Scaled Particle Theory and the Efficient Calculation of the Chemical Potential of Hard Spheres in the NVT Ensemble

Adjusting Catalytic Activity of β-Amyrin Synthase GgBAS by Utilizing the Plasticity Residues of an Active Site

β-Amyrin synthase (bAS) is a representative plant oxidosqualene cyclase (OSC), and previous studies have identified many functional residues and mutants that can alter its catalytic activity. However, the regulatory mechanism of the active site architecture for adjusting the catalytic activity remains unclear. In this study, we investigate the function of key residues and their regulatory effects on the catalytic activity of Glycyrrhiza glabra β-amyrin synthase (GgbAS) through molecular dynamics simulations and site-directed mutagenesis experiments. We identified the plasticity residues located in two active site regions and explored the interactions between these residues and tetracyclic/pentacyclic intermediates. Based on computational and experimental results, we further categorize these plasticity residues into three types: effector, adjuster, and supporter residues, according to their functions in the catalytic process. This study provides valuable insights into the catalytic mechanism and active site plasticity of GgbAS, offering important references for the rational enzyme engineering of other OSC enzyme.

Perfect confinement of crown ethers in MOF membrane for complete dehydration and fast transport of monovalent ions

Fast transport of monovalent ions is imperative in selective monovalent ion separation based on membranes. Here, we report the in situ growth of crown ether@UiO-66 membranes at a mild condition, where dibenzo-18-crown-6 (DB18C6) or dibenzo-15-crown-5 is perfectly confined in the UiO-66 cavity. Crown ether@UiO-66 membranes exhibit enhanced monovalent ion transport rates and mono-/divalent ion selectivity, due to the combination of size sieving and interaction screening effects toward the complete monovalent ion dehydration. Specifically, the DB18C6@UiO-66 membrane shows a permeation rate (e.g., K+) of 1.2 mol per square meter per hour and a mono-/divalent ion selectivity (e.g., K+/Mg2+) of 57. Theoretical calculations and simulations illustrate that, presumably, ions are completely dehydrated while transporting through the DB18C6@UiO-66 cavity with a lower energy barrier than that of the UiO-66 cavity. This work provides a strategy to develop efficient ion separation membranes via integrating size sieving and interaction screening and to illuminate the effect of ion dehydration on fast ion transport.

SHP-1 tyrosine phosphatase binding to c-Src kinase phosphor-dependent conformations: A comparative structural framework

SHP-1 is a cytosolic tyrosine phosphatase that is primarily expressed in hematopoietic cells. It acts as a negative regulator of numerous signaling pathways and controls multiple cellular functions involved in cancer pathogenesis. This study describes the binding preferences of SHP-1 (pY536) to c-Srcopen (pY416) and c-Srcclose (pY527) through in silico approaches. Molecular dynamics simulation analysis revealed more conformational changes in c-Srcclose upon binding to SHP-1, as compared to its active/open conformation that is stabilized by the cooperative binding of the C-SH2 domain and C-terminal tail of SHP-1 to c-Src SH2 and KD. In contrast, c-Srcclose and SHP-1 interaction is mediated by PTP domain-specific WPD-loop (WPDXGXP) and Q-loop (QTXXQYXF) binding to c-Srcclose C-terminal tail residues. The dynamic correlation analysis demonstrated a positive correlation for SHP-1 PTP with KD, SH3, and the C-terminal tail of c-Srcclose. In the case of the c-Srcopen-SHP-1 complex, SH3 and SH2 domains of c-Srcopen were correlated to C-SH2 and the C-terminal tail of SHP-1. Our findings reveal that SHP1-dependent c-Src activation through dephosphorylation relies on the conformational shift in the inhibitory C-terminal tail that may ease the recruitment of the N-SH2 domain to phosphotyrosine residue, resulting in the relieving of the PTP domain. Collectively, this study delineates the intermolecular interaction paradigm and underlying conformational readjustments in SHP-1 due to binding with the c-Src active and inactive state. This study will largely help in devising novel therapeutic strategies for targeting cancer development.

