Expanded interaction fingerprint method for analyzing ligand binding modes in docking and structure-based drug design

An expanded interaction fingerprint method has been developed for analyzing the binding modes of ligands in docking and structure-based design methods. Taking the basic premise of representing a ligand in terms of a binary string that denotes its interactions with a target protein, we have expanded the method to include additional interaction-specific information. By considering the hydrogen-bonding strength and/or accessibility of the hydrogen bonding groups within a binding site as well as their geometric arrangement we aim to provide a better representation of a ligand-protein interaction. These expanded methods have been applied to the postprocessing of binding poses generated in a docking study for 220 different proteins and to the analysis of ligands generated by an automated ligand-generation algorithm for the anthrax oedema factor. In the docking study, the application of the interaction fingerprint method as a postprocessing tool resulted in an increased success rate in identifying the crystallographic binding mode. In the analysis of the ligands generated for the anthrax oedema factor, the incorporation of additional interaction-specific information resulted in a more intuitive and comprehensive analysis of automated ligand-generation output.     

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations

The applicability of a computational method, Site Identification by Ligand Competitive Saturation (SILCS), to identify regions on a protein surface with which different types of functional groups on low-molecular weight inhibitors interact is demonstrated. The method involves molecular dynamics (MD) simulations of a protein in an aqueous solution of chemically diverse small molecules from which probability distributions of fragments types, termed FragMaps, are obtained. In the present application, SILCS simulations are performed with an aqueous solution of 1 M benzene and propane to map the affinity pattern of the protein for aromatic and aliphatic functional groups. In addition, water hydrogen and oxygen atoms serve as probes for hydrogen-bond donor and acceptor affinity, respectively. The method is tested using a set of 7 proteins for which crystal structures of complexes with several high affinity inhibitors are known. Good agreement is obtained between FragMaps and the positions of chemically similar functional groups in inhibitors as observed in the X-ray crystallographic structures. Quantitative capabilities of the SILCS approach are demonstrated by converting FragMaps to free energies, termed Grid Free Energies (GFE), and showing correlation between the GFE values and experimental binding affinities. For proteins for which ligand decoy sets are available, GFE values are shown to typically score the crystal conformation and conformations similar to it more favorable than decoys. Additionally, SILCS is tested for its ability to capture the subtle differences in ligand affinity across homologous proteins, information which may be of utility toward specificity-guided drug design. Taken together, our results show that SILCS can recapitulate the known location of functional groups of bound inhibitors for a number of proteins, suggesting that the method may be of utility for rational drug design.     

Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge

We continued prospective assessments of the Wilma–solvated interaction energy (SIE) platform for pose prediction, binding affinity prediction, and virtual screening on the challenging SAMPL4 data sets including the HIV-integrase inhibitor and two host–guest systems. New features of the docking algorithm and scoring function are tested here prospectively for the first time. Wilma–SIE provides good correlations with actual binding affinities over a wide range of binding affinities that includes strong binders as in the case of SAMPL4 host–guest systems. Absolute binding affinities are also reproduced with appropriate training of the scoring function on available data sets or from comparative estimation of the change in target’s vibrational entropy. Even when binding modes are known, SIE predictions lack correlation with experimental affinities within dynamic ranges below 2 kcal/mol as in the case of HIV-integrase ligands, but they correctly signaled the narrowness of the dynamic range. Using a common protein structure for all ligands can reduce the noise, while incorporating a more sophisticated solvation treatment improves absolute predictions. The HIV-integrase virtual screening data set consists of promiscuous weak binders with relatively high flexibility and thus it falls outside of the applicability domain of the Wilma–SIE docking platform. Despite these difficulties, unbiased docking around three known binding sites of the enzyme resulted in over a third of ligands being docked within 2 Å from their actual poses and over half of the ligands docked in the correct site, leading to better-than-random virtual screening results.     

