[Show abstract][Hide abstract] ABSTRACT: The multistep mechanism of the pentacyclo-undecane (PCU) cage lactam was investigated with DFT. ► B3LYP/6-31 + G(d) calculations in gas phase and with the SCRF solvent model is reported. ► Kinetic and thermodynamic properties of all species involved was investigated. ► The final product obtained is both thermodynamically and kinetically preferred. ► The observed rate determining step compared favourably to the experimentally observed intermediate.
Computational and Theoretical Chemistry. 04/2012; 986:63-70.
[Show abstract][Hide abstract] ABSTRACT: The current global outbreak of Clostridium difficile infection exemplifies the major public health threat posed by clostridial glucosylating toxins. In the western world, C. difficile infection is one of the most prolific causes of bacterial-induced diarrhea and potentially fatal colitis. Two pathogenic enterotoxins, TcdA and TcdB, cause the disease. Vancomycin and metronidazole remain readily available treatment options for C. difficile infection, but neither is fully effective as is evident by high clinical relapse and fatality rates. Thus, there is an urgent need to find an alternative therapy that preferentially targets the toxins and not the drug-resistant pathogen. Recently, we addressed these critical issues in a Nature Medicine letter, describing a novel host defense mechanism for subverting toxin virulence that we translated into prototypic allosteric therapy for C. difficile infection. In this addendum article, we provide a continued perspective of this antitoxin mechanism and consider the broader implications of therapeutic allostery in combating gut microbial pathogenesis.
[Show abstract][Hide abstract] ABSTRACT: β-Glucan is a (1→3)-β-linked glucose polymer with (1→6)-β-linked side chains and a major component of fungal cell walls. β-Glucans provide structural integrity to the fungal cell wall. The nature of the (1-6)-β-linked side chain structure of fungal (1→3,1→6)-β-D-glucans has been very difficult to elucidate. Herein, we report the first detailed structural characterization of the (1→6)-β-linked side chains of Candida glabrata using high-field NMR. The (1→6)-β-linked side chains have an average length of 4 to 5 repeat units spaced every 21 repeat units along the (1→3)-linked polymer backbone. Computer modeling suggests that the side chains have a bent curve structure that allows for a flexible interconnection with parallel (1→3)-β-D-glucan polymers, and/or as a point of attachment for proteins. Based on these observations we propose new approaches to how (1→6)-β-linked side chains interconnect with neighboring glucan polymers in a manner that maximizes fungal cell wall strength, while also allowing for flexibility, or plasticity.
PLoS ONE 11/2011; 6(11):e27614. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis.
Regulatory Toxicology and Pharmacology 03/2011; 60(1):151-60. · 2.13 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Glucans are structurally diverse fungal biopolymers that stimulate innate immunity and are fungal pathogen-associated molecular patterns. Dectin-1 is a C-type lectin-like pattern recognition receptor that binds glucans and induces innate immune responses to fungal pathogens. We examined the effect of glucan structure on recognition and binding by murine recombinant Dectin-1 with a library of natural product and synthetic (1-->3)-beta/(1-->6)-beta-glucans as well as nonglucan polymers. Dectin-1 is highly specific for glucans with a pure (1-->3)-beta-linked backbone structure. Although Dectin-1 is highly specific for (1-->3)-beta-d-glucans, it does not recognize all glucans equally. Dectin-1 differentially interacted with (1-->3)-beta-d-glucans over a very wide range of binding affinities (2.6 mM-2.2 pM). One of the most striking observations that emerged from this study was the remarkable high-affinity interaction of Dectin-1 with certain glucans (2.2 pM). These data also demonstrated that synthetic glucan ligands interact with Dectin-1 and that binding affinity increased in synthetic glucans containing a single glucose side-chain branch. We also observed differential recognition of glucans derived from saprophytes and pathogens. We found that glucan derived from a saprophytic yeast was recognized with higher affinity than glucan derived from the pathogen Candida albicans. Structural analysis demonstrated that glucan backbone chain length and (1-->6)-beta side-chain branching strongly influenced Dectin-1 binding affinity. These data demonstrate: 1) the specificity of Dectin-1 for glucans; 2) that Dectin-1 differentiates between glucan ligands based on structural determinants; and 3) that Dectin-1 can recognize and interact with both natural product and synthetic glucan ligands.
