Role of antibody heavy and light chain interface residues in affinity maturation of binding to HIV envelope glycoprotein

Cisneros, Alberto; Nargi, Rachel S.; Parrish, Erica H.; Haliburton, Christian Marie; Meiler, Jens; Crowe, James E.

doi:10.1039/c8me00080h

Cited by 5 publications

(7 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As noted in section 3.1, the mutant position L-K45 is a solvent accessible residue while L-Q48 is responsible for forming polar contacts with the heavy chain. The performance of these mutants a rms the importance of mutations at the heavy and light chain interface in improving binding a nity speci city as also shown by Cisneros and colleagues [29].…”

Section: Discussion and Conclusion 41 Mutationssupporting

confidence: 55%

Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

Saini

Agarwal

Pradhan

et al. 2021

Preprint

View full text Add to dashboard Cite

Introduction: Computational antibody engineering, affinity maturation, and screening greatly aid in vaccine and therapeutic antibody development by increasing the speed and accuracy of predictions. This study presents a protocol for designing affinity enhancing mutants of antibodies through in silico mutagenesis. A SARS-CoV-2 cross-reactive neutralizing antibody, CR3022, is considered as a case study.Methods: Our study aimed at generating antibody candidates from the human antibody CR3022 (derived from convalescent SARS patient) against the RBD of SARS-CoV-2 via in silico affinity maturation using site-directed mutagenesis in mutation hotspots. We optimized the paratope of the CR3022 antibody towards the RBD of SARS-CoV-2 for better binding affinity and stability, employing molecular modeling, docking, dynamics simulations, and molecular mechanics energies combined with generalized Born and surface area (MM-GBSA). Results: Nine antibody candidates were generated post in silico site-directed mutagenesis followed by preliminary screening. Molecular dynamics simulation of 100 nanoseconds and MM-GBSA analysis confirmed L-K45S as a lead antibody with the highest binding affinity against the RBD compared to wild-type and mutant counterparts. Three out of the remaining mutants were also found to have distinct epitopes and binding, possessing a potential to be developed against emerging SARS-CoV-2 variants of concern. Conclusion: The study demonstrates the use of an integrative antibody engineering protocol for enhancing affinity and neutralization potential through mutagenesis using robust open-source computational tools and predictors. This study highlights unique scoring and ranking methods for evaluating docking efficiency. It also underscores the importance of framework mutations for developing broadly neutralizing antibodies.

show abstract

Section: Discussion and Conclusion 41 Mutationssupporting

confidence: 55%

Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

Saini

Agarwal

Pradhan

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…First, we confirmed that the anti-NET immunoreactivity was completely lost in the GL counterpart whereas the anti-cit-H2B immunoreactivity was reduced by over 60%. Recent studies have shown that SHM in the HC/LC interface, distant from the region of contact between Ag/Ab, play an important role in the highaffinity recognition of the Ag (15). Moreover, it was recently proposed that SHM could generate new reactivity and/or polyreactivity toward cit-Ags, causing epitope spreading in the ACPA response (16)(17)(18).…”

Section: Discussionmentioning

confidence: 99%

H and L Chain Affinity Maturation and/or Fab N-Glycosylation Influence Immunoreactivity toward Neutrophil Extracellular Trap Antigens in Rheumatoid Arthritis Synovial B Cell Clones

Corsiero

Carlotti

Jagemann

et al. 2020

The Journal of Immunology

View full text Add to dashboard Cite

We previously showed that anti-neutrophil extracellular trap (NET) rheumatoid arthritis (RA)-rmAbs derived from CD19 + B cells within RA human synovial tissues frequently react against NETs. In this study, we aimed to characterize the importance of affinity maturation via somatic hypermutation (SHM) within the Ig variable H (VH) and variable L (VL) chains and Fab-N-linked glycosylation in RA synovial B cell clones reactive to NETs and NET-derived Ags such as citrullinated histones. Selected anti-NET RA-rmAbs derived from synovial RA CD19 + B cells were subjected to overlap-PCR to generate germline (GL; VH and VL reverted into GL), hybrid clones (VH/VL region reverted into GL), and N-glycosylation mutants (N→Q) and analyzed for anti-NETs and citrullinated histones (cit-H2B) immunoreactivity. Anti-NET/cit-H2B immunoreactivity of selected RA-rmAbs was abrogated in the VH and VL GL counterpart. In RA B cell hybrid clone RA015/11.88 and RA056/11.23.2, NET and/or cit-H2B immunoreactivity was solely dependent on SHM in the IgVH region whereas RA B cell hybrid clone RA015/11.91 required affinity maturation of both VH and VL for efficient binding to cit-H2B. In 7/80 RA-rmAb, SHM resulted in ex novo N-glycosylation sites in VH and/or VL regions. Removal of Fab-linked glycans in RA056/11.23.2 in the N-mutant counterpart resulted in 90% reduction in immunoreactivity to cit-H2B. Thus, SHM in the IgVH and/or VL regions of RA synovial B cells is necessary for the immunoreactivity to NET-Ags. Fab-N-linked-glycosylation introduction sites are observed in a minority of anti-NET B cell clones but can strongly influence NET-Ag binding.

show abstract

“…This modulation of chain interface relationships has been investigated recently by Cisneros et al, who found VH–VL interface residues were reverted to the germline sequence, which resulted in significant loss of affinity, and indicated that the rigidification of the VH–VL interface, which will determine its orientation, is a major driver for affinity maturation. 61 RosettaAntibody selects 10 different framework matches as starting structures for loop grafting. The selected template loops are superimposed on the framework based on two overlapping residues and optimized through a cycle of minimizations, random torsional sampling and cyclic coordinate descent (CCD).…”

Section: Methods For Antibody Structure Prediction and Designmentioning

confidence: 99%

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

et al. 2021

Self Cite

View full text Add to dashboard Cite

Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improvements in performance within the Rosetta software suite for biomolecular modeling have given rise to a greater breadth of structure prediction, including docking and design application cases for antibody and antigen modeling. Here, we present an overview of current protocols for antibody and antigen modeling using Rosetta and exemplify those by detailed tutorials originally developed for a Rosetta workshop at Vanderbilt University. These tutorials cover antibody structure prediction, docking, and design and antigen design strategies, including the addition of glycans in Rosetta. We expect that these materials will allow novice users to apply Rosetta in their own projects for modeling antibodies and antigens.

show abstract

Role of antibody heavy and light chain interface residues in affinity maturation of binding to HIV envelope glycoprotein

Abstract: Optimization of the heavy chain/light chain interface could serve as an important tool for maximizing antibody/antigen binding affinity without altering antigen contact residues.

Cited by 5 publications

References 43 publications

Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

H and L Chain Affinity Maturation and/or Fab N-Glycosylation Influence Immunoreactivity toward Neutrophil Extracellular Trap Antigens in Rheumatoid Arthritis Synovial B Cell Clones

Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design

Contact Info

Product

Resources

About