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise

Solvated interaction energy (SIE) is an end-point physics-based scoring function for predicting binding affinities from force-field nonbonded interaction terms, continuum solvation, and configurational entropy linear compensation. We tested the SIE function in the Community Structure-Activity Resource (CSAR) scoring challenge consisting of high-resolution cocrystal structures for 343 protein-ligand complexes with high-quality binding affinity data and high diversity with respect to protein targets. Particular emphasis was placed on the sensitivity of SIE predictions to the assignment of protonation and tautomeric states in the complex and the treatment of metal ions near the protein-ligand interface. These were manually curated from an originally distributed CSAR-HiQ data set version, leading to the currently distributed CSAR-NRC-HiQ version. We found that this manual curation was a critical step for accurately testing the performance of the SIE function. The standard SIE parametrization, previously calibrated on an independent data set, predicted absolute binding affinities with a mean-unsigned-error (MUE) of 2.41 kcal/mol for the CSAR-HiQ version, which improved to 1.98 kcal/mol for the upgraded CSAR-NRC-HiQ version. Half-half retraining-testing of SIE parameters on two predefined subsets of CSAR-NRC-HiQ led to only marginal further improvements to an MUE of 1.83 kcal/mol. Hence, we do not recommend altering the current default parameters of SIE at this time. For a sample of SIE outliers, additional calculations by molecular dynamics-based SIE averaging with or without incorporation of ligand strain, by MM-PB(GB)/SA methods with or without entropic estimates, or even by the linear interaction energy (LIE) formalism with an explicit solvent model, did not further improve predictions.     

Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach

A combined molecular dynamics simulation and multiple ligand docking approach is applied to study the binding specificity of acetylcholinesterase (AChE) with its natural substrate acetylcholine (ACh), a family of substrate analogues, and choline. Calculated docking energies are well correlated to experimental k(cat)/K(M) values, as well as to experimental binding affinities of a related series of TMTFA inhibitors. The "esteratic" and "anionic" subsites are found to act together to achieve substrate binding specificity. We find that the presence of ACh in the active site of AChE not only stabilizes the setup of the catalytic triad but also tightens both subsites to achieve better binding. The docking energy gained from this induced fit is 0.7 kcal/mol for ACh. For the binding of the substrate tailgroup to the anionic subsite, both the size and the positive charge of the tailgroup are important. The removal of the positive charge leads to a weaker binding of 1 kcal/mol loss in docking energy. Substituting each tail methyl group with hydrogen results in both an incremental loss in docking energy and also a decrease in the percentage of structures docked in the active site correctly set up for catalysis.     

Exploring potent ligand for proteins: insights from knowledge-based scoring functions and molecular interaction energies

Structural Chemistry - Two different scoring functions, Hirshfeld fingerprint-based scoring (HFBS) and molecular operating environment (MOE), and the kernel energy method (KEM) along with...     

Study of binding interaction of rivaroxaban with bovine serum albumin using multi-spectroscopic and molecular docking approach

Background

Rivaroxaban is a direct inhibitor of coagulation factor Xa and is used for venous thromboembolic disorders. The rivaroxaban interaction with BSA was studied to understand its PK and PD (pharmacokinetics and pharmacokinetics) properties. Multi-spectroscopic studies were used to study the interaction which included UV spectrophotometric, spectrofluorometric and three dimensional spectrofluorometric studies. Further elucidation of data was done by molecular simulation studies to evaluate the interaction behavior between BSA and rivaroxaban.

Results

Rivaroxaban quenched the basic fluorescence of BSA molecule by the process of static quenching since rivaroxaban and BSA form a complex that results in shift of the absorption spectra of BSA molecule. A decline in the values of binding constants was detected with the increase of temperatures (298–308 K) and the binding constants were in range from 1.32 × 10⁵ to 4.3 × 10³ L mol^?1 indicating the instability of the BSA and rivaroxaban complex at higher temperatures. The data of number of binding sites showed uniformity. The site marker experiments indicated site I (sub-domain IIA) as the principal site for rivaroxaban binding. The thermodynamic study experiments were carried at the temperatures of 298/303/308 K. The ?G⁰, ?H⁰ and ?S⁰ at these temperatures ranged between ? 24.67 and ? 21.27 kJ mol^?1 and the values for ?H⁰ and ?S⁰ were found to be ? 126 kJ mol^?1 and ?S ? 340 J mol^?1 K^?1 The negative value of ?G⁰ indicating spontaneous binding between the two molecules. The negative values in ?H⁰ and ?S⁰ indicated van der Waals interaction and hydrogen bonding were involved during the interaction between rivaroxaban and BSA.

Conclusions

The results of molecular docking were consistent with the results obtained from spectroscopic studies in establishing the principal binding site and type of bonds between rivaroxaban and BSA.

