Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19

Raihan, Topu; Rabbee, Muhammad Fazle; Roy, Puja; Choudhury, Swapnila; Baek, Kwang-Hyun; Azad, Abul Kalam

doi:10.3389/fmolb.2021.732256

REVIEW article

Front. Mol. Biosci., 07 September 2021

Sec. Metabolomics

Volume 8 - 2021 | https://doi.org/10.3389/fmolb.2021.732256

This article is part of the Research Topic Metabolomics in Infectious Diseases View all 8 articles

Microbial Metabolites: The Emerging Hotspot of Antiviral Compounds as Potential Candidates to Avert Viral Pandemic Alike COVID-19

Topu Raihan¹

Muhammad Fazle Rabbee²

¹Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
²Department of Biotechnology, Yeungnam University, Gyeongsan, South Korea
³Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh

The present global COVID-19 pandemic caused by the noble pleomorphic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a vulnerable situation in the global healthcare and economy. In this pandemic situation, researchers all around the world are trying their level best to find suitable therapeutics from various sources to combat against the SARS-CoV-2. To date, numerous bioactive compounds from different sources have been tested to control many viral diseases. However, microbial metabolites are advantageous for drug development over metabolites from other sources. We herein retrieved and reviewed literatures from PubMed, Scopus and Google relevant to antiviral microbial metabolites by searching with the keywords “antiviral microbial metabolites,” “microbial metabolite against virus,” “microorganism with antiviral activity,” “antiviral medicine from microbial metabolite,” “antiviral bacterial metabolites,” “antiviral fungal metabolites,” “antiviral metabolites from microscopic algae’ and so on. For the same purpose, the keywords “microbial metabolites against COVID-19 and SARS-CoV-2” and “plant metabolites against COVID-19 and SARS-CoV-2” were used. Only the full text literatures available in English and pertinent to the topic have been included and those which are not available as full text in English and pertinent to antiviral or anti-SARS-CoV-2 activity were excluded. In this review, we have accumulated microbial metabolites that can be used as antiviral agents against a broad range of viruses including SARS-CoV-2. Based on this concept, we have included 330 antiviral microbial metabolites so far available to date in the data bases and were previously isolated from fungi, bacteria and microalgae. The microbial source, chemical nature, targeted viruses, mechanism of actions and IC₅₀/EC₅₀ values of these metabolites are discussed although mechanisms of actions of many of them are not yet elucidated. Among these antiviral microbial metabolites, some compounds might be very potential against many other viruses including coronaviruses. However, these potential microbial metabolites need further research to be developed as effective antiviral drugs. This paper may provide the scientific community with the possible secret of microbial metabolites that could be an effective source of novel antiviral drugs to fight against many viruses including SARS-CoV-2 as well as the future viral pandemics.

Introduction

Viral infections are one of the major causes of morbidity and mortality in the world. It is very catastrophic due to the complexity, diversity, obligatory intracellular parasitic nature and pleomorphic character of viruses. These properties of viruses make it very difficult to counteract viral effects and transmission, which ultimately causes epidemics and/or pandemics (Graham et al., 2013; Meganck and Baric, 2021). Although the deadly influenza outbreak occurred in 1918, in the last 2 decades of the present century, there have been several viral epidemics or pandemics in humans (Figure 1). These viral epidemics or pandemics were caused with influenza A virus (H1N1), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), dengue virus (DENV), Zika virus (ZIKV), Ebola virus (EBOV), chikungunya virus (CHIKV), Henipavirus (HeV, NiV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Meganck and Baric, 2021). Moreover, human immunodeficiency virus (HIV) is life-threatening since its discovery in 1982. Some other viruses such as Crimean–Congo hemorrhagic fever virus, Herpes simplex virus, Hepatitis viruses, Rabies virus, Hantaviruses have caused outbreaks or have outbreak potential. Therefore, the increase of migration, global travel, and urbanization have made viruses outbreaks a crucial challenge for public health, especially when vaccines and antiviral therapies are still not available (Neiderud, 2015).

FIGURE 1

FIGURE 1. Viral outbreaks in the last 2 decades.

Viruses having a genome either RNA or DNA utilize the molecular apparatus of the host cells for their replication and cause several ailments (Tapparel et al., 2013; Cohen, 2016). Viral infections can be controlled by prophylactic strategy and/or drug therapy. However, for being obligatory intracellular parasite, most of the metabolic pathways involved in the viral replication are the same as in the host cells. From this point of view, it is difficult to design an appropriate treatment to attack the virus without triggering adverse events on the host. These aspects further highlight the main peculiarity of viruses (specificity, affinity, and self-defense mechanisms) and the difficulties of antiviral chemotherapy. Therefore, it is necessary to discover and identify new antiviral agents, which should possess primarily an adequate selectivity, power, in vivo stability profile and low toxicity (Akram et al., 2018).

Many natural and synthetic drugs having antiviral activity were considerably less effective when tested in virus-infected animal models (Martinez et al., 2015; Takizawa and Yamasaki, 2018; Mukherjee, 2019). Moreover, extraction of the natural products from the plants and the chemical synthesis of synthetic drugs have safety and economic concerns. Furthermore, conventional drugs become failed against viral infections and the onset of specific viral resistances against these drugs is a common phenomenon (Linnakoski et al., 2018; Mulwa and Stadler, 2018; Ma et al., 2020). Therefore, researchers need to search for alternative source of safe and economically cost-effective antiviral natural products. In this context, microbial metabolites might be a promising source of antiviral agents. Microorganisms are natural flora of the environment that play significant role in plenty of processes, and therefore, their metabolites have great potential to be used for antiviral treatment without severe side-effects (Cheung et al., 2014). In fact, microbial metabolites have already been a subject of intense research for the treatment of certain virus-mediated diseases (Berdy, 2005), and currently, there is an emerging trend in biotechnology for therapeutic applications of microbial metabolites as antiviral agents (Yasuhara-Bell et al., 2010a; Pham et al., 2019; Goris et al., 2021; Lobo-Galo et al., 2021). Several microbial metabolites have been demonstrated to offer promising antiviral activity against numerous DNA and RNA viruses (Tong et al., 2012; Linnakoski et al., 2018; Mulwa and Stadler, 2018). The whole world has been fighting against the current COVID-19 pandemic for more than one and a half years. As there is no newly developed specific approved drug, only repurposed drugs are used as the supportive treatment of the stormy COVID-19 caused by SARS-CoV-2 (Hakim et al., 2021), which has caused total death of 4,374,234 in the world as on August 15, 2021. Cases and death of COVID-19 is going on ceaselessly globally. As the trend of the history, more viral epidemics and/or pandemics may outbreak in the future. Therefore, it is essential to discover drugs with broad spectrum activity against SARS-CoV-2 including other catastrophic viruses. Screening and identification of natural compounds from microbial metabolites may be particularly important for drug discovery against the coronavirus alike SARS-CoV-2 as well as other viruses having potential outbreaks in the future.

