Redox-Mediated Amination of Pyrogallol-Based Polyphenols

Flavonoids are known to covalently modify amyloidogenic peptides by amination reactions. The underlying coupling process between polyphenols and N-nucleophiles is assessed by several in vitro and in silico approaches. The coupling reaction involves a sequence of oxidative dearomatization, amination, and reductive amination (ODARA) reaction steps. The C6-regioselectivity of the product is confirmed by crystallographic analysis. Under aqueous conditions, the reaction of baicalein with lysine derivatives yields C-N coupling as well as hydrolysis products of transient imine intermediates. The observed C-N coupling reactions work best for flavonoids combining a pyrogallol substructure with an electron-withdrawing group attached to the C4a-position. Thermodynamic properties such as bond dissociation energies also highlight the key role of pyrogallol units for the antioxidant ability. Combining the computed electronic properties and in vitro antioxidant assays suggests that the studied pyrogallol-containing flavonoids act by various radical-scavenging mechanisms working in synergy. Multivariate analysis indicates that a small number of descriptors for transient intermediates of the ODARA process generates a model with excellent performance (r=0.93) for the prediction of cross-coupling yields. The same model has been employed to predict novel antioxidant flavonoid-based molecules as potential covalent inhibitors, opening a new avenue to the design of therapeutically relevant anti-amyloid compounds.

Design, synthesis, and anticancer activity of some novel 1H-benzo[d]imidazole-5-carboxamide derivatives as fatty acid synthase inhibitors

Multiple malignancies exhibit aberrant FASN expression, associated with enhanced de novo lipogenesis to meet the metabolic demands of rapidly proliferating tumour cells. Furthermore, elevated FASN expression has been linked to tumour aggressiveness and poor prognosis in a variety of malignant tumours, making FASN is an attractive target for anticancer drug discovery. Herein, we report the de novo design and synthesis of (2-(2-hydroxyphenyl)-1H-benzo[d]imidazol-5-yl)(piperazin-1-yl)methanone derivatives as novel FASN inhibitors with potential therapeutic applications in breast and colorectal cancers. Twelve (2-(2-hydroxyphenyl)-1H-benzo[d]imidazol-5-yl)(piperazin-1-yl)methanone derivatives (CTL) were synthesized and evaluated for FASN inhibition and cytotoxicity against colon cancer (HCT-116, Caco-2 cell lines), breast cancer (MCF-7 cell line) and normal cell line (HEK-293). Compounds CTL-06 and CTL-12 were chosen as the most promising lead molecules based on FASN inhibition and selective cytotoxicity profiles against colon and breast cancer cell lines. Compounds CTL-06 and CTL-12 demonstrate promising FASN inhibitory activity at IC50 of 3 ± 0.25 µM and 2.5 ± 0.25 µM when compared to the FASN inhibitor orlistat, which has an IC50 of 13.5 ± 1.0 µM. Mechanistic investigations on HCT-116 revealed that CTL-06 and CTL-12 treatment led to cell cycle arrest in Sub-G1/S phase along with apoptosis induction. Western blot studies indicated that CTL-06 and CTL-12 inhibited FASN expression in a dose-dependent manner. CTL-06 and CTL-12 treatment of HCT-116 cells enhanced caspase-9 expression in a dose-dependent manner, while upregulating proapoptotic marker Bax and downregulating antiapoptotic Bcl-xL. Molecular docking experiments of CTL-06 and CTL-12 with FASN enzyme revealed the mode of binding of these analogues in the KR domain of the enzyme.

In silico guided designing of optimized benzochalcones derivatives as potent CYP1B1 inhibitors: An integrated in vitro and ONIOM study

Cytochrome P4501B1 (CYP1B1) is reported to be overexpressed in various malignancies including ovarian, lung, lymph, and breast cancers. The overexpression of this enzyme is accountable for the biotransformation-based inactivation of some anti-cancer drugs i.e. Docetaxel, Paclitaxel, and Cisplatin. To circumvent solutions to this issue, the current study reports some optimized derivatives of benzochalcone as selective CYP1B1 inhibitors. The optimized derivatives were screened using some structure-based drug-designing approaches including molecular docking and molecular dynamics. The implemented approaches revealed that all the designed molecules demonstrated not only essential interactions with key amino acid residues but also maintained stability within the active site of CYP1B1. Furthermore, to validate the in-silico results and develop a SAR, the designed molecules were subsequently synthesized and tested for their ability to selectively inhibit CYP1B1 over CYP1A1 using well established EROD assay. This assay results suggested that compounds 1(c), 1(d), and 1(e) are eightfold more selective CYP1B1 inhibitors over CYP1A1 with IC₅₀ values ranging from 0.06 to 0.09 μM respectively. Among these, compound 1(d) manifested potent inhibitory activity i.e. IC₅₀ of 0.06 μM with 24 folds selectivity over 1A1. To have a better insight into the binding pattern of 1(d) within CYP1B1 and precisely compute binding affinity for 1(d)-CYP1B1 complex, one of the advanced QM/MM approaches i.e. ONIOM has been implemented. Where 1(d)-CYP1B1 complex conferred comparable binding affinity in terms of ΔG (kcal/mol) with that of ANF-CYP1B1 complex. This research could provide a suitable starting point for the development of more potent multi-functional compounds with CYP1B1 inhibitory activity.

