Nanomedicine "New Food for an Old Mouth": Novel Approaches for the Treatment of COVID-19

Coronavirus disease (COVID-19) is an infectious disease caused by coronavirus. Devel-oping specific drugs for inhibiting replication and viral entry is crucial. Several clinical trial studies are underway to evaluate the efficacy of anti-viral drugs for COVID-19 patients. Nanomedicine formulations can present a novel strategy for targeting the virus life cycle. Nano-drug delivery systems can modify the pharmacodynamics and pharmacokinetics properties of anti-viral drugs and reduce their adverse effects. Moreover, nanocarriers can directly exhibit anti-viral effects. A number of nanocarriers have been studied for this purpose, including liposomes, dendrimers, exosomes and decoy nanoparticles (NPs). Among them, decoy NPs have been considered more as nanodecoys can efficiently protect host cells from the infection of SARS-CoV-2. The aim of this review article is to highlight the probable nanomedicine therapeutic strategies to develop anti-viral drug delivery systems for the treatment of COVID-19.Copyright © 2023 Bentham Science Publishers.

25 (S)-Hydroxycholesterol acts as a possible dual enzymatic inhibitor of SARS-CoV-2 Mpro and RdRp-: an insight from molecular docking and dynamics simulation approaches.

The coronavirus disease (COVID-19) pandemic has rapidly extended globally and killed approximately 5.83 million people all over the world. But, to date, no effective therapeutic against the disease has been developed. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and enters the host cell through the spike glycoprotein (S protein) of the virus. Subsequently, RNA-dependent RNA polymerase (RdRp) and main protease (Mpro) of the virus mediate viral transcription and replication. Mechanistically inhibition of these proteins can hinder the transcription as well as replication of the virus. Recently oxysterols and its derivative, such as 25 (S)-hydroxycholesterol (25-HC) has shown antiviral activity against SARS-CoV-2. But the exact mechanisms and their impact on RdRp and Mpro have not been explored yet. Therefore, the study aimed to identify the inhibitory activity of 25-HC against the viral enzymes RdRp and Mpro simultaneously. Initially, a molecular docking simulation was carried out to evaluate the binding activity of the compound against the two proteins. The pharmacokinetics (PK) and toxicity parameters were analyzed to observe the 'drug-likeness' properties of the compound. Additionally, molecular dynamics (MD) simulation was performed to confirm the binding stability of the compound to the targeted protein. Furthermore, molecular mechanics generalized Born surface area (MM-GBSA) was used to predict the binding free energies of the compound to the targeted protein. Molecular docking simulation identified low glide energy -51.0 kcal/mol and -35.0 kcal/mol score against the RdRp and Mpro, respectively, where MD simulation found good binding stability of the compound to the targeted proteins. In addition, the MM/GBSA approach identified a good value of binding free energies (ΔG bind) of the compound to the targeted proteins. Therefore, the study concludes that the compound 25-HC could be developed as a treatment and/or prevention option for SARS-CoV-2 disease-related complications. Although, experimental validation is suggested for further evaluation of the work.Communicated by Ramaswamy H. Sarma.

Binding properties of selective inhibitors of P323L mutated RdRp of SARS-CoV-2: a combined molecular screening, docking and dynamics simulation study.

Since 2019 the SARS-CoV-2 and its variants caused COVID-19, such incidents brought the world in pandemic situation. This happened due to furious mutations in SARS-CoV-2, in which some variants had high transmissibility and infective, this led the virus emerged as virulent and worsened the COVID-19 situation. Among the variants, P323L is one of the important mutants of RdRp in SARS-CoV-2. To inhibit the erroneous function of this mutated RdRp, we have screened 943 molecules against the P323L mutated RdRp with the criteria that the molecules with 90% similar to the structure of remdesivir (control drug) resulted nine molecules. Further, these molecules were evaluated by induced fit docking (IFD) identified two molecules (M2 & M4) which are forming strong intermolecular interactions with the key residues of mutated RdRp and has high binding affinity. Docking score of the M2 and M4 molecules with mutated RdRp are -9.24 and -11.87 kcal/mol, respectively. Further, to understand the intermolecular interactions, conformational stability, the molecular dynamics simulation and binding free energy calculations were performed. The binding free energy values of M2 and M4 molecules with the P323L mutated RdRp complexes are -81.60 and -83.07 kcal/mol, respectively. The results of this in silico study confirm that M4 is a potential molecule; hence, it may be considered as the potential inhibitor of P323L mutated RdRp to treat COVID-19 after clinical investigation.Communicated by Ramaswamy H. Sarma.

