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Su J, Guo W, Liu Y, Kong L, Zheng H, Zhu G. Cu-catalyzed cascade difluoroalkylation/5- endo cyclization/β-fluorine cleavage of ynones. Chem Commun (Camb) 2023; 59:1821-1824. [PMID: 36722869 DOI: 10.1039/d2cc06068j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A copper-catalyzed, redox-neutral cascade difluoroalkylation/5-endo annulation/β-fluorine cleavage of ynones is developed, providing a direct and stereoselective method to access synthetically important α-monofluoroalkenyl cyclopentanones. Mechanistic studies suggest an unprecedented CuII-assisted β-fluorine fragmentation, which may be valuable for the challenging but important C-F bond activation. Moreover, the in situ generated difluorocarbene was found to serve as an effective reductant for the regeneration of copper(I) catalyst, thus avoiding the addition of external reductants.
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Affiliation(s)
- Jingwen Su
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, P. R. China.
| | - Wenbin Guo
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, P. R. China.
| | - Yi Liu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, P. R. China.
| | - Lichun Kong
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, P. R. China.
| | - Hanliang Zheng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, P. R. China.
| | - Gangguo Zhu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, 688 Yingbin Road, Jinhua 321004, P. R. China.
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2
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Morales JF, Chuguransky S, Alberca LN, Alice JI, Goicoechea S, Ruiz ME, Bellera CL, Talevi A. Positive Predictive Value Surfaces as a Complementary Tool to Assess the Performance of Virtual Screening Methods. Mini Rev Med Chem 2021; 20:1447-1460. [PMID: 32072906 DOI: 10.2174/1871525718666200219130229] [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: 09/11/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Since their introduction in the virtual screening field, Receiver Operating Characteristic (ROC) curve-derived metrics have been widely used for benchmarking of computational methods and algorithms intended for virtual screening applications. Whereas in classification problems, the ratio between sensitivity and specificity for a given score value is very informative, a practical concern in virtual screening campaigns is to predict the actual probability that a predicted hit will prove truly active when submitted to experimental testing (in other words, the Positive Predictive Value - PPV). Estimation of such probability is however, obstructed due to its dependency on the yield of actives of the screened library, which cannot be known a priori. OBJECTIVE To explore the use of PPV surfaces derived from simulated ranking experiments (retrospective virtual screening) as a complementary tool to ROC curves, for both benchmarking and optimization of score cutoff values. METHODS The utility of the proposed approach is assessed in retrospective virtual screening experiments with four datasets used to infer QSAR classifiers: inhibitors of Trypanosoma cruzi trypanothione synthetase; inhibitors of Trypanosoma brucei N-myristoyltransferase; inhibitors of GABA transaminase and anticonvulsant activity in the 6 Hz seizure model. RESULTS Besides illustrating the utility of PPV surfaces to compare the performance of machine learning models for virtual screening applications and to select an adequate score threshold, our results also suggest that ensemble learning provides models with better predictivity and more robust behavior. CONCLUSION PPV surfaces are valuable tools to assess virtual screening tools and choose score thresholds to be applied in prospective in silico screens. Ensemble learning approaches seem to consistently lead to improved predictivity and robustness.
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Affiliation(s)
- Juan F Morales
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - Sara Chuguransky
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - Lucas N Alberca
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - Juan I Alice
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - Sofía Goicoechea
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - María E Ruiz
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - Carolina L Bellera
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
| | - Alan Talevi
- Laboratory of Bioactive Research and Development (LIDeB), Department of Biological Sciences, Faculty of Exact Sciences, University of La Plata (UNLP) - 47 & 115, La Plata (1900), Buenos Aires, Argentina
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van Veen BC, Wales SM, Clayden J. N-Methyl Allylic Amines from Allylic Alcohols by Mitsunobu Substitution Using N-Boc Ethyl Oxamate. J Org Chem 2021; 86:8538-8543. [PMID: 34101454 DOI: 10.1021/acs.joc.1c00918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the practical, scalable synthesis of a range of N-methyl allylic amines. Primary and secondary allylic alcohols underwent a regioselective Mitsunobu reaction with readily accessible N-Boc ethyl oxamate to deliver the corresponding N-Boc allylic amines, including in enantiopure form via stereospecific substitution. Subsequent N-methylation and Boc deprotection without chromatography yielded the amine products as hydrochloride salts. This method solves the problem of converting commercially available alcohols into often volatile N-methyl allylic amines, many of which have limited commercial availability.
