Green algae Caulerpa racemosa compounds as antiviral candidates for SARS-CoV-2: In silico study

Asmi CMAR. Tassakka; Israini W.  Iskandar; Andi BA.  Juniyazaki; St Zaenab; Jamaluddin F. Alam; Haerani  Rasyid; Kasmiati Kasmiati; Ellya  Sinurat; Fenny M.  Dwiany; Ronni  Martien; Abigail M.  Moore

doi:10.52225/narra.v3i2.179

Authors

Asmi CMAR. Tassakka Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar, Indonesia https://orcid.org/0000-0001-8967-210X
Israini W. Iskandar Postgraduate School of Biomedicine, Universitas Hasanuddin, Makassar, Indonesia https://orcid.org/0000-0001-9079-4147
Andi BA. Juniyazaki Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia https://orcid.org/0009-0007-7239-0035
St Zaenab Faculty of Fisheries, Universitas Cokroaminoto, Makassar, Indonesia https://orcid.org/0000-0003-2409-1464
Jamaluddin F. Alam Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar, Indonesia
Haerani Rasyid Faculty of Medicine, Universitas Hasanuddin, Makassar, Indonesia
Kasmiati Kasmiati Faculty of Marine Science and Fisheries, Universitas Hasanuddin, Makassar, Indonesia
Ellya Sinurat Indonesia National Research and Innovation Agency, Jakarta, Indonesia
Fenny M. Dwiany School of Life Science and Technology, Institute Teknologi Bandung, Bandung, Indonesia
Ronni Martien Faculty of Pharmacy, Universitas Gadjah Mada, Yogyakarta, Indonesia
Abigail M. Moore Graduate School, Universitas Hasanuddin, Makassar, Indonesia https://orcid.org/0000-0002-4122-3740

DOI:

https://doi.org/10.52225/narra.v3i2.179

Keywords:

Antiviral activity, binding affinity, Caulerpa racemosa, SARS-CoV-2, green algae

Abstract

Green algae (Caulerpa racemosa) are known to contain bioactive compounds which are hypothesized to have antiviral activities against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) pandemic. The aim of this study was to analyze the anti-SARS-CoV-2 potential of compounds extracted from the green alga Caulerpa racemosa using in silico analysis. The extract was obtained through maceration with 96% ethanol and the compounds present in the extract were identified through gas chromatography-mass spectroscopy (GC-MS). The binding affinities were analyzed in silico using the PyRx application and visualized in the PyMOL software. GC-MS analysis of Caulerpa racemosa extract showed 92 spectral peaks, each of which was assigned to a bioactive compound. Of the six compounds with a strong binding affinity, n-[1-(1-adamantan-1-yl-propyl)-2,5-dioxo-4-trifluoromethyl-imidazo lidin-4-yl] 4-methoxy-benzamide had the lowest score (-8.1 kcal/mol) against the SARS-CoV-2 3C-like protease binding site, similar with that of remdesivir. The molecular dynamics calculations demonstrated that root means square deviation values of the selected inhibitors remained stable throughout a 15-nanosecond simulation. In conclusion, the in silico analysis suggests that Caulerpa racemosa extract is a potential antiviral candidate against SARS-CoV-2.