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Meng F, Liu J, Cao Z, Yu J, Steurer B, Yang Y, Wang Y, Cai X, Zhang M, Ren F, Aliper A, Ding X, Zhavoronkov A. Discovery of macrocyclic CDK2/4/6 inhibitors with improved potency and DMPK properties through a highly efficient macrocyclic drug design platform. Bioorg Chem 2024; 146:107285. [PMID: 38547721 DOI: 10.1016/j.bioorg.2024.107285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
Cyclin-dependent kinases (CDKs) are critical cell cycle regulators that are often overexpressed in tumors, making them promising targets for anti-cancer therapies. Despite substantial advancements in optimizing the selectivity and drug-like properties of CDK inhibitors, safety of multi-target inhibitors remains a significant challenge. Macrocyclization is a promising drug discovery strategy to improve the pharmacological properties of existing compounds. Here we report the development of a macrocyclization platform that enabled the highly efficient discovery of a novel, macrocyclic CDK2/4/6 inhibitor from an acyclic precursor (NUV422). Using dihedral angle scan and structure-based, computer-aided drug design to select an optimal ring-closing site and linker length for the macrocycle, we identified compound 8 as a potent new CDK2/4/6 inhibitor with optimized cellular potency and safety profile compared to NUV422. Our platform leverages both experimentally-solved as well as generative chemistry-derived macrocyclic structures and can be deployed to streamline the design of macrocyclic new drugs from acyclic starting compounds, yielding macrocyclic compounds with enhanced potency and improved drug-like properties.
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Affiliation(s)
- Fanye Meng
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Jinxin Liu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Zhongying Cao
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Jiaojiao Yu
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Barbara Steurer
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong
| | - Yilin Yang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Yazhou Wang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Xin Cai
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Man Zhang
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Feng Ren
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China
| | - Alex Aliper
- Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong
| | - Xiao Ding
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China.
| | - Alex Zhavoronkov
- Insilico Medicine Shanghai Ltd., Shanghai 201203, China; Insilico Medicine Hong Kong Ltd., Hong Kong Science and Technology Park, Hong Kong; Insilico Medicine AI Limited, Masdar City, Abu Dhabi 145748, United Arab Emirates.
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2
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Saruengkhanphasit R, Butkinaree C, Ornnork N, Lirdprapamongkol K, Niwetmarin W, Svasti J, Ruchirawat S, Eurtivong C. Identification of new 3-phenyl-1H-indole-2-carbohydrazide derivatives and their structure-activity relationships as potent tubulin inhibitors and anticancer agents: A combined in silico, in vitro and synthetic study. Bioorg Chem 2021; 110:104795. [PMID: 33730670 DOI: 10.1016/j.bioorg.2021.104795] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 01/09/2023]
Abstract
Virtual screening of commercially available molecular entities by using CDRUG, structure-based virtual screening, and similarity identified eight new derivatives of 3-phenyl-1H-indole-2-carbohydrazide with anti-proliferative activities. The molecules were tested experimentally for inhibition of tubulin polymerisation, which revealed furan-3-ylmethylene-3-phenyl-1H-indole-2-carbohydrazide (27a) as the most potent candidate. Molecule 27a was able to induce G2/M phase arrest in A549 cell line, similar to other tubulin inhibitors. Synthetic modifications of 27a were focussed on small substitutions on the furan ring, halogenation at R1 position and alteration of furyl connectivity. Derivatives 27b, 27d and 27i exhibited the strongest tubulin inhibition activities and were comparable to 27a. Bromine substitution at R1 position showed most prominent anticancer activities; derivatives 27b-27d displayed the strongest activities against HuCCA-1 cell line and were more potent than doxorubicin and the parent molecule 27a with IC50 values <0.5 μM. Notably, 27b with a 5-methoxy substitution on furan displayed the strongest activity against HepG2 cell line (IC50 = 0.34 µM), while 27d displayed stronger activity against A549 cell line (IC50 = 0.43 µM) compared to doxorubicin and 27a. Fluorine substitutions at the R1 position tended to show more modest anti-tubulin and anticancer activities, and change of 2-furyl to 3-furyl was tolerable. The new derivatives, thiophenyl 26, displayed the strongest activity against A549 cell line (IC50 = 0.19 µM), while 1-phenylethylidene 21b and 21c exhibited more modest anticancer activities with unclear mechanisms of action; 26 and 21c demonstrated G2/M phase arrest, but showed weak tubulin inhibitory properties. Molecular docking suggests the series inhibit tubulin at the colchicine site, in agreement with the experimental findings. The calculated molecular descriptors indicated that the molecules obey Lipinski's rule which suggests the molecules are drug-like structures.
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Affiliation(s)
- Rungroj Saruengkhanphasit
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Chutikarn Butkinaree
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand; National Omics Center, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Narittira Ornnork
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | | | - Worawat Niwetmarin
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand
| | - Jisnuson Svasti
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Somsak Ruchirawat
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand; Laboratory of Medicinal Chemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Commission on Higher Education (CHE), Ministry of Education, Bangkok 10400, Thailand
| | - Chatchakorn Eurtivong
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology (EHT), Commission on Higher Education (CHE), Ministry of Education, Bangkok 10400, Thailand.
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3
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Hirata M, Asano A, Magata Y, Ohmomo Y, Temma T. Synthesis and evaluation of novel radioiodinated anthranilate derivatives for in vivo imaging of vascular endothelial growth factor receptor with single-photon emission computed tomography. Ann Nucl Med 2020; 34:486-495. [PMID: 32385783 DOI: 10.1007/s12149-020-01475-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/28/2020] [Indexed: 12/01/2022]
Abstract
OBJECTIVE Angiogenesis facilitates tumor survival and promotes malignancy. The vascular endothelial growth factor (VEGF)/VEGF receptor (VEGFR) tyrosine kinase (TK) signaling pathway is a key factor mediating angiogenesis, suggesting that this pathway may be a target for diagnosis and therapy. In this study, we aimed to develop small molecule radioiodinated probes applicable for in vivo VEGFR imaging considering the versatility and usefulness of single-photon emission computed tomography (SPECT). METHODS We designed and synthesized four radioiodinated anthranilate compounds (6a-d) based on the structure of an anticancer drug targeting VEGFR-TK. The inhibitory potencies of corresponding cold compounds 4a-d and in vitro stability of compounds 6a-d were assessed by cellular proliferation inhibition assays and radio thin-layer chromatography after incubation in neutral solution. In vivo biodistributions were evaluated by determining radioactivity in tissues of interest after intravenous injection of test compounds in tumor-bearing mice. In vitro and in vivo blocking experiments using a selective VEGFR-TK inhibitor and SPECT/computed tomography (CT) imaging were performed in tumor-bearing mice. RESULTS The radioiodinated compounds 6a-d were obtained with more than 68.0% radiochemical yield and more than 95% radiochemical purity. Because compounds 4a-d showed high inhibitory potencies and compounds 6c and 6d showed high in vitro stability, 6c ([125I]m-NPAM) and 6d ([125I]p-NPAM) were further evaluated. Analysis of the in vivo biodistribution revealed a tumor to blood radioactivity ratio of greater than 4 at 24 h after [125I]p-NPAM administration. Accumulation of radioactivity in cultured tumor cells and tumor xenografts after [125I]p-NPAM administration was significantly blocked by inhibitor pretreatment. Tumors were clearly imaged at 24 h after [125I]p-NPAM injection with SPECT/CT in comparison to that in inhibitor-pretreated tumor-bearing mice. CONCLUSION [125I]p-NPAM may have potential applications as a lead compound for future development of a clinically usable VEGFR imaging probe for SPECT.
