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Automated docking is one of the most important tools for structure-based drug design that allows prediction of ligand binding poses and also provides an estimate of how well small molecules fit in the binding site of a protein. A new scoring function based on AutoDock and AutoDock Vina has been introduced. The new hybrid scoring function is a linear combination of the two scoring function components derived from a multiple linear regression fitting procedure. The scoring function was built on a training set of 2412 protein-ligand complexes from pdbbind database (www.pdbbind.org.cn, version 2012). A test set of 313 complexes that appeared in the 2013 version was used for validation purposes. The new hybrid scoring function performed better than the original functions, both on training and test sets of protein-ligand complexes, as measured by the non-parametric Pearson correlation coefficient, R, mean absolute error (MAE), and root-mean-square error (RMSE) between the experimental binding affinities and the docking scores. The function also gave one of the best results among more than 20 scoring functions tested on the core set of the pdbbind database. The new AutoDock hybrid scoring function will be implemented in modified version of AutoDock.

In this study, we identified water-soluble C60 and C70 fullerene derivatives as a novel class of protein tyrosine phosphatase inhibitors. The evaluated compounds were found to inhibit CD45, PTP1B, TC-PTP, SHP2, and PTPβ with IC50 values in the low micromolar to high nanomolar range. These results demonstrate a new strategy for designing effective nanoscale protein tyrosine phosphatase inhibitors.

The cone shaped сalix[4]arene hydroxyphosponous, ketophosphonous, methylenebisphosphonous, and hydroxymethylenebisphosphonous acids are specific inhibitors of glutathione S-transferase, ATPases of smooth muscle cells, fibrin polymerization processes

Display Omitted A series of new predictive QSAR models is presented.Artificial Neural Networks used to build QSAR models.The models demonstrated good predictive ability.Cytotoxic activity of 3 compounds against Hep-2 cell line was the highest.Docking studies of 3 compounds predict their binding to the colchicine binding site of tubulin. Microtubules play a significant role in cell growth and functioning. Therefore inhibition of the microtubule assemblies has emerged as one of the most promising cancer treatment strategies. Predictive QSAR models were built on a series of selective inhibitors of the tubulin were performed by using Associative Neural Networks (ANN). To overcome the problem of data overfitting due to the descriptor selection, a 5-fold cross-validation with variable selection in each step of the analysis was used. All developed QSAR models showed excellent statistics on the training (total accuracy: 0.960.97) and test sets (total accuracy: 0.9597). The models were further validated by 11 synthesized 1,3-oxazole derivatives and all of them showed inhibitory effect on the Hep-2 cancer cell line. The most promising compound showed inhibitory activity IC50=60.2M. In order to hypothesize their mechanism of action the top three compounds were docked in the colchicine binding site of tubulin and showed reasonable docking scores as well as favorable interactions with the protein.

A series of dipropoxy-, tripropoxy- and tetrapropoxycalix(4)arenes bearing one or two fragments of α-hydroxymethylphosphonic acid at the upper rim of the macrocycle was prepared by the reaction of the corresponding mono- and di-formylcalixarenes with sodium salts of dialkyl phosphites or with trialkyl (tristrimethylsilyl)phosphites followed by dealkylation (desilylation) of the ester derivatives. The conformations of the macrocyclic skeleton and the stereoisomeric forms of the compounds obtained were investigated by 1 H NMR. The resulting α- hydroxymethylphosphonic acids were found to be able to inhibit the activity of glutathione S- transferase in vitro.

Hundred and two binding sites from 91 Protein Data Bank files for protein tyrosine phosphatase 1B with different ligands have been compared. It was found that they can be divided into five clusters. Additional clusters were formed by the unliganded and oxidized enzyme. The centroids of the clusters can be used as starting points for further studies of enzyme-inhibitor interaction by computer simulations. A special software tool has been created for the investigation of protein tyrosine phosphatase 1B and other enzymes. It performs multiple comparisons of selected parts of Protein Data Bank files, as well as further clustering, and determines mobility of separate residues.

