In silico quantitative prediction of peptides binding affinity to human MHC molecule: An intuitive quantitative structure-activity relationship approach

Amino Acids

Volumn 36, Issue 3, 2009, Pages 535-554

  Tian, F ^a,b   Yang, L ^b   Lv, F ^a   Yang, Q ^a   Zhou, P ^c  

^a THIRD MILITARY MEDICAL UNIVERSITY   (China)

^b CHONGQING UNIVERSITY   (China)

^c ZHEJIANG UNIVERSITY   (China)

Author keywords

Computer aided vaccine design; CTL epitope; Divided physicochemical property scores of amino acids; Genetic algorithm partial least square regression; HLA A*0201; Immunoinformatics; Quantitative structure activity relationship

Indexed keywords

AMINO ACID; EPITOPE; HYDROGEN; LIGAND; PEPTIDE;

ARTICLE; BINDING AFFINITY; COMPUTER MODEL; GENETIC ALGORITHM; HYDROGEN BOND; HYDROPHOBICITY; MAJOR HISTOCOMPATIBILITY COMPLEX; PARTIAL LEAST SQUARES REGRESSION; PHYSICAL CHEMISTRY; PREDICTION; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN INTERACTION; QUANTITATIVE ANALYSIS; STRUCTURE ACTIVITY RELATION;

ALGORITHMS; AMINO ACIDS; COMPUTER SIMULATION; EPITOPES, T-LYMPHOCYTE; HLA-A ANTIGENS; HUMANS; HYDROGEN BONDING; HYDROPHOBICITY; MODELS, CHEMICAL; PEPTIDES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; SEQUENCE ANALYSIS, PROTEIN;

EID: 67349182211     PISSN: 09394451     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00726-008-0116-8     Document Type: Article

References (70)

