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Németh BZ, Kiss B, Sahin-Tóth M, Magyar C, Pál G. The High-Affinity Chymotrypsin Inhibitor Eglin C Poorly Inhibits Human Chymotrypsin-Like Protease: Gln192 and Lys218 Are Key Determinants. Proteins 2024. [PMID: 39301701 DOI: 10.1002/prot.26750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/17/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024]
Abstract
Eglin C, a small protein from the medicinal leech, has been long considered a general high-affinity inhibitor of chymotrypsins and elastases. Here, we demonstrate that eglin C inhibits human chymotrypsin-like protease (CTRL) weaker by several orders of magnitude than other chymotrypsins. In order to identify the underlying structural aspects of this unique deviation, we performed comparative molecular dynamics simulations on experimental and AlphaFold model structures of bovine CTRA and human CTRL. Our results indicate that in CTRL, the primary determinants of the observed weak inhibition are amino-acid positions 192 and 218 (using conventional chymotrypsin numbering), which participate in shaping the S1 substrate-binding pocket and thereby affect the stability of the protease-inhibitor complexes.
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Affiliation(s)
- Bálint Zoltán Németh
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
- Institute of Molecular Life Sciences, Protein Bioinformatics Research Group, Hungarian Research Network, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Miklós Sahin-Tóth
- Department of Surgery, University of California Los Angeles, California, Los Angeles, USA
| | - Csaba Magyar
- Institute of Molecular Life Sciences, Protein Bioinformatics Research Group, Hungarian Research Network, Budapest, Hungary
| | - Gábor Pál
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
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Jung S, Woo SY, Park MH, Kim DY, Lee SU, Oh SR, Kim MO, Lee J, Ryu HW. Potent inhibition of human tyrosinase inhibitor by verproside from the whole plant of Pseudolysimachion rotundum var. subintegrum. J Enzyme Inhib Med Chem 2023; 38:2252198. [PMID: 37649388 PMCID: PMC10472861 DOI: 10.1080/14756366.2023.2252198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
Affinity-based ultrafiltration-mass spectrometry coupled with ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry was utilised for the structural identification of direct tyrosinase ligands from a crude Pseudolysimachion rotundum var. subintegrum extract. False positives were recognised by introducing time-dependent inhibition in the control for comparison. The P. rotundum extract contained nine main metabolites in the UPLC-QTOF-MS chromatogram. However, four metabolites were reduced after incubation with tyrosinase, indicating that these metabolites were bound to tyrosinase. The IC50 values of verproside (1) were 31.2 µM and 197.3 µM for mTyr and hTyr, respectively. Verproside showed 5.6-fold higher efficacy than that of its positive control (kojic acid in hTyr). The most potent tyrosinase inhibitor, verproside, features a 3,4-dihydroxybenzoic acid moiety on the iridoid glycoside and inhibits tyrosinase in a time-dependent and competitive manner. Among these three compounds, verproside is bound to the active site pocket with a docking energy of -6.9 kcal/mol and four hydrogen bonding interactions with HIS61 and HIS85.
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Affiliation(s)
- Sunin Jung
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
- Department of CBRN Medicine Research, center for Special Military Medicine, Armed Forces Medical Research Institute, Daejeon, South Korea
| | - So-Yeun Woo
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Mi Hyeon Park
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Doo-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Su Ui Lee
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Sei-Ryang Oh
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Mun-Ock Kim
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Jinhyuk Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyung Won Ryu
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
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Németh BZ, Nagy ZA, Kiss B, Gellén G, Schlosser G, Demcsák A, Geisz A, Hegyi E, Sahin-Tóth M, Pál G. Substrate specificity of human chymotrypsin-like protease (CTRL) characterized by phage display-selected small-protein inhibitors. Pancreatology 2023; 23:742-749. [PMID: 37604733 PMCID: PMC10528761 DOI: 10.1016/j.pan.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Chymotrypsin-like protease (CTRL) is one of the four chymotrypsin isoforms expressed in the human exocrine pancreas. Human genetic and experimental evidence indicate that chymotrypsins B1, B2, and C (CTRB1, CTRB2 and CTRC) are important not only for protein digestion but also for protecting the pancreas against pancreatitis by degrading potentially harmful trypsinogen. CTRL has not been reported to play a similar role, possibly due to its low abundance and/or different substrate specificity. To address this problem, we investigated the specificity of the substrate-binding groove of CTRL by evolving the substrate-like canonical loop of the Schistocerca gregaria proteinase inhibitor 2 (SGPI-2), a small-protein reversible chymotrypsin inhibitor to bind CTRL. We found that phage-associated SGPI-2 variants with strong affinity to CTRL were similar to those evolved previously against CTRB1, CTRB2 or bovine chymotrypsin A (bCTRA), indicating comparable substrate specificity. When tested as recombinant proteins, SGPI-2 variants inhibited CTRL with similar or slightly weaker affinity than bCTRA, confirming that CTRL is a typical chymotrypsin. Interestingly, an SGPI-2 variant selected with a Thr29His mutation in its reactive loop was found to inhibit CTRL strongly, but it was digested rapidly by bCTRA. Finally, CTRL was shown to degrade human anionic trypsinogen, however, at a much slower rate than CTRB2, suggesting that CTRL may not have a significant role in the pancreatic defense mechanisms against inappropriate trypsinogen activation and pancreatitis.
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Affiliation(s)
- Bálint Zoltán Németh
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary
| | - Zoltán Attila Nagy
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary
| | - Gabriella Gellén
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, H-1117, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/A, Budapest, H-1117, Budapest, Hungary
| | - Alexandra Demcsák
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrea Geisz
- Department of Surgery, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA
| | - Eszter Hegyi
- Institute for Translational Medicine, University of Pécs, Medical School, H-7624, Pécs, Hungary
| | - Miklós Sahin-Tóth
- Department of Surgery, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Gábor Pál
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, H-1117, Budapest, Hungary.
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Shah AB, Yoon S, Kim JH, Zhumanova K, Ban YJ, Lee KW, Park KH. Effectiveness of cyclohexyl functionality in ugonins from Helminthostachys zeylanica to PTP1B and α-glucosidase inhibitions. Int J Biol Macromol 2020; 165:1822-1831. [PMID: 33075336 DOI: 10.1016/j.ijbiomac.2020.10.061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022]
Abstract
Ugonins are unique flavonoids with cyclohexyl motif from Helminthostachys zeylanica. Ugonins (1-6) from the target plant displayed significant inhibitions against both PTP1B (IC50s = 0.6-7.3 μM) and α-glucosidase (IC50s = 3.9-32.9 μM), which are crucial enzymes associated with diabetes. A cyclohexyl motif was proved to be the key functionality for PTP1B and α-glucosidase. For example, 1 was 26-fold effective to PTP1B and 15-fold to α-glucosidase than its mother compound, luteolin. This tendency was well elucidated with distinctive differences of binding affinities (KSV) between ugonins and mother compounds to PTP1B enzyme. Inhibitory mechanisms to PTP1B and α-glucosidase were fully characterized to be competitive, non-competitive and mixed type I according to the position of cyclohexyl functionality. In particular, the ugonin J (1) has a cyclohexyl on the B ring was estimated as a reversible, competitive and a slow binding inhibitor with parameters: Kiapp = 0.1234 μM, k3 = 0.5713 μM-1 min-1, and k4 = 0.0705 min-1. In-depth molecular docking experiments disclosed the specific binding sites and residues of competitive inhibitor (1) and non-competitive inhibitor (4) to PTP1B enzymes. As well, all six ugonins (1-6) also inhibited α-glucosidase effectively, in which cyclohexyl motif was also the key functionality of inhibitions.
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Affiliation(s)
- Abdul Bari Shah
- Division of Applied Life Science (BK21 plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sanghwa Yoon
- Division of Life Science, Department of Bio & Medical Big-data (BK21 plus), RINS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeong Ho Kim
- Division of Applied Life Science (BK21 plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Kamila Zhumanova
- Division of Applied Life Science (BK21 plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yeong Jun Ban
- Division of Applied Life Science (BK21 plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Life Science, Department of Bio & Medical Big-data (BK21 plus), RINS, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ki Hun Park
- Division of Applied Life Science (BK21 plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea.
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Zueva IV, Lushchekina SV, Pottie IR, Darvesh S, Masson P. 1-(3- Tert-Butylphenyl)-2,2,2-Trifluoroethanone as a Potent Transition-State Analogue Slow-Binding Inhibitor of Human Acetylcholinesterase: Kinetic, MD and QM/MM Studies. Biomolecules 2020; 10:biom10121608. [PMID: 33260981 PMCID: PMC7760592 DOI: 10.3390/biom10121608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/14/2020] [Accepted: 11/24/2020] [Indexed: 12/11/2022] Open
Abstract
Kinetic studies and molecular modeling of human acetylcholinesterase (AChE) inhibition by a fluorinated acetophenone derivative, 1-(3-tert-butylphenyl)-2,2,2-trifluoroethanone (TFK), were performed. Fast reversible inhibition of AChE by TFK is of competitive type with Ki = 5.15 nM. However, steady state of inhibition is reached slowly. Kinetic analysis showed that TFK is a slow-binding inhibitor (SBI) of type B with Ki* = 0.53 nM. Reversible binding of TFK provides a long residence time, τ = 20 min, on AChE. After binding, TFK acylates the active serine, forming an hemiketal. Then, disruption of hemiketal (deacylation) is slow. AChE recovers full activity in approximately 40 min. Molecular docking and MD simulations depicted the different steps. It was shown that TFK binds first to the peripheral anionic site. Then, subsequent slow induced-fit step enlarged the gorge, allowing tight adjustment into the catalytic active site. Modeling of interactions between TFK and AChE active site by QM/MM showed that the “isomerization” step of enzyme-inhibitor complex leads to a complex similar to substrate tetrahedral intermediate, a so-called “transition state analog”, followed by a labile covalent intermediate. SBIs of AChE show prolonged pharmacological efficacy. Thus, this fluoroalkylketone intended for neuroimaging, could be of interest in palliative therapy of Alzheimer’s disease and protection of central AChE against organophosphorus compounds.
