Marine-Derived Bioactive Metabolites as a Potential Therapeutic Intervention in Managing Viral Diseases: Insights from the SARS-CoV-2 In Silico and Pre-Clinical Studies

Worldwide urbanization and subsequent migration have accelerated the emergence and spread of diverse novel human diseases. Among them, diseases caused by viruses could result in epidemics, typified by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which hit the globe towards the end of December 2019. The global battle against SARS-CoV-2 has reignited interest in finding alternative treatments for viral infections. The marine world offers a large repository of diverse and unique bioactive compounds. Over the years, many antiviral compounds from marine organisms have been isolated and tested in vitro and in vivo. However, given the increasing need for alternative treatment, in silico analysis appears to provide a time- and cost-effective approach to identifying the potential antiviral compounds from the vast pool of natural metabolites isolated from marine organisms. In this perspective review, we discuss marine-derived bioactive metabolites as potential therapeutics for all known disease-causing viruses including the SARS-CoV-2. We demonstrate the efficacy of marine-derived bioactive metabolites in the context of various antiviral activities and their in silico, in vitro, and in vivo capacities.


Introduction
Anthropogenic activities, including intensive agriculture and globalization, among others, have eroded biodiversity worldwide [1][2][3], accelerating the emergence and spread of numerous new human diseases [4,5].Emerging infectious diseases, especially those caused by viruses, pose a threat to global health capable of causing widespread mortality in pandemics or localized outbreaks with high fatality rates [6,7].Over the past five decades, there has been a continuous discovery of new emerging viruses of zoonotic origin.The first such case was the Ebola virus, which initially occurred in 1976 in Zaire and Sudan, and since then, there has been an ongoing report of Ebola outbreaks [8].In 1981, the first case of what would become known as AIDS was recorded as Pneumocystis carinii pneumonia, primarily among homosexual males in the United States, heralding the onset of the AIDS epidemic; the causative agent, a retrovirus, was subsequently identified in 1983 [9].The turn of the millennium witnessed the emergence of novel coronaviruses, with the Severe Acute Respiratory Syndrome (SARS) outbreak originating in Hong Kong in 2003.This was followed by the Middle East Respiratory Syndrome (MERS) in Saudi Arabia in 2012 [10].In December 2019, the city of Wuhan in China's Hubei Province became the epicenter for an outbreak of a pneumonia-like illness of unknown etiology, which was later identified as COVID-19, caused by a novel coronavirus designated SARS-CoV-2 [11].
Beyond their profound mortality and socioeconomic impacts, infectious diseases caused by emerging viruses represent escalating threats to global health.Accordingly, developing robust antiviral treatments and pre-emptive measures against potential pandemics has become a global public health priority [5,12].Currently, vaccines and antiviral drugs are the primary interventions employed for the prevention and treatment of human viral infections.Vaccines are regarded as the most effective method for preventing viral infections [13].Despite intensive research on a variety of viral pathogens, including the recent coronavirus strains, the repertoire of available antiviral treatments remains limited, compounded by the concerning decline in efficacy over time against certain viruses [14][15][16].
Since the approval of idoxuridine, the first antiviral drug, numerous others have been developed.However, the high mutation rate and genetic diversity of viruses often leads to treatment failure and rapid development of drug resistance [17].Another significant concern is the cytotoxicity associated with these antiviral agents, which can limit their therapeutic utility [17].On the other hand, vaccination is heralded as the most potent preventive strategy against viral infections, yet its effectiveness is not uniform across all populations, particularly among older adults, necessitating supplemental antiviral therapies [18].This was illustrated by a community-wide serosurvey assessing the effectiveness of the BNT162b2 and CoronaVac vaccines against the SARS-CoV-2 Omicron variant over 100 days.The results of the study showed that at 100 days, vaccine effectiveness decreased to 26 and 35% for 3 and 4 doses of BNT162b2 and 6 and 11% for 3 and 4 doses of CoronaVac vaccines [15].Given these challenges, it is crucial to explore and develop new therapeutic agents, particularly from natural sources such as marine-derived metabolites.
Over the years, natural products have provided resources/ingredients for developing drugs to treat and manage many human diseases.Covering over 70% of the earth's surface, oceans are home to a wide array of organisms, thus providing a unique source of various metabolites with significant health benefits [19].Research on marine microorganisms has steadily expanded since it started in the 1960s as a new area of study for natural products [20].The unique secondary metabolites found in marine organisms with a variety of biological functions have evolved because of ecological stresses such as competition for space, surface fouling, predation, and successful reproduction [21].For a long time, it was mainly disregarded how crucial these secondary metabolites are in the regulation of pathogenic and parasitic organisms.However, with improved extraction and characterization technologies, secondary metabolites can be sourced from marine organisms (both micro and macro).
Researchers have successfully isolated over 12,000 novel metabolites and continue to discover hundreds of new compounds annually from marine organisms, yielding new and potent natural bioactive ingredients [21,22].On one hand, the terrestrial environment contains various plant-derived natural ingredients and molecules used as medicines; however, on the other hand, the marine ecosystem offers more untapped species of organisms from which potential bioactive natural compounds may be isolated [23].These metabolites exhibit many biological activities of great pharmacological potentials, such as antimicrobial, antifungal, antifertility, antibiotic, and anticarcinogenic, and may serve as prophylaxis and treatment of human diseases.
Marine microorganisms, a subclass of marine organisms are recognized for their ability to produce antiviral agents, and they may offer limitless biological resources for obtaining therapeutic medications intended to treat and manage viral diseases in humans, as well as an endless supply of innovative compounds with promising medicinal properties and significant market potential [20].Marine fungi alone yield between 150 and 200 novel molecules per year, including sesquiterpenoids, polyketides, and alkaloids [24].Donia and Hamann reported the inhibitory potential of these marine-derived bioactive compounds against herpes simplex virus 1, poliovirus, yellow fever, dengue virus, rhinovirus, vesicular stomatitis virus, influenza viruses, and HIV-1 [21] with Griffithsin (a lectin extracted from red algae), suggested for anti-HIV activity, in clinical trials [19].Furthermore, the structural engineering of these compounds by adding different functional groups (e.g., amines and ketones) and introducing double bonds, as well as the use of polymeric nanosystems, can bring about improved antiviral properties [25,26].These agents, targeting various stages of the viral replication cycle, offer promising avenues for both therapeutic intervention and prophylactic measures against viral diseases, including COVID-19.
Thus, this perspective review discusses prospective marine-derived bioactive metabolites that may serve as therapeutic interventions in managing/treating various viral diseases.In addition, promising marine metabolites with potential inhibitory effects specifically against the replication mechanism of SARS-CoV-2 main proteases according to literature studies of molecular docking and simulation (in silico studies), coupled with in vitro and in vivo studies, are further discussed.

