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The anti-proliferative effect of β-carotene against a triple-negative breast cancer cell line is cancer cell-specific and JNK-dependent. PHARMANUTRITION 2022. [DOI: 10.1016/j.phanu.2022.100320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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2
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Martín-Alonso S, Kang D, Martínez Del Río J, Luczkowiak J, Frutos-Beltrán E, Zhang L, Cheng X, Liu X, Zhan P, Menéndez-Arias L. Novel RNase H Inhibitors Blocking RNA-directed Strand Displacement DNA Synthesis by HIV-1 Reverse Transcriptase. J Mol Biol 2022; 434:167507. [PMID: 35217069 DOI: 10.1016/j.jmb.2022.167507] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/27/2022]
Abstract
In retroviruses, strand displacement DNA-dependent DNA polymerization catalyzed by the viral reverse transcriptase (RT) is required to synthesize double-stranded proviral DNA. In addition, strand displacement during RNA-dependent DNA synthesis is critical to generate high-quality cDNA for use in molecular biology and biotechnology. In this work, we show that the loss of RNase H activity due to inactivating mutations in HIV-1 RT (e.g. D443N or E478Q) has no significant effect on strand displacement while copying DNA templates, but has a large impact on DNA polymerization in reactions carried out with RNA templates. Similar effects were observed with β-thujaplicinol and other RNase H active site inhibitors, including compounds with dual activity (i.e., characterized also as inhibitors of HIV-1 integrase and/or the RT DNA polymerase). Among them, dual inhibitors of HIV-1 RT DNA polymerase/RNase H activities, containing a 7-hydroxy-6-nitro-2H-chromen-2-one pharmacophore were found to be very potent and effective strand displacement inhibitors in RNA-dependent DNA polymerization reactions. These findings might be helpful in the development of transcriptomics technologies to obtain more uniform read coverages when copying long RNAs and for the construction of more representative libraries avoiding biases towards 5' and 3' ends, while providing valuable information for the development of novel antiretroviral agents.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Javier Martínez Del Río
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Joanna Luczkowiak
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Lina Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Xiqiang Cheng
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, PR China.
| | - Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa" (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain.
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3
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Notenboom S, Weigand KM, Proost JH, van Lipzig MM, van de Steeg E, van den Broek PH, Greupink R, Russel FG, Groothuis GM. Development of a mechanistic biokinetic model for hepatic bile acid handling to predict possible cholestatic effects of drugs. Eur J Pharm Sci 2018; 115:175-184. [DOI: 10.1016/j.ejps.2018.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/04/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
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4
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Ung PMU, Dunbar JB, Gestwicki JE, Carlson HA. An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. J Med Chem 2014; 57:6468-78. [PMID: 25062388 PMCID: PMC4136727 DOI: 10.1021/jm5008352] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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NMR
and MD simulations have demonstrated that the flaps of HIV-1 protease
(HIV-1p) adopt a range of conformations that are coupled with its
enzymatic activity. Previously, a model was created for an allosteric
site located between the flap and the core of HIV-1p, called the Eye
site (2008, 89, 643−65218381626). Here, results from our first study were
combined with a ligand-based, lead-hopping method to identify a novel
compound (NIT). NIT inhibits HIV-1p, independent of the presence of
an active-site inhibitor such as pepstatin A. Assays showed that NIT
acts on an allosteric site other than the dimerization interface.
MD simulations of the ligand–protein complex show that NIT
stably binds in the Eye site and restricts the flaps. That bound state
of NIT is consistent with a crystal structure of similar fragments
bound in the Eye site (2010, 75, 257−26820659109). Most importantly,
NIT is equally potent against wild-type and a multidrug-resistant
mutant of HIV-1p, which highlights the promise of allosteric inhibitors
circumventing existing clinical resistance.