Plant derived active compounds as potential anti SARS-CoV-2 agents: an in-silico study

Plants are a valued potential source of drugs for a variety of diseases and are often considered less toxic to humans. We investigated antiviral compounds that may potentially target SARS-CoV-2 antigenic spike (S) and host proteins; angiotensin-converting enzyme2 (ACE2), and transmembrane serine protease2 (TMPRSS2). We scrutinized 36 phytochemicals from 15 Indian medicinal plants known to be effective against RNA viruses via molecular docking. Besides, the TMPRSS2 structure was modeled and validated using the SWISS-MODEL. Docking was performed using Autodock Vina and 4.2 followed by visualization of the docking poses on Pymol version 2.4.0 and Discovery Studio Visualizer. Molecular docking showed that 12 out of 36 active compounds interacted efficiently with S, ACE2, and TMPRSS2 proteins. The ADMET profile generated using the swissADME and pkCSM server revealed that these compounds were possessed druggable properties. The Amber 12 simulation package was used to carry out energy minimizations and molecular dynamics (MD) simulations. The total simulation time for both S protein: WFA and S protein: WND complexes was 300 ns (100 ns per replica). A total of 120 structures were extracted from the last 60 ns of each MD simulation for further analysis. MM-PBSA and MM-GBSA were employed to assess the binding energy of each ligand and the receptor-binding domain of the viral S-protein. The methods suggested that WND and WFA showed thermodynamically favorable binding energies, and the S protein had a higher affinity with WND. Interestingly, Leu455 hotspot residue in the S protein, also predicted to participate in binding with ACE2, was engaged by WND and WFA. HighlightsPlants' natural active compounds may aid in the development of COVID-19 therapeutics.MD simulation study revealed stable binding of withanolide D and withaferin A with spike proteinWithanolide D and withaferin A could be effective against SARS-CoV-2 spike protein.Discovery of druggable agents that have less or lack of binding affinity with ACE2 to avoid the organs associated with comorbidities.According to ADMET selected phytochemicals may be used as druggable compounds.Communicated by Ramaswamy H. Sarma.

Intermolecular Copigmentation Between Delphinidin 3-O-Glucoside and Chlorogenic Acid: Taking into Account the Existence of Neutral and Negatively Charged Forms of the Copigment

Stopped flow corroborated by UV-vis measurements allowed for the calculation of the copigmentation constants of delphinidin 3-O-glucoside with the neutral (CP) and negatively charged CP(-) forms of chlorogenic acid. Solutions of delphinidin 3-O-glucoside in the absence and presence of the copigment were equilibrated at several pH values in the acidic region, pH < 6, and reverse pH jumps monitored by stopped flow were carried out by adding sufficient acid to give flavylium cation at pH ≤ 1. This procedure allows for the separation of three contributions: (i) all flavylium cation and quinoidal base species, (ii) all hemiketal species, and (iii) all cis-chalcone species. Reverse pH jumps can also be performed at fixed pH versus copigment addition. The contribution of trans-chalcone, minor species in the present system, requires reverse pH jumps from the equilibrium followed by a common spectrophotometer. The system was also studied by UV-vis as a function of the copigment addition at different pH values. A global fitting of all experimental data allowed for determination of the copigmentation constants with flavylium cation, K_AH⁺CP = 167 M^-1, K_AH⁺CP(-) = 338 M^-1; and quinoidal base, K_ACP = 1041 M^-1, K_ACP(-)= 221 M^-1. No significant copigmentation was observed for hemiketal and chalcones. Computational calculations confirm different geometries for the interactions of flavylium cation and quinoidal base with the neutral or the negatively charged forms of the copigment as well as predict identical relative order for the binding energies of the four adducts.

Epigenetic Anti‐Cancer Treatment With a Stabilized Carbocyclic Decitabine Analogue

5‐Aza‐2’‐deoxycytidine (Decitabine, AzadC) is a nucleoside analogue, which is in clinical use to treat patients with myelodysplastic syndrome or acute myeloid leukemia. Its mode of action is unusual because the compound is one of the few drugs that act at the epigenetic level of the genetic code. AzadC is incorporated as an antimetabolite into the genome and creates covalent, inhibitory links to DNA methyltransferases (DNMTs) that methylate 2’‐deoxycytidine (dC) to 5‐methyl‐dC (mdC). Consequently, AzadC treatment leads to a global loss of mdC, which presumably results in a reactivation of silenced genes, among them tumor suppressor and DNA damage response genes. Because AzadC suffers from severe instability, which limits its use in the clinic, a more sophisticated AzadC derivative would be highly valuable. Here, we report that a recently developed carbocyclic AzadC analogue (cAzadC) blocks DNMT1 in the AML cell line MOLM‐13 as efficient as AzadC. Moreover, cAzadC has a surprisingly strong anti‐proliferative effect and leads to a significantly higher number of double strand breaks compared to AzadC, while showing less off‐target toxicity. These results show that cAzadC triggers more deleterious repair and apoptotic pathways in cancer cells than AzadC, which makes cAzadC a promising next generation epigenetic drug.

