Molecular Epidemiology of SARS-CoV-2 Omicron Sub-Lineages Isolated from Turkish Patients Infected with COVID-19.

Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford University Coronavirus Antiviral & Resistance Database online tool was used for variant analyses of the strains uploaded to GISAID as Omicron (n = 20.959) between January 2021 and February,2023. Out of 288 different Omicron subvariants, B.1, BA.1, BA.2, BA.4, BE.1, BF.1, BM.1, BN.1, BQ.1, CK.1, CL.1, and XBB.1 were the main determined subvariants, and BA.1 (34.7%), BA.2 (30.8%), and BA.5 (23.6%) were reported most frequently. RdRp and 3CLPro-related resistance mutations were determined in n = 150, 0.72% sequences, while the rates of resistance against RdRp and 3CLpro inhibitors were reported at 0.1% and 0.6%, respectively. Mutations that were previously associated with a reduced susceptibility to remdesivir, nirmatrelvir/r, and ensitrelvir were most frequently detected in BA.2 (51.3%). The mutations detected at the highest rate were A449A/D/G/V (10.5%), T21I (10%), and L50L/F/I/V (6%). Our findings suggest that continuous monitoring of variants, due to the diversity of Omicron lineages, is necessary for global risk assessment. Although drug-resistant mutations do not pose a threat, the tracking of drug mutations will be necessary due to variant heterogenicity.

A New Cellular Interactome of SARS-CoV-2 Nucleocapsid Protein and Its Biological Implications.

There is still much to uncover regarding the molecular details of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. As the most abundant protein, coronavirus nucleocapsid (N) protein encapsidates viral RNAs, serving as the structural component of ribonucleoprotein and virion, and participates in transcription, replication, and host regulations. Virus-host interaction might give clues to better understand how the virus affects or is affected by its host during infection and identify promising therapeutic candidates. Considering the critical roles of N, we here established a new cellular interactome of SARS-CoV-2 N by using a high-specific affinity purification (S-pulldown) assay coupled with quantitative mass spectrometry and immunoblotting validations, uncovering many N-interacting host proteins unreported previously. Bioinformatics analysis revealed that these host factors are mainly involved in translation regulations, viral transcription, RNA processes, stress responses, protein folding and modification, and inflammatory/immune signaling pathways, in line with the supposed actions of N in viral infection. Existing pharmacological cellular targets and the directing drugs were then mined, generating a drug-host protein network. Accordingly, we experimentally identified several small-molecule compounds as novel inhibitors against SARS-CoV-2 replication. Furthermore, a newly identified host factor, DDX1, was verified to interact and colocalize with N mainly by binding to the N-terminal domain of the viral protein. Importantly, loss/gain/reconstitution-of-function experiments showed that DDX1 acts as a potent anti-SARS-CoV-2 host factor, inhibiting the viral replication and protein expression. The N-targeting and anti-SARS-CoV-2 abilities of DDX1 are consistently independent of its ATPase/helicase activity. Further mechanism studies revealed that DDX1 impedes multiple activities of N, including the N-N interaction, N oligomerization, and N-viral RNA binding, thus likely inhibiting viral propagation. These data provide new clues to better depiction of the N-cell interactions and SARS-CoV-2 infection and may help inform the development of new therapeutic candidates.

Impact of the COVID-19 pandemic on antiviral drug development for other community-acquired respiratory viruses' infections.

The coronavirus disease 2019 (COVID-19) pandemic indirectly resulted in missed therapeutic opportunities for many diseases. Here we focus on community-acquired respiratory viruses other than severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) [respiratory syncytial virus, parainfluenza and influenza A], and highlight the pandemics impact on clinical trials to develop novel therapies for other severe respiratory viral infections. We retrospectively reviewed inclusion rates within respiratory antiviral clinical trials in comparison with all other clinical trials in our clinical investigations center, before and during the COVID-19 pandemic. As opposed to the remaining clinical trials developed within our unit, respiratory antiviral trials inclusion rates did not recover after the initial recruitment decrease observed across all trials during the first pandemic wave. These results were discussed in the context of non-COVID-19 respiratory viral infection rates within our center, showing a general decline in seasonal respiratory viruses spread since the COVID-19 pandemic onset. Virus epidemiology changes upon the wide SARS-CoV-2 expansion as well as the lifestyle changes globally adopted to prevent SARS-CoV-2 transmission could have therefore contributed to the negative impact of the COVID-19 pandemic on antiviral drug development. Our study highlights the peculiarity of respiratory antiviral drug development during the COVID-19 pandemic era and describes potential explanations for such drug development halting.