This review focuses on microbial metabolites, which have shown activity against various viral pathogens. In addition, the current state of this research topic is briefly discussed, and gaps in the research are identified. Furthermore, the targets for antiviral therapeutic development and the advantages of microbial metabolites are briefly discussed. Finally, this review attempts to offer alternative conceptual framework for drug discovery for treatment of COVID-19 and alike future viral pandemics and/or epidemics.

Targets of Microbial Metabolites for Therapeutic Development

Despite of having different biology for infection, viruses share some basic steps for their replication (Figure 2A). The basic steps for viral replication include 1) viral attachment to host cells (host-viral interaction), 2) viral penetration into host cells, 3) viral uncoating into the cytoplasm, 4) viral genome replication and transcription, 5) viral protein translation and assembly, and 6) viral progeny release (Meganck and Baric, 2021). Due to having limited numbers of own coding genes, viruses must depend on the host machinery for accomplishment of viral lifecycle. The fundamental steps involved in viral lifecycle are associated with viral infection as well as pathogenesis and represent important targets for therapeutic development. The infection or the pathogenesis starts with the viral entry into the host cells (Ryu, 2017; Thaker et al., 2019). The prerequisite for viral entry is its binding on the cell surface. Viral proteins on the capsid or envelope interact with the specific receptor, which can be proteins, glycans and/or lipids in the host cell. For instance, the spike protein S of SARS-CoV-1 and SARS-CoV-2 interact with the angiotensin-converting enzyme 2 (ACE2) as the receptor expressed on the surface of the target cells (Lim et al., 2016; Fung and Liu, 2019; Chen et al., 2020; Hoffmann et al., 2020; Ou et al., 2020; Rahman et al., 2020; Walls et al., 2020; Yan et al., 2020). The interaction between the viral protein and host receptor facilitate the viral uptake often through endocytic pathways or through fusion at the plasma membrane (Millet and Whittaker, 2018; Milewska et al., 2020). Viruses escape the endosome by uncoating and the genomic material is released into the cytoplasm.

FIGURE 2

FIGURE 2. Viral lifecycle (A) and the proposed mode of actions of some of the antiviral microbial secondary metabolites (MSM) (B) listed in this review. The numbers in (A) denote the steps usually targeted by MSM. In (B), some of the antiviral MSM inhibiting targeted stages of viral lifecycle are listed. Cyan, red and green colors indicate the metabolites isolated from fungi, bacteria and microalgae, respectively. (C) Antiviral drug development strategy based on the viral and host factors.

Replication of DNA viruses is performed by using DNA dependent DNA polymerase. DNA viruses can integrate their genomes into the host genome and cause recurrent problem. RNA viruses replicate their genomes either by RNA-dependent RNA synthesis, or by RNA-dependent DNA synthesis (reverse transcription) which is followed by DNA replication and transcription. The genetic material of single-stranded positive sense RNA (ssRNA+) viruses is like mRNA which is directly translated by the host cell. The negative sense RNA (ssRNA−) viruses carry RNA that is complementary to mRNA and must be turned into ssRNA+ using RNA polymerase before translation. All positive sense RNA viruses like poliovirus, hepatitis C virus, dengue virus, ZIKV, SARS-coronavirus can arrange specialized membranous structures by remodeling host membranes where the viral genome is replicated (Cameron et al., 2009; Paul and Bartenschlager, 2013). Due to lack of RNA polymerase proofreading ability, RNA viruses have very high rate of mutation compared to DNA viruses, which eventually renders enhanced virulence and evolvability (Duffy, 2018).

Although all viruses utilize the host apparatus system for translation, viral translation is regulated differently from the host cell (Jan et al., 2016). Viral proteins and genomic materials are assembled to form the virion. The final stage of viral replication is the release of the new virions produced in the host organism. The new virions are then able to infect nearby cells and repeat the replication cycle. Some viruses are released when the host cell dies, while other viruses without directly killing the cell can leave infected cells by budding through the membrane (Lodish et al., 2000; Risco et al., 2014). The essential molecular elements involved in each of these steps in the viral lifecycle can be targeted by microbial metabolites as therapeutics.

The microbial metabolites may target either the viral or the host factors that are associated with viral pathogenesis or the completion of the viral lifecycle or viral replication (Figure 2B). The viral factors might be viral proteins associated with the binding of viruses to cells, viral protease, viral translation or others (Anderson et al., 1996; Klemm et al., 2020; Chen C. C. et al., 2021). Host-factors might be receptor on the cell surface, endocytosis, host proteases and kinases, and others (Inoue et al., 2007; Ivanov, 2008; Raj et al., 2013; Zhou et al., 2015; Kalil et al., 2021). However, the viral and the host factors associated with the viral pathogenesis and its lifecycle or replication may vary based on the viruses even of the same family. For instance, while the spike protein S of SARS-CoV-1 and SARS-CoV-2 bind with the ACE2 receptor, the S protein of MERS-CoV binds to dipeptidyl peptidase 4 (DPP4) receptor (Raj et al., 2013; Lim et al., 2016; Hoffmann et al., 2020; Rahman et al., 2020; Walls et al., 2020; Yan et al., 2020). Here, viral S protein may serve as the drug target for all these three SARS viruses, however, ACE2 might be the target for the earlier two SARS viruses and the DPP4 might be for the MERS-CoV. Similarly, a serine protease named TMPRSS2 found to be essential for the activation of hemagglutinin (HA), the key step for initiating the viral infection by the H7N9 variant of H1N1, may be an important therapeutic target. The HA activation was failed in H7N9 virus when the TMRSS2 was knocked out in the mice (Tarnow et al., 2014).

