Further quantitative in silico analysis of SARS-CoV-2 S-RBD Omicron BA.4, BA.5, BA.2.75, BQ.1, and BQ.1.1 transmissibility.

The Covid-19 variants' transmissibility was further quantitatively analyzed in silico to study the binding strength with ACE-2 and find the binding inhibitors. The molecular interaction energy values of their optimized complex structures (MIFS) demonstrated that Omicron BA.4 and 5's MIFS value (344.6 kcal mol-1) was equivalent to wild-type MIFS (346.1 kcal mol-1), that of Omicron BQ.1 and BQ. 1.1's MIFS value (309.9 and 364.6 kcal mol-1). Furthermore, the MIFS value of Omicron BA.2.75 (515.1 kcal mol-1) was about Delta-plus (511.3 kcal mol-1). The binding strength of Omicron BA.4, BA. 5, and BQ.1.1 may be neglectable, but that of Omicron BA.2.75 was urging. Furthermore, the 79 medicine candidates were analyzed as the binding inhibitors from binding strength with ACE-2. Only carboxy compounds were repulsed from the ACE-2 binding site indicating that further modification of medical treatment candidates may produce an effective binding inhibitor.

Quantitative in silico analysis of SARS-CoV-2 S-RBD omicron mutant transmissibility.

Covid-19 variants transmissibility was quantitatively analyzed in silico to understand the reaction mechanisms and to find the reaction inhibitors. Especially, SARS-CoV-2 omicron mutant (omicron S-RBD) binding affinity with human angiotensin-converting enzyme-2 (ACE-2) was quantitatively analyzed using molecular interaction (MI) energy values (kcal.mol-1) between the S-RBD and ACE-2. The MI of their optimized complex structures demonstrated that omicron's MI value (749.8) was 1.4 times delta MI (538.1) and 2.7 times alfa MI (276.9). The omicron S-RBD demonstrated the most vital transmissible strength. The 14 currently proposed medical treatment compounds did not show as the inhibitors to block the omicron S-RBD and ACE-2 binding; instead, they adsorbed at the ACE-2 active site and may inhibit the ACE-2 activity. A modified candidate (Gallo catechin gallate) whose two phenolic hydroxy groups were replaced with two carboxy groups was repulsed from ACE-2, indicating that further modification of medical treatment candidates may produce an effective docking inhibitor.

Quantitative analysis of selective glycosylation of saccharides with aromatic amines.

Glycosylation, a part of the Maillard reaction, occurs non-enzymatically in food and biological processes. The selectivity of N-glycosylation was analyzed based on the reactivity of monosaccharides with aromatic amines, including aromatic amino acids, and the degree of molecular interaction (MI) measured using liquid chromatography. Furthermore, the chemical structures of reaction products were determined using X-ray crystallography and/or NMR. The possible reaction products were estimated in silico using the optimized energy values of different conformations. The MI energy values of amino groups and saccharides were calculated using in silico analysis using a model phase. Saccharides having larger MI values easily produced stable crystals of N-glycosides. The reaction rate of glucose (an energy saccharide) was slow, and it easily produced the Amadori compounds. The study of the reactivity of aromatic amines with saccharides, the measurement of the retention of monosaccharides on amino phase in chromatography, and the synthesis of N-glycosides for the determination of their structures will provide useful information about selective glycosylation for the modification of drug candidates to improve their water solubility.

Quantitative In Silico Analysis of Retention of Nitrobenzofurazan-Amino Acids in Reversed-Phase Ion-Pair Liquid Chromatography.

The retention mechanisms of nitrobenzofurazan (NBD)-amino acids in reversed-phase ion-pair liquid chromatography were quantitatively analyzed in silico The most contributed interaction for the retention is the Lewis acid-base interaction between an aromatic ring of NBD-amino acids and hydroxyl-group hydrogen of tetra-butyl-ammonium hydroxide coated on the hydrophobic phase. Solvent effects significantly improved the relation between the calculated molecular interaction (MI) energy values using a molecular mechanics program and log k values measured in chromatography. The correlation coefficient between the calculated MI energy values and the log k values was >0.95.

Quantitative In Silico Analysis of Retention of Phenylthiohydantoin-Amino Acids in Reversed-Phase Ion-Pair Liquid Chromatography.

The retention mechanisms of phenylthiohydantoin (PTH)-amino acids in reversed-phase ion-pair liquid chromatography were quantitatively analyzed in silico. The most significant interaction for the retention was the Lewis acid-base interaction between an aromatic ring of a PTH-amino acid and a hydroxyl-group hydrogen of tetra-alkyl ammonium hydroxide. Solvent effects, addition of molecular interaction (MI) energy values between an analyte and solvent molecules, significantly improved the relationship between the MI energy values, calculated using a molecular mechanics program, and logk values, measured via chromatography. The correlation coefficient between the calculated MI energy values and the logk values was 0.98 (n = 19).