Structure based virtual screening of natural product molecules as glycosidase inhibitors

Objective of the present investigation comprised of the application of in silico methods to discover novel natural product (NP) based potential inhibitors for carbohydrate mediated diseases. Structure based drug design studies (molecular docking and structure based pharmacophore analysis)  were carried out on a series of natural product compounds to identify significant bioactive molecules to inhibit α-mannosidase (I and II) and β-galactosidase enzymes. Furthermore, protein ligand interaction fingerprint analysis, molecular dynamics simulations and molecular access system (MACCS) fingerprint analysis were performed to understand the binding behaviors of the studied molecules. The results derived from these analyses showed that the identified compounds exhibit significant binding interactions with the active site residues. The compounds, NP-51, NP-81 and NP-165 have shown significant docking score against the studied enzymes (α-mannosidases-I, α-mannosidases-II and β-galactosidases). The fingerprint studies showed that the presence of rings (aromatic or aliphatic) with sulfur atoms, nitrogen atoms, methyl groups, etc. have favorable effects on the α-mannosidase II inhibitory activity. However, the presence of halogen atoms substituted in the molecules have reduced inhibitory ability against α-mannosidase II. The compound, NP-165 has significant activity against both enzymes (α-mannosidases and β-galactosidases). These studies accomplished that the compounds identified through in silico methodologies can be used to develop semisynthetic derivatives of the glycosidase inhibitors and can be screened for the treatment of different carbohydrate mediated diseases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-021-00115-9.

Anthocyanin-Related Pigments: Natural Allies for Skin Health Maintenance and Protection

Human skin is commonly described as a particularly dynamic and complex environment, with a physiological balance continuously orchestrated by numerous internal and external factors. Intrinsic aging, exposure to UV radiation and skin pathogens are some of the key players that account for dermatological alterations and ailments. In this regard, this study intended to explore the potential skin-health beneficial properties of a group of molecules belonging to the anthocyanin family: cyanidin- and malvidin-3-O-glucosides and some of their structurally related pigments, resulting in a library of compounds with different structural properties and color hues. The inclusion of both purified compounds and crude extracts provided some insights into their distinctive effects when tested as individual agents or as part of multicomponent mixtures. Overall, most of the compounds were found to reduce biofilm production by S. aureus and P. aeruginosa reference strains, exhibit UV-filter capacity, attenuate the production of reactive oxygen species in human skin keratinocytes and fibroblasts and also showed inhibitory activity of skin-degrading enzymes, in the absence of cytotoxic effects. Carboxypyranocyanidin-3-O-glucoside stood out for its global performance which, combined with its greater structural stability, makes this a particular interesting compound for potential incorporation in topical formulations. Results provide strong evidence of the skin protective effects of these pigments, supporting their further application for cosmeceutical purposes.

The Role of Anthocyanins, Deoxyanthocyanins and Pyranoanthocyanins on the Modulation of Tyrosinase Activity: An In Vitro and In Silico Approach

Tyrosinase is the central enzyme involved in the highly complex process of melanin formation, catalyzing the rate-limiting steps of this biosynthetic pathway. Due to such a preponderant role, it has become a major target in the treatment of undesired skin pigmentation conditions and also in the prevention of enzymatic food browning. Numerous phenolic-based structures from natural sources have been pointed out as potential tyrosinase inhibitors, including anthocyanins. The aim of the present study was to individually assess the tyrosinase inhibitory activity of eight purified compounds with a variable degree of structural complexity: native anthocyanins, deoxyanthocyanins, and pyranoanthocyanins. The latter two, the groups of anthocyanin-related compounds with enhanced stability, were tested for the first time. Compounds 1 to 4 (luteolinidin, deoxymalvidin, cyanidin-, and malvidin-3-O-glucoside) revealed to be the most effective inhibitors, and further kinetic studies suggested their inhibition mechanism to be of a competitive nature. Structure–activity relationships were proposed based on molecular docking studies conducted with mushroom tyrosinase (mTYR) and human tyrosinase-related protein 1 (hTYRP1) crystal structures, providing information about the binding affinity and the different types of interactions established with the enzyme’s active center which corroborated the findings of the inhibition and kinetic studies. Overall, these results support the applicability of these compounds as pigmentation modulators.

