The Binding of Brazilin from C. sappan to the Full-Length SARS-CoV-2 Spike Proteins
Issued Date
2025-05-01
Resource Type
ISSN
16616596
eISSN
14220067
Scopus ID
2-s2.0-105004925322
Journal Title
International Journal of Molecular Sciences
Volume
26
Issue
9
Rights Holder(s)
SCOPUS
Bibliographic Citation
International Journal of Molecular Sciences Vol.26 No.9 (2025)
Suggested Citation
Bamrung P., Toviwek B., Samsudin F., Chairatana P., Bond P.J., Pongprayoon P. The Binding of Brazilin from C. sappan to the Full-Length SARS-CoV-2 Spike Proteins. International Journal of Molecular Sciences Vol.26 No.9 (2025). doi:10.3390/ijms26094100 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/110260
Title
The Binding of Brazilin from C. sappan to the Full-Length SARS-CoV-2 Spike Proteins
Corresponding Author(s)
Other Contributor(s)
Abstract
The emergence of coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a global issue since 2019. The prominent characteristic of SARS-CoV-2 is the presence of the spike (S) protein protruding from the virus particle envelope. The S protein is a major drug and vaccine target because it initiates the key step in infection. Medicinal herbs are a potential treatment option to enhance immunity to fight viral infections. Caesalpinia sappan L. has been reported to display promising anti-viral activities. Specifically, brazilin (BRA), a major bioactive compound in C. sappan, was reported to play a role in inhibiting viral infection. Thus, the ability of BRA as a COVID-19 treatment was tested. The S protein was used as the BRA target of this work. Understanding the binding mechanism of BRA to the S protein is crucial for future utilisation of C. sappan as a COVID-19 treatment or other coronavirus-caused pandemics. Here, we performed molecular docking of BRA onto the S protein receptor binding domain (RBD) and multimerisation (MM) pockets. Molecular dynamics (MD) simulations were conducted to study the stability of binding to glycosylated and non-glycosylated S protein constructs. BRA can bind to the Receptor-binding motif (RBM) on an RBD surface stably; however, it is too large to fit into the MM pocket, resulting in dissociation. Nonetheless, BRA is bound by residues near the S1/S2 interface. We found that glycosylation has no effect on BRA binding, as the proposed binding site is far from any glycans. Our results thus indicate that C. sappan may act as a promising preventive and therapeutic alternative for COVID-19 treatment.