Despite the viral life cycle, a number of factors regulate the host response towards certain viral infections (Fung and Liu, 2019; Azad et al., 2021; Hakim et al., 2021). The inaugural stages of diseases include the viral phase with the appearance of symptoms. However, with the progresses of the disease, the viral phase is replaced by the host inflammatory phase, which controls viral replication usually by damaging the host cells (Peiris et al., 2003). Antiviral therapeutics are active during the viral phase or viral life cycle after which these drugs become ineffective (Widagdo et al., 2017). Treatment options for controlling inflammatory damage during inflammatory phase usually include steroids as immunomodulatory and anti-inflammatory drugs (Yang J.-W. et al., 2020). In the ongoing pandemic, the hospitalized patients with COVID-19 are being treated with the corticosteroid dexamethasone (Group, 2021). Again baricitinib, a kinase inhibitor in the JAK/STAT signaling pathway, has been approved for COVID-19 treatment, which lowers cytokine release that is a hallmark in SARS-CoV-2 infection (Stebbing et al., 2020; Hakim et al., 2021; Kalil et al., 2021). Nevertheless, the interferon (IFN) alpha and beta activates the JAK/STAT signaling pathway that in turn triggers the synthesis of a number of antiviral gene products (Chiang and Liu, 2019). Therefore, any essential event involved in the viral phase and/or the host inflammatory phase might be an important target for treatment of the respective viral disease with microbial metabolites.

Microbial Metabolites as Potential Antiviral Candidates

Microbial metabolites are being used as important therapeutics for treatment of infections in health and agriculture arena (Demain, 2007; Raihan et al., 2021). For being advantageous over chemically synthesized and non-microbial natural products, research and development programs are continuously adopting approaches based on microbial products for the development of novel drugs. Microbial secondary metabolites (MSMs) have been being used as easy and reliable sources for the synthesis of new pharmaceuticals and therapeutics against different types of pathogens including viruses, bacteria, fungi and parasites (Demain, 2007; Selim et al., 2018). Many microorganisms such as bacteria, fungi, actinomycetes and microalgae from numerous sources have a variety of secondary metabolites like quinones, terpenoids, lignans, alkaloids, peptides, polysaccharides, lactones, polyketide, xanthone, ester, and so on having diverse antiviral activities (Selim et al., 2018; Pan et al., 2019). Several classes of such MSMs have been used as antiviral agents. From the literatures reported previously, only the antiviral metabolites from fungi, bacteria and microalgae have been listed in the present review (Tables 1–3). Fungi from different sources are the major reservoir of antiviral metabolites followed by bacteria and microalgae. Most of the MSMs were isolated from microorganisms of the marine source (Figure 3). The MSMs clusters to different groups (Figure 4) having different mechanism of actions against viruses. Although the mechanism of actions of most of the antiviral microbial metabolites are not yet elucidated, that of a few microbial metabolites has been reported (Tables 1–3). Elucidation of mode of actions and pharmacological properties of novel antiviral microbial bioactive metabolites may lead to the development of drugs for treating human diseases developed by catastrophic viral agents.

TABLE 1

TABLE 1. Antiviral bioactive compounds isolated from fungi.

TABLE 2

TABLE 2. Antiviral bioactive compounds isolated from bacteria and cyanobacteria.

TABLE 3

TABLE 3. Antiviral bioactive compounds obtained from microalgae.

FIGURE 3

FIGURE 3. Microbial source of antiviral compounds (A) and the source of microorganisms producing antiviral compounds (B).

FIGURE 4

FIGURE 4. Representative antiviral compounds from polyketone (A), alkaloid (B), peptide (C), polyphenol (D), pyrone (E), quinone (F), sterol (G), and terpenoid (H) groups.

Polysaccharides

Microbial polysaccharides (MPS), the biopolymers produced through microbial metabolic process, are widely found in bacteria, fungi and algae (Tables 1–3). The antiviral metabolites so far reported from algae are MPS (Table 3). However, bacteria and fungi produced a variety of MSM including MPS (Tables 1, 2). The advantages of MPS over plant polysaccharides include lack of seasonal, geographical, pest and diseases restriction; wide variety of sources as well as short production time (Chen and Huang, 2018). Some MPS are linear (cellulose, chitin, chitosan, pullulan, alginate, curdlan) and some are branched (dextran, levan, xanthan, scleroglucan, and in lesser degree gellan). Neutral (dextran, levan, pullulan, cellulose, scleroglucan and curdlan), anionic (alginate, xanthan, gellan), and cationic (chitin and chitosan) properties of these linear and branched MPS may make them suitable against a variety of viruses (Steed et al., 2017). Due to having diversified structural properties, the antiviral mechanisms of MPS are complex and diverse, and thus suitable for a variety of applications (Steed et al., 2017; Liu et al., 2020). The antiviral mechanisms of MPS include the inhibition of events involved in viral life cycle (attachment of virus to the host cell, penetration, genetic material and protein synthesis) and the improvement of the host immunity (Liu et al., 2020). However, the antiviral mechanism of many MPS is not yet known.

