Molecular Modeling Of Interaction Research Articles

DNA G-Quadruplex Recognition In Vitro and in Live Cells by a Structure-Specific Nanobody.

G-quadruplexes (G4s) are four-stranded DNA secondary structures that occur in the human genome and play key roles in transcription, replication, and genome stability. G4-specific molecular probes are of vital importance to elucidate the structure and function of G4s. The scFv antibody BG4 has been a widely used G4 probe but has various limitations, including relatively poor in vitro expression and the inability to be expressed intracellularly to interrogate G4s in live cells. To address these considerations, we describe herein the development of SG4, a camelid heavy-chain-only derived nanobody that was selected against the human Myc DNA G4 structure. SG4 exhibits low nanomolar affinity for a wide range of folded G4 structures in vitro. We employed AlphaFold combined with molecular dynamics simulations to construct a molecular model for the G4-nanobody interaction. The structural model accurately explains the role of key amino acids and Kd measurements of SG4 mutants, including arginine-to-alanine point mutations that dramatically diminish G4 binding affinity. Importantly, predicted amino acid-G4 interactions were subsequently confirmed experimentally by biophysical measurements. We demonstrate that the nanobody can be expressed intracellularly and used to image endogenous G4 structures in live cells. We also use the SG4 protein to positionally map G4s in situ and also on fixed chromatin. SG4 is a valuable, new tool for G4 detection and mapping in cells.

Effect of Fe and Al on phosphorus distribution characteristics during solidification of Si-Fe-Al alloy melt

Phosphorus (P) in metallurgical grade silicon (MG-Si) affects the production of downstream silicon materials. By ignoring the influence of minor elements on P, MG-Si can be approximated to a Si-Fe-Al system, and the distribution characteristics of P directly affect its separation. This study investigated the effect of Fe and Al on the P distribution characteristics during solidification of the Si-Fe-Al alloy melt. In an experiment, MG-Si and the Si-Fe-Al alloy, with similar composition and solidification route, were subjected to the same in situ corrosion and acid leaching. Their comparison shows that the total concentration of Fe and Al increased from 0.59 to 6.35 wt%, while the removal efficiency of P only increased from 7.23% to 25.00%. The residual percentage of P in the Si matrix of MG-Si and the Si-Fe-Al alloy were 92.77% and 75.00%, respectively. Additionally, the dissolution of AlP at the grain boundary is the main reason for the separation of P by acid leaching. At 1685 K, the activity interaction coefficients εPFe and εPAl are − 3.1348 and − 15.5498, respectively, as calculated by the molecular volume interaction model. During the initial crystallization of Si in the Si-Fe-Al system, Fe and Al can reduce the segregation coefficient of P and transform it into AlP, thereby theoretically promoting the separation of P from Si. However, AlP and Si have similar crystal structure, and the low mismatch factor and strong binding force between them facilitate the capture of AlP by primary Si, which hinders the enhanced separation of P from Si. An accurate understanding of the formation mechanism of the distribution characteristics of P in MG-Si is of great significance to the optimal design of MG-Si purification scheme.

Molecular interplay of ADAMTS13-MDTCS and von willebrand Factor-A2: deepened insights from extensive atomistic simulations

Thrombotic thrombocytopenic purpura (TTP) is a rare and life-threatening disease. One hallmark is severe ADAMTS13 deficiency, causing ultra-large von Willebrand factor (VWF) multimers to accumulate, leading to microthrombi and lastly to microangiopathic hemolytic anemia and severe thrombocytopenia. Despite great success in recent decades, the molecular picture of the interaction between VWF and ADAMTS13 remains vague. Here, we utilized modern replica-exchange molecular dynamics simulations with the TIGER2h method to sample a vast configurational space of the isolated ADAMTS13-MDTCS domains and the exposure to its substrate and activating cofactor – the unraveled VWF-A2 domain. The sampling of binding sites and conformations was guided and filtered in agreement with available experimental evidence. We provide comprehensive information on exosites for each domain and direct pairs of interacting amino acids, for the first time. The major binding cluster for the active site of the MP domain contrasts the previous mapping of VWF-A2 residues and reciprocal binding pockets. Two major binding modes are revealed and provide access to conformational changes of an extended gatekeeper tetrad upon overcoming local latency during substrate binding and to a dedicated recruitment mechanism. Our work adds the first molecular interaction model that places previous experimental results in perspective to better understand disease-related mutations towards improved therapies. Numerous empirical targets are proposed to verify the given binding modes, to refine the overall picture of MP binding pockets, the role of Dis binding in MP activation and the passage of the Cys-rich domain through VWF-A2, thus deepening the understanding of a highly dynamic interplay. Communicated by Ramaswamy H. Sarma