In silico Modeling Study on Molecular Interactions in Reversed-Phase Liquid Chromatography.

Homogeneous model phases were constructed for developing an in silico model study on molecular interactions in reversed-phase liquid chromatography. The different versions of molecular mechanics 2 (MM2) programs demonstrated the weight of hydrogen bonding energy contribution. The correlation coefficient between the energy values calculated using the latest version of MM2 and log k values of phenolic compounds measured using reversed-phase liquid chromatography was 0.95 (n = 48) using alkylbenzenes as calibration standard compounds.

RSC Chromatography Monographs Quantitative In Silico Chromatography Computational Modelling of Molecular Interactions.

All early chromatographic techniques, starting from the primitive "ancient" chromatography introduced by Tswett in the very early twentieth century, perfected in partition chromatography in the 1940s by Martin and Synge, and extended to a variety of additional separation mechanisms later, were first entirely experimental trial-and-error methods. The early years can also be characterized by searching for theoretical base of various separation techniques that would allow establishing relation between the structure of the analytes and their chromatographic behavior. The advent of computers followed by development of the new software then revolutionized the theoretical approaches and enabled detailed modeling instead of tedious experimentation. This book introduces the readers to the era of computational modeling in which molecular interactions are used to analyze the mechanisms of general molecular interactions with a special focus on biological applications. This article is protected by copyright. All rights reserved.

Quantitative in silico analysis of organic modifier effect on retention in reversed-phase liquid chromatography.

Retention times in reversed-phase liquid chromatography were quantitatively analyzed in silico using alkanes as standard compounds, much like they have been used for Kovats indices in gas chromatography. The molecular interaction energy was calculated between an analyte and a model hydrophobic phase using a molecular mechanics program. The solvation energy was calculated between an analyte and a model solvent phase. The correlation coefficients between the log k values and the combined molecular interaction and solvation energy values were 0.97 (n = 18) for alkanes, alkanols, alkylbenzenes and polycyclic aromatic hydrocarbons.

Role of the active site residues arginine-216 and arginine-237 in the substrate specificity of mammalian D-aspartate oxidase.

D-aspartate oxidase (DDO) and D-amino acid oxidase (DAO) are flavin adenine dinucleotide-containing flavoproteins that catalyze the oxidative deamination of D-amino acids. Unlike DAO, which acts on several neutral and basic D-amino acids, DDO is highly specific for acidic D-amino acids. Based on molecular modeling and simulated annealing docking analyses, a recombinant mouse DDO carrying two substitutions (Arg-216 to Leu and Arg-237 to Tyr) was generated (R216L-R237Y variant). This variant and two previously constructed single-point mutants of mouse DDO (R216L and R237Y variants) were characterized to investigate the role of Arg-216 and Arg-237 in the substrate specificity of mouse DDO. The R216L-R237Y and R216L variants acquired a broad specificity for several neutral and basic D-amino acids, and showed a considerable decrease in activity against acidic D-amino acids. The R237Y variant, however, did not show any additional specificity for neutral or basic D-amino acids and its activity against acidic D-amino acids was greatly reduced. The kinetic properties of these variants indicated that the Arg-216 residue is important for the catalytic activity and substrate specificity of mouse DDO. However, Arg-237 is, apparently, only marginally involved in substrate recognition, but is important for catalytic activity. Notably, the substrate specificity of the R216L-R237Y variant differed significantly from that of the R216L variant, suggesting that Arg-237 has subsidiary effects on substrate specificity. Additional experiments using several DDO and DAO inhibitors also suggested the involvement of Arg-216 in the substrate specificity and catalytic activity of mouse DDO and that Arg-237 is possibly involved in substrate recognition by this enzyme. Collectively, these results indicate that Arg-216 and Arg-237 play crucial and subsidiary role(s), respectively, in the substrate specificity of mouse DDO.

Thiolactomycin inhibits D-aspartate oxidase: a novel approach to probing the active site environment.

