RESUMO
A detailed theoretical investigation of cyclophanes with a divergent set of methods ranging from molecular mechanics through semiempirical to ab initio is presented. Cyclophanes have attracted interest over the years due to their unusual chemistry and increasing applications. There has been previous debate over the effects contributing to the greater stability of more-crowded in isomers of certain cyclophanes, and a higher strain in the out isomer was the prevailing explanation. Application of EDA-NOCV and SAPT analysis has enabled us to distinguish between different effects controlling isomer stability and determine the significance of all effects involved. Our results show that, although strain has a large significance, orbital stabilization within the molecule from the aromatic electron density is crucial. Furthermore, we analysed halogen-substituted cyclophanes in order to further understand these subtle effects.
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The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE(CCSD)(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type π â σ*(O-H) between the monomers also exists.
Assuntos
Água/química , Modelos Teóricos , TermodinâmicaRESUMO
We have analyzed the influence of anion-π interactions to the stability of Sm/LSm assemblies. The side chain of Glu is more likely to be in anion-π interactions than Asp. Phe has the highest occurrence in these interactions than the other two π residues. Among the anion-π residue pairs, Glu-Phe residue pair showed the maximum number of anion-π. We have found hot-spot residues forming anion-π interactions, and Glu-Phe is the most common hot-spot interacting pair. The significant numbers of anion-π interacting residues identified in the dataset were involved in the formation of multiple anion-π interactions. More than half of the residues involved in these interactions are evolutionarily conserved. The anion-π interaction energies are distance and orientation dependent. It was found that anion-π interactions showed energy less than -15 kcal mol(-1), and most of them have energy in the range -2 to -9 kcal mol(-1). Solvent accessibility pattern of Sm/LSm proteins reveals that all of the interacting residues are preferred to be in buried regions. Most of the interacting residues preferred to be in strand. A significant percentage of anion-π interacting residues are located as stabilization centers and thus might provide additional stability to these proteins. The simultaneous interaction of anions and cations on different faces of the same π-system has been observed. On the whole, the results presented in this work will be very useful for understanding the contribution of anion-π interaction to the stability of Sm/LSm proteins.
Assuntos
Proteínas de Ligação a RNA/química , Ribonucleoproteínas Nucleares Pequenas/química , Simulação por Computador , Estabilidade Proteica , Estrutura Secundária de Proteína , Relação Estrutura-AtividadeRESUMO
In search for novel biologically active metal based compounds, an evaluation of in vitro cytotoxic, antioxidant, and antimicrobial activity of new Pt(II) complex and its Zn(II), Cu(II), and Co(III) analogues, with NNO tridentately coordinated N-heteroaromatic Schiff base ligand (E)-2-[N'-(1-pyridin-2-yl-ethylidene)hydrazino]acetate, was performed. Investigation of antioxidative properties showed that all of the compounds have strong radical scavenging potencies. The Zn(II) complex showed potent inhibition of DNA cleavage by hydroxyl radical. A cytotoxic action of investigated compounds was evaluated on cultures of human promyelocitic leukaemia (HL-60), human glioma (U251), rat glioma (C6), and mouse melanoma (B16) cell lines. It was shown that binuclear pentacoordinated Zn(II) complex possesses a strong dose-dependent cytotoxic activity, of the same order of magnitude as cisplatin on B16, C6, and U251 cells. Furthermore, Zn(II) complex causes oxidative stress-induced apoptotic death of HL-60 leukemic cells, associated with caspase activation, phosphatidylserine externalization, and DNA fragmentation.
