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Ligand-decorated metal surfaces play a pivotal role in various areas of chemistry, particularly in selective catalysis. Molecular dynamics simulations at the molecular mechanics level of theory are best adapted to gain complementary insights to experiments regarding the structure and dynamics of such organic films. However, standard force fields tend to capture only weak physisorption interactions. This is inadequate for ligands that are strongly adsorbed such as carboxylates on metal surfaces. To address this limitation, we employ the Gaussian Lennard-Jones (GLJ) potential, which incorporates an attractive Gaussian potential between the surface and ligand atoms. Here, we develop this approach for the interaction between cobalt surfaces and carboxylate ligands. The accuracy of the GLJ approach is validated through the analysis of the interaction of oxygen with two distinct cobalt surfaces. The accuracy of this method reaches a root mean square deviation (RMSD) of about 3 kcal/mol across all probed configurations, which corresponds to a percentage error of roughly 4%. Application of the GLJ force field to the dynamics of the organic layer on these surfaces reveals how the ligand concentration influences the film order, and highlights differing mobility in the x and y directions, attributable to surface corrugation on Co(11 2 ̄ 0). GLJ is versatile, suitable for a broad range of metal/ligand systems, and can, subsequently, be utilized to study the organic film on the adsorption/desorption of reactants and products during a catalytic process. [ABSTRACT FROM AUTHOR]

Cyclodextrins (CDs) can enhance the stability and bioavailability of pharmaceutical compounds by encapsulating them within their cavities. This study utilized molecular dynamics simulations to investigate the interaction mechanisms between hydrocortisone (HC) and various methylated CD derivatives. The results reveal that the loading of HC into CD cavities follows different mechanisms depending on the degree and position of methylation. Loading into βCD and 6-MeβCD was more complete, with the hydroxyl groups of HC facing the primary hydroxyl rim (PHR) and the ketone side facing the secondary hydroxyl rim (SHR). In contrast, 2,3-D-MeβCD and 2,6-D-MeβCD showed a different loading mechanism, with the ketone side facing the PHR and the hydroxyl groups facing the SHR. The root mean square fluctuation (RMSF) analysis demonstrated that methylation increases the flexibility of CD heavy atoms, with 3-MeβCD and 2,3-D-MeβCD exhibiting the highest flexibility. However, upon inclusion of HC, 3-MeβCD, 2,3-D-MeβCD, 2-MeβCD, and 6-MeβCD showed a significant reduction in flexibility, suggesting a more rigid structure that effectively retains HC within their cavities. The radial distribution function revealed a significant reduction in the number of water molecules within the innermost layer of the methylated CD cavities, particularly in TMeβCD, indicating a decrease in polarity. The presence of HC led to the release of high-energy water molecules, creating more favorable conditions for HC loading. Conformational analysis showed that methylation caused a partial decrease in the area of the PHR, a significant decrease in the area of the middle rim, and a notable decrease in the area of the SHR. The loading of HC increased the area of the PHR in most derivatives, with the most pronounced increase observed in 2,6-D-MeβCD and 6-MeβCD. The analysis of interaction energies and binding free energies demonstrated that the binding of HC to methylated CD derivatives is thermodynamically more favorable than to βCD, with the strongest association observed for 6-MeβCD, 2-MeβCD, and 2,3-D-MeβCD. [ABSTRACT FROM AUTHOR]

Cellulose is a biopolymer with numerous advantages that make it an ecological, economical, and high-performing choice for various applications. To fully exploit the potential of cellulose, it is often necessary to dissolve it, which poses a current challenge. The aqueous zinc oxide/sodium hydroxide (ZnO/NaOH/Water) system is a preferred solvent for its rapid dissolution, non-toxicity, low cost, and environmentally friendly nature. In this context, the behavior of cellulose chains in the aqueous solution of ZnO/NaOH and the impact of temperature on the solubility of this polymer were examined through a molecular dynamics simulation. The analysis of the root means square deviation (RMSD), interaction energy, hydrogen bond curves, and radial distribution function revealed that cellulose is insoluble in the ZnO/NaOH solvent at room temperature (T = 298 K). Decreasing the temperature in the range of 273 K to 268 K led to a geometric deformation of cellulose chains, accompanied by a decrease in the number of interchain hydrogen bonds over the simulation time, thus confirming the solubility of cellulose in this system between T = 273 K and T = 268 K. [ABSTRACT FROM AUTHOR]

Content: Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. Methods: All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm. [ABSTRACT FROM AUTHOR]

In this study, a novel superalkali NLi 4 decorated Boron doped graphene/magnesium hydride heterojunction NLi 4 -BGra/MgH 2 was designed using density functional theory (DFT). Molecular dynamics (MD) confirmed that this material can release H 2 adsorbed near NLi 4 and H stored within MgH 2 at a fixed hydrogen-desorption temperature (T d) of 298 K and 570 K, respectively. Subsequently, 132 magnesium alloy hydrides Mg 1-X Me X H 2 with various hydrogen-storage capacities and hydrogen-desorption temperatures were predicted by DFT combined with machine learning (ML). Among them, Mg 0.875 Li 0.125 H 2 (T d = 400K) and Mg 0.875 Be 0.125 H 2 (T d = 500K) were selected to form NLi 4 -BGra/Mg 0.875 Me 0.125 H 2 (Me = Li, Be). The successful validation of Root Mean Square Deviation, diffusion coefficient and hydrogen-desorption trajectories to qualify the hydrogen-desorption capability of NLi 4 -BGra/Mg 0.875 Me 0.125 H 2 (Me = Li, Be) (T d = 400, 500K) confirms that the strategy of using Mg 1-X Me X H 2 to substitute MgH 2 in NLi 4 -BGra/MgH 2 enables the effective modulation of the hydrogen-desorption temperature ranges of NLi 4 -BGra/MgH 2 -based heterojunctions. In particular, partial density of state, electron localization function, and charge density difference were comprehensively analyzed to understand the hydrogen-storage mechanism and the nature of the hydrogen-desorption temperature variation. [ABSTRACT FROM AUTHOR]

Tyrosinase serves as the key enzyme in melanin biosynthesis, catalyzing the initial steps of the pathway, the hydroxylation of the amino acid L-tyrosine into L-3,4-dihydroxyphenylalanine (L-DOPA), followed by the subsequent oxidation of L-DOPA into dopaquinone (DQ), and it facilitates the conversion of 5,6-dihydroxyindole-2-carboxylic acid (DHICA) into 5,6-indolequinone-2-carboxylic acid (IQCA) and 5,6-dihydroxy indole (DHI) into indolequinone (IQ). Despite its versatile substrate capabilities, the precise mechanism underlying tyrosinase's multi-substrate activity remains unclear. Previously, we expressed, purified, and characterized the recombinant intra-melanosomal domain of human tyrosinase (rTyr). Here, we demonstrate that rTyr mimics native human tyrosinase's catalytic activities in vitro and in silico. Molecular docking and molecular dynamics (MD) simulations, based on rTyr's homology model, reveal variable durability and binding preferences among tyrosinase substrates and products. Analysis of root mean square deviation (RMSD) highlights the significance of conserved residues (E203, K334, F347, and V377), which exhibit flexibility during the ligands' binding. Additionally, in silico analysis demonstrated that the OCA1B-related P406L mutation in tyrosinase substantially influences substrate binding, as evidenced by the decreased number of stable ligand conformations. This correlation underscores the mutation's impact on substrate docking, which aligns with the observed reduction in rTyr activity. Our study highlights how rTyr dynamically adjusts its structure to accommodate diverse substrates and suggests a way to modulate rTyr ligand plasticity. [ABSTRACT FROM AUTHOR]