Chemical potential and surface free energy of a hard spherical particle in hard-sphere fluid over the full range of particle diameters

The excess chemical potential $\mu^\mathrm{ex}(\sigma,\eta)$ of a test hard spherical particle of diameter $\sigma$ in a fluid of hard spheres of diameter $\sigma_0$ and packing fraction $\eta$ can be computed with high precision using Widom's particle insertion method [J.~Chem.~Phys.~{\bf 39}, 2808 (1963)] for $\sigma$ between 0 and just larger than 1 and/or small $\eta$. Heyes and Santos [J.~Chem.~Phys.~{\bf 145}, 214504 (2016)] showed analytically that the only polynomial representation of $\mu^\mathrm{ex}$ consistent with the limits of $\sigma$ at zero and infinity has a cubic form. On the other hand, through the solvation free energy relationship between $\mu^\mathrm{ex}$ and the surface free energy $\gamma$ of hard-sphere fluid at a hard spherical wall, we can obtain precise measurements of $\mu^\mathrm{ex}$ for large $\sigma$, extending up to infinity (flat wall) [J.~Chem. Phys.~{\bf 149}, 174706 (2018)]. Within this approach, the cubic polynomial representation is consistent with the assumptions of Morphometric Thermodynamics. In this work, we present measurements of $\mu^\mathrm{ex}$ that combine the two methods to obtain high-precision results for the full range of $\sigma$ values from zero to infinity, which show statistically significant deviations from the cubic polynomial form. We propose an empirical functional form for $\mu^\mathrm{ex}$ dependence on $\sigma$ and $\eta$ which better fits the measurement data while remaining consistent with the analytical limiting behaviour at zero and infinite $\sigma$.

E2UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A computational study

Homologous to E6AP carboxyl-terminus (HECT)-type E3 ligase performs ubiquitin (Ub)-proteasomal protein degradation via forming a complex with E2∼Ub. Enveloped viruses including SARS-CoV-2 escape from the infected cells by harnessing the E-class vacuolar protein-sorting (ESCRT) machinery and mimic the cellular system through PPAY motif-based linking to HECT Ub ligase activity. In the present study, we have characterized the binding pattern of E2^UbcH5B to HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2 through in silico analysis to isolate the E2^UbcH5B-specific peptide inhibitors that may target SARS-CoV-2 viral egression. Molecular dynamics analysis revealed more opening of E2^UbcH5B-binding pocket upon binding to HECT^NEDD4L, HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2. We observed similar binding pattern for E2^UbcH5B and mentioned HECT domains as previously reported for HECT^NEDD4L where Trp762, Trp709, and Trp657 residues of HECT^NEDD4L, HECT^WWP1, and HECT^WWP2 are involved in making contacts with Ser94 residue of E2^UbcH5B. Similarly, corresponding to HECT^NEDD4L Tyr756 residue, HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2-specific Phe703, Phe651, Phe1387, and Phe1353 residues execute interaction with E2^UbcH5B. Our analysis suggests that corresponding to Cys942 of HECT^NEDD4L, Cys890, Cys838, Cys1574, and Cys1540 residues of HECT^WWP1, HECT^WWP2, HECT^HECW1, and HECT^HECW2, respectively are involved in E2-to-E3 Ub transfer. Furthermore, MM-PBSA free energy calculations revealed favorable energy values for E2^UbcH5B-HECT complexes along with the individual residue contributions. Subsequently, two E2^UbcH5B-derived peptides (His55-Phe69 and Asn81-Ala96) were tested for their binding abilities against HECT domains of NEDD4L, WWP1, WWP2, HECW1, and HECW2. Their binding was validated through substitution of Phe62, Pro65, Ile84, and Cys85 residues into Ala, which revealed an impaired binding, suggesting that the proposed peptide ligands may selectively target E2-HECT binding and Ub-transfer. Collectively, we propose that peptide-driven blocking of E2-to-HECT Ub loading may limit SARS-CoV-2 egression and spread in the host cells.

