Candidate drugs against SARS-CoV-2 and COVID-19

From a validated targeted method to a retrospective UHPLC-HRMS non-targeted analysis unveiling COVID-19-related contaminants in clams. Have we bias in marine model organisms for ecotoxicological studies?

This study explores a retrospective non-targeted analysis (NTA), based on Ultra High-Performance Liquid Chromatography coupled to High-Resolution Mass Spectrometry (UHPLC-HRMS), to assess hidden chemicals of emerging concern (CECs) in marine model organisms. Conventional ecotoxicological studies do not include evaluating the natural habitats of the collected organisms, missing the possibility of highlighting unexpected pollutants, and thus compromising the correctness and reliability of the experimental results. In this paper we reprocessed samples previously collected from the Venice Lagoon for ecotoxicological studies and used for targeted analysis of three bisphenols-related compounds (i.e. BPS, BPF and BPAF) on seawater and specimens of the clam Ruditapes philippinarum. Results from the validation were the following: accuracy, expressed as percentage recoveries (R%), in the range 80% Collapse

Key Words

• COVID-19
• bioaccumulation
• clam
• emerging contaminants
• non-targeted analysis
• pharmaceuticals

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Affiliation(s)

Graziano Rilievo Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy
Samuele Boscolo Department of Chemical Sciences,University of Padova,Via Marzolo 1, 35131 Padova,Italy
Silvia Pettenuzzo Department of Chemical Sciences,University of Padova,Via Marzolo 1, 35131 Padova,Italy
Valerio Matozzo Department of Biology,University of Padova,Via Ugo Bassi 58/B, 35131 Padova,Italy
Jacopo Fabrello Department of Biology,University of Padova,Via Ugo Bassi 58/B, 35131 Padova,Italy
Marco Roverso Department of Chemical Sciences,University of Padova,Via Marzolo 1, 35131 Padova,Italy
Sara Bogialli Department of Chemical Sciences,University of Padova,Via Marzolo 1, 35131 Padova,Italy

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Quercetin and taxifolin inhibits TMPRSS2 activity and its interaction with EGFR in paclitaxel-resistant breast cancer cells: An in silico and in vitro study

Transmembrane protease/serine (TMPRSS2), a type II transmembrane serine protease, plays a crucial role in different stages of cancer. Recent studies have reported that the triggering epidermal growth factor receptor (EGFR) activation through protease action promotes metastasis. However, there are no reports on the interaction of TMPRSS2 with EGFR, especially in triple-negative triple negative (TNBC). The current study investigates the unexplored interaction between TMPRSS2 and EGFR, which are key partners mediating metastasis. This interaction is explored for potential targeting using quercetin (QUE) and taxifolin (TAX). TMPRSS2 expression patterns in breast cancer (BC) tissues and subtypes have been predicted, with the prognostic significance assessed using the GENT2.0 database. Validation of TMPRSS2 expression was performed in normal and TNBC tissues, including drug-resistant cell lines, utilizing GEO datasets. TMPRSS2 was further validated as a predictive biomarker for FDA-approved chemotherapeutics through transcriptomic data from BC patients. The study demonstrated the association of TMPRSS2 with EGFR through in silico analysis and validates the findings in TNBC cohorts using the TIMER2.0 web server and the TCGA dataset through C-Bioportal. Molecular docking and molecular dynamic simulation studies identified QUE and TAX as best leads targeting TMPRSS2. They inhibited cell-free TMPRSS2 activity like clinical inhibitor of TMPRSS2, Camostat mesylate. In cell-based assays focused on paclitaxel-resistant TNBC (TNBC/PR), QUE and TAX demonstrated potent inhibitory activity against extracellular and membrane-bound TMPRSS2, with low IC50 values. Furthermore, ELISA and cell-based AlphaLISA assays demonstrated that QUE and TAX inhibit the interaction of TMPRSS2 with EGFR. Additionally, QUE and TAX exhibited significant inhibition of proliferation and cell cycle accompanied by notable alterations in the morphology of TNBC/PR cells. This study provides valuable insights into potential of QUE and TAX targeting TMPRSS2 overexpressing TNBC.

The Role and Implications of COVID-19 in Incident and Prevalent Heart Failure

PURPOSE OF REVIEW

This review examines the pathophysiological interactions between COVID-19 and heart failure, highlighting the exacerbation of heart failure in COVID-19 patients. It focuses on the complex mechanisms driving worse outcomes in these patients.

RECENT FINDINGS

Patients with pre-existing heart failure experience more severe symptoms and higher mortality rates due to mechanisms such as cytokine storms, myocardial infarction, myocarditis, microvascular dysfunction, thrombosis, and stress cardiomyopathy. Elevated biomarkers like troponin and natriuretic peptides correlate with severe disease. Long-term cardiovascular risks for COVID-19 survivors include increased incidence of heart failure, non-ischemic cardiomyopathy, cardiac arrest, and cardiogenic shock. COVID-19 significantly impacts patients with pre-existing heart failure, leading to severe symptoms and higher mortality. Elevated cardiac biomarkers are indicators of severe disease. Acute and long-term cardiovascular complications are common, calling for ongoing research into targeted therapies and improved management strategies to better prevent, diagnose, and treat heart failure in the context of COVID-19.

Using a static magnetic field to attenuate the severity in COVID-19-invaded lungs

Two important factors affecting the progress of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are the S-protein binding function of ACE2 receptors and the membrane fluidity of host cells. This study aimed to evaluate the effect of static magnetic field (SMF) on S-protein/ACE2 binding and cellular membrane fluidity of lung cells, and was performed in vitro using a Calu-3 cell model and in vivo using an animal model. The ability of ACE2 receptors to bind to SARS-CoV-2 spike protein on host cell surfaces under SMF stimulation was evaluated using fluorescence images. Host lung cell membrane fluidity was tested using fluorescence polarization to determine the effects of SMF. Our results indicate that 0.4 T SMF can affect binding between S-protein and ACE2 receptors and increase Calu-3 cell membrane fluidity, and that SMF exposure attenuates LPS-induced alveolar wall thickening in mice. These results may be of value for developing future non-contact, non-invasive, and low side-effect treatments to reduce disease severity in COVID-19-invaded lungs.

Role of Enhancing Aerobic Capacity in Countering COVID-19-induced Liver Injury in Elderlies

COVID-19 is still a world disaster; however, its vaccination is globally available. Liver and gastrointestinal disturbances occur in patients infected with COVID-19 at varying incidences. Aging decreases the functions of the liver. Thus, the elderly have a weaker response to the COVID-19 virus. The COVID-19 virus affects the liver directly through direct and indirect mechanisms. It directly affects the renin-angiotensin system or indirectly causes sepsis, uncontrolled immune reactions, drug-related hepatic injury, and cytokine storm. Also, COVID-19 vaccines and anti-drugs have adverse effects on the liver too. Thus, this review explores the effect of enhancing aerobic capacity as a nonpharmacological intervention on decreasing COVID- 19-induced liver injury. Enhancing aerobic capacity decreases COVID-19-induced liver injury through the following: 1) downregulating systemic and tissue ACE/ANG II/AT1R axis, upregulating ACE2/ANG 1-7/Mas axis, and moving the renin-angiotensin system to the direction of the ACE2/ANG (1-7)/Mas axis, 2) Improving mitochondrial function and oxygenation to body and lung tissues, causing a decrease in harmful oxidative reactions, 3) Increasing the processing of accumulated free radicals and inhibiting the acute respiratory distress syndrome, 4) Acting as an antioxidant to protect the liver from oxidative stress, 5) Increasing the effect of antiviral drugs and COVID-19 vaccines, which improves the function of immune biomarkers, decreases the viral load, and increases the body's defense against the virus, 6) Decreasing coagulation abnormalities and thrombosis. In conclusion, enhancing aerobic capacity may be an efficient nonpharmacological intervention to decrease COVID-19-induced liver injury in elderlies and regenerate the liver to its normal status after being infected by the COVID-19 virus. It also helps to strengthen the body's immunity for better effects of both COVID-19 vaccination and drugs.

