[1]
Ecker, D.M.; Jones, S.D.; Levine, H.L. The therapeutic monoclonal antibody market. MAbs, 2015, 7(1), 9-14.
[2]
Walsh, G. Biopharmaceutical benchmarks 2014. Nat. Biotechnol., 2014, 32(10), 992-1000.
[3]
Leader, B.; Baca, Q.J.; Golan, D.E. Protein therapeutics: A summary and pharmacological classification. Nat. Rev. Drug Discov., 2008, 7(1), 21-39.
[4]
Padlan, E.A. Anatomy of the antibody molecule. Mol. Immunol., 1994, 31(3), 169-217.
[5]
Carter, P.J. Potent antibody therapeutics by design. Nat. Rev. Immunol., 2006, 6(5), 343-357.
[6]
Jefferis, R. Antibody therapeutics: Isotype and glycoform selection. Expert Opin. Biol. Ther., 2007, 7(9), 1401-1413.
[7]
Jefferis, R. Isotype and glycoform selection for antibody therapeutics. Arch. Biochem. Biophys., 2012, 526(2), 159-166.
[8]
Krawczyk, K.; Dunbar, J.; Deane, C.M. Computational tools for aiding rational antibody design. Methods Mol. Biol., 2017, 1529, 399-416.
[9]
Bostrom, J.; Lee, C.V.; Haber, L.; Fuh, G. Improving antibody binding affinity and specificity for therapeutic development. Methods Mol. Biol., 2009, 525, 353-376.
[10]
Weiner, G.J. Building better monoclonal antibody-based therapeutics. Nat. Rev. Cancer, 2015, 15(6), 361-370.
[11]
Irani, V.; Guy, A.J.; Andrew, D.; Beeson, J.G.; Ramsland, P.A.; Richards, J.S. Molecular properties of human IgG subclasses and their implications for designing therapeutic monoclonal antibodies against infectious diseases. Mol. Immunol., 2015, 67(2 Pt A), 171-182.
[12]
Stanfield, R.L.; Takimoto-Kamimura, M.; Rini, J.M.; Profy, A.T.; Wilson, I.A. Major antigen-induced domain rearrangements in an antibody. Structure, 1993, 1(2), 83-93.
[13]
Gershoni, J.M.; Roitburd-Berman, A.; Siman-Tov, D.D.; Tarnovitski Freund, N.; Weiss, Y. Epitope mapping: The first step in developing epitope-based vaccines. BioDrugs, 2007, 21(3), 145-156.
[14]
Wang, W.; Ye, W.; Yu, Q.; Jiang, C.; Zhang, J.; Luo, R.; Chen, H.F. Conformational selection and induced fit in specific antibody and antigen recognition: SPE7 as a case study. J. Phys. Chem. B, 2013, 117(17), 4912-4923.
[15]
Bongini, L.; Fanelli, D.; Piazza, F.; De Los Rios, P.; Sandin, S.; Skoglund, U. Freezing immunoglobulins to see them move. Proc. Natl. Acad. Sci. USA, 2004, 101(17), 6466-6471.
[16]
Sandin, S.; Ofverstedt, L.G.; Wikstrom, A.C.; Wrange, O.; Skoglund, U. Structure and flexibility of individual immunoglobulin G molecules in solution. Structure, 2004, 12(3), 409-415.
[17]
Saphire, E.O.; Stanfield, R.L.; Crispin, M.D.; Parren, P.W.; Rudd, P.M.; Dwek, R.A.; Burton, D.R.; Wilson, I.A. Contrasting IgG structures reveal extreme asymmetry and flexibility. J. Mol. Biol., 2002, 319(1), 9-18.
[18]
Bongini, L.; Fanelli, D.; Piazza, F.; De Los Rios, P.; Sandin, S.; Skoglund, U. Dynamics of antibodies from cryo-electron tomography. Biophys. Chem., 2005, 115(2-3), 235-240.
[19]
Henzler-Wildman, K.; Kern, D. Dynamic personalities of proteins. Nature, 2007, 450(7172), 964-972.
[20]
Correia, I.; Sung, J.; Burton, R.; Jakob, C.G.; Carragher, B.; Ghayur, T.; Radziejewski, C. The structure of dual-variable-domain immunoglobulin molecules alone and bound to antigen. MAbs, 2013, 5(3), 364-372.