Assuntos
Anti-Infecciosos/farmacologia , Antioxidantes/farmacologia , Compostos Organometálicos/química , Compostos Organometálicos/farmacologia , Animais , Anti-Infecciosos/química , Antineoplásicos/química , Antineoplásicos/farmacologia , Antioxidantes/química , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Cobalto/farmacologia , Cobre/farmacologia , Relação Dose-Resposta a Droga , Avaliação Pré-Clínica de Medicamentos/métodos , Humanos , Camundongos , Estrutura Molecular , Compostos Organoplatínicos/química , Compostos Organoplatínicos/farmacologia , Estresse Oxidativo/efeitos dos fármacos , Ratos , Bases de Schiff , Zinco/farmacologiaRESUMO
Copper(II) complexes with an α-diimine show a wide variety of biological activities, such as antibacterial, antifungal, antioxidant and anticancer. In this work, we synthesized and structurally characterized two novel Cu(II) complexes with methyl 3-formyl-4-hydroxybenzoate (HL) and α-diimines: 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen). Crystal structure analysis shows that the formulas of the compounds are [Cu(bipy)(L)(BF4)] (1) and [Cu(phen)(L)(H2O)](BF4)·H2O (2), with BF4- as a ligand in complex 1, which is rarely coordinated to metals. Both complexes have a square pyramidal geometry, while DFT calculations showed that the most stable structures of complexes 1 and 2 in a water/DMSO mixture are square-planar derivatives [Cu(bipy)(L)]+ and [Cu(phen)(L)]+. The antibacterial activity of compounds was evaluated in vitro on four Gram-negative and four Gram-positive bacterial strains. Complex 2 showed greater antibacterial activity towards all bacterial strains comparable to the control compound Amikacin. Complex 2 exerted a strong cytotoxic effect against the tested cancer cell lines (IC50 values ranging from 0.32 to 0.44 µM). Both complexes caused apoptotic cell death in HeLa cells and a noticeable in vitro antiangiogenic effect. In the concentration range of 5 to 100 µM, the complexes showed the absence of a genotoxic effect and displayed a protective effect against oxidative DNA damage induced by H2O2 in human peripheral blood cells. The interaction between the compounds and calf-thymus DNA was evaluated by diverse techniques suggesting a tight binding, which was also confirmed by molecular docking. In addition, it was found that the complexes bind tightly and reversibly to bovine and human serum albumin.
Assuntos
Aldeídos , Complexos de Coordenação , Cobre , Animais , Bovinos , Humanos , Células HeLa , Cobre/farmacologia , Cobre/química , Complexos de Coordenação/química , Simulação de Acoplamento Molecular , Ligantes , Peróxido de Hidrogênio , Antibacterianos/farmacologia , Cristalografia por Raios XRESUMO
In this paper, three different Zn(II) complexes with (E)-2-(2-(1-(6-bromopyridin-2-yl)ethylidene)hydrazinyl)-N,N,N-trimethyl-2-oxoethan-1-aminium chloride (HLCl) have been synthesized and characterized by single crystal X-ray diffraction, elemental analysis, IR and NMR spectroscopy. All complexes are mononuclear, with the ligand (L) coordinated in a deprotonated formally neutral zwitterionic form via NNO donor set atoms. Complex 1 forms an octahedral geometry with the composition [ZnL2](BF4)2, while complexes 2 [ZnL(NCO)2] and 3 [ZnL(N3)2] form penta-coordinated geometry. Density functional theory (DFT) calculations were performed to enhance our understanding of the structures of the synthesized complexes and the cytotoxic activity of the complexes was tested against five human cancer cell lines (HeLa, A549, MDA-MB-231, K562, LS 174T) and normal human fibroblasts MRC-5. Additionally, antibacterial and antifungal activity of these complexes was tested against a panel of Gram-negative and Gram-positive bacteria, two fungal strains, and a yeast strain. It is noteworthy that all three complexes show selective antifungal activity comparable to that of amphotericin B. Molecular docking analysis predicted that geranylgeranyl pyrophosphate synthase, an enzyme essential for sterol biosynthesis, is the most likely target for inhibition by the tested complexes.
