Search Results (129)

This article presents a mini-review of the available data on the thermodynamics of the complexation of amino acids and peptides with some nucleic bases in a buffer medium. Data on changes in thermodynamic parameters (binding constants, Gibbs energy, enthalpy, entropy) during the complexation of nucleic bases with amino acids and peptides as a function of physicochemical properties are given at T = 298.15 K. The effects of complexation on the volumetric properties of nucleic bases, including apparent molar volumes, standard molar volumes, and limiting molar expansibility, over a temperature range of 288.15 to 313.15 K are considered in detail. Differences in the behavior of amino acids and peptides caused by different modes of coordination with nucleic bases are noted. These manifest in the stoichiometry of the formed complexes, the relationship with the acid dissociation constants of carboxyl and amino groups, enthalpy–entropy compensation in the complexation process, the temperature dependence of the transfer volumes, and the effect of hydrophobicity on volumetric characteristics. Full article

The aim of this study was to improve the water–gas shift efficiency of Co/CeO₂ catalyst by incorporating praseodymium and rhenium. The catalysts were synthesized via combustion method and characterized using X-ray diffraction (XRD), Brunauer–Emmett–Teller (BET) surface area analysis, Scanning Electron Microscope (SEM), H₂-temperature programmed reduction (H₂-TPR), NH₃-temperature programmed desorption (NH₃-TPD), Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS). These characterization techniques evaluate the increase of the surface acidity and oxygen vacancies in Co-based catalysts, which leads to an increase in water–gas shift performance because CO molecules prefer to react with surface oxygen, then followed by the production of CO₂ and oxygen vacancies which act as active sites for H₂O dissociation. The 1%Re4%Co/Ce-5%Pr-O catalyst exhibited a maximum CO conversion of 86% at 450 °C, substantially outperforming the 5%Co/Ce-5%Pr-O catalyst, which showed only 62% CO conversion at 600 °C. In addition, 1%Re4%Co/Ce-5%Pr-O catalyst is more resistant towards deactivation than 5%Co/Ce-5%Pr-O. The result presented that the catalytic activity of 1%Re4%Co/Ce-5%Pr-O catalyst was kept constant for the whole period of 50 h, while a 6% decrease in water–gas shift activity was found for the 5%Co/Ce-5%Pr-O catalyst. Moreover, the addition of rhenium into the Co/Ce-Pr-O catalyst reveals that the enhancement of oxygen vacancy concentration, oxygen mobility, and surface acidity, thereby enhances CO conversion efficiency. Full article

Cytokinins play an important role in plants and are targets of wheat breeding, particularly in terms of flowering and yield. The objective of this study was to determine relative synonymous codon usage (RSCU), molecular weight (g/mol), theoretical isoelectric point, instability index, aliphatic index, and hydrophobicity for the wheat cytokinin sequences from two different databases. The methods employed involved different formulas for calculations. The relative synonymous codon usage values were calculated as the ratio of the observed frequency to the expected frequency for the particular codon. The theoretical isoelectric point was calculated based on dissociation constant for groups of carboxylic acid and amino acids groups. The results showed that values of the relative synonymous codon usage divided amino acids of wheat into two groups. In the first group, values were above 1.6 (significant overrepresentation), such as those for phenylalanine (TTC), and Leucine (TTA). In the second group, values were below 0.6 (underrepresentation) such as those for leucine (CTA) and valine (GTT). In addition, the theoretical isoelectric point (pI) ranged from 4.81 to 6.6, and the instability index values were 34.3 and 38.16. A high degree of instability was observed at 1D and 5D of wheat genomes with values of 54.16 and 50.36, respectively. Principal component analysis (PCA) of the RSCU revealed that the main variation was attributed to PC1, accounting for a total variation of about 72.11%. The amino acids contributing to this variation included isoleucine, leucine, lysine, aspartic acid, and serine. PCA of the theoretical isoelectric point results found that the main variation was attributed to PC1, with a total variation of about 58.88%, and these chromosomes included 5D, 4D, 1A, 4B, and 3D of wheat genomes. Understanding the importance of RSCU in plant breeding helps breeders understand the mechanisms and functional aspects of wheat genomes, thereby enabling the development of wheat genomes for environmental adaptations. These results will provide a reference for nutrition and industrial applications, as well as supporting breeding programs. Full article

