Variable selection and model validation of 2D and 3D molecular descriptors>

We have found that molecular shape and electrostatics, in conjunction with 2D structural fingerprints, are important variables in discriminating classes of active and inactive compounds. The subject of this paper is how to explore the selection of these variables and identify their relative importance in quantitative structure-activity relationships (QSAR) analysis. We show the use of these variables in a form of similarity searching with respect to a crystal structure of a known bound ligand. This analysis is then validated through k-fold cross-validation of enrichments via several common classifiers. Additionally, we show an effective methodology using the variables in hypothesis generation; namely, when the crystal structure of a bound ligand is not known.     

De novo ligand design with explicit water molecules: an application to bacterial neuraminidase

Most computer-aided drug design methods ignore the presence of crystallographically-determined water molecules in the binding site of a target protein. In this paper, our de novo ligand design methods are applied to the X-ray crystal structure of bacterial neuraminidase in the presence of some selected water molecules. We have found that, for this particular protein, the complete removal of all bound water molecules leads to difficulties in generating any potential ligands if the unsatisfied hydrogen-bonding sitepoints left by removing these water molecules are to be satisfied by a ligand. As more of the crystallographically determined water molecules are allowed in the binding site, it becomes much easier to generate ligands in larger numbers and with wider chemical diversity. This example shows that, in some cases, bound water molecules can be more accessible for hydrogen bonding to an incoming ligand than the actual protein binding sitepoints associated with them. From the point of view of de novo ligand design, water molecules can thus act as versatile amphiprotic hydrogen-bonding sitepoints and reduce the conformational constraints of a particular binding site.     

Receptor‐Bound Conformation of Cilengitide Better Represented by Its Solution‐State Structure than the Solid‐State Structure

The X‐ray crystal and NMR spectroscopic structures of the peptide drug candidate Cilengitide (cyclo(RGDf(NMe)Val)) in various solvents are obtained and compared in addition to the integrin receptor bound conformation. The NMR‐based solution structures exhibit conformations closely resembling the X‐ray structure of Cilengitide bound to the head group of integrin αvβ3. In contrast, the structure of pure Cilengitide recrystallized from methanol reveals a different conformation controlled by the lattice forces of the crystal packing. Molecular modeling studies of the various ligand structures docked to the αvβ3 integrin revealed that utilization of the solid‐state conformation of Cilengitide leads—unlike the solution‐based structures—to a mismatch of the ligand–receptor interactions compared with the experimentally determined structure of the protein–ligand complex. Such discrepancies between solution and crystal conformations of ligands can be misleading during the structure‐based lead optimization process and should thus be taken carefully into account in ligand orientated drug design.     

Accurate prediction of the bound form of the Akt pleckstrin homology domain using normal mode analysis to explore structural flexibility

Molecular docking is often performed with rigid receptors. This can be a serious limitation, since the receptor often differs between bound and unbound forms or between bound forms with different ligands. We recently developed a normal-mode based docking method and showed that it is possible to obtain reasonable estimates of the complexed form of the pleckstrin homology (PH) domain of Akt, starting with the free form of the receptor. With inositol (1,3,4,5)-tetrakisphosphate (IP4) as the ligand the docked results agree with the known high-resolution X-ray crystal structure of the IP4-Akt PH domain complex. We also tested our methods with PH4, SC66, and PIT-1, several recently designed PH domain inhibitors. The results are shown to be consistent with available experimental data and previous modeling studies. The method we described can be used for molecular docking analysis even when only an approximation of the experimental structure or model is known.     

