4,799
Views
53
CrossRef citations to date
0
Altmetric
Reports

Boosting antibody developability through rational sequence optimization

, , , , , , , , & show all
Pages 505-515 | Received 01 Dec 2014, Accepted 06 Feb 2015, Published online: 01 May 2015

References

  • Reichert JM. Antibodies to watch in 2014. mAbs 2014; 6:5-14; PMID:24284914; http://dx.doi.org/10.4161/mabs.27333
  • Kola I, Landis J. Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov 2004; 3:711-6; PMID:15286737; http://dx.doi.org/10.1038/nrd1470
  • Cromwell MEM, Hilario E, Jacobson F. Protein aggregation and bioprocessing. AAPS J 2006; 8:E572-E579; PMID:17025275; http://dx.doi.org/10.1208/aapsj080366
  • Farid SS. Process economics of industrial monoclonal antibody manufacture. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 848: 8-18; PMID:16899415
  • Wu SJ, Luo J, O'Neil KT, Kang J, Lacy ER, Canziani G, Baker A, Huang M, Tang QM, Raju TS, et al. Structure-based engineering of a monoclonal antibody for improved solubility. Protein Eng Des Sel 2010; 23: 643-51; PMID:20543007; http://dx.doi.org/10.1093/protein/gzq037
  • Tiller T, Schuster I, Deppe D, Siegers K, Strohner R, Herrmann T, Berenguer M, Poujol D, Stehle J, Stark Y, et al. A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties. MAbs 2013; 5: 445-70; PMID:23571156
  • Neuber T, Frese K, Jaehrling J, Jäger S, Daubert D, Felderer K, Linnemann M, Höhne A, Kaden S, Kölln J, et al. Characterization and screening of IgG binding to the neonatal Fc receptor. mAbs 2014; 6: 928-42; PMID:24802048; http://dx.doi.org/10.4161/mabs.28744
  • Wang W, Nema S, Teagarden D. Protein aggregation–pathways and influencing factors. Int J Pharm 2010; 390: 89-99; PMID:20188160; http://dx.doi.org/10.1016/j.ijpharm.2010.02.025
  • Topp EM, Zhang L, Zhao H, Payne RW, Evans GJ, Manning MC. Chemical instability in peptide and protein pharmaceuticals, formulation and process development strategies for manufacturing biopharmaceuticals. Taylor & Francis.; 2010; 41-67.
  • Weiss WF, Young TM, Roberts CJ. Principles, approaches, and challenges for predicting protein aggregation rates and shelf life. J Pharm Sci 2009; 98: 1246-77; PMID:18683878; http://dx.doi.org/10.1002/jps.21521
  • Shire SJ, Shahrokh Z, Liu J. Challenges in the development of high protein concentration formulations. J Pharm Sci 2004; 93: 1390-402; PMID:15124199; http://dx.doi.org/10.1002/jps.20079
  • Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL. Design of therapeutic proteins with enhanced stability. Proc Natl Acad Sci USA 2009; 106: 11937-42; PMID:19571001; http://dx.doi.org/10.1073/pnas.0904191106
  • Chaudhri A, Zarraga IE, Kamerzell TJ, Brandt JP, Patapoff TW, Shire SJ, Voth GA. Coarse-grained modeling of the self-association of therapeutic monoclonal antibodies. J Phys Chem B 2012; 116(28):8045-57; PMID:22694284
  • Yearley EJ, Godfrin PD, Perevozchikova T, Zhang H, Falus P, Porcar L, Nagao M, Curtis JE, Gawande P, Taing R, et al. Observation of small cluster formation in concentrated monoclonal antibody solutions and its implications to solution viscosity. Biophys J 2014; 106: 1763-70; PMID:24739175; http://dx.doi.org/10.1016/j.bpj.2014.02.036
  • Roberts CJ. Therapeutic protein aggregation: mechanisms, design, and control. Trends Biotechnol 2014; 32: 372-80; PMID:24908382; http://dx.doi.org/10.1016/j.tibtech.2014.05.005
  • Zheng W, Doniach S. A comparative study of motor-protein motions by using a simple elastic-network model. Proc Natl Acad Sci U S A 2003; 100: 13253-8; PMID:14585932
