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Singh A, Ottavi S, Krieger I, Planck K, Perkowski A, Kaneko T, Davis AM, Suh C, Zhang D, Goullieux L, Alex A, Roubert C, Gardner M, Preston M, Smith DM, Ling Y, Roberts J, Cautain B, Upton A, Cooper CB, Serbina N, Tanvir Z, Mosior J, Ouerfelli O, Yang G, Gold BS, Rhee KY, Sacchettini JC, Fotouhi N, Aubé J, Nathan C. Redirecting raltitrexed from cancer cell thymidylate synthase to Mycobacterium tuberculosis phosphopantetheinyl transferase. SCIENCE ADVANCES 2024; 10:eadj6406. [PMID: 38489355 PMCID: PMC10942122 DOI: 10.1126/sciadv.adj6406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
There is a compelling need to find drugs active against Mycobacterium tuberculosis (Mtb). 4'-Phosphopantetheinyl transferase (PptT) is an essential enzyme in Mtb that has attracted interest as a potential drug target. We optimized a PptT assay, used it to screen 422,740 compounds, and identified raltitrexed, an antineoplastic antimetabolite, as the most potent PptT inhibitor yet reported. While trying unsuccessfully to improve raltitrexed's ability to kill Mtb and remove its ability to kill human cells, we learned three lessons that may help others developing antibiotics. First, binding of raltitrexed substantially changed the configuration of the PptT active site, complicating molecular modeling of analogs based on the unliganded crystal structure or the structure of cocrystals with inhibitors of another class. Second, minor changes in the raltitrexed molecule changed its target in Mtb from PptT to dihydrofolate reductase (DHFR). Third, the structure-activity relationship for over 800 raltitrexed analogs only became interpretable when we quantified and characterized the compounds' intrabacterial accumulation and transformation.
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Affiliation(s)
- Amrita Singh
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Samantha Ottavi
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Inna Krieger
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Kyle Planck
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrew Perkowski
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | | | - Christine Suh
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - David Zhang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | | | - Alexander Alex
- AMG Consultants Limited, Camburgh House, 27 New Dover Road, Canterbury, Kent, CT1 3DN, UK
- Evenor Consulting Limited, The New Barn, Mill Lane, Eastry, Kent CT13 0JW, UK
| | | | - Mark Gardner
- AMG Consultants Limited, Camburgh House, 27 New Dover Road, Canterbury, Kent, CT1 3DN, UK
| | - Marian Preston
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Dave M. Smith
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Yan Ling
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Bastien Cautain
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | - Anna Upton
- Evotec ID (Lyon), SAS 40 Avenue Tony Garnier, Lyon 69001, France
| | | | - Natalya Serbina
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - Zaid Tanvir
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - John Mosior
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Ouathek Ouerfelli
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guangli Yang
- Organic Synthesis Core, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ben S. Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
| | - Kyu Y. Rhee
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas Agricultural and Mechanical University, College Station, TX 77843, USA
| | - Nader Fotouhi
- Global Alliance for TB Drug Development, New York, NY 10005, USA
| | - Jeffrey Aubé
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10021, USA
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A guanidinium group is an effective mimic of the tertiary carbocation formed by isopentenyl diphosphate isomerase. Bioorg Med Chem Lett 2022; 75:128971. [PMID: 36064124 DOI: 10.1016/j.bmcl.2022.128971] [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: 07/21/2022] [Revised: 08/18/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022]
Abstract
Type I isopentenyl diphosphate isomerase is a metal-dependent enzyme that generates a tertiary carbocation intermediate during catalysis. This study describes an inhibitor (2-guanidinoethyl(dihydroxyphosphorylmethyl)phosphinate) of the isomerase that bears a guanidinium as a carbocation mimic and a phosphinylphosphonate as a non-hydrolyzable metal binding functionality. Inhibition kinetics show that the compound acts in a competitive manner with a Ki value of 129 nM (KM,IPP/Ki = 27). An analogous inhibitor bearing a tertiary ammonium as the carbocation mimic was 50-fold less potent, suggesting that the planar guanidinium is a more effective carbocation mimic. Inhibitors bearing an acylated methanesulfonamide or a hydroxamate group in place of the pyrophosphate inhibited the enzyme at millimolar concentrations indicating that the isomerase is highly specific for binding to the diphosphate portion of the intermediate.
