In silico prediction of human serum albumin binding for drug leads

Expert Opinion on Drug Discovery

Volumn 8, Issue 5, 2013, Pages 583-595

  Vallianatou, Theodosia ^a   Lambrinidis, George ^a   Tsantili Kakoulidou, Anna ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

HSA binding; HSA crystal structures; Ligand based modeling; Property based drug design; QSAR methodology; Structure based modeling

Indexed keywords

BENZODIAZEPINE DERIVATIVE; DICARBOXYLIC ACID; DIGITOXIN; SERUM ALBUMIN; WARFARIN;

BINDING AFFINITY; CHEMICAL STRUCTURE; CHINESE MEDICINE; COMPUTER MODEL; CRYSTAL STRUCTURE; DRUG BINDING; DRUG BINDING SITE; DRUG CLEARANCE; DRUG PENETRATION; DRUG SAFETY; HUMAN; HYDROGEN BOND; LIPOPHILICITY; MOLECULAR DOCKING; PARTITION COEFFICIENT; PHYSICAL CHEMISTRY; PLASMA PROTEIN BINDING; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTITATIVE STRUCTURE PROPERTY RELATION; REVIEW; THERMOSTABILITY;

COMPUTER SIMULATION; DRUG DISCOVERY; HUMANS; LIGANDS; MODELS, BIOLOGICAL; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; SERUM ALBUMIN;

EID: 84876745282     PISSN: 17460441     EISSN: 1746045X     Source Type: Journal    
DOI: 10.1517/17460441.2013.777424     Document Type: Review

References (109)

