1
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Yilmaz M, Inal AU. Microwave assisted synthesis of 2,3-dihydro-4H-benzo[4,5]thiazolo[3,2-a]furo[2,3-d] pyrimidin-4-ones by radical addition of 2-hydroxy-4H-benzo[4,5]thiazolo[3,2-a] pyrimidin-4-ones to various conjugated alkenes and dienes mediated Mn(OAc)3. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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2
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Transformational machine learning: Learning how to learn from many related scientific problems. Proc Natl Acad Sci U S A 2021; 118:2108013118. [PMID: 34845013 PMCID: PMC8670494 DOI: 10.1073/pnas.2108013118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
Machine learning (ML) is the branch of artificial intelligence (AI) that develops computational systems that learn from experience. In supervised ML, the ML system generalizes from labelled examples to learn a model that can predict the labels of unseen examples. Examples are generally represented using features that directly describe the examples. For instance, in drug design, ML uses features that describe molecular shape and so on. In cases where there are multiple related ML problems, it is possible to use a different type of feature: predictions made about the examples by ML models learned on other problems. We call this transformational ML. We show that this results in better predictions and improved understanding when applied to scientific problems. Almost all machine learning (ML) is based on representing examples using intrinsic features. When there are multiple related ML problems (tasks), it is possible to transform these features into extrinsic features by first training ML models on other tasks and letting them each make predictions for each example of the new task, yielding a novel representation. We call this transformational ML (TML). TML is very closely related to, and synergistic with, transfer learning, multitask learning, and stacking. TML is applicable to improving any nonlinear ML method. We tested TML using the most important classes of nonlinear ML: random forests, gradient boosting machines, support vector machines, k-nearest neighbors, and neural networks. To ensure the generality and robustness of the evaluation, we utilized thousands of ML problems from three scientific domains: drug design, predicting gene expression, and ML algorithm selection. We found that TML significantly improved the predictive performance of all the ML methods in all the domains (4 to 50% average improvements) and that TML features generally outperformed intrinsic features. Use of TML also enhances scientific understanding through explainable ML. In drug design, we found that TML provided insight into drug target specificity, the relationships between drugs, and the relationships between target proteins. TML leads to an ecosystem-based approach to ML, where new tasks, examples, predictions, and so on synergistically interact to improve performance. To contribute to this ecosystem, all our data, code, and our ∼50,000 ML models have been fully annotated with metadata, linked, and openly published using Findability, Accessibility, Interoperability, and Reusability principles (∼100 Gbytes).
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3
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Szumilak M, Wiktorowska-Owczarek A, Stanczak A. Hybrid Drugs-A Strategy for Overcoming Anticancer Drug Resistance? Molecules 2021; 26:2601. [PMID: 33946916 PMCID: PMC8124695 DOI: 10.3390/molecules26092601] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Despite enormous progress in the treatment of many malignancies, the development of cancer resistance is still an important reason for cancer chemotherapy failure. Increasing knowledge of cancers' molecular complexity and mechanisms of their resistance to anticancer drugs, as well as extensive clinical experience, indicate that an effective fight against cancer requires a multidimensional approach. Multi-target chemotherapy may be achieved using drugs combination, co-delivery of medicines, or designing hybrid drugs. Hybrid drugs simultaneously targeting many points of signaling networks and various structures within a cancer cell have been extensively explored in recent years. The single hybrid agent can modulate multiple targets involved in cancer cell proliferation, possesses a simpler pharmacokinetic profile to reduce the possibility of drug interactions occurrence, and facilitates the process of drug development. Moreover, a single medication is expected to enhance patient compliance due to a less complicated treatment regimen, as well as a diminished number of adverse reactions and toxicity in comparison to a combination of drugs. As a consequence, many efforts have been made to design hybrid molecules of different chemical structures and functions as a means to circumvent drug resistance. The enormous number of studies in this field encouraged us to review the available literature and present selected research results highlighting the possible role of hybrid drugs in overcoming cancer drug resistance.
