Dynamics Simulation Approach Research Articles

Identification of Novel PPAR-β/δ Agonists from Kaempferol, Quercetin, and Resveratrol Derivatives by Targeting Cancer: An Integrative Molecular Docking and Dynamics Simulation Approach

Background: Drug resistance in cancer is a serious threat to human well-being. There is a dire need to develop novel and efficient lead molecules to treat the disease. In lieu of anti-cancer activities, Peroxisome proliferator–activated receptors (PPARs)-β/δ proven to be potential therapeutic targets against cancer. However, there are yet no PPAR-β/δ agonists reported for clinical use. Objective: The present study features in silico screening and identification of 8708 derivatives based on backbone of natural compounds like Kaempferol, Quercetin and Resveratrol against PPAR-β/δ using molecular docking, and molecular dynamics (MD) simulations. Methods: Initial screening of 8708 derivatives was done by recruiting Lipinski’s rule of five. Docking calculations were assessed through FlexX software tool. GROMACS was used to analyze dynamic perturbations and binding free energy (MM/GBSA) analysis of the top compounds. SwissADME was used to analyze pharmacokinetic properties. Results: The results of molecular docking indicated that 2-[2-(2,4-Dihydroxyphenyl)-2- oxoethoxy]benzoate (DOB), (E)-1-(3,4,5-Trihydroxyphenyl)-3-(3,4-dihydroxyphenyl) propene (TDP) and 2-Hydroxy-3-(2,6,7-trihydroxy-3-oxo-3H-xanthen-9-YL) benzoic acid (HTOB); respective derivatives of Kaempferol, Resveratrol and Quercetin strongly binds to the active site residues of PPAR-β/δ. Furthermore, ADME (absorption, distribution, metabolism & excretion) profile conferred their high druglikeness properties. On monitoring their dynamic perturbations, HTOB acquired the most favorable interaction and stability within the vicinity of PPAR-β/δ protein. Conclusion: These outcomes constitute preliminary studies and the obtained lead derivatives could be great options to treat various types of cancer and formulate as oral drug candidates.

Evaluation of binding mechanism of dietary phytochemical, capsaicin, with human transferrin: targeting neurodegenerative diseases therapeutics.

Human transferrin (htf) plays a crucial role in regulating the balance of iron within brain cells; any disruption directly contributes to the development of Neurodegenerative Diseases (NDs) and other related pathologies, especially Alzheimer's Disease (AD). In recent times, a transition towards natural compounds is evident to treat diseases and this shift is mainly attributed to their broad therapeutic potential along with minimal side effects. Capsaicin, a natural compound abundantly found in red and chili peppers, possess neuroprotective potential. The current work targets to decipher the interaction mechanism of capsaicin with htf using experimental and computational approaches. Molecular docking analysis revealed that capsaicin occupies the iron binding pocket of htf, with good binding affinity. Further, the binding mechanism was investigated atomistically using Molecular dynamic (MD) simulation approach. The results revealed no significant alterations in the structure of htf implying the stability of the complex. In silico observations were validated by fluorescence binding assay. Capsaicin binds to htf with a binding constant (K) of 3.99 × 106M-1, implying the stability of the htf-capsaicin complex. This study lays a platform for potential applications of capsaicin in treatment of NDs in terms of iron homeostasis.

Investigation of the Several Aspects of Interaction between Human Serum Albumin and Oleic Acid by Molecular Dynamic Simulation Approaches and Spectroscopic Methods

Investigation of the Several Aspects of Interaction between Human Serum Albumin and Oleic Acid by Molecular Dynamic Simulation Approaches and Spectroscopic Methods

Structural insights into non-hotspot KRAS mutations and their potential as targets for effective cancer therapies

