Mapping the Binding Site of a Large Set of Quinazoline Type EGF-R Inhibitors Using Molecular Field Analyses and Molecular Docking Studies

In the current work, three-dimensional QSAR studies for one large set of quinazoline type epidermal growth factor receptor (EGF-R) inhibitors were conducted using two types of molecular field analysis techniques: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). These compounds belonging to six different structural classes were randomly divided into a training set of 122 compounds and a test set of 13 compounds. The statistical results showed that the 3D-QSAR models derived from CoMFA were superior to those generated from CoMSIA. The most optimal CoMFA model after region focusing bears significant cross-validated r(2)(cv) of 0.60 and conventional r(2) of 0.92. The predictive power of the best CoMFA model was further validated by the accurate estimation to these compounds in the external test set, and the mean agreement of experimental and predicted log(IC(50)) values of the inhibitors is 0.6 log unit. Separate CoMFA models were conducted to evaluate the influence of different partial charges (Gasteiger-Marsili, Gasteiger-Hückel, MMFF94, ESP-AM1, and MPA-AM1) on the statistical quality of the models. The resulting CoMFA field map provides information on the geometry of the binding site cavity and the relative weights of various properties in different site pockets for each of the substrates considered. Moreover, in the current work, we applied MD simulations combined with MM/PBSA (Molecular mechanics/Possion-Boltzmann Surface Area) to determine the correct binding mode of the best inhibitor for which no ligand-protein crystal structure was present. To proceed, we define the following procedure: three hundred picosecond molecular dynamics simulations were first performed for the four binding modes suggested by DOCK 4.0 and manual docking, and then MM/PBSA was carried out for the collected snapshots. The most favorable binding mode identified by MM/PBSA has a binding free energy about 10 kcal/mol more favorable than the second best one. The most favorable binding mode identified by MM/PBSA can give satisfactory explanation of the SAR data of the studied molecules and is in good agreement with the contour maps of CoMFA. The most favorable binding mode suggests that with the quinazoline-based inhibitor, the N3 atom is hydrogen-bonded to a water molecule which, in turn, interacts with Thr 766, not Thr 830 as proposed by Wissner et al. (J. Med. Chem. 2000, 43, 3244). The predicted complex structure of quinazoline type inhibitor with EGF-R as well as the pharmacophore mapping from CoMFA can interpret the structure activities of the inhibitors well and afford us important information for structure-based drug design.

[1]  M. Sanner,et al.  Reduced surface: an efficient way to compute molecular surfaces. , 1996, Biopolymers.

[2]  P. Kollman,et al.  Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. , 2000, Journal of medicinal chemistry.

[3]  W. Denny,et al.  Tyrosine kinase inhibitors. 11. Soluble analogues of pyrrolo- and pyrazoloquinazolines as epidermal growth factor receptor inhibitors: synthesis, biological evaluation, and modeling of the mode of binding. , 1997, Journal of medicinal chemistry.

[4]  Xiaojie Xu,et al.  Predictions of Binding of a Diverse Set of Ligands to Gelatinase-A by a Combination of Molecular Dynamics and Continuum Solvent Models , 2002 .

[5]  C. Cordon-Cardo,et al.  Expression of transforming growth factor-alpha and the epidermal growth factor receptor in human prostate tissues. , 1994, The Journal of urology.

[6]  A. Bridges,et al.  A specific inhibitor of the epidermal growth factor receptor tyrosine kinase. , 1994, Science.

[7]  G. Carpenter,et al.  Epidermal growth factor-receptor-protein kinase interactions. Co-purification of receptor and epidermal growth factor-enhanced phosphorylation activity. , 1980, The Journal of biological chemistry.

[8]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[9]  Xiaojie Xu,et al.  Three-dimensional quantitative structure–activity relationship study on paullones as CDK inhibitors using CoMSIA and CoMFA , 2001 .

[10]  P. Furet,et al.  4-(Phenylamino)pyrrolopyrimidines: potent and selective, ATP site directed inhibitors of the EGF-receptor protein tyrosine kinase. , 1996, Journal of medicinal chemistry.

[11]  Y. Yarden,et al.  Purification of an active EGF receptor kinase with monoclonal antireceptor antibodies. , 1985, The Journal of biological chemistry.

[12]  Peter Traxler,et al.  Protein tyrosine kinase inhibitors in cancer treatment , 1997 .

[13]  B. Honig,et al.  Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.

[14]  Peter A. Kollman,et al.  Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins , 1995, J. Comput. Chem..

[15]  G. Klebe,et al.  Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. , 1994, Journal of medicinal chemistry.

[16]  L Wang,et al.  Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  P. Kollman,et al.  Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .

[18]  W. Denny,et al.  Tyrosine kinase inhibitors. 9. Synthesis and evaluation of fused tricyclic quinazoline analogues as ATP site inhibitors of the tyrosine kinase activity of the epidermal growth factor receptor. , 1996, Journal of medicinal chemistry.

[19]  Z. Li,et al.  Three-Dimensional Quantitative Structure-Activity Relationship Analysis of the New Potent Sulfonylureas Using Comparative Molecular Similarity Indices Analysis , 2000, J. Chem. Inf. Comput. Sci..

[20]  P. Bross,et al.  Expression of transforming growth factor alpha and epidermal growth factor receptor in human bladder cancer. , 1999, Scandinavian journal of clinical and laboratory investigation.

[21]  Xiaojie Xu,et al.  Three-dimensional quantitative structure–activity relationship analyses of a series of cinnamamides , 2001 .

[22]  Andrew Streitwieser,et al.  Molecular orbital theory for organic chemists , 1961 .

[23]  R. Day,et al.  Levels of TGF-α and EGFR Protein in Head and Neck Squamous Cell Carcinoma and Patient Survival , 1998 .

[24]  K. Sharp,et al.  Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .

[25]  Ruth Halaban,et al.  Growth factors and tyrosine protein kinases in normal and malignant melanocytes , 1991, Cancer and Metastasis Reviews.

[26]  Johann Gasteiger,et al.  Prediction of proton magnetic resonance shifts: The dependence on hydrogen charges obtained by iterative partial equalization of orbital electronegativity , 1981 .

[27]  P. Kollman,et al.  Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding , 2000 .

[28]  Peter Traxler,et al.  Tyrosine kinase inhibitors in cancer treatment (Part II) , 1998 .

[29]  Todd J. A. Ewing,et al.  Critical evaluation of search algorithms for automated molecular docking and database screening , 1997 .

[30]  Bruce L. Bush,et al.  Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA , 1993, J. Comput. Aided Mol. Des..

[31]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[32]  T. Yamamoto,et al.  Evidence for the involvement of transforming growth factor alpha and epidermal growth factor receptor autocrine growth mechanism in primary human ovarian cancers in vitro. , 1991, Cancer research.

[33]  P. Kollman,et al.  Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. , 2001, Journal of the American Chemical Society.

[34]  W. Denny,et al.  Tyrosine kinase inhibitors. 5. Synthesis and structure-activity relationships for 4-[(phenylmethyl)amino]- and 4-(phenylamino)quinazolines as potent adenosine 5'-triphosphate binding site inhibitors of the tyrosine kinase domain of the epidermal growth factor receptor. , 1995, Journal of medicinal chemistry.

[35]  W. Denny,et al.  Tyrosine kinase inhibitors. 8. An unusually steep structure-activity relationship for analogues of 4-(3-bromoanilino)-6,7-dimethoxyquinazoline (PD 153035), a potent inhibitor of the epidermal growth factor receptor. , 1996, Journal of medicinal chemistry.

[36]  D. Boschelli,et al.  4-Anilino-6,7-dialkoxyquinoline-3-carbonitrile inhibitors of epidermal growth factor receptor kinase and their bioisosteric relationship to the 4-anilino-6,7-dialkoxyquinazoline inhibitors. , 2000, Journal of medicinal chemistry.

[37]  A Whitty,et al.  Structure-based design of a potent, selective, and irreversible inhibitor of the catalytic domain of the erbB receptor subfamily of protein tyrosine kinases. , 1997, Journal of medicinal chemistry.

[38]  D. Osguthorpe,et al.  Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system , 1988, Proteins.

[39]  R S Bohacek,et al.  Definition and display of steric, hydrophobic, and hydrogen-bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design. , 1992, Journal of medicinal chemistry.

[40]  WM. CHAPPELL,et al.  Molecular Vibrations , 1879, Nature.

[41]  Xiaojie Xu,et al.  Three-Dimension Quantitative Structure-Activity Relationship Analysis of Some Cinnamamides Using Comparative Molecular Similarity Indices Analysis (CoMSIA) , 2000 .

[42]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[43]  Y. Yarden,et al.  Self-phosphorylation of epidermal growth factor receptor: evidence for a model of intermolecular allosteric activation. , 1987, Biochemistry.

[44]  T. Halgren.  Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 , 1996, J. Comput. Chem..

[45]  F. Young.  Biochemistry , 1955, The Indian Medical Gazette.

[46]  J. Gasteiger,et al.  ITERATIVE PARTIAL EQUALIZATION OF ORBITAL ELECTRONEGATIVITY – A RAPID ACCESS TO ATOMIC CHARGES , 1980 .

[47]  P. Kollman,et al.  Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies , 1999 .