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Structure-based engineering of a novel CD3ε-targeting antibody for reduced polyreactivity

Article: 2189974 | Received 28 Nov 2022, Accepted 06 Mar 2023, Published online: 29 Mar 2023

References

  • Zhou S, Liu M, Ren F, Meng X, Yu J. The landscape of bispecific T cell engager in cancer treatment. Biomarker Res. 2021;9:38. doi:10.1186/s40364-021-00294-9. pmid = 34039409, pmcid = PMC8157659.
  • Baeuerle PA, Reinhardt C. Bispecific T-Cell engaging antibodies for cancer therapy. Cancer Res. 2009;69:4941–19. doi:10.1158/0008-5472.can-09-0547. pmid = 19509221.
  • Demaria O, Gauthier L, Debroas G, Vivier E. Natural killer cell engagers in cancer immunotherapy: next generation of immuno-oncology treatments. Eur J Immunol. 2021;51:1934–42mid = 34145579. doi:10.1002/eji.202048953.
  • Tian Z, Liu M, Zhang Y, Wang X. Bispecific T cell engagers: an emerging therapy for management of hematologic malignancies. J Hematol Oncol. 2021;14:75. doi:10.1186/s13045-021-01084-4. pmid = 33941237, pmcid = PMC8091790.
  • Bargou R, Leo E, Zugmaier G, Klinger M, Goebeler M, Knop S, Noppeney R, Viardot A, Hess G, Schuler M, et al. Tumor regression in cancer patients by very low doses of a T cell–Engaging antibody. Science. 2008;321:974–77mid = 18703743. doi:10.1126/science.1158545.
  • Kaplon H, Crescioli S, Chenoweth A, Reichert JV, Janice M. Antibodies to watch in 2023. mAbs. 2023. doi:10.1080/19420862.2022.2153410.
  • Ledbetter JA, Gentry LE, June CH, Rabinovitch PS, Purchio AF. Stimulation of T cells through the CD3/T-cell receptor complex: role of cytoplasmic calcium, protein kinase C translocation, and phosphorylation of pp60c-src in the activation pathway. Mol Cell Biol. 1987;7:650–56. doi:10.1128/mcb.7.2.650-656.1987. pmid = 2434833, pmcid = PMC365120.
  • Cibrián D, Sánchez-madrid F. CD69: from activation marker to metabolic gatekeeper. Eur J Immunol. 2017;47:946–53. doi:10.1002/eji.201646837. pmid = 28475283, pmcid = PMC6485631.
  • González-Amaro R, Cortés JR, Sánchez-Madrid F, Martín P. Is CD69 an effective brake to control inflammatory diseases? Trends Mol Med. 2013;19:625–32. doi:10.1016/j.molmed.2013.07.006. pmid = 23954168, pmcid = PMC4171681.
  • Li J, Stagg NJ, Johnston J, Harris MJ, Menzies SA, DiCara D, Clark V, Hristopoulos M, Cook R, Slaga D, et al. Membrane-Proximal epitope facilitates efficient T cell synapse formation by anti-FcRH5/CD3 and is a requirement for myeloma cell killing. Cancer Cell. 2017;31:383–95. pmid = 28262555, pmcid = PMC5357723. doi:10.1016/j.ccell.2017.02.001.
  • Razvag Y, Neve-Oz Y, Sajman J, Reches M, Sherman E. Nanoscale kinetic segregation of TCR and CD45 in engaged microvilli facilitates early T cell activation. Nat Commun. 2018;9:732. doi:10.1038/s41467-018-03127-w. pmid = 29467364, pmcid = PMC5821895.
  • Clynes RA, Desjarlais JR. Redirected T cell cytotoxicity in cancer therapy. Annu Rev Med. 2018;70:1–14mid = 30379598. doi:10.1146/annurev-med-062617-035821.
