1
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Guo H, Zhou B, Chang J, Chang W, Feng J, Zhang Z. Multicomponent cyclization with azides to synthesize N-heterocycles. Org Biomol Chem 2023; 21:8054-8074. [PMID: 37801029 DOI: 10.1039/d3ob01115a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Heterocyclic compounds, both naturally derived and synthetically produced, constitute a wide variety of biologically active and industrially important compounds. The synthesis and application of heterocyclic compounds have garnered significant attention and experienced rapid growth in recent decades. Organic azides, due to their unique properties and distinctive reactivity, have become a convenient chemical tool for achieving a wide range of heterocycles such as triazoles and tetrazoles. Importantly, the field of multicomponent reaction (MCR) chemistry provides a convergent approach to access various N-heterocyclic scaffolds, offering novelty, diversity, and complexity. However, the exploration of MCR pathways to N-heterocyclic compounds remains incomplete. Here, we review the use of multicomponent reactions for the preparation of N-heterocycles. A wide range of reactions based on azides for the synthesis of various types of N-heterocyclic systems have been developed.
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Affiliation(s)
- Hong Guo
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Bei Zhou
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Jingjing Chang
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Wenxu Chang
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Jiyao Feng
- College of Science, China Agricultural University, Beijing 100193, China.
| | - Zhenhua Zhang
- College of Science, China Agricultural University, Beijing 100193, China.
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2
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Tian H, Holyoke CW, Fleming FF. Stereoselective Synthesis of ( E)- and ( Z)-Isocyanoalkenes. Org Lett 2022; 24:8657-8661. [PMID: 36399331 DOI: 10.1021/acs.orglett.2c03461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
(E)- and (Z)-isocyanoalkenes were selectively synthesized via the sequential cross coupling of vinyl iodides with formamide, followed by dehydration. The optimal catalyst, generated in situ from CuII and trans-N,N'-dimethyl-1,2-cyclohexanediamine, rapidly coupled (E)- or (Z)-vinyl iodides with formamide, which minimized the isomerization of the resultant vinyl formamide. The method efficiently provided a range of acyclic, carbocyclic, and heterocyclic isocyanoalkenes; the versatility is illustrated with the selective, stereodivergent syntheses of the diastereomeric isocyanoalkene antibiotics, B371 and E-B371.
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Affiliation(s)
- Huan Tian
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Caleb W Holyoke
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Fraser F Fleming
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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3
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Silva EM, Albuquerque DY, Zukerman‐Schpector J, Schwab RS. Development of a Novel Three‐step Sonogashira Cross Coupling/Deacetonation/Cycloaddition Protocol for the Synthesis of 4‐aryl‐1,2,3‐triazoles Using 2‐methyl‐3‐butyn‐2‐ol as a Versatile Acetylene Surrogate. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Everton M. Silva
- Centre of Excellence for Research in Sustainable Chemistry (CERSusChem) Departamento de Química Universidade Federal de São Carlos – UFSCar Rodovia Washington Luís, km 235 – SP-310 São Carlos São Paulo 13565-905 Brazil
| | - Danilo Yano Albuquerque
- Centre of Excellence for Research in Sustainable Chemistry (CERSusChem) Departamento de Química Universidade Federal de São Carlos – UFSCar Rodovia Washington Luís, km 235 – SP-310 São Carlos São Paulo 13565-905 Brazil
| | - Julio Zukerman‐Schpector
- Departamento de Química Universidade Federal de São Carlos – UFSCar Rodovia Washington Luís, km 235 – SP-310 São Carlos São Paulo 13565-905 Brazil
| | - Ricardo S. Schwab
- Centre of Excellence for Research in Sustainable Chemistry (CERSusChem) Departamento de Química Universidade Federal de São Carlos – UFSCar Rodovia Washington Luís, km 235 – SP-310 São Carlos São Paulo 13565-905 Brazil
