RosettaAntibodyDesign (RAbD): A General Framework for Computational Antibody Design
Authors: Adolf-Bryfogle Jared , Kalyuzhniy Oleks , Kubitz Michael , Weitzner Brian D. , Hu Xiaozhen , Adachi Yumiko , Schief William R. , Dunbrack Roland L. 
Published: September 2017

A structural-bioinformatics-based computational methodology and framework have been developed for the design of antibodies to targets of interest. RosettaAntibodyDesign (RAbD) samples the diverse sequence, structure, and binding space of an antibody to an antigen in highly customizable protocols for the design of antibodies in a broad range of applications. The program samples antibody sequences and structures by grafting structures from a widely accepted set of the canonical clusters of CDRs (North et al.,J. Mol. Biol., 406:228-256, 2011). It then performs sequence design according to amino acid sequence profiles of each cluster, and samples CDR backbones using a flexible-backbone design protocol incorporating cluster-based CDR constraints. Starting from an existing experimental or computationally modeled antigen-antibody structure, RAbD can be used to redesign a single CDR or multiple CDRs with loops of different length, conformation, and sequence. We rigorously benchmarked RAbD on a set of 60 diverse antibody–antigen complexes, using two design strategies – optimizing total Rosetta energy and optimizing interface energy alone. We utilized two novel metrics for measuring success in computational protein design. The design risk ratio (DRR) is equal to the frequency of recovery of native CDR lengths and clusters divided by the frequency of sampling of those features during the Monte Carlo design procedure. Ratios greater than 1.0 indicate that the design process is picking out the native more frequently than expected from their sampled rate. We achieved DRRs for the non-H3 CDRs of between 2.4 and 4.0. The antigen risk ratio (ARR) is the ratio of frequencies of the native amino acid types, CDR lengths, and clusters in the output decoys for simulations performed in the presence and absence of the antigen. For CDRs, we achieved cluster ARRs as high as 2.5 for L1 and 1.5 for H2. For sequence design simulations without CDR grafting, the overall recovery for the native amino acid types for residues that contact the antigen in the native structures was 72% in simulations performed in the presence of the antigen and 48% in simulations performed without the antigen, for an ARR of 1.5. For the non-contacting residues, the ARR was 1.08. This shows that the sequence profiles are able to maintain the amino acid types of these conserved, buried sites, while recovery of the exposed, contacting residues requires the presence of the antigen-antibody interface. We tested RAbD experimentally on both a lambda and kappa antibody–antigen complex, successfully improving their affinities 10 to 50 fold by replacing individual CDRs of the native antibody with new CDR lengths and clusters.

Author Summary

Antibodies are proteins produced by the immune system to attack infections and cancer and are also used as drugs to treat cancer and autoimmune diseases. The mechanism that has evolved to produce them is able to make 10s of millions of different antibodies, each with a different surface used to bind the foreign or mutated molecule. We have developed a method to design antibodies computationally, based on the 1000s of experimentally determined three-dimensional structures of antibodies available. The method works by treating pieces of these structures as a collection of parts that can be combined in new ways to make better antibodies. Our method has been implemented in the protein modeling program Rosetta, and is called RosettaAntibodyDesign (RAbD). We tested RAbD both computationally and experimentally. The experimental test shows that we can improve existing antibodies by 10 to 50 fold, paving the way for design of entirely new antibodies in the future.