Using molecular dynamics simulations in an explicit aqueous solvent, we examine the binding of fluoride versus iodide to a spherical macromolecule with both hydrophobic and positively charged patches. Rationalizing our observations, we divide the ion association interaction into two mechanisms: (1) poorly solvated iodide ions are attracted to hydrophobic surface patches, while (2) the strongly solvated fluoride and to a minor extent also iodide bind via cation-anion interactions. Quantitatively, the binding affinities vary significantly with the accessibility of the charged groups as well as the surface potential; therefore, we expect the ion-macromolecule association to be modulated by the local surface characteristics of the (bio-)macromolecule. The observed cation-anion pairing preference is in excellent agreement with experimental data.
Pyrazine derivatives show a wide range of biological activities. 1-Pyrazin-2-ylethan-1-ones have served as food flavourants, and together with pyrazine-2-carbonitriles have been widely used as intermediates in the synthesis of various heterocyclic compounds. In our laboratory, substituted pyrazine-2-carbonitriles and 1-pyrazin-2-ylethan-1-ones have been used as intermediates for the preparation of potential antifungal and antimycobacterial drugs. Using established methods, a library of pyrazine derivatives was synthesized. Homolytic alkylation of commercially available pyrazine-2-carbonitrile yielded a series of 5-alkylpyrazine-2-carbonitriles which were converted into the corresponding 1-(5-alkylpyrazin-2-yl)ethan-1-ones (5-alkyl-2-acetylpyrazines) via the Grignard reaction. Homolytic acetylation of pyrazine-2-carbonitrile yielded 5-acetylpyrazine-2-carbonitrile. Using the same procedure, 3-acetyl-5-tert-butylpyrazine-2-carbonitrile was obtained with 5-tert-butylpyrazine-2-carbonitrile as a starting material. The hydrophobicity of the compounds was determined both experimentally (RP-HPLC) and by computation (CS ChemOffice Ultra version 9.0, ACD/LogP version 1.0 and ACD/LogP version 9.04), and both the approaches were compared. New hydrophobicity constants ? based on experimental results were derived. These constants are markedly different from tabulated constants ? valid for benzene rings, and can be widely used in estimating physicochemical properties of new biologically active pyrazines.
Hydrophobicity can either be determined experimentally or predicted by means of commercially available programs. In the studies concerning biological activities of pyrazine analogues of chalcones, 3-(2-hydroxyphenyl)-1-(pyrazin-2-yl)prop-2-en-1-ones were more potent than the corresponding 3-(4-hydroxyphenyl)-1-(pyrazin-2-yl)prop-2-en-1-ones. As the difference in lipophilicity may be a factor responsible for the difference in the potency, R(M) values of the compounds were determined by RP-TLC and compared with logP values calculated by various commercially available programs. Important discrepancies were found between experimental and computational lipophilicity data. Therefore, we have tried to find a reliable method for calculating R(M) values from in silico derived molecular parameters. The R(M) values obtained with the chromatographic system consisting of Silufol UV 254 plates impregnated with silicon oil as the stationary phase and acetone-citrate buffer (pH=3) 50:50 (v/v) as the mobile phase correlated well with van der Waals volumes (V(W)) and hydration energies [Formula: see text] derived of molecular models calculated on RHF/AM1 level.