  • Hötzel I, Theil F-P, Bernstein LJ, Prabhu S, Deng R, Quintana L, Lutman J, Sibia R, Chan P, Bumbaca D, et al. A strategy for risk mitigation of antibodies with fast clearance. mAbs. 2012;4:753–60. pmid = 23778268, pmcid = PMC3502242. doi:10.4161/mabs.22189.
  • 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. Proceedings of the National Academy of Sciences. 2017; 114:944–49. doi:10.1073/pnas.1616408114, pmid = 28096333.
  • Tessier PM, Jinkoji J, Cheng Y-C, Prentice JL, Lenhoff AM. Self-Interaction nanoparticle spectroscopy: a nanoparticle-based protein interaction assay. J Am Chem Soc. 2008;130:3106–12. doi:10.1021/ja077624q. pmid = 18271584.
  • Shehata L, Maurer DP, Wec AZ, Lilov A, Champney E, Sun T, Archambault K, Burnina I, Lynaugh H, Zhi X, et al. Affinity maturation enhances antibody specificity but compromises conformational stability. Cell Rep. 2019;28:3300–8.e3304mid = 31553901. doi:10.1016/j.celrep.2019.08.056.
  • Avery LB, Wade J, Wang M, Tam A, King A, Piche-Nicholas N, Kavosi MS, Penn S, Cirelli D, Kurz JC, et al. Establishing in vitro in vivo correlations to screen monoclonal antibodies for physicochemical properties related to favorable human pharmacokinetics. mAbs. 2017;10: pmid = 29271699, pmcid = PMC5825195. doi:10.1080/19420862.2017.1417718.
  • Kraft TE, Richter WF, Emrich T, Knaupp A, Schuster M, Wolfert A, Kettenberger H. Heparin chromatography as an in vitro predictor for antibody clearance rate through pinocytosis. mAbs. 2019;12:1683432. doi:10.1080/19420862.2019.1683432. pmid = 31769731, pmcid = PMC6927760.
  • Xu Y, Roach W, Sun T, Jain T, Prinz B, T-Y Y, Torrey J, Thomas J, Bobrowicz P, Vásquez M, et al. Addressing polyspecificity of antibodies selected from an in vitro yeast presentation system: a FACS-based, high-throughput selection and analytical tool. Protein Eng Design Select. 2013;26:663–70. pmid = 24046438. doi:10.1093/protein/gzt047.
  • Liu Y, Caffry I, Wu J, Geng SB, Jain T, Sun T, Reid F, Cao Y, Estep P, Yu Y, et al. High-throughput screening for developability during early-stage antibody discovery using self-interaction nanoparticle spectroscopy. mAbs. 2013;6:483–92. pmid = 24492294, pmcid = PMC3984336. doi:10.4161/mabs.27431.
  • Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem. 2022:1–18. doi:10.1038/s41570-022-00438-x.
  • Cunningham O, Scott M, Zhou ZS, Finlay WJJ. Polyreactivity and polyspecificity in therapeutic antibody development: risk factors for failure in preclinical and clinical development campaigns. mAbs. 2021;13:1999195mid = 34780320. doi:10.1080/19420862.2021.1999195.
  • Mouquet H, Scheid JF, Zoller MJ, Krogsgaard M, Ott RG, Shukair S, Artyomov MN, Pietzsch J, Connors M, Pereyra F, et al. Polyreactivity increases the apparent affinity of anti-HIV antibodies by heteroligation. Nature. 2010;467:591–95. pmid = 20882016, pmcid = PMC3699875. doi:10.1038/nature09385.
  • Yadav R, Sukumaran S, Zabka TS, Li J, Oldendorp A, Morrow G, Reyes A, Cheu M, Li J, Wallin JJ, et al. Nonclinical pharmacokinetics and pharmacodynamics characterization of anti-CD79b/CD3 T Cell-Dependent bispecific antibody using a surrogate molecule: a potential therapeutic agent for B cell malignancies. Pharmaceutics. 2022;14:970. pmid = 35631556, pmcid = PMC9147001. doi:10.3390/pharmaceutics14050970.