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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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Experimental and Computational Studies on N-alkylation Reaction of N-Benzoyl 5-(Aminomethyl)Tetrazole. CHEMISTRY 2021. [DOI: 10.3390/chemistry3030049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The N-alkylation reaction of N-benzoyl 5-(aminomethyl)tetrazole (5-AMT) with benzyl bromide was carried out in the presence of K2CO3 as a base. Two separable regioisomers were obtained, thus their purification led to determine the proportion of each of them, and their structures were attributed essentially based on 1H and 13C NMR spectroscopy in addition to the elemental analysis and MS data. In order to confirm the results obtained at the synthesis level, a computational study was carried out by application of density functional theory (DFT) using the Becke three-parameter hybrid exchange functional and the Lee-Yang-Parr correlation functional (B3LYP).
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Artificial intelligence in drug design: algorithms, applications, challenges and ethics. FUTURE DRUG DISCOVERY 2021. [DOI: 10.4155/fdd-2020-0028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The discovery paradigm of drugs is rapidly growing due to advances in machine learning (ML) and artificial intelligence (AI). This review covers myriad faces of AI and ML in drug design. There is a plethora of AI algorithms, the most common of which are summarized in this review. In addition, AI is fraught with challenges that are highlighted along with plausible solutions to them. Examples are provided to illustrate the use of AI and ML in drug discovery and in predicting drug properties such as binding affinities and interactions, solubility, toxicology, blood–brain barrier permeability and chemical properties. The review also includes examples depicting the implementation of AI and ML in tackling intractable diseases such as COVID-19, cancer and Alzheimer’s disease. Ethical considerations and future perspectives of AI are also covered in this review.
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Capon PK, Avery TD, Purdey MS, Abell AD. An improved synthesis of 4-aminobutanenitrile from 4-azidobutanenitrile and comments on room temperature stability. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1832527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Patrick K. Capon
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
| | - Thomas D. Avery
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
| | - Malcolm S. Purdey
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
| | - Andrew D. Abell
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, Australia
- Institute for Photonics and Advanced Sensing (IPAS), The University of Adelaide, Adelaide, Australia
- Australian Research Council Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, Australia
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7
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Popova EA, Trifonov RE, Ostrovskii VA. Tetrazoles for biomedicine. RUSSIAN CHEMICAL REVIEWS 2019. [DOI: 10.1070/rcr4864] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Reznikov AN, Ostrovskii VA, Klimochkin YN. Synthesis of Nonracemic Tetrazole GABA Analogs. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1070428018110155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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QSAR and Molecular Docking Studies of the Inhibitory Activity of Novel Heterocyclic GABA Analogues over GABA-AT. MOLECULES (BASEL, SWITZERLAND) 2018; 23:molecules23112984. [PMID: 30445747 PMCID: PMC6278377 DOI: 10.3390/molecules23112984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 11/20/2022]
Abstract
We have previously reported the synthesis, in vitro and in silico activities of new GABA analogues as inhibitors of the GABA-AT enzyme from Pseudomonas fluorescens, where the nitrogen atom at the γ-position is embedded in heterocyclic scaffolds. With the goal of finding more potent inhibitors, we now report the synthesis of a new set of GABA analogues with a broader variation of heterocyclic scaffolds at the γ-position such as thiazolidines, methyl-substituted piperidines, morpholine and thiomorpholine and determined their inhibitory potential over the GABA-AT enzyme from Pseudomonas fluorescens. These structural modifications led to compound 9b which showed a 73% inhibition against this enzyme. In vivo studies with PTZ-induced seizures on male CD1 mice show that compound 9b has a neuroprotective effect at a 0.50 mmole/kg dose. A QSAR study was carried out to find the molecular descriptors associated with the structural changes in the GABA scaffold to explain their inhibitory activity against GABA-AT. Employing 3D molecular descriptors allowed us to propose the GABA analogues enantiomeric active form. To evaluate the interaction with Pseudomonas fluorescens and human GABA-AT by molecular docking, the constructions of homology models was carried out. From these calculations, 9b showed a strong interaction with both GABA-AT enzymes in agreement with experimental results and the QSAR model, which indicates that bulky ligands tend to be the better inhibitors especially those with a sulfur atom on their structure.