The actin cytoskeleton is a dynamic structure that coordinates numerous fundamental processes in eukaryotic cells. Dozens of actin-binding proteins are known to be involved in the regulation of actin filament organization or turnover and many of these are stimulus-response regulators of phospholipid signaling. One of these proteins is the heterodimeric actin-capping protein (CP) which binds the barbed end of actin filaments with high affinity and inhibits both addition and loss of actin monomers at this end. The ability of CP to bind filaments is regulated by signaling phospholipids, which inhibit the activity of CP; however, the exact mechanism of this regulation and the residues on CP responsible for lipid interactions is not fully resolved. Here, we focus on the interaction of CP with two signaling phospholipids, phosphatidic acid (PA) and phosphatidylinositol (4,5)-bisphosphate (PIP(2)). Using different methods of computational biology such as homology modeling, molecular docking and coarse-grained molecular dynamics, we uncovered specific modes of high affinity interaction between membranes containing PA/phosphatidylcholine (PC) and plant CP, as well as between PIP(2)/PC and animal CP. In particular, we identified differences in the binding of membrane lipids by animal and plant CP, explaining previously published experimental results. Furthermore, we pinpoint the critical importance of the C-terminal part of plant CPα subunit for CP-membrane interactions. We prepared a GST-fusion protein for the C-terminal domain of plant α subunit and verified this hypothesis with lipid-binding assays in vitro.
- MeSH
- Actin Capping Proteins antagonists & inhibitors chemistry genetics metabolism MeSH
- Phosphatidylinositol Phosphates chemistry metabolism MeSH
- Phylogeny MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Chickens MeSH
- Phosphatidic Acids chemistry metabolism MeSH
- Models, Molecular MeSH
- Molecular Sequence Data MeSH
- Mutation MeSH
- Arabidopsis Proteins antagonists & inhibitors chemistry genetics metabolism MeSH
- Avian Proteins antagonists & inhibitors chemistry genetics metabolism MeSH
- Amino Acid Sequence MeSH
- Sequence Alignment MeSH
- Protein Binding MeSH
- Computational Biology MeSH
- Structure-Activity Relationship MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.
- MeSH
- Cysteine chemistry genetics metabolism MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Kinetics MeSH
- Protein Conformation MeSH
- Humans MeSH
- Models, Molecular MeSH
- Protein Multimerization * MeSH
- Mutation MeSH
- Computer Simulation MeSH
- 14-3-3 Proteins chemistry genetics metabolism MeSH
- Protein Stability MeSH
- Thermodynamics * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
OBJECTIVES: The herbal drug aristolochic acid (AA) derived from Aristolochia species has been shown to be the cause of aristolochic acid nephropathy (AAN), Balkan endemic nephropathy (BEN) and their urothelial malignancies. One of the common features of AAN and BEN is that not all individuals exposed to AA suffer from nephropathy and tumor development. One cause for these different responses may be individual differences in the activities of the enzymes catalyzing the biotransformation of AA. Thus, the identification of enzymes principally involved in the metabolism of AAI, the major toxic component of AA, and detailed knowledge of their catalytic specificities is of major importance. Human cytochrome P450 (CYP) 1A1 and 1A2 enzymes were found to be responsible for the AAI reductive activation to form AAI-DNA adducts, while its structurally related analogue, CYP1B1 is almost without such activity. However, knowledge of the differences in mechanistic details of CYP1A1-, 1A2-, and 1B1- mediated reduction is still lacking. Therefore, this feature is the aim of the present study. METHODS: Molecular modeling capable of evaluating interactions of AAI with the active site of human CYP1A1, 1A2 and 1B1 under the reductive conditions was used. In silico docking, employing soft-soft (flexible) docking procedure was used to study the interactions of AAI with the active sites of these human enzymes. RESULTS: The predicted binding free energies and distances between an AAI ligand and a heme cofactor are similar for all CYPs evaluated. AAI also binds to the active sites of CYP1A1, 1A2 and 1B1 in similar orientations. The carboxylic group of AAI is in the binding position situated directly above heme iron. This ligand orientation is in CYP1A1/1A2 further stabilized by two hydrogen bonds; one between an oxygen atom of the AAI nitro-group and the hydroxyl group of Ser122/Thr124; and the second bond between an oxygen atom of dioxolane ring of AAI and the hydroxyl group of Thr497/Thr498. For the CYP1B1:AAI complex, however, any hydrogen bonding of the nitro-group of AAI is prevented as Ser122/Thr124 residues are in CYP1B1 protein replaced by hydrophobic residue Ala133. CONCLUSION: The experimental observations indicate that CYP1B1 is more than 10× less efficient in reductive activation of AAI than CYP1A2. The docking simulation however predicts the binding pose and binding energy of AAI in the CYP1B1 pocket to be analogous to that found in CYP1A1/2. We believe that the hydroxyl group of S122/T124 residue, with its polar hydrogen placed close to the nitro group of the substrate (AAI), is mechanistically important, for example it could provide a proton required for the stepwise reduction process. The absence of a suitable proton donor in the AAI-CYP1B1 binary complex could be the key difference, as the nitro group is in this complex surrounded only by the hydrophobic residues with potential hydrogen donors not closer than 5 Å.