Safety Profile of Molnupiravir with Significant Effect on COVID-19: A Review

Background: As the COVID era unfolds, researchers reveal that rapid changes in viral genetic material allow viruses to circumvent challenges triggered by the host immune system and resist anti-viral drugs, potentially leading to persistent viral manifestations in host cells. Molnupiravir (RNA-dependent RNA polymerase inhibitor) is a novel anti-viral medicine promising a vital role in coming setbacks.Objectives: This review aims to clarify the safety and efficacy of the molnupiravir molecule in light of existing case studies. As a result, it is intended to explore and discuss the molecular structure, mechanism of action, discovery and development process, preclinical research, clinical investigations, and other subtopics.Methods: A total of 75 publications were searched using multiple engines, such as Google Scholar, PubMed, Web of Science, Embase, Cochrane Library, ClinicalTrials.gov, and others, with a constraint applied to exclude publications published over 11 years ago. Molnupiravir, safety, efficacy, COVID- 19, RdRp, PK-PD, and clinical study were utilized as keywords.Results: Clinical results on molnupiravir are supported by investigations that were recently disclosed in a study on both sex volunteers (male and female) with an age restriction of 19 to 60 years, followed by a Phase-3 Clinical Trial (NCT04575584) with 775 randomly assigned participants and no fatalities reported due to treatment.Conclusion: Molnupiravir proved a high level of safety, allowing it to be tested further. This review supports the safety and efficacy of this molecule based on the established evidence, which claims the most anticipated employment of molnupiravir in COVID protocol.

Identification of inhibitors of the RdRp and Mpro enzymes of SARS-CoV-2 virus by structural homology

TCOVID-19 has enormously impacted global public health due to the high infection and mortality rates associated with the SARS-CoV-2 virus-causing disease. The World Health Organization (WHO) approved 10 safe and effective vaccines. However, there are still significant limitations to their administration in developing countries and remote locations. Concerns remain about the emergence of virus variants that may evade immunity acquired through vaccination. In addition to preventing infection, effective therapeutic agents are needed to treat patients diagnosed with COVID-19. Under this context, the present study aimed to perform a structure-based virtual screening of the protease (Mpro) and RNA-dependent RNA polymerase (RdRp) enzymes of SARS-CoV-2. For this purpose, homologous protein inhibitors belonging to different viruses were tested. Multiple sequence alignment of these enzymes allowed us to recognize the high conservation of these enzymes between species, especially of the regions comprising the inhibitor binding sites. Therefore, it follows that it is possible to employ a redirection approach to inhibitors that were designed to treat other viral diseases. Molecular docking experiments identified that RTP inhibitors (binding affinity = -7.3 kcal/mol) and V3D (binding affinity = -8.0 kcal/mol) are excellent inhibitors of RdRp and Mpro, respectively. These results suggest that these molecules can virtually bind and inhibit the activity of RdRp and Mpro and thus constitute potential drugs to combat SARS-CoV-2. © 2022 by the authors.

Revealing the structural and molecular interaction landscape of the favipiravir-RTP and SARS-CoV-2 RdRp complex through integrative bioinformatics: Insights for developing potent drugs targeting SARS-CoV-2 and other viruses.