Kirsten rat sarcoma virus protein (KRAS) is a protein that plays a central role in signal transduction using extracellular signal regulated kinase (ERK) and mitogen activated protein kinase (MAPK) cellular signaling pathway. KRAS is a frequently mutated oncogene and plays a pivotal role in tumor initiation and progression. Hotspot mutations on codon 12, 13 and 61 in KRAS are well-known for their role in drug resistance and non-hotspot mutations also play a significant part in contributing to resistance mechanisms. The understanding of how these non-hotspot mutations might affect the signal transduction of KRAS and their contribution towards drug resistance is understudied. Here we provide structural insights into the interaction of non-hotspot KRAS mutants with GTP (the native ligand) using a molecular docking and molecular dynamics simulation approach. Extensive molecular docking and simulation studies suggest that non-hotspot mutations (E31D and E63K) show stable interaction with native ligand using all five trajectories, as evidenced by root mean square of distance (RMSD), root mean square of fluctuation (RMSF), radius of gyration (RoG), coulomb short-range energy and MMGBSA analysis. These results suggest that non-hotspot mutations do not undermine the oncogenic nature of KRAS. This observation is consistent with previous findings where overexpressing E31D and E63K mutations share phenotypic features with G12D and G13D transfected cells, including increased proliferative capacity, actin cytoskeleton organization, and migration rates. We further test whether FDA-approved KRAS inhibitors sotorasib and adagrasib successfully inhibit the E31D and E63K mutants. Results suggest that these two non-hotspot mutants can be inhibited by both drugs with following trend of structural stability (E31D > E63K > wild-KRAS > Q61H > G12C). Based on sharp coherence in trajectories between wild KRAS and non-hotspot mutants, it is suggested that these novel mutants do not contribute to drug resistance mechanism. Overall, we provide a comprehensive understanding of the impact of non-hotspot mutations on KRAS and their potential as targets for effective cancer therapies. Communicated by Ramaswamy H. Sarma

Molecular mechanisms of chaperone-directed protein folding: Insights from atomistic simulations.

Molecular chaperones, a family of proteins of which Hsp90 and Hsp70 are integral members, form an essential machinery to maintain healthy proteomes by controlling the folding and activation of a plethora of substrate client proteins. This is achieved through cycles in which Hsp90 and Hsp70, regulated by task-specific co-chaperones, process ATP and become part of a complex network that undergoes extensive compositional and conformational variations. Despite impressive advances in structural knowledge, the mechanisms that regulate the dynamics of functional assemblies, their response to nucleotides, and their relevance for client remodeling are still elusive. Here, we focus on the glucocorticoid receptor (GR):Hsp90:Hsp70:co-chaperone Hop client-loading and the GR:Hsp90:co-chaperone p23 client-maturation complexes, key assemblies in the folding cycle of glucocorticoid receptor (GR), a client strictly dependent upon Hsp90/Hsp70 for activity. Using a combination of molecular dynamics simulation approaches, we unveil with unprecedented detail the mechanisms that underpin function in these chaperone machineries. Specifically, we dissect the processes by which the nucleotide-encoded message is relayed to the client and how the distinct partners of the assemblies cooperate to (pre)organize partially folded GR during Loading and Maturation. We show how different ligand states determine distinct dynamic profiles for the functional interfaces defining the interactions in the complexes and modulate their overall flexibility to facilitate progress along the chaperone cycle. Finally, we also show that the GR regions engaged by the chaperone machinery display peculiar energetic signatures in the folded state, which enhance the probability of partial unfolding fluctuations. From these results, we propose a model where a dynamic cross-talk emerges between the chaperone dynamics states and remodeling of client-interacting regions. This factor, coupled to the highly dynamic nature of the assemblies and the conformational heterogeneity of their interactions, provides the basis for regulating the functions of distinct assemblies during the chaperoning cycle.

Raman spectroscopy study of 7,8-dihydrofolate inhibition on the Wuhan strain SARS-CoV-2 binding to human ACE2 receptor

