In Silico Virtual Screening of Marine Aldehyde Derivatives from Seaweeds against SARS-CoV-2

Abstract

Coronavirus disease 2019, caused by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing global pandemic that poses an unprecedented threat to the global economy and human health. Several potent inhibitors targeting SARS-CoV-2 have been published; however, most of them have failed in clinical trials. This study aimed to assess the therapeutic compounds among aldehyde derivatives from seaweeds as potential SARS-CoV-2 inhibitors using a computer simulation protocol. The absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties of the compounds were analyzed using a machine learning algorithm, and the docking simulation of these compounds to the 3C-like protease (Protein Data Bank (PDB) ID: 6LU7) was analyzed using a molecular docking protocol based on the CHARMm algorithm. These compounds exhibited good drug-like properties following the Lipinski and Veber rules. Among the marine aldehyde derivatives, 4-hydroxybenzaldehyde, 3-hydroxybenzaldehyde, 3,4-dihydroxybenzaldehyde, and 5-bromoprotocatechualdehyde were predicted to have good absorption and solubility levels and non-hepatotoxicity in the ADME/Tox prediction. 3-hydroxybenzaldehyde and 3,4-dihydroxybenzaldehyde were predicted to be non-toxic in TOPKAT prediction. In addition, 3,4-dihydroxybenzaldehyde was predicted to exhibit interactions with the 3C-like protease, with binding energies of −71.9725 kcal/mol. The computational analyses indicated that 3,4-dihydroxybenzaldehyde could be regarded as potential a SARS-CoV-2 inhibitor.

Novel fused pyran derivatives induce apoptosis and target cell cycle progression in anticancer efficacy against multiple cell lines

“…A multitude of parameters were computed, including the two-dimensional Fast Polar Surface Area (2D_FPSA), Atom-based Log P98 ( A Log P 98), the integrity of the Blood–Brain Barrier (BBB), the presence and influence of Cytochrome P4502D6 (CYP2D6), and the propensity for Hepatotoxicity (HEPATOX). 54–56…”

“…A multitude of parameters were computed, including the two-dimensional Fast Polar Surface Area (2D_FPSA), Atom-based Log P98 (A Log P98), the integrity of the Blood-Brain Barrier (BBB), the presence and influence of Cytochrome P4502D6 (CYP2D6), and the propensity for Hepatotoxicity (HEPATOX). [54][55][56] From Tables 2 and 3, it can be concluded that all the potent compounds displayed appropriate physicochemical properties and obeyed Lipinski's ''Rule of Five'' and ''Veber Rule'' and hence, they have drug-likeness and can be considered as probable A Log P = Ghose-Crippen-Viswanadhan octanol-water partition coefficient, M W = molecular weight, HBD = hydrogen bond donar, HBA = hydrogen bond acceptor, HT = hepatotoxic, HIA = human intestinal absorption, NI = non-inhibitor, NT = non-toxic. Solubility level: 0 (extremely low), 1 (very low), 2 (low), 3 (good), 4 (optimal), 5 (too soluble), 5 (molecules with one or more A Log P 98 types).…”

Screening Marine Microbial Metabolites as Promising Inhibitors of Borrelia garinii: A Structural Docking Approach towards Developing Novel Lyme Disease Treatment

“…In silico methods have played a crucial role in identifying and optimizing potential small molecule inhibitors from var-ious sources, including marine-derived products, offering a rapid and cost-effective approach to drug development [80][81][82]. Marine natural products have garnered significant attention in drug discovery due to their structural diversity and bioactive properties.…”

Structure-Based In Silico Screening of Marine Phlorotannins for Potential Walrus Calicivirus Inhibitor

“…Many recent studies have elucidated the 3D structures or the relevant homology models of several viruses, including SARS-CoV-2 [23][24][25][26]. This is part of the ongoing effort to expedite drug discovery when drug candidates can be identified based on such 3D-modeling approaches already available in the existing literature.…”