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Tokai S, Bito T, Shimizu K, Arima J. Methionine residues lining the substrate pathway in prolyl oligopeptidase from Pleurotus eryngii play an important role in substrate recognition. Biosci Biotechnol Biochem 2018; 82:1107-1115. [PMID: 29623768 DOI: 10.1080/09168451.2018.1459177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Family S9 prolyl oligopeptidases (POPs) are of interest as pharmacological targets. We recently found that an S9 POP from Pleurotus eryngii showed altered substrate specificity following H2O2 treatment. Oxidation of Met203 on the non-catalytic β-propeller domain resulted in decreased activity toward non-aromatic aminoacyl-para-nitroanilides (pNAs) while maintaining its activity toward aromatic aminoacyl-pNAs. Given that the other Met residues should also be oxidized by H2O2 treatment, we constructed mutants in which all the Met residues were substituted with other amino acids. Analysis of the mutants showed that Met570 in the catalytic domain is another potent residue for the altered substrate specificity following oxidation. Met203 and Met570 lie on the surfaces of two different domains and form part of a funnel from the surface to the active center. Our findings indicate that the funnel forms the substrate pathway and plays a role in substrate recognition.
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Affiliation(s)
- Shota Tokai
- a The United Graduate School of Agricultural Sciences , Tottori University , Tottori , Japan
| | - Tomohiro Bito
- b Faculty of Agriculture, Department of Agricultural, Biological and Environmental Sciences , Tottori University , Tottori , Japan
| | - Katsuhiko Shimizu
- c Organization for Regional Industrial Academic Cooperation, Tottori University , Tottori , Japan
| | - Jiro Arima
- b Faculty of Agriculture, Department of Agricultural, Biological and Environmental Sciences , Tottori University , Tottori , Japan
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Mikhailova AG, Rakitina TV, Timofeev VI, Karlinsky DM, Korzhenevskiy DA, Agapova YК, Vlaskina AV, Ovchinnikova MV, Gorlenko VA, Rumsh LD. Activity modulation of the oligopeptidase B from Serratia proteamaculans by site-directed mutagenesis of amino acid residues surrounding catalytic triad histidine. Biochimie 2017; 139:125-136. [DOI: 10.1016/j.biochi.2017.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 05/15/2017] [Accepted: 05/17/2017] [Indexed: 11/16/2022]
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3
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Tokai S, Bito T, Shimizu K, Arima J. Effect of oxidation of the non-catalytic β-propeller domain on the substrate specificity of prolyl oligopeptidase from Pleurotus eryngii. Biochem Biophys Res Commun 2017; 487:356-361. [DOI: 10.1016/j.bbrc.2017.04.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
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Bastos IMD, Motta FN, Grellier P, Santana JM. Parasite prolyl oligopeptidases and the challenge of designing chemotherapeuticals for Chagas disease, leishmaniasis and African trypanosomiasis. Curr Med Chem 2014; 20:3103-15. [PMID: 23514419 PMCID: PMC3778648 DOI: 10.2174/0929867311320250006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/16/2012] [Indexed: 11/22/2022]
Abstract
The trypanosomatids Trypanosoma cruzi, Leishmania spp. and Trypanosoma brucei spp. cause Chagas disease, leishmaniasis and human African trypanosomiasis, respectively. It is estimated that over 10 million people worldwide suffer from these neglected diseases, posing enormous social and economic problems in endemic areas. There are no vaccines to prevent these infections and chemotherapies are not adequate. This picture indicates that new chemotherapeutic agents must be developed to treat these illnesses. For this purpose, understanding the biology of the pathogenic trypanosomatid-host cell interface is fundamental for molecular and functional characterization of virulence factors that may be used as targets for the development of inhibitors to be used for effective chemotherapy. In this context, it is well known that proteases have crucial functions for both metabolism and infectivity of pathogens and are thus potential drug targets. In this regard, prolyl oligopeptidase and oligopeptidase B, both members of the S9 serine protease family, have been shown to play important roles in the interactions of pathogenic protozoa with their mammalian hosts and may thus be considered targets for drug design. This review aims to discuss structural and functional properties of these intriguing enzymes and their potential as targets for the development of drugs against Chagas disease, leishmaniasis and African trypanosomiasis.