Recently, studies on derivatives of MPS are given priorities because chemical modification generates enhanced or new activities to MPS (Chen and Huang, 2018). The most common derivatives are sulfonated, phosphorylated and selenizated. The derivatives of MPS having lower or no toxicity even at higher concentrations offer broad prospects for treatment of viral diseases (Saha et al., 2012; Chen and Huang, 2018; Liu et al., 2020). The bioactive sulfated polysaccharide, p-KG03, obtained from Gyrodinium impudicum showed antiviral activity (EC₅₀ = 26.9 µg/ml) against encephalomyocarditis virus (Yim et al., 2004) and inhibited H1N1 with an EC₅₀ value of 0.19–0.48 μg/ml through interfering the viral entry into the host cell (Kim et al., 2012). Another sulfated polysaccharide isolated from red microalgae Porphyridium sp. showed impressive antiviral activity against Herpes simplex viruses types 1 and 2 (HSV 1, 2) and Varicella zoster virus (VZV) with IC₅₀ 1 μg/ml (Huleihel et al., 2001). However, the same polysaccharide isolated from Haematococcus pluvialis showed similar inhibition rate against HSV-1 with IC₅₀ 75 µg/ml concentration (Santoyo et al., 2012). Furthermore, a number of MPS obtained from various microalgae and bacteria showed promising antiviral activity with unknown mechanism of action against numerous viruses such as HIV1, HSV-1, HSV-2, Vaccina virus, Murine sarcoma and leukemia viruses, Influenza A and B viruses, RSV-A, RSV-B, parainfluenza-2, VHSV, ASFV, hCMV, VACV mentioned in Tables 2, 3.

Peptides

Antiviral peptides (AVPs) obtained from natural sources are amphipathic and cationic nature. In addition, their hydrophobicity make them the promising drug candidate against enveloped viruses (Agarwal and Gabrani, 2020). The AVPs are reported from bacteria and fungi, however, not yet from algae (Tables 1, 2). Advantages of naturally produced microbial AVPs include high specificity and effectiveness, low toxicity and peptidase biodegradability, and low molecular weight (Boas et al., 2019). The AVPs can act at various stages of the viral life cycle through the suppression of viral gene expression. They can further prevent viral infection by many ways including inhibiting the viral particle or by competing for the receptor molecule in the host cell membrane and consequent adsorption, suppression of topoisomerase-mediated DNA-binding, DNA relaxation and formation of covalent complex (Galdiero et al., 2013; Heydari et al., 2021). Some of them can show activity by membrane destabilization of the virus (Rowley et al., 2004; Porotto et al., 2010). However, the mode of actions of most of the bacterial and fungal AVPs remains elusive (Tables 1, 2).

Sansalvamide A, a cyclic depsipeptide, isolated from marine Fusarium spp. showed antiviral activity against a poxvirus, molluscum contagiosum virus (MCV) by inhibiting the virus-encoded type-1 topoisomerase which is essential for MCV replication (Hwang et al., 1999). Simplicilliumtide J, a cyclic peptide, isolated from a deep sea derived fungal strain Simplicillium obclavatum EIODSF 020 and its analogues Verlamelin A and B showed very promising anti-HSV-1 activity with IC₅₀ values of 15.6 μM (Liang et al., 2017). The cyclodipeptide diketopiperazines (DKPs) obtained from endophytic fungus Aspergillus versicolor exhibited anti-HSV activity through inhibition of NS3/4A protease with the IC₅₀ value 8.2 μg/ml (Ahmed et al., 2017).

Alkaloids

Alkaloids are structurally diverse secondary metabolites which have many therapeutic applications including antiviral activity (Cushnie et al., 2014). Most of the alkaloids used as therapeutics to treat human diseases are natural products of plants although plants are unreliable, low-yielding, expensive and unstable source (Bradley et al., 2020). However, several recent studies showed that a number of fungi produce alkaloids as an MSM acting against pathogenic microbes including viruses (Table 1) (Peng et al., 2019; Sadahiro et al., 2020; Raihan et al., 2021). Nevertheless, despite the potentiality, bacterial and algal sources for alkaloids are not yet reported. Although the mechanisms of all microbial alkaloids are not yet known (Table 1), a number of studies report that alkaloids inhibit DNA polymerase, Topoisomerase, reverse transcriptase and protein synthesis (Thawabteh et al., 2019; Bleasel and Peterson, 2020; Wink, 2020), and deactivate the viral infection by acting as DNA intercalator (Croaker et al., 2016). Six indole alkaloids isolated from mangrove derived fungus Cladosporium sp. PJX-41 showed antiviral activity against H1N1 with IC₅₀ values 82–89 μM (Peng et al., 2013). Stachyflin, a sesquiterpenoidal alkaloid, obtained from Stachybotrys sp. RF-7260 by solid state fermentation showed a promising antiviral activity in vitro against H1N1 with IC₅₀ value 0.003 μM (Minagawa et al., 2002). Three new isoindolinone-type alkaloids named chartarutines B, G, and H isolated from sponge derived fungus Stachybotrys chartarum has been shown as antiviral agents to inhibit replication of HIV-1 with the IC₅₀ value 4.9–5.6 mM (Li et al., 2014). Recently, it has been shown that two aminosulfonyl group containing alkaloids named Scedapin C and scequinadoline A extracted from marine-derived fungus Scedosporium apiospermum, displayed significant anti-HCV activity by inhibiting HCV protease with the EC₅₀ values 110.35 and 128.60 μM, respectively (Huang L.-H. et al., 2017). Huang Z. et al. (2017) further showed that a deep-sea-derived fungus Aspergillus versicolor SCSIO 41502 produced Aspergilols H and I which displayed anti-HCV activity with EC₅₀ values 4.68 and 6.25 μM, respectively (Huang Z. et al., 2017).