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Affiliation(s)
- Peter M-U Ung
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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Elsinghorst PW, di Salvo ML, Parroni A, Contestabile R. Inhibition of human pyridoxal kinase by 2-acetyl-4-((1R,2S,3R)-1,2,3,4-tetrahydroxybutyl)imidazole (THI). J Enzyme Inhib Med Chem 2014; 30:336-40. [PMID: 24899377 DOI: 10.3109/14756366.2014.915396] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
2-Acetyl-4-((1R,2S,3R)-1,2,3,4-tetrahydroxybutyl)imidazole (THI) is observed as a minor contaminant in caramel food colourings (E 150c). Feeding experiments with rodents have revealed a significant lymphopenic effect that has been linked to the presence of THI in these food colourings. Pyridoxal kinase inhibition by THI has been suggested, but not demonstrated, as a mode of action as it leads to lowered levels of pyridoxal-5'-phosphate, which are known to cause lymphopenia. Recently, THI was also shown to inhibit sphingosine-1-phosphate lyase causing comparable immunosuppressive effects and derivatives of THI are being developed for the treatment of rheumatoid arthritis in humans. Interestingly, sphingosine-1-phosphate lyase activity depends on pyridoxal-5'-phosphate, which in turn is provided by pyridoxal kinase. This report shows that THI does inhibit pyridoxal kinase with competitive and mixed-type non-competitive behaviour towards its two substrates, pyridoxal and ATP, respectively. The corresponding inhibition constants are in the low millimolar range.
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Affiliation(s)
- Paul W Elsinghorst
- Pharmaceutical Chemistry I, Pharmaceutical Institute , University of Bonn, Bonn , Germany and
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6
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Intracellular antiviral activity of low-dose ritonavir in boosted protease inhibitor regimens. Antimicrob Agents Chemother 2014; 58:4042-7. [PMID: 24798279 DOI: 10.1128/aac.00104-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Protease inhibitors are largely used for the treatment of HIV infection in combination with other antiretroviral drugs. Their improved pharmacokinetic profiles can be achieved through the concomitant administration of low doses of ritonavir (RTV), a protease inhibitor currently used as a booster, increasing the exposure of companion drugs. Since ritonavir-boosted regimens are associated with long-term adverse events, cobicistat, a CYP3A4 inhibitor without antiviral activity, has been developed. Recently, high intracellular concentrations of ritonavir in lymphocytes and monocytes were reported even when ritonavir was administered at low doses, so we aimed to compare its theoretical antiviral activity with those of the associated protease inhibitors. Intracellular concentrations of ritonavir and different protease inhibitors were determined through the same method. Inhibitory constants were obtained from the literature. The study enrolled 103 patients receiving different boosted protease inhibitors, darunavir-ritonavir 600 and 100 mg twice daily and 800 and 100 mg once daily (n = 22 and 4, respectively), atazanavir-ritonavir 300 and 100 mg once daily (n = 40), lopinavir-ritonavir 400 and 100 mg twice daily (n = 21), or tipranavir-ritonavir 500 and 200 mg twice daily (n = 16). According to the observed concentrations, we calculated the ratios between the intracellular concentrations of ritonavir and those of the companion protease inhibitor and between the theoretical viral protease reaction speeds with each drug, with and without ritonavir. The median ratios were 4.04 and 0.63 for darunavir-ritonavir twice daily, 2.49 and 0.74 for darunavir-ritonavir once daily, 0.42 and 0.74 for atazanavir-ritonavir, 0.57 and 0.95 for lopinavir-ritonavir, and 0.19 and 0.84 for tipranavir-ritonavir, respectively. Therefore, the antiviral effect of ritonavir was less than that of the concomitant protease inhibitors but, importantly, mostly with darunavir. Thus, further in vitro and in vivo studies of the RTV antiviral effect are warranted.
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7
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Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: comparison of chrysin and flavopiridol. Food Chem Toxicol 2012; 61:14-27. [PMID: 23279842 DOI: 10.1016/j.fct.2012.12.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/18/2012] [Accepted: 12/20/2012] [Indexed: 11/21/2022]
Abstract
Flavonoids have been discovered as novel inhibitors of glycogen phosphorylase (GP), a target to control hyperglycemia in type 2 diabetes. To elucidate the mechanism of inhibition, we have determined the crystal structure of the GPb-chrysin complex at 1.9 Å resolution. Chrysin is accommodated at the inhibitor site intercalating between the aromatic side chains of Phe285 and Tyr613 through π-stacking interactions. Chrysin binds to GPb approximately 15 times weaker (Ki=19.01 μM) than flavopiridol (Ki=1.24 μM), exclusively at the inhibitor site, and both inhibitors display similar behavior with respect to AMP. To identify the source of flavopiridols' stronger affinity, molecular docking with Glide and postdocking binding free energy calculations using QM/MM-PBSA have been performed and compared. Whereas docking failed to correctly rank inhibitor binding conformations, the QM/MM-PBSA method employing M06-2X/6-31+G to model the π-stacking interactions correctly reproduced the experimental results. Flavopiridols' greater binding affinity is sourced to favorable interactions of the cationic 4-hydroxypiperidin-1-yl substituent with GPb, with desolvation effects limited by the substituent conformation adopted in the crystallographic complex. Further successful predictions using QM/MM-PBSA for the flavonoid quercetagetin (which binds at the allosteric site) leads us to propose the methodology as a useful and inexpensive tool to predict flavonoid binding.
