Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer

Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents

The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In this work, we used the previous results of a computational biochemistry protocol of a series of ligands designed in silico using thermolysin as a model for the search of antihypertensive agents. Here, thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family, was used to determine the most promising candidate as an antibacterial agent. Our results from docking, molecular dynamics simulation, molecular mechanics Poisson-Boltzmann (MM-PBSA) method, ligand efficiency, and ADME-Tox properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicate that the designed ligands were adequately oriented in the thermolysin active site. The Lig783, Lig2177, and Lig3444 compounds showed the best dynamic behavior; however, from the ADME-Tox calculated properties, Lig783 was selected as the unique antibacterial agent candidate amongst the designed ligands.

Recent Trends and Applications of Molecular Modeling in GPCR⁻Ligand Recognition and Structure-Based Drug Design

G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the recent progress in the computational studies focusing on the above issues. In the future, with continuous improvement in both computational hardware and algorithms, molecular modeling would serve as an indispensable tool in a wider scope of the research concerning GPCR–ligand recognition as well as drug design targeting GPCRs.

Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation

The rapid growth of structural information for G-protein-coupled receptors (GPCRs) has led to a greater understanding of their structure, function, selectivity, and ligand binding. Although novel ligands have been identified using methods such as virtual screening, computationally driven lead optimization has been possible only in isolated cases because of challenges associated with predicting binding free energies for related compounds. Here, we provide a systematic characterization of the performance of free-energy perturbation (FEP) calculations to predict relative binding free energies of congeneric ligands binding to GPCR targets using a consistent protocol and no adjustable parameters. Using the FEP+ package, first we validated the protocol, which includes a full lipid bilayer and explicit solvent, by predicting the binding affinity for a total of 45 different ligands across four different GPCRs (adenosine A_2AAR, β₁ adrenergic, CXCR4 chemokine, and δ opioid receptors). Comparison with experimental binding affinity measurements revealed a highly predictive ranking correlation (average spearman ρ = 0.55) and low root-mean-square error (0.80 kcal/mol). Next, we applied FEP+ in a prospective project, where we predicted the affinity of novel, potent adenosine A_2A receptor (A_2AR) antagonists. Four novel compounds were synthesized and tested in a radioligand displacement assay, yielding affinity values in the nanomolar range. The affinity of two out of the four novel ligands (plus three previously reported compounds) was correctly predicted (within 1 kcal/mol), including one compound with approximately a tenfold increase in affinity compared to the starting compound. Detailed analyses of the simulations underlying the predictions provided insights into the structural basis for the two cases where the affinity was overpredicted. Taken together, these results establish a protocol for systematically applying FEP+ to GPCRs and provide guidelines for identifying potent molecules in drug discovery lead optimization projects.

Exploring the binding mechanism of 5-hydroxy-3',4',7-trimethoxyflavone with bovine serum albumin: Spectroscopic and computational approach

The current study was carried out to investigate the binding mechanism of a potential flavonoid compound 5-hydroxy-3',4',7-trimethoxyflavone (HTMF) with bovine serum albumin (BSA) using ultraviolet-visible, fluorescence, circular dichroism (CD) spectral measurements along with molecular docking and molecular dynamics (MD) simulation. It was confirmed from fluorescence spectra that the intrinsic fluorescence of BSA was robustly quenched by HTMF through a static quenching mechanism. The number of binding sites (n) for HTMF binding on BSA was found to be about one. The thermodynamic parameters estimated from the van't Hoff plot specified that hydrophobic force was the predominant force in the HTMF-BSA complex and there also exist hydrogen bonds and electrostatic interactions. The effect of HTMF on the BSA conformation examined using CD studies revealed that there is a decrease in the helical content of BSA upon HTMF interaction. The results of molecular docking study shed light on the binding mode which exposed that HTMF bind within the hydrophobic pocket of the subdomain IIIA of BSA. The stability of HTMF-BSA complex with respect to free protein was analyzed from the molecular dynamic studies. The electronic structure analysis of HTMF was achieved by using density functional theory (DFT) calculations at B3LYP/6-31G** level to support its antioxidant role. The results of computational analysis are in good consistence with the experimental data and the present findings suggested that HTMF exhibits a good binding propensity to BSA protein which will be helpful for the drug design.

