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Ahmed Al-Hadhrami N, Ladwig A, Rahman A, Rozas I, Paul G Malthouse J, Evans P. Synthesis of 2-guanidinyl pyridines and their trypsin inhibition and docking. Bioorg Med Chem 2020; 28:115612. [PMID: 32690267 DOI: 10.1016/j.bmc.2020.115612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 10/24/2022]
Abstract
A range of guanidine-based pyridines, and related compounds, have been prepared (19 examples). These compounds were evaluated in relation to their competitive inhibition of bovine pancreatic trypsin. Results demonstrate that compounds in which the guanidinyl substituent can form an intramolecular hydrogen bond (IMHB) with the pyridinyl nitrogen atom (6a-p) are better trypsin inhibitors than their counterparts (10-13) that are unable to form an IMHB. Among the compounds 6a-p, examples containing a 5-halo substituent were, generally, found to be better trypsin inhibitors. This trend was inversely related to electronegativity, thus, 1-(5-iodopyridin-2-yl)guanidinium ion 6e (Ki = 0.0151 mM) was the optimum inhibitor in the 5-halo series. Amongst the isomeric methyl substituted compounds, 1-(3-methylpyridin-2-yl)guanidinium ion 6h demonstrated optimum levels of trypsin inhibition (Ki = 0.0140 mM). In order to rationalise the measured enzyme inhibition, selected compounds were docked with bovine and human trypsin with a view to understanding active site occupancy and taken together with the Ki values the order of inhibitory ability suggests that the 5-halo 2-guanidinyl pyridine inhibitors form a halogen bond with the catalytically active serine hydroxy group.
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Affiliation(s)
- Nahlah Ahmed Al-Hadhrami
- School of Chemistry, Centre for Synthesis and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland
| | - Angelique Ladwig
- School of Chemistry, Centre for Synthesis and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland
| | - Adeyemi Rahman
- School of Chemistry, TBSI, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, TBSI, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - J Paul G Malthouse
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, Conway Institute, University College Dublin, Dublin D04 N2E2, Ireland
| | - Paul Evans
- School of Chemistry, Centre for Synthesis and Chemical Biology, University College Dublin, Dublin D04 N2E2, Ireland.
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2
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Xu J, Ambrosini S, Tamahkar E, Rossi C, Haupt K, Tse Sum Bui B. Toward a Universal Method for Preparing Molecularly Imprinted Polymer Nanoparticles with Antibody-like Affinity for Proteins. Biomacromolecules 2015; 17:345-53. [DOI: 10.1021/acs.biomac.5b01454] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jingjing Xu
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Serena Ambrosini
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Emel Tamahkar
- Hitit University, Faculty
of Engineering, Department of Chemical Engineering, 19030 Çorum, Turkey
| | - Claire Rossi
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Karsten Haupt
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
| | - Bernadette Tse Sum Bui
- Sorbonne Universités, Université de Technologie de Compiègne, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
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3
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Ambrosini S, Beyazit S, Haupt K, Tse Sum Bui B. Solid-phase synthesis of molecularly imprinted nanoparticles for protein recognition. Chem Commun (Camb) 2013; 49:6746-8. [PMID: 23785709 DOI: 10.1039/c3cc41701h] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A solid-phase synthesis approach to prepare molecularly imprinted polymer nanoparticles (MIP-NPs) specific for trypsin is described. The protein is immobilized on a solid support upon which thermoresponsive MIP-NPs are synthesized. The MIP-NPs are released by a simple temperature change, resulting in synthetic antibody mimics exhibiting high specificity and selectivity for trypsin.