Emerging evidence suggests that elevated levels of folic acid in the bloodstream may confer protection against Wuhan-SARS-CoV-2 infection and mitigate its associated symptoms. Notably, two comprehensive studies of COVID-19 patients in Israel and UK uncovered a remarkable trend, wherein individuals with heightened folic acid levels exhibited only mild symptoms and necessitated no ventilatory support. In parallel, research has underscored the potential connection between decreased folic acid levels and the severity of Covid-19 among hospitalized patients. Yet, the underlying mechanisms governing this intriguing inhibition remain elusive. In a quest to elucidate these mechanisms, we conducted a molecular dynamics simulation approach followed by a Raman spectroscopy study to delve into the intricate interplay between the folic acid metabolite, 7,8-dihydrofolate (DHF), and the angiotensin-converting enzyme ACE2 receptor, coupled with its interaction with the receptor-binding domain (RBD) of the Wuhan strain of SARS-CoV-2. Through a meticulous exploration, we scrutinized the transformation of the ACE2 + RBD complex, allowing these reactants to form bonds. This was juxtaposed with a similar investigation where ACE2 was initially permitted to react with DHF, followed by the exposure of the ACE2 + DHF complex to RBD. We find that DHF, when bonded to ACE2, functions as a physical barrier, effectively inhibiting the binding of the Wuhan strain RBD. This physicochemical process offers a cogent explanation for the observed inhibition of host cell infection in subjects receiving supplementary folic acid doses, as epidemiologically substantiated in multiple studies. This study not only sheds light on a potential avenue for mitigating SARS-CoV-2 infection but also underscores the crucial role of folic acid metabolites in host-virus interactions. This research paves the way for novel therapeutic strategies in the battle against COVID-19 and reinforces the significance of investigating the molecular mechanisms underlying the protective effects of folic acid in the context of viral infections.

Simulating micelle self-assembly to assess potential for viscosity build in surfactant formulations

Self-assembly of surfactants into complex structures is key to the performance of many formulated products, which form a significant fraction of the world’s manufactured goods. Here we adopt the dissipative particle dynamics simulation approach to explore the self-assembly process of surfactants, with the aim of understanding what information can be obtained that may correlate with an increased zero-shear viscosity of surfactant based products. To this end we experimentally measured the zero-shear viscosity of mixed micelle systems comprised of cocoamidopropyl betaine (CAPB) and sodium lauryl sarcosinate (SLSar), as a function of the CAPB/SLSar mass ratio and pH, and characterised the early stages of self-assembly of the same systems computationally. From simulation we identify three distinct behaviors in the micellar self-assembly process (logarithmic, linear and cubic growth) which we find show some degree of correlation with the experimental zero-shear viscosity. Owing to the relatively short simulation times required, this may provide formulation scientists with a practical route to identify regions of interest (i. e. those with a desired zero-shear viscosity) prior to synthesising de novo (potentially natural) surfactants.

Magnesium Ion Gated Ion Rejection through Carboxylated Graphene Oxide Nanopore: A Theoretical Study.

While nanoporous graphene oxide (GO) is recognized as one of the most promising reverse osmosis desalination membranes, limited attention has been paid to controlling desalination performance through the large GO pores, primarily due to significant ion leakage resulting in the suboptimal performance of these pores. In this study, we employed a molecular dynamics simulation approach to demonstrate that Mg2+ ions, adhered to carboxylated GO nanopores, can function as gates, regulating the transport of ions (Na+ and Cl-) through the porous GO membrane. Specifically, the presence of divalent cations near a nanopore reduces the concentration of salt ions in the vicinity of the pore and prolongs their permeation time across the pore. This subsequently leads to a notable enhancement in salt rejection rates. Additionally, the ion rejection rate increases with more adsorbed Mg2+ ions. However, the presence of the adsorbed Mg2+ ions compromises water transport. Here, we also elucidate the impact of graphene oxidation degree on desalination. Furthermore, we design an optimal combination of adsorbed Mg2+ ion quantity and oxidation degree to achieve high water flux and salt rejection rates. This work provides valuable insights for developing new nanoporous graphene oxide membranes for controlled water desalination.