Metabolites from Marine Organisms
The marine ecosystem remains a repository of taxonomically diverse groups of unexplored micro-and macro-organisms, compared to its terrestrial counterpart.The complex marine habitats are exposed to extreme conditions and ecological pressures, including competition for space, pollution, and predation, which have powered the evolution of an assortment of potential secondary metabolites with different biological activities [21].Naturally occurring secondary metabolites remain the main source of active ingredients for new therapeutic agents.In this regard, secondary metabolites from marine organisms have attracted immense attention over the years as potential raw materials for new broadspectrum therapeutics due to the large ecological diversity of biological species contained in the marine environment [27].
These secondary metabolites are synthesized by marine organisms as a survival and defence mechanism against other organisms, thus making them potential sources of bioactive compounds.With the emergence of various infectious diseases coupled with the menace of antibiotic resistance, marine organisms serve as a rich source of novel bioactive compounds for managing current and future viral diseases.The diversity of marine species (Figure 1) allows all kinds of potent metabolites to be isolated and tested for their potential pharmacological benefits to humans.Some bioactive compounds isolated and identified from marine organisms include terpenes, peptides and proteins, polysaccharides, lipids, alkaloids, and macrolides.The range of these compounds is related to the diverse mechanisms used by marine organisms to increase survival.

Bacteria
Marine microorganisms are microbes that exist in the marine, brackish water (coastal estuaries), or seawater (oceans, seas) habitats, and they include prokaryotes (i.e., bacteria and archaea) and eukaryotes (i.e., protists and fungi).There are several bacterial phyla in marine ecosystems, including the economically and biotechnologically important actinobacteria.However, the predominant novel compounds with potential biological activity are sourced from the genus Streptomyces [28,29].Marine bacteria possess physiological and molecular characteristics that differ from their terrestrial counterparts, due to their symbiotic relationships with sponges, octocorallia, ascidians, and marine plants.Thus, they produce bioactive secondary metabolites for chemical defence by associated microflora (symbionts) or to survive in extreme environmental conditions [30,31].The myriad of bioactive natural compounds extracted from marine bacteria has significantly increased in recent years.Moreover, marine bacteria continue to be a prolific source of bioactive compounds (i.e., peptides, exopolysaccharides, polyketides, and macrolatones) to treat/manage many disease conditions [29].
Table 1 shows some of the reported antiviral compounds of marine bacteria.A novel compound, antimycin A1a (1), extracted from Streptomyces kaviengensis was effective against western equine encephalitis virus (WEEV; half maximal inhibitory concentration, IC50 = 4 nM) [32].The compound inhibited the cellular electron mitochondrial transport chain and suppressed de novo pyrimidine synthesis [32].Others have reported that furan-2-yl acetate (2) isolated from Streptomyces VITSDK1 spp.inhibited fish noda virus, an important viral pathogen in cultured marine fishes [33].Elsewhere, the heterogenous expression of type III polyketide synthase gene vioA (from deep-sea-derived Streptomyces somaliensis SCSIO ZH66) enhanced synthesis of antiviral methylated violapyrones (VLPs Q-T) (3)(4)(5)(6) in Streptomyces youssoufiensis OUC6819.The resultant VLPs Q-T (3)(4)(5)(6) showed inhibitory activity against strains of influenza A (IC50 = 30.6-68.4 μM against strain H1N1 and 45.3-95.0μM with regards to strain H3N2) compared to ribavirin and non-methylated VLPs [34].Butenolide analogue 3 (7) isolated from marine Streptomyces sp.AW28M48  Marine microorganisms are microbes that exist in the marine, brackish water (coastal estuaries), or seawater (oceans, seas) habitats, and they include prokaryotes (i.e., bacteria and archaea) and eukaryotes (i.e., protists and fungi).There are several bacterial phyla in marine ecosystems, including the economically and biotechnologically important actinobacteria.However, the predominant novel compounds with potential biological activity are sourced from the genus Streptomyces [28,29].Marine bacteria possess physiological and molecular characteristics that differ from their terrestrial counterparts, due to their symbiotic relationships with sponges, octocorallia, ascidians, and marine plants.Thus, they produce bioactive secondary metabolites for chemical defence by associated microflora (symbionts) or to survive in extreme environmental conditions [30,31].The myriad of bioactive natural compounds extracted from marine bacteria has significantly increased in recent years.Moreover, marine bacteria continue to be a prolific source of bioactive compounds (i.e., peptides, exopolysaccharides, polyketides, and macrolatones) to treat/manage many disease conditions [29].