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Tovar-Gudiño E, Guevara-Salazar JA, Bahena-Herrera JR, Trujillo-Ferrara JG, Martínez-Campos Z, Razo-Hernández RS, Santiago Á, Pastor N, Fernández-Zertuche M. Novel-Substituted Heterocyclic GABA Analogues. Enzymatic Activity against the GABA-AT Enzyme from Pseudomonas fluorescens and In Silico Molecular Modeling. Molecules 2018; 23:molecules23051128. [PMID: 29747438 PMCID: PMC6099672 DOI: 10.3390/molecules23051128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 11/16/2022] Open
Abstract
γ-Aminobutyric acid (GABA) is the most important inhibitory neurotransmitter in the central nervous system, and a deficiency of GABA is associated with serious neurological disorders. Due to its low lipophilicity, there has been an intensive search for new molecules with increased lipophilicity to cross the blood-brain barrier to raise GABA concentrations. We have designed and evaluated in vitro and in silico some new analogues of GABA, where the nitrogen atom at the γ-position is embedded in heterocyclic scaffolds and determined their inhibitory potential over the GABA-AT enzyme from Pseudomonas fluorescens. These modifications lead to compounds with inhibitory activity as it occurs with compounds 18a and 19a. The construction of Pseudomonas fluorescens and human GABA-AT models were carried out by homology modeling. Docking assays were done for these compounds over the GABA-AT enzyme models where 19a showed a strong interaction with both GABA-AT enzymes.
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Affiliation(s)
- Erika Tovar-Gudiño
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico.
| | - Juan Alberto Guevara-Salazar
- Departmento de Bioquímica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Cd Mexico 11340, Mexico.
| | - José Raúl Bahena-Herrera
- Departmento de Bioquímica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Cd Mexico 11340, Mexico.
| | | | - Zuleyma Martínez-Campos
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico.
| | - Rodrigo Said Razo-Hernández
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico.
| | - Ángel Santiago
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico.
| | - Nina Pastor
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico.
| | - Mario Fernández-Zertuche
- Instituto de Investigación en Ciencias Básicas y Aplicadas, Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, Morelos, Mexico.