A community effort in SARS-CoV-2 drug discovery

The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.

Anti-COVID-19 Potential of Withaferin-A and Caffeic Acid Phenethyl Ester

BACKGROUND

The recent COVID-19 (coronavirus disease 2019) pandemic triggered research on the development of new vaccines/drugs, repurposing of clinically approved drugs, and assessment of natural anti-COVID-19 compounds. Based on the gender difference in the severity of the disease, such as a higher number of men hospitalized and in intense care units, variations in sex hormones have been predicted to play a role in disease susceptibility. Cell surface receptors (Angiotensin-Converting Enzyme 2; ACE2 and a connected transmembrane protease serine 2- TMPSS2) are upregulated by androgens. Conversely, androgen antagonists have also been shown to lower ACE2 levels, implying their usefulness in COVID-19 management.

OBJECTIVES

In this study, we performed computational and cell-based assays to investigate the anti- COVID-19 potential of Withaferin-A and Caffeic acid phenethyl ester, natural compounds from Withania somnifera and honeybee propolis, respectively.

METHODS

Structure-based computational approach was adopted to predict binding stability, interactions, and dynamics of the two test compounds to three target proteins (androgen receptor, ACE2, and TMPRSS2). Further, in vitro, cell-based experimental approaches were used to investigate the effect of compounds on target protein expression and SARS-CoV-2 replication.

RESULTS

Computation and experimental analyses revealed that (i) CAPE, but not Wi-A, can act as androgen antagonist and hence inhibit the transcriptional activation function of androgen receptor, (ii) while both Wi-A and CAPE could interact with ACE2 and TMPRSS2, Wi-A showed higher binding affinity, and (iii) combination of Wi-A and CAPE (Wi-ACAPE) caused strong downregulation of ACE2 and TMPRSS2 expression and inhibition of virus infection.

CONCLUSION

Wi-A and CAPE possess multimodal anti-COVID-19 potential, and their combination (Wi-ACAPE) is expected to provide better activity and hence warrant further attention in the laboratory and clinic.

Design, synthesis, and structure-activity relationships of a novel class of quinazoline derivatives as coronavirus inhibitors

There remain great unmet needs to treat coronavirus infections in clinic, and the development of novel antiviral agents is highly demanded. In this work, a phenotypic screening against our in-house compound library identified several cajanine derivatives with moderate antiviral activity against HCoV-OC43. Based on the scaffold of cajanine, a series of quinazoline derivatives were designed employing a scaffold-hopping strategy. After an iterative structural optimization campaign, several quinazoline derivatives with potent antiviral efficacy (EC50: ∼0.1 μM) and high selectivity (SI > 1000) were successfully identified. The preliminary mechanism of action study indicated that such quinazoline derivatives functioned at the early stage of infection. In aggregate, this work delivered a new chemical type of coronavirus inhibitors, which could be employed not only for further development of antiviral drugs but also as important chemical tools to delineate the target of action.

Simultaneous quantification method for multiple antiviral drugs in serum using isotope dilution liquid chromatography-tandem mass spectrometry

We describe the simultaneous quantification of six antiviral drugs in serum based on high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS). The target drugs-hydroxychloroquine, chloroquine, favipiravir, umifenovir, ritonavir, and lopinavir-were extracted and purified from serum with 75 % v/v methanol as the precipitant reagent. The six analytes were clearly separated within 15 min using gradient elution and mixed-mode stationary phase. The measurement accuracy and precision were assured by adopting isotopes as internal standards. The optimized measurement procedure was strictly validated in linearity, sensitivity, accuracy, and precision. To confirm the robustness of the method in matrix, the method was additionally applied to various types of serum, namely hyperlipidemic and hyperglycemic serum. The method was then applied to assess the stability of the drugs in serum in order to set sample handling and storage guides for laboratory testing. Lastly, the method was implemented in different LC-MS systems to confirm its applicability across similar equipment commonly used in clinical testing laboratories. The overall results show that the optimized protocol is suitable for the accurate, simultaneous quantification of the six antiviral drugs in serum, and it is anticipated to satisfactorily serve as a reference protocol for the analysis of a wide range of other antiviral drugs for drug monitoring with various purposes.

Efficacy and Safety of Remdesivir in Hospitalized Pediatric COVID-19: A Retrospective Case-Controlled Study

Introduction

While most children experience mild coronavirus disease 2019 (COVID-19) infections, a minority of cases progress to severe or critical illness. This study aimed to assess the efficacy and safety of Remdesivir (RDV) therapy in children with moderate to severe COVID-19, enhancing clinical decision-making and expanding our understanding of antiviral treatments for pediatric patients.

Methods

The study included 60 patients, 38 receiving RDV treatment and 22 serving as the control group. Data was collected retrospectively from January 2021 to January 2022 through electronic hospital records.

Results

Regarding the main clinical symptoms reported, most patients experienced Upper Respiratory Tract Infections (93.3%), indicating respiratory involvement. Additional symptoms included Central Nervous System (11.7%) and Gastrointestinal (10.0%). Among the 38 cases in the RDV group included in the study, the adverse effects associated with using RDV: Hypoalbuminemia in 19 cases (50.0%) and anemia in 18 cases (47.4%), making them the most common adverse effects. Only one case in the RDV group experienced non-RDV-related death with a different clinical diagnosis. The results showed that RDV treatment was well-tolerated in pediatric patients, with no significant differences in hospital stay and oxygen treatment compared to the control group with P values (0.2, 0.18), respectively.

Conclusion

The outcomes indicate that Remdesivir may represent a safe and therapeutic choice for children with coronavirus disease 2019 (COVID-19).

A comprehensive review on the global efforts on vaccines and repurposed drugs for combating COVID-19

The recently discovered coronavirus, known as SARS-CoV-2, is a highly contagious and potentially lethal viral infection that was declared a pandemic by the World Health Organization on March 11, 2020. Since the beginning of the pandemic, an unprecedented number of COVID-19 vaccine candidates have been investigated for their potential to manage the pandemic. Herein, we reviewed vaccine development and the associated research effort, both traditional and forward-looking, to demonstrate the advantages and disadvantages of their technology, in addition to their efficacy limitations against mutant SARS-CoV-2. Moreover, we report repurposed drug discovery, which mainly focuses on virus-based and host-based targets, as well as their inhibitors. SARS-CoV-2 targets include the main protease (Mpro), and RNA-dependent RNA-polymerase (RdRp), which are the most well-studied and conserved across coronaviruses, enabling the development of broad-spectrum inhibitors of these enzymes.

