigma through the structure-based virtual screening. Bioorg Med Chem Lett 2012; 22:6333-7. [DOI: 10.1016/j.bmcl.2012.08.081] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 08/09/2012] [Accepted: 08/22/2012] [Indexed: 11/22/2022]
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Identification of common inhibitors of wild-type and T315I mutant of BCR-ABL through the parallel structure-based virtual screening. J Comput Aided Mol Des 2012; 26:983-92. [PMID: 22886487 DOI: 10.1007/s10822-012-9593-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 08/06/2012] [Indexed: 10/28/2022]
Abstract
Although the constitutively activated break-point cluster region-Abelson (BCR-ABL) tyrosine kinase was well known to be responsible for chronic myelogenous leukemia (CML), the existence of drug-resistant mutants of BCR-ABL has made it difficult to develop effective anti-CML drugs. Here, we report the first example for a successful application of the structure-based virtual screening to identify two common inhibitors equipotent for the wild type and the most drug-resistant T315I mutant of BCR-ABL. Because both inhibitors were screened for having desirable physicochemical properties as a drug candidate and revealed micromolar inhibitory activities, they deserve consideration for further development by structure-activity relationship (SAR) studies to optimize the anti-CML activity. We also address the structural features relevant to the stabilizations of the identified inhibitors in the ATP-binding sites. The results indicate that the inhibitors should be less stabilized by the hydrogen-bond interactions with the change of the receptor from the wild type to T315I mutant due to the replacement of the hydroxy group with the ethyl moiety in the ATP-binding site. Nonetheless, the inhibitors are found to be capable of maintaining the potency for the mutant through the strengthening of hydrophobic interactions to the extent sufficient to compensate for the loss of some hydrogen bonds. This differential binding mode may serve as key information for designing new common inhibitors of the wild type and T315I mutant of BCR-ABL.
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Park H, Lee S, Hong S. Discovery of MEK/PI3K dual inhibitor via structure-based virtual screening. Bioorg Med Chem Lett 2012; 22:4946-50. [PMID: 22771009 DOI: 10.1016/j.bmcl.2012.06.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/17/2022]
Abstract
Mitogen/extracellular signal-regulated kinase (MEK) and phosphoinositide 3-kinase (PI3Kα) are considered to be promising targets for the development of anticancer therapeutics. We report the first example of the successful application of structure-based virtual screening to identify novel inhibitors of MEK with IC(50) values ranging from 1 to 25 μM. One of the four newly identified MEK inhibitors was found to be also a potent inhibitor of PI3Kα with submicromolar inhibitory activity (IC(50)=0.3 μM). Because this dual inhibitor was screened for having desirable physicochemical properties as a drug candidate as well as the high inhibitory activities against MEK and PI3Kα, it warrants further development through structure-activity relationship (SAR) studies to optimize the inhibitory and anticancer activities. Structural features relevant to the stabilization of the dual inhibitor in the ATP-binding sites of MEK1 and PI3Kα are addressed in detail.
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Affiliation(s)
- Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul, Republic of Korea.
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Hong S, Kim J, Seo JH, Jung KH, Hong SS, Hong S. Design, Synthesis, and Evaluation of 3,5-Disubstituted 7-Azaindoles as Trk Inhibitors with Anticancer and Antiangiogenic Activities. J Med Chem 2012; 55:5337-49. [DOI: 10.1021/jm3002982] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Seunghee Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Jinhee Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
| | - Ju Hyeon Seo
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, 400-712, Korea
| | - Kyung Hee Jung
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, 400-712, Korea
| | - Soon-Sun Hong
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, 400-712, Korea
| | - Sungwoo Hong
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Korea
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Structure-based virtual screening approach to the discovery of p38 MAP kinase inhibitors. Bioorg Med Chem Lett 2012; 22:2195-9. [DOI: 10.1016/j.bmcl.2012.01.104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 01/25/2012] [Indexed: 11/23/2022]
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Ray D, Paul BK, Guchhait N. Effect of biological confinement on the photophysics and dynamics of a proton-transfer phototautomer: an exploration of excitation and emission wavelength-dependent photophysics of the protein-bound drug. Phys Chem Chem Phys 2012; 14:12182-92. [DOI: 10.1039/c2cp41292f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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