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Affiliation(s)
- Masahiko Hirata
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Akihiko Asano
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yasuhiro Magata
- Department of Molecular Imaging, Institute for Medical Photonics Research, Preeminent Medial Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Yoshiro Ohmomo
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan.
- Education and Research Center for Pharmaceutical Sciences, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan.
| | - Takashi Temma
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan.
- Department of Biofunctional Analysis, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan.
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Ji D, Zhang W, Xu Y, Zhang JJ. Design, synthesis and biological evaluation of anthranilamide derivatives as potent SMO inhibitors. Bioorg Med Chem 2020; 28:115354. [DOI: 10.1016/j.bmc.2020.115354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/17/2020] [Accepted: 01/31/2020] [Indexed: 01/20/2023]
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Gurbanov AV, Kuznetsov ML, Demukhamedova SD, Alieva IN, Godjaev NM, Zubkov FI, Mahmudov KT, Pombeiro AJL. Role of substituents on resonance assisted hydrogen bonding vs. intermolecular hydrogen bonding. CrystEngComm 2020. [DOI: 10.1039/c9ce01744e] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Resonance assisted hydrogen bond (RAHB) ring can be weakened/opened by a strong electron-donor (ED) group.
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Affiliation(s)
- Atash V. Gurbanov
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049–001 Lisboa
- Portugal
| | - Maxim L. Kuznetsov
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049–001 Lisboa
- Portugal
| | | | - Irada N. Alieva
- Institute for Physical Problems
- Baku State University
- Az 1148 Baku
- Azerbaijan
| | - Niftali M. Godjaev
- Institute for Physical Problems
- Baku State University
- Az 1148 Baku
- Azerbaijan
| | - Fedor I. Zubkov
- Organic Chemistry Department
- Faculty of Science
- Peoples' Friendship University of Russia (RUDN University)
- Moscow
- Russian Federation
| | - Kamran T. Mahmudov
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049–001 Lisboa
- Portugal
| | - Armando J. L. Pombeiro
- Centro de Química Estrutural
- Instituto Superior Técnico
- Universidade de Lisboa
- 1049–001 Lisboa
- Portugal
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Pro-angiogenic activity of isoliquiritin on HUVECs in vitro and zebrafish in vivo through Raf/MEK signaling pathway. Life Sci 2019; 223:128-136. [DOI: 10.1016/j.lfs.2019.03.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 12/21/2022]
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7
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Pillarisetti P, Myers KA. Identification and characterization of agnuside, a natural proangiogenic small molecule. Eur J Med Chem 2018; 160:193-206. [PMID: 30340142 PMCID: PMC6287603 DOI: 10.1016/j.ejmech.2018.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/02/2018] [Indexed: 12/29/2022]
Abstract
Due to its important role in regulating angiogenesis, vascular homeostasis and remodeling, and arteriogenesis in blood vascular and lymphatic endothelial cells, VEGFR2 stimulation has demonstrated promise in preclinical studies as an endovascular treatment for ischemic myocardial and peripheral disease. However, the short half-life of protein- and cytokine-based strategies and transduction inefficiency of vector-based modalities have hindered its clinical therapeutic applications. In the present study, we used a streamlined bioinformatics strategy combining ligand-based pharmacophore development and validation, virtual screening, and molecular docking to identify agnuside, a non-toxic, natural small molecule extract of Vitex agnus-castus possessing strong binding affinity, druggable physiochemical properties, and conformationally stable hydrogen bond and hydrophobic interactions with catalytically important residues within VEGFR2's active and allosteric sites. In-vitro proliferation, tube formation, and scratch wound migration assays provide evidence that agnuside promotes endothelial cell angiogenesis. Agnuside increases HUVEC proliferation with an EC50 of 1.376 μg/mL, stimulates tubulogenesis dose-dependently, and increases scratch wound migration rate. An additional angiogenesis assay suggests that agnuside may actively compete with a VEGFR2 inhibitor for VEGFR2 binding site occupancy to increase total length and branching length of HUVEC tubular networks. Chemometric analysis of molecular interaction fields (MIFs) by partial least squares (PLS)-derived quantitative structure activity relationship (QSAR) analysis and MIF contours provides the framework for the formulation of agnuside analogues possessing greater potency. Our research supports that agnuside may be a lead molecule for therapeutic angiogenesis.
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Affiliation(s)
- Piyush Pillarisetti
- Department of Biology, University of Pennsylvania, 433 S University Avenue, Philadelphia, PA, 19104, USA.
| | - Kenneth A Myers
- Department of Biological Sciences, 600 S 43rd Street, Philadelphia, PA, 19104, USA.
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Bártová K, Čechová L, Procházková E, Socha O, Janeba Z, Dračínský M. Influence of Intramolecular Charge Transfer and Nuclear Quantum Effects on Intramolecular Hydrogen Bonds in Azopyrimidines. J Org Chem 2017; 82:10350-10359. [PMID: 28829606 DOI: 10.1021/acs.joc.7b01810] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Intramolecular hydrogen bonds (IMHBs) in 5-azopyrimidines are investigated by NMR spectroscopy and DFT computations that involve nuclear quantum effects. A series of substituted 5-phenylazopyrimidines with one or two hydrogen bond donors able to form IMHBs with the azo group is prepared by azo coupling. The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is determined by variable temperature NMR spectroscopy and it is demonstrated that the barrier is significantly affected by intramolecular charge transfer. Through-hydrogen-bond scalar coupling is investigated in 15N labeled compounds and the stability of the IMHBs is correlated with experimental NMR parameters and rationalized by path integral molecular dynamics simulations that involve nuclear quantum effects. Detailed information on the hydrogen bond geometry upon hydrogen-to-deuterium isotope exchange is obtained from a comparison of experimental and calculated NMR data.
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Affiliation(s)
- Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Faculty of Science, Charles University , 116 36 Prague, Czech Republic
| | - Lucie Čechová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic.,Department of Chemistry of Natural Compounds, University of Chemistry and Technology Prague , Technická 5, 166 28 Prague, Czech Republic
| | - Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague, Czech Republic
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9
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Wang Y, Guo G, Yang BR, Xin QQ, Liao QW, Lee SMY, Hu YJ, Chen KJ, Cong WH. Synergistic effects of Chuanxiong-Chishao herb-pair on promoting angiogenesis at network pharmacological and pharmacodynamic levels. Chin J Integr Med 2017; 23:654-662. [PMID: 28551771 DOI: 10.1007/s11655-017-2408-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To investigate the synergistic effects of Chuanxiong-Chishao herb-pair (CCHP) on promoting angiogenesis in silico and in vivo. METHODS The mechanisms of action of an herb-pair, Chuanxiong-Chishao, were investigated using the network pharmacological and pharmacodynamic strategies involving computational drug target prediction and network analysis, and experimental validation. A set of network pharmacology methods were created to study the herbs in the context of targets and diseases networks, including prediction of target profiles and pharmacological actions of main active compounds in Chuanxiong and Chishao. Furthermore, the therapeutic effects and putative molecular mechanisms of Chuanxiong-Chishao actions were experimentally validated in a chemical-induced vascular insuffificiency model of transgenic zebrafifish in vivo. The mRNA expression of the predicted targets were further analyzed by real-time polymerase chain reaction (RT-PCR). RESULTS The computational prediction results found that the compounds in Chuanxiong have antithrombotic, antihypertensive, antiarrhythmic, and antiatherosclerotic activities, which were closely related to protecting against hypoxic-ischemic encephalopathy, ischemic stroke, myocardial infarction and heart failure. In addition, compounds in Chishao were found to participate in anti-inflflammatory effect and analgesics. Particularly, estrogen receptor α (ESRα) and hypoxia-inducible factor 1-α (HIF-1α) were the most important potential protein targets in the predicted results. In vivo experimental validation showed that post-treatment of tetramethylpyrazine hydrochloride (TMP•HCl) and paeoniflorin (PF) promoted the regeneration of new blood vessels in zebrafifish involving up-regulating ESRα mRNA expression. Co-treatment of TMP•HCl and PF could enhance the vessel sprouting in chemical-induced vascular insuffificiency zebrafifish at the optimal compatibility proportion of PF 10 μmol/L with TMP•HCl 1 μmol/L. CONCLUSIONS The network pharmacological strategies combining drug target prediction and network analysis identified some putative targets of CCHP. Moreover, the transgenic zebrafifish experiments demonstrated that the Chuanxiong-Chishao combination synergistically promoted angiogenic activity, probably involving ESRα signaling pathway.