1. MA Altfeld B Livingston N Reshamwala PT Nguyen MM Addo A Shea M Newman J Fikes J Sidney P Wentworth R Chesnut RL Eldridge ES Rosenberg GK Robbins C Brander PE Sax S Boswell T Flynn S Buchbinder PJR Goulder BD Walker A Sette SA Kalams 2001 Identification of novel HLA-A2-restricted human immunodeficiency virus type 1-specific cytotoxic T-lymphocyte epitopes predicted by the HLA-A2 supertype peptide-binding motif J Virol 75 1301 1311 (Pubitemid 32094689)
2. CC Bigelow 1967 On the average hydrophobicity of proteins and the relation between it and protein structure J Theor Biol 16 187 211
3. MJ Blythe IA Doytchinova DR Flower 2002 JenPep: a database of quantitative functional peptide data for immunology Bioinformatics 18 434 439 (Pubitemid 34284944)
4. V Brusic DR Flower 2007 Bioinformatics tools for identifying T-cell epitopes Drug Discov Today Biosilico 2 18 23
5. V Brusic G Rudy G Honeyman J Hammer L Harrison 1998 Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network Bioinformatics 14 121 130 (Pubitemid 28395870)
6. C Chang S Ekins P Bahadduri PW Swaan 2006 Pharmacophore-based discovery of ligands for drug transporters Adv Drug Deliv Rev 58 1431 1450
7. KC Chou 1996 Review: prediction of HIV protease cleavage sites in proteins Anal Biochem 233 1 14
8. KC Chou HB Shen 2007 Review: recent progresses in protein subcellular location prediction Anal Biochem 370 1 16 (Pubitemid 47404494)
9. ER Collantes WJ Dunn 1995 Amino acid side chain descriptors for quantitative structure activity relationship studies of peptide analogues J Med Chem 38 2705 2713
10. AJ Coyle JC Gutierrez-Ramos 2001 The expanding B7 superfamily: increasing complexity in costimulatory signals regulating T cell function Nat Immunol 2 203 209 (Pubitemid 33705995)
11. MF del Guercio J Sidney G Hermanson C Perez HM Grey RT Kubo A Sette 1995 Binding of a peptide antigen to multiple HLA alleles allows definition of an A2-like supertype J Immunol 154 685 693
12. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos
13. IA Doytchinova DR Flower 2001 Toward the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201 J Med Chem 44 3572 3581 (Pubitemid 33026664)
14. IA Doytchinova DR Flower 2002 Physicochemical explanation of peptide binding to HLA-A*0201 major histocompatibility complex: a three-dimensional quantitative structure-activity relationship-study Proteins 48 505 518
15. IA Doytchinova DR Flower 2007 Predicting class I major histocompatibility complex (MHC) binders using multivariate statistics: comparison of discriminant analysis and multiple linear regression J Chem Inf Model 47 234 238 (Pubitemid 46225579)
16. IA Doytchinova MJ Blythe DR Flower 2002 Additive method for the prediction of protein-peptide binding affinity: application to the MHC class I molecule HLA-A*0201 J Proteome Res 1 263 272 (Pubitemid 36050256)
17. QS Du YT Wei ZW Pang KC Chou RB Huang 2007 Predicting the affinity of epitope-peptides with class I MHC molecule HLA-A*0201: an application of amino acid-based peptide prediction Protein Eng Des Sel 20 417 423 (Pubitemid 47574737)
18. K Falk O Rötzschke S Stefanovic G Jung HG Rammensee 1991 Allele specific motifs revealed by sequencing of self-peptides eluted from MHC molecules Nature 351 290 296 (Pubitemid 21896578)
19. RN Germain 1994 MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation Cell 76 287 299 (Pubitemid 24046691)
20. A Golbraikh A Tropsha 2002 Beware of q2! J Mol Graphics Mod 20 269 276
21. P Guan IA Doytchinova VA Walshe P Borrow DR Flower 2005 Analysis of peptide-protein binding using amino acid descriptors: prediction and experimental verification for HLA-A*0201 J Med Chem 48 7418 7425
22. K Gulukota J Sidney A Sette C DeLisi 1997 Two complementary methods for predicting peptides binding major histocompatibility complex molecules J Mol Biol 267 1258 1267 (Pubitemid 27192636)
23. M Hagmann 2000 Computers aid vaccine design Science 290 80 82
24. CK Hattotuwagama CP Toseland P Guan DJ Taylor SL Hemsley IA Doytchinova DR Flower 2006 Toward prediction of class II mouse major histocompatibility complex peptide binding affinity: in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique J Chem Inf Model 46 1491 1502 (Pubitemid 43999192)