Combined in silico and in vitro studies to identify novel antidiabetic flavonoids targeting glycogen phosphorylase

Novel pharmacological strategies for the treatment of diabetic patients are now focusing on inhibiting glycogenolysis steps. In this regard, glycogen phosphorylase (GP) is a validated target for the discovery of innovative antihyperglycemic molecules. Natural products, and in particular flavonoids, have been reported as potent inhibitors of GP at the cellular level. Herein, free-energy calculations and microscale thermophoresis approaches were performed to get an in-depth assessment of the binding affinities and elucidate intermolecular interactions of several flavonoids at the inhibitor site of GP. To our knowledge, this is the first study indicating genistein, 8-prenylgenistein, apigenin, 8-prenylapigenin, 8-prenylnaringenin, galangin and valoneic acid dilactone as natural molecules with high inhibitory potency toward GP. We identified: i) the residues Phe285, Tyr613, Glu382 and/or Arg770 as the most relevant for the binding of the best flavonoids to the inhibitor site of GP, and ii) the 5-OH, 7-OH, 8-prenyl substitutions in ring A and the 4'-OH insertion in ring B to favor flavonoid binding at this site. Our results are invaluable to plan further structural modifications through organic synthesis approaches and develop more effective pharmaceuticals for Type 2 Diabetes treatment, and serve as the starting point for the exploration of food products for therapeutic usage, as well as for the development of novel bio-functional food and dietary supplements/herbal medicines.

Cell Wall Mannoproteins from Yeast Affect Salivary Protein-Flavanol Interactions through Different Molecular Mechanisms

It is known that interactions between wine flavanols and salivary proline-rich proteins (PRPs) are one of the main factors responsible for wine astringency. The addition of commercial yeast mannoproteins (MPs) to wines has been pointed to as a possible tool to modulate the excessive astringency due to a lack of phenolic maturity at harvest time that might occur as a consequence of global climate change. The aim of this work was to study by isothermal titration calorimetry and molecular dynamics simulation the molecular mechanisms by which mannoproteins could modulate astringency elicited by tannins and if it can be influenced by mannoprotein composition. Results obtained indicate that the MPs assayed had an important impact on astringency through the formation of ternary aggregates with different solubilities or by preventing the flavanol-PRP interaction by a competitive mechanism, although in a different strength, depending on the size and the compositional characteristic of the mannoprotein.

Anthocyanins as Antidiabetic Agents-In Vitro and In Silico Approaches of Preventive and Therapeutic Effects

Many efforts have been made in the past two decades into the search for novel natural and less-toxic anti-diabetic agents. Some clinical trials have assigned this ability to anthocyanins, although different factors like the food source, the amount ingested, the matrix effect and the time of consumption (before or after a meal) seem to result in contradictory conclusions. The possible mechanisms involved in these preventive or therapeutic effects will be discussed-giving emphasis to the latest in vitro and in silico approaches. Therapeutic strategies to counteract metabolic alterations related to hyperglycemia and Type 2 Diabetes Mellitus (T2DM) may include: (a) Inhibition of carbohydrate-metabolizing enzymes; (b) reduction of glucose transporters expression or activity; (c) inhibition of glycogenolysis and (d) modulation of gut microbiota by anthocyanin breakdown products. These strategies may be achieved through administration of individual anthocyanins or by functional foods containing complexes of anthocyanin:carbohydrate:protein.

A multi-spectroscopic study on the interaction of food polyphenols with a bioactive gluten peptide: From chemistry to biological implications

This study aims to exploit the molecular and cellular mechanisms concerning the functionality of dietary polyphenols (catechin, procyanidin B3, procyanidin C2, epigallocatechin and epigallocatechin gallate) in a nutritional context to prevent Celiac Disease (CD). In that sense, the interaction between the main CD bioactive peptide (32-mer peptide) and some polyphenols was fully characterized at the intestinal level under near physiological conditions by means of different spectroscopic techniques and dynamic simulations. Accordingly, it is proposed that the primarily polyphenol-binding sites on the 32-mer peptide correspond to leucine, tyrosine and phenylalanine containing domains being this interaction entropy-driven. Although procyanidin B3 and trimer C2 had a similar low-affinity constant at 310 K, both procyanidins were able to reduce the 32-mer peptide apical-to-basolateral translocation in in vitro simulated intestinal epithelial barrier thus prospecting the occurrence of additional and still unexplored regulatory mechanisms by which dietary polyphenols might modulate the transepithelial transport of CD bioactive peptides.

A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones

The potential of hydroxypyridinones for in vivo iron sequestration, in both biological and medical contexts, has been extensively discussed in the literature. Different chelators can be designed, with distinct lipophilicities that should alter their cell permeability, distribution, and rates of metabolism. However, for effective iron scavenging in biological systems, the redox potential and binding affinity of iron must fall within a proper range. Our objective was to assess the impact of different hydroxypyridinone chelators in 3:1 iron(III) complexes through comparison of these thermodynamic properties. For that purpose, we employed a cluster-continuum approach using density functional theory, on a dataset of 25 iron complexes. Whenever possible, our results were compared with experimental stability constants (log β) and with electrode potentials. We observed a good qualitative agreement between computed free energies of binding and log β values. In addition, we described which substitutions to the 3-hydroxypyridin-4-one ring should not markedly affect the redox properties and metal ion affinity considering iron. Graphical abstract Iron complexes of hydroxypyridinones.

