Enzyme-ligand Docking and Drug Design

Principal Investigator

Jill Gready

Division of Biochemistry and Molecular Biology

John Curtin School of Medical Research

The project is part of a drug design and development program, involving both computer-based and experimental work [synthesis, enzymology, cellular testing]. Dihydrofolate reductase (DHFR) is a key enzyme in nucleic acid biosynthesis and a target for cytotoxic drugs, and the overall goal of the program is development of new DHFR inhibitors for possible use as anticancer or antimicrobial agents. The work consists mostly of molecular dynamics studies with simulated annealing of designed pteridine analogues docked into DHFR. An x-ray structure of a human DHFR ternary complex is being used for starting co-ordinates. We are using a new parameterized method for estimating binding energies based on standard thermodynamic cycles and on linear approximation of polar and non-polar free energy contributions from MD averages. Computationally this is much more efficient than FEP (free energy perturbation) methods thus allowing the study of many related analogues.

The "docking" problem is related to the location, the conformation and the relative affinity of bound ligands. In the present project, the second and third aspects of the docking problem are investigated using energy-driven searching methods based on MD simulations. The aim is to determine the orientations of the heterocyclic ring (e.g.deazapterin ring) and the conformational preferences of groups appended to the ring in a set of substituted heterocyclic cations docked into the DHFR binding site. Absolute binding free energies for the different analogues are then calculated.


Peter Cummins

Division of Biochemistry and Molecular Biology

John Curtin School of Medical Research


u52 - VPP, PC

What are the results to date and the future of the work?

Based on exploratory studies, conditions of simulations for modelling the ligand in the DHFR active site have been refined. The methodology is based on the simulated annealing technique which involves "heating" and "cooling" the complex during the MD simulations in order to increase the efficiency of producing conformational transitions by overcoming larger potential energy barriers, and to relax towards conformations of low energies at the desired temperature.

- Appendix A

The correlation of the computed binding energies with experimental inhibition data for the initial series of compounds we studied appears sufficient for predicting which further analogues to synthesize. However, to obtain quantitative agreement with experiment the treatment of the long-range electrostatic interactions needs to be improved and longer simulation times may be required to reduce the uncertainties in the energies.

What computational techniques are used?

Molecular dynamics simulations have been undertaken with AMBER 4.1, which is vectorized for the VPP300.


Gorse, A.-D., Gready, J. E. Molecular dynamics simulations of the docking of substituted N5-deazapterins to dihydrofolate reductase, Protein Engineering,(1997) in press.