A comprehensive docking study on the selectivity of binding of aromatic compounds to proteins

Generally, computer-aided drug design is focused on screening of ligand molecules for a single protein target. The screening of several proteins for a ligand is a relatively new application of molecular docking. In the present study, complexes from the Brookhaven Protein Databank were used to investigate a docking approach of protein screening. Automated molecular docking calculations were applied to reproduce 44 protein-aromatic ligand complexes (31 different proteins and 39 different ligand molecules) of the databank. All ligands were docked to all different protein targets in altogether 12090 docking runs. Based on the results of the extensive docking simulations, two relative measures, the molecular interaction fingerprint (MIF) and the molecular affinity fingerprint (MAF), were introduced to describe the selectivity of aromatic ligands to different proteins. MIF and MAF patterns are in agreement with fragment and similarity considerations. Limitations and future extension of our approach are discussed.     

A weak Kantorovich existence theorem for the solution of nonlinear equations

The Kantorovich theorem is a fundamental tool in nonlinear analysis for proving the existence and uniqueness of solutions of nonlinear equations arising in various fields. This theorem was weakened recently by Argyros who used a combination of Lipschitz and center-Lipschitz conditions in place of the Lipschitz conditions of the Kantorovich theorem. In the present paper we prove a weak Kantorovich-type theorem that gives the same conclusions as the previous two results under weaker conditions. Illustrative examples are provided in the paper.     

Drug efficiency indices for improvement of molecular docking scoring functions

A dataset of protein‐drug complexes with experimental binding energy and crystal structure were analyzed and the performance of different docking engines and scoring functions (as well as components of these) for predicting the free energy of binding and several ligand efficiency indices were compared. The aim was not to evaluate the best docking method, but to determine the effect of different efficiency indices on the experimental and predicted free energy. Some ligand efficiency indices, such as ΔG/W (Wiener index), ΔG/NoC (number of carbons), and ΔG/P (partition coefficient), improve the correlation between experimental and calculated values. This effect was shown to be valid across the different scoring functions and docking programs. It also removes the common bias of scoring functions in favor of larger ligands. For all scoring functions, the efficiency indices effectively normalize the free energy derived indices, to give values closer to experiment. Compound collection filtering can be done prior or after docking, using pharmacokinetic as well as pharmacodynamic profiles. Achieving these better correlations with experiment can improve the ability of docking scoring functions to predict active molecules in virtual screening. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

A Unique Tryptophan C‐Prenyltransferase from the Kawaguchipeptin Biosynthetic Pathway

Cyanobactins are a rapidly growing family of linear and cyclic peptides produced by cyanobacteria. Kawaguchipeptins A and B, two macrocyclic undecapeptides reported earlier from Microcystis aeruginosa NIES‐88, are shown to be products of the cyanobactin biosynthetic pathway. The 9 kb kawaguchipeptin (kgp) gene cluster was identified in a 5.26 Mb draft genome of Microcystis aeruginosa NIES‐88. We verified that this gene cluster is responsible for the production of the kawaguchipeptins through heterologous expression of the kgp gene cluster in Escherichia coli. The KgpF prenyltransferase was overexpressed and was shown to prenylate C‐3 of Trp residues in both linear and cyclic peptides in vitro. Our findings serve to further enhance the structural diversity of cyanobactins to include tryptophan‐prenylated cyclic peptides.     

A generalized Kantorovich theorem for nonlinear equations based on function splitting

The Kantorovich theorem is a fundamental tool in nonlinear analysis for proving the existence and uniqueness of solutions of nonlinear equations arising in various fields. In the present paper we formulate and prove a generalized Kantorovich theorem that contains as special cases the Kantorovich theorem and a weak Kantorovich theorem recently proved by Uko and Argyros. An illustrative example is given to show that the new theorem is applicable in some situations in which the other two theorems are not applicable.     

Bis heteroannulation. 8. Total synthesis of (±)-paniculide-A

An efficient synthesis of the title compound 1 has been achieved beginning with 3-methylglutaric anhydride.     

A general treatment of solubility. 2. QSPR prediction of free energies of solvation of specified solutes in ranges of solvents

As part of our general QSPR treatment of solubility (started in the preceding paper), we now present quantitative relationships between solvent structures and the solvation free energies of individual solutes. Solvation free energies of 80 diverse organic solutes are each modeled in a range from 15 to 82 solvents using our CODESSA PRO software. Significant correlations (in terms of squared correlation coefficient) are found for all the 80 solutes: the best fit is obtained for n-propylamine (R(2) = 0.996); the lowest R(2) corresponds to toluene (0.604).     

Theoretical study of aminoalkylation in the Mannich reaction of furan with methyleneimminium salt

The potential energy surface for the reaction of furan and methyleneimminium cation with formation of a Mannich base has been studied using AM1 and PM3 semiempirical calculations. Nonspecific solvent effects were taken account of in the framework of the multicavity self-consistent reaction field approach. Characteristics of the reaction path elucidated for various media are discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 67: 359–366, 1998