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4
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Gambouz K, Abbouchi AE, Nassiri S, Suzenet F, Bousmina M, Akssira M, Guillaumet G, El Kazzouli S. Palladium‐Catalyzed Oxidative Arylation of 1
H
‐Indazoles with Arenes. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Khadija Gambouz
- Laboratoire de Chimie Physique et Chimie Bioorganique URAC 22 FSTM Université Hassan II – Casablanca BP 146 28800 Mohammedia Morocco
- Institut de Chimie Organique et Analytique Université d'Orléans UMR CNRS 7311 BP 6759 Orléans cedex 2 54067 France
- Euromed Research Center Engineering School of Biomedical and Biotechnology Euromed University of Fes (UEMF) Route de Meknès 30000 Fes Morocco
| | - Abdelmoula El Abbouchi
- Institut de Chimie Organique et Analytique Université d'Orléans UMR CNRS 7311 BP 6759 Orléans cedex 2 54067 France
- Euromed Research Center Engineering School of Biomedical and Biotechnology Euromed University of Fes (UEMF) Route de Meknès 30000 Fes Morocco
| | - Sarah Nassiri
- Institut de Chimie Organique et Analytique Université d'Orléans UMR CNRS 7311 BP 6759 Orléans cedex 2 54067 France
- Euromed Research Center Engineering School of Biomedical and Biotechnology Euromed University of Fes (UEMF) Route de Meknès 30000 Fes Morocco
| | - Franck Suzenet
- Institut de Chimie Organique et Analytique Université d'Orléans UMR CNRS 7311 BP 6759 Orléans cedex 2 54067 France
| | - Mostapha Bousmina
- Euromed Research Center Engineering School of Biomedical and Biotechnology Euromed University of Fes (UEMF) Route de Meknès 30000 Fes Morocco
| | - Mohamed Akssira
- Laboratoire de Chimie Physique et Chimie Bioorganique URAC 22 FSTM Université Hassan II – Casablanca BP 146 28800 Mohammedia Morocco
| | - Gérald Guillaumet
- Institut de Chimie Organique et Analytique Université d'Orléans UMR CNRS 7311 BP 6759 Orléans cedex 2 54067 France
- Euromed Research Center Engineering School of Biomedical and Biotechnology Euromed University of Fes (UEMF) Route de Meknès 30000 Fes Morocco
| | - Saïd El Kazzouli
- Euromed Research Center Engineering School of Biomedical and Biotechnology Euromed University of Fes (UEMF) Route de Meknès 30000 Fes Morocco
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5
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Ghosh S, Mondal S, Hajra A. Direct Catalytic Functionalization of Indazole Derivatives. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000423] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sumit Ghosh
- Department of Chemistry Visva-Bharati (A Central University) Santiniketan 731235 India
| | - Susmita Mondal
- Department of Chemistry Visva-Bharati (A Central University) Santiniketan 731235 India
| | - Alakananda Hajra
- Department of Chemistry Visva-Bharati (A Central University) Santiniketan 731235 India
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6
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Tontsch CJ, Gerster H, Maas G. Iminium-functionalized 1,2,3-triazoles by [3+2] cycloaddition reactions of internal acetylenic iminium triflates with organoazides. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2019. [DOI: 10.1515/znb-2019-0079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Propyne iminium triflates 1–6 react as dipolarophiles in thermal [3 + 2]-cycloadditions with sufficiently electron rich organoazides to form 1,4,5-trisubstituted 1,2,3-triazoles with iminium functionalization. The reactions require rather strong thermal activation, but can be accelerated by microwave irradiation. The regioselectivity of the cycloaddition at the internal acetylenic bond of 3-cyclopropylpropyne and 3-arylpropyne iminium ions (1–3 and 4, respectively) is very high, but is lowered in the presence of sterically demanding substituents at the opposite end of the iminium-substituted C,C triple bond. The iminium-functionalized triazoles can easily be transformed into neutral compounds; herein reported is the formation of triazolyl ketones 10 by hydrolysis and of tertiary triazolyldimethyl amines 12 by LiAlH4 reduction. When the reduction is performed with sodium boranate or sodium cyanoboranate, amine–borane complexes 15 and 16 are obtained.