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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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12
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Juncosa JI, Takaya K, Le HV, Moschitto MJ, Weerawarna PM, Mascarenhas R, Liu D, Dewey SL, Silverman RB. Design and Mechanism of (S)-3-Amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic Acid, a Highly Potent γ-Aminobutyric Acid Aminotransferase Inactivator for the Treatment of Addiction. J Am Chem Soc 2018; 140:2151-2164. [PMID: 29381352 PMCID: PMC5812813 DOI: 10.1021/jacs.7b10965] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
γ-Aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the central nervous system. Inhibition of GABA aminotransferase (GABA-AT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme that degrades GABA, has been established as a possible strategy for the treatment of substance abuse. The raised GABA levels that occur as a consequence of this inhibition have been found to antagonize the rapid release of dopamine in the ventral striatum (nucleus accumbens) that follows an acute challenge by an addictive substance. In addition, increased GABA levels are also known to elicit an anticonvulsant effect in patients with epilepsy. We previously designed the mechanism-based inactivator (1S,3S)-3-amino-4-difluoromethylenyl-1-cyclopentanoic acid (2), now called CPP-115, that is 186 times more efficient in inactivating GABA-AT than vigabatrin, the only FDA-approved drug that is an inactivator of GABA-AT. CPP-115 was found to have high therapeutic potential for the treatment of cocaine addiction and for a variety of epilepsies, has successfully completed a Phase I safety clinical trial, and was found to be effective in the treatment of infantile spasms (West syndrome). Herein we report the design, using molecular dynamics simulations, synthesis, and biological evaluation of a new mechanism-based inactivator, (S)-3-amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (5), which was found to be almost 10 times more efficient as an inactivator of GABA-AT than CPP-115. We also present the unexpected crystal structure of 5 bound to GABA-AT, as well as computational analyses used to assist the structure elucidation process. Furthermore, 5 was found to have favorable pharmacokinetic properties and low off-target activities. In vivo studies in freely moving rats showed that 5 was dramatically superior to CPP-115 in suppressing the release of dopamine in the corpus striatum, which occurs subsequent to either an acute cocaine or nicotine challenge. Compound 5 also attenuated increased metabolic demands (neuronal glucose metabolism) in the hippocampus, a brain region that encodes spatial information concerning the environment in which an animal receives a reinforcing or aversive drug. This multidisciplinary computational design to preclinical efficacy approach should be applicable to the design and improvement of mechanism-based inhibitors of other enzymes whose crystal structures and inactivation mechanisms are known.
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Affiliation(s)
- Jose I. Juncosa
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Kenji Takaya
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Hoang V. Le
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Matthew J. Moschitto
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Pathum M. Weerawarna
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
| | - Romila Mascarenhas
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Stephen L. Dewey
- Center for Neurosciences, Laboratory for Behavioral and Molecular Neuroimaging, Feinstein Institute for Medical Research, North Shore-LIJ Health System, Manhasset, New York 11030, United States
| | - Richard B. Silverman
- Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, Illinois 60208, United States
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Zhou Y, Gupta AK, Mukherjee M, Zheng L, Wulff WD. Multicomponent Catalytic Asymmetric Synthesis of trans-Aziridines. J Org Chem 2017; 82:13121-13140. [PMID: 29084386 DOI: 10.1021/acs.joc.7b02184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A multicomponent trans-aziridination of aldehydes, amines, and diazo compounds with BOROX catalysts is developed. The optimal protocol is slightly different for aryl aldehydes than for aliphatic aldehydes. The key to the success with aryl aldehydes was allowing the catalyst, aldehyde, and amine to react for 20 min before addition of the diazo compound. A variety of 11 different electron-poor and electron-rich aryl aldehydes were screened to give trans-aziridines in 73-90% yield with 82-99% ee and trans/cis selectivities of 19:1 to >99:1. The optimal protocol for the trans-aziridination of aliphatic aldehydes did not require prereaction of the catalyst, aldehyde, and amine, and instead, the diazo compound could be added directly. The scope of the reaction is limited to unbranched aliphatic aldehydes and was tolerant of a number of functional groups including ethers, esters, epoxides, carbamates, and phthalimides. A total of 10 aliphatic aldehydes were examined and found to give trans-aziridines in 60-88% yield with 60-98% ee and trans/cis selectivities of 6:1 to >99:1. Alkenyl aldehydes did not react, but an alkynyl aldehyde gave a 71% yield and 95% ee of an aziridine that was found to be the cis- and not the trans-diastereomer. The aryl and aliphatic aldehydes both gave the trans-aziridines with the same absolute configuration with the same catalyst; however, in those cases where cis-aziridines were formed, the configuration was opposite for those formed from aryl versus aliphatic aldehydes.