Assuntos
Antibacterianos , Antifúngicos , Antineoplásicos , Complexos de Coordenação , Teoria da Densidade Funcional , Hidrazonas , Testes de Sensibilidade Microbiana , Zinco , Humanos , Hidrazonas/química , Hidrazonas/farmacologia , Hidrazonas/síntese química , Zinco/química , Zinco/farmacologia , Complexos de Coordenação/farmacologia , Complexos de Coordenação/química , Complexos de Coordenação/síntese química , Antibacterianos/farmacologia , Antibacterianos/química , Antibacterianos/síntese química , Antifúngicos/farmacologia , Antifúngicos/química , Antifúngicos/síntese química , Antineoplásicos/farmacologia , Antineoplásicos/química , Antineoplásicos/síntese química , Linhagem Celular Tumoral , Estrutura Molecular , Simulação de Acoplamento Molecular , Ensaios de Seleção de Medicamentos Antitumorais , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Positivas/efeitos dos fármacos , Modelos Moleculares , Fungos/efeitos dos fármacos , Relação Estrutura-AtividadeRESUMO
Under simulated physiological conditions, this study investigates the interaction between nutraceutical phycocyanobilin (PCB) and the universal anti-protease protein human alpha-2-macroglobulin (α2M). Extensive molecular docking analyses on multiple α2M conformations, spectroscopic techniques, and α2M activity assays were utilized to examine the complex formation. The results revealed that for every protein conformation, two high energy binding sites exist: the first, conformationally independent, at the interface region between two monomer chains and the second, conformationally dependent, in the pocket composed of amino acids from four distinct domains (TED, RBD, CUB, and MG2) of the single protein chain. Spectrofluorimetric measurements indicated a moderate affinity between α2M and PCB with a moderately high binding constant of 6.3 × 105 M-1 at 25 °C. The binding of PCB to α2M resulted in minor changes in the secondary structure content of α2M. Furthermore, PCB protected α2M from oxidation and preserved its anti-protease activity in the oxidative environment. These findings suggest that PCB binding could indirectly impact the body's response to oxidative stress by influencing α2M's role in controlling enzyme activity during the inflammatory process.Communicated by Ramaswamy H. Sarma.
RESUMO
Apomyoglobin (apoMb), a model protein in biochemistry, exhibits a strong propensity to bind various ligands, which makes it a good candidate as a carrier of bioactive hydrophobic drugs. The stability of its hydrophobic pocket determines its potential as a carrier of bioactive compounds. High pressure (HP) is a potent tool for studying protein stability, revealing the specific role of hydrophobic cavities in unfolding. We probed the effects of biliverdin (BV) binding and its complex with Zn2+ ions on the structure and HP stability of apoMb. CD spectroscopy and SAXS measurements revealed that BV and BV-Zn2+ complexes make the apoMb structure more compact with higher α-helical content. We performed in situ HP measurements of apoMb intrinsic fluorescence to demonstrate the ability of BV to stabilise apoMb structure at HP conditions. Furthermore, the presence of Zn2+ within the apoMb-BV complex significantly enhances the BV stabilisation effect. In situ visible absorption study of BV chromophore confirmed the ability of Zn2+ to increase the stability of apoMb-BV complex under HP: the onset of complex dissociation is shifted by â¼100 MPa in presence of Zn2+. By combining HP-fluorescence and HP-visible absorption spectroscopy, our strategy highlights the crucial role of tetrapyrrole-metal complexes in stabilising apoMb hydrophobic pocket.
Assuntos
Biliverdina , Mioglobina , Biliverdina/farmacologia , Espalhamento a Baixo Ângulo , Difração de Raios X , Mioglobina/química , Apoproteínas/química , Íons , Zinco/farmacologiaRESUMO
In this article, cytotoxicity, the mechanisms of cytotoxic activity, genotoxicity, and interaction with DNA and proteins, of two Cu(II) complexes with a salicylaldehyde derivative (4-(diethylamino)salicylaldehyde) and α-diimine (2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)) are reported. Both Cu(II) complexes performed cytotoxic effects against all tested malignant cell lines. Complexes exerted highest cytotoxicity against HeLa and A375 malignant cell lines. The cytotoxic activity of Cu(II) complex with phen as a α-diimine co-ligand was significantly higher in comparison with cytotoxic activity of Cu(II) complex with bipy. Pretreatment with specific inhibitors of caspase-3, caspase-8 or caspase-9, in order to clear up the mode of cell death triggered by two Cu(II) complexes in HeLa cells, indicated the ability of these complexes to induce apoptosis through activation of target caspases. Cu(II)-phen complex exhibited significant antioxidant activity compared with Cu(II)-bipy complex, and showed a better effect on reducing intracellular ROS levels in HeLa cells. Tested complexes did not display genotoxic potential in human peripheral blood leucocytes, but exhibited an antigenotoxic effect in post-treatment, after H2O2 exposure. The study of the in vitro biological properties regarding their affinity towards CT (calf-thymus) DNA and serum albumins showed that the compounds can intercalate to CT DNA, and bind reversibly and tightly to the albumins. Molecular docking studies of the ability of compounds to bind to biomacromolecules are consistent with in vitro studies.
