Anti-HIV-drug and phyto-flavonoid combination against SARS-CoV-2: a molecular docking-simulation base assessment

Pathogenesis of SARS-CoV-2 induced cardiac injury from the perspective of the virus

COVID-19 pandemic caused by very severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) agent is an ongoing major global health concern. The disease has caused more than 452 million affected cases and more than 6 million death worldwide. Hence, there is an urgency to search for possible medications and drug treatments. There are no approved drugs available to treat COVID-19 yet, although several vaccine candidates are already available and some of them are listed for emergency use by the world health organization (WHO). Identifying a potential drug candidate may make a significant contribution to control the expansion of COVID-19. The in vitro biological activity of asymmetric disulfides against coronavirus through the inhibition of SARS-CoV-2 main protease (Mpro) protein was reported. Due to the lack of convincing evidence those asymmetric disulfides have favorable pharmacological properties for the clinical treatment of Coronavirus, in silico evaluation should be performed to assess the potential of these compounds to inhibit the SARS-CoV-2 Mpro.In this context, we report herein the molecular docking for a series of 40 unsymmetrical aromatic disulfides as SARS-CoV-2 Mpro inhibitor. The optimal binding features of disulfides within the binding pocket of SARS-CoV-2 endoribonuclease protein (Protein Data Bank [PDB]: 6LU7) was described. Studied compounds were ranked for potential effectiveness, and those have shown high molecular docking scores were proposed as novel drug candidates against SARS-CoV-2. Moreover, the outcomes of drug similarity and ADME (Absorption, Distribution, Metabolism, and Excretion) analyses have may have the effectiveness of acting as medicines, and would be of interest as promising starting point for designing compounds against SARS-CoV-2. Finally, the stability of these three compounds in the complex with Mpro was validated through molecular dynamics (MD) simulation, in which they displayed stable trajectory and molecular properties with a consistent interaction profile.

Background The outbreak of coronavirus disease 2019 (COVID-19) induced by the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in China and spread to cover the entire world with an ongoing pandemic. The magnitude of the situation and the fast spread of the new and deadly virus, as well as the lack of specific treatment, led to a focus on research to discover new therapeutic agents. Aim In this study, we explore the potential inhibitory effects of some active polyphenolic constituents of Rhus spp. (sumac) against the SARS-CoV-2 main protease enzyme (Mpro; 6LU7). Methods 26 active polyphenolic compounds of Rhus spp. were studied for their antiviral activity by molecular docking, drug likeness, and synthetic accessibility score (SAS) as inhibitors against the SARS-CoV-2 Mpro. Results The results show that all tested compounds of sumac provided good interaction with the main active site of SARS-CoV-2 Mpro, with better, lower molecular docking energy (kcal/mol) compared to the well-known drugs chloroquine and favipiravir (Avigan). Only six active polyphenolic compounds of Rhus spp. (sumac), methyl 3,4,5-trihydroxybenzoate, (Z)-1-(2,4-dihydroxyphenyl)-3-(3,4-dihydroxyphenyl)-2-hydroxyprop-2-en-1-one, (Z)-2-(3,4-dihydroxybenzylidene)-6-hydroxybenzofuran-3(2H)-one, 3,5,7-trihydroxy-2-(4-hydroxyphenyl)chroman-4-one, 2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-4H-chroman-4-one, and 3,7-dihydroxy-2-(4-hydroxyphenyl)chroman-4-one, were proposed by drug likeness, solubility in water, and SAS analysis as potential inhibitors of Mpro that may be used for the treatment of COVID-19. Conclusion Six phenolic compounds of Rhus spp. are proposed for synthesis as potential inhibitors against Mpro and have potential for the treatment of COVID-19. These results encourage further in vitro and in vivo investigations of the proposed ligands and research on the preventive use of Rhus spp. against SARS-CoV-2.

