CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications

ABSTRACT Bispecific immunoglobulins (Igs) typically contain at least two distinct variable domains (Fv) that bind to two different target proteins. They are conceived to facilitate clinical development of biotherapeutic agents for diseases where improved clinical outcome is obtained or expected by combination therapy compared to treatment by single agents. Almost all existing formats are linear in their concept and differ widely in drug-like and manufacture-related properties. To overcome their major limitations, we designed cross-over dual variable Ig-like proteins (CODV-Ig). Their design is akin to the design of circularly closed repeat architectures. Indeed, initial results showed that the traditional approach of utilizing (G4S)x linkers for biotherapeutics design does not identify functional CODV-Igs. Therefore, we applied an unprecedented molecular modeling strategy for linker design that consistently results in CODV-Igs with excellent biochemical and biophysical properties. CODV architecture results in a circular self-contained structure functioning as a self-supporting truss that maintains the parental antibody affinities for both antigens without positional effects. The format is universally suitable for therapeutic applications targeting both circulating and membrane-localized proteins. Due to the full functionality of the Fc domains, serum half-life extension as well as antibody- or complement-dependent cytotoxicity may support biological efficiency of CODV-Igs. We show that judicious choice in combination of epitopes and paratope orientations of bispecific biotherapeutics is anticipated to be critical for clinical outcome. Uniting the major advantages of alternative bispecific biotherapeutics, CODV-Igs are applicable in a wide range of disease areas for fast-track multi-parametric drug optimization.

[1]  R. Kontermann,et al.  Dual targeting strategies with bispecific antibodies , 2012, mAbs.

[2]  D. Haake,et al.  The modification of human immunoglobulin binding to staphylococcal protein A using diethylpyrocarbonate. , 1982, Journal of immunology.

[3]  Mieczyslaw Torchala,et al.  The scoring of poses in protein-protein docking: current capabilities and future directions , 2013, BMC Bioinformatics.

[4]  Z. Xiang,et al.  On the role of the crystal environment in determining protein side-chain conformations. , 2002, Journal of molecular biology.

[5]  Pamela J. Bjorkman,et al.  Crystal structure of the complex of rat neonatal Fc receptor with Fc , 1994, Nature.

[6]  Bruce Tidor,et al.  Quantitative methods for developing Fc mutants with extended half-lives. , 2005, Biotechnology and bioengineering.

[7]  E. Sasso,et al.  Human IgA and IgG F(ab')2 that bind to staphylococcal protein A belong to the VHIII subgroup. , 1991, Journal of immunology.

[8]  J. Marvin,et al.  Recombinant approaches to IgG-like bispecific antibodies , 2005, Acta Pharmacologica Sinica.

[9]  M. Kojima,et al.  The role of interface framework residues in determining antibody VH/VL interaction strength and antigen‐binding affinity , 2006, The FEBS journal.

[10]  U. Jacob,et al.  Crystal structure of the soluble form of the human Fcγ‐receptor IIb: a new member of the immunoglobulin superfamily at 1.7 Å resolution , 1999, The EMBO journal.

[11]  R. Kontermann,et al.  Improved Pharmacokinetics of Recombinant Bispecific Antibody Molecules by Fusion to Human Serum Albumin* , 2007, Journal of Biological Chemistry.

[12]  Chengbin Wu Diabodies: molecular engineering and therapeutic applications. , 2009, Drug news & perspectives.

[13]  Dongmei He,et al.  Protein design of IgG/TCR chimeras for the co-expression of Fab-like moieties within bispecific antibodies , 2015, mAbs.

[14]  J. Hess,et al.  The trifunctional antibody ertumaxomab destroys tumor cells that express low levels of human epidermal growth factor receptor 2. , 2009, Cancer research.

[15]  Daniela Bumbaca,et al.  Physiochemical and Biochemical Factors Influencing the Pharmacokinetics of Antibody Therapeutics , 2012, The AAPS Journal.

[16]  I. Pastan,et al.  Engineering antibody Fv fragments for cancer detection and therapy: Bisulfide-stabilized Fv fragments , 1996, Nature Biotechnology.