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Affiliation(s)
- Irina V. Zueva
- Arbuzov Institute of Organic and Physical Chemistry, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, Arbuzov str., 8, 420088 Kazan, Russia;
| | - Sofya V. Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin str. 4, 119334 Moscow, Russia;
| | - Ian R. Pottie
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, NS B3M 2J6, Canada; (I.R.P.); (S.D.)
- Department of Chemistry, Saint Mary’s University, Halifax, NS B3M 2J6, Canada
| | - Sultan Darvesh
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, NS B3M 2J6, Canada; (I.R.P.); (S.D.)
- Department of Medicine (Neurology and Geriatric Medicine) & Medical Neuroscience, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya str. 18, 480002 Kazan, Russia
- Correspondence:
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Slater CL, Winogrodzki J, Fraile-Ribot PA, Oliver A, Khajehpour M, Mark BL. Adding Insult to Injury: Mechanistic Basis for How AmpC Mutations Allow Pseudomonas aeruginosa To Accelerate Cephalosporin Hydrolysis and Evade Avibactam. Antimicrob Agents Chemother 2020; 64:e00894-20. [PMID: 32660987 PMCID: PMC7449160 DOI: 10.1128/aac.00894-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/01/2020] [Indexed: 12/27/2022] Open
Abstract
Pseudomonas aeruginosa is a leading cause of nosocomial infections worldwide and notorious for its broad-spectrum resistance to antibiotics. A key mechanism that provides extensive resistance to β-lactam antibiotics is the inducible expression of AmpC β-lactamase. Recently, a number of clinical isolates expressing mutated forms of AmpC have been found to be clinically resistant to the antipseudomonal β-lactam-β-lactamase inhibitor (BLI) combinations ceftolozane-tazobactam and ceftazidime-avibactam. Here, we compare the enzymatic activity of wild-type (WT) AmpC from PAO1 to those of four of these reported AmpC mutants, bearing mutations E247K (a change of E to K at position 247), G183D, T96I, and ΔG229-E247 (a deletion from position 229 to 247), to gain detailed insights into how these mutations allow the circumvention of these clinically vital antibiotic-inhibitor combinations. We found that these mutations exert a 2-fold effect on the catalytic cycle of AmpC. First, they reduce the stability of the enzyme, thereby increasing its flexibility. This appears to increase the rate of deacylation of the enzyme-bound β-lactam, resulting in greater catalytic efficiencies toward ceftolozane and ceftazidime. Second, these mutations reduce the affinity of avibactam for AmpC by increasing the apparent activation barrier of the enzyme acylation step. This does not influence the catalytic turnover of ceftolozane and ceftazidime significantly, as deacylation is the rate-limiting step for the breakdown of these antibiotic substrates. It is remarkable that these mutations enhance the catalytic efficiency of AmpC toward ceftolozane and ceftazidime while simultaneously reducing susceptibility to inhibition by avibactam. Knowledge gained from the molecular analysis of these and other AmpC resistance mutants will, we believe, aid in the design of β-lactams and BLIs with reduced susceptibility to mutational resistance.
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Affiliation(s)
- Cole L Slater
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | | | - Pablo A Fraile-Ribot
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Antonio Oliver
- Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | | | - Brian L Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Canada
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Lushchekina SV, Masson P. Slow-binding inhibitors of acetylcholinesterase of medical interest. Neuropharmacology 2020; 177:108236. [PMID: 32712274 DOI: 10.1016/j.neuropharm.2020.108236] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/11/2020] [Accepted: 07/10/2020] [Indexed: 12/15/2022]
Abstract
Certain ligands slowly bind to acetylcholinesterase. As a result, there is a slow establishment of enzyme-inhibitor equilibrium characterized by a slow onset of inhibition prior reaching steady state. Three mechanisms account for slow-binding inhibition: a) slow binding rate constant kon, b) slow ligand induced-fit following a fast binding step, c) slow conformational selection of an enzyme form. The slow equilibrium may be followed by a chemical step. This later that can be irreversible has been observed with certain alkylating agents and substrate transition state analogs. Slow-binding inhibitors present long residence times on target. This results in prolonged pharmacological or toxicological action. Through several well-known molecules (e.g. huperzine) and new examples (tocopherol, trifluoroacetophenone and a 6-methyluracil alkylammonium derivative), we show that slow-binding inhibitors of acetylcholinesterase are promising drugs for treatment of neurological diseases such as Alzheimer disease and myasthenia gravis. Moreover, they may be of interest for neuroprotection (prophylaxis) against organophosphorus poisoning. This article is part of the special issue entitled 'Acetylcholinesterase Inhibitors: From Bench to Bedside to Battlefield'.
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Affiliation(s)
- Sofya V Lushchekina
- Laboratory of Computer Modeling of Biomolecular Systems and Nanomaterials, Emanuel Institute of Biochemical Physics of RAS, 4 Kosygina St., Moscow, 119334, Russia.
| | - Patrick Masson
- Laboratory of Neuropharmacology, Kazan Federal University, 18 Kremlyovskaya St., Kazan, 420008, Russia.
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Holdgate GA, Meek TD, Grimley RL. Mechanistic enzymology in drug discovery: a fresh perspective. Nat Rev Drug Discov 2017; 17:115-132. [PMID: 29192286 DOI: 10.1038/nrd.2017.219] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Given the therapeutic and commercial success of small-molecule enzyme inhibitors, as exemplified by kinase inhibitors in oncology, a major focus of current drug-discovery and development efforts is on enzyme targets. Understanding the course of an enzyme-catalysed reaction can help to conceptualize different types of inhibitor and to inform the design of screens to identify desired mechanisms. Exploiting this information allows the thorough evaluation of diverse compounds, providing the knowledge required to efficiently optimize leads towards differentiated candidate drugs. This review highlights the rationale for conducting high-quality mechanistic enzymology studies and considers the added value in combining such studies with orthogonal biophysical methods.
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Affiliation(s)
- Geoffrey A Holdgate
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
| | - Thomas D Meek
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, USA
| | - Rachel L Grimley
- Discovery Sciences, IMED Biotech Unit, AstraZeneca, Building 310, Cambridge Science Park, Milton Road, Cambridge, CB4 0WG, UK
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9
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Tan XF, Uddin Z, Park C, Song YH, Son M, Lee KW, Park KH. Competitive protein tyrosine phosphatase 1B (PTP1B) inhibitors, prenylated caged xanthones from Garcinia hanburyi and their inhibitory mechanism. Bioorg Med Chem 2017; 25:2498-2506. [PMID: 28318895 DOI: 10.1016/j.bmc.2017.03.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/01/2017] [Accepted: 03/05/2017] [Indexed: 02/07/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) plays important role in diabetes, obesity and cancer. The methanol extract of the gum resin of Garcinia hanburyi (G. hanburyi) showed potent PTP1B inhibition at 10µg/ml. The active compounds were identified as prenylated caged xanthones (1-9) which inhibited PTP1B in dose-dependent manner. Carboxybutenyl group within caged motif (A ring) was found to play a critical role in enzyme inhibition such as 1-6 (IC50s=0.47-4.69µM), whereas compounds having hydroxymethylbutenyl 7 (IC50=70.25µM) and methylbutenyl 8 (IC50>200µM) showed less activity. The most potent inhibitor, gambogic acid 1 (IC50=0.47µM) showed 30-fold more potency than ursolic acid (IC50=15.5µM), a positive control. In kinetic study, all isolated xanthones behaved as competitive inhibitors which were fully demonstrated with Km, Vmax and Kik/Kiv ratio. It was also proved that inhibitor 1 operated under the enzyme isomerization model having k5=0.0751µM-1S-1, k6=0.0249µM-1S-1 and Kiapp=0.499µM. To develop a pharmacophore model, we explored the binding sites of compound 1 and 7 in PTP1B. These modeling results were in agreement with our findings, which revealed that the inhibitory activities are tightly related to caged motif and prenyl group in A ring.
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Affiliation(s)
- Xue Fei Tan
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Zia Uddin
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Chanin Park
- Division of Applied Life Science (BK21 Plus), PMBBRC, RINS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yeong Hun Song
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Minky Son
- Division of Applied Life Science (BK21 Plus), PMBBRC, RINS, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus), PMBBRC, RINS, Gyeongsang National University, Jinju 52828, Republic of Korea.
| | - Ki Hun Park
- Division of Applied Life Science (BK21 Plus), IALS, Gyeongsang National University, Jinju 52828, Republic of Korea.