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Affiliation(s)
- Yan Wang
- Clinical Medical College, Beijing University of Chinese Medicine, Beijing, 100029, China.,Laboratory of Cardiovascular Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China.,State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Gang Guo
- Department of Acupuncture and Moxibustion, Qilu Hospital Affiliated to Shandong University, Jinan, 250012, China
| | - Bin-Rui Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Qi-Qi Xin
- Laboratory of Cardiovascular Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China
| | - Qi-Wen Liao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Yuan-Jia Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China
| | - Ke-Ji Chen
- Laboratory of Cardiovascular Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China.
| | - Wei-Hong Cong
- Laboratory of Cardiovascular Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100091, China
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Structure-based discovery of novel 4,5,6-trisubstituted pyrimidines as potent covalent Bruton’s tyrosine kinase inhibitors. Bioorg Med Chem Lett 2016; 26:3052-3059. [DOI: 10.1016/j.bmcl.2016.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/19/2016] [Accepted: 05/04/2016] [Indexed: 11/23/2022]
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11
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Dračínský M, Čechová L, Hodgkinson P, Procházková E, Janeba Z. Resonance-assisted stabilisation of hydrogen bonds probed by NMR spectroscopy and path integral molecular dynamics. Chem Commun (Camb) 2016; 51:13986-9. [PMID: 26245988 DOI: 10.1039/c5cc05199a] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Path integral molecular dynamics and experimental NMR data are used to investigate resonance-assisted hydrogen bonds (RAHBs). When nuclear delocalisation is included in chemical shift calculations, the agreement with experiment is excellent, while static calculations show very poor performance. The results support the concept of RAHB, which has recently been questioned.
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Affiliation(s)
- M Dračínský
- Institute of Organic Chemistry and Biochemistry, AS CR, Flemingovo nám. 2, 166 10 Prague, Czech Republic.
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Zhao H, Huang H, Lin S. Chemical approaches to angiogenesis in development and regeneration. Methods Cell Biol 2016; 134:369-76. [PMID: 27312498 DOI: 10.1016/bs.mcb.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Vascular endothelial cells are essential building blocks of angiogenesis, which is required for normal embryonic development and tissue regeneration. In this chapter, we describe how to use transgenic zebrafish embryos expressing vascular-specific green fluorescent protein to evaluate differentiation, growth, and morphogenesis of endothelial cells. When combined with instrument automation and computational analysis, this method allows high-throughput screening for biologically active small chemical molecules that are effective in promoting angiogenesis. These molecules can be validated in mammalian endothelial cell differentiation and proliferation assays. These studies provide new reagents and therapeutic candidates for regenerative medicine studies.
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Affiliation(s)
- H Zhao
- University of California Los Angeles, Los Angeles, CA, United States; Jinan University, Guangzhou, China
| | - H Huang
- University of California Los Angeles, Los Angeles, CA, United States
| | - S Lin
- University of California Los Angeles, Los Angeles, CA, United States
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13
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Peng S, Zhang Y, Peng H, Ke Z, Xu L, Su T, Tsung A, Tohme S, Huang H, Zhang Q, Lencioni R, Zeng Z, Peng B, Chen M, Kuang M. Intracellular autocrine VEGF signaling promotes EBDC cell proliferation, which can be inhibited by Apatinib. Cancer Lett 2016; 373:193-202. [PMID: 26805764 DOI: 10.1016/j.canlet.2016.01.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/06/2016] [Accepted: 01/12/2016] [Indexed: 12/17/2022]
Abstract
Tumor cells produce vascular endothelial growth factor (VEGF) which can interact with membrane or cytoplasmic VEGF receptors (VEGFRs) to promote cell growth. We aimed to investigate the role of extracellular/intracellular autocrine VEGF signaling and Apatinib, a highly selective VEGFR2 inhibitor, in extrahepatic bile duct cancer (EBDC). We found conditioned medium or recombinant human VEGF treatment promoted EBDC cell proliferation through a phospholipase C-γ1-dependent pathway. This pro-proliferative effect was diminished by VEGF, VEGFR1 or VEGFR2 neutralizing antibodies, but more significantly suppressed by intracellular VEGFR inhibitor. The rhVEGF induced intracellular VEGF signaling by promoting nuclear accumulation of pVEGFR1/2 and enhancing VEGF promoter activity, mRNA and protein expression. Internal VEGFR2 inhibitor Apatinib significantly inhibited intracellular VEGF signaling, suppressed cell proliferation in vitro and delayed xenograft tumor growth in vivo, while anti-VEGF antibody Bevacizumab showed no effect. Clinically, overexpression of pVEGFR1 and pVEGFR2 was significantly correlated with poorer overall survival (P = .007 and P = .020, respectively). In conclusion, the intracellular autocrine VEGF loop plays a predominant role in VEGF-induced cell proliferation. Apatinib is an effective intracellular VEGF pathway blocker that presents a great therapeutic potential in EBDC.
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Affiliation(s)
- Sui Peng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yanyan Zhang
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Hong Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Lixia Xu
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Tianhong Su
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Allan Tsung
- Department of Surgery, University of Pittsburgh, Dallas, TX, USA
| | - Samer Tohme
- Department of Surgery, University of Pittsburgh, Dallas, TX, USA
| | - Hai Huang
- Department of Surgery, University of Pittsburgh, Dallas, TX, USA
| | - Qiuyang Zhang
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Riccardo Lencioni
- Division of Vascular Interventional Radiology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, USA
| | - Zhirong Zeng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Baogang Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Minhu Chen
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
| | - Ming Kuang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Division of Interventional Ultrasound, Department of Medical Ultrasound, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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Peng YH, Ueng SH, Tseng CT, Hung MS, Song JS, Wu JS, Liao FY, Fan YS, Wu MH, Hsiao WC, Hsueh CC, Lin SY, Cheng CY, Tu CH, Lee LC, Cheng MF, Shia KS, Shih C, Wu SY. Important Hydrogen Bond Networks in Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitor Design Revealed by Crystal Structures of Imidazoleisoindole Derivatives with IDO1. J Med Chem 2015; 59:282-93. [PMID: 26642377 DOI: 10.1021/acs.jmedchem.5b01390] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), promoting immune escape of tumors, is a therapeutic target for the cancer immunotherapy. A number of IDO1 inhibitors have been identified, but only limited structural biology studies of IDO1 inhibitors are available to provide insights on the binding mechanism of IDO1. In this study, we present the structure of IDO1 in complex with 24, a NLG919 analogue with potent activity. The complex structure revealed the imidazole nitrogen atom of 24 to coordinate with the heme iron, and the imidazoleisoindole core situated in pocket A with the 1-cyclohexylethanol moiety extended to pocket B to interact with the surrounding residues. Most interestingly, 24 formed an extensive hydrogen bond network with IDO1, which is a distinct feature of IDO1/24 complex structure and is not observed in the other IDO1 complex structures. Further structure-activity relationship, UV spectra, and structural biology studies of several analogues of 24 demonstrated that extensive hydrophobic interactions and the unique hydrogen bonding network contribute to the great potency of imidazoleisoindole derivatives. These results are expected to facilitate the structure-based drug design of new IDO inhibitors.
