Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.

The recent expansion of GPCR crystal structures provides the opportunity to assess the performance of structure-based drug design methods for the GPCR superfamily. Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA)-based methods are commonly used for binding affinity prediction, as they provide an intermediate compromise of speed and accuracy between the empirical scoring functions used in docking and more robust free energy perturbation methods. In this study, we systematically assessed the performance of MM/PBSA in predicting experimental binding free energies using twenty Class A GPCR crystal structures and 934 known ligands.

Correction: Synthesis and evaluation of nuciferine and roemerine enantiomers as 5-HT and α receptor antagonists.

[This corrects the article DOI: 10.1039/C7MD00629B.].

In vitro functional evaluation of isolaureline, dicentrine and glaucine enantiomers at 5-HT and α receptors.

Compounds with activity at serotonin (5-hydroxytryptamine) 5-HT and α adrenergic receptors have potential for the treatment of central nervous system disorders, drug addiction or overdose. Isolaureline, dicentrine and glaucine enantiomers were synthesized, and their in vitro functional activities at human 5-HT and adrenergic α receptor subtypes were evaluated. The enantiomers of isolaureline and dicentrine acted as antagonists at 5-HT and α receptors with (R)-isolaureline showing the greatest potency (pK  = 8.

Synthesis and evaluation of nuciferine and roemerine enantiomers as 5-HT and α receptor antagonists.

In this study, the ()-enantiomers of the aporphine alkaloids, nuciferine and roemerine, were prepared a synthetic route involving catalytic asymmetric hydrogenation and both stereoisomers were evaluated for functional activity at human 5-HT and adrenergic α receptor subtypes using a transforming growth factor-α shedding assay. Both enantiomers of each of the compounds were found to act as antagonists at 5-HT and α receptors. ()-roemerine was the most potent compound at 5-HT and 5-HT receptors (p = 7.

Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment.

GPCR crystal structures have become more readily accessible in recent years. However, homology models of GPCRs continue to play an important role as many GPCR structures remain unsolved. The new crystal structures now available provide not only additional templates for homology modelling but also the opportunity to assess the performance of homology models against their respective crystal structures and gain insight into the performance of such models.

A dual-application poly (dl-lactic-co-glycolic) acid (PLGA)-chitosan composite scaffold for potential use in bone tissue engineering.

The development of patient-friendly alternatives to bone-graft procedures is the driving force for new frontiers in bone tissue engineering. Poly (dl-lactic-co-glycolic acid) (PLGA) and chitosan are well-studied and easy-to-process polymers from which scaffolds can be fabricated. In this study, a novel dual-application scaffold system was formulated from porous PLGA and protein-loaded PLGA/chitosan microspheres.

Development and Validation of Decision Forest Model for Estrogen Receptor Binding Prediction of Chemicals Using Large Data Sets.

Some chemicals in the environment possess the potential to interact with the endocrine system in the human body. Multiple receptors are involved in the endocrine system; estrogen receptor α (ERα) plays very important roles in endocrine activity and is the most studied receptor. Understanding and predicting estrogenic activity of chemicals facilitates the evaluation of their endocrine activity.

Physicomechanical properties of sintered scaffolds formed from porous and protein-loaded poly(DL-lactic-co-glycolic acid) microspheres for potential use in bone tissue engineering.

An injectable poly(DL-lactic-co-glycolic acid) (PLGA) system comprising both porous and protein-loaded microspheres capable of forming porous scaffolds at body temperature was developed for tissue regeneration purposes. Porous and non-porous (lysozyme loaded) PLGA microspheres were formulated to represent 'low molecular weight' 22-34 kDa, 'intermediate molecular weight' (IMW) 53 kDa and 'high molecular weight' 84-109 kDa PLGA microspheres. The respective average size of the microspheres was directly related to the polymer molecular weight.

Flavonoids with M1 muscarinic acetylcholine receptor binding activity.

