Interpreting trends in the binding of cyclic ureas to HIV-1 protease

Journal of Molecular Biology

Volumn 309, Issue 2, 2001, Pages 507-517

  Mardis, Kristy L ^a   Luo, Ray ^a   Gilson, Michael K ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

Binding; Electrostatics; Free energy; HIV protease; Solvation

Indexed keywords

ARGININE; ASPARTIC ACID; PROTEINASE; UREA;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; ENZYME ACTIVE SITE; ENZYME BINDING; HUMAN IMMUNODEFICIENCY VIRUS 1; MODEL; NONHUMAN; PRIORITY JOURNAL; PROTON TRANSPORT;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 0035367150     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.4668     Document Type: Article

References (34)

1. Structure-based inhibitors of HIV-1 protease
2. Clinically effective HIV-1 protease inhibitors
3. Cyclic HIV protease inhibitors: Synthesis, conformational analysis, P2/P2′ structure-activity relationship, and molecular recognition of cyclic ureas
4. Design and selection of DMP 850 and DMP 851: The next generation of cyclic urea HIV protease inhibitors
5. Improved cyclic urea inhibitors of the HIV-I protease: Synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450
6. Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism
7. Kinetic studies of human-immunodeficiency virus type-1 protease and its active site hydrogen-bond mutant A28s
8. NMR and X-ray evidence that the HIV protease catalytic aspartyl groups are protonated in the complex formed by the protease and a nonpeptide cyclic urea-based inhibitor
9. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease
10. Calculating the electrostatic potential of molecules in solution - Method and error assessment
11. Calculation of the total electrostatic energy of a macromolecular system - Solvation energies, binding-energies, and conformational-analysis
12. Semianalytical treatment of solvation for molecular mechanics and dynamics
13. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii
14. Comparison of the generalized born and poisson models: Energetics and dynamics of the HIV-1 protease
15. A new class of models for computing receptor-ligand binding affinities
16. Differential adsorption of phenol derivatives onto a polymeric sorbent: A combined molecular modeling and experimental study
17. Computational study of KNI-272, a potent inhibitor of HIV-1 protease: On the mechanism of preorganization
18. Synthetic adenine receptors: Direct calculation of binding affinity and entropy
19. Nucleic acid base-pairing and N-methylacetamide self-association in chloroform: Affinity and conformation
20. The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known 3-dimensional structure
21. Development of a generalized born model parameterization for proteins and nucleic acids
22. The dielectric-constant of a folded protein
23. "Mining minima": Direct computation of conformational free energy
24. Strength of solvent-exposed saltbridges
25. The statistical-thermodynamic basis for computation of binding affinities: A critical review
26. CHARMM - A program for macromolecular energy, minimization, and dynamics calculations
27. The inclusion of electrostatic hydration energies in molecular mechanics calculations
28. Pk(a) shifts in small molecules and HIV protease: Electrostatics and conformation
29. A free-energy analysis of nucleic-acid base stacking in aqueous-solution
30. Competition between intra- and intermolecular hydrogen bonding: Effect on para/ortho adsorptive selectivity for substituted phenols
31. Intramolecular versus intermolecular hydrogen bonding in the adsorption of aromatic alcohols onto an acrylic ester sorbent
32. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
33. Ligand-receptor docking with the mining minima optimizer