Medicinal Chemistry Projects Requiring Imaginative Structure-Based Drug Design Methods

Accounts of Chemical Research

Volumn 49, Issue 9, 2016, Pages 1646-1657

  Moitessier, Nicolas ^a   Pottel, Joshua ^a   Therrien, Eric ^b   Englebienne, Pablo ^c   Liu, Zhaomin ^a   Tomberg, Anna ^a   Corbeil, Christopher R ^d  

^a MCGILL UNIVERSITY   (Canada)

^b Molecular Forecaster Inc   (Canada)

^c ROYAL HASKONINGDHV   (Netherlands)

^d NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENZYME INHIBITOR; GUANINE QUADRUPLEX; LIGAND; PROTEIN; RNA;

CHEMISTRY; DRUG DESIGN; GENETICS; HUMAN; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROTEIN CONFORMATION;

DNA; DRUG DESIGN; ENZYME INHIBITORS; G-QUADRUPLEXES; HUMANS; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; RNA;

EID: 84988643375     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/acs.accounts.6b00185     Document Type: Article

References (46)

1. J. Chem. Inf. Model. 2016, 56, 951-1099.
2. Totrov, M.; Abagyan, R. Flexible protein-ligand docking by global energy optimization in internal coordinates Proteins: Struct., Funct., Genet. 1997, 29, 215-220 10.1002/(SICI)1097-0134(1997)1+<215::AID-PROT29>3.0.CO;2-Q
3. Rarey, M.; Kramer, B.; Lengauer, T. The particle concept: Placing discrete water molecules during protein- ligand docking predictions Proteins: Struct., Funct., Genet. 1999, 34, 17-28 10.1002/(SICI)1097-0134(19990101)34:1<17::AID-PROT3>3.0.CO;2-1
4. Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; Corbeil, C. R. Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go Br. J. Pharmacol. 2008, 153, S7-S26 10.1038/sj.bjp.0707515
5. Corbeil, C. R.; Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of Fitted 1.0 J. Chem. Inf. Model. 2007, 47, 435-449 10.1021/ci6002637
6. Jain, A. N. Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search J. Comput.-Aided Mol. Des. 2007, 21, 281-306 10.1007/s10822-007-9114-2
7. Verdonk, M. L.; Chessari, G.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Nissink, J. W. M.; Taylor, R. D.; Taylor, R. Modeling water molecules in protein-ligand docking using GOLD J. Med. Chem. 2005, 48, 6504-6515 10.1021/jm050543p
8. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility J. Comput. Chem. 2009, 30, 2785-2791 10.1002/jcc.21256
9. Dock, version 6.7; University of California: San Francisco, CA, 2015; http://dock.compbio.ucsf.edu/DOCK-6/index.htm (accessed July 25, 2016).
10. Corbeil, C. R.; Therrien, E.; Moitessier, N. Modeling reality for optimal docking of small molecules to biological targets Curr. Comput.-Aided Drug Des. 2009, 5, 241-263 10.2174/157340909789577856
11. Hanessian, S.; Moitessier, N.; Therrien, E. A comparative docking study and the design of potentially selective MMP inhibitors J. Comput.-Aided Mol. Des. 2001, 15, 873-881 10.1023/A:1014356529909
12. Hanessian, S.; MacKay, D. B.; Moitessier, N. Design and synthesis of matrix metalloproteinase inhibitors guided by molecular modeling. Picking the S1 pocket using conformationally constrained inhibitors J. Med. Chem. 2001, 44, 3074-3082 10.1021/jm010096n
13. Hanessian, S.; Moitessier, N.; Cantin, L. D. Design and synthesis of MMP inhibitors using N-arylsulfonylaziridine hydroxamic acids as constrained scaffolds Tetrahedron 2001, 57, 6885-6900 10.1016/S0040-4020(01)00641-X
14. Moitessier, N.; Henry, C.; Chapleur, Y.; Maigret, B. Combining pharmacophore search, automated docking, and molecular dynamics simulations as a novel strategy for flexible docking. Proof of concept: Docking of arginine-glycine-aspartic acid-like compounds into the avb3 binding site J. Med. Chem. 2004, 47, 4178-4187 10.1021/jm0311386
15. Polgár, T.; Keseru, G. M. Structure-based β-secretase (BACE1) inhibitors Curr. Pharm. Des. 2014, 20, 3373-3379 10.2174/13816128113199990607
