1
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Nguyen TD, Tran DT, Huynh TN, Ly TM, Nguyen TT. Utilization of 2-nitrophenols in annulations with aryl isothiocyanates towards the synthesis of 2-aminobenzoxazoles. RSC Adv 2023; 13:18156-18159. [PMID: 37333726 PMCID: PMC10269044 DOI: 10.1039/d3ra02873a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023] Open
Abstract
A method for the annulation of 2-nitrophenols with aryl isothiocyanates is reported. The reactions proceeded in the presence of an iron(iii) acetylacetonate catalyst, elemental sulfur, NaOH as a base, and DMSO as a solvent. Derivatives of 2-aminobenzoxazoles bearing nitro, cyano, acetyl, sulfone, secondary amine, and pyrrolyl groups were successfully isolated.
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Affiliation(s)
- Thanh D Nguyen
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT) 268 Ly Thuong Kiet, District 10 Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Linh Trung Ward Ho Chi Minh City Vietnam
| | - Danh T Tran
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT) 268 Ly Thuong Kiet, District 10 Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Linh Trung Ward Ho Chi Minh City Vietnam
| | - Tan N Huynh
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT) 268 Ly Thuong Kiet, District 10 Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Linh Trung Ward Ho Chi Minh City Vietnam
| | - Thang M Ly
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT) 268 Ly Thuong Kiet, District 10 Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Linh Trung Ward Ho Chi Minh City Vietnam
| | - Tung T Nguyen
- Faculty of Chemical Engineering, Ho Chi Minh City University of Technology (HCMUT) 268 Ly Thuong Kiet, District 10 Ho Chi Minh City Vietnam
- Vietnam National University Ho Chi Minh City Linh Trung Ward Ho Chi Minh City Vietnam
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2
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Canh Pham E, Truong TN. Design, Microwave-Assisted Synthesis, Antimicrobial and Anticancer Evaluation, and In Silico Studies of Some 2-Naphthamide Derivatives as DHFR and VEGFR-2 Inhibitors. ACS OMEGA 2022; 7:33614-33628. [PMID: 36157776 PMCID: PMC9494668 DOI: 10.1021/acsomega.2c05206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Naphthamide is a common structural framework with diverse pharmacological activities. Ten novel 2-naphthamide derivatives have been designed, synthesized, and evaluated for their in vitro antibacterial, antifungal, and anticancer activities. The title compounds were synthesized from dimethoxybenzaldehyde derivatives through a four-step microwave-assisted synthesis process. The structures were confirmed by 1H NMR, 13C NMR, and MS spectra. Compound 8b showed good antibacterial activity against Escherichia coli, Streptococcus faecalis, Salmonella enterica, MSSA, and MRSA with MIC values of 16, 16, 16, 8, and 16 μg/mL, respectively, compared to ciprofloxacin (MIC = 8-16 μg/mL). Compounds 5b (IC50 = 3.59-8.38 μM) and 8b (IC50 = 2.97-7.12 μM) exhibited good cytotoxic activity against C26, HepG2, and MCF7 cancer cell lines as compared to paclitaxel (IC50 = 2.85-5.75 μM). Moreover, compounds 5b and 8b exhibited better anticancer activity than PTX against the C26 cell line. In particular, compound 8b showed potent in vitro VEGFR-2 inhibitory activity with the IC50 value of 0.384 μM compared with sorafenib (IC50 = 0.069 μM). Therefore, compound 8b is the most potent compound for anticancer activity as indicated by in vitro cell line inhibition, in silico ADMET, molecular docking, and in vitro VEGFR-2 inhibition studies.
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Affiliation(s)
- Em Canh Pham
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Hong Bang International University, 700000 Ho Chi Minh City, Vietnam
| | - Tuyen Ngoc Truong
- Department
of Organic Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, 700000 Ho Chi Minh
City, Vietnam
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3
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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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4
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Long L, Jieyan W, Li X, Peng S, Qiao L, Luo G, Chen Z. Hypervalent Iodine(III) Promoted Tandem Reaction of o-Fluoroanilines with Formamides to Construct 2-Aminobenzoxazoles. Org Chem Front 2022. [DOI: 10.1039/d2qo00049k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and practical synthesis of 2-aminobenzoxaoles has been developed from commercially available o-fluoroanilines, and formamides. The process can be performed in the absence of metal catalyst with high levels...
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5
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El-Adl K, Ibrahim MK, Khedr F, Abulkhair HS, Eissa IH. Design, synthesis, docking, and anticancer evaluations of phthalazines as VEGFR-2 inhibitors. Arch Pharm (Weinheim) 2021; 355:e2100278. [PMID: 34596910 DOI: 10.1002/ardp.202100278] [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: 07/30/2021] [Revised: 08/27/2021] [Accepted: 09/13/2021] [Indexed: 12/19/2022]
Abstract
Twenty new N-substituted-4-phenylphthalazin-1-amine derivatives were designed, synthesized, and evaluated for their anticancer activities against HepG2, HCT-116, and MCF-7 cells as VEGFR-2 inhibitors. HCT-116 was the most sensitive cell line to the influence of the new derivatives. In particular, compound 7f was found to be the most potent derivative among all the tested compounds against the three cancer cell lines, with 50% inhibition concentration, IC50 = 3.97, 4.83, and 4.58 µM, respectively, which is more potent than both sorafenib (IC50 = 9.18, 5.47, and 7.26 µM, respectively) and doxorubicin (IC50 = 7.94, 8.07, and 6.75 µM, respectively). Fifteen of the synthesized derivatives were selected to evaluate their inhibitory activities against VEGFR-2. Compound 7f was found to be the most potent derivative that inhibited VEGFR-2 at an IC50 value of 0.08 µM, which is more potent than sorafenib (IC50 = 0.10 µM). Compound 8c inhibited VEGFR-2 at an IC50 value of 0.10 µM, which is equipotent to sorafenib. Moreover, compound 7a showed very good activity with IC50 values of 0.11 µM, which is nearly equipotent to sorafenib. In addition, compounds 7d, 7c, and 7g possessed very good VEGFR-2-inhibitory activity, with IC50 values of 0.14, 0.17, and 0.23 µM, respectively.
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Affiliation(s)
- Khaled El-Adl
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Heliopolis University for Sustainable Development, El Salam City, Cairo, Egypt
| | - Mohamed K Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Fathalla Khedr
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
| | - Hamada S Abulkhair
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Al-Azhar University, Nasr City, Cairo, Egypt.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University, New Damietta, Egypt
| | - Ibrahim H Eissa
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
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6
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Cheng K, Liu CF, Rao GW. Anti-angiogenic Agents: A Review on Vascular Endothelial Growth Factor Receptor-2 (VEGFR-2) Inhibitors. Curr Med Chem 2021; 28:2540-2564. [PMID: 32407259 DOI: 10.2174/0929867327666200514082425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/18/2020] [Accepted: 04/23/2020] [Indexed: 11/22/2022]
Abstract
Tumor growth inhibition can be achieved by inhibiting angiogenesis, which has been a field of great concern in recent years. Important targets to inhibit angiogenesis include vascular endothelial growth factor receptor (VEGFR) and its homologous tyrosine kinase receptor. Anti-angiogenic therapy based on inhibition of VEGFR-2 is an effective clinical treatment strategy. The research progress of VEGFR-2 inhibitors is reviewed in this paper from the aspects of drug development and chemical synthesis.