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10
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Zhang R, Wong K. High performance enzyme kinetics of turnover, activation and inhibition for translational drug discovery. Expert Opin Drug Discov 2016; 12:17-37. [PMID: 27784173 DOI: 10.1080/17460441.2017.1245721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Enzymes are the macromolecular catalysts of many living processes and represent a sizable proportion of all druggable biological targets. Enzymology has been practiced just over a century during which much progress has been made in both the identification of new enzymes and the development of novel methodologies for enzyme kinetics. Areas covered: This review aims to address several key practical aspects in enzyme kinetics in reference to translational drug discovery research. The authors first define what constitutes a high performance enzyme kinetic assay. The authors then review the best practices for turnover, activation and inhibition kinetics to derive critical parameters guiding drug discovery. Notably, the authors recommend global progress curve analysis of dose/time dependence employing an integrated Michaelis-Menten equation and global curve fitting of dose/dose dependence. Expert opinion: The authors believe that in vivo enzyme and substrate abundance and their dynamics, binding modality, drug binding kinetics and enzyme's position in metabolic networks should be assessed to gauge the translational impact on drug efficacy and safety. Integrating these factors in a systems biology and systems pharmacology model should facilitate translational drug discovery.
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Affiliation(s)
- Rumin Zhang
- a Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc. , Kenilworth , NJ , USA
| | - Kenny Wong
- a Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc. , Kenilworth , NJ , USA
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11
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Tan XF, Kim DW, Song YH, Kim JY, Yuk HJ, Wang Y, Curtis-Long MJ, Park KH. Human neutrophil elastase inhibitory potential of flavonoids from Campylotropis hirtella and their kinetics. J Enzyme Inhib Med Chem 2016; 31:16-22. [PMID: 27558014 DOI: 10.3109/14756366.2015.1118683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Campylotropis hirtella is used as a food supplement in the subtropical region of China. In an intensive hunt for human neutrophil elastase inhibitors, we isolated eight flavonoids from C. hirtella three of which (1-3) emerged to be elastase inhibitors. Geranylated flavonoids (1-3) displayed significant inhibitory activity with IC50s between 8.5 and 30.8 μM. The most striking example was geranylated isofavanone 3 that inhibited elastase significantly (IC50 = 30.8 μM) but its parent compound (dalbergioidin) and isoflavone analog (5) were inactive (IC50 > 200 μM). Compounds (1-3) displayed different kinetic mechanisms (noncompetitive, competitive, and mixed type, respectively) that were dependent upon the parent skeleton. The competitive inhibitor, isoflavan-3-ol-4-one 2 manifested an inhibition of isomerization profile for elastase with kinetic parameters K5 = 0.0386 M-1S-1, K6 = 0.0244 μM-1S-1 and Kiapp = 16.3427 μM. The specific identification of metabolites was accomplished by LC-DAD-ESI/MS that was also used to analyze abundance of active components (1-3) within the plant.
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Affiliation(s)
- Xue Fei Tan
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
| | - Dae Wook Kim
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
| | - Yeong Hun Song
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
| | - Jeong Yoon Kim
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
| | - Heung Joo Yuk
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
| | - Yan Wang
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
| | - Marcus J Curtis-Long
- b Department of Chemistry and Chemical Biology , Cornell University , Ithaca , NY , USA
| | - Ki Hun Park
- a Division of Applied Life Science (BK21 Plus) , IALS, Gyeongsang National University , Jinju , Republic of Korea and
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12
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Slow-binding inhibition of cholinesterases, pharmacological and toxicological relevance. Arch Biochem Biophys 2016; 593:60-8. [DOI: 10.1016/j.abb.2016.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/20/2016] [Accepted: 02/05/2016] [Indexed: 11/20/2022]
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13
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Tan X, Song YH, Park C, Lee KW, Kim JY, Kim DW, Kim KD, Lee KW, Curtis-Long MJ, Park KH. Highly potent tyrosinase inhibitor, neorauflavane from Campylotropis hirtella and inhibitory mechanism with molecular docking. Bioorg Med Chem 2016; 24:153-9. [DOI: 10.1016/j.bmc.2015.11.040] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 11/28/2015] [Accepted: 11/28/2015] [Indexed: 11/26/2022]
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14
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Leroueil PR, DiMaggio S, Leistra AN, Blanchette CD, Orme C, Sinniah K, Orr BG, Banaszak Holl MM. Characterization of Folic Acid and Poly(amidoamine) Dendrimer Interactions with Folate Binding Protein: A Force-Pulling Study. J Phys Chem B 2015; 119:11506-12. [PMID: 26256755 DOI: 10.1021/acs.jpcb.5b05391] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic force microscopy force-pulling experiments have been used to measure the binding forces between folic acid (FA) conjugated poly(amidoamine) (PAMAM) dendrimers and folate binding protein (FBP). The generation 5 (G5) PAMAM conjugates contained an average of 2.7, 4.7, and 7.2 FA per dendrimer. The most probable rupture force was measured to be 83, 201, and 189 pN for G5-FA2.7, G5-FA4.7, and G5-FA7.2, respectively. Folic acid blocking experiments for G5-FA7.2 reduced the frequency of successful binding events and increased the magnitude of the average rupture force to 274 pN. The force data are interpreted as arising from a network of van der Waals and electrostatic interactions that form between FBP and G5 PAMAM dendrimer, resulting in a binding strength far greater than that expected for an interaction between FA and FBP alone.
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Affiliation(s)
| | - Stassi DiMaggio
- Department of Chemistry, Xavier University , New Orleans, Louisiana 70125, United States
| | - Abigail N Leistra
- Department of Chemistry & Biochemistry, Calvin College , Grand Rapids, Michigan 49546, United States
| | - Craig D Blanchette
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Christine Orme
- Physical and Life Sciences Division, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
| | - Kumar Sinniah
- Department of Chemistry & Biochemistry, Calvin College , Grand Rapids, Michigan 49546, United States
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15
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Daniel KB, Sullivan ED, Chen Y, Chan JC, Jennings PA, Fierke CA, Cohen SM. Dual-Mode HDAC Prodrug for Covalent Modification and Subsequent Inhibitor Release. J Med Chem 2015; 58:4812-21. [PMID: 25974739 PMCID: PMC4467547 DOI: 10.1021/acs.jmedchem.5b00539] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Histone deacetylase inhibitors (HDACi)
target abnormal epigenetic
states associated with a variety of pathologies, including cancer.
Here, the development of a prodrug of the canonical broad-spectrum
HDACi suberoylanilide hydroxamic acid (SAHA) is described. Although
hydroxamic acids are utilized universally in the development of metalloenzyme
inhibitors, they are considered to be poor pharmacophores with reduced
activity in vivo. We developed a prodrug of SAHA by appending a promoiety,
sensitive to thiols, to the hydroxamic acid warhead (termed SAHA-TAP).
After incubation of SAHA-TAP with an HDAC, the thiol of a conserved
HDAC cysteine residue becomes covalently tagged with the promoiety,
initiating a cascade reaction that leads to the release of SAHA. Mass
spectrometry and enzyme kinetics experiments validate that the cysteine
residue is covalently appended with the TAP promoiety. SAHA-TAP demonstrates
cytotoxicity activity against various cancer cell lines. This strategy
represents an original prodrug design with a dual mode of action for
HDAC inhibition.
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Affiliation(s)
- Kevin B Daniel
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Yao Chen
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Joshua C Chan
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Patricia A Jennings
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | | | - Seth M Cohen
- †Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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16
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Merzel RL, Chen JJ, Marsh ENG, Holl MMB. Folate binding protein—Outlook for drug delivery applications. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2014.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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17
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van Dongen MA, Silpe JE, Dougherty CA, Kanduluru AK, Choi SK, Orr BG, Low PS, Banaszak Holl MM. Avidity mechanism of dendrimer-folic acid conjugates. Mol Pharm 2014; 11:1696-706. [PMID: 24725205 PMCID: PMC4018099 DOI: 10.1021/mp5000967] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Multivalent conjugation of folic
acid has been employed to target
cells overexpressing folate receptors. Such polymer conjugates have
been previously demonstrated to have high avidity to folate binding
protein. However, the lack of a monovalent folic acid–polymer
material has prevented a full binding analysis of these conjugates,
as multivalent binding mechanisms and polymer-mass mechanisms are
convoluted in samples with broad distributions of folic acid-to-dendrimer
ratios. In this work, the synthesis of a monovalent folic acid–dendrimer
conjugate allowed the elucidation of the mechanism for increased binding
between the folic acid–polymer conjugate and a folate binding
protein surface. The increased avidity is due to a folate-keyed interaction
between the dendrimer and protein surfaces that fits into the general
framework of slow-onset, tight-binding mechanisms of ligand/protein
interactions.
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Affiliation(s)
- Mallory A van Dongen
- Department of Chemistry and ⊥Department of Physics, ‡Program in Macromolecular Sciences and Engineering, and §Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan , Ann Arbor, Michigan 48019, United States
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18
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Lavogina D, Enkvist E, Viht K, Uri A. Long Residence Times Revealed by Aurora A Kinase-Targeting Fluorescent Probes Derived from Inhibitors MLN8237 and VX-689. Chembiochem 2014; 15:443-50. [DOI: 10.1002/cbic.201300613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 11/10/2022]
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19
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Janthawornpong K, Krasutsky S, Chaignon P, Rohmer M, Poulter CD, Seemann M. Inhibition of IspH, a [4Fe-4S]2+ enzyme involved in the biosynthesis of isoprenoids via the methylerythritol phosphate pathway. J Am Chem Soc 2013; 135:1816-22. [PMID: 23316732 DOI: 10.1021/ja309557s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The MEP pathway, which is absent in animals but present in most pathogenic bacteria, in the parasite responsible for malaria and in plant plastids, is a target for the development of antimicrobial drugs. IspH, an oxygen-sensitive [4Fe-4S] enzyme, catalyzes the last step of this pathway and converts (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). A crucial step in the mechanism of this enzyme is the binding of the C4 hydroxyl of HMBPP to the unique fourth iron site in the [4Fe-4S](2+) moiety. Here, we report the synthesis and the kinetic investigations of two new extremely potent inhibitors of E. coli IspH where the OH group of HMBPP is replaced by an amino and a thiol group. (E)-4-Mercapto-3-methylbut-2-en-1-yl diphosphate is a reversible tight-binding inhibitor of IspH with K(i) = 20 ± 2 nM. A detailed kinetic analysis revealed that (E)-4-amino-3-methylbut-2-en-1-yl diphosphate is a reversible slow-binding inhibitor of IspH with K(i) = 54 ± 19 nM. The slow binding behavior of this inhibitor is best described by a one-step mechanism with the slow step consisting of the formation of the enzyme-inhibitor (EI) complex.