BACKGROUND: The global research community has made considerable progress in therapeutic and vaccine research during the COVID-19 pandemic. Several therapeutics have been repurposed for the treatment of COVID-19. One such compound is, favipiravir, which was approved for the treatment of influenza viruses, including drug-resistant influenza. Despite the limited information on its molecular activity, clinical trials have attempted to determine the effectiveness of favipiravir in patients with mild to moderate COVID-19. Here, we report the structural and molecular interaction landscape of the macromolecular complex of favipiravir-RTP and SARS-CoV-2 RdRp with the RNA chain. METHODS: Integrative bioinformatics was used to reveal the structural and molecular interaction landscapes of two macromolecular complexes retrieved from RCSB PDB. RESULTS: We analyzed the interactive residues, H-bonds, and interaction interfaces to evaluate the structural and molecular interaction landscapes of the two macromolecular complexes. We found seven and six H-bonds in the first and second interaction landscapes, respectively. The maximum bond length is 3.79 Å. In the hydrophobic interactions, five residues (Asp618, Asp760, Thr687, Asp623, and Val557) were associated with the first complex and two residues (Lys73 and Tyr217) were associated with the second complex. The mobilities, collective motion, and B-factor of the two macromolecular complexes were analyzed. Finally, we developed different models, including trees, clusters, and heat maps of antiviral molecules, to evaluate the therapeutic status of favipiravir as an antiviral drug. CONCLUSIONS: The results revealed the structural and molecular interaction landscape of the binding mode of favipiravir with the nsp7-nsp8-nsp12-RNA SARS-CoV-2 RdRp complex. Our findings can help future researchers in understanding the mechanism underlying viral action and guide the design of nucleotide analogs that mimic favipiravir and exhibit greater potency as antiviral drugs against SARS-CoV-2 and other infectious viruses. Thus, our work can help in preparing for future epidemics and pandemics.

In Vitro and In Vivo Therapeutic Potential of 6,6'-Dihydroxythiobinupharidine (DTBN) from Nuphar lutea on Cells and K18-hACE2 Mice Infected with SARS-CoV-2.

We have previously published research on the anti-viral properties of an alkaloid mixture extracted from Nuphar lutea, the major components of the partially purified mixture found by NMR analysis. These are mostly dimeric sesquiterpene thioalkaloids called thiobinupharidines and thiobinuphlutidines against the negative strand RNA measles virus (MV). We have previously reported that this extract inhibits the MV as well as its ability to downregulate several MV proteins in persistently MV-infected cells, especially the P (phospho)-protein. Based on our observation that the Nuphar extract is effective in vitro against the MV, and the immediate need that the coronavirus disease 2019 (COVID-19) pandemic created, we tested here the ability of 6,6'-dihydroxythiobinupharidine DTBN, an active small molecule, isolated from the Nuphar lutea extract, on COVID-19. As shown here, DTBN effectively inhibits SARS-CoV-2 production in Vero E6 cells at non-cytotoxic concentrations. The short-term daily administration of DTBN to infected mice delayed the occurrence of severe clinical outcomes, lowered virus levels in the lungs and improved survival with minimal changes in lung histology. The viral load on lungs was significantly reduced in the treated mice. DTBN is a pleiotropic small molecule with multiple targets. Its anti-inflammatory properties affect a variety of pathogens including SARS-CoV-2 as shown here. Its activity appears to target both pathogen specific (as suggested by docking analysis) as well as cellular proteins, such as NF-κB, PKCs, cathepsins and topoisomerase 2, that we have previously identified in our work. Thus, this combined double action of virus inhibition and anti-inflammatory activity may enhance the overall effectivity of DTBN. The promising results from this proof-of-concept in vitro and in vivo preclinical study should encourage future studies to optimize the use of DTBN and/or its molecular derivatives against this and other related viruses.

Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2.

Mutations drive viral evolution and genome variability that causes viruses to escape host immunity and to develop drug resistance. SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein. We consider the effects of mutations in some of the epitope region including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. We observe that the mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, we study the conformational stability of the epitope region and epitope:paratope interface under the mutation from the fluctuations in the dihedral angles. We observe that the mutation renders the epitope and the epitope:paratope interface unstable compared to the corresponding wild type ones. Thus, the mutations may help in escaping antibody mediated immunity of the hostCommunicated by Ramaswamy H. Sarma.