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Affiliation(s)
- Kang Cheng
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chen-Fu Liu
- School of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Guo-Wu Rao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
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7
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Isatin-Hydrazones with Multiple Receptor Tyrosine Kinases (RTKs) Inhibitory Activity and In-Silico Binding Mechanism. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11093746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recently, we have reported a series of isatin hydrazone, two of them, namely, 3-((2,6-dichlorobenzylidene)hydrazono)indolin-2-one (1) and 3-((2-chloro-6-fluorobenzylidene)hydrazono)indolin-2-one (2) having potent cytotoxicity, showing cyclin-dependent kinases (CDK2) inhibitory activity and bearing recommended drug likeness properties. Since both compounds (1 and 2) showed inhibitory activity against CDK2, we assumed it would also have multiple receptor tyrosine kinases (RTKs) inhibitory activity. Considering those points, here, above-mentioned two isatin hydrazone 1 and 2 were synthesized using previously reported method for further investigation of their potency on RTKs (EGFR, VEGFR-2 and FLT-3) inhibitory activity. As expected, Compound 1 exhibited excellent inhibitory activity against epidermal growth factor receptor (EGFR, IC50 = 0.269 µM), vascular epidermal growth factor receptor 2 (VEGFR-2, IC50 = 0.232 µM) and FMS-like tyrosine kinase-3 (FLT-3, IC50 = 1.535 µM) tyrosine kinases. On the other hand, Compound 2 also exhibited excellent inhibitory activity against EGFR (IC50 = 0.369 µM), VEGFR-2 (IC50 = 0.266 µM) and FLT-3 (IC50 = 0.546 µM) tyrosine kinases. A molecular docking study with EGFR, VEGFR-2 and FLT-3 kinase suggested that both compounds act as type I ATP competitive inhibitors against EGFR and VEGFR-2, and type II ATP non-competitive inhibitors against FLT-3.
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8
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Starikov AS, Kalashnikov VV, Tarakanov PA, Simakov AO, Simonov SV, Tkachev VV, Yarkov AV, Kazachenko VP, Chernyak AV, Zhurkin FE, Tomilova LG, Pushkarev VE. Synthesis of 1,2‐Dicyano‐3‐arylcycl[3.2.2]azines – First 1,2‐Dicarbonitriles Based on Cyclazine Heterocycle. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Andrei S. Starikov
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
| | - Valery V. Kalashnikov
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
| | - Pavel A. Tarakanov
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
| | - Anton O. Simakov
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
| | - Sergey V. Simonov
- Institute of Solid State Physics Russian Academy of Sciences 2 Academician Ossipyan street 142432 Chernogolovka Moscow Region Russian Federation
| | - Valery V. Tkachev
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
- Institute of Problems of Chemical Physics Russian Academy of Sciences 1 Academician Semenov avenue 142432 Chernogolovka Moscow Region Russian Federation
| | - Alexander V. Yarkov
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
| | - Vladimir P. Kazachenko
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
| | - Alexander V. Chernyak
- Institute of Problems of Chemical Physics Russian Academy of Sciences 1 Academician Semenov avenue 142432 Chernogolovka Moscow Region Russian Federation
| | - Fedor E. Zhurkin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR CNRS 8601 Université de Paris 45 rue des Saints‐Pères 75006 Paris France
| | - Larisa G. Tomilova
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
- Department of Chemistry M.V. Lomonosov Moscow State University 1 Leninskie Gory 119991 Moscow Russian Federation
| | - Victor E. Pushkarev
- Institute of Physiologically Active Compounds Russian Academy of Sciences 1 Severny proezd 142432 Chernogolovka Moscow Region Russian Federation
- Department of Chemistry M.V. Lomonosov Moscow State University 1 Leninskie Gory 119991 Moscow Russian Federation
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9
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Sharma N, Sharma M, Rahman QI, Akhtar S, Muddassir M. Quantitative structure activity relationship and molecular simulations for the exploration of natural potent VEGFR-2 inhibitors: an in silico anti-angiogenic study. J Biomol Struct Dyn 2020; 39:2806-2823. [PMID: 32363995 DOI: 10.1080/07391102.2020.1754916] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
VEGFR-2 has recently become an eye-catching molecular target for the novel therapeutic designs against cancer for its well known role in persuading angiogenesis in tumor cells. The current study set sights on the exploration of novel potent natural compound targeting VEGFR-2 via computational ligand-based modeling and database screening followed by binding pattern analysis, reactivity site prediction and MD simulation studies. The known 53 VEGFR-2 inhibitors (with IC50 ranging from 0.7 nM to 9700 nM) were headed for development of Ligand based pharmacophore model using 3 D QSAR pharmacophore generation module of DS Client. Training set inhibitors (23 compounds) were exploited to create pharmacophore model based on their chemical features. The model was validated through 30 test set inhibitors and exploited further for screening of 62,082 natural compounds from InterBioscreen natural compound database. Screened compounds further went through Drug-Likeliness study, ADMET prediction, Binding pattern analysis, In silico prediction of reactivity sites, Biological activity spectra prediction, pan assay interference compound identification and MD simulation analysis. Out of 5 screened compounds, Compound A and Compound B exhibited highest binding energy judged against the standard drug "Sorafenib". On further conducting reactivity site prediction, BAS prediction, and pan assay interference compound identification, Compound B exhibited better result which was carried forward for MD simulation study for 50 ns. MD simulation results suggested that Compound B exhibited more stable binding to the active site of VEGFR-2 without causing any conformational changes in protein-ligand complex. Thereby, the investigation proposes Compound B to hold potent antiangiogenic potential targeting VEGFR-2. [Formula: see text] Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neha Sharma
- Department of Bioengineering, Integral University, Lucknow, India
| | - Mala Sharma
- Department of Biosciences, Integral University, Lucknow, India
| | | | - Salman Akhtar
- Department of Bioengineering, Integral University, Lucknow, India.,Novel Global Community Educational Foundation, Hebersham, Australia
| | - Mohd Muddassir
- Department of Chemistry, College of Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
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10
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Park H, Christian LS, Kim MJ, Li QJ, Hong J. Synthesis and Biological Evaluation of Subglutinol Analogs for Immunomodulatory Agents. J Med Chem 2019; 63:283-294. [PMID: 31793781 DOI: 10.1021/acs.jmedchem.9b01579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autoimmune diseases are chronic inflammatory diseases associated with high morbidity and mortality. Treatment options for autoimmune diseases have increased over the past several decades, but they are, in general, limited in their clinical efficacy due to high toxicity and lack of selectivity. Thus, efforts must be made to identify new immunomodulatory agents that are effective through a novel mechanism to circumvent existing side effects. To define the structural requirements of subglutinols for immunomodulatory activity and to provide guiding principles on future therapeutic development, we prepared and evaluated several subglutinol analogs for their immunomodulatory activities. Our efforts identified a subglutinol analog with reduced structural complexity as a potential lead compound for future autoimmune drug development. Our study will provide an important framework for the design of potent and nontoxic immunomodulating agents derived from subglutinols.