Assuntos
Antineoplásicos , Complexos de Coordenação , Cobre , Albuminas , Aldeídos , Antineoplásicos/farmacologia , Antioxidantes/farmacologia , Complexos de Coordenação/farmacologia , Cobre/farmacologia , DNA/metabolismo , Células HeLa , Humanos , Peróxido de Hidrogênio , Simulação de Acoplamento Molecular , Fenantrolinas/farmacologiaRESUMO
In this study, ß-keto esters as readily available bio-based building blocks were used to decorate the C60 sphere. Generally, cyclopropanated fullerene derivatives are obtained by the standard Bingel-Hirsch procedure. Herein, omitting the iodine from the reaction mixture and adding TEMPO afforded dihydrofuran fused C60 fullerene derivatives. The mechanism of the reaction shifted from nucleophilic aliphatic substitution to oxidative [3 + 2] cycloaddition via fullerenyl cations as an intermediate. This mechanism is proposed based on a series of control experiments with radical scavengers. Therefore, dihydrofuran-fused C60 derivatives were selectively obtained in good yields and their structures were established based on UV-Vis, IR, NMR spectroscopy and mass spectrometry. The electrochemical properties of the synthesized compounds were investigated by cyclic voltammetry. DFT calculations were performed in order to investigate the difference in stability, electronic properties and π-electron delocalization between methano and furano fullerenes.
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In this study, the interaction between clozapine, an atypical antipsychotic drug, and alpha-2-macroglobulin (α2M), a multipurpose anti-proteinase, was investigated under simulated (patho) physiological conditions using multiple spectroscopic techniques and molecular modeling. It was found that α2M binds clozapine with a moderate affinity (the binding constant of 0.9 × 105 M-1 at 37 °C). The preferable binding site for both clozapine's atropisomers was revealed to be a large pocket at the interface of C and D monomer subunits of the protein. Hydrogen bonds and the hydrophobic effect were proposed as dominant forces in complex formation. The binding of clozapine did not induce significant conformational change of the protein, as confirmed by virtually unaltered α2M secondary structure and anti-proteinase activity. However, both clozapine and α2M shielded each other from the deleterious influence of strong oxidants: sodium hypochlorite and 2,2'-azobis-2-methyl-propanimidamide dihydrochloride (AAPH). Moreover, clozapine in a concentration range that is usually targeted in the plasma during patients' treatment effectively protected the anti-proteinase activity of α2M under AAPH-induced free radical overproduction. Our results suggest that the cooperation between α2M and clozapine may be a path by which these two molecules synergistically protect neural tissue against injury caused by disturbed proteostasis or oxidative stress.