[21]
Zhang, X.; Zhang, L.; Tong, H.; Peng, B.; Rames, M.J.; Zhang, S.; Ren, G. 3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography. Sci. Rep., 2015, 5, 9803.
[22]
Zhang, H.M.; Li, C.; Lei, M.; Lundin, V.; Lee, H.Y.; Ninonuevo, M.; Lin, K.; Han, G.; Sandoval, W.; Lei, D.; Ren, G.; Zhang, J.; Liu, H. Structural and functional characterization of a hole-hole homodimer variant in a “Knob-Into-Hole” bispecific antibody. Anal. Chem., 2017, 89(24), 13494-13501.
[23]
Harris, L.J.; Larson, S.B.; Hasel, K.W.; McPherson, A. Refined structure of an intact IgG2a monoclonal antibody. Biochemistry, 1997, 36(7), 1581-1597.
[24]
Harris, L.J.; Skaletsky, E.; McPherson, A. Crystallographic structure of an intact IgG1 monoclonal antibody. J. Mol. Biol., 1998, 275(5), 861-872.
[25]
Saphire, E.O.; Parren, P.W.; Pantophlet, R.; Zwick, M.B.; Morris, G.M.; Rudd, P.M.; Dwek, R.A.; Stanfield, R.L.; Burton, D.R.; Wilson, I.A. Crystal structure of a neutralizing human IGG against HIV-1: A template for vaccine design. Science, 2001, 293(5532), 1155-1159.
[26]
Dunbar, J.; Krawczyk, K.; Leem, J.; Baker, T.; Fuchs, A.; Georges, G.; Shi, J.; Deane, C.M. SAbDab: The structural antibody database. Nucleic Acids Res., 2014, 42(D1), D1140-D1146.
[27]
Sung, J.J.; Pardeshi, N.N.; Mulder, A.M.; Mulligan, S.K.; Quispe, J.; On, K.; Carragher, B.; Potter, C.S.; Carpenter, J.F.; Schneemann, A. Transmission electron microscopy as an orthogonal method to characterize protein aggregates. J. Pharm. Sci., 2015, 104(2), 750-759.
[28]
Krissinel, E.; Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol., 2007, 372(3), 774-797.
[29]
Plath, F.; Ringler, P.; Graff-Meyer, A.; Stahlberg, H.; Lauer, M.E.; Rufer, A.C.; Graewert, M.A.; Svergun, D.; Gellermann, G.; Finkler, C.; Stracke, J.O.; Koulov, A.; Schnaible, V. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs. MAbs, 2016, 8(5), 928-940.
[30]
Lapelosa, M.; Patapoff, T.W.; Zarraga, I.E. Molecular simulations of the pairwise interaction of monoclonal antibodies. J. Phys. Chem. B, 2014, 118(46), 13132-13141.
[31]
De Vivo, M.; Masetti, M.; Bottegoni, G.; Cavalli, A. Role of molecular dynamics and related methods in drug discovery. J. Med. Chem., 2016, 59(9), 4035-4061.
[32]
Soler, M.A.; de Marco, A.; Fortuna, S. Molecular dynamics simulations and docking enable to explore the biophysical factors controlling the yields of engineered nanobodies. Sci. Rep., 2016, 6, 34869.
[33]
Paul, R.; Graff-Meyer, A.; Stahlberg, H.; Lauer, M.E.; Rufer, A.C.; Beck, H.; Briguet, A.; Schnaible, V.; Buckel, T.; Boeckle, S. Structure and function of purified monoclonal antibody dimers induced by different stress conditions. Pharm. Res., 2012, 29(8), 2047-2059.
[34]
Brandt, J.P.; Patapoff, T.W.; Aragon, S.R. Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody. Biophys. J., 2010, 99(3), 905-913.
[35]
Lin, J.C.; Glover, Z.K.; Sreedhara, A. Assessing the utility of circular dichroism and FTIR spectroscopy in monoclonal-antibody comparability studies. J. Pharm. Sci., 2015, 104(12), 4459-4466.
[36]
Razinkov, V.I.; Treuheit, M.J.; Becker, G.W. Methods of high throughput biophysical characterization in biopharmaceutical development. Curr. Drug Discov. Technol., 2013, 10(1), 59-70.
[37]
Benevides, J.M.; Overman, S.A.; Thomas, G.J. Jr. Raman spectroscopy
of proteins. Curr. Protoc. Protein Sci , 2004. Chap. 17, unit
17.8.
