Order this document
Proteins 1997 Feb;27(2):195-203
Laboratory of Mathematical Biology, NCI-Frederick Cancer Research Facility and Development Center, MD 21702, USA.
Six models of the catalytic site of HIV-1 protease complexed with a reduced peptide inhibitor, MVT-101, were investigated. These studies focused on the details of protonation of the active site, its total net charge and hydrogen bonding pattern, which was consistent with both the observed coplanar configuration of the acidic groups of the catalytic aspartates (Asp-25 and Asp-125) and the observed binding mode of the inhibitor. Molecular dynamic simulations using AMBER 4.0 indicated that the active site should be neutral. The planarity of the aspartate dyad may be due to the formation of two hydrogen bonds: one between the inner O delta 1 oxygen atoms of the two catalytic aspartates and another between the O delta 2 atom of Asp-125 and the nitrogen atom of the reduced peptide bond of the bound inhibitor. This would require two additional protonations, either of both aspartates, or of one Asp and the amido nitrogen atom of Nle-204. Our results favor the Asp-inhibitor protonation but the other one is not excluded. Implications of these findings for the mechanism of enzymatic catalysis are discussed. Dynamic properties of the hydrogen bond network in the active site and an analysis of the interaction energy between the inhibitor and the protease are presented.
MeSH Terms:
Substances:
Grant support:
Other Formats: Links:
Proteins 1997 Feb;27(2):184-94
Macromolecular Structure Laboratory, NCI-Frederick Cancer Research Facility and Development Center, MD 21702, USA.
The structure of a complex between a hexapeptide-based inhibitor, MVT-101, and the chemically synthesized (Aba 67,95,167,195; Aba: L-alpha-amino-n-butyric acid) protease from the human immunodeficiency virus (HIV-1), reported previously at 2.3 A has now been refined to a crystallographic R factor of 15.4% at 2.0 A resolution. Root mean square deviations from ideality are 0.18 A for bond lengths and 2.4 degrees for the angles. The inhibitor can be fitted to the difference electron density map in two alternative orientations. Drastic differences are observed for positions and interactions at P3/S3 and P3'/S3' subsites of the two orientations due to different crystallographic environments.
Pept Res 1995 Nov-Dec;8(6):328-34
University of Trieste, Italy.
HIV-1 aspartic protease (PR) is a promising target for acquired immunodeficiency syndrome (AIDS) therapy, and the development of PR inhibitors can be accelerated by computer-aided design methods. We describe an approach for the design of new inhibitors, based on the modification of a known reference inhibitor, and the calculation of relative binding energies, taking into account contributions from all species in the binding equilibrium (inhibitor, PR and inhibitor/PR complex), as well as their solvation. This allows for a rational selection of new structures that are likely to have increased inhibition potency. We have analyzed reduced amide bond hexapeptides (Ac-P3-P2-P1-phi[CH2-NH]-P1'-P2-P3'-NH2), based on the structure of the known inhibitor MVT-101. A maximum gain in binding energy (approximately -55 kcal/mol) is observed when Phe or Tyr are present in positions P1 and P1', Glu in position P2' and aromatic residues (Phe, Trp or Tyr) in positions P3 and P3', while, in general, the presence of positively charged residues is destabilizing. This specificity is explained in terms of the interaction of individual inhibitor residues with proximal and distal PR residues. The validity of this computational approach has been confirmed by solid-phase synthesis of several of the designed pseudopeptides, followed by in vitro enzyme inhibition assaying. The best candidate structures show IC50 values in the low nanomolar range.
Protein Eng 1995 Jul;8(7):677-91
Agouron Pharmaceuticals Inc., San Diego, CA 92121-1121, USA.
The steadily increasing number of high-resolution human immunodeficiency virus (HIV) 1 protease complexes has been the impetus for the elaboration of knowledge-based mean field ligand-protein interaction potentials. These potentials have been linked with the hydrophobicity and conformational entropy scales developed originally to explain protein folding and stability. Empirical free energy calculations of a diverse set of HIV-1 protease crystallographic complexes have enabled a detailed analysis of binding thermodynamics. The thermodynamic consequences of conformational changes that HIV-1 protease undergoes upon binding to all inhibitors, and a substantial concomitant loss of conformational entropy by the part of HIV-1 protease that forms the ligand-protein interface, have been examined. The quantitative breakdown of the entropy-driven changes occurring during ligand-protein association, such as the hydrophobic contribution, the conformational entropy term and the entropy loss due to a reduction of rotational and translational degrees of freedom, of a system composed to ligand, protein and crystallographic water molecules at the ligand-protein interface has been carried out. The proposed approach provides reasonable estimates of distinctions in binding affinity and gives an insight into the nature of enthalpyentropy compensation factors detected in the binding process.
Nat Struct Biol 1995 Apr;2(4):255-7
Publication Types:
Comments:
J Med Chem 1994 Aug 19;37(17):2664-77
Parke-Davis Pharmaceutical Research, Division of Warner Lambert, Ann Arbor, Michigan 48105-2430.
HIV-1 protease has been identified as a significant target enzyme in AIDS research. While numerous peptide-derived inhibitors have been described, the identification of a nonpeptide inhibitor remains an important goal. Using an HIV-1 protease mass screening technique, 4-hydroxy-3-(3-phenoxypropyl)-2H-1-benzopyran-2-one (1) was identified as a nonpeptide competitive inhibitor of the enzyme. Employing a Monte Carlo-based docking procedure, the coumarin was docked in the active site of the enzyme, revealing a binding mode that was later confirmed by the X-ray crystal analysis. Several analogs were prepared to test the binding interactions and improve the overall binding affinity. The most active compound in the study was 4,7-dihydroxy-3-[4-(2-methoxyphenyl)butyl]-2H-1-benzopyran-2-one (31).
J Med Chem 1991 Aug;34(8):2344-56
Department of Medicinal Chemistry, Upjohn Company, Kalamazoo, Michigan 49001.
The peptidomimetic template and the dihydroxyethylene isostere insert that were applied successfully to the design of renin inhibitors have been extended to the related protease from human immunodeficiency virus (HIV). The present report describes the structure-activity study leading to the identification of an inhibitor with a Ki of less than 1 nM for the HIV type-1 protease (compound II). This compound, containing a diol insert, is highly effective in blocking polyprotein processing in in vitro cell culture assays. Results obtained from kinetic analysis, studies of the stereochemistry of the insert, and modeling have led to insights as to the requisites involved in the active site-inhibitor interaction.
Adv Exp Med Biol 1991;306:433-41
Macromolecular Structure Laboratory, NCI-Frederick Cancer Research and Development Center, Maryland 21702-1201.
Science 1989 Dec 1;246(4934):1149-52
NCI-Frederick Cancer Research Facility, BRI-Basic Research Program, MD 21701.
The structure of a complex between a peptide inhibitor with the sequence N-acetyl-Thr-Ile-Nle-psi[CH2-NH]-Nle-Gln-Arg.amide (Nle, norleucine) with chemically synthesized HIV-1 (human immunodeficiency virus 1) protease was determined at 2.3 A resolution (R factor of 0.176). Despite the symmetric nature of the unliganded enzyme, the asymmetric inhibitor lies in a single orientation and makes extensive interactions at the interface between the two subunits of the homodimeric protein. Compared with the unliganded enzyme, the protein molecule underwent substantial changes, particularly in an extended region corresponding to the "flaps" (residues 35 to 57 in each chain), where backbone movements as large as 7 A are observed.
the above reports in Macintosh PC UNIX Text HTML format documents on this page through Loansome Doc