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Affiliation(s)
- Serena Ambrosini
- Compiègne University of Technology, CNRS Enzyme and Cell Engineering Laboratory, Rue Roger Couttolenc, CS 60319, 60203 Compiègne Cedex, France
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4
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Behnen J, Köster H, Neudert G, Craan T, Heine A, Klebe G. Experimental and computational active site mapping as a starting point to fragment-based lead discovery. ChemMedChem 2011; 7:248-61. [PMID: 22213702 DOI: 10.1002/cmdc.201100490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 11/23/2011] [Indexed: 11/06/2022]
Abstract
Small highly soluble probe molecules such as aniline, urea, N-methylurea, 2-bromoacetate, 1,2-propanediol, nitrous oxide, benzamidine, and phenol were soaked into crystals of various proteins to map their binding pockets and to detect hot spots of binding with respect to hydrophobic and hydrophilic properties. The selected probe molecules were first tested at the zinc protease thermolysin. They were then applied to a wider range of proteins such as protein kinase A, D-xylose isomerase, 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, endothiapepsin, and secreted aspartic protease 2. The crystal structures obtained clearly show that the probe molecules populate the protein binding pockets in an ordered fashion. The thus characterized, experimentally observed hot spots of binding were subjected to computational active site mapping using HotspotsX. This approach uses knowledge-based pair potentials to detect favorable binding positions for various atom types. Good agreement between the in silico hot spot predictions and the experimentally observed positions of the polar hydrogen bond forming functional groups and hydrophobic portions was obtained. Finally, we compared the observed poses of the small-molecule probes with those of much larger structurally related ligands. They coincide remarkably well with the larger ligands, considering their spatial orientation and the experienced interaction patterns. This observation confirms the fundamental hypothesis of fragment-based lead discovery: that binding poses, even of very small molecular probes, do not significantly deviate or move once a ligand is grown further into the binding site. This underscores the fact that these probes populate given hot spots and can be regarded as relevant seeds for further design.
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Affiliation(s)
- Jürgen Behnen
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Banerjee D, Srivastava SK, Pal SK. Spectroscopic studies on ligand-enzyme interactions: complexation of alpha-chymotrypsin with 4',6-diamidino-2-phenylindole (DAPI). J Phys Chem B 2008; 112:1828-33. [PMID: 18205349 DOI: 10.1021/jp709621c] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present study, the interaction of two structurally related proteolytic enzymes trypsin and alpha-chymotrypsin (CHT) with 4',6-Diamidino-2-phenylindole (DAPI) has been addressed. The binding of DAPI to CHT has been characterized by steady-state and picosecond time-resolved spectroscopic techniques. Enzymatic activity of CHT and simultaneous binding of the well-known inhibitor proflavin (PF) in the presence of DAPI clearly rule out the possibility of DAPI binding at the catalytic site of the enzyme. The spectral overlap between the emission of DAPI and absorption of PF offers the opportunity to explore the binding site of DAPI using Förster resonance energy transfer (FRET). FRET studies between DAPI and PF indicate that DAPI is bound to CHT with its transition dipole nearly perpendicular to that of PF. Competitive binding of DAPI with another fluorescent probe 2,6-p-toluidinonaphthalene sulfonate (TNS), having a well-defined binding site, indicates that DAPI and TNS bind at the same hydrophobic site of the enzyme CHT. The difference in the interactions of two well-studied, structurally similar enzymes with the same molecule may find its application in the design of specific substrate mimics or inhibitors of the enzymes.
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Affiliation(s)
- Debapriya Banerjee
- Unit for Nano Science & Technology, Department of Chemical, Biological & Macromolecular Sciences, SN Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India
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6
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Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 2005; 26:915-31. [PMID: 15841474 PMCID: PMC3920598 DOI: 10.1002/jcc.20222] [Citation(s) in RCA: 293] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The extent to which accuracy of electric charges plays a role in protein-ligand docking is investigated through development of a docking algorithm, which incorporates quantum mechanical/molecular mechanical (QM/MM) calculations. In this algorithm, fixed charges of ligands obtained from force field parameterization are replaced by QM/MM calculations in the protein environment, treating only the ligands as the quantum region. The algorithm is tested on a set of 40 cocrystallized structures taken from the Protein Data Bank (PDB) and provides strong evidence that use of nonfixed charges is important. An algorithm, dubbed "Survival of the Fittest" (SOF) algorithm, is implemented to incorporate QM/MM charge calculations without any prior knowledge of native structures of the complexes. Using an iterative protocol, this algorithm is able in many cases to converge to a nativelike structure in systems where redocking of the ligand using a standard fixed charge force field exhibits nontrivial errors. The results demonstrate that polarization effects can play a significant role in determining the structures of protein-ligand complexes, and provide a promising start towards the development of more accurate docking methods for lead optimization applications.