Due to the length of time required to develop specific antiviral agents, the World Health Organization adopted the strategy of repurposing existing medications to treat Coronavirus disease 2019 infection. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease is possible biological target for potential antiviral drugs. We selected various compounds from PubChem database based on the structure of main protease inhibitors in Protein Data Bank database. Ten compounds showed nontumorigenic and nonmutagenic potential and met Egan's and Lipinski's rules. Molecular docking analysis was performed using AutoDock Vina software. Based on number and type of key binding interactions, as well as docking scores, we selected compounds 6, 8, and 17 that demonstrated the highest binding affinity for the target protein. Molecular dynamics simulations were then carried out on the protein-top docked ligand complexes which were subjected to molecular mechanics/generalized Born and surface area calculations. The molecular dynamics simulation results indicated that protein-top docked ligand complexes showed good conformational stability. Among analyzed molecules, compound 17 emerged as the best in silico hit based on the docking score, MM/GBSA binding energy and MD results.

Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (Mpro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a -7 kcal/mol binding energy score, the top-2 docked complex with a -6.9 kcal/mol binding energy score, and the top-3 docked complex with a -6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were -24.23 kcal/mol, -26.38 kcal/mol, and -25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as -17.23 kcal/mol (top-1 complex), -24.75 kcal/mol (top-2 complex), and -24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.

Since the end of 2019, the emergence of novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has accelerated the research on host immune responses toward the coronaviruses. When there is no approved drug or vaccine to use against these culprits, host immunity is the major strategy to fight such infections. Type I interferons are an integral part of the host innate immune system and define one of the first lines of innate immune defense against viral infections. The in vitro antiviral role of type I IFNs against Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV (severe acute respiratory syndrome coronavirus) is well established. Moreover, the involvement of type I IFNs in disease pathology has also been reported. In this study, we have reviewed the protective and the immunopathogenic role of type I IFNs in the pathogenesis of MERS-CoV, SARS-CoV, and SARS-CoV-2. This review will also enlighten the potential implications of type I IFNs for the treatment of COVID-19 when used in combination with IFN-γ.

By May 15, 2020, 65 days after the World Health Organization (WHO) declared the novel coronavirus disease 2019 (COVID-19) pandemic, 4.2 million individuals were confirmed as being infected with the causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and 294,000 people had died from the disease1. These numbers are almost certainly an underestimation of the true morbidity and mortality of the disease to this point. From the beginning of this public health crisis, attention has focused on the development of vaccines against SARS-CoV-2. Many believe that immunization is the key advance in the war against COVID-19 and that control of SARS-CoV-2 allowing approximations of pre-pandemic social conditions will not be possible without a viable vaccine2. Until a viable vaccine is developed, extensive diagnostic testing, quarantining, and social distancing are the only control methods that we have3. This article was written for musculoskeletal physicians and scientists without immunology backgrounds. It seeks to provide a concise but comprehensive understanding of vaccine development with a special emphasis on efforts to establish immunization directed against SARS-CoV-2. This will help to inform readers of the challenges to be hurdled and allow them to track milestones reached as the global community labors toward an effective vaccine. In-depth reviews of complex immunology topics, viral epidemiology, the myriad historic aspects of vaccine development, and the economics of developing and utilizing different types of vaccines are beyond the scope of this work. Background SARS-CoV-2 To understand the process of vaccine development, one must start with a basic understanding of the pathogen against which it will be directed. SARS-CoV-2 is a beta coronavirus4. The virus has been found to be similar to another coronavirus whose usual hosts are bats. It is believed that wild animals being sold at a market in Wuhan, Hubei Province, the People's Republic of China, led to the transmission of SARS-CoV-2 to humans5. Members of the Coronaviridae family have a positive-sense, single-stranded RNA ([+]ssRNA) genome6. The (+)ssRNA can serve as messenger RNA (mRNA) in the host cell, allowing utilization of host ribosomal