- MeSH
- DNA Adducts chemistry metabolism MeSH
- Aristolochia chemistry MeSH
- Aryl Hydrocarbon Hydroxylases chemistry genetics metabolism MeSH
- Models, Chemical MeSH
- Cytochrome P-450 CYP1A1 chemistry genetics metabolism MeSH
- Cytochrome P-450 CYP1A2 chemistry genetics metabolism MeSH
- Hydrophobic and Hydrophilic Interactions drug effects MeSH
- Catalytic Domain drug effects MeSH
- Aristolochic Acids adverse effects chemistry pharmacokinetics MeSH
- Drugs, Chinese Herbal adverse effects chemistry pharmacokinetics MeSH
- Humans MeSH
- Molecular Sequence Data MeSH
- Kidney Diseases chemically induced MeSH
- Nitroreductases adverse effects chemistry pharmacokinetics MeSH
- Computer Simulation MeSH
- Amino Acid Sequence MeSH
- Protein Structure, Tertiary drug effects MeSH
- Hydrogen Bonding drug effects MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Nine new dihydrochloride salts of 3-(4-arylpiperazin-1-yl)-2-hydroxypropyl 4-alkoxyethoxybenzoates were designed and synthesized. The physicochemical properties such as lipophilicity index (log kw) and dissociation constant (pKa) were experimentally determined and compared to the software calculated data. The lipophilicity index was determined by means of reversed-phase high performance liquid chromatography (RP-HPLC). The pKa values were determined by means of capillary zone electrophoresis. The "drug-likeness" properties according to the Lipinski Rule of Five and prediction of possible blood-brain barrier penetration were computed and discussed.
- MeSH
- Benzoates chemical synthesis chemistry MeSH
- Chemical Phenomena MeSH
- Chromatography, Reverse-Phase methods MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Hydrogen-Ion Concentration MeSH
- Lipids chemistry MeSH
- Software * MeSH
- Chromatography, High Pressure Liquid methods MeSH
- Publication type
- Journal Article MeSH
In this study, we have carried out a combined experimental and computational investigation to elucidate several bred-in-the-bone ideas standing out in rational design of novel cationic surfactants as antibacterial agents. Five 3-hydroxypyridinium salts differing in the length of N-alkyl side chain have been synthesized, analyzed by high performance liquid chromatography, tested for in vitro activity against a panel of pathogenic bacterial and fungal strains, computationally modeled in water by a SCRF B3LYP/6-311++G(d,p) method, and evaluated by a systematic QSAR analysis. Given the results of this work, the hypothesis suggesting that higher positive charge of the quaternary nitrogen should increase antimicrobial efficacy can be rejected since 3-hydroxyl group does increase the positive charge on the nitrogen but, simultaneously, it significantly derogates the antimicrobial activity by lowering the lipophilicity and by escalating the desolvation energy of the compounds in comparison with non-hydroxylated analogues. Herein, the majority of the prepared 3-hydroxylated substances showed notably lower potency than the parent pyridinium structures, although compound 8 with C12 alkyl chain proved a distinctly better antimicrobial activity in submicromolar range. Focusing on this anomaly, we have made an effort to reveal the reason of the observed activity through a molecular dynamics simulation of the interaction between the bacterial membrane and compound 8 in GROMACS software.