Journal of Pharmacology and Experimental Therapeutics 04/2008; 325(1):115-23. · 3.89 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. AVAILABILITY: The InterProSurf web server is available at http://curie.utmb.edu/
[Show abstract][Hide abstract] ABSTRACT: Apurinic/apyrimidinic endonuclease (APE-1) is essential for base excision repair (BER) of damaged DNA. Here molecular dynamics (MD) simulations of APE1 complexed with cleaved and uncleaved damaged DNA were used to determine the role and position of the metal ion(s) in the active site before and after DNA cleavage. The simulations started from an energy minimized wild-type structure of the metal-free APE1/damaged-DNA complex (1DE8). A grid search with one Mg2+ ion located two low energy clusters of Mg2+ consistent with the experimentally determined metal ion positions. At the start of the longer MD simulations, Mg2+ ions were placed at different positions as seen in the crystal structures and the movement of the ion was followed over the course of the trajectory. Our analysis suggests a "moving metal mechanism" in which one Mg2+ ion moves from the B- (more buried) to the A-site during substrate cleavage. The anticipated inversion of the phosphate oxygens occurs during the in-line cleavage reaction. Experimental results, which show competition between Ca2+ and Mg2+ for catalyzing the reaction, and high concentrations of Mg2+ are inhibitory, indicate that both sites cannot be simultaneously occupied for maximal activity.
Proteins Structure Function and Bioinformatics 07/2007; 68(1):313-23. · 3.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The adenylyl cyclase toxins produced by bacteria (such as the edema factor (EF) of Bacillus anthracis and CyaA of Bordetella pertussis) are important virulence factors in anthrax and whooping cough. Co-crystal structures of these proteins differ in the number and positioning of metal ions in the active site. Metal ions bound only to the ligands in the crystal structures are not included during the docking. To determine what effect these "missing" metals have on docking results, the AutoDock, LigandFit/Cerius2, and FlexX programs were compared for their ability to correctly place substrate analogues and inhibitors into the active sites of the crystal structures of EF, CyaA, and mammalian adenylate cyclase. Protonating the phosphates of substrate analogues improved the accuracy of docking into the active site of CyaA, where the grid did not account for one of the three Mg2+ ions in the crystal structure. The AutoDock ranking (based on docking energies) of a test group of compounds was relatively unaffected by protonation of carboxyl groups. However, the ranking by FlexX-ChemScore varied significantly, especially for docking to CyaA, suggesting that alternate protonation states should be tested when screening compound libraries with this program. When the charges on the bound metal were set correctly, AutoDock was the most reliable program of the three tested with respect to positioning substrate analogues and ranking compounds according to their experimentally determined ability to inhibit EF.
Proteins Structure Function and Bioinformatics 06/2007; 67(3):593-605. · 3.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The regioselective protection of alcohols, amines and a cage lactam with acetic anhydride was previously investigated. A six-membered cyclic transition state of acetic anhydride with the reagent was found. The same computational model was applied to three lactam systems, namely 5-methylhydantoin, 5,5-dimethyl-hydantoin and a pentacyclo-undecane cage hydantoin. The density functional hybrid method B3LYP was employed along with the 6-31 + G(d) basis set to obtain the optimised geometries and corresponding energies of the different reagents, transition states and products. The computational model described herein correctly predicts the experimentally observed products. The synthesis and the NMR elucidation of three novel mono-Boc protected hydantoins are reported. (c) 2006 Elsevier B.V. All rights reserved.
[Show abstract][Hide abstract] ABSTRACT: The regioselective acetylation of 8,11-dihydroxy-pentacyclo[5.4.0.02,6.03,10.05,9]undecane-8,11-lactam with acetic anhydride was investigated. Only one of four possible structural isomers, namely 8-hydroxy-11-acetoxy-pentacyclo[5.4.0.02,6.03,10.05,9]undecane-8,11-lactam, was obtained. Ab initio [RHF/6-31+G(d)] and DFT [B3LYP/6-31+G(d)] calculations were employed to obtain the optimised geometries and corresponding energies of the different possible structural isomers, precomplexes and corresponding transition states. A six-membered cyclic transition state of acetic anhydride with the reagent was found. The computational model correctly predicts which isomer would preferentially form and suggests that the product obtained is both thermodynamically and kinetically preferred. The computational results were verified using a kinetically controlled experiment and 2D NMR techniques.
Journal of Molecular Structure THEOCHEM 03/2004; · 1.37 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bis-cage-annulated 18-crown-6 and 20-crown-6 macrocyclic ethers (i.e., 1 and 2, respectively) have been synthesized, and their alkali metal picrate extraction profiles have been determined. Host system 1 proved to be a significantly more avid alkali metal cation complexant than 2 and somewhat more avid than 18-crown-6. Both 1 and 18-crown-6 display modest selectivity toward K+ and Rb+. A stable host–guest complex was prepared by slow evaporation of a CH2Cl2–hexane solution of an equimolar mixture of 2 and potassium picrate. The X-ray crystal structure of this complex reveals that picrate anion functions as a bidentate ligand therein. The gas-phase interaction energy between the 2 · K+ complex and picrate anion was calculated to be ca. -64.9 kcal mol-1, thereby indicating that participation of picrate anion as an additional bidentate ligand results in significant stabilization of complex 10.
