1
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Reddi R, Ganji RJ, Marapaka AK, Bala SC, Yerra NV, Haque N, Addlagatta A. Puromycin, a selective inhibitor of PSA acts as a substrate for other M1 family aminopeptidases: Biochemical and structural basis. Int J Biol Macromol 2020; 165:1373-1381. [PMID: 33045297 DOI: 10.1016/j.ijbiomac.2020.10.035] [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: 04/06/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 10/23/2022]
Abstract
Puromycin sensitive aminopeptidase (PSA or NPEPPS) is a M1 class aminopeptidase is selectively inhibited by the natural product puromycin, an aminonucleoside antibiotic produced by the bacterium Streptomyces alboniger. The molecular basis for this selective inhibition has not been understood well. Here, we report the basis for selectivity of puromycin using biochemical, structural and molecular modeling tools on four different M1 family enzymes including human PSA. Except for PSA, the other three enzymes were not inhibited. Instead, the peptide bond in the puromycin is hydrolyzed to O-methyl-L-tyrosine (OMT) and puromycin aminonucleoside (PAN). Neither of the hydrolyzed products, individually or together inhibit any of the four enzymes. Crystal structure of ePepN using crystals that are incubated with puromycin contained the hydrolyzed products instead of intact puromycin. On the other hand, intact puromycin molecule was observed in the crystal structure of the inactive mutant ePepN (E298A)-puromycin complex. Surprisingly, puromycin does not enter the active site of the mutant enzyme but binds near the entrance. Comparison of puromycin binding region in ePepN mutant enzyme and molecular modeling studies suggest that PSA might be inhibited by similar mode of binding there by blocking the entrance of the active site.
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Affiliation(s)
- Ravikumar Reddi
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Roopa Jones Ganji
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Anil Kumar Marapaka
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sandeep Chowdary Bala
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Naga Veera Yerra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Department of Analytical and Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Neshatul Haque
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India
| | - Anthony Addlagatta
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Localization and enzyme kinetics of aminopeptidase N3 from Toxoplasma gondii. Parasitol Res 2019; 119:357-364. [PMID: 31836922 DOI: 10.1007/s00436-019-06512-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/15/2019] [Indexed: 10/25/2022]
Abstract
Aminopeptidase N is an important metalloenzyme from the M1 zinc metallopeptidase family, which is present in numerous apicomplexan parasites, including Plasmodium, Eimeria, and Cryptosporidium. Aminopeptidase N is a potential drug target, and hence, its properties have been widely investigated. In the current study, the cellular localization and enzyme characteristics of Toxoplasma gondii aminopeptidase N3 (TgAPN3) were evaluated in vitro. Cellular localization analysis revealed that TgAPN3 and GRA protein were co-located in the organelle and parasitophorous vacuole of T. gondii. The secretion assay showed that TgAPN3 could be co-secreted from the tachyzoites with GRA protein. A functional recombinant Toxoplasma aminopeptidase N3 (rTgAPN3) was produced in Escherichia coli. The enzyme activity was first determined using a fluorogenic H-Ala-MCA substrate. Some activity of rTgAPN3 was observed between pH 3.0 and 8.0, with a peak at pH 7.0. The activity was significantly enhanced in the presence of Co2+ ions. Substrate specificity of rTgAPN3 was then evaluated. The enzyme showed a preference for substrates containing N-terminal Ala residues, followed by Tyr and Cys. The rTgAPN3 activity was significantly inhibited by bestatin and phebestatin. In general, TgAPN3 was a structurally conserved member of the M1 family, although it also displayed unique biochemical characteristics. These results lay the foundation for a functional study of TgAPN3 and constitute its putative identification as a drug target.
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3
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Salomon E, Schmitt M, Marapaka AK, Stamogiannos A, Revelant G, Schmitt C, Alavi S, Florent I, Addlagatta A, Stratikos E, Tarnus C, Albrecht S. Aminobenzosuberone Scaffold as a Modular Chemical Tool for the Inhibition of Therapeutically Relevant M1 Aminopeptidases. Molecules 2018; 23:molecules23102607. [PMID: 30314342 PMCID: PMC6222927 DOI: 10.3390/molecules23102607] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 01/22/2023] Open
Abstract
The synthesis of racemic substituted 7-amino-5,7,8,9-tetrahydrobenzocyclohepten-6-one hydrochlorides was optimized to enhance reproducibility and increase the overall yield. In order to investigate their specificity, series of enzyme inhibition assays were carried out against a diversity of proteases, covering representative members of aspartic, cysteine, metallo and serine endopeptidases and including eight members of the monometallic M1 family of aminopeptidases as well as two members of the bimetallic M17 and M28 aminopeptidase families. This aminobenzosuberone scaffold indeed demonstrated selective inhibition of M1 aminopeptidases to the exclusion of other tested protease families; it was particularly potent against mammalian APN and its bacterial/parasitic orthologues EcPepN and PfAM1.
