Abstract
Rational engineering methods can be applied with success to optimize physicochemical characteristics of antibodies. Application of in silico analysis and prediction methods to antibody Fv regions can help to find residues affecting antibody–antigen affinity when high-resolution antibody structures or antibody–antigen complex structures are known. In these cases, the identification of residues affecting affinity can facilitate the selection of candidates for guided maturation by PCR using degenerate oligonucleotides. Here, we describe the utilization of a semi-rational approach to enhance the affinity of antibodies by combining in silico and traditional wet lab-based methods.
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References
Jain M, Kamal N, Batra SK (2007) Engineering antibodies for clinical applications. Trends Biotechnol 25:307–316
Rajpal A, Beyaz N, Haber L, Cappuccilli G, Yee H, Bhatt RR, Takeuchi T, Lerner RA, Crea R (2005) A general method for greatly improving the affinity of antibodies by using combinatorial libraries. Proc Natl Acad Sci U S A 102:8466–8471
Cauerhff A, Goldbaum FA, Braden BC (2004) Structural mechanism for affinity maturation of an anti-lysozyme antibody. Proc Natl Acad Sci U S A 101:3539–3544
Presta LG (2006) Engineering of therapeutic antibodies to minimize immunogenicity and optimize function. Adv Drug Deliv Rev 58:640–656
Valjakka J, Hemminki A, Niemi S, Soderlund H, Takkinen K, Rouvinen J (2002) Crystal structure of an in vitro affinity- and specificity-matured anti-testosterone Fab in complex with testosterone. Improved affinity results from small structural changes within the variable domains. J Biol Chem 277:44021–44027
Tomlinson IM, Walter G, Jones PT, Dear PH, Sonnhammer EL, Winter G (1996) The imprint of somatic hypermutation on the repertoire of human germline V genes. J Mol Biol 256:813–817
Clark LA, Boriack-Sjodin PA, Eldredge J, Fitch C, Friedman B, Hanf KJ, Jarpe M, Liparoto SF, Li Y, Lugovskoy A, Miller S, Rushe M, Sherman W, Simon K, Van Vlijmen H (2006) Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design. Protein Sci 15:949–960
Fontayne A, De Maeyer B, De Maeyer M, Yamashita M, Matsushita T, Deckmyn H (2007) Paratope and epitope mapping of the antithrombotic antibody 6B4 in complex with platelet glycoprotein Ibalpha. J Biol Chem 282:23517–23524
Fontayne A, Vanhoorelbeke K, Pareyn I, Van Rompaey I, Meiring M, Lamprecht S, Roodt J, Desmet J, Deckmyn H (2006) Rational humanization of the powerful antithrombotic anti-GPIbalpha antibody: 6B4. Thromb Haemost 96:671–684
Barderas R, Desmet J, Timmerman P, Meloen R, Casal JI (2008) Affinity maturation of antibodies assisted by in silico modeling. Proc Natl Acad Sci U S A 105:9029–9034
Yang WP, Green K, Pinz-Sweeney S, Briones AT, Burton DR, Barbas CF 3 (1995) CDR walking mutagenesis for the affinity maturation of a potent human anti-HIV-1 antibody into the picomolar range. J Mol Biol 254:392–403
Goletz S, Christensen PA, Kristensen P, Blohm D, Tomlinson I, Winter G, Karsten U (2002) Selection of large diversities of antiidiotypic antibody fragments by phage display. J Mol Biol 315:1087–1097
Chen R, Li L, Weng Z (2003) ZDOCK: an initial-stage protein-docking algorithm. Proteins 52:80–87
Barderas R, Shochat S, Timmerman P, Hollestelle MJ, Martinez-Torrecuadrada JL, Hoppener JW, Altschuh D, Meloen R, Casal JI (2008) Designing antibodies for the inhibition of gastrin activity in tumoral cell lines. Int J Cancer 122:2351–2359
Webster DM, Henry AH, Rees AR (1994) Antibody-antigen interactions. Curr Opin Struct Biol 4:123–129
Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ (2009) Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins 74:497–514
Liwo A, Czaplewski C, Oldziej S, Scheraga HA (2008) Computational techniques for efficient conformational sampling of proteins. Curr Opin Struct Biol 18:134–139
Olson MA, Feig M, Brooks CL 3 (2008) Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. J Comput Chem 29:820–831
Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125:1731–1737
Barderas R, Shochat S, Martinez-Torrecuadrada J, Altschuh D, Meloen R, Ignacio Casal J (2006) A fast mutagenesis procedure to recover soluble and functional scFvs containing amber stop codons from synthetic and semisynthetic antibody libraries. J Immunol Methods 312:182–189
Babel I, Barderas R, Pelaez-Garcia A, Casal JI (2011) Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen. BMC Biotechnol 11:61–71
Martinez-Torrecuadrada JL, Cheung LH, Lopez-Serra P, Barderas R, Canamero M, Ferreiro S, Rosenblum MG, Casal JI (2008) Antitumor activity of fibroblast growth factor receptor 3-specific immunotoxins in a xenograft mouse model of bladder carcinoma is mediated by apoptosis. Mol Cancer Ther 7:862–873
Acknowledgements
Rodrigo Barderas is recipient of a JAE-DOC Contract of the CSIC. This work was supported by a grant from the Spanish Ministry of Science and Innovation BIO2009-08818.
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Barderas, R., Desmet, J., Alard, P., Casal, J.I. (2012). Affinity Maturation by Semi-rational Approaches. In: Chames, P. (eds) Antibody Engineering. Methods in Molecular Biology, vol 907. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-974-7_27
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DOI: https://doi.org/10.1007/978-1-61779-974-7_27
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