A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series

We introduce the "Prime-ligand" method for ranking ligands in congeneric series. The method employs a single scoring function, the OPLS-AA/GBSA molecular mechanics/implicit solvent model, for all stages of sampling and scoring. We evaluate the method using 12 test sets of congeneric series for which experimental binding data is available in the literature, as well as the structure of one member of the series bound to the protein. Ligands are "docked" by superimposing a common stem fragment among the compounds in the series using a crystal complex from the Protein Data Bank and sampling the conformational space of the variable region. Our results show good correlation between our predicted rankings and the experimental data for cases in which binding affinities differ by at least 1 order of magnitude. For 11 out of 12 cases, >90% of such ligand pairs could be correctly ranked, while for the remaining case, Factor Xa, 76% of such pairs were correctly ranked. A small number of compounds could not be docked using the current protocol because of the large size of functional groups that could not be accommodated by a rigid receptor. CPU requirements for the method, involving CPU minutes per ligand, are modest compared with more rigorous methods that use similar force fields, such as free energy perturbation. We also benchmark the scoring function using series of ligands bound to the same protein within the CSAR data set. We demonstrate that energy minimization of ligands in the crystal structures is critical to obtain any correlation with experimentally determined binding affinities.     

Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities

Summary Exploitation of protein structures for potential drug leads by molecular docking is critically dependent on methods for scoring putative protein-ligand interactions. An ideal function for scoring must exhibit predictive accuracy and high computational speed, and must be tolerant of variations in the relative protein-ligand molecular alignment and conformation. This paper describes the development of an empirically derived scoring function, based on the binding affinities of protein-ligand complexes coupled with their crystallographically determined structures. The function's primary terms involve hydrophobic and polar complementarity, with additional terms for entropic and solvation effects. The issue of alignment/conformation dependence was solved by constructing a continuous differentiable nonlinear function with the requirement that maxima in ligand conformation/alignment space corresponded closely to crystallographically determined structures. The expected error in the predicted affinity based on cross-validation was 1.0 log unit. The function is sufficiently fast and accurate to serve as the objective function of a molecular-docking search engine. The function is particularly well suited to the docking problem, since it has spatially narrow maxima that are broadly accessible via gradient descent.     

A general mass spectrometry-based assay for the quantitation of protein-ligand binding interactions in solution

A new method that utilizes matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and exploits the hydrogen/deuterium (H/D) exchange properties of proteins was developed for measuring the thermodynamic properties of protein-ligand complexes in solution. Dissociation constants (Kd values) determined by the method for five model protein-ligand complexes that included those with small molecules, nucleic acids, peptides, and other proteins were generally in good agreement with Kd values measured by conventional methods. Important experimental advantages of the described method over existing methods include: the ability to make measurements in a high-throughput and automated fashion, the ability to make measurements using only picomole quantitities of protein, and the ability to analyze either purified or unpurified protein-ligand complexes.     

High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing

We have developed a system for performing computations on an enterprise grid using a freely available package for grid computing that allows us to harvest unused CPU cycles off of employee desktop computers. By modifying the traditional formulation of Molecular Mechanics with Poisson-Boltzmann Surface Area (MM-PBSA) methodology, in combination with a coarse-grain parallelized implementation suitable for deployment onto our enterprise grid, we show that it is possible to produce rapid physics-based estimates of protein-ligand binding affinities that have good correlation to experimental data. This is demonstrated by examining the correlation of our calculated binding affinities to experimental data and also by comparison to the correlation obtained from the binding-affinity calculations using traditional MM-PBSA that are reported in the literature.     

Three-dimensional distribution function theory for the prediction of protein-ligand binding sites and affinities: application to the binding of noble gases to hen egg-white lysozyme in aqueous solution

The three-dimensional distribution function theory of molecular liquids is applied to lysozyme in mixtures of water and noble gases. The results indicate that the theory has the capability of predicting the protein-ligand binding sites and affinities. First, it is shown that the theory successfully reproduces the binding sites of xenon found by X-ray crystallography. Then, the ability of the theory to predict the size selectivity of noble gases is demonstrated. The effect of water on the selectivity is clarified by a theoretical analysis. Finally, it is demonstrated that the dose-response curve, which is employed in experiments for examining the binding affinity, is realized by the theory.     

Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities

Binding mode calculations for complexes between an artificial paracyclophane receptor and digoxins, cholic acids as well as cortisone steroids show encapsulation of different ring combinations. Docking experiments were performed between the 26-10 antibody and digoxins. Coordination affinity arises from hydrophobic desolvation and van der Waals interactions rather than from hydrogen bonds. The specificity and affinity arises mainly from shape complementarity. Computed binding free energies and Kohonen neural network computations both point to physicochemical and structural similarities of natural antibodies and artificial receptors.     

