1
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Undheim K. Bond Formation at C8 in the Nucleoside and Nucleotide Purine Scaffold: An Informative Selection. Molecules 2024; 29:1815. [PMID: 38675636 PMCID: PMC11054916 DOI: 10.3390/molecules29081815] [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: 03/06/2024] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
This paper presents methods for the introduction and exchange of substituents in a nucleobase and its nucleosides and nucleotides with emphasis on the C8-position in the purine skeleton. The nucleobase is open for electrophilic and nucleophilic chemistry. The nucleophilic chemistry consists mainly of displacement reactions when the C8-substituent is a good leaving group such as a halogen atom. The heteroatom in amines, sulfides, or oxides is a good nucleophile. Halides are good reaction partners. Metal-promoted cross-coupling reactions are important for carbylations. Direct oxidative metalation reactions using sterically hindered metal amides offer chemo- and regio-selectivity besides functional tolerance and simplicity. The carbon site is highly nucleophilic after metalation and adds electrophiles resulting in chemical bond formation. Conditions for metal-assisted reactions are described for nucleobases and their glycosides.
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Affiliation(s)
- Kjell Undheim
- Department of Chemistry, University of Oslo, 0315 Oslo, Norway
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2
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Shet H, Sahu R, Sanghvi YS, Kapdi AR. Strategies for the Synthesis of Fluorinated Nucleosides, Nucleotides and Oligonucleotides. CHEM REC 2022; 22:e202200066. [PMID: 35638251 DOI: 10.1002/tcr.202200066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/11/2022] [Indexed: 11/09/2022]
Abstract
Fluorinated nucleosides and oligonucleotides are of specific interest as probes for studying nucleic acids interaction, structures, biological transformations, and its biomedical applications. Among various modifications of oligonucleotides, fluorination of preformed nucleoside and/or nucleotides have recently gained attention owing to the unique properties of fluorine atoms imparting medicinal properties with respect to the small size, electronegativity, lipophilicity, and ability for stereochemical control. This review deals with synthetic protocols for selective fluorination either at sugar or base moiety in a preformed nucleosides, nucleotides and nucleic acids using specific fluorinating reagents.
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Affiliation(s)
- Harshita Shet
- Department of Chemistry, Institute of Chemical Technology -, Indian Oil Odisha Campus, IIT Kharagpur Extension Centre, Mouza Samantpuri, Bhubaneswar, Odisha-751013, India.,Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
| | - Rajesh Sahu
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
| | - Yogesh S Sanghvi
- Rasayan Inc., 2802, Crystal Ridge, Encinitas, CA92024-6615, California, USA
| | - Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai-400019, India
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3
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Sebastian D, Satishkumar S, Pradhan P, Yang L, Lakshman MK. General Approach to N6,C5'-Difunctionalization of Adenosine. J Org Chem 2021; 87:18-39. [PMID: 34905365 DOI: 10.1021/acs.joc.1c01587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among the C6-halo purine ribonucleosides, the readily accessible 6-chloro derivative has been known to undergo slow SNAr reactions with amines, particularly aryl amines. In this work, we show that in 0.1 M AcOH in EtOH, aryl amines react quite efficiently at the C6-position of 2',3',5'-tri-O-(t-BuMe2Si)-protected 6-chloropurine riboside (6-ClP-riboside), with concomitant cleavage of the 5'-silyl group. These two-step processes proceeded in generally good yields, and notably, reactions in the absence of AcOH were much slower and/or lower yielding. Corresponding reactions of 2',3',5'-tri-O-(t-BuMe2Si)-protected 6-ClP-riboside with alkyl amines proceeded well but without desilylation at the primary hydroxyl terminus. These differences are likely due to the acidities of the ammonium chlorides formed in these reactions, and the role of AcOH was not desilylation but possibly only purine activation. With 50% aqueous TFA in THF at 0 °C, cleavage of the 5'-silyl group from 2',3',5'-tri-O-(t-BuMe2Si)-protected N6-alkyl adenosine derivatives and from 6-ClP-riboside was readily achieved. Reactions of the 5'-deprotected 6-ClP-riboside with alkyl amines proceeded in high yields and under mild conditions. Because these complementary methodologies yielded N6-aryl and -alkyl adenosine derivatives containing a free 5'-hydroxyl group, a variety of product functionalizations were undertaken to yield N6,C5'-doubly modified nucleoside analogues.