Assuntos
Antipsicóticos/metabolismo , Clozapina/metabolismo , Estresse Oxidativo , alfa-Macroglobulinas/metabolismo , Antipsicóticos/química , Sítios de Ligação , Clozapina/química , Humanos , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Simulação de Acoplamento Molecular , Oxirredução , Ligação Proteica , Conformação Proteica , Relação Estrutura-Atividade , alfa-Macroglobulinas/químicaRESUMO
Electronic interactions in donor-π-linker-acceptor systems with barbituric acid as an electron acceptor and possible electron donor were investigated to screen promising candidates with a push-pull character based on experimental and quantum chemical studies. The tautomeric properties of 5-benzylidenebarbituric acid derivatives were studied with NMR spectra, spectrophotometric determination of the pKa values, and quantum chemical calculations. Linear solvation energy relationships (LSER) and linear free energy relationships (LFER) were applied to the spectral data - UV frequencies and 13C NMR chemical shifts. The experimental studies of the nature of the ground and excited state of investigated compounds were successfully interpreted using a computational chemistry approach including ab initio MP2 geometry optimization and time-dependent DFT calculations of excited states. Quantification of the push-pull character of barbituric acid derivatives was performed by the 13CNMR chemical shift differences, Mayer π bond order analysis, hole-electron distribution analysis, and calculations of intramolecular charge transfer (ICT) indices. The results obtained show, that when coupled with a strong electron-donor, barbituric acid can act as the electron-acceptor in push-pull systems, and when coupled with a strong electron-acceptor, barbituric acid can act as the weak electron-donor.
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α-Lactalbumin (ALA) is a Ca2+-binding protein which constitutes up to 20% of whey protein. At acidic pH, and in the apo-state at elevated temperatures, ALA is the classic 'molten globule' (MG). This study examined epigallocatechin-3-gallate (EGCG) binding to ALA in its apo form (apoALA) and stabilizing effect on protein structure thereof. EGCG binds to apoALA in both native and MG state. The complex of EGCG and ALA is more stable to thermal denaturation. The docking analysis and molecular dynamic simulation (MDS) showed that Ca2+ removal decreased conformational stability of ALA, because of the local destabilization of Ca2+-binding region. EGCG binding to apoALA increases its stability by reverting of conformation and stability of Ca2+-binding region. Therefore, EGCG-induced thermal stability of apoALA is based on increased apoALA conformational rigidity. This study implies that during gastric digestion of tea with milk EGCG would remain bound to ALA, albeit in the Ca2+-free form.
Assuntos
Apoproteínas/química , Catequina/análogos & derivados , Lactalbumina/química , Simulação de Dinâmica Molecular , Animais , Apoproteínas/metabolismo , Sítios de Ligação , Cálcio/química , Catequina/química , Catequina/metabolismo , Concentração de Íons de Hidrogênio , Lactalbumina/metabolismo , Ligação Proteica , Desnaturação Proteica , Estabilidade Proteica , Estrutura Secundária de Proteína , Espectrometria de FluorescênciaRESUMO
With regard to the harmful effects of heavy metals on human health and the environment, the demand for synthesis and investigation of macromolecules with large capacity of harmful substances sorption is ever greater. Quantum-chemical methods may be applied in structural modeling, prediction, and characterization of such molecules and reactions. Sorption of metal ions (Cu2+, Cd2+, Co2+, and Ni2+) to triethylenetetramine-functionalized copolymer poly(GMA-co-EGDMA)-teta was successfully modeled by quantum chemical calculations, at the B3LYP//6-311++G**/lanl2dz level. Optimized structures of metal complexes were used for calculation of real binding energy of metal ion within the complex (ΔEr). Solvent and hydrolyzation effects were essential for obtaining the objective values. Solvent effect was included in ΔEr by using the total solvation energy for reaction of formation of tetaOH complex (ΔEs1, the first approach) or by using dehydration energy of free metal ion (ΔEs2, the second approach). Experimental results were confirmed in our theoretical analyses (using the second approach). Graphical abstract Theoretical modeling of divalent metal ions sorption on triethylenetetramine-functionalized copolymer poly(GMA-co-EGDMA)-teta.
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Phycocyanobilin (PCB) is a blue tetrapyrrole chromophore of C-phycocyanin, the main protein of the microalga Spirulina, with numerous proven health-related benefits. We examined binding of PCB to bovine serum albumin (BSA) and how it affects protein and ligand stability. Protein fluorescence quenching and microscale thermophoresis demonstrated high-affinity binding (Ka=2×106M-1). Spectroscopic titration with molecular docking analysis revealed two binding sites on BSA, at the inter-domain cleft and at subdomain IB, while CD spectroscopy indicated stereo-selective binding of the P conformer of the pigment to the protein. The PCB protein complex showed increased thermal stability. Although complex formation partly masked the antioxidant properties of PCB and BSA, a mutually protective effect against free radical-induced oxidation was found. BSA could be suitable for delivery of PCB as a food colorant or bioactive component. Our results also highlight subtle differences between PCB binding to bovine vs. human serum albumin.
