3D-QSAR based on quantum-chemical molecular fields: Toward an improved description of halogen interactions

Journal of Chemical Information and Modeling

Volumn 52, Issue 9, 2012, Pages 2441-2453

  Güssregen, Stefan ^a   Matter, Hans ^a   Hessler, Gerhard ^a   Müller, Marco ^a   Schmidt, Friedemann ^a   Clark, Timothy ^b,c  

^a SANOFI AVENTIS DEUTSCHLAND GMBH   (Germany)

^b UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

^c UNIVERSITY OF PORTSMOUTH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ATOMS; BIOACTIVITY; COMPLEXATION; ELECTRON AFFINITY; ELECTROSTATICS; HYDROGEN BONDS; IONS; LEAST SQUARES APPROXIMATIONS; LIGANDS; POLARIZATION; QUANTUM CHEMISTRY; QUANTUM THEORY; REGRESSION ANALYSIS;

BIOLOGICAL AFFINITY; CLASSICAL FORCE FIELDS; LOCAL IONIZATION ENERGIES; NON-COVALENT INTERACTION; PARTIAL LEAST-SQUARES REGRESSION; POLARIZABILITY EFFECTS; QUANTUM MECHANICAL; SPECIFIC INTERACTION;

COMPUTATIONAL CHEMISTRY;

HALOGEN;

ARTICLE; METABOLISM; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM THEORY;

HALOGENS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; QUANTUM THEORY;

EID: 84866693984     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300253z     Document Type: Article

References (78)