machinery to translate viral proteins. This coronavirus genome is highly conserved6. The first gene (open reading frame [ORF]1a and ORF1b) is involved in replication and transcription. Subsequent genes are related to structural proteins (Fig. 1). The spike protein (S) has an exposed location on the virion and is necessary for entry into the cell. Blocking of the spike protein epitopes that interact with angiotensin-converting enzyme 2 (ACE2), the host cellular receptor for SARS-CoV-2, should lead to neutralization (Fig. 2). ACE2 degrades angiotensin II (AngII), downregulating the renin-angiotensin-aldosterone system. ACE2 is distinct from the angiotensin type-I receptor, which leads to activating signal transduction by AngII7.Fig. 1: Illustration of the SARS-CoV-2 genome showing expressed structural component proteins and their location within the virion. The open reading frame (ORF) codes for nonstructural viral proteins participating in viral genome replication, transcription, and protein processing. The spike protein (S) binds to the ACE2 receptor, allowing virus entry into host cells. The envelope protein (E) has been found to bind to host gene regulatory proteins and putatively influences host cell gene expression. The membrane protein (M) seems to cooperate with S during binding and entry into the cell. The nucleocapsid protein (N) coils the viral mRNA inside the viral particle, organizing and protecting it.Fig. 2: SARS-CoV-2 virion entry into the host cell. The virus enters the host cell via the S protein interacting with ACE2. It is important to generate antibodies to the S protein rather than ACE2. This allows ACE2 to remain open to receive the host ligand and to avoid the possibility that the blocking antibody interferes with its normal physiologic function.COVID-19 is usually characterized by fever, cough, dyspnea, fatigue, and sore throat. Radiographic findings have demonstrated pneumonia with infiltrates on chest imaging8. Typically, radiographic changes appear on presentation. In Wuhan, 76% of diagnosed patients demonstrated changes on chest radiographs9. It is unknown whether radiographic changes arise prior to the onset of symptoms. Currently, there are no known curative treatments for COVID-19. Treatment is centered around supportive care while the afflicted individual clears the infection. In some cases, supplemental oxygen needs to be administered to help those with the associated pneumonia to maintain their oxygen saturation. Severe cases may benefit from antiviral medications, dexamethasone10, and ventilatory support with or without extracorporeal membrane oxygenation11,12. In March 2020, the WHO estimated the global mortality rate for those confirmed to have a SARS-CoV-2 infection to be 4.3%, although this varies by region13. Vaccines Vaccines meet the definition of a drug because they are substances other than food used in the prevention, diagnosis, alleviation, treatment, or cure of a disease14. They are administered to healthy individuals to prevent diseases caused by infectious agents to which they might be exposed in the future or, in some cases, to which they have been recently exposed. Immunization is the process of presenting antigens to a live host to induce an immune response. Vaccines can be utilized therapeutically and prophylactically. Most vaccines are developed as prophylaxis against infection. A primary goal of prophylaxis is to generate neutralizing antibodies that prevent viral entry into cells. However, in some cases, vaccines can be administered for short-term protection. This short-term protection is termed passive immunization. A smaller proportion of vaccines are developed for the therapeutic treatment of infections that have already become initiated. An example of this is the vaccine used after exposure to rabies15. Epidemiology of Infectious Disease and Vaccination During infectious disease outbreaks, vaccines have the ability to break chains of transmission, drastically slowing the propagation of infection and eventually eradicating the disease. The vast majority of individuals in modernized societies are immunized against a host of pathogens as children. This global public health effort has resulted in the worldwide elimination of smallpox16 and substantial progress toward the elimination of polio17. These accomplishments required concerted international efforts that were sustained over many decades. The epidemiologic dynamics of vaccination, especially in a population with a disease presence (either endemic or epidemic), can be described mathematically. The basic reproduction number (R0) is the intrinsic measure of transmissibility of a pathogen. It describes the mean number of secondary infections resulting from a single infection within a fully susceptible population (Fig. 3). For SARS-CoV-2, R0 has been estimated to be between 2 and 318.Fig. 3: Illustration of the basic reproduction number (R0) values for representative infectious diseases, demonstrating increasing infectivity with increasing values of R0. HIV = human