[38]
Ma, L.; Yang, F.; Zheng, J. Application of fluorescence resonance energy transfer in protein studies. J. Mol. Struct., 2014, 1077, 87-100.
[39]
Goulet, D.R.; Orcutt, S.J.; Zwolak, A.; Rispens, T.; Labrijn, A.F.; de Jong, R.N.; Atkins, W.M.; Chiu, M.L. Kinetic mechanism of controlled Fab-arm exchange for the formation of bispecific immunoglobulin G1 antibodies. J. Biol. Chem., 2018, 293(2), 651-661.
[40]
Rispens, T.; Davies, A.M.; Ooijevaar-de Heer, P.; Absalah, S.; Bende, O.; Sutton, B.J.; Vidarsson, G.; Aalberse, R.C. Dynamics of inter-heavy chain interactions in human immunoglobulin G (IgG) subclasses studied by kinetic Fab arm exchange. J. Biol. Chem., 2014, 289(9), 6098-6109.
[41]
Pervushin, K.; Riek, R.; Wider, G.; Wuthrich, K. Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. USA, 1997, 94(23), 12366-12371.
[42]
Fiaux, J.; Bertelsen, E.B.; Horwich, A.L.; Wuthrich, K. NMR analysis of a 900K GroEL GroES complex. Nature, 2002, 418, 207-211.
[43]
Arbogast, L.W.; Brinson, R.G.; Formolo, T.; Hoopes, J.T.; Marino, J.P., II (1)H(N), (15)N Correlated NMR methods at natural abundance for obtaining structural maps and statistical comparability of monoclonal antibodies. Pharm. Res., 2016, 33(2), 462-475.
[44]
Arbogast, L.W.; Brinson, R.G.; Marino, J.P. Mapping monoclonal antibody structure by 2D 13C NMR at natural abundance. Anal. Chem., 2015, 87(7), 3556-3561.
[45]
Eschweiler, J.D.; Kerr, R.; Rabuck-Gibbons, J.; Ruotolo, B.T. Sizing up protein-ligand complexes: The rise of structural mass spectrometry approaches in the pharmaceutical sciences. Annu. Rev. Anal. Chem. (Palo Alto, Calif.), 2017, 10(1), 25-44.
[46]
Zhang, Y.; Cui, W.; Wecksler, A.T.; Zhang, H.; Molina, P.; Deperalta, G.; Gross, M.L. Native MS and ECD characterization of a fab-antigen complex may facilitate crystallization for X-ray diffraction. J. Am. Soc. Mass Spectrom., 2016, 27(7), 1139-1142.
[47]
Haberger, M.; Leiss, M.; Heidenreich, A.K.; Pester, O.; Hafenmair, G.; Hook, M.; Bonnington, L.; Wegele, H.; Haindl, M.; Reusch, D.; Bulau, P. Rapid characterization of biotherapeutic proteins by size-exclusion chromatography coupled to native mass spectrometry. MAbs, 2016, 8(2), 331-339.
[48]
Ferguson, C.N.; Gucinski-Ruth, A.C. Evaluation of ion mobility-mass spectrometry for comparative analysis of monoclonal antibodies. J. Am. Soc. Mass Spectrom., 2016, 27(5), 822-833.
[49]
Zhang, Z.; Smith, D.L. Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation. Protein Sci., 1993, 2(4), 522-531.
[50]
Englander, S.W. Hydrogen exchange and mass spectrometry: A historical perspective. J. Am. Soc. Mass Spectrom., 2006, 17(11), 1481-1489.
[51]
Maleknia, S.D.; Brenowitz, M.; Chance, M.R. Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry. Anal. Chem., 1999, 71(18), 3965-3973.
[52]
Xu, G.H.; Chance, M.R. Hydroxyl radical-mediated modification of proteins as probes for structural proteomics. Chem. Rev., 2007, 107, 3514-3543.
[53]
Zhang, H.; Wen, J.; Huang, R.Y.; Blankenship, R.E.; Gross, M.L. Mass spectrometry-based carboxyl footprinting of proteins: Method evaluation. Int. J. Mass Spectrom., 2012, 312, 78-86.
[54]
Zhang, Y.; Fonslow, B.R.; Shan, B.; Baek, M.C.; Yates, J.R., III Protein analysis by shotgun/bottom-up proteomics. Chem. Rev., 2013, 113, 2343-2394.