Assuntos
Ficobilinas/química , Ficocianina/química , Soroalbumina Bovina/química , Animais , Sítios de Ligação , Bovinos , Humanos , Simulação de Acoplamento Molecular , Ligação Proteica , Espectrometria de FluorescênciaRESUMO
Binding of three ruthenium(ii) compounds of general formula mer-[Ru(L3)(N-N)X][Y] (where L3 = 4'-chloro-2,2':6',2''-terpyridine (Cl-tpy); N-N = 1,2-diaminoethane (en), 1,2-diaminocyclohexane (dach) or 2,2'-bipyridine (bipy); X = Cl; Y = Cl) to human serum albumin (HSA) has been investigated by nano-LC/nano-ESI MS and docking studies. A bottom-up proteomics approach has been applied for the structural characterization of metallated proteins and the data were analyzed in both the positive and negative ion mode. The negative ion mode was achieved after the post-column addition of an isopropanol solution of formaldehyde that enabled sample ionization at micro-flow rates. The negative ion mode MS has been proved to be beneficial for the analysis of binding sites on ruthenated protein in terms of ion charge reduction and consequent simplification of target sequence identification based on isotopic differences between ruthenated and non-ruthenated peptides. Moreover, the negative ion mode ESI MS shows the advantage of singly charged ion formation and, unlike MALDI MS, it does not cause complete ligand fragmentation, merging the benefits of each method into a single experiment. Six target sequences were identified for the binding of en and dach compounds, and four sequences for the binding of bipy. All compounds have been found to bind histidine and one aspartate residue. Docking studies showed that the identified sequences are the constituents of five distinct binding sites for en and dach, or two sites for the bipy complex. The selection of binding sites seems to be dependent on the chelate ligand and the form of the complex prior or after hydrolysis of the leaving chloride ligand.
Assuntos
Angiotensina II/metabolismo , Complexos de Coordenação/metabolismo , Simulação de Acoplamento Molecular , Nanotecnologia/métodos , Rutênio/metabolismo , Albumina Sérica Humana/metabolismo , Espectrometria de Massas por Ionização por Electrospray/métodos , Angiotensina II/química , Sítios de Ligação , Complexos de Coordenação/química , Humanos , Ligação Proteica , Rutênio/química , Albumina Sérica Humana/químicaRESUMO
In this study, we investigated structural aspects of covalent binding of food derived blue pigment phycocyanobilin (PCB) to bovine ß-lactoglobulin (BLG), major whey protein, by spectroscopic, electrophoretic, mass spectrometry and computational methods. At physiological pH (7.2), we found that covalent pigment binding via free cysteine residue is slow (kaâ¯=â¯0.065â¯min-1), of moderate affinity (Kaâ¯=â¯4â¯×â¯104â¯M-1), and stereo-selective. Binding also occurs at a broad pH range and under simulated gastrointestinal conditions. Adduct formation rises with pH, and in concentrated urea (kaâ¯=â¯0.101â¯min-1). The BLG-PCB adduct has slightly altered secondary and tertiary protein structure, and bound PCB has higher fluorescence and more stretched conformation than free chromophore. Combination of steered molecular dynamic for disulfide exchange, non-covalent and covalent docking, favours Cys119 residue in protein calyx as target for covalent BLG-PCB adduct formation. Our results suggest that this adduct can serve as delivery system of bioactive PCB.