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8
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Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries. Biochem J 2010; 429:527-32. [PMID: 20507280 DOI: 10.1042/bj20091645] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Clinically approved inhibitors of the HIV-1 protease function via a competitive mechanism. A particular vulnerability of competitive inhibitors is their sensitivity to increases in substrate concentration, as may occur during virion assembly, budding and processing into a mature infectious viral particle. Advances in chemical synthesis have led to the development of new high-diversity chemical libraries using rapid in-solution syntheses. These libraries have been shown previously to be effective at disrupting protein-protein and protein-nucleic acid interfaces. We have screened 44000 compounds from such a library to identify inhibitors of the HIV-1 protease. One compound was identified that inhibits wild-type protease, as well as a drug-resistant protease with six mutations. Moreover, analysis of this compound suggests an allosteric non-competitive mechanism of inhibition and may represent a starting point for an additional strategy for anti-retroviral therapy.
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Schenker P, Baici A. Simultaneous interaction of enzymes with two modifiers: Reappraisal of kinetic models and new paradigms. J Theor Biol 2009; 261:318-29. [DOI: 10.1016/j.jtbi.2009.07.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 07/13/2009] [Accepted: 07/24/2009] [Indexed: 11/27/2022]
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Dimitriou-Christidis P, Autenrieth RL. Kinetics of biodegradation of binary and ternary mixtures of PAHs. Biotechnol Bioeng 2007; 97:788-800. [PMID: 17115447 DOI: 10.1002/bit.21269] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The kinetics of biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by Sphingomonas paucimobilis strain EPA505 were investigated. The investigation focused on three- and four-ring PAHs, specifically 2-methylphenanthrene, fluoranthene, and pyrene. Uptake rates in aerobic batch suspended cultivations were measured for the individual PAHs and their binary and ternary mixtures. It was observed that kinetics were influenced by the mixture composition and the kinetic properties of the components. A material balance equation containing the Monod model was numerically fitted to uptake data to determine extant kinetic parameters for the individual PAHs. Similarly, equations containing kinetic interaction models derived from enzyme kinetics were fitted to the uptake data obtained from experiments with binary and ternary mixtures. The investigation considered the following interaction types: no-interaction (Monod), pure competitive interaction, noncompetitive or mixed-type interaction, uncompetitive inhibition, and nonspecific interaction based on pure competition (SKIP). Model fit was evaluated based on probabilistic and statistical criteria and inferences were reached about underlying interaction mechanisms based on model fit. Mixture kinetics were most adequately simulated by the pure competitive interaction model with mutual substrate exclusivity. This model is fully predictive, relying only on parameters determined in the sole-PAH experiments. It was shown that for low percent inhibition values and with limited data, pure competitive interaction kinetics may not be evident, resembling no-interaction kinetics. This study is a reasonable starting point for understanding and modeling biodegradation of complex PAH mixtures in engineered and natural systems.
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Affiliation(s)
- Petros Dimitriou-Christidis
- Department of Civil Engineering, Environmental Engineering Division, Texas A&M University, 3136 TAMU, College Station, Texas 77843-3136, USA
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11
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Carvajal N, Orellana MS, Salas M, Enríquez P, Alarcón R, Uribe E, López V. Kinetic studies and site-directed mutagenesis of Escherichia coli agmatinase. A role for Glu274 in binding and correct positioning of the substrate guanidinium group. Arch Biochem Biophys 2004; 430:185-90. [PMID: 15369817 DOI: 10.1016/j.abb.2004.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2004] [Revised: 06/29/2004] [Indexed: 11/20/2022]
Abstract
The interaction of Escherichia coli agmatinase (EC 3.5.3.11) with the substrate guanidinium group was investigated by kinetic and site-directed mutagenesis studies. Putrescine and guanidinium ions (Gdn+) were slope-linear, competitive inhibitors with respect to agmatine and their bindings to the enzyme were not mutually exclusive. By site-directed mutagenesis, the E274A variant exhibiting about 1-2% of wild-type activity was obtained. Mutation produced a moderate, but significant, increase in the Km value for agmatine (from 1.1 +/- 0.2 mM to 6.3 +/- 0.3 mM) and the Ki value for competitive inhibition by Gdn+ (from 15.0 +/- 0.1 mM to 44.2 +/- 2.1 mM), but the Ki value for putrescine inhibition (2.8 +/- 0.2 mM) was not altered. The tryptophan fluorescence properties (lambdamax = 342 nm) and circular dichroism spectra were not significantly altered by the Glu274 --> Ala mutation. The dimeric structure of the enzyme was also maintained. We conclude that Glu274 is involved in binding and positioning of the guanidinium moiety of the substrate for efficient catalysis. A kinetic mechanism involving rapid equilibrium random release of products is proposed for E. coli agmatinase.