25. S Hellberg M Sjostrom B Skagerberg S Wold 1987 Peptide quantitative structure-activity relationships, a multivariate approach J Med Chem 30 1126 1135 (Pubitemid 17117970)
26. AV Hill J Elvin AC Willis M Aidoo CE Allsopp FM Gotch XM Gao M Takiguchi BM Greenwood AR Townsend 1992 Molecular analysis of the association of HLA-B53 and resistance to severe malaria Nature 360 434 439
27. MC Honeyman V Brusic NL Stone LC Harrison 1998 Neural network-based prediction of candidate T-cell epitopes Nat Biotechnol 16 966 969 (Pubitemid 28483627)
28. R Horton L Wilming V Rand RC Lovering EA Bruford VK Khodiyar MJ Lush S Povey CC Talbot Jr MW Wright HM Wain J Trowsdale A Ziegler S Beck 2004 Gene map of the extended human MHC Nat Rev Genet 5 889 899 (Pubitemid 39564252)
29. WM Kast RM Brandt J Sidney JW Drijfhout RT Kubo HM Grey CJ Melief A Sette 1994 Role of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus type 16 E6 and E7 proteins J Immunol 152 3904 3912 (Pubitemid 24111062)
30. DB Kitchen H Decornez JR Furr J Bajorath 2004 Docking and scoring in virtual screening for drug discovery: Methods and applications Nat Rev 3 935 949 (Pubitemid 39529931)
31. RT Kubo A Sette HM Grey E Appella K Sakaguchi NZ Zhu D Arnott N Sherman J Shabanowitz H Michel 1994 Definition of specific peptide motifs for four major HLA-A alleles J Immunol 152 3913 3925 (Pubitemid 24111063)
32. I Kawashima H Ogata M Kanehisa 1999 AAindex: amino acid index database Nucleic Acids Res 27 368 369 (Pubitemid 29209488)
33. I Kawashima V Tsai S Southwood K Takesako A Sette E Celis 1999 Identification of HLA-A3-restricted cytotoxic T lymphocyte epitopes from carcinoembryonic antigen and HER-2/neu by primary in vitro immunization with peptide-pulsed dendritic cells Cancer Res 59 431 435 (Pubitemid 29048879)
34. A Kidera Y Konishi M Oka T Ooi HA Scheraga 1985 A statistical analysis of the physical properties of the 20 naturally occurring amino acids J Protein Chem 4 23 55 (Pubitemid 15245426)
35. TJ Kirksey RR Pogue-Caley JA Frelinger EJ Collins 1999 The structural basis for the increased immunogenicity of two HIV-reverse transcriptase peptide variant/class I major histocompatibility complexes J Biol Chem 274 37259 37264 (Pubitemid 30016804)
36. AR Khan BM Baker P Ghosh WE Biddison DC Wiley 2000 The structure and stability of an HLA-A*0201/octameric Tax peptide complex with an empty conserved peptide-N-terminal binding site J Immunol 164 6398 6405 (Pubitemid 30408822)
37. H Kubinyi 1997 QSAR and 3D-QSAR in drug design Drug Discov Today 2 457 467
38. Z Lin Y Wu B Zhu B Ni L Wang 2004 Toward the quantitative prediction of T-Cell. epitopes: QSAR studies on peptides having affinity with the class I MHC molecular HLA-A*0201 J Comput Boil 11 683 694 (Pubitemid 39238380)
39. A Logean A Sette D Rognan 2001 Customized versus universal scoring functions: application to class I MHC-peptide binding free energy predictions Bioorg Med Chem Lett 11 675 679 (Pubitemid 32187953)
40. Y Lu B Bulka M desJardins SJ Freeland 2007 Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids Protein Eng Des Sel 20 347 351 (Pubitemid 47327721)
41. DR Madden 1995 The three-dimensional structure of peptide-MHC complexes Annu Rev Immunol 13 587 622
42. DR Madden DN Garboczi DC Wiley 1993 The antigenic identity of peptide/MHC complexes, a comparison of the conformations of five viral peptides presented by HLA-A2 Cell 75 693 708 (Pubitemid 23346368)
43. EG Pamer JT Harty MJ Bevan 1991 Precise prediction of a dominant class I MHC-restricted epitope of Listeria monocytogenes Nature 353 852 855 (Pubitemid 21912640)
44. KC Parker MA Bednarek JE Coligan 1994 Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chain J Immunol 152 163 175 (Pubitemid 24009753)
45. GE Peoples PS Goedegebuure R Smith DC Linehan I Yoshino TY Eberlein 1995 Breast and ovarian cancer-specific cytotoxic T lymphocytes recognize the same HER2/neu-derived peptide Proc Natl Acad Sci USA 92 432 436
46. HG Rammensee 1995 Chemistry of peptides associated with MHC class 1 and class II molecules Curr Opin Immunol 7 85 96