Marine Fungi
Marine fungi are also a rich source of natural bioactive compounds with various biological activities, including antiviral effects (Table 2, Figure S1).It has been reported that marine fungi have developed specific metabolic pathways compared to their terrestrial showed anti-adenoviral activity at EC50 of 91 μM with no prominent cytotoxicity effects at 2 mM [35].Furthermore, a marine exopolysaccharide (EPS) (8) extracted from Pseudoalteromonas spp.exerted a remarkable antiviral activity against herpes simplex (HSV-1) [36].WSSV (white spot syndrome virus), HSV (herpes simplex virus), H1N1 (a subtype of influenza A virus), half maximal effective concentration (EC50); half maximal inhibitory concentration (IC50).

Marine Fungi
Marine fungi are also a rich source of natural bioactive compounds with various biological activities, including antiviral effects (Table 2, Figure S1).It has been reported that marine fungi have developed specific metabolic pathways compared to their terrestrial showed anti-adenoviral activity at EC50 of 91 μM with no prominent cytotoxicity effects at 2 mM [35].Furthermore, a marine exopolysaccharide (EPS) (8) extracted from Pseudoalteromonas spp.exerted a remarkable antiviral activity against herpes simplex (HSV-1) [36].WSSV (white spot syndrome virus), HSV (herpes simplex virus), H1N1 (a subtype of influenza A virus), half maximal effective concentration (EC50); half maximal inhibitory concentration (IC50).

Marine Fungi
Marine fungi are also a rich source of natural bioactive compounds with various biological activities, including antiviral effects (Table 2, Figure S1).It has been reported that marine fungi have developed specific metabolic pathways compared to their terrestrial showed anti-adenoviral activity at EC50 of 91 μM with no prominent cytotoxicity effects at 2 mM [35].Furthermore, a marine exopolysaccharide (EPS) (8) extracted from Pseudoalteromonas spp.exerted a remarkable antiviral activity against herpes simplex (HSV-1) [36].WSSV (white spot syndrome virus), HSV (herpes simplex virus), H1N1 (a subtype of influenza A virus), half maximal effective concentration (EC50); half maximal inhibitory concentration (IC50).

Marine Fungi
Marine fungi are also a rich source of natural bioactive compounds with various biological activities, including antiviral effects (Table 2, Figure S1).It has been reported that marine fungi have developed specific metabolic pathways compared to their terrestrial

Streptomyces koyangensis SCSIO5802
Sediment sample collected from the South China Sea Antiviral activity against HSV at a concentration of 10 µM [40] WSSV (white spot syndrome virus), HSV (herpes simplex virus), H1N1 (a subtype of influenza A virus), half maximal effective concentration (EC 50 ); half maximal inhibitory concentration (IC 50 ).

Marine Algae
Marine algae are photosynthetic plant-like organisms that are categorized into three groups: microalgae, macroalgae, and multicellular organisms.Microalgae are tiny unicellular microorganisms that form the phytoplankton and comprise approximately 50,000 species.Conversely, sea algae, also known as seaweed, have become prominent in the food and cosmetic industries due to their nutrients and rich sulfated polysaccharides content, among others, which have been shown to exert various biological activities such as anticancer, antioxidant, immunoregulatory, antiviral, antithrombic, and anti-inflammatory properties [77].

Marine Algae
Marine algae are photosynthetic plant-like organisms that are categorized into three groups: microalgae, macroalgae, and multicellular organisms.Microalgae are tiny unicellular microorganisms that form the phytoplankton and comprise approximately 50,000 species.Conversely, sea algae, also known as seaweed, have become prominent in the food and cosmetic industries due to their nutrients and rich sulfated polysaccharides content, among others, which have been shown to exert various biological activities such as anticancer, antioxidant, immunoregulatory, antiviral, antithrombic, and anti-inflammatory properties [77].

Marine Algae
Marine algae are photosynthetic plant-like organisms that are categorized into three groups: microalgae, macroalgae, and multicellular organisms.Microalgae are tiny unicellular microorganisms that form the phytoplankton and comprise approximately 50,000 species.Conversely, sea algae, also known as seaweed, have become prominent in the food and cosmetic industries due to their nutrients and rich sulfated polysaccharides content, among others, which have been shown to exert various biological activities such as anticancer, antioxidant, immunoregulatory, antiviral, antithrombic, and anti-inflammatory properties [77].
Antiviral activities of other reported compounds isolated from marine macro-organisms (vertebrates and invertebrates) are summarized in Table 3.
Table 3. Antiviral properties of metabolites from marine macro-organisms.

Group of Compounds
Compound Name and Structural Formula (PubChem CID)
Table 3. Antiviral properties of metabolites from marine macro-organisms.

Group of Compounds
Compound Name and Structural Formula (PubChem CID) isms (vertebrates and invertebrates) are summarized in Table 3.