Inhibition of Yersinia protein tyrosine phosphatase by calix[4]arene mono-, bis-, and tetrakis(methylenebisphosphonic) acids as well as calix[4]arene and thiacalix[4]arene tetrakis(methylphosphonic) acids have been investigated. The kinetic studies revealed that some compounds in this class are potent competitive inhibitors of Yersinia PTP with inhibition constants in the low micromolar range. The binding modes of macrocyclic phosphonate derivatives in the enzyme active center have been explained using computational docking approach. The results obtained indicate that calix[4]arenes are promising scaffolds for the development of inhibitors of Yersinia PTP.

Monoester derivatives of thiacalix[4]arene tetrakis(methylphosphonic) acid were found to be capable of inhibiting protein tyrosine phosphatase 1B. In addition, these compounds can strongly bind to human serum albumin.

α,α-Difluoro-β-ketophosphonated derivatives of tetraazamacrocycles were synthesized and found to be potential inhibitors of protein tyrosine phosphatases. N-Substituted conjugates of cyclam and cyclen with bioisosteric phosphonate groups displayed good activities toward T-cell protein tyrosine phosphatase with IC50 values in the micromolar to nanomolar range and showed selectivity over PTP1B, CD45, SHP2, and PTPβ. Kinetic studies indicated that the inhibitors can occupy the region of the active site of TC-PTP. This study demonstrates a new approach which employs tetraazamacrocycles as a molecular platform for designing inhibitors of protein tyrosine phosphatases.

Inhibition of some PTPases by mono-, bis-, and tetrakisphosphorylated calix[4]arenes have been investigated. Kinetics and computational docking studies provide a basis for understanding the mechanism of enzyme–inhibitor complexation, which may be useful for the development of potent inhibitors of the PTPases.

Phosphorylated derivatives of calix[4]arene were evaluated as inhibitors of glutathione S-transferase. Computer-simulated docking studies showed that phosphorylated macrocycle is located near the G-site of the enzyme.

The inhibition effects of enantiomerically pure α-(N-benzylamino)benzylphosphonic acids and their derivatives on human prostatic acid phosphatase have been investigated. As expected, (R)-α-(N-benzylamino)benzylphosphonic acid demonstrated higher affinity for the enzyme than (S)-enantiomer. At the same time, (1R,2S)-phenyl[(1-phenylethyl)amino]methylphosphonic acid was found to be a significantly weaker inhibitor than its (1S,2R)-analogue. The enantioselectivity has been explained using a molecular modeling approach by computational docking of inhibitors into active center of prostatic acid phosphatase.

Isoindolin-1-one-2-ylmethylphosphonic acid derivatives have been synthesized as potential inhibitors of protein tyrosine phosphatases. Molecular docking calculations and assays in vitro showed that isoindolin-1-one-2-ylmethylphosphonic acid can be used as a scaffold for the design of new inhibitors of the enzymes.

In this paper we describe an Internet Java-based technology that allows scientists to make their analytical software available worldwide. The implementation of this technology is exemplified by programs for the calculation of the lipophilicity and water solubility of chemical compounds available at http://www.lnh.unil.ch/~itetko/logp. Both these molecular properties are key parameters in quantitative structure-activity relationship studies and are used to provide invaluable information for the overall understanding of the uptake distribution, biotransformation, and elimination of a wide variety of chemicals. The compounds can be analyzed in batch or single-compound mode. The single-compound analysis offers the possibility to compare our results with several popular lipophilicity calculation methods, including CLOGP, KOWWIN, and XLOGP. The chemical compounds are analyzed according to SMILES line notation that can be prepared with the JME molecular editor of Peter Ertl. Conversion to SMILES from 56 formats is also available using the molecular structure information interchange hub developed by Pat Walters and Matt Stahl.

The inhibition of alkaline phosphatase from bovine intestine mucosa and bovine kidney by calix[4]arenes functionalized at the marcocyclic upper rim by one or two methylene bisphosphonic acid fragments have been investigated. The mechanisms of enzyme inhibition have been discussed using a molecular docking approach by computational modeling of inhibitors into active centers of E. coli alkaline phosphatase.