1. Böhm, H.-J.; Banner, D.; Bendels, S.; Kansy, M.; Kuhn, B.; Müller, K.; Obst-Sander, U.; Stahl, M. Fluorine in medicinal chemistry ChemBioChem 2004, 5, 637-643
2. Hagmann, W. K. The Many Roles for Fluorine in Medicinal Chemistry J. Med. Chem. 2008, 51, 4359-4369
3. Ismael, F. M. D. Important fluorinated drugs in experimental and clinical use J. Fluorine Chem. 2002, 118, 27-33
4. Gerebtzoff, G.; Li-Blatter, X.; Fischer, H.; Frentzel, A.; Seelig, A. Halogenation of drugs enhances membrane binding and permeation ChemBioChem 2004, 5, 676-684
5. Politzer, P.; Murray, J. S.; Clark, T. Halogen bonding: an electrostatically-driven highly directional noncovalent interaction Phys. Chem. Chem. Phys. 2010, 12, 7748-7757
6. El Kerdawy, A.; Wick, C. R.; Hennemann, M.; Clark, T. Predicting the Sites and Energies of Noncovalent Intermolecular Interactions Using Local Properties, J. Chem. Inf. Model., 2012, 52, 1061 - 1071.
7. Murray, J. S.; Riley, K. E.; Politzer, P.; Clark, T. Directional Weak Interactions: σ-Hole Bonding Aus. J. Chem 2010, 63, 1598-1607
8. Clark, T.; Hennemann, M.; Murray, J. S.; Politzer, P. Halogen bonding: the σ-hole J. Mol. Model. 2007, 13, 291-296
9. Murray, J. S.; Lane, P.; Clark, T.; Politzer, P. σ-Hole bonding: molecules containing group VI atoms J. Mol. Model. 2007, 13, 1033-1038
10. Murray, J. S.; Lane, P.; Clark, T.; Riley, K. E.; Politzer, P. σ-Holes, π-holes and electrostatically-driven interactions J. Mol. Model. 2012, 18, 541-548
11. Metrangolo, P.; Resnati, G. Halogen Bonding: Fundamentals and Applications; Springer: Berlin, 2008.
12. Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. An overview of halogen bonding J. Mol. Model. 2007, 13, 305-311
13. Hardegger, L. A.; Kuhn, B.; Spinnler, B.; Anselm, L.; Ecabert, R.; Stihle, M.; Gsell, B.; Thoma, R.; Diez, J.; Benz, J.; Plancher, J.-M.; Hartmann, G.; Banner, D. W.; Haap, W.; Diederich, F. Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions Angew. Chem., Int. Ed. 2011, 50, 314-318
14. Hardegger, L. A.; Kuhn, B.; Spinnler, B.; Anselm, L.; Ecabert, R.; Stihle, M.; Gsell, B.; Thoma, R.; Diez, J.; Benz, J.; Plancher, J.-M.; Hartmann, G.; Isshiki, Y.; Morikami, K.; Shimma, N.; Haap, W.; Banner, D. W.; Diederich, F. Halogen Bonding at the Active Sites of Human Cathepsin L and MEK1 Kinase: Efficient Interactions in Different Environments ChemMedChem 2011, 6, 2048-2054
15. Clark, M.; Cramer, R. D.; Van Opdenbosch, N. Validation of the general purpose Tripos 5.2 force field J. Comput. Chem. 1989, 10, 982-1012
16. Halgren, T. A. Maximally diagonal force constants in dependent angle-bending coordinates. II. Implications for the design of empirical force fields J. Am. Chem. Soc. 1990, 112, 4710-4723
17. Halgren, T. A. MMFF VI. MMFF94s option for energy minimization studies J. Comput. Chem. 1999, 20, 720-729
18. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
19. Ibrahim, M. A. A. Molecular Mechanical Study of Halogen Bonding in Drug Discovery J. Comput. Chem. 2011, 32, 2564-2574
20. Kolar, M.; Hobza, P. On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds J. Chem. Theory Comput. 2012, 8, 1325-1333
21. Jorgensen, W. L.; Schyman, P. Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents. J. Chem. Theory Comput., DOI: 10.1021/ct300180w
22. Politzer, P.; Murray, J. S.; Concha, M. C. σ-hole bonding between like atoms; a fallacy of atomic charges J. Mol. Model. 2008, 14, 659-665
23. 3D-QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden (NL), 1993.
24. Cramer, R. D., III; Patterson, D. E.; Bunce, J. E. Comparative Molecular Field Analysis (CoMFA). 1. Effect of Shape on Binding of Steroids to Carrier Proteins J. Am. Chem. Soc. 1988, 110, 5959-5967
25. Clark, M.; Cramer, R. D., III; Jones, D. M.; Patterson, D. E.; Simeroth, P. E. Comparative Molecular Field Analysis (CoMFA). 2. Towards its use with 3D-Structural Databases Tetrahed. Comp. Meth. 1990, 3, 47-59
26. Geerlings, P.; De Proft, F.; Langenaeker, W. Conceptual Density Functional Theory Chem. Rev. 2003, 103, 1793-1874
27. Van Damme, S.; Bultinck, P. 3D QSAR based on conceptual DFT molecular fields: Antituberculotic activity J. Mol. Struct. THEOCHEM 2010, 943, 83-89
28. Beck, M. E.; Schindler, M. Quantitative structure-activity relations based on quantum theory and wavelet transformations Chem. Phys. 2009, 356, 121-130
29. Ehresmann, B.; Martin, B.; Horn, A.H. C.; Clark, T. Local molecular properties and their use in predicting reactivity J. Mol. Model. 2003, 9, 342-347