Optimisation of SARS-CoV-2 peptide stimulation and measurement of cytokine output by intracellular flow cytometry and bio-plex analysis

Our study was conducted to optimise a peptide stimulation and an intracellular cytokine staining protocol, alongside Bio-Plex supernatant analysis, for use in patients who had previously contracted SARS-CoV-2 or received vaccination against this virus in a clinical laboratory setting. Peripheral Blood Mononuclear Cell extraction and cryopreservation allowed for cells to be stored long term and enhanced logistical processing of samples. Viability and functionality of cells were analysed by flow cytometric methodology using viability staining monoclonal antibodies conjugated to fluorochromes. Antibiotics and Benzonase Nuclease did not impact lymphocyte viability and so cell culture conditions were optimised in terms of retaining viability and functionality. Optimisation of peptide stimulation with Influenza and SARS-CoV-2 peptide pools was conducted through stimulation experiments assessing peptide concentration, peptide stimulation time and enrichment studies to increase precursor frequency. Cytokine output was measured by flow cytometry and Bio-Plex methodologies, with positive cytokine readings predominantly detected in the cell culture supernatant. Analysis of both intracellular and extracellular compartments allowed for detection of cytokines and established the retained cellular functionality post cryopreservation. These results also indicated that our peptide stimulation method can generate antigen-specific T lymphocytes upon exposure to SARS-CoV-2 peptide pools. Moreover, the measurement of specific cytokines could be applied to an array of conditions, such as chronic inflammatory diseases, but to also offer an alternative method of measuring vaccine responses. This platform is easily adaptable and can remain relevant alongside changing vaccine composition, thus ensuring its applicability to future vaccination programmes.

Acute and subacute oral toxicity characterization and safety assessment of COVID organics® (Madagascar's Anti-COVID Herbal Tea) in animal models

Introduction

Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2. No drug has been generally approved as safe and effective for the treatment of COVID-19. Several therapeutic agents such as COVID Organics® (CVO) have been explored as treatment options. CVO is an herbal tea composed of 62% of Artemisia annua and 38% of other plants. There is presently no existing scientific report and data on the safety and efficacy of CVO herbal drug. Thus, acute and subacute toxicity studies were undertaken to evaluate the safety and toxicity of CVO on short- and long-term usage in animal models.

Materials and Methods

Phytochemical and nutritional compositions of CVO were determined using standard methods. Acute oral toxicity was investigated using female Swiss albino mice (three per group). While subacute oral toxicity was done using female and male Swiss albino rats (five per group). The animals were administered 2000 mg/kg, 5000 mg/kg, therapeutic dose; 5500 mg/kg and supratherapeutic dose; 11,000 mg/kg of CVO herbal product. The control group received water ad libitum. The oral toxicity studies were done in accordance with Organization for Economic Corporation and Development guidelines. The experimental protocol was approved by the Institutional Animal Care and Use Committee, Nigerian Institute of Medical Research (Ethics No. IRB/17/043).

Results

CVO is rich in antioxidants: flavonoids (10.3%), tannins (29.1%), and phenolics (434.4 mg). It contains proteins (33.8%), carbohydrates (34.5%), fat (6.8%), and fiber (0.5%). In the acute toxicity study, no mortality was recorded in all the treated and untreated groups. The lethal dose of CVO is >5000 mg/kg body weight. The hematological, biochemical, lipid profile, and histologic parameters were all normal at therapeutic doses when compared to the control group.

Conclusion

The acute and subacute oral toxicity studies revealed that CVO is not toxic. The specific organ toxicity evaluations also indicated that CVO has no toxic effects on blood parameters and vital organs structure and function at therapeutic dose. Thus, CVO is safe for short- and long-term usage. We recommend that CVO should be subjected to efficacy studies to investigate whether it is effective for COVID-19 treatment as claimed by the manufacturer.

An approach to rapid distributed manufacturing of broad spectrum anti-viral griffithsin using cell-free systems to mitigate pandemics

This study describes the cell-free biomanufacturing of a broad-spectrum antiviral protein, griffithsin (GRFT) such that it can be produced in microgram quantities with consistent purity and potency in less than 24 h. We demonstrate GRFT production using two independent cell-free systems, one plant and one microbial. Griffithsin purity and quality were verified using standard regulatory metrics. Efficacy was demonstrated in vitro against SARS-CoV-2 and HIV-1 and was nearly identical to that of GRFT expressed in vivo. The proposed production process is efficient and can be readily scaled up and deployed wherever a viral pathogen might emerge. The current emergence of viral variants of SARS-CoV-2 has resulted in frequent updating of existing vaccines and loss of efficacy for front-line monoclonal antibody therapies. Proteins such as GRFT with its efficacious and broad virus neutralizing capability provide a compelling pandemic mitigation strategy to promptly suppress viral emergence at the source of an outbreak.

Hybrid molecules based on an emodin scaffold. Synthesis and activity against SARS-CoV-2 and Plasmodium

Since the Covid-19 epidemic, it has been clear that the availability of small and affordable drugs that are able to efficiently control viral infections in humans is still a challenge in medicinal chemistry. The synthesis and biological activities of a series of hybrid molecules that combine an emodin moiety and other structural moieties expected to act as possible synergistic pharmacophores in a single molecule were studied. Emodin has been reported to block the entry of the SARS-CoV-2 virus into human cells and might also inhibit cytokine production, resulting in the reduction of pulmonary injury induced by SARS-CoV-2. The pharmacophore associated with emodin was either a polyamine residue (emodin-PA series), a choice driven by the fact that a natural alkyl PA like spermine and spermidine play regulatory roles in immune cell functions, or a diphenylmethylpiperazine derivative of the norchlorcyclizine series (emoxyzine series). In fact, diphenylmethylpiperazine antagonists of the H1 histamine receptor display activity against several viruses by multiple interrelated mechanisms. In the emoxyzine series, the most potent drug against SARS-CoV-2 was (R)-emoxyzine-2, with an EC50 value = 1.9 μM, which is in the same range as that of the reference drug remdesivir. However, the selectivity index was rather low, indicating that the dissociation of antiviral potency and cytotoxicity remains a challenge. In addition, since emodin was also reported to be a relatively high-affinity inhibitor of the virulence regulator FIKK kinase from the malaria parasite Plasmodium vivax, the antimalarial activity of the synthesized hybrid compounds has been evaluated. However, these molecules cannot efficiently compete with the currently used antimalarial drugs.

Conformational response to ligand binding of TMPRSS2, a protease involved in SARS-CoV-2 infection: Insights through computational modeling

Thanks to the considerable research which has been undertaken in the last few years to improve our understanding of the biology and mechanism of action of SARS-CoV-2, we know how the virus uses its surface spike protein to infect host cells. The transmembrane prosthesis, serine 2 (TMPRSS2) protein, located on the surface of human cells, recognizes the cleavage site in the spike protein, leading to the release of the fusion peptide and entry of the virus into the host cells. Because of its role, TMPRSS2 has been proposed as a drug target to prevent infection by the virus. In this study, we aim to increase our understanding of TMPRSS2 using long scale microsecond atomistic molecular dynamics simulations, focusing on the conformational changes over time. The comparison between simulations conducted on the protein in the native (apo) and inhibited form (holo), has shown that in the holo form the inhibitor stabilizes the catalytic site and induces rearrangements in the extracellular domain of the protein. In turn, it leads to the formation of a new cavity in the vicinity of the ligand binding pocket that is stable in the microsecond time scale. Given the low specificity of known protease inhibitors, these findings suggest a new potential drug target site that can be used to improve TMPRSS2 specific recognition by newly designed inhibitors.

Current state-of-the-art and potential future therapeutic drugs against COVID-19

The novel coronavirus disease (COVID-19) continues to endanger human health, and its therapeutic drugs are under intensive research and development. Identifying the efficacy and toxicity of drugs in animal models is helpful for further screening of effective medications, which is also a prerequisite for drugs to enter clinical trials. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) invades host cells mainly by the S protein on its surface. After the SARS-CoV-2 RNA genome is injected into the cells, M protein will help assemble and release new viruses. RdRp is crucial for virus replication, assembly, and release of new virus particles. This review analyzes and discusses 26 anti-SARS-CoV-2 drugs based on their mechanism of action, effectiveness and safety in different animal models. We propose five drugs to be the most promising to enter the next stage of clinical trial research, thus providing a reference for future drug development.