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Affiliation(s)
- Art E Cho
- Center for Biomolecular Simulations, Columbia University, New York, NY 10027, USA
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8
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Cho AE, Wendel JA, Vaidehi N, Kekenes-Huskey PM, Floriano WB, Maiti PK, Goddard WA. The MPSim-Dock hierarchical docking algorithm: application to the eight trypsin inhibitor cocrystals. J Comput Chem 2005; 26:48-71. [PMID: 15529328 DOI: 10.1002/jcc.20118] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To help improve the accuracy of protein-ligand docking as a useful tool for drug discovery, we developed MPSim-Dock, which ensures a comprehensive sampling of diverse families of ligand conformations in the binding region followed by an enrichment of the good energy scoring families so that the energy scores of the sampled conformations can be reliably used to select the best conformation of the ligand. This combines elements of DOCK4.0 with molecular dynamics (MD) methods available in the software, MPSim. We test here the efficacy of MPSim-Dock to predict the 64 protein-ligand combinations formed by starting with eight trypsin cocrystals, and crossdocking the other seven ligands to each protein conformation. We consider this as a model for how well the method would work for one given target protein structure. Using as a criterion that the structures within 2 kcal/mol of the top scoring include a conformation within a coordinate root mean square (CRMS) of 1 A of the crystal structure, we find that 100% of the 64 cases are predicted correctly. This indicates that MPSim-Dock can be used reliably to identify strongly binding ligands, making it useful for virtual ligand screening.
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Affiliation(s)
- Art E Cho
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, USA
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9
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Clark SM, Konermann L. Determination of Ligand−Protein Dissociation Constants by Electrospray Mass Spectrometry-Based Diffusion Measurements. Anal Chem 2004; 76:7077-83. [PMID: 15571362 DOI: 10.1021/ac049344o] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel approach for the quantification of ligand-protein interactions is presented. Electrospray ionization mass spectrometry (ESI-MS) is used to monitor the diffusion behavior of noncovalent ligands in the presence of their protein receptors. These data allow the fraction of free ligand in solution to be determined, such that the corresponding dissociation constants can be calculated. A set of conditions is developed that provides an "allowable range" of concentrations for this type of assay. The method is tested by applying it to two different inhibitor-enzyme systems. The dissociation constants measured for benzamidine-trypsin and for N,N',N' '-triacetylchitotriose-lysozyme are (50 +/- 10) and (6 +/- 1) mM, respectively. Both of these results are in good agreement with previous data from the literature. In contrast to traditional ESI-MS-based methods, the approach used in this work does not rely on the preservation of specific solution-type noncovalent interactions in the gas phase. It is shown that this method allows an accurate determination of dissociation constants, even in cases in which the ion abundance ratio of free to ligand-bound protein in ESI-MS does not reflect the corresponding concentration ratio in solution.
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Affiliation(s)
- Sonya M Clark
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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10
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Kunert C, Voigt D, Friedel P, Komber H, Böhme F. Polymers containing formamidine groups. VI. Structural influences on the formation of cyclic trimers. ACTA ACUST UNITED AC 2001. [DOI: 10.1002/pola.1105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Federico R, Leone L, Botta M, Binda C, Angelini R, Venturini G, Ascenzi P. Inhibition of pig liver and Zea mays L. polyamine oxidase: a comparative study. JOURNAL OF ENZYME INHIBITION 2001; 16:147-55. [PMID: 11342283 DOI: 10.1080/14756360109162364] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Polyamine oxidase (PAO) is involved in polyamine metabolism and production of hydrogen peroxide in animal and plants, thus representing a key system in development and programmed cell death. In the present study, the inhibitory effect of amiloride, p-aminobenzamidine, clonidine, 4',6-diamidino-2-phenyl-indole (DAPI), gabexate mesylate, guazatine, and N,N'-bis(2,3-butadienyl)-1,4-butane-diamine (MDL72527) on the catalytic activity of pig liver and Zea mays L. PAO, Lens culinaris L. and Pisum sativum L. and swine kidney copper amine oxidase, bovine trypsin, as well as neuronal constitutive nitric oxide synthase (NOS-I) was investigated. Moreover, agmatine and N(3) -prenylagmatine (G3) were observed to inhibit pig liver and Zea mays L. PAO, bovine trypsin, and NOS-I action, but were substrates for Lens culinaris L., Pisum sativum L. and swine kidney copper amine oxidase. Guazatine and G3 inhibited selectively Zea mays L. PAO with K(i) values of 7.5 x 10(-9) M and 1.5 x 10(-8) M, respectively (at pH 6.5 and 25.0 degrees C). As a whole, the data reported here represent examples of enzyme cross-inhibition, and appear to be relevant in view of the use of cationic L-arginine-and imidazole-based compounds as drugs.