Determining the glycation site specificity of human holo-transferrin

Understanding the effect of glycation on the function of transferrin, the systemic iron transporter, is fundamental to fully grasp the mechanisms leading to the loss of iron homeostasis observed in diabetes mellitus (DM). The spontaneous reaction with protein amino groups is one of the main causes of glucose toxicity, but the site specificity of this reaction is still poorly understood. Here in, an in vitro approach was used to study human holo-transferrin glycation in detail. Lysine residues 103, 312 and 380 proved to be the most reactive sites, and overall glycation specificity was found to be remarkably different from that described for apo-transferrin. A computational biochemistry approach was subsequently applied to rationalize lysine reactivity. Even though pK_a values, solvent accessible surface area, hydrogen bonds or the presence of nearby charged/polar residues could be related to lysine reactivity, these parameters do not suffice to describe glycation site specificity in holo-transferrin. Furthermore, analysis of the most reactive residues suggests that the correct lysine side chain orientation may play a fundamental role in reactivity. Nevertheless, in holo-transferrin, glycation occurs away from the iron-binding sites and, despite the observed iron release, the modification of apo-transferrin should play a more relevant role for the loss of iron-binding capacity observed in the blood serum of DM patients.

Molecular insights on the interaction and preventive potential of epigallocatechin-3-gallate in Celiac Disease

Celiac Disease (CD) is now recognized as a worldwide epidemic. Although a gluten free diet usually induces clinical improvements within days or weeks, adhering to this routine is still troublesome. Therefore, new solutions are needed for quality-of-life improvement of CD patients. The present work intends to bring molecular and thermodynamic insights on the ability of green tea epigalhocatechin-3-gallate (EGCG) to interact and modulate the bioavailability of a major CD immunodominant peptide (32-mer). Characterization of peptide binding was assessed by means of both 1D and 2D ¹H NMR experiments, ITC and Molecular Dynamics simulations. Accordingly, EGCG not only exhibits a high reactivity towards the 32-mer peptide as its binding appears to be entropy-driven and involves two sequential binding events, each with different binding strengths. Structural rearrangements were also detected during the interaction, contributing to a greater stability of the formed complexes. In vitro transepithelial transport assays using a Caco-2 cell line model were also performed and highlighted the ability of EGCG to significantly reduce the concentration of free peptide in the basolateral compartment. Overall, this study provides important evidences regarding the structural features and molecular mechanisms by which EGCG could interact and potentially modulate the function of some bioactive CD peptides.

Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

Human α-phosphoglucomutase 1 (α-PGM) catalyzes the isomerization of glucose-1-phosphate into glucose-6-phosphate (G6P) through two sequential phosphoryl transfer steps with a glucose-1,6-bisphosphate (G16P) intermediate. Given that the release of G6P in the gluconeogenesis raises the glucose output levels, α-PGM represents a tempting pharmacological target for type 2 diabetes. Here, we provide the first theoretical study of the catalytic mechanism of human α-PGM. We performed transition-path sampling simulations to unveil the atomic details of the two catalytic chemical steps, which could be key for developing transition state (TS) analogue molecules with inhibitory properties. Our calculations revealed that both steps proceed through a concerted S_N 2-like mechanism, with a loose metaphosphate-like TS. Even though experimental data suggests that the two steps are identical, we observed noticeable differences: 1) the transition state ensemble has a well-defined TS region and a late TS for the second step, and 2) larger coordinated protein motions are required to reach the TS of the second step. We have identified key residues (Arg23, Ser117, His118, Lys389), and the Mg²⁺ ion that contribute in different ways to the reaction coordinate. Accelerated molecular dynamics simulations suggest that the G16P intermediate may reorient without leaving the enzymatic binding pocket, through significant conformational rearrangements of the G16P and of specific loop regions of the human α-PGM.

Membrane partition of bis-(3-hydroxy-4-pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations

The class of 3-hydroxy-4-pyridinone ligands is widely known and valuable for biomedical and pharmaceutical purposes. Their chelating properties towards biologically-relevant transition metal ions highlight their potential biomedical utility. A set of 3-hydroxy-4-pyridinone Zn(ii) complexes at different concentrations was studied for their ability to interact with lipid phases. We employed umbrella sampling simulations to attain the potential-of-mean force for a set of ligands and one Zn(ii) complex, as these permeated a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) hydrated bilayer system. In addition, we used conventional molecular dynamics simulations to study the behavior of various Zn(ii) complexes in hydrated bilayer systems. This work discusses: (i) the partition of 3-hydroxy-4-pyridinone ligands to bilayer phases; (ii) self-aggregation in crowded environments of Zn(ii) complexes; and (iii) possible mechanisms for the membrane translocation of Zn(ii) complexes. We observed distinct interactions for the studied complexes, and distinct membrane partition coefficients (K_mem) depending on the considered ligand. The more hydrophobic ligand, 1-hexyl-3-hydroxy-2-methyl-4(1H)-pyridinone, partitioned more favorably to lipid phases (at least two orders of magnitude higher K_mem when compared to the other ligands), and the corresponding Zn(ii) complex was also prone to self-aggregation when an increased concentration of the complex was employed. We also observed that the inclusion of a coordinated water molecule in the parameterization of the Zn(ii) coordination sphere, as proposed in the available crystallographic structure of the complex, decreased the partition coefficient and membrane permeability for the tested complex.