Cancer is a mechanistically complex and diverse disease with a plethora of fundamental genetic and epigenetic factors. Signal transducer and activator of transcription-3 (STAT3) is a transcription factor, and its constitutive activation executes promotion of cellular proliferation, cell cycle, angiogenesis, metastasis, immunosuppression, and chemo-resistance in cancer cells. Here, we aimed to design natural potential STAT3 inhibitors. For this purpose, we investigated 92 phytochemical compounds by molecular docking studies because they are diversified, multitargeted, affordable, easily available, and less- or non-toxic. We selected only 6 compounds such as sarsasapogenin (L3), peiminine (L9), solasodine (L10), tormentic acid (L23), obacunone (L29), and echinocystic acid (L34) due to their greater binding affinity than reference STAT3 inhibitor (S3I-201) with STAT3. The study was further continued by molecular dynamic (MD) simulations and ADMET (absorption, distribution, metabolism, excretion, and toxicity) analysis. The results of molecular docking showed that all selected ligands exhibited binding affinity range from -9.3 Kcal/mol to -7.9 Kcal/mol and predicted inhibition constant (K i pred .) values range from 0.14 μ M to 1.5 μ M. These compounds showed effective hydrogen bonding and hydrophobic interactions with DNA binding domain as well as SH2-domain of STAT3. The MD simulations performed by nanoscale molecular dynamics (NAMD) calculated root mean square deviations (RMSD), root mean square fluctuations (RMSF), radius of gyration ( R g ), solvent accessible surface area (SASA) and number of hydrogen bond dynamics. All selected ligands with protein exhibited stability over 120 ns by MD simulation. Moreover, these ligands showed favorable ADMET profiling and drug likeness. So, our current computational investigations showed that these novel drug candidates can be potential STAT3 inhibitors and evoke the scientific interest for their further verification by in vitro and in vivo studies. [ABSTRACT FROM AUTHOR]

Introduction: Computational simulation study was carried out on bioactive compounds of Ganoderma lucidum (G. lucidum). Methods: Molecular docking and molecular dynamics (MD) simulations were performed. The input files for protein and ligands were retrieved from Protein Data Bank (PDB) and PubChem database. Human maltase-glucoamylase (PDB ID: 3L4Y) is the protein (a-glucosidase enzyme). The ligands are thirteen compounds derived from G. lucidum together with acarbose and miglitol as controls. Results: Docking result showed the lowest binding energy is from Ganomycin B (-7.8 kcal/mol) compared to acarbose and miglitol (-5.0 kcal/mol and -4.4 kcal/mol) respectively. MD simulation showed interaction of 3L4Y-Ganomycin B achieved stable interaction and conformation as follows: root mean square deviation (RMSD) is ± 2.7 Å, average distance of ±1.8 Å and constant hydrogen bonds around 1 - 3. Conclusion: Ganomycin B was found to have good binding affinity, embarking its potential as a potent α-glucosidase inhibitor. [ABSTRACT FROM AUTHOR]

Modifications at the harmine (HAM) 9‐N position demonstrated effective antitumor activity in previous studies. However, the difficult preparation, low yield and poor stability of derivatives limited their applications. A partial activity priming was carried out by converting the 9‐position substituted propargyl group of HAM to propynyl group. Molecular docking simulations of compound 9i with DYRK1A kinase showed that it was able to embed itself into the active pocket of the DYRK1A protein and formed hydrogen bonds with multiple active amino acid residues at a low binding energy. The results of molecular dynamics simulations showed that the RMSD (root mean square deviation) fluctuations of the complex were more gentle, and the trends of the changes in Rg (radius of gyration) and SASA (solvent accessible surface area) were lower, indicating that the DYRK1A protein was less disturbed and the structure of the complex was more compact and stable. The cytotoxicity assay indicated that compound 9i displayed good antiproliferative activity against human cancer cells MGC‐803, HepG2, and PANC‐1. In addition, 9i was able to reduce the ratio of polynomials induced by the Ras overexpression model of Caenorhabditis elegans, which showed anti‐Ras activity, and the RT‐qPCR results suggested that its anti‐Ras ability was not achieved by directly inhibiting the expression of the let‐60/Ras genes, and that 9i was able to upregulate the expression of SOD‐3 activation of oxidative stress, which means that it may be useful as a pro‐oxidant for the treatment of cancers caused by Ras over‐activation. [ABSTRACT FROM AUTHOR]

This paper investigates the impact of taurine as an additive on the structural and functional stability of urate oxidase. First, the effect of the processing parameters for the stabilization of Urate Oxidase (UOX) using taurine was examined using the response surface methodology (RSM) and the central composite design (CCD) model. Also, the study examines thermodynamic and kinetic parameters as well as structural changes of urate oxidase with and without taurine. Fluorescence intensity changes indicated static quenching during taurine binding. The obtained result indicates that taurine has the ability to preserve the native structural conformation of UOX. Furthermore, molecular dynamics simulation is conducted in order to get insights into the alterations in the structure of urate oxidase in the absence and presence of taurine under optimal conditions. The molecular dynamics simulation section investigated the formation of hydrogen bonds (H-bonds) between different components as well as analysis of root mean square deviation (RMSD), root mean square fluctuations (RMSF) and secondary structure. Lower Cα-RMSD and RMSF values indicate greater stabilization of the taurine-treated UOX structure compared to the free enzyme. The results of molecular docking indicate that the binding of taurine to the UOX enzyme through hydrophobic interactions is associated with a negative value for the Gibbs free energy. [ABSTRACT FROM AUTHOR]

Emulsion is of great concern in the process of crude oil production. In the later stages of heavy oil reservoir development, the crude oil produced on the surface exists in the form of emulsion, accompanied by sand production. Some sand particles are transported to the surface with the fluid. It is necessary to determine the mechanism by which the type and size of clay particles affect the performance of emulsions in order to aid in demulsification. Therefore, the effects of different clay particles and sizes on the shape and stability of the emulsion and stability was studied. The research results show that emulsion droplets with added montmorillonite contain more clay particles in their interior compared to droplets with added kaolin and illite systems. The diameter of the droplets in the montmorillonite system is larger and mostly ranges between 10–12 μm. The proportion of droplets with a diameter of 12–20 μm in the kaolin and illite systems is smaller than that in the montmorillonite system. When the same type of clay particles are added, with the increase in particle size, the late-stage water volume and viscosity of the montmorillonite system are the highest. The range of water volume is 6.38–7.3 mL, and the viscosity slightly increases within the range of .07–.66 mPa·s. When the clay particles are 8–10 μm, the viscosity increase of each system also gradually becomes smaller. The molecular dynamics simulation results show that the effects of adding clay particles on the root mean square displacement in different directions are z-axis > y-axis > x-axis. The addition of clay particles in the system has a lower crude oil migration speed compared to the blank system, ranging from .0001 to .0003 Å2 /ps. The addition of clay particles mainly affects the root mean square displacement of oil droplets in the vertical direction. Through this study, the effects of different clay particles on the emulsion of heavy oil have been preliminarily determined, providing guidance for the treatment of heavy oil emulsions. [ABSTRACT FROM AUTHOR]

Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlphaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequentMDsimulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the U-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113!Phe182!(Leu259 or Tyr260)!Tyr291 induced by the ligand binding with a time scale of 4-6 ns. [ABSTRACT FROM AUTHOR]

