Humanized Anti-PD-1 Antibodies Generated Using The Conditional Kernel-Elastic Autoencoder

Abstract

The human immune system excels at generating highly effective antibodies through natural selection and somatic hypermutation, but adapting these antibodies for therapeutic use, referred to as "antibody medicine-likeness", requires careful consideration of biochemical and physiological properties. Traditional redesign methods are often slow and limited in scope. In this study, we introduce a machine learning-based approach to evolve new anti-PD-1 antibodies within a chemically informed latent space using a conditional kernel-elastic autoencoder (CKEA) between nivolumab and pembrolizumab, both of which bind the FG-loop "hotspot" of PD-1 in the most distantly related orientations, differing by 174{degrees}. This generative framework is designed to preserve favorable therapeutic features while exploring variants with different potency, ultimately for improved potency. To evaluate structural and functional viability, we performed molecular dynamics (MD) simulations of the generated antibody - PD-1 complexes and described their MD properties. These simulations reveal detailed free-energy landscapes and identify stable binding conformations, providing a strong basis for experimental validation. To validate our designs, we expressed and experimentally tested the antibodies for binding affinity to PD-1. Upon expression and purification, three out of six designed antibodies exhibited some binding to PD-1, whose properties could likely be improved using other computational saturation mutagenesis or laboratory evolution. Our results demonstrate the potential of artificial intelligence (AI)-guided interpolation methods to generate novel, high-affinity antibodies with therapeutic promise, offering a powerful strategy for next-generation antibody development. SYNOPSIS TOCCombination of MD simulations with machine learning algorithms could revolutionize the antibody-breeding sciences to lead to new antibody discovery that is compatible with or better than naturally occurring antibodies. Topics of Content (TOC)Fingerprints of R86 finger of PD-1 are recognized by our designed P2N_2 anti-PD-1 antibody according to our MD simulations O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/742579v1_ufig1.gif" ALT="Figure 1000"> View larger version (49K): org.highwire.dtl.DTLVardef@130fd5aorg.highwire.dtl.DTLVardef@1495cd8org.highwire.dtl.DTLVardef@16e822forg.highwire.dtl.DTLVardef@25004c_HPS_FORMAT_FIGEXP M_FIG C_FIG