[55]
Zhang, Z.; Pan, H.; Chen, X. Mass spectrometry for structural characterization of therapeutic antibodies. Mass Spectrom. Rev., 2009, 28(1), 147-176.
[56]
Mo, J.; Tymiak, A.A.; Chen, G. Structural mass spectrometry in biologics discovery: Advances and future trends. Drug Discov. Today, 2012, 17(23-24), 1323-1330.
[57]
Chalmers, M.J.; Busby, S.A.; Pascal, B.D.; He, Y.; Hendrickson, C.L.; Marshall, A.G.; Griffin, P.R. Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry. Anal. Chem., 2006, 78(4), 1005-1014.
[58]
Wales, T.E.; Fadgen, K.E.; Gerhardt, G.C.; Engen, J.R. High-speed and high-resolution UPLC separation at zero degrees Celsius. Anal. Chem., 2008, 80(17), 6815-6820.
[59]
Balasubramanian, B.; Pogozelski, W.K.; Tullius, T.D. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA, 1998, 95(17), 9738-9743.
[60]
Galas, D.J.; Schmitz, A. DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res., 1978, 5(9), 3157-3170.
[61]
Sclavi, B.; Woodson, S.; Sullivan, M.; Chance, M.R.; Brenowitz, M. Time-resolved synchrotron X-ray “footprinting”, a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. J. Mol. Biol., 1997, 266(1), 144-159.
[62]
Aydogan, B.; Marshall, D.T.; Swarts, S.G.; Turner, J.E.; Boone, A.J.; Richards, N.G.; Bolch, W.E. Site-specific OH attack to the sugar moiety of DNA: A comparison of experimental data and computational simulation. Radiat. Res., 2002, 157(1), 38-44.
[63]
Kent, O.; Chaulk, S.G.; MacMillan, A.M. Kinetic analysis of the M1 RNA folding pathway. J. Mol. Biol., 2000, 304(5), 699-705.
[64]
Ralston, C.Y.; He, Q.; Brenowitz, M.; Chance, M.R. Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation. Nat. Struct. Biol., 2000, 7(5), 371-374.
[65]
Ralston, C.Y.; Sclavi, B.; Sullivan, M.; Deras, M.L.; Woodson, S.A.; Chance, M.R.; Brenowitz, M. Time-resolved synchrotron X-ray footprinting and its application to RNA folding. Methods Enzymol., 2000, 317, 353-368.
[66]
Brenowitz, M.; Chance, M.R.; Dhavan, G.; Takamoto, K. Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical “footprinting”. Curr. Opin. Struct. Biol., 2002, 12(5), 648-653.
[67]
Adilakshmi, T.; Bellur, D.L.; Woodson, S.A. Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly. Nature, 2008, 455(7217), 1268-1272.
[68]
Kiselar, J.G.; Maleknia, S.D.; Sullivan, M.; Downard, K.M.; Chance, M.R. Hydroxyl radical probe of protein surfaces using synchrotron X-ray radiolysis and mass spectrometry. Int. J. Radiat. Biol., 2002, 78(2), 101-114.
[69]
Xu, G.; Chance, M.R. Radiolytic modification of acidic amino acid residues in peptides: probes for examining protein-protein interactions. Anal. Chem., 2004, 76(5), 1213-1221.
[70]
Hambly, D.M.; Gross, M.L. Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale. J. Am. Soc. Mass Spectrom., 2005, 16(12), 2057-2063.
[71]
Gau, B.C.; Sharp, J.S.; Rempel, D.L.; Gross, M.L. Fast photochemical oxidation of protein footprints faster than protein unfolding. Anal. Chem., 2009, 81(16), 6563-6571.
[72]
Konermann, L.; Vahidi, S.; Sowole, M.A. Mass spectrometry methods for studying structure and dynamics of biological macromolecules. Anal. Chem., 2014, 86(1), 213-232.
[73]
Wang, L.; Chance, M.R. Protein footprinting comes of age: Mass spectrometry for biophysical structure assessment. Mol. Cell. Proteomics, 2017, 16(5), 706-716.
[74]
Aye, T.T.; Low, T.Y.; Sze, S.K. Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry. Anal. Chem., 2005, 77(18), 5814-5822.
[75]
Sharp, J.S.; Tomer, K.B. Analysis of the oxidative damage-induced conformational changes of apo- and holocalmodulin by dose-dependent protein oxidative surface mapping. Biophys. J., 2007, 92(5), 1682-1692.