47. HG Rammensee 2003 Immunoinformatics: bioinformatic strategies for better understanding of immune function Novartis Found Symp 254 1 2
48. D Rogers AJ Hopfinger 1994 Application of genetic function approximation to quantitative-structure activity relationships and quantitative structure-property relationships J Chem Inf Comput Sci 34 854 866
49. J Ruppert J Sidney E Celis RT Kubo HM Grey A Sette 1993 Prominent role of secondary anchor residues in peptide binding to HLA-A*0201 molecules Cell 74 929 937 (Pubitemid 23270612)
50. M Sandberg L Eriksson J Jonsson S Wold 1998 New chemical descriptors for the design of biologically active peptides. A multivariate charaterrization of 87 amino acids J Med Chem 41 2481 2491 (Pubitemid 28321898)
51. MA Sapper PJ Bjorkman 1991 Refined structure of the human histocompatibility antigen HLA-A2 at 2.6Å resolution J Mol Biol 219 277 319
52. P Sarobe CD Pendleton TD Akatsuka VH Engelhard SM Feinstone JA Berzofsky 1998 Enhanced in vitro potency and in vivo immunogenicity of a CTL epitope from hepatitis C virus core protein following amino acid replacement at secondary HLA-A 2.1 binding positions J Clin Invest 102 1239 1248 (Pubitemid 28436284)
53. S Schefzick M Bradley 2004 Comparison of commercially available genetic algorithms: GAs as variable selection tool J Comput Aided Mol Des 18 511 521
54. O Schueler-Furman 2000 Structure-based prediction of binding peptides to MHC class I molecules: application to a broad range of MHC alleles Protein Sci 9 1838 1846
55. A Sette 2000 Tools of the trade in vaccine design Science 290 2074 2075 (Pubitemid 32001567)
56. A Sette S Buus E Appella JA Smith R Chesnut C Miles SM Colon HM Grey 1989 Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis Proc Natl Acad Sci USA 86 3296 3300 (Pubitemid 19129598)
57. A Sette J Sidney 1998 HLA supertypes and supermotifs: a functional perspective on HLA polymorphism Curr Opin Immunol 10 478 482 (Pubitemid 28393833)
58. HB Shen KC Chou 2007 EzyPred: a top-down approach for predicting enzyme functional classes and subclasses Biochem Biophys Res Comm 364 53 59 (Pubitemid 47599445)
59. HB Shen KC Chou 2007 Signal-3L: a 3-layer approach for predicting signal peptide Biochem Biophys Res Comm 363 297 303 (Pubitemid 47484331)
60. M Šoškić 1996 Link between orthogonal and standard multiple linear regression models J Chem Inf Comput Sci 36 829 832
61. T Sturniolo E Bono J Ding L Raddrizzani O Tuereci U Sahin M Braxenthaler F Gallazzi MP Protti F Sinigaglia J Hammer 1999 Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices Nat Biotechnol 17 555 561 (Pubitemid 29262918)
62. JM Sutter SL Dixon PC Jurs 1995 Automated descriptor selection for quantitative structure-activity relationships using generalized simulated annealing J Chem Inf Comput Sci 35 77 84
63. A Tropsha P Gramatica VK Gombar 2003 The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models QSAR Comb Sci 22 69 77 (Pubitemid 36717473)
64. J Trowsdale J Ragoussis RD Campbell 1991 Map of the human MHC Immunol Today 12 443 446 (Pubitemid 23198168)
65. K Udaka H Mamitsuka Y Nakaseko N Abe 2002 Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides J Immunol 169 5744 5753 (Pubitemid 35291676)
66. AC Wallace RA Laskowski JM Thornton 1995 LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions Protein Engin 8 127 134
67. X Xiao S Shao Y Ding Z Huang X Chen KC Chou 2005 An application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutation J Theor Biol 235 555 565 (Pubitemid 40780944)
68. P Zhou F Tian M Zhang Z Li 2006 Applying generalized hydrophobicity scale of amino acids to quantitative prediction of human leukocyte antigen-A0201-restricted cytotoxic T lymphocyte epitope Chin Sci Bull 51 1439 1443 (Pubitemid 44432190)
69. P Zhou F Tian Z Li 2007 A structure-based, quantitative structure-activity relationship approach for predicting HLA-A0201-restricted cytotoxic T lymphocyte epitopes Chem Biol Drug Des 69 56 67 (Pubitemid 46277786)
70. Zhou P, Tian F, Wu Y, Li Z, Shang Z. (2008) Quantitative sequence-activity model (QSAM): Applying QSAR strategy to model and predict bioactivity and function of peptides, proteins and nucleic acids. Curr Comput Aided Drug Des (in press)