30. Clark, T. QSAR and QSPR based solely on surface properties? J. Mol. Graphics Model. 2004, 22, 519-525
31. El Kerdawy, A.; Wick, C. R.; Hennemann, M.; Clark, T. Predicting the Sites and Energies of Non-Covalent Intermolecular Interactions Using Local Properties. J. Chem. Inf. Model. 2012, not supplied.
32. Sjoberg, P.; Murray, J. S.; Brinck, T.; Politzer, P. Average local ionization energies on the molecular surfaces of aromatic systems as guides to chemical reactivity Can. J. Chem. 1990, 68, 1440-1443
33. Clark, T. The Local Electron Affinity for Non-Minimal Basis Sets J. Mol. Model. 2010, 16, 1231-1238
34. Mulliken, R. S. New electroaffinity scale; together with data on valence states and on valence ionization potentials and electron affinities J. Chem. Phys. 1934, 2, 782-793
35. Pearson, R. G. Absolute electronegativity and hardness: application to inorganic chemistry Inorg. Chem. 1988, 27, 734-740
36. Matter, H.; Will, D. W.; Nazaré, M.; Schreuder, H.; Laux, V.; Wehner, V. Structural Requirements for Factor Xa Inhibition by 3-Oxybenzamides with Neutral P1 Substituents: Combining X-ray Crystallography, 3D-QSAR, and Tailored Scoring Functions J. Med. Chem. 2005, 48, 3290-3312
37. Wong, G.; Koehler, K. F.; Skolnick, P.; Gu, Z. Q.; Ananthan, S.; Schönholzer, P.; Hunkeler, W.; Zhang, W.; Cook, J. M. Synthetic and computer-assisted analysis of the structural requirements for selective, high-affinity ligand binding to diazepam-insensitive benzodiazepine receptors J. Med. Chem. 1993, 36, 1820-1830
38. Wold, S.; Albano, C.; Dunn, W. J.; Edlund, U.; Esbenson, K.; Geladi, P.; Hellberg, S.; Lindberg, W.; Sjöström, M., In Chemometrics: Mathematics and Statistics in Chemistry; Kowalski, B., Ed.; Reidel, Dortrecht: The Netherlands, 1984, pp 17-95.
39. Dunn, W. J.; Wold, S.; Edlund, U.; Hellberg, S.; Gasteiger, J. Multivariate Structure-Activity Relationship Between Data from a Battery of Biological Tests and an Ensemble of Structure Descriptors: The PLS Method Quant. Struct.-Act. Relat. 1984, 3, 31-137
40. Geladi, P. Notes on the History and nature of Partial Least Squares (PLS) Modelling J. Chemom. 1988, 2, 231-246
41. Wold, S. Cross-Validatory Estimation of the Number of Component in Factor and Principal Component Models Technometrics 1978, 4, 397-405
42. Diaconis, P.; Efron, B. Computer-Intensive Methods for Statistics Sci. Am. 1984, 116, 96-117
43. Cramer, R. D., III.; Bunce, J. D.; Patterson, D. E. Crossvalidation, Bootstrapping and Partial Least Squares Compared wih Multiple Regression in Conventional QSAR Studies Quant.-Struct.-Act. Relat. 1988, 7, 18-25
44. McMartin, C.; Bohacek, R. S. QXP: powerful, rapid computer algorithms for structure-based drug design J. Comput.-Aided Mol. Des. 1997, 11, 333-344
45. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins J. Am. Chem. Soc. 1984, 106, 765-784
46. Allinger, N. L. Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms J. Am. Chem. Soc. 1977, 99, 8127-8134
47. Binkley, J. S.; Pople, J. A.; Hehre, W. J. Self-consistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements J. Am. Chem. Soc. 1980, 102, 939-947
48. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 1985, 107, 3902-3909
49. Stewart, J. J. P. MOPAC2000, Fujitsu, Ltd, Tokyo, Japan, 1999.
50. MOPAC 6.0 was once available as Stewart, J. J. P. QCPE no. 455, Quantum Chemistry Program Exchange; Bloomsville, IN, 1990.
51. MOPAC6; Cepos InSilico Ltd., Bedford MK42 8BQ, UK, 2009.
52. Parasurf'10; Cepos InSilico Ltd, Bedford MK42 8BQ, UK, 2010.
53. Sybyl x1.3; Tripos International, St. Louis, MO, USA, 2010.
54. Sheridan, R. P.; Nachbar, R. B.; Bush, B. L. Extending the trend vector: The trend matrix and sample-based partial least squares J. Comput.-Aided Mol. Des. 1994, 8, 323-340
55. Thibaut, U.; Folkers, G.; Klebe, G.; Kubinyi, H.; Merz, A.; Rognan, D. Recommendations for CoMFA Studies and 3D QSAR Publications. In 3D QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993; pp 711-717.
56. Folkers, G.; Merz, A.; Rognan, D. CoMFA: Scope and Limitations. In 3D QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993; pp 583-616.
57. Cramer, R. D., III; DePriest; S. A.; Patterson; D. E.; Hecht, P. The Developing Practice of Comparative Molecular Field Analysis. In 3D QSAR in Drug Design. Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, The Netherlands, 1993; pp 443-485.
58. Klebe, G.; Abraham, U.; Mietzner, T. Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity J. Med. Chem. 1994, 37, 4130-4146