Polyelectrolytes for Enzyme Immobilization and the Regulation of Their Properties.

In this review, we considered aspects related to the application of polyelectrolytes, primarily synthetic polyanions and polycations, to immobilize enzymes and regulate their properties. We mainly focused on the description of works in which polyelectrolytes were used to create complex and unusual systems (self-regulated enzyme–polyelectrolyte complexes, artificial chaperones, polyelectrolyte brushes, layer-by-layer immobilization and others). These works represent the field of “smart polymers”, whilst the trivial use of charged polymers as carriers for adsorption or covalent immobilization of proteins is beyond the scope of this short review. In addition, we have included a section on the molecular modeling of interactions between proteins and polyelectrolytes, as modeling the binding of proteins with a strictly defined, and already known, spatial structure, to disordered polymeric molecules has its own unique characteristics.

Modeling Interfacial Interaction between Gas Molecules and Semiconductor Metal Oxides: A New View Angle on Gas Sensing.

With the development of internet of things and artificial intelligence electronics, metal oxide semiconductor (MOS)-based sensing materials have attracted increasing attention from both fundamental research and practical applications. MOS materials possess intrinsic physicochemical properties, tunable compositions, and electronic structure, and are particularly suitable for integration and miniaturization in developing chemiresistive gas sensors. During sensing processes, the dynamic gas-solid interface interactions play crucial roles in improving sensors' performance, and most studies emphasize the gas-MOS chemical reactions. Herein, from a new view angle focusing more on physical gas-solid interactions during gas sensing, basic theory overview and latest progress for the dynamic process of gas molecules including adsorption, desorption, and diffusion, are systematically summarized and elucidated. The unique electronic sensing mechanisms are also discussed from various aspects including molecular interaction models, gas diffusion mechanism, and interfacial reaction behaviors, where structure-activity relationship and diffusion behavior are overviewed in detail. Especially, the surface adsorption-desorption dynamics are discussed and evaluated, and their potential effects on sensing performance are elucidated from the gas-solid interfacial regulation perspective. Finally, the prospect for further research directions in improving gas dynamic processes in MOS gas sensors is discussed, aiming to supplement the approaches for the development of high-performance MOS gas sensors.

Applying the quantum chemical simulation to describe electrical conductivity in silicate-based materials

Introduction. It is confirmed that a dispersion of carbon black when it added to concrete is likely to increase its electrical conductivity. These materials are of great importance for construction for example for civil engineering, transportation and energy industries. In that branches such materials could be used as snow melting systems, protective materials for metal bars, electromagnetically shielded materials. This study is about probable reason of electrically conductive properties in silicate-based material with carbon particles.
 
 Materials and methods. Small molecular fragments which are the parts of modified concrete have been considered to investigate contact areas between carbon particles in silicate based material. Fire Fly has been chosen as software. Exchange-correlation phenomenon has been included by using B3LYP.
 
 Results. An optimum percentage of modifier in mineral binder leads to the formation of an electrically conductive grid made of carbon nanoparticles. Electrical conductivity of material is influenced by contact areas between these nanoparticles. Quantum chemical molecular models of molecular fragments and interactions between these fragments have been made. Also, the impact of these areas on electrical conductivity was estimated.
 
 Conclusions. Quantum chemical molecular models and analysis based on the optimum percentage of the modifier showed that electrical conductivity of the modified concrete depended on an electrons movement along the grid of carbon nanoparticles formed within the mineral matrix. The key role in electrical conductivity of the material plays contact areas between these particles. Electrical conductivity is increasing due to silicate-based components in molecular fragments.