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Affiliation(s)
- Marta Szumilak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland
| | - Anna Wiktorowska-Owczarek
- Department of Pharmacology and Toxicology, Medical University of Lodz, Zeligowskiego 7/9, 90-752 Lodz, Poland;
| | - Andrzej Stanczak
- Department of Community Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland;
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4
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An efficient diastereoselective synthesis of novel fused 5H-furo[2,3-d]thiazolo[3,2-a]pyrimidin-5-ones via one-pot three-component reaction. Mol Divers 2021; 26:183-190. [PMID: 33389558 DOI: 10.1007/s11030-020-10173-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 12/11/2020] [Indexed: 10/22/2022]
Abstract
Herein, a convenient and efficient synthesis of 7-benzoyl-6-(aryl)-6,7-dihydro-5H-furo[2,3-d]thiazolo[3,2-a]pyrimidin-5-one derivatives was achieved from the reaction of isoquinolinium N-ylides, aromatic aldehydes, and heterocyclic 1,3-dicarbonyl compounds via one-pot three-component diastereoselective domino reaction in good-to-excellent yields. The advantages of this protocol are easily available starting materials, operational simplicity, and avoidance of hazardous organic solvents and catalyst. The synthesized products were characterized by IR, 1H NMR, 13C NMR and mass spectra. Additionally, the conclusive structure of target compounds was confirmed by X-Ray diffraction analysis.
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5
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Regioselective synthesis of spirobarbiturate-dihydrofurans and dihydrofuro[2,3-d]pyrimidines via one-pot cascade reaction of barbiturate-based olefins and ethyl acetoacetate. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Ghoneim AA, El-Farargy AF, Elkanzi NAA. Synthesis of some novel phenylfuro[3,2-d]pyrimidine glycosides derivatives with expected antimicrobial activity. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2020. [DOI: 10.1007/s13738-019-01768-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Design, synthesis and biological evaluation of novel substituted purine isosters as EGFR kinase inhibitors, with promising pharmacokinetic profile and in vivo efficacy. Eur J Med Chem 2019; 176:393-409. [DOI: 10.1016/j.ejmech.2019.05.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/07/2019] [Accepted: 05/07/2019] [Indexed: 01/07/2023]
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8
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Zhou J, Jiang X, He S, Jiang H, Feng F, Liu W, Qu W, Sun H. Rational Design of Multitarget-Directed Ligands: Strategies and Emerging Paradigms. J Med Chem 2019; 62:8881-8914. [PMID: 31082225 DOI: 10.1021/acs.jmedchem.9b00017] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Due to the complexity of multifactorial diseases, single-target drugs do not always exhibit satisfactory efficacy. Recently, increasing evidence indicates that simultaneous modulation of multiple targets may improve both therapeutic safety and efficacy, compared with single-target drugs. However, few multitarget drugs are on market or in clinical trials, despite the best efforts of medicinal chemists. This article discusses the systematic establishment of target combination, lead generation, and optimization of multitarget-directed ligands (MTDLs). Moreover, we analyze some MTDLs research cases for several complex diseases in recent years and the physicochemical properties of 117 clinical multitarget drugs, with the aim to reveal the trends and insights of the potential use of MTDLs.
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Affiliation(s)
- Junting Zhou
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Xueyang Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Siyu He
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
| | - Hongli Jiang
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China.,Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Feng Feng
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China.,Jiangsu Food and Pharmaceutical Science College , Huaian 223003 , People's Republic of China
| | - Wenyuan Liu
- Department of Analytical Chemistry , China Pharmaceutical University , Nanjing 210009 , People's Republic of China
| | - Wei Qu
- Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , 211198 , People's Republic of China
| | - Haopeng Sun
- Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing 211198 , People's Republic of China
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9
