Design, synthesis, and activity of a novel series of factor Xa inhibitors: optimization of arylamidine groups

Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model

A variable dielectric model based on residue types for better description of protein-ligand electrostatics in MM-GBSA scoring is reported. The variable dielectric approach provides better correlation with binding data and reduces the score dynamic range, typically observed in the standard MM-GB/SA method. The latter supports the view that exaggerated enthalpic separation between weak and potent compounds due to the lack of shielding effects in the model is greatly responsible for the wide scoring spread.

Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases

The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.

Synthesis and SAR of alkanediamide-linked bisbenzamidines with anti-trypanosomal and anti-pneumocystis activity

A series of alkanediamide-linked bisbenzamidines was synthesized and tested in vitro against a drug-sensitive strain of Trypanosoma brucei brucei, a drug-resistant strain of Trypanosoma brucei rhodesiense and Pneumocystiscarinii. Bisbenzamidines linked with longer alkanediamide chains were potent inhibitors of both strains of T. brucei. However, bisbenzamidines linked with shorter alkanediamide chains were the most potent compounds against P. carinii. N,N'-Bis[4-(aminoiminomethyl)phenyl] hexanediamide, 4 displayed potent inhibition (IC50=2-3 nM) against T. brucei and P. carinii, and was non-cytotoxic in the A549 human lung carcinoma cell line. The inhibitory bioactivity was significantly reduced when the amidine groups in 4 were moved from the para to the meta positions or replaced with amides.

MM-GB/SA rescoring of docking poses in structure-based lead optimization

The critical issues in docking include the prediction of the correct binding pose and the accurate estimation of the corresponding binding affinity. Different docking methodologies have all been successful in reproducing the crystallographic binding modes but struggle when predicting the corresponding binding affinities. The aim of this work is to evaluate the performance of the MM-GB/SA rescoring of docking poses in structure-based lead optimization. To accomplish that, a diverse set of pharmaceutically relevant targets, including CDK2, FactorXa, Thrombin, and HIV-RT were selected. The correlation between the MM-GB/SA results and experimental data in all cases is remarkable. It even qualifies this approach as a more attractive alternative for rank-ordering than the Free Energy Perturbation and Thermodynamic Integration methodologies because, while as accurate, it can handle more structurally dissimilar ligands and provides results at a fraction of the computational cost. On the technical side, the benefit of performing a conformational analysis and having an ensemble of conformers to represent each ligand in the unbound state during the MM-GB/SA rescoring procedure was investigated. In addition, the estimation of conformational entropy penalties for the ligands upon binding, computed from the Boltzmann distribution in water, was evaluated and compared to a commonly used approach employed by many docking scoring functions.

Prediction of factor Xa inhibitors by machine learning methods

Factor Xa (FXa) inhibitors have been explored as anticoagulants for treatment and prevention of thrombotic diseases. Molecular docking, pharmacophore, quantitative structure-activity relationships, and support vector machines (SVM) have been used for computer prediction of FXa inhibitors. These methods achieve promising prediction accuracies of 69-80% for FXa inhibitors and 85-99% for non-inhibitors. Prediction performance, particularly for inhibitors, may be further improved by exploring methods applicable to more diverse range of compounds and by using more appropriate set of molecular descriptors. We tested the capability of several machine learning methods (C4.5 decision tree, k-nearest neighbor, probabilistic neural network, and support vector machine) by using a much more diverse set of 1098 compounds (360 inhibitors and 738 non-inhibitors) than those in other studies. A feature selection method was used for selecting molecular descriptors appropriate for distinguishing FXa inhibitors and non-inhibitors. The prediction accuracies of these methods are 89.1-97.5% for FXa inhibitors and 92.3-98.1% for non-inhibitors. In particular, compared to other studies, support vector machine gives a substantially improved accuracy of 94.6% for FXa non-inhibitors and maintains a comparable accuracy of 98.1% for inhibitors, based-on a more rigorous test with more diverse range of compounds. Our study suggests that machine learning methods such as SVM are useful for facilitating the prediction of FXa inhibitors.

The rational design of inhibitors of nitric oxide formation by inducible nitric oxide synthase

A series of compounds was rationally designed as inhibitors of dimer formation of the inducible isoform of nitric oxide synthase, and subsequent nitric oxide production. The conformation of two fragments obtained from a crystal structure was utilized to design a tether connecting those same two fragments. The resulting compounds were potent dimerization inhibitors that bound to the enzyme in a similar conformation as the fragments.

The role of hydrophobic properties of chemicals in promoting allosteric reactions

An allosteric reaction has been found in a variety of instances where an inverted parabolic relationship between biological activity and hydrophobicity is apparent, that is the activity first decreases as hydrophobicity increases and after a certain point, activity begins to increase. This could be attributed to the ligands causing a change in the receptor structure. In this report, the role of hydrophobic properties of chemicals in promoting allosteric reactions have been discussed in term of hydrophobicity (logP) by the formulation of a total number of 50 QSAR equations. The QSAR model of this type may be represented by Eq. I.