Immunoinformatics, molecular docking and dynamics simulation approaches unveil a multi epitope-based potent peptide vaccine candidate against avian leukosis virus

Lymphoid leukosis is a poultry neoplastic disease caused by avian leukosis virus (ALV) and is characterized by high morbidity and variable mortality rates in chicks. Currently, no effective treatment and vaccination is the only means to control it. This study exploited the immunoinformatics approaches to construct multi-epitope vaccine against ALV. ABCpred and IEDB servers were used to predict B and T lymphocytes epitopes from the viral proteins, respectively. Antigenicity, allergenicity and toxicity of the epitopes were assessed and used to construct the vaccine with suitable adjuvant and linkers. Secondary and tertiary structures of the vaccine were predicted, refined and validated. Structural errors, solubility, stability, immune simulation, dynamic simulation, docking and in silico cloning were also evaluated.The constructed vaccine was hydrophilic, antigenic and non-allergenic. Ramchandran plot showed most of the residues in the favored and additional allowed regions. ProsA server showed no errors in the vaccine structure. Immune simulation showed significant immunoglobulins and cytokines levels. Stability was enhanced by disulfide engineering and molecular dynamic simulation. Docking of the vaccine with chicken’s TLR7 revealed competent binding energies.The vaccine was cloned in pET-30a(+) vector and efficiently expressed in Escherichia coli. This study provided a potent peptide vaccine that could assist in tailoring a rapid and cost-effective vaccine that helps to combat ALV. However, experimental validation is required to assess the vaccine efficiency.

A comparison of the use of traditional glazing and a novel concentrated photovoltaic glazing (CoPVG) for building solar gain analysis using IESVE

The aim of this study is to compare the difference in solar gain for an internal space when a novel Concentrated Photovoltaic Glazing (CoPVG) unit is compared against traditional glazing modules. The CoPVG is an innovative glazing system developed by Ulster University, that takes advantage of Total Internal Reflection (TIR) to direct solar radiation into the internal space during periods of low solar altitude (around winter) harnessing the thermal contribution of solar gain and daylight. During periods of higher solar altitude (around summer), the solar radiation is mostly directed onto embedded photovoltaic cells. Previous work assessed the concept’s optical functionality, through experimental measurement and computational ray-tracing. Dynamic simulation in Matrix Laboratory (MATLAB) using a series of codes to represent the optical function of the CoPVG’s and Integrated Environmental Solutions Virtual Environment (IESVE) was validated by the experimental data. This work investigates methodologies in determining the transmissivty of the system in a dynamic simulation approach using ray tracing and Radiance in IESVE for visualisation, thereby building on the versability of this software to allow building designers and consultants to investigate energy and economic benefits of this system and systems like it in real building applications. The impact of integrating CoPVG as a replacement to traditonal glazing on a sun-facing building facade is assessed and the solar gain in the adjaciant space is compared throughout the year. During the summer months the integrated system reduces solar gain in the space by 34% but only 11% in the winter months, representing a reduction in the overall annual building energy needs. The study presents the potential economic and environmental savings provided by reduced cooling.

Multiscale Molecular Dynamics Simulations of an Active Self-Assembling Material.

Inspired by the adaptability observed in biological materials, self-assembly processes have attracted significant interest for their potential to yield novel materials with unique properties. However, experimental methods have often fallen short in capturing the molecular details of the assembly process. In this study, we employ a multiscale molecular dynamics simulation approach, complemented by NMR quantification, to investigate the mechanism of self-assembly in a redox-fueled bioinspired system. Contrary to conventional assumptions, we have uncovered a significant role played by the monomer precursor in the assembly process, with its presence varying with concentration and the extent of conversion of the monomer to the dimer. Experimental confirmation through NMR quantification underscores the concentration-dependent incorporation of monomers into the fibrous structures. Furthermore, our simulations also shed light on the diverse intermolecular interactions, including T-shaped and parallel π stacking, as well as hydrogen bonds, in stabilizing the aggregates. Overall, the open conformation of the dimer is preferred within these aggregates. However, inside the aggregates, the distribution of conformations shifts slightly to the closed conformation compared to on the surface. These findings contribute to the growing field of bioinspired materials science by providing valuable mechanistic and structural insights to guide the design and development of self-assembling materials with biomimetic functionalities.