- MeSH
- Anti-Bacterial Agents chemistry pharmacology toxicity MeSH
- Bacteria drug effects MeSH
- CHO Cells MeSH
- Cricetulus MeSH
- Fungi drug effects MeSH
- Hydrophobic and Hydrophilic Interactions MeSH
- Cricetinae MeSH
- Quantitative Structure-Activity Relationship * MeSH
- Molecular Conformation MeSH
- Pyridines chemistry pharmacology toxicity MeSH
- Molecular Dynamics Simulation * MeSH
- Cell Survival drug effects MeSH
- Animals MeSH
- Check Tag
- Cricetinae MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
BACKGROUND: The Nse1, Nse3 and Nse4 proteins form a tight sub-complex of the large SMC5-6 protein complex. hNSE3/MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen) protein family and the Nse4 kleisin subunit is related to the EID (E1A-like inhibitor of differentiation) family of proteins. We have recently shown that human MAGE proteins can interact with NSE4/EID proteins through their characteristic conserved hydrophobic pocket. METHODOLOGY/PRINCIPAL FINDINGS: Using mutagenesis and protein-protein interaction analyses, we have identified a new Nse3/MAGE-binding domain (NMBD) of the Nse4/EID proteins. This short domain is located next to the Nse4 N-terminal kleisin motif and is conserved in all NSE4/EID proteins. The central amino acid residues of the human NSE4b/EID3 domain were essential for its binding to hNSE3/MAGEG1 in yeast two-hybrid assays suggesting they form the core of the binding domain. PEPSCAN ELISA measurements of the MAGEC2 binding affinity to EID2 mutant peptides showed that similar core residues contribute to the EID2-MAGEC2 interaction. In addition, the N-terminal extension of the EID2 binding domain took part in the EID2-MAGEC2 interaction. Finally, docking and molecular dynamic simulations enabled us to generate a structure model for EID2-MAGEC2. Combination of our experimental data and the structure modeling showed how the core helical region of the NSE4/EID domain binds into the conserved pocket characteristic of the MAGE protein family. CONCLUSIONS/SIGNIFICANCE: We have identified a new Nse4/EID conserved domain and characterized its binding to Nse3/MAGE proteins. The conservation and binding of the interacting surfaces suggest tight co-evolution of both Nse4/EID and Nse3/MAGE protein families.
- MeSH
- Protein Interaction Domains and Motifs MeSH
- Intracellular Signaling Peptides and Proteins chemistry genetics metabolism MeSH
- Nuclear Proteins chemistry MeSH
- Conserved Sequence MeSH
- Humans MeSH
- Models, Molecular MeSH
- Molecular Sequence Data MeSH
- Mutagenesis, Site-Directed MeSH
- Peptide Fragments chemistry genetics metabolism MeSH
- Computer Simulation MeSH
- Cell Cycle Proteins genetics metabolism MeSH
- Recombinant Proteins chemistry genetics metabolism MeSH
- Schizosaccharomyces pombe Proteins chemistry MeSH
- Schizosaccharomyces MeSH
- Amino Acid Sequence MeSH
- Amino Acid Substitution MeSH
- Two-Hybrid System Techniques MeSH
- Carrier Proteins chemistry genetics metabolism MeSH
- Protein Binding MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
... The Hydrophobic Effect 158 -- 8.6. The Hydrophobic Interaction 161 -- 8.7. ... ... Experimental Measurements of Double-Layer and DLVO Forces 331 -- 14.23. ... ... Experimental Measurements and Properties of Oscillatory Forces 355 -- 15.8. ... ... Hydrophobic Energy of Transfer 514 -- 19.8. ... ... Attractive Hydrophobic Forces 595 -- 21.6. ...
Third edition xxx, 674 stran : 24 cm il. ;
- MeSH
- Chemistry, Physical MeSH
- Publication type
- Monograph MeSH
- Conspectus
- Fyzikální chemie
- NML Fields
- chemie, klinická chemie