16. Cosconati, S.; Marinelli, L.; Di Leva, F. S.; La Pietra, V.; De Simone, A.; Mancini, F.; Andrisano, V.; Novellino, E.; Goodsell, D. S.; Olson, A. J. Protein flexibility in virtual screening: The BACE-1 case study J. Chem. Inf. Model. 2012, 52, 2697-2704 10.1021/ci300390h
17. Moitessier, N.; Therrien, E.; Hanessian, S. A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic β-secretase (BACE 1) inhibitors J. Med. Chem. 2006, 49, 5885-5894 10.1021/jm050138y
18. Hanessian, S.; Tremblay, M.; Kornienko, A.; Moitessier, N. Design, modeling and synthesis of functionalized paromamine analogs Tetrahedron 2001, 57, 3255-3265 10.1016/S0040-4020(01)00194-6
19. Moitessier, N.; Westhof, E.; Hanessian, S. Docking of aminoglycosides to hydrated and flexible RNA J. Med. Chem. 2006, 49, 1023-1033 10.1021/jm0508437
20. Englebienne, P.; Fiaux, H.; Kuntz, D. A.; Corbeil, C. R.; Gerber-Lemaire, S.; Rose, D. R.; Moitessier, N. Evaluation of Docking Programs for Predicting Binding of Golgi alpha-Mannosidase II Inhibitors: A Comparison with Crystallography Proteins: Struct., Funct., Genet. 2007, 69, 160-176 10.1002/prot.21479
21. Corbeil, C. R.; Englebienne, P.; Yannopoulos, C. G.; Chan, L.; Das, S. K.; Bilimoria, D.; L'Heureux, L.; Moitessier, N. Docking Ligands into Flexible and Solvated Macromolecules. 2. Development and Application of Fitted 1.5 to the Virtual Screening of Potential HCV Polymerase Inhibitors J. Chem. Inf. Model. 2008, 48, 902-909 10.1021/ci700398h
22. Therrien, E.; Englebienne, P.; Arrowsmith, A. G.; Mendoza-Sanchez, R.; Corbeil, C. R.; Weill, N.; Campagna-Slater, V.; Moitessier, N. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulatorswith Forecaster, a novel platform for drug discovery J. Chem. Inf. Model. 2012, 52, 210-224 10.1021/ci2004779
23. Fay, A. M. L.; Corbeil, C. R.; Brown, P.; Moitessier, N.; Bowie, D. Functional characterization and in silico docking of full and partial GluK2 kainate receptor agonists Mol. Pharmacol. 2009, 75, 1096-1107 10.1124/mol.108.054254
24. Schiavini, P.; Dawe, G. B.; Bowie, D.; Moitessier, N. Discovery of novel small-molecule antagonists for GluK2 Bioorg. Med. Chem. Lett. 2015, 25, 2416-2420 10.1016/j.bmcl.2015.04.008
25. Corbeil, C. R.; Moitessier, N. Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs J. Chem. Inf. Model. 2009, 49, 997-1009 10.1021/ci8004176
26. Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? J. Chem. Inf. Model. 2009, 49, 1568-1580 10.1021/ci8004308
27. Verdonk, M. L.; Chessari, G.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Nissink, J. W. M.; Taylor, R. D.; Taylor, R. Modeling water molecules in protein-ligand docking using GOLD J. Med. Chem. 2005, 48, 6504-6515 10.1021/jm050543p
28. Kendall, M. A New Measure of Rank Correlation Biometrika 1938, 30, 81-93 10.1093/biomet/30.1-2.81
29. Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 5. Force-field-based prediction of binding affinities of ligands to proteins J. Chem. Inf. Model. 2009, 49, 2564-2571 10.1021/ci900251k
30. Kieltyka, R.; Englebienne, P.; Fakhoury, J.; Autexier, C.; Moitessier, N.; Sleiman, H. F. A platinum supramolecular square as an effective G-quadruplex binder and telomerase inhibitor J. Am. Chem. Soc. 2008, 130, 10040-10041 10.1021/ja8014023
31. Kieltyka, R.; Fakhoury, J.; Moitessier, N.; Sleiman, H. F. Platinum phenanthroimidazole complexes as G-quadruplex DNA selective binders Chem.-Eur. J. 2008, 14, 1145-1154 10.1002/chem.200700783
32. Castor, K. J.; Mancini, J.; Fakhoury, J.; Weill, N.; Kieltyka, R.; Englebienne, P.; Avakyan, N.; Mittermaier, A.; Autexier, C.; Moitessier, N.; Sleiman, H. F. Platinum(II) phenanthroimidazoles for targeting telomeric G-quadruplexes ChemMedChem 2012, 7, 85-94 10.1002/cmdc.201100453
