Molecular insights into the interaction of apo-lactoferrin with the receptor binding domain of the SARS-CoV-2 spike protein: a molecular dynamics simulation study

Abstract

LF is a bioactive protein, derived from colostrum and milk that has been found to possess various immunomodulatory, iron chelating, and antimicrobial properties, especially in its apo-form. Recent studies have demonstrated the functionality of LF in attaching to the S proteins of SARS-CoV-2, thereby preventing it from interacting with the ACE-2 receptor. However, the molecular mechanism mediating the process is poorly understood. In this study, molecular docking and MD simulations coupled with free energy calculations were applied to elucidate the key interaction of apo-LF and its N-lobe and C-lobe derivative forms with the RBD of coronavirus S proteins. This has also been extended into evaluating the L452R mutant, which is associated with the delta variant of SARS-CoV-2. The results demonstrate the efficacy of the apo-LF C-lobe in binding to the RBD of both variants, primarily through electrostatic attractions between the acidic residues of the former and the basic residues of each RBD. Furthermore, due to the additional arginine in the L452R variant, the interaction between the C-lobe and the latter is stronger, resulting in a more favourable binding and tightly bound structure. The simulations highlight that the C-lobe, followed by full-length apo-LF can form a multimeric complex with the RBD of SARS-CoV-2, indicating their potential use as novel therapeutics, particularly the cleaved C-lobe of apo-LF to disrupt the S proteins from binding to the host ACE-2 receptor.

Communicated by Ramaswamy H. Sarma

Keywords:

• Coronavirus
• Spike proteins
• COVID-19
• antimicrobials
• nutraceuticals

Disclosure statement

We hereby certify that, to the best of our knowledge, no person(s) has any potential interest in the publication of this article, with regards to either the practical or writing aspects that may corrupt its authenticity. If any information indicating otherwise comes to light, then the relevant people will be contacted and procedures followed as outlined by RMIT University.

Acknowledgements

KKD gratefully acknowledges the Australian Government for providing Research Training Program (RTP) scholarship in the form of Research Stipend Scholarship (RSS) and International tuition fee offset scholarship. We thank the National Computing Infrastructure (NCI), and the Pawsey Supercomputing Centre in Australia, which are funded by the Australian Government as well as the LIEF HPC-GPGPU Facility hosted at the University of Melbourne, which was established with the assistance of LIEF Grant LE170100200.

Funding

The author(s) reported there is no funding associated with the work featured in this article.