Comparison of the Old and New - Novel Mechanisms of Action for Anti-coronavirus Nucleoside Analogues

Over the past two and a half years the world has seen a desperate scramble to find a treatment for SARS-CoV-2 and COVID. In that regard, nucleosides have long served as the cornerstone to antiviral treatments due to their resemblance to the naturally occurring nucleosides that are involved in numerous biological processes. Unlike other viruses however, it was found early on during the search for drugs to treat SARS-1 and later MERS, that the coronaviruses possess a unique repair enzyme, an exonuclease (ExoN)[3] which rendered nucleoside analogues useless, thus negating their use.[4] During the current outbreak however, as both well-known and new nucleoside analogues were investigated or reinvestigated as a possible cure for SARS-CoV-2, several novel and/or lesser-known mechanisms of action were uncovered. This review briefly describes these mechanisms.

Dual computational and biological assessment of some promising nucleoside analogs against the COVID-19-Omicron variant.

Nucleoside analogs/derivatives (NAs/NDs) with potent antiviral activities are now deemed very convenient choices for the treatment of coronavirus disease 2019 (COVID-19) arisen by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. At the same time, the appearance of a new strain of SARS-CoV-2, the Omicron variant, necessitates multiplied efforts in fighting COVID-19. Counteracting the crucial SARS-CoV-2 enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) jointly altogether using the same inhibitor is a quite successful new plan to demultiplicate SARS-CoV-2 particles and eliminate COVID-19 whatever the SARS-CoV-2 subtype is (due to the significant conservation nature of RdRps and ExoNs in the different SARS-CoV-2 strains). Successive in silico screening of known NAs finally disclosed six different promising NAs, which are riboprine/forodesine/tecadenoson/nelarabine/vidarabine/maribavir, respectively, that predictably can act through the planned dual-action mode. Further in vitro evaluations affirmed the anti-SARS-CoV-2/anti-COVID-19 potentials of these NAs, with riboprine and forodesine being at the top. The two NAs are able to effectively antagonize the replication of the new virulent SARS-CoV-2 strains with considerably minute in vitro anti-RdRp and anti-SARS-CoV-2 EC50 values of 189 and 408 nM for riboprine and 207 and 657 nM for forodesine, respectively, surpassing both remdesivir and the new anti-COVID-19 drug molnupiravir. Furthermore, the favorable structural characteristics of the two molecules qualify them for varied types of isosteric and analogistic chemical derivatization. In one word, the present important outcomes of this comprehensive dual study revealed the anticipating repurposing potentials of some known nucleosides, led by the two NAs riboprine and forodesine, to successfully discontinue the coronaviral-2 polymerase/exoribonuclease interactions with RNA nucleotides in the SARS-CoV-2 Omicron variant (BA.5 sublineage) and accordingly alleviate COVID-19 infections, motivating us to initiate the two drugs' diverse anti-COVID-19 pharmacological evaluations to add both of them betimes in the COVID-19 therapeutic protocols.

Electrochemiluminescence resonance energy transfer biosensing platform between g-C3N4 nanosheet and Ru-SiO2@FA for dual-wavelength ratiometric detection of SARS-CoV-2 RdRp gene.

Rational detection of syndrome coronavirus 2 (SARS-CoV-2) is crucial to prevention, control, and treatment of disease. Herein, a dual-wavelength ratiometric electrochemiluminescence (ECL) biosensor based on resonance energy transfer (RET) between g-C3N4 nanosheets and Ru-SiO2@folic acid (FA) nanomaterials was designed to realize ultrasensitive detection of SARS-CoV-2 virus (RdRp gene). Firstly, the unique g-C3N4 nanosheets displayed very intense and stable ECL at 460 nm, then the triple helix DNA was stably and vertically bound to g-C3N4 on electrode by high binding affinity between ssDNA and g-C3N4. Meanwhile, trace amounts of target genes were converted to a large number of output by three-dimensional (3D) DNA walker multiple amplification, and the output bridged a multifunctional probe Ru-SiO2@FA to electrode. Ru-SiO2@FA not only showed high ECL at 620 nm, but also effectively quenched g-C3N4 ECL. As a result, ECL decreased at 460 nm and increased at 620 nm, which was used to design a rational ECL biosensor for detection of SARS gene. The results show that the biosensor has excellent detection sensitivity for RdRp gene with a dynamic detection range of 1 fM to 10 nM and a limit of detection (LOD) of 0.18 fM. The dual-wavelength ratio ECL biosensor has inestimable value and application prospects in the fields of biosensing and clinical diagnosis.

