1
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Wang H, Blind RD, Shears SB. X-ray crystallographic analyses of 14 IPMK inhibitor complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593385. [PMID: 38766172 PMCID: PMC11100778 DOI: 10.1101/2024.05.09.593385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Inositol polyphosphate multikinase (IPMK) is a ubiquitously expressed kinase that has been linked to several cancers. Here, we report 14 new co-crystal structures (1.7Å - 2.0Å resolution) of human IPMK complexed with various IPMK inhibitors developed by another group. The new structures reveal two ordered water molecules that participate in hydrogen-bonding networks, and an unoccupied pocket in the ATP-binding site of human IPMK. New Protein Data Bank (PDB) codes of these IPMK crystal structures are: 8V6W (1.95Å), 8V6X (1.75Å), 8V6Y (1.70Å), 8V6Z (1.85Å), 8V70 (1.85Å), 8V71 (1.70Å), 8V72 (2.0Å), 8V73 (1.90Å), 8V74 (1.85Å), 8V75 (1.85Å), 8V76 (1.95Å), 8V77 (1.95Å), 8V78 (1.95Å), 8V79 (1.95Å).
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2
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Abdel Rahman DE, Fouad MA, Mohammed ER, El-Zoheiry HH, Abdelrasheed Allam H. Novel VEGFR-2 inhibitors as antiangiogenic and apoptotic agents via paracrine and autocrine cascades: Design, synthesis, and biological evaluation. Bioorg Chem 2023; 139:106678. [PMID: 37354661 DOI: 10.1016/j.bioorg.2023.106678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/31/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
Appertaining to its paracrine and autocrine signaling loops, VEGFR-2 succeeded in grabbing attention as one of the leading targets in cancer treatment. Based on the foregoing and our comprehensive studies regarding pharmacophoric features and activity of sorafenib, novel phenylpyridazinone based VEGFR-2 inhibitors 4, 6a-e, 7a,b, 9a,b, 12a-c, 13a,b, 14a,b, 15a,b, and 17a-d were optimized. An assortment of biological assays was conducted to assess the antiangiogenic and apoptotic activities of the synthesized derivatives. In vitro VEGFR-2 kinase assay verified the inhibitory activity of the synthesized derivatives with IC50 values from 49.1 to 418.0 nM relative to the reference drug sorafenib (IC50 = 81.8 nM). Antiproliferative activity against HUVECs revealed that compounds 2-{2-[2-(6-oxo-3-phenylpyridazin-1(6H)-yl)acetyl]hydrazineyl}-N-(p-tolyl)acetamide (12c) and 2-[(5-mercapto-4-methyl-4H-1,2,4-triazol-3-yl)methyl]-6-phenylpyridazin-3(2H)-one (13a) possessed superior activity (IC50 values = 11.5 and 12.3 nM, respectively) in comparison to sorafenib (IC50 = 23.2 nM). For the purpose of appraising their antiproliferative effect, derivatives 12c and 13a were exposed to cell cycle analysis, apoptotic, cell invasion and migration assays in addition to determination of VEGFR-2 in protein level. Moreover, cytotoxicity as well as selectivity index against WI-38 cell line was measured to examine safety of derivatives 12c and 13a. After that, molecular docking study was executed on the top five compounds in the in vitro VEGFR-2 kinase assay 6d, 12c, 13a, 14a and 17c to get a deep perception on binding mode of the synthesized compounds and correlate the design strategy with biological results. Finally, physicochemical, pharmacokinetic properties, and drug-likeness studies were performed on the top five derivative in in vitro VEGFR-2 kinase assay.