The photochemical behavior of the phototoxic antidepressant drug venlafaxine (VLF, 1) was studied under aerobic conditions in UV-A light. Irradiation of a phosphate buffer solution of the drug produces N-Demethylated (2) and O-Demethylated (3) as two major photoproducts. The formation of photoproducts (2) and (3) occurs through a singlet oxygen-mediated mechanism, i.e., type-II photodynamic action, involving an irreversible trapping of the self-photogenerated singlet molecular oxygen (1O2) and through free radical-mediated mechanism, i.e., type 1 photodynamic action, respectively. The generation of singlet oxygen and free radicals during photolysis was confirmed by singlet oxygen scavenger sodium azide (NaN3) and free radical scavenger reduced glutathione (GSH). In addition, the comparative antioxidant potentials of the parent drug and its photoproducts were examined utilizing in-silico molecular docking against tyrosinase to better understand the in vivo relevance of drug pharmacological action as a result of drug-light interaction. Photoproduct (2) exhibited less activity as compared to the parent drug, VLF (1), whereas photoproduct (3) formed a stable protein–ligand complex. In order to determine the nature of stability of complex between protein and ligand, further, molecular dynamics (MD) simulation on photoproduct (3) was performed for 100 ns, and the results were analyzed by monitoring root mean square deviations (RMSD), the radius of gyration (Rg), and solvent accessible surface area (SASA). The results proved the formation of a better protein–ligand complex with photoproduct (3). These findings imply that drug users should avoid their exposure to light (natural or artificial) to prevent drug-induced photosensitivity. This study also opens new vistas for the development of novel drugs with desired tyrosinase binding affinity, improved biological features, and low phototoxic manifestations. [ABSTRACT FROM AUTHOR]

A comprehensive understanding of molecular interactions and functions is imperative for unraveling the intricacies of viral protein behavior and conformational dynamics during cellular entry. Focusing on the SARS-CoV-2 spike protein (SARS-CoV-2 sp), a Principal Component Analysis (PCA) on a subset comprising 131 A-chain structures in presence of various inhibitors was conducted. Our analyses unveiled a compelling correlation between PCA modes and Anisotropic Network Model (ANM) modes, underscoring the reliability and functional significance of low-frequency modes in adapting to diverse inhibitor binding scenarios. The role of HR1 in viral processing, both linear Normal Mode Analysis (NMA) and Nonlinear NMA were implemented. Linear NMA exhibited substantial inter-structure variability, as evident from a higher Root Mean Square Deviation (RMSD) range (7.30 Å), nonlinear NMA show stability throughout the simulations (RMSD 4.85 Å). Frequency analysis further emphasized that the energy requirements for conformational changes in nonlinear modes are notably lower compared to their linear counterparts. Using simulations of molecular dynamics at constant pH (cpH-MD), we successfully predicted the pKa order of the interconnected residues within the HR1 mutations at lower pH values, suggesting a transition to a post-fusion structure. The pKa determination study illustrates the profound effects of pH variations on protein structure. Key results include pKa values of 9.5179 for lys-921 in the D936H mutant, 9.50 for the D950N mutant, and a slightly higher value of 10.49 for the D936Y variant. To further understand the behavior and physicochemical characteristics of the protein in a biologically relevant setting, we also examine hydrophobic regions in the prefused states of the HR1 protein mutants D950N, D936Y, and D936H in our study. This analysis was conducted to ascertain the hydrophobic moment of the protein within a lipid environment, shedding light on its behavior and physicochemical properties in a biologically relevant context. [ABSTRACT FROM AUTHOR]

Galidesivir (BCX4430) is known to treat different viruses under Filoviridae family and it has proved as a potential antiviral drug against Ebola virus. Therefore, for treating Ebola virus in particular there is a need for the identification a drug compound. In this work, derivatives of Pyrrolopyrimidine are designed to investigate their antiviral activity against Ebola virus receptors (VP24, VP30, VP35 and VP40). FBDD‐based virtual screening resulted in eight compounds, based on pharmacokinetics and Density Functional Theory (DFT) analysis; four compounds were shortlisted. Further, docking simulation resulted that, compound 4 exhibited −9.8, −9.6, −9.7, −9.5 kcal/mol binding energy against each Ebola receptor, respectively. The predicted docking results of the above compound against each receptor were better than BCX4430. Docking results were validated and compared to BCX4430 by performing Molecular Dynamic simulations at 100 ns, in order to study the Root Mean Square Deviation, Root Mean Square Fluctuation, Radius of Gyration and MM/PBSA of the docked complexes. Therefore, the study lays the foundation for the designed and screened compound to act as a probable drug compound against Ebola. [ABSTRACT FROM AUTHOR]

Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL−1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL−1 for rGILCC 1 and 5291.665 ± 45.83 UL−1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10−2 mM for rGILCC 1 and 3.72 × 10−2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10−2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1–ABTS and POXA 1B–ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model–ABTS interactions (GILCC 1–ABTS and POXA 1B–ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme–substrate interactions, offering potential applications in environmental substrate treatments. [ABSTRACT FROM AUTHOR]

RuBisCO is the main photosynthetic enzyme of carbon assimilatory pathways in nature. Despite being the most abundant protein on earth, RuBisCO is still relatively underutilised in the food chain. Although there are sequence and structure details in the database, there are few instances of studies on evolutionary relationships. A bioinformatics and in silico study was conducted to check sequence and structural differences of RuBisCO among different photosynthetic organisms. RuBisCO from Oryza sativa showed an abundance of charged amino acids, salt-bridges, and intra-protein interactions and was more hydrophilic in nature compared to Nostoc sp., Chlamydomonas reinhardtii, and Nicotiana tabacum. From molecular dynamics simulations, lower root mean square deviation and root mean square fluctuation indicate that RuBisCO from Oryza sativa was more stable, followed by Nicotiana tabacum, and a lower radius of gyrations indicates their tight packing. From this study, it was clear that some specific evolutions in charged amino acids of RuBisCO of monocot, i.e., Oryza sativa, make it more stable and stronger than other plant groups. The study concludes that a more stable nature of RuBisCO is gained from monocot Oryza sativa. [ABSTRACT FROM AUTHOR]

Acylphosphatase (Acp) is a hydrolase which specifically cleaves carboxyl-phosphate bond of intermediates of metabolic pathways. It is a small cytosolic enzyme found in both prokaryotic and eukaryotic organisms. Previous crystal structures of acylphosphatase from different organisms have provided insights into the active site but the complete understanding of substrate binding and catalytic mechanisms in acylphosphatase remain elusive. Here we report the crystal structure of phosphate bound acylphosphatase from a mesothermic bacterium, Deinococcus radiodurans (drAcp) at resolution of 1.0 Å. Our structural analysis shows how the terminal phosphate group of substrates is bound to the active site, highlighting the importance of arginine in substrate recognition, role of asparagine in mode of catalysis and shedding light on the reaction mechanism. Additionally, the protein can refold after thermal melting by gradually lowering the temperature. To further explore the dynamics of drAcp, molecular dynamics simulation of drAcp and homologs from thermophilic organisms were carried out which revealed similar root mean square fluctuation profile but drAcp showed comparatively higher fluctuations. • Structure of Acylphosphatase (Acp) with end product phosphate at active site. • Substrate mediated catalysis by acylphosphatase. • Acylphosphatase can refold after thermal denaturation. [ABSTRACT FROM AUTHOR]

This study conducted an in silico approach to determine which among the known Moringa oleifera phytochemicals demonstrate the most comparable anti-inflammatory activity compared to dexamethasone. Initial screening for druglikeness was performed using Lipinski’s rule of five while the ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties were investigated. Molecular docking analysis via AutoDock Vina revealed that pterygospermin demonstrated the strongest binding affinity to the target NF-κB p50 (−5.0 kcal/mol), higher than dexamethasone (−4.8 kcal/mol). PharmaGist also provided an overview of the structural features of pterygospermin that could ascertain binding interaction with NF-κB p50. Molecular dynamics simulation using CABS-flex strongly suggested that pterygospermin can stably bind to NF-κB p50 as evidenced by the minimal root mean square fluctuations between the apo and bound structures (p = 0.4595). These results suggest that pterygospermin can be a candidate inhibitor of NF-κB p50. Screening for the antiinflammatory activity of M. oleifera leaves, pod, and seed aqueous extract on lipopolysaccharide-induced human THP-1 macrophage cells afforded significant downregulation of proinflammatory IL1-β and TNF-α transcripts via qRT-PCR (p < 0.0001) when compared to non-induced controls. Results from in silico studies revealed that Moringa oleifera can be a potential source of novel phytochemicals capable of targeting NF-κB and thus impede inflammation. [ABSTRACT FROM AUTHOR]