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Petraitytė G, Vaitkevičius V, Özer B, Masevičius V. Synthesis of 5-substituted and 5,6-disubstituted furo[2,3-d]pyrimidines from 2-methylthio-4,6-pyrimidindione and bifunctional electrophiles. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Synthesis and evaluation of new 2,6-diamino-5-hetarylpyrimidines as inhibitors of dihydrofolate reductase. MONATSHEFTE FUR CHEMIE 2018. [DOI: 10.1007/s00706-017-2032-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Sheikhhosseini E. Design and effective synthesis of novel furo[2,3-d]pyrimidine derivatives containing ethylene ether spacers. JOURNAL OF SAUDI CHEMICAL SOCIETY 2018. [DOI: 10.1016/j.jscs.2016.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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One-pot three component isocyanide-based reaction: Synthesis of novel tetracyclic fused furo[2′,3′:4,5]pyrimido[2,1- b ][1,3]benzothiazole. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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13
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Pavana RK, Choudhary S, Bastian A, Ihnat MA, Bai R, Hamel E, Gangjee A. Discovery and preclinical evaluation of 7-benzyl-N-(substituted)-pyrrolo[3,2-d]pyrimidin-4-amines as single agents with microtubule targeting effects along with triple-acting angiokinase inhibition as antitumor agents. Bioorg Med Chem 2017; 25:545-556. [PMID: 27894589 PMCID: PMC5191990 DOI: 10.1016/j.bmc.2016.11.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/08/2016] [Accepted: 11/11/2016] [Indexed: 02/07/2023]
Abstract
The utility of cytostatic antiangiogenic agents (AA) in cancer chemotherapy lies in their combination with cytotoxic chemotherapeutic agents. Clinical combinations of AA with microtubule targeting agents (MTAs) have been particularly successful. The discovery, synthesis and biological evaluations of a series of 7-benzyl-N-substituted-pyrrolo[3,2-d]pyrimidin-4-amines are reported. Novel compounds which inhibit proangiogenic receptor tyrosine kinases (RTKs) including vascular endothelial growth factor receptor-2 (VEGFR-2), platelet-derived growth factor receptor-β (PDGFR-β) and epidermal growth factor receptor (EGFR), along with microtubule targeting in single molecules are described. These compounds also inhibited blood vessel formation in the chicken chorioallantoic membrane (CAM) assay, and some potently inhibited tubulin assembly (with activity comparable to that of combretastatin A-4 (CA)). In addition, some of the analogs circumvent the most clinically relevant tumor resistance mechanisms (P-glycoprotein and β-III tubulin expression) to microtubule targeting agents (MTA). These MTAs bind at the colchicine site on tubulin. Two analogs displayed two to three digit nanomolar GI50 values across the entire NCI 60 tumor cell panel and one of these, compound 7, freely water soluble as its HCl salt, afforded excellent in vivo antitumor activity against an orthotopic triple negative 4T1 breast cancer model and was superior to doxorubicin.
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Affiliation(s)
- Roheeth Kumar Pavana
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States
| | - Shruti Choudhary
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States
| | - Anja Bastian
- Department of Physiology, University of Oklahoma College of Medicine, Oklahoma City, OK 73104, United States
| | - Michael A Ihnat
- Department of Pharmaceutical Sciences, University of Oklahoma College of Pharmacy, Oklahoma City, OK 73117, United States
| | - Ruoli Bai
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Ernest Hamel
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, United States.
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14
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Enaminonitrile as Building Block in Heterocyclic Synthesis: Synthesis of Novel 4H-Furo[2,3-d][1,3]oxazin-4-one and Furo[2,3-d]pyrimidin-4(3H)-one Derivatives. J CHEM-NY 2017. [DOI: 10.1155/2017/5610707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
2-Amino-4,5-diphenylfuran-3-carbonitrile 1 was utilized as building block for the construction of new furo[2,3-d]pyrimidin-4(3H)-one derivative 2 and 4H-furo[2,3-d][1,3]oxazin-4-one derivative 3 via treatment with acetic anhydride and benzoyl chloride, respectively. The 4H-furo[2,3-d][1,3]oxazin-4-one derivative 3 was transformed into novel furo[2,3-d]pyrimidin-4(3H)-ones 4–8, tetrazolylfuran derivative 10, and furo[3,2-d]imadazolone derivative 11 via reaction with various nitrogen nucleophiles. The structure features of the synthesized compounds were established from their spectral and elemental analyses.