Muscarinic acetylcholine receptor-active compounds have potential for the treatment of Alzheimer's disease. In this study, a series of natural and synthetic flavones and flavonols was assayed in vitro for their ability to inhibit radioligand binding at human cloned M1 muscarinic receptors. Several compounds were found to possess competitive binding affinity (Ki=40-110 µM), comparable to that of acetylcholine (Ki=59 µM).

Toward activated homology models of the human M1 muscarinic acetylcholine receptor.

Structure-based virtual screening offers a good opportunity for the discovery of selective M1 muscarinic acetylcholine receptor (mAChR) agonists for the treatment of Alzheimer's disease. However, no 3-D structure of an M1 mAChR is yet available and the homology models that have been previously reported are only able to identify antagonists in virtual screening experiments. In this study, we generated a homology model of the human M1 mAChR, based on the crystal structure of an M3 mAChR as the template.

Molecular dynamics simulations of the adenosine A2a receptor in POPC and POPE lipid bilayers: effects of membrane on protein behavior.

Analysis of 300 ns (ns) molecular dynamics (MD) simulations of an adenosine A2a receptor (A2a AR) model, conducted in triplicate, in 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) and 1-palmitoyl-2-oleoylphosphatidylethanolamine (POPE) bilayers reveals significantly different protein dynamical behavior. Principal component analysis (PCA) shows that the dissimilarities stem from interhelical rather than intrahelical motions. The difference in the hydrophobic thicknesses of these simulated lipid bilayers is potentially a significant reason for the observed difference in results.

The influence of substituted phenols on the sol:gel transition of hydroxypropyl methylcellulose (HPMC) aqueous solutions.

The influence of the physicochemical parameters of substituted aromatic molecules on the phase transition from sol to gel of hydroxypropyl methylcellulose (HPMC) has been investigated using a homologous series of substituted phenols. Using a turbimetric methodology, concentration dependent suppression of phase transition temperature of HPMC was observed for phenol and its derivatives, including methyl-, nitro- and chloro-substituted molecules. Although no strong direct relationship between single molecular physicochemical properties of the phenolic compounds (such as pKa, LogP and other molecular descriptors) and ΔCPT was found for the compounds tested, a successful prediction of behaviour could be obtained by using a combination of parameters.

Conversion of a non-selective adenosine receptor antagonist into A3-selective high affinity fluorescent probes using peptide-based linkers.

Advances in fluorescence-based imaging technologies have helped propel the study of real-time biological readouts and analysis across many different areas. In particular the use of fluorescent ligands as chemical tools to study proteins such as G protein-coupled receptors (GPCRs) has received ongoing interest. Methods to improve the efficient chemical synthesis of fluorescent ligands remain of paramount importance to ensure this area of bioanalysis continues to advance.

Molecular dynamics simulations of the adenosine A2a receptor: structural stability, sampling, and convergence.

Molecular dynamics (MD) simulations of membrane-embedded G-protein coupled receptors (GPCRs) have rapidly gained popularity among the molecular simulation community in recent years, a trend which has an obvious link to the tremendous pharmaceutical importance of this group of receptors and the increasing availability of crystal structures. In view of the widespread use of this technique, it is of fundamental importance to ensure the reliability and robustness of the methodologies so they yield valid results and enable sufficiently accurate predictions to be made. In this work, 200 ns simulations of the A2a adenosine receptor (A2a AR) have been produced and evaluated in the light of these requirements.

Structure-based identification of aporphines with selective 5-HT(2A) receptor-binding activity.

Selective blockade of the serotonin 5-HT(2A) receptor is a useful therapeutic approach for a number of disorders, including schizophrenia, insomnia and ischaemic heart disease. A series of aporphines were docked into a homology model of the rat 5-HT(2A) receptor using AutoDock. Selected compounds with high in silico binding affinities were screened in vitro using radioligand-binding assays against rat serotonin (5-HT(1A) and 5-HT(2A)) and dopamine (D1 and D2) receptors.

Homology modeling of the human 5-HT1A, 5-HT 2A, D1, and D2 receptors: model refinement with molecular dynamics simulations and docking evaluation.