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Affiliation(s)
- Doaa E Abdel Rahman
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Marwa A Fouad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt; Pharmaceutical Chemistry Department, School of Pharmacy, New Giza University, Newgiza, km 22 Cairo-Alexandria Desert Road, Cairo, Egypt
| | - Eman R Mohammed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
| | - Haidy H El-Zoheiry
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt.
| | - Heba Abdelrasheed Allam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr El-Aini St., Cairo 11562, Egypt
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3
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Elrayess R, Elgawish MS, Nafie MS, Ghareb N, Yassen ASA. 2‐Phenylquinazolin‐4(3
H
)‐one scaffold as newly designed, synthesized VEGFR‐2 allosteric inhibitors with potent cytotoxicity through apoptosis. Arch Pharm (Weinheim) 2023:e2200654. [DOI: 10.1002/ardp.202200654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023]
Affiliation(s)
- Ranza Elrayess
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
| | - Mohamed S. Elgawish
- Medicinal Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
| | - Mohamed S. Nafie
- Chemistry Department (Biochemistry program), Faculty of Science Suez Canal University Ismailia Egypt
| | - Nagat Ghareb
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
| | - Asmaa S. A. Yassen
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy Suez Canal University Ismailia Egypt
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4
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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.
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Affiliation(s)
| | | | | | - Mutasem Taha
- Faculty of pharmacy,University of jordan, JORDAN
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5
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Salem MG, El-Maaty DMA, El-Deen YIM, Elesawy BH, Askary AE, Saleh A, Saied EM, Behery ME. Novel 1,3-Thiazole Analogues with Potent Activity against Breast Cancer: A Design, Synthesis, In Vitro, and In Silico Study. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27154898. [PMID: 35956848 PMCID: PMC9370021 DOI: 10.3390/molecules27154898] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/24/2022] [Accepted: 07/27/2022] [Indexed: 01/23/2023]
Abstract
Breast cancer is the most common cancer in women, responsible for over half a million deaths in 2020. Almost 75% of FDA-approved drugs are mainly nitrogen- and sulfur-containing heterocyclic compounds, implying the importance of such compounds in drug discovery. Among heterocycles, thiazole-based heterocyclic compounds have demonstrated a broad range of pharmacological activities. In the present study, a novel set of 1,3-thiazole derivatives was designed and synthesized based on the coupling of acetophenone derivatives, and phenacyl bromide was substituted as a key reaction step. The activity of synthesized compounds was screened against the proliferation of two breast cancer cell lines (MCF-7 and MDA-MB-231). Almost all compounds exhibited a considerable antiproliferative activity toward the breast cancer cells as compared to staurosporine, with no significant cytotoxicity toward the epithelial cells. Among the synthesized compounds, compound 4 exhibited the most potent antiproliferative activity, with an IC50 of 5.73 and 12.15 µM toward MCF-7 and MDA-MB-231 cells, respectively, compared to staurosporine (IC50 = 6.77 and 7.03 µM, respectively). Exploring the mechanistic insights responsible for the antiproliferative activity of compound 4 revealed that compound 4 possesses a significant inhibitory activity toward the vascular endothelial growth factor receptor-2 (VEGFR-2) with (IC50 = 0.093 µM) compared to Sorafenib (IC50 = 0.059 µM). Further, compound 4 showed the ability to induce programmed cell death by triggering apoptosis and necrosis in MCF-7 cells and to induce cell cycle arrest on MCF-7 cells at the G1 stage while decreasing the cellular population in the G2/M phase. Finally, detailed in silico molecular docking studies affirmed that this class of compounds possesses a considerable binding affinity toward VEGFR2 proteins. Overall, these results indicate that compound 4 could be a promising lead compound for developing potent anti-breast cancer compounds.
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Affiliation(s)
- Manar G. Salem
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (M.G.S.); (Y.I.M.E.-D.)
| | - Dina M. Abu El-Maaty
- Biochemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 415222, Egypt;
| | - Yassmina I. Mohey El-Deen
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt; (M.G.S.); (Y.I.M.E.-D.)
| | - Basem H. Elesawy
- Department of Pathology, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ahmad El Askary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Asmaa Saleh
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Essa M. Saied
- Chemistry Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
- Institute for Chemistry, Humboldt Universität zu Berlin, Brook-Taylor-Str. 2, 12489 Berlin, Germany
- Correspondence: (E.M.S.); (M.E.B.)
| | - Mohammed El Behery
- The Division of Biochemistry, Chemistry Department, Faculty of Science, Port Said University, Port Said 42526, Egypt
- Correspondence: (E.M.S.); (M.E.B.)