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Affiliation(s)
- Karnjapan Janthawornpong
- Université de Strasbourg, CNRS UMR 7177, Institut Le Bel, 4 rue Blaise Pascal, CS 90032, 67081 Strasbourg Cedex, France
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20
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Zhang R, Windsor WT. In vitro kinetic profiling of hepatitis C virus NS3 protease inhibitors by progress curve analysis. Methods Mol Biol 2013; 1030:59-79. [PMID: 23821260 DOI: 10.1007/978-1-62703-484-5_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Kinetic profiling of drug binding to its target reveals important mechanistic parameters including drug-target residence time. In this chapter, we focus on global progress curve analysis as a convenient method for kinetic profiling. Detailed guidelines with pros and cons for various experimental designs and data analysis are provided. Kinetic profiling of Boceprevir and Telaprevir is illustrated.
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Affiliation(s)
- Rumin Zhang
- In Vitro Pharmacology, Merck Research Laboratories, Kenilworth, NJ, USA
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21
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Hall RS, Fedorov AA, Xu C, Fedorov EV, Almo SC, Raushel FM. Three-dimensional structure and catalytic mechanism of cytosine deaminase. Biochemistry 2011; 50:5077-85. [PMID: 21545144 DOI: 10.1021/bi200483k] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytosine deaminase (CDA) from E. coli is a member of the amidohydrolase superfamily. The structure of the zinc-activated enzyme was determined in the presence of phosphonocytosine, a mimic of the tetrahedral reaction intermediate. This compound inhibits the deamination of cytosine with a K(i) of 52 nM. The zinc- and iron-containing enzymes were characterized to determine the effect of the divalent cations on activation of the hydrolytic water. Fe-CDA loses activity at low pH with a kinetic pK(a) of 6.0, and Zn-CDA has a kinetic pK(a) of 7.3. Mutation of Gln-156 decreased the catalytic activity by more than 5 orders of magnitude, supporting its role in substrate binding. Mutation of Glu-217, Asp-313, and His-246 significantly decreased catalytic activity supporting the role of these three residues in activation of the hydrolytic water molecule and facilitation of proton transfer reactions. A library of potential substrates was used to probe the structural determinants responsible for catalytic activity. CDA was able to catalyze the deamination of isocytosine and the hydrolysis of 3-oxauracil. Large inverse solvent isotope effects were obtained on k(cat) and k(cat)/K(m), consistent with the formation of a low-barrier hydrogen bond during the conversion of cytosine to uracil. A chemical mechanism for substrate deamination by CDA was proposed.
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Affiliation(s)
- Richard S Hall
- Department of Chemistry, Texas A&M University, College Station, Texas 77842-3012, United States
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22
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Forcella M, Cardona F, Goti A, Parmeggiani C, Cipolla L, Gregori M, Schirone R, Fusi P, Parenti P. A membrane-bound trehalase from Chironomus riparius larvae: purification and sensitivity to inhibition. Glycobiology 2010; 20:1186-95. [DOI: 10.1093/glycob/cwq087] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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23
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Sikora AL, Wilson DJ, Aldrich CC, Blanchard JS. Kinetic and inhibition studies of dihydroxybenzoate-AMP ligase from Escherichia coli. Biochemistry 2010; 49:3648-57. [PMID: 20359185 DOI: 10.1021/bi100350c] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Inhibition of siderophore biosynthetic pathways in pathogenic bacteria represents a promising strategy for antibacterial drug development. Escherichia coli synthesize and secrete the small molecule iron chelator siderophore, enterobactin, in response to intracellular iron depletion. Here we describe a detailed kinetic analysis of EntE, one of six enzymes in the enterobactin synthetase gene cluster. EntE catalyzes the ATP-dependent condensation of 2,3-dihydroxybenzoic acid (DHB) and phosphopantetheinylated EntB (holo-EntB) to form covalently arylated EntB, a product that is vital for the final assembly of enterobactin. Initial velocity studies show that EntE proceeds via a bi-uni-uni-bi ping-pong kinetic mechanism with a k(cat) equal to 2.8 s(-1) and K(m) values of 2.5, 430, and 2.9 microM for DHB, ATP, and holo-EntB-ArCP, respectively. Inhibition and direct binding experiments suggest that, during the first half-reaction (adenylation), DHB binds first to the free enzyme, followed by ATP and the release of pyrophosphate to form the adenylate intermediate. During the second half-reaction (ligation), phosphopantetheinylated EntB binds to the enzyme followed by the release of products, AMP and arylated EntB. Two hydrolytically stable adenylate analogues, 5'-O-[N-(salicyl)sulfamoyl]adenosine (Sal-AMS) and 5'-O-[N-(2,3-dihydroxybenzoyl)sulfamoyl]adenosine (DHB-AMS), are shown to act as slow-onset tight-binding inhibitors of the enzyme with (app)K(i) values of 0.9 and 3.8 nM, respectively. Direct binding experiments, via isothermal titration calorimetry, reveal low picomolar dissociation constants for both analogues with respect to EntE. The tight binding of Sal-AMS and DHB-AMS to EntE suggests that these compounds may be developed further as effective antibiotics targeted to this enzyme.
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Affiliation(s)
- Alison L Sikora
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
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24
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Gloster TM, Davies GJ. Glycosidase inhibition: assessing mimicry of the transition state. Org Biomol Chem 2010; 8:305-20. [PMID: 20066263 PMCID: PMC2822703 DOI: 10.1039/b915870g] [Citation(s) in RCA: 191] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 09/30/2009] [Indexed: 12/15/2022]
Abstract
Glycoside hydrolases, the enzymes responsible for hydrolysis of the glycosidic bond in di-, oligo- and polysaccharides, and glycoconjugates, are ubiquitous in Nature and fundamental to existence. The extreme stability of the glycosidic bond has meant these enzymes have evolved into highly proficient catalysts, with an estimated 10(17) fold rate enhancement over the uncatalysed reaction. Such rate enhancements mean that enzymes bind the substrate at the transition state with extraordinary affinity; the dissociation constant for the transition state is predicted to be 10(-22) M. Inhibition of glycoside hydrolases has widespread application in the treatment of viral infections, such as influenza and HIV, lysosomal storage disorders, cancer and diabetes. If inhibitors are designed to mimic the transition state, it should be possible to harness some of the transition state affinity, resulting in highly potent and specific drugs. Here we examine a number of glycosidase inhibitors which have been developed over the past half century, either by Nature or synthetically by man. A number of criteria have been proposed to ascertain which of these inhibitors are true transition state mimics, but these features have only be critically investigated in a very few cases.
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Affiliation(s)
- Tracey M. Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. ; ; Fax: +44 1904 328266; Tel: +44 1904 328260
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK. ; ; Fax: +44 1904 328266; Tel: +44 1904 328260
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25
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Yan K, Lok CN, Bierla K, Che CM. Gold(i) complex of N,N′-disubstituted cyclic thiourea with in vitro and in vivo anticancer properties—potent tight-binding inhibition of thioredoxin reductase. Chem Commun (Camb) 2010; 46:7691-3. [DOI: 10.1039/c0cc01058h] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Abbate V, Bassindale AR, Brandstadt KF, Lawson R, Taylor PG. Enzyme mediated silicon–oxygen bond formation; the use of Rhizopus oryzae lipase, lysozyme and phytase under mild conditions. Dalton Trans 2010; 39:9361-8. [DOI: 10.1039/c0dt00151a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Berg AK, Yu Q, Qian SY, Haldar MK, Srivastava DK. Solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:704-13. [PMID: 19922819 DOI: 10.1016/j.bbapap.2009.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Revised: 10/23/2009] [Accepted: 11/09/2009] [Indexed: 10/20/2022]
Abstract
Due to its potential as an antibiotic target, E. coli peptide deformylase (PDF(Ec)) serves as a model enzyme system for inhibitor design. While investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (AMT) served as a slow-binding inhibitor of PDF(Ec) when the above compound was dissolved only in dimethylformamide (DMF), but not in any other solvent, and allowed to age. The time dependent inhibitory potency of the DMF-dissolved AMT was correlated with the broadening of the inhibitor's 295 nm spectral band toward the visible region, concomitant with the increase in the mass of the parent compound by about 2-fold. These data led to the suggestion that DMF facilitated the slow dimerization of AMT (via the formation of a disulfide bond), and that the dimeric form of AMT served as an inhibitor for PDF(Ec). The latter is not caused by the simple oxidation of sulfhydryl groups by oxidizing agents such as H(2)O(2). Newly synthesized dimeric/dithiolated form of AMT ("bis-AMT") exhibited similar spectral and inhibitory features as given by the parent compound when incubated with DMF. The computer graphic modeling data revealed that bis-AMT could be reliably accommodated within the active site pocket of PDF(Ec), and the above enzyme-ligand interaction involves coordination with the enzyme resident Ni(2+) cofactor. The mechanism of the DMF-assisted activation of AMT (generating bis-AMT), the overall microscopic pathway for the slow-binding inhibition of PDF(Ec) by bis-AMT, and the potential of bis-AMT to serve as a new class of antibiotic agent are presented.