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Affiliation(s)
- R Federico
- Dipartimento di Biologia, Università degli Studi 'Roma Tre', Viale G. Marconi 446, I-00146 Roma, Italy
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12
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Amiconi G, Amoresano A, Boumis G, Brancaccio A, De Cristofaro R, De Pascalis A, Di Girolamo S, Maras B, Scaloni A. A novel venombin B from agkistrodon contortrix contortrix: evidence for recognition properties in the surface around the primary specificity pocket different from thrombin. Biochemistry 2000; 39:10294-308. [PMID: 10956019 DOI: 10.1021/bi000145i] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel thrombin-like enzyme (named contortrixobin) has been purified to homogeneity from the venom of Agkistrodon contortrix contortrix by affinity chromatography on arginine-Sepharose, anionic exchange chromatography, and HPLC. The complete amino acid sequence has been determined by Edman degradation and by mass spectral analysis of peptides generated by enzymatic cleavage. A microheterogeneity at the level of residue 234 has been detected, as demonstrated by peptides differing for the occurrence of Pro234 ( approximately 85%) or Asp234 ( approximately 15%). Contortrixobin (i) has six disulfide bonds whose sequence positions have been determined by mass spectrometry and (ii) does not contain carbohydrates in its structure. As expected, the 234 residue sequence of contortrixobin exhibits strong homology with snake venom serine proteases acting on either fibrinogen or other blood coagulation components. The interaction of contortrixobin with chromogenic substrates indicates a higher specificity for arginine over lysine in the primary subsite and a faster attack to ester than amides. The hydrolytic activity of contortrixobin is strongly inhibited by diisopropyl fluorophosphate and to a less extent by phenylmethylsulfonyl fluoride, benzamidine, and 4', 6-diamidino-2-phenylindole; hirudin (a specific alpha-thrombin inhibitor) as well as basic pancreatic trypsin inhibitor has a small effect on contortrixobin's catalytic properties. Contortrixobin (i) preferentially releases fibrinopeptide B from human fibrinogen, (ii) activates blood coagulation Factors V and XIII with a rate 250-500-fold lower than human alpha-thrombin, and (iii) does not induce thrombocyte aggregation, intracytoplasmatic calcium ion increase in platelets, and activation of Factor VIII. Evidence for biorecognition properties different from thrombin is also reported.
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Affiliation(s)
- G Amiconi
- Department of Biochemical Sciences, University of Rome "La Sapienza", Italy.
