Data processing: structural design – modeling – simulation – and em – Simulating nonelectrical device or system – Biological or biochemical
Reexamination Certificate
1998-06-02
2001-05-01
Teska, Kevin J. (Department: 2763)
Data processing: structural design, modeling, simulation, and em
Simulating nonelectrical device or system
Biological or biochemical
C703S012000, C702S019000, C702S027000
Reexamination Certificate
active
06226603
ABSTRACT:
BACKGROUND
1. Technical Field
This invention relates to computer assisted methods for identifying target binding sites on a molecule of interest and methods for designing ligands which bind to a molecule of interest.
2. Background Information
Structure-based drug design is a major activity in pharmaceutical laboratories. The recent development of HIV-1 protease inhibitors is a major testimony to that effect. In structure-based drug design, the overall goal is to design a small molecule that binds to a specific site in a target molecule, usually a protein or other macromolecule. Where the target protein is an enzyme, the specific target site is often the substrate binding site or active site of the enzyme. Where the target protein is a receptor, the specific target site is often the binding site for a natural ligand of the receptor. In all cases the goal is to alter the behavior of the target molecule in a predetermined way as a result of the binding of the small molecule.
The starting point in the design process is the availability of the high resolution structure of the target protein. As noted above, in most situations, the target site for binding of the small molecule drug is the substrate binding or active site of an enzyme or the ligand binding site of a receptor. In some cases the location of these sites on the surface of the target protein is known from biochemical or structural studies. For this reason, most lead compounds are analogues of natural ligands or substrates. The situation is more complicated if the location of these sites is not known or if targeting a second binding site is required (a situation necessary, e.g., in cases where resistance towards an existing drug develops). Furthermore, the optimization of lead compounds is a very demanding endeavor requiring the chemical synthesis and characterization of a very large number of derivatives. It is evident that the availability of an algorithm that can identify, map, and rank binding sites and design ligands would have a positive impact in drug design. The present invention provides such capabilities.
SUMMARY
The invention features a computer-based method for the identification of binding targets in proteins and other macromolecules. More particularly, the invention includes an algorithm aimed at predicting binding targets in proteins and other macromolecules. The algorithm, referred to as “Woolford”, requires knowledge of the three-dimensional structure of the selected target protein or target macromolecule. However, Woolford does not require knowledge of the location or identity of natural binding sites or ligands. Binding targets in the protein are identified and classified according to their expected optimal affinities. Binding targets can be located at the protein surface or at internal surfaces that become exposed as a result of partial unfolding, conformational changes, subunit dissociation, or other events. The entire protein is mapped according to the binding potential of its constituent atoms. In another aspect of the invention, once binding targets are identified, optimal ligands are designed and progressively built by the addition of individual atoms or amino acids in the csae of peptide design that complement structurally and energetically the selected target site.
The Woolford algorithm and the associated methods of the invention are expected to have significant applications in structure-based drug design since they allow: 1) identification of binding targets in proteins and other macromolecules; 2) identification of additional binding targets if a primary binding target is known; 3) design of molecules (“ligand”) with optimal binding affinities for the selected binding target; and 4) refinement of lead compounds by defining the location and nature of chemical groups for optimal binding affinity.
The invention features methods for the identification of binding targets in proteins and other macromolecules. Binding targets can be located at the protein surface or at internal surfaces that become exposed as a result of partial unfolding, conformational changes, subunit dissociation, or other events.
The method for the identification of internal binding targets includes the identification of the most probable partially folded conformations of a protein and/or the dissociation energetics.
The invention also features methods for the design of synthetic organic ligands and peptide ligands which bind identified binding targets.
The invention also features methods for optimization of the conformation of ligands and the calculation of the expected binding affinities of ligands.
The invention also features methods for calculating the Gibbs free energy of binding of a ligand to a macromolecule. The method entails the steps of: (a) inputting into the programmed computer, through an input device, data which includes the three-dimensional coordinates and identity of each of the atoms in the ligand, the three-dimensional coordinates and identity of each of the atoms in the macromolecule, and the three-dimensional coordinates of each of the atoms in the complex of the ligand bound to the macromolecule; (b) determining, using the processor, the difference between the Gibbs free energy of the complex of the ligand and the macromolecule and the Gibbs free energy of the uncomplexed ligand and the uncomplexed macromolecule; (c) outputting to the output device the difference between the Gibbs free energy of the complex of the ligand and the macromolecule and the Gibbs free energy of the uncomplexed ligand and the uncomplexed macromolecule.
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Freire Ernesto
Luque Irene
Choi Kyle J.
McGuireWoods LLP
Teska Kevin J.
The Johns Hopkins University
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