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Affiliation(s)
- Yi-Hui Peng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Shau-Hua Ueng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chen-Tso Tseng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Ming-Shiu Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Jen-Shin Song
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Jian-Sung Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Fang-Yu Liao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Yu-Shiou Fan
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Mine-Hsine Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Wen-Chi Hsiao
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Ching-Cheng Hsueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chia-Yi Cheng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chih-Hsiang Tu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Lung-Chun Lee
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Ming-Fu Cheng
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Kak-Shan Shia
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Chuan Shih
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
| | - Su-Ying Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan, ROC
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15
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Ruan JQ, Li S, Li YP, Wu WJ, Lee SMY, Yan R. The Presystemic Interplay between Gut Microbiota and Orally Administered Calycosin-7-O-β-d-Glucoside. Drug Metab Dispos 2015; 43:1601-11. [DOI: 10.1124/dmd.115.065094] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/22/2015] [Indexed: 12/31/2022] Open
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16
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Chen LY. Computing membrane-AQP5-phosphatidylserine binding affinities with hybrid steered molecular dynamics approach. Mol Membr Biol 2015; 32:19-25. [PMID: 25955791 DOI: 10.3109/09687688.2015.1006275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In order to elucidate how phosphatidylserine (PS6) interacts with AQP5 in a cell membrane, we developed a hybrid steered molecular dynamics (hSMD) method that involved: (1) Simultaneously steering two centers of mass of two selected segments of the ligand, and (2) equilibrating the ligand-protein complex with and without biasing the system. Validating hSMD, we first studied vascular endothelial growth factor receptor 1 (VEGFR1) in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide (8ST), for which the binding energy is known from in vitro experiments. In this study, our computed binding energy well agreed with the experimental value. Knowing the accuracy of this hSMD method, we applied it to the AQP5-lipid-bilayer system to answer an outstanding question relevant to AQP5's physiological function: Will the PS6, a lipid having a single long hydrocarbon tail that was found in the central pore of the AQP5 tetramer crystal, actually bind to and inhibit AQP5's central pore under near-physiological conditions, namely, when AQP5 tetramer is embedded in a lipid bilayer? We found, in silico, using the CHARMM 36 force field, that binding PS6 to AQP5 was a factor of 3 million weaker than "binding" it in the lipid bilayer. This suggests that AQP5's central pore will not be inhibited by PS6 or a similar lipid in a physiological environment.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, University of Texas at San Antonio , One UTSA Circle, San Antonio, Texas , USA
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17
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Dank C, Kirchknopf B, Mastalir M, Kählig H, Felsinger S, Roller A, Arion VB, Gstach H. Hybrids of salicylalkylamides and Mannich bases: control of the amide conformation by hydrogen bonding in solution and in the solid state. Molecules 2015; 20:1686-711. [PMID: 25608856 PMCID: PMC6272445 DOI: 10.3390/molecules20011686] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/04/2015] [Accepted: 01/12/2015] [Indexed: 11/23/2022] Open
Abstract
3-Aminomethylation of salicylalkylamides afforded hybrids with a Mannich base. In addition, it triggered the rotation of the amide bond. The observed conformational switch is driven by strong intramolecular hydrogen bonding between the Mannich base and phenolic group. Crystal structure analysis reveals the stabilization of the hybrid molecules by double hydrogen bonding of the phenolic OH, which acts as an acceptor and donor simultaneously. The molecules contain an amide site and a Mannich base site in an orthogonal spatial arrangement. The intramolecular hydrogen bonds are persistent in a nonpolar solvent (e.g., chloroform). The conformational change can be reversed upon protection or protonation of the Mannich base nitrogen.
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Affiliation(s)
- Christian Dank
- Institute of Medical Chemistry, Center of Pathobiochemistry and Genetics, Medical University of Vienna, Währingerstrasse 10, Vienna 1090, Austria.
| | - Barbara Kirchknopf
- University of Applied Sciences Wiener Neustadt, Konrad-Lorenz-Strasse 10, Tulln a. d. Donau 3430, Austria.
| | - Matthias Mastalir
- Institute of Medical Chemistry, Center of Pathobiochemistry and Genetics, Medical University of Vienna, Währingerstrasse 10, Vienna 1090, Austria.
| | - Hanspeter Kählig
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, Vienna 1090, Austria.
| | - Susanne Felsinger
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, Vienna 1090, Austria.
| | - Alexander Roller
- Structure Analysis Centre, University of Vienna, Währingerstrasse 38, Vienna 1090, Austria.
| | - Vladimir B Arion
- Structure Analysis Centre, University of Vienna, Währingerstrasse 38, Vienna 1090, Austria.
| | - Hubert Gstach
- Institute of Medical Chemistry, Center of Pathobiochemistry and Genetics, Medical University of Vienna, Währingerstrasse 10, Vienna 1090, Austria.
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18
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Li J, Zhang Z, Xu X, Shao X, Li Z. Nematicidal Activities of Diamides with Diphenylacetylene Scaffold Against Meloidogyne Incognita. Aust J Chem 2015. [DOI: 10.1071/ch15065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
With the goal of searching for new potential nematicides with high activity and low toxicity, new molecules are needed as potential prototypes for the synthesis of new nematicidal compounds. A series of novel diamides based on diphenylacetylene scaffold were designed and synthesised. The conformation of the amide was restricted through the ten-membered H-bonded ring. Their structures were characterised by 1H NMR, 13C NMR, 19F NMR, and high-resolution mass spectrometry. The preliminary bioassays evaluated against Meloidogyne Incognita indicated that most of the title compounds were endowed with moderate-to-good activities at the concentration of 25 mg L–1. In particular, compounds 9a, 9c, 9g, 9h, 9k, and 9l displayed >50 % nematicidal activity at 5 mg L–1. It is possible that the novel diamides with diphenylacetylene scaffold, which possess good nematicidal activities, provide distinct nematicidal chemotypes that can be used as leads for further optimisation.
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19
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Design and synthesis of novel 5-(3,4,5-trimethoxybenzoyl)-4-aminopyrimidine derivatives as potent and selective phosphodiesterase 5 inhibitors: Scaffold hopping using a pseudo-ring by intramolecular hydrogen bond formation. Bioorg Med Chem Lett 2014; 24:5175-80. [DOI: 10.1016/j.bmcl.2014.09.082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 09/23/2014] [Accepted: 09/27/2014] [Indexed: 11/20/2022]
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20
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Li S, Dang YY, Oi Lam Che G, Kwan YW, Chan SW, Leung GPH, Lee SMY, Hoi MPM. VEGFR tyrosine kinase inhibitor II (VRI) induced vascular insufficiency in zebrafish as a model for studying vascular toxicity and vascular preservation. Toxicol Appl Pharmacol 2014; 280:408-20. [DOI: 10.1016/j.taap.2014.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/22/2014] [Accepted: 09/04/2014] [Indexed: 12/17/2022]
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21
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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22
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Čechová L, Procházková E, Císařová I, Dračínský M, Janeba Z. Separation of planar rotamers through intramolecular hydrogen bonding in polysubstituted 5-nitrosopyrimidines. Chem Commun (Camb) 2014; 50:14892-5. [DOI: 10.1039/c4cc06978a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unique isolation of pairs of planar rotamers, planamers, as chemical species differing only in nitroso group orientation, separable through the presence of a single intramolecular hydrogen bond, is reported.