Molecular dynamics and structural analysis of the binding of COP1 E3 ubiquitin ligase to β-catenin and TRIB pseudokinases

Tribbles pseudokinases, Tribbles homolog 1 (TRIB1), Tribbles homolog 2 (TRIB2), and Tribbles homolog 3 (TRIB3), bind to constitutive photomorphogenesis protein 1 (COP1) E3 ligase to mediate the regulation of β-catenin expression. The interaction mechanism between COP1 E3 ligase and β-catenin has not been addressed to date. Based on the functional presence of TRIBs in wingless-related integration site (WNT) signaling, we analyzed their interaction patterns with β-catenin and COP1. Here, through in silico approaches, we ascribe the COP1 binding pattern against TRIBs and β-catenin. TRIB1 (355-DQIVPEY-361), TRIB2 (326-DQLVPDV-332), and TRIB3 (333-AQVVPDG-339) peptides revealed a shallow binding pocket at the COP1 interface to accommodate the V-P sequence motif. Reinvigoration of the comparative binding pattern and subtle structural analysis via docking, molecular dynamics simulations, molecular mechanics Poisson-Boltzmann surface area, topological, and tunnel analysis revealed that both β-catenin phosphodegron (DSGXXS) and TRIB (D/E/AQXVPD/E) motifs occupied a common COP1 binding site. Current study suggests a structural paradigm of TRIB homologs bearing a conserved motif that may compete with β-catenin phosphodegron signature for binding to WD40 domain of COP1. Thorough understanding of the structural basis for TRIB-mediated regulation of WNT/β-catenin signaling may help in devising more promising therapeutic strategy for liver and colorectal cancers.

EVI1 phosphorylation at S436 regulates interactions with CtBP1 and DNMT3A and promotes self-renewal

The transcriptional regulator EVI1 has an essential role in early development and haematopoiesis. However, acute myeloid leukaemia (AML) driven by aberrantly high EVI1 expression has very poor prognosis. To investigate the effects of post-translational modifications on EVI1 function, we carried out a mass spectrometry (MS) analysis of EVI1 in AML and detected dynamic phosphorylation at serine 436 (S436). Wild-type EVI1 (EVI1-WT) with S436 available for phosphorylation, but not non-phosphorylatable EVI1-S436A, conferred haematopoietic progenitor cell self-renewal and was associated with significantly higher organised transcriptional patterns. In silico modelling of EVI1-S436 phosphorylation showed reduced affinity to CtBP1, and CtBP1 showed reduced interaction with EVI1-WT compared with EVI1-S436A. The motif harbouring S436 is a target of CDK2 and CDK3 kinases, which interacted with EVI1-WT. The methyltransferase DNMT3A bound preferentially to EVI1-WT compared with EVI1-S436A, and a hypomethylated cell population associated by EVI1-WT expression in murine haematopoietic progenitors is not maintained with EVI1-S436A. These data point to EVI1-S436 phosphorylation directing functional protein interactions for haematopoietic self-renewal. Targeting EVI1-S436 phosphorylation may be of therapeutic benefit when treating EVI1-driven leukaemia.

Molecular Dynamics Simulation of Cetyl Phosphate Adsorption in Flotation of Magnesite and Pertinent Chemical Aspects

Magnesite ores are important resources in the production of value-added magnesium materials. Generally, low selectivity of conventional collectors and the requirement of a large amount of depressant has been a motivation for researchers to identify alternate collectors. In this work, the role of potassium cetyl phosphate (PCP) as a new collector in magnesite flotation is investigated using molecular dynamics (MD) simulations and chemical equilibria, electrokinetics and wettability. The results indicate that PCP exhibits a strong collecting ability for magnesite particles even with low concentrations. The presence of PCP leads to significant alterations in the electric double layer and contact angle behavior of magnesite, which results in rapid adsorption of PCP on magnesite surface. The results from chemical computations show that the monoanionic forms of PCP are the dominant species in the weakly acidic pH range, where monohydroxy magnesium species and the ion concentration of magnesite in suspension can be controlled by adjusting pH. The adsorption models indicate that the stable adsorption of PCP on magnesite surfaces occurs spontaneously, supporting the potentiality for selective magnesite flotation in its separation from other carbonate minerals.

Evidence for NAD+-dependent histone dynamics and tunneling associated conformational transitions in circadian deacetylase SIRT1