Ab initio computational modeling of long loops in G-protein coupled receptors

A newly developed approach for predicting the structure of segments that connect known elements of secondary structure in proteins has been applied to some of the longer loops in the G-protein coupled receptors (GPCRs) rhodopsin and the dopamine receptor D2R. The algorithm uses Monte Carlo (MC) simulation in a temperature annealing protocol combined with a scaled collective variables (SCV) technique to search conformation space for loop structures that could belong to the native ensemble. Except for rhodopsin, structural information is only available for the transmembrane helices (TMHs), and therefore the usual approach of finding a single conformation of lowest energy has to be abandoned. Instead the MC search aims to find the ensemble located at the absolute minimum free energy, i.e., the native ensemble. It is assumed that structures in the native ensemble can be found by an MC search starting from any conformation in the native funnel. The hypothesis is that native structures are trapped in this part of conformational space because of the high-energy barriers that surround the native funnel. In this work it is shown that the crystal structure of the second extracellular loop (e2) of rhodopsin is a member of this loop’s native ensemble. In contrast, the crystal structure of the third intracellular loop is quite different in the different crystal structures that have been reported. Our calculations indicate, that of three crystal structures examined, two show features characteristic of native ensembles while the other one does not. Finally the protocol is used to calculate the structure of the e2 loop in D2R. Here, the crystal structure is not known, but it is shown that several side chains that are involved in interaction with a class of substituted benzamides assume conformations that point into the active site. Thus, they are poised to interact with the incoming ligand.     

Revealing the Absolute Configuration of the CO and CN− Ligands at the Active Site of a [NiFe] Hydrogenase

Combined molecular dynamics (MD) and quantum mechanical/molecular mechanical (QM/MM) calculations were performed on the crystal structure of the reduced membrane‐bound [NiFe] hydrogenase (MBH) from Ralstonia eutropha to determine the absolute configuration of the CO and the two CN^? ligands bound to the active‐site iron of the enzyme. For three models that include the CO ligand at different positions, often indistinguishable on the basis of the crystallographic data, we optimized the structures and calculated the ligand stretching frequencies. Comparison with the experimental IR data reveals that the CO ligand is in trans position to the substrate‐binding site of the bimetallic [NiFe] cluster.     

Synthesis, spectroscopic characterization and crystal structure of mixed ligand Ni(II) complex of N-4-diethylaminosalicylidine-N′-4-nitrobenzoyl hydrazone and 4-picoline

A novel mixed ligand nickel complex [NiLB] [H₂L-N-4-diethylaminosalicylidine-N′-4-nitrobenzoyl hydrazone and B-4-picoline] has been synthesized and characterized by elemental analysis, IR spectrum, UV-Vis spectrum and structure has been confirmed by single crystal X-ray structure analysis. The crystal structure reveals that the complex adopts distorted square planar structure with ONO donor atoms of primary ligand and N donor atom of the secondary ligand 4-picoline.     

Electron nuclear double resonance determined structures of enzyme reaction intermediates: structural evidence for substrate destabilization

Angle selective ENDOR of nitroxyl spin-labels is briefly reviewed to illustrate the methodology of structure analysis developed in our laboratory for characterizing catalytically competent intermediates of enzyme catalyzed reactions. ENDOR structure determination of a reaction intermediate of α-chymotrypsin formed with a kinetically specific spin-labeled substrate and of an enzyme-inhibitor complex formed with a spin-labeled transition-state inhibitor analog is briefly described. Both spin-labeled molecules bound in the active site of the enzyme are found in torsionally distorted conformations. It is suggested that this torsionally distorted state in which the bound ligand is of higher potential energy than in the ground state conformation reflects substrate destabilization in the course of the enzyme catalyzed reaction.     

A molecular mechanics/grid method for evaluation of ligand–receptor interactions

We present a computational method for prediction of the conformation of a ligand when bound to a macromolecular receptor. The method is intended for use in systems in which the approximate location of the binding site is known and no large-scale rearrangements of the receptor are expected upon formation of the complex. The ligand is initially placed in the vicinity of the binding site and the atomic motions of the ligand and binding site are explicitly simulated, with solvent represented by an implicit solvation model and using a grid representation for the bulk of the receptor protein. These two approximations make the method computationally efficient and yet maintain accuracy close to that of an all-atom calculation. For the benzamidine/trypsin system, we ran 100 independent simulations, in many of which the ligand settled into the low-energy conformation observed in the crystal structure of the complex. The energy of these conformations was lower than and well-separated from that of others sampled. Extensions of this method are also discussed. © 1995 by John Wiley & Sons, Inc.     