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Affiliation(s)
- Yubai Zhou
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Anil K Gupta
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Munmun Mukherjee
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - Li Zheng
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
| | - William D Wulff
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States
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14
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Abstract
AIM The similarity in the biological function of the bioisosteric pair, carboxyl and sulfonamide functional groups, is studied using the quantitative tool, average electron density of the bioisosteric moiety in drug molecules and the qualitative tool, electrostatic potential. Results/methodology: Five different capping groups (methyl, phenyl, chlorine, hydrogen and amine) were considered to investigate the effect of the environment on the properties of the bioisosteres. The molecules were considered in their neutral and anionic forms to account for the change in pH depending on the medium of the drug-receptor interactions. CONCLUSION The new developed approach, average electron density, is not only advantageous as a qualitative descriptor, it is also more consistent compared with the conventionally accepted method, electrostatic potential, especially for the anions.
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Saeed A, Larik FA, Lal B, Faisal M, El-Seedi H, Channar PA. Recent resurgence toward the oxidation of heteroatoms using dimethyldioxirane as an exquisite oxidant. SYNTHETIC COMMUN 2017. [DOI: 10.1080/00397911.2017.1291816] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Aamer Saeed
- Department of Chemistry, Quaid-I-Azam University, Islamabad, Pakistan
| | - Fayaz Ali Larik
- Department of Chemistry, Quaid-I-Azam University, Islamabad, Pakistan
| | - Bhajan Lal
- Department of Energy Systems Engineering, Sukkur Institute of Business Administration, Sukkur, Pakistan
| | - Muhammad Faisal
- Department of Chemistry, Quaid-I-Azam University, Islamabad, Pakistan
| | - Hesham El-Seedi
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
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16
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Electrostatic potentials and average electron densities of bioisosteres in methylsquarate and acetic acid. Future Med Chem 2016; 8:361-71. [DOI: 10.4155/fmc.16.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The bioisosterism in −CO2H and −C4HO3 is exploited using the quantum theory of atoms in molecules and molecular electrostatic potentials (ESP). Results & discussion: Bioisosteres in methylsquarate and acetic acid, in the neutral/anionic forms, have average electron densities that differ by less than 2% (i.e., ∼0.01 atomic units) while irrespective of the capping group. The topography of the ESP reveals similarities in the case of the neutral species but not in the anionic forms. Conclusion: The nonclassical bioisosteres in methylsquarate and acetic acid have average electron densities that are similar and relatively insensitive to the ionization state (neutral or anionic) or its studied capping group (H, CH3, Cl or phenyl). The ESP reveals similarities in the topography of neutral molecules.
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17
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Popova EA, Trifonov RE. Synthesis and biological properties of amino acids and peptides containing a tetrazolyl moiety. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4527] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Peralta-Hernández E, Blé-González EA, Gracia-Medrano-Bravo VA, Cordero-Vargas A. A practical free-radical approach to 1,4-dicarbonyl compounds. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.02.077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Łukowska-Chojnacka E, Mierzejewska J. Enzymatic Hydrolysis of Esters Containing a Tetrazole Ring. Chirality 2014; 26:811-6. [DOI: 10.1002/chir.22360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/10/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Edyta Łukowska-Chojnacka
- Faculty of Chemistry, Institute of Biotechnology; Warsaw University of Technology; Warsaw Poland
| | - Jolanta Mierzejewska
- Faculty of Chemistry, Institute of Biotechnology; Warsaw University of Technology; Warsaw Poland
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Bouasla R, Berredjem H, Berredjem M, Ibrahim-Oualid M, Allaoui A, Lecouvey M, Aouf NE. Synthesis and Biological Activity of New ChiralN-Acylsulfonamide Bis-oxazolidin-2-ones. J Heterocycl Chem 2013. [DOI: 10.1002/jhet.1987] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Radia Bouasla
- Laboratoire de Chimie Organique Appliquée, Groupe de Chimie Bioorganique; Université Badji Mokhtar; Annaba BP 12 Algeria
| | - Hadjira Berredjem
