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Yasuda S, Svergja H, Olsen CE, Hoff BH. Promotion of Water as Solvent in Amination of 4-Chloropyrrolopyrimidines and Related Heterocycles under Acidic Conditions. ACS OMEGA 2024; 9:14142-14152. [PMID: 38559978 PMCID: PMC10976386 DOI: 10.1021/acsomega.3c09673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/22/2024] [Accepted: 02/28/2024] [Indexed: 04/04/2024]
Abstract
A switch of reaction medium from organic solvents to water can improve the safety and lower the cost of production processes. Hydrochloric acid-promoted amination of fused pyrimidines has been studied using 4-chloro-7H-pyrrolo[2,3-d]pyrimidine and aniline as model compounds. Higher rate was observed in water than in four alcoholic solvents and DMF. An important aspect is that the amount of acid should be kept low to minimize the competing solvolysis. The substrate scope for the amination in water was evaluated by reacting 4-chloro-7H-pyrrolo[2,3-d]pyrimidine with 20 aniline derivatives with variance in steric and electronic properties. Preparative useful reactions were seen for 14 of the 20 derivatives. Unsuited nucleophiles are ortho-substituted anilines with a pKa below 1. Amination of the corresponding quinazoline, thienopyrimidine, and purine also proceeded well in water. Highly lipophilic and crystalline compounds are more efficiently aminated in 2-propanol. Aliphatic and benzylic amines react poorly under acidic conditions, but these aminations can be done in water without acid.
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Affiliation(s)
- Shuhei Yasuda
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Ho̷gskoleringen 5, NO-7491 Trondheim, Norway
| | | | - Cecilie Elisabeth Olsen
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Ho̷gskoleringen 5, NO-7491 Trondheim, Norway
| | - Bård Helge Hoff
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), Ho̷gskoleringen 5, NO-7491 Trondheim, Norway
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2
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Huo D, Sun Z, Wang M, Yan A. Ligand and structure based hierarchical virtual screening cascade for finding novel epidermal growth factor receptor inhibitors. Chem Biol Drug Des 2024; 103:e14375. [PMID: 37849030 DOI: 10.1111/cbdd.14375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 09/11/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023]
Abstract
The epidermal growth factor receptor (EGFR) tyrosine kinase plays an important role in tumor formation and growth by mediating cell growth and other physiological processes. Therefore, EGFR is a promising target for the treatment of cancer. In this work, we combined ligand-based and structure-based virtual screening methods to identify novel EGFR inhibitors from a library of more than 103 thousand compounds. We first obtained hundreds of compounds with similar physiochemical properties through 3D molecular shape and electrostatic similarity screening with potent inhibitors AEE788 and Afatinib as queries. Next, we identified compounds with strong binding affinities to the EGFR pocket through molecular docking, which makes good use of the structure information of the receptor. After molecular scaffold analysis, our bioassay confirmed 13 compounds with EGFR inhibitory activity and three compounds had IC50 values below 1000 nM. In addition, we collected 5371 EGFR inhibitors from online databases, and clustered them into 7 groups by K-means method using their ECFP4 fingerprints as input. Each cluster had typical molecular fragments and corresponding activity characteristics, which could guide the design of EGFR inhibitors, and we concluded that the fragments from some of the hits are indicated in the highly active scaffolds.