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Affiliation(s)
- Branca C van Veen
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Steven M Wales
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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4
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Silverman RB. Design and Mechanism of GABA Aminotransferase Inactivators. Treatments for Epilepsies and Addictions. Chem Rev 2018; 118:4037-4070. [PMID: 29569907 DOI: 10.1021/acs.chemrev.8b00009] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
When the brain concentration of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) diminishes below a threshold level, the excess neuronal excitation can lead to convulsions. This imbalance in neurotransmission can be corrected by inhibition of the enzyme γ-aminobutyric acid aminotransferase (GABA-AT), which catalyzes the conversion of GABA to the excitatory neurotransmitter l-glutamic acid. It also has been found that raising GABA levels can antagonize the rapid elevation and release of dopamine in the nucleus accumbens, which is responsible for the reward response in addiction. Therefore, the design of new inhibitors of GABA-AT, which increases brain GABA levels, is an important approach to new treatments for epilepsy and addiction. This review summarizes findings over the last 40 or so years of mechanism-based inactivators (unreactive compounds that require the target enzyme to catalyze their conversion to the inactivating species, which inactivate the enzyme prior to their release) of GABA-AT with emphasis on their catalytic mechanisms of inactivation, presented according to organic chemical mechanism, with minimal pharmacology, except where important for activity in epilepsy and addiction. Patents, abstracts, and conference proceedings are not covered in this review. The inactivation mechanisms described here can be applied to the inactivations of a wide variety of unrelated enzymes.
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Affiliation(s)
- Richard B Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Center for Developmental Therapeutics , Northwestern University , 2145 Sheridan Road , Evanston , Illinois 60208-3113 , United States
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5
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Lee H, Le HV, Wu R, Doud E, Sanishvili R, Kellie JF, Compton PD, Pachaiyappan B, Liu D, Kelleher NL, Silverman RB. Mechanism of Inactivation of GABA Aminotransferase by (E)- and (Z)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic Acid. ACS Chem Biol 2015; 10:2087-98. [PMID: 26110556 DOI: 10.1021/acschembio.5b00212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
When γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter in the mammalian central nervous system, falls below a threshold level, seizures occur. One approach to raise GABA concentrations is to inhibit GABA aminotransferase (GABA-AT), a pyridoxal 5'-phosphate-dependent enzyme that degrades GABA. We have previously developed (1S,3S)-3-amino-4-difluoromethylene-1-cyclopentanoic acid (CPP-115), which is 186 times more efficient in inactivating GABA-AT than vigabatrin, the only FDA-approved inactivator of GABA-AT. We also developed (E)- and (Z)-(1S,3S)-3-amino-4-fluoromethylenyl-1-cyclopentanoic acid (1 and 2, respectively), monofluorinated analogs of CPP-115, which are comparable to vigabatrin in inactivating GABA-AT. Here, we report the mechanism of inactivation of GABA-AT by 1 and 2. Both produce a metabolite that induces disruption of the Glu270-Arg445 salt bridge to accommodate interaction between the metabolite formyl group and Arg445. This is the second time that Arg445 has interacted with a ligand and is involved in GABA-AT inactivation, thereby confirming the importance of Arg445 in future inactivator design.
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Affiliation(s)
- Hyunbeom Lee
- Departments
of Chemistry and Molecular Biosciences, Chemistry of Life Processes
Institute, and the Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Hoang V. Le
- Departments
of Chemistry and Molecular Biosciences, Chemistry of Life Processes
Institute, and the Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Rui Wu
- Department
of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Emma Doud
- Departments
of Chemistry and Molecular Biosciences, and the Proteomics Center
of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Ruslan Sanishvili
- X-ray
Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - John F. Kellie
- Departments
of Chemistry and Molecular Biosciences, and the Proteomics Center
of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Phillip D. Compton
- Departments
of Chemistry and Molecular Biosciences, and the Proteomics Center
of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Boobalan Pachaiyappan
- Departments
of Chemistry and Molecular Biosciences, Chemistry of Life Processes
Institute, and the Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
| | - Dali Liu
- Department
of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences, and the Proteomics Center
of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard B. Silverman
- Departments
of Chemistry and Molecular Biosciences, Chemistry of Life Processes
Institute, and the Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, United States
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Pinto A, Tamborini L, Pennacchietti E, Coluccia A, Silvestri R, Cullia G, De Micheli C, Conti P, De Biase D. Bicyclic γ-amino acids as inhibitors of γ-aminobutyrate aminotransferase. J Enzyme Inhib Med Chem 2015; 31:295-301. [DOI: 10.3109/14756366.2015.1021251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Andrea Pinto
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy,
| | - Lucia Tamborini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy,
| | - Eugenia Pennacchietti
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze e Biotecnologie Medico-Chirurgiche, Sapienza Università di Roma, Latina, Italy, and
| | - Antonio Coluccia
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Romano Silvestri
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Gregorio Cullia
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy,
| | - Carlo De Micheli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy,
| | - Paola Conti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy,
| | - Daniela De Biase
- Istituto Pasteur – Fondazione Cenci Bolognetti, Dipartimento di Scienze e Biotecnologie Medico-Chirurgiche, Sapienza Università di Roma, Latina, Italy, and
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7
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Kiss L, Nonn M, Sillanpää R, Fustero S, Fülöp F. Efficient regio- and stereoselective access to novel fluorinated β-aminocyclohexanecarboxylates. Beilstein J Org Chem 2013; 9:1164-9. [PMID: 23843909 PMCID: PMC3701410 DOI: 10.3762/bjoc.9.130] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/21/2013] [Indexed: 11/26/2022] Open
Abstract
A regio- and stereoselective method has been developed for the synthesis of novel fluorinated 2-aminocyclohexanecarboxylic acid derivatives with the fluorine attached to position 4 of the ring. The synthesis starts from either cis- or trans-β-aminocyclohex-4-enecarboxylic acids and involves regio- and stereoselective transformation of the ring C–C double bond through iodooxazine formation and hydroxylation, followed by hydroxy–fluorine or oxo–fluorine exchange.
