Search results for "Structure based"

Conf-VLKA: A structure-based revisitation of the Virtual Lock-and-key Approach

2016

In a previous work, we developed the in house Virtual Lock-and-Key Approach (VLKA) in order to evaluate target assignment starting from molecular descriptors calculated on known inhibitors used as an information source. This protocol was able to predict the correct biological target for the whole dataset with a good degree of reliability (80%), and proved experimentally, which was useful for the target fishing of unknown compounds. In this paper, we tried to remodel the previous in house developed VLKA in a more sophisticated one in order to evaluate the influence of 3D conformation of ligands on the accuracy of the prediction. We applied the same previous algorithm of scoring and ranking b…

Structure-Based Discovery of Small Molecules Binding to RNA

2017

Ribonucleic acids (RNAs) constitute attractive drug targets. The wealth of structural information about RNAs is steadily increasing making it possible to use this information for the design of new ligands. Two methods that make heavy use of structural knowledge for ligand discovery are molecular docking and fragment screening. In molecular docking the structure of the binding site is used as a template for the design of new ligands using computational methods whereas in fragment screening biophysical methods are used for the detection of weak binding ligands which are subsequently elaborated into tighter binding molecules. In this chapter, we give an overview of both methods in the context …

Targeting Bacterial Sortase A with Covalent Inhibitors: 27 New Starting Points for Structure-Based Hit-to-Lead Optimization.

2019

Because of its essential role as a bacterial virulence factor, enzyme sortase A (SrtA) has become an attractive target for the development of new antivirulence drugs against Gram-positive infections. Here we describe 27 compounds identified as covalent inhibitors of

Off-Target-Based Design of Selective HIV-1 PROTEASE Inhibitors

2021

The approval of the first HIV-1 protease inhibitors (HIV-1 PRIs) marked a fundamental step in the control of AIDS, and this class of agents still represents the mainstay therapy for this illness. Despite the undisputed benefits, the necessary lifelong treatment led to numerous severe side-effects (metabolic syndrome, hepatotoxicity, diabetes, etc.). The HIV-1 PRIs are capable of interacting with “secondary” targets (off-targets) characterized by different biological activities from that of HIV-1 protease. In this scenario, the in-silico techniques undoubtedly contributed to the design of new small molecules with well-fitting selectivity against the main target, analyzing possible undesirabl…

El debat sobre l'estructura causal de la teoria evolutiva: lleis, forces i analogies

2021

Resum: Aquest article analitza l’estructura de la teoria evolutiva i les discussions produides als seu voltant en les ultimes decades. En primer lloc, presente l’anomenada “interpretacio de forces” o “analogia newtoniana” i la seua estructura basada en l’elaboracio de tres lleis fonamentals. Mes endavant, mostre les critiques a aquesta interpretacio per diferents autors, en especial l’anomenada “versio estadistica” de la teoria evolutiva. Posteriorment, analitze la idoneitat de la interpretacio de forces i elabore una reformulacio de la mateixa que permet explicar el seu sorgiment i la seua utilitat dins de la literatura biologica. Abstract: This article analyses the structure of evolutiona…

Innenrücktitelbild: Structure-Based Design of an RNA-Bindingp-Terphenylene Scaffold that Inhibits HIV-1 Rev Protein Function (Angew. Chem. 50/2013)

2013

Structure-Based Design of an RNA-Bindingp-Terphenylene Scaffold that Inhibits HIV-1 Rev Protein Function

2013

Inside Back Cover: Structure-Based Design of an RNA-Bindingp-Terphenylene Scaffold that Inhibits HIV-1 Rev Protein Function (Angew. Chem. Int. Ed. 50…

2013

The Repurposing of Old Drugs or Unsuccessful Lead Compounds by in Silico Approaches: New Advances and Perspectives

2015

Have you a compound in your lab, which was not successful against the designed target, or a drug that is no more attractive? The drug repurposing represents the right way to reconsider them. It can be defined as the modern and rationale approach of the traditional methods adopted in drug discovery, based on the knowledge, insight and luck, alias known as serendipity. This repurposing approach can be applied both in silico and in wet. In this review we report the molecular modeling facilities that can be of huge support in the repurposing of drugs and/or unsuccessful lead compounds. In the last decades, different methods were proposed to help the scientists in drug design and in drug repurpo…

An Experimental Toolbox for Structure‐Based Hit Discovery for P. aeruginosa FabF, a Promising Target for Antibiotics

2021

Abstract FabF (3‐oxoacyl‐[acyl‐carrier‐protein] synthase 2), which catalyses the rate limiting condensation reaction in the fatty acid synthesis II pathway, is an attractive target for new antibiotics. Here, we focus on FabF from P. aeruginosa (PaFabF) as antibiotics against this pathogen are urgently needed. To facilitate exploration of this target we have set up an experimental toolbox consisting of binding assays using bio‐layer interferometry (BLI) as well as saturation transfer difference (STD) and WaterLOGSY NMR in addition to robust conditions for structure determination. The suitability of the toolbox to support structure‐based design of FabF inhibitors was demonstrated through the …