The structural analysis of proteins is a major domain of biomedical research. Such analysis requires resolved three-dimensional structures of proteins. Advancements in computer technology have led to progress in biomedical research. In silico prediction and modeling approaches have facilitated the construction of protein structures, with or without structural templates. In this study, we used three neural network-based de novo modeling approaches—AlphaFold2 (AF2), Robetta-RoseTTAFold (Robetta), and transform-restrained Rosetta (trRosetta)—and two template-based tools—the Molecular Operating Environment (MOE) and iterative threading assembly refinement (I-TASSER)—to construct the structure of a viral capsid protein, hepatitis C virus core protein (HCVcp), whose structure have not been fully resolved by laboratory techniques. Templates with sufficient sequence identity for the homology modeling of complete HCVcp are currently unavailable. Therefore, we performed domain-based homology modeling for MOE simulations. The templates for each domain were obtained through sequence-based searches on NCBI and the Protein Data Bank. Then, the modeled domains were assembled to construct the complete structure of HCVcp. The full-length structure and two truncated forms modeled using various computational tools were compared. Molecular dynamics (MD) simulations were performed to refine the structures. The root mean square deviation of backbone atoms, root mean square fluctuation of Cα atoms, and radius of gyration were calculated to monitor structural changes and convergence in the simulations. The model quality was evaluated through ERRAT and phi–psi plot analysis. In terms of the initial prediction for protein modeling, Robetta and trRosetta outperformed AF2. Regarding template-based tools, MOE outperformed I-TASSER. MD simulations resulted in compactly folded protein structures, which were of good quality and theoretically accurate. Thus, the predicted structures of certain proteins must be refined to obtain reliable structural models. MD simulation is a promising tool for this purpose. [ABSTRACT FROM AUTHOR]

Context: Molecular docking is an important and rapid tool that provides a comprehensive view of different molecular mechanisms. It is often used to verify the binding interactions of many pairs of molecules and is much faster than more rigorous approaches. However, its application requires carefully preprocessing each molecule and selecting a series of simulation parameters, which is not always done correctly. We show how preprocessing and simulation parameters can positively or negatively impact molecular docking performance. For example, the inclusion of hydrogen atoms leads to better redocking scores, but molecular dynamics simulations must be performed under certain constraints; otherwise, it may worsen performance rather than improve it. This study clarifies the importance and influence of these different parameters in the simulation results. Methods: We analyzed the influence of different parameters on the predictive ability of molecular docking techniques using two software packages: AutoDock Vina and AutoDock-GPU. Thus, 90 receptor-ligand complexes were redocked, evaluating the root mean square deviation (RMSD) between the original position of the ligand (receptor-ligand complex obtained experimentally) and that obtained by the software for every analysis. We investigated the influence of hydrogen atoms (on the receptor and on the receptor-ligand complex), partial charges (QEq, QTPIE, EEM, EEM2015ha, MMFF94, Gasteiger-Marsili, and no charge), search boxes (size and exhaustiveness), ligand characteristics (size and number of torsions), and the use of molecular dynamics (of the receptor or the receptor-ligand complex) before docking analyses. [ABSTRACT FROM AUTHOR]

Chronic periodontitis can cause the overgrowth of harmful bacteria in the mouth, which leads to the progressive destruction of the tissues that support the teeth. Fusobacterium nucleatum plays a role in the inflammatory response during periodontal disease. Phosphoenolpyruvate protein phosphotransferase (PEP) is found in bacteria and contributes to the virulence of F. nucleatum. Inhibition of PEP is a key role in finding more efficacious and safer drugs for treating chronic periodontitis. The research aimed to reveal the potential compounds able to inhibit PEP through molecular docking simulation by in silico analysis. The compounds were drawn from the DrugBank database, then the test ligands conducted virtual screening using the AutoDock Vina program on Google Colab Pro and assessed based on the affinity value against PEP by molecular dynamics analysis. Of 8364 compounds screened, pteroic acid showed the highest binding affinity of -6.8 kcal/mol. Root mean square deviations ranging from 0.3 to 5.5 nm were found in the molecular dynamics of pteroic acid and PEP. In vitro, investigation for pteroic acid against F. nucleatum is further needed. [ABSTRACT FROM AUTHOR]

Carbon nanotubes (CNTs) have a wide range of applications in nanotechnology engineering. This research aims to quantify the effect of wall vibration on n-decane molecules' diffusion in double-walled CNTs (DWNTs) with different diameters and determine the diffusion mechanisms behind it. Molecular dynamics simulations are performed to generate mass density profiles of confined n-decane molecules. The root mean square fluctuation and mean squared displacement analyses show that the confinement suppresses n-decane molecules' fluctuations. A self-diffusion coefficient of n-decane molecules in a 13.6 Å-diameter DWNT is the largest. However, the vibration enhancement of the n-decane molecules' diffusion in a 27.1 Å-diameter DWNT is 207%, more extensive than that in 13.6 Å-diameter and 10.8 Å-diameter DWNTs. The n-decane–CNT attractive interactions, extreme confinement, and surface friction affect the n-decane molecules' diffusion in CNTs with vibration. [ABSTRACT FROM AUTHOR]

Lipid nanoparticles (LNPs) have emerged as a promising delivery system, particularly for genetic therapies and vaccines. LNP formation requires a specific mixture of nucleic acid in a buffered solution and lipid components in ethanol. Ethanol acts as a lipid solvent, aiding the formation of the nanoparticle's core, but its presence can also affect LNP stability. In this study, we used molecular dynamics (MD) simulations to investigate the physicochemical effect of ethanol on LNPs and gain a dynamic understanding of its impact on the overall structure and stability of LNPs. Our results demonstrate that ethanol destabilizes LNP structure over time, indicated by increased root mean square deviation (RMSD) values. Changes in the solvent-accessible surface area (SASA), electron density, and radial distribution function (RDF) also suggest that ethanol affects LNP stability. Furthermore, our H-bond profile analysis shows that ethanol penetrates the LNP earlier than water. These findings emphasize the importance of immediate ethanol removal in lipid-based systems during LNP production to ensure stability. [ABSTRACT FROM AUTHOR]

Purpose: The current study is aimed to perform structure-based screening of FDA-approved drugs that can act as novel inhibitor of the 11beta- hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme. Methods: Structural analogs of carbenoxolone (CBX) were selected from DrugBank database and their Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) parameters were investigated by SwissADME. Molecular docking of CBX analogs against 11β-HSD1 was performed by AutoDock tool, their binding patterns were visualized using PyMOL and the interacting amino acids were determined by ProteinPlus tool. Molecular dynamics simulation was performed on the docked structure of 11β-HSD1 (Protein Data Bank (PDB) code: 2ILT) using GROMACS 2018.1. Results: The binding energies of hydrocortisone succinate, medroxyprogesterone acetate, testolactone, hydrocortisone cypionate, deoxycorticosterone acetate, and hydrocortisone probutate were lower than that of substrate corticosterone. The molecular dynamics simulation of 11β-HSD1 and hydrocortisone cypionate docked structure showed that it formed a stable complex with the inhibitor. The Root mean square deviation (RMSD) of the protein (0.37 ± 0.05 nm) and ligand (0.41 ± 0.06 nm) shows the stability of the ligand-protein interaction. Conclusion: The docking study revealed that hydrocortisone cypionate has a higher binding affinity than carbenoxolone and its other analogs. The molecular dynamics simulation indicated the stability of the docked complex of 11β-HSD1 and hydrocortisone cypionate. These findings indicate the potential use of this FDA approved drug in the treatment of type 2 diabetes. However, validation by in vitro inhibitory studies and clinical trials on type 2 diabetes patients is essential to confirm the current findings. [ABSTRACT FROM AUTHOR]

