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Peptides – Potential Agents Against 2019-nCoV, SARS, and MERS-CoV

Currently, news headlines from around the world are filled with reports of the coronavirus epidemic, initially erupting in the People’s Republic of China and now spreading to other, especially neighboring, countries. The total number of individuals infected with the 2019-nCoV coronavirus has crossed a million, with tens of thousands of fatalities [1, 2].

Bloomberg agency has compiled lists of virus-related fatalities, specifying symptoms, gender, and age as of January 23, 2020 [3]. Lethal outcomes are predominantly observed in elderly men over 60 years old. The most common symptoms include fever, cough, and difficulty breathing. Disease progression can lead to progressive respiratory failure due to alveolar damage and even death. Clinicians have identified the disease as virus-induced pneumonia based on clinical symptoms and other criteria, including elevated body temperature, decreased lymphocytes and leukocytes, new lung infiltrates on chest X-rays, and a lack of apparent improvement with antibiotic treatment for three days.

The virus is spreading rapidly worldwide. As of January 28, 2020, confirmed infection cases by country [2] (an continually updated interactive map with new infection and death cases is available at the link, but may experience interruptions due to high traffic): Mainland China – 4,409, Hong Kong – 8, Thailand – 8, Macao – 6, Australia – 5, Taiwan – 5, USA – 5, Japan – 4, Malaysia – 4, Singapore – 5, South Korea – 4, France – 3, Germany – 1, Vietnam – 2, Cambodia – 1, Canada – 1, Nepal – 1, Sri Lanka – 1. Russia has not yet reported any confirmed cases. The rate of infected individuals in mainland China is following an exponential growth trend. Quarantine measures are being implemented in China, with restrictions on travel to some affected areas, essentially isolating millions of people [3]. The World Health Organization (WHO) stated on Thursday that the outbreak has not yet become a global emergency but that WHO is closely monitoring the situation.

The infectious agent is the 2019-nCoV virus (Wuhan coronavirus, Wuhan seafood market pneumonia virus), a new strain of coronavirus discovered in December 2019 during the pneumonia outbreak in Wuhan, China [4]. 2019-nCoV can be transmitted from person to person. It is still unclear how easily this happens, but human coronaviruses typically spread through the air via coughing and sneezing. The incubation period can be up to 14 days, during which transmission between humans is also possible. By mid-January, the genome of the 2019-nCoV virus had already been decoded and added to the database [5]. 2019-nCoV is a single-stranded RNA virus with a genome sequence of 29,903 nucleotides. Due to reports that initial cases had epidemiological links to a large seafood and animal market, it is believed that the virus has a zoonotic origin, although this has not been confirmed. Comparisons of genetic sequences between this virus and other existing virus samples showed a 79.5% similarity with SARS-CoV and 96% with a bat coronavirus (BatCoV RaTG13, previously found in the Asian horseshoe bat, Rhinolophus affinis) [6], suggesting a probable origin from bats. The name SARS-CoV (severe acute respiratory syndrome-related coronavirus) stands for “coronavirus related to severe acute respiratory syndrome.” It has already been established that the new 2019-nCoV virus uses the same cell entry receptor, ACE2, as SARS-CoV [6].

In general, coronaviruses (CoVs) are a group of viruses that cause diseases in mammals and birds. In humans, CoVs cause respiratory infections that are typically mild but can be fatal in rare cases. In cattle and pigs, they can cause diarrhea, while in chickens, they can lead to upper respiratory tract disease. As of now, there are no vaccines or antiviral drugs approved for the prevention or treatment of diseases caused by CoVs. By classification, coronaviruses are viruses of the subfamily Orthocoronavirinae in the family Coronaviridae, order Nidovirales. Coronaviruses are enveloped viruses with a positive-polarity single-stranded RNA genome ((+)ssRNA) and a nucleocapsid with helical symmetry. The size of the CoV genome is approximately 26 to 32 kilobases, making it the largest among RNA viruses.