[17]  John D. Davis,et al.  Projecting human pharmacokinetics of monoclonal antibodies from nonclinical data: comparative evaluation of prediction approaches in early drug development. , 2016, Biopharmaceutics & drug disposition.

[18]  Sahana Bose,et al.  Simultaneous targeting of multiple disease mediators by a dual-variable-domain immunoglobulin , 2007, Nature Biotechnology.

[19]  A. Plückthun,et al.  Stability engineering of antibody single-chain Fv fragments. , 2001, Journal of molecular biology.

[20]  M. Mack,et al.  A small bispecific antibody construct expressed as a functional single-chain molecule with high tumor cell cytotoxicity. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Shohei Koide,et al.  Design of protein function leaps by directed domain interface evolution , 2008, Proceedings of the National Academy of Sciences.

[22]  D. Roopenian,et al.  Clinical Ramifications of the MHC Family Fc Receptor FcRn , 2010, Journal of Clinical Immunology.

[23]  J. Deisenhofer Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. , 1981, Biochemistry.

[24]  U. Jacob,et al.  Molecular basis for immune complex recognition: a comparison of Fc-receptor structures. , 2001, Journal of molecular biology.

[25]  Hiroki Noguchi,et al.  Computational design of a self-assembling symmetrical β-propeller protein , 2014, Proceedings of the National Academy of Sciences.

[26]  Andrew Leaver-Fay,et al.  Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface , 2014, Nature Biotechnology.

[27]  B. Carragher,et al.  The structure of dual-variable-domain immunoglobulin molecules alone and bound to antigen , 2013, mAbs.

[28]  O. Ortmann,et al.  Trifunctional antibody ertumaxomab: Non-immunological effects on Her2 receptor activity and downstream signaling , 2012, mAbs.

[29]  E. Sasso,et al.  Human IgM molecules that bind staphylococcal protein A contain VHIII H chains. , 1989, Journal of immunology.

[30]  A. Urvoas,et al.  Artificial proteins from combinatorial approaches. , 2012, Trends in biotechnology.

[31]  M. Taussig,et al.  Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[32]  W Wang,et al.  Monoclonal Antibody Pharmacokinetics and Pharmacodynamics , 2008, Clinical pharmacology and therapeutics.

[33]  Chan Hyuk Kim,et al.  Bispecific small molecule–antibody conjugate targeting prostate cancer , 2013, Proceedings of the National Academy of Sciences.

[34]  R. Landgraf,et al.  Signaling through ERBB receptors: multiple layers of diversity and control. , 2006, Cellular signalling.

[35]  Pei Zhou,et al.  Suppression of conformational heterogeneity at a protein–protein interface , 2015, Proceedings of the National Academy of Sciences.

[36]  Andrew C Doxey,et al.  Modular evolution and the origins of symmetry: reconstruction of a three-fold symmetric globular protein. , 2012, Structure.

[37]  Marc F Lensink,et al.  Docking, scoring, and affinity prediction in CAPRI , 2013, Proteins.

[38]  Yanay Ofran,et al.  A Systematic Comparison of Free and Bound Antibodies Reveals Binding-Related Conformational Changes , 2012, The Journal of Immunology.

[39]  J. Chaparro-Riggers,et al.  The neonatal Fc receptor (FcRn) binds independently to both sites of the IgG homodimer with identical affinity , 2015, mAbs.

[40]  D. Röthlisberger,et al.  Domain interactions in the Fab fragment: a comparative evaluation of the single-chain Fv and Fab format engineered with variable domains of different stability. , 2005, Journal of molecular biology.

[41]  Kenneth C. Anderson,et al.  Daratumumab, a Novel Therapeutic Human CD38 Monoclonal Antibody, Induces Killing of Multiple Myeloma and Other Hematological Tumors , 2011, The Journal of Immunology.

[42]  Diego Ellerman,et al.  Bispecific antibodies with natural architecture produced by co-culture of bacteria expressing two distinct half-antibodies , 2013, Nature Biotechnology.