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Affiliation(s)
- Dellamol Sebastian
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sakilam Satishkumar
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States
| | - Padmanava Pradhan
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States
| | - Lijia Yang
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
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4
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Abstract
3′,5′-O-Bis(tert-butyldimethylsilyl)-8-fluoro-N-2-isobutyryl-2′-deoxyguanosine was synthesized from 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-isobutyryl-2′-deoxyguanosine by the treatment with N-fluorobenzenesulfonimide. A similar fluorination reaction with 3′,5′-O-bis(tert-butyldimethylsilyl)-N-2-(N,N-dimethylformamidine)-2′-deoxyguanosine, however, failed to give the corresponding fluorinated product. It was found that 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine is labile under acidic conditions, but sufficiently stable in dichloroacetic acid used in solid phase synthesis. Incorporation of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis failed to give the desired products. Furthermore, treatment of 8-fluoro-N-2-isobutyryl-2′-deoxyguanosine with aqueous ammonium hydroxide did not give 8-fluoro-2′-deoxyguanosine, but led to the formation of a mixture consisting of 8-amino-N-2-isobutyryl-2′-deoxyguanosine and C8:5′-O-cyclo-2′-deoxyguanosine. Taken together, an alternative N-protecting group and possibly modified solid phase synthetic cycle conditions will be required for the incorporation of 8-fluoro-2′-deoxyguanosine into oligonucleotides through the phosphoramidite chemistry-based solid phase synthesis.
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5
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Torres Hernandez AX, Weeramange CJ, Desman P, Fatino A, Haney O, Rafferty RJ. Efforts in redesigning the antileukemic drug 6-thiopurine: decreasing toxic side effects while maintaining efficacy. MEDCHEMCOMM 2018; 10:169-179. [PMID: 30774864 DOI: 10.1039/c8md00463c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/15/2018] [Indexed: 01/14/2023]
Abstract
6-Thiopurine (6TP) is a currently prescribed drug in the treatment of diseases ranging from Crohn's disease to acute lymphocytic leukemia. While its potent mode of action is through incorporation into DNA as a thiol mimic of deoxyguanosine, severe toxicities are associated with its administration which hinder the potential therapeutic application. We have previously reported in vitro that the oxidative metabolites of 6TP, specifically 6-thiouric acid (6TU, K i 7 μM), are potent inhibitors of UDP-glucose dehydrogenase (UDPGDH), an enzyme that is responsible for the formation of UDP-glucuronic acid (UDPGA), an essential substrate that is used in detoxification processes in the liver. An in vivo investigation was undertaken to probe if 6TU inhibits UDPGDH in rat hepatocytes, and it was observed that 6TU does greatly suppress the conjugation of bilirubin with UDPGA. The failed excretion of bilirubin is linked to a majority of the reported toxicities associated with 6TP administration. Efforts were undertaken for the construction of 6TP analogs, substituted at the C8 position, to reduce inhibition of UDPGDH while retaining therapeutic efficacy. Three new 6TP analogs bearing a halogen (Br, Cl, and F) at the C8 position have been achieved over five-synthetic steps in overall yields of 16 to 32%. Each of these analogs were shown to have reduced inhibition towards UDPGDH, with K i values of 192, 163, 215 μM, respectively. In addition, the bromine, chlorine, and fluorine analogs were shown to possess cytotoxicity towards the REH cell line (acute lymphocytic leukemia) having IC50 values of 9.54 μM (±0.97), 3.95 μM (±1.94), and 4.71 μM (±1.40), respectively. These three new 6TP analogs represent the first steps in the redesign of this potent anticancer agent into a better drug that possesses reduced toxic side effects while retaining therapeutic potency.
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Affiliation(s)
- Arnaldo X Torres Hernandez
- Department of Chemistry , Pontifical Catholic University of Puerto Rico , 2250 Boulevard Luis A. Ferré Aguayo, Suite 626 , Ponce , PR 00717-0777 , Puerto Rico.,Department of Chemistry , Kansas State University , 1212 Mid-Campus Drive North , Manhattan , KS 66506 , USA .
| | - Chamitha J Weeramange
- Department of Chemistry , Kansas State University , 1212 Mid-Campus Drive North , Manhattan , KS 66506 , USA .
| | - Prathibha Desman
- Department of Chemistry , Kansas State University , 1212 Mid-Campus Drive North , Manhattan , KS 66506 , USA .
| | - Anthony Fatino
- Department of Chemistry , Kansas State University , 1212 Mid-Campus Drive North , Manhattan , KS 66506 , USA .
| | - Olivia Haney
- Department of Chemistry , Kansas State University , 1212 Mid-Campus Drive North , Manhattan , KS 66506 , USA .
| | - Ryan J Rafferty
- Department of Chemistry , Kansas State University , 1212 Mid-Campus Drive North , Manhattan , KS 66506 , USA .