 

Coronaviruses were first discovered in the 1960s, with the earliest ones found in the infectious bronchitis virus of chickens and two viruses from the nasal cavities of patients with the common cold. These later became known as human coronavirus 229E and human coronavirus OC43. Since then, other members of this family have been identified, including SARS-CoV in 2003, HCoV NL63 in 2004, HKU1 in 2005, MERS-CoV in 2012, and 2019-nCoV in 2019, with most of them being associated with severe respiratory infections.
Beta-coronaviruses, including BatCoV RaTG13, which is closely related to the new virus 2019-nCoV, belong to one of the four genera of coronaviruses. In earlier literature, this genus was also known as group 2 coronaviruses.Among Beta-CoVs, those of clinical significance to humans include lineage A strains OC43 and HKU1, lineage B strains SARS-CoV and 2019-nCov, and lineage C strain MERS-CoV. MERS-CoV was the first Beta-coronavirus belonging to lineage C to affect humans. Alpha and Beta coronaviruses originate from the genetic pool of bats.In the past two decades, coronaviruses have caused two major pandemics: SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome).SARS is a coronavirus that caused an epidemic of severe atypical pneumonia in 2002, beginning in China. During replication, SARS destroys the cells of the lung alveoli, which can lead to death. There were confirmed 8098-8422 cases of infection, resulting in 774 deaths in 17 countries (mortality rate 9.6-11%).Middle East Respiratory Syndrome (MERS), caused by a Beta-coronavirus, led to an outbreak primarily in Middle Eastern countries in 2012. Most patients developed severe acute respiratory illness requiring hospitalization, with a mortality rate ranging from 30% to 60%. Approximately 2000 people were affected, and the virus was initially isolated from bats. MERS-CoV is closely related to bat coronaviruses Tylonycteris HKU4 and Pipistrellus HKU5, sharing genetic sequences of more than 90%.As of March 2017, the World Health Organization (WHO) reported 1905 confirmed cases of MERS, including 677 deaths in 27 countries. MERS spreads among humans, causing severe complications leading to death, highlighting the need for effective therapeutic and preventive measures. Transmission of the virus from human to human was responsible for an outbreak of MERS in a hospital. Currently, there is no registered treatment or vaccine for this disease, but MERS-CoV infection is managed primarily through supportive care, along with some preventive measures to avoid reinfection. Several studies have shown that various therapeutic agents can inhibit MERS-CoV replication in cell cultures.In 2018, an extensive review of contemporary treatments for Middle East Respiratory Syndrome (MERS) and the role of peptides as potential therapeutic components was published. This review briefly describes important drug targets of MERS-CoV, presents therapeutic options available for MERS treatment, discusses their efficacy, and explores the role of peptide research in virology. It also emphasizes the significance of antimicrobial peptides (AMPs) as potential therapeutic agents against MERS. The rapid development of computational biology approaches is expected to lead to new and effective therapies for MERS utilizing AMPs.

Structural and non-structural proteins of MERS-CoV as drug targets

The transmission pathway of MERS-CoV from animals to humans has not been definitively determined, but it is believed to have been transmitted from bats through camels, serving as intermediate hosts. MERS-CoV has been shown to modulate the innate immune response, antigen production, mitogen-activated protein kinase (MAPK), and apoptosis.