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Affiliation(s)
- I M D Bastos
- Pathogen-Host Interface Laboratory, Department of Cell Biology, The University of Brasília, Brasília, Brazil
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Fukumoto J, Ismail NIM, Kubo M, Kinoshita K, Inoue M, Yuasa K, Nishimoto M, Matsuki H, Tsuji A. Possible role of inter-domain salt bridges in oligopeptidase B from Trypanosoma brucei: critical role of Glu172 of non-catalytic -propeller domain in catalytic activity and Glu490 of catalytic domain in stability of OPB. J Biochem 2013; 154:465-73. [PMID: 23946505 DOI: 10.1093/jb/mvt077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Junki Fukumoto
- Department of Biological Science and Technology, The University of Tokushima Graduate School, 2-1 Minamijosanjima, Tokushima 770-8506, Japan; Faculty of Science, Universiti Tunku Abdul Rahman, Jalam Universiti, Bandar Barat, 31900 Kampar, Perak D.R., Malaysia; and Department of Parasitology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka 830-0011, Japan
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Arthur IN, Hennessy JE, Padmakshan D, Stigers DJ, Lesturgez S, Fraser SA, Liutkus M, Otting G, Oakeshott JG, Easton CJ. In Situ Deprotection and Incorporation of Unnatural Amino Acids during Cell-Free Protein Synthesis. Chemistry 2013; 19:6824-30. [DOI: 10.1002/chem.201203923] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/15/2013] [Indexed: 01/15/2023]
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Mikhailova AG, Khairullin RF, Kolomijtseva GY, Rumsh LD. Oligopeptidase B from Serratia proteamaculans. III. Inhibition analysis. Specific interactions with metalloproteinase inhibitors. BIOCHEMISTRY (MOSCOW) 2012; 77:300-6. [DOI: 10.1134/s0006297912030091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mikhailova AG, Khairullin RF, Demidyuk IV, Gromova TY, Kostrov SV, Rumsh LD. Oligopeptidase B from Serratia proteamaculans. II. Enzymatic characteristics: Substrate analysis, influence of calcium ions, pH and temperature dependences. BIOCHEMISTRY (MOSCOW) 2011; 76:480-90. [DOI: 10.1134/s0006297911040122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kaszuba K, Rog T, St Pierre JF, Mannisto PT, Karttunen M, Bunker A. Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2009; 20:595-609. [PMID: 20024801 DOI: 10.1080/10629360903438198] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We used the crystal structure of prolyl oligopeptidase (POP) with bound Z-pro-prolinal (ZPP) inhibitor (Protein Data Bank (PDB) structure 1QFS) to perform an intensive molecular dynamics study of the POP-ZPP complex. We performed 100 ns of simulation with the hemiacetal bond, through which the ZPP is bound to the POP, removed in order to better investigate the binding cavity environment. From basic analysis, measuring the radius of gyration, root mean square deviation, solvent accessible surface area and definition of the secondary structure of protein, we determined that the protein structure is highly stable and maintains its structure over the entire simulation time. This demonstrates that such long time simulations can be performed without the protein structure losing stability. We found that water bridges and hydrogen bonds play a negligible role in binding the ZPP thus indicating the importance of the hemiacetal bond. The two domains of the protein are bound by a set of approximately 12 hydrogen bonds, specific to the particular POP protein.