[Show abstract][Hide abstract] ABSTRACT: Diels–Alder cycloaddition of hexacyclo[7.5.1.01,6.06,13.08,12.010,14]pentadeca-2,4-diene-7,15-dione (1) to ethyl propiolate proceeds with π-facial selectivity to afford two cycloadducts, 4b and 5b (product ratio: 4b/5b=80:20). Thermal [4+2] cycloaddition of hexacyclo[7.5.2.01,6.06,13.08,12.010,14]hexadeca-2,4-diene-7,16-dione (2) to ethyl propiolate affords two isomeric cycloadducts, i.e. 6c and 6d (product ratio: 6c/6d=40:60). Cycloadducts 6c and 6d are formed with a high degree of endo π-facial selectivity but with only modest proximal/distal regioselectivity. The corresponding [4+2] cycloaddition of 2 (diene) to dimethyl acetylenedicarboxylate (dienophile) produced a single cycloadduct, 7b. These observations have been further examined by employing Hartree–Fock relative energies of transition states presumably formed enroute to the various products. Interestingly, filled orbital electrostatic repulsion between the incoming dienophile and the CO groups in the diene substrate does not appear to be a significant factor that might influence π-facial selection in this [4+2] cycloaddition. Finally, thermal [4+2] cycloaddition of cyclopentadiene (diene) to dienophile 3 proceeded with a high degree of π-facial selectivity to afford a single cycloadduct, 9b.
[Show abstract][Hide abstract] ABSTRACT: Compound 5, a cage-annulated monoaza-18-crown-6 macrocyclic polyether, has been synthesized, and its alkali metal picrate extraction capabilities have been assessed relative to those of the parent monoaza-18-crown-6 host system. It was observed that both 5 and monoaza-18-crown-6 are selective K+ picrate extractants; however, 5 appears generally to be a somewhat more efficient alkali metal picrate extractant than monoaza-18-crown-6. Interestingly, both the avidity and selectivity of 5 toward extraction of alkali metal picrates from aqueous solution into CHCl3 appears to be pH dependent. In addition, the X-ray crystal structure of an unusual hydronium ion complex of 5 [i.e., 5(HCl)(H
2] has been determined. The X-ray structure thus determined is compared with the corresponding structure of 5(HCl)(H
O) that has been calculated via application of B3LYP Density Functional Theory.
[Show abstract][Hide abstract] ABSTRACT: Grignard addition of excess vinylmagnesium bromide to 1-methyland 3-methylpentacyclo[5.4.0.02,6.03,10.05,9]undecane-8,11-diones (1a and 1b, respectively) and to 1-methylhexacyclo[10.2.1.02,11.04,9.04,14.09,13]pentadeca-5,7-diene-3,10-dione (4) each proceed regiospecifically to afford a single hemiketal adduct (i.e., 2a, 3a, and 5a, respectively). The structure of each of the three reaction products was established unequivocally via application of X-ray crystallographic methods. Relative energies for the model transition states obtained from geometry optimizations at the Hartree–Fock level of theory in basis set 3-21G(d) indicate that these reactions are kinetically controlled.
[Show abstract][Hide abstract] ABSTRACT: Irradiation of 1 with visible light results in intramolecular [2 + 2] photocyclization to afford the corresponding pentacyclic cage diketone, i.e., pentacyclo [220.127.116.11(2.6).0(3,10).0(5,9)] undecane-8,11-dione (2). The mechanism of this reaction has been scrutinized by using ab initio theoretical methods. The results of these calculations provide new evidence which supports earlier suggestions that alkene-enedione photocyclizations may actually proceed via a diradical stepwise mechanism through the triplet excited state rather than as concerted [2 + 2] cycloadditions.
[Show abstract][Hide abstract] ABSTRACT: The syntheses of pyridyl containing calixarene receptors (4, 5, and 11) that adopt the cone conformation are reported. The complexation properties of these host molecules were estimated via the results of alkali metal picrate extraction experiments. A singly-bridged bis-calixarene, i.e. 4 does not appear to be an efficient alkali metal picrate extractant. A doubly-bridged bis-calixarene, i.e. 5, displays elevated extraction avidity toward Rb+ and Cs+ picrates when compared with that of 4. A pyridyl containing calixarene-crown-5, i.e. 11, shows improved avidity and selectivity toward extraction of K+ and Rb+ picrates vis-a-vis the corresponding behavior of 4 and 5.