Screening of benzamidine-based thrombin inhibitors via a linear interaction energy in continuum electrostatics model

Abstract  

A series of 27 benzamidine inhibitors covering a wide range of biological activity and chemical diversity was analysed to derive a Linear Interaction Energy in Continuum Electrostatics (LIECE) model for analysing the thrombin inhibitory activity. The main interactions occurring at the thrombin binding site and the preferred binding conformations of inhibitors were explicitly biased by including into the LIECE model 10 compounds extracted from X-ray solved thrombin-inhibitor complexes available from the Protein Data Bank (PDB). Supported by a robust statistics (r ² = 0.698; q ² = 0.662), the LIECE model was successful in predicting the inhibitory activity for about 76% of compounds (r _ext² ≥ 0.600) from a larger external test set encompassing 88 known thrombin inhibitors and, more importantly, in retrieving, at high sensitivity and with better performance than docking and shape-based methods, active compounds from a thrombin combinatorial library of 10240 mimetic chemical products. The herein proposed LIECE model has the potential for successfully driving the design of novel thrombin inhibitors with benzamidine and/or benzamidine-like chemical structure.     

Synthesis and pharmacological effects of novel benzenesulfonamides carrying benzamide moiety as carbonic anhydrase and acetylcholinesterase inhibitors

N -(1-(4-Methoxyphenyl)-3-oxo-3-((4-( N -(substituted)sulfamoyl)phenyl)amino)prop-1-en-1-yl)benzamides 3a – g were designed since sulfonamide and benzamide pharmacophores draw great attention in novel drug design due to their wide range of bioactivities including acetylcholinesterase (AChE) and human carbonic anhydrase I and II (hCA I and hCA II) inhibitory potencies. Structure elucidation of the compounds was carried out by 1H NMR, 13C NMR, and HRMS spectra. In vitro enzyme assays showed that the compounds had significant inhibitory potential against hCA I, hCA II, and AChE enzymes at nanomolar levels. Ki values were in the range of 4.07 ± 0.38 – 29.70 ± 3.18 nM for hCA I and 10.68 ± 0.98 – 37.16 ± 7.55 nM for hCA II while Ki values for AChE were in the range of 8.91 ± 1.65 – 34.02 ± 5.90 nM. The most potent inhibitors 3g (Ki = 4.07 ± 0.38 nM, hCA I), 3c (Ki = 10.68 ± 0.98 nM, hCA II ) , and 3f (Ki = 8.91 ± 1.65 nM, AChE) can be considered as lead compounds of this study with their promising bioactivity results. Secondary sulfonamides showed promising enzyme inhibitory effects on AChE while primary sulfonamide derivative was generally effective on hCA I and hCA II isoenzymes.     

Amidino-containing Schiff base copper(II) and iron(III) chelates as a thrombin inhibitor

Four series of Schiff base copper(II) and iron(III) chelates were synthesized from 4-formyl-3-hydroxybenzamidine or 3-formyl-4-hydroxybenzamidine and various L- or D-amino acids. Their inhibitory activities for bovine alpha-thrombin (abbreviated as thrombin) were determined. The most potent thrombin inhibitor in this series is copper(II) chelate (1g') derived from 4-formyl-3-hydroxybenzamidine and D-Trp. Its Ki value, 2.7x10(-8) M, is comparable to that of Argatroban (MD-805), which is a clinically used compound. The iron(III) chelates derived from 4-formyl-3-hydroxybenzamidine and hydrophobic L-amino acids (Val, Ile, Leu, Phe, Trp, Met) also exhibited higher inhibitory potency. It appears that coordination geometry composed of metal ion, amidino group, amino acid side chain is well accommodated to the thrombin active site. From the Ki values of Schiff base metal chelates for thrombin, the structure-activity relationships between the chelates and active site of thrombin were discussed.     

Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors

Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free enthalpy of protein-ligand complexation. The lactam derivatives are much more potent and more selective inhibitors (K(i) values between 0.065 and 0.005 microM, selectivity for thrombin over trypsin between 361- and 1609-fold) than the imide compounds (Ki values between 0.057 and 23.7 microM, selectivity for thrombin over trypsin between 3- and 67-fold). The increase in potency and selectivity is explained by the favorable occupancy of the P-pocket of thrombin by the additional isopropyl substituent in the lactam derivatives. The nature of the substituent on the benzyl ring filling the D pocket strongly influences binding potency in the imide series, with Ki values increasing in the sequence: F < OCH2O < Cl < H < OMe < OH < N(pyr)< Br. This sequence can be explained by both steric fit and the occurrence of orthogonal multipolar interactions with the backbone C[double bond, length as m-dash]O moiety of Asn98. In contrast, the substituent on the benzyl ring hardly affects the ligand potency in the lactam series. This discrepancy was clarified by the comparison of X-ray structures solved for co-crystals of thrombin with imide and lactam ligands. Whereas the benzyl substituents in the imide inhibitors are sufficiently close (< or =3.5 Angstroms) to the C=O group of Asn98 to allow for attractive orthogonal multipolar interactions, the distances in the lactam series are too large (> or =4 Angstroms) for attractive dipolar contacts to be effective.     

Prediction of enzyme binding: human thrombin inhibition study by quantum chemical and artificial intelligence methods based on X-ray structures

Thrombin is a serine protease which plays important roles in the human body, the key one being the control of thrombus formation. The inhibition of thrombin has become a target for new antithrombotics. The aim of our work was to (i) construct a model which would enable us to predict Ki values for the binding of an inhibitor into the active site of thrombin based on a database of known X-ray structures of inhibitor-enzyme complexes and (ii) to identify the structural and electrostatic characteristics of inhibitor molecules crucially important to their effective binding. To retain as much of the 3D structural information of the bound inhibitor as possible, we implemented the quantum mechanical/molecular mechanical (QM/MM) procedure for calculating the molecular electrostatic potential (MEP) at the van der Waals surfaces of atoms in the protein's active site. The inhibitor was treated quantum mechanically, while the rest of the complex was treated by classical means. The obtained MEP values served as inputs into the counter-propagation artificial neural network (CP-ANN), and a genetic algorithm was subsequently used to search for the combination of atoms that predominantly influences the binding. The constructed CP-ANN model yielded Ki values predictions with a correlation coefficient of 0.96, with Ki values extended over 7 orders of magnitude. Our approach also shows the relative importance of the various amino acid residues present in the active site of the enzyme for inhibitor binding. The list of residues selected by our automatic procedure is in good correlation with the current consensus regarding the importance of certain crucial residues in thrombin's active site.     

Design of small-molecule thrombin inhibitors based on the <Emphasis Type="Italic">cis</Emphasis>-5-phenylproline scaffold

The design of novel organic compounds containing no strongly basic amidine or guanidine functional groups typical of serine protease inhibitors was performed to develop an oral anticoagulant drug. A three-dimensional computational model for thrombin active site was constructed and optimized for docking of small-molecule organic compounds and calculating the energies of inhibitor-enzyme interactions. Novel racemic derivatives of 1-[2-(4-chlorophenylthio)acetyl]-5-phenylpyrrolidine-2,4-dicarboxylic acids were synthesized for which Cl-π interactions between the inhibitors and the S1 pocket of thrombin active site are predicted by modeling. The compounds synthesized deactivate thrombin in vitro and the inhibition properties show good correlations with the results of calculations.     

7-Azabicycloheptane carboxylic acid: a proline replacement in a boroarginine thrombin inhibitor

[formula: see text] The synthesis of thrombin inhibitor 3, which incorporates conformationally constrained 7-azabicycloheptane carboxylic acid (1) as a proline replacement, is described. The inhibition constant (Ki(thrombin) = 2.9 nM) indicates that 1 is a reasonable replacement of proline in the formation of a beta-turn tripeptide mimetic.     

Synthesis,In vitro Coagulation Activities and Molecular Docking Studies on Three L-Histidine Amide Derivatives

Three novel L-histidine amide derivatives were synthesized and the corresponding chemical structures were characterized by means of melting point analysis, IR, MS, ¹H NMR as well as ¹³C NMR. The coagulation acti- vities of the compounds were evaluated by an MOE(molecular operating environment) docking technique and coagulation test. The results obtained from molecular docking show that the interactions between the compounds and thrombin exhibit procoagulant activity in combination with an improved combinatory effect. Moreover, the results of in vitro coagulation tests show that the L-histidine amide derivatives feature coagulant activities in common coagulation pathways. Compared with the blank control group, the optimal shortening rates of compounds 1―3 were 39.08%(0.5 mmol/L), 22.94%(1.0 mmol/L) and 15.38%(0.0625 mmol/L), respectively.     

