A Free Energy Based Computational Pathway from Chemical Templates to Lead Compounds: A Case Study of COX-2 Inhibitors

4-quinolones as noncovalent inhibitors of high molecular mass penicillin-binding proteins

Penicillin-binding proteins (PBPs) are important bacterial enzymes that carry out the final steps of bacterial cell wall assembly. Their DD-transpeptidase activity accomplishes the essential peptide cross-linking step of the cell wall. To date, all attempts to discover effective inhibitors of PBPs, apart from β-lactams, have not led to new antibiotics. Therefore, the need for new classes of efficient inhibitors of these enzymes remains. Guided by a computational fragment-based docking procedure, carried out on Escherichia coli PBP5, we have designed and synthesized a series of 4-quinolones as potential inhibitors of PBPs. We describe their binding to the PBPs of E. coli and Bacillus subtilis. Notably, these compounds bind quite tightly to the essential high molecular mass PBPs.

Preparation and characterization of inclusion complex of iprodione and beta-cyclodextrin to improve fungicidal activity

The effect of beta-cyclodextrin (beta-CD) on the improvement of the fungicidal activity of iprodione has been investigated. The inclusion complexation of beta-CD with iprodione has been prepared and characterized by integrating some analytical techniques (such as electrospray ionization-mass spectrometry, differential scanning calorimetry, thermogravimetry, x-ray diffraction, and scanning electron microscopy) and molecular simulation methods. The beta-CD/iprodione inclusion complex has exhibited different spectroscopic features and properties from iprodione. The stoichiometric ratio and stability constant describing the extent of formation of inclusion complexes have been determined by phase solubility studies. The calculated apparent stability constant of the iprodione/beta-CD complex was 407.5 M-1. The obtained inclusion complexes were found to significantly improve the water solubility of iprodione, and there is a 4.7-fold increase in the presence of 13 mM beta-CD as compared with the solubility of iprodione in deionized water in the absence of beta-CD. The bioassay demonstrated that the complex displayed over two-fold increase of the fungicidal activity. In addition, the possible structure of the beta-CD/iprodione complex was proposed according to the results of the molecular dynamic simulation. The present study provided useful information for a more rational application of iprodione, diminishing the use of organic solvents and increasing its efficacy.

Protein Structure Evaluation using an All-Atom Energy Based Empirical Scoring Function

Arriving at the native conformation of a polypeptide chain characterized by minimum most free energy is a problem of long standing interest in protein structure prediction endeavors. Owing to the computational requirements in developing free energy estimates, scoring functions--energy based or statistical--have received considerable renewed attention in recent years for distinguishing native structures of proteins from non-native like structures. Several cleverly designed decoy sets, CASP (Critical Assessment of Techniques for Protein Structure Prediction) structures and homology based internet accessible three dimensional model builders are now available for validating the scoring functions. We describe here an all-atom energy based empirical scoring function and examine its performance on a wide series of publicly available decoys. Barring two protein sequences where native structure is ranked second and seventh, native is identified as the lowest energy structure in 67 protein sequences from among 61,659 decoys belonging to 12 different decoy sets. We further illustrate a potential application of the scoring function in bracketing native-like structures of two small mixed alpha/beta globular proteins starting from sequence and secondary structural information. The scoring function has been web enabled at www.scfbio-iitd.res.in/utility/proteomics/energy.jsp.