[43]  Nicholas Sawyer,et al.  All repeats are not equal: a module-based approach to guide repeat protein design. , 2013, Journal of molecular biology.

[44]  K. Garcia,et al.  Molecular architecture of the αβ T cell receptor–CD3 complex , 2014, Proceedings of the National Academy of Sciences.

[45]  R. Kontermann,et al.  Half-life extension of a single-chain diabody by fusion to domain B of staphylococcal protein A. , 2012, Protein engineering, design & selection : PEDS.

[46]  C. Bokemeyer Catumaxomab – trifunctional anti-EpCAM antibody used to treat malignant ascites , 2010, Expert opinion on biological therapy.

[47]  D. Burton,et al.  Molecular selection of human antibodies with an unconventional bacterial B cell antigen. , 1993, Journal of immunology.

[48]  Piet Gros,et al.  Complement Is Activated by IgG Hexamers Assembled at the Cell Surface , 2014, Science.

[49]  D. Dimitrov,et al.  Engineered antibody domains with significantly increased transcytosis and half-life in macaques mediated by FcRn , 2015, mAbs.

[50]  M. Heiss,et al.  The trifunctional antibody catumaxomab in treatment of malignant ascites and peritoneal carcinomatosis. , 2010, Future oncology.

[51]  Herren Wu,et al.  Insights into the molecular basis of a bispecific antibody's target selectivity , 2015, mAbs.

[52]  A. Hemminki,et al.  Fc-gamma receptor polymorphisms as predictive and prognostic factors in patients receiving oncolytic adenovirus treatment , 2013, Journal of Translational Medicine.

[53]  Brian Kuhlman,et al.  Fab-based bispecific antibody formats with robust biophysical properties and biological activity , 2015, mAbs.

[54]  S. Qiao,et al.  Neonatal Fc Receptor: From Immunity to Therapeutics , 2010, Journal of Clinical Immunology.

[55]  J. Reichert,et al.  World Bispecific Antibody Summit, September 27–28, 2011, Boston, MA , 2012, mAbs.

[56]  Hirotsugu Ogi,et al.  Concentration dependence of IgG-protein A affinity studied by wireless-electrodeless QCM. , 2007, Biosensors & bioelectronics.

[57]  R. Yeh,et al.  Effect of FCGR2A and FCGR3A variants on CLL outcome. , 2010, Blood.

[58]  C. Klein,et al.  Crystal Structure of an Anti-Ang2 CrossFab Demonstrates Complete Structural and Functional Integrity of the Variable Domain , 2013, PloS one.

[59]  P. Carter,et al.  Bispecific human IgG by design. , 2001, Journal of immunological methods.

[60]  R. Majeti,et al.  A bispecific antibody targeting CD47 and CD20 selectively binds and eliminates dual antigen expressing lymphoma cells , 2015, mAbs.

[61]  Jihong Wang,et al.  Improving target cell specificity using a novel monovalent bispecific IgG design , 2015, mAbs.

[62]  Misha V Golynskiy,et al.  Rational design of FRET sensor proteins based on mutually exclusive domain interactions. , 2013, Biochemical Society transactions.

[63]  G. A. Lazar,et al.  Engineered antibody Fc variants with enhanced effector function. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Inbal Sela-Culang,et al.  The Structural Basis of Antibody-Antigen Recognition , 2013, Front. Immunol..

[65]  M. Wittekind,et al.  Enhancing Antibody Fc Heterodimer Formation through Electrostatic Steering Effects , 2010, The Journal of Biological Chemistry.

[66]  L. Regan,et al.  NextGen protein design. , 2013, Biochemical Society transactions.

[67]  J. Desjarlais,et al.  Optimization of antibody binding to FcγRIIa enhances macrophage phagocytosis of tumor cells , 2008, Molecular Cancer Therapeutics.

[68]  Dan S. Tawfik,et al.  Functional β-propeller lectins by tandem duplications of repetitive units. , 2011, Protein engineering, design & selection : PEDS.

