4,378
Views
48
CrossRef citations to date
0
Altmetric
Reports

Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies

, , , , , , , , , , , & show all
Pages 646-653 | Received 05 Jan 2017, Accepted 31 Jan 2017, Published online: 10 Mar 2017

References

  • Hawe A, Wiggenhorn M, van de Weert M, Garbe JH, Mahler HC, Jiskoot W. Forced degradation of therapeutic proteins. J Pharm Sci 2012; 101:895-913; PMID: 22083792; http://dx.doi.org/10.1002/jps.22812
  • Torosantucci R, Schoneich C, Jiskoot W. Oxidation of therapeutic proteins and peptides: structural and biological consequences. Pharm Res 2014; 31:541-53; PMID: 24065593; http://dx.doi.org/10.1007/s11095-013-1199-9
  • Wang W, Vlasak J, Li Y, Pristatsky P, Fang Y, Pittman T, Roman J, Wang Y, Prueksaritanont T, Ionescu R. Impact of methionine oxidation in human IgG1 Fc on serum half-life of monoclonal antibodies. Mol Immunol 2011; 48:860-6; PMID: 21256596; http://dx.doi.org/10.1016/j.molimm.2010.12.009
  • Pan H, Chen K, Chu L, Kinderman F, Apostol I, Huang G. Methionine oxidation in human IgG2 Fc decreases binding affinities to protein A and FcRn. Protein Sci 2009; 18:424-33; PMID: 19165723; http://dx.doi.org/10.1002/pro.45
  • Davies MJ. The oxidative environment and protein damage. Biochim Biophys Acta 2005; 1703:93-109; PMID: 15680218; http://dx.doi.org/10.1016/j.bbapap.2004.08.007
  • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971; 55:379-400; PMID: 5551392; http://dx.doi.org/10.1016/0022-2836(71)90324-X
  • Chu JW, Yin J, Wang DI, Trout BL. Molecular dynamics simulations and oxidation rates of methionine residues of granulocyte colony-stimulating factor at different pH values. Biochemistry 2004; 43:1019-29; PMID: 14744147; http://dx.doi.org/10.1021/bi0356000
  • Chennamsetty N, Quan Y, Nashine V, Sadineni V, Lyngberg O, Krystek S. Modeling the oxidation of methionine residues by peroxides in proteins. J Pharm Sci 2015; 104:1246-55; PMID: 25641333; http://dx.doi.org/10.1002/jps.24340
  • Sharma VK, Patapoff TW, Kabakoff B, Pai S, Hilario E, Zhang B, Li C, Borisov O, Kelley RF, Chorny I, et al. In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability. Proc Natl Acad Sci U S A 2014; 111;18601-6; PMID: 24324143; http://dx.doi.org/10.1073/pnas.1421779112
  • Thirumangalathu R, Krishnan S, Bondarenko P, Speed-Ricci M, Randolph TW, Carpenter JF, Brems DN. Oxidation of methionine residues in recombinant human interleukin-1 receptor antagonist: Implications of conformational stability on protein oxidation kinetics. Biochemistry 2007; 46:6213-24; PMID: 17480058; http://dx.doi.org/10.1021/bi700321g
  • Jain T, Sun T, Durand S, Hall A, Houston NR, Nett JH, Sharkey B, Bobrowicz B, Caffry I, Yu Y, et al. Biophysical properties of the clinical-stage antibody landscape. Proc Natl Acad Sci U S A 2017; PMID:28096333; http://dx.doi.org/10.1073/pnas.1616408114
  • Gao X, Ji JA, Veeravalli K, Wang YJ, Zhang T, McGreevy W, Zheng K, Kelley RF, Laird MW, Liu J, et al. Effect of individual Fc methionine oxidation on FcRn binding: Met252 oxidation impairs FcRn binding more profoundly than Met428 oxidation. J Pharm Sci 2015; 104:368-77; PMID: 25175600; http://dx.doi.org/10.1002/jps.24136
  • Chu JW, Brooks BR, Trout BL. Oxidation of methionine residues in aqueous solutions: Free methionine and methionine in granulocyte colony-stimulating factor. J Am Chem Soc 2004; 126:16601-7; PMID: 15600366; http://dx.doi.org/10.1021/ja0467059