     

Prediction of multiple binding modes of the CDK2 inhibitors, anilinopyrazoles, using the automated docking programs GOLD, FlexX, and LigandFit: an evaluation of performance

Anilinopyrazoles as CDK2 inhibitors can adopt multiple binding modes depending on the substituents at the 5-position of the pyrazole ring, based on CDK2/cyclin A crystallographic studies. Three commercially available docking programs, FlexX, GOLD, and LigandFit, were tested with 63 anilinopyrazole analogues in an attempt to reproduce the binding modes observed in the crystal structures. Each docking program gave different ligand conformations depending on the scoring or energy functions used. FlexX/drugscore, GOLD/chemscore, and LigandFit/plp were the best combinations of each docking program in reproducing the ligand conformations observed in the crystal structures. The 63 analogues were divided into two groups, type-A and type-B, depending on the substituent at the 5-position of the pyrazole ring. Although an alternate binding mode, observed in a crystal structure of one type-B compound, could not be reproduced with any of the above docking/scoring combinations, GOLD, with a template constraint based on the crystal structure coordinates, was able to reproduce the pose. As for type-A compounds, all docking conditions yielded similar poses to those observed in crystal structures. When predicting activities by scoring programs, the combination of docking with LigandFit/plp and scoring with LIGSCORE1_CFF gave the best correlation coefficient (r=0.60) between experimental pIC50 values and top-ranked rescores of 30 poses of each compound. With regard to type-A compounds, the correlation was 0.69. However, when 11 compounds, whose top-ranked rescored poses did not demonstrate the correct binding modes in reference to the crystal structure, were removed, the correlation rose to 0.75. Consequently, predicting activity on the basis of correct binding modes was found to be reliable.     

Competition between coordination bonds and hydrogen bonds: the nitrile-silver(I) interaction using dicyanobithiophene as ligand

Reactions of the ligand 5,5′-dicyano-2,2′-bithiophene (T₂CN₂) with a variety of silver(I) salts are presented. In most cases, the ligand precipitates by itself without incorporating the silver(I) metal. However, when the counterion is triflate, in benzene or THF, a coordination compound is formed. The crystal structure of the species grown from benzene, a double-stranded one-dimensional polymer, is reported. In this structure, the bithiophene ligand is twisted into the uncommon syn orientation. The reasons for the lack of reactivity of the ligand are discussed by comparing the relative strengths of the interligand hydrogen bond with the ligand–metal bond.     

Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space

We present a binding free energy function that consists of force field terms supplemented by solvation terms. We used this function to calibrate the solvation model along with the binding interaction terms in a self-consistent manner. The motivation for this approach was that the solute dielectric-constant dependence of calculated hydration gas-to-water transfer free energies is markedly different from that of binding free energies (J. Comput. Chem. 2003, 24, 954). Hence, we sought to calibrate directly the solvation terms in the context of a binding calculation. The five parameters of the model were systematically scanned to best reproduce the absolute binding free energies for a set of 99 protein-ligand complexes. We obtained a mean unsigned error of 1.29 kcal/mol for the predicted absolute binding affinity in a parameter space that was fairly shallow near the optimum. The lowest errors were obtained with solute dielectric values of Din = 20 or higher and scaling of the intermolecular van der Waals interaction energy by factors ranging from 0.03 to 0.15. The high apparent Din and strong van der Waals scaling may reflect the anticorrelation of the change in solvated potential energy and configurational entropy, that is, enthalpy-entropy compensation in ligand binding (Biophys. J. 2004, 87, 3035-3049). Five variations of preparing the protein-ligand data set were explored in order to examine the effect of energy refinement and the presence of bound water on the calculated results. We find that retaining water in the final protein structure used for calculating the binding free energy is not necessary to obtain good results; that is the continuum solvation model is sufficient. Virtual screening enrichment studies on estrogen receptor and thymidine kinase showed a good ability of the binding free energy function to recover true hits in a collection of decoys.     

Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.     

Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide

Fragment-based drug discovery approaches allow for a greater coverage of chemical space and generally produce high efficiency ligands. As such, virtual and experimental fragment screening are increasingly being coupled in an effort to identify new leads for specific therapeutic targets. Fragment docking is employed to create target-focussed subset of compounds for testing along side generic fragment libraries. The utility of the program Glide with various scoring schemes for fragment docking is discussed. Fragment docking results for two test cases, prostaglandin D2 synthase and DNA ligase, are presented and compared to experimental screening data. Self-docking, cross-docking, and enrichment studies are performed. For the enrichment runs, experimental data exists indicating that the docking decoys in fact do not inhibit the corresponding enzyme being examined. Results indicate that even for difficult test cases fragment docking can yield enrichments significantly better than random. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evaluating the enthalpic contribution to ligand binding using QM calculations: effect of methodology on geometries and interaction energies