Three α-dicarbonyl compounds, methylglyoxal (MGO), diacetyl (DA) and glyoxal (GO) were common highly reactive glycosylation intermediates that can cause damage to biological macromolecules (e. g. DNA) in the body. The interaction properties of MGO, DA and GO with calf thymus DNA (ctDNA) were determined by multispectral methods combined with computer simulation techniques. Analysis of UV spectra indicated that MGO, DA and GO binding to ctDNA spontaneously were mainly driven by van der Waals forces and hydrogen bonding, and the energy distribution in molecular dynamics simulations supported this conclusion. The binding constants of MGO, DA and GO with ctDNA at 25 ℃ were close to those of classical groove-binders, with corresponding values of 2.99×10³, 1.96×10³ and 1. 05×10³ L·mol-1, respectively. NaCl, single and double-stranded DNA, thermal denaturation, viscosity and CD spectroscopy experiments demonstrated that MGO, DA and GO were all bound to ctDNA via groove binding. Molecular docking visualization showed that MGO, DA and GO were bound in the AT-rich minor groove region of DNA, with DT7 and DA18 being the active sites of binding. Molecular dynamics simulations of the MGO-ctDNA complex had higher root mean square deviation, radius of gyration, and root mean square fluctuation values than free DNA, indicating that the binding of MGO loosened and tended to destabilise parts of the DNA structure. Gel electrophoresis experiments showed that MGO, DA and GO could damage plasmid DNA in the presence of lysine and Cu2+, and MGO and GO even completely disrupted the superhelical morphology of DNA. [ABSTRACT FROM AUTHOR]

Acinetobacter baumannii (A. baumannii) is an opportunistic bacterium that has developed multidrug resistance (MDR) to most of today's antibiotics, posing a significant risk to human health. Considering the fact that developing novel drugs is a time-consuming and expensive procedure, this research focuses on utilizing computational resources for repurposing antibacterial agents for A. baumannii. We targeted shikimate kinase, an essential enzyme in A. baumannii, that plays a significant role in the metabolic process. The basis for generating new therapeutic compounds is to inhibit the shikimate kinase and thereby targeting the shikimate pathway. Herein, 1941 drug-like compounds were investigated in different in silico techniques for assessing drug-likeness properties, ADMET (absorption, distribution, metabolism, excretion, and toxicity) profiling, binding affinity, and conformation analysis utilizing Autodock-vina and SwissDock. CHEMBL1237, CHEMBL1237119, CHEMBL2018096, and CHEMBL39167178 were determined as potential drug candidates for suppressing shikimate kinase protein. Molecular Dynamics Simulation (MDS) results for root mean square deviation, root mean square fluctuation, hydrogen bond, and gyration radius confirm the drug candidates' molecular stability with the target protein. According to this study, CHEMBL1237 (Lisinopril) could be the most suitable candidate for A. baumannii. Our investigation suggests that the inhibitors of shikimate kinase could represent promising treatment options for A. baumannii. However, further in vitro and in vivo studies are necessary to validate the therapeutic potential of the suggested drug candidates. [ABSTRACT FROM AUTHOR]

Spherical nanocarriers can lead to a bright future to lessen problems of virus infected people. Spherical polyethylene glycol (PEG) and spherical silica (SiO2) are novel attractive nanocarriers as drug delivery agents, especially they are recently noticed to be reliable for antiviral drugs like anti-HIV, anti-covid-19, etc. Lamivudine (3TC) is used as a first line drug for antiviral therapy and the atomic view of 3TC-PEG/SiO2 complexes enable scientist to help improve treatment of patients with viral diseases. This study investigates the interactions of 3TC with Spherical PEG/SiO2, using molecular dynamics simulations. The mechanism of adsorption, the stability of systems and the drug concentration effect are evaluated by analyzing the root mean square deviation, the solvent accessible surface area, the radius of gyration, the number of hydrogen bonds, the radial distribution function, and Van der Waals energy. Analyzed data show that the compression of 3TC is less on PEG and so the stability is higher than SiO2; the position and intensity of the RDF peaks approve this stronger binding of 3TC to PEG as well. Our studies show that PEG and also SiO2 are suitable for loading high drug concentrations and maintaining their stability; therefore, spherical PEG/SiO2 can reduce drug dosage efficiently. [ABSTRACT FROM AUTHOR]

Hexaconazole is widely used as a fungicide for agricultural purposes. However, the endocrine-disrupting potential of hexaconazole is still under investigation. In addition, an experimental study found that hexaconazole may disrupt the normal synthesis of steroidal hormones. The potency of hexaconazole to bind with sex hormone-binding globulin (SHBG), a plasma carrier protein that binds androgens and oestrogens, is unknown. In this study, we evaluated the efficacy of hexaconazole to bind with SHBG by molecular interaction, a molecular dynamics method. In addition, principal component analysis was performed to understand the dynamical behaviour of hexaconazole with SHBG in comparison with dihydrotestosterone and aminoglutethimide. The binding scores of hexaconazole, dihydrotestosterone, and aminoglutethimide with SHBG were found to be −7.12 kcal/mol, −11.41 kcal/mol, and −6.84 kcal/mol, respectively. With respect to stable molecular interaction, hexaconazole showed similar molecular dynamics patterns of root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), and hydrogen bonding. The solvent surface area (SASA) and principal component analysis (PCA) of hexaconazole exhibit similar patterns in comparison with dihydrotestosterone and aminoglutethimide. These results show that hexaconazole has a stable molecular interaction with SHBG, which may acquire the active site of the native ligand, resulting in significant endocrine disruption during agricultural work. [ABSTRACT FROM AUTHOR]

Identification of novel drugs for anti-African swine fever (ASF) applications is of utmost urgency, as it negatively affects pig farming and no effective vaccine or treatment is currently available. African swine fever virus (ASFV) encoded pS273R is a cysteine protease that plays an important role in virus replication. E64, acting as an inhibitor of cysteine protease, has been established as exerting an inhibitory effect on pS273R. In order to obtain a better understanding of the interaction between E64 and pS273R, common docking, restriction docking, and covalent docking were employed to analyze the optimal bonding position between pS273R−E64 and its bonding strength. Additionally, three sets of 100 ns molecular dynamics simulations were conducted to examine the conformational dynamics of pS273R and the dynamic interaction of pS273R−E64, based on a variety of analytical methods including root mean square deviation (RMSD), root mean square fluctuation (RMSF), free energy of ligand (FEL), principal component analysis (PCA), and molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) analysis. The results show that E64 and pS273R exhibited close binding degrees at the activity center of ASFV pS273R protease. The data of these simulations indicate that binding of E64 to pS273R results in a reduction in flexibility, particularly in the ARM region, and a change in the conformational space of pS273R. Additionally, the ability of E64 to interact with polar amino acids such as ASN158, SER192, and GLN229, as well as charged amino acids such as LYS167 and HIS168, seems to be an important factor in its inhibitory effect. Finally, Octet biostratigraphy confirmed the binding of E64 and pS273R with a KD value of 903 uM. Overall, these findings could potentially be utilized in the development of novel inhibitors of pS273R to address the challenges posed by ASFV. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations were applied to human 5-LOX to obtain detailed information on its structure and dynamics with and without ligands. The dynamical properties evaluated based on root mean square deviations, root mean square fluctuations and secondary structure prediction helped decipher the contrast dynamic behavior of the systems pointing toward the ligand binding effect. The ligand binding to the protein also perturbed other properties of the protein such as the central bending of the protein and water coordination to the metal ion. The central bending in the protein was reported to be very significant that was associated with the allosteric modulation in the lipoxygenases; therefore, on a similar line, the central bending was evaluated in terms of hinge angle analysis which showed substantial bending between the C-terminal and the N-terminal domain via the linker residues which connects the two domains. On the other hand, the suspected water coordination to the metal ion in the protein was ruled out by computing the iron-water radial distribution function which showed that the water molecule was not found to be in the vicinity of the metal ion. Finally, the binding free energy was estimated for Zileuton and CAPE1 inhibitors bound to 5-LOX via the thermodynamic integration approach which showed that CAPE1 had a strong binding potential for the active site of the protein compared to Zileuton, and the free energy data correlated well with their IC50 values corresponding to the high inhibition potential of CAPE1 compared to Zileuton. [ABSTRACT FROM AUTHOR]