The membrane partition of hydroxypyridinones and of zinc complexes explored by molecular dynamics.

Reactivity of Cork Extracts with (+)-Catechin and Malvidin-3-O-glucoside in Wine Model Solutions: Identification of a New Family of Ellagitannin-Derived Compounds (Corklins)

The aim of this study was to evaluate the reactivity of phenolic compounds extracted from cork stoppers to wine model solutions with two major wine components, namely, (+)-catechin and malvidin-3-O-glucoside. Besides the formation of some compounds already described in the literature, these reactions also yielded a new family of ellagitannin-derived compounds, named herein as corklins. This new family of compounds that were found to result from the interaction between ellagitannins in alcoholic solutions and (+)-catechin were structurally characterized by mass spectroscopy, nuclear magnetic resonance, and computational methods.

Interaction between Wine Phenolic Acids and Salivary Proteins by Saturation-Transfer Difference Nuclear Magnetic Resonance Spectroscopy (STD-NMR) and Molecular Dynamics Simulations

The interaction between phenolic compounds and salivary proteins is highly related to the astringency perception. Recently, it has been proven the existence of synergisms on the perceived astringency when phenolic acids were tested as mixtures in comparison to individual compounds, maintaining constant the total amount of the stimulus. The interactions between wine phenolic acids and the peptide fragment IB7₁₂ have been studied by saturation-transfer difference (STD) NMR spectroscopy. This technique provided the dissociation constants and the percentage of interaction between both individual and mixtures of hydroxybenzoic and hydroxycinnamic acids and the model peptide. It is noteworthy that hydroxybenzoic acids showed higher affinity for the peptide than hydroxycinnamic acids. To obtain further insights into the mechanisms of interaction, molecular dynamics simulations have been performed. Results obtained not only showed the ability of these compounds to interact with salivary proteins but also may justify the synergistic effect observed in previous sensory studies.

Molecular Approach to the Synergistic Effect on Astringency Elicited by Mixtures of Flavanols

The interactions between salivary proteins and wine flavanols (catechin, epicatechin, and mixtures thereof) have been studied by HPLC-DAD, isothermal titration microcalorimetry, and molecular dynamics simulations. Chromatographic results suggest that the presence of these flavanol mixtures could facilitate the formation of precipitates to the detriment of soluble aggregates. Comparison between the thermodynamic parameters obtained showed remarkably higher negative values of ΔG in the system containing the mixture of both flavanols in comparison to the systems containing individual flavanols, indicating a more favorable scenario in the mixing system. Also, the apparent binding constants were higher in this system. Furthermore, molecular dynamics simulations suggested a faster and greater cooperative binding of catechin and epicatechin to IB7₁₄ peptides when both types of flavanols are present simultaneously in solution.

Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations

3-O-Sulfotransferase (3-OST) is one of the enzymes involved in heparan sulfate (HS) biosynthesis. HSs are polysaccharides with variable patterns of sulfation and acetylation that serve as entry receptors for herpes simplex virus type 1 (HSV-1). 3-OST is responsible for the transfer of a sulfate group from 3'-phosphoadenosine-5'-phosphosulfate (PAPS) to glucosamine units of HS. In this work, the catalytic mechanism of 3-OST was studied with atomic detail, using computational methods. We investigated the protonation state of key residues using the H++ web-based pKa prediction tool and molecular dynamics (MD) simulations and estimated the most relevant protonation state of the catalytic residues during catalysis. Catalytic histidine (His186) is predominantly protonated, while catalytic aspartate and glutamate (Asp189 and Glu184) are predominantly deprotonated. Subsequently, to study the catalytic mechanism, we applied a QM/MM method at the ONIOM(B3LYP/6-31G(d):ff94) level, starting from three geometries extracted from the 3, 6 and 8 ns point on the MD simulation. The results show that the reaction mechanism of 3-OST occurs by a single elementary step, consisting of an associative SN2 transfer of the sulfate group from PAPS to the HS glucosamine units, with the transfer of a proton from glucosamine to the catalytic Glu184. The activation free energies for this reaction were determined at the ONIOM(M06-2X-D3/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94) level of theory. Despite the free energy differences among the three conformations (10.2, 20.9 and 16.1 kcal mol(-1)), our results are consistent with the upper limit determined experimentally for the full cycle (20.4 kcal mol(-1)). The data obtained in this study will be useful for further studies on the inhibition of this enzyme, which is a useful target for drugs that block HSV-1 viral infections.

The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac

Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl-enzyme covalent complex. The leaving group Ala-Tyr-Asp-Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1-P1' bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. The formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal mol(-1) and 19.8 kcal mol(-1) respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.

