The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands

Normal mode analysis and comparative study of intrinsic dynamics of alcohol oxidase enzymes from GMC protein family

Glucose-Methanol-Choline (GMC) family enzymes are very important in catalyzing the oxidation of a wide range of structurally diverse substrates. Enzymes that constitute the GMC family, share a common tertiary fold but < 25% sequence identity. Cofactor FAD, FAD binding signature motif, and similar structural scaffold of the active site are common features of oxidoreductase enzymes of the GMC family. Protein functionality mainly depends on protein three-dimensional structures and dynamics. In this study, we used the normal mode analysis method to search the intrinsic dynamics of GMC family enzymes. We have explored the dynamical behavior of enzymes with unique substrate catabolism and active site characteristics from different classes of the GMC family. Analysis of individual enzymes and comparative ensemble analysis of enzymes from different classes has shown conserved dynamic motion at FAD binding sites. The present study revealed that GMC enzymes share a strong dynamic similarity (Bhattacharyya coefficient >90% and root mean squared inner product >52%) despite low sequence identity across the GMC family enzymes. The study predicts that local deformation energy between atoms of the enzyme may be responsible for the catalysis of different substrates. This study may help that intrinsic dynamics can be used to make meaningful classifications of proteins or enzymes from different organisms.Communicated by Ramaswamy H. Sarma.

Allosteric Modulators of Dopamine D2 Receptors for Fine-Tuning of Dopaminergic Neurotransmission in CNS Diseases: Overview, Pharmacology, Structural Aspects and Synthesis

Allosteric modulation of G protein-coupled receptors (GPCRs) is nowadays a hot topic in medicinal chemistry. Allosteric modulators, i.e., compounds which bind in a receptor site topologically distinct from orthosteric sites, exhibit a number of advantages. They are more selective, safer and display a ceiling effect which prevents overdosing. Allosteric modulators of dopamine D₂ receptor are potential drugs against a number of psychiatric and neurological diseases, such as schizophrenia and Parkinson's disease. In this review, an insightful summary of current research on D₂ receptor modulators is presented, ranging from their pharmacology and structural aspects of ligand-receptor interactions to their synthesis.

Mind the Gap—Deciphering GPCR Pharmacology Using 3D Pharmacophores and Artificial Intelligence

G protein-coupled receptors (GPCRs) are amongst the most pharmaceutically relevant and well-studied protein targets, yet unanswered questions in the field leave significant gaps in our understanding of their nuanced structure and function. Three-dimensional pharmacophore models are powerful computational tools in in silico drug discovery, presenting myriad opportunities for the integration of GPCR structural biology and cheminformatics. This review highlights success stories in the application of 3D pharmacophore modeling to de novo drug design, the discovery of biased and allosteric ligands, scaffold hopping, QSAR analysis, hit-to-lead optimization, GPCR de-orphanization, mechanistic understanding of GPCR pharmacology and the elucidation of ligand–receptor interactions. Furthermore, advances in the incorporation of dynamics and machine learning are highlighted. The review will analyze challenges in the field of GPCR drug discovery, detailing how 3D pharmacophore modeling can be used to address them. Finally, we will present opportunities afforded by 3D pharmacophore modeling in the advancement of our understanding and targeting of GPCRs.

Investigation of potential descriptors of chemical compounds on prevention of nephrotoxicity via QSAR approach

Drug-induced nephrotoxicity remains a common problem after exposure to medications and diagnostic agents, which may be heightened in the kidney microenvironment and deteriorate kidney function. In this study, the toxic effects of fourteen marked drugs with the individual chemical structure were evaluated in kidney cells. The quantitative structure–activity relationship (QSAR) approach was employed to investigate the potential structural descriptors of each drug-related to their toxic effects. The most reasonable equation of the QSAR model displayed that the estimated regression coefficients such as the number of ring assemblies, three-membered rings, and six-membered rings were strongly related to toxic effects on renal cells. Meanwhile, the chemical properties of the tested compounds including carbon atoms, bridge bonds, H-bond donors, negative atoms, and rotatable bonds were favored properties and promote the toxic effects on renal cells. Particularly, more numbers of rotatable bonds were positively correlated with strong toxic effects that displayed on the most toxic compound. The useful information discovered from our regression QSAR models may help to identify potential hazardous moiety to avoid nephrotoxicity in renal preventive medicine.