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Affiliation(s)
- Hyeri Park
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | | | - Mi Jung Kim
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | | | - Jiyong Hong
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
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11
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Šlachtová V, Chasák J, Brulíková L. Synthesis of Various 2-Aminobenzoxazoles: The Study of Cyclization and Smiles Rearrangement. ACS OMEGA 2019; 4:19314-19323. [PMID: 31763555 PMCID: PMC6868899 DOI: 10.1021/acsomega.9b02702] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
This study reports two synthetic approaches leading to 2-aminobenzoxazoles and their N-substituted analogues. Our first synthetic strategy involves a reaction between various o-aminophenols and N-cyano-N-phenyl-p-toluenesulfonamide as a nonhazardous electrophilic cyanating agent in the presence of Lewis acid. The second synthetic approach uses the Smiles rearrangement upon activation of benzoxazole-2-thiol with chloroacetyl chloride. Both developed synthetic protocols are widely applicable, afford the desired aminobenzoxazoles in good to excellent yields, and use nontoxic and inexpensive starting material.
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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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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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14
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Design and synthesis of novel ribofuranose nucleoside analogues as antiproliferative agents: A molecular docking and DFT study. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Tankam T, Srisa J, Sukwattanasinitt M, Wacharasindhu S. Microwave-Enhanced On-Water Amination of 2-Mercaptobenzoxazoles To Prepare 2-Aminobenzoxazoles. J Org Chem 2018; 83:11936-11943. [DOI: 10.1021/acs.joc.8b01824] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Theeranon Tankam
- Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University Bangkok 10330, Thailand
| | - Jakkrit Srisa
- Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University Bangkok 10330, Thailand
| | - Mongkol Sukwattanasinitt
- Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University Bangkok 10330, Thailand
| | - Sumrit Wacharasindhu
- Nanotec-CU Center of Excellence on Food and Agriculture, Department of Chemistry, Faculty of Science, Chulalongkorn University Bangkok 10330, Thailand
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16
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Design, synthesis and biological evaluation of a series of novel 2-benzamide-4-(6-oxy-N-methyl-1-naphthamide)-pyridine derivatives as potent fibroblast growth factor receptor (FGFR) inhibitors. Eur J Med Chem 2018; 154:9-28. [PMID: 29775937 DOI: 10.1016/j.ejmech.2018.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/08/2018] [Accepted: 05/04/2018] [Indexed: 02/08/2023]
Abstract
Starting from the phase II clinical FGFR inhibitor lucitanib (2), we conducted a medicinal chemistry approach by opening the central quinoline skeleton coupled with a scaffold hopping process thus leading to a series of novel 2-benzamide-4-(6-oxy-N-methyl-1-naphthamide)-pyridine derivatives. Compound 25a was identified to show selective and equally high potency against FGFR1/2 and VEGFR2 with IC50 values less than 5.0 nM. Significant antiproliferative effects on both FGFR1/2 and VEGFR2 aberrant cancer cells were observed. In the SNU-16 xenograft model, compound 25a showed tumor growth inhibition rates of 25.0% and 81.0% at doses of 10 mg/kg and 50 mg/kg, respectively, with 5% and 10%body weight loss. In view of the synergistic potential of FGFs and VEGFs in tumor angiogenesis observed in preclinical studies, the FGFR/VEGFR2 dual inhibitor 25a may achieve better clinical benefits.
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17
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In silico quest of selective naphthyl-based CREBBP bromodomain inhibitor. In Silico Pharmacol 2018; 6:1. [PMID: 30607314 DOI: 10.1007/s40203-018-0038-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/02/2018] [Indexed: 10/17/2022] Open
Abstract
The reader proteins like bromodomains have recently gained increased attentions in the area of epigenetic drug discovery, as they are the potent regulators in gene transcription process. Among the other bromodomains, cAMP response element-binding protein (CREB) binding protein or CREBBP bomodomain involved in various cancer progressions and therefore, efforts to develop specific inhibitors of CREBBP bomodomain are of clinical value. In this study, we tried to identify selective CREBBP bromodomain inhibitor, which was accomplished by using molecular docking, free energy calculation and molecular dynamics (MD) simulation studies, considering a series of naphthyl based compounds. The docking procedure was validated by comparing root mean square deviations (RMSDs) of crystallographic complex to docked complex. Favorable electrostatic interactions with the Arg1173 side chain were considered to attain selectivity for CREBBP bromodomain over other human bromodomain subfamilies. We found that naphthyl-based compounds have greater binding affinities towards the CREBBP bromodomain, and formed non-bonded interactions with various side chain residues that are important for bromodomain inhibition. From detailed investigation by induced fit docking, compound 31 was found to have favorable electrostatic interactions with the Arg1173 side chain by forming conventional hydrogen bonds. This result was further confirmed by analyzing hydrogen bond occupancy and bonding distance during the molecular dynamics simulation. We believe that these findings offer useful insight for the designing of target specific new bromodomain inhibitor and also promote further structure guided synthesis of analogues for identification of potent CREBBP bromodomain inhibitors as well as detailed in vitro and in vivo analyses.
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18
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Dvořáková P, Bušek P, Knedlík T, Schimer J, Etrych T, Kostka L, Stollinová Šromová L, Šubr V, Šácha P, Šedo A, Konvalinka J. Inhibitor-Decorated Polymer Conjugates Targeting Fibroblast Activation Protein. J Med Chem 2017; 60:8385-8393. [PMID: 28953383 DOI: 10.1021/acs.jmedchem.7b00767] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteases are directly involved in cancer pathogenesis. Expression of fibroblast activation protein (FAP) is upregulated in stromal fibroblasts in more than 90% of epithelial cancers and is associated with tumor progression. FAP expression is minimal or absent in most normal adult tissues, suggesting its promise as a target for the diagnosis or treatment of various cancers. Here, we report preparation of a polymer conjugate (an iBody) containing a FAP-specific inhibitor as the targeting ligand. The iBody inhibits both human and mouse FAP with low nanomolar inhibition constants but does not inhibit close FAP homologues dipeptidyl peptidase IV, dipeptidyl peptidase 9, and prolyl oligopeptidase. We demonstrate the applicability of this iBody for the isolation of FAP from cell lysates and blood serum as well as for its detection by ELISA, Western blot, flow cytometry, and confocal microscopy. Our results show the iBody is a useful tool for FAP targeting in vitro and potentially also for specific anticancer drug delivery.