1. Kola I, Landis J. Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov 2004;3:711-15
2. Gaviraghi G, Barnaby RJ, Pellegatti M. Pharmacokinetic challenges in lead optimization. In: Testa B, van de Waterbeemd H, Folkers G, Guy R, editors. Pharmacokinetic optimization in drug research. Verlag Helvetica Chimica Acta, Zürich; 2001. p. 3-14
3. Testa B, Vistoli G, Pedretti A. Musings on ADME predictions and structure - activity relations. Chem Biodiver 2005;2:1411-27
4. Rogge MC, Taft DR. Preclinical drug development. In: Swarbrick J, editor. Drugs and the pharmaceutical sciences. Volume 187. Informa Healthcare, USA; 2010
5. Smith DA, van de Waterbeemd H. Pharmacokinetics and metabolism in early drug discovery. Curr Opin Chem Biol 1999;4:373-8
6. Hollósy F, Valkó K, Hersey A, et al. Estimation of volume of distribution in humans from high throughput HPLC-based measurements of human serum albumin binding and immobilized artificial membrane. J Med Chem 2006;49:6958-71
7. Ito K, Iwatsubo T, Kanamitsu S, et al. Quantitative prediction of in vivo drug clearance and drug interactions from in vitro data on metabolism together with binding and transport. Ann Rev Pharmacol Toxicol 1998;38:461-99
8. Rowley M, Kulagowski JJ, Watt AP, et al. Effect of plasma protein binding on in vivo activity and brain penetration of glycine/NMDA receptor antagonists. J Med Chem 1997;40:4053-68
9. Rolan PE. Plasma protein binding displacement interactions-Why are they regarded as clinically important? Br J Clin Pharmacol 1994;37:125-8
10. Hage DS. High performance affinity chromatography: a powerful tool for studying serum protein binding. J Chromatogr B 2002;768:3-30
11. Noctor TAG, Wainer IW, Hage DS. Allosteric and competitive displacement of drugs from human serum albumin by octanoic acid, as revealed by high-performance liquid affinity chromatography, on a human serum albumin-based stationary phase. J Chromatogr Biomed Appl 1992;577:305-15
12. Benet LZ, Hoener B. Changes in plasma protein binding have little clinical relevance. Clin Pharmacol Ther 2002;71:115-21
13. Smith DA, Di L, Kerns EH. The effect of plasma protein binding on in vivo efficacy: misconceptions in drug discovery. Nat Rev Drug Discov 2010;9:929-39
14. Stamler JS, Jaraki O, Osborne J, et al. Nitric oxide circulates in mammalian plasma primarily as a S-nitroso adduct of serum albumin. Proc Natl Acad Sci USA 1992;89:7674-7
15. Torres E, Aburto J. Chloroperoxidase-catalyzed oxidation of 4,6-dimethyldibenzothiophene as dimer complexes: evidence for kinetic cooperativity. Arch Biochem Biophys 2005;437:224-32
16. Bertucci C, Andrisano V, Gotti R, Cavrini VJ. Use of an immobilised human serum albumin HPLC column as a probe of drug-protein interactions: the reversible binding of valproate. J Chromatogr B 2002;768:147-55
17. Nobeli I, Favia AD, Thornton JM. Protein promiscuity and its implications for biotechnology. Nat Biotechnol 2009;27:157-67
18. Leo A, Hansch C, Elkins D. Partition coefficients and their uses. Chem Rev 1971;71:525-616 . Most cited historical publication.
19. Lejon S, Frick IM, Bjorck L, et al. Crystal structure and biological implications of a bacterial albumin binding module in complex with human serum albumin. J Biol Chem 2004;279:42924-8
20. Curry S, Brick P, Franks NP. Fatty acid binding to human serum albumin: new insights from crystallographic studies. Biochim Biophys Acta 1999;1441:131-40
21. Bujacz A. Structures of bovine, equine and leporine serum albumin. Acta Crystallogr D Biol Crystallogr 2012;68:1278-89
22. Carter DC, Ho JX. Structure of serum albumin. Adv Protein Chem 1994;45:153-203
23. Deeb O, Rosales-Hernández MC, Gómez-Castro C, et al. Exploration of human serum albumin binding sites by docking and molecular dynamics flexible ligand-protein interactions. Biopolymers 2010;93:161-70
24. Kratochwil NA, Huber W, Mu?ller F, et al. Predicting plasma protein binding of drugs: a new approach. Biochem Pharmacol 2002;64:1355-74
25. Petitpas I, Bhattacharya AA, Twine S, et al. Crystal structure analysis of warfarin binding to human serum albumin: anatomy of drug site I. J Biol Chem 2001;276:22804-9
26. Sudlow G, Birkett DJ, Wade DN. The characterization of two specific drug binding sites on human serum albumin. Mol Pharmacol 1975;11:824-32
27. Sjoholm I, Ekman B, Kober A, et al. Binding of drugs to human serum albumin:XI. The specificity of three binding sites as studied albumin immobilized in microparticles. Mol Pharmacol 1979;16:767-77
28. Petitpas I, Petersen CE, Ha CE, et al. Structural basis of albumin-thyroxine interactions and familial dysalbuminemic hyperthyroxinemia. Proc Natl Acad Sci USA 2003;100:6440-5