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6
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Levchenko V, Dmytriv YV, Tymtsunik AV, Liubchak K, Rudnichenko A, Melnyk AV, Veselovych SY, Borodulin YV, Otsalyuk OM, Tolmachev AA, Mykhailiuk PK. Preparation of 5-Fluoropyrazoles from Pyrazoles and N-Fluorobenzenesulfonimide (NFSI). J Org Chem 2018; 83:3265-3274. [DOI: 10.1021/acs.joc.8b00199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vitalina Levchenko
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
| | - Yurii V. Dmytriv
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
- Department of Chemical Technology, National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, Prosp. Peremohy 37, Kyiv 03056, Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
- Department of Chemical Technology, National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, Prosp. Peremohy 37, Kyiv 03056, Ukraine
| | - Konstantin Liubchak
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
| | - Alexander Rudnichenko
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
- Department of Chemistry, National Taras Shevchenko University of Kyiv, Volodymyrska 64, Kyiv 01033, Ukraine
| | - Anton V. Melnyk
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
| | - Stanislav Y. Veselovych
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
| | - Yurii V. Borodulin
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
| | - Oleksandr M. Otsalyuk
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
| | - Andrei A. Tolmachev
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
- Department of Chemistry, National Taras Shevchenko University of Kyiv, Volodymyrska 64, Kyiv 01033, Ukraine
| | - Pavel K. Mykhailiuk
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine (www.enamine.net;
www.mykhailiukchem.org)
- Department of Chemistry, National Taras Shevchenko University of Kyiv, Volodymyrska 64, Kyiv 01033, Ukraine
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7
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Akula HK, Kokatla H, Andrei G, Snoeck R, Schols D, Balzarini J, Yang L, Lakshman MK. Facile functionalization at the C4 position of pyrimidine nucleosides via amide group activation with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) and biological evaluations of the products. Org Biomol Chem 2017; 15:1130-1139. [PMID: 28054092 PMCID: PMC5367150 DOI: 10.1039/c6ob02334g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reactions of O-t-butyldimethylsilyl-protected thymidine, 2'-deoxyuridine, and 3'-azidothymidine (AZT) with (benzotriazol-1-yloxy)tris(dimethylamino)phosphonium hexafluorophosphate (BOP) leads to activation of the C4 amide carbonyl by formation of putative O4-(benzotriazol-1-yl) derivatives. Subsequent substitution with alkyl and aryl amines, thiols, and alcohols leads to facile functionalization at this position. Reactions with amines and thiols were conducted either as a two-step, one-pot transformation, or as a one-step conversion. Reactions with alcohols were conducted as two-step, one-pot transformations. In the course of these investigations, the formation of 1-(4-pyrimidinyl)-1H-benzotriazole-3-oxide derivatives from the pyrimidine nucleosides was identified. However, these too underwent conversion to the desired products. Products obtained from AZT were converted to the 3'-amino derivatives by catalytic reduction. All products were assayed for their abilities to inhibit cancer cell proliferation and for antiviral activities. Many were seen to be active against HIV-1 and HIV-2, and one was active against herpes simplex virus-1 (HSV-1).
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Affiliation(s)
- Hari K Akula
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA. and The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
| | - Hariprasad Kokatla
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Jan Balzarini
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, Postbus 1043, 3000 Leuven, Belgium
| | - Lijia Yang
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA. and The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, USA
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8
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Abstract
Fluorination reactions of medicinal and biologically-active compounds will be discussed. Late stage fluorination strategies of medicinal targets have recently attracted considerable attention on account of the influence that a fluorine atom can impart to targets of medicinal importance, such as modulation of lipophilicity, electronegativity, basicity and bioavailability, the latter as a consequence of membrane permeability. Therefore, the recourse to late-stage fluorine substitution on compounds with already known and relevant biological activity can provide the pharmaceutical industry with new leads with improved medicinal properties. The fluorination strategies will take into account different fluorinating reagents, either of nucleophilic or electrophilic, and of radical nature. Diverse families of organic compounds such as (hetero)aromatic rings, and aliphatic substrates (sp(3), sp(2), and sp carbon atoms) will be studied in late-stage fluorination reaction strategies.
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Affiliation(s)
- Damian E Yerien
- Departamento de Química Orgánica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires-CONICET, Junín 954 CP, 1113-Buenos Aires, Argentina.