Communication between the active site and the allosteric site in class A beta-lactamases

Bacterial production of beta-lactamases, which hydrolyze beta-lactam type antibiotics, is a common antibiotic resistance mechanism. Antibiotic resistance is a high priority intervention area and one strategy to overcome resistance is to administer antibiotics with beta-lactamase inhibitors in the treatment of infectious diseases. Unfortunately, beta-lactamases are evolving at a rapid pace with new inhibitor resistant mutants emerging every day, driving the design and development of novel beta-lactamase inhibitors. Here, we examined the inhibitor recognition mechanism of two common beta-lactamases using molecular dynamics simulations. Binding of beta-lactamase inhibitor protein (BLIP) caused changes in the flexibility of regions away from the binding site. One of these regions was the H10 helix, which was previously identified to form a lid over an allosteric inhibitor binding site. Closer examination of the H10 helix using sequence and structure comparisons with other beta-lactamases revealed the presence of a highly conserved Trp229 residue, which forms a stacking interaction with two conserved proline residues. Molecular dynamics simulations on the Trp229Ala mutants of TEM-1 and SHV-1 resulted in decreased stability in the apo form, possibly due to loss of the stacking interaction as a result of the mutation. The mutant TEM-1 beta-lactamase had higher H10 fluctuations in the presence of BLIP, higher affinity to BLIP and higher cross-correlations with BLIP. Our results suggest that the H10 helix and specifically W229 are important modulators of the allosteric communication between the active site and the allosteric site.     

The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.     

A new technique to determine organic and inorganic acid contamination

A new acid indicator pad was developed for the detection of acid breakthrough of gloves and chemical protective clothing. The pad carries a reagent which responds to acid contaminant by producing a color change. The pad was used to detect both organic and inorganic acids permeating through glove materials using the modified ASTM F-739 and direct permeability testing procedures. Breakthrough times for each type of glove were determined, and found to range from 4 min to > 4 h for propionic acid, from 3 min to > 4 h for acrylic acid, and from 26 min to > 4 h for HCl. A quantification was performed for propionic and acrylic acids following solvent desorption and gas chromatography. Both acids exhibited > 99% adsorption [the acid and its reactivity (the acid reacted with an indicator to contribute the color change)] on the pads at a spiking level of 1.8 microL for each acid. Acid recovery during quantification was calculated for each acid, ranging from 52-72% (RSD < or = 4.0%) for both acids over the spiking range 0.2-1.8 microL. The quantitative mass of the acids on the pads at the time of breakthrough detection ranged from 260-282 and 270-296 microg cm(-2) for propionic acid and acrylic acid, respectively. The new colorimetric indicator pad should be useful in detecting and collecting acid permeation samples through gloves and chemical protective clothing in both laboratory and field studies, for quantitative analysis.     

A simple gas chromatographic technique to determine trace impurities in gases

A new method is described which allows the determination of trace impurities in flowing gases without removing a sample. The technique is based upon gas fractionation by a sudden change of flow through a small orifice or capillary.     

A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections

We present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.     

Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation

The computational determination of binding modes for a ligand into a protein receptor is much more successful than the prediction of relative binding affinities (RBAs) for a set of ligands. Here we consider the binding of a set of 26 synthetic A-CD ligands into the estrogen receptor ERα. We show that the MOE default scoring function (London dG) used to rank the docked poses leads to a negligible correlation with experimental RBAs. However, switching to an energy-based scoring function, using a multiple linear regression to fit experimental RBAs, selecting top-ranked poses and then iteratively repeating this process leads to exponential convergence in 4–7 iterations and a very strong correlation. The method is robust, as shown by various validation tests. This approach may be of general use in improving the quality of predicted binding affinities.     

Micelle-mediated extractions using nonionic surfactant mixtures and HPLC-UV to determine endocrine-disrupting phenols in seawaters

An environmentally friendly method to extract endocrine-disrupting phenols (EDPs) from seawaters was realized using nonionic surfactant mixtures and micelle-mediated extractions. The preconcentration step was achieved directly in the seawater matrix, and was followed by high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection without any clean-up steps to remove the surfactant mixture prior to injection. Various nonionic surfactant mixtures were used, and polyoxyethylene-10-laurylether (POLE) with polyoxyethylene-4-laurylether (Brij 30) was found to be the best to work with. Method optimization involved maximizing the preconcentration factor using the studied mixtures. The proposed method gave extraction recoveries ranging from 83.3 to 114.4% for an EDP spiking level of 46.7 μg L⁻¹, and from 63.4 to 112.4% for a spiking level of 4.7 μg L⁻¹ for EDPs studied in real seawater matrices, with relative standard deviations of <12.1%. The detection limits of the method varied from 0.18 μg L⁻¹ for bisphenol A (BPA) to 1.17 μg L⁻¹ for 4-cumylphenol (4-CP). The method was applied to seawaters from the Canary Islands with successful results. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A test for the reliability of the controlled potential coulometric method to determine plutonium in uranium-plutonium mixtures