In silico exploration of the potential inhibitory activities of in-house and ZINC database lead compounds against alpha-glucosidase using structure-based virtual screening and molecular dynamics simulation approach

Inhibitors of α-glucosidase have been used to treat type-2 diabetes (T2DM) by preventing the breakdown of carbohydrates into glucose and prevent enhancing glucose conversion. Structure-based virtual screening (SBVS) was used to generate novel chemical scaffold-ligand α-glucosidase inhibitors. The databases were screened against the receptor α-glucosidase using SBVS and molecular dynamics simulation (MDS) techniques in this study. Based on molecular docking studies, three and two compounds of α-glucosidase inhibitors were chosen from a commercial database (ZINC) and an In-house database for this study respectively. The mode of binding interactions of the selected compounds later predicted their α-glucosidase inhibitory potential. Finally, one out of three lead compound from ZINC and one out of two lead compound from In-house database were shortlisted based on interactions. Furthermore, MDS and post-MDS strategies were used to refine and validate the shortlisted leads along with the reference acarbose/α-glucosidase. The Hits’ ability to inhibit α-glucosidase was predicted by SBVS, indicating that these compounds have good inhibitory activities. The lead inhibitor’s structure may serve as templates for the design of novel inhibitors, and in vitro testing to confirm their anti-diabetic potential is necessary. These insights can help rationally design new effective anti-diabetic drugs. Communicated by Ramaswamy H. Sarma

Secondary metabolites of Trichoderma spp. as EGFR tyrosine kinase inhibitors: Evaluation of anticancer efficacy through computational approach.

The present study explores the epidermal growth factor receptor (EGFR) tyrosine kinase inhibition efficacy of secondary metabolites in Trichoderma spp. through molecular docking, molecular dynamics (MD) simulation and MM-PBSA approach. The result of molecular docking confirmed that out of 200 metabolites screened, three metabolites such as Harzianelactone A, Pretrichodermamide G and Aspochalasin M, potentially bound with the active binding site of EGFR tyrosine kinase domain(PDB ID: 1M17) with a threshold docking score of ≤- 9.0 kcal/mol when compared with the standard EGFR inhibitor (Erlotinib). The MD simulation was run to investigate the potential for stable complex formation in EGFR tyrosine kinase domain-unbound/lead metabolite (Aspochalasin M)-bound/standard inhibitor (Erlotinib)-bound complex. The MD simulation analysis at 100 ns revealed that Aspochalasin M formed the stable complex with EGFR. Besides, the in silico predication of pharmacokinetic properties further confirmed that Aspochalasin M qualified the drug-likeness rules with no harmful side effects (viz., hERG toxicity, hepatotoxicity and skin sensitization), non-mutagenicity and favourable logBB value. Moreover, the BOILED-Egg model predicted that Aspochalasin M showed a higher gastrointestinal absorption with improved bioavailability when administered orally and removed from the central nervous system (CNS). The results of the computational studies concluded that Aspochalasin M possessed significant efficacy in binding EGFR's active sites compared to the known standard inhibitor (Erlotinib). Therefore, Aspochalasin M can be used as a possible anticancer drug candidate and further in vitro and in vivo experimental validation of Aspochalasin M of Trichoderma spp. are required to determine its anticancer potential.

Identification of antiviral phytochemicals from cranberry as potential inhibitors of SARS-CoV-2 main protease (Mpro)

Cranberry phytochemicals are known to possess antiviral activities. In the current study, we explored the therapeutic potential of cranberry against SARS-CoV-2 by targeting its main protease (Mpro) enzyme. Firstly, phytochemicals of cranberry origin were identified from three independent databases. Subsequently, virtual screening, using molecular docking and molecular dynamics simulation approaches, led to the identification of three lead phytochemicals namely, cyanidin 3-O-galactoside, β-carotene and epicatechin. Furthermore, in vitro enzymatic assays revealed that cyanidin 3-O-galactoside had the highest inhibitory potential with IC50 of 9.98 μM compared to the other two phytochemicals. Cyanidin 3-O-galactoside belongs to the class of anthocyanins. Anthocyanins extracted from frozen cranberry also exhibited the highest inhibitory potential with IC50 of 23.58 μg/ml compared to the extracts of carotenoids and flavanols, the class for β-carotene and epicatechin, respectively. Finally, we confirm the presence of the phytochemicals in the cranberry extracts using targeted LC-MS/MS analysis. Our results, therefore, indicate that the identified cranberry-derived bioactive compounds as well as cranberry could be used for therapeutic interventions against SARS-CoV-2.

