Maximum common binding modes (MCBM): consensus docking scoring using multiple ligand information and interaction fingerprints

Improving the scoring functions for small molecule-protein docking is a highly challenging task in current computational drug design. Here we present a novel consensus scoring concept for the prediction of binding modes for multiple known active ligands. Similar ligands are generally believed to bind to their receptor in a similar fashion. The presumption of our approach was that the true binding modes of similar ligands should be more similar to each other compared to false positive binding modes. The number of conserved (consensus) interactions between similar ligands was used as a docking score. Patterns of interactions were modeled using ligand receptor interaction fingerprints. Our approach was evaluated for four different data sets of known cocrystal structures (CDK-2, dihydrofolate reductase, HIV-1 protease, and thrombin). Docking poses were generated with FlexX and rescored by our approach. For comparison the CScore scoring functions from Sybyl were used, and consensus scores were calculated thereof. Our approach performed better than individual scoring functions and was comparable to consensus scoring. Analysis of the distribution of docking poses by self-organizing maps (SOM) and interaction fingerprints confirmed that clusters of docking poses composed of multiple ligands were preferentially observed near the native binding mode. Being conceptually unrelated to commonly used docking scoring functions our approach provides a powerful method to complement and improve computational docking experiments.     

A novel subshape molecular descriptor

Molecules with similar shapes and features often have similar biological activity. Several computational approaches search chemical databases for new leads or templates based on overall molecular shape similarity. However, active molecules often present critical subshapes that are required for binding, which may be missed by comparing overall shape similarity. We present a new approach to compare molecular shapes of different sizes and to calculate subshape similarity. We developed a skeletal representation of the shape which is topologically unrelated to covalent chemical connectivity. This simplifies rotational and translational sampling. We test initial possible alignments by matching similar triangles. This triangle-matching filter rapidly eliminates most geometrically impossible matches. Surviving matches are filtered further in successive stages. These stages involve direction, feature, and shape matching procedures. Our approach is applied to several situations demonstrating lead discovery and evolution.     

Application of an integrated cheminformatics-molecular docking approach for discovery for physicochemically similar analogs of fluoroquinolones as putative HCV inhibitors

BackgroundHepatitis C Virus (HCV) infection is a major public health concern across the globe. At present, direct-acting antivirals are the treatment of choice. However, the long-term effect of this therapy has yet to be ascertained. Previously, fluoroquinolones have been reported to inhibit HCV replication by targeting NS3 protein. Therefore, it is logical to hypothesize that the natural analogs of fluoroquinolones will exhibit NS3 inhibitory activity with substantially lesser side effects.MethodIn this study, we tested the application of a recently devised integrated in-silico Cheminformatics-Molecular Docking approach to identify physicochemically similar natural analogs of fluoroquinolones from the available databases (Ambinter, Analyticon, Indofines, Specs, and TimTec). Molecular docking and ROC curve analyses were performed, using PatchDock and Graphpad software, respectively, to compare and analyze drug-protein interactions between active natural analogs, Fluoroquinolones, and HCV NS3 protein.ResultIn our analysis, we were able to shortlist 18 active natural analogs, out of 10,399, that shared physicochemical properties with the template drugs (fluoroquinolones). These analogs showed comparable binding efficacy with fluoroquinolones in targeting 32 amino acids in the HCV NS3 active site that are crucial for NS3 activity. Our approach had around 80 % sensitivity and 70 % specificity in identifying physicochemically similar analogs of fluoroquinolones.ConclusionOur current data suggest that our approach can be efficiently applied to identify putative HCV drug inhibitors that can be taken for in vitro testing. This approach can be applied to discover physicochemically similar analogs of virtually any drug, thus providing a speedy and inexpensive approach to complement drug discovery and design, which can tremendously economize on time and money spent on the screening of putative drugs.     

The free radical distribution in emulsion polymerization using oil-soluble initiators

A new approach is presented to calculate both the distribution of particles with iradicals and the average number of radicals per particle in emulsion polymerizations carried out using oil-soluble initiators. The convergence and accuracy of the approach were examined. It was found that, in agreement with previously published experimental results, the present approach predicts a kinetic behavior similar to that found for water-soluble initiators. This effect is primarily due to the desorption of initiator radicals from the polymer particles rather than the contribution of the fraction of oil-soluble initiator dissolved in the aqueous phase.     

A comparison of the analysis of covariance (ANCOVA) and range-based approaches for assessing batch-to-batch variability of the stability of pharmaceutical products

Stability data were generated by the Monte Carlo method, and batch-to-batch variability was evaluated by analysis of differences in slope and intercept according to the analysis of covariance (ANCOVA) approach recommended in the FDA Guidance. Using the same generated data, batch-to-batch variability was also evaluated by assessing the equivalence of shelf lives estimated for individual batches based on the range (Range-based approach) in order to compare the ability of the two approaches to detect stability differences among batches. The results of the study indicated that the Range-based approach can detect a 30% difference in the slope of degradation curves among batches with a similar beta error as the ANCOVA approach, provided that degradation data are obtained with assay errors below 0.5. The range-based approach appears to be useful as an alternative method to ANCOVA, if it is modified such that the variance of estimates is taken into account.     

Valence bond description for structures of O3, SO2 and NO

A modern valence bond approach, namely bonded tableau unitary group approach, is applied to ozone, sulphur dioxide and nitrite systems, respectively. It is shown that the biradical structure is in the primary position in describing the molecular structure of ozone. Thus three instead of two resonance structures are needed to describe the ground state of ozone. The case of sulphur dioxide is similar to that of ozone. It is found that, however, for the nitrite anion four resonance structures are needed.     