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Affiliation(s)
- Donghui Huo
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, China Petroleum & Chemical Corporation (SINOPEC), Dalian, China
| | - Zhiqi Sun
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Maolin Wang
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Physiology, School of Basic Medical Sciences, Shenzhen University Health Sciences Center, Shenzhen, Guangdong, China
| | - Aixia Yan
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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3
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Yadav TT, Moin Shaikh G, Kumar MS, Chintamaneni M, YC M. A Review on Fused Pyrimidine Systems as EGFR Inhibitors and Their Structure–Activity Relationship. Front Chem 2022; 10:861288. [PMID: 35769445 PMCID: PMC9234326 DOI: 10.3389/fchem.2022.861288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/28/2022] [Indexed: 01/05/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) belongs to the family of tyrosine kinase that is activated when a specific ligand binds to it. The EGFR plays a vital role in the cellular proliferation process, differentiation, and apoptosis. In the case of cancer, EGFR undergoes uncontrolled auto-phosphorylation that results in increased cellular proliferation and decreased apoptosis, causing cancer promotion. From the literature, it shows that pyrimidine is one of the most commonly studied heterocycles for its antiproliferative activity against EGFR inhibition. The authors have collated some interesting results in the heterocycle-fused pyrimidines that have been studied using different cell lines (sensitive and mutational) and in animal models to determine their activity and potency. It is quite clear that the fused systems are highly effective in inhibiting EGFR activity in cancer cells. Therefore, the structure–activity relationship (SAR) comes into play in determining the nature of the heterocycle and the substituents that are responsible for the increased activity and toxicity. Understanding the SAR of heterocycle-fused pyrimidines will help in getting a better overview of the molecules concerning their activity and potency profile as future EGFR inhibitors.
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Affiliation(s)
| | | | | | | | - Mayur YC
- *Correspondence: Mayur YC, mayur
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4
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Yahyazadehfar M, Sheikhhosseini E, Ahmadi SA, Ghazanfari D. One Pot Unexpected Isocyanide-based Three-component Synthesis of Pyrrole-3-carboxamides Containing Ether Groups. ORG PREP PROCED INT 2021. [DOI: 10.1080/00304948.2021.1973275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | | | - Sayed Ali Ahmadi
- Department of Chemistry, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Dadkhoda Ghazanfari
- Department of Chemistry, Kerman Branch, Islamic Azad University, Kerman, Iran
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5
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Bhosale JD, Dabur R, Jadhav GP, Bendre RS. Facile Syntheses and Molecular-Docking of Novel Substituted 3,4-Dimethyl-1H-pyrrole-2-carboxamide/carbohydrazide Analogues with Antimicrobial and Antifungal Properties. Molecules 2018; 23:molecules23040875. [PMID: 29641457 PMCID: PMC6017109 DOI: 10.3390/molecules23040875] [Citation(s) in RCA: 5] [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: 03/03/2018] [Revised: 03/28/2018] [Accepted: 04/05/2018] [Indexed: 11/20/2022] Open
Abstract
The article describes the use of facile one-pot, high-yielding reactions to synthesize substituted 3,4-dimethyl-1H-pyrrole-2-carboxamides 3a–m and carbohydrazide analogues 5a–l as potential antifungal and antimicrobial agents. The structural identity and purity of the synthesized compounds were assigned based on appropriate spectroscopic techniques. Synthesized compounds were assessed in vitro for antifungal and antibacterial activity. The compounds 5h, 5i and 5j were found to be the most potent against Aspergillusfumigatus, with MIC values of 0.039 mg/mL. The compound 5f bearing a 2, 6-dichloro group on the phenyl ring was found to be the most active broad spectrum antibacterial agent with a MIC value of 0.039 mg/mL. The mode of action of the most promising antifungal compounds (one representative from each series; 3j and 5h) was established by their molecular docking with the active site of sterol 14α-demethylase. Molecular docking studies revealed a highly spontaneous binding ability of the tested compounds in the access channel away from catalytic heme iron of the enzyme, which suggested that the tested compounds inhibit this enzyme and would avoid heme iron-related deleterious side effects observed with many existing antifungal compounds.
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Affiliation(s)
- Jitendra D Bhosale
- School of Chemical Sciences, North Maharashtra University, Jalgaon 425001, India.
| | - Rajesh Dabur
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India.
| | - Gopal P Jadhav
- School of Medicine, Department of clinical & translational sciences, Creighton University, Omaha, NE 68178, USA.
| | - R S Bendre
- School of Chemical Sciences, North Maharashtra University, Jalgaon 425001, India.