- Laboratoire de Toxicologie Cellulaire; Universite Badji Mokhtar; Annaba BP 12 Algeria
| | - Malika Berredjem
- Laboratoire de Chimie Organique Appliquée, Groupe de Chimie Bioorganique; Université Badji Mokhtar; Annaba BP 12 Algeria
| | - Malika Ibrahim-Oualid
- Institut des Sciences Moléculaires de Marseille; UMR 7313 CNRS and Université d'Aix Marseille, Faculté des Sciences et Techniques de Saint Jérôme, Avenue Escadrille Normandie-Niemen; 13397 Marseille Cedex 20 France
| | - Assia Allaoui
- Laboratoire de Chimie Organique Appliquée, Groupe de Chimie Bioorganique; Université Badji Mokhtar; Annaba BP 12 Algeria
| | - Marc Lecouvey
- Laboratoire de Chimie Bioorganique et Bionanomatériaux, CSPBAT, FRE 3043 CNRS; Université Paris 13; Bobigny Cedex France
| | - Nour-Eddine Aouf
- Laboratoire de Chimie Organique Appliquée, Groupe de Chimie Bioorganique; Université Badji Mokhtar; Annaba BP 12 Algeria
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21
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Lopes SMM, Brigas AF, Palacios F, Lemos A, Pinho e Melo TMVD. [4+2] Cycloadditions of 3-Tetrazolyl-1,2-diaza-1,3-butadienes: Synthesis of 3-Tetrazolyl-1,4,5,6-tetrahydropyridazines. European J Org Chem 2012. [DOI: 10.1002/ejoc.201101826] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Łukowska-Chojnacka E, Bernaś U, Plenkiewicz J. Lipase-catalyzed enantioseparation of alcohols containing a tetrazole ring. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.tetasy.2012.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Lopes SM, Palacios F, Lemos A, Pinho e Melo TM. Diels–Alder reactions of 3-(1H-tetrazol-5-yl)-nitrosoalkenes: synthesis of functionalized 5-(substituted)-1H-tetrazoles. Tetrahedron 2011. [DOI: 10.1016/j.tet.2011.09.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design. Future Med Chem 2011; 3:969-94. [PMID: 21707400 DOI: 10.4155/fmc.11.65] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.
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25
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26
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Lopes SM, Lemos A, Melo TMPE. A hetero-Diels–Alder approach to functionalized 1H-tetrazoles: synthesis of tetrazolyl-1,2-oxazines, -oximes and 5-(1-aminoalkyl)-1H-tetrazoles. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.10.095] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Alexiou P, Demopoulos VJ. A Diverse Series of Substituted Benzenesulfonamides as Aldose Reductase Inhibitors with Antioxidant Activity: Design, Synthesis, and in Vitro Activity. J Med Chem 2010; 53:7756-66. [DOI: 10.1021/jm101008m] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Polyxeni Alexiou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
| | - Vassilis J. Demopoulos
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki 54 124, Greece
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28
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Synthesis of γ-aminobutyric acid analogs based on carbohydrate scaffolds. Carbohydr Res 2010; 345:1099-106. [DOI: 10.1016/j.carres.2010.03.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/18/2010] [Accepted: 03/25/2010] [Indexed: 11/23/2022]
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29
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Matta CF, Arabi AA, Weaver DF. The bioisosteric similarity of the tetrazole and carboxylate anions: clues from the topologies of the electrostatic potential and of the electron density. Eur J Med Chem 2010; 45:1868-72. [PMID: 20133027 DOI: 10.1016/j.ejmech.2010.01.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 11/16/2022]
Abstract
There is a need for an a priori method with which to demonstrate the physical similarities between non-classical bioisosteres. In this study we explore the utility of the electron density and the electrostatic potential as the basis for a systematic investigation of the physical and chemical similarities between bioisosteres. The tetrazole and carboxylate bioisosteric pair is used as an illustrative example. It is shown that tetrazole and carboxylate anions give rise to electrostatic potentials (ESP) that exhibit a remarkable local similarity in the disposition of four coplanar local minima at positions consistent with lone pairs. The similarity of the disposition of these ESP minima generated by the two bioisosteres is in sharp contrast with their differences in the number and types of atoms, their nuclear geometrical arrangements, their total volumes, their partial charges, and their electron populations. The topology and geometrical disposition of these minima are shown to be independent of the capping group used in the model, and thus an inherent property of this bioisosteric pair. A model of the receptor region responsible for binding to either of these bioisosteres is proposed on the basis of an electrostatic "lock-and-key".