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Affiliation(s)
- L. Čechová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- CZ-166 10 Prague 6, Czech Republic
- Department of Chemistry of Natural Compounds
- Institute of Chemical Technology Prague
| | - E. Procházková
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- CZ-166 10 Prague 6, Czech Republic
- Faculty of Science
- Charles University in Prague
| | - I. Císařová
- Faculty of Science
- Charles University in Prague
- CZ-128 40 Prague 2, Czech Republic
| | - M. Dračínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- CZ-166 10 Prague 6, Czech Republic
| | - Z. Janeba
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- CZ-166 10 Prague 6, Czech Republic
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23
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Procházková E, Čechová L, Janeba Z, Dračínský M. A Switchable Intramolecular Hydrogen Bond in Polysubstituted 5-Nitrosopyrimidines. J Org Chem 2013; 78:10121-33. [DOI: 10.1021/jo401441z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
| | - Lucie Čechová
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 166 10 Prague, Czech Republic
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24
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Musumeci F, Radi M, Brullo C, Schenone S. Vascular endothelial growth factor (VEGF) receptors: drugs and new inhibitors. J Med Chem 2012; 55:10797-822. [PMID: 23098265 DOI: 10.1021/jm301085w] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The recent launch onto the market of five VEGFR inhibitors indicates the therapeutic value of these agents and the importance of the research in the field of angiogenesis inhibitors for future oncologic therapy. In this Perspective we briefly report the inhibitors that are in clinical use, while we dedicate two wider sections to the compounds that are in clinical trials and to the new derivatives appearing in the literature. We especially consider the medicinal chemistry aspect of the topic and report the structure-activity relationship studies and the binding mode of some inhibitors as well as the biological data of the compounds discovered in the past 5 years.
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Affiliation(s)
- Francesca Musumeci
- Dipartimento di Farmacia, University of Genoa, Viale Benedetto XV 3, 16132 Genova, Italy
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25
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Sun H, Tawa G, Wallqvist A. Classification of scaffold-hopping approaches. Drug Discov Today 2012; 17:310-24. [PMID: 22056715 PMCID: PMC3328312 DOI: 10.1016/j.drudis.2011.10.024] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
Abstract
The general goal of drug discovery is to identify novel compounds that are active against a preselected biological target with acceptable pharmacological properties defined by marketed drugs. Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties. In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping. We review the structural diversity of original and final scaffolds with respect to each category. We discuss the advantages and limitations of small, medium and large-step scaffold hopping. Finally, we summarize software that is frequently used to facilitate different kinds of scaffold-hopping methods.
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Affiliation(s)
- Hongmao Sun
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Frederick, MD 21702, USA.
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26
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Li Z, Tan JH, He JH, Long Y, Ou TM, Li D, Gu LQ, Huang ZS. Disubstituted quinazoline derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA. Eur J Med Chem 2011; 47:299-311. [PMID: 22104971 DOI: 10.1016/j.ejmech.2011.10.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 12/12/2022]
Abstract
A series of 2,4-disubstituted quinazoline derivatives found to be a new type of highly selective ligand to bind with telomeric G-quadruplex DNA, and their biological properties were reported for the first time.Their interactions with telomeric G-quadruplex DNA were evaluated by using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and molecular modeling. Our results showed that these derivatives could well recognize G-quadruplex and have high selectivity toward G-quadruplex over duplex DNA. The structure-activity relationships (SARs) study revealed that the disubstitution of quinazoline and the length of the amide side chain were important for its interaction with the G-quadruplex. Furthermore, telomerase inhibition of the quinazoline derivatives and their cellular effects were studied.
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Affiliation(s)
- Zeng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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27
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Design, synthesis of some 2,6,9-trisubstituted purinyl thioureido derivatives and evaluation of antimicrobial activity. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9682-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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Huang D, Caflisch A. Fragment-Based Approaches in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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29
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Honda T, Nagahara H, Mogi H, Ban M, Aono H. KDR inhibitor with the intramolecular non-bonded interaction: conformation-activity relationships of novel indole-3-carboxamide derivatives. Bioorg Med Chem Lett 2011; 21:1782-5. [PMID: 21324683 DOI: 10.1016/j.bmcl.2011.01.063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 01/04/2011] [Accepted: 01/18/2011] [Indexed: 11/16/2022]
Abstract
We previously reported that compound 1, having a similar conformation to PTK787 (2) by forming a pseudo ring structure with an intramolecular non-bonded S-O interaction, exhibited a potent inhibitory activity against VEGFR2 tyrosine kinase (KDR). Applying the ideas of pseudo ring formations, we have designed three types of novel indole carboxamide derivatives 5-7 with an intramolecular hydrogen bonding or non-bonded S-O interaction. We describe the design and synthesis of 5-7, and also discuss the relationships of their KDR inhibitory activity and conformations that were stabilized by their intramolecular non-bonded interactions.
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Affiliation(s)
- Takahiro Honda
- Research and Development Center, Santen Pharmaceutical Co. Ltd, Ikoma-shi, Nara, Japan.
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30
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G. Tsoungas P, Cordopatis P, Gardikis Y, Potamitis C, Zervou M, Pairas G. Xanthones in Heterocyclic Synthesis. An Efficient and General Route for the Synthesis of Regioselectively Substituted Phthalazines. HETEROCYCLES 2011. [DOI: 10.3987/com-11-12168] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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31
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Liu KKC, Huang X, Bagrodia S, Chen JH, Greasley S, Cheng H, Sun S, Knighton D, Rodgers C, Rafidi K, Zou A, Xiao J, Yan S. Quinazolines with intra-molecular hydrogen bonding scaffold (iMHBS) as PI3K/mTOR dual inhibitors. Bioorg Med Chem Lett 2010; 21:1270-4. [PMID: 21269826 DOI: 10.1016/j.bmcl.2010.12.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 12/01/2010] [Accepted: 12/06/2010] [Indexed: 11/24/2022]
Abstract
Intra-molecular hydrogen bonding was introduced to the quinazoline motif to form a pseudo ring (intra-molecular H-bond scaffold, iMHBS) to mimic our previous published core structures, pyrido[2.3-D]pyrimidin-7-one and pteridinone, as PI3K/mTOR dual inhibitors. This design results in potent PI3K/mTOR dual inhibitors and the purposed intra-molecular hydrogen bonding structure is well supported by co-crystal structure in PI3Kγ enzyme. In addition, a novel synthetic route was developed for these analogs.
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Affiliation(s)
- Kevin K C Liu
- Pfizer Global Research and Development, Chemistry Department, 10770 Science Center Drive, La Jolla, CA 92120, USA.
