Influence of Sequential Modifications and Carbohydrate Variations in Synthetic AFGP Analogues on Conformation and Antifreeze Activity

Certain Arctic and Antarctic ectotherm species have developed strategies for survival under low temperature conditions that, among others, consist of antifreeze glycopeptides (AFGP). AFGP form a class of biological antifreeze agents that exhibit the ability to inhibit ice growth in vitro and in vivo and, hence, enable life at temperatures below the freezing point. AFGP usually consist of a varying number of (Ala‐Ala‐Thr)_n units (n=4–55) with the disaccharide β‐D ‐galactosyl‐(1→3)‐α‐N‐acetyl‐D ‐galactosamine glycosidically attached to every threonine side chain hydroxyl group. AFGP have been shown to adopt polyproline II helical conformation. Although this pattern is highly conserved among different species, microheterogeneity concerning the amino acid composition usually occurs; for example, alanine is occasionally replaced by proline in smaller AFGP. The influence of minor and major sequence mutations on conformation and antifreeze activity of AFGP analogues was investigated by replacement of alanine by proline and glycosylated threonine by glycosylated hydroxyproline. The target compounds were prepared by using microwave‐enhanced solid phase peptide synthesis. Furthermore, artificial analogues were obtained by copper‐catalyzed azide–alkyne cycloaddition (CuAAC): propargyl glycosides were treated with polyproline helix II‐forming peptides comprising (Pro‐Azp‐Pro)_n units (n=2–4) that contained 4‐azidoproline (Azp). The conformations of all analogues were examined by circular dichroism (CD). In addition, microphysical analysis was performed to provide information on their inhibitory effect on ice recrystallization.     

Synthesis and biological activities of lipid A analogs: modification of a glycosidically bound group with chemically stable polar acidic groups and lipophilic groups on the disaccharide backbone with tetradecanoyl or N-dodecanoylglycyl groups.

Six novel lipid A analogs were synthesized. The first two analogs, 4 and 5, have an alpha-glycosidically bound carboxymethyl or 1,3-dicarboxyisopropyl group on the disaccharide backbone with four tetradecanoyl groups. The next three analogs, 6, 7 and 8, have two or four N-dodecanoylglycyl groups on the 1-alpha-O-phosphonooxyethylated disaccharide backbone. Analog 6 bears N-dodecanoylglycyl groups on the hydroxyl functions at positions 3 and 3', and tetradecanoyl groups on the amino functions at positions 2 and 2'. Analog 7 is a 2, 3, 2' and 3'-tetrakis(N-dodecanoylglycyl) derivative, and analog 8 resembles compound 6, but the binding of the N-dodecanoylglycyl and tetradecanoyl groups at positions 2, 2' and 3, 3' are reversed. The third analog, 9, has the same acyl group configuration as compound 6, but has a 1,3-dicarboxyisopropyl group at position C-1. Compounds 4 and 5 exhibited definite antitumor activity against Meth A fibrosarcoma, indicating that the phosphate group at the C-1 position in lipid A could be replaced by the carboxylic acid without reducing the antitumor activity. In rabbits, compounds 6 and 9 exhibited potent antitumor activity, but their toxicity was extremely low. On the other hand, compounds 7 and 8 showed no antitumor activity. The levels of antitumor activity of 6 and 9 were similar to those of the natural-type lipid A. The antitumor activities of analogs with a N-dodecanoylglycyl group on the disaccharide backbone depended on the connecting sites of the acyl groups.     

Ice surface reconstruction as antifreeze protein-induced morphological modification mechanism

The crystal growth process by which fish antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) modify the ice morphology is analyzed in the AFP-ice system. A newly identified AFP-induced surface reconstruction mechanism enables one-dimensional helical and irregular globular ice binding surfaces to stabilize secondary, kinetically less stable ice surfaces with variable face indices. Not only are the relative growth rates controlled by the IBS engagement but also the secondary face indices themselves become adjusted in the process of maximizing the AFP-substrate interaction, through attaining the best structural match. The theoretical formulation leads to comprehensive agreement with experiment.     