  • Haber L, Olson K, Kelly MP, Crawford A, DiLillo DJ, Tavaré R, Ullman E, Mao S, Canova L, Sineshchekova O, et al. Generation of T-cell-redirecting bispecific antibodies with differentiated profiles of cytokine release and biodistribution by CD3 affinity tuning. Sci Rep. 2021;11:14397mid = 34257348. doi:10.1038/s41598-021-93842-0.
  • Mandikian D, Takahashi N, Lo AA, Li J, Eastham-Anderson J, Slaga D, Ho J, Hristopoulos M, Clark R, Totpal K, et al. Relative target affinities of T-Cell–dependent bispecific antibodies determine biodistribution in a solid tumor mouse model. Mol Cancer Ther. 2018;17:molcanther.0657.2017. pmid = 29339550. doi:10.1158/1535-7163.mct-17-0657.
  • Poussin M, Sereno A, Wu X, Huang F, Manro J, Cao S, Carpenito C, Glasebrook A Jr, Demarest S, Demarest SJ. Dichotomous impact of affinity on the function of T cell engaging bispecific antibodies. J ImmunoTher Cancer. 2021;9:e002444. pmid = 34253637, pmcid = PMC8276301. doi:10.1136/jitc-2021-002444.
  • Staflin K, Zafra CLZD, Schutt LK, Clark V, Zhong F, Hristopoulos M, Clark R, Li J, Mathieu M, Chen X, et al. Target arm affinities determine preclinical efficacy and safety of anti-HER2/CD3 bispecific antibody. JCI Insight. 2020;5:e133757. pmid = 32271166, pmcid = PMC7205277. doi:10.1172/jci.insight.133757.
  • Bortoletto N, Scotet E, Myamoto Y, D’oro U, Lanzavecchia A. Optimizing anti-cd3 affinity for effective T cell targeting against tumor cells. Eur J Immunol. 2002;32:3102–07. doi:10.1002/1521-4141(200211)32:11<3102:aid-immu3102>3.0.co;2-c. pmid = 12385030.
  • Ellerman D. Bispecific T-cell engagers: towards understanding variables influencing the in vitro potency and tumor selectivity and their modulation to enhance their efficacy and safety. Methods. 2019;154:102–17. pmid = 30395966. doi:10.1016/j.ymeth.2018.10.026.
  • Zorn JA, Wheeler ML, Barnes RM, Kaberna J, Morishige W, Harris M, Huang RYC, Lohre J, Chang YC, Chau B, et al. Humanization of a strategic CD3 epitope enables evaluation of clinical T-cell engagers in a fully immunocompetent in vivo model. Sci Rep. 2022;12:3530mid = 35241687. doi:10.1038/s41598-022-06953-7.
  • Camacho CJ, Kimura SR, DeLisi C, Vajda S. Kinetics of Desolvation-Mediated Protein–Protein Binding. Biophys J. 2000;78:1094–105. doi:10.1016/s0006-3495(00)76668-9. pmid = 10692300, pmcid = PMC1300713.
  • Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces11edited by J. Wells. J Mol Biol. 1998;280:1–9. doi:10.1006/jmbi.1998.1843. pmid = 9653027.
  • The antibody society. Therapeutic monoclonal antibodies approved or in regulatory review. [accessed June 15, 2020].
  • Chen Xiaocheng, Dennis Mark S, Ebens, Jr Allen J, Junttila, Teemu T, Kelley Robert F, Mathieu Mary A, Sun Liping L. 2015. Anti-CD3 antibodies and methods of use. US10174124B2.
  • Datta-Mannan A, Lu J, Witcher DR, Leung D, Tang Y, Wroblewski VJ. The interplay of non-specific binding, target-mediated clearance and FcRn interactions on the pharmacokinetics of humanized antibodies. mAbs. 2015;7:1084–93. doi:10.1080/19420862.2015.1075109. pmid = 26337808, pmcid = PMC4966429.