immunodeficiency virus.Once substantial immunity, through either vaccination or natural exposure to the disease, starts to be established in the population, R0 becomes a less accurate measure of transmissibility, and a second number, the effective reproduction number (Re), becomes more representative of transmissibility. Re represents the actual number of transmissions per infection. For an explanation of how these numbers are calculated and their effect on viral epidemiology (Fig. 4), please see Appendix I.Fig. 4: The relationship between the basic reproduction number (R0) and the effective reproduction number (Re) of a pathogen. Re changes based on the percentage of the population that is immune, demonstrated by the different lines on the chart. For a disease with an R0 of 3.5, immunization of 70% of the population will be necessary to bring Re below 1.0. This can be compared with an immunization level of only 50% needed to bring Re below 1.0 for a disease with an R0 of 2.0. If Re, a measure of disease transmissibility, is <1, a disease outbreak will end without further measures being taken.Herd Immunity Herd immunity is a condition achieved in a population when the indirect protection of susceptible individuals against a specific pathogen is conferred by immune individuals. In effect, those with immunity within a population shield those without immunity from transmission, thereby limiting the spread of the disease19 (Fig. 5). A further explanation of how R0 and Re affect herd immunity (Figs. 6 and 7) is found in Appendix II.Fig. 5: Illustration demonstrating herd immunity. The spread of a hypothetical illness within a population is shown under 3 different conditions. The top row is a time early after the introduction of the pathogen within a population. The second row represents 1 replication cycle and the third row represents 2 replication cycles following the time represented in the top row. In the left column, the population is fully susceptible (no naturally acquired immunity or immunity through vaccination) to the pathogen. The middle column represents an intermediate state between full susceptibility and achievement of the herd immunity threshold (Pcrit). The column on the right represents how spread is hindered in a population that has already achieved Pcrit.Fig. 6: The relationship between the basic reproduction number of a virus, R0, and the proportion of the population that needs to be immunized to enter into a state in which herd immunity takes effect, Pcrit. R0 is unitless and Pcrit is measured as the percentage of the population. The slope of the curve is greatest between R0 values of 1 and 4, indicating that a large increase in the proportion of immune individuals within the population is needed to achieve Pcrit for an infectious disease with an R0 that is just slightly larger than another. The estimated R0 for SARS-CoV-2 is between 2 and 3, which is demarcated in the area between the dotted lines on the graph. This R0 range indicates that the percentage of the population that needs to become immune to reach Pcrit, either through infection or vaccination, is between 50% and 66.7%.Fig. 7: Vaccination affects the achievement of herd immunity. This graph shows vaccination affecting herd immunity to diphtheria. Diphtheria-tetanus-pertussis (DTP3) immunization coverage is expressed as a percentage of the population from 1982 to 2016. The red line on this graph represents the number of diphtheria cases reported worldwide by year. The blue line represents the immunization coverage as a percentage of the population by year. The dashed orange line represents the herd immunity threshold (Pcrit) for diphtheria assuming that it has an R0 of 6. The graph demonstrates how achieving immunization levels just slightly above Pcrit can drive the number of cases down to just a few thousand per year.SARS-CoV-2 Vaccines Under Development It is through recombinant nucleic acid technology that most efforts against COVID-19 are progressing. Theoretically, vaccines using recombinant nucleic acid technology can be developed and, therefore, deployed more quickly than those using more traditional means. However, a few are based on immunologic techniques used widely in the mid-twentieth century for the development of vaccines used in standard childhood immunization schedules. Table I summarizes the types of vaccines as well as their advantages and disadvantages. By June 2, 2020, >130 candidate vaccines targeting SARS-CoV-2 were under development worldwide according to the WHO20. Ten of these candidate vaccines have entered into human trials. Table II summarizes the SARS-CoV-2 vaccines currently in development. TABLE I - Advantages and Disadvantages of Different Vaccine Types* Type of Vaccine Example Vaccine(s) Advantages Disadvantages Potential Solutions to Development Problems Attenuated Sabin polio (host-range mutant) Smallpox (Jennerian method) Reliable Confer both humoral and cell-mediated immunity Limited need for booster doses Relatively inexpensive technology May yield less