Development of an ethanol-free salbutamol sulfate metered-dose inhaler: Application of molecular dynamic simulation-based prediction of intermolecular interaction

IntroductionMore than fifty years after the commercialization of the Ventolin metered-dose inhaler (MDI), its constituent active ingredient, salbutamol sulfate (SS), remains the most prescribed short-acting beta agonist for the first-line treatment of acute asthma attacks and the metered-dose inhaler remains its primary dosage form. The first generation of Ventolin MDI was developed at a time when environmental and regulatory concerns were less stringent than today. The MDI industry is now on the verge of a second major reformulation effort in response to environmental concerns. This paper serves to illustrate how modern computational modeling of molecular interactions can aid the reformulation process. By way of a case study, computational modeling was performed to compare poly(ethylene glycol) 400 (PEG400) and, separately, isopropyl myristate (IPM) as substitutes for the ethanol used in some generic salbutamol sulfate suspension-based hydrofluoroalkane MDIs. MethodsPEG400 and IPM were investigated as potential alternative cosolvents to ethanol in HFA134a-based SS suspension MDI formulations. Density functional theory (DFT) molecular dynamics simulations were used to evaluate the compatibility of the candidate cosolvents with the formulation's components. Corresponding physical formulations were filled into polyethylene terephthalate (PET) and, separately, aluminium canisters. In-vitro pharmaceutical product performance and macroscopic visual appearance were assessed and compared to the results of the simulation studies. ResultsThe simulation studies indicated that PEG400 would be a good candidate as a replacement for ethanol whereas IPM would not. The in-vitro and visual assessments support the predicted outcome of the simulation studies. ConclusionThis work suggests that molecular dynamics simulations may provide a useful tool to aid the selection of compatible excipients when reformulating MDI suspension-based products, thereby reducing the time and cost associated with manufacturing and testing of physical samples.

Adsorption of the most common non-steroidal analgesics from aquatic environment on agricultural wastes-based activated carbons; experimental adsorption study supported by molecular modeling

Adsorption experiments and force-field based molecular modeling of analgesics interactions with carbon structures were applied to study the adsorption of diclofenac sodium salt, paracetamol and ibuprofen on activated carbons prepared from six different agro-wastes. Revealing the role of pore size, various carbon structural properties and surface functionalization in analgesic adsorption led to the determination of the affinity of individual analgesics for carbon: diclofenac sodium salt > paracetamol > ibuprofen. Diclofenac sodium salt bonds predominantly via electrostatic attractions, paracetamol and ibuprofen bond via weak hydrogen bonds and π-π interactions flat on the carbon graphitic surface. The micropore volume and size play the key role. Diclofenac sodium salt and ibuprofen adsorption is favoured in micropores with size < 1.2 nm, while smaller pores (<0.86 nm) are the most important for paracetamol adsorption. For diclofenac sodium salt adsorption the high surface polarity (COOH groups) is the second most important property. For adsorption of ibuprofen and paracetamol, the high graphitization rate is determining. Diclofenac sodium salt adsorption is preferred on graphitic edges rather than on the flat graphitic surface. The combination of experiment and molecular modeling was found to be a simple but powerful tool for prediction of adsorption properties.

Molecular Modeling of Penicillin Acylase Binding with a Penicillin Nucleus by High Performance Computing: Can Enzyme or its Mutants Possess beta-lactamase Activity?

High-performance computing has been used for molecular modeling of penicillin acylase interaction with a penicillin nucleus 6-aminopenicillanic acid (6-APA) to assess whether the wild-type enzyme or its mutants could possess β-lactamase activity. Applying parallel hybrid GPU/CPU computing technologies for metadynamics calculations with the PLUMED library in conjunction with AMBER software suite it has been shown that trace amounts of wild-type penicillin acylase6-APA complexes leading to a β-lactamase reaction can be formed. Higher β-lactamase activity can be observed in enzyme mutants by introducing charged residue in the substrate binding pocket and its proper positioning with respect to a catalytic nucleophile, including stabilization of the tetrahedral intermediate in the oxyanion hole. Thus, it has been shown that the certain mutations facilitate the orientation of the substrate required for the manifestation of β-lactamase activity in the penicillin acylase active center.