Optimized synthesis of anti-COVID-19 drugs aided by retrosynthesis software

Considering the millions of COVID-19 patients worldwide, a global critical challenge of low-cost and efficient anti-COVID-19 drug production has emerged. Favipiravir is one of the potential anti-COVID-19 drugs, but its original synthetic route with 7 harsh steps gives a low product yield (0.8%) and has a high cost ($68 per g). Herein, we demonstrated a low-cost and efficient synthesis route for favipiravir designed using improved retrosynthesis software, which involves only 3 steps under safe and near-ambient air conditions. A yield of 32% and cost of $1.54 per g were achieved by this synthetic route. We also used the same strategy to optimize the synthesis of sabizabulin. We anticipate that these synthetic routes will contribute to the prevention and treatment of COVID-19.

Identifying hub genes and common biological pathways between COVID-19 and benign prostatic hyperplasia by machine learning algorithms

Background

COVID-19, a serious respiratory disease that has the potential to affect numerous organs, is a serious threat to the health of people around the world. The objective of this article is to investigate the potential biological targets and mechanisms by which SARS-CoV-2 affects benign prostatic hyperplasia (BPH) and related symptoms.

Methods

We downloaded the COVID-19 datasets (GSE157103 and GSE166253) and the BPH datasets (GSE7307 and GSE132714) from the Gene Expression Omnibus (GEO) database. In GSE157103 and GSE7307, differentially expressed genes (DEGs) were found using the "Limma" package, and the intersection was utilized to obtain common DEGs. Further analyses followed, including those using Protein-Protein Interaction (PPI), Gene Ontology (GO) function enrichment analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Potential hub genes were screened using three machine learning methods, and they were later verified using GSE132714 and GSE166253. The CIBERSORT analysis and the identification of transcription factors, miRNAs, and drugs as candidates were among the subsequent analyses.

Results

We identified 97 common DEGs from GSE157103 and GSE7307. According to the GO and KEGG analyses, the primary gene enrichment pathways were immune-related pathways. Machine learning methods were used to identify five hub genes (BIRC5, DNAJC4, DTL, LILRB2, and NDC80). They had good diagnostic properties in the training sets and were validated in the validation sets. According to CIBERSORT analysis, hub genes were closely related to CD4 memory activated of T cells, T cells regulatory and NK cells activated. The top 10 drug candidates (lucanthone, phytoestrogens, etoposide, dasatinib, piroxicam, pyrvinium, rapamycin, niclosamide, genistein, and testosterone) will also be evaluated by the P value, which is expected to be helpful for the treatment of COVID-19-infected patients with BPH.

Conclusion

Our findings reveal common signaling pathways, possible biological targets, and promising small molecule drugs for BPH and COVID-19. This is crucial to understand the potential common pathogenic and susceptibility pathways between them.

Synthesis and anti-SARS-CoV-2 evaluation of lipid prodrugs of β-D-N4-hydroxycytidine (NHC) and a 3′-fluoro-substituted analogue of NHC

β-D-N⁴-hydroxycytidine (NHC, EIDD-1931) is a nucleoside analogue that exhibits broad spectrum antiviral activity against a variety of RNA viruses. Herein, we report the synthesis of a series of lipid prodrugs of NHC and a novel 3′-fluoro modified NHC analogue, and evaluation of their antiviral activity against five variants of SARS-CoV-2. All lipid prodrugs showed potent antiviral activity against the tested SARS-CoV-2 variants with EC₅₀ values in the range of 0.31–3.51 μM, which were comparable to those of NHC or higher than those of remdesivir and molnupiravir. An increase in the cytostatic activity of the lipid prodrugs was found, but prodrug 2d proved equally selective as molnupinavir. The 3′-F analogue of NHC (6) only displayed minor antiviral activity against the SARS-CoV-2 Omicron variant (EC₅₀ = 29.91 μM), while no activity was found for other variants at the highest concentration tested. The promising antiviral data of the lipid prodrugs of NHC suggest that they deserve further investigation as new anti-SARS-CoV-2 drugs.

Marine drugs as putative inhibitors against non-structural proteins of SARS-CoV-2: an in silico study

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is an unprecedented pandemic, threatening human health worldwide. The need to produce novel small-molecule inhibitors against the ongoing pandemic has resulted in the use of drugs such as chloroquine, azithromycin, dexamethasone, favipiravir, ribavirin, remdesivir and azithromycin. Moreover, the reports of the clinical trials of these drugs proved to produce detrimental effects on patients with side effects like nephrotoxicity, retinopathy, cardiotoxicity and cardiomyopathy. Recognizing the need for effective and non-harmful therapeutic candidates to combat COVID-19, we aimed to develop promising drugs against SARS-COV-2.

DISCUSSION

In the current investigation, high-throughput virtual screening was performed using the Comprehensive Marine Natural Products Database against five non-structural proteins: Nsp3, Nsp5, Nsp12, Nsp13 and Nsp15. Furthermore, standard precision (SP) docking, extra precision (XP) docking, binding free energy calculation and absorption, distribution, metabolism, excretion and toxicity studies were performed using the Schrӧdinger suite. The top-ranked 5 hits obtained by computational studies exhibited to possess a greater binding affinity with the selected non-structural proteins. Amongst the five hits, CMNPD5804, CMNPD20924 and CMNPD1598 hits were utilized to design a novel molecule (D) that has the capability of interacting with all the key residues in the pocket of the selected non-structural proteins. Furthermore, 200 ns of molecular dynamics simulation studies provided insight into the binding modes of D within the catalytic pocket of selected proteins.

CONCLUSION

Hence, it is concluded that compound D could be a promising inhibitor against these non-structural proteins. Nevertheless, there is still a need to conduct in vitro and in vivo studies to support our findings.

A dispersion-corrected DFT calculation on encapsulation of favipiravir drug used as antiviral against COVID-19 into carbon-, boron-, and aluminum-nitride nanotubes for optimal drug delivery systems combined with molecular docking simulations

Favipiravir (FAV) (6-fluoro-3-oxo-3,4-dihydropyrazine-2-carboxamide) is one of the most effective antiviral drugs which is cited for action against RNA-viral infections of COVID-19. In this study, density functional theory (DFT) calculations were used to investigate three nanotubes (NTs) with FAV drug as delivery systems. The encapsulated systems (ESs) consist of FAV drug inside carbon-carbon, aluminum nitride, and boron nitride. At B3LYP-D/6-31G(d,p) and CPCM/B3LYP-D/6-31G(d,p), the optimization of NTs, FAV, and its tautomeric forms and six ESs was investigated in gas and water environments. Five tautomeric forms of FAV were investigated, two keto forms (K1 and K2) and three enol forms (E1, E2, and E3). The results revealed that E3 and K2 isomeric forms represented the most stable structures in both media; thus, these two forms were encapsulated into the NTs. The stability and the synthesis feasibility of NTs have been proven by calculating their interaction energies. Non-covalent interactions (NCIs) were investigated in the ESs to show the type of NCI with the molecular voids. The binding energies, thermochemical parameters, and recovery times were investigated to understand the mechanism of FAV encapsulation and release. The encapsulated AlNNT systems are more favorable than those of BNNTs and CNTs in gas and aqueous environments with much higher binding energies. The quantum theory of atoms in molecules (QTAIM) and recovery time analysis revealed the easier releasing of E3 from AlNNT over K2 form. Based on molecular docking simulations, we found that E3 and K2 FAV forms showed a high level of resistance to SARS-CoV-6M3M/6LU7/6W9C proteases.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11224-023-02182-4.

