Exploring the binding mechanism of dihydropyrimidinones to human serum albumin: spectroscopic and molecular modeling techniques

The binding mechanism of molecular interaction between 5-(ethoxycarbonyl)-6-methyl-4-phenyl-3,4-dihydropyrimidin-2(1H)-one (a dihydropyrimidinones derivative, EMPD) and human serum albumin (HSA) was studied using spectroscopic methods and modeling technique. The quenching mechanism was investigated in terms of the binding constants and the basic thermodynamic parameters. The results of spectroscopic measurements suggested that EMPD have a strong ability to quench the intrinsic fluorescence of HSA through static quenching procedure. The drug-protein complex was stabilized by hydrophobic forces and hydrogen bonding as indicated from the thermodynamic parameters and synchronous fluorescence spectra, which was consistent with the results of molecular docking and accessible surface area calculation. Competitive experiments indicated that a displacement of warfarin by EMPD, which revealed that the binding site of EMPD to HSA was located at the subdomains IIA. The distance between the donor and the acceptor was 4.85nm as estimated according to F?rster's theory of non-radiation energy transfer. The effect of metal ions on the binding constants was also investigated. The results indicated that the binding constants between EMPD and HSA increased in the presence of common metal ions.     

Exploring the mechanism of Cremastra Appendiculata (SUANPANQI) against breast cancer by network pharmacology and molecular docking

BackgroundSUANPANQI, the pseudo phosphorous stem of Cremastra appendiculata, is one of the most well-known traditional Chinese medicine, which has been shown to inhibit tumorigenesis in various human cancers. However, the underlying mechanism of SUANPANQI treatment against breast cancer (BRCA) remains unclear. In this study. we aim to investigate the bioactive compounds and mechanisms of SUANPANQI in the treatment of BRCA based on network pharmacology and molecular docking.MethodsThe compounds were collected from previous research. SwissADME was used to screen bioactive compounds. The targets corresponding to SUANPANQI and BRCA were obtained using MalaCards and SwissTargetPrediction. SUANPANQI-related and BRCA-related targets were found and then overlapped to get intersections, which represented potential anti-BRCA targets of SUANPANQI. The Cytoscape software was used to construct bioactive compounds targeting the BRCA network. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the targets was extracted from the metascape database, then conducted using the Cluster Profiler package in R software. Protein-Protein interaction (PPI) network was constructed using the STRING online database and analyzed using Cytoscape software. Pivotal genes were screened using the topological analysis, survival analysis, and pathological stage analysis. Molecular docking analysis was used to verify whether the bioactive compounds had a definite affinity with the pivotal targets.ResultsSixty-five bioactive compounds of SUANPANQI were involved with 225 predicted BRCA targets. Then, a compound-target network and a PPI network were constructed. The GO analysis and KEGG enrichment analysis suggested that SUANPANQI worked against BRCA via PI3K-Akt, Ras, FoxO, Rap1, and ErbB signaling pathways, etc. After topological analysis, survival analysis, and pathological stage analysis of the SUANPANQI potential targets against BRCA, 6 pivotal target genes (AR, HSP90AA1, MMP9, PGR, PTGS2, TNF) that were highly responsible for the therapeutic effects of SUANPANQI against BRCA were obtained. Molecular docking results showed that 6 bioactive compounds of SUANPANQI had strong binding efficiency with the 6 pivotal genes.ConclusionsThe present study clarifies the mechanism of SUANPANQI against BRCA through multiple targets and pathways, and provides evidence to support its clinical use.     

Exploring chemistry with the fragment molecular orbital method

The fragment molecular orbital (FMO) method makes possible nearly linear scaling calculations of large molecular systems, such as water clusters, proteins and DNA. In particular, FMO has been widely used in biochemical applications involving protein-ligand binding and drug design. The method has been efficiently parallelized suitable for petascale computing. Many commonly used wave functions and solvent models have been interfaced with FMO. We review the historical background of FMO, and summarize its method development and applications.     

Carbon-13 NMR distinction between categories of molecular order and disorder in cellulose

Differences between values of proton rotating-frame spin relaxation time constants can be exploited to separate a solid-state¹³C NMR spectrum of cellulose into subspectra of crystalline and noncrystalline regions. Variations in chemical shifts and¹³C spin-lattice relaxation time constants can then be used to study variations in molecular order and disorder within each of the two broader categories. Mechanical damage during Wiley milling increases the content of noncrystalline cellulose and changes the nature of molecular disorder within that category. Resolution enhancement of the subspectrum assigned to crystalline cellulose reveals pairs of signals at 83.9 and 84.9 ppm (cellulose I) or 86.8 and 88.3 ppm (cellulose II) assigned to C-4 on well-ordered crystal surfaces. A broader peak in the subspectrum of crystalline cellulose I is assigned to poorly-ordered surfaces. Relative proportions in Avicel microcrystalline cellulose were estimated as: 54% in crystal interiors, 22% on well-ordered surfaces, 8% on poorly-ordered surfaces, 16% in domains of disorder extending more than a few nanometres.     

Exploring antibiotic resistant mechanism by microcalorimetry

In an effort to probe the reaction of antibiotic hydrolysis catalyzed by B3 metallo-??-lactamase (M??L), the thermodynamic parameters of penicillin G hydrolysis catalyzed by M??L L1 from Stenotrophomonas maltophilia were determined by microcalorimetric method. The values of activation free energy ??G _?? ^?? are 88.26, 89.44, 90.49, and 91.57?kJ?mol^?1 at 293.15, 298.15, 303.15, and 308.15?K, respectively, activation enthalpy ??H _?? ^?? is 24.02?kJ?mol^?1, activation entropy ??S _?? ^?? is ?219.2511?J?mol^?1?K^?1, apparent activation energy E is 26.5183?kJ?mol^?1, and the reaction order is 1.0. The thermodynamic parameters reveal that the penicillin G hydrolysis catalyzed by M??L L1 is an exothermic and spontaneous reaction.     