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Affiliation(s)
- Loránd Kiss
- University of Szeged, Institute of Pharmaceutical Chemistry, Szeged, Hungary
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8
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Hawker DD, Silverman RB. Synthesis and evaluation of novel heteroaromatic substrates of GABA aminotransferase. Bioorg Med Chem 2012; 20:5763-73. [PMID: 22944334 PMCID: PMC3448830 DOI: 10.1016/j.bmc.2012.08.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/02/2012] [Accepted: 08/08/2012] [Indexed: 11/21/2022]
Abstract
Two principal neurotransmitters are involved in the regulation of mammalian neuronal activity, namely, γ-aminobutyric acid (GABA), an inhibitory neurotransmitter, and L-glutamic acid, an excitatory neurotransmitter. Low GABA levels in the brain have been implicated in epilepsy and several other neurological diseases. Because of GABA's poor ability to cross the blood-brain barrier (BBB), a successful strategy to raise brain GABA concentrations is the use of a compound that does cross the BBB and inhibits or inactivates GABA aminotransferase (GABA-AT), the enzyme responsible for GABA catabolism. Vigabatrin, a mechanism-based inactivator of GABA-AT, is currently a successful therapeutic for epilepsy, but has harmful side effects, leaving a need for improved GABA-AT inactivators. Here, we report the synthesis and evaluation of a series of heteroaromatic GABA analogues as substrates of GABA-AT, which will be used as the basis for the design of novel enzyme inactivators.
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Affiliation(s)
- Dustin D. Hawker
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208-3113, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, and Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208-3113, USA
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9
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Kiss L, Forró E, Fustero S, Fülöp F. Regio- and diastereoselective fluorination of alicyclic β-amino acids. Org Biomol Chem 2011; 9:6528-34. [PMID: 21773624 DOI: 10.1039/c1ob05648d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A regio- and stereoselective approach to fluorinated β-aminocyclohexene or cyclohexane esters has been developed, starting from a bicyclic β-lactam (1). The procedure involves six or seven steps, based on regio- and stereoselective iodolactonization, lactone opening and hydroxy-fluorine exchange. The method has been extended to the synthesis of fluorinated amino ester enantiomers.
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Affiliation(s)
- Loránd Kiss
- Institute of Pharmaceutical Chemistry, University of Szeged, H-6720, Szeged, Eötvös u. 6, Szeged, Hungary
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10
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Kiss L, Forró E, Fustero S, Fülöp F. Selective Synthesis of New Fluorinated Alicyclic β-Amino Ester Stereoisomers. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100583] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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11
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Synthesis of conformationally restricted 1,2,3-triazole-substituted ethyl β- and γ-aminocyclopentanecarboxylate stereoisomers. Multifunctionalized alicyclic amino esters. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.030] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Wnuk SF, Lalama J, Garmendia CA, Robert J, Zhu J, Pei D. S-Ribosylhomocysteine analogues with the carbon-5 and sulfur atoms replaced by a vinyl or (fluoro)vinyl unit. Bioorg Med Chem 2008; 16:5090-102. [PMID: 18375129 DOI: 10.1016/j.bmc.2008.03.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Revised: 03/05/2008] [Accepted: 03/10/2008] [Indexed: 11/28/2022]
Abstract
Treatment of the protected ribose or xylose 5-aldehyde with sulfonyl-stabilized fluorophosphonate gave (fluoro)vinyl sulfones. Stannyldesulfonylation followed by iododestannylation afforded 5,6-dideoxy-6-fluoro-6-iodo-d-ribo or xylo-hex-5-enofuranoses. Coupling of the hexenofuranoses with alkylzinc bromides gave 10-carbon ribosyl- and xylosylhomocysteine analogues incorporating a fluoroalkene. The fluoroalkenyl and alkenyl analogues were evaluated for inhibition of Bacillus subtilis S-ribosylhomocysteinase (LuxS). One of the compounds, 3,5,6-trideoxy-6-fluoro-d-erythro-hex-5-enofuranose, acted as a competitive inhibitor of moderate potency (K(I)=96microM).
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Affiliation(s)
- Stanislaw F Wnuk
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA.
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13
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Kiss L, Forró E, Sillanpää R, Fülöp F. Diastereo- and Enantioselective Synthesis of Orthogonally Protected 2,4-Diaminocyclopentanecarboxylates: A Flip from β-Amino- to β,γ-Diaminocarboxylates. J Org Chem 2007; 72:8786-90. [DOI: 10.1021/jo701332v] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Loránd Kiss
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
| | - Enikó Forró
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
| | - Reijo Sillanpää
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry and Research Group of Stereochemistry of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös utca 6, Hungary, and Department of Chemistry, University of Jyväskylä, FIN-40351, Jyväskylä, Finland
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