Mimicking the properties of antifreeze glycoproteins: synthesis and characterization of a model system for ice nucleation and antifreeze studies

Synthesis of beta-D-Gal-(1 --> 3)-beta-D-GalNAc coupled to HOC2H4NHCOC15H30SH is described. This compound was coadsorbed at various proportions with C2H5OC2H4NHCOC15H30SH to form statistically mixed self-assembled monolayers (SAMs) on gold in an attempt to mimic the properties of the active domain in antifreeze glycoproteins (AFGPs). The monolayers were characterized by null ellipsometry, contact angle goniometry, X-ray photoelectron spectroscopy, and infrared reflection-absorption spectroscopy. The disaccharide compound adsorbed preferentially, and SAMs prepared at a solution molar ratio >0.3 displayed total wetting. The mixed SAMs showed well-organized alkyl chains up to a disaccharide surface fraction of 0.8. The amount of gauche conformers in the alkyls increased rapidly above this point, and the monolayers became disordered and less densely packed. Furthermore, the generated mixed SAMs were subjected to water vapor at constant relative humidity and the subsequent ice crystallization on a cooled substrate was monitored via an optical microscope. Interestingly, rapid crystallization occurred within a narrow range of temperatures on mixed SAMs with a high disaccharide content, surface fraction >0.3. The reported crystallization temperatures and the ice layer topography were compared with results obtained for a much simpler reference system composed of -OH/-CH3 terminated n-alkanethiols in order to account for changes in topography of the water/ice layer with surface energy. Although preliminary, the obtained results can be useful in the search for the molecular mechanism behind the antifreeze activity of AFGPs.     

Pattern formation of antifreeze glycoproteins via solvent evaporation

Surface patterning of antifreeze glycoprotein fraction 8 (AFGP 8) via a solvent evaporation method is reported here. In this process, lines of AFGP 8 particles and gridlike patterns were formed as as result of the receding of the droplet contact line and the accumulation of the solute during evaporation. The solution concentration strongly affects the protein line spacing. The average height of the protein was measured to be 8.1 +/- 2.5 A, which may be attributed to the height of a single molecule.     

Characterization of the restricted rotation of the dimethyl groups in chemically N-terminal 13C-labeled antifreeze glycoproteins: a temperature-dependent study in water to ice through the supercooled state

Site-specific chemical modification, especially with isotopically enriched groups, allows one to study the structure and dynamics of proteins for which uniform enrichment is difficult. When the N-terminal alanine in antifreeze glycoprotein (AFGP) is replaced with an N,N-dimethyl alanine the methyl groups show signatures of slow rotation about the C-N bond. In order to separate the local dynamics of the N-terminus from the overall protein dynamics, we present a complete characterization of this dynamics. Temperature-dependent nuclear magnetic-resonance experiments from room temperature to subzero temperatures, including the supercooled state and in the presence of ice, are presented. Quantum chemical calculations are also performed on a localized N-terminus of the AFGP. Our results show that in the solution state at room temperature and in the super cooled regime, the dimethyl groups undergo a slow, restricted rotation with an unequal distribution of population between two major conformations. At lower temperatures in the presence of ice, the dynamics become much more complex due to freezing out of several conformational states. Based on these results, we conclude that the segmental dynamics of the N-terminus are local to the first residue and do not affect the overall dynamics of the protein.     