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Affiliation(s)
- Alexander K Berg
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, ND 58102, USA
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28
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Munos JW, Pu X, Mansoorabadi SO, Kim HJ, Liu HW. A secondary kinetic isotope effect study of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase-catalyzed reaction: evidence for a retroaldol-aldol rearrangement. J Am Chem Soc 2009; 131:2048-9. [PMID: 19159292 DOI: 10.1021/ja807987h] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
1-Deoxy-d-xylulose 5-phosphate (DXP) reductoisomerase (DXR, also known as methyl-d-erythritol 4-phosphate (MEP) synthase) is a NADPH-dependent enzyme, which catalyzes the conversion of DXP to MEP in the nonmevalonate pathway of isoprene biosynthesis. Two mechanisms have been proposed for the DXR-catalyzed reaction. In the alpha-ketol rearrangement mechanism, the reaction begins with deprotonation of the C-3 hydroxyl group followed by a 1,2-migration to give methylerythrose phosphate, which is then reduced to MEP by NADPH. In the retroaldol/aldol rearrangement mechanism, DXR first cleaves the C3-C4 bond of DXP in a retroaldol manner to generate a three-carbon and a two-carbon phosphate bimolecular intermediate. These two species are then reunited by an aldol reaction to form a new C-C bond, yielding an aldehyde intermediate. Subsequent reduction by NADPH affords MEP. To differentiate these mechanisms, we have prepared [3-(2)H]- and [4-(2)H]-DXP and carried out a competitive secondary kinetic isotope effect (KIE) study of the DXR reaction. The normal 2 degrees KIEs observed for [3-(2)H]- and [4-(2)H]-DXP provide compelling evidence supporting a retroaldol/aldol mechanism for the rearrangement catalyzed by DXR, with the rate-limiting step being cleavage of the C3-C4 bond of DXP.
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Affiliation(s)
- Jeffrey W Munos
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
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29
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Golicnik M, Olguin LF, Feng G, Baxter NJ, Waltho JP, Williams NH, Hollfelder F. Kinetic analysis of beta-phosphoglucomutase and its inhibition by magnesium fluoride. J Am Chem Soc 2009; 131:1575-88. [PMID: 19132841 DOI: 10.1021/ja806421f] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isomerization of beta-glucose-1-phosphate (betaG1P) to beta-glucose-6-phosphate (G6P) catalyzed by beta-phosphoglucomutase (betaPGM) has been examined using steady- and presteady-state kinetic analysis. In the presence of low concentrations of beta-glucose-1,6-bisphosphate (betaG16BP), the reaction proceeds through a Ping Pong Bi Bi mechanism with substrate inhibition (kcat = 65 s(-1), K(betaG1P) = 15 microM, K(betaG16BP) = 0.7 microM, Ki = 122 microM). If alphaG16BP is used as a cofactor, more complex kinetic behavior is observed, but the nonlinear progress curves can be fit to reveal further catalytic parameters (kcat = 74 s(-1), K(betaG1P) = 15 microM, K(betaG16BP) = 0.8 microM, Ki = 122 microM, K(alphaG16BP) = 91 microM for productive binding, K(alphaG16BP) = 21 microM for unproductive binding). These data reveal that variations in the substrate structure affect transition-state affinity (approximately 140,000-fold in terms of rate acceleration) substantially more than ground-state binding (110-fold in terms of binding affinity). When fluoride and magnesium ions are present, time-dependent inhibition of the betaPGM is observed. The concentration dependence of the parameters obtained from fitting these progress curves shows that a betaG1P x MgF3(-) x betaPGM inhibitory complex is formed under the reaction conditions. The overall stability constant for this complex is approximately 2 x 10(-16) M(5) and suggests an affinity of the MgF3(-) moiety to this transition-state analogue (TSA) of < or = 70 nM. The detailed kinetic analysis shows how a special type of TSA that does not exist in solution is assembled in the active site of an enzyme. Further experiments show that under the conditions of previous structural studies, phosphorylated glucose only persists when bound to the enzyme as the TSA. The preference for TSA formation when fluoride is present, and the hydrolysis of substrates when it is not, rules out the formation of a stable pentavalent phosphorane intermediate in the active site of betaPGM.
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Affiliation(s)
- Marko Golicnik
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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30
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Ryu YB, Ha TJ, Curtis-Long MJ, Ryu HW, Gal SW, Park KH. Inhibitory effects on mushroom tyrosinase by flavones from the stem barks of Morus lhou (S.) Koidz. J Enzyme Inhib Med Chem 2009; 23:922-30. [PMID: 18608767 DOI: 10.1080/14756360701810207] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Five flavones displaying tyrosinase inhibitory activity were isolated from the stem barks of Morus lhou (S.) Koidz., a cultivated edible plant. The isolated compounds were identified as mormin (1), cyclomorusin (2), morusin (3), kuwanon C (4), and norartocarpetin (5). Mormin (1) was characterized as a new flavone possesing a 3-hydroxymethyl-2-butenyl at C-3. The inhibitory potencies of these flavonoids toward monophenolase activity of mushroom tyrosinase were investigated. The IC50 values of compounds 1-5 for monophenolase activity were determined to be 0.088, 0.092, 0.250, 0.135 mM, and 1.2 microM, respectively. Mormin (1), cyclomorusin (2), kuwanon C (4) and norartocarpetin (5) exhibited competitive inhibition characteristics. Interestingly norartocarpetin (5) showed a time-dependent inhibition against oxidation of L-tyrosine: it also operated under the enzyme isomerization model (k5 = 0.8424 min(-1), k6 = 0.0576 min(-1), K(app)(i) = 1.354 microM).
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Affiliation(s)
- Y B Ryu
- Division of Applied Life Science (BK21 program), EB-NCRC, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 660-701, Korea
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31
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Baek YS, Ryu YB, Curtis-Long MJ, Ha TJ, Rengasamy R, Yang MS, Park KH. Tyrosinase inhibitory effects of 1,3-diphenylpropanes from Broussonetia kazinoki. Bioorg Med Chem 2009; 17:35-41. [DOI: 10.1016/j.bmc.2008.11.022] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 11/08/2008] [Accepted: 11/11/2008] [Indexed: 11/26/2022]
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Garrido-Del Solo C, Yago JM, García-Moreno M, Havsteen BH, García-Cánovas F, Varón R. The influence of product instability on slow-binding inhibition. J Enzyme Inhib Med Chem 2008; 20:309-16. [PMID: 16206824 DOI: 10.1080/14756360500096651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
We present a kinetic study of an enzyme reaction that takes place with slow-binding inhibition where the immediate product undergoes a spontaneous or induced process of decomposition. A kinetic study of an enzyme process, in which a slow-binding inhibition process and a decomposition of the immediate product of the reaction take place simultaneously is performed. The corresponding explicit concentration-time equations were obtained. Using the analytical solutions obtained, which were tested numerically, we suggest a procedure that allows the discrimination between the particular cases considered and the evaluation of the principal kinetic parameters of the reaction.
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Affiliation(s)
- C Garrido-Del Solo
- Departamento de Química-Física, Escuela Politécnica Superior, Universidad de Castilla-La Mancha Avda, España, s/n Campus Universitario, E-02071 Albacete, Spain
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33
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Preclinical characteristics of the hepatitis C virus NS3/4A protease inhibitor ITMN-191 (R7227). Antimicrob Agents Chemother 2008; 52:4432-41. [PMID: 18824605 DOI: 10.1128/aac.00699-08] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Future treatments for chronic hepatitis C virus (HCV) infection are likely to include agents that target viral components directly. Here, the preclinical characteristics of ITMN-191, a peptidomimetic inhibitor of the NS3/4A protease of HCV, are described. ITMN-191 inhibited a reference genotype 1 NS3/4A protein in a time-dependent fashion, a hallmark of an inhibitor with a two-step binding mechanism and a low dissociation rate. Under preequilibrium conditions, 290 pM ITMN-191 half-maximally inhibited the reference NS3/4A protease, but a 35,000-fold-higher concentration did not appreciably inhibit a panel of 79 proteases, ion channels, transporters, and cell surface receptors. Subnanomolar biochemical potency was maintained against NS3/4A derived from HCV genotypes 4, 5, and 6, while single-digit nanomolar potency was observed against NS3/4A from genotypes 2b and 3a. Dilution of a preformed enzyme inhibitor complex indicated ITMN-191 remained bound to and inhibited NS3/4A for more than 5 h after its initial association. In cell-based potency assays, half-maximal reduction of genotype 1b HCV replicon RNA was afforded by 1.8 nM; 45 nM eliminated the HCV replicon from cells. Peginterferon alfa-2a displayed a significant degree of antiviral synergy with ITMN-191 and reduced the concentration of ITMN-191 required for HCV replicon elimination. A 30-mg/kg of body weight oral dose administered to rats or monkeys yielded liver concentrations 12 h after dosing that exceeded the ITMN-191 concentration required to eliminate replicon RNA from cells. These preclinical characteristics compare favorably to those of other inhibitors of NS3/4A in clinical development and therefore support the clinical investigation of ITMN-191 for the treatment of chronic hepatitis C.