[76]
Hambly, D.; Gross, M. Laser flash photochemical oxidation to locate heme binding and conformational changes in myoglobin. Int. J. Mass Spectrom., 2007, 259, 124-129.
[77]
Kaur, P.; Tomechko, S.; Kiselar, J.; Shi, W.; Deperalta, G.; Wecksler, A.T.; Gokulrangan, G.; Ling, V.; Chance, M.R. Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting. MAbs, 2014, 6(6), 1486-1499.
[78]
Mendoza, V.L.; Vachet, R.W. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. Mass Spectrom. Rev., 2009, 28(5), 785-815.
[79]
Xu, G.; Kiselar, J.; He, Q.; Chance, M.R. Secondary reactions and strategies to improve quantitative protein footprinting. Anal. Chem., 2005, 77(10), 3029-3037.
[80]
Chance, M.R.; Sclavi, B.; Woodson, S.A.; Brenowitz, M. Examining the conformational dynamics of macromolecules with time-resolved synchrotron X-ray ‘footprinting’. Structure, 1997, 5(7), 865-869.
[81]
Woodson, S.A.; Deras, M.L.; Brenowitz, M. Time-resolved hydroxyl radical footprinting of RNA with X-rays; , 2001.
[82]
Zhang, Y.; Rempel, D.L.; Zhang, H.; Gross, M.L. An improved Fast Photochemical Oxidation of Proteins (FPOP) platform for protein therapeutics. J. Am. Soc. Mass Spectrom., 2015, 26(3), 526-529.
[83]
Niu, B.; Zhang, H.; Giblin, D.; Rempel, D.L.; Gross, M.L. Dosimetry determines the initial OH radical concentration in Fast Photochemical Oxidation of Proteins (FPOP). J. Am. Soc. Mass Spectrom., 2015, 26(5), 843-846.
[84]
Vahidi, S.; Konermann, L. Probing the time scale of FPOP (Fast Photochemical Oxidation of Proteins): Radical reactions extend over tens of milliseconds. J. Am. Soc. Mass Spectrom., 2016, 27(7), 1156-1164.
[85]
Kaur, P.; Kiselar, J.G.; Chance, M.R. Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry. Anal. Chem., 2009, 81(19), 8141-8149.
[86]
Charvatova, O.; Foley, B.L.; Bern, M.W.; Sharp, J.S.; Orlando, R.; Woods, R.J. Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: Application to galectin-1. J. Am. Soc. Mass Spectrom., 2008, 19(11), 1692-1705.
[87]
Bern, M.; Kil, Y.J.; Becker, C. , 2012.
[88]
Rey, M.; Sarpe, V.; Burns, K.M.; Buse, J.; Baker, C.A.; van Dijk, M.; Wordeman, L.; Bonvin, A.M.; Schriemer, D.C. Mass spec studio for integrative structural biology. Structure, 2014, 22(10), 1538-1548.
[89]
Rinas, A.; Espino, J.A.; Jones, L.M. An efficient quantitation strategy for hydroxyl radical-mediated protein footprinting using Proteome Discoverer. Anal. Bioanal. Chem., 2016, 408(11), 3021-3031.
[90]
Jones, L.M. J, B.S.; J, A.C.; Gross, M.L. Fast photochemical oxidation of proteins for epitope mapping. Anal. Chem., 2011, 83(20), 7657-7661.
[91]
Tong, X.; Wren, J.C.; Konermann, L. Effects of protein concentration on the extent of gamma-ray-mediated oxidative labeling studied by electrospray mass spectrometry. Anal. Chem., 2007, 79(16), 6376-6382.
[92]
Gupta, S.; Sullivan, M.; Toomey, J.; Kiselar, J.; Chance, M.R. The beamline X28C of the center for synchrotron biosciences: A national resource for biomolecular structure and dynamics experiments using synchrotron footprinting. J. Synchrotron Radiat., 2007, 14(Pt 3), 233-243.
[93]
Xie, B.; Sharp, J. Hydroxyl radical dosimetry for high flux hydroxyl radical protein footprinting applications using a simple optical detection method. Anal. Chem., 2015, 87(21), 10719-10723.
[94]
Guttman, M.; Garcia, N.K.; Cupo, A.; Matsui, T.; Julien, J.P.; Sanders, R.W.; Wilson, I.A.; Moore, J.P.; Lee, K.K. CD4-induced activation in a soluble HIV-1 Env trimer. Structure, 2014, 22(7), 974-984.