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Affiliation(s)
- Christian J. Tontsch
- Institute of Organic Chemistry I , Ulm University , Albert-Einstein-Allee 11, D-89081 Ulm , Germany
| | - Holger Gerster
- Institute of Organic Chemistry I , Ulm University , Albert-Einstein-Allee 11, D-89081 Ulm , Germany
| | - Gerhard Maas
- Institute of Organic Chemistry I , Ulm University , Albert-Einstein-Allee 11, D-89081 Ulm , Germany , Fax: +49-731-5022803
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7
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Ghanakota P, DasGupta D, Carlson HA. Free Energies and Entropies of Binding Sites Identified by MixMD Cosolvent Simulations. J Chem Inf Model 2019; 59:2035-2045. [PMID: 31017411 DOI: 10.1021/acs.jcim.8b00925] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In our recent efforts to map protein surfaces using mixed-solvent molecular dynamics (MixMD) (Ghanakota, P.; Carlson, H. A. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. J. Phys. Chem. B 2016, 120, 8685-8695), we were able to successfully capture active sites and allosteric sites within the top-four most occupied hotspots. In this study, we describe our approach for estimating the thermodynamic profile of the binding sites identified by MixMD. First, we establish a framework for calculating free energies from MixMD simulations, and we compare our approach to alternative methods. Second, we present a means to obtain a relative ranking of the binding sites by their configurational entropy. The theoretical maximum and minimum free energy and entropy values achievable under such a framework along with the limitations of the techniques are discussed. Using this approach, the free energy and relative entropy ranking of the top-four MixMD binding sites were computed and analyzed across our allosteric protein targets: Abl Kinase, Androgen Receptor, Pdk1 Kinase, Farnesyl Pyrophosphate Synthase, Chk1 Kinase, Glucokinase, and Protein Tyrosine Phosphatase 1B.
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Affiliation(s)
- Phani Ghanakota
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Debarati DasGupta
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109-1065 , United States
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8
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Xi YK, Zhang H, Li RX, Kang SY, Li J, Li Y. Total Synthesis of Spirotryprostatins through Organomediated Intramolecular Umpolung Cyclization. Chemistry 2019; 25:3005-3009. [DOI: 10.1002/chem.201806411] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Yong-Kai Xi
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Hongbin Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Rui-Xi Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Shi-Yuan Kang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Jin Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
| | - Yan Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan province, State Key Laboratory for, Conservation and Utilization of Bio-Resources in Yunnan; School of, Chemical Science and Technology; Yunnan University; Kunming Yunnan 650091 P. R. China
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9
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Keim M, Maas G. Terminal Acetylenic Iminium Salts: Cycloaddition Reactions with Azides Leading to 1,2,3-Triazoles and Bicyclic 1,2,3-Triazolium Salts. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801749] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Michael Keim
- Institute of Organic Chemistry I; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Gerhard Maas
- Institute of Organic Chemistry I; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
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10
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Lessing T, van Mark H, Müller TJJ. Substituted 1H-1,2,3-Triazol-4-yl-1H-pyrrolo[2,3-b]pyridines by De Novo One-Pot Ring-Forming Coupling/Cyclization/Desilylation Cu Alkyne/Azide Cycloaddition (AAC) Sequence. Chemistry 2018; 24:8974-8979. [PMID: 29726615 DOI: 10.1002/chem.201801632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Indexed: 11/06/2022]
Abstract
Substituted 1H-1,2,3-triazol-4-yl-pyrrolo[2,3-b]pyridines are efficiently prepared by a one-pot coupling/cyclization/desilylation Cu alkyne/azide cycloaddition (CuAAC) sequence in the sense of a consecutive three-component fashion. The key feature of this new de novo formation of azole and triazole anellation is the sequentially Pd/Cu-catalyzed process employing tri(iso-propyl)silyl (TIPS) butadiyne as a four-carbon building block. In addition, the sequence can be expanded in a four-component fashion also employing the in situ formation of the required azides.