  • Igawa T, Tsunoda H, Tachibana T, Maeda A, Mimoto F, Moriyama C, Nanami M, Sekimori Y, Nabuchi Y, Aso Y, et al. Reduced elimination of IgG antibodies by engineering the variable region. Protein Eng Design Select. 2010;23:385–92mid = 20159773. doi:10.1093/protein/gzq009.
  • Li B, Tesar D, Boswell CA, Cahaya HS, Wong A, Zhang J, Meng YG, Eigenbrot C, Pantua H, Diao J, et al. Framework selection can influence pharmacokinetics of a humanized therapeutic antibody through differences in molecule charge. mAbs. 2014;6:1255–64. pmid = 25517310, pmcid = PMC4623330. doi:10.4161/mabs.29809.
  • Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, et al.Zwart\it PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D. 2010; 66:213–21. doi:10.1107/S0907444909052925.
  • Emsley Bl P, Scott WG, Cowtan K, Cowtan K. Features and development of Coot. Acta Crystal Sec D. 2010;66:486–501. doi:10.1107/S0907444910007493.
  • Emsley P, Cowtan K. Cowtan PEaK.\it Coot: model-building tools for molecular graphics. Acta Crystal Sec D. 2004;60:2126–32. doi:10.1107/S0907444904019158.
  • McCoy RWG-K AJ, Adams PD, Winn MD, Storoni LC, Storoni LC, Read RJ. Phaser crystallographic software. J App Crystal. 2007;40:658–74. doi:10.1107/S0021889807021206.
  • Yu Y, Schürpf T, Springer TA. How Natalizumab Binds and Antagonizes α4 Integrins*. J Biol Chem. 2013;288:32314–25. doi:10.1074/jbc.m113.501668. pmid = 24047894.
  • Sheffler W, Baker D. RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci. 2009;18:229–39. doi:10.1002/pro.8. pmid = 19177366, pmcid = PMC2708028.
  • Kjer-Nielsen L, Dunstone MA, Kostenko L, Ely LK, Beddoe T, Mifsud NA, Purcell AW, Brooks AG, McCluskey J, Rossjohn J Crystal structure of the human T cell receptor CD3εγ heterodimer complexed to the therapeutic mAb OKT3. Proceedings of the National Academy of Sciences. 2004; 101:7675–80. doi:10.1073/pnas.0402295101, pmid = 15136729, pmcid = PMC419665.
  • Arnett KL, Harrison SC, Wiley DC Crystal structure of a human CD3-ε/δ dimer in complex with a UCHT1 single-chain antibody fragment. Proceedings of the National Academy of Sciences of the United States of America. 2004; 101:16268–73. doi:10.1073/pnas.0407359101, pmid = 15534202.
  • Dong D, Zheng L, Lin J, Zhang B, Zhu Y, Li N, Xie S, Wang Y, Gao N, Huang Z. Structural basis of assembly of the human T cell receptor–cd3 complex. Nature. 2019;573:546–52mid = 31461748. doi:10.1038/s41586-019-1537-0.
  • Sušac L, Vuong MT, Thomas C, Bülow Sv OB, Santos C, Am FR, Hummer G, Tampé R, Davis SJ, Davis SJ. Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell. 2022;185:3201–13.e3219. doi:10.1016/j.cell.2022.07.010.
  • Chen Y, Zhu Y, Li X, Gao W, Zhen Z, Dong D, Huang B, Ma Z, Zhang A, Song X, et al. Cholesterol inhibits TCR signaling by directly restricting TCR-CD3 core tunnel motility. Mol Cell. 2022;82:1278–87.e1275mid = 35271814. doi:10.1016/j.molcel.2022.02.017.
  • Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci. 2018;27:112–28. pmid = 28836357, pmcid = PMC5734301, eprint = 1707.00027. doi:10.1002/pro.3280.