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32
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Tang JY, Li S, Li ZH, Zhang ZJ, Hu G, Cheang LCV, Alex D, Hoi MPM, Kwan YW, Chan SW, Leung GPH, Lee SMY. Calycosin promotes angiogenesis involving estrogen receptor and mitogen-activated protein kinase (MAPK) signaling pathway in zebrafish and HUVEC. PLoS One 2010; 5:e11822. [PMID: 20686605 PMCID: PMC2912279 DOI: 10.1371/journal.pone.0011822] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 06/16/2010] [Indexed: 01/01/2023] Open
Abstract
Background Angiogenesis plays an important role in a wide range of physiological processes, and many diseases are associated with the dysregulation of angiogenesis. Radix Astragali is a Chinese medicinal herb commonly used for treating cardiovascular disorders and has been shown to possess angiogenic effect in previous studies but its active constituent and underlying mechanism remain unclear. The present study investigates the angiogenic effects of calycosin, a major isoflavonoid isolated from Radix Astragali, in vitro and in vivo. Methodology Tg(fli1:EGFP) and Tg(fli1:nEGFP) transgenic zebrafish embryos were treated with different concentrations of calycosin (10, 30, 100 µM) from 72 hpf to 96 hpf prior morphological observation and angiogenesis phenotypes assessment. Zebrafish embryos were exposed to calycosin (10, 100 µM) from 72 hpf to 78 hpf before gene-expression analysis. The effects of VEGFR tyrosine kinase inhibitor on calycosin-induced angiogenesis were studied using 72 hpf Tg(fli1:EGFP) and Tg(fli1:nEGFP) zebrafish embryos. The pro-angiogenic effects of calycosin were compared with raloxifene and tamoxifen in 72 hpf Tg(fli1:EGFP) zebrafish embryos. The binding affinities of calycosin to estrogen receptors (ERs) were evaluated by cell-free and cell-based estrogen receptor binding assays. Human umbilical vein endothelial cell cultures (HUVEC) were pretreated with different concentrations of calycosin (3, 10, 30, 100 µM) for 48 h then tested for cell viability and tube formation. The role of MAPK signaling in calycosin-induced angiogenesis was evaluated using western blotting. Conclusion Calycosin was shown to induce angiogenesis in human umbilical vein endothelial cell cultures (HUVEC) in vitro and zebrafish embryos in vivo via the up-regulation of vascular endothelial growth factor (VEGF), VEGFR1 and VEGFR2 mRNA expression. It was demonstrated that calycosin acted similar to other selective estrogen receptor modulators (SERMs), such as raloxifene and tamoxifen, by displaying selective potency and affinity to estrogen receptors ERα and ERβ. Our results further indicated that calycosin promotes angiogenesis via activation of MAPK with the involvement of ERK1/2 and ER. Together, this study revealed, for the first time, that calycosin acts as a selective estrogen receptor modulator (SERM) to promote angiogenesis, at least in part through VEGF-VEGFR2 and MAPK signaling pathways.
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Affiliation(s)
- Jing Yan Tang
- Institute of Chinese Medical Sciences, University of Macau, Macao, China
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33
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Andersson MK, Göransson M, Olofsson A, Andersson C, Aman P. Nuclear expression of FLT1 and its ligand PGF in FUS-DDIT3 carrying myxoid liposarcomas suggests the existence of an intracrine signaling loop. BMC Cancer 2010; 10:249. [PMID: 20515481 PMCID: PMC2889895 DOI: 10.1186/1471-2407-10-249] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 06/01/2010] [Indexed: 01/05/2023] Open
Abstract
Background The FUS-DDIT3 fusion oncogene encodes an abnormal transcription factor that has a causative role in the development of myxoid/round-cell liposarcomas (MLS/RCLS). We have previously identified FLT1 (VEGFR1) as a candidate downstream target gene of FUS-DDIT3. The aim of this study was to investigate expression of FLT1 and its ligands in MLS cells. Methods HT1080 human fibrosarcoma cells were transiently transfected with FUS-DDIT3-GFP variant constructs and FLT1 expression was measured by quantitative real-time PCR. In addition, FLT1, PGF, VEGFA and VEGFB expression was measured in MLS/RCLS cell lines, MLS/RCLS tumors and in normal adiopocytes. We analyzed nine cases of MLS/RCLS and one cell line xenografted in mice for FLT1 protein expression using immunohistochemistry. MLS/RCLS cell lines were also analyzed for FLT1 by immunofluorescence and western blot. MLS/RCLS cell lines were additionally treated with FLT1 tyrosine kinase inhibitors and assayed for alterations in proliferation rate. Results FLT1 expression was dramatically increased in transfected cells stably expressing FUS-DDIT3 and present at high levels in cell lines derived from MLS. The FLT1 protein showed a strong nuclear expression in cells of MLS tissue as well as in cultured MLS cells, which was confirmed by cellular fractionation. Tissue array analysis showed a nuclear expression of the FLT1 protein also in several other tumor and normal cell types including normal adipocytes. The FLT1 ligand coding gene PGF was highly expressed in cultured MLS cells compared to normal adipocytes while the other ligand genes VEGFA and VEGFB were expressed to lower levels. A more heterogeneous expression pattern of these genes were observed in tumor samples. No changes in proliferation rate of MLS cells were detected at concentrations for which the kinase inhibitors have shown specific inhibition of FLT1. Conclusions Our results imply that FLT1 is induced as an indirect downstream effect of FUS-DDIT3 expression in MLS. This could be a consequence of the ability of FUS-DDIT3 to hijack parts of normal adipose tissue development and reprogram primary cells to a liposarcoma-like phenotype. The findings of nuclear FLT1 protein and expression of corresponding ligands in MLS and normal tissues may have implications for tissue homeostasis and tumor development through auto- or intracrine signaling.
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Affiliation(s)
- Mattias K Andersson
- Lundberg Laboratory for Cancer Research, Department of Pathology, Sahlgrenska Academy at Göteborg University, Göteborg, Sweden.
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34
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Zhou H, Zhang W, Yan B. Use of cyclohexylisocyanide and methyl 2-isocyanoacetate as convertible isocyanides for microwave-assisted fluorous synthesis of 1,4-benzodiazepine-2,5-dione library. ACTA ACUST UNITED AC 2010; 12:206-14. [PMID: 19947585 DOI: 10.1021/cc900157w] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A new protocol in which cyclohexylisocyanide and methyl 2-isocyanoacetate are used as convertible isocyanides for Ugi/de-Boc/cyclization/Suzuki synthesis of biaryl-substituted 1,4-benzodiazepine-2,5-diones has been developed. Ugi reactions of Boc-protected anthranilic acids, fluorous benzaldehydes, amines, and cyclohexylisocyanide or methyl 2-isocyanoacetate were carried out at room temperature. Microwave-promoted de-Boc/cyclization reactions afforded 1,4-benzodiazepine-2,5-diones (BZDs). Suzuki coupling reactions further derivatized the BZD ring by removing the fluorous tag and introducing the biaryl group. A thirty three-member biaryl-substituted BZD library containing four points of diversity was prepared by microwave-assisted solution-phase fluorous parallel synthesis.
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Affiliation(s)
- Hongyu Zhou
- St. Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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35
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Kuhn B, Mohr P, Stahl M. Intramolecular Hydrogen Bonding in Medicinal Chemistry. J Med Chem 2010; 53:2601-11. [DOI: 10.1021/jm100087s] [Citation(s) in RCA: 401] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Bernd Kuhn
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
| | - Peter Mohr
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
| | - Martin Stahl
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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36
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Karskela T, Lönnberg H. Solid-Phase Synthesis of 4(5),1′,5′-Trisubstituted 2,4′-Biimidazoles. J Org Chem 2009; 74:9446-51. [DOI: 10.1021/jo902122e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tuomas Karskela
- Department of Chemistry, University of Turku, Turku, FIN-20014, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, Turku, FIN-20014, Finland
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37
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Naik S, Dothager RS, Marasa J, Lewis CL, Piwnica-Worms D. Vascular Endothelial Growth Factor Receptor-1 Is Synthetic Lethal to Aberrant {beta}-Catenin Activation in Colon Cancer. Clin Cancer Res 2009; 15:7529-7537. [PMID: 20008853 DOI: 10.1158/1078-0432.ccr-09-0336] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE: The Wnt/beta-catenin (beta-cat) signaling cascade is a key regulator of development, and dysregulation of Wnt/beta-cat contributes to selected cancers, such as colorectal, breast, and hepatocellular carcinoma, through abnormal activation of Wnt target genes. To identify novel modulators of the Wnt/beta-cat pathway that may emerge as therapeutic targets, we did an unbiased high-throughput RNA interference screen. EXPERIMENTAL DESIGN: A synthetic oligonucleotide small interfering RNA library targeting 691 known and predicted human kinases was screened in Wnt3a-stimulated human cells in a live cell luciferase assay for modulation of Wnt/beta-cat-dependent transcription. Follow-up studies of a selected high-confidence "hit" were conducted. RESULTS: A robust quartile-based statistical analysis and secondary screen yielded several kinases worthy of further investigation, including Cdc2L1, Lmtk3, Pank2, ErbB3, and, of note, vascular endothelial growth factor receptor (VEGFR)1/Flt1, a receptor tyrosine kinase (TK) with putative weak kinase activity conventionally believed to be a negative regulator of angiogenesis. A series of loss-of-function, genetic null, and VEGFR TK inhibitor assays further revealed that VEGFR1 is a positive regulator of Wnt signaling that functions in a glycogen synthase kinase-3beta (GSK3beta)-independent manner as a potential synthetic lethal target in Wnt/beta-cat-addicted colon carcinoma cells. CONCLUSIONS: This unanticipated non-endothelial link between VEGFR1 TK activity and Wnt/beta-cat signaling may refine our understanding of aberrant Wnt signaling in colon carcinoma and points to new combinatorial therapeutics targeted to the tumor cell compartment, rather than angiogenesis, in the context of colon cancer. (Clin Cancer Res 2009;15(24):7529-37).