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Affiliation(s)
- Timo Lessing
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, d-40225, Düsseldorf, Germany
| | - Hauke van Mark
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, d-40225, Düsseldorf, Germany
| | - Thomas J J Müller
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, d-40225, Düsseldorf, Germany
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11
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Zhang Y, Borrel A, Ghemtio L, Regad L, Boije af Gennäs G, Camproux AC, Yli-Kauhaluoma J, Xhaard H. Structural Isosteres of Phosphate Groups in the Protein Data Bank. J Chem Inf Model 2017; 57:499-516. [DOI: 10.1021/acs.jcim.6b00519] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Alexandre Borrel
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
| | | | - Leslie Regad
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
| | | | - Anne-Claude Camproux
- Laboratoire
Molécules Thérapeutiques in silico (MTi), UMRS-973, Université Paris Diderot, Sorbonne Paris Cité, INSERM, F-75013 Paris, France
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12
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Bonacorso HG, Dal Forno GM, Wiethan C, Ketzer A, Zanatta N, Frizzo CP, Martins MAP, Stradiotto M. Sequential one-pot three-step synthesis of polysubstituted 4-(5-(trifluoromethyl)-1H-pyrazol-4-yl)-1H-1,2,3-triazole systems. RSC Adv 2017. [DOI: 10.1039/c7ra07960e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sequential one-pot, three-step synthesis of polysubstituted 4-(5-(trifluoromethyl)-1H-pyrazol-4-yl)-1H-1,2,3-triazoles.
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Affiliation(s)
- Helio G. Bonacorso
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Gean M. Dal Forno
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Carson Wiethan
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Alex Ketzer
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Nilo Zanatta
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Clarissa P. Frizzo
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Marcos A. P. Martins
- Núcleo de Química de Heterociclos – NUQUIMHE
- Departamento de Química
- Universidade Federal de Santa Maria
- 97105-900 Santa Maria
- Brazil
| | - Mark Stradiotto
- Department of Chemistry
- Dalhousie University
- Halifax
- B3H 4R2 Canada
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13
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Malvezzi S, Angelov T, Sturla SJ. Minor Groove 3-Deaza-Adenosine Analogues: Synthesis and Bypass in Translesion DNA Synthesis. Chemistry 2016; 23:1101-1109. [PMID: 27862447 DOI: 10.1002/chem.201604289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Indexed: 11/07/2022]
Abstract
Anticancer drugs that alkylate DNA in the minor groove may give rise to 3-alkyl-adenosine adducts that interfere with replication, inducing apoptosis in rapidly dividing cancer cells. However, translesion DNA synthesis (TLS) by polymerase enzymes (Pols) with the capacity to bypass DNA adducts may contribute to damage tolerance and drug resistance. 3-Alkyl-adenosine adducts are unstable and depurinate, which is a barrier to addressing chemical and enzymatic aspects of how they impact the progress of DNA Pols. To characterize structure-based relationships of 3-adenine alkylation relevant to cancer drugs on duplex stability and DNA Pol-catalyzed DNA synthesis, we synthesized stable 3-deaza-3-alkyl-adenosine analogues, including 3-deaza-3-phenethyl-adenosine and 3-deaza-3-methoxynaphthylethyl-adenosine, and incorporated them into oligonucleotides. A moderate reduction of duplex stability was observed on the basis of thermal denaturation data. Replication studies using purified Y-family human DNA Pols hPol η, κ, and ι indicated that these enzymes can perform TLS over the modified bases. hPol η had higher misincorporation rates when synthesizing opposite the modified bases compared with adenine, whereas hPol κ and ι maintained high fidelity. These results provide insight into how alterations in chemical structure reduce bypass of minor-groove adducts, and provide novel chemical probes for evaluating minor-groove DNA alkylation.