Polyketones

Many polyketides (derived from polyketones) isolated from microorganisms such as fungi and bacteria have been shown to inhibit the viral infection in a various way (Tables 1, 2). However, mechanisms of actions of most of the polyketones mentioned in this paper have to be elucidated. A group of polyketides are capable to inhibit viral replication. Two of such polyketides named as Alternariol and Balticolid isolated from Pleospora tarda and Ascomycetous strain exhibited potent antiviral activity with IC₅₀ value 13.5 μM and 0.01 mg/ml, respectively (Shushni et al., 2011; Selim et al., 2018). While these polyketones inhibit viral replication, Sclerotiorin, another polyketone isolated from an endophyte Penicillium sclerotiorum essentially interferes with HIV-1 integrase and protease—two essential enzymes for maintaining the life cycle of the virus inside the host cell (Arunpanichlert et al., 2010). Furthermore, a group of polyketides namely sulfangolid C, soraphen F, spirangien B and epothilon D isolated from Sorangium cellulosum protects against HIV by interacting with the Acetyl-CoA carboxylate transferase enzyme (Martinez et al., 2013). Martinez et al. (2013) further found that Rhizopodin, derived from M. stipitatus is a potential antiviral agent although the mechanism of inhibition of the compound has not been elucidated. Another study found that marine microbe Phoma sp. produced Phomasetin which inhibited the HIV integrase, rendering it a potential drug compound against HIV (Singh et al., 1999). In fact, most of the microbial polyketides have been isolated till date is from the marine microorganisms. However, several fungi obtained from other sources are also reported to produce antiviral compounds having promising activity against DENV, ZIKV, Influenza virus, HCV and others (Table 1).

Terpenoids

Terpenoids are one of the most abundant natural aromatic compounds mostly found in plants. However, some microorganisms can synthesize terpenoids (Yamada et al., 2015). Furthermore, microbial strains can be engineered to produce such terpenoids that have antiviral activities (Ma et al., 2020). The properties and medicinal uses of terpenoids are being continuously investigated by researchers for anticancer, antioxidant, antiviral, and anti-atherosclerotic activities (Nazaruk and Borzym-Kluczyk, 2015). Based on the number of carbon atoms, terpenoids are of different types (Wang et al., 2018). Different modes of actions of different terpinoids make them important against viral infection. For instance, ochraceopone A, isoasteltoxin, and asteltoxin obtained from antarctic fungus Aspergillus ochraceopetaliformis exhibited antiviral activities against the H1N1 and H3N2 influenza viruses by inhibiting viral growth through their protease suppression with IC₅₀ values of >20.0/12.2 ± 4.10, 0.23 ± 0.05/0.66 ± 0.09, and 0.54 ± 0.06/0.84 ± 0.02 μM, respectively (Wang et al., 2016). Three sesquiterpenes named as (Z)-5-(Hydroxymethyl)-2-(6′)-methylhept-2′-en-2′-yl)-phenol, diorcinol, cordyol C were extracted from sponge-associated fungus Aspergillus sydowii which showed anti H3N2 activity with IC₅₀ values of 57.4, 66.5 and 78.5 μM, respectively (Wang et al., 2014). In addition, a terpenoid compound called xiamycin derived from a bacterial endophyte (Streptomyces sp.) acts as anti-HIV agent through prohibition of beta-chemokine receptor CCR5 with IC₅₀ value of > 30 μM (Ding et al., 2010). This class of metabolites can be produced in engineered fungi such Saccharomyces cerevisiae and Yarrowia. Lipolytica (Ma et al., 2020). Oleanolic acid is such a terpenoid produced from genetically modified S. cerevisiae, which inhibited genome replication and transcription of HCV (Zhao et al., 2018a). Another metabolite named betulinic acid produced from both S. cerevisiae and Y. lipolytica showed promising anti-HIV activity by inhibiting viral release from the host cell (Huang H. et al., 2019; Sun et al., 2019). Furthermore, a lot of terpinoids derived from fungi exhibited antiviral activity against numerous viruses such as H3N2, hEV71, H1N1, HBV, HIV, PRV, and DENV (Table 1).

Quinone

Quinones are aromatic organic compounds and found ubiquitously in prokaryotes and eukaryotes. Quinones act through inhibition of electron transport as well as uncoupling of oxidative phosphorylation (Obach and Kalgutkar, 2018). Furthermore, they can act as inducers of reactive oxygen species and bioreductive alkylators of biomolecules, and suppress DNA function by interpolation into DNA (Roa-Linares et al., 2019). Quinones are used as antioxidant, antimicrobial, anticancer, anti-inflammatory, antitumor agents (El-Najjar et al., 2011; Teng et al., 2020). The coccoquinone A, an anthraquinone derivative, obtained from Aspergillus versicolor function as an anti-HSV agent with the EC₅₀ value 6.25 µM (Huang Z. et al., 2017). Furthermore, 4-hydroxymethyl-quinoline isolated from myxobacteria Labilithrix luteola exhibited antiviral activity against HCV (Mulwa et al., 2018). Moreover, Alatinone, Emodin, and Hydroxyemodin, isolated from red alga Liagora viscida derived endophytic fungi Penicillium chrysogenum showed antiviral activity against HCV through inhibition HCV protease (Hawas et al., 2013). A citrinin dimer, seco-penicitrinol A obtained by coculturing of two marine algal-derived endophytic fungal strains Aspergillus sydowii and Penicillium citrinum showed inhibitory activity towards influenza neuraminidase in vitro with an IC₅₀ value 24.7 µM (Yang et al., 2018). An anthraquinone derivatives called (‒)-2′R-1-hydroxyisorhodoptilometrin obtained from marine fungi Penicillium sp. OUCMDZ acted as an antiviral agent against HBV (Jin et al., 2018). Furthermore, some other promising antiviral quinone type compounds have been listed in Table 1.

Sterols

Sterols, also known as steroid alcohols, found ubiquitously in numerous plant, animals as well as microorganisms are considered as common natural bioactive compounds (Hisham Shady et al., 2021). These natural compounds inhibit viral infection through suppression of lipid dependent viral attachment to the host (Hisham Shady et al., 2021). A highly oxygenated sterol compound called Cladosporisteroid B isolated from a sponge-derived fungus Cladosporium sp. acted as an antiviral agent against H3N2 with an IC₅₀ value 16.2 µM (Pang et al., 2018). Another new compound named 3α-hydroxy-7-ene-6,20-dione containing a rare 3α-OH configuration and synthesized by the fungus Cladosporium sp. showed antiviral activity against the respiratory syncytial virus (RSV) with the IC₅₀ value of 0.12 µM (Yu et al., 2018). Furthermore, an ergostane analogous metabolite named 3β-hydroxyergosta-8, 14, 24 (28)-trien-7-one isolated from the marine Penicillium sp. displayed broad-spectrum antiviral activities against HIV and H1N1 with the IC₅₀ value of 3.5 and 0.5 µM, respectively (Li et al., 2019c).