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Affiliation(s)
- Snehal Naik
- Authors' Affiliation: Molecular Imaging Center, Mallinckrodt Institute of Radiology, and Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri
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38
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Kolb P, Kipouros CB, Huang D, Caflisch A. Structure-based tailoring of compound libraries for high-throughput screening: discovery of novel EphB4 kinase inhibitors. Proteins 2009; 73:11-8. [PMID: 18384152 DOI: 10.1002/prot.22028] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
High-throughput docking is a computational tool frequently used to discover small-molecule inhibitors of enzymes or receptors of known three-dimensional structure. Because of the large number of molecules in chemical libraries, automatic procedures to prune multimillion compound collections are useful for high-throughput docking and necessary for in vitro screening. Here, we propose an anchor-based library tailoring approach (termed ALTA) to focus a chemical library by docking and prioritizing molecular fragments according to their binding energy which includes continuum electrostatics solvation. In principle, ALTA does not require prior knowledge of known inhibitors, but receptor-based pharmacophore information (hydrogen bonds with the hinge region) is additionally used here to identify molecules with optimal anchor fragments for the ATP-binding site of the EphB4 receptor tyrosine kinase. The 21,418 molecules of the focused library (from an initial collection of about 730,000) are docked into EphB4 and ranked by force-field-based energy including electrostatic solvation. Among the 43 compounds tested in vitro, eight molecules originating from two different anchors show low-micromolar activity in a fluorescence-based enzymatic assay. Four of them are active in a cell-based assay and are potential anti-angiogenic compounds.
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Affiliation(s)
- Peter Kolb
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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39
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40
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Conformation–activity relationship on novel 4-pyridylmethylthio derivatives with antiangiogenic activity. Bioorg Med Chem Lett 2008; 18:2939-43. [DOI: 10.1016/j.bmcl.2008.03.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 03/06/2008] [Accepted: 03/25/2008] [Indexed: 11/21/2022]
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41
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Furet P, Caravatti G, Guagnano V, Lang M, Meyer T, Schoepfer J. Entry into a new class of protein kinase inhibitors by pseudo ring design. Bioorg Med Chem Lett 2008; 18:897-900. [DOI: 10.1016/j.bmcl.2007.12.041] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 12/14/2007] [Accepted: 12/19/2007] [Indexed: 10/22/2022]
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42
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Jansma A, Zhang Q, Li B, Ding Q, Uno T, Bursulaya B, Liu Y, Furet P, Gray NS, Geierstanger BH. Verification of a Designed Intramolecular Hydrogen Bond in a Drug Scaffold by Nuclear Magnetic Resonance Spectroscopy. J Med Chem 2007; 50:5875-7. [DOI: 10.1021/jm700983a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Piguel S, Legraverend M. Selective Amidation of 2,6-Dihalogenopurines: Application to the Synthesis of New 2,6,9-Trisubstituted Purines. J Org Chem 2007; 72:7026-9. [PMID: 17685576 DOI: 10.1021/jo071196p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report herein the palladium(0)/Xantphos-catalyzed cross-coupling of various amides with 2,6-dihalogenopurines, with substituent-dependent regioselectivity. Furthermore, subjecting the same 2,6-dihalogenopurines to SNAr conditions with amide/NaH in DMF leads to inverted regioselectivity albeit in lower yield. These methodologies allow the two-step synthesis of new 2,6,9-trisubstituted purines from readily available 2,6-dihalogenopurines.
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44
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Wickens P, Kluender H, Dixon J, Brennan C, Achebe F, Bacchiocchi A, Bankston D, Bierer D, Brands M, Braun D, Brown MS, Chuang CY, Dumas J, Enyedy I, Hofilena G, Hong Z, Housley T, Jones B, Khire U, Kreiman C, Kumarasinghe E, Lowinger T, Ott-Morgan R, Perkins L, Phillips B, Schoenleber R, Scott WJ, Sheeler R, Redman A, Sun X, Taylor I, Wang L, Wilhelm S, Zhang X, Zhang M, Sullivan E, Carter C, Miglarese M, Levy J. SAR of a novel ‘Anthranilamide Like’ series of VEGFR-2, multi protein kinase inhibitors for the treatment of cancer. Bioorg Med Chem Lett 2007; 17:4378-81. [PMID: 17574417 DOI: 10.1016/j.bmcl.2007.02.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 02/23/2007] [Accepted: 02/26/2007] [Indexed: 11/29/2022]
Abstract
Novel anthranilamides were surprisingly found to exert additional activity on B-RAF. Corresponding thiophene, pyrazole, and thiazole core analogs were prepared as VEGFR-2 inhibitors with c-KIT, and B-RAF activity. Compounds in the phenyl, thiophene, and thiazole series are in vivo active.
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Affiliation(s)
- Philip Wickens
- Department of Chemistry Research, Bayer Research Center, 400 Morgan Lane, West Haven, CT 06516, USA.
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45
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Velaparthi U, Wittman M, Liu P, Stoffan K, Zimmermann K, Sang X, Carboni J, Li A, Attar R, Gottardis M, Greer A, Chang CY, Jacobsen BL, Sack JS, Sun Y, Langley DR, Balasubramanian B, Vyas D. Discovery and initial SAR of 3-(1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-ones as inhibitors of insulin-like growth factor 1-receptor (IGF-1R). Bioorg Med Chem Lett 2007; 17:2317-21. [PMID: 17317169 DOI: 10.1016/j.bmcl.2007.01.102] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Revised: 01/12/2007] [Accepted: 01/18/2007] [Indexed: 11/29/2022]
Abstract
The discovery and synthesis of 3-(1H-benzo[d]imidazol-2-yl)pyridin-2(1H)-one inhibitors of insulin-like growth factor 1-receptor (IGF-1R) are presented. Installing amine containing side chains at the 4-position of pyridone ring significantly improved the enzyme potency. SAR and biological activity of these compounds is presented.
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Affiliation(s)
- Upender Velaparthi
- Department of Discovery Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, 5 Research Parkway, Wallingford, CT 06492, USA.
