Characterization of epitopes recognized by monoclonal antibodies: experimental approaches supported by freely accessible bioinformatic tools

被引：25

作者：

Clementi, Nicola ^{[1
]}

Mancini, Nicasio ^{[1
]}

Castelli, Matteo ^{[1
]}

Clementi, Massimo ^{[1
]}

Burioni, Roberto ^{[1
]}

机构：

[1] Univ Vita Salute San Raffaele, Microbiol & Virol Unit, I-20132 Milan, Italy

来源：

DRUG DISCOVERY TODAY | 2013年 / 18卷 / 9-10期

关键词：

HEPATITIS-C VIRUS; PROTEIN-PROTEIN DOCKING; MOLECULAR-DYNAMICS SIMULATIONS; RANDOM PEPTIDE LIBRARIES; MASS-SPECTROMETRY; CRYSTAL-STRUCTURE; PHAGE DISPLAY; INFLUENZA HEMAGGLUTININ; COMPUTATIONAL DOCKING; LIQUID-CHROMATOGRAPHY;

D O I：

10.1016/j.drudis.2012.11.006

中图分类号：

R9 [药学];

学科分类号：

1007 ;

摘要：

Monoclonal antibodies (mAbs) have been used successfully both in research and for clinical purposes. The possible use of protective mAbs directed against different microbial pathogens is currently being considered. The fine definition of the epitope recognized by a protective mAb is an important aspect to be considered for possible development in epitope-based vaccinology. The most accurate approach to this is the X-ray resolution of mAb/antigen crystal complex. Unfortunately, this approach is not always feasible. Under this perspective, several surrogate epitope mapping strategies based on the use of bioinformatics have been developed. In this article, we review the most common, freely accessible, bioinformatic tools used for epitope characterization and provide some basic examples of molecular visualization, editing and computational analysis.

引用

页码：464 / 471

页数：8

共 75 条

[1] Selective Flexibility of Side-Chain Residues Improves VEGFR-2 Docking Score using AutoDock Vina [J].

Abreu, Rui M. V. ;

Froufe, Hugo J. C. ;

Queiroz, Maria-Joao R. P. ;

Ferreira, Isabel C. F. R. .

CHEMICAL BIOLOGY & DRUG DESIGN, 2012, 79 (04) :530-534

[2] Crystal structure of the M1 protein-binding domain of the influenza A virus nuclear export protein (NEP/NS2) [J].

Akarsu, H ;

Burmeister, WP ;

Petosa, C ;

Petit, I ;

Müller, CW ;

Ruigrok, RWH ;

Baudin, F .

EMBO JOURNAL, 2003, 22 (18) :4646-4655

[3] Benchmarking B cell epitope prediction: Underperformance of existing methods [J].

Blythe, MJ ;

Flower, DR .

PROTEIN SCIENCE, 2005, 14 (01) :246-248

[4] Free modeling with Rosetta in CASP6 [J].

Bradley, P ;

Malmström, L ;

Qian, B ;

Schonbrun, J ;

Chivian, D ;

Kim, DE ;

Meiler, K ;

Misura, KMS ;

Baker, D .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 61 :128-134

[5] Evaluation of DOCK 6 as a pose generation and database enrichment tool [J].

Brozell, Scott R. ;

Mukherjee, Sudipto ;

Balius, Trent E. ;

Roe, Daniel R. ;

Case, David A. ;

Rizzo, Robert C. .

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2012, 26 (06) :749-773

[6] Monoclonal antibodies isolated from human B cells neutralize a broad range of H1 subtype influenza A viruses including swine-origin Influenza virus (S-OIV) [J].

Burioni, Roberto ;

Canducci, Filippo ;

Mancini, Nicasio ;

Clementi, Nicola ;

Sassi, Monica ;

De Marco, Donata ;

Diotti, Roberta Antonia ;

Saita, Diego ;

Sampaolo, Michela ;

Sautto, Giuseppe ;

Pianezze, Matteo ;

Clementi, Massimo .

VIROLOGY, 2010, 399 (01) :144-152

[7]

Burioni R, 2009, NEW MICROBIOL, V32, P319

[8] Anti-HIV-1 Response Elicited in Rabbits by Anti-Idiotype Monoclonal Antibodies Mimicking the CD4-Binding Site [J].

Burioni, Roberto ;

Mancini, Nicasio ;

De Marco, Donata ;

Clementi, Nicola ;

Perotti, Mario ;

Nitti, Giovanni ;

Sassi, Monica ;

Canducci, Filippo ;

Shvela, Krisha ;

Bagnarelli, Patrizia ;

Mascola, John R. ;

Clementi, Massimo .

PLOS ONE, 2008, 3 (10)

[9] Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles [J].

Chaudhury, Sidhartha ;

Gray, Jeffrey J. .

JOURNAL OF MOLECULAR BIOLOGY, 2008, 381 (04) :1068-1087

[10] ZDOCK: An initial-stage protein-docking algorithm [J].

Chen, R ;

Li, L ;

Weng, ZP .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2003, 52 (01) :80-87

← 1 2 3 4 5 6 7 8 →