Therapeutic Targets in the Virological Mechanism and in the Hyperinflammatory Response of Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2)

This work is a bibliographic review. The search for the necessary information was carried out in the months of November 2022 and January 2023. The databases used were as follows: Pubmed, Academic Google, Scielo, Scopus, and Cochrane library. Results: In total, 101 articles were selected after a review of 486 articles from databases and after applying the inclusion and exclusion criteria. The update on the molecular mechanism of human coronavirus (HCoV) infection was reviewed, describing possible therapeutic targets in the viral response phase. There are different strategies to prevent or hinder the introduction of the viral particle, as well as the replicative mechanism ((protease inhibitors and RNA-dependent RNA polymerase (RdRp)). The second phase of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) involves the activation of hyperinflammatory cascades of the host's immune system. It is concluded that there are potential therapeutic targets and drugs under study in different proinflammatory pathways such as hydroxychloroquine, JAK inhibitors, interleukin 1 and 6 inhibitors, and interferons. © 2023 by the authors.

Teriflunomide and COVID-19: A Friend or Foe?!

Unfortunately, the coronavirus disease 2019 (COVID-19) pandemic has become an irritating universal crisis. Thus, the discovery/identification of prospective drug candidates to disband the branched health issues caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has become urgent. This current research sheds light on the repositioning possibility of the potent antirheumatic drug teriflunomide to act as an efficient anti-SARS-CoV-2/anti-COVID-19 remedy. Herein, a motivating in silico molecular docking/modeling study of teriflunomide explores its potential inhibitory actions on the novel coronaviral-2 RNA-dependent RNA polymerase (nCoV-RdRp) enzyme/protein was reported. Interestingly, the computational analysis of the teriflunomide superior inhibitory binding mode in the binding cavity of one of the active sites of the nCoV-RdRp detected that teriflunomide molecule shows considerably stronger inhibitory binding interactions and better inhibitory binding affinities (it shows lower binding energies which reached-9.70 kcal/mol) than both used references. It was reported that teriflunomide potently impairs viral replication/reproduction by employing two distinct action mechanisms. Thus, the existing study's findings surprisingly uphold teriflunomide's double mode of action. In conclusion, the presented research work paves the way to biologically and clinically begin exploring the promising properties of teriflunomide to strongly hit the SARS-CoV-2 particles of the different strains and inhibit their pathogenic replication in an integrative triple mode of action. Hopingly, the potential sextet COVID-19 attacker teriflunomide can be rapidly subjected to the various in vitro/in vivo/clinical anti-COVID-19 assays/trials in a serious attempt to assess its comprehensive bioactivities against COVID-19 to be effectively used in SARS-CoV-2 infections therapy soon. © 2022 by the authors.

Molecular Docking and Dynamics of Phytochemicals From Chinese Herbs With SARS-CoV-2 RdRp

The novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is causing coronavirus disease 2019 (COVID-19) pandemic. Ancient Chinese herbal formulas are effective for diseases caused by viral infection, and their effects on COVID-19 are currently being examined. To directly evaluate the role of Chinese herbs in inhibiting replication of SARS-CoV-2, we investigated how the phytochemicals from Chinese herbs interact with the viral RNA-dependent RNA polymerase (RdRP). Total 1025 compounds were screened, and then 181compounds were selected for molecular docking analysis. Four phytochemicals licorice glycoside E, diisooctyl phthalate, (-)-medicocarpin, and glycyroside showed good binding affinity with RdRp. The best complex licorice glycoside E/RdRp forms 3 hydrogen bonds, 4 hydrophobic interactions, 1 pair of Pi-cation/stacking, and 4 salt bridges. Furthermore, docking complexes licorice glycoside E/RdRp and diisooctyl phthalate/RdRp were optimized by molecular dynamics simulation to obtain the stable conformation. These studies indicate that they are promising as antivirals against SARS-CoV-2.Copyright © The Author(s) 2022.