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Affiliation(s)
- Nelson Carvajal
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Chile.
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12
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Crouch SR, Cullen TF, Scheeline A, Kirkor ES. Kinetic Determinations and Some Kinetic Aspects of Analytical Chemistry. Anal Chem 1998. [DOI: 10.1021/a1980005s] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Martinez-Irujo JJ, Villahermosa ML, Mercapide J, Cabodevilla JF, Santiago E. Analysis of the combined effect of two linear inhibitors on a single enzyme. Biochem J 1998; 329 ( Pt 3):689-98. [PMID: 9445400 PMCID: PMC1219094 DOI: 10.1042/bj3290689] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Different methods for studying the concurrent effects of two linear inhibitors on a single enzyme have been published, including the fractional product of Webb, the Yonetani-Theorell plot or the method of Chou and Talalay. Recently the use of combination plots has also been advocated for this purpose. We have evaluated the applicability of these methods and found that most of them depend on assumptions about the mechanism of action of the inhibitors. If the mechanism of action is not completely understood, or if some assumptions about the mechanism are unfounded, the parameters obtained may be meaningless. Even if these assumptions are correct, the interaction can be advantageously measured using an alternative representation that does not require a knowledge of the inhibition constants and allows experimental data to be retrieved from the plot. In other cases it is the interpretation of the results rather than the validity of the method that is misleading. A common mistake is to take the exclusivity of the effects of two inhibitors as exclusivity of their binding. We show that this assumption is seldom justified. In any case, it is possible to decide whether the combination of two or more inhibitors is more effective than their individual use by means of isobolographic analysis, even when no information about their mechanism of action is available.
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Affiliation(s)
- J J Martinez-Irujo
- Department of Biochemistry and Molecular Biology, University of Navarra, Pamplona, Spain
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Asante-Appiah E, Seetharaman J, Sicheri F, Yang DS, Chan WW. Gem-dialkyl succinic acids: a novel class of inhibitors for carboxypeptidases. Biochemistry 1997; 36:8710-5. [PMID: 9220957 DOI: 10.1021/bi970354b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
gem-Dimethylsuccinic acid and its higher homolog, 2-methyl-2-ethylsuccinic acid (MESA) are highly potent inhibitors of both carboxypeptidase A (CPA) and B. The inhibition constant of MESA for CPA (0.11 microM for the racemic mixture) is remarkable considering the relatively simple structure of the compound. The molecular feature which is crucial for high affinity binding to both carboxypeptidases appears to be the nonpolar gem-dialkyl locus. The structure of the complex between MESA and CPA has been determined by X-ray crystallography to 2.0 A resolution and shows the R enantiomer of the inhibitor to be bound in a generally substrate-like manner. The carboxymethyl group is coordinated to the Zn ion in the active site, and the gem-dialkyl locus corresponds in position to the alpha-carbon of the C-terminal amino acid in a peptide substrate. The methyl group of the inhibitor occupies a cavity in the enzyme which is apparently not filled upon substrate-binding. We postulate that this cavity (the alpha-methyl hole) is designed to allow the proximal Glu-270 residue to undergo a critical movement during catalysis. The hydrophobic nature of the above cavity may play a role in modulating the reactivity of this residue. These results suggest that similar cenophilic(empty-loving) inhibitors may be found for other enzymes.
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Affiliation(s)
- E Asante-Appiah
- Department of Biochemistry, McMaster University, Hamilton, Ontario, Canada L8N 3Z5
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