Formation of carbonylrhenium cryptates with alkali metal cations: Coordination chemistry studies of [Ph2P(E)NP(E)Ph2], E = O,S, Se towards ReBr(CO)5

Reaction of ReBr(CO)₅ with Li[Ph₂P(O)NP(O)Ph₂] afforded the cryptate Li[Re₂(CO)₆{μ-Ph₂P(O)NP(O)Ph₂-κ²O,O’}₃]; whereas K[Ph₂P(O)NP(O)Ph₂] reacted with ReBr(CO)₅ to give K[Re₂(CO)₆{μ-Ph₂P(O)NP(O)Ph₂-κ²O,O′}{Ph₂P(O)NP(O)Ph₂-κ²O,O′}₂]. Other chalcogen ligands’ salts M[Ph₂P(E)NP(E)Ph₂], E = Se and S, M = K and Li gave dirhenium carbonyls with bromido and Ph₂P(E)NP(E)Ph₂, E = Se or S bridges upon reaction with ReBr(CO)₅.     

Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking

HIV infection is initiated by fusion of the virus with the target cell through binding of the viral gp120 protein with the CD4 cell surface receptor protein and the CXCR4 or CCR5 co-receptors. There is currently considerable interest in developing novel ligands that can modulate the conformations of these co-receptors and, hence, ultimately block virus-cell fusion. This article describes a detailed comparison of the performance of receptor-based and ligand-based virtual screening approaches to find CXCR4 and CCR5 antagonists that could potentially serve as HIV entry inhibitors. Because no crystal structures for these proteins are available, homology models of CXCR4 and CCR5 have been built, using bovine rhodopsin as the template. For ligand-based virtual screening, several shape-based and property-based molecular comparison approaches have been compared, using high-affinity ligands as query molecules. These methods were compared by virtually screening a library assembled by us, consisting of 602 known CXCR4 and CCR5 inhibitors and some 4700 similar presumed inactive molecules. For each receptor, the library was queried using known binders, and the enrichment factors and diversity of the resulting virtual hit lists were analyzed. Overall, ligand-based shape-matching searches yielded higher enrichments than receptor-based docking, especially for CXCR4. The results obtained for CCR5 suggest the possibility that different active scaffolds bind in different ways within the CCR5 pocket.     

Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach

In this work, we analyze the structure–activity relationships (SAR) of epigenetic inhibitors (lysine mimetics) against lysine methyltransferase (G9a or EHMT2) using a combined activity landscape, molecular docking and molecular dynamics approach. The study was based on a set of 251 G9a inhibitors with reported experimental activity. The activity landscape analysis rapidly led to the identification of activity cliffs, scaffolds hops and other active an inactive molecules with distinct SAR. Structure-based analysis of activity cliffs, scaffold hops and other selected active and inactive G9a inhibitors by means of docking followed by molecular dynamics simulations led to the identification of interactions with key residues involved in activity against G9a, for instance with ASP 1083, LEU 1086, ASP 1088, TYR 1154 and PHE 1158. The outcome of this work is expected to further advance the development of G9a inhibitors.

     

Centralizing discovery information: from logistics to knowledge at a public organization

Due to the huge amount of data generated in drug discovery programs, their success strongly depends on both the workflows and platforms to manage and, more importantly, to integrate different chemical and biological data sources. At Experimental Therapeutics Program in the Spanish National Cancer Research Center (CNIO), we have addressed our efforts in the design and optimal implementation of those key processes that enable dynamic workflows and interfaces between the different information blocks. Our approach focuses on the development of a common chemical and biological repository (CCBR) that gathers all data that pass quality control criteria. An integral web application (WACBIP) was designed to query against CCBR while providing decision making tools. Currently, our CCBR contains more than 43,000 unique structures as well as experimental data from more than 350 different biological assays. As input sources of the CCBR, we federated a series of Laboratory Information Management Systems (LIMS) which cover sections as follows: chemical synthesis, analytical department, compound logistics, biochemical and cellular data (including high-throughput and high-content screenings; HTS and HCS), computational chemistry (in-silico chemogenomics and physico-chemical profiling) and in-vivo pharmacology. With regard to the last section, an integral In-Vivo Management e-Biobook (IVMB) that handles the entire workflow of in-vivo labs was designed and implemented. Herein we describe the processes and tools that we have developed and implemented, balancing purchase and development, for centralizing discovery information as well as providing decision-making and project management tools - a clear unmet need in public organizations and networks.     

Fine tuning for success in structure-based virtual screening

Journal of Computer-Aided Molecular Design - Structure-based virtual screening plays a significant role in drug-discovery. The method virtually docks millions of compounds from corporate or public...