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Affiliation(s)
- Petra Dvořáková
- Institute of Organic Chemistry and Biochemistry of The Czech Academy of Sciences , Flemingovo nám 2, 16610 Prague 6, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University , Viničná 7, 12843 Prague 2, Czech Republic
| | - Petr Bušek
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University , U Nemocnice 5, 12853 Prague 2, Czech Republic
| | - Tomáš Knedlík
- Institute of Organic Chemistry and Biochemistry of The Czech Academy of Sciences , Flemingovo nám 2, 16610 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University , Hlavova 8, 12843 Prague 2, Czech Republic
| | - Jiří Schimer
- Institute of Organic Chemistry and Biochemistry of The Czech Academy of Sciences , Flemingovo nám 2, 16610 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University , Hlavova 8, 12843 Prague 2, Czech Republic
| | - Tomáš Etrych
- Institute of Macromolecular Chemistry, The Czech Academy of Sciences , Heyrovského nám 2, 16206 Prague 6, Czech Republic
| | - Libor Kostka
- Institute of Macromolecular Chemistry, The Czech Academy of Sciences , Heyrovského nám 2, 16206 Prague 6, Czech Republic
| | - Lucie Stollinová Šromová
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University , U Nemocnice 5, 12853 Prague 2, Czech Republic
| | - Vladimír Šubr
- Institute of Macromolecular Chemistry, The Czech Academy of Sciences , Heyrovského nám 2, 16206 Prague 6, Czech Republic
| | - Pavel Šácha
- Institute of Organic Chemistry and Biochemistry of The Czech Academy of Sciences , Flemingovo nám 2, 16610 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University , Hlavova 8, 12843 Prague 2, Czech Republic
| | - Aleksi Šedo
- Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University , U Nemocnice 5, 12853 Prague 2, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of The Czech Academy of Sciences , Flemingovo nám 2, 16610 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University , Hlavova 8, 12843 Prague 2, Czech Republic
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19
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Synthesis of piperazine-based thiazolidinones as VEGFR2 tyrosine kinase inhibitors inducing apoptosis. Future Med Chem 2017; 9:1709-1729. [DOI: 10.4155/fmc-2017-0072] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: VEGFR2 tyrosine kinase is a main target in suppressing cancer growth and metastasis. Materials & methods: Piperazine-based thiazolidinones were synthesized and screened for their anticancer and VEGFR2 tyrosine kinase inhibitory activity. Results: Compounds 11, 13 and 16 displayed potent anticancer activity against HepG-2 with IC50 values 0.03–0.06 μM. They were safe on normal human fibroblasts with selectivity indices 8.09, 11.40 and 4.37, respectively. Also, these compounds showed VEGFR2 tyrosine kinase inhibitory activities more than the reference staurosporine with IC50 values <0.3 μM. Lineweaver–Burk plot revealed that these compounds behaved as uncompetitive VEGFR2 tyrosine kinase inhibitors. They also induced caspase-dependent apoptosis in HepG-2. In addition, these compounds revealed good binding within VEGFR2 tyrosine kinase enzyme in comparison with sorafenib reference. Conclusion: Compounds 11, 13 and 16 comprise a new promising scaffold of selective VEGFR2 tyrosine kinase inhibitors with caspase-dependent apoptotic activities.
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20
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Shukla R, Saeed A, Simpson J, Chopra D. Quantitative investigation of C–H⋯π and other intermolecular interactions in a series of crystalline N-(substituted phenyl)-2-naphthamide derivatives. CrystEngComm 2017. [DOI: 10.1039/c7ce01310h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we have investigated the nature and characteristics of different intermolecular interactions present in a series of sevenN-(substituted phenyl)-2-naphthamides.
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Affiliation(s)
- Rahul Shukla
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
| | - Aamer Saeed
- Department of Chemistry
- Quaid-i-Azam University-45320
- Islamabad
- Pakistan
| | - Jim Simpson
- Department of Chemistry
- University of Otago
- Dunedin 9054
- New Zealand
| | - Deepak Chopra
- Crystallography and Crystal Chemistry Laboratory
- Department of Chemistry
- IISER Bhopal
- Bhopal 462066
- India
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21
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Yan W, Huang Z, Wang Z, Cao S, Tong L, Zhang T, Wang C, Zhou L, Ding J, Luo C, Zhou J, Xie H, Duan W. Discovery of 1,3-Diaryl-pyridones as Potent VEGFR-2 Inhibitors: Design, Synthesis, and Biological Evaluation. Chem Biol Drug Des 2016; 87:694-703. [DOI: 10.1111/cbdd.12703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/04/2015] [Accepted: 12/03/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Wei Yan
- School of Pharmacy; East China University of Science & Technology; Shanghai 200237 China
| | - Zhaoru Huang
- Division of Anti-Tumor Pharmacology; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
- Department of Gastroenterology; The First Affiliated Hospital of Zhengzhou University; Zhengzhou Henan Province 450014 China
| | - Zhengyu Wang
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Sufen Cao
- School of Pharmacy; East China University of Science & Technology; Shanghai 200237 China
| | - Linjiang Tong
- Division of Anti-Tumor Pharmacology; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
| | - Tao Zhang
- Division of Anti-Tumor Pharmacology; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
| | - Chen Wang
- Drug Discovery and Design Center; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
| | - Lin Zhou
- Department of Gastroenterology; The First Affiliated Hospital of Zhengzhou University; Zhengzhou Henan Province 450014 China
| | - Jian Ding
- Division of Anti-Tumor Pharmacology; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
| | - Cheng Luo
- Drug Discovery and Design Center; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
| | - Jinpei Zhou
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 China
| | - Hua Xie
- Division of Anti-Tumor Pharmacology; State Key Laboratory of Drug Research; Shanghai Institute of Materia Medica; Shanghai 201203 China
| | - Wenhu Duan
- School of Pharmacy; East China University of Science & Technology; Shanghai 200237 China
- Department of Medicinal Chemistry; Shanghai Institute of Materia Medica; Shanghai 201203 China
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22
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Wang J, Shu M, Wen X, Wang Y, Wang Y, Hu Y, Lin Z. Discovery of vascular endothelial growth factor receptor tyrosine kinase inhibitors by quantitative structure–activity relationships, molecular dynamics simulation and free energy calculation. RSC Adv 2016. [DOI: 10.1039/c6ra03743g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Employing the combined strategy to understand the features of KDR–ligands complexes, and provide a basis for rational design of inhibitors.
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Affiliation(s)
- Juan Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
| | - Mao Shu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Xiaorong Wen
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yuanliang Wang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education)
- Research Center of Bioinspired Material Science and Engineering
- Bioengineering College
- Chongqing University
- Chongqing 400044
| | - Yuanqiang Wang
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Yong Hu
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
| | - Zhihua Lin
- School of Pharmacy and Bioengineering
- Chongqing University of Technology
- Chongqing 400054
- China
- College of Chemistry and Chemical Engineering
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23
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Investigation of new 2-aryl substituted Benzothiopyrano[4,3-d]pyrimidines as kinase inhibitors targeting vascular endothelial growth factor receptor 2. Eur J Med Chem 2015; 103:29-43. [PMID: 26318056 DOI: 10.1016/j.ejmech.2015.08.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/28/2015] [Accepted: 08/11/2015] [Indexed: 02/06/2023]
Abstract
Vascular Endothelial Growth Factor (VEGF) pathway has emerged as one of the most important positive modulators of Angiogenesis, a central process implicated in tumour growth and metastatic dissemination. This led to the design and development of anti-VEGF monoclonal antibodies and small-molecule ATP-competitive VEGFR-inhibitors. In this study, we describe the synthesis and the biological evaluation of novel 2-aryl substituted benzothiopyrano-fused pyrimidines 1a-i, 2a-i and 3a-i. The ability of the compounds to target the VEGF pathway was determined in vitro exploiting the compounds' antiproliferative efficacy against HUVEC cells. The VEGFR-2 inhibition was confirmed by enzymatic assays on recombinant human kinase insert domain receptor (KDR), by cell-based phospho-VEGFR-2 inhibition assays, and by ex vivo rat aortic ring tests. The selectivity profile of the best performing derivatives belonging to series 2 was further explored combining modeling studies and additional assays in a panel of human cell lines and other kinases.
