Natércia F. Brás

QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions

Carbohydrates perform a wide range of crucial functions in biological systems and are of great interest for the food and pharmaceutical industries. β-Galactosidase from Escherichia coli catalyzes both the hydrolytic breaking of the very stable glycosidic bond of lactose and a series of transglycosylation reactions. These reactions are crucial for the development of new carbohydrate molecules, as well as the optimization of their syntheses. In this work we have used computational methods to study the catalytic mechanism of hydrolysis and a set of distinct transglycosylation reactions of a retaining galactosidase, with atomic detail, with lactose as the natural substrate. The ONIOM method (BB1K:AMBER//B3LYP:AMBER calculations) was employed to address such a large enzymatic system. Such a methodology can efficiently account for the stereochemistry of the reactive residues, as well as the long-range enzyme-substrate interactions. The possible importance of the magnesium ion in the catalytic reaction was investigated, and it was found that, indeed, the magnesium ion catalyzes the transformation, lowering the activation barrier by 14.9 kcal/mol. The calculations indicate that the formation of β(1-3) glycosidic linkages is thermodynamically very unfavorable. In contrast, the formation of β(1-6) glycosidic bonds is the most favored, in complete agreement with the enantioselectivity observed experimentally. The data also clearly show the importance of the enzyme scaffold beyond the first-shell amino acids in the stabilization of the transition states. It is fundamental to include the enzyme explicitly in computational studies.

Receptor-based virtual screening protocol for drug discovery

Computational aided drug design (CADD) is presently a key component in the process of drug discovery and development as it offers great promise to drastically reduce cost and time requirements. In the pharmaceutical arena, virtual screening is normally regarded as the top CADD tool to screen large libraries of chemical structures and reduce them to a key set of likely drug candidates regarding a specific protein target. This chapter provides a comprehensive overview of the receptor-based virtual screening process and of its importance in the present drug discovery and development paradigm. Following a focused contextualization on the subject, the main stages of a virtual screening campaign, including its strengths and limitations, are the subject of particular attention in this review. In all of these stages special consideration will be given to practical issues that are normally the Achilles heel of the virtual screening process.

Understanding the molecular mechanism of anthocyanin binding to pectin.

Association between anthocyanins and carbohydrates has drawn attention over the past few years and this interaction is of particularly importance in food chemistry since these compounds are often found together in plants and foodstuffs. This work intended to bring insights on the interaction between ionic carbohydrates (pectin) and two anthocyanins (cyanidin-3-O-glucoside, cy3glc and delphinidin-3-O-glucoside, dp3glc). The interaction between the flavylium cation and hemiketal anthocyanin forms was characterized by saturation transfer difference (STD) NMR spectroscopy and the respective dissociation constant (Kd) was obtained. This binding was also studied by Molecular Dynamics simulation. In the presence of the anthocyanin hemiketal form a weak interaction between anthocyanins and pectin seems to occur. A variation in the extent of this interaction was also noticed for the two anthocyanins with dp3glc bearing three hydroxyl groups, revealing to be a stronger binder to pectin (Kd ≈ 180 μM for dp3glc and Kd ≈ 250 μM for cy3glc). Experiments performed at acidic pH (flavylium cation) revealed a much stronger interaction (Kd ≈ 2 μM). These experimental results were also supported by theoretical studies which also revealed a stronger interaction in the presence of the anthocyanin flavylium cation and also a stronger interaction between pectin and dp3glc than with cy3glc (for the hemiketal form).

Mechanistic studies on the formation of glycosidase‐substrate and glycosidase‐inhibitor covalent intermediates

Glycoside hydrolases catalyze the breaking of the glycosidic bond. This type of bond fashioned between two monosaccharides is very stable, and the polymers created are involved in multiple cellular processes, being crucial to life. In this article, computational methods were used to study the first step of the mechanism of reaction of retaining glycoside hydrolases in atomic detail. The systems modeled included a simplified reaction center and a small substrate/inhibitor. Using DFT calculations we were able to corroborate and provide molecular‐level detail to the dissociative mechanism proposed in the literature. The role of the hydrogen bridge between the nucleophile and the C2OH group of the ring was also investigated. Therefore, we concluded that this bridge is responsible for lowering the activation barrier by 5.1 kcal mol−1 with functional BB1K/6‐311+G(2d,2p), and the absence of the bridge explains, at least in part, the inhibitory effect of fluoro‐substituted glycosides in the −2 position. The hydrogen bridge could also be involved in favoring the ring distortion verified in the transition state, and the dissociative character of the reaction mechanism. Using the NBO method, point atomic charges were calculated. In the transition state, the positive charge generated in the sugar ring is distributed nearly equally between the anomeric carbon and the ring oxygen, through a partial double bond involving the two atoms.