Preferential Coupling of Dopamine D2S and D2L Receptor Isoforms with Gi1 and Gi2 Proteins-In Silico Study

The dopamine D₂ receptor belongs to rhodopsin-like G protein-coupled receptors (GPCRs) and it is an important molecular target for the treatment of many disorders, including schizophrenia and Parkinson's disease. Here, computational methods were used to construct the full models of the dopamine D₂ receptor short (D_2S) and long (D_2L) isoforms (differing with 29 amino acids insertion in the third intracellular loop, ICL3) and to study their coupling with G_i1 and G_i2 proteins. It was found that the D_2L isoform preferentially couples with the G_i2 protein and D_2S isoform with the G_i1 protein, which is in accordance with experimental data. Our findings give mechanistic insight into the interplay between isoforms of dopamine D₂ receptors and G_i proteins subtypes, which is important to understand signaling by these receptors and their mediation by pharmaceuticals, in particular psychotic and antipsychotic agents.

Conformational Flexibility of the Protein-Protein Interfaces of the Ebola Virus VP40 Structural Matrix Filament

The Ebola virus (EBOV) is a virulent pathogen that causes severe hemorrhagic fever with a high fatality rate in humans. The EBOV transformer protein VP40 plays crucial roles in viral assembly and budding at the plasma membrane of infected cells. One of VP40's roles is to form the long, flexible, pleomorphic filamentous structural matrix for the virus. Each filament contains three unique interfaces: monomer NTD-NTD to form a dimer, dimer-to-dimer NTD-NTD oligomerization to form a hexamer, and end-to-end hexamer CTD-CTD to build the filament. However, the atomic-level details of conformational flexibility of the VP40 filament are still elusive. In this study, we have performed explicit-solvent, all-atom molecular dynamic simulations to explore the conformational flexibility of the three different interface structures of the filament. Using dynamic network analysis and other calculational methods, we find that the CTD-CTD hexamer interface with weak interdomain amino acid communities is the most flexible, and the NTD-NTD oligomer interface with strong interdomain communities is the least flexible. Our study suggests that the high flexibility of the CTD-CTD interface may be essential for the supple bending of the Ebola filovirus, and such flexibility may present a target for molecular interventions to disrupt the Ebola virus functioning.

Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays

In the current work, we developed a computational pipeline method for predicting the binding affinities of studied compounds at the specific target sites. Since many approved therapeutic compounds involve indole or indole-derivative rings, in the current study we focused compounds including these fingerprints. Initially, 212520 compounds were retrieved from Specs-SC library and after the conversion of IUPAC text file format, compounds that include 'indol' keyword (5194 compounds) were used in binary QSAR-based models to screen against a defined therapeutic activity "Alzheimer's disease" (AD). The molecules that have higher AD therapeutic activity values (>0.5) were then used in the 26 different toxicity-QSAR models. Binary QSAR models resulted 89 hits that have high AD therapeutic activity and no toxicity. Selected 89 molecules were then screened against acetylcholinesterase (AChE) targets using molecular docking and top-docking poses of compounds were used in initially short (10 ns) molecular dynamics (MD) simulations. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations were performed for 89 ligands and tightly bound 17 ligands based on average MM/GBSA scores were selected for long (100 ns) MD simulations. The same protocol was also applied for the known 4 AChE inhibitors. Selected hits were also docked to the binding pocket of butyrylcholinesterase (BChE). Finally, based on MM/GBSA scores, as well as their corresponding docking scores and metabolite production profiles, 7 compounds were selected and their in vitro tests were performed. Out of 7 compounds, 6 of them showed μM-level inhibition for both AChE and BChE targets.Communicated by Ramaswamy H. Sarma.

Probing Binding Landscapes and Molecular Recognition Mechanisms of Atypical Antipsychotic Drugs towards the Selective Targeting of D2 Dopamine Receptor

Dopamine receptors constitute a unique class of G-protein coupled receptors that mediate the activities of dopamine, a neurotransmitter implicated in diverse neurological diseases when dysregulated. Over the years, antipsychotic drugs have been primarily directed towards D₂ dopamine receptor (DRD2) while associable adverse effects have been centred on non-selective targeting. The recent crystal structure of DRD2 in complex with atypical antipsychotic could further aid the structure-based design of highly DRD2-selective antipsychotics. Therefore, in this study, we comprehensively investigate the molecular recognition and differential binding landscapes of class-I and II DRD2 atypical antipsychotics, using membrane-bilayer molecular dynamics simulation and binding free energy techniques. Findings revealed that selected class-I antipsychotics exhibited binding dynamics and poses dissimilar to the class-II types with different interactive mechanisms at the binding cavity of DRD2. More interestingly, the class-II drugs established a highly coordinated binding at the DRD2 active site with a pertinent and recurrent involvement of Asp114 via strong hydrogen interactions. Furthermore, while these compounds exert distinct effects on DRD2 structure, findings revealed that the class-II types favourably engaged the deep hydrophobic pocket of DRD2 compared to the class-I drugs. We speculate that these findings will be fundamental to the discovery of highly selective DRD2 antipsychotics.

