Thermodynamic contributions of the ordered water molecule in HIV-1 protease

Binding between biomolecules is usually accompanied by the formation of direct interactions with displacement of water from the binding sites. In some cases, however, the interactions are mediated by ordered water molecules, whose effect on binding affinity and the other thermodynamic functions is unclear. In this work, we compute the contribution of one such water molecule, the strongly bound water molecule at the binding site of HIV-1 protease, to the thermodynamic properties using statistical mechanical formulas for the energy and entropy. The requisite correlation functions are obtained by molecular dynamics simulations. We find that the entropic penalty of ordering is large but is outweighed by the favorable water-protein interactions. We also find a large negative contribution from this water molecule to the heat capacity. This approach could be useful in rational drug design by estimating which bound water molecules would be most favorable to displace.     

Synthesis of C 2 Symmetric Potential Inhibitors of HIV-1 Protease From D-Mannitol

ABSTRACT

D-Mannitol was used as precursor for the synthesis of acyclic C ₂ symmetric potential HIV-1 protease inhibitors. The 1- and 6-hydroxy groups of D-mannitol were substituted by -NHBoc, -NHValZ, -SAr, -SOAr and -SO₂Ar and the 2-and 5-hydroxy groups were benzylated. In some products one of the central hydroxyl groups was either inverted or deoxygenated. Despite a close structural similarity to previously published inhibitors none of the products showed significant inhibitory activity against HIV-1 protease.

     

Quantum study of HIV-1 protease-bridge water interaction

We present a fully quantum mechanical calculation for binding interaction between HIV-1 protease (PR) and the water molecule W301 which bridges the flaps of the protease with the inhibitors of PR. The quantum calculation is made possible by applying a recently developed molecular fractionation with conjugate caps (MFCC) method which divides a protein molecule into capped amino acid-based fragments and their conjugate caps. These individual fragments are properly treated to preserve the chemical property of bonds that are cut. Ab initio methods at HF, B3LYP, and MP2 levels with a fixed basis set 6-31+G* have been employed in the present calculation. The MFCC calculation produces a quantum mechanical interaction "map" representing interactions between individual residues of PR and W301. This enables a detailed quantitative analysis on binding of W301 to specific residues of PR at quantum mechanical level.     

Building molecular charge distributions from fragments: Application to HIV-1 protease inhibitors

Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon—carbon rather than carbon—nitrogen bonds. © 1997 by John Wiley & Sons, Inc.     

Modeling of ion complexation and extraction using substructural molecular fragments

A substructural molecular fragment (SMF) method has been developed to model the relationships between the structure of organic molecules and their thermodynamic parameters of complexation or extraction. The method is based on the splitting of a molecule into fragments, and on calculations of their contributions to a given property. It uses two types of fragments: atom/bond sequences and "augmented atoms" (atoms with their nearest neighbors). The SMF approach is tested on physical properties of C2-C9 alkanes (boiling point, molar volume, molar refraction, heat of vaporization, surface tension, melting point, critical temperature, and critical pressures) and on octanol/water partition coefficients. Then, it is applied to the assessment of (i) complexation stability constants of alkali cations with crown ethers and phosphoryl-containing podands, and of beta-cyclodextrins with mono- and 1,4-disubstituted benzenes, and (ii) solvent extraction constants for the complexes of uranyl cation by phosphoryl-containing ligands.