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6
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Davoine C, Pardo A, Pochet L, Fillet M. Fragment Hit Discovery and Binding Site Characterization by Indirect Affinity Capillary Electrophoresis: Application to Factor XIIa. Anal Chem 2021; 93:14802-14809. [PMID: 34694784 DOI: 10.1021/acs.analchem.1c03611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fragment-based lead discovery is a usual strategy in drug discovery to identify innovative lead compounds. The success of this approach strongly relies on the capacity to detect weak binders and characterize their binding site. NMR and X-ray crystallography are the conventional technologies used to tackle this challenge. However, their large protein consumption and the cost of equipment reduce their accessibility. Here, an affinity capillary electrophoresis methodology was developed that enables the detection of mM binders, the determination of dissociation constants, and the characterization of the fragment binding site. On the basis of multiple equilibrium theory, dissociation constants in the μM-mM range were determined, and a new methodology is proposed to establish graphically if two fragments bind the same protein pocket. The applicability of this methodology was demonstrated experimentally on coagulation factor XIIa by evaluating pairs of fragments with expected behavior. This study reinforces the significance of using affinity capillary electrophoresis to gather valuable information for medicinal chemistry projects.
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Affiliation(s)
- Clara Davoine
- Namur Medicine & Drug Innovation Center (NAMEDIC─NARILIS), University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium.,Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| | - Alissia Pardo
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
| | - Lionel Pochet
- Namur Medicine & Drug Innovation Center (NAMEDIC─NARILIS), University of Namur, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines (LAM), Department of Pharmacy, CIRM, University of Liege, Avenue Hippocrate 15, B36 Tour 4 +3, 4000 Liège, Belgium
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7
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Design and synthesis of novel furan, furo[2,3-d]pyrimidine and furo[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine derivatives as potential VEGFR-2 inhibitors. Bioorg Chem 2021; 116:105336. [PMID: 34530235 DOI: 10.1016/j.bioorg.2021.105336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 12/30/2022]
Abstract
Novel furan 6a-c, furo[2,3-d]pyrimidine 7a-f, 9, 10a-f, 12a,b, 14a-d and furo[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine 8a-f derivatives were designed based on their structural similarity to a previously described oxazole VEGFR-2 back pocket binding fragment. The designed compounds were synthesized and screened for their in vitro VEGFR-2 inhibitory activity where they exhibited good to moderate nanomolar inhibition with improved ligand efficiencies. 8b and 10c (IC50 = 38.72 ± 1.7 and 41.40 ± 1.8 nM, respectively) were equipotent to sorafenib and 6a, 6c, 7f, 8a, 8c, 10b, 10f, 12b, 14c and 14d showed good activity (IC50 = 43.31-98.31 nM). The furotriazolopyrimidines 8a-c and furopyrimidine derivative 10c were further evaluated for their in vitro antiproliferative activity against human umbilical vein endothelial cells (HUVECs) where 8b showed higher potency than sorafenib and resulted in cell cycle arrest at G2/M phase whereas 8c revealed good antiproliferative activity with cell cycle arrest at G1 phase. Moreover, 8a-c and 10c showed significant inhibitory effects on the invasion and migration of HUVECs. Molecular docking study was conducted to gain insight about the potential binding mode. The furo[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine derivatives 8b and 8c represent interesting starting point for antiangiogenic compounds based on their activity and favorable drug likeness profiles.
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8
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Anil D, Caykoylu EU, Sanli F, Gambacorta N, Karatas OF, Nicolotti O, Algul O, Burmaoglu S. Synthesis and biological evaluation of 3,5-diaryl-pyrazole derivatives as potential antiprostate cancer agents. Arch Pharm (Weinheim) 2021; 354:e2100225. [PMID: 34467575 DOI: 10.1002/ardp.202100225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Prostate cancer is the most frequently diagnosed tumor in men and the second leading cause of cancer-associated mortality in most developed countries. 3,5-Diaryl substituted pyrazole derivatives (20-28) were prepared starting from related chalcones and biologically evaluated for in vitro growth inhibition activity against PC3 and DU145 human prostate cancer cell lines. Compounds 23, 26, and 28 were found to be more potent as compared to the other halogen-substituted derivatives. Especially, the 2-bromo-substituted pyrazole derivative (26) was found to be more potent against PC3 and DU145 cells. Epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor 2 (VEGFR2) are known to be expressed in DU145 and PC3 cancer cells. The binding mode of the most selective compound 26 toward EGFR and VEGFR2 was investigated by employing docking simulations based on GLIDE standard precision (-5.912 and -6.949 kcal/mol, respectively).