  • Liu YD, Goetze AM, Bass RB, Flynn GC. N-terminal Glutamate to Pyroglutamate Conversion in vivo for Human IgG2 Antibodies. J Biol Chem. 2011;286:11211–17. doi:10.1074/jbc.m110.185041. pmid = 21282104, pmcid = PMC3064176.
  • Leong SR, Sukumaran S, Hristopoulos M, Totpal K, Stainton S, Lu E, Wong A, Tam L, Newman R, Vuillemenot BR, et al. An anti-CD3/anti–CLL-1 bispecific antibody for the treatment of acute myeloid leukemia. Blood. 2017;129:609–18. doi:10.1182/blood-2016-08-735365. pmid = 27908880, pmcid = PMC5290988.
  • Yadav S, Laue TM, Kalonia DS, Singh SN, Shire SJ. The influence of charge distribution on self-Association and viscosity behavior of monoclonal antibody solutions. Mol Pharm. 2012;9:791–802mid = 22352470. doi:10.1021/mp200566k.
  • Birtalan S, Zhang Y, Fellouse FA, Shao L, Schaefer G, Sidhu SS. The intrinsic contributions of tyrosine, serine, glycine and arginine to the affinity and specificity of antibodies. J Mol Biol. 2008;377:1518–28. doi:10.1016/j.jmb.2008.01.093. pmid = 18336836.
  • DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, et al. Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires. Proceedings of the National Academy of Sciences. 2016; 113:E2636–45. doi:10.1073/pnas.1525510113, pmid = 27114511, pmcid = PMC4868480.
  • Sheinerman FB, Norel R, Honig B. Electrostatic aspects of protein–protein interactions. Curr Opin Struct Biol. 2000;10:153–59. doi:10.1016/s0959-440x(00)00065-8. pmid = 10753808.
  • Marvin JS, Lowman HB. Redesigning an antibody fragment for faster association with its antigen. Biochemistry. 2003;42:7077–83mid = 12795603. doi:10.1021/bi026947q.
  • Gabdoulline RR, Wade RC. Biomolecular diffusional association. Curr Opin Struct Biol. 2002;12:204–13mid = 11959498. doi:10.1016/s0959-440x(02)00311-1.
  • Bugelski PJ, Achuthanandam R, Capocasale RJ, Treacy G, Bouman-Thio E. Monoclonal antibody-induced cytokine-release syndrome. Expert Rev Clin Immunol. 2009;5:499–521. doi:10.1586/eci.09.31. pmid = 20477639.
  • Dudgeon K, Rouet R, Kokmeijer I, Schofield P, Stolp J, Langley D, Stock D, Christ D General strategy for the generation of human antibody variable domains with increased aggregation resistance. Proceedings of the National Academy of Sciences. 2012; 109:10879–84. doi:10.1073/pnas.1202866109, pmid = 22745168, pmcid = PMC3390889.
  • Perchiacca JM, Ladiwala ARA, Bhattacharya M, Tessier PM. Aggregation-resistant domain antibodies engineered with charged mutations near the edges of the complementarity-determining regions. Protein Eng Design Select. 2012;25:591–602mid = 22843678. doi:10.1093/protein/gzs042.
  • Wec AZ, Wrapp D, Herbert AS, Maurer DP, Haslwanter D, Sakharkar M, Jangra RK, Dieterle ME, Lilov A, Huang D, et al. Broad neutralization of SARS-related viruses by human monoclonal antibodies. Science. 2020;369:731–36mid = 32540900. doi:10.1126/science.abc7424.
  • Akari H, Nam K-H, Mori K, Otani I, Shibata H, Adachi A, Terao K, Yoshikawa Y. Effects of SIVmac Infection on Peripheral Blood CD4+CD8+T Lymphocytes in Cynomolgus Macaques. Clin Immun. 1999;91:321–29mid = 10370378. doi:10.1006/clim.1999.4700.