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6
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Whitehead A, Zhang Y, McCabe Dunn J, Sherer EC, Lam YH, Stelmach J, Sun A, Shiroda M, Orr RK, Waddell ST, Raghavan S. Selective Formation of Functionalized α-Quaternary Malononitriles toward 5,5-Disubstituted Pyrrolopyrimidinones. Org Lett 2017; 19:4448-4451. [PMID: 28812897 DOI: 10.1021/acs.orglett.7b01930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A modular, selective approach to complex α-tertiary substituted malononitriles is reported. The method takes advantage of β-ester-substituted α,α-dinitrile alkenes as highly reactive, chemoselective electrophiles for 1,4-additions with organometallic nucleophiles to produce functionally and sterically dense all-carbon quaternary centers. In the presence of a chiral ester auxiliary bearing an aromatic ring, the 1,4-addition occurs with good to excellent selectivity due to favorable cation-π interactions. The highly functionalized malononitriles represent versatile building blocks and can be applied toward efficient, highly selective syntheses of 5,5-disubstituted pyrrolopyrimidinones.
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Affiliation(s)
- Alan Whitehead
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yong Zhang
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | | | | | | | - John Stelmach
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Aaron Sun
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Melisa Shiroda
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | | | - Sherman T Waddell
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Subharekha Raghavan
- Discovery Chemistry, Merck & Co., Inc. , 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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7
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Gogoi D, Baruah VJ, Chaliha AK, Kakoti BB, Sarma D, Buragohain AK. 3D pharmacophore-based virtual screening, docking and density functional theory approach towards the discovery of novel human epidermal growth factor receptor-2 (HER2) inhibitors. J Theor Biol 2016; 411:68-80. [PMID: 27693363 DOI: 10.1016/j.jtbi.2016.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/06/2016] [Accepted: 09/20/2016] [Indexed: 11/24/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same. Identification of novel HER2 inhibitors with improved therapeutics index was performed with a highly correlating (r=0.975) ligand-based pharmacophore model (Hypo1) in this study. Hypo1 was generated from a training set of 22 compounds with HER2 inhibitory activity and this well-validated hypothesis was subsequently used as a 3D query to screen compounds in a total of four databases of which two were natural product databases. Further, these compounds were analyzed for compliance with Veber's drug-likeness rule and optimum ADMET parameters. The selected compounds were then subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of HER2. The findings thus presented would be an important starting point towards the development of novel HER2 inhibitors using well-validated computational techniques.
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Affiliation(s)
- Dhrubajyoti Gogoi
- DBT-Bioinformatics Infrastructure Facility, Centre for Biotechnology and Bioinformatics, School of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Vishwa Jyoti Baruah
- DBT-Bioinformatics Infrastructure Facility, Centre for Biotechnology and Bioinformatics, School of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Amrita Kashyap Chaliha
- DBT-Bioinformatics Infrastructure Facility, Centre for Biotechnology and Bioinformatics, School of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Bibhuti Bhushan Kakoti
- DBT-Bioinformatics Infrastructure Facility, Centre for Biotechnology and Bioinformatics, School of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Diganta Sarma
- Department of Chemistry, School of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India
| | - Alak Kumar Buragohain
- DBT-Bioinformatics Infrastructure Facility, Centre for Biotechnology and Bioinformatics, School of Science and Engineering, Dibrugarh University, Dibrugarh, Assam, India.