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Affiliation(s)
- K Kaszuba
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
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Usuki H, Uesugi Y, Iwabuchi M, Hatanaka T. Activation of oligopeptidase B from Streptomyces griseus by thiol-reacting reagents is independent of the single reactive cysteine residue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1673-83. [PMID: 19665591 DOI: 10.1016/j.bbapap.2009.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
Abstract
Oligopeptidase B from Streptomyces griseus was cloned and characterized to clarify the substrate recognition mechanism and the role of a reactive cysteine residue in family S9 prolyl oligopeptidases (POPs). The cloned enzyme, SGR-OpdB, was annotated as a putative family S9 prolyl oligopeptidase based on its deduced amino acid sequence, in which a sole cysteine residue Cys(544) is present close to the catalytic Asp residue in the C-terminal region. The protein was identified as oligopeptidase B, a member of the subfamily S9a of the family S9 POPs, as judged by its substrate specificity and enzymatic characteristics. Its enzymatic activity was markedly enhanced by high NaCl concentration and the reducing reagents dithiothreitol (DTT) and reduced glutathione (GSH). It is particularly interesting that oxidized glutathione (GSSG) also enhanced SGR-OpdB activity. The SGR-OpdB C544A mutant was constructed and characterized to clarify the role of the putative reactive Cys residue, Cys(544). Surprisingly, the enzymatic activity of the Cys-free mutant was also markedly activated by the general thiol-reacting reagent DTT, GSH, and GSSG. To our knowledge, this is the first report of activity-enhancing effects of thiol-reacting reagents toward Cys-free enzymes. Results clarified the role of additives in inducing conformational change of SGR-OpdB into active peptidase.
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Affiliation(s)
- Hirokazu Usuki
- Research Institute for Biological Sciences (RIBS), Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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Oligopeptidase B: A processing peptidase involved in pathogenesis. Biochimie 2008; 90:336-44. [DOI: 10.1016/j.biochi.2007.10.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Accepted: 10/25/2007] [Indexed: 11/20/2022]
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12
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Yu WY, Yang LX, Xie JS, Zhou L, Jiang XY, Zhu DX, Muramatsu M, Wang MW. Derivatives of aryl-4-guanidinomethylbenzoate and N-aryl-4-guanidinomethylbenzamide as new antibacterial agents: synthesis and bioactivity. Acta Pharmacol Sin 2008; 29:267-77. [PMID: 18215358 DOI: 10.1111/j.1745-7254.2008.00720.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
AIM The aim of the present study was to design, synthesize, and evaluate novel antibacterial agents, derivatives of aryl-4-guanidinomethylbenzoate and N-aryl-4-guanidinomethylbenzamide. METHODS A total of 44 derivatives of aryl-4-guanidin-omethylbenzoate (series A) and N-aryl-4-guanidinomethylbenzamide (series B) were synthesized and their antibacterial activities were assessed in vitro against a variety of Gram-positive and Gram-negative bacteria by an agar dilution method. RESULTS Twelve compounds showed potent bactericidal effects against a panel of Gram-positive germs, including methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), vancomycin-intermediate Staphylococcus aureus (VISA), and methicillin-resistant coagulase-negative staphylococci (MRCNS), with minimum inhibitory concentrations (MIC) ranging between 0.5 and 8 microg/mL, which were comparable to the MIC values of several marketed antibiotics. They exhibited weak or no activity on the Gram-negative bacteria tested. In addition, these compounds displayed high inhibitory activities towards oligopeptidase B of bacterial origin. CONCLUSION In comparison with the previously reported MIC values of several known antibiotics, the derivatives of aryl-4-guanidinomethylbenzoate and N-aryl-4-guanidinomethylbenzamide showed comparable in vitro bactericidal activities against VRE and VISA as linezolid. Their growth inhibitory effects on MRSA were similar to vancomycin, but were less potent than linezolid and vancomycin against MRCNS. This class of compounds may have the potential to be developed into narrow spectrum antibacterial agents against certain drug-resistant strains of bacteria.