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Affiliation(s)
- Emmanuel Salomon
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Marjorie Schmitt
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Anil Kumar Marapaka
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Dehli 110001, India.
| | - Athanasios Stamogiannos
- Protein Chemistry Laboratory, INRASTES, National Centre for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece.
| | - Germain Revelant
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Céline Schmitt
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Sarah Alavi
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CNRS, 75231 Paris, France.
| | - Anthony Addlagatta
- Centre for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, Telangana, India.
- Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Dehli 110001, India.
| | - Efstratios Stratikos
- Protein Chemistry Laboratory, INRASTES, National Centre for Scientific Research Demokritos, Agia Paraskevi, 15310 Athens, Greece.
| | - Céline Tarnus
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
| | - Sébastien Albrecht
- Laboratoire d'Innovation Moléculaire et Applications, Université de Haute-Alsace, Université de Strasbourg, CNRS, 68093 Mulhouse, France.
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4
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Marapaka AK, Pillalamarri V, Gumpena R, Haque N, Bala SC, Jangam A, Addlagatta A. Discovery, Structural and Biochemical Studies of a rare Glu/Asp Specific M1 Class Aminopeptidase from Legionella pneumophila. Int J Biol Macromol 2018; 120:1111-1118. [PMID: 30172821 DOI: 10.1016/j.ijbiomac.2018.08.172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Aminopeptidases catalyze the hydrolysis of amino acids from the N-terminus of protein or peptide substrates. M1 family aminopeptidases are important for the pathogenicity of bacteria and play critical role in many physiological processes such as protein maturation, regulation of peptide hormone levels in humans. Most of the M1 family aminopeptidases reported till date display broad substrates specificity, mostly specific to basic and hydrophobic residues. In the current study we report the discovery of a novel M1 class aminopeptidase from Legionella pneumophila (LePepA), which cleaves only acidic residues. Biochemical and structural studies reveal that the S1 pocket is polar and positively charged. Bioinformatic analysis suggests that such active site is unique to only Legionella species and probably evolved for special needs of the microbe. Given its specific activity, LePepA could be useful in specific biotechnological applications.
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Affiliation(s)
- Anil Kumar Marapaka
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Vijaykumar Pillalamarri
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Rajesh Gumpena
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Neshatul Haque
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Sandeep Chowdary Bala
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India
| | - Aruna Jangam
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India
| | - Anthony Addlagatta
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500 007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Rafi Marg, New Delhi 110001, India.
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5
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Kok GPY, Yang H, Wong MW, Zhao Y. Cu-Catalyzed [3 + 3] Cycloaddition of Isocyanoacetates with Aziridines and Stereoselective Access to α,γ-Diamino Acids. Org Lett 2018; 20:5112-5115. [PMID: 30141633 DOI: 10.1021/acs.orglett.8b01948] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report herein an efficient Cu-catalyzed formal [3 + 3] cycloaddition of isocyanoacetates with readily available aziridines of different substitution patterns, which provides a practical access to valuable 1,4,5,6-tetrahydropyrimidine derivatives. In particular, the use of enantiopure aziridines delivers disubstituted tetrahydropyrimidines bearing a 1,3-diamino unit in good yields as a single stereoisomer (>20:1 dr, > 99% ee). The heterocyclic products can also be easily converted to synthetically useful amino alcohol derivatives or α,γ-diamino acids.