Pyrone

Pyrones, found as two isomers namely 2-pyrone and 4-pyrone, are comprised of an unsaturated six-membered ring with one oxygen atom and a ketone functional group (Teng et al., 2020). An endophytic Fusarium equiseti isolated from a marine brown alga Padina pavonica, secretes various extracellular metabolites in different media compositions (Hawas et al., 2016). When this endophytic fungus was cultivated in biomalt-peptone medium, it produced 12 known metabolites of diketopeprazines and anthraquinones which were very potent anti-HCV (HCV protease inhibitor) agent with an IC₅₀ from 19 to 77 μM, and the most potent anti-HCV compound in this condition was Griseoxanthone C with IC₅₀ value of 19.8 μM (Hawas et al., 2016). However, the same fungus released nine different types of anti-HCV agents with IC₅₀ value of 10–37 μM in the presence of Czapek’smedia, and the most potent anti-HCV compound was ω-hydroxyemodin with IC₅₀ value of 10.7 μM (Hawas et al., 2016). “One strain many compounds” (OSMAC) has been proposed as a very effective approach to discover novel bioactive compounds (Pan et al., 2019). With the OSMAC approach, a coastal saline soil-derived fungus Aspergillus iizukae produces different antiviral compounds namely Methyl-(2-chloro-l,6-dihydroxy-3-methylxanthone)-8-carboxylate; methyl-(4-chloro-l,6-dihydroxy-3-methylxanthone)-8-carboxylate; methyl-(4-chloro-6-hydroxy-1-methoxy-3-methylxanthone)-8-carboxylate; methyl-(6-hydroxy-1-methoxy-3-methylxanthone)-8-carboxylate; 4-chloro-1,6-dihydroxy-3-methylxanthone-8-carboxylic acid; and 2,4-dichloro-1,6-dihydroxy-3-methylxanthone-8-carboxylic acid (Kang et al., 2018). Among these compounds, methyl-(4-chloro-l,6-dihydroxy-3-methylxanthone)-8-carboxylate exhibits strong antiviral activities against H1N1, HSV-1, and HSV-2 with IC₅₀ values 44.6, 21.4, and 76.7 µM, respectively. However, the other compounds show week antiviral activity (Kang et al., 2018). A marine bacteria Streptomyces youssoufiensis can produce antiviral violapyrones (VLPs) Q–T through heterologous expression of the type III polyketide synthase (PKS) gene VioA (Hou et al., 2018). The antimicrobial activity of violapyrones mainly depends on the modification of 4-OH (methylation/non-methylation) (Teng et al., 2020). The compound showed antiviral activity in methylated condition but it showed anti-MRSA (Methicillin-resistant Staphylococcus aureus) activity in non-methylated condition with losing antiviral activity. The results support the notion that methylation at 4-OH of these compounds enhanced anti-virus activity but reduced anti-MRSA activity (Hou et al., 2018).

Polyphenol

Polyphenols or phenolic compounds are one of the prominent bioactive compounds found as secondary metabolites in plants and microorganisms (Othman et al., 2019; Carpine and Sieber, 2021). For instance, a soil fungus Exophiala pisciphila produces a novel dimeric 2,4-dihydroxy alkyl benzoic acid which exhibits anti-HIV activity by inhibiting integrase, a most crucial enzyme for HIV pathogenesis and is one of the most promising drug targets for anti-retroviral therapy (Ondeyka et al., 2003). Some antiviral polyphenol compounds have been produced through genetically engineered Saccharomyces cerevisiae, E. coli, Penicillium brevicompactum, Streptomyces avermitilis, Streptomyces lavendulae, and Yarrowia lipolytica (Ma et al., 2020). These prominent bioactive compounds exhibit antiviral activities through numerous mechanisms such as inhibition of viral attachment, penetration, genome replication and transcription as well as translation and viral assembly (Tables 1, 2) (Ma et al., 2020).

Lectin, Lipid, Lignan

A unique 95 amino acid long antiviral lectin obtained from a cyanobacterium Scytonema varium inhibits HIV attachment to the host cell through binding with the viral coat proteins gp120, gp160, and gp41 with EC₅₀ values ranging from 0.3 to 22 nM (Bokesch et al., 2003). In addition, two prominent antiviral compounds namely cyanovirin-N and agglutinin obtained from cyanobacterium Nostoc ellipsosporum and Oscillatoria agardhii, respectively act as anti-HIV agents. The former compound inhibits viral attachment by binding with gp120 and the later one inhibits viral replication (Boyd et al., 1997; Sato et al., 2007). Furthermore, a glycolipid derived from cyanobacterium showed remarkable antiviral activity against HIV-1 (Gustafson et al., 1989). Phenylpropanoid units containing compound such as podophyllotoxin of endophytic Fusarium oxysporum isolated from Juniperus recurva showed anti-HIV activity (Kour et al., 2008). Furthermore, lots of bioactive compounds show antiviral activity against various viruses such as Human cytomegalovirus; HIV, H1N1, HSV, DENV, Enterovirus 71, ZIKV, RSV, HBV, HCV, Western equine encephalitis virus, and Pseudorabies virus (Tables 1, 2).