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13
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Venturini G, Colasanti M, Persichini T, Fioravanti E, Federico R, Ascenzi P. Selective inhibition of nitric oxide synthase type I by clonidine, an anti-hypertensive drug. Biochem Pharmacol 2000; 60:539-44. [PMID: 10874128 DOI: 10.1016/s0006-2952(00)00352-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Clonidine, clinically used in the treatment of hypertension, is a central alpha(2)-adrenergic agonist that reduces blood pressure and slows heart rate by reducing sympathetic stimulation. Considering the structural similarity between clonidine and hydrophobic heterocyclic nitric oxide synthase (NOS) inhibitors, the effect of clonidine on the nitric oxide (NO) pathway was investigated. This was verified by determination of NOS activity in vitro and by analysis of inducible Ca(2+)-independent NOS (NOS-II) mRNA expression and measurement of nitrite levels in rat C6 glioma cells, taken as a cellular model. Clonidine inactivated neuronal Ca(2+)-dependent NOS (NOS-I) competitively without affecting NOS-II and endothelial Ca(2+)-dependent NOS (NOS-III) activity. However, the value of K(i) for clonidine binding to NOS-I depended on tetrahydrobiopterin (BH(4)) concentration, as reported for NOS inhibition by other nitrogen heterocyclic compounds. In particular, the value of K(i) for clonidine binding to NOS-I increased (from [7. 9 +/- 0.4] x 10(-5) M to [8.0 +/- 0.4] x 10(-3) M) as BH(4) concentration was increased (between 3.0 x 10(-7) M and 1.0 x 10(-3) M), at pH 7.5 and 37.0 degrees. In addition, clonidine (1.0 x 10(-4) M) enhanced NOS-II mRNA expression in rat C6 glioma cells, as induced by Escherichia coli lipopolysaccharide (LPS) plus interferon-gamma (IFN-gamma). Finally, clonidine (1.0 x 10(-4) M to 1.0 x 10(-3) M) dose dependently increased the levels of LPS/IFN-gamma-induced nitrites, the breakdown product of NO, in supernatants of rat C6 glioma cells. As reported for other NOS inhibitors, clonidine was also able to regulate NOS-I and NOS-II inversely.
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Affiliation(s)
- G Venturini
- Department of Biology, University of Roma Tre, I-00146, Rome, Italy
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14
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Nienaber VL, Boxrud PD, Berliner LJ. Thrombin inhibitor design: X-ray and solution studies provide a novel P1 determinant. JOURNAL OF PROTEIN CHEMISTRY 2000; 19:327-33. [PMID: 11043938 DOI: 10.1023/a:1007055615190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The crystal structures of proflavin and 6-fluorotryptamine thrombin have been completed showing binding of both ligands at the active site S1 pocket. The structure of proflavin:thrombin was confirmatory, while the structure of 6-fluorotryptamine indicated a novel binding mode at the thrombin active site. Furthermore, speculation that the sodium atom identified in an extended solvent channel beneath the S pocket may play a role in binding of these ligands was investigated by direct proflavin titrations as well as chromogenic activity measurements as a function of sodium concentration at constant ionic strength. These results suggested a linkage between the sodium site and the S1 pocket. This observation could be due to a simple ionic interaction between Asp189 and the sodium ion or a more complicated structural rearrangement of the thrombin S1 pocket. Finally, the unique binding mode of 6-fluorotryptamine provides ideas toward the design of a neutrally charged thrombin inhibitor.
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Affiliation(s)
- V L Nienaber
- Department of Chemical and Physical Sciences, DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880, USA
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15
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Cortesi R, Ascenzi P, Colasanti M, Persichini T, Venturini G, Bolognesi M, Pesce A, Nastruzzi C, Menegatti E. Cross-enzyme inhibition by gabexate mesylate: formulation and reactivity study. J Pharm Sci 1998; 87:1335-40. [PMID: 9811486 DOI: 10.1021/js980079u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gabexate mesylate (GM; commercialized under the brand name FOY) is a nonantigenic synthetic inhibitor of plasmatic and pancreatic serine proteinases that is used therapeutically in the treatment of pancreatitis and disseminated intravascular coagulation and as a regional anticoagulant for hemodialysis. The inhibitory effect of GM on nitric oxide synthase as well as serine proteinases and swine kidney copper amine oxidase, all acting on cationic substrates, has been investigated. On the basis of the available X-ray crystal structures of the enzymes considered, the possible binding mode(s) of GM has(have) been analyzed. The enzyme cross-inhibition by GM suggests that the use of this drug should be under careful control. With the aim to improve the scarce plasma stability of GM, the positively charged drug has been complexed to the surface of preformed anionic liposomes. The liposome-complexed GM half-life increases about five-fold, indicating the protective effect of liposomes on GM degradation. Moreover, the GM complexation with liposomes does not alter its inhibitory activity on NOS-I and porcine pancreatic trypsin.