5-HT(1A) serotonin and D1 dopamine receptor agonists have been postulated to be able to improve negative and cognitive impairment symptoms of schizophrenia, while partial agonists and antagonists of the D2 and 5-HT(2A) receptors have been reported to be effective in reducing positive symptoms. There is therefore a need for well-defined homology models for the design of more selective antipsychotic agents, since no three-dimensional (3D) crystal structures of these receptors are currently available. In this study, homology models were built based on the high-resolution crystal structure of the β(2)-adrenergic receptor (2RH1) and further refined via molecular dynamics simulations in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer system with the GROMOS96 53A6 united atom force field.

A quantitative assessment of inhaled drug particle-pulmonary surfactant interaction by atomic force microscopy.

To date limited consideration has been given to the physical interaction between inhaled drug particles and pulmonary surfactant (PS). This study combines atomic force microscopy (AFM) with a Langmuir-Blodgett (LB) approach to quantify the force of adhesion between micronised budesonide particles and simulated PS monolayers. A LB approach was used to prepare Survanta monolayers at pre-determined surface pressures and AFM was employed to facilitate their visualisation.

Crystallization and preliminary X-ray characterization of the Bacillus amyloliquefaciens YwrO enzyme.

CB1954 is an anticancer prodrug that is currently in clinical trials coupled with the Escherichia coli flavoenzyme nitroreductase (NTR) for use in directed-enzyme prodrug therapy (DEPT). The NTR enzyme is responsible for the conversion of the prodrug into a cytotoxic agent. The bifunctional alkylating agent produced by this bioactivation process leads to DNA damage and death of cancer cells.

Modelling the restoration of wild-type dynamic behaviour in DeltaF508-CFTR NBD1 by 8-cyclopentyl-1,3-dipropylxanthine.

Cystic fibrosis (CF) is the most frequently occurring severe, genetic disease in western populations with an incidence as high as 1 in 2500. The principal biochemical defect in CF is a mutation in a membrane transport protein, namely the cystic fibrosis transmembrane conductance regulator (CFTR), which is responsible for the conductance of chloride ions across cell membranes. In 70% of cases a single mutation in CFTR, namely the deletion of amino acid 508 (called DeltaF508) is sufficient to cause severe disease.

Inhibition of cobalamin-dependent methionine synthase by substituted benzo-fused heterocycles.

The cobalamin-dependent cytosolic enzyme, methionine synthase (EC.2.1.

Binding of the anticancer prodrug CB1954 to the activating enzyme NQO2 revealed by the crystal structure of their complex.

CB1954 is an attractive prodrug for directed-enzyme prodrug therapy (DEPT) and a conventional prodrug against tumors in which the enzyme NQO2 is highly expressed. We have determined the crystal structure of the NQO2-CB1954 complex to 2.0 A resolution.

Characterization of drug particle surface energetics and young's modulus by atomic force microscopy and inverse gas chromatography.

Purpose: Particulate interactions are dominated by aspects such as surface topography, exposed chemical moieties, environmental conditions, and thermodynamic properties such as surface free energy (gamma). The absolute value and relative magnitude of surface energies of a drug and excipients within a formulation can significantly influence manufacture, processing, and use. This study utilizes and compares the potentially complementary analytical techniques of atomic force microscopy (AFM) and inverse gas chromatography (IGC) in the quantitative determination of the surface energy of drug (budesonide) particles (micronized and unmilled) relevant to inhaled delivery.

Chemical modification of the naphthoyl 3-position of JWH-015: in search of a fluorescent probe to the cannabinoid CB2 receptor.

In silico modelling was used to guide the positioning of the fluorescent dye NBD-F on the cannabinoid CB2 receptor agonist JWH-015. While the ultimate fluorescent conjugate lost extensive binding affinity to the cannabinoid CB2 receptor, affinity and efficacy studies on the naphthoyl 3-position modified precursor molecules have provided new insight into structure-activity relationships associated with this position.