Development and validation of an LC-MS/MS method for quantification of favipiravir in human plasma

Favipiravir (FVP) is a broad-spectrum antiviral that selectively inhibits viral RNA-dependent RNA polymerase, first trialled for the treatment of influenza infection. It has been shown to be effective against a number of RNA virus families including arenaviruses, flaviviruses and enteroviruses. Most recently, FVP has been investigated as a potential therapeutic for severe acute respiratory syndrome coronavirus 2 infection. A liquid chromatography tandem mass spectrometry method for the quantification of FVP in human plasma has been developed and validated for use in clinical trials investigating favipiravir as treatment for coronavirus disease-2019. Samples were extracted by protein precipitation using acetonitrile, using ¹³C, ¹⁵N- Favipiravir as internal standard. Elution was performed on a Synergi Polar-RP 150 × 2.1 mm 4 µm column using a gradient mobile phase programme consisting of 0.2% formic acid in water and 0.2% formic acid in methanol. The assay was validated over the range 500-50,000 ng/mL; this method was found to be precise and accurate and recovery of FVP from the matrix was high. Stability experiments confirmed and expanded on the known stability of FVP, including under heat treatment and for a period of 10 months at - 80 °C.

Potential treatments of COVID-19: Drug repurposing and therapeutic interventions

The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The infection is caused when Spike-protein (S-protein) present on the surface of SARS-CoV-2 interacts with human cell surface receptor, Angiotensin-converting enzyme 2 (ACE2). This binding facilitates SARS-CoV-2 genome entry into the human cells, which in turn causes infection. Since the beginning of the pandemic, many different therapies have been developed to combat COVID-19, including treatment and prevention. This review is focused on the currently adapted and certain other potential therapies for COVID-19 treatment, which include drug repurposing, vaccines and drug-free therapies. The efficacy of various treatment options is constantly being tested through clinical trials and in vivo studies before they are made medically available to the public.

Autophagy and SARS-CoV-2-Old Players in New Games

At present it is well-defined that autophagy is a fundamental process essential for cell life but its pro-viral and anti-viral role has been stated out with the COVID pandemic. However, viruses in turn have evolved diverse adaptive strategies to cope with autophagy driven host defense, either by blocking or hijacking the autophagy machinery for their own benefit. The mechanisms underlying autophagy modulation are presented in the current review which summarizes the accumulated knowledge on the crosstalk between autophagy and viral infections, with a particular emphasizes on SARS-CoV-2. The different types of autophagy related to infections and their molecular mechanisms are focused in the context of inflammation. In particular, SARS-CoV-2 entry, replication and disease pathogenesis are discussed. Models to study autophagy and to formulate novel treatment approaches and pharmacological modulation to fight COVID-19 are debated. The SARS-CoV-2-autophagy interplay is presented, revealing the complex dynamics and the molecular machinery of autophagy. The new molecular targets and strategies to treat COVID-19 effectively are envisaged. In conclusion, our finding underline the importance of development new treatment strategies and pharmacological modulation of autophagy to fight COVID-19.

Nanomedicine for drug resistant pathogens and COVID-19 using mushroom nanocomposite inspired with bacteriocin – A Review

Multidrug resistant (MDR) pathogens have become a major global health challenge and have severely threatened the health of society. Current conditions have gotten worse as a result of the COVID-19 pandemic, and infection rates in the future will rise. It is necessary to design, respond effectively, and take action to address these challenges by investigating new avenues. In this regard, the fabrication of metal NPs utilized by various methods, including green synthesis using mushroom, is highly versatile, cost-effective, eco-compatible, and superior. In contrast, biofabrication of metal NPs can be employed as a powerful weapon against MDR pathogens and have immense biomedical applications. In addition, the advancement in nanotechnology has made possible to modify the nanomaterials and enhance their activities. Metal NPs with biomolecules composite to prevents their microbial adhesion and kills the microbial pathogens through biofilm formation. Bacteriocin is an excellent antimicrobial peptide that works well as an augmentation substance to boost the antimicrobial effects. As a result, we concentrate on the creation of new, eco-compatible mycosynthesized metal NPs with bacteriocin nanocomposite via electrostatic, covalent, or non-covalent bindings. The synergistic benefits of metal NPs with bacteriocin to combat MDR pathogens and COVID-19, as well as other biomedical applications, are discussed in this review. Moreover, the importance of the adverse outcome pathway (AOP) in risk analysis of manufactured metal nanocomposite nanomaterial and their future possibilities also discussed.

Radiation Protection of Polydatin Against Radon Exposure Injury of Epithelial Cells and Mice

Radon exposure is significantly associated with lung cancer. Radon concentration is currently reduced mainly by physical methods, but there is a lack of protective drugs or biochemical reagents for radon damage. This study aimed to explore the protective effect of polydatin (PD) on the radon-exposed injury. The results showed that PD can significantly reduce ROS level, raise SOD activity, weaken the migration ability, increase E-cad, and decrease mesenchymal cell surface markers (FN1, Vimentin, N-cad, α-SMA, and Snail) in radon-exposed epithelial cells. In vivo, PD increased the mice weight, promoted SOD activity, and decreased MDA content, the number of bullae, pulmonary septum thickness, lung collagenous fibers, and mesenchymal cell surface markers. Furthermore, PD inhibited p-PI3K, p-AKT, and p-mTOR expression. Compared with directly adding PD on radon-exposed cells, adding PD before and after radon exposure could more obviously improve the adhesion of radon-exposed cells, significantly alleviate the migration ability, and more significantly reduce mesenchyme markers and p-AKT and p-mTOR. These results indicate that PD can reduce oxidative stress, weaken epithelial-mesenchymal transition (EMT) and lung fibrosis in radon-exposed cells/mice, and have good radiation protection against radon injury. The mechanism is related to the inhibition of the PI3K/AKT/mTOR pathway.

Drugs for COVID-19 Treatment: A New Challenge

COVID-19 infection is a new disease and our knowledge is limited; day in and day out more and more interesting yet diverse observations are reported by the different research groups from different corners of the world. So, there is an urgent requirement of the invention of some effective and efficient drugs that can carry out the end of the deadly viral infection. Throughout the world, there have been many efforts carried out in different labs to invent such a drug and also identifying any pre-existing drugs which can carry out the killing of the virus. In this review, an effort has been made to understand the potential drugs which can be used against the SARS-CoV-2 viral infection. Again, the strategies on the current and the future drug discovery mechanisms against the SARS-CoV-2 are also mentioned. The different drugs made and the drugs re-used and also the drugs which are in the making process in different research laboratories across the world are also mentioned. To combat this unexpected crisis, we still need some more efforts from the different scientific communities around the world for finding a cure against this viral infection and this is needed to be done for the prevention of more loss of human life.

Functionally Collaborative Nanostructure for Direct Monitoring of Neurotransmitter Exocytosis in Living Cells

Neurotransmitter exocytosis of living cells plays a vital role in neuroscience. However, the available amperometric technique with carbon fiber electrodes typically measures exocytotic events from one cell during one procedure, which requires professional operations and takes time to produce statistical results of multiple cells. Here, we develop a functionally collaborative nanostructure to directly measure the neurotransmitter dopamine (DA) exocytosis from living rat pheochromocytoma (PC12) cells. The functionally collaborative nanostructure is constructed of metal-organic framework (MOF)-on-nanowires-on-graphene oxide, which is highly sensitive to DA molecules and enables direct detection of neurotransmitter exocytosis. Using the microsensor, the exocytosis from PC12 cells pretreated with the desired drugs (e.g., anticoronavirus drug, antiflu drug, or anti-inflammatory drug) has been successfully measured. Our achievements demonstrate the feasibility of the functionally collaborative nanostructure in the real-time detection of exocytosis and the potential applicability in the highly efficient assessment of the modulation effects of medications on exocytosis.