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Affiliation(s)
- Stefano Malvezzi
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zurich, Switzerland
| | - Todor Angelov
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zurich, Switzerland
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14
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Functionalization of indazoles by means of transition metal-catalyzed cross-coupling reactions. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.08.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Wucherer-Plietker M, Merkul E, Müller TJ, Esdar C, Knöchel T, Heinrich T, Buchstaller HP, Greiner H, Dorsch D, Finsinger D, Calderini M, Bruge D, Grädler U. Discovery of novel 7-azaindoles as PDK1 inhibitors. Bioorg Med Chem Lett 2016; 26:3073-3080. [DOI: 10.1016/j.bmcl.2016.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/02/2016] [Accepted: 05/03/2016] [Indexed: 11/30/2022]
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16
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Ghanakota P, Carlson HA. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. J Phys Chem B 2016; 120:8685-95. [PMID: 27258368 DOI: 10.1021/acs.jpcb.6b03515] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mixed-solvent molecular dynamics (MixMD) is a hotspot-mapping technique that relies on molecular dynamics simulations of proteins in binary solvent mixtures. Previous work on MixMD has established the technique's effectiveness in capturing binding sites of small organic compounds. In this work, we show that MixMD can identify both competitive and allosteric sites on proteins. The MixMD approach embraces full protein flexibility and allows competition between solvent probes and water. Sites preferentially mapped by probe molecules are more likely to be binding hotspots. There are two important requirements for the identification of ligand-binding hotspots: (1) hotspots must be mapped at very high signal-to-noise ratio and (2) the hotspots must be mapped by multiple probe types. We have developed our mapping protocol around acetonitrile, isopropanol, and pyrimidine as probe solvents because they allowed us to capture hydrophilic, hydrophobic, hydrogen-bonding, and aromatic interactions. Charged probes were needed for mapping one target, and we introduce them in this work. In order to demonstrate the robust nature and wide applicability of the technique, a combined total of 5 μs of MixMD was applied across several protein targets known to exhibit allosteric modulation. Most notably, all the protein crystal structures used to initiate our simulations had no allosteric ligands bound, so there was no preorganization of the sites to predispose the simulations to find the allosteric hotspots. The protein test cases were ABL Kinase, Androgen Receptor, CHK1 Kinase, Glucokinase, PDK1 Kinase, Farnesyl Pyrophosphate Synthase, and Protein-Tyrosine Phosphatase 1B. The success of the technique is demonstrated by the fact that the top-four sites solely map the competitive and allosteric sites. Lower-ranked sites consistently map other biologically relevant sites, multimerization interfaces, or crystal-packing interfaces. Lastly, we highlight the importance of including protein flexibility by demonstrating that MixMD can map allosteric sites that are not detected in half the systems using FTMap applied to the same crystal structures.
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Affiliation(s)
- Phani Ghanakota
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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17
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D'Attoma J, Cozien G, Brun PL, Robin Y, Bostyn S, Buron F, Routier S. Fast functionalization of (7-aza)indoles using continuous flow processes. ChemistrySelect 2016. [DOI: 10.1002/slct.201600012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Grégoire Cozien
- ISOCHEM, 4 rue Marc Sangnier; BP 16729 45300 Pithiviers France
| | | | - Yves Robin
- ISOCHEM, 4 rue Marc Sangnier; BP 16729 45300 Pithiviers France
| | - Stéphane Bostyn
- Institut de Combustion, Aérothermique, Réactivité; et Environnement (ICARE); 1c, avenue de la recherche scientifique 45071 Orléans cedex 2 France
| | - Frédéric Buron
- Univ Orleans, CNRS, ICOA; UMR 7311 F-45067 Orléans France
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18
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Elayadi H, Lazrek HB. CuSO4/KI As Catalyst for the Synthesis of 1,4-Disubstituted-1,2,3-Triazolo-Nucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 34:433-41. [PMID: 25965332 DOI: 10.1080/15257770.2015.1014047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A simple and inexpensive procedure has been developed for the selective formation of 1,4-disubstituted-1,2,3-triazolo-nucleosides starting from organic azides and terminal alkynes, mediated by in situ generated copper(I) catalyst from readily available CuSO4 and KI.