SARS-CoV-2 Virology and Mode of Entry
The SARS-CoV-2 which caused the severe acute respiratory coronavirus disease 2019 (COVID-19) belongs to the Coronaviridae family with a zoonotic potential, thus transmitted from humans and other mammals [134].It shares a similar genomic sequence with the original SARS-CoV (~79.5% similarity) and BatCoV RaTG13 (~96% similarity).SARS-CoV-2 is a 50-200 nM positive-sense single-stranded enveloped RNA virus (+ssRNA) with a genome size of 28-30 kb [135][136][137].The genome of SARS-CoV-2 consists of over 29,000 bases and codes for 29 proteins.Of the 29 proteins, the viral genome encodes 4 structural proteins and 16 non-structural replicate polyproteins which play a crucial role in the viral replication complex (Figure 2).The structural proteins include the spike (S) glycoprotein which binds to the host ACE2 receptor to initiate infection, small envelope (E) glycoprotein, and membrane (M) glycoprotein distributed along the viral envelope, and nucleocapsid (N) phosphoprotein which is an RNA-binding protein that facilitates the packaging of the genome and protects the viral genome [137,138].Structural proteins are important for infection and replication in the host cell, thus making them ideal candidates or targets for antiviral therapies.The non-structural proteins (NsPs) are synthesized as long polypeptides which release the RNA-dependent RNA polymerase (RdRp), Nsp12, when activated by the main protease (MP), Nsp5.MP can be targeted by antiviral drugs against SARS-CoV-2, given its key role in virus replication and transcription [139,140].
the genome and protects the viral genome [137,138].Structural proteins are important for infection and replication in the host cell, thus making them ideal candidates or targets for antiviral therapies.The non-structural proteins (NsPs) are synthesized as long polypeptides which release the RNA-dependent RNA polymerase (RdRp), Nsp12, when activated by the main protease (MP), Nsp5.MP can be targeted by antiviral drugs against SARS-CoV-2, given its key role in virus replication and transcription [139,140].Infection of host cells by SARS-CoV-2 transmission occurs via endocytosis, which involves the interaction of host cell surface receptors (fusion) with endosomal components.The spike proteins are essential for the entry of the virus into a host cell.Particularly, the S1/S2 subunit facilitates attachment to the cell and subsequent fusion.It requires initial priming by the transmembrane protease, serine 2 (TMPRSS2), cysteine protease, and cathepsin L (CatL).In the host cell, the angiotensin-converting enzyme 2 (ACE2), a type I membrane receptor protein found in the lungs and arteries [137], serves as the binding site for SARS-CoV.The SARS-CoV-2 virion attaches to the enzymatic domain of ACE2 on the surface of cells via the receptor-binding domain (RBD) of the S1 unit, and Infection of host cells by SARS-CoV-2 transmission occurs via endocytosis, which involves the interaction of host cell surface receptors (fusion) with endosomal components.The spike proteins are essential for the entry of the virus into a host cell.Particularly, the S1/S2 subunit facilitates attachment to the cell and subsequent fusion.It requires initial priming by the transmembrane protease, serine 2 (TMPRSS2), cysteine protease, and cathepsin L (CatL).In the host cell, the angiotensin-converting enzyme 2 (ACE2), a type I membrane receptor protein found in the lungs and arteries [137], serves as the binding site for SARS-CoV.The SARS-CoV-2 virion attaches to the enzymatic domain of ACE2 on the surface of cells via the receptor-binding domain (RBD) of the S1 unit, and subsequently, the cell TMPRSS2 opens the S protein, allowing for the fusion of the S2 subunit and ACE2 [141].This results in endocytosis and the translocation of both the virus and enzyme into endosomes [142].The virus subsequently escapes when the pH of the endosome drops or is cleaved by cathepsin, thus releasing its RNA into the cell cytoplasm.The virus then replicates and spreads new copies of the virus to infect more cells [136,141].

Therapeutic Target Site to Inhibit SARS-CoV-2 Entry and Replication
At present, vaccines, monoclonal antibodies, peptides, small molecule drugs, and interferon therapies serve as viable options to manage SARS-CoV-2.Nevertheless, targeting the replication machinery of the virus remains a promising therapeutic approach.In this regard, viral proteases are suitable targets, as these enzymes play critical roles in the replication of the virus by cleaving proproteins after translation into the host cell cytosol during viral protein maturation [143].Figure 3 shows the entry and replication cycle of SARS-CoV-2 entry with inhibition sites of some marine-derived metabolites.SARS-CoV-2 spike (S) glycoprotein binds to the ACE2 receptor on the host cell surface, and the virus subsequently enters the cells via endocytosis to release its positive-sense ribonucleic acid (RNA) into the host cell.The viral genomic RNA is then transcribed and translated to produce non-structural proteins (nsps), including replicase polyproteins (RNA-dependent RNA polymerase and helicase), which then creates an RdRp complex.Within the RdRp complex, subgenomic transcription and RNA replication occur to synthesize negative-strand guide RNA (gRNA) and a set of subgenomic RNAs for viral replication and transcription.Subgenomic RNAs are synthesized and translated into viral structural proteins such as the spike (S), nucleocapsid (N), membrane (M), and envelope (E).After viral structural proteins are translated, S, E, and M proteins are processed in the Endoplasmic Reticulum-Golgi (ERG) intermediate compartment of the host cell.In the cytoplasm, nucleocapsids assemble and bud into the lumen of the ERG intermediate compartment.Finally, the mature virus inside the Golgi vesicle is exocytosed from the infected cell.Through ACE-2 receptors, a mature virus can infect the lung, endothelium, intestine, heart, testis, and kidney [140,144].

