In-silico prediction of concentration-dependent viscosity curves for monoclonal antibody solutions

References

• Reichert JM. Which are the antibodies to watch in 2013? mAbs 2013; 5:1-4; PMID:23254906; http://dx.doi.org/10.4161/mabs.22976
   PubMed Web of Science ®Google Scholar
• Reichert JM. Antibodies to watch in 2016. mAbs 2016; 8:197-204; PMID:26651519; http://dx.doi.org/10.1080/19420862.2015.1125583
   PubMed Web of Science ®Google Scholar
• Ecker DM, Jones SD, Levine HL. The therapeutic monoclonal antibody market. MAbs 2015; 7:9-14; PMID:25529996; http://dx.doi.org/10.4161/19420862.2015.989042
   PubMed Web of Science ®Google Scholar
• Brady JL, Harrison LC, Goodman DJ, Cowan PJ, Hawthorne WJ, O'Connell PJ, Sutherland RM, Lew AM. Preclinical screening for acute toxicity of therapeutic monoclonal antibodies in a hu-SCID model. Clin Trans Immunol 2014; 3:e29; PMID:25587392; http://dx.doi.org/10.1038/cti.2014.28
   Google Scholar
• Brennan FR, Morton LD, Spindeldreher S, Kiessling A, Allenspach R, Hey A, Muller PY, Frings W, Sims J. Safety and immunotoxicity assessment of immunomodulatory monoclonal antibodies. MAbs 2010; 2:233-55; PMID:20421713; http://dx.doi.org/10.4161/mabs.2.3.11782
   PubMed Web of Science ®Google Scholar
• Tomar DS, Kumar S, Singh SK, Goswami S, Li L. Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development. mAbs 2016; 8:216-28; PMID:26736022; http://dx.doi.org/10.1080/19420862.2015.1128606
   PubMed Web of Science ®Google Scholar
• Druin ML, Kreps SI. Prediction of viscosity of liquid hydrocarbons. Ind Eng Chem Fund 1970; 9:79-83; http://dx.doi.org/10.1021/i160033a012
   Google Scholar
• Katritzky AR, Chen K, Wang Y, Karelson M, Lucic B, Trinajstic N, Suzuki T, Schüürmann G. Prediction of liquid viscosity for organic compounds by a quantitative structure–property relationship. J Phys Org Chem 2000; 13:80-6; ; http://dx.doi.org/10.1002/(SICI)1099-1395(200001)13:1<80::AID-POC179>3.0.CO;2-8
   Web of Science ®Google Scholar
• Ivanciuc O, Ivanciuc T, Filip PA, Cabrol-Bass D. Estimation of the liquid viscosity of organic compounds with a quantitative structure−property model. J Chem Inform Comput Sci 1999; 39:515-24; ; http://dx.doi.org/10.1021/ci980117v
   Google Scholar
• Li L, Kumar S, Buck PM, Burns C, Lavoie J, Singh SK, Warne NW, Nichols P, Luksha N, Boardman D. Concentration dependent viscosity of monoclonal antibody solutions: explaining experimental behavior in terms of molecular properties. Pharm Res 2014; 31:3161-78; PMID:24906598; http://dx.doi.org/10.1007/s11095-014-1409-0
   PubMed Web of Science ®Google Scholar
• 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:25512516; http://dx.doi.org/10.1073/pnas.1421779112
   PubMed Web of Science ®Google Scholar
• Agrawal NJ, Helk B, Kumar S, Mody N, Sathish HA, Samra HS, Buck PM, Li L, Trout BL. Computational tool for the early screening of monoclonal antibodies for their viscosities. mAbs 2016; 8:43-8; PMID:26399600; http://dx.doi.org/10.1080/19420862.2015.1099773
   Web of Science ®Google Scholar
• Nichols P, Li L, Kumar S, Buck PM, Singh SK, Goswami S, Balthazor B, Conley TR, Sek D, Allen MJ. Rational design of viscosity reducing mutants of a monoclonal antibody: hydrophobic versus electrostatic inter-molecular interactions. MAbs 2015; 7:212-30; PMID:25559441; http://dx.doi.org/10.4161/19420862.2014.985504
   PubMed Web of Science ®Google Scholar
• Geoghegan JC, Fleming R, Damschroder M, Bishop SM, Sathish HA, Esfandiary R. Mitigation of reversible self-association and viscosity in a human IgG1 monoclonal antibody by rational, structure-guided Fv engineering. mAbs 2016; 8:941-50; PMID:27050875; http://dx.doi.org/10.1080/19420862.2016.1171444
   Web of Science ®Google Scholar
• Buck PM, Chaudhri A, Kumar S, Singh SK. Highly viscous antibody solutions are a consequence of network formation caused by domain-domain electrostatic complementarities: insights from coarse-grained simulations. Mol Pharm 2015; 12:127-39; PMID:25383990; http://dx.doi.org/10.1021/mp500485w
   PubMed Web of Science ®Google Scholar
• Saltzman WM, Radomsky ML, Whaley KJ, Cone RA. Antibody diffusion in human cervical mucus. Biophys J 1994; 66:508-15; PMID:8161703; http://dx.doi.org/10.1016/S0006-3495(94)80802-1
   PubMed Web of Science ®Google Scholar
• Connolly BD, Petry C, Yadav S, Demeule B, Ciaccio N, Moore JM, Shire SJ, Gokarn YR. Weak interactions govern the viscosity of concentrated antibody solutions: high-throughput analysis using the diffusion interaction parameter. Biophys J 2012; 103:69-78; PMID:22828333; http://dx.doi.org/10.1016/j.bpj.2012.04.047
   PubMed Web of Science ®Google Scholar
• Creighton TE. The physical and chemical basis of molecular biology. Helvetian Press 2010.