Novel modes of capillary electrophoresis for the determination of endocrine disrupting chemicals

The synthesis and usage of a wide range of organic chemicals has increased dramatically over the last five decades. These compounds sometimes termed endocrine disrupting chemicals include agricultural pesticides, industrial solvents, dyes, plasticisers, detergents and heat exchangers. Concerns have been raised about the potential adverse effects of these compounds on humans and wildlife species. Our objectives are to develop a method to identify, using novel capillary electrophoretic techniques, the endocrine disrupting compounds that are reported to be present in environmental samples. The CE modes, capillary zone electrophoresis, micellar electrokinetic chromatography (MEKC), cyclodextrin-modified MEKC (CD-MEKC) and electroosmotic flow-suppressed CD-MEKC were investigated for the determination of a range of endocrine disrupting chemical compounds. This paper shows some initial results obtained.     

Dysinosin A: a novel inhibitor of Factor VIIa and thrombin from a new genus and species of Australian sponge of the family Dysideidae

A new marine natural product dysinosin A 1 has been isolated from a new genus and species of sponge of the family Dysideidae found near Lizard Island, North Queensland, Australia. Dysinosin A is a potent inhibitor of the blood coagulation cascade factor VIIa and an inhibitor of the serine protease thrombin. Among the distinctive features of dysinosin A are the presence of a 5,6-dihydroxy-octahydroindole-2-carboxylic acid, 3-amino-ethyl 1-N-amidino-Delta-3-pyrroline, a sulfated glyceric acid, and d-leucine, assembled through three peptidic linkages. Dysinosin A inhibited factor VIIa at a Ki of 108 nM and thrombin at a Ki of 452 nM. The identification of the 1-N-amidino-Delta-3-pyrroline and 5,6-dihydroxy-octahydroindole-2-carboxylic acid as P1 and P2 moieties respectively, should pave the way for the design and synthesis of new structure-based inhibitors.     

Label free binding assay with spectroscopic detection for pharmaceutical screening

Many therapeutic drugs exert their effects by interaction with well defined molecular targets. Increasing knowledge in molecular biology allows identification of more and more molecular key compounds and in consequence a molecular approach to disease and therapy. As binding of drugs to their target compounds is a key event, binding assays with an appropriate target molecule are useful means for primary screening of novel substances. We have investigated the potential of thin film interference spectroscopy (RIFS) as a label free detection method for pharmaceutical screening in a binding inhibition assay. To meet the throughput requirements in pharmaceutical screening a parallel detection system based on imaging spectroscopy was constructed. Thrombin/thrombin inhibitor interaction was investigated as a model system. The thin film transducer was covalently modified with a thrombin inhibitor. Specific binding of thrombin and binding inhibition by inhibitor compounds could be observed. A test cycle of less than 10 min could be reached. The parallel setup allows the simultaneous detection of 96 binding curves and can reach a throughput of more than 10⁶ samples per year.     

Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase.

BACKGROUND: The substrate sites of enzymes are attractive targets for structure-based inhibitor design. Two difficulties hinder efforts to discover and elaborate new (nonsubstrate-like) inhibitors for these sites. First, novel inhibitors often bind at nonsubstrate sites. Second, a novel scaffold introduces chemistry that is frequently unfamiliar, making synthetic elaboration challenging. RESULTS: In an effort to discover and elaborate a novel scaffold for a substrate site, we combined structure-based screening with in-parallel synthetic elaboration. These techniques were used to find new inhibitors that bound to the folate site of Lactobacillus casei thymidylate synthase (LcTS), an enzyme that is a potential target for proliferative diseases, and is highly studied. The available chemicals directory was screened, using a molecular-docking computer program, for molecules that complemented the three-dimensional structure of this site. Five high-ranking compounds were selected for testing. Activity and docking studies led to a derivative of one of these, dansyltyrosine (Ki 65 microM). Using solid-phase in-parallel techniques 33 derivatives of this lead were synthesized and tested. These analogs are dissimilar to the substrate but bind competitively with it. The most active analog had a Ki of 1.3 microM. The tighter binding inhibitors were also the most specific for LcTS versus related enzymes. CONCLUSIONS: TS can recognize inhibitors that are dissimilar to, but that bind competitively with, the folate substrate. Combining structure-based discovery with in-parallel synthetic techniques allowed the rapid elaboration of this series of compounds. More automated versions of this approach can be envisaged.     