  • Li X, Xu W, Wang Y, Zhao J, Liu YH, Richardson D, Li H, Shameem M, Yang X. High throughput peptide mapping method for analysis of site specific monoclonal antibody oxidation. J Chromatogr A 2016; 1460:51-60; PMID: 27432793; http://dx.doi.org/10.1016/j.chroma.2016.06.085
  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28:235-42; PMID: 10592235; http://dx.doi.org/10.1093/nar/28.1.235
  • Lefranc MP. IMGT, the International ImMunoGeneTics Information System. Cold Spring Harb Protoc 2011; 2011:595-603; PMID: 21632786; http://dx.doi.org/10.1101/pdb.top115
  • Lefranc MP, Pommi?? C, Kaas Q, Duprat E, Bosc N, Guiraudou D, Jean C, Ruiz M, Da Piédade I, Rouard M, et al. IMGT unique numbering for immunoglobulin and T cell receptor constant domains and Ig superfamily C-like domains. Dev Comp Immunol 2005; 29:185-203; PMID: 15572068; http://dx.doi.org/10.1016/j.dci.2004.07.003
  • Al-Lazikani B, Lesk aM, Chothia C. Standard conformations for the canonical structures of immunoglobulins. J Mol Biol 1997; 273:927-48; PMID: 9367782; http://dx.doi.org/10.1006/jmbi.1997.1354
  • Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K. Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8. Proteins 2009; 77 Suppl 9:114-22; PMID: 19768677; http://dx.doi.org/10.1002/prot.22570
  • Pierce Na, Spriet Ja, Desmet J, Mayo SL. Conformational splitting: A more powerful criterion for dead-end elimination. Journal of Computational Chemistry 2000; 21:999-1009; http://dx.doi.org/10.1002/1096-987X(200008)21:11%3c999::AID-JCC9%3e3.0.CO;2-A
  • Canutescu Aa, Shelenkov Aa, Dunbrack RL. A graph-theory algorithm for rapid protein side-chain prediction. Protein science : a publication of the Protein Society 2003; 12:2001-14; PMID: 12930999; http://dx.doi.org/10.1110/ps.03154503
  • Dunbrack RL, Others. Rotamer libraries in the 21st century. Current opinion in structural biology 2002; 12:431-40; PMID: 12163064; http://dx.doi.org/10.1016/S0959-440X(02)00344-5
  • Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides †. The Journal of Physical Chemistry B 2001; 105:6474-87; http://dx.doi.org/10.1021/jp003919d
  • Pokala N, Handel TM. Energy functions for protein design I: efficient and accurate continuum electrostatics and solvation. Protein science : a publication of the Protein Society 2004; 13:925-36; PMID: 15010542; http://dx.doi.org/10.1110/ps.03486104
  • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations. J Mol Biol 2003; 331:281-99; PMID: 12875852; http://dx.doi.org/10.1016/S0022-2836(03)00670-3
  • Pierce B, Weng Z. ZRANK : Reranking Protein Docking Predictions With an Optimized Energy Function. Bioinformatics 2007; 1086:1078-86; PMID:17373710; http://dx.doi.org/10.1002/prot.21373
  • Chennamsetty N, Quan Y, Nashine V, Sadineni V, Lyngberg O, Krystek S. Modeling the Oxidation of Methionine Residues by Peroxides in Proteins. J Pharm Sci 2015; 104:1246-55; PMID: 25641333; http://dx.doi.org/10.1002/jps.24340
  • Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL. Prediction of aggregation prone regions of therapeutic proteins. J Phys Chem B 2010; 114:6614-24; PMID: 20411962; http://dx.doi.org/10.1021/jp911706q
  • Liaw A, Wiener M. Classification and Regression by randomForest. R News 2002; 2:18-22.
  • Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003; 24:1999-2012; PMID: 14531054; http://dx.doi.org/10.1002/jcc.10349

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.