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Affiliation(s)
- Derya Anil
- Department of Chemistry and Chemical Process Technologies, Erzurum Technical Science Vocational School, Atatürk University, Erzurum, Turkey
| | - Emine U Caykoylu
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
| | - Fatma Sanli
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey.,Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Nicola Gambacorta
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Omer F Karatas
- Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey.,Molecular Cancer Biology Laboratory, High Technology Application and Research Center, Erzurum Technical University, Erzurum, Turkey
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Oztekin Algul
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erzincan Binali Yildirim University, Erzincan, Turkey
| | - Serdar Burmaoglu
- Department of Chemistry, Faculty of Science, Atatürk University, Erzurum, Turkey
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9
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Tao Y, Hao X, Ding X, Cherukupalli S, Song Y, Liu X, Zhan P. Medicinal chemistry insights into novel CDC25 inhibitors. Eur J Med Chem 2020; 201:112374. [PMID: 32603979 DOI: 10.1016/j.ejmech.2020.112374] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
Cell division cycle 25 (CDC25) phosphatases, a kind of cell cycle regulators, have become an attractive target for drug discovery, as they have been found to be over-expressed in various human cancer cells. Several CDC25 inhibitors have achieved significant attention in clinical trials with possible mechanistic actions. Prompted by the significance of CDC25 inhibitors with medicinal chemistry prospect, it is an apt time to review the various drug discovery methods involved in CDC25 drug discovery including high throughput screening (HTS), virtual screening (VS), fragment-based drug design, substitution decorating approach, structural simplification approach and scaffold hopping method to seek trends and identify promising new avenues of CDC25 drug discovery.
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Affiliation(s)
- Yucen Tao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xia Hao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Xiao Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Srinivasulu Cherukupalli
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China
| | - Yuning Song
- Department of Clinical Pharmacy, Qilu Hospital of Shandong University, 250012, Jinan, China.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012, Jinan, Shandong, PR China.
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10
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Wang CY, Kim D, Zhu YK, Oh DC, Huang RZ, Wang HS, Liang D, Lee SK. Glechomanamides A-C, Germacrane Sesquiterpenoids with an Unusual Δ 8-7,12-Lactam Moiety from Salvia scapiformis and Their Antiangiogenic Activity. JOURNAL OF NATURAL PRODUCTS 2019; 82:3056-3064. [PMID: 31668072 DOI: 10.1021/acs.jnatprod.9b00648] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Three new germacrane sesquiterpenoid-type alkaloids with an unusual Δ8-7,12-lactam moiety, glechomanamides A-C (1-3), and two pairs of 7,12-hemiketal sesquiterpenoid epimers (4a/b, 5a/b) were isolated from Salvia scapiformis. Their structures were elucidated by spectroscopic methods including HRESIMS, IR, UV, and 1D and 2D NMR and also confirmed by single-crystal X-ray diffraction analysis. The chemical transformation of compounds 1-5 in a solution environment was analyzed by 2D NMR spectroscopy. The aza acetallactams (1-3) were stable in organic solvent, while single crystals of the hemiacetal esters (4a/b, 5a/b) underwent a tautomeric equilibrium after being dissolved. Single crystals of 4a, 4b, and 5a were obtained for the first time as their naturally occurring forms. Glechomanamide B (2) exhibited antiangiogenic activity by suppression of vascular endothelial growth factor (VEGF)-induced tube formation through modulation of VEGF receptor 2 (VEGFR2)-mediated signaling pathways in human umbilical vascular endothelial cells (HUVECs). In addition, compound 2 also showed the significant suppression of mRNA expression associated with glycolysis and angiogenesis biomarkers in high glucose (30 mM)-induced HUVECs. These findings suggest that compound 2 might be a potential lead compound candidate for the management of diabetic retinopathy.