  • Sakharkar M, Rappazzo CG, Wieland-Alter WF, Hsieh C-L, Wrapp D, Esterman ES, Kaku CI, Wec AZ, Geoghegan JC, McLellan JS, et al. Prolonged evolution of the human B cell response to SARS-CoV-2 infection. Sci Immun. 2021;6:eabg6916. pmid = 33622975, pmcid = PMC8128290. doi:10.1126/sciimmunol.abg6916.
  • Myszka DG. Improving biosensor analysis. J Mol Recogn. 1999;12:279–84. doi:10.1002/(sici)1099-1352(199909/10)12:5<279:aid-jmr473>3.0.co;2-3. pmid = 10556875.
  • Sule Shantanu V, Sukumar M, Weiss William F, Marcelino-Cruz Anna M, Sample T, Tessier Peter M. High-Throughput analysis of concentration-Dependent antibody self-Association. Biophys J. 2011;101:1749–57. doi:10.1016/j.bpj.2011.08.036. pmid = 21961601, pmcid = PMC3183799.
  • Kelly RL, Geoghegan JC, Feldman J, Jain T, Kauke M, Le D, Zhao J, Wittrup KD. Chaperone proteins as single component reagents to assess antibody nonspecificity. mAbs. 2017;9:1036–40. doi:10.1080/19420862.2017.1356529. pmid = 28745541, pmcid = PMC5627595.
  • Kozlowski LP. IPC – Isoelectric point calculator. Biol Direct. 2016;11:55. doi:10.1186/s13062-016-0159-9. pmid = 27769290, pmcid = PMC5075173.
  • EMBOSS. Date.
  • Evans PR, Murshudov GN, GN EPaM. How good are my data and what is the resolution? Acta Crystal Sec D. 2013;69:1204–14. doi10.1107/S0907444913000061.
  • Kabsch W. It XDS. Acta crystallographica section D. Acta Crystallogr D Biol Crystallogr. 2010;66(2):125–32. doi:10.1107/S0907444909047337.
  • Vonrhein C, Cf PK, Sharff O, Smart A, Paciorek T, Womack W, Bricogne G, Bricogne G. Data processing and analysis with the autoPROC toolbox. Acta Crystal Sec D. 2011;67:293–302. doi:10.1107/S0907444911007773.
  • He F, Woods CE, Becker GW, Narhi LO, Razinkov VI., Razinkov VI. High-throughput assessment of thermal and colloidal stability parameters for monoclonal antibody formulations. J Pharm Sci. 2011;100:5126–41. doi:10.1002/jps.22712.
  • Rappazzo CG, Tse LV, Kaku CI, Wrapp D, Sakharkar M, Huang D, Deveau LM, Yockachonis TJ, Herbert AS, Battles MB, et al. Broad and potent activity against SARS-like viruses by an engineered human monoclonal antibody. Science. pp.eabf4830. 2021. doi:10.1126/science.abf4830
  • Stein C, Pejchal R, Mccreary J, Barlow K, Sivasubramanian A, Battles MB inventors; Adimab; WO2022150785A2s assignee.^assignees. variant Ch3 Domains engineered for preferential Ch3 heterodimerization, multi-Specific antibodies comprising the same, and methods of making thereof.
  • Barlow K, Sivasubramanian A, Battles MB inventors; Adimab; WO2022150787A2s assignee.^assignees. Variant Ch1 Domains and Variant Cl Domains engineered for preferential chain pairing and multi-specific antibodies comprising the same.
  • Sharkey B, Pudi S, Moyer IW, Zhong L, Prinz B, Baruah H, Lynaugh H, Kumar S, Wittrup KD, Nett JH. Purification of common light chain IgG-like bispecific antibodies using highly linear pH gradients. mAbs. 2017;9:257–68. doi:10.1080/19420862.2016.1267090. pmid = 27937066, pmcid = PMC5297495.