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Affiliation(s)
- Wen-yuan Yu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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Yun YS, Lee W, Shin S, Oh BH, Choi KY. Arg-158 Is Critical in Both Binding the Substrate and Stabilizing the Transition-state Oxyanion for the Enzymatic Reaction of Malonamidase E2. J Biol Chem 2006; 281:40057-64. [PMID: 17077089 DOI: 10.1074/jbc.m604515200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malonamidase E2 (MAE2) from Bradyrhizobium japonicum is an enzyme that hydrolyzes malonamate to malonate and has a Ser-cis-Ser-Lys catalytic triad at the active site. The crystal structures of wild type and mutant MAE2 exhibited that the guanido group of Arg-158 could be involved in the binding of malonamate in which the negative charge of the carboxyl group could destabilize a negatively charged transition-state oxyanion in the enzymatic reaction. In an attempt to elucidate the specific roles of Arg-158, site-directed mutants, R158Q, R158E, and R158K, were prepared (see Table 1). The crystal structure of R158Q determined at 2.2 Angstrom resolution showed that the guanido group of Arg-158 was important for the substrate binding with the marginal structural change upon the mutation. The k(cat) value of R158Q significantly decreased by over 1500-fold and the catalytic activity of R158E could not be detected. The k(cat) value of R158K was similar to that of the wild type with the K(m) value drastically increased by 100-fold, suggesting that Lys-158 of R158K can stabilize the negative charge of the carboxylate in the substrate to some extent and contribute to the stabilization of the transition-state oxyanion, but a single amine group of Lys-158 in R158K could not precisely anchor the carboxyl group of malonamate compared with the guanido group of Arg-158. Our kinetic and structural evidences demonstrate that Arg-158 in MAE2 should be critical to both binding the substrate and stabilizing the transition-state oxyanion for the catalytic reaction of MAE2.
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Affiliation(s)
- Young Sung Yun
- Department of Life Sciences, National CRI Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang 790-784, South Korea
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Bincoletto C, Tersariol ILS, Oliveira CR, Dreher S, Fausto DM, Soufen MA, Nascimento FD, Caires ACF. Chiral cyclopalladated complexes derived from N,N-dimethyl-1-phenethylamine with bridging bis(diphenylphosphine)ferrocene ligand as inhibitors of the cathepsin B activity and as antitumoral agents. Bioorg Med Chem 2005; 13:3047-55. [PMID: 15781414 DOI: 10.1016/j.bmc.2005.01.057] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2004] [Revised: 01/26/2005] [Accepted: 01/26/2005] [Indexed: 11/20/2022]
Abstract
Chiral cyclopalladated complexes derived from N,N-dimethyl-1-phenethylamine and the coordinating ligand 1,1'-bis(diphenylphosphine)ferrocene were synthesized and studied as Cathepsin B inhibitors and antitumoral agents against solid tumors. Our results revealed that the palladium compound [Pd2(C2,N-S(-)dmpa)2(mu-dppf)Cl2] (2) was able to inhibit Cathepsin B activity in a reversible fashion. This palladacycle compound binds to free cathepsin B (E) as well as to the enzyme-substrate complex (ES) with dissociation constants of KH=12+/-1 microM and alphaKH=2.4+/-0.3 microM, respectively. The application of this complex, in Walker tumor-bearing rats, resulted in 90% inhibition of the tumor growth. Subcutaneous inoculations of 10(6) tumoral cells produced solid tumors with a mass of 4.0+/-1.0 g in 12 days Walker tumor-bearing rats. However, when these animals were treated with one dose of the palladacycle compound (2.0 mg/kg), the tumoral mass was reduced to 0.3+/-0.1 g. On the other hand, the same complex (2) did not afford any protection to mice bearing the non-metastatic Ehrlich Ascites tumor treated with doses of 0.5, 5.0, and 30 mg/kg for a period of four, three and one day, respectively, beginning 72 h after tumor inoculation. Toxicological studies using mice treated with one high dose of the complex (2) (100 mg/kg) did not show any alterations in red and white blood cell morphology 14 days after the drug administration. Similar results were obtained with hepatic, kidney, and spleen tissues. The results presented in this work introduce the title cyclopalladated complexes as promising antitumoral drugs with reduced toxicity in experimental studies.