Study of the Mechanical Properties of a CMDB Propellant Over a Wide Range of Strain Rates Using a Group Interaction Model

Composite modified double base (CMDB) propellants are heterogeneous propellants in which properties are significantly improved by adding solid particles into the polymer matrix. A molecular group interaction model that can predict the mechanical properties of polymers through a molecular structure is used to predict the viscoelastic behavior of the CMDB propellant. Considering that the addition of solid particles will improve the crosslinking degree between polymer molecules and reduce its secondary loss peak, the input parameters of the model are modified through dynamic mechanical analysis (DMA) experimental data. By introducing the strain rate into the expression of model glass transition temperature, the mechanical properties of propellant over a wide strain range ( 1.7 × 10 − 4 s-1 ~ 3000 s-1) are obtained. The reliability of the model is verified by comparison with uniaxial compression test data. By modifying the input parameters of the model, the effects of different mass ratios of nitrocellulose (NC)/nitroglycerin (NG) on the mechanical properties of the CMDB propellant were analyzed. The results show that the glass transition loss increases with increasing mass ratio of NC/NG, while Young’s modulus and yield stress decrease.

Molecular modeling of chemical admixtures; opportunities and challenges

Chemical admixtures are an essential ingredient of modern concrete mix, but many of their molecular scale working mechanisms remain poorly described. In this respect, recent advances in computational methods, provide a unique opportunity to gain the needed molecular level insights into the mechanism of action of chemical admixtures in cementitious systems. Such studies are slowly increasing in number and this paper proposes a review on approaches that deal with molecular simulations of chemical admixtures. The key properties studied so far are mainly adsorption behaviors and conformations of monomers, oligomers and polymers (molecular weight ~ 10,000 g/mol). Our aim is to identify opportunities, challenges and give perspectives on the future of molecular modeling of chemical admixture-cement interactions.

Allosteric cross-talk between the hydrophobic cleft and the BH4 domain of Bcl-2 in control of inositol 1,4,5-trisphosphate receptor activity.

Aim:Inositol 1,4,5-trisphosphate receptor (IP3R) is a ubiquitous calcium (Ca2+) channel involved in the regulation of cellular fate and motility. Its modulation by anti-apoptotic protein B-cell lymphoma 2 (Bcl-2) plays an important role in cancer progression. Disrupting this interaction could overcome apoptosis avoidance, one of the hallmarks of cancer, and is, thus, of great interest. Earlier reports have shown the involvement of both the Bcl-2 homology 4 (BH4) and the transmembrane domains (TMDs) of Bcl-2 in regulating IP3R activity, while the Bcl-2 hydrophobic cleft was associated primarily with its anti-apoptotic and IP3R-independent action at the mitochondria (Oncotarget. 2016;7:55704–20. doi: 10.18632/oncotarget.11005). The aim of this study was to investigate how targeting the BH3 hydrophobic cleft of Bcl-2 affects IP3R:Bcl-2 interaction.Methods:Organelle membrane-derived (OMD) patch-clamp and circular dichroism (CD) thermal melting experiments were used to elucidate the effects of the ABT-199 (venetoclax) on the IP3R:Bcl-2 interaction. Molecular dynamics (MD) simulations of free and ABT-199 bound Bcl-2 were used to propose a molecular model of such interaction.Results:It was shown that occlusion of Bcl-2’s hydrophobic cleft by the drug ABT-199 finely modulates IP3R gating in the low open probability (Po) regime, characteristic of the basal IP3R activity in non-excited cells. Complementary MD simulations allowed to propose a model of this modulation, involving an allosteric interaction with the BH4 domain on the opposite side of Bcl-2.Conclusions:Bcl-2 is an important regulator of IP3R activity and, thus of Ca2+ release from internal stores and associated processes, including cellular proliferation and death. The presence of multiple regulatory domains in both proteins suggests a complex interaction. Thus, it was found that the occlusion of the hydrophobic cleft of Bcl-2 by ABT-199 disrupts IP3R activity, leading to Bcl-2 rebinding with smaller affinity and lesser inhibitory effect. MDs simulations of free and ABT-199 bound Bcl-2 propose a molecular model of such disruption, involving an allosteric interaction with the BH4 domain on the opposite side of Bcl-2.