protective mutant viruses if passages are performed in non-human cell lines63 Can cause disease in immunocompromised individuals Enhanced storage and maintenance requirements (e.g., refrigeration, culture media) Inactivated Typhoid Salk polio Rabies Influenza Relatively fast Easy to scale up Relatively inexpensive development Alternate routes of administration (e.g., oral) Inactivation can sometimes damage key epitopes Can still theoretically cause disease (if not fully inactivated) Labor-intensive process to ensure no viable virion remains after inactivation Greater amounts of inoculum required to achieve immunity Immune response is less durable, requiring booster doses64 Titration of inactivation methods to prevent overtreatment, maintaining key epitopes Subunit Hepatitis B surface antigen Safe Easy to use Requires large amounts of isolated antigen Immunopotentiation2,65 Recombinant technology has made large-scale production possible Adjuvants can be added to vaccine preparations66 mRNA29 HIV† Zika† Influenza† Rabies† Can replicate using host machinery Highly potent Relatively fast Easy to scale up • Relative low cost of manufacturing Safe Confer both humoral and cell-mediated immunity dsRNA byproducts of production are PAMPs‡ and lead to immune recognition and degradation29 Inefficient delivery to target cells Instability of mRNA Modified nucleosides avoid host immune recognition Purification to eliminate dsRNA Multiple delivery methods devised to improve efficiency Inclusion of upstream and downstream untranslated sequences improves stability of mRNA DNA plasmid Prostate cancer† Melanoma† Can replicate using host machinery Highly potent Relatively fast Easy to scale up • Safe Confer both humoral and cell-mediated immunity Inefficient delivery to target cells Coupled treatments (e.g., electroporation) to improve DNA plasmid entry into human cells34 and enhance immune response32–33- Vector-based recombinant (e.g., adenovirus vector) Malaria† HIV† Ebola (in development) Confer both humoral and cell-mediated immunity Enter host cells via ubiquitously expressed cell surface receptors Can incorporate additional transgenes for biological adjuvants37,67 Highly potent Relatively fast Easy to scale up in low-resource settings68 Safe Easier, alternate routes of administration favoring IgA production (e.g., oral, intranasal)69,70 Vector immunity due to host recognition of adenovirus71 If replication-competent viral vectors are utilized, could cause adenovirus infection Administration via mucosa may require dose escalation Repeated immunizations can diminish neutralizing antibodies to adenovirus vectors, thereby decreasing vector immunity71 Utilize different adenovirus strains to evade vector immunity70,72,73 Utilize chimpanzee adenovirus vectors to evade vector immunity due to highly conserved genome74 Use of replication-competent viral vectors can boost immunogenicity *HIV = human immunodeficiency virus, dsRNA = double-stranded RNA, PAMP = pathogen-associated molecular pattern, and IgA = immunoglobulin A.†In trials.‡These are present and invariant in the pathogen but not in the potential host organism; PAMPs allow early recognition and immune activation by the host organism75. TABLE II - SARS-CoV-2 Candidate Vaccines Currently in Clinical Development* Vaccine Type Clinical Phase of Development Trial No. (Location) Chimpanzee adenovirus vector-based (nonreplicating) Phase 2b/3 2020-001228-32 (EU) mRNA (lipid nanoparticle encapsulated) Phase 2: scheduled to conclude September 2021 NCT04405076 (USA) Adenovirus-5 vector-based (nonreplicating) Phase 2: scheduled to conclude January 2021 ChiCTR2000031781 (China) Subunit (recombinant spike protein) Phase 1 and 2: scheduled to conclude July 2021 NCT04368988 (USA) mRNA (lipid nanoparticle encapsulated) Phase 1 and 2: scheduled to conclude June 2021 NCT04368728 (USA), 2020-001038-36 (EU) Inactivated with aluminum adjuvant Phase 1 and 2: scheduled to conclude July/August 2020 NCT04383574 (USA), NCT04352608 (USA) Inactivated Phase 1 and 2: scheduled to conclude November 2021 ChiCTR2000031809 (China) Inactivated Phase 1 and 2: scheduled to conclude November 2021 ChiCTR2000032459 (China) DNA plasmid (with electroporation) Phase 1: scheduled to conclude July 2021 NCT04336410 (USA) Inactivated Phase 1 China *As of June 2, 2020. Attenuated Vaccines Vaccines that use a weakened but viable form of the pathogen to establish an immune response are termed attenuated vaccines. The establishment of attenuated strains is an empiric rather than a designed process, the duration of which is influenced by the scale of the process and the time necessary to complete the passage of the virus in the cell culture. In rare cases, the attenuated variant can revert to a virulent form, resulting in the establishment of the disease in the immunized cohort. There are 4 different types of attenuated vaccines. At least 3 different groups are seeking to develop attenuated vaccines against COVID-1920. The most common form of an attenuated vaccine is the host range mutant. This