Study the solubility of pharmaceutical ingredients and their eutectic mixtures: An in-depth density functional theory and molecular dynamics simulations approaches

Solubility is a major concern for many active pharmaceutical ingredients (APIs) and drugs. Owing to their better solubility, biodegradability and low toxicity of APIs and drugs, eutectic mixtures are emerging as the system to enhance their solubility with no loss of biological activity. In the present work, authors have taken camizestrant, deucravacitinib, and iclepertin as the active pharmaceutical ingredients (API) because they have poor solubility in water. Authors have designed eutectic mixtures (EMs) of the selected APIs with the amino acids (aspartic acid, lysine, phenylalanine, and proline) and studied for their physiochemical properties in default and water using density functional theory calculations, performed by Gaussian. The solubility of the APIs, amino acids and the designed eutectic mixtures of APIs have been determined and discussed using the dipole moment. The results showed that the solubility of the designed eutectic mixtures have better aqueous solubility than the APIs alone. Further, molecular dynamics (MD) simulations were done for APIs and EMs to study their stability and interactions.

Analysing the nexus between clean energy expansion, natural resource extraction, and load capacity factor in China: a step towards achieving COP27 targets

AbstractThe excessive use of non-renewable energy in 21st-century economic growth has continued to hurt the environment by accumulating carbon dioxide and other greenhouse gases. However, promoting environmental sustainability requires expanding clean energy utilisation. In this study, we examine the effects of clean energy expansion and natural resource extraction on load capacity factor (LCF) in China from 1970 to 2018. Using the dynamic autoregressive distributed lag simulations approach, we extend the standard load capacity curve (LCC) hypothesis by incorporating clean energy expansion and natural resource extraction as main determinants of the LCF. The empirical outcomes reveal that economic expansion is, although positively associated with the LCF, but its squared term degrades the LCF. This confirms that the LCC hypothesis is not valid for China. Moreover, while clean energy expansion has a positive effect on the LCF, the effect of natural resource extraction is negative. These effects are stronger and statistically significant only in the long run. Therefore, this study highlights the potentials for a sustainable decarbonized economy in China by investing not only in clean energy sources but also efficiently use the available natural resources in the country.

Integrating molecular docking and molecular dynamics simulation approaches for the investigation of the affinity and interactions of curcumin with Class D β-lactamase

ntroduction: Antimicrobial resistance has become major concern of treating infectious disease due to their extensive use, which led to bacterial gen modification and secretion of some enzymes by these microorganisms that make them survival despite the presence of antibiotics. Searching of inhibitors for these resistant pathogens were helpful to elevate the impact of antibiotics in curing diseases. Curcumin is a natural compound which has several medicinal effects, can be used to inhibit OXA-10 β-lactamase class D enzymes. Materials and Methods: Molecular docking and Molecular dynamic simulation utilized to understand the binding pose, structural integrity, stability and binding energy of class D beta lactamase with Curcumin using Autodock 4.2.2 software and GROMACS 2019.6 program applying AMBER99SB force field respectively. Results: Molecular docking results and interaction analysis of molecular dynamics simulations indicated stable hydrogen bonds and van der Waals interactions of Curcumin with OXA-10 β-lactamase. Conclusion: This paper indicates that curcumin which is a natural ingredient can be used as a potential inhibitor of class D β -lactamase OXA-10.