HIV-1 maturation is the final step in the retroviral lifecycle that is regulated by the proteolytic cleavage of the Gag precursor protein. As a first-in-class HIV-1 maturation inhibitor (MI), bevirimat blocks virion maturation by disrupting capsid-spacer peptide 1 (CA-SP1) cleavage, which acts as the target of MIs. Previous alterations of beesioside I (1) produced (20S,24S)-15ꞵ,16ꞵ-diacetoxy-18,24; 20,24-diepoxy-9,19-cyclolanostane-3ꞵ,25-diol 3-O-3′,3′-dimethylsuccinate (3, DSC), showing similar anti-HIV potency compared to bevirimat. To ascertain the binding modes of this derivative, further modification of compound 1 was conducted. Three-dimensional quantitative structure–activity relationship (3D-QSAR) analysis combined with docking simulations and molecular dynamics (MD) were conducted. Five new derivatives were synthesized, among which compound 3b showed significant activity against HIV-1NL4-3 with an EC50 value of 0.28 µM. The developed 3D-QSAR model resulted in great predictive ability with training set (r2 = 0.99, q2 = 0.55). Molecular docking studies were complementary to the 3D-QSAR analysis, showing that DSC was differently bound to CA-SP1 with higher affinity than that of bevirimat. MD studies revealed that the complex of the ligand and the protein was stable, with root mean square deviation (RMSD) values <2.5 Å. The above results provided valuable insights into the potential of DSC as a prototype to develop new antiviral agents. [ABSTRACT FROM AUTHOR]

Background: The emergence of Coronavirus disease (COVID-19) has been declared a pandemic and made a medical emergency worldwide. Various attempts have been made, including optimizing effective treatments against the disease or developing a vaccine. Since the SARS-CoV-2 protease crystal structure has been discovered, searching for its inhibitors by in silico technique becomes possible. Objective: This study aims to virtually screen the potential of phytoconstituents from the Begonia genus as 3Cl pro-SARS-CoV-2 inhibitors, based on its crucial role in viral replication, hence making these proteases "promising" for the anti-SARS-CoV-2 target. Methods: In silico screening was carried out by molecular docking on the web-based program DockThor and validated by a retrospective method. Predictive binding affinity (Dock Score) was used for scoring the compounds. Further molecular dynamics on Desmond was performed to assess the complex stability. Results: Virtual screening protocol was valid with the area under curve value 0.913. Molecular docking revealed only ß-sitosterol-3-O-ß-D-glucopyranoside with a lower docking score of - 9.712 kcal/mol than positive control of indinavir. The molecular dynamic study showed that the compound was stable for the first 30 ns simulations time with Root Mean Square Deviation <3 Å, despite minor fluctuations observed at the end of simulation times. Root Mean Square Fluctuation of catalytic sites HIS41 and CYS145 was 0.756 Å and 0.773 Å, respectively. Conclusions: This result suggests that ß-sitosterol-3-O-ß-Dglucopyranoside might be a prospective metabolite compound that can be developed as anti-SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Fascin is a filamentous actin (F‐actin) bundling protein, which cross‐links F‐actin into bundles and becomes an important component of filopodia on the cell surface. Fascin is overexpressed in many types of cancers. The mutation of fascin affects its ability to bind to F‐actin and the progress of cancer. In this paper, we have studied the effects of residues of K22, K41, K43, K241, K358, K399, and K471 using molecular dynamics (MD) simulation. For the strong‐effect residues, that is, K22, K41, K43, K358, and K471, our results show that the mutation of K to A leads to large values of root mean square fluctuation (RMSF) around the mutated residues, indicating those residues are important for the flexibility and thermal stability. On the other hand, based on residue cross‐correlation analysis, alanine mutations of these residues reinforce the correlation between residues. Together with the RMSF data, the local flexibility is extended to the entire protein by the strong correlations to influence the dynamics and function of fascin. By contrast, for the mutants of K241A and K399A those do not affect the function of fascin, the RMSF data do not show significant differences compared with wild‐type fascin. These findings are in a good agreement with experimental studies. [ABSTRACT FROM AUTHOR]

Diabetes is a chronic disease that leads to abnormal carbohydrate digestion and hyperglycemia. The long-term use of marketed drugs results in secondary infections and side effects that demand safe and natural substitutes for synthetic drugs. The objective of this study is to evaluate the antidiabetic potential of compounds from the leaves of Tradescantia pallida. Thirteen phenolic compounds were identified from the ethyl acetate fraction of leaves of Tradescantia pallida using liquid chromatography-mass spectrometry. The compounds were then studied for the type of interactions between polyphenols and human α-glucosidase protein using molecular docking analysis. Prime Molecular Mechanics/Generalized Born Surface Area (MM-GBSA) calculations were performed to measure the binding free energies responsible for the formation of ligand–protein complexes. The compounds were further investigated for the thermodynamic constraints under a specified biological environment using molecular dynamic simulations. The flexibility of the ligand–protein systems was verified by Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and molecular interactions. The results authenticated the antidiabetic potential of polyphenols identified from the leaves of Tradescantia pallida. Our investigations could be helpful in the design of safe antidiabetic agents, but further in vitro and in vivo investigations are required. [ABSTRACT FROM AUTHOR]

In this study, in-silico interaction analysis between Human serum albumin (HSA) and serum protein acidic and rich in cysteine (SPARC)–Collagen complex was performed to determine the binding affinity between the two proteins. Structure-based molecular interaction studies of the HSA–SPARC–Collagen complex were performed using ClusPro 2.0, ZDOCK and PatchDock servers. Molecular dynamics analysis was performed for the first-ranked complex structure (HSA–SPARC–Collagen complex) using GROMACS for a period of 125 nanoseconds to determine the stability of the complex. The results show higher structural interactive cumulative scores between the HSA and SPARC–Collagen complex. HSA–SPARC–Collagen complex predominantly has the Pi-alkyl and Pi-sigma interactions. The root mean square fluctuation (RMSF), root mean square deviation, solvent accessible surface area, radius of gyration and the number of hydrogen bonds show that formed complex is stable. In conclusion, our study provides an add-on for tuning drugs concerning albumin as a drug carrier by targeting the SPARC–Collagen complex for treating different ailments. Human serum albumin (HSA) bypasses the degradative lysozyme system and interacts with the SPARC-Collagen complex in the interstitium. Molecular docking and molecular dynamics studies between HSA and SPARC-Collagen complex have shown a greater affinity and stability. Tuning the drug molecules with the HSA and targeting SPARC-Collagen complex protein helps deliver the drugs in low doses to the tumor cells. [ABSTRACT FROM AUTHOR]

