Antibodies VRC01 and 10E8 Neutralize HIV-1 with High Breadth and Potency Even with Ig-Framework Regions Substantially Reverted to Germline

Abs capable of effectively neutralizing HIV-1 generally exhibit very high levels of somatic hypermutation, both in their CDR and framework-variable regions. In many cases, full reversion of the Ab-framework mutations back to germline results in substantial to complete loss of HIV-1–neutralizing activity. However, it has been unclear whether all or most of the observed framework mutations would be necessary or whether a small subset of these mutations might be sufficient for broad and potent neutralization. To address this issue and to explore the dependence of neutralization activity on the level of somatic hypermutation in the Ab framework, we applied a computationally guided framework-reversion procedure to two broadly neutralizing anti–HIV-1 Abs, VRC01 and 10E8, which target two different HIV-1 sites of vulnerability. Ab variants in which up to 78% (38 of 49 for VRC01) and 89% (31 of 35 for 10E8) of framework mutations were reverted to germline retained breadth and potency within 3-fold of the mature Abs when evaluated on a panel of 21 diverse viral strains. Further, a VRC01 variant with an ∼50% framework-reverted L chain showed a 2-fold improvement in potency over the mature Ab. Our results indicate that only a small number of Ab-framework mutations may be sufficient for high breadth and potency of HIV-1 neutralization by Abs VRC01 and 10E8. Partial framework revertants of HIV-1 broadly neutralizing Abs may present advantages over their highly mutated counterparts as Ab therapeutics and as targets for immunogen design.

[1]  Ron Diskin,et al.  HIV therapy by a combination of broadly neutralizing antibodies in humanized mice , 2012, Nature.

[2]  Young Do Kwon,et al.  Multidonor analysis reveals structural elements, genetic determinants, and maturation pathway for HIV-1 neutralization by VRC01-class antibodies. , 2013, Immunity.

[3]  Pablo Gainza,et al.  Osprey: Protein Design with Ensembles, Flexibility, and Provable Algorithms , 2022 .

[4]  J. Whittle,et al.  Structural and genetic basis for development of broadly neutralizing influenza antibodies , 2012, Nature.

[5]  I. Georgiev,et al.  Elicitation of HIV-1-neutralizing antibodies against the CD4-binding site. , 2013, Current opinion in HIV and AIDS.

[6]  D. Burton,et al.  Very Few Substitutions in a Germ Line Antibody Are Required To Initiate Significant Domain Exchange , 2010, Journal of Virology.

[7]  Richard T. Wyatt,et al.  Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals , 2009, Nature.

[8]  M. Neuberger,et al.  Molecular mechanisms of antibody somatic hypermutation. , 2007, Annual review of biochemistry.

[9]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[10]  Benny K. C. Lo,et al.  Antibody humanization by CDR grafting. , 2004, Methods in molecular biology.

[11]  Pham Phung,et al.  Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target , 2009, Science.

[12]  G. Nabel,et al.  The design and evaluation of HIV-1 vaccines. , 2012, AIDS.

[13]  Mario Roederer,et al.  Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1 , 2010, Science.

[14]  Xiping Wei,et al.  Human Immunodeficiency Virus Type 1 env Clones from Acute and Early Subtype B Infections for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies , 2005, Journal of Virology.

[15]  Tongqing Zhou,et al.  Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01 , 2010, Science.

[16]  Tongqing Zhou,et al.  Delineating Antibody Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate Neutralization , 2013, Science.

[17]  J. Cyster,et al.  Germinal-center organization and cellular dynamics. , 2007, Immunity.

[18]  J. Mascola,et al.  Crystal Structure of PG16 and Chimeric Dissection with Somatically Related PG9: Structure-Function Analysis of Two Quaternary-Specific Antibodies That Effectively Neutralize HIV-1 , 2010, Journal of Virology.

[19]  Jamie K. Scott,et al.  Comparison of Antibody Repertoires Produced by HIV-1 Infection, Other Chronic and Acute Infections, and Systemic Autoimmune Disease , 2011, PloS one.

[20]  David Baltimore,et al.  Antibody-based Protection Against HIV Infection by Vectored ImmunoProphylaxis , 2011, Nature.

[21]  Pham Phung,et al.  Broad neutralization coverage of HIV by multiple highly potent antibodies , 2011, Nature.

[22]  J. Crowe,et al.  Reversion of Somatic Mutations of the Respiratory Syncytial Virus–Specific Human Monoclonal Antibody Fab19 Reveal a Direct Relationship between Association Rate and Neutralizing Potency , 2013, The Journal of Immunology.

[23]  Tongqing Zhou,et al.  Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization , 2013, Cell.

[24]  Tongqing Zhou,et al.  Mechanism of Human Immunodeficiency Virus Type 1 Resistance to Monoclonal Antibody b12 That Effectively Targets the Site of CD4 Attachment , 2009, Journal of Virology.

[25]  Chaim A. Schramm,et al.  Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus , 2013, Nature.

[26]  Mario Roederer,et al.  Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing , 2011, Science.

[27]  David Nemazee,et al.  Rational immunogen design to target specific germline B cell receptors , 2012, Retrovirology.

[28]  Noreen R. Gonzales,et al.  Grafting of “Abbreviated” Complementarity-Determining Regions Containing Specificity-Determining Residues Essential for Ligand Contact to Engineer a Less Immunogenic Humanized Monoclonal Antibody , 2002, The Journal of Immunology.

[29]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[30]  H. Hong,et al.  Humanization by CDR grafting and specificity-determining residue grafting. , 2012, Methods in molecular biology.

[31]  Amy C. Anderson,et al.  Computational structure-based redesign of enzyme activity , 2009, Proceedings of the National Academy of Sciences.

[32]  Ron Diskin,et al.  Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding , 2011, Science.

[33]  Holly Janes,et al.  Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies , 2009, Journal of Virology.

[34]  D. Burton,et al.  Highly potent HIV-specific antibody neutralization in vitro translates into effective protection against mucosal SHIV challenge in vivo , 2012, Proceedings of the National Academy of Sciences.

[35]  Q. Sattentau,et al.  Analysis of Memory B Cell Responses and Isolation of Novel Monoclonal Antibodies with Neutralizing Breadth from HIV-1-Infected Individuals , 2010, PloS one.

[36]  Baoshan Zhang,et al.  Broad and potent neutralization of HIV-1 by a gp41-specific human antibody , 2012, Nature.