This study presents a detailed thermodynamic investigation on the protonation behavior of tartronic acid in aqueous solutions of various ionic media, including sodium chloride, potassium chloride, tetramethylammonium chloride, and tetraethylammonium iodide. Specifically, potentiometric measurements were performed at temperatures ranging from 288.15 to 310.15 K and ionic strengths between 0.1 and 1.0 mol dm⁻³ to determine stoichiometric protonation constants in different ionic media. The formation of weak complexes between tartronate and alkaline metal cations was obtained by means of the ΔpK method. Moreover, data were modeled using the Debye–Hückel equation and Specific Ion Interaction Theory (SIT), allowing for the calculation of standard thermodynamic parameters and the assessment of the dependence of protonation constants on ionic strength. Additionally, the protonation behavior of tartronic acid was compared with that of structurally related acids, such as malonic and mesoxalic acids, providing insights into the role of molecular structure in acid dissociation. The results emphasize the significant role of entropic contributions in the protonation process and provide a comprehensive model for the thermodynamic properties of tartronic acid across a wide range of experimental conditions. Full article

3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition of endogenous translational termination machinery. Here, we employed a special in vitro protein expression system that facilitates the efficiency of DOPA incorporation into proteins by removing essential Class I peptide release factors through targeted degradation. In the absence of both RF1 and RF2, we successfully demonstrated DOPA incorporation at all three stop codons (TAG, TAA, and TGA). By optimizing the concentration of engineered DOPA-specific aminoacyl-tRNA synthetase (DOPARS), DOPA, and DNA template, we achieved a synthesis yield of 2.24 µg of sfGFP with 100% DOPA incorporation in a 20 μL reaction system. DOPARS exhibited a dissociation constant (Kd) of 11.7 μM for DOPA but showed no detectable binding to its native counterpart, tyrosine. Additionally, DOPA was successfully incorporated into a reverse transcriptase, which interfered with its activity. This system demonstrates a fast and efficient approach for precise DOPA incorporation into proteins, paving the way for advanced protein engineering applications. Full article

The acidity of anatase titania before and after KOH doping was probed by pyridine adsorption in a pulse microreactor and modeled by DFT optimization of the geometry of CO and pyridine adsorption on a periodic slab of (101) and (100) surfaces using a GGA/PBE functional and verified by an example of a single-point calculation of the optimized geometry using an HSE-06 hybrid functional. The anatase (101) surface was slightly more acidic compared to the (100) surface. Both experimental and computational methods show that the acidity of anatase surfaces decreased after KOH doping and increased after the dissociative adsorption of water. Higher acidity of Ti metal centers was indicated by the shortening of the Ti-N, Ti-C, and C-O bond lengths, increasing the IR frequency of CO and pyridine ring vibrations and energy of adsorption. The DFT calculated energy of pyridine adsorption was analyzed in terms of binding energy and the energy of lattice distortion. The latter was used to construct Hammett plots for the adsorption of 4-substituted pyridines with electron-donating and -withdrawing substituents. The Hammett rho constant was obtained and used to characterize the acidity of various metal centers of −1.51 vs. −1.46 on pristine (101) and (100) surfaces, which were lowered to −1.07 and −1.19 values on KOH-doped (101) and (100) surfaces, respectively. The mechanism of lowering surface acidity via KOH doping proceeds through the stabilization of the atomic structure of Lewis acid centers. When an alkaline metal cation binds to several lattice oxygen atoms, the surface structure becomes more rigid. The ability of Ti atoms to move toward the adsorbate is restricted. Consequently, the lattice distortion energy and binding energy are decreased. In contrast, higher flexibility of the outermost layer of Ti atoms as a result of electron density redistribution, for example, in the presence of water on the surface, allows them to move farther outward, make shorter contacts with the adsorbate, and attain higher energies of binding and lattice distortion. Full article