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8
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Lawhorn BG, Philp J, Zhao Y, Louer C, Hammond M, Cheung M, Fries H, Graves AP, Shewchuk L, Wang L, Cottom JE, Qi H, Zhao H, Totoritis R, Zhang G, Schwartz B, Li H, Sweitzer S, Holt DA, Gatto GJ, Kallander LS. Identification of Purines and 7-Deazapurines as Potent and Selective Type I Inhibitors of Troponin I-Interacting Kinase (TNNI3K). J Med Chem 2015; 58:7431-48. [PMID: 26355916 DOI: 10.1021/acs.jmedchem.5b00931] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A series of cardiac troponin I-interacting kinase (TNNI3K) inhibitors arising from 3-((9H-purin-6-yl)amino)-N-methyl-benzenesulfonamide (1) is disclosed along with fundamental structure-function relationships that delineate the role of each element of 1 for TNNI3K recognition. An X-ray structure of 1 bound to TNNI3K confirmed its Type I binding mode and is used to rationalize the structure-activity relationship and employed to design potent, selective, and orally bioavailable TNNI3K inhibitors. Identification of the 7-deazapurine heterocycle as a superior template (vs purine) and its elaboration by introduction of C4-benzenesulfonamide and C7- and C8-7-deazapurine substituents produced compounds with substantial improvements in potency (>1000-fold), general kinase selectivity (10-fold improvement), and pharmacokinetic properties (>10-fold increase in poDNAUC). Optimal members of the series have properties suitable for use in in vitro and in vivo experiments aimed at elucidating the role of TNNI3K in cardiac biology and serve as leads for developing novel heart failure medicines.
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Affiliation(s)
- Brian G Lawhorn
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joanne Philp
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Yongdong Zhao
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Christopher Louer
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Marlys Hammond
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Mui Cheung
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Harvey Fries
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Alan P Graves
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Lisa Shewchuk
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Liping Wang
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Joshua E Cottom
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Hongwei Qi
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Huizhen Zhao
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Rachel Totoritis
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Guofeng Zhang
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Benjamin Schwartz
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Hu Li
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Sharon Sweitzer
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Dennis A Holt
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Gregory J Gatto
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Lara S Kallander
- Heart Failure Discovery Performance Unit and ‡Platform Technology and Sciences, GlaxoSmithKline , 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
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9
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Kobayashi K, Ono R, Yuba S, Hiyoshi H. Two-Step Synthesis of 5-Hydroxy-5,7-dihydro-6H-pyrrolo[2,3-d]pyrimidin-6-one Derivatives from 4-Chloro-6-methoxy-2-(methylsulfanyl)pyrimidine. HETEROCYCLES 2015. [DOI: 10.3987/com-15-13202] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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10
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Discovery of 2-aryl-8-hydroxy (or methoxy)-isoquinolin-1(2H)-ones as novel EGFR inhibitor by scaffold hopping. Bioorg Med Chem 2013; 21:6956-64. [DOI: 10.1016/j.bmc.2013.09.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/04/2013] [Accepted: 09/10/2013] [Indexed: 12/18/2022]
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11
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Hao BY, Liu JQ, Zhang WH, Chen XZ. Chiral Pool Synthesis of N-Cbz-cis-(3R,4R)-3-methylamino-4-methylpiperidine from L-Malic acid. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.5.1371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Xu B, Ding J, Chen KX, Miao ZH, Huang H, Liu H, Luo XM. Advances in Cancer Chemotherapeutic Drug Research in China. RECENT ADVANCES IN CANCER RESEARCH AND THERAPY 2012. [PMCID: PMC7158183 DOI: 10.1016/b978-0-12-397833-2.00012-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Bin Xu