Synthesis,Crystal Structures,Thermal and Magnetic Properties of New Selenocyanato Coordination Polymers with Pyrazine as Co‐Ligand

Reaction of iron(II), cobalt(II) and nickel(II) selenocyanate with pyrazine in water at room temperature leads to the formation of the isotypic new ligand‐rich 1:2 (1:2 = ratio between metal and co‐ligand) compounds [M(NCSe)₂(pyrazine)₂]_n (M = Fe ( 1 ), Co ( 2 ), Ni ( 3 )). The crystal structure of 2 was determined by X‐ray single crystal analysis and those of 1 and 3 were refined from X‐ray powder data with the Rietveld method. In their crystal structure the metal(II) cations are coordinated by four pyrazine co‐ligands, which connect them into layers, and two terminally N‐bonded selenocyanato anions in a distorted octahedral arrangement. The terminal coordination mode of the selenocyanato anions was further emphasized by IR spectroscopic investigations. On heating, all compounds decompose in a single heating step without the formation of ligand‐deficient intermediates like previously reported for related thiocyanato compounds. Magnetic measurements of compound 1 show a long‐range antiferromagnetic ordering with an ordering temperature of T_N = 6.7 K, which must be mediated by the aromatic π‐system of the pyrazine ligand, whereas 2 and 3 show only Curie–Weiss behavior with antiferromagnetic exchange interactions.     

New polymorphic modification of the crystal structure of bromopeganol

The crystal structure of 6-bromopeganol in a new polymorphic modification is found and determined by single crystal X-ray diffraction analysis. For the crystal structure of the new polymorph the formation of a centrosymmetric closed dimer (associate) is also characteristic. It consists of two bromopeganol molecules bound by centrosymmetric reciprocal hydrogen bonds O-H...N(1). This polymorph differs from the known one in the mutual arrangement and interaction of these associates. Original Russian Text Copyright ? 2009 by R. Ya. Okmanov, A. G. Tozhiboev, K. K. Turgunov, B. Tashkhodzhaev, N. I. Mukarramov, and Kh. M. Shakhidoyatov __________ Translated from Zhurnal Strukturnoi Khimii, Vol. 50, No. 2, pp. 396–398, March–April, 2009.     

Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4

Drug Design Data Resource (D3R) Grand Challenge 4 (GC4) offered a unique opportunity for designing and testing novel methodology for accurate docking and affinity prediction of ligands in an open and blinded manner. We participated in the beta-secretase 1 (BACE) Subchallenge which is comprised of cross-docking and redocking of 20 macrocyclic ligands to BACE and predicting binding affinity for 154 macrocyclic ligands. For this challenge, we developed machine learning models trained specifically on BACE. We developed a deep neural network (DNN) model that used a combination of both structure and ligand-based features that outperformed simpler machine learning models. According to the results released by D3R, we achieved a Spearman's rank correlation coefficient of 0.43(7) for predicting the affinity of 154 ligands. We describe the formulation of our machine learning strategy in detail. We compared the performance of DNN with linear regression, random forest, and support vector machines using ligand-based, structure-based, and combining both ligand and structure-based features. We compared different structures for our DNN and found that performance was highly dependent on fine optimization of the L2 regularization hyperparameter, alpha. We also developed a novel metric of ligand three-dimensional similarity inspired by crystallographic difference density maps to match ligands without crystal structures to similar ligands with known crystal structures. This report demonstrates that detailed parameterization, careful data training and implementation, and extensive feature analysis are necessary to obtain strong performance with more complex machine learning methods. Post hoc analysis shows that scoring functions based only on ligand features are competitive with those also using structural features. Our DNN approach tied for fifth in predicting BACE-ligand binding affinities.

     

<Emphasis Type="Italic">In-silico</Emphasis> Screening using Flexible Ligand Binding Pockets: A Molecular Dynamics-based Approach

Summary In-silico screening of flexible ligands against flexible ligand binding pockets (LBP) is an emerging approach in structure-based drug discovery. Here, we describe a molecular dynamics (MD) based docking approach to investigate the influence on the high-throughput in-silico screening of small molecules against flexible ligand binding pockets. In our approach, an ensemble of 51 energetically favorable structures of the LBP of human estrogen receptor α (hERα) were collected from 3 ns MD simulations. In-silico screening of 3500 endocrine disrupting compounds against these flexible ligand binding pockets resulted in thousands of ER–ligand complexes of which 582 compounds were unique. Detailed analysis of MD generated structures showed that only 17 of the LBP residues significantly contribute to the overall binding pocket flexibility. Using the flexible LBP conformations generated, we have identified 32 compounds that bind better to the flexible ligand-binding pockets compared to the crystal structure. These compounds, though chemically divergent, are structurally similar to the natural hormone. Our MD-based approach in conjunction with grid–based distributed computing could be applied routinely for in-silico screening of large databases against any given target.     