Adsorption-induced conformational changes of antifreeze glycoproteins at the ice/water interface

The conformation of antifreeze glycoprotein (AFGP) molecules adsorbed at the ice/water interface was studied by attenuated total reflection (ATR)-FTIR spectroscopy. Measurements were carried out for AFGP/D2O solution films formed on the surface of an ATR prism as a function of temperature. Using the FTIR spectrum from the O-D stretching band of D2O molecules, we monitored the supercooled and frozen states of the film and measured the thickness of the quasi-liquid layer (QLL) at the ice/prism interfaces. The AFGP structure was determined for the liquid, supercooled, and frozen states of the solution film using the amide I band spectra. No noticeable differences in conformation were observed in the solution conformation from room temperature down to the 15 K supercooling studied, whereas the alpha-helical content of AFGP suddenly increased when the supercooled solution film froze at -15 degrees C. This change in conformation can increase the overall interaction between the AFGP molecules and ice surface and allow a stronger adsorption. In contrast, the alpha-helical content of AFGP in the frozen film gradually decreased with increasing temperature and finally returned to its solution-state level at the melting point of D2O ice. This gradual decrease in the alpha-helix content directly correlates with the measured increase in QLL thickness. Finally, we conclude that the differences in the alpha-helix signals between the frozen and supercooled states indicate the conformational change of AFGP molecules upon adsorption at the ice/water interface, emphasizing the importance of the structure-function relationship, even for this highly flexible antifreeze.     

Subtle structural changes in tetrahydroquinolines, a new class of nonsteroidal selective androgen receptor modulators, induce different functions

Tetrahydroquinolines (THQs), a new class of nonsteroidal selective androgen receptor (AR) modulators, have two indispensable functional groups, that is, a hydroxyl group for AR binding and a nitro group for agonistic activity. Interestingly, switching the nitro to a cyano group, the compound acts as an antagonist. To understand this phenomenon, molecular dynamics simulations were applied for dihydrotestosterone (DHT) and representative THQs complexes with AR. Upon ligand binding, the hydroxyl group formed a tight hydrogen-bond (H-bond) with Asn705 on Helix 3 (H3). The immobilization of Asn705 on H3 is helpful in the formation of tight H-bonds with Asp890 on loop 11-12, and this immobilization consequently leads to a stabilization of H12. The difference in the DHT carbonyl isosteres affected the presence or absence of the H-bonds between the hydroxyl group of THQ and Thr877 and the distortion of H12, which is caused by the methyl group of THQ. Thus, the binding, agonist, and antagonist functions were controlled by subtle structural changes in THQ.     

Facile One‐Step Syntheses of Modified O‐Glycoprotein Galβ1‐3GalNAc Structures by Transglycosylation Employing Three β‐Galactosidases from Bovine Testes,Xanthomonas manihotis,and Bacillus circulans *

Natural O‐glycoproteins such as the Thomsen‐Friedenreich antigen or gangliosides contain the motif Galβ1‐3GalNAc as an important disaccharide with significant biologic activity. The arrangement of spatial functionalities in this structure are of particular interest with regard to the development of potential leads en route to pharmaceuticals. Therefore, it was desired to obtain access to a range of modified derivatives of the aforementioned motif paying particular attention to introducing specific deoxy functions instead of hydroxyl groups.     

Facile solid-phase synthesis of an antifreeze glycoprotein

The antifreeze glycoproteins (AFGPs) 1 are composed of a repeating tripeptide unit (Ala-Thr-Ala) in which the threonine residue is glycosylated with the disaccharide beta-D-Gal-(1-->3)-alpha-D-GalNAc. A new procedure for synthesizing AFGPs using Fmoc-(Ac4-beta-D-Gal-(1-->3)-benzylidene- alpha-D-GalNAc)Thr-OH (10) as a building block has been developed. Total synthesis of the AFGPs (n = 4, 8) in overall yields of 61% and 33 %, respectively, has demonstrated the usefulness of the method. The synthetic AFGPs 1 (n = 4, 8) showed a similar conformation to the native AFGPs in their circular dichroism spectra.     