Therapeutically important bioactive compounds of the genus Polygonum L. and their possible interventions in clinical medicine

OBJECTIVES

Increasing literature data have suggested that the genus Polygonum L. possesses pharmacologically important plant secondary metabolites. These bioactive compounds are implicated as effective agents in preclinical and clinical practice due to their pharmacological effects such as anti-inflammatory, anticancer, antidiabetic, antiaging, neuroprotective or immunomodulatory properties among many others. However, elaborate pharmacological and clinical data concerning the bioavailability, tissue distribution pattern, dosage and pharmacokinetic profiles of these compounds are still scanty.

KEY FINDINGS

The major bioactive compounds implicated in the therapeutic effects of Polygonum genus include phenolic and flavonoid compounds, anthraquinones and stilbenes, such as quercetin, resveratrol, polydatin and others, and could serve as potential drug leads or as adjuvant agents. Data from in-silico network pharmacology and computational molecular docking studies are also highly helpful in identifying the possible drug target of pathogens or host cell machinery.

SUMMARY

We provide an up-to-date overview of the data from pharmacodynamic, pharmacokinetic profiles and preclinical (in-vitro and in-vivo) investigations and the available clinical data on some of the therapeutically important compounds of genus Polygonum L. and their medical interventions, including combating the outbreak of the COVID-19 pandemic.

Analytical approaches for determination of COVID-19 candidate drugs in human biological matrices

Since the outbreak of the COVID-19 pandemic, the use of antiviral and other available drugs has been considered to combat or reduce the clinical symptoms of patients. In this regard, it would be necessary to choose sensitive and selective analytical techniques for pharmacokinetic and pharmacodynamic studies, monitoring of drug concentration in biological fluids, and determination of the most appropriate dose to achieve the desired effect on the disease. In the present study, the analytical techniques based on spectroscopy and chromatography with different detectors for diagnosis and determination of candidate drugs in the treatment of COVID-19 in human biological fluids are reviewed during the period 2015-2022. Moreover, various sample preparation and extraction techniques, are being used for this purpose, such as protein precipitation (PP), solid-phase extraction (SPE), liquid-liquid extraction (LLE), and QuEChERS (quick, easy, cheap, effective, rugged, and safe) are investigated.

COVID-19 signalome: Potential therapeutic interventions

The COVID-19 pandemic has triggered intensive research and development of drugs and vaccines against SARS-CoV-2 during the last two years. The major success was especially observed with development of vaccines based on viral vectors, nucleic acids and whole viral particles, which have received emergent authorization leading to global mass vaccinations. Although the vaccine programs have made a big impact on COVID-19 spread and severity, emerging novel variants have raised serious concerns about vaccine efficacy. Due to the urgent demand, drug development had originally to rely on repurposing of antiviral drugs developed against other infectious diseases. For both drug and vaccine development the focus has been mainly on SARS-CoV-2 surface proteins and host cell receptors involved in viral attachment and entry. In this review, we expand the spectrum of SARS-CoV-2 targets by investigating the COVID-19 signalome. In addition to the SARS-CoV-2 Spike protein, the envelope, membrane, and nucleoprotein targets have been subjected to research. Moreover, viral proteases have presented the possibility to develop different strategies for the inhibition of SARS-CoV-2 replication and spread. Several signaling pathways involving the renin-angiotensin system, angiotensin-converting enzymes, immune pathways, hypoxia, and calcium signaling have provided attractive alternative targets for more efficient drug development.

SARS-CoV-2 RdRp uses NDPs as a substrate and is able to incorporate NHC into RNA from diphosphate form molnupiravir

The coronavirus disease 2019 has been ravaging throughout the world for three years and has severely impaired both human health and the economy. The causative agent, severe acute respiratory syndrome coronavirus 2 employs the viral RNA dependent RNA polymerase (RdRp) complex for genome replication and transcription, making RdRp an appealing target for antiviral drug development. Systematic characterization of RdRp will undoubtedly aid in the development of antiviral drugs targeting RdRp. Here, our research reveals that RdRp can recognize and utilize nucleoside diphosphates as a substrate to synthesize RNA with an efficiency of about two thirds of using nucleoside triphosphates as a substrate. Nucleoside diphosphates incorporation is also template-specific and has high fidelity. Moreover, RdRp can incorporate β-d-N4-hydroxycytidine into RNA while using diphosphate form molnupiravir as a substrate. This incorporation results in genome mutation and virus death. It is also observed that diphosphate form molnupiravir is a better substrate for RdRp than the triphosphate form molnupiravir, presenting a new strategy for drug design.

Chronic alcohol intake regulates expression of SARS-CoV2 infection-relevant genes in an organ-specific manner

BACKGROUND

Chronic alcohol consumption and alcohol use disorder have a tremendous impact on the patient's psychological and physiological health. There is evidence that chronic alcohol consumption influences SARS-CoV2 infection risk, but so far, the molecular mechanism underlying such an effect is unknown.

METHODS

We generated the expression data of SARS-CoV2 infection-relevant genes (Ace2, Tmprss2, and Mas) in different organs in rat models of chronic alcohol exposure and alcohol dependence. Ace2 and Tmprss2 represent the virus entry point, whereas Mas activates the anti-inflammatory response once the cells are infected.

RESULTS

Across three different chronic alcohol test conditions, we found a consistent upregulation of Ace2 gene expression in the lung, which has been shown to be the most affected organ in COVID-19 patients. Other organs such as liver, ileum, kidney, heart, and brain also showed upregulation of Ace2 and Mas gene expression but less consistently across the different animal models, while Tmprss2 expression was unaffected in all conditions.

CONCLUSIONS

We conclude that alcohol-induced upregulation of Ace2 gene expression can lead to an elevated stochastic probability of virus entry into cells and may thus confer a molecular risk for SARS-CoV2 infection.

A hypothesis on designing strategy of effective RdRp inhibitors for the treatment of SARS-CoV-2

Vaccines are used as one of the major weapons for the eradication of pandemic. However, the rise of different variants of the SARS-CoV-2 virus is creating doubts regarding the end of the pandemic. Hence, there is an urgent need to develop more drug candidates which can be useful for the treatment of COVID-19. In the present research for the scientific hypothesis, emphasis was given on the direct antiviral therapy available for the treatment of COVID-19. In lieu of this, the available molecular targets which include Severe Acute Respiratory Syndrome Chymotrypsin-like Protease (SARS-3CLpro), Papain-Like Cysteine Protease (PLpro), and RNA-Dependent RNA Polymerase (RdRp) were explored. As per the current scientific reports and literature, among all the available molecular targets, RNA-Dependent RNA Polymerase (RdRp) was found to be a crucial molecular target for the treatment of COVID-19. Most of the inhibitors which are reported against this target consisted of the free amine group and carbonyl group which might be playing an important role in the binding interaction with the RdRp protein. Among all the reported RdRp inhibitors, remdesivir, favipiravir, and molnupiravir were found to be the most promising drugs against COVID-19. Overall, the structural features of this RNA-Dependent RNA Polymerase (RdRp) inhibitors proved the importance of pyrrolo-triazine and pyrimidine scaffolds. Previous computational models of these drug molecules indicated that substitution with the polar functional group, hydrogen bond donor, and electronegative atoms on these scaffolds may increase the activity against the RdRp protein. Hence, in line with the proposed hypothesis, in the present research work for the evaluation of the hypothesis, new molecules were designed from the pyrrolo-triazine and pyrimidine scaffolds. Further, molecular docking and MD simulation studies were performed with these designed molecules. All these designed molecules (DM-1, DM-2, and DM-3) showed the results as per the proposed hypothesis. Among all the designed molecules, DM-1 showed promising results against the RdRp protein of SARS-CoV-2. In the future, these structural features can be used for the development of new RdRp inhibitors with improved activity. Also, in the future lead compound DM-1 can be explored against the RdRp protein for the treatment of COVID-19.