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9
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Efficient functionalization of 2-amino-6-chloropurine derivatives at C-8 via 8-lithiated species. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.09.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Champagne PA, Desroches J, Hamel JD, Vandamme M, Paquin JF. Monofluorination of Organic Compounds: 10 Years of Innovation. Chem Rev 2015; 115:9073-174. [PMID: 25854146 DOI: 10.1021/cr500706a] [Citation(s) in RCA: 673] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Pier Alexandre Champagne
- Canada Research Chair in Organic and Medicinal Chemistry, CGCC, PROTEO, Département de Chimie, Université Laval , 1045 Avenue de la Médecine, Québec (QC), Canada G1V 0A6
| | - Justine Desroches
- Canada Research Chair in Organic and Medicinal Chemistry, CGCC, PROTEO, Département de Chimie, Université Laval , 1045 Avenue de la Médecine, Québec (QC), Canada G1V 0A6
| | - Jean-Denys Hamel
- Canada Research Chair in Organic and Medicinal Chemistry, CGCC, PROTEO, Département de Chimie, Université Laval , 1045 Avenue de la Médecine, Québec (QC), Canada G1V 0A6
| | - Mathilde Vandamme
- Canada Research Chair in Organic and Medicinal Chemistry, CGCC, PROTEO, Département de Chimie, Université Laval , 1045 Avenue de la Médecine, Québec (QC), Canada G1V 0A6
| | - Jean-François Paquin
- Canada Research Chair in Organic and Medicinal Chemistry, CGCC, PROTEO, Département de Chimie, Université Laval , 1045 Avenue de la Médecine, Québec (QC), Canada G1V 0A6
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11
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Picaud S, Strocchia M, Terracciano S, Lauro G, Mendez J, Daniels D, Riccio R, Bifulco G, Bruno I, Filippakopoulos P. 9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain. J Med Chem 2015; 58:2718-36. [PMID: 25703523 PMCID: PMC4403932 DOI: 10.1021/jm501893k] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Indexed: 12/20/2022]
Abstract
The 2-amine-9H-purine scaffold was identified as a weak bromodomain template and was developed via iterative structure based design into a potent nanomolar ligand for the bromodomain of human BRD9 with small residual micromolar affinity toward the bromodomain of BRD4. Binding of the lead compound 11 to the bromodomain of BRD9 results in an unprecedented rearrangement of residues forming the acetyllysine recognition site, affecting plasticity of the protein in an induced-fit pocket. The compound does not exhibit any cytotoxic effect in HEK293 cells and displaces the BRD9 bromodomain from chromatin in bioluminescence proximity assays without affecting the BRD4/histone complex. The 2-amine-9H-purine scaffold represents a novel template that can be further modified to yield highly potent and selective tool compounds to interrogate the biological role of BRD9 in diverse cellular systems.
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Affiliation(s)
- Sarah Picaud
- Nuffield
Department of Clinical Medicine, Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Maria Strocchia
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Stefania Terracciano
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Gianluigi Lauro
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Jacqui Mendez
- Promega
Corporation, 2800 Woods
Hollow Road, Madison, Wisconsin 53711, United States
| | - Danette
L. Daniels
- Promega
Corporation, 2800 Woods
Hollow Road, Madison, Wisconsin 53711, United States
| | - Raffaele Riccio
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Giuseppe Bifulco
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Ines Bruno
- Department
of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084 Fisciano, Italy
| | - Panagis Filippakopoulos
- Nuffield
Department of Clinical Medicine, Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Nuffield
Department of Clinical Medicine, Ludwig
Cancer Research, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.
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12
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Zimdars S, Jourdin XMD, Crestey F, Carell T, Knochel P. Trifunctionalization of the Purine Scaffold Using Mg and Zn Organometallic Intermediates. Org Lett 2011; 13:792-5. [DOI: 10.1021/ol103057k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Silvia Zimdars
- Department Chemie & Biochemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - Xavier Mollat du Jourdin
- Department Chemie & Biochemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - François Crestey
- Department Chemie & Biochemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - Thomas Carell
- Department Chemie & Biochemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
| | - Paul Knochel
- Department Chemie & Biochemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377 München, Germany
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13
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Regioselective Sonogashira cross-coupling reactions of 6-chloro-2,8-diiodo-9-THP-9H-purine with alkyne derivatives. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.11.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1573-80. [PMID: 20559630 PMCID: PMC2975913 DOI: 10.1007/s00249-010-0614-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/21/2010] [Accepted: 05/26/2010] [Indexed: 11/20/2022]
Abstract
The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs were performed. The calculated values agree well with the available experimental data, and the main contribution to the free energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble average of the coupling constants 3J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the relative binding affinities to FtsZ, indicating their dominant contribution.
