23
DOI: https://doi.org/10.1186/s43141-023-00569-8
English
eng
Hessel, Sofia Safitri
Contributor
<div id="abs0005" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0010" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Background</h3><div class="u-margin-s-bottom" id="sp0090" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">The ongoing concern surrounding <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/coronavirinae" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">coronavirus</a><span style="margin: 0px; padding: 0px;"> disease 2019 (COVID-19) primarily stems from continuous mutations in the genome of the <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/severe-acute-respiratory-syndrome-coronavirus-2" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">severe acute respiratory syndrome coronavirus 2</a><span style="margin: 0px; padding: 0px;"> (SARS-CoV-2), leading to the emergence of numerous variants. The receptor-binding domain (RBD) in the S1 subunit of the <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/vitronectin" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">S protein</a><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> of the virus plays a crucial role in recognizing the host’s angiotensin-converting enzyme 2 (hACE2) receptor and facilitating cell <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/membrane-fusion" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">membrane fusion</a> processes, making it a potential target for preventing viral entrance into cells. This research aimed to determine the potential of banana </span><a href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/lectin" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">lectin</a> (BanLec) proteins to inhibit SARS-CoV-2 attachment to host cells by interacting with RBD through computational modeling.</span></span></span></div></div><div id="abs0010" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0015" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Materials and methods</h3><div class="u-margin-s-bottom" id="sp0095" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;">The BanLecs were selected through a sequence analysis process. Subsequently, the genes encoding BanLec proteins were retrieved from the Banana Genome Hub database. The FGENESH online tool was then employed to predict <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/peptide-sequence" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">protein sequences</a>, while web-based tools were utilized to assess the physicochemical properties, </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/allergenicity" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">allergenicity</a><span style="margin: 0px; padding: 0px;">, and toxicity of BanLecs. The RBDs of SARS-CoV-2 were modeled using the SWISS-MODEL in the following step. <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/docking-molecular" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Molecular docking</a> procedures were conducted with the aid of ClusPro 2.0 and HDOCK web servers. The three-dimensional structures of the docked complexes were visualized using PyMOL. Finally, molecular dynamics simulations were performed to investigate and validate the interactions of the complexes exhibiting the highest interactions, facilitating the simulation of their dynamic properties.</span></div></div><div id="abs0015" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0020" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Results</h3><div class="u-margin-s-bottom" id="sp0100" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;">The BanLec proteins were successfully modeled based on the <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/rna-sequence" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">RNA sequences</a> from two species of banana (</span><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/musa" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Musa</a></span></span><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> sp.). Moreover, an <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/amino-acids" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">amino acid</a> modification in the BanLec protein was made to reduce its </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/mitogenicity" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">mitogenicity</a>. Theoretical </span><a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/allergenicity" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">allergenicity</a><span style="margin: 0px; padding: 0px;"> and toxicity predictions were conducted on the BanLecs, which suggested they were likely non-allergenic and contained no discernible toxic domains. <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/docking-molecular" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Molecular docking</a><span style="margin: 0px; padding: 0px;"> analysis demonstrated that both altered and wild-type BanLecs exhibited strong affinity with the RBD of different SARS-CoV-2 variants. Further analysis of the molecular docking results showed that the BanLec proteins interacted with the active site of RBD, particularly the key amino acids residues responsible for RBD’s binding to hACE2. Molecular dynamics simulation indicated a stable interaction between the <a href="https://www.sciencedirect.com/topics/medicine-and-dentistry/omicron-coronavirus-variant" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Omicron</a> RBD and BanLec, maintaining a root-mean-square deviation (RMSD) of approximately 0.2 nm for a duration of up to 100 ns. The individual proteins also had stable structural conformations, and the complex demonstrated a favorable binding-free energy (BFE) value.</span></span></span></div></div><div id="abs0020" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0025" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Conclusions</h3><div class="u-margin-s-bottom" id="sp0105" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">These results confirm that the BanLec protein is a promising candidate for developing a potential therapeutic agent for combating COVID-19. Furthermore, the results suggest the possibility of BanLec as a broad-spectrum antiviral agent and highlight the need for further studies to examine the protein’s safety and effectiveness as a potent antiviral agent.</div></div>
Elsevier
December 2023
pdf
Journal of Genetic Engineering and Biotechnology
A computational simulation appraisal of banana lectin as a potential anti-SARS-CoV-2 candidate by targeting the receptor-binding domain
mixed material
Elsevier