A mononuclear zinc(II) complex with piroxicam: crystal structure, DNA- and BSA-binding studies; in vitro cell cytotoxicity and molecular modeling of oxicam complexes

A new mononuclear Zn(II) complex, trans-[Zn(Pir)2(DMSO)2], where Pir(-) is 4-hydroxy-2-methyl-N-2-pyridyl-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (piroxicam), has been synthesized and characterized. The crystal structure of the complex was obtained by the single crystal X-ray diffraction technique. The interaction of the complex with DNA and BSA was investigated. The complex interacts with FS-DNA by two binding modes, viz., electrostatic and groove binding (major and minor). The microenvironment and the secondary structure of BSA are changed in the presence of the complex. The anticancer effects of the seven complexes of oxicam family were also determined on the human K562 cell lines and the results showed reasonable cytotoxicities. The interactions of the oxicam complexes with BSA and DNA were modeled by molecular docking and molecular dynamic simulation methods.

Experimental and molecular modeling studies of the interaction of the polypyridyl Fe(II) and Fe(III) complexes with DNA and BSA

Two mononuclear iron complexes, [Fe(tppz)₂](PF₆)₂·H₂O (1) and Fe(tppz)Cl₃·2CHCl₃ (2) where tppz is (2,3,5,6-tetra(2-pyridyl)pyrazine), have been synthesized and characterized by elemental analysis, spectroscopic methods (UV-Vis and IR) and single crystal X-ray structure analysis. The interaction of (1) as the nitrate salt ([Fe(tppz)₂](NO₃)₂) with calf-thymus DNA (CT-DNA) has been monitored by UV-Vis spectroscopy, competitive fluorescence titration, circular dichroism (CD), voltammetric techniques, viscosity measurement, and gel electrophoresis. Gel electrophoresis of DNA with [Fe(tppz)₂](NO₃)₂ demonstrated that the complex also has the ability to cleave supercoiled plasmid DNA. The results have indicated that the complex binds to CT-DNA by three binding modes, viz., electrostatic, groove and partial insertion of the pyridyl rings between the base stacks of double-stranded DNA. Molecular docking of [Fe(tppz)₂](NO₃)₂ with the DNA sequence d(ACCGACGTCGGT)₂ suggests the complex fits into the major groove. The water-insoluble complex (2) can catalyze the cleavage of BSA at 40 °C. There are no reports of the catalytic effect of polypyridyl metal complexes on the BSA cleavage. Molecular docking of (2) with BSA suggests that, when the chloro ligands in the axial positions are replaced by water molecules, the BSA can interact with the Fe(III) complex more easily.

Design and synthesis of a novel trinuclear palladium(ii) complex containing an oxime chelate ligand: determining the interaction mechanism with the DNA groove and BSA site I by spectroscopic and molecular dynamics simulation approaches

The trinuclear Pd(II) complex containing an oxime ligand showed significant interaction with both CT-DNA and BSA.

Comparative amino acid decomposition analysis of potent type I p38α inhibitors

Background and purpose of the study

p38α is a member of mitogen-activated protein kinases (MAPK) considered as a prominent target in development of anti-inflammatory agents. Any abnormality in the phosphorylation process leads to the different human diseases such as cancer, diabetes and inflammatory diseases. Several small molecule p38α inhibitors have been developed up to now. In this regard, structural elucidation of p38 inhibitors needs to be done enabling us in rational lead development strategies.

Methods

Various interactions of three potent inhibitors with p38α active site have been evaluated in terms of binding energies and bond lengths via density function theory and MD simulations.

Results

Our comparative study showed that both ab initio and MD simulation led to the relatively similar results in pharmacophore discrimination of p38α inhibitors.

Conclusion

The results of the present study may find their usefulness in pharmacophore based modification of p38α inhibitors.