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Affiliation(s)
- Germaine Pui Yann Kok
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543
| | - Hui Yang
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543
| | - Ming Wah Wong
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543
| | - Yu Zhao
- Department of Chemistry , National University of Singapore , 3 Science Drive 3 , Republic of Singapore 117543
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6
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Peng G, McEwen AG, Olieric V, Schmitt C, Albrecht S, Cavarelli J, Tarnus C. Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis. Proteins 2017; 85:1413-1421. [DOI: 10.1002/prot.25301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/17/2017] [Accepted: 04/03/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Guanya Peng
- Paul Scherrer Institut (SLS) WSLB; 5232 Villigen Suisse Switzerland
| | - Alastair G. McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Illkirch France
- Centre National de la Recherche Scientifique; UMR7104; Illkirch France
- Institut National de la Santé et de la Recherche Médicale; U964; Illkirch France
- Université de Strasbourg; Illkirch France
| | - Vincent Olieric
- Paul Scherrer Institut (SLS) WSLB; 5232 Villigen Suisse Switzerland
| | - Celine Schmitt
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
| | - Sebastien Albrecht
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
| | - Jean Cavarelli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire; Illkirch France
- Centre National de la Recherche Scientifique; UMR7104; Illkirch France
- Institut National de la Santé et de la Recherche Médicale; U964; Illkirch France
- Université de Strasbourg; Illkirch France
| | - Celine Tarnus
- Laboratoire de Chimie Organique et Bioorganique; EA4566; Université de Haute Alsace, Institut Jean Baptiste Donnet; Mulhouse France
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7
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Węglarz-Tomczak E, Berlicki Ł, Pawełczak M, Nocek B, Joachimiak A, Mucha A. A structural insight into the P1S1 binding mode of diaminoethylphosphonic and phosphinic acids, selective inhibitors of alanine aminopeptidases. Eur J Med Chem 2016; 117:187-96. [PMID: 27100031 DOI: 10.1016/j.ejmech.2016.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/04/2016] [Accepted: 04/06/2016] [Indexed: 10/22/2022]
Abstract
N'-substituted 1,2-diaminoethylphosphonic acids and 1,2-diaminoethylphosphinic dipeptides were explored to unveil the structural context of the unexpected selectivity of these inhibitors of M1 alanine aminopeptidases (APNs) versus M17 leucine aminopeptidase (LAP). The diaminophosphonic acids were obtained via aziridines in an improved synthetic procedure that was further expanded for the phosphinic pseudodipeptide system. The inhibitory activity, measured for three M1 and one M17 metalloaminopeptidases of different sources (bacterial, human and porcine), revealed several potent compounds (e.g., Ki = 65 nM of 1u for HsAPN). Two structures of an M1 representative (APN from Neisseria meningitidis) in complex with N-benzyl-1,2-diaminoethylphosphonic acid and N-cyclohexyl-1,2-diaminoethylphosphonic acid were determined by the X-ray crystallography. The analysis of these structures and the models of the phosphonic acid complexes of the human ortholog provided an insight into the role of the additional amino group and the hydrophobic substituents of the ligands within the S1 active site region.
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Affiliation(s)
- Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | | | - Bogusław Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Artur Mucha
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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8
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Aeluri R, Ganji RJ, Marapaka AK, Pillalamarri V, Alla M, Addlagatta A. Highly functionalized tetrahydropyridines are cytotoxic and selective inhibitors of human puromycin sensitive aminopeptidase. Eur J Med Chem 2015; 106:26-33. [DOI: 10.1016/j.ejmech.2015.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 01/17/2023]
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9
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Romero JM, Martin M, Ramirez CL, Dumas VG, Marti MA. Efficient Calculation of Enzyme Reaction Free Energy Profiles Using a Hybrid Differential Relaxation Algorithm: Application to Mycobacterial Zinc Hydrolases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 100:33-65. [PMID: 26415840 DOI: 10.1016/bs.apcsb.2015.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Determination of the free energy profile for an enzyme reaction mechanism is of primordial relevance, paving the way for our understanding of the enzyme's catalytic power at the molecular level. Although hybrid, mostly DFT-based, QM/MM methods have been extensively applied to this type of studies, achieving accurate and statistically converged results at a moderate computational cost is still an open challenge. Recently, we have shown that accurate results can be achieved in less computational time, combining Jarzynski's relationship with a hybrid differential relaxation algorithm (HyDRA), which allows partial relaxation of the solvent during the nonequilibrium steering of the reaction. In this work, we have applied this strategy to study two mycobacterial zinc hydrolases. Mycobacterium tuberculosis infections are still a worldwide problem and thus characterization and validation of new drug targets is an intense field of research. Among possible drug targets, recently two essential zinc hydrolases, MshB (Rv1170) and MA-amidase (Rv3717), have been proposed and structurally characterized. Although possible mechanisms have been proposed by analogy to the widely studied human Zn hydrolases, several key issues, particularly those related to Zn coordination sphere and its role in catalysis, remained unanswered. Our results show that mycobacterial Zn hydrolases share a basic two-step mechanism. First, the attacking water becomes deprotonated by the conserved base and establishes the new C-O bond leading to a tetrahedral intermediate. The intermediate requires moderate reorganization to allow for proton transfer to the amide N and C-N bond breaking to occur in the second step. Zn ion plays a key role in stabilizing the tetrahedral intermediate and balancing the negative charge of the substrate during hydroxide ion attack. Finally, comparative analysis of other Zn hydrolases points to a convergent mechanistic evolution.
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Affiliation(s)
- Juan Manuel Romero
- Instituto de Química Física de los Materiales Medio Ambiente y Energía (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Mariano Martin
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Claudia Lilián Ramirez
- Instituto de Química Física de los Materiales Medio Ambiente y Energía (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Victoria Gisel Dumas
- Instituto de Química Física de los Materiales Medio Ambiente y Energía (INQUIMAE), UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo Adrián Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina.