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34
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Kuzmič P. A steady state mathematical model for stepwise “slow-binding” reversible enzyme inhibition. Anal Biochem 2008; 380:5-12. [DOI: 10.1016/j.ab.2007.11.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Revised: 11/17/2007] [Accepted: 11/17/2007] [Indexed: 10/22/2022]
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35
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Affiliation(s)
- Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO 63110, USA.
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36
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Gloster TM, Meloncelli P, Stick RV, Zechel D, Vasella A, Davies GJ. Glycosidase Inhibition: An Assessment of the Binding of 18 Putative Transition-State Mimics. J Am Chem Soc 2007; 129:2345-54. [PMID: 17279749 DOI: 10.1021/ja066961g] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The inhibition of glycoside hydrolases, through transition-state mimicry, is important both as a probe of enzyme mechanism and in the continuing quest for new drugs, notably in the treatment of cancer, HIV, influenza, and diabetes. The high affinity with which these enzymes are known to bind the transition state provides a framework upon which to design potent inhibitors. Recent work [for example, Bülow, A. et al. J. Am. Chem. Soc. 2000, 122, 8567-8568; Zechel, D. L. et al. J. Am. Chem. Soc. 2003, 125, 14313-14323] has revealed quite confusing and counter-intuitive patterns of inhibition for a number of glycosidase inhibitors. Here we describe a synergistic approach for analysis of inhibitors with a single enzyme 'model system', the Thermotoga maritima family 1 beta-glucosidase, TmGH1. The pH dependence of enzyme activity and inhibition has been determined, structures of inhibitor complexes have been solved by X-ray crystallography, with data up to 1.65 A resolution, and isothermal titration calorimetry was used to establish the thermodynamic signature. This has allowed the characterization of 18 compounds, all putative transition-state mimics, in order to build an 'inhibition profile' that provides an insight into what governs binding. In contrast to our preconceptions, there is little correlation of inhibitor chemistry with the calorimetric dissection of thermodynamics. The ensemble of inhibitors shows strong enthalpy-entropy compensation, and the random distribution of similar inhibitors across the plot of DeltaH degrees a vs TDeltaS degrees a likely reflects the enormous contribution of solvation and desolvation effects on ligand binding.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
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37
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Kumar A, Rao M. Biochemical characterization of a low molecular weight aspartic protease inhibitor from thermo-tolerant Bacillus licheniformis: Kinetic interactions with Pepsin. Biochim Biophys Acta Gen Subj 2006; 1760:1845-56. [PMID: 16982155 DOI: 10.1016/j.bbagen.2006.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 08/04/2006] [Accepted: 08/07/2006] [Indexed: 11/17/2022]
Abstract
The present article reports a low molecular weight aspartic protease inhibitor, API, from a newly isolated thermo-tolerant Bacillus licheniformis. The inhibitor was purified to homogeneity as shown by rp-HPLC and SDS-PAGE. API is found to be stable over a broad pH range of 2-11 and at temperature 90 degrees C for 2 1/2h. It has a Mr (relative molecular mass) of 1363 Da as shown by MALDI-TOF spectra and 1358 Da as analyzed by SDS-PAGE . The amino acid analysis of the peptide shows the presence of 12 amino acid residues having Mr of 1425 Da. The secondary structure of API as analyzed by the CD spectra showed 7% alpha-helix, 49% beta-sheet and 44% aperiodic structure. The Kinetic studies of Pepsin-API interactions reveal that API is a slow-tight binding competitive inhibitor with the IC(50) and Ki values 4.0 nM and (3.83 nM-5.31 nM) respectively. The overall inhibition constant Ki* value is 0.107+/-0.015 nM. The progress curves are time-dependent and consistent with slow-tight binding inhibition: E+I -->/<-- (k(4), k(5)) EI -->/<-- (k(6), k(7)) EI*. Rate constant k(6)=2.73+/-0.32 s(-1) reveals a fast isomerization of enzyme-inhibitor complex and very slow dissociation as proved by k(7)=0.068+/-0.009 s(-1). The Rate constants from the intrinsic tryptophanyl fluorescence data is in agreement with those obtained from the kinetic analysis; therefore, the induced conformational changes were correlated to the isomerization of EI to EI*.
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Affiliation(s)
- Ajit Kumar
- Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
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38
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Sharpley MS, Hirst J. The inhibition of mitochondrial complex I (NADH:ubiquinone oxidoreductase) by Zn2+. J Biol Chem 2006; 281:34803-9. [PMID: 16980308 DOI: 10.1074/jbc.m607389200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a highly complicated, membrane-bound enzyme. It is central to energy transduction, an important source of cellular reactive oxygen species, and its dysfunction is implicated in neurodegenerative and muscular diseases and in aging. Here, we describe the effects of Zn2+ on complex I to define whether complex I may contribute to mediating the pathological effects of zinc in states such as ischemia and to determine how Zn2+ can be used to probe the mechanism of complex I. Zn2+ inhibits complex I more strongly than Mg2+, Ca2+, Ba2+, and Mn2+ to Cu2+ or Cd2+. It does not inhibit NADH oxidation or intramolecular electron transfer, so it probably inhibits either proton transfer to bound quinone or proton translocation. Thus, zinc represents a new class of complex I inhibitor clearly distinct from the many ubiquinone site inhibitors. No evidence for increased superoxide production by zinc-inhibited complex I was detected. Zinc binding to complex I is mechanistically complicated. During catalysis, zinc binds slowly and progressively, but it binds rapidly and tightly to the resting state(s) of the enzyme. Reactivation of the inhibited enzyme upon the addition of EDTA is slow, and inhibition is only partially reversible. The IC50 value for the Zn2+ inhibition of complex I is high (10-50 microm, depending on the enzyme state); therefore, complex I is unlikely to be a major site for zinc inhibition of the electron transport chain. However, the slow response of complex I to a change in Zn2+ concentration may enhance any physiological consequences.
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Affiliation(s)
- Mark S Sharpley
- Medical Research Council (MRC) Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 2XY, United Kingdom
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39
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de Carvalho LPS, Argyrou A, Blanchard JS. Slow-onset feedback inhibition: inhibition of Mycobacterium tuberculosis alpha-isopropylmalate synthase by L-leucine. J Am Chem Soc 2005; 127:10004-5. [PMID: 16011356 DOI: 10.1021/ja052513h] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This report describes the first demonstration of slow-onset feedback inhibition of an enzyme that catalyzes the first committed step in a biosynthetic pathway. alpha-Isopropylmalate synthase (IPMS) catalyzes the first committed step of the l-leucine biosynthetic pathway and is feedback-inhibited by l-leucine. Initial velocity experiments on the Mycobacterium tuberculosis IPMS indicate that inhibition by l-leucine is linearly noncompetitive versus alpha-ketoisovalerate. Time-courses displayed a burst of product formation followed by a linear steady-state rate when reactions were initiated by the addition of enzyme. The burst rate showed a hyperbolic dependence on the concentration of l-leucine indicating that inhibition proceeds in two steps, an initial rapid binding step followed by slow isomerization to a more tightly bound complex.
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Affiliation(s)
- Luiz P S de Carvalho
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York, 10461, USA
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40
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Kuntz L, Tritsch D, Grosdemange-Billiard C, Hemmerlin A, Willem A, Bach T, Rohmer M. Isoprenoid biosynthesis as a target for antibacterial and antiparasitic drugs: phosphonohydroxamic acids as inhibitors of deoxyxylulose phosphate reducto-isomerase. Biochem J 2005; 386:127-35. [PMID: 15473867 PMCID: PMC1134774 DOI: 10.1042/bj20041378] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Isoprenoid biosynthesis via the methylerythritol phosphate pathway is a target against pathogenic bacteria and the malaria parasite Plasmodium falciparum. 4-(Hydroxyamino)-4-oxobutylphosphonic acid and 4-[hydroxy(methyl)amino]-4-oxobutyl phosphonic acid, two novel inhibitors of DXR (1-deoxy-D-xylulose 5-phosphate reducto-isomerase), the second enzyme of the pathway, have been synthesized and compared with fosmidomycin, the best known inhibitor of this enzyme. The latter phosphonohydroxamic acid showed a high inhibitory activity towards DXR, much like fosmidomycin, as well as significant antibacterial activity against Escherichia coli in tests on Petri dishes.