Template Entrance Channel as Possible Allosteric Inhibition and Resistance Site for Quinolines Tricyclic Derivatives in RNA Dependent RNA Polymerase of Bovine Viral Diarrhea Virus.

The development of potent non-nucleoside inhibitors (NNIs) could be an alternate strategy to combating infectious bovine viral diarrhea virus (BVDV), other than the traditional vaccination. RNA-dependent RNA polymerase (RdRp) is an essential enzyme for viral replication; therefore, it is one of the primary targets for countermeasures against infectious diseases. The reported NNIs, belonging to the classes of quinolines (2h: imidazo[4,5-g]quinolines and 5m: pyrido[2,3-g] quinoxalines), displayed activity in cell-based and enzyme-based assays. Nevertheless, the RdRp binding site and microscopic mechanistic action are still elusive, and can be explored at a molecular level. Here, we employed a varied computational arsenal, including conventional and accelerated methods, to identify quinoline compounds' most likely binding sites. Our study revealed A392 and I261 as the mutations that can render RdRp resistant against quinoline compounds. In particular, for ligand 2h, mutation of A392E is the most probable mutation. The loop L1 and linker of the fingertip is recognized as a pivotal structural determinant for the stability and escape of quinoline compounds. Overall, this work demonstrates that the quinoline inhibitors bind at the template entrance channel, which is governed by conformational dynamics of interactions with loops and linker residues, and reveals structural and mechanistic insights into inhibition phenomena, for the discovery of improved antivirals.

SARS-CoV-2: Molecular Biology and Therapeutic Targets

A century after the outbreak of the Spanish flu, the world is suffering from another pandemic because of the coronavirus. The virus took a toll on more than millions of lives worldwide and continues to affect the health and socio-economic infrastructure all over the world. This study explores the epidemiology, etiology, and transmission of the virus and its phylogenetic relationship with SARS and MERS coronavirus responsible for the 2002 and 2012 viral outbreak. Furthermore, this review highlights the key features of the viral genome and essential viral proteins responsible for the viral life cycle, evading host immune response, and viral immunopathology with therapeutics from "Recovery" and "Solidarity" trials. The review culminates with a discussion on different classes of prominent vaccines and their efficacy. An overall understanding of essential viral proteins and their role in pathogenesis, repurposed drugs, and vaccine development is the rationale of the present review.Copyright © 2021 Bentham Science Publishers.

Feasibility of targeted antiviral therapy for acute respiratory viral infections in the COVID-19 pandemic.

The aim of this study was to analyze the efficacy and safety of using etiotropic therapy with favipiravir and molnupiravir that can selectively bind and inhibit not only SARS-CoV-2 proteins but also other RNA-containing pathogens of acute respiratory diseases. High transmission of pathogens, the risk of becoming chronic, frequent complications, cases of co-infection with several pathogens, which can lead to a more severe course of the disease, insufficient vaccination effectiveness, all this requires additional strategies for both prevention and treatment of acute respiratory viral infections. RNA-dependent RNA polymerase (RdRp), which has no equivalent in human cells, is involved in RNA synthesis and is an excellent therapeutic target for diseases caused by RNA viruses, including SARS-CoV-2. The long process of drug development and the "reuse" of drugs approved for other indications or successfully tested in terms of safety and tolerability pose the challenge of rapid establishment of an effective drug, including for the treatment of severe cases of COVID-19.Copyright © 2022, Dynasty Publishing House.

