Elucidation of bezlotoxumab binding specificity to toxin B in Clostridioides difficile

Abstract

C. difficile or Clostridioides difficile infection (CDI) is currently one of the major causes of epidemics worldwide. Toxin B from Clostridioides difficile toxin B (TcdB) infection is the main target protein inhibiting CDI recurrence. Clinical research suggested that bezlotoxumab’s (Bez) efficiency is significantly reduced in neutralizing the B2 strain compared to the B1 strain. The monoclonal antibody (mAb) functions by binding to the epitope 1 and 2 regions in the combined repetitive oligopeptide (CROP) domain. Some binding residues are distinctively different between B1 and B2 strains. In this work, we aimed to elucidate and compare insights into the interaction of toxins B1 and B2 in complex with Bez by using all-atom molecular dynamics (MD) simulations and binding free energy calculations. The predicted ΔG_binding values suggested that the antibody (Ab) could bind to toxin B1 significantly better than B2, supported by higher salt bridge and hydrogen bonding (H-bonding) interactions, as well as the number of contact residues between the two focused proteins. The toxin B1 residues important for binding with Bez were E1878, T1901, E1902, F1905, N1941, V1946, N2031, T2032, E2033, V2076, V2077, and E2092. The lower susceptibility of Bez towards toxin B2 was primarily due to a change of residue E2033 from glutamate to alanine (A2033) and the loss of E1878 and E1902 contributions, as determined by the intermolecular interaction changes from the dynamic residue interaction network (dRIN) analysis. The obtained data strengthen our understanding of Bez/toxin B binding.

Communicated by Ramaswamy H. Sarma

Keywords:

• Clostridioides difficile
• Toxin B
• bezlotoxumab
• molecular dynamics
• dynamic residue interaction network

Acknowledgments

K.K. would like to thank the Bioinformatics and Computational Biology Program Scholarship, and the Overseas Presentations of Graduate Level Academic Thesis from Graduate School, Chulalongkorn University. C.H. thanks the Science Achievement Scholarship of Thailand (SAST).

Disclosure statement

The authors report there is no conflict of interest, financial or otherwise.

Additional information

Funding

K.K. would like to thank Chulalongkorn University for financing this research as part of the 90^th Anniversary of Chulalongkorn University (GCUGR1125651009M).