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Affiliation(s)
- Cai Yi Wang
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Donghwa Kim
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yan Kui Zhu
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences , Guangxi Normal University , Guilin 541004 , People's Republic of China
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
| | - Ri Zhen Huang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences , Guangxi Normal University , Guilin 541004 , People's Republic of China
- Department of Pharmaceutical Engineering, School of Chemistry and Chemical Engineering , Southeast University , Nanjing 211189 , People's Republic of China
| | - Heng-Shan Wang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences , Guangxi Normal University , Guilin 541004 , People's Republic of China
| | - Dong Liang
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences , Guangxi Normal University , Guilin 541004 , People's Republic of China
| | - Sang Kook Lee
- Natural Products Research Institute, College of Pharmacy , Seoul National University , Seoul 08826 , Republic of Korea
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11
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Rampogu S, Baek A, Park C, Son M, Parate S, Parameswaran S, Park Y, Shaik B, Kim JH, Park SJ, Lee KW. Discovery of Small Molecules that Target Vascular Endothelial Growth Factor Receptor-2 Signalling Pathway Employing Molecular Modelling Studies. Cells 2019; 8:E269. [PMID: 30901950 PMCID: PMC6468367 DOI: 10.3390/cells8030269] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/08/2019] [Accepted: 03/16/2019] [Indexed: 12/15/2022] Open
Abstract
Angiogenesis is defined as the formation of new blood vessels and is a key phenomenon manifested in a host of cancers during which tyrosine kinases play a crucial role. Vascular endothelial growth factor receptor-2 (VEGFR-2) is pivotal in cancer angiogenesis, which warrants the urgency of discovering new anti-angiogenic inhibitors that target the signalling pathways. To obtain this objective, a structure-based pharmacophore model was built from the drug target VEGFR-2 (PDB code: 4AG8), complexed with axitinib and was subsequently validated and employed as a 3D query to retrieve the candidate compounds with the key inhibitory features. The model was escalated to molecular docking studies resulting in seven candidate compounds. The molecular docking studies revealed that the seven compounds displayed a higher dock score than the reference-cocrystallised compound. The GROningen MAchine for Chemical Simulations (GROMACS) package guided molecular dynamics (MD) results determined their binding mode and affirmed stable root mean square deviation. Furthermore, these compounds have preserved their key interactions with the residues Glu885, Glu917, Cys919 and Asp1046. The obtained findings deem that the seven compounds could act as novel anti-angiogenic inhibitors and may further assist as the prototype in designing and developing new inhibitors.
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Affiliation(s)
- Shailima Rampogu
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Ayoung Baek
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Chanin Park
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Minky Son
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Shraddha Parate
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Saravanan Parameswaran
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
| | - Yohan Park
- College of Pharmacy, Inje University, 197 Inje-ro, Gimhae, Gyeongnam 50834, Korea;
| | - Baji Shaik
- Department of Chemistry (BK 21 plus), Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, Gyeongnam 52828, Korea; (B.S.); (J.H.K.)
| | - Ju Hyun Kim
- Department of Chemistry (BK 21 plus), Research Institute of Natural Science (RINS), Gyeongsang National University, Jinju, Gyeongnam 52828, Korea; (B.S.); (J.H.K.)
| | - Seok Ju Park
- Department of Internal Medicine, College of Medicine, Busan Paik Hospital, Inje University, Gyeongnam 47392, Korea
| | - Keun Woo Lee
- Division of Life Sciences, Division of Applied Life Science (BK21 Plus), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju 52828, Korea; (S.R.); (A.B.); (C.P.); (M.S.); (S.P.); (S.P.)