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Affiliation(s)
- R Cortesi
- Department of Pharmaceutical Sciences, University of Ferrara, Via Fossato di Mortara 19, I-44100 Ferrara, Rome
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16
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Ercolini L, Angelini R, Federico R, Rea G, Venturini G, Ascenzi P. Competitive inhibition of Lens culinaris L. copper amine oxidase by amiloride, p-aminobenzamidine, clonidine, 4',6-diamidino-2-phenylindole and gabexate mesylate: a comparative study. JOURNAL OF ENZYME INHIBITION 1998; 13:465-71. [PMID: 9825309 DOI: 10.3109/14756369809020550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The competitive inhibition of Lens culinaris L. copper amine oxidase by amiloride (Ki = 4.1 x 10(-4) M), p-aminobenzamidine (Ki = 6.0 x 10(-4) M), clonidine (Ki = 5.0 x 10(-4) M), 4',6-diamidino-2-phenylindole (DAPI; Ki = 1.9 x 10(-5) M) and gabexate mesylate (Ki = 2.5 x 10(-4) M) has been investigated, at pH 7.0 and 25 degrees C. The affinity of p-aminobenzamidine, clonidine and DAPI for plant and mammalian copper amine oxidase is closely similar. However, values of Ki for amiloride and gabexate mesylate binding to swine kidney copper amine oxidase are lower than those observed for inhibitor binding to Lens culinaris L. cooper amine oxidase. Thus, amiloride and gabexate mesylate may represent useful model compounds for the development of selective inhibitors of mammalian copper amine oxidase, which may be important in view of the potential use of plant copper amine oxidase as drugs.
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Affiliation(s)
- L Ercolini
- Department of Biology, Third University of Rome, Italy
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17
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Schaefer M, van Vlijmen HW, Karplus M. Electrostatic contributions to molecular free energies in solution. ADVANCES IN PROTEIN CHEMISTRY 1998; 51:1-57. [PMID: 9615168 DOI: 10.1016/s0065-3233(08)60650-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- M Schaefer
- Laboratoire de Chimie Biophysique, Institut le Bel, Université Louis Pasteur, Strasbourg, France
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18
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Federico R, Angelini R, Ercolini L, Venturini G, Mattevi A, Ascenzi P. Competitive inhibition of swine kidney copper amine oxidase by drugs: amiloride, clonidine, and gabexate mesylate. Biochem Biophys Res Commun 1997; 240:150-2. [PMID: 9367901 DOI: 10.1006/bbrc.1997.7630] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Competitive inhibition of swine kidney copper amine oxidase by diuretic, antihypertensive, and anticoagulant drugs, amiloride, clonidine, and gabexate mesylate, respectively, is reported. The affinity of these compounds for swine kidney copper amine oxidase is similar to that observed for inhibitor binding to nitric oxide synthase and trypsin-like serine proteinases. This finding suggests that amiloride, clonidine, and gabexate mesylate should be administrated under careful control, since enzyme cross-inhibition may occur also in vivo.
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Affiliation(s)
- R Federico
- Department of Biology, Third University of Rome, Italy
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19
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Favilla R, Parisoli A, Mazzini A. Alkaline denaturation and partial refolding of pepsin investigated with DAPI as an extrinsic probe. Biophys Chem 1997; 67:75-83. [PMID: 9397520 DOI: 10.1016/s0301-4622(97)00016-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The binding parameters of DAPI to porcine stomach pepsin have been described in the previous article in this issue (A. Mazzini et al.). Here we exploit the differences in the spectroscopic (fluorescence and circular dichroism) properties of DAPI bound to either native or alkali denatured pepsin. We follow the kinetics of pepsin denaturation around neutrality (pH range 6.8-7.4), at several phosphate buffer ionic strengths (range 0.02-0.25). The dependence of the apparent dissociation rate constant on pH clearly shows that the rate limiting step follows the dissociation of about three acidic protein residues. The accelerating effect by ionic strength we observed can be accounted for by a simple treatment based on both transition state theory and Debye-Hueckel's limiting law. Furthermore, when a solution of pepsin, rapidly denatured at pH 7, is reacidified to a pH between 4.5 and 5.5, a substantial recovery of protein secondary structure, with no enzymatic activity, is observed, judging by the far UV circular dichroism of the protein. This process of partial refolding can easily be followed using DAPI as an extrinsic reporter group, able to monitor the kinetics of formation and decay of a highly fluorescent intermediate. This process becomes faster at a lower pH, at least in the limited range investigated (pH 4.5-5.5), in which the refolded protein does not aggregate, but, in contrast to unfolding, is almost independent in ionic strength.