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Affiliation(s)
- Hanane Elayadi
- a Laboratory of Biomolecular and Medicinal Chemistry, Faculty of Science Semlalia , Cadi Ayyad University , Marrakech , Morocco
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Barbie P, Kazmaier U. Total synthesis of cyclomarins A, C and D, marine cyclic peptides with interesting anti-tuberculosis and anti-malaria activities. Org Biomol Chem 2016; 14:6036-54. [DOI: 10.1039/c6ob00800c] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cyclomarins are cyclic heptapeptides containing four unusual amino acids.
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Affiliation(s)
- Philipp Barbie
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
| | - Uli Kazmaier
- Institute of Organic Chemistry
- Saarland University
- 66041 Saarbrücken
- Germany
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20
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Sequentially Palladium-Catalyzed Processes in One-Pot Syntheses of Heterocycles. APPLIED SCIENCES-BASEL 2015. [DOI: 10.3390/app5041803] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Hassan S, Müller TJJ. Multicomponent Syntheses based upon Copper-Catalyzed Alkyne-Azide Cycloaddition. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201400904] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Gehringer M, Forster M, Laufer SA. Solution-phase parallel synthesis of ruxolitinib-derived Janus kinase inhibitors via copper-catalyzed azide-alkyne cycloaddition. ACS COMBINATORIAL SCIENCE 2015; 17:5-10. [PMID: 25405713 DOI: 10.1021/co500122h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A solution-phase parallel synthesis of triazole-derived ruxolitinib analogues was developed in the current study. The method employs copper-catalyzed azide-alkyne cycloaddition to build up the central triazole template. Product isolation by precipitation and centrifugation is straightforward and yields high purity compounds suited for biological profiling. A simple protocol for accessing the terminal alkyne precursors in high yields was established and a library of ruxolitinib-like triazoles featuring diverse functional groups was prepared. In addition, a model for the binding mode of ruxolitinib to Janus kinase (JAK) 2 is proposed. In contrast to previous models, the pose explains the compound selectivity for JAK1/JAK2 and is in accordance with published structure-activity data. On this basis, a structure-based design hypothesis for inverting the selectivity profile of ruxolitinib is deduced. Application of this strategy identified a moderately potent JAK3 inhibitor (35 nM) with high selectivity against other JAKs, potentially exploiting a covalent binding mode.
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Affiliation(s)
- Matthias Gehringer
- Department
of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Michael Forster
- Department
of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Stefan A. Laufer
- Department
of Pharmaceutical
and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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Abstract
PDK1 is a key member of the AGC protein kinase family. It plays an important role in a variety of cellular functions, leading to the activation of the PI3K signaling pathway, an event often associated with the onset and progression of several human cancers. Numerous recent observations suggest that PDK1 inhibitors may provide novel opportunities for the development of effective classes of therapeutics. On these premises, recent years have witnessed an increased effort by medicinal chemists to develop novel scaffolds to derive potent and selective PDK1 inhibitors. The intent of this review is to update the reader on the recent patent literature, covering applications published between June 2008 and September 2011 that report on PDK1 inhibitors.