[69]  S. Kadono,et al.  Novel asymmetrically engineered antibody Fc variant with superior FcγR binding affinity and specificity compared with afucosylated Fc variant , 2013, mAbs.

[70]  C. Jakob,et al.  Structure reveals function of the dual variable domain immunoglobulin (DVD-Ig™) molecule , 2013, mAbs.

[71]  J. Huston,et al.  SEEDbodies: fusion proteins based on strand-exchange engineered domain (SEED) CH3 heterodimers in an Fc analogue platform for asymmetric binders or immunofusions and bispecific antibodies. , 2010, Protein engineering, design & selection : PEDS.

[72]  F Bender,et al.  Comparative study of IgG binding to proteins G and A: nonequilibrium kinetic and binding constant determination with the acoustic waveguide device. , 2003, Analytical chemistry.

[73]  Zhiping Weng,et al.  Docking unbound proteins using shape complementarity, desolvation, and electrostatics , 2002, Proteins.

[74]  W. Sherman,et al.  Probing the α‐Helical Structural Stability of Stapled p53 Peptides: Molecular Dynamics Simulations and Analysis , 2010, Chemical biology & drug design.

[75]  Zhiping Weng,et al.  Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library , 2011, PloS one.

[76]  Kunihiro Hattori,et al.  Crystal structure of a novel asymmetrically engineered Fc variant with improved affinity for FcγRs. , 2014, Molecular immunology.

[77]  Guy Georges,et al.  Immunoglobulin domain crossover as a generic approach for the production of bispecific IgG antibodies , 2011, Proceedings of the National Academy of Sciences.

[78]  G. Winter,et al.  Retargeting serum immunoglobulin with bispecific diabodies , 1997, Nature Biotechnology.

[79]  Gili Bisker,et al.  Mechanism of immobilized protein A binding to immunoglobulin G on nanosensor array surfaces. , 2015, Analytical Chemistry.

[80]  P. Moore,et al.  A CD3xCD123 bispecific DART for redirecting host T cells to myelogenous leukemia: Preclinical activity and safety in nonhuman primates , 2015, Science Translational Medicine.

[81]  John Kelly,et al.  Improving biophysical properties of a bispecific antibody scaffold to aid developability , 2013, mAbs.

[82]  K. Avery,et al.  Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies , 2013, Proceedings of the National Academy of Sciences.

[83]  B. Honig,et al.  A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.

[84]  Michael Blaber,et al.  Designing proteins from simple motifs: opportunities in Top-Down Symmetric Deconstruction. , 2012, Current opinion in structural biology.

[85]  P. Bjorkman,et al.  Fc receptors and their interactions with immunoglobulins. , 1996, Annual review of cell and developmental biology.

[86]  R. Raag,et al.  Single‐chain Fvs , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[87]  Diego Ellerman,et al.  Anti-CD20/CD3 T cell–dependent bispecific antibody for the treatment of B cell malignancies , 2015, Science Translational Medicine.

[88]  Robert Huber,et al.  The 3.2-Å crystal structure of the human IgG1 Fc fragment–FcγRIII complex , 2000, Nature.

[89]  B. Bast,et al.  Killing of human leukaemia/lymphoma B cells by activated cytotoxic T lymphocytes in the presence of a bispecific monoclonal antibody (αCD3/αCD19) , 1992 .

[90]  C. Jakob,et al.  Ligand association rates to the inner-variable-domain of a dual-variable-domain immunoglobulin are significantly impacted by linker design , 2011, mAbs.

[91]  Woody Sherman,et al.  Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments , 2013, Journal of Computer-Aided Molecular Design.

[92]  Yan Feng,et al.  Alteration of substrate specificities of thermophilic α/β hydrolases through domain swapping and domain interface optimization. , 2012, Acta biochimica et biophysica Sinica.

[93]  D. Driver,et al.  FcRn Affinity-Pharmacokinetic Relationship of Five Human IgG4 Antibodies Engineered for Improved In Vitro FcRn Binding Properties in Cynomolgus Monkeys , 2012, Drug Metabolism and Disposition.