Potential In Silico and Pre-Clinical Studies of Marine-Derived Metabolites against Target Sites of SARS-CoV-2 as Therapeutics
Various in vitro and in vivo anti-SARS-CoV and anti-MERS-CoV studies have been carried out using a wide myriad of bioactive compounds during the previous outbreaks.Considering that they share some similarities with SARS-CoV-2, some of these bioactive compounds may be repurposed to screen for their potential against SARS-CoV-2.Designing an efficient broad-spectrum antiviral therapy against coronaviruses is an efficient way to counter various mutant strains of SARS-CoV-2, which hinder the effectiveness of the current vaccines [150].Natural bioactive compounds can be used to design new antiviral drugs against viral infections, coupled with boosting the innate immune system.However, there are challenges involved considering the diversity of natural metabolites, chemical intricacies, and different extraction methodologies [135].
To save time in screening bioactive compounds for potential activity, a virtual or computational screening approach is recommended.In this regard, in silico techniques such as molecular docking, molecular dynamics simulations, and network pharmacology are useful for the preliminary identification of natural compounds that can directly inhibit target proteins [5,135,151].Molecular docking evaluates the binding and interaction between the specified molecules (i.e., marine-derived metabolites) and the target protein(s), whereas network pharmacology employs computationally simulated drug-targeted inter- Overall, the ACE2 protein, transmembrane protease serine 2 (TMPRSS2), papain-like protease (PL2pro), and main protease (Mpro)/chymotrypsin-like protease (3CLpro), which are crucial for viral replication and proliferation in the human host, are all potential targets under investigation for therapeutic interventions against SARS-CoV-2 [134,135,137,143,145].PL2pro and 3CLpro/Mpro cleave large polyproteins of SARS-CoV-2 before being proteolytically processed to generate the individual proteins required for viral replication [141,142].3CLpro/Mpro plays a leading role in transcription, releasing replicative proteins, including the viral RNA polymerase and helicase proteins [146,147].3CLpro/Mpro is the main protease found only in the coronavirus family and is considered the most suitable target for virus inhibition as it cleaves the coronavirus polyprotein at eleven conserved sites.It is worth noting that glycan-protein interactions are important during viral binding to the host cell, considering that glycosylation of the S-protein shields the proteins from immune recognition.Hence, disrupting S-protein glycosylation significantly impairs viral entry, thus serving as another potential target for vaccine development and therapeutic interventions [137].Furthermore, neuropilin 1 (NRP1), a host protein, aids virus entry, making it an attractive target [148].In addition, RNA-dependent RNA polymerase (RdRp), which catalyzes the replication of the viral RNA genome, is a probable target as well [149].Also, more focus has been placed on decreasing the levels of ACE2, a part of the reninangiotensin system that regulates blood pressure, given that it is the main entry point of the virus in humans.However, this may not be a good approach since it can alter the central pressure control system and cause stroke or other medical conditions [148].

Potential In Silico and Pre-Clinical Studies of Marine-Derived Metabolites against Target Sites of SARS-CoV-2 as Therapeutics
Various in vitro and in vivo anti-SARS-CoV and anti-MERS-CoV studies have been carried out using a wide myriad of bioactive compounds during the previous outbreaks.Considering that they share some similarities with SARS-CoV-2, some of these bioactive compounds may be repurposed to screen for their potential against SARS-CoV-2.Designing an efficient broad-spectrum antiviral therapy against coronaviruses is an efficient way to counter various mutant strains of SARS-CoV-2, which hinder the effectiveness of the current vaccines [150].Natural bioactive compounds can be used to design new antiviral drugs against viral infections, coupled with boosting the innate immune system.However, there are challenges involved considering the diversity of natural metabolites, chemical intricacies, and different extraction methodologies [135].
To save time in screening bioactive compounds for potential activity, a virtual or computational screening approach is recommended.In this regard, in silico techniques such as molecular docking, molecular dynamics simulations, and network pharmacology are useful for the preliminary identification of natural compounds that can directly inhibit target proteins [5,135,151].Molecular docking evaluates the binding and interaction between the specified molecules (i.e., marine-derived metabolites) and the target protein(s), whereas network pharmacology employs computationally simulated drug-targeted interactions to identify potential inhibitors for a particular target and mode of action [152,153].Additionally, the process evaluates the stability of the predicted protein-ligand complex considering factors such as the nature of the solvent [154].By including biological circumstances, such as structural motions and the 3D structure of the targets, more reliable affinity values of the metabolites are estimated [155].Nevertheless, most studies about network pharmacology for SARS-CoV-2 are related to existing traditional drugs with limited studies available for marine-derived drugs [156,157].

In Silico, In Vitro, and In Vivo Studies of Major Classes of Metabolites against Entry and Replication of SARS-CoV-2
Diverse and unique polysaccharides, proteins, lipids, terpenoids, flavonoids, steroids, and alkaloids with virucidal activities have been extracted from marine organisms [158].Some of these metabolites and their derivatives are reported to be protease inhibitors that can inhibit DNA and RNA viruses, and thus may serve as potential protease inhibitors against SARS-CoV-2 [5].