Molecular dynamics simulation of biased agonists at the dopamine D2 receptor suggests the mechanism of receptor functional selectivity

The dopamine D2 receptor (D2R) is the primary target for antipsychotic drugs. Besides schizophrenia, this receptor is linked to dementia, Parkinson's disease, and depression. Recent studies have shown that β-arrestin biased agonists at this receptor treat schizophrenia with less side effects. Although the high resolution structure of this receptor exists, the mechanism of biased agonism at the receptor is unknown. In this study, dopamine, the endogenous unbiased G-protein agonist, MLS1547, a G-protein biased agonist, and UNC9975, a G-protein antagonist and a β-arrestin biased agonist, were docked to a homology model of the whole D2R including all flexible loops, and molecular dynamics simulations were conducted to study the potential mechanisms of biased agonism. Our thorough analysis on the protein-ligand interaction, secondary structure, tertiary structure, structure dynamics, and molecular switches of all three systems indicates that ligand binding to transmembrane 3 might be essential for G-protein recruitment, while ligand binding to transmembrane 6 might be essential for β-arrestin recruitment. Our analysis also suggests changes in both the secondary and the tertiary structures of TM5 and TM7, molecular switches and ICL3 flexibility are important in biased signaling. Communicated by Ramaswamy H. Sarma.

Comparative molecular field analysis and molecular dynamics studies of the dopamine D2 receptor antagonists without a protonatable nitrogen atom

The dopaminergic hypothesis of schizophrenia is the main concept explaining the direct reasons of schizophrenia and the effectiveness of current antipsychotics. All antipsychotics present on the market are potent dopamine D₂ receptor antagonists or partial agonists. In this work we investigate a series of dopamine D₂ receptor antagonists which do not fulfill the criteria of the classical pharmacophore model as they do not possess a protonatable nitrogen atom necessary to interact with the conserved Asp(3.32). Such compounds are interesting, inter alia, due to possible better pharmacokinetic profile when compared to basic, ionizable molecules. By means of homology modeling, molecular docking and molecular dynamics we determined that the compounds investigated interact with Asp(3.32) via their amide nitrogen atom. It was found that the studied compounds stabilize the receptor inactive conformation through the effect on the ionic lock, which is typical for GPCR antagonists. We constructed a CoMFA model for the studied compounds with the following statistics: R² = 0.95, Q² = 0.63. The quality of the CoMFA model was confirmed by high value of R² of the test set, equal 0.96. The CoMFA model indicated two regions where bulky substituents are favored and two regions where bulky substituents are not beneficial. Two red contour regions near carbonyl groups were identified meaning that negative charge would be favored here. Furthermore, the S-oxide group is connected with blue contour region meaning that positive charge is favored in this position. These findings may be applied for further optimization of the studied compound series.

Molecular Mechanism and Dynamics of S-Deoxyephedrine Moving through Molecular Channels within D3R

In this article, the trajectories of S-deoxyephedrine (SBD) along molecular channels within the complex protein structure of third dopamine receptor (D₃R) are analyzed via molecular dynamic techniques, including potential mean force calculations of umbrella samplings from the 4.5 version of the GROMACS program. Changes in free energy due to the movement of SBD within D₃R are determined, and the molecular dynamic mechanisms of SBD transmitting along molecular channels are probed. Molecular simulated results show that the change in free energy is calculated as 171.7 kJ·mol^-1 for the transmission of SBD toward the outside of the cell along the y+ axis functional molecular channel and is 275.0 kJ·mol^-1 for movement toward the intracellular structure along the y- axis. Within the internal structure of D₃R, the changes in free energy are determined to be 103.6, 242.1, 459.7, and 127.8 kJ·mol^-1 for transmission of SBD along the x+, x-, z+, and z- axes, respectively, toward the cell bilayer membrane, which indicates that SBD leaves much more easily along the x+ axis through the gap between the TM5 (the fifth transmembrane helix) and TM6 (the sixth transmembrane helix) from the internal structure of D₃R. The values of free-energy changes indicate that SBD molecules can clear the protective channel within D₃R, which helps dopamine molecules to leave the D₃R internal structure along the x+ axis and to prevent them for exerting excessive neurotransmitter function. Therefore, our results suggest that SBD is effective for development as a drug for treating schizophrenia and its pharmacology is closely related to its dynamics and mechanisms within the molecular pathway of dopamine receptors.

Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking

Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2^HighR and D2^LowR dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2^HighR and D2^LowR targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2^HighR and D2^LowR with binding affinities (K_i) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [³H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2^HighR. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2^HighR binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2^LowR. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.