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24
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Yin Y, Sha S, Wang YT, Wu X, Wang SF, Qiao F, Lv PC, Zhu HL. Discovery of new 4-alkoxyquinazoline-based derivatives as potent VEGFR2 inhibitors. Chem Biol Drug Des 2015; 86:1323-9. [PMID: 26032487 DOI: 10.1111/cbdd.12596] [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] [Received: 01/19/2015] [Revised: 04/19/2015] [Accepted: 04/27/2015] [Indexed: 01/23/2023]
Abstract
VEGFR2 has been proved to play a major role in the regulation of tumor angiogenesis. Twenty-one 4-alkoxyquinazoline-based derivatives have been designed and synthesized as vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors, and their biological activities were evaluated. Among these compounds, compound 3h exhibited the most potent inhibitory activities against VEGFR2 tyrosine kinase and cell proliferation, with the IC50 values of 2.89 nm (for VEGFR2) and 0.25 μm (for MCF-7), which were comparable with the control compound. Docking simulation was performed to position compound 3h into the 4ASE active site, and the result showed that compound 3h could bind well at the 4ASE active site.
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Affiliation(s)
- Yong Yin
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Shao Sha
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Yan-Ting Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Xun Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - She-Feng Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Fang Qiao
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Peng-Cheng Lv
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210093, China
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25
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Branch A, Bobilev A, Negrao NW, Cai H, Shen P. Prevention of palatable diet-induced hyperphagia in rats by central injection of a VEGFR kinase inhibitor. Behav Brain Res 2015; 278:506-13. [DOI: 10.1016/j.bbr.2014.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/30/2014] [Accepted: 10/02/2014] [Indexed: 12/22/2022]
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26
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Lv Y, Li M, Cao S, Tong L, Peng T, Wei L, Xie H, Ding J, Duan W. Discovery of anilinopyrimidine-based naphthamide derivatives as potent VEGFR-2 inhibitors. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00191a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) plays an important role in tumor angiogenesis, and inhibition of the VEGFR-2 signaling pathway has emerged as an attractive strategy for the treatment of cancer.
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Affiliation(s)
- Yongcong Lv
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- China
| | - Mengyuan Li
- Division of Anti-Tumor Pharmacology
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Sufen Cao
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- China
| | - Linjiang Tong
- Division of Anti-Tumor Pharmacology
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Ting Peng
- Division of Anti-Tumor Pharmacology
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Lixin Wei
- Northwest Institute of Plateau Biology
- Chinese Academy of Sciences
- China
| | - Hua Xie
- Division of Anti-Tumor Pharmacology
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Jian Ding
- Division of Anti-Tumor Pharmacology
- State Key Laboratory of Drug Research
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
| | - Wenhu Duan
- Department of Medicinal Chemistry
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203
- China
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27
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Molecular dynamics simulation and free energy calculation studies of kinase inhibitors binding to active and inactive conformations of VEGFR-2. J Mol Graph Model 2014; 56:103-12. [PMID: 25594497 DOI: 10.1016/j.jmgm.2014.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 12/04/2014] [Accepted: 12/16/2014] [Indexed: 11/21/2022]
Abstract
Vascular endothelial growth factors receptor-2 (VEGFR-2) inhibitors have been proved as very effective anticancer agents. Structurally similar ligands 1 and 2 show almost the same inhibitory activities against VEGFR-2, but they bind to the enzyme in distinct binding mode. Ligand 1 targets DFG-in active conformation of VEGFR-2, known as Type I inhibitor. On the other hand, ligand 2 targets DFG-out inactive conformation of VEGFR-2, known as Type II inhibitor or allosteric kinase inhibitor. Ligand 2 shows high inhibitory activity, while the compound 3, a close analog of 2 with the cyclopropylamide replaced by tert-butylamide, exhibits drastically diminished potency. In this work, molecular dynamics simulations and free energy calculations were performed on inhibitors 1-3 binding to active and inactive conformation of VEGFR-2. Molecular dynamics simulations find that the active conformation binding to Type I inhibitor 1 appears more flexible when compared to the unbound form. In contrast, binding of Type II inhibitor 2 to the inactive conformation helps to stabilize the inactive conformation of the protein. Binding free energy calculations verify that inhibitors 1 and 2 have almost the same activities against VEGFR-2, and that ligand 1 binds to and stabilizes the DFG-in conformation of VEGFR-2, which is in agree with the experimental observation. Molecular dynamics simulations and binding free energy calculations of 3 binding to VEGFR-2 can give a good explanation of the drastically diminished potency. Free energy analysis revealed that van der Waals interactions provided the substantial driving force for the binding process. The important hydrophobic property of the terminal 4-Cl phenyl was required to be Type II inhibitors. Furthermore, per-residue free energy decomposition analysis revealed that the most favorable contribution came from Leu840, Val848, Ala866, Lys868, Leu889, Val899, Thr916, Phe918, Cys919, Leu1035, Cys1045, Asp1046, and Phe1047. These results are expected to be useful for future rational design of novel potent VEGFR-2 inhibitors.
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28
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Lv Y, Li M, Liu T, Tong L, Peng T, Wei L, Ding J, Xie H, Duan W. Discovery of a New Series of Naphthamides as Potent VEGFR-2 Kinase Inhibitors. ACS Med Chem Lett 2014; 5:592-7. [PMID: 24900886 DOI: 10.1021/ml5000417] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/24/2014] [Indexed: 02/08/2023] Open
Abstract
Inhibition of VEGFR-2 signaling pathway has already become one of the most promising approaches for the treatment of cancer. In this study, we describe the design, synthesis, and biological evaluation of a new series of naphthamides as potent inhibitors of VEGFR-2. Among these compounds, 14c exhibited high VEGFR-2 inhibitory potency in both enzymatic and HUVEC cellular proliferation assays, with IC50 values of 1.5 and 0.9 nM, respectively. Kinase selectivity profiling revealed that 14c was a multitargeted inhibitor, and it also exhibited good potency against VEGFR-1, PDGFR-β, and RET. Furthermore, 14c effectively blocked tube formation of HUVEC at nanomolar level. Overall, 14c might be a promising candidate for the treatment of cancer.