A combined spectroscopic, docking and molecular dynamics simulation approach to probing binding of a Schiff base complex to human serum albumin

The molecular mechanism of a Schiff base complex ((E)-((E)-2-(3-((E)-((E)-3(mercapto (methylthio) methylene)cyclopentylidene) amino) propylimino) cyclopentylidene) (methylthio) methanethiol) binding to Human Serum Albumin (HSA) was investigated by fluorescence quenching, absorption spectroscopy, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of HSA was quenched by this Schiff base complex that has been analyzed for estimation of binding parameters. The titration of Schiff base solution by various amount of HSA was also followed by UV-Vis absorption spectroscopy and the corresponding data were analyzed by suitable models. The results revealed that this Schiff base has an ability to bind strongly to HSA and formed 1:1 complex. Energy transfer mechanism of quenching was discussed and the value of 5.45 ± 0.06 nm was calculated as the mean distance between the bound complex and the Trp residue. This is implying the high possibility of energy transfer from HSA to this Schiff base complex. Molecular docking results indicated that the main active binding site for this Schiff base complex is site III in subdomain IB. Moreover, MD simulation results suggested that this Schiff base complex can interact with HSA, without affecting the secondary structure of HSA but probably with a slight modification of its tertiary structure. MD simulations, molecular docking and experimental data reciprocally supported each other.

Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor

Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the development of clinically useful agents. In this study, the effects of lipid bilayer, N-acetylglucosamine and S-palmitoyl on the dynamic behavior of A(2B)AR model is explored. Homology modeling, molecular docking and molecular dynamics simulations were performed to explore structural features of A(2B)AR in the presence of lipid bilayer. Twenty ns MD simulation was performed on the constructed model inserted in a hydrated lipid bilayer to examine stability of the best model. OSIP339391 as the most potent antagonist was docked in the active site of the model. Another MD simulation was performed on the ligand-protein complex to explore effects of the bilayer on this complex. A similar procedure was performed for the modified protein with N-acetylglucosamine and S-palmitoyl moieties in its structure. Phe173 and Glu174 located in EL2 were determined to be involved in ligand-receptor interactions through π-π stacking and hydrogen bonding. Asn254 was crucial to form hydrogen-bonding. The reliability of the model was assessed through docking using both commercial and synthetic antagonists and an r(2) of 0.70 was achieved. Our results show that molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B)AR in its native environment is a possible approach and this model can be used for designing potent and selective A(2B)AR antagonists.

The use of G-protein coupled receptor models in lead optimization

With the emerging new crystal structures of G-protein coupled receptors (GPCRs), the number of reported in silico receptor models vastly increases every year. The use of these models in lead optimization (LO) is investigated here. Although there are many studies where GPCR models are used to identify new chemotypes by virtual screening, the classical application in LO is rarely reported. The reason for this may be that the quality of a model, which is appropriate for atomistic modeling, must be very high, and the biology of GPCR ligand-dependent signaling is still not fully understood. However, the few reported studies show that GPCR models can be used efficiently in LO for various problems, such as affinity optimization or tuning of physicochemical parameters.

Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation

In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of some inhibitors of chemokine receptor type 5 (CCR5), and to construct a model for designing new CCR5 inhibitors for preventing HIV attachment to the host cell. A homology modeling procedure was employed to construct a 3D model of CCR5. For this procedure, the X-ray crystal structure of bovine rhodopsin (1F88A) at 2.80Å resolution was used as template. After inserting the constructed model into a hydrated lipid bilayer, a 20ns molecular dynamics (MD) simulation was performed on the whole system. After reaching the equilibrium, twenty-four CCR5 inhibitors were docked in the active site of the obtained model. The binding models of the investigated antagonists indicate the mechanism of binding of the studied compounds to the CCR5 obviously. Moreover, 3D pictures of inhibitor-protein complex provided precious data regarding the binding orientation of each antagonist into the active site of this protein. One additional 20 ns MD simulation was performed on the initial structure of the CCR5-ligand 21 complex, resulted from the previous docking calculations, embedded in a hydrated POPE bilayer to explore the effects of the presence of lipid bilayer in the vicinity of CCR5-ligand complex. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.

Synthesis of Quinoline Derivatives as 5-HT4 Receptor Ligands

A general and convenient synthesis of 6-methoxyquinoline-3-carboxamides commencing with a cyclization step that involves ρ-anisidine and diethyl (ethoxymethylene)malonate is described. An additional tetrahydroquinoline scaffold 19 is prepared from 6-methoxyquinoline-3-carboxamide and this represents a novel serotinergic lead structure. These compounds show reasonable affinity at 1 × 10–6 M, and docking experiments suggest that they may bind in a similar manner to serotonin.