type is usually achieved by the passage of the virus in the cell culture to generate nonvirulent mutants. Over multiple passages, the host range mutant acquires mutations, rendering it harmless while retaining the necessary antigens to generate immunity. The second type is naturally attenuated. This method requires empiric identification and recovery of variant or minimally variant strains during periods of outbreak21. The third type of attenuated vaccine is the temperature-sensitive mutant. This method isolates mutants that at of strains that can be at is the found at the respiratory but become nonvirulent at the or The type of attenuated termed is not being in the COVID-19 vaccine development Inactivated Vaccine vaccine requires large amounts of viral to be in and by either or (Fig. The of inactivation is to the virus nonvirulent without the epitopes to which an immune response is and can virus A needs to be achieved in the of vaccines. will lead to and of key to a neutralizing antibody response that is and protective with a live However, if complete inactivation not of the disease can from the vaccination through some vaccine types that are being developed against SARS-CoV-2. Inactivated viral are in and through or means. The of viral allows the of an immune response without of infection. Subunit viral proteins are and These proteins are into patients to be The proteins are by the host cells and the antigens are that an antibody response is mRNA mRNA the viral S protein is in the and is using technology as These mRNA are and are into viral proteins using host and the antigens are that an antibody response is DNA plasmid DNA for the viral S protein is into a DNA This plasmid enters host and machinery viral proteins. These viral proteins generate an antibody response. vector-based the gene for the viral S protein is into an adenovirus genome in These adenovirus vectors with entry into the host cell and the host machinery to viral proteins that generate an antibody Vaccines Subunit vaccines generate immunity by administration of a virus antigen (Fig. These antigens are by the immune to generate an antibody response. Typically, antigens are that will generate an immune response. For SARS-CoV-2, one of the candidate antigens for vaccine development is the spike A number of the of and are on developing spike protein mRNA Vaccines In this mRNA for the SARS-CoV-2 spike protein is into the host cells to it (Fig. proteins made by host cells will be as by the immune which will generate both an antibody and the response to mRNA vaccines have had that effective but have of these mRNA vaccine delivery and the of the and methods are standard at this 1 developing an mRNA vaccine against SARS-CoV-2 has that it could be as an measure to as early as DNA Vaccine the of the of SARS-CoV-2, the development of a DNA vaccine the (+)ssRNA genome of SARS-CoV-2, DNA sequences can be These sequences can be into or double-stranded DNA that for antigen DNA (Fig. can replicate using host is into host it can viral antigens that are as the host immune to generate an antibody and the response. This method of vaccine development advantages similar to those for mRNA vaccines nucleic are that the potential with protein which can recombinant multiple have demonstrated that can enter host cells and can in a immune This technology has been shown to be and in to there have been no DNA vaccines for use in Recombinant Vaccines Recombinant viral vectors have been as vaccine over the few for their ability to antigens and their immunogenicity (Fig. are DNA of recombinant adenovirus vector-based vaccines is that they can be made and highly effective through recombinant The of recombinant adenovirus vector-based vaccines is by rendering the virion replication This is achieved by the antigen in the of the adenovirus genome for viral replication, thereby its ability to most vaccines are administered either or adenovirus vector-based vaccines provide the possibility of This is a more administration than For these many different recombinant adenovirus vector-based vaccines targeting SARS-CoV-2 are currently under development. Immunization immunization may be achieved by administration of to a or recently infected protection against pathogens within the immunized The protective of the are eventually down or this the protective effect is because not or the immune to provide immunization. There are with and patients develop the at a of infection. Currently, there are a number of for the treatment of patients with Immunity to COVID-19 There and should a to develop a vaccine against SARS-CoV-2. health measures will need to the development, and administration of a vaccine against SARS-CoV-2 to a large proportion of the population. with these morbidity and mortality will The potential rate increase from to between and of the population while the the herd immunity threshold (Pcrit) may be to A number of potential immunity, immunity, and vaccine could the of a COVID-19 vaccine TABLE - and the of COVID-19 Vaccine Immunization