The accurate determination of acid/base constants (proton dissociation constants—pK_a, or equivalently protonation constants—logK) is essential for the physicochemical characterization of new molecules, especially in drug design and development, as these parameters thoroughly influence the pharmacokinetics and pharmacodynamics of drug action. While pH/potentiometric titration remains the gold standard method for determining acid/base constants, spectroscopic techniques—particularly nuclear magnetic resonance spectroscopy (as NMR/pH titrations)—have emerged as powerful alternatives for specific challenges in analytical chemistry, providing also information on the structure and site of protonation. In this study, we performed a comprehensive meta-analysis of protonation constants reported in the literature, measured using both potentiometry and NMR titrations. Our analysis compiled the available literature data and assessed the agreement between the two methods, taking into consideration various experimental conditions, such as temperature and ionic strength. The results provide insights into the reliability and applicability of NMR titrations compared with potentiometry, offering guidance for selecting appropriate methodologies in drug design. Full article

An imbalance between production and excretion of amyloid β peptide (Aβ) in the brain tissues of Alzheimer’s disease (AD) patients leads to Aβ accumulation and the formation of noxious Aβ oligomers/plaques. A promising approach to AD prevention is the reduction of free Aβ levels by directed enhancement of Aβ binding to its natural depot, human serum albumin (HSA). We previously demonstrated the ability of specific low-molecular-weight ligands (LMWLs) in HSA to improve its affinity for Aβ. Here we develop this approach through a bioinformatic search for the clinically approved AD-related LMWLs in HSA, followed by classification of the candidates according to the predicted location of their binding sites on the HSA surface, ranking of the candidates, and selective experimental validation of their impact on HSA affinity for Aβ. The top 100 candidate LMWLs were classified into five clusters. The specific representatives of the different clusters exhibit dramatically different behavior, with 3- to 13-fold changes in equilibrium dissociation constants for the HSA–Aβ40 interaction: prednisone favors HSA–Aβ interaction, mefenamic acid shows the opposite effect, and levothyroxine exhibits bidirectional effects. Overall, the LMWLs in HSA chosen here provide a basis for drug repurposing for AD prevention, and for the search of medications promoting AD progression. Full article

The selection of a “perfect tool” for the theoretical determination of acid-base dissociation constants (Ka) is still puzzling. Recently, we developed a user-friendly model exploiting CAM-B3LYP for determining pKa with impressive reliability. Herein, a new challenge is faced, examining a panel of functionals belonging to different rungs of the “Jacob’s ladder” organization, which classifies functionals according to their level of theory. Specifically, meta-generalized gradient approximations (GGAs), hybrid-GGAs, and the more complex range-separated hybrid (RSH)-GGAs were investigated in predicting the pKa of differently substituted carboxylic acids. Therefore, CAM-B3LYP, WB97XD, B3PW91, PBE1PBE, PBEPBE and TPSSTPSS were used, with 6-311G+(d,p) as the basis set and the solvation model based on density (SMD). CAM-B3LYP showed the lowest mean absolute error value (MAE = 0.23) with relatively high processing time. PBE1PBE and B3PW91 provided satisfactory predictions (MAE = 0.34 and 0.38, respectively) with moderate computational time cost, while PBEPBE, TPSSTPSS and WB97XD led to unreliable results (MAE > 1). These findings validate the reliability of our model in predicting carboxylic acids pKa, with MAE well below 0.5 units, using a simplistic theoretical level and a low-cost computational approach. Full article