Polysaccharides
Marine-derived polysaccharides are considered important biological macromolecules with unique and diverse structures and are considered valuable resources for drug discovery and design [159].Moreover, marine-derived polysaccharides are cheaply available in nature, non-toxic, safe, biocompatible, and biodegradable [160].a. Sulfated Polysaccharide (SP) Found in the cell walls of marine microbes, sulfated polysaccharides (SP) are naturally occurring water-soluble complex polymers extracted using water as a solvent [159].Others have speculated that SP-derived therapy may be used to manage COVID-19 disease because it prevents/inhibits adherence of the S-protein to the heparin sulfate co-receptor and thus decreases viral infection by acting as a decoy in host tissues [159,160].Various concentrations of fucoidan (RPI-27 (151) and RPI-28 (152)) extracted from Saccharina japon-ica showed antiviral activity against SARS-CoV-2 in Vero cells.RPI-27 (151) significantly inhibited SARS-CoV-2 infection in Vero cells (EC 50 = 0.08 µM) compared to RPI-28 (152) (EC 50 = 1.2 µM) [161].
Glycosaminoglycans are another class of sulfated polysaccharides with potential SARS-CoV-2 inhibitory properties.Song et al. [164] checked the inhibitory properties of sulfated glycosaminoglycans (SCSP) (156) isolated from sea cucumber Stichopus japonicus and observed that SCSP exhibited the highest inhibitory activity (IC 50 of 9.10 µg/mL) compared to fucoidan from brown algae, and chondroitin sulfate C from sharks (CS).They further demonstrated that SCSP can bind specifically to the S glycoprotein to inhibit entry of SARS-CoV-2 into host cells using pseudotype virus with S glycoprotein of SARS-CoV-2.The authors postulated that the binding of SCSP was facilitated by the high structural flexibility.Flexibility is necessary for the binding of polysaccharides to the S glycoprotein [164,165].Another sulfated glycosaminoglycan (156) from the bacteria, Pseudomonas sp. was reported to have a high binding energy with Mpro at −7.98 kcal/mol in silico [5].

Proteins a. Peptides
Bioactive peptides, arising from the hydrolysis of proteins, possess unique amino acid sequences that confer on them various biological activities.Marine organisms are a cheap source of proteins for acquiring bioactive peptides.Yao et al. [171] reported that oligopeptides (2-8 amino acids long) (161) arising from in silico hydrolysis of proteins from salmon, squid, tuna, mackerel, and pomfret exhibited high binding affinity to SARS-CoV-2 Mpro and monoamine oxidase A. Peptides that interrupt the binding of SARS-CoV-2 spike proteins to ACE are particularly enticing candidates against SARS-CoV-2 cell entry.For instance, peptides (sequences GDLGKTTTVSNWSPPKYKDTP (162) and VW ( 163)) obtained from Thunnus obesus and Undaria pinnatifida have been shown to stably bind to both hACE2 (−246.50 and −117.65 kcal/mol) and spike RBD-ACE2 complex (−223.60 and −123.42 kcal/mole) [23].The binding of these peptides may disrupt the interaction of SARS-CoV-s2 spike proteins with ACE2 and thus prevent cell entry of the virus.Also, peptides (Asp-Trp (164) and Val-Tyr ( 165)) isolated from tilapia viscera hydrolysate exhibited great binding affinity to four SARS-CoV-2 components including Mpro, S-glycoprotein, RBD-ACE2, and deubiquitinase inhibitors [172].

b. Lectins
Lectins from marine organisms have been garnering interest lately, especially those from algae [158].Lectins are carbohydrate-binding non-immunoglobulin-type proteins that recognize specific sugar groups on other molecules [158,177].Compared to lectins from other sources, marine lectins recognize and bind to a wide variety of sugar moieties including sugar monomers and oligosaccharides [149,158].Considering that SARS-CoV-2 uses spike glycoproteins to bind and facilitate on the cell surface glycans of potential hosts to initiate entry into cells, this makes them a perfect target for lectins.
Griffithsin ( 81) is a lectin found in the red-algae Griffithsia sp., which has a strong specificity for mannose residues of viral glycol proteins [149,158,178].They have the potential to interrupt the self-assembly of viruses during replication.It has been reported that treatment of SARS-CoV-2-infected rats with 10 mg/kg (b.w.)/day of Griffithsin (81) resulted in a 100% survival rate compared to the nontreated group [149,158,178].Griffithsin (81) has been shown to inhibit the s-protein-mediated adhesion of the RBD to hACE2 with an IC 50 of 0.3 µM [179].Consequently, Griffithsin (81) significantly inhibited SARS-CoV-2 pseudovirus infection in a dose-dependent manner in vitro, with an IC 50 of 293 nmol/L.Treatment of cells with Griffithsin (81) before or at the early stages of infection (0-0.5 h) resulted in up to 80% inhibition of SARS-CoV-2 compared to 32% inhibition when administered 8 h after infection [179].This suggests that Griffithsin (81) is effective against the virus at the initial stages of infection.c.Protein-bound pigments Some studies have also highlighted protein-bound pigments as potential inhibitors of SARS-CoV-2 infection.Phycobilins are light-capturing tetrapyrrole chromophores found in certain cyanobacteria, rhodophytes, chloroplasts of red algae, glaucophytes, and some cryptomonads.In recent times, these molecules have been widely studied for their antioxidant and antiviral activities [149,150].In silico studies have shown that phycocyanobilins (PCB) (174), a group of blue phycobilins, have a high binding energy of −8.6 and −9.3 kcal/mol for PCB-Mpro and PCB-RdRp, respectively [180].Pendyala et al. [150] further showed that PCB (174) can bind to Mpro and PLpro via polar interactions with specific binding pockets of amino acids such as G143 (38.5),N119, S46, and Y54 for Mpro, and D164(C), R166(C), D164(A), and G271(A) for PLpro.Petit et al. [181] also reported that PCB (174) obtained from Arthrospira sp. also exhibited strong binding affinity to SARS-CoV-2 S-glycoprotein using molecular docking studies.They also reported that both van der Waals attractions and hydrogen bonding contributed to the binding of PCB to spike RBD in silico.The molecular docking studies further revealed that PCB interacted with several amino acid residues of the spike RBD including TYR453, GLN493, TYR495, PHE497, ASN501, TYR505, SER494, GLN498, and GLY496 via different bonds [181].