D-Aspartate oxidase (DDO) and D-amino acid oxidase (DAO) are flavin adenine dinucleotide (FAD)-containing flavoproteins that catalyze the oxidative deamination of D-amino acids. While several functionally and structurally important amino acid residues have been identified in the DAO protein, little is known about the structure-function relationships of DDO. In the search for a potent DDO inhibitor as a novel tool for investigating its structure-function relationships, a large number of biologically active compounds of microbial origin were screened for their ability to inhibit the enzymatic activity of mouse DDO. We discovered several compounds that inhibited the activity of mouse DDO, and one of the compounds identified, thiolactomycin (TLM), was then characterized and evaluated as a novel DDO inhibitor. TLM reversibly inhibited the activity of mouse DDO with a mixed type of inhibition more efficiently than meso-tartrate and malonate, known competitive inhibitors of mammalian DDOs. The selectivity of TLM was investigated using various DDOs and DAOs, and it was found that TLM inhibits not only DDO, but also DAO. Further experiments with apoenzymes of DDO and DAO revealed that TLM is most likely to inhibit the activities of DDO and DAO by competition with both the substrate and the coenzyme, FAD. Structural models of mouse DDO/TLM complexes supported this finding. The binding mode of TLM to DDO was validated further by site-directed mutagenesis of an active site residue, Arg-237. Collectively, our findings show that TLM is a novel, active site-directed DDO inhibitor that will be useful for elucidating the molecular details of the active site environment of DDO.

The generation of lucigenin chemiluminescence from the reaction of guanidino compounds with phenylglyoxal under alkaline conditions and its application.

It is shown that o-carboxyphenylglyoxal, which is converted from ninhydrin by alkali, produces a chemiluminescent lucigenin reaction under alkaline conditions when with reacted with guanidino compounds. It is also demonstrated that phenylglyoxal, which is a model compound of o-carboxyphenylglyoxal, produces a strong chemiluminescent lucigenin reaction under alkaline conditions when reacted with guanidino compounds. Moreover, ESR spectra showed the presence of 5,5-dimethyl-1-pyrroline N-oxide (DMPO)-spin adducts of superoxide anions in a mixture of phenylglyoxal and guanidino compounds under alkaline conditions. It was confirmed that the superoxide anions were generated by the reaction of phenylglyoxal with guanidino compounds under alkaline conditions, thereby causing lucigenin chemiluminescence. The chemiluminescent reaction of lucigenin in a mixture of phenylglyoxal and the guanidino compounds was applied to HPLC for guanidino compounds. The present chemiluminescence-HPLC system has a 2-fold greater sensitivity than chemiluminescence-HPLC using ninhydrin. Arginine, guanidine and methylguanidine were detected in serum from a hemodialysis patient with chronic renal failure.

Quantitative in silico analysis of the selectivity of graphitic carbon synthesized by different methods.

Molecular interaction energy (MI) values calculated by molecular mechanics (MM2) using a model graphitic carbon phase were used for studying the selectivity of different types of graphitic carbon columns. The MI values well correlated with logk values measured on a graphitic carbon synthesized from 100% organic materials (r = 0.961, n = 13) but not with logk values measured on a graphitic carbon synthesized using silica matrix (r = 0.558, n = 17). The latter logk values correlated well with the hydrogen bonding energy values calculated using a model silica phase (r = 0.856, n = 17). The reason for the poor correlation of the logk values measured on the latter graphitic carbon is that the silica matrix might not be completely eliminated in the production process.

Retention behaviour of polyunsaturated fatty acid methyl esters on porous graphitic carbon.

Retention with porous graphitic carbon was investigated with 25 structures of fatty acid methyl esters (FAMEs) with two different mobile phases: CH(3)CN:CHCl(3) 60:40 (v/v) and CH(3)OH:CHCl(3) 60:40 (v/v) with both 0.1% triethylamine (TEA) and an equimolar amount of HCOOH. Preliminary results showed that the use of TEA/HCOOH led to the response increase of saturated FAMEs with evaporative light scattering detection. No increase was observed for unsaturated one. These modifiers may slightly reduce the retention of FAMEs but did not significantly modify the separation factor with porous graphitic carbon. Thermodynamic parameters were calculated for each structure using Van't Hoff plot measured over the temperature range from 10 to 50 degrees C, with the both mobile phase conditions. All the studied compounds were found linked by the same retention mechanism on porous graphitic carbon. Quantitative in silico analysis of the retention using a molecular mechanics calculation demonstrated a good correlation between the retention factors and the molecular interaction energy values (r>0.93). Especially the Van der Waals energy was predominant, and the contribution of electrostatic energy was negligible for the quantitative analysis of the retention. The results indicate that Van der Waals force, hydrophobic interaction, is predominant for the retention of FAMEs on this packing material. The relative retention for highly unsaturated homologues can be changed by the selection of the weak solvent CH(3)CN or CH(3)OH. Then isomers differing only in the position of the carbon double bond on the alkyl chain can be separated and their behaviour is summarised as the closer the carbon double bonds to the FAME polar head, the more the retention decreases. Finally, the more important the number of carbon double bonds in the alkyl chain is, the smaller the retention is.

