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Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
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Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
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Journal Article
Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
2025
Overview
The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining region (CDR) grafting approach for designing nanobodies (Nbs) that target specific epitopes, with the aid of computer simulation and machine learning. As a proof-of-concept, we designed, evaluated, and characterized a high-affinity Nb against the spike protein of SARS-CoV-2, the causative agent of the COVID-19 pandemic. The designed Nb, referred to as Nb Ab.2, was synthesized and displayed high-affinity for both the purified receptor-binding domain protein and to the virus-like particle, demonstrating affinities of 9 nM and 60 nM, respectively, as measured with microscale thermophoresis. Circular dichroism showed the designed protein’s structural integrity and its proper folding, whereas molecular dynamics simulations provided insights into the internal dynamics of Nb Ab.2. This study shows that our computational pipeline can be used to efficiently design high-affinity Nbs with diagnostic and prophylactic potential, which can be tailored to tackle different viral targets.
Publisher
Public Library of Science,Public Library of Science (PLoS)
Subject
/ Binding
/ Complementarity Determining Regions - chemistry
/ Complementarity Determining Regions - immunology
/ Complementarity-determining region
/ Computer and Information Sciences
/ Computer-generated environments
/ COVID-19
/ Design
/ Epitopes
/ Ethylenediaminetetraacetic acid
/ Grafting
/ Humans
/ Medicine and health sciences
/ Molecular Dynamics Simulation
/ Proteins
/ Research and Analysis Methods
/ Severe acute respiratory syndrome coronavirus 2
/ Single-Domain Antibodies - chemistry
/ Single-Domain Antibodies - immunology
/ Spike Glycoprotein, Coronavirus - chemistry
/ Spike Glycoprotein, Coronavirus - immunology
/ Vaccines
/ Viruses