33. Castor, K. J.; Liu, Z.; Fakhoury, J.; Hancock, M. A.; Mittermaier, A.; Moitessier, N.; Sleiman, H. F. A platinum(ii) phenylphenanthroimidazole with an extended side-chain exhibits slow dissociation from a c-kit G-quadruplex motif Chem.-Eur. J. 2013, 19, 17836-17845 10.1002/chem.201301590
34. Lawandi, J.; Toumieux, S.; Seyer, V.; Campbell, P.; Thielges, S.; Juillerat-Jeanneret, L.; Moitessier, N. Constrained Peptidomimetics Reveal Detailed Geometric Requirements of Covalent Prolyl Oligopeptidase Inhibitors J. Med. Chem. 2009, 52, 6672-6684 10.1021/jm901013a
35. De Cesco, S.; Deslandes, S.; Therrien, E.; Levan, D.; Cueto, M.; Schmidt, R.; Cantin, L. D.; Mittermaier, A.; Juillerat-Jeanneret, L.; Moitessier, N. Virtual screening and computational optimization for the discovery of covalent prolyl oligopeptidase inhibitors with activity in human cells J. Med. Chem. 2012, 55, 6306-6315 10.1021/jm3002839
36. Ouyang, X.; Zhou, S.; Su, C. T. T.; Ge, Z.; Li, R.; Kwoh, C. K. CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints J. Comput. Chem. 2013, 34, 326-336 10.1002/jcc.23136
37. London, N.; Miller, R. M.; Krishnan, S.; Uchida, K.; Irwin, J. J.; Eidam, O.; Gibold, L.; Cimermančič, P.; Bonnet, R.; Shoichet, B. K.; Taunton, J. Covalent docking of large libraries for the discovery of chemical probes Nat. Chem. Biol. 2014, 10, 1066-1072 10.1038/nchembio.1666
38. Mariaule, G.; De Cesco, S.; Airaghi, F.; Kurian, J.; Schiavini, P.; Rocheleau, S.; Huskić, I.; Auclair, K.; Mittermaier, A.; Moitessier, N. 3-Oxo-hexahydro-1H-isoindole-4-carboxylic Acid as a Drug Chiral Bicyclic Scaffold: Structure-Based Design and Preparation of Conformationally Constrained Covalent and Noncovalent Prolyl Oligopeptidase Inhibitors J. Med. Chem. 2016, 59, 4221-4234 10.1021/acs.jmedchem.5b01296
39. Campagna-Slater, V.; Pottel, J.; Therrien, E.; Cantin, L.-D.; Moitessier, N. Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s J. Chem. Inf. Model. 2012, 52, 2471-2483 10.1021/ci3003073
40. Schiavini, P.; Pottel, J.; Moitessier, N.; Auclair, K. Metabolic Instability of Cyanothiazolidine-Based Prolyl Oligopeptidase Inhibitors: A Structural Assignment Challenge and Potential Medicinal Chemistry Implications ChemMedChem 2015, 10, 1174-1183 10.1002/cmdc.201500114
41. Bernard-Gauthier, V.; Aliaga, A.; Aliaga, A.; Boudjemeline, M.; Hopewell, R.; Kostikov, A.; Rosa-Neto, P.; Thiel, A.; Schirrmacher, R. Syntheses and evaluation of carbon-11- and fluorine-18-radiolabeled pan-tropomyosin receptor kinase (Trk) inhibitors: Exploration of the 4-aza-2-oxindole scaffold as Trk PET imaging agents ACS Chem. Neurosci. 2015, 6, 260-276 10.1021/cn500193f
42. Pottel, J.; Therrien, E.; Gleason, J. L.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 6. Development and application to the docking of HDACs and other zinc metalloenzymes inhibitors J. Chem. Inf. Model. 2014, 54, 254-265 10.1021/ci400550m
43. Santos-Martins, D.; Forli, S.; Ramos, M. J.; Olson, A. J. AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins J. Chem. Inf. Model. 2014, 54, 2371-2379 10.1021/ci500209e
44. Mendoza-Sanchez, R.; Cotnoir-White, D.; Kulpa, J.; Jutras, I.; Pottel, J.; Moitessier, N.; Mader, S.; Gleason, J. L. Design, synthesis and evaluation of antiestrogen and histone deacetylase inhibitor molecular hybrids Bioorg. Med. Chem. 2015, 23, 7597-7606 10.1016/j.bmc.2015.11.005
45. Therrien, E.; Weill, N.; Tomberg, A.; Corbeil, C. R.; Lee, D.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy J. Chem. Inf. Model. 2014, 54, 3198-3210 10.1021/ci500299h
46. Xu, W.; Lucke, A. J.; Fairlie, D. P. Comparing sixteen scoring functions for predicting biological activities of ligands for protein targets J. Mol. Graphics Modell. 2015, 57, 76-88 10.1016/j.jmgm.2015.01.009