59. Horn, A. H. C.; Lin, J.-H.; Clark, T. Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets Theor. Chem. Acc. 2005, 114, 159-168
60. Theor. Chem. Acc. 2007, 117, 461-465.
61. Colapietro, M.; Domenicano, A. Structural studies of benzene derivatives. X. Refinement of the structure of p-chlorobenzoic acid Acta Crystallogr. Sect. B: Struct. Crystallogr. Cryst. Chem. 1982, B38, 1953-1957
62. CSD, version 5.33 (November 2011), available from The Cambridge Crystallographic Data Centre (CCDC): 12 Union Road, Cambridge, CB2, 1EZ, UK.
63. IUPAC. Compendium of Chemical Terminology, 2 nd ed. (the ″Gold Book″); McNaught, A. D.,; Wilkinson, A. Blackwell Scientific Publications: Oxford, 1997.
64. Nic, M.; Jirat, J.; Kosata, B. XML on-line corrected version. http://goldbook.iupac.org (2006); Jenkins, A., Ed.; doi: 10.1351/goldbook.
65. Golbraikh, A.; Tropsha, A. Beware of q2! J. Mol. Graph. Model. 2002, 20, 269-276
66. Matter, H.; Nazaré, M.; Güssregen, S.; Will, D. W.; Schreuder, H.; Bauer, A.; Urmann, M.; Ritter, K.; Wagner, M.; Wehner, V. Evidence for C-Cl/C-Br...π Interactions as an Important Contribution to Protein-Ligand Binding Affinity Angew. Chem., Int. Ed. 2009, 48, 2911-2916
67. Nazaré, M.; Will, D. W.; Matter, H.; Schreuder, H.; Ritter, K.; Urmann, M.; Essrich, M.; Bauer, A.; Wagner, M.; Czech, J.; Lorenz, M.; Laux, V.; Wehner, V. Probing the Subpockets of Factor Xa Reveals Two Binding Modes for Inhibitors Based on a 2-Carboxyindole Scaffold: A Study Combining Structure-Activity Relationship and X-ray Crystallography J. Med. Chem. 2005, 48, 4511-4525
68. Tucker, T. J.; Brady, S. F.; Lumma, W. C.; Lewis, S. D.; Gardell, S. J.; Naylor-Olsen, A. M.; Yan, Y.; Sisko, J. T.; Stauffer, K. J.; Lucas, B. J.; Lynch, J. J.; Cook, J. J.; Stranieri, M. T.; Holahan, M. A.; Lyle, E. A.; Baskin, E. P.; Chen, I. W.; Dancheck, K. B.; Krueger, J. A.; Cooper, C. M.; Vacca, J. P. Design and Synthesis of a Series of Potent and Orally Bioavailable Noncovalent Thrombin Inhibitors That Utilize Nonbasic Groups in the P1 Position J. Med. Chem. 1998, 41, 3210-3219
69. Adler, M.; Kochanny, M. J.; Ye, B.; Rumnenik, G.; Light, D. R.; Biancalana, S.; Whitlow, M. Crystal Structures of Two Potent Nonamidine Inhibitors Bound to Factor Xa Biochemistry 2002, 41, 15514-15523
70. Stubbs, M. T.; Reyda, S.; Dullweber, F.; Moller, M.; Klebe, G.; Dorsch, D.; Mederski, W. W. K. R.; Wurziger, H. pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design ChemBioChem 2002, 3, 246-249
71. Maignan, S.; Guilloteau, J.-P.; Choi-Sledeski, Y. M.; Becker, M. R.; Ewing, W. R.; Pauls, H. W.; Spada, A. P.; Mikol, V. Molecular Structures of Human Factor Xa Complexed with Ketopiperazine Inhibitors: Preference for a Neutral Group in the S1 Pocket J. Med. Chem. 2003, 46, 685-690
72. Roehrig, S.; Straub, A.; Pohlmann, J.; Lampe, T.; Pernerstorfer, J.; Schlemmer, K.-H.; Reinemer, P.; Perzborn, E. Discovery of the Novel Antithrombotic Agent 5-Chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]- 1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): An Oral, Direct Factor Xa Inhibitor J. Med. Chem. 2005, 48, 5900-5908
73. Hartshorn, M. J.; Murray, C. W.; Cleasby, A.; Frederickson, M.; Tickle, I. J.; Jhoti, H. Fragment-Based Lead Discovery Using X-Ray Crystallography J. Med. Chem. 2005, 48, 403-413
74. Shi, Y.; Sitkoff, D.; Zhang, J.; Klei, H. E.; Kish, K.; Liu, E.C.-K.; Hartl, K. S.; Seiler, S. M.; Chang, M.; Huang, C.; Youssef, S.; Steinbacher, T. E.; Schumacher, W. A.; Grazier, N.; Pudzianowski, A.; Apedo, A.; Discenza, L.; Yanchunas, J.; Stein, P. D.; Atwal, K. S. Design, Structure-Activity Relationships, X-ray Crystal Structure, and Energetic Contributions of a Critical P1 Pharmacophore: 3-Chloroindole-7-yl-Based Factor Xa Inhibitors J. Med. Chem. 2008, 51, 7541-7551
75. Straub, A.; Roehrig, S.; Hillisch, A. Entering the era of non-basic P1 site groups: discovery of Xarelto (Rivaroxaban) Curr. Top. Med. Chem. 2010, 10, 257-269
76. Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding J. Am. Chem. Soc. 2008, 130, 2817-2831
77. Abel, R.; Salam, N. K.; Shelley, J.; Farid, R.; Friesner, R. A.; Sherman, W. Contribution of Explicit Solvent Effects to the Binding Affinity of Small-Molecule Inhibitors in Blood Coagulation Factor Serine Proteases ChemMedChem 2011, 6, 1049-1066
78. Hansch, C.; Leo, A.; Hoekman, D. Exploring QSAR: Hydrophobic, Electronic and Steric Constants; Americal Chemical Society: Washington DC, US, 1995.