  • Suhre K, Sanejouand YH. ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 2004; 32: W610-W614; PMID:15215461; http://dx.doi.org/10.1093/nar/gkh368
  • Seeliger D, Haas J, de Groot BL. Geometry-based sampling of conformational transitions in proteins. Structure 2007; 15: 1482-92; PMID:17997973; http://dx.doi.org/10.1016/j.str.2007.09.017
  • Guerois R, Nielsen JE, Serrano L. Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations. J Mol Biol 2002; 320: 369-87; PMID:12079393; http://dx.doi.org/10.1016/S0022-2836(02)00442-4
  • Seeliger D, de Groot BL. Protein thermostability calculations using alchemical free energy simulations. Biophys J 2010; 98: 2309-16; PMID:20483340; http://dx.doi.org/10.1016/j.bpj.2010.01.051
  • Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins 2011; 79: 830-8; http://dx.doi.org/10.1002/prot.22921
  • Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997; 272: 133-43; PMID:9299343; http://dx.doi.org/10.1006/jmbi.1997.1233
  • Fernandez-Escamilla AM, Rousseau F, Schymkowitz J, Serrano L. Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins. Nat.Biotechnol. 2004; 22: 1302-6.
  • Tartaglia GG, Cavalli A, Pellarin R, Caflisch A. Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences. Protein Sci 2005; 14: 2723-34; PMID:16195556; http://dx.doi.org/10.1110/ps.051471205
  • Conchillo-Solé O, de Groot NS, Avilés FX, Vendrell J, Daura X, Ventura S. AGGRESCAN: A server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. BMC Bioinformatics 2007; 8:65.
  • Trovato A, Seno F, Tosatto SCE. The PASTA server for protein aggregation prediction. Protein Engineering, Design and Selection 2007; 20: 521-3; http://dx.doi.org/10.1093/protein/gzm042
  • Tartaglia GG, Pawar AP, Campioni S, Dobson CM, Chiti F, Vendruscolo M. Prediction of aggregation-prone regions in structured proteins. J Mol Biol 2008; 380: 425-36; PMID:18514226; http://dx.doi.org/10.1016/j.jmb.2008.05.013
  • Frousios KK, Iconomidou VA, Karletidi CM, Hamodrakas SJ. Amyloidogenic determinants are usually not buried. BMC Struct Biol 2009; 9:44; PMID:19589171; http://dx.doi.org/10.1186/1472-6807-9-44
  • Wines BD, Powell MS, Parren PWHI, Barnes N, Hogarth PM. The IgG Fc contains distinct Fc receptor (FcR) binding sites: The leukocyte receptors FcgRI and FcgRIIa bind to a region in the Fc distinct from that recognized by neonatal FcR and protein A. J Immunol 2000; 164: 5313-8; http://dx.doi.org/10.4049/jimmunol.164.10.5313
  • Seeliger D. Development of scoring functions for antibody sequence assessment and optimization. PLoS One 2013; 8:e76909
  • Garidel P, Hegyi M, Bassarab S, Weichel M. A rapid, sensitive and economical assessment of monoclonal antibody conformational stability by intrinsic tryptophan fluorescence spectroscopy. Biotechnol J 2008; 3: 1201-11; PMID:18702089; http://dx.doi.org/10.1002/biot.200800091
  • Garber E, Demarest SJ. A broad range of Fab stabilities within a host of therapeutic IgGs. Biochemical Biophys Rese Commun 2007; 355: 751-7; PMID:17321501; http://dx.doi.org/10.1016/j.bbrc.2007.02.042
  • Ionescu RM, Vlasak J, Price C, Kirchmeier M. Contribution of variable domains to the stability of humanized IgG1 monoclonal antibodies. J Pharm Sci 2008; 97: 1414-26; PMID:17721938; http://dx.doi.org/10.1002/jps.21104