Protection of protein secondary structure by saccharides of different molecular weights during freeze-drying

The protective effects of saccharides with various molecular weights (glucose, maltose, maltotriose, maltotetraose, maltopentaose, maltoheptaose, dextran 1060, dextran 4900, and dextran 10200) against lyophilization-induced structural perturbation of model proteins (BSA, ovalbumin) were studied. Fourier transform infrared (FT-IR) analysis of the proteins in initial solutions and freeze-dried solids indicated that maltose conferred the greatest protection against secondary structure change. The structure-stabilizing effect of maltooligosaccharides decreased in increasing the number of saccharide units. Larger molecules of dextran also showed a smaller structure-stabilizing effect. Increasing the effective saccharide molecular size by a borate-saccharide complexation reduced the protein structure-stabilizing effect of all of the saccharides except glucose. The results indicate that the larger saccharide molecules, and/or the complex formation with borate ion, reduce the free and accessible hydroxyl groups to interact with and stabilize the protein structure by a water-substitution mechanism.     

Synthesis of thio-linked disaccharides by 1-->2 intramolecular thioglycosyl migration: oxacarbenium versus episulfonium ion intermediates

The conversion of 1,1'-thio-linked glucopyranosyl alpha-D-mannopyranosides to 1,2-thio-linked methyl sophorosides or methyl kojibiosides is described. The method involves the 1-->2-migration of the thioglucopyranosyl portion of the nonreducing disaccharide with inversion of configuration at C-2 of the mannopyranose ring and concomitant formation of the methyl glucopyranoside. The thioglucosyl migration does not occur when electron-withdrawing benzoate protecting groups are present. The rearrangement occurs with retention of configuration in the migrating thioglucoside but the methyl glycoside is formed as a mixture of alpha- and beta-isomers. This is attributed to a mechanism involving an oxacarbenium-ion intermediate rather than an episulfonium-ion intermediate. The relevance of this work to recent theoretical predictions concerning the relative stability of such intermediates is discussed.     

Reactions of pyrimidine nucleosides with aqueous alkalies: kinetics and mechanisms

Kinetics for the reactions of various cytosine and uracil nucleosides and their alkyl derivatives with aqueous sodium hydroxide have been studied by liquid chromatography. Blocking of the glycosyl hydroxyl groups with alkyl groups and changes in the glycon moiety configuration have been observed to exert only moderate effects on the rate of deamination of cytosine nucleosides. Methylation of the 4-amino group retards deamination considerably, while a methyl substituent at C5 is rate accelerating and at C6 only moderately rate retarding. These findings have been accounted for by a mechanism involving a rate limiting bimolecular displacement of the 4-amino group by a hydroxide ion. Analogous comparisons with uracil nucleosides suggest that the decomposition of uridine is initiated by an intermolecular attack of hydroxide ion on the C5 atom of the base moiety. In contrast, beta-D-arabino- and beta-D-lyxo-furanosyl derivatives appear to be cleaved via an intramolecular nucleophilic attack of the ionized 2'-hydroxyl group.     

An improved method for synthesizing antennary β-d-mannopyranosyl disaccharide units

The merits of an indirect protecting method for hydroxyl groups using allyl groups via allyloxycarbonyl groups in the synthesis of antennary β-d-mannopyranosyl disaccharides from β-d-galactopyranosyl disaccharides were studied. Regioselective allyloxycarbonylation and conversion reactions involving simultaneous double S_N2 nucleophilic substitution at C-2′ and C-4′ of benzyl O-[β-d-galactopyranosyl]-(1-4)-3,6-di-O-benzyl-2-deoxy-2-N-phthalimido-β-d-glucopyranoside were examined for comparison with the direct allylation method. The required β-d-mannopyranosyl disaccharide having proper protecting groups was obtained using this indirect method in 52% yield. In contrast, the reported direct allylation method using methyl O-(β-d-galactopyranosyl) disaccharide gave the corresponding β-d-mannopyranosyl disaccharide in only 7.5% yield.     