Summary A method has been developed for the determination of trimethylsilyl groups in N-silylated compounds and in trimethylsilyl esters of carboxylic acids. The method is based on the desilylation of the compound to be analysed with phenol followed by gas-chromatographic determination of the trimethylphenoxysilane formed. The relative error of the determination is around 1% and the standard deviation is 1.20 × 10^–3 (3.12%). A single determination takes less than 2 h.

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Gas-chromatographische Bestimmung von Trimethylsilyl-Gruppen in N-silylierten Verbindungen und in Trimethylsilyl-Estern von Carbonsäuren

Zusammenfassung Das Verfahren beruht auf der Desilylierung der zu analysierenden Verbindung mit Phenol und der anschlie\enden gas-chromatographischen Bestimmung des gebildeten Trimethylphenoxysilans. Der relative Fehler der Bestimmung beträgt ca. 1% und die Standardabweichung 1,20 × 10^–3 (3,12%). Die Bestimmungszeit ist kürzer als 2 h.

     

Coherent forward scattering technique to determine copper in steels,zinc and tin

Coherent forward scattering spectroscopy having the Voigt configuration was applied in the determination of copper in steels, zinc and tin. Copper (0.0005–0.2%) in these metals could be determined without preconcentration procedure. The relative standard deviations were 4.4% for 0.0035% copper and 7.1% for 0.067% copper in steel. The reproducibility of calibration curves for copper in steels (log-log plotting with a slope of about two) was about 18% and the limit of detection was about 0.4 ± 0.07 ng/10 μl.     

Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin

The binding of a set of 10 triphenoxypyridine derivatives to two serine proteases, factor Xa and trypsin, has been used to analyze factors related to sampling and convergence in free energy calculations based on molecular dynamics simulation techniques. The inhibitors investigated were initially proposed as part of the Critical Assessment of Techniques for Free Energy Evaluation (CATFEE) project for which no experimental results nor any assessment of the predictions submitted by various groups have ever been published. The inhibitors studied represent a severe challenge for explicit free energy calculations. The mutations from one compound to another involve up to 19 atoms, the creation and annihilation of net charge and several alternate binding modes. Nevertheless, we demonstrate that it is possible to obtain highly converged results (+/- 5-10 kJ/mol) even for such complex multi-atom mutations by simulating on a nanosecond time scale. This is achieved by using soft-core potentials to facilitate the creation and deletion of atoms and by a careful choice of mutation pathway. The results show that given modest computational resources, explicit free energy calculations can be successfully applied to realistic problems in drug design.     

Ozonolysis in solvent/water mixtures: direct conversion of alkenes to aldehydes and ketones

Ozonolysis of alkenes in the presence of solubilized water results in the direct formation of aldehydes and/or ketones, avoiding the need to isolate or decompose ozonides.     

Convection, diffusion and reaction in a surface-based biosensor: modeling of cooperativity and binding site competition on the surface and in the hydrogel

We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.     

A comparison of direct methods to determine n-th order kinetic parameters of solid thermal decomposition for use in fire models

Pyrolysis models for burning solids in fire simulations are sensitive to the values of the activation energy, frequency factor, and reaction order that characterize the thermal decomposition of the solid to gaseous fuel, so direct measurement of these kinetic parameters is recommended, and simple methods are preferred. Three direct methods were evaluated with regard to the ability of their kinetic parameters to reproduce the thermal decomposition of five polymers measured by differential thermogravimetric analysis using the reaction order model. It was found that the two multiple heating rate methods produced identical, physically based kinetic parameters, while the peak property method produced non-physical kinetic parameters. However, all of these kinetic parameters in a single-step reaction order model gave reasonably good conversion histories for non-charring and moderately charring polymers. For a highly charring polymer, the conversion histories were poorly described without a multiple step reaction. The temperature at the maximum rate of conversion was found to be essentially independent of the reaction order, which decouples the frequency factor from the reaction order in the direct kinetic methods. Any of the direct methods are sufficiently accurate to obtain kinetic parameters for pyrolysis models because of the inherent spatial and temporal averaging of reaction rates at the burning surface of a thick solid and the uncertainty in the heat transfer mechanisms and thermo-physical parameters used in the models.