Circadian rhythm is a biological cycle that is involved in all processes over 24 h day and night period. Sirtuin 1 (SIRT1) is a 747 amino acid-long class III Nicotinamide adenine dinucleotide (NAD⁺)-dependent histone that acts as a circadian deacetylase. Here we present a detailed in-silico analysis to address comparative structure-function relationship and interaction pattern of SIRT1-NAD⁺/Zn⁺² and SIRT1^NAD+/Zn+2-acetylated histone H4 (H4^KAC16) complexes. MD-based ensemble analysis suggested an overall loss of helical content (21.144-17.230%) in H4^KAC16-bound SIRT1^NAD+/Zn+2 due to conformational readjustments of 32 residues, as compared to SIRT1^NAD+/Zn+2. Due to increased flexibility, SIRT1-specific SER275, SER442 and ARG466 residues involved in NAD⁺ association facilitated in the formation of a transient tunnel (17.77 Å) that was further elongated to 19.25 Å upon SIRT1^NAD+/Zn+2 binding to H4^KAC16. A close conformation of SIRT1^NAD+/Zn+2 was achieved due to binding of H4^KAC16 that results in the movement of helical module towards Zn⁺² binding module together with Rossmann fold at NAD⁺ binding region. Furthermore, a 2-fold increase (4.31-8.82 Å) in the measured inter-atomic distance between imidazole nitrogen of conserved HIS363 and NAD⁺-specific 2'-hydroxyl group of ribose ring was evident in SIRT1^NAD+/Zn+2-H4^KAC16 complex. At 90 ns time scale, the distance between C6A of adenine ring and C2N of nicotinamide ring was more extended (19.32 Å) in SIRT1^NAD+/Zn+2-H4^KAC16 as compared to SIRT1^NAD+/Zn+2 (11.54 Å). These data suggest that H4^KAC16 binding to SIRT1 may coordinate an unusual conformational readjustment of nicotinamide ring at site-b and reposition of HIS363 to facilitate SIRT1-dependent deacetylase activity. Taken together, our findings will help in understanding the precise structural changes occurring in response to SIRT1 deacetylase activity of core histone.

Structural basis of βTrCP1-associated GLI3 processing

Controlled ubiquitin-mediated protein degradation is essential for various cellular processes. GLI family regulates the transcriptional events of the sonic hedgehog pathway genes that are implicated in almost one fourth of human tumors. GLI3 phosphorylation by Ser/Thr kinases is a primary factor for their transcriptional activity that incurs the formation of both GLI3 repressor and activator forms. GLI3 processing is triggered in an ubiquitin-dependent manner via SCF^βTrCP1 complex; however, structural characterization, mode of action based on sequence of phosphorylation signatures and induced conformational readjustments remain elusive. Here, through structural analysis and molecular dynamics simulation assays, we explored comparative binding pattern of GLI3 phosphopeptides against βTrCP1. A comprehensive and thorough analysis demarcated GLI3 presence in the binding cleft shared by inter-bladed binding grooves of β-propeller. Our results revealed the involvement of all seven WD40 repeats of βTrCP1 in GLI3 interaction. Conversely, GLI3 phosphorylation pattern at primary protein kinase A (PKA) sites and secondary casein kinase 1 (CK1) or glycogen synthase kinase 3 (GSK3) sites was carefully evaluated. Our results indicated that GLI3 processing depends on the 19 phosphorylation sites (849, 852, 855, 856, 860, 861, 864, 865, 868, 872, 873, 876, 877, 880, 899, 903, 906, 907 and 910 positions) by a cascade of PKA, GSK3β and CSKI kinases. The presence of a sequential phosphorylation in the binding induction of GLI3 and βTrCP1 may be a hallmark to authenticate GLI3 processing. We speculate that mechanistic information of the individual residual contributions through structure-guided approaches may be pivotal for the rational design of specific and more potent inhibitors against activated GLI3 with a special emphasis on the anticancer activity.

Equations of the state of hard sphere fluids based on recent accurate virial coefficients B5–B12

A review on the numerical virial coefficients, compressibility factor, fluid–solid phase transition point and equations of the state of hard sphere fluids.

Structural basis for renal cancer by the dynamics of pVHL-dependent JADE1 stabilization and β-catenin regulation