Potential Microbial Metabolites Against SARS-CoV-2

No newly developed specific drug has been approved by the WHO, FDA or any other global regulatory body to treat SARS-CoV-2. However, some drugs for other diseases have been approved for emergency usage during the pandemic situation (Hakim et al., 2021). For instance, the microbial-derived anti-parasitic drug ivermectin (Patridge et al., 2016) has been approved by the FDA to treat COVID-19 patients. Nevertheless, the time was not also enough to discover specific drug against SARS-CoV-2. However, research is going on globally to find drug against SARS-CoV-2 either from microbial or plant sources. A semisynthetic pentacyclic sixteen-membered lactone obtained from the soil bacterium Streptomyces avermitilis, has been found in vitro as inhibitor of SARS-CoV-2 replication (Caly et al., 2020). To find anti-SARS-CoV-2 drug from either microbial or plant sources, mostly in silico studies have been done. In silico screening, molecular docking, ADMET (Absorption, Distribution, Metabolism, Elimination, and Toxicity) prediction and molecular dynamic simulation (MDS) carried out by a number of studies predicted several phytocompounds as the potential inhibitors of SARS-CoV-2 and could be candidates to the discovery of novel drugs for the treatment of COVID-19 (Basu et al., 2020; Bhuiyan et al., 2020; Choudhary et al., 2020; Prasanth et al., 2020; Puttaswamy et al., 2020; Zhang et al., 2020; Chandra et al., 2021; Prasanth et al., 2021; Sankar et al., 2021). A study screened six potential candidates (Citriquinochroman, Holyrine B, Proximicin C, Pityriacitrin B, (+)-Anthrobenzoxoconone, and Penimethavone A) as anti-SARS-CoV-2 from >24,000 natural microbial compounds (Sayed et al., 2020). Docking andMDS analysis suggests that these microbial metabolites are potential inhibitor of protease involved in the host-SARS-CoV-2 interaction. However, experimental validation is required for the hypothesis derived from the in silico studies of plant and microbial metabolites.

Since the outbreaks of SARS in 2002/2003, MERS in 2012 and the COVID-19 pandemic in 2019/2020 (all caused by β-coronaviruses), different antiviral natural compounds have been tested against coronaviruses, such as remdesivir, ribavirin or herbacetin (Cherian et al., 2020). A numbers of microbial metabolites have been discussed in the aforementioned section to show antiviral activity including viral respiratory infections. Most of the microbial metabolites listed in Tables 1–3 are experimentally reported. Some of these metabolites especially those that show activity against viral respiratory infection can be potential for repurposing drugs against SARS-CoV-2. However, it would be worth for the researchers to elucidate the mechanism of actions of all antiviral microbial metabolites. Therefore, it will be interesting to perform docking and MDS of these microbial metabolites against proteins of SARS-CoV-2 and/or humans to predict their mechanism of actions, and finally experimentally validate the prediction of the in silico study. Metabolites from probiotic bacteria and/or gut microflora have been suggested to prevent viral respiratory infections including COVID-19 (Chen J. et al., 2021; Gautier et al., 2021). Probiotic bacterial metabolites such as butyrate, desaminotyrosine, and secondary bile acid may be transported to the lung via the circulation and could prevent viral respiratory infections by inhibiting viral replication or improving the immune response against viruses (Tiwari et al., 2020; Gautier et al., 2021). However, extensive studies are required to conclude the benefits of metabolites from probiotic bacteria and/or gut micro flora in COVID-19.

Advantages of the Microbial Source for Antiviral Metabolites

Currently, researchers are focusing on natural bioactive compounds to control viral infections that are considered as the main cause for human death worldwide (Akram et al., 2018). They are designing natural broad-spectrum antiviral agents by targeting a common pathway but essential for functions in many viruses (Vigant et al., 2015). The sources of natural bioactive compounds are plants, animals and microorganisms. However, as the leading producers of essential natural bioactive compounds, microorganisms are preferred more. Microorganisms are advantageous over other natural sources such as plants and animals due to their certain unique characteristics. Most of microorganisms are available as a wide range of genetically specified strains, fast growth, high density, high production rate, efficient secretion, easy handling and propagate, and can be easily manipulated (Singh et al., 2017). Microorganisms in general act as the source of essential natural product having the advantage of viable and sustainable production of secondary metabolites by large scale fermentation with reasonable cost (Waites et al., 2009; Sun X. et al., 2015). Furthermore, microorganisms can be grown at large amount in a small space such as in a fermenter under a wide range of environmental conditions for production of MSM of versatile groups. However, plants and animals need large space and longer period for cultivation, and are not amicable to versatile environmental conditions and/or metabolic engineering is technically challenging to plants and animals (Tatsis and O’Connor, 2016).

Metabolic and genetic engineering can easily be applied to microorganisms. Genomic information of a microbe makes it easy to apply metabolic engineering to scale up the production and/or modify the natural bioactive compound (Ma et al., 2020). Modified natural bioactive compounds may be suitable to get rid of drug resistance of viruses with their high genetic variability, and microbes are the most preferable candidates in this case (Lin et al., 2014). Furthermore, metabolic engineering to contrive the microbial cellular metabolic machinery and the fermentation technology to scale up the production has introduced a low-cost microbial system for large scale production of many natural bioactive compounds including antiviral agents (Liu and Nielsen, 2019; Pham et al., 2019; Ma et al., 2020). For instance, Violacein is a bis-indole pigment produced by several Gram-negative bacterial species by the vioABCDE operon (Choi et al., 2015). Due to antimicrobial (antibacterial, antiviral and antifungal) properties, this compound has become an interesting target for metabolic engineering strategy. Recently, the Y. lipolytica chassis strain was engineered for increased production of this compound. Introduction of five genes of bacterial vioABCDE operon and overexpression of endogenous anthranilate synthase 2 and 3 of Y. lipolytica increased violacein production 2.9 fold in comparison with the control (Zheng et al., 2020). Thus, heterologous synthesis of many antiviral compounds in genetically engineered microbes which are safer and economically beneficial offers some significant advantages over plant extraction and chemical synthesis (Ma et al., 2020). However, expression of the biosynthetic pathways for production of particular compounds in microbial factories may not be cost-effective sometimes due to mainly complexity of the pathways involving a number of enzymatic steps (Pandey et al., 2016; Yang D. et al., 2020). Introduction of a number of foreign proteins in a single microbial cell may lead to unwanted interaction between genetic factors and overload of the cell capacity, resulting in decreased microbial growth and low yields of the metabolite (Johnston et al., 2020). In this case, coculturing might be a highly promising approach to overcome these complexities with high yield. Furthermore, recombinant DNA technology used for large scale industrial production of bioactive compounds is feasible in microbial systems. The advancement of recombinant DNA technology has opened new windows for development of bioactive natural products and biologics (Pham et al., 2019; Ma et al., 2020). However, the choice of microbial host cells is very crucial for production of natural and recombinant products. Different tools and strategies for engineering host cells as microbial cell factories for production of natural bioactive compounds and recombinant products have been discussed elsewhere (Pham et al., 2019; Ma et al., 2020).