Discovery of Promising Inhibitors of Epidermal Growth Factor Receptor (EGFR), Human Epidermal Growth Factor Receptor 2 (HER2), Estrogen Receptor (ER), and Phosphatidylinositol-3-kinase a (PI3Ka) for Personalized Breast Cancer Treatment.

Despite the rapid developments and advancements to improve treatments, Breast cancer remains one of the deadliest health challenges and the most frequently diagnosed tumor. One of the major problems with treatment is the unique difference that each cancerous cell exhibits. As a result, treatment of breast cancer has now become more personalized based on the specific features of the tumor such as overexpression of growth factor receptors (Epidermal growth factor receptor (EGFR), Human Epidermal Growth Factor Receptor 2 (HER2)), hormone receptors (Human Estrogen receptor alpha (ER)) and kinases involved in pivotal signaling associated with growth (Phosphatidylinositol 3-kinase (PI3K)). Several chemotherapeutic agents have been developed to curb the menace, but the associated adverse drug effects cannot be overlooked. To this end, this study employed a molecular modeling approach to identify novel compounds of natural origin that can potentially antagonize the receptors (mentioned above) associated with the pathophysiology of breast cancer and at the same time pose very little or no side effects. The results of the molecular model of biological interactions between a library of 118 anthocyanins and the binding pockets of the protein targets identified 5 compounds (Pelargonin, Delphinidin 3-O-rutinoside, Malvin, Cyanidin-3-(6-acetylglucoside), and Peonidin 3-O-rutinoside) with good binding affinities to the protein targets. Further MM-GBSA calculations returned high binding energies. The specific molecular interactions between the compounds and the targets were analyzed and reported herein. Also, all the compounds exhibited good pharmacokinetic profiles and are therefore recommended for further analyses as they could be explored as new treatment options for a broad range and personalized breast cancer treatments.

Efficacy of Chondroprotective Food Supplements Based on Collagen Hydrolysate and Compounds Isolated from Marine Organisms.

Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increased incidence in older patients. The bioactivities of collagen hydrolysates, sulfated glucosamine and a special fatty acid enriched dog-food were tested in a dog patient study of 52 dogs as potential therapeutic treatment options in early osteoarthritis. Biophysical, biochemical, cell biological and molecular modeling methods support that these well-defined substances may act as effective nutraceuticals. Importantly, the applied collagen hydrolysates as well as sulfated glucosamine residues from marine organisms were strongly supported by both an animal model and molecular modeling of intermolecular interactions. Molecular modeling of predicted interaction dynamics was evaluated for the receptor proteins MMP-3 and ADAMTS-5. These proteins play a prominent role in the maintenance of cartilage health as well as innate and adapted immunity. Nutraceutical data were generated in a veterinary clinical study focusing on mobility and agility. Specifically, key clinical parameter (MMP-3 and TIMP-1) were obtained from blood probes of German shepherd dogs with early osteoarthritis symptoms fed with collagen hydrolysates. Collagen hydrolysate, a chondroprotective food supplement was examined by high resolution NMR experiments. Molecular modeling simulations were used to further characterize the interaction potency of collagen fragments and glucosamines with protein receptor structures. Potential beneficial effects of collagen hydrolysates, sulfated glycans (i.e., sulfated glucosamine from crabs and mussels) and lipids, especially, eicosapentaenoic acid (extracted from fish oil) on biochemical and physiological processes are discussed here in the context of human and veterinary medicine.

Dynorphin Neuropeptides Decrease Apparent Proton Affinity of ASIC1a by Occluding the Acidic Pocket.