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Affiliation(s)
- Lionel Kuntz
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Denis Tritsch
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | | | - Andréa Hemmerlin
- †CNRS-UPR 2357, Institut de Biologie Moléculaire des Plantes, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Audrey Willem
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
| | - Thomas J. Bach
- †CNRS-UPR 2357, Institut de Biologie Moléculaire des Plantes, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Michel Rohmer
- *Université Louis Pasteur/CNRS-UMR 7123, Institut Le Bel, 4 rue Blaise Pascal, 67070 Strasbourg Cedex, France
- To whom correspondence should be addressed (email )
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41
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Van Aller GS, Nandigama R, Petit CM, DeWolf WE, Quinn CJ, Aubart KM, Zalacain M, Christensen SB, Copeland RA, Lai Z. Mechanism of Time-Dependent Inhibition of Polypeptide Deformylase by Actinonin. Biochemistry 2004; 44:253-60. [PMID: 15628866 DOI: 10.1021/bi048632b] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polypeptide deformylase (PDF) is an essential bacterial metalloenzyme responsible for the removal of the N-formyl group from the N-terminal methionine of nascent polypeptides. Inhibition of bacterial PDF enzymes by actinonin, a naturally occurring antibacterial agent, has been characterized using steady-state and transient kinetic methods. Slow binding of actinonin to these enzymes is observed under steady-state conditions. Progress curve analysis is consistent with a two-step binding mechanism, in which tightening of the initial encounter complex (EI) results in a final complex (EI*) with an extremely slow, but observable, off-rate (t(1/2) for inhibitor dissociation >or=0.77 days). Stopped-flow measurement of PDF fluorescence confirms formation of EI and provides a direct measurement of the association rate. Rapid dilution studies establish that the potency of actinonin is enhanced by more than 2000-fold upon tightening of EI to form EI*, from K(i) = 530 nM (EI) to Ki*<or= 0.23 nM (EI*). In sharp contrast, the previously reported small molecule PDF inhibitor, SB-543668, is a competitive, readily reversible inhibitor (t(1/2) for dissociation = 2.8 s). In addition, we demonstrate that BB-3497 is also a time-dependent inhibitor of PDF with an extremely slow off-rate. The two-step inhibition model detailed herein for the inhibition of Staphylococcus aureus PDF by actinonin and BB-3497 is consistent with a recent report on the time-dependent inhibition of Escherichia coli PDF by a macrocyclic peptidomimetic inhibitor [Ngugen, K. T., et al. (2004) Bioorg. Chem. 32, 178-191]. This study substantially extends our understanding of PDF inhibition and may facilitate the development of novel antibiotics.
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Affiliation(s)
- Glenn S Van Aller
- Enzymology and Mechanistic Pharmacology, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA
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42
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Vathipadiekal V, Rao M. Inhibition of 1,4-beta-D-xylan xylanohydrolase by the specific aspartic protease inhibitor pepstatin: probing the two-step inhibition mechanism. J Biol Chem 2004; 279:47024-33. [PMID: 15317808 DOI: 10.1074/jbc.m407866200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This is the first report that describes the inhibition mechanism of xylanase from Thermomonospora sp. by pepstatin A, a specific inhibitor toward aspartic proteases. The kinetic analysis revealed competitive inhibition of xylanase by pepstatin A with an IC50 value 3.6 +/- 0.5 microm. The progress curves were time-depended, consistent with a two-step slow tight binding inhibition. The inhibition followed a rapid equilibrium step to form a reversible enzyme-inhibitor complex (EI), which isomerizes to the second enzyme-inhibitor complex (EI*), which dissociated at a very slow rate. The rate constants determined for the isomerization of EI to EI* and the dissociation of EI* were 15 +/- 1 x 10(-5) and 3.0 +/- 1 x 10(-8) s(-1), respectively. The Ki value for the formation of EI complex was 1.5 +/- 0.5 microm, whereas the overall inhibition constant Ki* was 28.0 +/- 1 nm. The conformational changes induced in Xyl I by pepstatin A were monitored by fluorescence spectroscopy, and the rate constants derived were in agreement with the kinetic data. Thus, the conformational alterations were correlated to the isomerization of EI to EI*. Pepstatin A binds to the active site of the enzyme and disturbs the native interaction between the histidine and lysine, as demonstrated by the abolished isoindole fluorescence of o-phthalaldehyde-labeled xylanase. Our results revealed that the inactivation of xylanase is due to the interference in the electronic microenvironment and disruption of the hydrogen-bonding network between the essential histidine and other residues involved in catalysis, and a model depicting the probable interaction between pepstatin A with xylanase has been proposed.
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Affiliation(s)
- Vinod Vathipadiekal
- Division of Biochemical Sciences, National Chemical Laboratory, Pune 411-008, India
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43
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Kapoor M, Reddy C, Krishnasastry M, Surolia N, Surolia A. Slow-tight-binding inhibition of enoyl-acyl carrier protein reductase from Plasmodium falciparum by triclosan. Biochem J 2004; 381:719-24. [PMID: 15086316 PMCID: PMC1133881 DOI: 10.1042/bj20031821] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2003] [Revised: 03/05/2004] [Accepted: 04/16/2004] [Indexed: 11/17/2022]
Abstract
Triclosan is a potent inhibitor of FabI (enoyl-ACP reductase, where ACP stands for acyl carrier protein), which catalyses the last step in a sequence of four reactions that is repeated many times with each elongation step in the type II fatty acid biosynthesis pathway. The malarial parasite Plasmodium falciparum also harbours the genes and is capable of synthesizing fatty acids by utilizing the enzymes of type II FAS (fatty acid synthase). The basic differences in the enzymes of type I FAS, present in humans, and type II FAS, present in Plasmodium, make the enzymes of this pathway a good target for antimalarials. The steady-state kinetics revealed time-dependent inhibition of FabI by triclosan, demonstrating that triclosan is a slow-tight-binding inhibitor of FabI. The inhibition followed a rapid equilibrium step to form a reversible enzyme-inhibitor complex (EI) that isomerizes to a second enzyme-inhibitor complex (EI*), which dissociates at a very slow rate. The rate constants for the isomerization of EI to EI* and the dissociation of EI* were 5.49x10(-2) and 1x10(-4) s(-1) respectively. The K(i) value for the formation of the EI complex was 53 nM and the overall inhibition constant K(i)* was 96 pM. The results match well with the rate constants derived independently from fluorescence analysis of the interaction of FabI and triclosan, as well as those obtained by surface plasmon resonance studies [Kapoor, Mukhi, N. Surolia, Sugunda and A. Surolia (2004) Biochem. J. 381, 725-733].
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Affiliation(s)
- Mili Kapoor
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | | | | | - Namita Surolia
- ‡Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Avadhesha Surolia
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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44
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Goliĉnik M, Stojan J. Slow-binding inhibition: A theoretical and practical course for students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2004; 32:228-235. [PMID: 21706729 DOI: 10.1002/bmb.2004.494032040358] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Tyrosinase (EC 1.14.18.1) catalyzes the oxidation of L-3,4-dihydroxyphenylalanine (L-DOPA) to 2,3,5,6-tetrahydro-5,6-dioxo-1H-indole-2-carboxylate (dopachrome), according to the classical Michaelis-Menten kinetic mechanism. The enzyme is strongly but slowly inhibited by α-amino-β-[N-(3-hydroxy-4-pyridone)] propionic acid (L-mimosine), a toxic plant amino acid. Easily available reagents and simple spectrophotometric detection of the product make the experimental characterization and kinetic analysis of tyrosinase action convenient and interesting for teaching purposes. In the present article, we present a theoretical and practical guide to the kinetic analysis of slow-binding inhibition. The effect of L-mimosine on tyrosinase is established by progress curve measurements, carried out on a conventional spectrophotometer equipped with a rapid kinetic accessory. In the analysis, we recommend a classical linearization approach but we also took advantage of a more reliable nonlinear regression method to avoid subjective bias. A multistep procedure starts by careful inspection of the curves to discriminate between candidate mechanisms. Next, the evaluation of initial and steady-state velocities provides information on the enzyme catalytic and Michaelis-Menten constants, as well as the corresponding inhibition constants. Subsequently, an appropriate mathematical derivation enables estimation of the isomerization rate constants characteristic for a slow-binding inhibitor. To conclude, we suggest simultaneous multivariable regression, using all the progress curve data, to cross-check the proposed reaction mechanism and evaluated kinetic constants.
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Affiliation(s)
- Marko Goliĉnik
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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45
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Ehmann DE, Demeritt JE, Hull KG, Fisher SL. Biochemical characterization of an inhibitor of Escherichia coli UDP-N-acetylmuramyl-l-alanine ligase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1698:167-74. [PMID: 15134649 DOI: 10.1016/j.bbapap.2003.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Accepted: 11/07/2003] [Indexed: 11/24/2022]
Abstract
UDP-N-acetylmuramyl-l-alanine ligase (MurC) is an essential bacterial enzyme involved in peptidoglycan biosynthesis and a target for the discovery of novel antibacterial agents. As a result of a high-throughput screen (HTS) against a chemical library for inhibitors of MurC, a series of benzofuran acyl-sulfonamides was identified as potential leads. One of these compounds, Compound A, inhibited Escherichia coli MurC with an IC(50) of 2.3 microM. Compound A exhibited time-dependent, partially reversible inhibition of E. coli MurC. Kinetic studies revealed a mode of inhibition consistent with the compound acting competitively with the MurC substrates ATP and UDP-N-acetyl-muramic acid (UNAM) with a K(i) of 4.5 microM against ATP and 6.3 microM against UNAM. Fluorescence binding experiments yielded a K(d) of 3.1 microM for the compound binding to MurC. Compound A also exhibited high-affinity binding to bovine serum albumin (BSA) as evidenced by a severe reduction in MurC inhibition upon addition of BSA. This finding is consistent with the high lipophilicity of the compound. Advancement of this compound series for further drug development will require reduction of albumin binding.
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Affiliation(s)
- David E Ehmann
- Department of Biochemistry, Infection Discovery, Cancer and Infection Research Area, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA.