The characteristic alkaloid component of the leaves of the catnip shrub (Catha edulis) is cathinone, and its synthetic analogs form a major group of recreational drugs. Cathinone derivatives are chiral compounds. In the literature, several chiral methods using cyclodextrins (CDs) have been achieved so far for diverse sets of analogs; however, a comprehensive investigation of the stability of their CD complexes has not been performed yet. To characterize the enantioselective complex formation, a systematic experimental design was developed in which a total number of 40 neutral, positively, and negatively charged CD derivatives were screened by affinity capillary electrophoresis and compared according to their cavity size, substituent type, and location. The functional groups responsible for the favorable interactions were identified in the case of para-substituted cathinone analog mephedrone, flephedrone, and 4-methylethcathinone (4-MEC) and in the case of 3,4-methylendioxy derivative butylone and methylenedioxypyrovalerone (MDPV). The succinylated-β-CD and subetadex exhibited the highest complex stabilities among the studied drugs. The complex stoichiometry was determined using the Job’s plot method, and the complex structures were further studied using ROESY NMR measurements. The results of our enantioselective complex formation study can facilitate chiral method development and may lead to evaluate potential CD-based antidotes for cathinone analogs. Full article

Histidine residues play crucial roles in shaping the function and structure of proteins due to their unique ability to act as both acids and bases. In other words, they can serve as proton donors and acceptors at physiological pH. This exceptional property is attributed to the side-chain imidazole ring of histidine residues. Consequently, determining the acid-base dissociation constant (Ka) of histidine imidazole rings in proteins often yields valuable insights into protein functions. Significant efforts have been dedicated to measuring the pKa values of histidine residues in various proteins, with nuclear magnetic resonance (NMR) spectroscopy being the most commonly used technique. However, NMR-based methods encounter challenges in assigning signals to individual imidazole rings and require a substantial amount of proteins. To address these issues associated with NMR-based approaches, a mass-spectrometry-based method known as histidine hydrogen–deuterium exchange mass spectrometry (His-HDX-MS) has been developed. This technique not only determines the pKa values of histidine imidazole groups but also quantifies their solvent accessibility. His-HDX-MS has proven effective across diverse proteins, showcasing its utility. This review aims to clarify the fundamental principles of His-HDX-MS, detail the experimental workflow, explain data analysis procedures and provide guidance for interpreting the obtained results. Full article

Intact Transition Epitope Mapping—One-step Non-covalent force Exploitation (ITEM-ONE) analysis reveals an assembled epitope on the surface of Pertuzumab, which is recognized by the anti-Pertuzumab affimer 00557_709097. It encompasses amino acid residues NSGGSIYNQRFKGR, which are part of CDR2, as well as residues FTLSVDR, which are located on the variable region of Pertuzumab’s heavy chain and together form a surface area of 1381.46 Ų. Despite not being part of Pertuzumab’s CDR2, the partial sequence FTLSVDR marks a unique proteotypic Pertuzumab peptide. Binding between intact Pertuzumab and the anti-Pertuzumab affimer was further investigated using the Intact Transition Epitope Mapping—Thermodynamic Weak-force Order (ITEM-TWO) approach. Quantitative analysis of the complex dissociation reaction in the gas phase afforded a quasi-equilibrium constant (${\mathrm{K}}_{\mathrm{D} \mathrm{m}0\mathrm{g}}^{\#}$) of 3.07 × 10⁻¹². The experimentally determined apparent enthalpy (${\mathsf{\Delta }\mathrm{H}}_{\mathrm{m}0\mathrm{g}}^{\#}$) and apparent free energy (${\mathsf{\Delta }\mathrm{G}}_{\mathrm{m}0\mathrm{g}}^{\#}$) of the complex dissociation reaction indicate that the opposite reaction—complex formation—is spontaneous at room temperature. Due to strong binding to Pertuzumab and because of recognizing Pertuzumab’s unique partial amino acid sequences, the anti-Pertuzumab affimer 00557_709097 is considered excellently suitable for implementation in Pertuzumab quantitation assays as well as for the accurate therapeutic drug monitoring of Pertuzumab in biological fluids. Full article