Small molecule antiviral compound collection (SMACC): A comprehensive, highly curated database to support the discovery of broad-spectrum antiviral drug molecules.

Diseases caused by new viruses cost thousands if not millions of human lives and trillions of dollars. We have identified, collected, curated, and integrated all chemogenomics data from ChEMBL for 13 emerging viruses that hold the greatest potential threat to global human health. By identifying and solving several challenges related to data annotation accuracy, we developed a highly curated and thoroughly annotated database of compounds tested in both phenotypic and target-based assays for these viruses that we dubbed SMACC (Small Molecule Antiviral Compound Collection). The pilot version of the SMACC database contains over 32,500 entries for 13 viruses. By analyzing data in SMACC, we have identified ∼50 compounds with polyviral inhibition profile, mostly covering flavi- and coronaviruses. The SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel BSA agents in preparation for future viral outbreaks. SMACC is publicly available at https://smacc.mml.unc.edu.

Curcumin as a potential multiple-target inhibitor against SARS-CoV-2 Infection: A detailed interaction study using quantum chemical calculations

Curcumin is one of the important naturally occurring compounds having several medicinal properties such as: antiviral, antioxidant, antifibrotic, antineoplastic as well as anti-inflammatory. SARS-CoV-2 has emerged as inf-ectious virus, which severely infected a large number of people all over the world. Many efforts have been made to prepare novel antiviral compound, but it is still challenging. Naturally occurring compound, curcumin, can be used as an alternative to antiviral compound against SARS-CoV-2. Its effect against SARS-CoV-2 is already highlighted in the literature. But the quantitative study of its interaction with various precursors of SARS-CoV-2 is not reported till date. This paper reports the interaction of curcumin with angiotensin-convert-ing enzyme2, transmembrane serine protease 2, 3-chymotrypsin-like protease and papain-like protease through molecular docking and quantum chemistry calculations to achieve quantitative understanding of underlying interactions. Here the conformational flexibility of curcumin is also highlighted, which helps it to accommodate in the four different docking sites. The study has been performed using calculations of geometrical parameter, atomic charge, electron density, Laplacian of electron density, dipole moment and the energy gap between highest occupied and lowest unoccupied molecular orbitals. The non--covalentinteraction (NCI) analysis is performed to visualize the weak inter-action present in the active sites. Combinedly molecular docking and detailed quantum chemistry calculations revealed that curcumin can be adopted as a potential multiple-target inhibitor against SARS-CoV-2.

Hypothesis of a potential antiviral drug

The approval of mRNA vaccine technique against COVID-19 opens a door to research and the creation of new drugs against different infectious pathologies or even cancer, since for several diseases the therapeutic options are limited, and different viral diseases are treated only symptomatically. For these reasons, this study proposed a hypothesis supported by biological studies, that it provides a theoretical basis for the possible development of a drug that used the mRNA technique and the ribonucleolytic action of a ribonuclease for a possible antiviral therapy, and analyzed a future perspective of this technique in order to provide a bibliographic basis on this hypothesis and motivate researchers to carry out biological studies on this topic.Copyright © 2022, Health Biotechnology and Biopharma. All rights reserved.

A Comparison of Etiology, Pathogenesis, Vaccinal and Antiviral Drug Development between Influenza and COVID-19.