29. Ghuman J, Zunszain PA, Petitpas I, et al. Structural basis of the drug-binding specificity of human serum albumin. J Mol Biol 2005;353:38-52
30. Peters T. All about albumin: biochemistry, genetics and medical applications. Academic Press, San Diego; 1995
31. Curry S. Lessons from the crystallographic analysis of small molecule binding to human serum albumin. Drug Metab Pharmacokinet 2009;24:342-57
32. Kwong TC. Free drug measurements: methodology and clinical significance. Clin Chim Acta 1985;151:193-216
33. Barre J, Didey F, Delion F, Tillement JP. Problems in therapeutic drug monitoring: free drug level monitoring. Ther Drug Monit 1988;10:133-43
34. Chaiken IM. editor. Analytical affinity chromatography. CRC Press, Boca Raton, FL; 1987
35. Noctor TAG, Pham CD, Kaliszan R, Wainer IW. Stereochemical aspects of benzodiazepine binding to human serum albumin. I. Enantioselective high performance liquid affinity chromatographic examination of chiral and achiral binding interactions between 1,4-benzodiazepines and human serum albumin. Mol Pharm 1992;42:506-11
36. Nakano NI, Shimamori Y, Yamaguchi S. Binding capacities of human serum albumin monomer and dimer by continuous frontal affinity chromatography. J Chromatogr 1982;237:225-32
37. Ashton DS, Beddell CR, Cockerill GS, et al. Binding measurements of indolocarbazole derivatives to immobilised human serum albumin by high-performance liquid chromatography. J Chromatogr B 1996;677:194-8
38. Chrysanthakopoulos M, Giaginis C, Tsantili-Kakoulidou A. Retention of structurally diverse drugs in human serum albumin chromatography and its potential to simulate plasma protein binding. J Chromatogr A 2010;1217:5761-8
39. Fournier T, Medjoubi-N N, Porquet D. Alpha-1-acid glycoprotein. Biochim Biophys Acta 2000;1482:157-71
40. Huang Z. Effect of Alpha-1-Acid Glycoprotein binding on pharmacokinetics and Pharmacodynamics. Curr Drug Metab 2012; Epub ahead of print
41. Hervé F, Caron G, Duché JC, et al. Ligand specificity of the genetic variants of human alpha-1-acid glycoprotein. Generation of a 3D-QSAR model for drug binding to the A variant. Mol Pharm 1998;54:129-38
42. Kaliszan R, Nasal A, Turowski M. Binding site for basic drugs on alpha 1-acid glycoprotein as revealed by chemometric analysis of biochromatographic data. Biomed Chromatogr 1995;9:211-15
43. He XM, Carter DC. Atomic structure and chemistry of human serum albumin. Nature 1992;358:209-15
44. Zhu L, Yang F, Chen L, et al. A new drug binding subsite on human serum albumin and drug-drug interaction studied by X-ray crystallography. J Struct Biol 2008;162:40-9
45. Lejon S, Cramera JF, Nordberg P. Structural basis for the binding of naproxen to human serum albumin in the presence of fatty acids and the GA module. Acta Cryst 2008;F64:64-9
46. Almogren A, Furtado PB, Sun Z, et al. Purification, properties and extended solution structure of the complex formed between human immunoglobulin A1 and human serum albumin by scattering and ultracentrifugation. J Mol Biol 2006;356:413-31
47. Curry S, Mandelkow H, Brick P, Franks N. Crystal structure of human serum albumin complexed with fatty acid reveals an asymmetric distribution of binding sites. Nat Struct Biol 1998;5:827-35
48. Sugio S, Kashima A, Mochizuki S, et al. Crystal structure of human serum albumin at 2.5 A ° resolution. Protein Eng 1999;12:439-46
49. Bhattacharya AA, Gru?ne T, Curry S. Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin. J Mol Biol 2000;303:721-32
50. Bhattacharya AA, Curry S, Franks NP. Binding of the general anesthetics propofol and halothane to human serum albumin. J Biol Chem 2000;275:38731-8
51. Petitpas I, Gru?ne T, Bhattacharya AA, Curry S. Crystal structures of human serum albumin complexed with monounsaturated and polyunsaturated fatty acids. J Mol Biol 2001;314:955-60
52. Zunszain PA, Ghuman J, Komatsu T, et al. Crystal structural analysis of human serum albumin complexed with hemin and fatty acid. BMC Struct Biol 2003;3:6-14
53. Wardell M, Wang Z, Ho JX, et al. The atomic structure of human methemalbumin at 1.9 A ° . Biochem Biophys Res Commun 2002;291:813-19
54. Yang F, Bian C, Zhu L, et al. Effect of human serum albumin on drug metabolism: structural evidence of esterase activity of human serum albumin. J Struct Biol 2007;157:348-55
55. Zunszain PA, Ghuman J, McDonagh AF, Curry S. Crystallographic analysis of human serum albumin complexed with 4Z,15Ebilirubin- IXalpha. J Mol Biol 2008;381:394-406
56. Guo S, Shi X, Yang F, et al. Structural basis of transport of lysophospholipids by human serum albumin. Biochem J 2009;423:23-30
57. Ryan AJ, Ghuman J, Zunszain PA, et al. Structural basis of binding of fluorescent, site-specific dansylated amino acids to human serum albumin. J Struct Biol 2011;174:84-91