Molecular dynamics studies show solvation structure of type III antifreeze protein is disrupted at low pH

Antifreeze proteins are a class of biological molecules of interest in many research and industrial applications due to their highly specialized function, but there is little information of their stability and properties under varied pH derived from computational studies. To gain novel insights in this area, we conducted molecular dynamics (MD) simulations with the antifreeze protein 1KDF at varied temperatures and pH. Water solvation and H-bond formation around specific residues – ASN14, THR18 and GLN44 – involved in its antifreeze activity were extensively studied. We found that at pH1 there was a disruption in water solvation around the basal and the ice binding surfaces of the molecule. This was induced by a small change in the secondary structure propensities of some titrable residues, particularly GLU35. This change explains the experimentally observed reduction in antifreeze activity previously reported for this protein at pH1. We also found that THR18 showed extremely low H-bond formation, and that the three antifreeze residues all had very low average H-bond lifetimes. Our results confirm long-standing assumptions that these small, compact molecules can maintain their antifreeze activity in a wide range of pH, while demonstrating the mechanism that may reduce antifreeze activity at low pH. This aspect is useful when considering industrial and commercial use of antifreeze proteins subject to extreme pH environments, in particular in food industrial applications.     

Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations

Atomistic molecular dynamics simulations are used to investigate the mechanism by which the antifreeze protein from the spruce budworm, Choristoneura fumiferana, binds to ice. Comparison of structural and dynamic properties of the water around the three faces of the triangular prism-shaped protein in aqueous solution reveals that at low temperature the water structure is ordered and the dynamics slowed down around the ice-binding face of the protein, with a disordering effect observed around the other two faces. These results suggest a dual role for the solvation water around the protein. The preconfigured solvation shell around the ice-binding face is involved in the initial recognition and binding of the antifreeze protein to ice by lowering the barrier for binding and consolidation of the protein:ice interaction surface. Thus, the antifreeze protein can bind to the molecularly rough ice surface by becoming actively involved in the formation of its own binding site. Also, the disruption of water structure around the rest of the protein helps prevent the adsorbed protein becoming covered by further ice growth.     

Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations

The cyclic urea inhibitors of HIV-1 protease generally have two hydroxyl groups on the seven-membered ring. In this study, free energy perturbation and continuum electrostatic calculations were used to study the contributions of the two hydroxyl groups to the binding affinity and solubility of a cyclic urea inhibitor DMP323. The results indicated that the inhibitor with one hydroxyl group has better binding affinity and solubility than the inhibitor with two hydroxyl groups. Therefore, removal of one hydroxyl group from DMP323 may help to improve the properties of DMP323. This is also likely to be true for other cyclic urea inhibitors. The study also illustrated the difficulty in accurate modeling of the binding affinities of HIV-1 protease inhibitors, which involves many possible protonation states of the two catalytic aspartic acids in the active site of the enzyme.     

Selective Binding of Dopamine and Epinephrine in Water by Molecularly Imprinted Fluorescent Receptors

Catecholamines play important roles in biology but their structural similarity makes it challenging to construct synthetic receptors with selective binding. A combination of covalent and noncovalent binding groups in the hydrophobic core of water‐soluble nanoparticles enabled them to recognize dopamine and epinephrine with an association constant (K_a) of 3–4×10⁴ M^?1 in water, an order of magnitude higher than those of previously reported synthetic hosts. In addition, minute structural changes among analogues were detected including the addition or removal of a single hydroxyl or methyl group.     

Synthesis and antibacterial activity of emodin and its derivatives against methicillin-resistant Staphylococcus aureus

Synthesis of the antibacterial emodin was improved using Friedel-Crafts acylation as a key step leading to 37% overall yield. In addition, 21 analogues were synthesized by structural modification of the hydroxyl and methyl groups, as well as the aromatic ring of emodin. Antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and cytotoxicity against noncancerous Vero cells were evaluated. A structure-activity relationship (SAR) study indicated that the hydroxyl groups and the methyl group in the emodin skeleton were crucial for anti-MRSA activity. Furthermore, the presence of an iodine atom or ethylamino group on the aromatic ring enhanced the anti-MRSA activity with higher selectivity indices, while derivatives containing bromine, chlorine atoms or quaternary ammonium salt were as active as emodin. The quaternary ammonium group on the aromatic ring also led to non-cytotoxicity against Vero cells.     

Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.