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Affiliation(s)
- R Favilla
- Istituto Nazionale di Fisica della Materia (INFM), Dipartimento di Fisica, Università di Parma, Italy.
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20
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Mazzini A, Incerti M, Favilla R. Interaction of DAPI with pepsin as a function of pH and ionic strength. Biophys Chem 1997; 67:65-74. [PMID: 9397519 DOI: 10.1016/s0301-4622(97)00015-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The fluorescent probe 4',6-diamidino-2-phenylindole (DAPI), extensively used with nucleic acids, has also recently been used with membranes and proteins (Favilla et al., Biophys. Chem., 46 (1993) 217-226 and Mazzini et al., Biophys. Chem. 52 (1994) 145-156, respectively). The spectroscopic changes of DAPI observed, namely a considerable enhancement of fluorescence, induced circular dichroism (CD) and absorbance spectral shifts, have been exploited to study the binding of this dye to both native and alkali denatured pepsin. Fluorescence and CD titrations show that nearly two molecules of DAPI bind to either native or alkali denatured pepsin with pH and ionic strength dependent Kd values, whereas absorbance titrations evidentiate an interaction characterized by a lower affinity and a larger number of binding sites. Therefore two kinds of interaction are proposed: a specific one, involving both hydrophobic and electrostatic forces; and a non-specific one, involving surface protein negative charges only. Finally, the behaviour of DAPI as a competitive inhibitor and the remarkable effect of pepstatin A, a specific inhibitor of pepsin, on both the CD and fluorescence spectra of DAPI in the presence of pepsin, show the involvement of the protein active site in the interaction.
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Affiliation(s)
- A Mazzini
- Istituto Nazionale di Fisica della Materia (INFM), Dipartimento di Fisica, Università di Parma, Italy.
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21
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Fiorucci L, Erba F, Bolognesi M, Coletta M, Ascoli F. pH dependence of bovine mast cell tryptase catalytic activity and of its inhibition by 4',6-diamidino-2-phenylindole. FEBS Lett 1997; 408:85-8. [PMID: 9180274 DOI: 10.1016/s0014-5793(97)00395-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tryptases are oligomeric enzymes localized in the secretory granules of mast cells. Their role(s) in vivo has yet to be clarified and the lack of powerful and specific inhibitors has hampered the comprehension of the biological functions of these enzymes. In this paper, we identify 4',6-diamidino-2-phenylindole as a potent inhibitor for bovine tryptase. This inhibitory effect and the enzyme catalyzed hydrolysis of the synthetic substrate Boc-Phe-Ser-Arg-methyl-coumarin were investigated in the pH range of 6.0-9.0. On the basis of the pK shifts occurring upon formation of the inhibitor(substrate)/enzyme complexes, some aminoacidic groups are proposed to play a role in such interactions.
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Affiliation(s)
- L Fiorucci
- Department of Experimental Medicine and Biochemical Sciences, University Tor Vergata, Rome, Italy
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22
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Venturini G, Menegatti E, Ascenzi P. Competitive inhibition of nitric oxide synthase by p-aminobenzamidine, a serine proteinase inhibitor. Biochem Biophys Res Commun 1997; 232:88-90. [PMID: 9125158 DOI: 10.1006/bbrc.1997.6228] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
p-Aminobenzamidine competitively inhibits bovine trypsin, human and bovine thrombin, and human plasmin, all of which act on substrates containing preferentially the L-arginyl side chain at their P1 position. Considering the structural and functional similarity between p-aminobenzamidine and the L-arginyl side chain in trypsin-like serine proteinases, we investigated the interaction of p-aminobenzamidine with mouse brain nitric oxide synthase (NOS), which uses L-arginine as the substrate for generating NO and L-citrulline. p-Aminobenzamidine is a competitive NOS inhibitor (Ki = 1.2 x 10(-4) M, at pH 7.5 and 37.0 degrees C), but not an NO precursor. Therefore, p-aminobenzamidine affects the NO production and the trypsin-like serine proteinase action.