Highly Enantioselective Adsorption of Small Prochiral Molecules on a Chiral Intermetallic Compound

Intrinsically chiral surfaces of intermetallic compounds are shown to be novel materials for enantioselective processes. Their advantage is the significantly higher thermal and chemical stability, and therefore their extended application range for catalyzed chiral reactions compared to surfaces templated with chiral molecular modifiers or auxiliaries. On the Pd₁‐terminated PdGa(111) surface, room‐temperature adsorption of a small prochiral molecule (9‐ethynylphenanthrene) leads to exceptionally high enantiomeric excess ratios of up to 98 %. Our findings highlight the great potential of intrinsically chiral intermetallic compounds for the development of novel, enantioselective catalysts that can be operated at high temperatures and potentially also in harsh chemical environments.     

Antibody-based fluorescence polarization assay to screen combinatorial libraries for sweet taste compounds

Technological advances in instrumentation, chemical synthesis methods, molecular biology and biochemistry have fueled the recent growth in high throughput screening. Assays are available in a vast range for formats, including fluorescence, luminescence, absorbance, and scintillation detection. Antibodies represent a powerful tool for novel compound discovery and their utility in this regard should not be underestimated. We have designed a fluorescence polarization immunoassay for the identification of novel sweeteners. The assay is based on monoclonal antibodies that bind superpotent sweet taste compounds and libraries of suitable test compounds can be rapidly screened using these antibodies as "artificial taste receptors."     

Time-resolved fluorescence aptamer-based sandwich assay for thrombin detection

In the present study, the authors report a novel sensitive method for the detection of thrombin using time-resolved fluorescence sensing platform based on two different thrombin aptamers. The thrombin 15-mer aptamer as a capture probe was covalently attached to the surface of glass slide, and the thrombin 29-mer aptamer was fluorescently labeled as a detection probe. A bifunctional europium complex was used as the fluorescent label. The introduction of thrombin triggers the two different thrombin aptamers and thrombin to form a sandwich structure. The fluorescence intensity is proportional to the thrombin concentration. The present sensing system could provide both a wide linear dynamic range and a low detection limit. The proposed sensing system also presented satisfactory specificity and selectivity. Results showed that thrombin was retained at the aptamer-modified glass surface while nonspecific proteins were removed by rinsing with buffer solution. This approach successfully showed the suitability of aptamers as low molecular weight receptors on glass slides for sensitive and specific protein detection.     

Synthesis and liquid crystalline properties of a series of cholesterol-based dimesogenic compounds

The synthesis and mesomorphic properties of a series of novel dimesogenic compounds containing the cholesteryl ester unit and a phenyl benzoate group are reported. The two mesogenic units of these compounds are linked through dicarboxylic ester bonds, with alkylene spacer lengths of 2, 4, 6 and 8 methylene units. The chemical structures and liquid crystalline properties of this series of compounds were characterized by FTIR, ¹H NMR, hot stage-coupled polarizing microscopy and DSC. The results show that this series of compounds are cholesteric liquid crystals over a wide range, both during heating and cooling, and they exhibit iridescent colours in the liquid crystalline state.     

Synthesis and liquid crystalline properties of a series of cholesterol‐based dimesogenic compounds

The synthesis and mesomorphic properties of a series of novel dimesogenic compounds containing the cholesteryl ester unit and a phenyl benzoate group are reported. The two mesogenic units of these compounds are linked through dicarboxylic ester bonds, with alkylene spacer lengths of 2, 4, 6 and 8 methylene units. The chemical structures and liquid crystalline properties of this series of compounds were characterized by FTIR, ¹H NMR, hot stage‐coupled polarizing microscopy and DSC. The results show that this series of compounds are cholesteric liquid crystals over a wide range, both during heating and cooling, and they exhibit iridescent colours in the liquid crystalline state.