Lipids
Lipids are involved extensively in the life cycle of SARS-CoV-2.They form the basis of host cell and viral membranes and act as the initial point of interaction between the virus and its potential host [158].
The receptor binding domain (RBD) of SARS-CoV-2 has been revealed to have three fatty acid binding pockets (FABP), which are lined by hydrophobic amino acids forming a bent tube that serves as an anchor for free fatty acids (FFA) [184].Linoleic acid (LA) (179), an omega 6 (ω-6) PUFA, has been reported to fit into the FABP and occupy all pockets [184].The binding of LA to the S protein induces the protein to adopt a stable closed S conformation, resulting in a reduced interaction with ACE2 [184].Similarly, long-chain omega 3 (ω-3) PUFAs, including docosahexaenoic acid (DHA) (180) and eicosapentaenoic acid (EPA) (181), bind to the FABP and induce the closed conformation of the spike protein, to an even greater extent than LA (179) [155].ω-3 PUFAs therefore have the potential to interrupt the interaction of ACE2 and RBD, thus reducing viral entry.Additionally, increased intake of ω-3 PUFAs decreases inflammation and coagulation caused by COVID-19 [155].
Another group of natural metabolites with a prominent role in cell-cell interactions are cerebrosides.These metabolites also carry out cell regulation and signal transduction.The molecular docking and dynamics analysis by Zahran et al. [185] revealed that cerebrosides such as A1 (182) and C1 (183) (from the Korean sponge Haliclona renier), LAMA-1 and penicilloside B (184) (from the Egyptian Penicillium chrysogenum), and asperiamide B (185) (from the Chinese-Sea-water-derived fungus Aspergillus niger) exhibit binding affinity to hACE2 (−7.1 to −7.6, kcal/mol).Moreover, Tassakka et al. [186] found that FAs/lipids were the prominent metabolites both in ethanolic and ethyl acetate extracts of Halymenia durvillei, which inhibited the activity of Mpro.