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15
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Dutta L, Bhuyan PJ. One-pot Three-component Reaction of Barbituric acids, Aldehydes and 4-Hydroxycoumarins: Synthesis of Some Novel Functionalized Furo[2,3-d]pyrimidines. ChemistrySelect 2016. [DOI: 10.1002/slct.201601320] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Leema Dutta
- Applied Organic Chemistry Group; CSIR-North East Institute of Science & Tehnology; Jorhat 785006, Assam India
| | - Pulak J. Bhuyan
- Applied Organic Chemistry Group; CSIR-North East Institute of Science & Tehnology; Jorhat 785006, Assam India
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16
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Dutta L, Sharma M, Bhuyan PJ. Regioisomeric synthesis of dihydrofuro[2,3-d]pyrimidines in a diastereoselective manner involving nitrogen ylides in one-pot three-component reaction. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.08.084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Furo[2,3-d]pyrimidine based derivatives as kinase inhibitors and anticancer agents. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2016. [DOI: 10.1016/j.fjps.2015.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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18
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Cody V, Pace J, Namjoshi OA, Gangjee A. Structure-activity correlations for three pyrido[2,3-d]pyrimidine antifolates binding to human and Pneumocystis carinii dihydrofolate reductase. Acta Crystallogr F Struct Biol Commun 2015; 71:799-803. [PMID: 26057816 PMCID: PMC4461351 DOI: 10.1107/s2053230x15008468] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/29/2015] [Indexed: 11/10/2022] Open
Abstract
To further define the interactions that enhance the selectivity of binding and to directly compare the binding of the most potent analogue {N(6)-methyl-N(6)-(3,4,5-trifluorophenyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine; compound 26} in the series of bicyclic pyrido[2,3-d]pyrimidine analogues of piritrexim (PTX) with native human (h), Pneumocystis carinii (pc) and Pneumocystis jirovecii (pj) dihydrofolate reductase (DHFR) enzymes, the crystal structures of hDHFR complexed with N(6)-methyl-N(6)-(4-isopropylphenyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine (compound 22), of hDHFR complexed with compound 26 and of pcDHFR complexed with N(6)-methyl-N(6)-1-naphthylpyrido[2,3-d]pyrimidine-2,4,6-triamine (compound 24) are reported as ternary complexes with NADPH. This series of bicyclic pyrido[2,3-d]pyrimidines were designed in which there was a transposition of the 5-methyl group of PTX to the N9 position of the pyrido[2,3-d]pyrimidine. It was hypothesized that the N9-methyl group would preferentially interact with Ile123 of pcDHFR (and Ile123 of pjDHFR), but not with the shorter Val115 in hDHFR. Structure-activity data for this series of antifolates revealed that a trifluoro derivative (26) was the most selective against pjDHFR compared with mammalian DHFR (h/pj = 35.7). Structural data for the hDHFR-26 complex revealed that 26 binds in a different conformation from that observed in the pcDHFR-26 complex. In the hDHFR-26 complex the trifluorophenyl ring of 26 occupies a position near the cofactor-binding site, with close intermolecular contacts with Asp21, Ser59 and Ile60, whereas this ring in the pcDHFR-26 complex is positioned away from the cofactor site and near Ile65, with weaker contacts with Ile65, Phe69 and Ile123. Comparison of the intermolecular contacts between the N9-methyl group with Val115/Ile123 validates the hypothesis that the N9-methyl substituent preferentially interacts with Ile123 compared with Val115 of hDHFR, as the weaker contact with Val115 in the hDHFR structure is consistent with its weaker binding affinity compared with pcDHFR. The results for the structures of hDHFR-22 and pcDHFR-24 show that their inhibitor-binding orientation is similar to that observed in pcDHFR-26 and the pcDHFR variant (F69N) reported previously. The naphthyl moiety of 24 makes several intermolecular contacts with the active-site residues in pcDHFR that help to stabilize the binding, resulting in a more potent inhibitor.
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Affiliation(s)
- Vivian Cody
- Structural Biology Department, Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Structural Biology Department, School of Medicine and Biomedical Sciences, University at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Jim Pace
- Structural Biology Department, Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Ojas A. Namjoshi
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15213, USA
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15213, USA
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19
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Soleimany M, Lari J, Vahedi H, Imanpour M. New Facile Route to Synthesize Furo[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine and Furo[3,2-e][1,2,4]triazolo[1,5-c]pyrimidine Derivatives. SYNTHETIC COMMUN 2014. [DOI: 10.1080/00397911.2014.943344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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20
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Zhang X, Raghavan S, Ihnat M, Thorpe JE, Disch BC, Bastian A, Bailey-Downs LC, Dybdal-Hargreaves NF, Rohena CC, Hamel E, Mooberry SL, Gangjee A. The design and discovery of water soluble 4-substituted-2,6-dimethylfuro[2,3-d]pyrimidines as multitargeted receptor tyrosine kinase inhibitors and microtubule targeting antitumor agents. Bioorg Med Chem 2014; 22:3753-72. [PMID: 24890652 PMCID: PMC4089508 DOI: 10.1016/j.bmc.2014.04.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/16/2014] [Accepted: 04/25/2014] [Indexed: 12/13/2022]
Abstract
The design, synthesis and biological evaluations of fourteen 4-substituted 2,6-dimethylfuro[2,3-d]pyrimidines are reported. Four compounds (11-13, 15) inhibit vascular endothelial growth factor receptor-2 (VEGFR-2), platelet-derived growth factor receptor β (PDGFR-β), and target tubulin leading to cytotoxicity. Compound 11 has nanomolar potency, comparable to sunitinib and semaxinib, against tumor cell lines overexpressing VEGFR-2 and PDGFR-β. Further, 11 binds at the colchicine site on tubulin, depolymerizes cellular microtubules and inhibits purified tubulin assembly and overcomes both βIII-tubulin and P-glycoprotein-mediated drug resistance, and initiates mitotic arrest leading to apoptosis. In vivo, its HCl salt, 21, reduced tumor size and vascularity in xenograft and allograft murine models and was superior to docetaxel and sunitinib, without overt toxicity. Thus 21 affords potential combination chemotherapy in a single agent.