on COVID-19 Vaccine Immunization immunity are of Immunity in individuals may require vaccination individuals may not be fully immune Vaccine is only effective May require vaccination or vaccination of more individuals than Pcrit Vaccine or use of vaccines to achieve Pcrit for development for vaccine development and is 4 the development can only if necessary the first Vaccine takes to develop similar efforts have of vaccine development, we still not have a vaccine Vaccine takes to develop molecular techniques more effective of recombinant Development Vaccines or manufacturing complete of vaccine development to from and Over worldwide on vaccine Development Vaccine to by the is especially A by the for that of not and were if they when a vaccine becomes A of found that were at and an additional were in a COVID-19 is an that could Pcrit or lead to the of COVID-19 The COVID-19 vaccine will not be the This was with polio and both of which through in the and types that were used when or were in the early The vaccines which groups to they are administered and toward and their delivery methods will with limiting vaccine is immunity. illness are of the This that SARS-CoV-2 may exposed individuals. may be due to either antibody and cell or The need for vaccination could the establishment of Pcrit. possibility is that only some individuals have full immunity. immunity is still it the numbers of infected individuals and those requiring care on the level of an care The of developed vaccines will most be by of blocking Vaccines that have entered into have already been for blocking antibodies in their The administration of different vaccines has been in achieving immunity. attenuated and polio vaccines administered have a for viruses with substantial as immunizations help to neutralizing antibody for conserved There is a complex of and on immune In antibody to vaccines are in while both humoral immune to novel that are related to multiple affect the time for immunity to a is 2 to 3 following the Problems that are of in developing a vaccine to RNA viruses are the of and is the of the viral disease rather than its This has led to and in immunized has been with a number of those against is the of infection. of infection when viruses are by cells via their or This has been shown to in human cells with It is not that vaccine administration will have a musculoskeletal However, the time to testing, and will have for the and of care It is standard methods or will be during the production and of viable as many of the currently being used have resulted in doses at that multiple vaccines and their will be to more and effective and administration to the Immunization with candidate vaccines should not lead to should be to allow the establishment of an immune response and of severe morbidity and mortality associated with The for the development of effective vaccines should be with the that the to achieve will be There will be many and we must to this The protective measures that we have social protective and the use of testing, will be a of COVID-19 has morbidity and Pcrit will be in to a of social Pcrit will be through immunization. an early and response toward developing a COVID-19 remain in Recombinant techniques may this A between the community and should the need for vaccine development with Appendix by the is with the of this article as a at

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Identification of natural peptides from “PlantPepDB” database as anti-SARS-CoV-2 agents: A protein-protein docking approach

To date, very few small drug molecules are used for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has been discovered since the epidemic commenced in November 2019. SARS-CoV-2 RdRp and spike protein are essential targets for drug development amidst whole variants of coronaviruses. This study aims to discover and recognize the most effective and promising small molecules against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and spike protein targets through molecular docking screening of 39 phytochemicals from five different Ayurveda medicinal plants. The phytochemicals were downloaded from PubChem, and SARS-CoV-2 RdRp and spike protein were taken from the protein data bank. The molecular interactions, binding energy, and ADMET properties were analyzed. Molecular docking analysis identified some phytochemicals, oleanolic acid, friedelin, serratagenic acid, uncinatone, clemaphenol A, sennosides B, trilobine and isotrilobine from ayurvedic medicinal plants possessing greater affinity against SARS-CoV-2-RdRp and spike protein targets. Two molecules, namely oleanolic acid and sennosides B, with low binding energies, were the most promising. Furthermore, based on the docking score, we carried out MD simulations for the oleanolic acid and sennosides B-protein complexes. Molecular ADMET profile estimation showed that the docked phytochemicals were safe. The present study suggested that active phytochemicals from medicinal plants could inhibit RdRp and spike protein of SARS-CoV-2.