Establishing the catalytic mechanism of human pancreatic α-amylase with QM/MM methods

In this work, we studied the catalytic mechanism of human pancreatic α-amylase (HPA). Our goal was to determine the catalytic mechanism of HPA with atomic detail using computational methods. We demonstrated that the HPA catalytic mechanism consists of two steps, the first of which (glycosylation step) involves breaking the glycosidic bond to culminate in the formation of a covalent intermediate. The second (deglycosylation step) consists of the addition of a water molecule to release the enzyme/substrate covalent intermediate, completing the hydrolysis of the sugar. The active site was very open to the solvent. Our mechanism basically differs from the previously proposed mechanism by having two water molecules instead of only one near the active site that participate in the mechanism. We also demonstrate the relevant role of the three catalytic amino acids, two aspartate residues and a glutamate (D197, E233, and D300), during catalysis. It was also shown that the rate limiting step was glycosylation, and its activation energy was in agreement with experimental values obtained for HPA. The experimental activation energy was 14.4 kcal mol(-1), and the activation energy obtained computationally was 15.1 kcal mol(-1).

Impact of a pectic polysaccharide on oenin copigmentation mechanism

Copigmentation plays an important role in the colors provided by anthocyanins. However, little attention has been paid to the interaction between anthocyanins and cell wall compounds (e.g. polysaccharides) and the impact of this interaction on anthocyanins color, a fundamental issue to be considered in industrial applications of these pigments as food colorants. The copigmentation binding constants (KCP) for the interaction between malvidin-3-O-glucoside and (+)-catechin in the presence of low methoxylated pectic polysaccharide were determined. The values obtained showed that in the presence of pectic polysaccharide the copigmentation binding constants decreased. These results probably suggest the occurrence of competition equilibrium in which the presence of pectin limited the association between catechin and oenin. (1)H NMR studies revealed that the dissociation constant determined for these complexes was very similar in absence and presence of 1.5g/L pectin with this polysaccharide apparently not affecting the strength of anthocyanin-catechin binding.

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.

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.

A study of anthocyanin self-association by NMR spectroscopy

Malvidin-3-O-coumaroylglucoside molecules self-associate, with this interaction occurring mainly by dispersive contacts (direct π–π stacking and van der Waals interactions).

Relevant interactions of antimicrobial iron chelators and membrane models revealed by nuclear magnetic resonance and molecular dynamics simulations

The dynamics and interaction of 3-hydroxy-4-pyridinone fluorescent iron chelators, exhibiting antimicrobial properties, with biological membranes were evaluated through NMR and molecular dynamics simulations. Both NMR and MD simulation results support a strong interaction of the chelators with the lipid bilayers that seems to be strengthened for the rhodamine containing compounds, in particular for compounds that include ethyl groups and a thiourea link. For the latter type of compounds the interaction reaches the hydrophobic core of the lipid bilayer. The molecular docking and MD simulations performed for the potential interaction of the chelators with DC-SIGN receptors provide valuable information regarding the cellular uptake of these compounds since the results show that the fluorophore fragment of the molecular framework is essential for an efficient binding. Putting together our previous and present results, we put forward the hypothesis that all the studied fluorescent chelators have access to the cell, their uptake occurs through different pathways and their permeation properties correlate with a better access to the cell and its compartments and, consequently, with the chelators antimicrobial properties.

Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases

In this work, a combination of homology modeling and molecular dynamics (MD) simulations was used to investigate the factors that modulate substrate specificity and activity of the mouse AOX isoforms: mAOX1, mAOX2 (previously mAOX3l1), mAOX3 and mAOX4. The results indicate that the AOX isoform structures are highly preserved and even more conserved than the corresponding amino acid sequences. The only differences are at the protein surface and substrate-binding site region. The substrate-binding site of all isoforms consists of two regions: the active site, which is highly conserved among all isoforms, and a isoform-specific region located above. We predict that mAOX1 accepts a broader range of substrates of different shape, size and nature relative to the other isoforms. In contrast, mAOX4 appears to accept a more restricted range of substrates. Its narrow and hydrophobic binding site indicates that it only accepts small hydrophobic substrates. Although mAOX2 and mAOX3 are very similar to each other, we propose the following pairs of overlapping substrate specificities: mAOX2/mAOX4 and mAOX3/mAXO1. Based on these considerations, we propose that the catalytic activity between all isoforms should be similar but the differences observed in the binding site might influence the substrate specificity of each enzyme. These results also suggest that the presence of several AOX isoforms in mouse allows them to oxidize more efficiently a wider range of substrates. This contrasts with the same or other organisms that only express one isoform and are less efficient or incapable of oxidizing the same type of substrates.

Grape anthocyanin oligomerization: a putative mechanism for red color stabilization?

The equilibrium forms of malvidin-3-O-glucoside trimer present in grape skins were studied in aqueous solution at different pH values through UV-Visible spectroscopy. It was observed that the reactivity of this compound is strongly dominated by acid-base chemistry (pKa1=3.61±0.03; pKa2=6.83±0.06), with the reaction sequence hydration-tautomerization-isomerization accounting less than 10% of the overall reactivity. The decrease of hydration of this flavylium cation derivative when compared to the original anthocyanins results from the formation of a cluster of the pigment with a high-energy of solvation that inhibits the access of water molecules to the flavylium cation core preventing by this way the hydration reactions. Overall of these results raise the hypothesis that polymerization may be a natural stabilization mechanism for the red color of anthocyanins.