- Corresponding author: Bin Xu, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zi Road, Shanghai 201203, People’s Republic of China. Tel: O21-54920515 (o), 13501793936 (mobile), Fax: 021-54920568, e-mail:
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13
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Yang SC, Chang SS, Chen CYC. Identifying HER2 inhibitors from natural products database. PLoS One 2011; 6:e28793. [PMID: 22174899 PMCID: PMC3236219 DOI: 10.1371/journal.pone.0028793] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/15/2011] [Indexed: 01/09/2023] Open
Abstract
The relationship between abnormal HER2 expression and cancer is important in cancer therapeutics. Formation and spread of cancer cells may be restricted by inhibiting HER2. We conducted ligand-based and structure-based studies to assess the potency of natural compounds as potential HER2 inhibitors. Multiple linear regression (MLR) and support vector machine (SVM) models were constructed to predict biological activities of natural compounds, and molecular dynamics (MD) was used to assess their stability with HER2 under a dynamic environment. Predicted bioactivities of the natural compounds ranged from 6.014–9.077 using MLR (r2 = 0.7954) and 5.122–6.950 using SVM (r2 = 0.8620). Both models were in agreement and suggest bioactivity based on candidate structure. Conformation changes caused by MD favored the formation of stabilizing H-bonds. All candidates had higher stability than Lapinatib, which may be due to the number and spatial distribution of additional H-bonds and hydrophobic interactions. Amino acids Lys724 and Lys736 are critical for binding in HER2, and Thr798, Cys805, and Asp808 are also important for increased stability. Candidates may block the entrance to the ATP binding site located within the inner regions and prevent downstream activation of HER2. Our multidirectional approach indicates that the natural compounds have good ligand efficacy in addition to stable binding affinities to HER2, and should be potent candidates of HER2 inhibitors. With regard to drug design, designing HER2 inhibitors with carboxyl or carbonyl groups available for H-bond formation with Lys724 and Lys736, and benzene groups for hydrophobic contact with Cys805 may improve protein-ligand stability.
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Affiliation(s)
- Shun-Chieh Yang
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
| | - Su-Sen Chang
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
| | - Calvin Yu-Chian Chen
- Laboratory of Computational and Systems Biology, China Medical University, Taichung, Taiwan
- Department of Bioinformatics, Asia University, Taichung, Taiwan
- China Medical University Beigang Hospital, Yunlin, Taiwan
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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14
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Wu C, Tang Z, Fan W, Zhu W, Wang C, Somoza E, Owino N, Li R, Ma PC, Wang Y. In vivo positron emission tomography (PET) imaging of mesenchymal-epithelial transition (MET) receptor. J Med Chem 2010; 53:139-46. [PMID: 19968287 DOI: 10.1021/jm900803q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report the radiosynthesis and evaluation of 3-[3,5-dimethyl-4-(4-[11C]methylpiperazinecarbonyl)-1H-pyrrol-2-ylmethylene]-2-oxo-2,3-dihydro-1H-indole-5-sulfonic acid (3-chlorophenyl)methylamide, termed [11C]SU11274 ([11C]14) for in vivo imaging of mesenchymal-epithelial transition (MET) receptor by positron emission tomography (PET). Following the synthesis of the precursor (13) that was achieved in 10 steps with a total yield of 9.7%, [11C]14 was obtained through radiomethylation in a range of 5-10% radiochemical yield and over 95% radiochemical purity. For in vivo PET studies, two human lung cancer xenograft models were established using MET-positive NCI-H1975 and MET-negative NCI-H520 cell lines. Quantitative [11C]14-PET studies showed that the tumor uptake of [11C]14 in the NCI-H1975 xenografts was significantly higher than that in the NCI-H520 xenografts, which is consistent with their corresponding immunohistochemical tissue staining patterns of MET receptors from the same animals. These studies demonstrated that [11C]14-PET is an appropriate imaging marker for quantification of MET receptor in vivo, which can facilitate efficacy evaluation in the clinical development of MET-targeted cancer therapeutics.