Influenza virus and coronavirus, two kinds of pathogens that exist widely in nature, are common emerging pathogens that cause respiratory tract infections in humans. In December 2019, a novel coronavirus SARS-CoV-2 emerged, causing a severe respiratory infection named COVID-19 in humans, and raising a global pandemic which has persisted in the world for almost three years. Influenza virus, a seasonally circulating respiratory pathogen, has caused four global pandemics in humans since 1918 by the emergence of novel variants. Studies have shown that there are certain similarities in transmission mode and pathogenesis between influenza and COVID-19, and vaccination and antiviral drugs are considered to have positive roles as well as several limitations in the prevention and control of both diseases. Comparative understandings would be helpful to the prevention and control of these diseases. Here, we review the study progress in the etiology, pathogenesis, vaccine and antiviral drug development for the two diseases.

Octyl gallate targeting the 3C-like protease exhibits highly efficient antiviral activity against swine enteric coronavirus PEDV.

Infection with porcine epidemic diarrhea virus (PEDV) causes severe watery diarrhea in newborn piglets, leading to substantial financial losses for the swine industry. In this study, we screened small molecule drugs targeting 3 C-like protease (3CLpro) by molecular docking, and further evaluated the antiviral activity of the screened drugs against PEDV. Results showed that octyl gallate (OG), a widely used food additive, exhibited strong binding affinity with the 3CLpro active sites of PEDV. Bio-layer interferometry and fluorescence resonance energy transfer revealed that OG directly interacts with PEDV 3CLpro (KD = 549 nM) and inhibits 3CLpro activity (IC50 = 22.15 µM). OG showed a strong inhibition of PEDV replication in vitro. Virus titers were decreased by 0.58 and 0.71 log10 TCID50/mL for the CV777 and HM2017 strains, respectively. In vivo, all piglets in the PEDV-infected group died at 48 h post-infection (hpi), while 75% of piglets in the OG treatment group showed significant relief from the clinical symptoms, pathological damage, and viral loads in the jejunum and ileum. Moreover, the western blotting results showed that OG also has strong antiviral activity against other swine enteric coronaviruses, including transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and swine acute diarrhea syndrome coronavirus (SADS-CoV). Our findings revealed that OG could be developed as a novel antiviral drug against PEDV. The OG exhibited a potential broad-spectrum antiviral drug for control of other swine enteric coronaviruses.

Comparative Study of Molecular Docking, Structural, Electronic, and Fukui Function Studies on Favipiravir and its Newly Designed Derivatives (Potential Inhibitors) for COVID-19 Protease

Favipiravir is an antiviral medication currently being trialed as a COVID-19 treatment. These results motivate us to develop new species (possibly drugs) from favipiravir, perform comparative molecular docking, and reexamine their biological and pharmacological activities. Detailed quantum chemical research on favipiravir and its newly designed derivatives has been carried out with the help of DFT/B3LYP/6–311 + + G (d, p). In the present work, the structure of favipiravir has been modified and 12 new species have been modeled (all species are inherently stable because no virtual frequency is found during the vibration analysis). Reactivity of all species using various descriptors (local) such as Fukui function, local softness, electrophilicity, and global, i.e., electronegativity, hardness, HOMO–LUMO gap, etc. of the same are calculated and discussed. In silico studies such as molecular docking of all species and complete quantum chemistry studies suggest that four of them may mitigate the effects of the COVID-19 protease. © 2023 Wiley-VCH GmbH.

Drug therapy in hospitalized patients with very severe symptoms following COVID-19

Implication for health policy/practice/research/medical education: To treat COVID-19, the first choice should be antiviral drugs and sometimes a small dose of anti-inflammatory drugs to reduce inflammation. In this regard, chloroquine has both features including antiviral activity and anti-inflammatory effect.Copyright © 2020 The Author(s);.

A Novel Oral Antiviral Drug for COVID-19. Can It Make a Difference?

Countries across the world are striving to vaccinate their citizens against the virus that brings about COVID-19. Not only developed countries but also developing ones have had success in vaccinating a huge number of people. Advance and improved treatments are still required to reduce hospitalizations and deaths. They also aid in the prevention of virus propagation. It is important to recognize that, despite being vaccinated, there is still a need for alternative and more effective COVID treatment options. In the quest to create a solution for battling COVID-19, antiviral medicine was developed. The good thing about this solution is that it can be taken orally rather than intravenously which can be provided outside of a hospital setting before COVID-19 has progressed to a critical level. © 2023, Army Medical College. All Rights Reserved.