In Silico Studies of Other Secondary Metabolites (Phytochemicals) with Potential Antiviral
and Therapeutic Properties against SARS-CoV-2 5.2.1.Polyphenols SARS-CoV-1 and 2 infections generate reactive oxygen species (ROS) which are known to cause oxidative damage, inflammation, lung infection, and epithelial tissue degeneration.3CLpro/Mpro activates the NF-kB-dependent reporter gene which causes ROS generation in the HL-CZ cells, leading to a disruption of the oxidation-reduction processes of the cell [178].Marine organisms are a rich source of antioxidants and several other secondary metabolites classified as broad-spectrum compounds, which can be used as therapies to manage SARS-CoV-2 infection together with antivirals.Polyphenols such as phloroglucinol oligomers and phlorotannins are a type of tannin found in brown algae and have shown promising antiviral action [181].In silico analysis showed that the phlorotannin dieckol (86) can bind to the Spike RBD of SARS-CoV-2 high affinity (−8.1 kcal/mol) [181].Aatif et al. [187] also reported that dieckol (86) from Ecklonia cava exhibited similar binding affinity (−8.326 kcal/mol) towards the RBD of the spike protein.Eckol (186) and trifucol (188) are other phlorotannins obtained from the brown alga Ecklonia cava and Himanthalia elongate.Eckol (186) has a high binding affinity, in silico, to the Mpro (−8.19 kcal/mol), while trifucol (187) binds to both the S-glycoprotein (−7.5 kcal/mol) and the Mpro (−6.3 kcal/mol) [160].
Caulerpin (214) is another low toxic bis-indole alkaloid found in distinct species of marine algae, especially the Caulpera genus.It has been isolated from the green macroalgae (Caulerpa racemose), the red algae (Chondria armata), and the brown algae (Sargassum platycarpum).Caulerpin (214) and some of its derivatives are known to possess a lot of biological properties.Ahmed et al. [147] carried out a molecular docking analysis of caulerpin (214) and its analogs against the SARS-CoV-2 Mpro and spike protein.They showed that the derivatives had a higher binding affinity towards Mpro and s-protein than chemical drugs like lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir.
ACE2 produced by marine organisms can also serve as a receptor binding domain to the SARS-CoV-2 spike glycoprotein to suppress its transmission.For instance, ACE2 (234) of Delphinapterus leucas (Beluga whale) had a binding affinity of −988.5 kcal/mol towards the SARS-CoV-2 spike glycoprotein which is comparable to the hACE2 binding affinity (−946.4kcal/mol) to the spike glycoprotein.Thus, ACE2 and ACE2-like structures from the marine biota could be used as decoys for viral binding [197].Fayed et al. [198] screened several marine compounds for their pharmacophore potentials against SARS-CoV-2 Mpro (6lu7 and 6y2f), spike glycoprotein, and RNA Polymerase, and reported that compounds with a flavonoid core, acyl indole, and pyrrole carboxamide alkaloids performed better.The co-crystallized ligands of Mpro showed perfect overlay with the pyrroles sceptrin (235) and debromo sceptrin (237).Among all the target proteins, thalassiolin (A-C) (237-239) had the best binding and similarity values.Also, ACE2 and Mpro were shown to interact well with compounds isolated from marine sponges including microspinosamide (240) (−16.8 and 13.7 kcal/mol), neamphamide A (241) (−13.7 and 13.1 kcal/mol), mirabamide A (242) (−11.3 and 10.3 kcal/mol), and sterol clathsterol (243) (−10.5 and 10.1 kcal/mol) [199].However, the drug-likeness test of all compounds was below Lipinski's rule of 5, even though all the compounds had shown potential inhibition against the HIV-1 virus.
Structurally, the natural inorganic polyphosphate (polyP), considered a physiological, metabolic energy (ATP)-providing and morphogenetically active linear polymer of orthophosphate released from human blood platelets, is expressed in every cell including marine bacteria and sponges [200,201].Polyphosphate (polyP) helps in the mediation of blood clots due to interaction with the protease coagulation factor VII; however, its production is reduced in COVID-19 patients due to a deficiency in platelet count [201].Müller et al. [202] and Neufurth et al. [200] found that polyp (244) blocks the binding of the receptor binding domain (RBD), thus preventing the binding of the spike protein to host ACE-2 receptor at concentrations ranging from 1 to 100 µg/mL with 70% effectiveness at 10 µg/mL.Neufurth et al. [200] proposed that the 15 phosphate units of polyP (244) interacted with the basic residues, Arg, Lys, and His on the spike protein.Müller et al. [202] also reported polyp (244) increased ATP production, cell attachment, and expression of the membrane-tethered mucin MUC1 and the secreted mucin MUC5AC genes in the mucus layer, thus enhancing the barrier against inhaled pathogens such as the coronavirus SARS-CoV-2 [202,203].
Structural characteristics of some selected compounds from marine organisms with SARS-CoV-2 inhibitory properties are shown in Figure 4 and Figure S8.Additionally, Table S1 shows some selected marine compounds with potential inhibitory properties against SARS-CoV-2 in silico.

A Promising Future for Marine Bioactive Metabolites to Tackle SARS-CoV-2
Due to the vast and diverse organisms with naturally occurring metabolites found in bodies of water, researchers are increasingly turning to the oceans, rivers, and seas for new natural compounds with antiviral potentials to help create the basis for novel therapeutics.Compounds of various structural classes, including polysaccharides, terpenes, steroids, alkaloids, and peptides that inhibit both RNA and DNA viruses have been isolated from marine micro-and macro-organisms.There is much hope to discover novel resources from marine organisms, which would serve as potential drug leads that would, in addition to controlling viral replication, help manage the symptoms presented by viral diseases.Such compounds could either block the penetration of viruses into the host cells, inhibit viral fusion to host proteins, or inhibit the activity of major viral proteins such as those involved in replication.However, drug development is cost-intensive.Even with significant efforts being made in designing novel SARS-CoV-2 inhibitors from marine organisms, with some (such as plitidepsin ( 166)) already under clinical trials, most available studies appear exceptionally preliminary and based on computer-aided findings that employed molecular docking, molecular dynamics simulation techniques, and network pharmacology.The scarcity of comprehensive pre-clinical research involving various cell lines and animal models underscores the need for in-depth future investigations.Such studies should examine the compounds identified through in silico analysis for their potential drug-like properties, laying the groundwork for subsequent clinical trials.

Figure 1 .
Figure 1.Sources of bioactive metabolites from marine organisms.

Figure 1 .
Figure 1.Sources of bioactive metabolites from marine organisms.

Figure 3 .
Figure 3. SARS-CoV-2 entry and replication cycle with potential inhibition sites for marine metabolites.

Figure 4 .
Figure 4.Chemical structure of some selected compounds from marine organisms with SARS-CoV-2 inhibitory properties.Figure 4. Chemical structure of some selected compounds from marine organisms with SARS-CoV-2 inhibitory properties.

Figure 4 .
Figure 4.Chemical structure of some selected compounds from marine organisms with SARS-CoV-2 inhibitory properties.Figure 4. Chemical structure of some selected compounds from marine organisms with SARS-CoV-2 inhibitory properties.

Table 1 .
Antiviral properties of metabolites from marine bacteria.

Table 1 .
Antiviral properties of metabolites from marine bacteria.

Table 1 .
Antiviral properties of metabolites from marine bacteria.

Table 2 .
Antiviral activities of marine-derived bioactive compounds extracted from marine fungi.

Table 2 .
Antiviral activities of marine-derived bioactive compounds extracted from marine fungi.

Table 2 .
Antiviral activities of marine-derived bioactive compounds extracted from marine fungi.
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