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46
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Pandhare J, Dash C, Rao M, Deshpande V. Slow Tight Binding Inhibition of Proteinase K by a Proteinaceous Inhibitor. J Biol Chem 2003; 278:48735-44. [PMID: 14507912 DOI: 10.1074/jbc.m308976200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The kinetics of slow onset inhibition of Proteinase K by a proteinaceous alkaline protease inhibitor (API) from a Streptomyces sp. is presented. The kinetic analysis revealed competitive inhibition of Proteinase K by API with an IC50 value 5.5 +/- 0.5 x 10-5 m. The progress curves were time-dependent, consistent with a two-step slow tight binding inhibition. The first step involved a rapid equilibrium for formation of reversible enzyme-inhibitor complex (EI) with a Ki value 5.2 +/- 0.6 x 10-6 m. The EI complex isomerized to a stable complex (EI*) in the second step because of inhibitor-induced conformational changes, with a rate constant k5 (9.2 +/- 1 x 10-3 s-1). The rate of dissociation of EI* (k6) was slower (4.5 +/- 0.5 x 10-5 s-1) indicating the tight binding nature of the inhibitor. The overall inhibition constant Ki* for two-step inhibition of Proteinase K by API was 2.5 +/- 0.3 x 10-7 m. Time-dependent dissociation of EI* revealed that the complex failed to dissociate after a time point and formed a conformationally altered, irreversible complex EI**. These conformational states of enzyme-inhibitor complexes were characterized by fluorescence spectroscopy. Tryptophanyl fluorescence of Proteinase K was quenched as a function of API concentration without any shift in the emission maximum indicating a subtle conformational change in the enzyme, which is correlated to the isomerization of EI to EI*. Time-dependent shift in the emission maxima of EI* revealed the induction of gross conformational changes, which can be correlated to the irreversible conformationally locked EI** complex. API binds to the active site of the enzyme as demonstrated by the abolished fluorescence of 5-iodoacetamidofluorescein-labeled Proteinase K. The chemoaffinity labeling experiments lead us to hypothesize that the inactivation of Proteinase K is because of the interference in the electronic microenvironment and disruption of the hydrogen-bonding network between the catalytic triad and other residues involved in catalysis.
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Affiliation(s)
- Jui Pandhare
- Division of Biochemical Sciences, National Chemical Laboratory, Pune-411 008, India
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47
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Mans BJ, Louw AI, Neitz AWH. Amino acid sequence and structure modeling of savignin, a thrombin inhibitor from the tick, Ornithodoros savignyi. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2002; 32:821-828. [PMID: 12044499 DOI: 10.1016/s0965-1748(01)00169-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The full-length gene of savignin, a potent thrombin (E.C. 3.4.21.5) inhibitor from the tick Ornithodoros savignyi has been cloned and sequenced. Both 5' and 3' UTR's, a signal peptide from the translated amino acid sequence and an unusual poly-adenylation signal (AATACA) has been identified. The translated protein sequence shows high identity (63%) with ornithodorin, the thrombin inhibitor from the tick, Ornithodoros moubata. Molecular modeling using the structure of ornithodorin as reference gave a structure with an RMSD of 0.25 A for the full-length protein, 0.11 A for the N-terminal BPTI-like domain and 0.11 A for the C-terminal BPTI-like domain, indicating that maximum deviation occurs in the mobile bridge (0.18 A) between the two domains. Docking of savignin to thrombin shows that the interaction is similar to the ornithodorin-thrombin complex. The N-terminal amino acid residues of savignin bind inside the active site cleft, while the C-terminal domain of savignin has a net negative electrostatic potential and interacts with the basic fibrinogen recognition exosite of thrombin through hydrogen bonds and hydrophobic interactions. These results correlate with kinetic data obtained, which showed that savignin is a competitive, slow, tight-binding inhibitor that requires thrombin's fibrinogen-binding exo-site for optimal inhibition.
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Affiliation(s)
- B J Mans
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa
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Golicnik M, Stojan J. Multi-step analysis as a tool for kinetic parameter estimation and mechanism discrimination in the reaction between tight-binding fasciculin 2 and electric eel acetylcholinesterase. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1597:164-72. [PMID: 12009416 DOI: 10.1016/s0167-4838(02)00285-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The mechanism of action of a potent peptidic inhibitor fasciculin 2 (Fas2) on electric eel acetylcholinesterase (eleelAChE) has been examined in a three-level analysis. Classical steps included equilibration experiments for the evaluation of high affinity binding constant and the existence of residual hydrolytic activity in a solution of completely Fas2 saturated enzyme. The two rate constants for the association (k(on)) and the dissociation (k(off)) of Fas2 with free enzyme were determined by the time course of residual enzyme activity measurements. In the third step, with a nonclassical progress curve analysis, we found that the Fas2-enzyme complex exhibited hydrolytic activity in a butyrylcholinesterase-like kinetics. The switch appears to be a consequence of steric obstruction, but also the consequence of subtle rapid conformational changes around catalytic site, upon slow single-step binding of large Fas2 molecule at the peripheral site. An unusual unilateral effect of bound Fas2 is reflected by acylation-independent association and dissociation rates and might indeed be due to inability of small acylation agent to influence the binding of a large opponent.
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Affiliation(s)
- Marko Golicnik
- Institute of Biochemistry, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
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Dash C, Vathipadiekal V, George SP, Rao M. Slow-tight binding inhibition of xylanase by an aspartic protease inhibitor: kinetic parameters and conformational changes that determine the affinity and selectivity of the bifunctional nature of the inhibitor. J Biol Chem 2002; 277:17978-86. [PMID: 11844793 DOI: 10.1074/jbc.m111250200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The first report of slow-tight inhibition of xylanase by a bifunctional inhibitor alkalo-thermophilic Bacillus inhibitor (ATBI), from an extremophilic Bacillus sp. is described. ATBI inhibits aspartic protease (Dash, C., and Rao, M. (2001) J. Biol. Chem., 276, 2487-2493) and xylanase (Xyl I) from a Thermomonospora sp. The steady-state kinetics revealed time-dependent competitive inhibition of Xyl I by ATBI, consistent with two-step inhibition mechanism. The inhibition followed a rapid equilibrium step to form a reversible enzyme-inhibitor complex (EI), which isomerizes to the second enzyme-inhibitor complex (EI*), which dissociated at a very slow rate. The rate constants determined for the isomerization of EI to EI*, and the dissociation of EI* were 13 +/- 1 x 10(-6) s(-1) and 5 +/- 0.5 x 10(-8) s(-1), respectively. The K(i) value for the formation of EI complex was 2.5 +/- 0.5 microm, whereas the overall inhibition constant K(i)* was 7 +/- 1 nm. The conformational changes induced in Xyl I by ATBI were monitored by fluorescence spectroscopy and the rate constants derived were in agreement with the kinetic data. Thus, the conformational alterations were correlated to the isomerization of EI to EI*. ATBI binds to the active site of the enzyme and disturbs the native interaction between the histidine and lysine, as demonstrated by the abolished isoindole fluorescence of o-phthalaldehyde (OPTA)-labeled Xyl I. Our results revealed that the inactivation of Xyl I is due to the disruption of the hydrogen-bonding network between the essential histidine and other residues involved in catalysis and a model depicting the probable interaction between ATBI or OPTA with Xyl I has been proposed.
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Affiliation(s)
- Chandravanu Dash
- Division of Biochemical Sciences, National Chemical Laboratory, Pune, Maharashtra 411 008, India
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Dash C, Phadtare S, Deshpande V, Rao M. Structural and mechanistic insight into the inhibition of aspartic proteases by a slow-tight binding inhibitor from an extremophilic Bacillus sp.: correlation of the kinetic parameters with the inhibitor induced conformational changes. Biochemistry 2001; 40:11525-32. [PMID: 11560501 DOI: 10.1021/bi010594y] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present here the first report of a hydrophilic peptidic inhibitor, ATBI, from an extremophilic Bacillus sp. exhibiting a two-step inhibition mechanism against the aspartic proteases, pepsin and F-prot from Aspergillus saitoi. Kinetic analysis shows that these proteases are competitively inhibited by ATBI. The progress curves are time-dependent and consistent with slow-tight binding inhibition: E + I right arrow over left arrow (k(3), k(4)) EI right arrow over left arrow (k(5), k(6)) EI. The K(i) values for the first reversible complex (EI) of ATBI with pepsin and F-prot were (17 +/- 0.5) x 10(-9) M and (3.2 +/- 0.6) x 10(-6) M, whereas the overall inhibition constant K(i) values were (55 +/- 0.5) x 10(-12) M and (5.2 +/- 0.6) x 10(-8) M, respectively. The rate constant k(5) revealed a faster isomerization of EI for F-prot [(2.3 +/- 0.4) x 10(-3) s(-1)] than pepsin [(7.7 +/- 0.3) x 10(-4) s(-1)]. However, ATBI dissociated from the tight enzyme-inhibitor complex (EI) of F-prot faster [(3.8 +/- 0.5) x 10(-5) s(-1)] than pepsin [(2.5 +/- 0.4) x 10(-6) s(-1)]. Comparative analysis of the kinetic parameters with pepstatin, the known inhibitor of pepsin, revealed a higher value of k(5)/k(6) for ATBI. The binding of the inhibitor with the aspartic proteases and the subsequent conformational changes induced were monitored by exploiting the intrinsic tryptophanyl fluorescence. The rate constants derived from the fluorescence data were in agreement with those obtained from the kinetic analysis; therefore, the induced conformational changes were correlated to the isomerization of EI to EI. Chemical modification of the Asp or Glu by WRK and Lys residues by TNBS abolished the antiproteolytic activity and revealed the involvement of two carboxyl groups and one amine group of ATBI in the enzymatic inactivation.
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Affiliation(s)
- C Dash
- Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India
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