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Affiliation(s)
- Yongcong Lv
- Department
of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Mengyuan Li
- Division
of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- Northwest
Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning
Road, Qinghai 81008, China
| | - Ting Liu
- Department
of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
- Medical College of Nanchang University, 461 Bayi Road, Nanchang, Jiangxi 330066, China
| | - Linjiang Tong
- Division
of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Ting Peng
- Division
of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Lixin Wei
- Northwest
Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning
Road, Qinghai 81008, China
| | - Jian Ding
- Division
of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Hua Xie
- Division
of Anti-Tumor Pharmacology, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
| | - Wenhu Duan
- Department
of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, China
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29
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Colzani M, Noberini R, Romanenghi M, Colella G, Pasi M, Fancelli D, Varasi M, Minucci S, Bonaldi T. Quantitative chemical proteomics identifies novel targets of the anti-cancer multi-kinase inhibitor E-3810. Mol Cell Proteomics 2014; 13:1495-509. [PMID: 24696502 PMCID: PMC4047469 DOI: 10.1074/mcp.m113.034173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Novel drugs are designed against specific molecular targets, but almost unavoidably they bind non-targets, which can cause additional biological effects that may result in increased activity or, more frequently, undesired toxicity. Chemical proteomics is an ideal approach for the systematic identification of drug targets and off-targets, allowing unbiased screening of candidate interactors in their natural context (tissue or cell extracts). E-3810 is a novel multi-kinase inhibitor currently in clinical trials for its anti-angiogenic and anti-tumor activity. In biochemical assays, E-3810 targets primarily vascular endothelial growth factor and fibroblast growth factor receptors. Interestingly, E-3810 appears to inhibit the growth of tumor cells with low to undetectable levels of these proteins in vitro, suggesting that additional relevant targets exist. We applied chemical proteomics to screen for E-3810 targets by immobilizing the drug on a resin and exploiting stable isotope labeling by amino acids in cell culture to design experiments that allowed the detection of novel interactors and the quantification of their dissociation constant (Kd imm) for the immobilized drug. In addition to the known target FGFR2 and PDGFRα, which has been described as a secondary E-3810 target based on in vitro assays, we identified six novel candidate kinase targets (DDR2, YES, LYN, CARDIAK, EPHA2, and CSBP). These kinases were validated in a biochemical assay and—in the case of the cell-surface receptor DDR2, for which activating mutations have been recently discovered in lung cancer—cellular assays. Taken together, the success of our strategy—which integrates large-scale target identification and quality-controlled target affinity measurements using quantitative mass spectrometry—in identifying novel E-3810 targets further supports the use of chemical proteomics to dissect the mechanism of action of novel drugs.
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Affiliation(s)
- Mara Colzani
- From the ‡Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy; §Center of Genomic Science, Istituto Italiano di Tecnologia, via Adamello 16, 20139 Milano, Italy
| | - Roberta Noberini
- From the ‡Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy; §Center of Genomic Science, Istituto Italiano di Tecnologia, via Adamello 16, 20139 Milano, Italy
| | - Mauro Romanenghi
- From the ‡Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Gennaro Colella
- ¶EOS S.p.A., Via Monte di Pietà 1/A, 20121 Milano, Italy; ‖Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Amadeo 42, 20133 Milano, Italy
| | - Maurizio Pasi
- **Drug Discovery Program, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Daniele Fancelli
- **Drug Discovery Program, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Mario Varasi
- **Drug Discovery Program, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Saverio Minucci
- From the ‡Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy; **Drug Discovery Program, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy; ‡‡Department of Bioscience, University of Milan, 20133 Milano, Italy
| | - Tiziana Bonaldi
- From the ‡Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milano, Italy;
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30
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Zhang Y, Yang S, Jiao Y, Liu H, Yuan H, Lu S, Ran T, Yao S, Ke Z, Xu J, Xiong X, Chen Y, Lu T. An Integrated Virtual Screening Approach for VEGFR-2 Inhibitors. J Chem Inf Model 2013; 53:3163-77. [DOI: 10.1021/ci400429g] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yanmin Zhang
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Shangyan Yang
- State
Key Laboratory of Natural Medcines, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Yu Jiao
- State
Key Laboratory of Natural Medcines, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
| | - Haichun Liu
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Haoliang Yuan
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Shuai Lu
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Ting Ran
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Sihui Yao
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Zhipeng Ke
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jinxing Xu
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Xiao Xiong
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Yadong Chen
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Tao Lu
- Laboratory
of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
- State
Key Laboratory of Natural Medcines, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing, 210009, China
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Liu B, Yin M, Gao H, Wu W, Jiang H. Synthesis of 2-Aminobenzoxazoles and 3-Aminobenzoxazines via Palladium-Catalyzed Aerobic Oxidation of o-Aminophenols with Isocyanides. J Org Chem 2013; 78:3009-20. [DOI: 10.1021/jo400002f] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Bifu Liu
- School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, People’s Republic
of China
| | - Meizhou Yin
- School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, People’s Republic
of China
| | - Hanling Gao
- School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, People’s Republic
of China
| | - Wanqing Wu
- School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, People’s Republic
of China
| | - Huanfeng Jiang
- School of Chemistry and
Chemical Engineering, South China University of Technology, Guangzhou 510640, People’s Republic
of China
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32
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Abstract
VEGF is an important signaling protein involved in both vasculogenesis and angiogenesis. As an essential receptor protein tyrosine kinase propagating cellular signal transduction processes, VEGFR-2 is a central target for drug discovery against tumor-associated angiogenesis. Since the autophosphorylation of VEGFR-2 represents a key step in this signal pathway that contributes to angiogenesis, the discovery of small molecule inhibitors that block this reaction has attracted great interest for novel drugs research and development. Advances in the understanding of catalytic cleft and the conformational changes of DFG motif have resulted in the development of small molecule inhibitors known as type I and type II. High-resolution crystal structures of various inhibitors in complex with the receptor offer an insight into the relationship among binding modes, inhibition mechanisms, activity, selectivity and resistance. To control selectivity, improve activity and introduce intellectual property novelty, the strategies for the further development are discussed through structural and conformational analysis in this review.
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Design, synthesis, and evaluation of imidazo[1,2-b]pyridazine derivatives having a benzamide unit as novel VEGFR2 kinase inhibitors. Bioorg Med Chem 2012; 20:7051-8. [DOI: 10.1016/j.bmc.2012.10.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/04/2012] [Accepted: 10/05/2012] [Indexed: 11/21/2022]
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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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35
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Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors. Proc Natl Acad Sci U S A 2012; 109:18281-9. [PMID: 22988103 DOI: 10.1073/pnas.1207759109] [Citation(s) in RCA: 336] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analyses of compounds in clinical development have shown that ligand efficient-molecules with privileged physical properties and low dose are less likely to fail in the various stages of clinical testing, have fewer postapproval withdrawals, and are less likely to receive black box safety warnings. However, detailed side-by-side examination of molecular interactions and properties within single drug classes are lacking. As a class, VEGF receptor tyrosine kinase inhibitors (VEGFR TKIs) have changed the landscape of how cancer is treated, particularly in clear cell renal cell carcinoma, which is molecularly linked to the VEGF signaling axis. Despite the clear role of the molecular target, member molecules of this validated drug class exhibit distinct clinical efficacy and safety profiles in comparable renal cell carcinoma clinical studies. The first head-to-head randomized phase III comparative study between active VEGFR TKIs has confirmed significant differences in clinical performance [Rini BI, et al. (2011) Lancet 378:193-1939]. To elucidate how fundamental drug potency-efficiency is achieved and impacts differentiation within the VEGFR TKI class, we determined potencies, time dependence, selectivities, and X-ray structures of the drug-kinase complexes using a VEGFR2 TK construct inclusive of the important juxtamembrane domain. Collectively, the studies elucidate unique drug-kinase interactions that are dependent on distinct juxtamembrane domain conformations, resulting in significant potency and ligand efficiency differences. The identified structural trends are consistent with in vitro measurements, which translate well to clinical performance, underscoring a principle that may be broadly applicable to prospective drug design for optimal in vivo performance.