Harmonic modes as variables to approximately account for receptor flexibility in ligand–receptor docking simulations: Application to DNA minor groove ligand complex

An approach to approximately account for receptor flexibility in ligand–receptor docking simulations is described and applied to a DNA/Hoechst 33258 analogue complex. Harmonic modes corresponding to eigenvectors with small eigenvalues of the Hessian matrix of the potential energy function were used as independent variables to describe receptor flexibility. For the DNA minor groove ligand case most of the conformational difference between an energy minimized free DNA and ligand-bound structure could be assigned to 5–40 harmonic receptor modes with small eigenvalues. During docking, deformations of the DNA receptor structure in the subset of harmonic modes were limited using a simple penalty function that avoided the summation over all intrareceptor atom pairs. Significant improvement of the sterical fit between ligand and receptor was found upon relaxation of the DNA in the subset of harmonic modes after docking of the ligand at the position found in the known crystal structure. In addition, the harmonic mode relaxation resulted in DNA structures that were more similar to the energy minimized ligand-bound form. Although harmonic mode relaxation also leads to improved sterical fit for other ligand placements, the placement as observed in the crystal structure could still be identified as the site with the most favorable sterical interactions. Because relaxation in the harmonic modes is orders of magnitude faster than conventional energy minimization using all atom coordinates as independent variables, the approach might be useful as a preselection tool to recognize ligand binding sites accessible only upon small conformational changes of the receptor. The harmonic mode relaxed structures can only be considered as approximate structures because deformation of the receptor in the harmonic modes can lead to small perturbations of the stereochemical geometry of the molecule. Energy minimization of preselected ligand–DNA docking candidates in all atom coordinates is required to reduce these deviations. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 287–300, 1999     

A gadolinium(III) complex: synthesis,structure, photophysical profile and its role in the degradation of nitroaromatics

The synthesis and structural characterization of a gadolinium(III) complex with phenanthroline and thiocyanate ligands have been accomplished. The X-ray crystal structure reveals that Gd(III) in a slightly distorted square anti-prism coordinated with four thiocyanate ions and two phenanthroline molecules; one phenanthroline is protonated which compensates the charge of Gd(III) center. The crystal structure shows chemically significant non-covalent interactions like hydrogen bonding involving the thiocyanate ligand and π–π interactions between uncoordinated phenanthrolinium and coordinated phen. Investigation on the intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that close contacts are mainly associated with weak interactions. The fingerprint plots demonstrate that these weak interactions are important for crystal packing. The Gd(III) complex shows photophysical activity. The compound is capable of degrading toxic pollutants like nitroaromatics and may have far reaching consequences for cleaning these toxic pollutants from industrial effluents.     

Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase

[NiFe] hydrogenases catalyse the reaction H₂↔2H⁺+2e⁻. Several states of the enzyme have been observed by spectroscopic methods. Among these, the two most oxidized states, called the unready Ni–A and Ni–SU states, have been especially intriguing, because they take a much longer time to activate than the corresponding ready Ni–B and Ni–SI states. It has recently been suggested that the unready states actually contain a (hydro)peroxide bridge between the Ni and Fe ions, in contrast to the hydroxide bridge in the ready states. In this paper, we use quantum refinement (crystallographic refinement, in which the molecular mechanics [MM] calculations, normally employed to supplement the crystallographic data, are replace by more accurate quantum mechanics [QM] calculations), combined QM/MM calculations, and accurate energy estimates to study the nature of a recent oxidised crystal structure of [NiFe] hydrogenase from Desulfovibrio fructosovorans. We show that the structure contains a mixture of several states in the active site. The experimental data is best explained by structures with a hydroxide bridge but with two of the cysteine ligands (one bridging and one terminal) partly oxidised. When the terminal Cys-543 ligand is oxidised, the sulphur occupies an alternative position, observed in several crystal structures. The Glu-25 residue, that forms a hydrogen bond to this sulphur, also changes position. A peroxide ligand may exist as a minor component in the crystal and the suggested structure is supported by the calculations. We suggest that oxidised states are slow-equilibrium mixtures of structures with a peroxide bound and structures with oxidised Cys residues, and that the former can be activated by replacement of the protonated peroxide with a H₂ or CO ligand, as has been observed in electrochemical experiments.     