Chromatography in silico, quantitative analysis of retention of aromatic acid derivatives.

A quantitative analysis of the retention of aromatic acid derivatives in reversed-phase liquid chromatography (RPLC) is conducted using a molecular mechanics calculation in the CAChe program. The molecular interaction energy value is calculated by subtracting the energy value of the complex from the sum of energy values of a model phase and an analyte. Several model phases are constructed, and the feasibility of applying the method to a variety of compounds is examined based on improving the contact surface area and the capability of computer software and hardware. Interaction energy values are calculated for both molecular and ionic forms. The predicted retention factors of partially ionized acids obtained using a combination of dissociation constants correlated well with the values measured by RPLC with pH-controlled eluents.

Chromatography in silica, quantitative analysis of retention mechanisms of benzoic acid derivatives.

A quantitative analysis of the retention of benzoic acid derivatives in reversed-phase liquid chromatography was achieved using a molecular mechanics calculation in the CAChe program. Interaction energy values were calculated for both molecular and ionic forms. The predicted retention factors of partially ionized acids obtained using a combination of dissociation constants well correlated with the values measured by reversed-phase liquid chromatography with pH-controlled eluents. The molecular interaction energy value was calculated by subtracting the energy value of the complex from the sum of energy values of a model-phase and an analyte.

Chromatography in silico, basic concept in reversed-phase liquid chromatography.

Basic phenomena in reversed-phase liquid chromatography have been quantitatively analyzed using a computational chemical calculation. Pyridine interacted with an ionized silica surface under neutral conditions. Alkyl-chain length affected the contact surface area with an analyte. Steric hindrance was demonstrated using a model graphitic carbon phase and unsaturated alkenes. Quantitative structure-retention relationships in reversed-phase liquid chromatography were demonstrated for phenolic compounds and acidic and basic drugs. The correlations between predicted and measured retention factors were satisfactory. Dissociation constants were derived from the atom partial charge and used to predict retention factors of partially ionized compounds.

Chromatography and computational chemical analysis for drug discovery.

Analytical chemists have increasingly turned their attention to drug discovery and drug analysis and to solve fundamental questions of biological significance in physiology and genetics. New technologies have been developed, and a variety of instruments have been redesigned for biomedical applications. The development of high-performance liquid chromatography (HPLC) opened a new era in biorelated fields and allowed faster separations of fragile macromolecules. Capillary column gas chromatography (GC)/mass spectrometry (MS) have been used to achieve more powerful separation and to perform structural analysis of molecules, and laboratory automation including robotics has become a powerful trend in both analysis and synthesis. Liquid chromatography (LC)/MS is more suitable for biomedical applications than GC/MS because almost all biomolecules are heat sensitive. Furthermore, a combination of various mass spectrometers has been used even for proteins directly. Improving the sensitivity of nuclear magnetic resonance spectrometry (NMR) has permitted a direct connection with LC. Purification of biomolecules on-line by LC has been performed since the development of chip-electrophoresis, On the other hand, computational chemical analysis is a promising technique given the advancing the hardware and software for use in chemical fields. In this review, a combination of chromatography and computational chemistry for use in drug discovery studies is described. Fast LC analysis using a column switching technique was introduced for aromatic amino acid metabolites and guanidino compounds. Recent developments in related technologies are also included from review papers.

Computational chemical analysis of the retention of acidic drugs on a pentyl-bonded silica gel in reversed-phase liquid chromatography.

A fast method to obtain a quantitative structure-retention relationship is required in chromatography for the rapid optimization of chromatographic separation conditions. Chromatographic data of acidic drugs are analyzed by a computational chemical method to simulate chromatographic simulation. The direct interaction between a model phase and a drug is calculated as an energy value using the molecular mechanics calculation of CAChe. Computational chemistry using a model adsorbent is a new method for quantitative analysis of retention in reversed-phase liquid chromatography. The correlation coefficient is 0.878 (n = 19) between the retention factors of acidic drugs and interaction energy values of the final structure (DeltaFS) between an acidic drug and model pentyl-bonded phase.

Analysis of the mechanism of retention on graphitic carbon by a computational chemical method.

Retention mechanism on a graphitic carbon was analyzed by computational chemical calculation. The model graphitic carbon phase was a large polycyclic aromatic hydrocarbon (PAH) and analytes were carbohydrates and hydrocarbons separated by liquid and gas chromatography. Molecular mechanics calculation was fast and suggested their retention order and main retention force. Molecular orbital package calculation (MOPAC) demonstrated their complex form.