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36
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Lovering F, McDonald J, Whitlock GA, Glossop PA, Phillips C, Bent A, Sabnis Y, Ryan M, Fitz L, Lee J, Chang JS, Han S, Kurumbail R, Thorarensen A. Identification of type-II inhibitors using kinase structures. Chem Biol Drug Des 2012; 80:657-64. [PMID: 22759374 DOI: 10.1111/j.1747-0285.2012.01443.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spleen tyrosine kinase is a non-receptor tyrosine kinase, overactivation of which is thought to contribute to autoimmune diseases as well as allergy and asthma. Protein kinases have a highly conserved ATP binding site, thus making challenging the design of selective small molecule inhibitors. It has been well documented that some protein kinases can be stabilized in their inactive conformations (Type-II inhibitors). Herein, we describe a protein structure/ligand-based approach to successfully identify ligands that bind to novel conformations of spleen tyrosine kinase. By utilizing kinase protein crystal structures both in the public domain (RCSB) and within Pfizer's protein crystal database, we report the discovery of the first spleen tyrosine kinase Type-II ligands. Compounds 1 and 3 were found to bind to the DFG-out conformation of spleen tyrosine kinase, while compound 2 binds to a DFG-in, C-Helix-out conformation. In this instance, the C-helix moved significantly to create a large hydrophobic pocket rarely seen in kinase protein crystal structures.
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Affiliation(s)
- Frank Lovering
- World Wide Medicinal Chemistry, Pfizer Worldwide R & D, 200 Cambridgepark Drive, Cambridge, MA 02140, USA.
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37
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Han SY, Choi JW, Yang J, Chae CH, Lee J, Jung H, Lee K, Ha JD, Kim HR, Cho SY. Design and synthesis of 3-(4,5,6,7-tetrahydro-3H-imidazo[4,5-c]pyridin-2-yl)-1H-quinolin-2-ones as VEGFR-2 kinase inhibitors. Bioorg Med Chem Lett 2012; 22:2837-42. [DOI: 10.1016/j.bmcl.2012.02.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/14/2012] [Accepted: 02/23/2012] [Indexed: 11/30/2022]
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38
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Chanda K, Maiti B, Tseng CC, Sun CM. Microwave-assisted linear approach toward highly substituted benzo[d]oxazol-5-yl-1H-benzo[d]imidazole on ionic liquid support. ACS COMBINATORIAL SCIENCE 2012; 14:115-23. [PMID: 22263632 DOI: 10.1021/co200188g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A novel and efficient diversity-oriented synthetic approach was employed to access the benzo[d]oxazol-5-yl-1H-benzo[d]imidazole on ionic liquid support, which helps to absorb microwave irradiation. In this paper, we successfully coupled 4-hydroxy-3-nitrobenzoic acid onto ionic liquid-immobilized o-phenylenediamine, which subsequently underwent an acid mediated, ring closure reaction leading to benzimidazole derivatives. After hydrogenation of the nitro group to an amine, the resulting ionic liquid conjugate was reacted with 1,1-thiocarbonyldiimidazols to yield an ionic liquid tagged-benzoxazol. Final skeletal diversity of the present scaffold was further achieved by S-alkylation with alkyl and aryl bromides. The benzo[d]oxazol-5-yl-1H-benzo[d]imidazole was finally cleaved smoothly from the ionic liquid support with sodium methoxide in methanol under microwave irradiation. This methodology has provided access to a small, diverse library by straightforward and simple operations and could be applied readily in various drug discovery programs.
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Affiliation(s)
- Kaushik Chanda
- Laboratory of Combinatorial Drug Design, Department
of Applied Chemistry, National Chiao-Tung University, Hsinchu 300-10, Taiwan
| | - Barnali Maiti
- Laboratory of Combinatorial Drug Design, Department
of Applied Chemistry, National Chiao-Tung University, Hsinchu 300-10, Taiwan
| | - Chih-Chung Tseng
- Laboratory of Combinatorial Drug Design, Department
of Applied Chemistry, National Chiao-Tung University, Hsinchu 300-10, Taiwan
| | - Chung-Ming Sun
- Laboratory of Combinatorial Drug Design, Department
of Applied Chemistry, National Chiao-Tung University, Hsinchu 300-10, Taiwan
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39
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Coxon A, Bready J, Kaufman S, Estrada J, Osgood T, Canon J, Wang L, Radinsky R, Kendall R, Hughes P, Polverino A. Anti-tumor activity of motesanib in a medullary thyroid cancer model. J Endocrinol Invest 2012; 35:181-90. [PMID: 21422803 DOI: 10.3275/7609] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Medullary thyroid cancer (MTC) is frequently associated with mutations in the tyrosine kinase Ret and with increased expression of vascular endothelial growth factor (VEGF) and VEGF receptor 2 (VEGFR2). Motesanib is an investigational, orally administered small molecule antagonist of VEGFR1, 2, and 3; platelet-derived growth factor receptor (PDGFR); Kit; and possibly Ret. AIM The aim of this study was to investigate the effects of motesanib on wildtype and mutant Ret activity in vitro and on tumor xenograft growth in a mouse model of MTC. METHODS/RESULTS In cellular phosphorylation assays, motesanib inhibited the activity of wild-type Ret (IC(50)=66 nM), while it had limited activity against mutant Ret C634W (IC(50)=1100 nM) or Ret M918T (IC(50)>2500 nM). In vivo, motesanib significantly inhibited the growth of TT tumor cell xenografts (expressing Ret C634W) and significantly reduced tumor blood vessel area and tumor cell proliferation, compared with control. Treatment with motesanib resulted in substantial inhibition of Ret tyrosine phosphorylation in TT xenografts and, at comparable doses, in equivalent inhibition of VEGFR2 phosphorylation in both TT xenografts and in mouse lung tissue. CONCLUSIONS The results of this study demonstrate that motesanib inhibited thyroid tumor xenograft growth predominantly through inhibition of angiogenesis and possibly via a direct inhibition of VEGFR2 and Ret expressed on tumor cells. These data suggest that targeting angiogenesis pathways and specifically the VEGF pathway may represent a novel therapeutic approach in the treatment of MTC.
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Affiliation(s)
- A Coxon
- Department of Oncology Research, Amgen Inc., Thousand Oaks, CA 91320, USA.
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40
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Abreu RMV, Froufe HJC, Queiroz MJRP, Ferreira ICFR. Selective flexibility of side-chain residues improves VEGFR-2 docking score using AutoDock Vina. Chem Biol Drug Des 2012; 79:530-4. [PMID: 22188672 DOI: 10.1111/j.1747-0285.2011.01313.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selective side-chain residue flexibility is an option available on AutoDock Vina docking software. This approach is promising as it attempts to provide a more realistic ligand-protein interaction environment without an unmanageable increase in computer processing time. However, studies validating this approach are still scarce. VEGFR-2 (vascular endothelial growth factor receptor 2), a known protein target for anti-angiogenic agents, was used in this study. Four residues located in the VEGFR-2 kinase site were selected and made flexible: Lys868, Glu885, Cys919, and Asp1046. The docking scores for all possible combinations of flexible residues were compared to the docking scores using a rigid conformation. The best overall docking scores were obtained using the Glu885 flexible conformation, with Pearson and Spearman rank correlation values of 0.568 and 0.543, respectively, and a 51% increase in processing time. Using different VEGFR-2 crystal structures, a similar trend was observed with the Glu885 flexible conformation presenting best scores. This study demonstrates that careful use of selective side-chain residue flexibility can improve AutoDock Vina docking score accuracy, without a significant increase in processing time. This methodology can be a valuable tool in drug design projects using VEGFR-2 but will also probably be useful if applied to other protein targets.