Renal cancer is the major cause of mortality due to abnormal functioning of von Hippel-Lindau (pVHL) and Jade Family PHD Finger 1 (JADE1) complex. E3 ubiquitin ligase JADE1 is stabilized by pVHL interaction through its plant homeodomains (PHDs). JADE1 acts as a renal tumor suppressor that promotes the ubiquitination and degradation of β-catenin by inhibiting canonical WNT signalling. Current study focuses on the structural characterization of reported missense mutations in pVHL through in silico approaches. The predicted 3-dimensional structures of pVHL^WT, pVHL^Y98H, pVHL^Y112H, pVHL^L118P and pVHL^R167W were subjected to binding analysis against JADE1 through molecular docking and simulation assays. In all cases, JADE1 binding was observed at the β-domain, except pVHL^L118P that exhibited binding with JADE1 through its α-domain. Our results signify that JADE1 stabilization is induced by pVHL α-domain, while β-domain is required for JADE1 binding. pVHL binding was mediated through β1 and β2-strands against the concave surface of the JADE1-PHD domain. The pVHL-JADE1 complex was evaluated to scrutinize the β-catenin-binding interface, which suggested the contribution of both α and β-domains of pVHL in β-catenin binding. The eleven-residue (Tyr30-Thr40) β-catenin segment exhibited association in a bipartite manner with pVHL-JADE1 complex. The presented model depicts a pVHL-JADE1 interface for the cooperative regulation of β-catenin binding. We propose that reduced JADE1 stabilization in case of pVHL^L118P and pVHL^R167W may correlate with the increased activity of β-catenin that may lead to renal cancer through β-catenin de-repression. Overall, β-catenin targeting mechanism coupled with the structural knowledge of JADE1-pVHL complex will provide better understanding of renal cancer pathogenesis.

Antagonistic role of Klotho-derived peptides dynamics in the pancreatic cancer treatment through obstructing WNT-1 and Frizzled binding

Klotho is an anti-aging protein that is engaged in the suppression of canonical WNT signaling. In this study, we investigated the expression pattern of human WNTs and Klotho in the pancreatic cancer. In the cancerous cells, WNT-1 exhibited much higher expression as compared to other WNTs, while no WNT expression was detected in the normal tissue. In contrast, Klotho expression was significantly low in the cancerous tissue. Based on these observations, we intended to explore Klotho binding to WNT-1 and cystein-rich domains (CRDs) of Frizzled (FZD) homologs through molecular docking and dynamics simulation assays. Interestingly, similar region of WNT-1 was detected in binding with Klotho and CRDs of FZD-1/2. FZD-CRDs were grasped by the association of peripheral hydrophobic residues of WNT-1 U-shaped cavity. Subsequently, WNT-1-bound Klotho-peptides were isolated and reevaluated for their binding abilities against WNT-1 and FZD-CRDs., The conformational readjustements of these complexes were deeply analyzed by calculating the size of WNT-1 U-shaped cavity. In comparison to apo-WNT-1, cavity opening was markedly enhanced (8.2 Å to 15.64 Å, 32.89 Å and 35.11 Å) in WNT-1-a, WNT-1-c and WNT-1-e complexes, respectively. Thus Klotho-derived peptides may facilitate distinct conformational changes in the WNT-1-FZD associated region. As a result, aberrant loss of FZD binding may lead to augment WNT signaling. Overall, current study opens up new avenues in the pancreatic cancer therapeutics through antagonizing WNT-1 by Klotho.

Chemical potential of a test hard sphere of variable size in hard-sphere fluid mixtures

A detailed comparison between the Boublík-Mansoori-Carnahan-Starling-Leland (BMCSL) equation of state of hard-sphere mixtures is made with Molecular Dynamics (MD) simulations of the same compositions. The Labík and Smith simulation technique [S. Labík and W. R. Smith, Mol. Simul. 12, 23-31 (1994)] was used to implement the Widom particle insertion method to calculate the excess chemical potential, βμ₀^ex, of a test particle of variable diameter, σ₀, immersed in a hard-sphere fluid mixture with different compositions and values of the packing fraction, η. Use is made of the fact that the only polynomial representation of βμ₀^ex which is consistent with the limits σ₀ → 0 and σ₀ → ∞ has to be of the cubic form, i.e., c₀(η)+c¯₁(η)σ₀/M₁+c¯₂(η)(σ₀/M₁)²+c¯₃(η)(σ₀/M₁)³, where M₁ is the first moment of the distribution. The first two coefficients, c₀(η) and c¯₁(η), are known analytically, while c¯₂(η) and c¯₃(η) were obtained by fitting the MD data to this expression. This in turn provides a method to determine the excess free energy per particle, βa^ex, in terms of c¯₂, c¯₃, and the compressibility factor, Z. Very good agreement between the BMCSL formulas and the MD data is found for βμ₀^ex, Z, and βa^ex for binary mixtures and continuous particle size distributions with the top-hat analytic form. However, the BMCSL theory typically slightly underestimates the simulation values, especially for Z, differences which the Boublík-Carnahan-Starling-Kolafa formulas and an interpolation between two Percus-Yevick routes capture well in different ranges of the system parameter space.