The discovery of antibiotics initiated the era of drug innovation and implementation for human and animal health. Very soon, antibiotic resistance started evolving due to over-prescription and heavy usage of drugs leading to deleterious side effects. However, using plant extracts or medicinal plants has emerged as a new approach to dealing with the current problem. One such medicinal plant Sisymbrium irio L. is widely used in Unani therapy as an antimicrobial, analgesic, antipyretic, antioxidant, anti-inflammatory, hepatoprotective, bronchoprotective etc. The phytochemicals extracted from the aerial part of the plant have been used as a natural compound library and screened against a well-known anti-bacterial drug target Dihydrofolate reductase (DHFR) enzyme of Staphylococcus aureus. The top two phytochemicals with lower docking score along with the positive control were subjected to molecular dynamics (MD) simulation studies to examine the stabilities of the complexes over 100 ns, followed by binding free energy estimation. The Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF) and Radius of Gyration (Rg) yielded established results throughout the MD run. Moreover, the derived phytochemicals exhibited lower binding free energy values than the positive control that can be tested for its in vitro efficacy, followed by further optimization to attain a potent therapeutic against S. aureus. Taken together, the present study suggests two promising phytochemicals derived from the aerial part of the plant S. irio with stable MD simulation results, strong binding affinity and no side effects. [ABSTRACT FROM AUTHOR]

COVID-19 in Indonesia is considered to be entering the endemic phase, and the population is expected to live side by side with the SARS-CoV 2 viruses and their variants. In this study, procyanidin, oleic acid, methyl linoleic acid, and vitexin, four compounds from binahong leaves-tropical/subtropical plant, were examined for their interactions with the major protease (Mpro) of the SARS-CoV 2 virus. Molecular dynamics simulation shows that procyanidin and vitexin have the best docking scores of −9.132 and −8.433, respectively. Molecular dynamics simulation also shows that procyanidin and vitexin have the best Root Mean Square Displacement (RMSD) and Root Mean Square Fluctuation (RMSF) performance due to dominant hydrogen, hydrophobic, and water bridge interactions. However, further strain energy calculation obtained from ligand torsion analyses, procyanidin and vitexin do not conform as much as quercetin as ligand control even though these two ligands have good performance in terms of interaction with the target protein. [ABSTRACT FROM AUTHOR]

The HA3 influenza (H3N2) influenza was originally found in 2011 and later appeared in January 2021. As per WHO report, H3N2 has the potential of causing a pandemic; therefore, an inhibitor for H3N2 should be designed. The hemagglutinin variants have typical 18 subtypes present in humans. Therefore, in the study, we generated the phylogenetic tree for understanding the similarity sequence between 18 subtypes and also the sequence of similarity was compared to H3N2. Thereafter, scaffold structures of FDA-approved Peramivir were generated, among which, four compounds were selected based on their drug-likeness and synthetic feasibility for performing docking and MD simulations. Theoretical evaluations, such as electronic, spectroscopic, binding energy, Root Mean Square Deviation (RMSD), Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET), were performed to validate the derived chemical structures and identify their potential of acting as drug compounds. In the present work, derivatives of 2-methyl tetrahydrofuran- n -carboxylic acids show the inhibitory activity with H3N2 (PDB ID: 4WEA) with stable conformations. In silico study for physical, chemical and biological activity of scaffolds of Peramivir. Comparative study for docking and MD simulation of complexes (scaffolds with HA3). Phylogenetic tree analysis and genomic sequence analysis for classes of influenza hemagglutinin. [ABSTRACT FROM AUTHOR]

Alkaline pectate lyase has developmental prospects in the textile, pulp, paper, and food industries. In this study, we selected BacPelA, the pectin lyase with the highest expression activity from Bacillus clausii, modified and expressed in Escherichia coli BL21(DE3). Through fragment replacement, the catalytic activity of the enzyme was significantly improved. The optimum pH and temperature of the modified pectin lyase (PGLA-rep4) were 11.0 and 70 °C, respectively. It also exhibited a superior ability to cleave methylated pectin. The enzyme activity of PGLA-rep4, measured at 235 nm with 0.2% apple pectin as the substrate, was 554.0 U/mL, and the specific enzyme activity after purification using a nickel column was 822.9 U/mg. After approximately 20 ns of molecular dynamics simulation, the structure of the pectin lyase PGLA-rep4 tended to be stable. The root mean square fluctuation (RMSF) values at the key catalytically active site, LYS168, were higher than those of the wildtype PGLA. In addition, PGLA-rep4 was relatively stable in the presence of metal ions. PGLA-rep4 has good enzymatic properties and activities and maintains a high pH and temperature. This study provides a successful strategy for enhancing the catalytic activity of PGLA-rep4, making it the ultimate candidate for degumming and various uses in the pulp, paper, and textile industries. [ABSTRACT FROM AUTHOR]

This study explored the mechanisms by which the stability of super-secondary structures of the 3β-corner type autonomously outside the protein globule are maintained in an aqueous environment. A molecular dynamic (MD) study determined the behavioral diversity of a large set of non-homologous 3β-corner structures of various origins. We focused on geometric parameters such as change in gyration radius, solvent-accessible area, major conformer lifetime and torsion angles, and the number of hydrogen bonds. Ultimately, a set of 3β-corners from 330 structures was characterized by a root mean square deviation (RMSD) of less than 5 Å, a change in the gyration radius of no more than 5%, and the preservation of amino acid residues positioned within the allowed regions on the Ramachandran map. The studied structures retained their topologies throughout the MD experiments. Thus, the 3β-corner structure was found to be rather stable per se in a water environment, i.e., without the rest of a protein molecule, and can act as the nucleus or "ready-made" building block in protein folding. The 3β-corner can also be considered as an independent object for study in field of structural biology. [ABSTRACT FROM AUTHOR]

Chlorothricin (CHL) belongs to a spirotetronate antibiotic family produced by Streptomyces antibioticus that inhibits pyruvate carboxylase and malate dehydrogenase. For the biosynthesis of CHL, ChlB3 plays a crucial role by introducing the 6-methylsalicylic acid (6MSA) moiety to ChlB2, an acyl carrier protein (ACP). However, the structural insight and catalytic mechanism of ChlB3 was unclear. In the current study, the crystal structure of ChlB3 was solved at 3.1 Å-resolution and a catalytic mechanism was proposed on the basis of conserved residues of structurally related enzymes. ChlB3 is a dimer having the same active sites as CerJ (a structural homologous enzyme) and uses a KSIII-like fold to work as an acyltransferase. The relaxed substrate specificity of ChlB3 was defined by its catalytic efficiencies (kcat/Km) for non-ACP tethered synthetic substrates such as 6MSA-SNAC, acetyl-SNAC, and cyclohexonyl-SNAC. ChlB3 successfully detached the 6MSA moiety from 6MSA-SNAC substrate and this hydrolytic activity demonstrated that ChlB3 has the potential to catalyze non-ACP tethered substrates. Structural comparison indicated that ChlB3 belongs to FabH family and showed 0.6–2.5 Å root mean square deviation (RMSD) with structural homologous enzymes. Molecular docking and dynamics simulations were implemented to understand substrate active site and structural behavior such as the open and closed conformation of the ChlB3 protein. The resultant catalytic and substrate recognition mechanism suggested that ChlB3 has the potential to use non-native substrates and minimize the labor of expressing ACP protein. This versatile acyltransferase activity may pave the way for manufacturing CHL variants and may help to hydrolyze several thioester-based compounds. [ABSTRACT FROM AUTHOR]

In the present work, the molecular dynamics study method has been utilised to investigate the effects of pressure on the volatilisation of pure Bi nanoparticles and Bi–Fe core–shell nanoparticles during continuous heating. Computational total energy curves between 300 and 2000 K are used to explore the structural changes of nanoparticles under different pressures. On the other hand, the radial distribution function is examined to determine the structural evolution of a system. The calculated root mean square displacement curves under pressures of 0–5 GPa between 300 and 2000 K are employed to explore the diffusion of Bi element and the calculated volatilisation rate of Bi element is used to quantitatively obtain the volatilisation characteristics. The volatilisation patterns of pure Bi nanoparticles and Bi–Fe core–shell nanoparticles are different under different temperatures and pressures. The results show that the volatilisation of Bi element is increasing during the heating from 300 to 2000 K, and the volatilisation decreases with the increase of pressure. Furthermore, the Fe shell can effectively decrease the volatilisation of the Bi element. [ABSTRACT FROM AUTHOR]