[95]
Niu, B.; Mackness, B.C.; Rempel, D.L.; Zhang, H.; Cui, W.; Matthews, C.R.; Zitzewitz, J.A.; Gross, M.L. Incorporation of a reporter peptide in FPOP compensates for adventitious scavengers and permits time-dependent measurements. J. Am. Soc. Mass Spectrom., 2017, 28(2), 389-392.
[96]
Kaur, P.; Kiselar, J.; Shi, W.; Yang, S.; Chance, M.R. , 2015.
[97]
Huang, W.; Ravikumar, K.M.; Chance, M.R.; Yang, S.C. Quantitative mapping of protein structure by hydroxyl radical footprinting mediated structural mass spectrometry: A protection factor analysis. Biophys. J., 2015, 108(1), 107-115.
[98]
Kamal, J.K.A.; Chance, M.R. Modeling of protein binary complexes using structural mass spectrometry data. Protein Sci., 2008, 17(1), 79-94.
[99]
Pan, L.Y.; Salas-Solano, O.; Valliere-Douglass, J.F. Antibody structural integrity of site-specific antibody-drug conjugates investigated by hydrogen/deuterium exchange mass spectrometry. Anal. Chem., 2015, 87(11), 5669-5676.
[100]
Pan, L.Y.; Salas-Solano, O.; Valliere-Douglass, J.F. Conformation and dynamics of interchain cysteine-linked antibody-drug conjugates as revealed by hydrogen/deuterium exchange mass spectrometry. Anal. Chem., 2014, 86(5), 2657-2664.
[101]
Houde, D.; Arndt, J.; Domeier, W.; Berkowitz, S.; Engen, J.R. Characterization of IgG1 conformation and conformational dynamics by hydrogen/deuterium exchange mass spectrometry. Anal. Chem., 2009, 81(7), 2644-2651.
[102]
Houde, D.; Peng, Y.; Berkowitz, S.A.; Engen, J.R. Post-translational modifications differentially affect IgG1 conformation and receptor binding. Mol. Cell. Proteomics, 2010, 9(8), 1716-1728.
[103]
Lei, M.; Kao, Y.H.; Schoneich, C. Using lysine-reactive fluorescent dye for surface characterization of a mAb. J. Pharm. Sci., 2015, 104(3), 995-1004.
[105]
Gresl, T.; Storz, U.; Sandercock, C. An update on obtaining and enforcing therapeutic antibody patent claims. Nat. Biotechnol., 2016, 34(12), 1242-1245.
[106]
Baerga-Ortiz, A.; Hughes, C.A.; Mandell, J.G.; Komives, E.A. Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci., 2002, 11(6), 1300-1308.
[107]
Wecksler, A.T.; Kalo, M.S.; Deperalta, G. Mapping of Fab-1:VEGF interface using carboxyl group footprinting mass spectrometry. J. Am. Soc. Mass Spectrom., 2015, 26(12), 2077-2080.
[108]
Zhang, Y.; Wecksler, A.T.; Molina, P.; Deperalta, G.; Gross, M.L. Mapping the binding interface of VEGF and a monoclonal antibody Fab-1 fragment with Fast Photochemical Oxidation of Proteins (FPOP) and mass spectrometry. J. Am. Soc. Mass Spectrom., 2017, 28(5), 850-858.
[109]
Li, J.; Wei, H.; Krystek, S.R.; Bond, D.; Brender, T.M.; Cohen, D.; Feiner, J.; Hamacher, N.; Harshman, J.; Huang, R.Y.C.; Julien, S.H.; Lin, Z.; Moore, K.; Mueller, L.; Noriega, C.; Sejwal, P.; Sheppard, P.; Stevens, B.; Chen, G.D.; Tyrniak, A.A.; Gross, M.L.; Schneeweis, L.A. Mapping the energetic epitope of an Antibody/Interleukin-23 interaction with hydrogen/deuterium exchange, fast photochemical oxidation of proteins mass spectrometry, and alanine shave mutagenesis. Anal. Chem., 2017, 89(4), 2250-2258.
[110]
Li, X.Y.; Li, Z.X.; Xie, B.; Sharp, J.S. Improved identification and relative quantification of sites of peptide and protein oxidation for hydroxyl radical footprinting. J. Am. Soc. Mass Spectrom., 2013, 24(11), 1767-1776.