Vertex metric resolvability of COVID antiviral drug structures

In November of 2019 year, there was the first case of COVID-19 (Coronavirus) recorded, and up to 3rd of April of 2020, 1,116,643 confirmed positive cases, and around 59,158 dying were recorded. Novel antiviral structures of the 2019 pandemic disease Coronavirus are discussed in terms of the metric basis of their molecular graph. These structures are named arbidol, chloroquine, hydroxy-chloroquine, thalidomide, and theaflavin. Metric dimension or metric basis is a concept in which the whole vertex set of a structure is uniquely identified with a chosen subset named as resolving set. Moreover, the fault-tolerant concept of those structures is also included in this study. By this concept of vertex-metric resolvability of COVID antiviral drug structures are uniquely identified and help to study the structural properties of the structure. © 2023 - IOS Press. All rights reserved.

Smart Organic-Inorganic Polyoxomolybdates in Forward Osmosis for Antiviral-Drug Wastewater Treatment and Drug Reclamation.

The demand to effectively treat medical wastewater has escalated with the much greater use of antiviral drugs since the COVID-19 pandemic. Forward osmosis (FO) has great potential in wastewater treatment only when appropriate draw solutes are available. Here, we synthesize a series of smart organic-inorganic polyoxomolybdates (POMs), namely, (NH4)6[Mo7O24], (PrNH3)6[Mo7O24], (iPrNH3)6[Mo7O24], and (BuNH3)6[Mo7O24], for FO to treat antiviral-drug wastewater. Influential factors of separation performance have been systematically studied by tailoring the structure, organic characteristics, and cation chain length of POMs. POMs at 0.4 M produce water fluxes ranging from 14.0 to 16.4 LMH with negligible solute losses, at least 116% higher than those of NaCl, NH4HCO3, and other draw solutes. (NH4)6[Mo7O24] creates a water flux of 11.2 LMH, increased by more than 200% compared to that of NaCl and NH4HCO3 in long-term antiviral-drug wastewater reclamation. Remarkably, the drugs treated with NH4HCO3 and NaCl are either contaminated or denatured, while those with (NH4)6[Mo7O24] remain intact. Moreover, these POMs are recovered by sunlight-assisted acidification owing to their light and pH dual sensitivity and reusability for FO. POMs prove their suitability as draw solutes and demonstrate their superiority over the commonly studied draw solutes in wastewater treatment.

Risk of Underlying Diseases and Effectiveness of Drugs on COVID-19 Inpatients Assessed Using Medical Claims in Japan: Retrospective Observational Study.

Background: Results of earlier studies have demonstrated underlying diseases such as cancer, diabetes mellitus, immunodeficiency, hypertension and heart failure to be risk factors for severe outcomes and mortality. Furthermore, clinical trials have shown that drugs such as antiviral drugs, antibody cocktails, steroids and anti-inflammatory drugs can be expected to prevent severe COVID-19 outcomes and death. Methods: This study, using inpatient records from the Medical Information Analysis Databank covering national hospital organizations in Japan, was conducted to evaluate the effects of underlying diseases and/or administered drugs on mortality. Subjects were all inpatients receiving oxygen administration and inpatients using respiratory ventilators, categorized by three age classes: all ages, patients 65 years old or older, and patients younger than 65 years old. We used logistic regression to analyze outcomes for underlying diseases, administered drugs, age, sex, the proportion of the mutated strains, and vaccine coverage. Results: Patients with hypertension, except for younger inpatients, have a lower risk of mortality (estimated coefficient 0.67 among all inpatients (p < 0.01): 0.77 among inpatients with oxygen therapy (p = 0.02) and 0.57 among inpatients with respiratory ventilation w (p = 0.01)). Except for younger inpatients, antibody cocktail (casirivimab/imdevimab or sotrovimab) administration was associated with a higher probability of survival (estimated coefficient 0.27 among all inpatients (p < 0.01)). It raised the survival probability consistently, although other drugs might have reduced the probability of survival. Conclusion: These findings suggest that antiviral drugs (remdesivir, estimated coefficient 1.44 (p < 0.01)), steroids (dexamethasone, estimated coefficient 1.85 (p < 0.01)), and anti-inflammatory drugs (baricitinib, estimated coefficient 1.62 (p < 0.01), and tocilizumab, estimated coefficient 2.73 (p < 0.01)) might not contribute to survival. These results have not been reported from earlier studies. More sophisticated estimation procedures, such as treatment effect models, are necessary to obtain conclusive results.