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Affiliation(s)
- Xin Zhang
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Sudhir Raghavan
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States
| | - Michael Ihnat
- College of Pharmacy, University of Oklahoma Health Science Center, 1110 North Stonewall, Oklahoma City, OK 73117, United States
| | - Jessica E Thorpe
- College of Pharmacy, University of Oklahoma Health Science Center, 1110 North Stonewall, Oklahoma City, OK 73117, United States
| | - Bryan C Disch
- College of Pharmacy, University of Oklahoma Health Science Center, 1110 North Stonewall, Oklahoma City, OK 73117, United States
| | - Anja Bastian
- College of Pharmacy, University of Oklahoma Health Science Center, 1110 North Stonewall, Oklahoma City, OK 73117, United States
| | - Lora C Bailey-Downs
- College of Pharmacy, University of Oklahoma Health Science Center, 1110 North Stonewall, Oklahoma City, OK 73117, United States
| | - Nicholas F Dybdal-Hargreaves
- Department of Pharmacology, Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, United States
| | - Cristina C Rohena
- Department of Pharmacology, Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, United States
| | - Ernest Hamel
- Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Institutes of Health, 1050 Boyles Street, Frederick, MD 21702, United States
| | - Susan L Mooberry
- Department of Pharmacology, Cancer Therapy & Research Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, United States
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, 600 Forbes Avenue, Pittsburgh, PA 15282, United States.
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21
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Kozielewicz P, Paradowska K, Erić S, Wawer I, Zloh M. Insights into mechanism of anticancer activity of pentacyclic oxindole alkaloids of Uncaria tomentosa by means of a computational reverse virtual screening and molecular docking approach. MONATSHEFTE FUR CHEMIE 2014. [DOI: 10.1007/s00706-014-1212-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Gangjee A, Pavana RK, Ihnat MA, Thorpe JE, Disch BC, Bastian A, Bailey-Downs LC, Hamel E, Bai R. Discovery of antitubulin agents with antiangiogenic activity as single entities with multitarget chemotherapy potential. ACS Med Chem Lett 2014; 5:480-4. [PMID: 24900865 DOI: 10.1021/ml4004793] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/27/2014] [Indexed: 01/09/2023] Open
Abstract
Antiangiogenic agents (AA) are cytostatic, and their utility in cancer chemotherapy lies in their combination with cytotoxic chemotherapeutic agents. Clinical combinations of vascular endothelial growth factor receptor-2 (VEGFR2) inhibitors with antitubulin agents have been particularly successful. We have discovered a novel, potentially important analogue, that combines potent VEGFR2 inhibitory activity (comparable to that of sunitinib) with potent antitubulin activity (comparable to that of combretastatin A-4 (CA)) in a single molecule, with GI50 values of 10(-7) M across the entire NCI 60 tumor cell panel. It potently inhibited tubulin assembly and circumvented the most clinically relevant tumor resistance mechanisms (P-glycoprotein and β-III tubulin expression) to antimicrotubule agents. The compound is freely water-soluble as its HCl salt and afforded excellent antitumor activity in vivo, superior to docetaxel, sunitinib, or Temozolomide, without any toxicity.