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12
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Elsayed NM, Serya RA, Tolba MF, Ahmed M, Barakat K, Abou El Ella DA, Abouzid KA. Design, synthesis, biological evaluation and dynamics simulation of indazole derivatives with antiangiogenic and antiproliferative anticancer activity. Bioorg Chem 2019; 82:340-359. [DOI: 10.1016/j.bioorg.2018.10.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 10/26/2018] [Accepted: 10/31/2018] [Indexed: 02/07/2023]
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13
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Mioc M, Avram S, Bercean V, Kurunczi L, Ghiulai RM, Oprean C, Coricovac DE, Dehelean C, Mioc A, Balan-Porcarasu M, Tatu C, Soica C. Design, Synthesis and Biological Activity Evaluation of S-Substituted 1 H-5-Mercapto-1,2,4-Triazole Derivatives as Antiproliferative Agents in Colorectal Cancer. Front Chem 2018; 6:373. [PMID: 30234098 PMCID: PMC6134806 DOI: 10.3389/fchem.2018.00373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
Colon cancer is a widespread pathology with complex biochemical etiology based on a significant number of intracellular signaling pathways that play important roles in carcinogenesis, tumor proliferation and metastasis. These pathways function due to the action of key enzymes that can be used as targets for new anticancer drug development. Herein we report the synthesis and biological antiproliferative evaluation of a series of novel S-substituted 1H-3-R-5-mercapto-1,2,4-triazoles, on a colorectal cancer cell line, HT-29. Synthesized compounds were designed by docking based virtual screening (DBVS) of a previous constructed compound library against protein targets, known for their important role in colorectal cancer signaling: MEK1, ERK2, PDK1, VEGFR2. Among all synthesized structures, TZ55.7, which was retained as a possible PDK1 (phospholipid-dependent kinase 1) inhibitor, exhibited the most significant cytotoxic activity against HT-29 tumor cell line. The same compound alongside other two, TZ53.7 and TZ3a.7, led to a significant cell cycle arrest in both sub G0/G1 and G0/G1 phase. This study provides future perspectives for the development of new agents containing the 1,2,4-mercapto triazole scaffold with antiproliferative activities in colorectal cancer.
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Affiliation(s)
- Marius Mioc
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Sorin Avram
- Department of Computational Chemistry, Institute of Chemistry Timisoara of the Romanian Academy, Timisoara, Romania
| | | | - Ludovic Kurunczi
- Department of Computational Chemistry, Institute of Chemistry Timisoara of the Romanian Academy, Timisoara, Romania
| | - Roxana M Ghiulai
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Camelia Oprean
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania.,"Pius Brinzeu" Timisoara County Emergency Clinical Hospital, Oncogen Institute, Timisoara, Romania
| | - Dorina E Coricovac
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Cristina Dehelean
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Alexandra Mioc
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | | | - Calin Tatu
- "Pius Brinzeu" Timisoara County Emergency Clinical Hospital, Oncogen Institute, Timisoara, Romania
| | - Codruta Soica
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
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14
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Rampogu S, Baek A, Zeb A, Lee KW. Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations. BMC Cancer 2018. [PMID: 29514608 PMCID: PMC5842552 DOI: 10.1186/s12885-018-4050-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Angiogenesis is a process of formation of new blood vessels and is an important criteria demonstrated by cancer cells. Over a period of time, these cancer cells infect the other parts of the healthy body by a process called progression. The objective of the present article is to identify a drug molecule that inhibits angiogenesis and progression. Methods In this pursuit, ligand based pharmacophore virtual screening was employed, generating a pharmacophore model, Hypo1 consisting of four features. Furthermore, this Hypo1 was validated recruiting, Fischer’s randomization, test set method and decoy set method. Later, Hypo1 was allowed to screen databases such as Maybridge, Chembridge, Asinex and NCI and were further filtered by ADMET filters and Lipinski’s Rule of Five. A