Article

Ligand-guided receptor optimization.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.
Methods in molecular biology (Clifton, N.J.) (Impact Factor: 1.29). 01/2012; 857:189-205. DOI: 10.1007/978-1-61779-588-6_8
Source: PubMed

ABSTRACT Receptor models generated by homology or even obtained by crystallography often have their binding pockets suboptimal for ligand docking and virtual screening applications due to insufficient accuracy or induced fit bias. Knowledge of previously discovered receptor ligands provides key information that can be used for improving docking and screening performance of the receptor. Here, we present a comprehensive ligand-guided receptor optimization (LiBERO) algorithm that exploits ligand information for selecting the best performing protein models from an ensemble. The energetically feasible protein conformers are generated through normal mode analysis and Monte Carlo conformational sampling. The algorithm allows iteration of the conformer generation and selection steps until convergence of a specially developed fitness function which quantifies the conformer's ability to select known ligands from decoys in a small-scale virtual screening test. Because of the requirement for a large number of computationally intensive docking calculations, the automated algorithm has been implemented to use Linux clusters allowing easy parallel scaling. Here, we will discuss the setup of LiBERO calculations, selection of parameters, and a range of possible uses of the algorithm which has already proven itself in several practical applications to binding pocket optimization and prospective virtual ligand screening.

0 Bookmarks
 · 
74 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Despite tremendous successes of GPCR crystallog-raphy, the receptors with available structures repre-sent only a small fraction of human GPCRs. An important role of the modeling community is to maxi-mize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smooth-ened receptor. Forty-four modeling groups partici-pated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accu-racy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain un-solved problems. INTRODUCTION
    Structure 08/2014; 22:1-20. · 5.99 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The biological response to the activation of G protein-coupled receptors (GPCRs) typically originates from the simultaneous modulation of various signaling pathways that lead to distinct biological consequences. Hence, 'biased agonists' (i.e., compounds that selectively activate one of the pathways while blocking the others) are highly sought-after molecules to provide fine-tuned pharmacological interventions. This review describes strategies that can be deployed to model the conformation of GPCRs in complex with ligands endowed with specific signaling profiles useful for the generation of hypotheses on the structural requirements for the activation of different signaling pathways or for rational computer-aided ligand discovery campaigns. In particular, it focuses on strategies potentially applicable to model the global or local conformational states of GPCRs stabilized by specific ligands.
    Trends in Pharmacological Sciences 05/2014; · 9.25 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Firemaster 550 (FM550) is an additive flame retardant mixture used within polyurethane foam and is increasingly found in house dust and the environment due to leaching. Despite the widespread use of FM550, very few studies have investigated the potential toxicity of its ingredients during early vertebrate development. In the current study, we sought to specifically investigate mono-substituted isopropylated triaryl phosphate (mITP), a component comprising approximately 32% of FM550, which has been shown to cause cardiotoxicity during zebrafish embryogenesis. Previous research showed that developmental defects are rescued using an aryl hydrocarbon receptor (AHR) antagonist (CH223191), suggesting that mITP-induced toxicity was AHR-dependent. As zebrafish have three known AHR isoforms, we used a functional AHR2 knockout line along with AHR1A- and AHR1B-specific morpholinos to determine which AHR isoform, if any, mediates mITP-induced cardiotoxicity. As in silico structural homology modeling predicted that mITP may bind favorably to both AHR2 and AHR1B isoforms, we evaluated AHR involvement in vivo by measuring CYP1A mRNA and protein expression following exposure to mITP in the presence or absence of CH223191 or AHR-specific morpholinos. Based on these studies, we found that mITP interacts with both AHR2 and AHR1B isoforms to induce CYP1A expression. However, while CH223191 blocked mITP-induced CYP1A induction and cardiotoxicity, knockdown of all three AHR isoforms failed to block mITP-induced cardiotoxicity in the absence of detectable CYP1A induction. Overall, these results suggest that, while mITP is an AHR agonist, mITP causes AHR-independent cardiotoxicity through a pathway that is also antagonized by CH223191.
    Aquatic toxicology (Amsterdam, Netherlands) 05/2014; 154C:71-79. · 3.12 Impact Factor