58. Hein KL, Kragh-Hansen U, Morth JP, et al. Crystallographic analysis reveals a unique lidocaine binding site on human serum albumin. J Struct Biol 2010;171:353-60
59. Buttar D, Colclough N, Gerhardt S, et al. A combined spectroscopic and crystallographic approach to probing drug-human serum albumin interactions. Bioorg Med Chem 2010;18:7486-96
60. Yamaguchi S, Aldini G, Ito S, et al. D12-Prostaglandin J2 as a product and ligand of human serum albumin: formation of an unusual covalent adduct at his146. J Am Chem Soc 2010;132:824-32
61. Ryan AJ, Chung C-W, Curry S. Crystallographic analysis reveals the structural basis of the high-affinity binding of iophenoxic acid to human serum albumin. Bmc Struct Biol 2011;11:18-24
62. He Y, Ning T, Xie T, et al. Large-scale production of functional human serum albumin from transgenic rice seeds. Proc Natl Acad Sci USA 2011;108:19078-83
63. Yang F, Ma Z, Ma L, et al. Human serum albumin-myristate-amantadine hydrochloride complex. Available from: http://www.rcsb.org/pdb/explore/explore. do?structureId=3uiv
64. Luo Z, Shi X, Hu Q, et al. Structural evidence of perfluorooctane sulfonate transport by human serum albumin. Chem Res Toxicol 2012;25:990-2
65. Wang Y, Luo Z, Shi X, et al. A fluorescent fatty acid probe, DAUDA, selectively displaces two myristates bound in human serum albumin. Protein Sci 2011;20:2095-101
66. Mao H, Hajduk PJ, Craig R, et al. Rational design of diflunisal analogues with reduced affinity for human serum albumin. J Am Chem Soc 2001;123:10429-35 . Successful case for optimization on both HSA and target receptor.
67. Sheppard GS, Wang J, Kawai M, et al. Discovery and optimization of anthranilic acid sulfonamides as inhibitors of methionine aminopeptidase-2: a structural basis for the reduction of albumin binding. J Med Chem 2006;49:3832-49 . Successful case for optimization on both HSA and target receptor.
68. Lu Y, Feng Q, Cui F, et al. Interaction of 3'-azido-3'-deamino daunorubicin with human serum albumin: investigation by fluorescence spectroscopy and molecular modeling methods. Bioorg Med Chem Lett 2010;20:6899-904
69. Wendt MD, Shen W, Kunzer A, et al. Discovery and structure-activity relationship of antagonists of b-cell lymphoma 2 family proteins with chemopotentiation activity in vitro and in vivo. J Med Chem 2006;49:1165-81 . Successful case for optimization on both HSA and target receptor.
70. Keseru? GM. A virtual high throughput screen for high affinity cytochrome P450cam substrates. Implications for in silico prediction of drug metabolism. J Comput Aided Mol Des 2001;15:649-57
71. Enyedy IJ, Egan WJ. Can we use docking and scoring for hit-to-lead optimization? J Comput Aided Mol Des 2008;22:161-8
72. Brandt T, Holzmann N, Muley L, et al. Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties. J Mol Biol 2011;405:1170-87
73. Gumede NJ, Singh P, Sabela MI, et al. Experimental-like affinity constants and enantioselectivity estimates from flexible docking. J Chem Inf Model 2012;52:2754-9
74. Chen L, Chen X. Results of molecular docking as descriptors to predict human serum albumin binding affinity. J Mol Graph Model 2012;33:35-43
75. Kaliszan R. Structure and retention in chromatography: a chemometric approach. Harwood Academic Publishers, Amsterdam, The Netherlands; 1997 . Classical book on QSRR.
76. Kaliszan R, Noctor TA, Wainer IW. Stereochemical aspects of benzodiazepine binding to human serum albumin. II. Quantitative relationships between structure and enantioselective retention in high performance liquid affinity chromatography. Mol Pharmacol 1992;42:512-17
77. Kaliszan R, Noctor TAG, Wainer IW. Quantitative structure- enantioselective retention relationships for the chromatography of 1,4-benzodiazepines on a human serum albumin based HPLC chiral stationary phase: an approach to the computational prediction of retention and enantioselectivity. Chromatographia 1992;33:546-50
78. Ashton DS, Beddell C, Ray AD, Valkó K. Quantitative structure-retention relationships of acyclovir esters using immobilised albumin high-performance liquid chromatography and reversed-phase high-performance liquid chromatography. J Chromatogr A 1995;707:367-72
79. Aureli L, Cruciani G, Cesta MC, et al. Predicting human serum albumin affinity of interleukin-8 (CXCL8) inhibitors by 3D-QSPR approach. J Med Chem 2005;48:2469-79
80. Milano Chemometrics and QSAR Research Group, Talete, Milano, Italy. Available from: http://www.disat.unimib. it/chm/Dragon.htm
81. CODESSA PRO, University of Florida. Available from: http://www.codessa- pro. com/descriptors/index.htm
82. Todeschini R, Consonni V. Handbook of molecular descriptors. Wiley, Weinheim; 2000 . A very important compilation of descriptors.
