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Epitopes prediction for microcystin-LR by molecular docking.

Yuan Liu1, Shu Liu1, Chongxin Xu2

  • 1School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; Key Laboratory of Food Quality and Safety of Jiangsu Province, Nanjing 210014, China.

Ecotoxicology and Environmental Safety
|October 30, 2021
PubMed
Summary

Researchers identified key binding sites on microcystin-LR (MC-LR), a harmful cyanobacterial toxin, using a single-chain variable fragment (scFv) antibody. This study reveals crucial interactions for antibody development and toxin detection.

Keywords:
EpitopeMicrocystin-LRMolecular dockingSingle chain variable fragment

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Area of Science:

  • Environmental toxicology
  • Immunochemistry
  • Structural biology

Background:

  • Microcystin-LR (MC-LR) is a prevalent and potent cyanobacterial toxin with significant public health implications.
  • Existing antibodies against MC-LR lack detailed epitope mapping, hindering precise detection and therapeutic development.
  • Understanding MC-LR-antibody interactions is crucial for developing sensitive diagnostic tools and potential neutralization strategies.

Purpose of the Study:

  • To elucidate the specific epitopes of MC-LR recognized by an antibody.
  • To characterize the binding mode between MC-LR and its corresponding single-chain variable fragment (scFv).
  • To provide insights for designing improved MC-LR detection methods and antibodies.

Main Methods:

  • Cloning and expression of a mouse hybridoma-derived scFv against MC-LR in E. coli.
  • Quantification of binding affinity (IC50, IC10) using competitive ELISA.
  • Assessment of antibody cross-reactivity with related microcystin variants (MC-RR, MC-YR, MC-LA).
  • Molecular docking simulations to predict the MC-LR-scFv binding interface.
  • Analysis of antibody variable region sequences (VH, Vκ) and complementarity-determining regions (CDRs).

Main Results:

  • The MC-LR-specific scFv demonstrated high affinity, with IC50 and IC10 values in the nanomolar range.
  • Significant cross-reactivity was observed with MC-RR and MC-YR, and moderate cross-reactivity with MC-LA.
  • Molecular docking revealed key interactions, including a hydrogen bond between Adda5 of MC-LR and the scFv, and involvement of Arg4 and Adda5.
  • VH-CDR1 was identified as critical for MC-LR binding, with potential for specificity tuning via Vκ-CDR1 and Vκ-CDR3.

Conclusions:

  • The study successfully mapped critical epitopes of MC-LR and demonstrated its binding mode with a specific scFv antibody.
  • The identified interactions and key antibody regions provide a foundation for rational design of MC-LR haptens and antibody engineering.
  • These findings are valuable for advancing the development of sensitive and specific MC-LR detection assays and immunotherapies.