Design, synthesis, and evaluation of oxyanion-hole selective inhibitor substituents for the S1 subsite of factor Xa

We have designed, synthesized, and evaluated the factor Xa inhibitory activities of p-amidinophenyl-sulfones, amines, and alcohols intended to take advantage of the polarity and hydrogen-bonding potential of the oxyanion hole region of the S1 specificity pocket. We demonstrate that placement of an anionic group within the oxyanion hole region of the catalytic site substantially enhances activity, with small flexible groups favored over bulkier ones. Ab initio pKa calculations suggest that the hydroxyl substituent frequently used for benzamidine moieties may be ionized to form an anionic group, consistent with the general trend. One nonamidine based substituent also shows promising activity.

Current trends in quantitative structure activity relationships on FXa inhibitors: Evaluation and comparative analysis

This article evaluates the quantitative structure activity relationships of FXa inhibitors, using the C-QSAR program of Biobyte. Diaryloxypyridines, aminophenols, biaryl isoxazoline derivatives, 1,2-dibenzamidobenzenes, 3-amidinophenylalanine derivatives, benzoxazinones, naphthoanilides, tetrazoles, glucolic and mandelic acid derivatives were included in this survey. Clog P plays a significant role in the QSAR, especially as hydrophilicity. In the most of the cases, CMR/MR molar refractivity as well as sterimol parameters (B5 and L) are important. Electronic effects with the exception of the Hammett's constant sigmam, are not found to govern the biological activity. Es was found to be important indicator variables were used after the best model was found to account for the usual structural features.

Understanding Protein–Ligand Interactions: The Price of Protein Flexibility

In order to design selective, high-affinity ligands to a target protein, it is advantageous to understand the structural determinants for protein-ligand complex formation at the atomic level. In a model system, we have successively mapped the factor Xa binding site onto trypsin, showing that certain mutations influence both protein structure and inhibitor specificity. Our previous studies have shown that introduction of the 172SSFI175 sequence of factor Xa into rat or bovine trypsin results in the destabilisation of the intermediate helix with burial of Phe174 (the down conformation). Surface exposure of the latter residue (the up conformation) is critical for the correct formation of the aromatic box found in factor Xa-ligand complexes. In the present study, we investigate the influence of aromatic residues in position 174. Replacement with the bulky tryptophan (SSWI) shows reduced affinity for benzamidine-based inhibitors (1) and (4), whereas removal of the side-chain (alanine, SSAI) or exchange with a hydrophilic residue (arginine, SSRI) leads to a significant loss in affinity for all inhibitors studied. The variants could be crystallised in the presence of different inhibitors in multiple crystal forms. Structural characterisation of the variants revealed three different conformations of the intermediate helix and 175 loop in SSAI (down, up and super-up), as well as a complete disorder of this region in one crystal form of SSRI, suggesting that the compromised affinity of these variants is related to conformational flexibility. The influence of Glu217, peripheral to the ligand-binding site in factor Xa, was investigated. Introduction of Glu217 into trypsin variants containing the SSFI sequence exhibited enhanced affinity for the factor Xa ligands (2) and (3). The crystal structures of these variants also exhibited the down and super-up conformations, the latter of which could be converted to up upon soaking and binding of inhibitor (2). The improved affinity of the Glu217-containing variants appears to be due to a shift towards the up conformation. Thus, the reduction in affinity caused by conformational variability of the protein target can be partially or wholly offset by compensatory binding to the up conformation. The insights provided by these studies will be helpful in improving our understanding of ligand binding for the drug design process.

Analyses of Activity for Factor Xa Inhibitors Based on Monte Carlo Simulations

Monte Carlo/Extended Linear Response (MC/ELR) simulations have been conducted on 60 inhibitors of human factor Xa to determine the important interactions associated with their activity. A variety of physicochemical descriptors were configurationally averaged during the course of the simulations of each inhibitor bound to factor Xa and free in water. A regression equation was then derived; it reproduces the experimental inhibition data with a correlation coefficient, r(2), of 0.74, an rms error of 0.67 kcal/mol, and an average unsigned error of 0.60 kcal/mol using only two physically reasonable descriptors. The two factors that emerged as important in determining inhibitory potential are (1) favorable van der Waals interactions between protein and ligand and (2) direct hydrogen bonding between the inhibitor and protein. The conclusions were supported with structural analyses and results of MC/free energy perturbation (FEP) calculations.

ZZ made EZ: influence of inhibitor configuration on enzyme selectivity

Selectivity of drug targeting is necessary in order to forestall undesired side-effects. Here, we examine the structural grounds for the configuration-dependent selectivity of 2,7-bis(4-amidinobenzylidene)-cycloheptan-1-one (1) for factor Xa and trypsin: Previous studies showed that factor Xa is preferentially inhibited by the (Z,Z) configuration isomer of (1), whilst trypsin binds equally well to both (E,Z) and (Z,Z) forms. Using engineered trypsin variants, we find similar overall binding modes for the (E,Z) and (Z,Z) isomers. Minor changes in van der Waals' contacts to Tyr99 (Leu in trypsin) explain the differential inhibition of factor Xa. We note differences in the experimental electron densities observed from co-crystallisation and soaking experiments: while the co-crystallisation of (1) with variants containing Tyr99 (Leu99) reveal the exclusive presence of the (Z,Z) ((E,Z)) configurations respectively, soaking experiments with either variant result in mixtures of (E,Z), (Z,Z) and (E,E). This discrepancy arises presumably from differences in the spatial (packing considerations) or chemical (crystallisation conditions) microenvironments. The results presented here represent an extreme example of the problems that face structure-based drug design, in particular the dangers inherent in relying on a single crystal structure for interpreting protein-ligand interactions.