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Palladium and copper-supported on charcoal: A heterogeneous multi-task catalyst for sequential Sonogashira–Click and Click–Heck reactions. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.01.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Klukas F, Grunwald A, Menschel F, Müller TJJ. Rapid pseudo five-component synthesis of intensively blue luminescent 2,5-di(hetero)arylfurans via a Sonogashira-Glaser cyclization sequence. Beilstein J Org Chem 2014; 10:672-9. [PMID: 24778719 PMCID: PMC3999768 DOI: 10.3762/bjoc.10.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 02/12/2014] [Indexed: 11/23/2022] Open
Abstract
2,5-Di(hetero)arylfurans are readily accessible in a pseudo five-component reaction via a Sonogashira–Glaser coupling sequence followed by a superbase-mediated (KOH/DMSO) cyclization in a consecutive one-pot fashion. Besides the straightforward synthesis of natural products and biologically active molecules all representatives are particularly interesting due to their bright blue luminescence with remarkably high quantum yields. The electronic structure of the title compounds is additionally studied with DFT computations.
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Affiliation(s)
- Fabian Klukas
- Heinrich-Heine Universität Düsseldorf, Institut für Organische Chemie und Makromolekulare Chemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Alexander Grunwald
- Heinrich-Heine Universität Düsseldorf, Institut für Organische Chemie und Makromolekulare Chemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Franziska Menschel
- Heinrich-Heine Universität Düsseldorf, Institut für Organische Chemie und Makromolekulare Chemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Thomas J J Müller
- Heinrich-Heine Universität Düsseldorf, Institut für Organische Chemie und Makromolekulare Chemie, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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Kotasthane A, Mulakala C, Viswanadhan VN. Applying conformational selection theory to improve crossdocking efficiency in 3-phosphoinositide dependent protein kinase-1. Proteins 2013; 82:436-51. [PMID: 23999908 DOI: 10.1002/prot.24410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/22/2013] [Accepted: 08/23/2013] [Indexed: 11/11/2022]
Abstract
The emerging picture of biomolecular recognition is that of conformational selection followed by induced-fit. Conformational selection theory states that binding partners exist in various conformations in solution, with binding involving a "selection" between complementary conformers. In this study, we devise a docking protocol that mimics conformational selection in protein-ligand binding and demonstrate that it significantly enhances crossdocking accuracy over Glide's flexible docking protocol, which is widely used in the pharmaceutical industry. Our protocol uses a pregenerated conformational ensemble to simulate ligand flexibility. The ensemble was generated by thorough conformational sampling coupled with conformer minimization. The generated conformers were then rigidly docked in the active site of the protein along with a postdocking minimization step that allows limited induced fit effects to be modeled for the ligand. We illustrate the improved performance of our protocol through crossdocking of 31 ligands to cocomplexed proteins of the kinase 3-phosphoinositide dependent protein kinase-1 extracted from the crystal structures 1H1W (ATP bound), 1OKY (staurosporine bound) and 3QD0 (bound to a potent inhibitor). Consistent with conformational selection theory, the performance of our protocol was the best for crossdocking to the cognate protein bound to the natural ligand, ATP.
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Affiliation(s)
- Anuja Kotasthane
- Department of Computational Chemistry, Jubilant Biosys Limited, Yeshwanthpur, Bangalore, 560 022, Karnataka, India
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Mangsang W, Sirion U, Saeeng R. One-pot synthesis of O-glycosyl triazoles by O-glycosylation–click reaction. Carbohydr Res 2013; 375:79-89. [DOI: 10.1016/j.carres.2013.04.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/20/2013] [Accepted: 04/24/2013] [Indexed: 11/25/2022]
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Sokolova NV, Nenajdenko VG. Recent advances in the Cu(i)-catalyzed azide–alkyne cycloaddition: focus on functionally substituted azides and alkynes. RSC Adv 2013. [DOI: 10.1039/c3ra42482k] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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30
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Yao B, Jaccoud C, Wang Q, Zhu J. Synergistic Effect of Palladium and Copper Catalysts: Catalytic Cyclizative Dimerization of ortho-(1-Alkynyl)benzamides Leading to Axially Chiral 1,3-Butadienes. Chemistry 2012; 18:5864-8. [DOI: 10.1002/chem.201200215] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 02/27/2012] [Indexed: 11/10/2022]
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