As a result of research on ligand efficiency in the pharmaceutical industry, there is greater focus on optimizing the strength of polar interactions within receptors, so that the contribution of overall size and lipophilicity to binding can be decreased. A number of quantum mechanical (QM) methods involving simple probes are available to assess the H-bonding potential of different heterocycles or functional groups. However, in most receptors, multiple features are present, and these have distinct directionality, meaning very minimalist models may not be so ideal to describe the interactions. We describe how the use of gas phase QM models of kinase protein-ligand complex, which can more closely mimic the polar features of the active site region, can prove useful in assessing alterations to a core template, or different substituents. We investigate some practical issues surrounding the use of QM cluster models in structure based design (SBD). These include the choice of the method; semi-empirical, density functional theory or ab-initio, the choice of the basis set, whether to include implicit or explicit solvation, whether BSSE should be included, etc. We find a combination of the M06-2X method and the 6-31G* basis set is sufficiently rapid, and accurate, for the computation of structural and energetic parameters for this system.     

GalaxyDock2: Protein–ligand docking using beta‐complex and global optimization

In this article, an enhanced version of GalaxyDock protein–ligand docking program is introduced. GalaxyDock performs conformational space annealing (CSA) global optimization to find the optimal binding pose of a ligand both in the rigid‐receptor mode and the flexible‐receptor mode. Binding pose prediction has been improved compared to the earlier version by the efficient generation of high‐quality initial conformations for CSA using a predocking method based on a beta‐complex derived from the Voronoi diagram of receptor atoms. Binding affinity prediction has also been enhanced by using the optimal combination of energy components, while taking into consideration the energy of the unbound ligand state. The new version has been tested in terms of binding mode prediction, binding affinity prediction, and virtual screening on several benchmark sets, showing improved performance over the previous version and AutoDock, on which the GalaxyDock energy function is based. GalaxyDock2 also performs better than or comparable to other state‐of‐the‐art docking programs. GalaxyDock2 is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html . © 2013 Wiley Periodicals, Inc.     

N,S-donor acetamide ligand: silver (I) binding and test silver (I) extraction studies

Transition Metal Chemistry - Ligands bearing soft donors including N- and S- have found applications in selective metal recovery due to the ability to preferentially bind soft acceptors like Ag+....     

A [2 x 2] nickel(ii) grid and a copper(ii) square result from differing binding modes of a pyrazine-based diamide ligand

The potentially bis-terdentate diamide ligand N,N'-bis[2-(2-pyridyl)ethyl]pyrazine-2,3-dicarboxamide (H(2)L(Et)) was structurally characterised. Potentiometric titrations revealed rather low pK(a) values for the deprotonation of the first amide group of H(2)L(Et) (14.2) and N,N'-bis(2-pyridylmethyl)pyrazine-2,3-dicarboxamide (H(2)L(Me), 13.1). Two tetranuclear copper(ii) square complexes of H(2)L(Et) with a paddle-wheel appearance, in which each ligand strand acts as a linear N(3)-NO hybrid terdentate-bidentate chelate, have been isolated and structurally characterised. Complex [Cu(II)(4)(H(2)L(Et))(2)(HL(Et))(2)](BF(4))(6).3MeCN.0.5H(2)O (.3MeCN.0.5H(2)O), with two nondeprotonated zwitterionic ligand strands and two monodeprotonated ligand strands, is formed in the 1 : 1 reaction of H(2)L(Et) and Cu(BF(4))(2).4H(2)O. It has a polymeric chain structure of tetranuclear subunits connected by N-H[dot dot dot]N hydrogen bonds. The same reaction carried out with one equivalent of base gives the related compound [Cu(II)(4)(HL(Et))(4)](BF(4))(4) (), with all four ligand strands monodeprotonated. It consists of isolated tetranuclear units. In both .3MeCN.0.5 H(2)O and the copper(ii) ions are in five-coordinate N(4)O environments but the degree of trigonality (tau) differs [.3MeCN.0.5H(2)O 0.14 相似文献   

Design and nonlinear optical properties (NLO) using DFT approach of new Cr(III), VO(II), and Ni(II) chelates incorporating tri-dentate imine ligand for DNA interaction,antimicrobial, anticancer activities and molecular docking studies