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become heritable traits (sic). We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein–ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTO DOCK , and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein–ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard error of 9.11 kJ mol⁻¹ (2.177 kcal mol⁻¹) and was chosen as the new energy function. The new search methods and empirical free energy function are available in AUTO DOCK , version 3.0. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1639–1662, 1998     

Conservation of mus-ms enzyme motions in the apo- and substrate-mimicked state

Solution NMR spin-relaxation experiments were used to compare mus-ms dynamics in RNase A in the apo form and as complexed to the substrate-mimic, pTppAp. The crystal structure of the RNase A/pTppAp complex was determined and demonstrates that this ligand binds at the active site and utilizes established substrate binding sites in its interaction with RNase A. Relaxation-compensated CPMG experiments identify flexible residues in and around the active site in both the apo and pTppAp-bound enzyme. Quantitative analysis of the NMR spin-relaxation dispersion curves show that the time scale of motion in RNase A is unchanged when pTppAp binds and is similar to the time scale for the rate-determining step of the catalytic reaction. Temperature-dependent measurements provide an activation barrier for motion of 5.2 +/- 1.0 kcal/mol and 4.5 +/- 1.2 kcal/mol for the apo and pTppAp forms of RNase A, respectively. These data indicate very similar motion exists in the free and bound enzyme. Additionally, chemical shift data suggests that the magnitude of motion is also similar for these two forms and that it is likely that apo enzyme interconverts to a structure that resembles a ligand-bound form. Likewise, it appears that the bound conformation samples the apo enzyme form even when ligand is present. Taken together the data imply that RNase A is in a preexisting dynamic equilibrium between two conformations that represent the open and closed enzyme forms. These data suggest that ligand binding stabilizes the bound conformer but does not induce it.     

Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach

Manganese superoxide dismutases catalyze the disproportionation of the superoxide radical anion to molecular oxygen and hydrogen peroxide. Recently, atomic-resolution crystal structures of the reduced and oxidized enzymes have been reported. They show an active site with the manganese ion bound to one aspartate, three histidine residues, and a solvent molecule. In this paper, we combine crystallographic refinement with quantum mechanical methods to show that the solvent ligand is undoubtedly a water molecule in the reduced state. However, the putative oxidized structure is to a large extent reduced during data collection, so that it contains a mixture of the Mn2+ and Mn3+ structure. The crystal structures show that the Mn-bound solvent molecule accepts a hydrogen bond from the side chain of the conserved Gln-146 residue. If the solvent ligand is water, then this could lead to a steric clash, but it is avoided by the plane of water molecule forming an angle of 72 degrees to the Mn-O bond. Such a conformation is also found outside the enzyme, giving a minimal destabilization of the reduced state. We show by molecular dynamics simulations that the suggested Mn2+-H2O and Mn3+-OH- structures are stable. Moreover, we show that the superoxide substrate may bind both in the first coordination sphere of the Mn ion, opposite to the aspartate ligand, or in the second sphere, close to the conserved Tyr-34 and His-30 residues, approximately 5 A from Mn. However, the second-sphere structures are not stable in long molecular dynamics simulations. We see no difference in the coordination between the reduced and the oxidized states of the enzyme.     

Molecular Rectangle Formed by Head-to-tail Self-Assembly of 1-(Dipyrrin-2-yl)-1-(dipyrrin-3-yl)methane

Summary. 1-(Dipyrrin-2-yl)-1-(dipyrrin-3-yl)methane, the N-confused analog of biladiene-ac, is prepared by condensation of 2,3-dipyrromethane with two molecules of 2-formylpyrrole in dichloromethane in the presence of hydrogen bromide. Self-assembly of the ligand with Zn(II) in dichloromethane and methanol offers a dinuclear dimeric complex with a ligand:metal ratio of 2:2. X-Ray crystal structure analysis reveals two ligands bound through a head-to-tail pattern to two zinc centers to form a severely distorted helical conformation, which has the shape of a rectangle.