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Affiliation(s)
- Rui M V Abreu
- CIMO-ESA, Instituto Politécnico de Bragança, Campus de Sta Apolónia, Apartado 1172, 5301-855 Bragança, Portugal.
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41
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Chanda K, Maiti B, Yellol GS, Chien MH, Kuo ML, Sun CM. Polymer supported synthesis of novel benzoxazole linked benzimidazoles under microwave conditions: in vitro evaluation of VEGFR-3 kinase inhibition activity. Org Biomol Chem 2011; 9:1917-26. [PMID: 21283915 DOI: 10.1039/c0ob00547a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An efficient soluble polymer-supported method has been developed for the parallel synthesis of substituted benzimidazole linked benzoxazoles using focused microwave irradiation. The key step involves the amidation of 4-hydroxy-3-nitrobenzoic acid with polymer-immobilized o-phenylenediamine. Application of mild acidic conditions promoted the ring closure to furnish the benzimidazole ring. After hydrogenation of the nitro-group to amine, the resulted polymer conjugates underwent efficient ring closure with various alkyl, aryl and heteroaryl isothiocyanates to generate the polymer-bound benzimidazolyl benzoxazoles. The polymer-bound compounds were finally cleaved from the support to furnish benzimidazole linked benzoxazole derivatives. The efficacy of the resultant angular bis-heterocyclic library was studied against vascular endothelial growth factor receptor (VEGFR-3). The preliminary screening of these novel compounds exhibits moderate to high inhibition (IC(50) = 0.56-1.42 μM). This protocol provides an easy access to novel angular bis-heterocycles which have potential for the discovery of novel leads for targeted cancer therapeutics.
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Affiliation(s)
- Kaushik Chanda
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300-10, Taiwan
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42
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Martin MW, Machacek MR. Update on lymphocyte specific kinase inhibitors: a patent survey. Expert Opin Ther Pat 2010; 20:1573-93. [PMID: 20831362 DOI: 10.1517/13543776.2010.517749] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
IMPORTANCE OF THE FIELD Lck (p56(lck) or lymphocyte specific kinase) is a cytoplasmic tyrosine kinase of the Src family expressed in T cells and natural killer (NK) cells. Genetic evidence from knockout mice and human mutations demonstrates that Lck kinase activity is critical for T cell receptor (TCR)-mediated signaling, leading to normal T-cell development and activation. Selective inhibition of Lck is expected to offer a new therapy for the treatment of T-cell-mediated autoimmune and inflammatory disorders and/or organ transplant rejection. AREAS COVERED IN THIS REVIEW This review covers the patents, patent applications and associated publications for small molecule kinase inhibitors of Lck since 2005 and attempts to place them in context from a structural point of view. WHAT THE READER WILL GAIN Readers will gain an overview of the structural classes and binding modes of Lck inhibitors, the major players in this area and an insight into the current state of the field. TAKE HOME MESSAGE The search for a potent and orally active inhibitor of Lck has been an intense area of research for a number of years. Despite tremendous efforts, the identification of a highly selective and potent Lck inhibitor suitable for use as an immunosuppressive agent remains elusive.
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Affiliation(s)
- Matthew W Martin
- Amgen, Inc., Department of Medicinal Chemistry, Cambridge, Massachusetts 02142, USA.
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43
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Sun M, Chen J, Cai J, Cao M, Yin S, Ji M. Simultaneously Optimized Support Vector Regression Combined With Genetic Algorithm for QSAR Analysis of KDR/VEGFR-2 Inhibitors. Chem Biol Drug Des 2010; 75:494-505. [DOI: 10.1111/j.1747-0285.2010.00958.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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44
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Littler DR, Walker JR, Davis T, Wybenga-Groot LE, Finerty PJ, Newman E, Mackenzie F, Dhe-Paganon S. A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:143-51. [PMID: 20124709 DOI: 10.1107/s1744309109052543] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 12/07/2009] [Indexed: 12/16/2022]
Abstract
The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 A resolution crystal structure of the isolated kinase domain from the alpha2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKalpha2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function.
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Affiliation(s)
- Dene R Littler
- The Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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45
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Papakyriakou A, Katsarou M, Belimezi M, Karpusas M, Vourloumis D. Discovery of Potent Vascular Endothelial Growth Factor Receptor-2 Inhibitors. ChemMedChem 2010; 5:118-29. [DOI: 10.1002/cmdc.200900373] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Lu X, Chen Y, You Q. Pharmacophore Guided 3D-QSAR CoMFA Analysis of Amino Substituted Nitrogen Heterocycle Ureas as KDR Inhibitors. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200960032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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48
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Wang LM, Hu L, Chen HJ, Sui YY, Shen W. One-pot synthesis of quinoline-4-carboxylic acid derivatives in water: Ytterbium perfluorooctanoate catalyzed Doebner reaction. J Fluor Chem 2009. [DOI: 10.1016/j.jfluchem.2009.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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49
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Du J, Lei B, Qin J, Liu H, Yao X. Molecular modeling studies of vascular endothelial growth factor receptor tyrosine kinase inhibitors using QSAR and docking. J Mol Graph Model 2008; 27:642-54. [PMID: 19081278 DOI: 10.1016/j.jmgm.2008.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 10/17/2008] [Accepted: 10/20/2008] [Indexed: 10/21/2022]
Abstract
The vascular endothelial growth factor (VEGF) and its receptor tyrosine kinases VEGFR-2 or kinase insert domain receptor (KDR) are attractive targets for the development of novel anticancer agents. In the present work, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of selective inhibitors of KDR. Docking studies were performed to explore the binding mode between all of the inhibitors and the KDR and produce the bioactive conformation of each compound in the whole dataset. Two conformer-based alignment strategies were employed to construct reliable 3D-QSAR models. The docked conformer-based alignment strategy gave the best 3D-QSAR models. The best CoMFA and CoMSIA models gave a cross-validated coefficient q(2) of 0.546 and 0.715, non-cross-validated r(2) values of 0.936 and 0.961, predicted r(2) values of 0.673 and 0.797, respectively. The information obtained from molecular modeling studies were very helpful to design some novel selective inhibitors of KDR with desired activity.
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Affiliation(s)
- Juan Du
- Department of Chemistry, Lanzhou University, Lanzhou, China
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50
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Teffera Y, Colletti AE, Harmange JC, Hollis LS, Albrecht BK, Boezio AA, Liu J, Zhao Z. Chemical Reactivity of Methoxy 4-O-Aryl Quinolines: Identification of Glutathione Displacement Products in Vitro and in Vivo. Chem Res Toxicol 2008; 21:2216-22. [DOI: 10.1021/tx800307n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yohannes Teffera
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - Adria E. Colletti
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - Jean Christophe Harmange
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - L. Steven Hollis
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - Brian K. Albrecht
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - Alessandro A. Boezio
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - Jingzhou Liu
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
| | - Zhiyang Zhao
- Pharmacokinetics and Drug Metabolism and Medicinal Chemistry, Amgen, Inc., One Kendall Square, Building 1000, Cambridge, Massachusetts 02139
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