In recent years, metals based antitumor complexes have played a vital role in chemotherapy. Therefore, in this study, some new imine Cr(III), VO(II) and Ni(II) complexes incorporating ESAP imine ligand (2-Ethoxy-6-((2-hydroxy-phenylimino)-methyl)-phenol were designed and synthesized. The investigated complexes were fully characterized by micro analysis, infrared, electronic spectra, thermal analysis (TGA), conductivity as well as magnetic susceptibility measurements. Moreover, the stability constants of the prepared complexes were determined spectrophotometrically. The results suggest that the titled ESAP imine ligand serves as tri-dentate moiety through deprotonated two phenolic oxygen and azomethene nitrogen atoms for coordination to Cr(III) in octahedral geometry, tetrahedral to Ni(II) and distorted square pyramidal to VO(II). The electronic structure and nonlinear optical parameters NLO of the newly synthesized complexes are investigated theoretically at the B3LYP/GEN level of theory. The studied complexes show promising optical properties. Indeed, the prepared compounds were evaluated for antimicrobial effect against some types of bacteria and fungi. The investigated complexes exhibit a stronger antimicrobial efficiency compared to its ligand. Moreover, the interaction of the complexes with CT-DNA was monitored using spectral studies, viscosity and gel electrophoreses measurements. Furthermore, the cytotoxic activity of the prepared imine complexes on human colon carcinoma cells, hepatic cellular carcinoma cells and breast carcinoma cells have shown promising results and enhancement of the anti-proliferative activity compared to its ligand. The molecular docking into TRK (PDB: 1t46) was done for the optimization of the investigated compounds as potential TRK inhibitors.     

Sn(3) and Sn(10) sulfonate-oxide-hydroxide clusters with two different sulfonate binding modes

A tin sulfonate-oxide-hydroxide tetracation with two different sulfonate bindings, an electrostatic and a monohapto covalent one, and a tin sulfonate-oxide-hydroxide monocation with two other kinds of sulfonate bindings, an electrostatic and a dihapto bridging one are described here.     

Synthesis, structure and isomerization of arylphosphoranes with anti-apicophilic bonding modes using a novel bidentate ligand with two C(2)F(5) groups

A series of anti-apicophilic pentacoordinate phosphoranes (with one chelating substituent in an O-equatorial, C-apical bonding mode at pentacoordinated phosphorus atom) bearing a para-substituted aryl group (-C(6)H(4)(p-X); X = H, CF(3), F, OMe) or a mesityl (2,4,6-trimethylphenyl) group were isolated using a novel bulky bidentate ligand with two C(2)F(5) groups. These phosphoranes were stable to isomerization at room temperature, and quantitatively converted into the corresponding more stable isomers (O-apical) at elevated temperatures in solution. On the basis of a kinetic study, the free energy of activation (DeltaG(double dagger)) of the stereomutation of the O-equatorial mesitylphosphorane to its O-apical isomer was higher than that of the CF(3) derivative by 2.6 kcal mol(-1), giving rise to a further example of the steric effect of the C(2)F(5) group to freeze the isomerization of the pentacoordinate phosphorus compounds. Kinetic measurements of the isomerization of the O-equatorial ortho-unsubstituted derivatives (-C(6)H(4)(p-X)) to the corresponding O-apical isomers suggested that the O-equatorial isomers were stabilized by the pi --> sigma*(P-O) interaction in the ground state.     

Five- to six-coordination in (nitrosyl)iron(II) porphyrinates: effects of binding the sixth ligand

We report structural and spectroscopic data for a series of six-coordinate (nitrosyl)iron(II) porphyrinates. The structures of three tetraphenylporphyrin complexes [Fe(TPP)(NO)(L)], where L = 4-(dimethylamino)pyridine, 1-methylimidazole, 4-methylpiperidine, are reported here to a high degree of precision and allow observation of several previously unobserved structural features. The tight range of bonding parameters for the [FeNO] moiety for these three complexes suggests a canonical representation for six-coordinate systems (Fe-N(p) = 2.007 A, Fe-N(NO) = 1.753 A, angle FeNO = 138.5 degrees ). Comparison of these data with those obtained previously for five-coordinate systems allows the precise determination of the structural effects of binding a sixth ligand. These include lengthening of the Fe-N(NO) bond and a decrease in the Fe-N-O angle. Several other aspects of the geometry of these systems are also discussed, including the first examples of off-axis tilting of a nitrosyl ligand in a six-coordinate [FeNO](7) heme system. We also report the first examples of M?ssbauer studies for these complexes. Measurements have been made in several applied magnetic fields as well as in zero field. The spectra differ from those of their five-coordinate analogues. To obtain reasonable fits to applied magnetic field data, rotation of the electrical field gradient is required, consistent with differing g-tensor orientations in the five- vs six-coordinate species.