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Affiliation(s)
- Chunying Wu
- Division of Radiopharmaceutical Science, Case Center for Imaging Research, Department of Radiology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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15
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Rheault TR, Caferro TR, Dickerson SH, Donaldson KH, Gaul MD, Goetz AS, Mullin RJ, McDonald OB, Petrov KG, Rusnak DW, Shewchuk LM, Spehar GM, Truesdale AT, Vanderwall DE, Wood ER, Uehling DE. Thienopyrimidine-based dual EGFR/ErbB-2 inhibitors. Bioorg Med Chem Lett 2009; 19:817-20. [DOI: 10.1016/j.bmcl.2008.12.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 12/01/2008] [Accepted: 12/03/2008] [Indexed: 10/21/2022]
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16
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Li HH, Huang H, Zhang XH, Luo XM, Lin LP, Jiang HL, Ding J, Chen KX, Liu H. Discovering novel 3-nitroquinolines as a new class of anticancer agents. Acta Pharmacol Sin 2008; 29:1529-38. [PMID: 19026174 DOI: 10.1111/j.1745-7254.2008.00907.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
AIM To design and synthesize a novel class of antitumor agents, featuring the 3-nitroquinoline framework. METHODS Based on the enzyme-binding features of Ekb1, introducing a nitro group at the 3-position of the quinoline core, a series of novel 3-nitroquinolines was designed and synthesized. The inhibition of epidermal growth factor receptor (EGFR) activity by these compounds was evaluated and analyzed by the sulforhodamine B assay for their inhibitory activities toward human epidermoid carcinoma (A431) cells and breast cancer (MDA-MB-468) cells, which are known to overexpress the EGFR kinase. RESULTS A series of novel 3-nitroquinoline derivatives were synthesized and evaluated for their antiproliferative effect against the EGFR-overexpressing tumor cell lines. Several compounds for concentration-response studies showed prominent inhibitory activities with IC50 values in the micromolar or nanomolar range. The structure-activity relationship was discussed in terms of the inhibitory activity against the proliferation of 2 human carcinoma cell lines. CONCLUSION This study was the first to identify new structural types of antiproliferative agents against the EGFR-overexpressing tumor cell lines by the incorporation of the nitro group at the 3-position of the quinoline core structure, providing promising new templates for the further development of anticancer agents.
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Affiliation(s)
- Hai-hong Li
- Drug Discovery and Design Centre, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Jones MA, Morton JD, Coxon JM, McNabb SB, Lee HYY, Aitken SG, Mehrtens JM, Robertson LJ, Neffe AT, Miyamoto S, Bickerstaffe R, Gately K, Wood JM, Abell AD. Synthesis, biological evaluation and molecular modelling of N-heterocyclic dipeptide aldehydes as selective calpain inhibitors. Bioorg Med Chem 2008; 16:6911-23. [DOI: 10.1016/j.bmc.2008.05.048] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/21/2008] [Accepted: 05/22/2008] [Indexed: 11/26/2022]
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Kang SS, Li HL, Zeng HS, Wang HB. Ethyl 5-formyl-2,4-dimethyl-1H-pyrrole-3-carboxyl-ate. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o1125. [PMID: 21202636 PMCID: PMC2961598 DOI: 10.1107/s1600536808014542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 05/14/2008] [Indexed: 11/23/2022]
Abstract
The molecule of the title compound, C10H13NO3, is approximately planar. A network of N—H⋯O and weak C—H⋯O hydrogen bonds helps to consolidate the crystal structure.