Future Prospects and Conclusion

The microbial source and system for antiviral natural bioactive compounds is attracting the researchers due to its advantages over plant and animal sources. Consequently, the demand of antiviral microbial metabolites is gradually increasing because the plant extraction and chemical synthesis cannot meet the global demand due to environmental, longer time and economic concerns. Microbial fermentation technology and metabolic and genetic engineering in microbial cells provide an alternate for scalable synthesis of these compounds. The global market value for MSM including antiviral agents was 277 billion USD in 2015, which is predicted to be 400 USD by 2025 (Park et al., 2019). Again, about 77% of FDA approved antimicrobial agents are produced from microbial sources, indicating microbial bioactive compounds as the pivotal source of antimicrobial drugs (Patridge et al., 2016). Therefore, antiviral microbial metabolites may pose great possibility in the field of pharmaceutical research and commercialization in near future. However, the vast diversity of antiviral microbial natural products yet requires extensive research and evaluation to find out the specific bioactive compounds with desired medicinal properties. Hence, from selection of appropriate microorganisms to formulation of drugs from their metabolites is a long term, expensive process that deserves relentless efforts and continuous exploration (Park et al., 2019).

Despite of some drawbacks such as final product purification and structural identification, microbial metabolite is still the unparalleled source of plenty of novel antiviral drug compounds (Park et al., 2019; Ma et al., 2020; Yi et al., 2020). Advancement of OMIC sciences (genomics, proteomics, metabolomics and so on) and gene based molecular approaches such genome editing, protein engineering and mutagenesis may offer more convenient drug design. Metabolomics being an emerging area in OMICs play pivotal roles in screening of lead compound, identifying drug target and assess bioactivity, potentiality and toxicity of the metabolites. Therefore, metabolomics in addition to proteomics that allows the structural and functional evaluation of the protein or antigenic compound targeted for the drug might be a great demand now-a-days in the term of drug designing and pharmacological research (Jain, 2004; Wishart, 2016). Furthermore, the most recent genome editing tool known as CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) can also be implemented in order to make desired change in the genome, especially while designing recombinant proteins in microbial cells to explore novel antiviral drugs (Liu et al., 2016). Similar site-specific gene editing by Zinc-finger nucleases (ZFNs) and transcription activator like effector nucleases (TALENs) possess great potentiality to be used in therapeutic purpose (Gaj et al., 2013). Therefore, OMICs and gene editing approaches collectively can be feasible in achieving the desired goal in screening and modifying microbial metabolites for antiviral drugs. Another efficient approach is microbial genome mining which comes with an outstanding opportunity of evaluating activity of the silent gene and discovering novel metabolites with the assistance of the information from genome sequencing (Bachmann et al., 2014). It also enables the understanding of biochemical pathways taking place inside the microbial cell, thus allowing the potential antiviral drug compounds to be discovered and analyzed (Fields et al., 2017; Xia, 2017). Furthermore, in the near future, metabolic engineering will contribute a lot to the discovery and development of antiviral drugs from microbial metabolites. Microbial system is becoming popular for expressing heterologous antiviral bioactive compounds. However, it paves challenges to the researchers to design and express the multiple enzymatic pathways involved in biosynthesis of antiviral bioactive compounds.

A wide array of plant-based secondary metabolites show promising antiviral activity against coronaviruses (Bhuiyan et al., 2020). Microbial biotechnology may contribute to large scale production of antiviral plant secondary metabolites or to get novel pharmaceutically active metabolites. However, many of the antiviral microbial metabolites included in this study are synthesized by endophytes. Therefore, the promising plant-based metabolites can be achieved through the screening of endophytic organisms of the targeted plant because various endophytic bacteria and fungi have the ability to produce the same or similar compounds as their host plants (Xu et al., 2009; Gouda et al., 2016; Raihan et al., 2021). For example, taxol, a billion dollar anticancer drug, initially produced by Taxus brevifolia and now it is produced from its endophyte Taxomyces andreanae (Stierle et al., 1993). Similarly, camptothecin, podophyllotoxin, hypericin and azadirachtin, are produced both by the endophyte and its host plant (Kusari and Spiteller, 2011; Bhalkar et al., 2016). Therefore, metabolites of endophytic microorganisms could be an emerging source of antiviral bioactive compounds (Schulz et al., 2002; Xu et al., 2009; Gouda et al., 2016; Raihan et al., 2021). Finally, researchers should pay attention to research with microbial metabolites using the approaches aforementioned to combat against catastrophic viral infections including COVID-19 and potential outbreaks of future viral pandemic and/or epidemics. For this, it is necessary to adopt initiatives to conduct systematic longitudinal studies by applying available and newly discovered microbial metabolites against catastrophic viruses including SARS-CoV-2.

Author Contributions

Concept and design: TR and AKA; whole draft manuscript writing: TR; partial draft manuscript writing: MFR, PR, and SC; Data collection and analysis, figures preparation: TR and AKA; critical review and suggestion for editing: K-HB; Data interpretation, compilation, supervision and editing of the whole manuscript: AKA. All authors contributed to the article and approved the submitted version.

Funding

This work was partially supported by grants in aid from the Research Centre, Shahjalal University of Science and Technology, Sylhet, Bangladesh (No. LS/2020/1/17).

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Publisher’s Note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

References

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