Prolonged acidosis, as it occurs during ischemic stroke, induces neuronal death via acid-sensing ion channel 1a (ASIC1a). Concomitantly, it desensitizes ASIC1a, highlighting the pathophysiological significance of modulators of ASIC1a acid sensitivity. One such modulator is the opioid neuropeptide big dynorphin (Big Dyn) which binds to ASIC1a and enhances its activity during prolonged acidosis. The molecular determinants and dynamics of this interaction remain unclear, however. Here, we present a molecular interaction model showing a dynorphin peptide inserting deep into the acidic pocket of ASIC1a. We confirmed experimentally that the interaction is predominantly driven by electrostatic forces, and using noncanonical amino acids as photo-cross-linkers, we identified 16 residues in ASIC1a contributing to Big Dyn binding. Covalently tethering Big Dyn to its ASIC1a binding site dramatically decreased the proton sensitivity of channel activation, suggesting that Big Dyn stabilizes a resting conformation of ASIC1a and dissociates from its binding site during channel opening.

Structural analysis and prediction of potent bioactive molecule for eNOS protein through molecular docking

Reactive oxygen species by uncoupled eNOS is linked to endothelial dysfunction. Ellagic acid (EA), a polyphenol possesses numerous biological activities including radical scavenging. whether EA exerts a vasculo-protective effect via antioxidant mechanisms in blood vessels remains unknown. Molecular docking provides an initial model of protein and molecular interactions in various physiological and/or pathological functions. To identify a eNOS modulatory biomolecule through molecular docking as possible vascular protective agent. On the basis of binding affinities and other physicochemical features, a molecular docking-based approach was used to classify and evaluate eNOS binding micronutrients found in natural sources, Lipinski's rule was used taking into account their adsorption, delivery, metabolism, and excretion (ADME). An insilico approach focused on the ligand-protein interaction technique to determine the therapeutic potential of certain phytochemical-based drugs for the vascular remodelling.20 bioactive molecules were screened, docking analysis on human eNOS proteins was performed. The best poses for target protein was established based on binding energy and inhibition constant. EA and caffeine acid are the strongest candidates for eNOS protein functional norms. This provides a novel insight into the interaction properties of known human eNOS protein with EA and used as a therapeutic agent in various pathologies. Predicting interaction of ellagic acid with eNOS protein by molecular docking in endothelial dysfunction.

Interaction between a Novel Oligopeptide Fragment of the Human Neurotrophin Receptor TrkB Ectodomain D5 and the C-Terminal Fragment of Tetanus Neurotoxin.

This article presents experimental evidence and computed molecular models of a potential interaction between receptor domain D5 of TrkB with the carboxyl-terminal domain of tetanus neurotoxin (Hc-TeNT). Computational simulations of a novel small cyclic oligopeptide are designed, synthesized, and tested for possible tetanus neurotoxin-D5 interaction. A hot spot of this protein-protein interaction is identified in analogy to the hitherto known crystal structures of the complex between neurotrophin and D5. Hc-TeNT activates the neurotrophin receptors, as well as its downstream signaling pathways, inducing neuroprotection in different stress cellular models. Based on these premises, we propose the Trk receptor family as potential proteic affinity receptors for TeNT. In vitro, Hc-TeNT binds to a synthetic TrkB-derived peptide and acts similar to an agonist ligand for TrkB, resulting in phosphorylation of the receptor. These properties are weakened by the mutagenesis of three residues of the predicted interaction region in Hc-TeNT. It also competes with Brain-derived neurotrophic factor, a native binder to human TrkB, for the binding to neural membranes, and for uptake in TrkB-positive vesicles. In addition, both molecules are located together in vivo at neuromuscular junctions and in motor neurons.

Fuzzy binding model of molecular interactions between tropoelastin and integrin alphaVbeta3

Tropoelastin is the highly flexible monomer subunit of elastin, required for the resilience of the extracellular matrix in elastic tissues. To elicit biological signaling, multiple sites on tropoelastin bind to cell surface integrins in a poorly understood multifactorial process. We constructed a full atomistic molecular model of the interactions between tropoelastin and integrin αvβ3 using ensemble-based computational methodologies. Conformational changes of integrin αvβ3 associated with outside-in signaling were more frequently facilitated in an ensemble in which tropoelastin bound the integrin’s α1 helix rather than the upstream canonical binding site. Our findings support a model of fuzzy binding, whereby many tropoelastin conformations and defined sites cooperatively interact with multiple αvβ3 regions. This model explains prior experimental binding to distinct tropoelastin regions, domains 17 and 36, and points to the cooperative participation of domain 20. Our study highlights the utility of ensemble-based approaches in helping to understand the interactive mechanisms of functionally significant flexible proteins.