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Affiliation(s)
- Si-Shun Kang
- College of Science, Nanjing University of Technolgy, Xinmofan Road No.5, Nanjing 210009, People's Republic of China
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Gangjee A, Namjoshi OA, Yu J, Ihnat MA, Thorpe JE, Warnke LA. Design, synthesis and biological evaluation of substituted pyrrolo[2,3-d]pyrimidines as multiple receptor tyrosine kinase inhibitors and antiangiogenic agents. Bioorg Med Chem 2008; 16:5514-28. [PMID: 18467105 DOI: 10.1016/j.bmc.2008.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 04/04/2008] [Accepted: 04/04/2008] [Indexed: 01/05/2023]
Abstract
Direct and indirect involvement of receptor tyrosine kinases (RTKs) in tumor growth and metastasis makes them ideal targets for anticancer therapy. A paradigm shift from inhibition of single RTK to inhibition of multiple RTKs has been recently demonstrated. We designed and synthesized eight N(4)-phenylsubstituted-6-(2-phenylethylsubstituted)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamines as homologated series of our previously published RTK inhibitors. We reasoned that increased flexibility of the side chain, which determines potency and selectivity, would improve the spectrum of RTK inhibition. These compounds were synthesized using a bis-electrophilic cyclization to afford substituted pyrrolo[2,3-d]pyrimidines followed by chlorination and substitution at the 4-position with various anilines. Five additional compounds of this series were previously reported by Gangjee et al.(1) with activities against IGFR only. Their synthesis, characterization and biological activities against a variety of other RTKs are reported in this study for the first time. The biological evaluation, in whole cell assays, showed several analogs had remarkable inhibitory activity against epithelial growth factor receptor (EGFR), vascular endothelial growth factor receptor-1 (VEGFR-1), platelet-derived growth factor receptor-beta (PDGFR-beta), the growth of A431 cells in culture, and in the chicken embryo chorioallantoic membrane (CAM) angiogenesis assay. The inhibitory data against the RTKs in this study demonstrate that variation of the 6-ethylaryl substituents as well as the N(4)-phenyl substituents of these analogs does indeed control both the potency and specificity of inhibitory activity against RTKs. In addition, homologation of the chain length of the 6-substituent from a methylene to an ethyl increases the spectrum of RTK inhibition. New multi-RTK inhibitors (8, 12) and potent inhibitors of angiogenesis (15, 19) were identified with the best compound, N(4)-(3-trifluromethylphenyl)-6-(2-phenylethyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine (15), with an IC(50) value of 30nM in the CAM angiogenesis inhibition assay.
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Affiliation(s)
- Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA.
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Werner S, Iyer PS, Fodor MD, Coleman CM, Twining LA, Mitasev B, Brummond KM. Solution-phase synthesis of a tricyclic pyrrole-2-carboxamide discovery library applying a stetter-Paal-Knorr reaction sequence. JOURNAL OF COMBINATORIAL CHEMISTRY 2006; 8:368-80. [PMID: 16677007 PMCID: PMC3433767 DOI: 10.1021/cc050160c] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution-phase synthesis of a discovery library of 178 tricyclic pyrrole-2-carboxamides was accomplished in nine steps and seven purifications starting with three benzoyl-protected amino acid methyl esters. Further diversity was introduced by two glyoxaldehydes and 41 primary amines. The combination of Pauson-Khand, Stetter, and microwave-assisted Paal-Knorr reactions was applied as a key sequence. The discovery library was designed with the help of QikProp 2.1, and physicochemical data are presented for all pyrroles. Library members were synthesized and purified in parallel and analyzed by LC/MS. Selected compounds were fully characterized.
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Affiliation(s)
- Stefan Werner
- University of Pittsburgh Center for Chemical Methodologies and Library Development, Pennsylvania 15260, USA.
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Kamath S, Buolamwini JK. Targeting EGFR and HER-2 receptor tyrosine kinases for cancer drug discovery and development. Med Res Rev 2006; 26:569-94. [PMID: 16788977 DOI: 10.1002/med.20070] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Conventional anticancer therapy using cytotoxic drugs lacks selectivity and is prone to toxicity and drug resistance. Anticancer therapies targeting aberrant growth factor receptor signaling are gaining interest. The erbB receptor family belongs to the type I, the receptor tyrosine kinases class, and comprises EGFR, HER-2, HER-3, and HER-4. It has been targeted for solid tumor therapy, including breast, ovarian, colon, head-and-neck, and non-small-cell lung cancers. This review summarizes structural aspects of this class of growth factor receptors, their oncogenic expression, and various pharmacological interventions including biological products and small molecules that inhibit these enzymes. We have also discussed various mutations that occur in EGFR and their consequences on anticancer therapy.
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Affiliation(s)
- Shantaram Kamath
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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