A molecular dynamics simulation study of peptide deformylase from Leptospira interrogans complex：Exploring the closing mechanism of the substrate pocket

To explore the closing mechanism of the substrate pocket,we perform a 16,000 ps molecular dynamics simulation separately on the ligand-free and actinonin-bound peptide deformylase from Leptospira interrogans.Our results show that the CD-loop, hydrophilic inhibitor and hydrophobic cluster are necessary for the formation of semi-open conformation,and Tyr71 plays an important role in mediating the movements of CD-loop.The average MD structure of the actinonin-bound LiPDF complex approaches to the crystal structure.These are consistent with experiment very well.     

Exploring the mechanism for the amine-catalyzed isomerization of dimethyl maleate. A computational study

The main objective of this study was to investigate the amine-catalyzed isomerization of dimethyl maleate into dimethyl fumarate in order to utilize the former as a prodrug for the latter. Mechanistic study of this reaction using DFT at B3LYP/6-31G(d,p) level revealed that the reaction is first order in dimethyl maleate, second order in the amine, and overall third order. Moreover, the calculations revealed the existence of a linear correlation between the basicity of the amine catalyst and the isomerization rate.     

Charge-transfer as a mechanism for controlling molecular fragmentation

We investigate control over molecular fragmentation in the halogen substituted acetone 1,1-dibromo-3,3,3-trifluoroacetone using shaped ultrafast laser pulses. Following insight gained from closed-loop learning control experiments, further tests reveal that control over the CF₃⁺/CHBr₂⁺ ratio exploits a charge-transfer mechanism. We interpret the control in terms of adiabatic rapid passage.     

Exploring the no-man's land between molecular nanomagnets and magnetic nanoparticles

The comparison of the structural and magnetic properties of molecular nanomagnets (MNM) and magnetic nanoparticles (MNP) can be instructive to get a deeper understanding of the magnetic behavior on the intermediate scale between molecular and bulk objects. In this respect iron oxo based clusters are particularly interesting, since they provide an increasing number of molecular systems with sizes close to that of iron oxide MNP. In this Minireview we report a survey of literature data aimed at improving our understanding of the emergence of MNP properties from MNM ones.     

Exploring antibiotic resistant mechanism by microcalorimetry II

In an effort to understand the reaction of antibiotic hydrolysis with B2 metallo-??-lactamases (M??Ls), the thermodynamic parameters of imipenem hydrolysis catalyzed by metallo-??-lactamase ImiS from Aeromonas veronii bv. sobria were determined by microcalorimetric method. The values of activation free energy $ \Updelta G_{ \ne }^{\theta } $ are 86.400?±?0.043, 87.543?±?0.034, 88.772?±?0.024, and 89.845?±?0.035?kJ?mol^?1 at 293.15, 298.15, 303.15, and 308.15?K, respectively, activation enthalpy $ \Updelta H_{ \ne }^{\theta } $ is 18.586?±?0.009?kJ?mol^?1, activation entropy $ \Updelta S_{ \ne }^{\theta } $ is ?231.34?±?0.12?J?mol^?1?K^?1, apparent activation energy E is 21.084?kJ?mol^?1, and the reaction order is 1.5. The thermodynamic parameters reveal that the imipenem hydrolysis catalyzed by metallo-??-lactammase ImiS is an exothermic and spontaneous reaction.     

A new molecular mechanism of blue color development with protocyanin,a supramolecular pigment from cornflower,Centaurea cyanus

Protocyanin (1), a blue pigment of Centaurea cyanus, is composed of six molecules each of malonylflavone (2) and succinylcyanin (3), complexed with magnesium and ferric ions. The blue color of 1 is developed by an LMCT interaction between anthocyanin and ferric ion, rather than arising from the formation of a simple anhydrobase anion of the chromophore. The supramolecular structure of 1 was elucidated.     

Exploring the elution mechanism of selenium species on liquid chromatography

In the present work, the chromatographic behavior of eight selenium species, namely selenites (Se(IV)), selenates (Se(VI)), seleno‐DL ‐methionine (Se‐Met), selenocystine (Se‐Cyst), selenocystamine (Se‐CM), selenourea (Se‐U), dimethylselenide ((CH₃)₂Se) and dimethyldiselenide ((CH₃)₂Se₂), was investigated under different stationary and mobile phase conditions, in an effort to unravel secondary interferences in their underlying elution mechanism. For this purpose, two end‐capped and a polar‐embedded reversed‐phase stationary phases were employed using different mobile phase conditions. Retention factors (log k_w) were compared with octanol–water distribution coefficients (log D) as well as with log k_w values on two immobilized artificial membrane (IAM) columns and two immobilized artificial plasma proteins stationary phases, obtained in our previous work. The role of electrostatic interactions was confirmed by introducing the net charge of the investigated Se species as an additional term in the log k_w/log D interrelation, which in most cases proved to be statistically significant. Principal component analysis of retention factors on all stationary phases and octanol–water log D values, however, showed that the elution of the investigated selenium species is mainly governed by partitioning mechanism under all different chromatographic conditions, while the pH of the mobile phase and the special column characteristics have only a minor effect.     

Centrifugal mechanism for molecular dissociation in high-energy collisions with solid surfaces

A simple model is proposed for molecular dissociation probabilities in impulsive collisions with surfaces. Dissociation is assumed to follow rotational excitation high enough to break the molecule. The model was tested against exact classical simulations for I₂, Li₂ colliding with smooth surfaces. Agreement is better than a factor of 2 over a wide range of energies.