ArticleACS omega2026
Exploring Trop-2-Nanobody PPI Interactions through Molecular Dynamics Simulations and Biovalidations.
Article in ACS omega, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Authors and funding
10 authors.
Funding
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Abstract
The transmembrane glycoprotein Trop-2 has garnered significant attention as a potential therapeutic target due to its involvement in various malignancies, including breast, lung, and prostate cancers. Specifically, the exploration of Trop-2-specific antibodies and nanobodies has emerged as a promising avenue for innovative treatment strategies. Despite advancements, a comprehensive understanding of the intricate molecular interactions between Trop-2 and specific nanobodies remains elusive. In this study, molecular dynamics (MD) simulations with MM/GBSA were employed to investigate the binding poses, key residues, and detailed interactions between Trop-2 and three distinct nanobodies (Nb60, Nb65, and Nb108), which will further guide the development of Trop-2-targeting nanobodies. Our findings corroborated the docking results, highlighting the reliability of binding pose 1. Additionally, our simulations elucidated key residues involved in the interaction interface, particularly within the C-terminal cysteine-poor domain (CPD) and an α-helix region (S170-Y185) on Trop-2. Furthermore, we identified the critical role of the complementarity-determining region 3 (CDR3) length and the key residues involved in the binding of nanobodies to Trop-2. Potential key residues predicted by MD simulations guided the redesign of the CDR3 region of Nb60, generating variants Nb-6, Nb-7, and Nb-14. Experimental data showed that alterations in the CDR3 significantly impacted binding affinity, with Nb-7 exhibiting the highest affinity (
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