The structure of MERS-CoV consists of four structural proteins, including the spike protein (S), envelope protein (E), membrane protein (M), and nucleocapsid protein (N). The S protein is a transmembrane type I glycoprotein located on the virus’s surface in a trimeric state. It consists of subunits S1 and S2 and plays a role in virus entry, binding, and fusion. The S1 subunit contains the receptor-binding domain (RBD), responsible for binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). The S2 subunit includes two regions, heptad repeat 1 and 2 (HR1 and HR2), which assemble into a fusion core, playing a key role in membrane fusion. The E protein is 82 amino acids long and is primarily found in intracellular viral membranes, playing a major role in virus assembly, budding, and intracellular transport. The M protein is a component of the viral envelope, involved in virion morphogenesis and assembly through its interaction with other viral proteins. Proteins S, M, and E are integrated into the endoplasmic reticulum membrane and transported to the Golgi complex, where they interact with N proteins to form viral particles. This interaction ultimately hinders the fusion of cellular and viral membranes. Thus, the mentioned peptides can be of significant importance in peptide-based therapy. Additionally, MERS-CoV consists of two large polyproteins, pp1a and pp1ab, which are then cleaved into 16 non-structural proteins (nsps). Two proteases, papain-like protease (PLpro or nsp3) and 3C-like protease (3CLpro or nsp5), are responsible for processing all 16 nsps, which are essential for replication and transcription. PLpro cleaves positions 1-3 to develop three nsps, while 3CLpro cleaves the remaining positions 4-16. These nsps are responsible for viral RNA-dependent RNA polymerase activity (nsp12), DNA primase activity (nsp8), RNA helicase activity (nsp13), exoribonuclease activity (nsp14), endoribonuclease activity (nsp15), and 2′-O-methyltransferase activity (nsp16). The activity of 2′-O-methyltransferase is stimulated by nsp10, which acts as an allosteric activator of nsp16. Studies show that coronavirus nsps can be used as targets for the development of new treatment methods (see references in the review [20]). Both structural and non-structural proteins can serve as therapeutic targets, where various therapeutic options can be implemented, and they will be discussed further.

The Role of Peptides as Potential Antiviral/Anti-Coronavirus Agents

There is a growing interest in peptide-based drugs and their mimetics as potential antagonists against various pathogens. Peptide research is a crucial aspect of pharmaceutical investigations, with approximately 140 peptide-based drugs currently in clinical trials.

The reasons for using peptides in drug development are manifold. They can inhibit protein-protein interactions, serve as alternative therapies for challenging diseases, have advanced methods for extending peptide half-life, and can have a quicker time to market compared to chemical drugs. Peptide-based medications often exhibit minimal side effects and good tolerability compared to chemical drugs. However, they require special storage conditions, as the protein function may become inactive, leading to low oral bioavailability and susceptibility to rapid metabolism.

Many peptide inhibitors have shown activity against viruses and other pathogens. For example, the peptide RVFV-6, derived from the stem region of the glycoprotein Gc of Rift Valley Fever virus, prevents virus fusion during Rift Valley fever. It also exhibits activity against unrelated viruses such as EBOV and VSV. A derivative of scorpion toxin peptide Kn2-7 was identified as a potential agent against HIV-1 with low cytotoxic effects.

The lack of effective treatments has led to the development of additional therapeutic agents with improved efficacy to overcome side effects associated with current MERS treatment. In recent years, there has been a growing interest in peptide therapy due to numerous side effects associated with chemical drugs.

Antimicrobial peptides (AMPs) are excellent candidates for new therapeutic agents because they have shown antiviral activity. AMPs are components of the first line of defense in both eukaryotic and prokaryotic organisms. These small, positively charged peptides exhibit selective toxicity against Gram-positive and Gram-negative bacteria, protozoa, fungi, and viruses. Their selective toxicity is due to the negatively charged bacterial membrane compared to the positive charge of AMPs. Antiviral AMPs act through various mechanisms, including blocking virus entry through interaction with heparan sulfate, inhibiting virus entry through fusion with specific cell receptors, and preventing virus fusion through interaction with viral glycoproteins, membrane, and envelope.

Conclusion

There is an urgent need for the development of more effective therapies against coronaviruses such as MERS, 2019-nCoV, and potentially new, unknown, and dangerous agents. The development of protocols for use in randomized controlled trials is also essential. Research has shown that peptides have become highly effective agents in signal transmission during viral diseases. Antimicrobial peptides are expected to be a successful therapeutic option for the new MERS pathogen. Computational biology combined with virology can expedite the advanced development of peptide therapy against MERS-CoV. Additionally, repurposing existing clinically approved antiviral peptide drugs may be a promising direction for developing new agents against MERS-CoV and similar coronaviruses.

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