Anti-HIV and anti-HCV small molecule protease inhibitors in-silico repurposing against SARS-CoV-2 Mpro for the treatment of COVID-19

The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is a global health emergency warranting development and implementation of targeted treatment. The enzyme main protease (M^pro; also known as 3C-like protease) is emerging as an attractive drug target. This enzyme plays an indispensable role in processing the translated polyproteins of viral RNA. Inhibiting the activity of M^pro would wedge viral replication. To facilitate the discovery of targeted therapy for COVID-19, we carried out the structure-assisted repurposing of existing protease inhibiting small molecules to target SARS-CoV-2 M^pro. Based on the structure of SARS-CoV-2 M^pro, here we report the small drug molecule namely saquinavir as its potent inhibitor. Findings support the premise that this promising antiviral protease inhibiting small drug molecule can be validated and implemented for the treatment and clinical management of COVID-19 pandemic disease.Communicated by Ramaswamy H. Sarma.

An approach to rapid distributed manufacturing of broad spectrum anti-viral griffithsin using cell-free systems to mitigate pandemics

This study describes the cell-free biomanufacturing of a broad-spectrum antiviral protein, griffithsin (GRFT) such that it can be produced with consistent purity and potency in less than 24 hours. We demonstrate GRFT production using two independent cell-free systems, one plant and one microbial. Griffithsin purity and quality were verified using standard regulatory metrics. Efficacy was demonstrated in vitro against SARS-CoV-2 and HIV-1 and was nearly identical to that of GRFT expressed in vivo . The proposed production process is efficient and can be readily scaled up and deployed anywhere in the world where a viral pathogen might emerge. The current emergence of viral variants has resulted in frequent updating of existing vaccines and loss of efficacy for front-line monoclonal antibody therapies. Proteins such as GRFT with its efficacious and broad virus neutralizing capability provide a compelling pandemic mitigation strategy to promptly suppress viral emergence at the source of an outbreak.

Significant perspectives on various viral infections targeted antiviral drugs and vaccines including COVID-19 pandemicity

A virus enters a living organism and recruits host metabolism to reproduce its own genome and proteins. The viral infections are intricate and cannot be completely removed through existing antiviral drugs. For example, the herpes, influenza, hepatitis and human immunodeficiency viruses are a few dreadful ones amongst them. Significant studies are needed to understand the viral entry and their growth in host cells to design effective antivirals. This review emphasizes the range of therapeutical antiviral drugs, inhibitors along with vaccines to fight against viral pathogens, especially for combating COVID-19. Moreover, we have provided the basic and in depth information about viral targets, drugs availability, their mechanisms of action, method of prevention of viral diseases and highlighted the significances of anticoagulants, convalescent plasma for COVID-19 treatment, scientific details of airborne transmission, characteristics of antiviral drug delivery using nanoparticles/carriers, nanoemulsions, nanogels, metal based nanoparticles, alike the future nanosystems through nanobubbles, nanofibers, nanodiamonds, nanotraps, nanorobots and eventually, the therapeutic applications of micro- and nanoparticulates, current status for clinical development against COVID-19 together with environmental implications of antivirals, gene therapy etc., which may be useful for repurposing and designing of novel antiviral drugs against various dreadful diseases, especially the SARS-CoV-2 and other associated variants.

Natural Products Against COVID-19 Inflammation: A Mini-Review

Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) is a virus whose genetic material is positive single-stranded RNA, being responsible for coronavirus disease 2019 (COVID- 19), an infection that compromises the lungs and consequently the respiratory capacity of the infected individual, according to the WHO in November 2021, 249,743,428 cases were confirmed, of which 5,047,652 individuals died due to complications resulting from the infection caused by SARSCOV- 2. As the infection progresses, the individual may experience loss of smell and taste, as well as breathing difficulties, severe respiratory failure, multiple organ failure, and death. Due to this new epidemiological agent in March 2020 it was announced by the director general of the World Health Organization (WHO) a pandemic status, and with that, many research groups are looking for new therapeutic alternatives through synthetic and natural bioactives. This research is a literature review of some in silico studies involving natural products against COVID-19 inflammation published in 2020 and 2021. Work like this presents relevant information to the scientific community, boosting future research and encouraging the use of natural products for the search for new antivirals against COVID-19.

Research and development of Chinese anti-COVID-19 drugs

The outbreak and spread of coronavirus disease 2019 (COVID-19) highlighted the importance and urgency of the research and development of therapeutic drugs. Very early into the COVID-19 pandemic, China has begun developing drugs, with some notable progress. Herein, we summarizes the anti-COVID-19 drugs and promising drug candidates originally developed and researched in China. Furthermore, we discussed the developmental prospects, mechanisms of action, and advantages and disadvantages of the anti-COVID-19 drugs in development, with the aim to contribute to the rational use of drugs in COVID-19 treatment and more effective development of new drugs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the variants. Neutralizing antibody is an effective approach to overcome COVID-19. However, drug resistance induced by rapid virus mutation will likely to challenge neutralizing antibodies. Taking into account current epidemic trends, small molecule drugs have a crucial role in fighting COVID-19 due to their significant advantage of convenient administration and affordable and broad-spectrum. Traditional Chinese medicines, including natural products and traditional Chinese medicine prescriptions, contribute to the treatment of COVID-19 due to their unique mechanism of action. Currently, the research and development of Chinese anti-COVID-19 drugs have led to some promising achievements, thus prompting us to expect even more rapidly available solutions.

Role of trace TEMPO as electron shuttle in enhancing chloroquine phosphate elimination in UV-LED-driven persulfate activation process

Chloroquine Phosphate (CP) is an antiviral drug used for treatment of COVID-19. It is released into wastewater and eventually contaminates natural water. This study reports an effective homogeneous catalysis way for CP degradation by the 2,2,6,6-Tetramethylpiperidine-N-oxyl (TEMPO) enhanced persulfate (PDS) activation under UVB-LEDs irradiation at 305 nm. TEMPO at a low concentration (0.1 μM) enhanced CP degradation in UV₃₀₅/PDS process in deionized water at different pHs, in different anions and different molecular weight dissolved organic matter solutions and in real surface water. The enhancement was verified to be attributed to the electron shuttle role of TEMPO, which promoted the yield of SO₄ ^•- by enhancing electron donating capacity of the reacting system. The degradation products of CP and their acute toxicities suggested that UV₃₀₅/PDS/TEMPO process has better performance on CP detoxification than UV₃₀₅/PDS process. This study provides a new way to tackle the challenge of pharmaceutical pollutions in homogeneous photocatalysis process for natural water and sewage restoration.