Repurposing of approved drug molecules for viral infectious diseases: a molecular modelling approach.

The identification of new viral drugs has become a task of paramount significance due to the frequent occurrence of viral infections and especially during the current pandemic. Despite the recent advancements, the development of antiviral drugs has not made parallel progress. Reduction of time frame and cost of the drug development process is the major advantage of drug repurposing. Therefore, in this study, a drug repurposing strategy using molecular modelling techniques, i.e. biological activity prediction, virtual screening, and molecular dynamics simulation was employed to find promising repurposing candidates for viral infectious diseases. The biological activities of non-redundant (4171) drug molecules were predicted using PASS analysis, and 1401 drug molecules were selected which showed antiviral activities in the analysis. These drug molecules were subjected to virtual screening against the selected non-structural viral proteins. A series of filters, i.e. top 10 drug molecules based on binding affinity, mean value of binding affinity, visual inspection of protein-drug complexes, and number of H-bond between protein and drug molecules were used to narrow down the drug molecules. Molecular dynamics simulation analysis was carried out to validate the intrinsic atomic interactions and binding conformations of protein-drug complexes. The binding free energies of drug molecules were assessed by employing MMPBSA analysis. Finally, nine drug molecules were prioritized, as promising repurposing candidates with the potential to inhibit the selected non-structural viral proteins.Communicated by Ramaswamy H. Sarma.

Aptamer-Mediated Antiviral Approaches for SARS-CoV-2.

2020 and 2021 were disastrous years across the world, with the emergence of the severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) virus as a pandemic, which continues to be a top global health issue. There are still many countries and regions struggling to fight coronavirus disease 2019 (COVID-19), and, with the emergence of the various variants of the virus, we are still far from considering this global pandemic over. In addition to having good diagnostic tools and a variety of vaccines with high efficacy, it is of utmost importance to develop effective antiviral drugs or therapies to battle COVID-19. Aptamers known as the next-generation targeting elements can offer promising opportunities in developing antiviral drugs against SARS-CoV-2. This is owing to their high specificity and affinity, making them ideal for targeting ligands and neutralizers to impede both, viral entry and replication or even further enhance the anti-infection effects in the infected host cells. Also, aptamers are extremely attractive as they can be rapidly synthesized and scalable with a lower production cost. This work provides in-depth discussions on the potential of aptamers in therapeutic applications, their mode of action, and current progress on the use of aptamer-based therapies against SARS-CoV-2 and other viruses. The article also discusses the limitations associated with aptamer-based SARS-CoV-2-antiviral therapy with several proposed ideas to resolve them. Lastly, theranostic applications of aptamer nanoformulated dendrimers against viral infections are discussed.

Remdesivir.

Remdesivir, marketed under the brand name Veklury, is an antiviral drug with a broad spectrum of activity. There were various countries where the use of Remdesivir for the treatment of COVID-19 was authorized during the pandemic. Remdesivir was first designed to treat hepatitis C, but it was later tested for Ebola virus sickness and Marburg virus infections. Remdesivir is a prodrug designed to facilitate the intracellular transport of GS-441524 monophosphate and its subsequent biotransformation into GS-441524 triphosphate, a ribonucleotide analogue inhibitor of viral RNA polymerase. The objective of this chapter is to provide a comprehensive review of Remdesivir (GS-5734), including its nomenclature, physiochemical properties, preparation methods, identification procedures, numerous qualitative and quantitative analytical techniques, ADME profiles, and pharmacological effects. In addition, the chapter provides a variety of chromatographic and spectroscopic techniques for separating brimonidine from other drugs in combination formulations.