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Affiliation(s)
- Cláudia Bincoletto
- Centro Interdisciplinar de Investigação Bioquímica-CIIB, Universidade de Mogi das Cruzes, Av. Cândido Xavier de Almeida Souza, 200-CEP: 08701-970, CP: 411, Mogi das Cruzes-SP, Brazil
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Lindner AB, Kim SH, Schindler DG, Eshhar Z, Tawfik DS. Esterolytic antibodies as mechanistic and structural models of hydrolases-a quantitative analysis. J Mol Biol 2002; 320:559-72. [PMID: 12096909 DOI: 10.1016/s0022-2836(02)00418-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Understanding enzymes quantitatively and mimicking their remarkable catalytic efficiency is a paramount challenge. Here, we applied esterolytic antibodies (the D-Abs) to dissect and quantify individual elements of enzymatic catalysis such as transition state (TS) stabilization, nucleophilic reactivity and conformational changes. Kinetic and mutagenic analysis of the D-Abs were combined with existing structural evidence to show that catalysis by the D-Abs is driven primarily by stabilization of the tetrahedral oxyanionic intermediate of ester hydrolysis formed by the nucleophilic attack of an exogenous (solution) hydroxide anion. The side-chain of TyrH100d is shown to be the main H-bond donor of the D-Abs oxyanion hole. The pH-rate and pH-binding profiles indicate that the strength of this H-bond increases dramatically as the neutral substrate develops into the oxyanionic TS, resulting in TS stabilization of 5-7 kcal/mol, which is comparable to oxyanionic TS stabilization in serine hydrolases. We show that the rate of the exogenous (intermolecular) nucleophilic attack can be enhanced by 2000-fold by replacing the hydroxide nucleophile with peroxide, an alpha-nucleophile that is much more reactive than hydroxide. In the presence of peroxide, the rate saturates (k(cat)(max)) at 6 s(-1). This rate-ceiling appears to be dictated by the rate of the induced-fit conformational rearrangement leading to the active antibody-TS complex. The selective usage of negatively charged exogenous nucleophiles by the D-Abs led to the identification of a positively charged channel. Imprinted by the negatively-charged TS-analogue against which these antibodies were elicited, this channel presumably directs the nucleophile to the antibody-bound substrate. Our findings are discussed in comparison with serine esterases and, in particular, with cocaine esterase (cocE), which possesses a tyrosine based oxyanion hole.
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Affiliation(s)
- Ariel B Lindner
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
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Morty RE, Fülöp V, Andrews NW. Substrate recognition properties of oligopeptidase B from Salmonella enterica serovar Typhimurium. J Bacteriol 2002; 184:3329-37. [PMID: 12029050 PMCID: PMC135088 DOI: 10.1128/jb.184.12.3329-3337.2002] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2002] [Accepted: 03/26/2002] [Indexed: 01/27/2023] Open
Abstract
Oligopeptidase B (OpdB) is a serine peptidase broadly distributed among unicellular eukaryotes, gram-negative bacteria, and spirochetes which has emerged as an important virulence factor and potential therapeutic target in infectious diseases. We report here the cloning and expression of the opdB homologue from Salmonella enterica serovar Typhimurium and demonstrate that it exhibits amidolytic activity exclusively against substrates with basic residues in P(1). While similar to its eukaryotic homologues in terms of substrate specificity, Salmonella OpdB differs significantly in catalytic power and inhibition and activation properties. In addition to oligopeptide substrates, restricted proteolysis of histone proteins was observed, although no cleavage was seen at or near residues that had been posttranslationally modified or at defined secondary structures. This supports the idea that the catalytic site of OpdB may be accessible only to unstructured oligopeptides, similar to the closely related prolyl oligopeptidase (POP). Salmonella OpdB was employed as a model enzyme to define determinants of substrate specificity that distinguish OpdB from POP, which hydrolyzes substrates exclusively at proline residues. Using site-directed mutagenesis, nine acidic residues that are conserved in OpdBs but absent from POPs were converted to their corresponding residues in POP. In this manner, we identified a pair of glutamic acid residues, Glu(576) and Glu(578), that define P(1) specificity and direct OpdB cleavage C terminal to basic residues. We have also identified a second pair of residues, Asp(460) and Asp(462), that may be involved in defining P(2) specificity and thus direct preferential cleavage by OpdB after pairs of basic residues.
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Affiliation(s)
- Rory E Morty
- Section of Microbial Pathogenesis, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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