Evidence for copigmentation interactions between deoxyanthocyanidin derivatives (oaklins) and common copigments in wine model solutions

The aim of this study was to investigate interactions possibly taking place in red wine between oaklins, which are deoxyanthocyanidin derivatives (guaiacylcatechin-pyrylium and syringylcatechin-pyrylium), and several copigments: catechin (CP1), epicatechin (CP2), chlorogenic acid (CP3), epigallocatechin (CP4), and procyanidin B3 (CP5). The results show that oaklins, like common anthocyanins, also present copigmentation interactions that further stabilize the flavylium cation in hydroalcoholic solutions. Molecular dynamics simulations were also performed to interpret the binding data, to specify the relative arrangement of the pigment and copigment molecules within the complexes, and to interpret their absorption properties in the visible range.

Antioxidant features of red wine pyranoanthocyanins: experimental and theoretical approaches

This work is focused on the study of the antioxidant properties of red wine anthocyanin derivatives (carboxypyranoanthocyanins, methylpyranoanthocyanins, oxovitisins, and pyranoanthocyanin-phenolics) derived from malvidin-3-glucoside. Some antioxidant features were determined using the DPPH assay and the ability to delay lipid peroxidation in a liposome membrane system by monitoring oxygen consumption. The pyranoanthocyanin-phenolics have higher antioxidant potential than that of malvidin-3-glucoside, suggesting that the addition of a catechol or flavanol moiety increases the antioxidant capacity. The only derivatives that showed lower antioxidant features than malvidin-3-glucoside were oxovitisins and methylpyranomalvidin-3-glucoside. Also, the radical scavenging capacity of these pyranoanthocyanins was computationally explored using DFT methods. All pyranoanthocyanins were suggested as good candidates as antioxidant compounds because they easily donate an H atom to the free radicals, originating stable species. Altogether, these results support the fact that the antioxidant potential arising from anthocyanins is not impaired by some of their transformations during red wine aging.

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).

Discovery of new sites for drug binding to the hypertension-related renin-angiotensinogen complex

Renin (REN) is a key drug target to stop the hypertension cascade, but thus far only one direct inhibitor has been made commercially available. In this study, we assess an innovative REN inhibition strategy, by targeting the interface of the renin:angiotensinogen (REN:ANG) complex. We characterized the energetic role of interfacial residues of REN:ANG and identified the ones responsible for protein:protein binding, which can serve as drug targets for disruption of the REN:ANG association. For this purpose, we applied a computational alanine scanning mutagenesis protocol, which measures the contribution of each side chain for the protein:protein binding free energy with an accuracy of ≈ 1 kcal/mol. As a result, in REN and ANG, six and eight residues were found to be critical for binding, respectively. The leading force behind REN:ANG complexation was found to be the hydrophobic effect. The binding free energy per residue was found to be proportional to the buried area. Residues responsible for binding were occluded from water at the complex, which promotes an efficient pairing between the two proteins. Two druggable pockets involving critical residues for binding were found on the surface of REN, where small druglike molecules can bind and disrupt the ANG:REN association that may provide an efficient way to achieve REN inhibition and control hypertension.

Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors

In this study a novel renin and ACE inhibitor was developed from natural products using computational techniques. Molecular dynamic simulations showed that the new lead compound has significant binding to the targets.

Identification of crucial amino acids in mouse aldehyde oxidase 3 that determine substrate specificity

In order to elucidate factors that determine substrate specificity and activity of mammalian molybdo-flavoproteins we performed site directed mutagenesis of mouse aldehyde oxidase 3 (mAOX3). The sequence alignment of different aldehyde oxidase (AOX) isoforms identified variations in the active site of mAOX3 in comparison to other AOX proteins and xanthine oxidoreductases (XOR). Based on the structural alignment of mAOX3 and bovine XOR, differences in amino acid residues involved in substrate binding in XORs in comparison to AOXs were identified. We exchanged several residues in the active site to the ones found in other AOX homologues in mouse or to residues present in bovine XOR in order to examine their influence on substrate selectivity and catalytic activity. Additionally we analyzed the influence of the [2Fe-2S] domains of mAOX3 on its kinetic properties and cofactor saturation. We applied UV-VIS and EPR monitored redox-titrations to determine the redox potentials of wild type mAOX3 and mAOX3 variants containing the iron-sulfur centers of mAOX1. In addition, a combination of molecular docking and molecular dynamic simulations (MD) was used to investigate factors that modulate the substrate specificity and activity of wild type and AOX variants. The successful conversion of an AOX enzyme to an XOR enzyme was achieved exchanging eight residues in the active site of mAOX3. It was observed that the absence of the K889H exchange substantially decreased the activity of the enzyme towards all substrates analyzed, revealing that this residue has an important role in catalysis.