  • Burstein EA, Vedenkina NS, Ivkova MN. Fluorescence and the location of tryptophan residues in protein molecules. Photochem Photobiol 1973; 18: 263-79; PMID:4583619; http://dx.doi.org/10.1111/j.1751-1097.1973.tb06422.x
  • Vivian JT, Callis PR. Mechanisms of tryptophan fluorescence shifts in proteins. Biophys J 2001; 80: 2093-109; PMID:11325713; http://dx.doi.org/10.1016/S0006-3495(01)76183-8
  • Brandts JF, Hu CQ, Lin LN, Mos MT. A simple model for proteins with interacting domains. Applications to scanning calorimetry data. Biochemistry 1989; 28: 8588-96; PMID:2690944; http://dx.doi.org/10.1021/bi00447a048
  • Feige MJ, Groscurth S, Marcinowski M, Shimizu Y, Kessler H, Hendershot LM, Buchner J. An Unfolded CH1 Domain Controls the Assembly and Secretion of IgG Antibodies. Mol Cell 2009; 34: 569-79; PMID:19524537; http://dx.doi.org/10.1016/j.molcel.2009.04.028
  • Röthlisberger D, Honegger A, Plückthun A. Domain interactions in the Fab fragment: A comparative evaluation of the single-chain Fv and Fab format engineered with variable domains of different stability. J Mol Biol 2005; 347: 773-89; PMID:15769469; http://dx.doi.org/10.1016/j.jmb.2005.01.053
  • Rowe ES. Dissociation and denaturation equilibria and kinetics of a homogeneous human immunoglobulin fab fragment. Biochemistry 1976; 15: 905-16; PMID:813765
  • Brummitt RK, Nesta DP, Roberts CJ. Predicting accelerated aggregation rates for monoclonal antibody formulations, and challenges for low-temperature predictions. J Pharm Sci 2011; 100(10):4234-43.
  • Youssef AMK, Winter G. A critical evaluation of microcalorimetry as a predictive tool for long term stability of liquid protein formulations: Granulocyte Colony Stimulating Factor (GCSF). Eur J Pharm Biopharm 2013; 84: 145-55; PMID:23333898
  • Costanzo JA, O'Brien CJ, Tiller K, Tamargo E, Robinson AS, Roberts CJ, Fernandez EJ. Conformational stability as a design target to control protein aggregation. Protein Eng Des Sel 2014; 27(5):157-67; PMID:24722670
  • Maddux NR, Iyer V, Cheng W, Youssef AMK, Joshi SB, Volkin DB, Ralston JP, Winter G, Middaugh CR. High throughput prediction of the long-term stability of pharmaceutical macromolecules from short-term multi-instrument spectroscopic data. J Pharm Sci 2014; 103: 828-39; PMID:24421157; http://dx.doi.org/10.1002/jps.23849
  • Garidel P. Right angle light scattering protein thermostability screening: From research to development. 2012; 24: 13-8
  • Leslie A, Powell H. Processing diffraction data with mosflm, In: Read R, Sussman J, eds., Evolving methods for macromolecular crystallography. Taylor & Francis Netherlands; 2007; 41-51
  • Kabsch W. XDS. Acta Crystallogr D Biol.Crystallogr 2010; 66: 125-32; http://dx.doi.org/10.1107/S0907444909047337
  • Evans P. Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 2006; 62: 72-82; http://dx.doi.org/10.1107/S0907444905036693
  • Vonrhein C, Flensburg C, Keller P, Sharff A, Smart O, Paciorek W, Womack T, Bricogne G. Data processing and analysis with the autoPROC toolbox. Acta Crystallogr.D Biol.Crystallogr 2011; 67: 293-302; http://dx.doi.org/10.1107/S0907444911007773
  • McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr 2007; 40: 658-74; PMID:19461840; http://dx.doi.org/10.1107/S0021889807021206
  • Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 2010; 66: 486-501; http://dx.doi.org/10.1107/S0907444910007493
  • Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 2010; 66: 12-21; http://dx.doi.org/10.1107/S0907444909042073

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.