83. Tropsha A, Gramatica P, Gombar VK. The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. QSAR Comb Sci 2003;22:69-77
84. Chirico N, Gramatica P. Real external predictivity of QSAR models. Part 2. New intercomparable thresholds for different validation criteria and the need for scatter plot inspection. J Chem Inf Model 2012;52:2044-58
85. Roy K, Mitra I, Kar S, et al. Comparative studies on some metrics for external validation of QSPR models. J Chem Inf Model 2012;52:396-408
86. Stanforth RW, Kolossov E, Mirkin B. A measure of domain of applicability for QSAR modelling based on intelligent K-means clustering. QSAR Comb Sci 2007;26:837-44
87. Hertzberg RP, Pope AJ. High-throughput screening: new technology for the 21st century. Curr Opin Chem Biol 2000;4:445-51
88. Rodgers SL, Davis AM, van de Waterbeemd H. Time-series QSAR analysis of human plasma protein binding. QSAR Comb Sci 2007;26:511-21
89. Rodgers SL, Davis AM, Tomkinson NP, van de Waterbeemd H. Predictivity of simulated ADME AutoQSAR models over time data. Mol Inf 2011;30:256-66 . A very important publication on the methodology for continuous updating of the models.
90. Cartmell J, Enoch S, Krstajic D, Leahy DE. Automated QSPR through competitive workflow. J Comput Aided Mol Des 2005;19:821-33 . Very important contribution to automation in HSA binding predictions.
91. Valkó K. Application of high-performance liquid chromatography based measurements of lipophilicity to model biological distribution. J Chromatogr A 2004;1037:299-310
92. Colmenarejo G. In silico prediction of drug-binding strengths to human serum albumin. Med Res Rev 2003;23:275-301 . Many other authors have used the same data set for establishing HSA QSAR models.
93. Wen Y, Liu H, Luan F, Gao Y. Application of quantitative structure-activity relationship to the determination of binding constant based on fluorescence quenching. J Luminescence 2011;131:126-33
94. Saiakhov RD, Stefan LR, Klopman G. Multiple computer-automated structure evaluation model of the plasma protein binding affinity of diverse drugs. Perspect Drug Discov Des 2000;19:133-55
95. Klopman G. The MultiCASE program II. Baseline activity identification algorithm (BAIA). J Chem Inf Comput Sci 1998;38:78-81
96. Colmenarejo G, Alvarez-Pedraglio A, Lavandera JL. Cheminformatic models to predict binding affinities to human serum albumin. J Med Chem 2001;44:4370-8
97. Hall LM, Lowell H, Kier LBJ. Modeling drug albumin binding affinity with E-state topological structure representation. Chem Inf Comput Sci 2003;43:2120-8
98. Valkó K, Nunhuck S, Bevan C, et al. Fast gradient HPLC method to Determine compounds binding to human serum albumin. Relationships with octanol/water and immobilized artificial membrane lipophilicity. J Pharm Sci 2003;92:2236-48
99. Abraham MH, Chadha HS, Whiting GS, Mitchell RC. Hydrogen bonding. 32. An analysis of water-octanol and water-alkane partitioning and the delta log P parameter of Seiler. J Pharm Sci 1994;83:1085-100
100. Gunturi SB, Narayanan R, Khandelwal A. In silico ADME modelling 2: computational models to predict human serum albumin binding affinity using ant colony systems. Bioorg Med Chem 2006;14:4118-29
101. Deeb O, Hemmateenejad B. ANN-QSAR Model of drug-binding to human serum albumin. Chem Biol Drug Des 2007;70:19-29
102. Wichmann K, Diedenhofen M, Klamt A. Prediction of blood-brain partitioning and human serum albumin binding based on COSMO-RS sigma-moments. J Chem Inf Model 2007;47:228-33
103. Liu J, Yang L, Li Y, et al. Constructing plasma protein binding model based on a combination of cluster analysis and 4D-fingerprint molecular similarity analyses. Bioorg Med Chem 2006;14:611-21
104. Votano JR, Parham M, Hall LM, et al. QSAR modeling of human serum protein binding with several modeling techniques utilizing structure-information representation. J Med Chem 2006;49:7169-81
105. Hajduk PJ, Mendoza R, Petros AM, et al. Ligand binding to domain-3 of human serum albumin: a chemometric analysis. J Comp Aided Mol Des 2003;17:93-102
106. Cruciani G, Pastor M, Clementi S. Handling information from 3D grid maps for QSAR studies. In: Gundertofte K, Jørgensen FE, editors. Molecular modeling and prediction of bioactivity. Kluwer Academic/Plenum Publishers, New York; 2000. p. 73-82
107. Li H, Chen Z, Xu X, et al. Predicting human plasma protein binding of drugs using plasma protein interaction QSAR analysis (PPI-QSAR). Biopharm Drug Dispos 2011;32:333-42
108. Estrada E, Uriarte E, Molina E, et al. An integrated in silico analysis of drug-binding to human serum albumin. J Chem Inf Model 2006;46:2709-24
109. Zsila F, Bikadi Z, Malik D, et al. Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking. Bioinformatics 2011;27:1806-13