   Google Scholar
• Long WF, Labute P. Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors. J Comput-Aided Mol Des 2010; 24:907-16; PMID:20842408; http://dx.doi.org/10.1007/s10822-010-9383-z
   PubMed Web of Science ®Google Scholar
• Roberts CJ. Protein aggregation and its impact on product quality. Curr Opin Biotechnol 2014; 30:211-7; PMID:25173826; http://dx.doi.org/10.1016/j.copbio.2014.08.001
   PubMed Web of Science ®Google Scholar
• Sarangapani Prasad S, Hudson Steven D, Jones Ronald L, Douglas Jack F, Pathak Jai A. Critical examination of the colloidal particle model of globular proteins. Biophys J 2015; 108:724-37; PMID:25650939; http://dx.doi.org/10.1016/j.bpj.2014.11.3483
   PubMed Web of Science ®Google Scholar
• The MathWorks, Inc., Natick, Massachusetts, United States. MATLAB 2013a.
   Google Scholar
• Wilkinson GN, Rogers CE. Symbolic description of factorial models for analysis of variance. J Roy Stat Soc C (Applied Statistics) 1973; 22:392-9; http://dx.doi.org/10.2307/2346786
   Web of Science ®Google Scholar
• Liu H, May K. Disulfide bond structures of IgG molecules. mAbs 2012; 4:17-23; PMID:22327427; http://dx.doi.org/10.4161/mabs.4.1.18347
   PubMed Web of Science ®Google Scholar
• Wang X, Kumar S, Buck PM, Singh SK. Impact of de-glycosylation and thermal stress on conformational stability of a full length murine IgG2a monoclonal antibody: Observations from molecular dynamics simulations. Proteins: Structure, Function, and Bioinformatics 2013; 81:443-60; PMID:23065923; http://dx.doi.org/10.1002/prot.24202
   Google Scholar
• Harding SE, Johnson P. The concentration-dependence of macromolecular parameters. Biochem J 1985; 231:543-7; PMID:4074322; http://dx.doi.org/10.1042/bj2310543.
   PubMed Web of Science ®Google Scholar
• Chemical Computing Group Inc. SSW, Suite #910, Montreal, QC, Canada, H3A 2R7. Mol Operating Environ 2014. 09. 2016
   Google Scholar
• Saphire EO, Parren PW, Pantophlet R, Zwick MB, Morris GM, Rudd PM, Dwek RA, Stanfield RL, Burton DR, Wilson IA. Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design. Science 2001; 293:1155-9; PMID:11498595; http://dx.doi.org/10.1126/science.1061692
   PubMed Web of Science ®Google Scholar
• Harris LJ, Larson SB, Hasel KW, McPherson A. Refined Structure of an Intact IgG2a Monoclonal Antibody. Biochemistry 1997; 36:1581-97; PMID:9048542; http://dx.doi.org/10.1021/bi962514+
   PubMed Web of Science ®Google Scholar
• Scapin G, Yang X, Prosise WW, McCoy M, Reichert P, Johnston JM, Kashi RS, Strickland C. Structure of full-length human anti-PD1 therapeutic IgG4 antibody pembrolizumab. Nat Struct Mol Biol 2015; 22:953-8; PMID:26595420; http://dx.doi.org/10.1038/nsmb.3129
   PubMed Web of Science ®Google Scholar
• Guo J, Kumar S, Prashad A, Starkey J, Singh SK. Assessment of physical stability of an antibody drug conjugate by higher order structure analysis: Impact of thiol- maleimide chemistry. Pharm Res 2014; 31:1710-23; PMID:24464270; http://dx.doi.org/10.1007/s11095-013-1274-2
   PubMed Web of Science ®Google Scholar
• Wang X, Kumar S, Singh SK. Disulfide scrambling in IgG2 monoclonal antibodies: Insights from molecular dynamics simulations. Pharm Res 2011; 28:3128-44; PMID:21671135; http://dx.doi.org/10.1007/s11095-011-0503-9
   PubMed Web of Science ®Google Scholar
• Padlan EA. Anatomy of the antibody molecule. Mol Immunol 1994; 31:169-217; PMID:8114766; http://dx.doi.org/10.1016/0161-5890(94)90001-9
   PubMed Web of Science ®Google Scholar
• Maurer-Stroh S, Debulpaep M, Kuemmerer N, de la Paz ML, Martins IC, Reumers J, Morris KL, Copland A, Serpell L, Serrano L, et al. Exploring the sequence determinants of amyloid structure using position-specific scoring matrices. Nat Meth 2010; 7:237-42; PMID:20154676; http://dx.doi.org/10.1038/nmeth.1432
   PubMed Web of Science ®Google Scholar
• 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; PMID:15361882; http://dx.doi.org/10.1038/nbt1012
   PubMed Web of Science ®Google Scholar
• Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res 2013; 41:W34-W40; PMID:23671333; http://dx.doi.org/10.1093/nar/gkt382
   PubMed Web of Science ®Google Scholar
• Kumar S, Tsai CJ, Nussinov R. Temperature Range of Thermodynamic Stability for the Native State of Reversible Two-State Proteins. Biochemistry 2003; 42:4864-73; PMID:12718527; http://dx.doi.org/10.1021/bi027184+
   PubMed Web of Science ®Google Scholar
• Weisberg S. Weights, Lack of Fit, and More. Applied Linear Regression: John Wiley & Sons, Inc., 2005:96-114; http://dx.doi.org/10.1002/0471704091
   Google Scholar
• Chatterjee S, Hadi AS. Variable Selection Procedures. Regression Analysis by Example: John Wiley & Sons, Inc., 2006:281-315.
   Google Scholar