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Affiliation(s)
- Aleem Gangjee
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Roheeth Kumar Pavana
- Division
of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, United States
| | - Michael A. Ihnat
- Department
of Pharmaceutical Sciences, University of Oklahoma College of Pharmacy, Oklahoma
City, Oklahoma 73117, United States
| | - Jessica E. Thorpe
- Department
of Pharmaceutical Sciences, University of Oklahoma College of Pharmacy, Oklahoma
City, Oklahoma 73117, United States
| | | | - Anja Bastian
- Department
of Pharmaceutical Sciences, University of Oklahoma College of Pharmacy, Oklahoma
City, Oklahoma 73117, United States
| | - Lora C. Bailey-Downs
- Department
of Pharmaceutical Sciences, University of Oklahoma College of Pharmacy, Oklahoma
City, Oklahoma 73117, United States
| | - Ernest Hamel
- Screening
Technologies Branch, Developmental Therapeutics Program, Division
of Cancer Treatment and Diagnosis, Frederick National Laboratory for
Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Rouli Bai
- Screening
Technologies Branch, Developmental Therapeutics Program, Division
of Cancer Treatment and Diagnosis, Frederick National Laboratory for
Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
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23
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Schumann M, Armen RS. Identification of distant drug off-targets by direct superposition of binding pocket surfaces. PLoS One 2013; 8:e83533. [PMID: 24391782 PMCID: PMC3877058 DOI: 10.1371/journal.pone.0083533] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/04/2013] [Indexed: 01/23/2023] Open
Abstract
Correctly predicting off-targets for a given molecular structure, which would have the ability to bind a large range of ligands, is both particularly difficult and important if they share no significant sequence or fold similarity with the respective molecular target ("distant off-targets"). A novel approach for identification of off-targets by direct superposition of protein binding pocket surfaces is presented and applied to a set of well-studied and highly relevant drug targets, including representative kinases and nuclear hormone receptors. The entire Protein Data Bank is searched for similar binding pockets and convincing distant off-target candidates were identified that share no significant sequence or fold similarity with the respective target structure. These putative target off-target pairs are further supported by the existence of compounds that bind strongly to both with high topological similarity, and in some cases, literature examples of individual compounds that bind to both. Also, our results clearly show that it is possible for binding pockets to exhibit a striking surface similarity, while the respective off-target shares neither significant sequence nor significant fold similarity with the respective molecular target ("distant off-target").
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Affiliation(s)
- Marcel Schumann
- Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Roger S. Armen
- Department of Pharmaceutical Sciences, School of Pharmacy, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
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24
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Zhang HJ, Qian Y, Zhu DD, Yang XG, Zhu HL. Synthesis, molecular modeling and biological evaluation of chalcone thiosemicarbazide derivatives as novel anticancer agents. Eur J Med Chem 2011; 46:4702-8. [PMID: 21816517 DOI: 10.1016/j.ejmech.2011.07.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Revised: 05/24/2011] [Accepted: 07/09/2011] [Indexed: 11/19/2022]
Affiliation(s)
- Hong-Jia Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, People's Republic of China
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25
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Teimouri MB, Eskandari M. An Efficient Synthesis of Novel Chromone-Containing Furopyrimidines. JOURNAL OF CHEMICAL RESEARCH 2011. [DOI: 10.3184/174751911x13146322603355] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The one-pot three-component reaction of 1,3-disubstituted barbituric acid derivatives, 3-formylchromones and alkyl isocyanides proceed smoothly at room temperature to give the corresponding chromone-containing furopyrimidines derivatives in good yields within 10 minutes in DMF. This three-component reaction represents a facile and efficient route to the furo[2,3-d]pyrimidine derivatives, which have become synthetic targets for many organic and medicinal chemists. In the course of the creation of a fused furopyrimidine ring, three bonds (C=C, C–C and C–O bonds) are newly formed.