Pharmacoinformatics exploration of polyphenol oxidases leading to novel inhibitors by virtual screening and molecular dynamic simulation study

Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis. The 3D structures of PPO1 and PPO2 were built through homology modeling, while the 3D crystal structures of PPO3 and PPO4 were retrieved from PDB. Pharmacophore modeling was performed using LigandScout 3.1 software and top five models were selected to screen the libraries (2601 of Aurora and 727, 842 of ZINC). Top 10 hit compounds (C1-10) were short-listed having strong binding affinities for PPO1-4. Drug and synthetic accessibility (SA) scores along with absorption, distribution, metabolism, excretion and toxicity (ADMET) assessment were employed to scrutinize the best lead hit. C4 (name) hit showed the best predicted SA score (5.75), ADMET properties and drug-likeness behavior among the short-listed compounds. Furthermore, docking simulations were performed to check the binding affinity of C1-C10 compounds against target proteins (PPOs). The binding affinity values of complex between C4 and PPOs were higher than those of other complexes (-11.70, -12.1, -9.90 and -11.20kcal/mol with PPO1, PPO2, PPO3, or PPO4, respectively). From comparative docking energy and binding analyses, PPO2 may be considered as better target for melanogenesis than others. The potential binding modes of C4, C8 and C10 against PPO2 were explored using molecular dynamics simulations. The root mean square deviation and fluctuation (RMSD/RMSF) graphs results depict the significance of C4 over the other compounds. Overall, bioactivity and ligand efficiency profiles suggested that the proposed hit may be more effective inhibitors for melanogenesis.

Computational analysis of histidine mutations on the structural stability of human tyrosinases leading to albinism insurgence

Misfolding and structural alteration in proteins lead to serious malfunctions and cause various diseases in humans.

Synthesis, Bioevaluation and Molecular Dynamic Simulation Studies of Dexibuprofen-Antioxidant Mutual Prodrugs

Dexibuprofen–antioxidant conjugates were synthesized with the aim to reduce its gastrointestinal effects. The esters analogs of dexibuprofen 5a–c were obtained by reacting its –COOH group with chloroacetyl derivatives 3a–c. The in vitro hydrolysis data confirmed that synthesized prodrugs 5a–c were stable in stomach while undergo significant hydrolysis in 80% human plasma and thus release free dexibuprofen. The minimum reversion was observed at pH 1.2 suggesting that prodrugs are less irritating to stomach than dexibuprofen. The anti-inflammatory activity of 5c (p < 0.001) is more significant than the parent dexibuprofen. The prodrug 5c produced maximum inhibition (42.06%) of paw-edema against egg-albumin induced inflammation in mice. Anti-pyretic effects in mice indicated that prodrugs 5a and 5b showed significant inhibition of pyrexia (p < 0.001). The analgesic activity of 5a is more pronounced compared to other synthesized prodrugs. The mean percent inhibition indicated that the prodrug 5a was more active in decreasing the number of writhes induced by acetic acid than standard dexibuprofen. The ulcerogenic activity results assured that synthesized prodrugs produce less gastrointestinal adverse effects than dexibuprofen. The ex vivo antiplatelet aggregation activity results also confirmed that synthesized prodrugs are less irritant to gastrointestinal mucosa than the parent dexibuprofen. Molecular docking analysis showed that the prodrugs 5a–c interacts with the residues present in active binding sites of target protein. The stability of drug–target complexes is verified by molecular dynamic simulation study. It exhibited that synthesized prodrugs formed stable complexes with the COX-2 protein thus support our wet lab results. It is therefore concluded that the synthesized prodrugs have promising pharmacological activities with reduced gastrointestinal adverse effects than the parent drug.