Search for new pharmacological alternatives for obesity is based on the design and development of compounds that can aid in weight loss so that they can be used safely and effectively over a long period while maintaining their function. The endocannabinoid system is related to obesity by increasing orexigenic signals and reducing satiety signals. Cannabis sativa is a medicinal plant of polypharmaceutical potential that has been widely studied for various medicinal purposes. The in silico evaluation of their natural cannabinoids (also called phytocannabinoids) for anti-obesity purpose stems from the existence of synthetic cannabinoid compounds that have already presented this result, but which did not guarantee patient safety. In order to find new molecules from C. sativa phytocannabinoids, with the potential to interact peripherally with the pharmacological target cannabinoid receptor 1, a pharmacophore-based virtual screening was performed, including the evaluation of physicochemical, pharmacokinetic, toxicological predictions and molecular docking. The results obtained from the ZINC12 database pointed to Zinc 69 (ZINC33053402) and Zinc 70 (ZINC19084698) molecules as promising anti-obesity agents. Molecular dynamics (MD) studies disclose that both complexes were stable by analyzing the RMSD (root mean square deviation) values, and the binding free energy values demonstrate that the selected structures can interact and inhibit their catalytic activity. [ABSTRACT FROM AUTHOR]

A novel series of benzothiazole‐rhodanine derivatives (A1‐A10) were designed and synthesized, with the aim of developing possible antidiabetic agents and the spectral characterization of these compounds was done using infrared spectroscopy (IR), proton‐nuclear magnetic resonance (1H‐NMR), carbon‐nuclear magnetic resonance (C13‐NMR), and high resolution mass spectroscopy (HR‐MS) techniques. In vitro hypoglycemic potential of the compounds was evaluated by performing α‐amylase and α‐glucosidase enzyme inhibitory assays. In addition, these compounds were subjected to in silico analysis. Based on the results, compounds A5, A6, and A9 displayed good activity in comparison with the standard acarbose. Based on Lineweaver‐Burk plots, it was concluded that compounds A5 and A9 displayed competitive type of enzyme inhibition. Molecular dynamic simulations were conducted to evaluate the stability of the ligand‐protein complex by the calculation of the root mean square deviation, root means square fluctuation, and solvent accessible surface area. [ABSTRACT FROM AUTHOR]

Eight novel fluorescent antifolates were designed and docked with folate receptors FRα and FRβ. The structures of the complexes were further calculated by molecular dynamic (MD) simulations. The binding energies were calculated by molecular docking and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) studies. The binding energy differences between FRα and FRβ (|Ebα|–|Ebβ|) values for compounds 3 and 8 were 1.3 and 1.1 kcal/mol calculated by molecular docking, and 13.9 and 10.4 kcal/mol by MM-PBSA simulation, respectively. The results indicated that compounds 3 and 8 may be the best candidates for targeted drug delivery to FRα. The binding structures, interaction residues, negatively charged pocket volume, and surface area were analyzed for all the complexes. We further calculated the root mean square displacement and secondary structural elements of the bound complexes using molecular dynamics simulations. The purpose of this study is to design novel antifolates targeted to FRα and FRβ, and to further distinguish between cancer cells and inflammation. [ABSTRACT FROM AUTHOR]

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a pivotal enzyme in tocopherol and plastoquinone synthesis and a potential target for novel herbicides. Thirty-five pyridine derivatives were selected to establish a Topomer comparative molecular field analysis (Topomer CoMFA) model to obtain correlation information between HPPD inhibitory activity and the molecular structure. A credible and predictive Topomer CoMFA model was established by "split in two R-groups" cutting methods and fragment combinations (q2 = 0.703, r2 = 0.957, ONC = 6). The established model was used to screen out more active compounds and was optimized through the auto in silico ligand directing evolution (AILDE) platform to obtain potential HPPD inhibitors. Twenty-two new compounds with theoretically good HPPD inhibition were obtained by combining the high-activity contribution substituents in the existing molecules with the R-group search via Topomer search. Molecular docking results revealed that most of the 22 fresh compounds could form stable π-π interactions. The absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction and drug-like properties made 9 compounds potential HPPD inhibitors. Molecular dynamics simulation indicated that Compounds Y12 and Y14 showed good root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values and stability. According to the AILDE online verification, 5 new compounds with potential HPPD inhibition were discovered as HPPD inhibitor candidates. This study provides beneficial insights for subsequent HPPD inhibitor design. [ABSTRACT FROM AUTHOR]

Molecular dynamics (MD) simulation was used to study the influence of electric field on Glucagon-like Peptide-2 (GLP-2). Different electric field strengths (0 V/nm ≤ E ≤ 1 V/nm) were mainly carried out on GLP-2. The structural changes in GLP-2 were analyzed by the Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), Solvent Accessible Surface Area (SASA), Secondary Structure and the number of hydrogen bonds. The stable α—helix structure of GLP-2 was unwound and transformed into an unstable Turn and Coil structure since the stability of the GLP-2 protein structure was reduced under the electric field. Our results show that the degree of unwinding of the GLP-2 structure was not linearly related to the electric field intensity. E = 0.5 V/nm was a special point where the degree of unwinding of the GLP-2 structure reached the maximum at this electric field strength. Under a weak electric field, E < 0.5 V/nm, the secondary structure of GLP-2 becomes loose, and the entropy of the chain increases. When E reaches a certain value (E > 0.5 V/nm), the electric force of the charged residues reaches equilibrium, along the z-direction. Considering the confinement of moving along another direction, the residue is less free. Thus, entropy decreases and enthalpy increases, which enhance the interaction of adjacent residues. It is of benefit to recover hydrogen bonds in the middle region of the protein. These investigations, about the effect of an electric field on the structure of GLP-2, can provide some theoretical basis for the biological function of GLP-2 in vivo. [ABSTRACT FROM AUTHOR]

Phytochemicals derived from Cydonia oblonga have been investigated for their anti-oxidant and anti-cancer activities in various cancer cell lines. The reported bioactive compounds are evaluated in silico to develop a novel antagonist against pTEN (phosphatase and tensin homolog) and HBx (hepatitis B X-interacting protein) to target hepatocellular carcinoma. Lower expression of pTEN or higher expression of HBx represents the progression of hepatocellular carcinoma. This research is intended to identify the best candidate who interacts with our target proteins (pTEN and HBx) from the quince seeds by using computational methodologies. The ternary structures of the proteins and phytochemicals are retrieved from the online databases (RCSB and PubChem). The drug likeness analysis of the reported seventeen compounds was done, but only five follow the selection criteria. ADMET profiling of these five compounds was done, followed by docking analysis and molecular dynamics study of the best complexes to determine the stability of the complexes. A docking study revealed that caffeoylquinic acids (CQA) derivatives have the significant inhibitory potential of 3-O-caffeoylquinic acid (3CQA) and 5-O-caffeoylquinic acid (5CQA) with binding affinity of − 7.53 and − 7.49 against pTEN and − 5.94 and − 6.01 against HBx in comparison to the doxorubicin. The average root mean square deviation and root mean square fluctuation values for protein–ligand complexes were found quite stable compared to the standard, while parameters like gyration and SASA (solvent-accessible surface area) supported the complexes significant binding and stability. The results obtained from the evaluation show that 3CQA and 5CQA have the best stability, especially with the pTEN protein target. Hence, these compounds have to be considered for detailed experimental studies to understand their biological function against hepato-carcinoma. [ABSTRACT FROM AUTHOR]