Molecular determinants of ligand specificity in family 11 carbohydrate binding modules – an NMR, X‐ray crystallography and computational chemistry approach

The direct conversion of plant cell wall polysaccharides into soluble sugars is one of the most important reactions on earth, and is performed by certain microorganisms such as Clostridium thermocellum (Ct). These organisms produce extracellular multi‐subunit complexes (i.e. cellulosomes) comprising a consortium of enzymes, which contain noncatalytic carbohydrate‐binding modules (CBM) that increase the activity of the catalytic module. In the present study, we describe a combined approach by X‐ray crystallography, NMR and computational chemistry that aimed to gain further insight into the binding mode of different carbohydrates (cellobiose, cellotetraose and cellohexaose) to the binding pocket of the family 11 CBM. The crystal structure of C. thermocellum CBM11 has been resolved to 1.98 Å in the apo form. Since the structure with a bound substrate could not be obtained, computational studies with cellobiose, cellotetraose and cellohexaose were carried out to determine the molecular recognition of glucose polymers by CtCBM11. These studies revealed a specificity area at the CtCBM11 binding cleft, which is lined with several aspartate residues. In addition, a cluster of aromatic residues was found to be important for guiding and packing of the polysaccharide. The binding cleft of CtCBM11 interacts more strongly with the central glucose units of cellotetraose and cellohexaose, mainly through interactions with the sugar units at positions 2 and 6. This model of binding is supported by saturation transfer difference NMR experiments and linebroadening NMR studies.

Structural Features of Copigmentation of Oenin with Different Polyphenol Copigments

The copigmentation binding constants (K) for the interaction of different copigments with oenin (major red wine anthocyanin) were determined. All tests were performed in a 12% ethanol citrate buffer solution (0.2 M) at pH 3.5, with an ionic strength adjusted to 0.5 M by the addition of sodium chloride. Over the past years, several copigmentation studies were made and many copigments were tested, but none of them included prodelphinidin B3 or a dimeric-type adduct like oenin-(O)-catechin, probably due to the difficulty in obtaining them. The data yielded from this study allowed concluding that (a) the presence of a pyrogallol group in the B ring of the flavan-3-ol structure slightly increases the copimentation potential and (b) within all copigments tested oenin-(O)-catechin was revealed to be the best. According to computational studies performed on epicatechin/oenin, epigallocatechin/oenin, procyanidin B3/oenin, and oenin-(O)-catechin/oenin complexes, the ΔGbinding energy of the oenin-(O)-catechin/oenin complex is the most negative compared to the other copigmentation complexes, hence being more stable and thermodynamically favored. All structural data show that oenin-(O)-catechin and epigallocatechin are closer to the pigment molecule, which is in accordance with these two copigments having the highest experimental copigmentation binding constants for oenin.

Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains

The ionization states of amino acids influence the structure, function, stability, solubility, and reactivity of proteins and are difficult to determine unambiguously by experimental means. Thus, it is very important to be able to determine them theoretically and with high reliability. We have analyzed how well DFT functionals, often used to characterize complex and large models such as proteins, describe the zero-point-exclusive proton affinity at 0 K, PAel0K, for the ionizable side chains of lysine (Lys), histidine (His), arginine (Arg), and aspartate (Asp–) as well as the cysteine (Cys–), serine (Ser–), and tyrosine (Tyr–) anions. The reference values PAel0K were determined at the very accurate CCSD(T)/CBS level. Those values were obtained by the sum of the complete basis set limit of the MP2 energies plus a CCSD(T) correction term evaluated with the aug-cc-pVTZ basis set. The complete basis set limit of MP2 energies was determined using the Truhlar and Helgaker extrapolation schemes. A new, important,...

Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Quantum mechanics/molecular mechanics (QM/MM) methods offer a very appealing option for the computational study of enzymatic reaction mechanisms, by separating the problem into two parts that can be treated with different computational methods. Hence, in a QM/MM formalism, the part of the system in which catalysis actually occurs and that involves the active site, substrates and directly participating amino acid residues is treated at an adequate quantum mechanical level to describe the chemistry taking place. For the remaining of the enzyme, which does not participate directly in the reaction, but that typically involves a much larger number of atoms, molecular mechanics is employed, traditionally through the application of a biomolecular force field. When applied with care, QM/MM methods can be used with great advantage in comparing, at a structural and energetic level, different mechanistic proposals, discarding mechanistic alternatives and proposing new mechanistic pathways that are consistent with the available experimental data. With time, diverse flavors within the QM/MM methods have emerged, differing in a variety of technical and conceptual aspects. Hence present alternatives differ between additive and subtractive QM/MM schemes, the type of boundary schemes, and the way in which the electrostatic interactions between the two regions are accounted for. Also, single‐conformation QM/MM, multi‐PES approaches, and QM/MM Molecular Dynamics coexist today, each type with its own advantages and limitations. This review focuses on the application of QM/MM methods in the study of enzymatic reaction mechanisms, briefly presenting also the most important technical aspects involved in these calculations. Particular attention is dedicated to the application of the single‐conformation QM/MM, multi‐PES QM/MM studies, and QM/MM‐FEP methods and to the advantages and disadvantages of the different types of QM/MM. Recent breakthroughs are also introduced. A selection of hand‐picked examples is used to illustrate such features. WIREs Comput Mol Sci 2017, 7:e1281. doi: 10.1002/wcms.1281

Understanding the binding of procyanidins to pancreatic elastase by experimental and computational methods.

Human diets are rich in secondary metabolites such as polyphenols. These compounds perform a wide range of crucial functions in biological systems and are of great interest for the pharmaceutical and food industries. In this work, the binding mode of the natural polyphenolic compounds from grape seed on the porcine pancreatic elastase surface was studied by experimental and computational methods. Fluorescence quenching, circular dichroism, nephelometry, dynamic light scattering (DLS), molecular docking, and molecular dynamics simulation studies were performed. A decrease in fluorescence intensities was observed with addition of increasing polyphenol concentrations. The order of binding ability obtained was oligomeric fraction of procyanidins (OFP) > tetramer > trimer > dimer B3 procyanidins. Thus a relationship between higher molecular weight and binding ability was observed. The interaction between these molecules and the enzyme occurs by a static mechanism, as inferred from the high apparent fluorescence and bimolecular quenching constants. A blue shift in the maximal emission wavelength could be seen, which indicates that the tryptophan residues acquire a more hydrophobic character upon procyanidin binding. Molecular docking and dynamics simulations also demonstrate that the SASA (solvent-accessible surface area) values of tryptophans decrease with the binding of these compounds, preventing the accessibility of water molecules, which agrees with the referred blue shift. Circular dichroism studies indicate a decrease in alpha-helix content, followed by an increase in the beta-sheet component of secondary structures of this enzyme. DLS and nephelometry techniques also indicate a relationship between large procyanidins and aggregate formation ability.

Experimental and Theoretical Data on the Mechanism by Which Red Wine Anthocyanins Are Transported through a Human MKN-28 Gastric Cell Model

The gastric absorption of red wine anthocyanins was evaluated using a gastric MKN-28 cell barrier model. Anthocyanin transport was not affected by the presence of 4% ethanol and decreased with the increase of pH. Gastric cells pretreated with anthocyanins were found to increase anthocyanin transport. The presence of d-(+)-glucose was found to decrease anthocyanin uptake, suggesting the involvement of glucose transporters. RT-PCR assays revealed that GLUT1, GLUT3, and MCT1 transporters were expressed in MKN-28 cells. Computational studies were performed to provide a structural characterization of the binding site of hGLUT1 to glucose or different anthocyanins under different forms. Docking results demonstrated that anthocyanins can bind to glucose transporters from both intracellular and extracellular sides. Anthocyanins seem to enter into the transporter by two main conformations: B ring or glucose. From MD simulations, hGLUT1 was found to form complexes with all anthocyanins tested in the different protonation states.