total of 699 molecules that passed the above criteria, were challenged against 4AG8, an angiogenic drug target employing GOLD v5.2.2. Results The results rendered by molecular docking, DFT and the MD simulations showed only one molecule (Hit) obeyed the back-to-front approach. This molecule displayed a dock score of 89.77, involving the amino acids, Glu885 and Cys919, Asp1046, respectively and additionally formed several important hydrophobic interactions. Furthermore, the identified lead molecule showed interactions with key residues when challenged with CDK2 protein, 1URW. Conclusion The lead candidate showed several interactions with the crucial residues of both the targets. Furthermore, we speculate that the residues Cys919 and Leu83 are important in the development of dual inhibitor. Therefore, the identified lead molecule can act as a potential inhibitor for angiogenesis and progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailima Rampogu
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Ayoung Baek
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Amir Zeb
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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15
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Eriocalyxin B, a natural diterpenoid, inhibited VEGF-induced angiogenesis and diminished angiogenesis-dependent breast tumor growth by suppressing VEGFR-2 signaling. Oncotarget 2018; 7:82820-82835. [PMID: 27756875 PMCID: PMC5347735 DOI: 10.18632/oncotarget.12652] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 10/02/2016] [Indexed: 12/29/2022] Open
Abstract
Eriocalyxin B (EriB), a natural ent-kaurane diterpenoid isolated from the plant Isodon eriocalyx var. laxiflora, has emerged as a promising anticancer agent. The effects of EriB on angiogenesis were explored in the present study. Here we demonstrated that the subintestinal vein formation was significantly inhibited by EriB treatment (10, 15 μM) in zebrafish embryos, which was resulted from the alteration of various angiogenic genes as shown in transcriptome profiling. In human umbilical vein endothelial cells, EriB treatment (50, 100 nM) could significantly block vascular endothelial growth factors (VEGF)-induced cell proliferation, tube formation, cell migration and cell invasion. Furthermore, EriB also caused G1 phase cell cycle arrest which was correlated with the down-regulation of the cyclin D1 and CDK4 leading to the inhibition of phosphorylated retinoblastoma protein expression. Investigation of the signal transduction revealed that EriB inhibited VEGF-induced phosphorylation of VEGF receptor-2 via the interaction with the ATP-binding sites according to the molecular docking simulations. The suppression of VEGFR-2 downstream signal transduction cascades was also observed. EriB was showed to inhibit new blood vessel formation in Matrigel plug model and mouse 4T1 breast tumor model. EriB (5 mg/kg/day) treatment was able to decrease tumor vascularization and suppress tumor growth and angiogenesis. Taken together, our findings suggested that EriB is a novel inhibitor of angiogenesis through modulating VEGFR-2 signaling pathway, which could be developed as a promising anti-angiogenic agent for treatment of angiogenesis-related human diseases, such as cancer.
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16
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Murray CW, Berdini V, Buck IM, Carr ME, Cleasby A, Coyle JE, Curry JE, Day JEH, Day PJ, Hearn K, Iqbal A, Lee LYW, Martins V, Mortenson PN, Munck JM, Page LW, Patel S, Roomans S, Smith K, Tamanini E, Saxty G. Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors. ACS Med Chem Lett 2015; 6:798-803. [PMID: 26191369 DOI: 10.1021/acsmedchemlett.5b00143] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/04/2015] [Indexed: 12/24/2022] Open
Abstract
The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either at the hinge or in the back pocket associated with the DFG-out conformation of the kinase. Modeling based on crystal structures of potent kinase inhibitors facilitated the "back-to-front" design of potent DDR1/2 inhibitors that incorporated one of the DFG-out fragments. Further optimization led to low nanomolar, orally bioavailable inhibitors that were selective for DDR1 and DDR2. The inhibitors were shown to potently inhibit DDR2 activity in cells but in contrast to unselective inhibitors such as dasatinib, they did not inhibit proliferation of mutant DDR2 lung SCC cell lines.
