Molecular dynamics simulation of 1,2-dilauroyl-L-phosphatidylethanolamine binding to phospholipase A2: an attempt to explain the selective hydrolysis of substrate fatty acid ester at position 2

Prospects and Challenges of Phospholipid-Based Prodrugs

Nowadays, the prodrug approach is used already at the early stages of drug development. Lipidic prodrug approach is a growing field for improving a number of drug properties/delivery/therapy aspects, and can offer solutions for various unmet needs. This approach includes drug moiety bound to the lipid carrier, which can be triglyceride, fatty acids, steroid, or phospholipid (PL). The focus of this article is PL-based prodrugs, which includes a PL carrier covalently bound to the active drug moiety. An overview of relevant physiological lipid processing pathways and absorption barriers is provided, followed by drug delivery/therapeutic application of PL-drug conjugates, as well as computational modeling techniques, and a modern bioinformatics tool that can aid in the optimization of PL conjugates. PL-based prodrugs have increased lipophilicity comparing to the parent drug, and can therefore significantly improve the pharmacokinetic profile and overall bioavailability of the parent drug, join the endogenous lipid processing pathways and therefore accomplish drug targeting, e.g., by lymphatic transport, drug release at specific target site(s), or passing the blood-brain barrier. Moreover, an exciting gateway for treating inflammatory diseases and cancer is presented, by utilizing the PL sn-2 position in the prodrug design, aiming for PLA₂-mediated activation. Overall, a PL-based prodrug approach shows great potential in improving different drug delivery/therapy aspects, and is expected to grow.

[Overview of structural study on conformations and intermolecular interactions of biomolecules]

Information on the conformational feature and specific intermolecular interaction of biomolecules is important to understand the biological function and to develop device for treating disorder caused by the abnormal function. Thus the 3D structures of the biologically active molecules and the specific interactions with their target molecules at the atomic level have been investigated by various physicochemical approaches. Herein, the following five subjects are reviewed: (1) function-linked conformations of biomolecules including natural annular products, opioid peptides and neuropeptides; (2) π-π stacking interactions of tryptophan derivatives with coenzymes and nucleic acid bases; (3) mRNA cap recognition of eukaryotic initiation factor 4E and its regulation by 4E-binding protein; (4) conformational feature of histamine H2 receptor antagonists and design of cathepsin B inhibitors; (5) self-aggregation mechanism of tau protein and its inhibition.

Modulation of the positional specificity of lecithin-cholesterol acyltransferase by the acyl group composition of its phosphatidylcholine substrate: role of the sn-1-acyl group

Human lecithin-cholesterol acyltransferase (LCAT), which is normally specific for the sn-2 position of phosphatidylcholine (PC), derives a significant percentage of acyl groups from the sn-1 position, when sn-2 is occupied by 18:0, 20:4, or 22:6. We investigated the relative importance of the two acyl groups of PC in determining the positional specificity by first analyzing the cholesteryl esters formed in the presence of symmetric PCs labeled at sn-2. Both human and rat LCATs transferred exclusively the sn-2-acyl group from all symmetric PCs, including 18:0-18:0, and 20:4-20:4, showing that the presence of these fatty acids at sn-2 does not automatically alter the positional specificity. The role of the sn-1-acyl group was then tested by using PCs containing 20:4 or 18:0 at sn-2 and fatty acids of various chain lengths and unsaturation at sn-1. With 20:4 at sn-2 and saturated fatty acids of various chain lengths at sn-1, human and rat LCATs derived, respectively, 5-72% and 1-20% of the total acyl groups from the sn-1 position. However, the chain length of the sn-1-acyl did not correlate with its utilization by either enzyme. Various unsaturated fatty acids at sn-1 also were transferred by human LCAT at a higher rate (5-75% of total) than they were transferred by rat LCAT (0-21%). With sn-2-18:0 PCs, however, rat LCAT exhibited greater alteration in positional specificity (30-95% from sn-1) than human LCAT (15-83% from sn-1). These results show that while the primary determinant of positional specificity is the sn-2-acyl group of PC, the structure of sn-1-acyl significantly modifies it.

Molecular dynamics simulations of adipocyte lipid-binding protein: effect of electrostatics and acyl chain unsaturation

Molecular dynamics (MD) simulations have been performed on adipocyte lipid-binding protein, using the apo and holo forms, bound with stearic and oleic acid. The contribution of electrostatics to protein dynamics and ligand stabilization was assayed by perturbing the electrostatic charge of Arg106 and Arg126 (positive-->neutral) and the fatty acid (132H) headgroup (negative-->neutral). MD simulations for charged holo forms demonstrated significantly greater electrostatic binding energy and a more stabilized hydrogen bond network than simulations performed using neutral forms. Electrostatics, however, appeared to have little effect on fatty acid behavior, e.g., fluctuation of the dihedral head group; number of dihedral transitions within the acyl chain; and change in the end-to-end distance for fatty acid. Instead, fatty acid behavior appeared to be dictated by the presence or absence of an unsaturated bond within the acyl chain. A significantly greater number of transitions were observed during MD simulations in oleic than stearic acid. In addition, significantly greater fluctuation was observed for oleic acid, within the C2 headgroup and C9 and C11 dihedrals (which lie adjacent to the olefin bond of oleic acid). The dynamic behavior of the acyl chain may thereby be more a property of van der Waals contact, and the degree of acyl chain unsaturation, than a function of electrostatics. In the absence of fatty acid, an increase in distance between guanidino carbon centered atoms of Arg126 and Arg106 was observed during MD simulations of the charged apo form. This effect not observed with the neutral apo form or in any of the holo complexes and, presumbably, was a result of repulsion between the negatively charged arginine sidechains. Conserved waters reflected substantially lower mean-square displacement (msd) in all simulations, except the neutral apo form. This suggests that the presence of either charged amino acids or lipid provides increased order for water within the binding pocket. These results provide a dynamic perspective of the interactive nature within the FABP binding pocket regulated in a complex manner by the electrostatics within the binding cavity, acyl chain structure and behavior, and water energetics.

X-ray crystal structure and molecular dynamics simulation of bovine pancreas phospholipase A2-n-dodecylphosphorylcholine complex

The crystal structure of n-dodecylphosphorylcholine (n-C12PC)-bovine pancreas phospholipase A2 (PLA2) complex provided the following structural characteristics: (1) the dodecyl chain of n-C12PC was located at the PLA2 N-terminal helical region by hydrophobic interactions, which corresponds to the binding pocket of 2-acyl fatty acid chain (beta-chain) of the substrate phospholipid, (2) the region from Lys-53 to Lys-56 creates a choline-receiving pocket of n-C12PC and (3) the N-terminal group of Ala-1 shifts significantly toward the Tyr-52 OH group by the binding of the n-C12PC inhibitor. Since the accuracy of the X-ray analysis (R = 0.275 at 2.3 A resolution) was insufficient to establish these important X-ray insights, the complex structure was further investigated through the molecular dynamics (MD) simulation, assuming a system in aqueous solution at 310K. The MD simulation covering 176 ps showed that the structural characteristics observed by X-ray analysis are intrinsic and also stable in the dynamic state. Furthermore, the MD simulation made clear that the PLA2 binding pocket is large enough to permit the conformational fluctuation of the n-C12PC hydrocarbon chain.