[111]
Wang, L.; Qin, Y.; Ilchenko, S.; Bohon, J.; Shi, W.; Cho, M.W.; Takamoto, K.; Chance, M.R. Structural analysis of a highly glycosylated and unliganded gp120-based antigen using mass spectrometry. Biochemistry, 2010, 49(42), 9032-9045.
[112]
Li, X.; Grant, O.C.; Ito, K.; Wallace, A.; Wang, S.; Zhao, P.; Wells, L.; Lu, S.; Woods, R.J.; Sharp, J.S. Structural analysis of the glycosylated intact HIV-1 gp120-b12 antibody complex using hydroxyl radical protein footprinting. Biochemistry, 2017, 56(7), 957-970.
[113]
Guttman, M.; Cupo, A.; Julien, J.P.; Sanders, R.W.; Wilson, I.A.; Moore, J.P.; Lee, K.K. Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env. Nat. Commun., 2015, 6, 6144.
[114]
Harris, R.J.; Shire, S.J.; Winter, C. Commercial manufacturing scale formulation and analytical characterization of therapeutic recombinant antibodies. Drug Dev. Res., 2004, 61(3), 137-154.
[115]
Beck, A.; Wagner-Rousset, E.; Ayoub, D.; Van Dorsselaer, A.; Sanglier-Cianferani, S. Characterization of therapeutic antibodies and related products. Anal. Chem., 2013, 85(2), 715-736.
[116]
Liu, H.C.; Gaza-Bulseco, G.; Faldu, D.; Chumsae, C.; Sun, J. Heterogeneity of monoclonal antibodies. J. Pharm. Sci., 2008, 97(7), 2426-2447.
[117]
Liu, H.C.; Nowak, C.; Shao, M.; Ponniah, G.; Neill, A. Impact of cell culture on recombinant monoclonal antibody product heterogeneity. Biotechnol. Prog., 2016, 32(5), 1103-1112.
[118]
Manning, M.C.; Chou, D.K.; Murphy, B.M.; Payne, R.W.; Katayama, D.S. Stability of protein pharmaceuticals: An update. Pharm. Res., 2010, 27(4), 544-575.
[119]
Majumdar, R.; Manikwar, P.; Hickey, J.M.; Samra, H.S.; Sathish, H.A.; Bishop, S.M.; Middaugh, C.R.; Volkin, D.B.; Weis, D.D. Effects of salts from the hofmeister series on the conformational stability, aggregation propensity, and local flexibility of an IgG1 monoclonal antibody. Biochemistry, 2013, 52(19), 3376-3389.
[120]
Manikwar, P.; Majumdar, R.; Hickey, J.M.; Thakkar, S.V.; Samra, H.S.; Sathish, H.A.; Bishop, S.M.; Middaugh, C.R.; Weis, D.D.; Volkin, D.B. Correlating excipient effects on conformational and storage stability of an IgG1 monoclonal antibody with local dynamics as measured by hydrogen/deuterium-exchange mass spectrometry. J. Pharm. Sci., 2013, 102(7), 2136-2151.
[121]
Majumdar, R.; Middaugh, C.R.; Weis, D.D.; Volkin, D.B. Hydrogen-deuterium exchange mass spectrometry as an emerging analytical tool for stabilization and formulation development of therapeutic monoclonal antibodies. J. Pharm. Sci., 2015, 104(2), 327-345.
[122]
Arora, J.; Hickey, J.M.; Majumdar, R.; Esfandiary, R.; Bishop, S.M.; Samra, H.S.; Middaugh, C.R.; Weis, D.D.; Volkin, D.B. Hydrogen exchange mass spectrometry reveals protein interfaces and distant dynamic coupling effects during the reversible self-association of an IgG1 monoclonal antibody. MAbs, 2015, 7(3), 525-539.
[123]
Arora, J.; Hu, Y.; Esfandiary, R.; Sathish, H.A.; Bishop, S.M.; Joshi, S.B.; Middaugh, C.R.; Volkin, D.B.; Weis, D.D. Charge-mediated Fab-Fc interactions in an IgG1 antibody induce reversible self-association, cluster formation, and elevated viscosity. MAbs, 2016, 8(8), 1561-1574.