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15
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Abstract
The Julia-Kocienski olefination provides a versatile platform for the synthesis of fluorovinyl compounds. This review describes our efforts as well as those of others in the synthesis of various fluorinated aryl and heteroaryl sulfones and their utility as olefination reagents for the modular assembly of fluoroalkenes. Where data is available, the influence of the fluorine atom on the reactivity of the olefination reagents and the stereochemical outcome of the olefination are described.
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Affiliation(s)
- Barbara Zajc
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031
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16
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Hritz J, Oostenbrink C. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers. J Phys Chem B 2009; 113:12711-20. [PMID: 19722597 DOI: 10.1021/jp902968m] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such compounds. We present an enhanced sampling-one step perturbation method (ES-OS) to tackle this problem in a highly efficient way. A single molecular dynamics simulation of a judiciously chosen reference state (using two sets of soft-core interactions) is sufficient to determine conformational distributions of chemically similar compounds and the free energy differences between them. The ES-OS method is applied to a set of five biologically relevant 8-substituted GTP analogs having high energy barriers between the anti and the syn conformations of the base with respect to the ribose part. The reliability of ES-OS is verified by comparing the results to Hamiltonian replica exchange simulations of GTP and 8-Br-GTP and the experimentally determined 3J(C4,H1') coupling constant for GMP in water. Additional simulations in vacuum and octanol allow us to calculate differences in the solvation free energies and in lipophilicities (log P). Free energy contributions from individual conformational regions are also calculated, and their relationship with the overall free energy is derived leading to a set of multiconformational free energy formulas. These relationships are of general applicability and can be used in free energy calculations for a more diverse set of compounds.
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Affiliation(s)
- Jozef Hritz
- Leiden Amsterdam Center for Drug Research, Division of Molecular Toxicology, VU University Amsterdam, The Netherlands
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17
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Ghosh AK, Zajc B. Fluorinated 1-phenyl-1H-tetrazol-5-yl sulfone derivatives as general reagents for fluoroalkylidene synthesis. J Org Chem 2009; 74:8531-40. [PMID: 19831343 PMCID: PMC3045538 DOI: 10.1021/jo901313k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Julia-Kocienski olefination reagents 1-fluoropropyl, (cyclopropyl)fluoromethyl, 1-fluoro-2-methyl-2-propenyl, and 1-fluoro-5-hexenyl 1-phenyl-1H-tetrazol-5-yl (PT) sulfones were prepared by metalation followed by electrophilic fluorination. Although metalation-fluorination of n-propyl, 5-hexenyl, and (cyclopropyl)methyl PT-sulfones proceeded under homogeneous conditions, fluorination of 2-methyl-2-propenyl PT-sulfone required heterogeneous fluorination conditions. Condensation reactions of fluoro PT-sulfones with aldehydes resulted in fluoroalkylidenes in high yields. Screening of olefination conditions showed that stereoselectivity depended on reagent and carbonyl structure and can in many cases be tuned either toward E- or Z-selectivity. For example, LHMDS-mediated condensations of 1-fluoropropyl PT-sulfone in the presence of MgBr(2) x OEt(2) were Z-selective with electron-rich aromatic aldehydes, a hindered aromatic aldehyde, and cinnamaldehyde. Low-temperature KHMDS-mediated condensations were E-selective with electron-rich and electron-deficient aromatic aldehydes and Z-selective with n-octanal. Dialkyl, aryl alkyl, and diaryl ketones reacted as well to give fluoro olefin products in 71-99% yields.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031
| | - Barbara Zajc
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, NY 10031
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Seela F, Xu K. DNA with stable fluorinated dA and dG substitutes: syntheses, base pairing and 19F-NMR spectra of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine. Org Biomol Chem 2008; 6:3552-60. [PMID: 19082156 DOI: 10.1039/b806145a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fluorinated DNA containing stable fluorine substituents in the "purine" base were synthesized for the first time. For this, the phosphoramidites of 7-fluoro-7-deaza-2'-deoxyadenosine and 7-fluoro-7-deaza-2'-deoxyguanosine were prepared and oligonucleotides were synthesized. The 7-fluoro substitution leads to increased duplex stability and more selective base pairing compared to the non-functionalized 7-deazapurine oligonucleotides. (19)F NMR spectra of fluorinated nucleosides, single stranded oligonucleotides and DNA duplex show only a single signal for one fluorine modification. The NMR sensitive (19)F spin or the positron emitting (18)F isotope make these compounds applicable for DNA detection or imaging in vitro and in vivo.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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