Structure-based ligand design for flexible proteins: Application of new F-DycoBlock

A method of structure-based ligand design – DycoBlock – has been proposed and tested by Liu et al.[1]. It was further improved by Zhu et al. and applied to design new selective inhibitors of cyclooxygenase 2 [2]. In the current work, we present a new methodology – F-DycoBlock that allows for the incorporation of receptor flexibility. During the designing procedure, both the receptor and molecular building blocks are subjected to the multiple-copy stochastic molecular dynamics (MCSMD) simulation [1], while the protein moves in the mean field of all copies. It is tested for two enzymes studied previously – cyclooxygenase 2 (COX-2) and human immunodeficiency type 1 (HIV-1) protease. To identify the applicability of F-DycoBlock, the binding protein structure was used as starting point to explore the conformational space around the bound state. This method can be easily extended to accommodate the flexibility in different degree. Four types of treatment of the receptor flexibility – all-atom restrained, backbone restrained, intramolecular hydrogen-bond restrained and active-site flexible – were tested with or without the grid approximation. Two inhibitors, SC-558 for COX-2 and L700417 for HIV-1 protease, are used in this testing study for comparison with previous results. The accuracy of recovery, binding energy, solvent accessible surface area (SASA) and positional root-mean-square (RMS) deviation are used as criteria. The results indicate that F-DycoBlock is a robust methodology for flexible drug design. It is particularly notable that the protein flexibility has been perfectly associated with each stage of drug design – search for the binding sites, dynamic assembly and optimization of candidate compounds. When all protein atoms were restrained, F-DycoBlock yielded higher accuracy of recovery than DycoBlock (100%). If backbone atoms were restrained, the same ratio of accuracy was achieved. Moreover, with the intramolecular hydrogen bonds restrained, reasonable conformational changes were observed for HIV-1 protease during the long-time MCSMD simulation and L700417 was reassembled at the active site. It makes it possible to study the receptor motion in the binding process.

[1]  M Karplus,et al.  HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site , 1994, Proteins.

[2]  H Liu,et al.  Structure‐based ligand design by dynamically assembling molecular building blocks at binding site , 1999, Proteins.

[3]  Eveline,et al.  The aspirin and heme-binding sites of ovine and murine prostaglandin endoperoxide synthases. , 1990, The Journal of biological chemistry.

[4]  A. Leach,et al.  Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.

[5]  Gennady M Verkhivker,et al.  Predicting structural effects in HIV‐1 protease mutant complexes with flexible ligand docking and protein side‐chain optimization , 1998, Proteins.

[6]  R. Elber,et al.  Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations , 1991 .

[7]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[8]  P Koehl,et al.  Mean-field minimization methods for biological macromolecules. , 1996, Current opinion in structural biology.

[9]  J A McCammon,et al.  Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.

[10]  W. F. Gunsteren,et al.  Optimization methods for conformational sampling using a Boltzmann‐weighted mean field approach , 1998 .

[11]  Wei-Mou Zheng,et al.  An analytical derivation of the locally enhanced sampling approximation , 1997 .

[12]  J. Onuchic,et al.  Navigating the folding routes , 1995, Science.

[13]  D J Kyle,et al.  Multiple copy sampling: Rigid versus flexible protein , 1994, Proteins.

[14]  H. Chan.  Kinetics of protein folding , 1995, Nature.

[15]  Haiyan Liu,et al.  Design of new selective inhibitors of cyclooxygenase-2 by dynamic assembly of molecular building blocks , 2001, J. Comput. Aided Mol. Des..

[16]  Rakefet Rosenfeld,et al.  Theoretical analysis of the multicopy sampling method in molecular modeling , 1993 .

[17]  M. Karplus,et al.  Functionality maps of binding sites: A multiple copy simultaneous search method , 1991, Proteins.

[18]  J A McCammon,et al.  Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. , 1994, Journal of molecular biology.

[19]  J. Tainer,et al.  Screening a peptidyl database for potential ligands to proteins with side‐chain flexibility , 1998, Proteins.

[20]  Collin M. Stultz,et al.  Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin , 2000, Proteins.

[21]  M. Karplus,et al.  Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin , 1990 .

[22]  R. Nussinov,et al.  Folding funnels and binding mechanisms. , 1999, Protein engineering.

[23]  E. Fischer.  Einfluss der Configuration auf die Wirkung der Enzyme , 1894 .

[24]  M Karplus,et al.  "New view" of protein folding reconciled with the old through multiple unfolding simulations. , 1997, Science.

[25]  C. Sander,et al.  An effective solvation term based on atomic occupancies for use in protein simulations , 1993 .

[26]  M. Murcko,et al.  CONCERTS: dynamic connection of fragments as an approach to de novo ligand design. , 1996, Journal of medicinal chemistry.

[27]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[28]  Collin M. Stultz,et al.  MCSS functionality maps for a flexible protein , 1999, Proteins.

[29]  P. Wolynes,et al.  Intermediates and barrier crossing in a random energy model , 1989 .

[30]  L. Serrano,et al.  Obligatory steps in protein folding and the conformational diversity of the transition state , 1998, Nature Structural &Molecular Biology.

[31]  John E. Straub,et al.  ENERGY EQUIPARTITIONING IN THE CLASSICAL TIME-DEPENDENT HARTREE APPROXIMATION , 1991 .