Influenza antivirals and their role in pandemic preparedness.

Effective antivirals provide crucial benefits during the early phase of an influenza pandemic, when vaccines are still being developed and manufactured. Currently, two classes of viral protein-targeting drugs, neuraminidase inhibitors and polymerase inhibitors, are approved for influenza treatment and post-exposure prophylaxis. Resistance to both classes has been documented, highlighting the need to develop novel antiviral options that may include both viral and host-targeted inhibitors. Such efforts will form the basis of management of seasonal influenza infections and of strategic planning for future influenza pandemics. This review focuses on the two classes of approved antivirals, their drawbacks, and ongoing work to characterize novel agents or combination therapy approaches to address these shortcomings. The importance of these topics in the ongoing process of influenza pandemic planning is also discussed.

Assessment of influenza A (H1N1, H3N2) oseltamivir resistance during 2017-2019 in Iran.

Background and Objectives: Neuraminidase inhibitors (NAIs) as an imperative antiviral for influenza prophylaxis and treatment are being consumed worldwide. Increasing use of these antivirals might be associated with drug resistance. Regarding the significance of these variations, this study aimed to investigate the mutations occurring in the NA gene of influenza A viruses leading to oseltamivir resistance during 2017-2019 in Iran. Materials and Methods: In this cross-sectional study, 40 influenza A (H1N1, H3N2) strains, isolated in National Influenza Center (NIC) from patients with Severe Acute Respiratory Infection (SARI) during 2017-2019 were subjected to RT-PCR and sequencing of NA complete gene. The frequency of oseltamivir resistance and variation of NA amino acids in these strains were investigated. Results: No significant mutation conferring oseltamivir resistance was detected. However, NA antigenic sites in these strains depicted minor changes compared to the vaccine strains. Among H3N2 isolates, mutations at 329, 344, 346 and 385 and among H1N1 isolates mutations at 143 and 188 residues occurred in NA antigenic regions. Conclusion: Evaluation of NA gene sequences, showed no resistant viruses to oseltamivir. Given that the viruses in the present study were the last viruses circulating in Iran before COVID-19 pandemic, the results will be beneficial to have a worthy comparison with the strains circulating after the pandemic. Constant monitoring for the emergence of drug-resistant variants and antigenic changes are crucial for all countries.

Targeting an evolutionarily conserved "E-L-L" motif in spike protein to identify a small molecule fusion inhibitor against SARS-CoV-2.

As newer variants of SARS-CoV-2 continue to pose major threats to global human health and economy, identifying novel druggable antiviral targets is the key toward sustenance. Here, we identify an evolutionarily conserved "Ex3Lx6L" ("E-L-L") motif present within the HR2 domain of all human and nonhuman coronavirus spike (S) proteins that play a crucial role in stabilizing its postfusion six-helix bundle (6-HB) structure and thus, fusion-mediated viral entry. Mutations within this motif reduce the fusogenicity of the S protein without affecting its stability or membrane localization. We found that posaconazole, an FDA-approved drug, binds to this "E-L-L" motif and impedes the formation of 6-HB, thus effectively inhibiting SARS-CoV-2 infection in cells. While posaconazole exhibits high efficacy in blocking S protein-mediated viral entry, mutations within the "E-L-L" motif rendered the protein completely resistant to the drug, establishing its specificity toward this motif. Our data demonstrate that posaconazole restricts early stages of infection through specific inhibition of membrane fusion and viral genome release into the host cell and is equally effective toward all major variants of concerns of SARS-CoV-2, including Beta, Kappa, Delta, and Omicron. Together, we show that this conserved essential "E-L-L" motif is an ideal target for the development of prophylactic and therapeutic interventions against SARS-CoV-2.