Integrating molecular docking and molecular dynamics simulation approaches for investigation of the affinity and interactions of Berberine with Class C β-Lactamase

Background: Antibiotic resistance is a significant health concern, as bacteria produce enzymes that inhibit antimicrobial drug activity, increasing disease generation. This study investigates the inhibitory effect of berberine on β-lactamase enzyme activity and antibiotic effectiveness. Methods: Molecular docking was utilized to find the binding pose and binding affinity of a new inhibitory ligand with the AmpC enzyme using Autodock software version 4.2.2. MD simulations were performed in free form and complicated to understand the stability of the protein-ligand docked complex. Results: The molecular docking result indicated the proper interaction between berberine and the AmpC β-lactamase enzyme with a suitable binding pose and binding energy of -6.55 kcal/mol. The MD simulation of systems verifies the docking result, which shows stable hydrogen bonds of berberine with AmpC and good equivalence between RMSD, RMSF, SASA, etc. Conclusion: This paper reveals that berberine, which is a natural ingredient with multiple medicinal characteristics, can be applied as a potential inhibitor of class C β-lactamase AmpC. Hence, the outcome of the calculations performed provides valuable data to design new inhibitors with therapeutic potential to control the β-lactamase activity.

Effect of Solute on Interfacial Properties and Micelle Structure of Dodecylbenzenesulfonate (DBS): Experimental and Molecular Dynamics Studies.

A combined experimental and molecular dynamic simulation approach was used to examine the structure and interfacial properties of solute-saturated micelles. The properties of dodecylbenzenesulfonate (DBS) micelles were examined in dodecane and benzene hydrocarbon systems. Pyrene fluorescence was used to determine the aggregation number of surfactant monomers in the micelle systems. Molecular dynamic (MD) simulations using energy minimization applying the CHARMm force field with the TIP3P model for water. Comparison of the DBS/benzene and DBS/Dodecane micelles equilibrium structures via radial distribution function (RDF) and probability distribution function (PDF) analysis indicates that the area per head group for the DBS/Benzene micelle interface is significantly larger than that of the DBS/Dodecane at the interface. It was also determined that benzene molecules can move freely within the micelle while dodecane is strictly confined in the core of the micelle. The increased interfacial area per monomer caused by the insertion of benzene also reduces the effectiveness of the surfactant, which has implications for use in various environmental applications. However, the DBS/benzene micelle can solubilize many more hydrocarbon molecules in one micelle with less surfactant monomer (i.e., lower aggregation number) per micelle due to the increased available packing positions within the micelle. This, in turn, increases the efficiency of the surfactant in real-world applications which is consistent with previous laboratory results. Understanding the differing solubilization characteristics of surfactants against various classes of hydrocarbons in single solute systems is a necessary step to beginning to understand their solubilization properties in the mixed waste systems prevalent in most surfactant enhanced remediation (SEAR) strategies.

Comprehensive characterization of coding and non-coding single nucleotide polymorphisms of the Myoneurin (MYNN) gene using molecular dynamics simulation and docking approaches.

Genome-wide association studies (GWAS) identified a coding single nucleotide polymorphism, MYNN rs10936599, at chromosome 3q. MYNN gene encodes myoneurin protein, which has been associated with several cancer pathogenesis and disease development processes. However, there needed to be a more detailed characterization of this polymorphism's (and other coding and non-coding polymorphisms) structural, functional, and molecular impact. The current study addressed this gap and analyzed different properties of rs10936599 and non-coding SNPs of MYNN via a thorough computational method. The variant, rs10936599, was predicted functionally deleterious by nine functionality prediction approaches, like SIFT, PolyPhen-2, and REVEL, etc. Following that, structural modifications were estimated through the HOPE server and Mutation3D. Moreover, the mutation was found in a conserved and active residue, according to ConSurf and CPORT. Further, the secondary structures were predicted, followed by tertiary structures, and there was a significant deviation between the native and variant models. Similarly, molecular simulation also showed considerable differences in the dynamic pattern of the wildtype and mutant structures. Molecular docking revealed that the variant binds with better docking scores with ligand NOTCH2. In addition to that, non-coding SNPs located at the MYNN locus were retrieved from the ENSEMBL database. These were found to disrupt the transcription factor binding regulatory regions; nonetheless, only two affect miRNA target sites. Again, eight non-coding variants were detected in the testes with normalized expression, whereas HaploReg v4.1 unveiled annotations for non-coding variants. In summary, in silico comprehensive characterization of coding and non-coding single nucleotide polymorphisms of MYNN gene will assist researchers to work on MYNN gene and establish their association with certain types of cancers.