Assuntos
Lactoglobulinas/química , Ficobilinas/química , Ficocianina/química , Animais , Sítios de Ligação , Bovinos , Concentração de Íons de Hidrogênio , PigmentaçãoRESUMO
The ratios of E/Z isomers of sixteen synthesized 1,3-dihydro-3-(substituted phenylimino)-2H-indol-2-one were studied using experimental and theoretical methodology. Linear solvation energy relationships (LSER) rationalized solvent influence of the solvent-solute interactions on the UV-Vis absorption maxima shifts (νmax) of both geometrical isomers using the Kamlet-Taft equation. Linear free energy relationships (LFER) in the form of single substituent parameter equation (SSP) was used to analyze substituent effect on pKa, NMR chemical shifts and νmax values. Electron charge density was obtained by the use of Quantum Theory of Atoms in Molecules, i.e. Bader's analysis. The substituent and solvent effect on intramolecular charge transfer (ICT) were interpreted with the aid of time-dependent density functional (TD-DFT) method. Additionally, the results of TD-DFT calculations quantified the efficiency of ICT from the calculated charge-transfer distance (DCT) and amount of transferred charge (QCT). The antimicrobial activity was evaluated using broth microdilution method. 3D QSAR modeling was used to demonstrate the influence of substituents effect as well as molecule geometry on antimicrobial activity.
Assuntos
Anti-Infecciosos/química , Anti-Infecciosos/farmacologia , Isatina/química , Isatina/farmacologia , Bactérias/efeitos dos fármacos , Isomerismo , Espectroscopia de Ressonância Magnética , Testes de Sensibilidade Microbiana , Modelos Moleculares , Relação Quantitativa Estrutura-Atividade , Bases de Schiff , Solventes , Espectrofotometria Ultravioleta , TermodinâmicaRESUMO
Phycocyanobilin (PCB) binds with high affinity (2.2 x 106 M-1 at 25°C) to human serum albumin (HSA) at sites located in IB and IIA subdomains. The aim of this study was to examine effects of PCB binding on protein conformation and stability. Using 300 ns molecular dynamics (MD) simulations, UV-VIS spectrophotometry, CD, FT-IR, spectrofluorimetry, thermal denaturation and susceptibility to trypsin digestion, we studied the effects of PCB binding on the stability and rigidity of HSA, as well as the conformational changes in PCB itself upon binding to the protein. MD simulation results demonstrated that HSA with PCB bound at any of the two sites showed greater rigidity and lower overall and individual domain flexibility compared to free HSA. Experimental data demonstrated an increase in the α-helical content of the protein and thermal and proteolytic stability upon ligand binding. PCB bound to HSA undergoes a conformational change to a more elongated conformation in the binding pockets of HSA. PCB binding to HSA stabilizes the structure of this flexible transport protein, making it more thermostable and resistant to proteolysis. The results from this work explain at molecular level, conformational changes and stabilization of HSA structure upon ligand binding. The resultant increased thermal and proteolytic stability of HSA may provide greater longevity to HSA in plasma.
Assuntos
Simulação de Acoplamento Molecular , Ficobilinas/farmacologia , Ficocianina/farmacologia , Albumina Sérica/química , Sítios de Ligação , Ficobilinas/química , Ficocianina/química , Ligação Proteica , Estabilidade Proteica , Albumina Sérica/metabolismo , Spirulina/químicaRESUMO
Conglutins represent the major peanut allergens and are renowned for their resistance to gastro-intestinal digestion. Our aim was to characterize the digestion-resistant peptides (DRPs) of conglutins by biochemical and biophysical methods followed by a molecular dynamics simulation in order to better understand the molecular basis of food protein allergenicity. We have mapped proteolysis sites at the N- and C-termini and at a limited internal segment, while other potential proteolysis sites remained unaffected. Molecular dynamics simulation showed that proteolysis only occurred in the vibrant regions of the proteins. DRPs appeared to be conformationally stable as intact conglutins. Also, the overall secondary structure and IgE-binding potency of DRPs was comparable to that of intact conglutins. The stability of conglutins toward gastro-intestinal digestion, combined with the conformational stability of the resulting DRPs provide conditions for optimal exposure to the intestinal immune system, providing an explanation for the extraordinary allergenicity of peanut conglutins.