Comparative analysis of HPLC retention: A thermodynamic approach to the interpretation of correlation equations

That correlation equations in the method of comparative analysis of chromatographic retention are linear was explained by the fact that relationships between the Gibbs energies are linear. The specifics of the application of the thermodynamic approach to an analysis of the retention of substances under conditions of reversed-phase partition chromatography were discussed. It was shown that a similar approach can be applied to an analysis of incremental relationships for the retention of three substances.     

Applications of ultrashort shaped pulses in microscopy and for controlling chemical reactions

This article presents a new perspective on laser control based on insights into the effect of spectral phase on nonlinear optical processes. Gaining this understanding requires the systematic evaluation of the molecular response as a function of a series of pre-defined accurately shaped laser pulses. The effort required is rewarded with robust, highly reproducible, results. This approach is illustrated by results on selective two-photon excitation microscopy of biological samples, where higher signal and less photobleaching damage are achieved by accurate phase measurement and elimination of high-order phase distortions from the ultrashort laser pulses. A similar systematic approach applied to laser control of gas phase chemical reactions reveals surprising general trends. Molecular fragmentation pattern is found to be dependent on phase shaping. Differently shaped pulses with similar pulse duration have been found to produce similar fragmentation patterns. This implies that any single parameter that is proportional to the pulse duration, such as second harmonic generation intensity, allows us to predict the molecular fragmentation pattern within the experimental noise. This finding, is illustrated here for a series of isomers. Bond selectivity, coherent photochemistry and their applications are discussed in light of results from these systematic studies.     

A combinatorial/geometric analysis of parallelogram-like benzenoids

We recently reported an algorithm to count Kekulé (resonance) structures for convex cyclofusenes using a combinatorial/geometric approach. Previously, we presented an algorithm for counting resonance structures for parallelogram-like benzenoids with holes by counting descending paths using rectangular meshes with holes. In this article, we employ a similar combinatorial/geometric approach to determine algorithms that will facilitate counting of the resonance structures in parallelogram-like benzenoids with no holes.     

Solid phase peptide templated glycosidic bond formation

Glycosylation reactions performed between a glycosyl donor and acceptor covalently linked to a peptide template both in the solution and solid phase give similar yields and product distributions. The adoption of a solid phase approach opens the way for the synthesis of libraries of peptide templates in an attempt to screen for particular peptide sequences that effect complete regio-and stereochemical control during glycosidic bond formation, whilst the use of second generation donors allows the possibility of an iterative approach.     

Evaluating uncertainty in routine analysis

In this article, we critically describe the different approaches proposed so far for calculating uncertainty in chemical measurements: (1) the ISO approach, adapted for the analytical field by EURACHEM (commonly known as `bottom-up'), and (2) the Analytical Methods Committee approach (commonly known as `top-down'), based on interlaboratory information. We also propose a new procedure, which is totally consistent with the ISO approach in the sense that all the sources of error are identified, quantified and combined, but which is conceptually more similar to the `top-down' approach because of its holistic character. This new procedure estimates uncertainty from the information generated during the process of assessing accuracy.     

Investigation of the low temperature effect in reversed phase micro high performance liquid chromatography

The low temperature effect has been investigated in reversed phase micro high performance liquid chromatography with various aqueous mobile phase systems by an approach based on enthalpy-entropy compensation. The compensation temperatures, Tc , were determined for these systems, and the results show that the retention mechanism in a lower temperature column is similar to that in a normal temperature column in the reversed phase mode at mobile phase water contents above 9.8%. At lower water contents, the separation mechanism is different from that in the reversed phase mode, but otherwise very similar to that in the normal phase mode.     

SURFCOMP: a novel graph-based approach to molecular surface comparison

Analysis of the distributions of physicochemical properties mapped onto molecular surfaces can highlight important similarities or differences between compound classes, contributing to rational drug design efforts. Here we present an approach that uses maximal common subgraph comparison and harmonic shape image matching to detect locally similar regions between two molecular surfaces augmented with properties such as the electrostatic potential or lipophilicity. The complexity of the problem is reduced by a set of filters that implement various geometric and physicochemical heuristics. The approach was tested on dihydrofolate reductase and thermolysin inhibitors and was shown to recover the correct alignments of the compounds bound in the active sites.     

单源前体合成水溶性的CdS和ZnS纳米晶

0引言量子点(QuantumDots)一般指半径小于或接近玻尔激子半径的半导体纳米晶颗粒。和有机染料分子相比,无机半导体纳米晶的带隙宽度可通过简单     

Combining unsupervised and supervised artificial neural networks to predictaquatic toxicity

Most quantitative structure-activity relationship (QSAR) models are linear relationships and significant for only a limited domain of compounds. Here we propose a data-driven approach with a flexible combination of unsupervised and supervised neural networks able to predict the toxicity of a large set of different chemicals while still respecting the QSAR postulates. Since QSAR is applicable only to similar compounds, which have similar biological and physicochemical properties, large numbers of compounds are clustered before building local models, and local models are ensembled to obtain the final result. The approach has been used to develop models to predict the fish toxicity of Pimephales promelas and Tetrahymena pyriformis, a protozoan.     

A critical comparison of search algorithms applied to the optimization of protein side-chain conformations

Three different optimization algorithms are applied to solving the problem of finding the best side-chain conformations with a test set of 14 globular proteins having known crystallographic conformations. It is shown that simulated annealing, simple and modified genetic algorithms, and a heuristic combinatorial approach achieve similar optimal solutions, with the exception of simulated annealing applied to the largest proteins. The efficiency of the different algorithms, however, shows wide variations. General conclusions are drawn concerning the optimal approach to such problems. © 1993 John Wiley & Sons, Inc.