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Affiliation(s)
- G Venturini
- Department of Biology, Third University of Rome, Italy
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23
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Engh RA, Brandstetter H, Sucher G, Eichinger A, Baumann U, Bode W, Huber R, Poll T, Rudolph R, von der Saal W. Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design. Structure 1996; 4:1353-62. [PMID: 8939759 DOI: 10.1016/s0969-2126(96)00142-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The explosive growth in the rate of X-ray determination of protein structures is fuelled largely by the expectation that structural information will be useful for pharmacological and biotechnological applications. For example, there have been intensive efforts to develop orally administrable antithrombotic drugs using information about the crystal structures of blood coagulation factors, including thrombin. Most of the low molecular weight thrombin inhibitors studied so far are based on arginine and benzamidine. We sought to expand the database of information on thrombin-inhibitor binding by studying new classes of inhibitors. RESULTS We report the structures of three new inhibitors complexed with thrombin, two based on 4-aminopyridine and one based on naphthamidine. We observe several geometry changes in the protein main chain and side chains which accompany inhibitor binding. The two inhibitors based on 4-aminopyridine bind in notably different ways: one forms a water-mediated hydrogen bond to the active site Ser195, the other induces a rotation of the Ser214-Trp215 peptide plane that is unprecedented in thrombin structures. These binding modes also differ in their 'weak' interactions, including CH-O hydrogen bonds and interactions between water molecules and aromatic pi-clouds. Induced-fit structural changes were also seen in the structure of the naphthamidine inhibitor complex. CONCLUSIONS Protein flexibility and variable water structures are essential elements in protein-ligand interactions. Ligand design strategies that fail to take this into account may overlook or underestimate the potential of lead structures. Further, the significance of 'weak' interactions must be considered both in crystallographic refinement and in analysis of binding mechanisms.
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Affiliation(s)
- R A Engh
- Max-Planck-Institut für Biochemie, D82152 Martinsried, Germany.
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24
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Raspi G. Kallikrein and kallikrein-like proteinases: purification and determination by chromatographic and electrophoretic methods. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL APPLICATIONS 1996; 684:265-87. [PMID: 8906477 DOI: 10.1016/0378-4347(96)00144-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Kallikreins and kallikrein-like enzymes make up a family of serine proteinases present in tissues and body fluids of mammals and in some snake venoms. This review deals with the procedures of purification, detection and determination of these enzymes by chromatographic and electrophoretic methods. The procedures are reported in tables, described and discussed with the aim of illustrating the state-of-the-art of research in the field.
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Affiliation(s)
- G Raspi
- Dipartimento di Chimica e Chimica Industriale dell'Università and Istituto di Chimica Analitica Strumentale del C.N.R. Pisa, Italy
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25
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von der Saal W, Engh RA, Eichinger A, Gabriel B, Kucznierz R, Sauer J. Syntheses and selective inhibitory activities of terphenyl-bisamidines for serine proteases. Arch Pharm (Weinheim) 1996; 329:73-82. [PMID: 8851470 DOI: 10.1002/ardp.19963290204] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Biphenyl nitriles 5a-c, terphenyl dinitriles 11a-d, and naphthalene-bis(benzonitrile) 11c were prepared by palladium-catalyzed cross coupling reactions and subsequently converted to biphenyl amidines 8a-c and bis(benzamidines) 4a-e. Among the biphenyl amidines 8 only the meta-derivative 8b inhibits factor Xa and trypsin (Ki = 10 microM). The terphenyl bisamidine 4c does not inhibit factor Xa, trypsin, thrombin, and plasmin, while 4a and 4d are almost equipotent inhibitors of these enzymes (Ki 1-6 microM), and 4b and 4e are selective for trypsin (Ki = 0.2 and 0.3 microM; but Ki > 1 microM for factor Xa, thrombin, and plasmin). X-ray analysis of crystals of 4b complexed with bovine trypsin revealed a unique binding mode: one benzamidino group binds in the S1 site to the side chain carboxylate of Arg189. The central phenyl group is twisted away from the S2/S3 sites and the second amidino group contacts the Asn143 side chain.
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Affiliation(s)
- W von der Saal
- Chemical Research Department, Boehringer Mannheim, Germany
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