Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide

Abstract

The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic APF provided a platform to study amino acid modifications and their effect on APF activity, based on which a structure-activity relationship (SAR) for APF activity was previously proposed. However, this SAR model could not explain the change in activity associated with minor alterations in the peptide sequence. Presented is computational analysis of 14 APF derivatives to identify structural trends from which a more detailed SAR is obtained. The APF activity is found to be dictated by the close interplay between carbohydrate-peptide and peptide-peptide interactions. The former involves hydrogen bond and hydrophobic interactions and the latter is dominated by hydrophobic interactions. The highly flexible hydrophobic peptide adopts collapsed conformations separated by low energy barriers. APF activity correlates with hydrophobic clustering associated with amino acids 4A, 6V and 8V. Peptide conformations are highly sensitive to single point mutations, which explain the experimental trends. The presented SAR will act as a guide for lead optimization of more potent APF analogues of potential therapeutic utility.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

“…12 Validation MD studies included examining the conformational properties and stability of oligomeric hyaluronan, sialyl Lewis X and the acetamido group in GlcNAc, as well as 4 larger glycoprotein systems and the intermolecular interactions in a lectin-sucrose complex. Subsequently, the model has been applied to study glycopeptides, including the anti-proliferative factor, 73 and validated against NMR data for di- and trisaccharides; 74 these efforts included targeting the 1–6 linkage, which led to additional optimization of associated dihedral parameters. 75 The presence of a broad carbohydrate model that is consistent with the remainder of the CHARMM36 force field is anticipated to facilitate studies of complex systems, such as glycolipids, glycoproteins and a range of carbohydrate-containing antibiotics.…”

Conformational Sampling of Oligosaccharides Using Hamiltonian Replica Exchange with Two-Dimensional Dihedral Biasing Potentials and the Weighted Histogram Analysis Method (WHAM)

“…Traditionally, only the ground-state, unbiased replica is used for data analysis. 15, 17, 50-51, 62-63 In this study, we propose to combine all the replicas with the weighted histogram analysis method (WHAM) to obtain an optimal distribution under the original potential of the system. Following the original WHAM 64 implementation, the probability distribution from H-REX can be expressed as the combination of the distribution from each replica, 64-65 …”

“…49-50 Our previous studies show that H-REX simulations with 1D and 2D biasing potentials applied to the glycosidic linkage dihedrals can greatly enhance conformational sampling for disaccharides and for disaccharides in a glycopeptide. 15, 17 In addition, H-REX has been adopted using a 2D Gaussian-like biasing potential for each linkage in di- and trisaccharides in solution. 51 In the studies in our laboratory the 2D biasing potentials were constructed as the negative of the potential of mean force (PMF) along two linkage dihedrals using the grid-based correction map (CMAP) method, which was originally developed for the protein backbone Φ/Ψ dihedrals in the CHARMM force field.…”

Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations

“…The intriguing relationship between functional variation and conformational heterogeneity of saccharides has stimulated intensive studies using both experimental and simulation approaches in recent years. 9, 13–18 …”

“…The C36 force field has been carefully calibrated against both QM calculations and experimental measurements 28, 30, 40 and has been successfully used for the study of (1→4)- and (1→6)-linked disaccharides and oligo-saccharides. 9, 10, 13, 14, 35, 36 …”