Rna-Dependent Rna Polymerase (Rdrp) Inhibitor Drugs against Sars-Cov-2: A Molecular Docking Study

Objective: SARS-CoV-2 associated viral pandemic was first reported in Wuhan, China, in December 2019. Due to the rapid increase in its pathogenicity, SARS-CoV-2 was declared a global pandemic by WHO on March 11, 2020. For that reason, determining the most attractive viral protein targets became a must. One of the most important target proteins is SARS-COV-2 RNA-dependent RNA polymerase (RdRp) on which COVID-19 depends in its replication process. This study aimed to examine the possible interactions between RdRp and the most promising RdRp nucleoside inhibitors especially Purine nucleoside analogs, to detect the most important residues that commonly interact with RdRp's inhibitors and to investigate whether if there any mutations have been observed so far in these residues or not. Material(s) and Method(s): Molecular docking studies were carried out using AutoDock Vina between SARS-CoV-2 RdRp and drugs approved against different viral RdRps (Galidesivir, Remdesivir, Ribavirin, Sofosbuvir, and Favipiravir) as well as physiological nucleotides (ATP and GTP). Based on the obtained results, a detailed surface-interaction analysis was also performed using Pymol and Discovery Studio Visualizer software for the models that exhibited the most suitable location and configuration in space. Result and Discussion: All the tested molecules were able to bind to SARS-CoV-2 RdRp successfully. Also, they all commonly interact with 9 different amino acids (Arg553, Arg555, Asp618, Asp623, Ser682, Asn691, Ser759, Asp760, and Asp761), and 3 different Template-primer RNA nucleotides (U10, A11, and U20) causing inhibition of viral RdRp via non obligate RNA chain termination.Copyright © 2022 University of Ankara. All rights reserved.

Diagnosing COVID-19: diagnostic importance of detecting E gene of the SARS-CoV-2 genome

Aim: To evaluate the significance of E gene analysis in addition to N and RdRp genes of SARS-CoV-2, and to compare the specificity and sensitivity of targets. Material(s) and Method(s): We used two reverse transcription-PCR assays: one targeting N, E and RdRp and the other targeting N and RdRp genes and analyzed variation in threshold cycle (Ct) values. Result(s): Of the 155 samples, 70.32% tested positive: all three genes were detected in 45.87%, N and RdRp in 19.27% and only N in 34.86%. Patients negative for the E gene were tested after symptoms disappeared and Ct values were significantly higher. Conclusion(s): Samples negative for the E gene were potentially false positive and clinical conditions should be assessed while interpreting results.Copyright © 2023 Future Medicine Ltd.

In Silico Analysis of 14-Deoxy 11, 12-Didehydro Andrographolide (AGP 2) From Sambiloto (Andrographis paniculata) As Drug Candidate Against SARS-CoV-2

The outbreak of the COVID-19 pandemic in the world has urged researchers to develop a vaccine or therapeutic drugs to fight this virus. This study aimed to assay 14 deoxy-11,12-didehydroandrographolide (AGP 2) ability as an inhibitor of 3-chymotrypsin like-protease (3CLPro), Papain-like protease (PLPro), and RNA-dependent RNA-polymerase (RdRp), the viral proteins of SARS-CoV-2 and to evaluate it safeness as a drug candidate. In-silico technique was performed in this study to analyze the binding interaction, complex stability between protein and ligand, and drug-likeness properties. The proteins and ligands were obtained from Protein Data Bank (PDB) and PubChem web tools, then using PyRx to identify the binding affinity score, PyMoL to visualize the 3D binding interaction, and WebGro web tools to analyze the stability of each complex. A drug-likeness evaluation was done using SwissADME, pkCSM, and Way2drug web tools. The result of this study showed that the binding affinity score for each complex is;AGP 2-3CLPro (-6.7 kcal/mol), AGP 2-PLPro (-6.4 kcal/mol), and AGP 2-RdRp (-7.0 kcal/mol) where the AGP 2-RdRp and AGP 2-3CLPro showed a stable form indicating the inhibitor ability of AGP 2. This study also demonstrates that the drug-likeness properties of AGP 2 are safe to use. Additionally, it has been proved that AGP 2 can be developed into a therapeutic drug with further studies. © 2023, Bogor Agricultural University. All rights reserved.