[124]
Moussa, E.M.; Singh, S.K.; Kimmel, M.; Nema, S.; Topp, E.M. Probing the conformation of an IgG1 monoclonal antibody in lyophilized solids using solid-state Hydrogen-Deuterium Exchange with Mass Spectrometric Analysis (ssHDX-MS). Mol. Pharm., 2018, 15(2), 356-368.
[125]
Moussa, E.M.; Wilson, N.E.; Zhou, Q.T.; Singh, S.K.; Nema, S.; Topp, E.M. Effects of drying process on an IgG1 monoclonal antibody using solid-state Hydrogen Deuterium Exchange with Mass Spectrometric analysis (ssHDX-MS). Pharm. Res., 2018, 35(35), 12.
[126]
Moorthy, B.S.; Zarraga, I.E.; Kumar, L.; Walters, B.T.; Goldbach, P.; Topp, E.M.; Allmendinger, A. Solid-state hydrogen-deuterium exchange mass spectrometry: Correlation of deuterium uptake and long-term stability of lyophilized monoclonal antibody formulations. Mol. Pharm., 2018, 15(1), 1-11.
[127]
Sharma, V.K.; Patapoff, T.W.; Kabakoff, B.; Pai, S.; Hilario, E.; Zhang, B.; Li, C.; Borisov, O.; Kelley, R.F.; Chorny, I.; Zhou, J.Z.; Dill, K.A.; Swartz, T.E. In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability. Proc. Natl. Acad. Sci. USA, 2014, 111(52), 18601-18606.
[128]
Chaudhri, A.; Zarraga, I.E.; Yadav, S.; Patapoff, T.W.; Shire, S.J.; Voth, G.A. The role of amino acid sequence in the self-association of therapeutic monoclonal antibodies: Insights from coarse-grained modeling. J. Phys. Chem. B, 2013, 117(5), 1269-1279.
[130]
Kuhn, A.B.; Kube, S.; Karow-Zwick, A.R.; Seeliger, D.; Garidel, P.; Blech, M.; Schafer, L.V. Improved solution-state properties of monoclonal antibodies by targeted mutations. J. Phys. Chem. B, 2017, 121(48), 10818-10827.
[131]
Chennamsetty, N.; Voynov, V.; Kayser, V.; Helk, B.; Trout, B.L. Design of therapeutic proteins with enhanced stability. Proc. Natl. Acad. Sci. USA, 2009, 106(29), 11937-11942.
[132]
Watson, C.; Sharp, J.S. Conformational analysis of therapeutic proteins by hydroxyl radical protein footprinting. AAPS J., 2012, 14(2), 206-217.
[133]
Deperalta, G.; Alvarez, M.; Bechtel, C.; Dong, K.; McDonald, R.; Ling, V. Structural analysis of a therapeutic monoclonal antibody dimer by hydroxyl radical footprinting. MAbs, 2013, 5(1), 86-101.
[134]
Jones, L.M.; Zhang, H.; Cui, W.D.; Kumar, S.; Sperry, J.B.; Carroll, J.A.; Gross, M.L. Complementary MS methods assist conformational characterization of antibodies with altered S-S bonding networks. J. Am. Soc. Mass Spectrom., 2013, 24(6), 835-845.
[135]
Beck, A.; Wurch, T.; Bailly, C.; Corvaia, N. Strategies and challenges for the next generation of therapeutic antibodies. Nat. Rev. Immunol., 2010, 10(5), 345-352.
[136]
Salfeld, J.G. Isotype selection in antibody engineering. Nat. Biotechnol., 2007, 25(12), 1369-1372.
[137]
Jhan, S.Y.; Huang, L.J.; Wang, T.F.; Chou, H.H.; Chen, S.H. Dimethyl labeling coupled with mass spectrometry for topographical characterization of primary amines on monoclonal antibodies. Anal. Chem., 2017, 89(7), 4255-4263.
[138]
Harmonised Tripartate Guideline, ICH 2009.
[139]
Alt, N.; Zhang, T.Y.; Motchnik, P.; Taticek, R.; Quarmby, V.; Schlothauer, T.; Beck, H.; Emrich, T.; Harris, R.J. Determination of critical quality attributes for monoclonal antibodies using quality by design principles. Biologicals, 2016, 44(5), 291-305.
[140]
Houde, D.; Berkowitz, S.A.; Engen, J.R. The utility of hydrogen/deuterium exchange mass spectrometry in biopharmaceutical comparability studies. J. Pharm. Sci., 2011, 100(6), 2071-2086.
Download PDF Flyer