Computational prediction of structure-Activity Relationships for the Binding of Aminocyclitols to β-Glucocerebrosidase

Journal of Chemical Information and Modeling

Volumn 51, Issue 3, 2011, Pages 601-611

  Díaz, Lucía ^a,c   Bujons, Jordi ^b   Delgado, Antonio ^a,c   Gutiérrez De Terán, Hugo ^d   Åqvist, Johan ^e  

^a Research Unit on Bioactive Molecules (RUBAM)   (Spain)

^b INSTITUTE OF ADVANCED CHEMISTRY OF CATALONIA IQAC CSIC   (Spain)

^c UNIVERSITY OF BARCELONA   (Spain)

^d HOSPITAL CLÍNICO UNIVERSITARIO   (Spain)

^e UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; FREE ENERGY; LIGANDS; MOLECULAR DYNAMICS;

BINDING FREE ENERGY; COMPUTATIONAL APPROACH; COMPUTATIONAL MODEL; COMPUTATIONAL PREDICTIONS; INTERACTION ENERGIES; MEAN UNSIGNED ERRORS; NEW THERAPEUTIC AGENT; STRUCTURE ACTIVITY RELATIONSHIPS;

BINDING ENERGY;

CYCLITOL; GLUCOSYLCERAMIDASE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DOCKING; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION;

CYCLITOLS; GLUCOSYLCERAMIDASE; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 79953230555     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci100453a     Document Type: Article

References (43)