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Affiliation(s)
- Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Valerio Berdini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Ildiko M. Buck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Maria E. Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Anne Cleasby
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joseph E. Coyle
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Jayne E. Curry
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - James E. H. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Phillip J. Day
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Keisha Hearn
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Aman Iqbal
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Lydia Y. W. Lee
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Vanessa Martins
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Paul N. Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Joanne M. Munck
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Lee W. Page
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Sahil Patel
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Susan Roomans
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Kirsten Smith
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Emiliano Tamanini
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
| | - Gordon Saxty
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K
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Novel approaches for targeting kinases: allosteric inhibition, allosteric activation and pseudokinases. Future Med Chem 2014; 6:541-61. [PMID: 24649957 DOI: 10.4155/fmc.13.216] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein kinases are involved in many essential cellular processes and their deregulation can lead to a variety of diseases, including cancer. The pharmaceutical industry has invested heavily in the identification of kinase inhibitors to modulate these disease-promoting pathways, resulting in several successful drugs. However, the field is challenging as it is difficult to identify novel selective inhibitors with good pharmacokinetic/pharmacodynamic properties. In addition, resistance to kinase inhibitor treatment frequently arises. The identification of non-ATP site targeting ('allosteric') inhibitors, the identification of kinase activators and the expansion of kinase target space to include the less studied members of the family, including atypical- and pseudo-kinases, are potential avenues to overcome these challenges. In this perspective, the opportunities and challenges of following these approaches and others will be discussed.
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18
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Gadhe CG, Balupuri A, Kothandan G, Cho SJ. Theoretical Characterization of Binding Mode of Organosilicon Inhibitor with p38: Docking, MD Simulation and MM/GBSA Free Energy Approach. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.8.2494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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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.
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Affiliation(s)
- Rebecca Horbert
- Institute of Pharmacy, Christian-Albrechts-University of Kiel , Gutenbergstraße 76, D-24116 Kiel, Germany
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Shi H, Guo T, Zhang-Negrerie D, Du Y, Zhao K. Synthesis of substituted tetrahydron-1H-carbazol-1-one and analogs via PhI(OCOCF3)2-mediated oxidative C–C bond formation. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.02.083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Mortenson PN, Berdini V, O'Reilly M. Fragment-based approaches to the discovery of kinase inhibitors. Methods Enzymol 2014; 548:69-92. [PMID: 25399642 DOI: 10.1016/b978-0-12-397918-6.00003-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.
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22
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Sanphanya K, Phowichit S, Wattanapitayakul SK, Fokin VV, Vajragupta O. Novel VEGFR-2 kinase inhibitors identified by the back-to-front approach. Bioorg Med Chem Lett 2013; 23:2962-7. [PMID: 23562241 PMCID: PMC3942623 DOI: 10.1016/j.bmcl.2013.03.042] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 02/10/2013] [Accepted: 03/12/2013] [Indexed: 01/06/2023]
Abstract
We report a novel VEGFR-2 inhibitor, developed by the back-to-front approach. Docking experiments indicated that the 3-chloromethylphenylurea motif of the lead compound occupied the back pocket of VEGFR-2 kinase. An attempt was made to enhance the binding affinity of 1 by expanding the structure to access the front pocket using a triazole linker. A library of 1,4-(disubstituted)-1H-1,2,3-triazoles were screened in silico, and one compound (VH02) was identified with an IC50 against VEGFR-2 of 0.56μM. VH02 showed antiangiogenic effects, inhibiting tube formation in HUVEC cells (EA.hy926) at 0.3μM, 13 times lower than its cytotoxic dose. These enzymatic and cellular activities suggest that VH02 has potential as a lead for further optimization.
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Affiliation(s)
- Kingkan Sanphanya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayudya Rd, Bangkok 10400, Thailand
| | - Suwadee Phowichit
- Department of Pharmacology, Faculty of Medicine, Srinakharinwirot University, 114 Sukhumvit 23, Bangkok 10110, Thailand
| | - Suvara K. Wattanapitayakul
- Department of Pharmacology, Faculty of Medicine, Srinakharinwirot University, 114 Sukhumvit 23, Bangkok 10110, Thailand
| | - Valery V. Fokin
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Opa Vajragupta
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayudya Rd, Bangkok 10400, Thailand
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23
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Balewski Ł, Sączewski F, Gdaniec M, Bednarski PJ, Jara I. Synthesis of N-(2-pyridyl)imidazolidin-2-ones and 1-(2-pyridyl)-2,3,7,8-tetrahydro-1H-imidazo[2,1-b][1,3,5]triazepin-5(6H)-ones with potential biological activities. HETEROCYCL COMMUN 2013. [DOI: 10.1515/hc-2013-0125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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