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Affiliation(s)
| | - Mehrdad Eskandari
- Faculty of Chemistry, Omidiyeh Branch, Islamic Azad University, Omidiyeh, Iran
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26
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Cody V, Piraino J, Pace J, Li W, Gangjee A. Preferential selection of isomer binding from chiral mixtures: alternate binding modes observed for the E and Z isomers of a series of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines as ternary complexes with NADPH and human dihydrofolate reductase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1271-7. [PMID: 21123866 PMCID: PMC2995722 DOI: 10.1107/s0907444910035808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 09/06/2010] [Indexed: 11/10/2022]
Abstract
The crystal structures of six human dihydrofolate reductase (hDHFR) ternary complexes with NADPH and a series of mixed E/Z isomers of 5-substituted 5-[2-(2-methoxyphenyl)-prop-1-en-1-yl]furo[2,3-d]pyrimidine-2,4-diamines substituted at the C9 position with propyl, isopropyl, cyclopropyl, butyl, isobutyl and sec-butyl (E2-E7, Z3) were determined and the results were compared with the resolved E and Z isomers of the C9-methyl parent compound. The configuration of all of the inhibitors, save one, was observed as the E isomer, in which the binding of the furopyrimidine ring is flipped such that the 4-amino group binds in the 4-oxo site of folate. The Z3 isomer of the C9-isopropyl analog has the normal 2,4-diaminopyrimidine ring binding geometry, with the furo oxygen near Glu30 and the 4-amino group interacting near the cofactor nicotinamide ring. Electron-density maps for these structures revealed the binding of only one isomer to hDHFR, despite the fact that chiral mixtures (E:Z ratios of 2:1, 3:1 and 3:2) of the inhibitors were incubated with hDHFR prior to crystallization. Superposition of the hDHFR complexes with E2 and Z3 shows that the 2'-methoxyphenyl ring of E2 is perpendicular to that of Z3. The most potent inhibitor in this series is the isopropyl analog Z3 and the least potent is the isobutyl analog E6, consistent with data that show that the Z isomer makes the most favorable interactions with the active-site residues. The isobutyl moiety of E6 is observed in two orientations and the resultant steric crowding of the E6 analog is consistent with its weaker activity. The alternative binding modes observed for the furopyrimidine ring in these E/Z isomers suggest that new templates can be designed to probe these binding regions of the DHFR active site.
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Affiliation(s)
- Vivian Cody
- Structural Biology Department, Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA.
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27
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Hu YG, Wang Y, Du SM, Chen XB, Ding MW. Efficient synthesis and biological evaluation of some 2,4-diamino-furo[2,3-d]pyrimidine derivatives. Bioorg Med Chem Lett 2010; 20:6188-90. [PMID: 20850310 DOI: 10.1016/j.bmcl.2010.08.122] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Revised: 07/28/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
Abstract
The carbodiimides 2, obtained from aza-Wittig reactions of iminophosphorane 1 with aromatic isocyanates, reacted with ammonia to give ethyl 3,4-dihydro-6-methyl-4-oxo-2-arylamino-furo[2,3-d]pyrimidine-5-carboxylate 3. Further reaction of 3 with POCl(3) and various amines generated ethyl 4-alkylamino-2-arylamino-6-methyl-furo[2,3-d]pyrimidine-5-carboxylate 5 in good yields. Their structures were confirmed by (1)H NMR, EI-Ms, IR and elemental analysis. Compound 5b was further analyzed by single crystal X-ray diffraction. Compound 5 exhibited cytotoxicity against two lung cancer cell lines. For example, compound 5a showed the best inhibition activities against A459 with IC(50) 0.8μM.
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Affiliation(s)
- Yang-Gen Hu
- Institute of Medicinal Chemistry, Hubei Medical University, Shiyan 442000, China; Department of Pharmacy, Taihe Hospital of Hubei Medical University, Shiyan 442000, China.
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28
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Qian Y, Zhang HJ, Zhang H, Xu C, Zhao J, Zhu HL. Synthesis, molecular modeling, and biological evaluation of cinnamic acid metronidazole ester derivatives as novel anticancer agents. Bioorg Med Chem 2010; 18:4991-6. [PMID: 20594859 DOI: 10.1016/j.bmc.2010.06.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 06/02/2010] [Accepted: 06/03/2010] [Indexed: 10/19/2022]
Abstract
A series of novel cinnamic acid metronidazole ester derivatives have been designed and synthesized, and their biological activities were also evaluated as potential EGFR and HER-2 kinase inhibitors. Compound 3h showed the most potent biological activity (IC50=0.62 microM for EGFR and IC50=2.15 microM for HER-2). Docking simulation was performed to position compound 3h into the EGFR active site to determine the probable binding model. Antiproliferative assay results demonstrated that some of these compounds possessed good antiproliferative activity against MCF-7. Compound 3h with potent inhibitory activity in tumor growth inhibition may be a potential anticancer agent.
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Affiliation(s)
- Yong Qian
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, People's Republic of China
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