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Affiliation(s)
- Chérif F Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia, Canada B3M 2J6; Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3.
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Affiliation(s)
- Mohannad Abdo
- Department of Chemistry & Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854
| | - Spencer Knapp
- Department of Chemistry & Chemical Biology, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854
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Delain-Bioton L, Villemin D, Lohier JF, Sopkova J, Jaffrès PA. Synthesis of triazolyl-alkylphosphonate starting from ω-azidoalkylphosphonates or ω-alkynylphosphonates. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.07.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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32
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An expeditious and convenient synthesis of acylsulfonamides utilizing polymer-supported reagents. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.05.158] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Yuan H, Silverman RB. Structural modifications of (1S,3S)-3-amino-4-difluoromethylenecyclopentanecarboxylic acid, a potent irreversible inhibitor of GABA aminotransferase. Bioorg Med Chem Lett 2007; 17:1651-4. [PMID: 17267220 PMCID: PMC1853296 DOI: 10.1016/j.bmcl.2006.12.119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Accepted: 12/22/2006] [Indexed: 11/18/2022]
Abstract
Low brain levels of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) lead to convulsions. Inhibition of GABA aminotransferase increases the concentration of GABA and can terminate the convulsions. Earlier we reported the synthesis of (1S,3S)-3-amino-4-difluoromethylenecyclopentanecarboxylic acid (2), which is 186 times more potent an inactivator of GABA aminotransferase than the epilepsy drug S-vigabatrin. The corresponding dichloromethylene analogue of 2 (compound 3) has been made, but it shows only weak reversible inhibition of GABA aminotransferase. However, the tetrazole isostere of 2 (compound 4) has been found to be a time-dependent inactivator of GABA aminotransferase. Although it is 20 times less potent than carboxylic acid 2, it is 2.5 times more potent than S-vigabatrin. A calculation of the ClogP values indicates that 4 is the most lipophilic of the three, being 69 times more lipophilic than 2 and 55 times more lipophilic than S-vigabatrin, indicating potential for improved bioavailability.
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Affiliation(s)
| | - Richard B. Silverman
- *To whom correspondence should be addressed at the Department of Chemistry. Phone: 1-847-491-5653. Fax: 1-847-491-7713.
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Schwarz JB, Colbry NL, Zhu Z, Nichelson B, Barta NS, Lin K, Hudack RA, Gibbons SE, Galatsis P, DeOrazio RJ, Manning DD, Vartanian MG, Kinsora JJ, Lotarski SM, Li Z, Dickerson MR, El-Kattan A, Thorpe AJ, Donevan SD, Taylor CP, Wustrow DJ. Carboxylate bioisosteres of pregabalin. Bioorg Med Chem Lett 2006; 16:3559-63. [PMID: 16621528 DOI: 10.1016/j.bmcl.2006.03.083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2006] [Revised: 03/23/2006] [Accepted: 03/24/2006] [Indexed: 10/24/2022]
Abstract
Several beta-amino tetrazole analogs of gabapentin 1 and pregabalin 2 were prepared by one of two convergent, highly efficient routes, and their affinity for the alpha(2)-delta protein examined. Two select compounds with potent affinity for alpha(2)-delta, 8a and 16a, were subsequently tested in vivo in an audiogenic seizure model and found to elicit protective effects.
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Affiliation(s)
- Jacob B Schwarz
- Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, 48105, USA.
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