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46
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Kolb P, Caflisch A. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. J Med Chem 2007; 49:7384-92. [PMID: 17149868 DOI: 10.1021/jm060838i] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The computer program DAIM (Decomposition and Identification of Molecules) has been developed to automatically break up compounds in small-molecule libraries for fragment-based docking as well as database analysis. Here, DAIM is evaluated on 130 ligands derived from known crystal structures of ligand-protein complexes. The decomposition and a new fingerprint-based identification technique are used to select anchor fragments for docking. The docking results show that the DAIM selection is superior to size-based or random selection of fragments. To evaluate the usefulness for analyzing the fragment composition of a large library, DAIM is applied to a collection of about 1.85 million commercially available compounds. Interestingly, it is found that the set of most frequent cyclic and acyclic fragments originating from the decomposition of the 1.85 million molecules shows a large overlap with the most frequent fragments in a library of 5120 known drugs. DAIM has been successfully used in the in silico screening for inhibitors of beta-secretase and EphB4 kinase by fragment-based high-throughput docking. Possible future applications for de novo ligand design are briefly discussed.
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Affiliation(s)
- Peter Kolb
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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47
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Radioiodinated VEGF to image tumor angiogenesis in a LS180 tumor xenograft model. Nucl Med Biol 2006; 33:963-9. [PMID: 17127168 DOI: 10.1016/j.nucmedbio.2006.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 08/09/2006] [Accepted: 08/10/2006] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Angiogenesis is essential for tumor growth or metastasis. A method involving noninvasive detection of angiogenic activity in vivo would provide diagnostic information regarding antiangiogenic therapy targeting vascular endothelial cells as well as important insight into the role of vascular endothelial growth factor (VEGF) and its receptor (flt-1 and KDR) system in tumor biology. We evaluated radioiodinated VEGF(121), which displays high binding affinity for KDR, and VEGF(165), which possesses high binding affinity for flt-1 and low affinity for KDR, as angiogenesis imaging agents using the LS180 tumor xenograft model. METHODS VEGF(121) and VEGF(165) were labeled with (125)I by the chloramine-T method. Biodistribution was observed in an LS180 human colon cancer xenograft model. Additionally, autoradiographic imaging and immunohistochemical staining of tumors were performed with (125)I-VEGF(121). RESULTS (125)I-VEGF(121) and (125)I-VEGF(165) exhibited strong, continuous uptake by tumors and the uterus, an organ characterized by angiogenesis. (125)I-VEGF(121) uptake in tumors was twofold higher than that of (125)I-VEGF(165) (9.12+/-98 and 4.79+/-1.08 %ID/g at 2 h, respectively). (125)I-VEGF(121) displayed higher tumor to nontumor (T/N) ratios in most normal organs in comparison with (125)I-VEGF(165). (125)I-VEGF(121) accumulation in tumors decreased with increasing tumor volume. Autoradiographic and immunohistochemical analyses confirmed that the difference in (125)I-VEGF(121) tumor accumulation correlated with degree of tumor vascularity. CONCLUSION Radioiodinated VEGF(121) is a promising tracer for noninvasive delineation of angiogenesis in vivo.
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48
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Stewart KD, Shiroda M, James CA. Drug Guru: a computer software program for drug design using medicinal chemistry rules. Bioorg Med Chem 2006; 14:7011-22. [PMID: 16870456 DOI: 10.1016/j.bmc.2006.06.024] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/06/2006] [Accepted: 06/08/2006] [Indexed: 11/23/2022]
Abstract
Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.
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Affiliation(s)
- Kent D Stewart
- Abbott Laboratories, Global Pharmaceuticals Research and Development, Abbott Park, IL 60064, USA.
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49
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El-Araby M, Guo H, Pottorf RS, Player MR. Solid-phase synthesis of an alkylaminobenzanilide library. ACTA ACUST UNITED AC 2006; 6:789-95. [PMID: 15360215 DOI: 10.1021/cc0499284] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The synthesis of a library of 2- and 3-substituted benzanilides has been achieved on solid phase. Attachment of anilines to formyldimethoxyphenyl (FDMP) resin via reductive amination was optimized to allow a wide range of anilines to be used. Acylation of this resin-bound aniline was accomplished with 2- or 3-nitrobenzoyl chloride to yield nitrobenzanilides. Following reduction of the nitro group, the resulting amine was alkylated using aromatic and heteroaromatic aldehydes in the presence of NaBH(OAc)(3) under controlled conditions. Finally, the products were cleaved from the resin using trifluoroacetic acid to produce a 10 800-member library.
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Affiliation(s)
- Moustafa El-Araby
- 3-Dimensional Pharmaceuticals, Inc., 8 Clarke Drive, Cranbury, New Jersey 08512, USA
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50
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Borzilleri RM, Zheng X, Qian L, Ellis C, Cai ZW, Wautlet BS, Mortillo S, Jeyaseelan R, Kukral DW, Fura A, Kamath A, Vyas V, Tokarski JS, Barrish JC, Hunt JT, Lombardo LJ, Fargnoli J, Bhide RS. Design, synthesis, and evaluation of orally active 4-(2,4-difluoro-5-(methoxycarbamoyl)phenylamino)pyrrolo[2,1-f][1,2,4]triazines as dual vascular endothelial growth factor receptor-2 and fibroblast growth factor receptor-1 inhibitors. J Med Chem 2005; 48:3991-4008. [PMID: 15943473 DOI: 10.1021/jm0501275] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of substituted 4-(2,4-difluoro-5-(methoxycarbamoyl)phenylamino)pyrrolo[2,1-f][1,2,4]triazines was identified as potent and selective inhibitors of the tyrosine kinase activity of the growth factor receptors VEGFR-2 (Flk-1, KDR) and FGFR-1. The enzyme kinetics associated with the VEGFR-2 inhibition of compound 50 (K(i) = 52 +/- 3 nM) confirmed that the pyrrolo[2,1-f][1,2,4]triazine analogues are competitive with ATP. Several analogues demonstrated low-nanomolar inhibition of VEGF- and FGF-dependent human umbilical vein endothelial cell (HUVEC) proliferation. Replacement of the C6-ester substituent of the pyrrolo[2,1-f][1,2,4]triazine core with heterocyclic bioisosteres, such as substituted 1,3,5-oxadiazoles, afforded compounds with excellent oral bioavailability in mice (i.e., 50 F(po) = 79%). Significant antitumor efficacy was observed with compounds 44, 49, and 50 against established L2987 human lung carcinoma xenografts implanted in athymic mice. A full account of the synthesis, structure-activity relationships, pharmacology, and pharmacokinetic properties of analogues within the series is presented.
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MESH Headings
- Administration, Oral
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Biological Availability
- Blood Proteins/metabolism
- Cell Proliferation/drug effects
- Drug Design
- Endothelium, Vascular/cytology
- Humans
- Hydroxamic Acids/chemical synthesis
- Hydroxamic Acids/chemistry
- Hydroxamic Acids/pharmacology
- In Vitro Techniques
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Microsomes, Liver/metabolism
- Models, Molecular
- Oxadiazoles/chemical synthesis
- Oxadiazoles/chemistry
- Oxadiazoles/pharmacology
- Protein Binding
- Pyrroles/chemical synthesis
- Pyrroles/chemistry
- Pyrroles/pharmacology
- Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor, Fibroblast Growth Factor, Type 1
- Receptors, Fibroblast Growth Factor/antagonists & inhibitors
- Receptors, Fibroblast Growth Factor/chemistry
- Structure-Activity Relationship
- Triazines/chemical synthesis
- Triazines/chemistry
- Triazines/pharmacology
- Vascular Endothelial Growth Factor Receptor-2/antagonists & inhibitors
- Vascular Endothelial Growth Factor Receptor-2/chemistry
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Robert M Borzilleri
- Department of Oncology Chemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000, USA.
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