Chemical potential of a test hard sphere of variable size in a hard-sphere fluid

The Labík and Smith Monte Carlo simulation technique to implement the Widom particle insertion method is applied using Molecular Dynamics (MD) instead to calculate numerically the insertion probability, P₀(η,σ₀), of tracer hard-sphere (HS) particles of different diameters, σ₀, in a host HS fluid of diameter σ and packing fraction, η, up to 0.5. It is shown analytically that the only polynomial representation of -ln⁡P₀(η,σ₀) consistent with the limits σ₀→0 and σ₀→∞ has necessarily a cubic form, c₀(η)+c₁(η)σ₀/σ+c₂(η)(σ₀/σ)²+c₃(η)(σ₀/σ)³. Our MD data for -ln⁡P₀(η,σ₀) are fitted to such a cubic polynomial and the functions c₀(η) and c₁(η) are found to be statistically indistinguishable from their exact solution forms. Similarly, c₂(η) and c₃(η) agree very well with the Boublík-Mansoori-Carnahan-Starling-Leland and Boublík-Carnahan-Starling-Kolafa formulas. The cubic polynomial is extrapolated (high density) or interpolated (low density) to obtain the chemical potential of the host fluid, or σ₀→σ, as βμ^ex=c₀+c₁+c₂+c₃. Excellent agreement between the Carnahan-Starling and Carnahan-Starling-Kolafa theories with our MD data is evident.

Elucidation, functional clustering and structural characterization of βTrCP1 substrates through a molecular dynamics study

Structural knowledge of substrate recognition by SKP1–CUL1–βTrCP1 complex for targeted cancer therapeutic strategy.

Field induced gradient simulations: a high throughput method for computing chemical potentials in multicomponent systems

We present a simulation method for direct computation of chemical potentials in multicomponent systems. The method involves application of a field to generate spatial gradients in the species number densities at equilibrium, from which the chemical potential of each species is theoretically estimated. A single simulation yields results over a range of thermodynamic states, as in high throughput experiments, and the method remains computationally efficient even at high number densities since it does not involve particle insertion at high densities. We illustrate the method by Monte Carlo simulations of binary hard sphere mixtures of particles with different sizes in a gravitational field. The results of the gradient Monte Carlo method are found to be in good agreement with chemical potentials computed using the classical Widom particle insertion method for spatially uniform systems.

Analytical expressions for the fourth virial coefficient of a hard-sphere mixture

A method of numerical calculation of the fourth virial coefficients of the mixture of additive hard spheres is proposed. The results are compared with an exact analytical formula for the fourth partial virial coefficient B4[1] (i.e., three spheres of diameters sigma1 and one sphere of diameter sigma2) and a semiempirical expression for B4[2] (i.e., two spheres of each kind). It is shown that the first formula is nonanalytic and the implication to the equations of state for hard-sphere mixtures is discussed.

Neighbor network in a polydisperse hard-disk fluid: degree distribution and assortativity

The neighbor network in a two-dimensional polydisperse hard-disk fluid with diameter distribution p(sigma) approximately sigma(-4) is examined using constant-pressure Monte Carlo simulations. Graphs are constructed from vertices (disks) with edges (links) connecting each vertex to k neighboring vertices defined by a radical tessellation. At packing fractions in the range 0.24< or =eta< or =0.36, the decay of the network degree distribution is observed to be consistent with the power law k(-gamma) where the exponent lies in the range 5.6< or =gamma< or =6.0 . Comparisons with the predictions of a maximum-entropy theory suggest that this apparent power-law behavior is not the asymptotic one and that p(k) approximately k(-4) in the limit k-->infinity. This is consistent with the simple idea that for large disks, the number of neighbors is proportional to the disk diameter. A power-law decay of the network degree distribution is one of the characteristics of a scale-free network. The assortativity of the network is measured and is found to be positive, meaning that vertices of equal degree are connected more often than in a random network. Finally, the equation of state is determined and compared with the prediction from a scaled-particle theory. Very good agreement between simulation and theory is demonstrated.

Fundamental measure theory in cylindrical geometry

Density functional theory as proposed by Rosenfeld [Phys. Rev. Lett. 63, 980 (1989)] is used to study hard sphere mixture exposed by cylindrically symmetric external field. Exploiting the symmetry of the system, explicit formulas for the weighted densities are derived. The resulting density profiles are compared with new grand canonical Monte Carlo simulations. The comparison reveals very good agreement between the predicted and simulated results even at high densities and very narrow pores. Finally, simple algorithms for computing complete elliptic functions of the first and second kinds that occur in the derived formulae are presented to make the paper self-contained.