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10
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Vassiliou S, Węglarz-Tomczak E, Berlicki Ł, Pawełczak M, Nocek B, Mulligan R, Joachimiak A, Mucha A. Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases. J Med Chem 2014; 57:8140-51. [PMID: 25192493 PMCID: PMC4331105 DOI: 10.1021/jm501071f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Seven crystal structures of alanyl aminopeptidase from Neisseria meningitides (the etiological agent of meningitis, NmAPN) complexed with organophosphorus compounds were resolved to determine the optimal inhibitor-enzyme interactions. The enantiomeric phosphonic acid analogs of Leu and hPhe, which correspond to the P1 amino acid residues of well-processed substrates, were used to assess the impact of the absolute configuration and the stereospecific hydrogen bond network formed between the aminophosphonate polar head and the active site residues on the binding affinity. For the hPhe analog, an imperfect stereochemical complementarity could be overcome by incorporating an appropriate P1 side chain. The constitution of P1'-extended structures was rationally designed and the lead, phosphinic dipeptide hPhePψ[CH2]Phe, was modified in a single position. Introducing a heteroatom/heteroatom-based fragment to either the P1 or P1' residue required new synthetic pathways. The compounds in the refined structure were low nanomolar and subnanomolar inhibitors of N. meningitides, porcine and human APNs, and the reference leucine aminopeptidase (LAP). The unnatural phosphinic dipeptide analogs exhibited a high affinity for monozinc APNs associated with a reasonable selectivity versus dizinc LAP. Another set of crystal structures containing the NmAPN dipeptide ligand were used to verify and to confirm the predicted binding modes; furthermore, novel contacts, which were promising for inhibitor development, were identified, including a π-π stacking interaction between a pyridine ring and Tyr372.
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Affiliation(s)
- Stamatia Vassiliou
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens , Panepistimiopolis, Zografou, 15701 Athens, Greece
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11
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Patra CR, Chaudhuri A. Chemical Biologists Meet at ICCB-2014, the First Annual Conference of the Newly Born Chemical Biology Society of India, at the City of Pearls. ACS Chem Biol 2014. [DOI: 10.1021/cb5003653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chitta Ranjan Patra
- Biomaterials Group, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, India
| | - Arabinda Chaudhuri
- Biomaterials Group, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007, India
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12
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Yoshimura T, Kinoshita T, Yoshioka H, Kawabata T. Asymmetric Intermolecular Conjugate Addition of Amino Acid Derivatives via Memory of Chirality: Total Synthesis of Manzacidin A. Org Lett 2013; 15:864-7. [DOI: 10.1021/ol303568f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | - Hiroyasu Yoshioka
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
| | - Takeo Kawabata
- Institute for Chemical Research, Kyoto University, Uji 611-0011, Japan
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13
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Węglarz-Tomczak E, Poręba M, Byzia A, Berlicki Ł, Nocek B, Mulligan R, Joachimiak A, Drąg M, Mucha A. An integrated approach to the ligand binding specificity of Neisseria meningitidis M1 alanine aminopeptidase by fluorogenic substrate profiling, inhibitory studies and molecular modeling. Biochimie 2012; 95:419-28. [PMID: 23131591 DOI: 10.1016/j.biochi.2012.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/15/2012] [Indexed: 12/11/2022]
Abstract
Neisseria meningitides is a gram-negative diplococcus bacterium and is the main causative agent of meningitis and other meningococcal diseases. Alanine aminopeptidase from N. meningitides (NmAPN) belongs to the family of metallo-exopeptidase enzymes, which catalyze the removal of amino acids from the N-terminus of peptides and proteins, and are found among all the kingdoms of life. NmAPN is suggested to be mostly responsible for proteolysis and nutrition delivery, similar to the orthologs from other bacteria. To explore the possibility of NmAPN being a potential drug target for inhibition and development of novel therapeutic agents, the specificity of the S1 and S1' binding sites was explored using an integrated approach. Initially, an extensive library consisting of almost 100 fluorogenic substrates derived from both natural and unnatural amino acids, were used to obtain a detailed substrate fingerprint of the S1 pocket of NmAPN. A broad substrate tolerance of NmAPN was revealed, with bulky basic and hydrophobic ligands being the most favored substrates. Additionally, the potency of a set of organophosphorus inhibitors of neutral aminopeptidases, amino acid and dipeptide analogs was determined. Inhibition constants in the nanomolar range, determined for phosphinic dipeptides, proves the positive increase in inhibition impact of the P1' ligand elongation. The results were further verified via molecular modeling and docking of canonical aminopeptidase phosphinic dipeptide inhibitors in the NmAPN active site. These studies present comprehensive characterization of interactions responsible for specific ligand binding. This knowledge provides invaluable insight into understanding of the enzyme and development of novel NmAPN inhibitors.
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Affiliation(s)
- Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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14
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Synthesis, cytotoxic, and DNA binding studies of novel fluorinated condensed pyrano pyrazoles. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0239-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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