MOLECULAR DESIGN OF N-ACYL DERIVATIVES OF 2-(2-OXOPYROLIDIN-1-YL)-ACETAMIDE WITH GABA-ERGIC AND GLUTAMATERGIC ACTIVITIES

The first of the most successfully implemented nootropic drugs in medical practice is piracetam, which should be attributed to cyclic derivatives of gamma-aminobutyric acid. The production of new piracetam derivatives with high nootropic activity is a promising direction in the development of new neuroprotective drugs.The aim of the study is to predict GABA-ergic and glutamatergic activities of N-acyl derivatives of 2-(2-oxopyrolidin-1-yl)- acetamide by a molecular docking method through the energy analysis of interaction of modeled structures with GABAA and AMPA receptors with their subsequent targeted synthesis.Materials and methods. The objects of the research are new N-acyl derivatives of 2-oxo-1-pyrrolidineacetamide and a virtual model of the GABAA receptor of the Homo sapiens organism with the identification code 6D6U and a three-dimensional model of the AMPA-receptor of the Rattus norvegicus organism with the identification code 3LSF from the RCSB PDB database. The simulated compounds were designed in the HyperChem 8.0.8 program. This program was also used to optimize geometry using the force field of molecular mechanics MM+. Molecular docking was carried out using the Molegro Virtual Docker 6.0.1 program. The preparation of N-acyl derivatives of 2-(2-oxopyrrolidin-1-yl)-acetamide was carried out by the interaction of 2-(2-oxopyrrolidin-1-yl)-acetamide with an excess of the corresponding anhydride under conditions of acid catalysis.Results. Based on the results of molecular docking, a high affinity of all simulated compounds for the binding site of GABAA and AMPA receptors can be estimated. According to the predict, the maximum GABA-ergic activity should be expected for (N-[2-(2-oxopyrrolidin-1-yl)-acetyl]-butyramide. N-acyl derivatives of 2-oxo-1-pyrrolidineacetamide form a more stable complex with amino acid residues Arg207, Phe200, Thr202, Tyr97, Tyr157, Tyr205 and Phe65 of the GABAA receptor binding site than the GABA molecule. In terms of the minimum interaction energy, the N-acyl derivatives of 2-(2-oxopyrrolidin-1-yl)- acetamide are superior to a number of known ligands such as GABA, piracetam, anipiracetam, picamilon and pramiracetam. The tested compounds have also shown a high affinity for the binding site of the AMPA receptor. The leader compound is also the compound PirBut, as in the case of the GABAА receptor.Conclusion. Molecular modeling of the ligands interaction with the active binding site of gamma-aminobutyric acid of the GABAA receptor by molecular docking showed that all virtual N-acyl derivatives of 2-oxo-1-pyrrolidineacetamide can exceed a number of nootropic drugs by activity. In the course of molecular design, a method for predicting a glutamatergic activity for 2-pyrrolidone derivatives has been developed. It suggests a significant nootropic activity for N-[2-(2-oxopyrrolidin-1-yl)- acetamide amides.

Substrate curvature dependence of intrinsic contact angles

The intrinsic contact angle is an essential wetting parameter between a liquid and a substrate and had long been regarded as an intrinsic interfacial property. Recent investigations showed that the intrinsic contact angles depend on substrate curvatures. However, the reported trends were contradictory, and the underlying physics has not been revealed. This paper presents a molecular perspective to understand the intrinsic nature of the curvature effect on the contact angles. Molecular dynamics simulations quantitatively validate the theoretical model without fitting. This general molecular interaction model provides a unified curvature effect on different fluids that the contact angle decreases on a concave substrate and increases on a convex substrate. This curvature effect is amplified on a more wettable substrate and enlarged by a longer-range molecular interaction. We anticipate that the new understanding of nanoscale wetting will give new insights into the design of nano-flow systems and stable superhydrophobic surfaces.