1. De Benedetti, P. G.; Fanelli, F. Ligand-receptor communication and drug design Curr. Protein Pept. Sci. 2009, 10, 186-193
2. Ringe, D.; Petsko, G. A. What are pharmacological chaperones and why are they interesting? J. Biol. 2009, 8, 80
3. Grabowski, G. A. Treatment perspectives for the lysosomal storage diseases Expert Opin. Emerging Drugs 2008, 13, 197-211 (Pubitemid 351448710)
4. Butters, T. D. Gaucher disease Curr. Opin. Chem. Biol. 2007, 11, 412-418 (Pubitemid 47302848)
5. Parenti, G. Treating lysosomal storage diseases with pharmacological chaperones: from concept to clinics EMBO Mol. Med. 2009, 1, 268-279
6. Sanchez-Ruiz, J. M. Ligand effects on protein thermodynamic stability Biophys. Chem. 2007, 126, 43-9 (Pubitemid 46186638)
7. Serrano, P.; Llebaria, A.; Delgado, A. Regio- and stereoselective synthesis of aminoinositols and 1,2-diaminoinositols from conduritol B epoxide J. Org. Chem. 2005, 70, 7829-7840 (Pubitemid 41377487)
8. Serrano, P.; Casas, J.; Zucco, M.; Emeric, G.; Egido-Gabas, M.; Llebaria, A.; Delgado, A. Combinatorial Approach to N-Substituted Aminocyclitol Libraries by Solution-Phase Parallel Synthesis and Preliminary Evaluation as Glucocerebrosidase Inhibitors J. Comb. Chem. 2007, 9, 43-52
9. Egido-Gabas, M.; Canals, D.; Casas, J.; Llebaria, A.; Delgado, A. Aminocyclitols as Pharmacological Chaperones for Glucocerebrosidase, a Defective Enzyme in Gaucher Disease ChemMedChem 2007, 2, 992-994
10. Sawkar, A. R.; Cheng, W. C.; Beutler, E.; Wong, C. H.; Balch, W. E.; Kelly, J. W. Chemical chaperones increase the cellular activity of N370S beta -glucosidase: a therapeutic strategy for Gaucher disease Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15428-15433 (Pubitemid 35403951)
11. Sanchez-Olle, G.; Duque, J.; Egido-Gabas, M.; Casas, J.; Lluch, M.; Chabas, A.; Grinberg, D.; Vilageliu, L. Promising results of the chaperone effect caused by iminosugars and aminocyclitol derivatives on mutant glucocerebrosidases causing Gaucher disease Blood Cells, Mol., Dis. 2009, 42, 159-166
12. Diaz, L.; Bujons, J.; Casas, J.; Llebaria, A.; Delgado, A. Click Chemistry Approach to New N-Substituted Aminocyclitols as Potential Pharmacological Chaperones for Gaucher Disease J. Med. Chem. 2010, 53, 5248-5255
13. Egido-Gabas, M.; Serrano, P.; Casas, J.; Llebaria, A.; Delgado, A. New aminocyclitols as modulators of glucosylceramide metabolism Org. Biomol. Chem. 2005, 3, 1195-201 (Pubitemid 40538238)
14. Brumshtein, B.; Greenblatt, H. M.; Butters, T. D.; Shaaltiel, Y.; Aviezer, D.; Silman, I.; Futerman, A. H.; Sussman, J. L. Crystal structures of complexes of N-butyl- and N-nonyl-deoxynojirimycin bound to acid beta-glucosidase: insights into the mechanism of chemical chaperone action in Gaucher disease J. Biol. Chem. 2007, 282, 29052-29058 (Pubitemid 47606022)
15. Lieberman, R. L.; Wustman, B. A.; Huertas, P.; Powe, A. C., Jr.; Pine, C. W.; Khanna, R.; Schlossmacher, M. G.; Ringe, D.; Petsko, G. A. Structure of acid beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease Nat. Chem. Biol. 2007, 3, 101-107 (Pubitemid 46134996)
16. Bas, D. C.; Rogers, D. M.; Jensen, J. H. Very fast prediction and rationalization of pKa values for protein-ligand complexes Proteins 2008, 73, 765-783 (Pubitemid 352788657)
17. Li, H.; Robertson, A. D.; Jensen, J. H. Very fast empirical prediction and rationalization of protein pKa values Proteins 2005, 61, 704-721 (Pubitemid 41753142)
18. Maestro, version 8.5; Schrödinger, LLC: New York, NY, 2008.
19. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, 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 (Pubitemid 26399746)
20. LigPrep, version 2.2; Schrödinger, LLC: New York, NY, 2005.
21. Glide, version 5.0; Schrödinger, LLC: New York, NY, 2008.
22. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 2004, 47, 1739-1749 (Pubitemid 38380917)
23. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes J. Med. Chem. 2006, 49, 6177-6196 (Pubitemid 44595196)
24. Diaz, L.; Bujons, J.; Casas, J.; Llebaria, A.; Delgado, A. New glucocerebrosidase inhibitors by exploration of chemical diversity of N substituted aminocyclitols using click chemistry and in situ screening. J. Med. Chem. 2011, 54, accepted.
25. Marelius, J.; Kolmodin, K.; Feierberg, I.; Åqvist, J. Q An MD program for free energy calculations and empirical valence bond simulations in biomolecular systems J Mol. Graph. Modell. 1999, 16, 213-225 (Pubitemid 30069589)
26. MacroModel, version 9.6; Schrödinger, LLC: New York, NY, 2005.
27. Jorgensen, W.; Chandrasekhar, J.; Madura, J.; Rw, I.; Klein, M. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
28. King, G.; Warshel, A. A Surface Constrained All-Atom Solvent Model for Effective Simulations of Polar Solutions J. Chem. Phys. 1989, 91, 3647-3661
29. Lee, F. S.; Chu, Z. T.; Bolger, M. B.; Warshel, A. Calculations of Antibody-Antigen Interactions: Microscopic and Semi-Microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603 Protein Eng. 1992, 5, 215-228
30. Åqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design Protein Eng. 1994, 7, 385-391 (Pubitemid 24063137)
31. Hansson, T.; Marelius, J.; Åqvist, J. Ligand binding affinity prediction by linear interaction energy methods J. Comput.-Aided Mol. Des. 1998, 12, 27-35 (Pubitemid 128513811)
32. Almlof, M.; Carlsson, J.; Aqvist, J. Improving the accuracy of the linear interaction energy method for solvation free energies J. Chem. Theory Comput. 2007, 3, 2162-2175
33. Almlöf, M.; Brandsdal, B. O.; Åqvist, J. Binding Affinity Prediction with Different Force Fields: Examination of the Linear Interaction Energy Method J. Comput. Chem. 2004, 25, 1242-1254
34. Cheng, Y.; Prusoff, W. H. Relationship between the inhibition constant (Ki) and the concentration of inhibitor which causes 50% inhibition (I50) of an enzymatic reaction Biochem. Pharmacol. 1973, 22, 3099-3108
35. Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of drug binding affinities by comparative binding energy analysis J. Med. Chem. 1995, 38, 2681-2691
36. SIMCA-P+, version 12.0; Umetrics: Umeå, Sweden.
37. Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Combining docking and molecular dynamic simulations in drug design Med. Res. Rev. 2006, 26, 531-568 (Pubitemid 44230412)
38. Sham, Y.; Chu, Z. T.; Tao, H.; Warshel, A. Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease Proteins 2000, 39, 393-407 (Pubitemid 30414177)
39. Gutiérrez-de-Terán, H.; Nervall, M.; Ersmark, K.; Dunn, B. M.; Hallberg, A.; Åqvist, J. Inhibitor Binding to the Plasmepsin IV Aspartic Protease from Plasmodium Falciparum Biochemistry 2006, 45, 10529-10541 (Pubitemid 44320469)
40. Wang, W.; Wang, J.; Kollman, P. A. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations? Proteins 1999, 34, 395-402 (Pubitemid 29071680)
41. Carlsson, J.; Boukharta, L.; Aqvist, J. Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase J. Med. Chem. 2008, 51, 2648-2656 (Pubitemid 351620786)
42. Bjelic, S.; Nervall, M.; Gutierrez-de-Teran, H.; Ersmark, K.; Hallberg, A.; Aqvist, J. Computational inhibitor design against malaria plasmepsins Cell. Mol. Life Sci. 2007, 64, 2285-2305 (Pubitemid 47347955)
43. Nervall, M.; Hanspers, P.; Carlsson, J.; Boukharta, L.; Aqvist, J. Predicting binding modes from free energy calculations J. Med. Chem. 2008, 51, 2657-2667 (Pubitemid 351620787)