The present work describes the complexation of the anti-inflammatory sialorphin derivative Pal-Lys-Lys-Gln-His-Asn-Pro-Arg (palmitic acid-lysine-lysine-glutamine-histidine-asparagine-proline-arginine) with Cu(II) ions in an aqueous solution, at a temperature of 25.0 ± 0.1 °C, over the whole pH range. The complexing properties were characterized by potentiometric and UV-Vis spectrophotometric methods. The potentiometric method was used to calculate the logarithms of the overall stability constants (log β) and the values of the stepwise dissociation constants (pK_a) of the studied complexes. The percentage of each species formed in an aqueous solution was estimated from the species distribution curve as a function of pH. The absorbance (A) and molar absorption coefficient (ε) values for the Cu(II)-sialorphin derivative system were determined with UV-Vis spectroscopy. Our studies indicate that the sialorphin derivative forms stable complexes with Cu(II) ions, which may lead to future biological and therapeutic applications. Full article

Lipophilic oligonucleotide derivatives are a potent approach to the intracellular delivery of nucleic acids. The binding of these derivatives to serum albumin is a determinant of their fate in the body, as its structure contains several sites of high affinity for hydrophobic compounds. This study focuses on the features of self-association and non-covalent interactions with human serum albumin of novel self-penetrating oligonucleotide derivatives. The study revealed that the introduction of a triazinyl phosphoramidate modification bearing two dodecyl groups at the 3′ end region of the oligonucleotide sequence has a negligible effect on its affinity for the complementary sequence. Dynamic light scattering verified that the amphiphilic oligonucleotides under study can self-assemble into micelle-like particles ranging from 8 to 15 nm in size. The oligonucleotides with dodecyl groups form stable complexes with human serum albumin with a dissociation constant of approximately 10⁻⁶ M. The oligonucleotide micelles are simultaneously destroyed upon binding to albumin. Using an electrophoretic mobility shift assay and affinity modification, we examined the ability of DNA duplexes containing triazinyl phosphoramidate oligonucleotides to interact with Ku antigen and PARP1, as well as the mutual influence of PARP1 and albumin or Ku antigen and albumin upon interaction with DNA duplexes. These findings, together with the capability of dodecyl-containing derivatives to effectively penetrate different cells, such as HEK293 and T98G, indicate that the oligonucleotides under study can be considered as a platform for the development of therapeutic preparations with a target effect. Full article

Among the different drug targets of SARS-CoV-2, a multi-domain protein known as NSP3 is a critical element of the translational and replication machinery. The macrodomain-I, in particular, has been reported to have an essential role in the viral attack on the innate immune response. In this study, we explore natural medicinal compounds and identify potential inhibitors to target the SARS-CoV-2–NSP3 macrodomain-I. Computational modeling and simulation tools were utilized to investigate the structural-dynamic properties using triplicates of 100 ns MD simulations. In addition, the MM/GBSA method was used to calculate the total binding free energy of each inhibitor bound to macrodomain-I. Two significant hits were identified: 3,5,7,4′-tetrahydroxyflavanone 3′-(4-hydroxybenzoic acid) and 2-hydroxy-3-O-beta-glucopyranosyl-benzoic acid. The structural-dynamic investigation of both compounds with macrodomain-I revealed stable dynamics and compact behavior. In addition, the total binding free energy for each complex demonstrated a robust binding affinity, of ΔG −61.98 ± 0.9 kcal/mol for Compound A, while for Compound B, the ΔG was −45.125 ± 2.8 kcal/mol, indicating the inhibitory potential of these compounds. In silico bioactivity and dissociation constant (K_D) determination for both complexes further validated the inhibitory potency of each compound. In conclusion, the aforementioned natural products have the potential to inhibit NSP3, to directly rescue the host immune response. The current study provides the basis for novel drug development against SARS-CoV-2 and its variants. Full article