WLLP: A weighted reconstruction-based linear label propagation algorithm for predicting potential therapeutic agents for COVID-19

The global coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV) has led to a huge health and economic crises. However, the research required to develop new drugs and vaccines is very expensive in terms of labor, money, and time. Owing to recent advances in data science, drug-repositioning technologies have become one of the most promising strategies available for developing effective treatment options. Using the previously reported human drug virus database (HDVD), we proposed a model to predict possible drug regimens based on a weighted reconstruction-based linear label propagation algorithm (WLLP). For the drug–virus association matrix, we used the weighted K-nearest known neighbors method for preprocessing and label propagation of the network based on the linear neighborhood similarity of drugs and viruses to obtain the final prediction results. In the framework of 10 times 10-fold cross-validated area under the receiver operating characteristic (ROC) curve (AUC), WLLP exhibited excellent performance with an AUC of 0.8828 ± 0.0037 and an area under the precision-recall curve of 0.5277 ± 0.0053, outperforming the other four models used for comparison. We also predicted effective drug regimens against SARS-CoV-2, and this case study showed that WLLP can be used to suggest potential drugs for the treatment of COVID-19.

Insight into designing of 2-pyridone derivatives for COVID-19 drug discovery - A computational study

Presently, the prime global focus is on SARS-CoV-2, as no fully established, licensed medicine has been found thus far, in spite of the existence of various reports and administration of partially proven certain class of natural products. However, in case of natural products, the extraction and purification limit their application. This situation drives researchers to explore synthetically viable drugs. In the present investigation, twenty-three 2-pyridone synthetic derivatives (P1-P23) have been theoretically tested for their suitability as potential inhibitors for COVID-19 main protease through DFT, molecular docking, and molecular dynamics simulations. DFT calculations offer insights into structure-property relationships, while ADMET studies indicate the pharmacological characteristics of these molecules. Molecular docking studies ascertain the nature and mode of interactions of these entities with COVID-19 main protease. Furthermore, covalent docking has been carried out to verify the feasibility of the formation of a covalent bond with the active site. The top protein-inhibitor complexes, such as P18, P11, and P12, were identified based on their glide score. These molecules, along with the covalent docked complexes, namely P18 and P16, were selected and subjected to molecular dynamics simulations. The 100 ns simulation process exhibited that the covalent docked ones, due to their stable form could serve as lead compounds against SARS-CoV-2. Hence, this study affirms the potential candidature of 2-pyridone-based inhibitors.

Broad Tricyclic Ring Inhibitors Block SARS-CoV-2 Spike Function Required for Viral Entry

The entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells requires binding of the viral spike glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor, which triggers subsequent conformational changes to facilitate viral and cellular fusion at the plasma membrane or following endocytosis. Here, we experimentally identified selective and broad inhibitors of SARS-CoV-2 entry that share a tricyclic ring (or similar) structure. The inhibitory effect was restricted to early steps during infection and the entry inhibitors interacted with the receptor binding domain of the SARS-CoV-2 spike but did not significantly interfere with receptor (ACE2) binding. Instead, some of these compounds induced conformational changes or affected spike assembly and blocked SARS-CoV-2 spike cell-cell fusion activity. The broad inhibitors define a highly conserved binding pocket that is present on the spikes of SARS-CoV-1, SARS-CoV-2, and all circulating SARS-CoV-2 variants tested and block SARS-CoV spike activity required for mediating viral entry. These compounds provide new insights into the SARS-CoV-2 spike topography, as well as into critical steps on the entry pathway, and can serve as lead candidates for the development of broad-range entry inhibitors against SARS-CoVs.

Antiviral and Anti-Inflammatory Plant-Derived Bioactive Compounds and Their Potential Use in the Treatment of COVID-19-Related Pathologies

The highly contagious coronavirus disease (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic and public health emergency as it has taken the lives of over 5.7 million in more than 180 different countries. This disease is characterized by respiratory tract symptoms, such as dry cough and shortness of breath, as well as other symptoms, including fever, chills, and fatigue. COVID-19 is also characterized by the excessive release of cytokines causing inflammatory injury to the lungs and other organs. It is advised to undergo precautionary measures, such as vaccination, social distancing, use of masks, hygiene, and a healthy diet. This review is aimed at summarizing the pathophysiology of COVID-19 and potential biologically active compounds (bioactive) found in plants and plant food. We conclude that many plant food bioactive compounds exhibit antiviral and anti-inflammatory properties and support in attenuating organ damage due to reduced cytokine release and improving the recovery process from COVID-19 infection.

Molecular mechanisms involved in anosmia induced by SARS-CoV-2, with a focus on the transmembrane serine protease TMPRSS2

Since 2020, SARS-CoV-2 has caused a pandemic virus that has posed many challenges worldwide. Infection with this virus can result in a number of symptoms, one of which is anosmia. Olfactory dysfunction can be a temporary or long-term viral complication caused by a disorder of the olfactory neuroepithelium. Processes such as inflammation, apoptosis, and neuronal damage are involved in the development of SARS-CoV-2-induced anosmia. One of the receptors that play a key role in the entry of SARS-CoV-2 into the host cell is the transmembrane serine protease TMPRSS2, which facilitates this process by cleaving the viral S protein. The gene encoding TMPRSS2 is located on chromosome 21. It contains 15 exons and has many genetic variations, some of which increase the risk of disease. Delta strains have been shown to be more dependent on TMPRSS2 for cell entry than Omicron strains. Blockade of this receptor by serine protease inhibitors such as camostat and nafamostat can be helpful for treating SARS-CoV-2 symptoms, including anosmia. Proper understanding of the different functional aspects of this serine protease can help to overcome the therapeutic challenges of SARS-CoV-2 symptoms, including anosmia. In this review, we describe the cellular and molecular events involved in anosmia induced by SARS-CoV-2 with a focus on the function of the TMPRSS2 receptor.

DRPADC: A novel drug repositioning algorithm predicting adaptive drugs for COVID-19

Given that the usual process of developing a new vaccine or drug for COVID-19 demands significant time and funds, drug repositioning has emerged as a promising therapeutic strategy. We propose a method named DRPADC to predict novel drug-disease associations effectively from the original sparse drug-disease association adjacency matrix. Specifically, DRPADC processes the original association matrix with the WKNKN algorithm to reduce its sparsity. Furthermore, multiple types of similarity information are fused by a CKA-MKL algorithm. Finally, a compressed sensing algorithm is used to predict the potential drug-disease (virus) association scores. Experimental results show that DRPADC has superior performance than several competitive methods in terms of AUC values and case studies. DRPADC achieved the AUC value of 0.941, 0.955 and 0.876 in Fdataset, Cdataset and HDVD dataset, respectively. In addition, the conducted case studies of COVID-19 show that DRPADC can predict drug candidates accurately.

Targeted therapy in Coronavirus disease 2019 (COVID-19): Implication from cell and gene therapy to immunotherapy and vaccine

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is a highly pathogenic and transmissible virus. Infection caused by SARS-CoV-2 known as Coronavirus disease 2019 (COVID-19) can be severe, especially among high risk populations affected of underlying medical conditions. COVID-19 is characterized by the severe acute respiratory syndrome, a hyper inflammatory syndrome, vascular injury, microangiopathy and thrombosis. Antiviral drugs and immune modulating methods has been evaluated. So far, a particular therapeutic option has not been approved for COVID-19 and a variety of treatments have been studied for COVID-19 including, current treatment such as oxygen therapy, corticosteroids, antiviral agents until targeted therapy and vaccines which are diverse in each patient and have various outcomes. According to the findings of different in vitro and in vivo studies, some novel approach such as gene editing, cell based therapy, and immunotherapy may have significant potential in the treatment of COVID-19. Based on these findings, this paper aims to review the different strategies of treatment against COVID-19 and provide a summary from traditional and newer methods in curing COVID-19.

Using In Silico Bioinformatics Algorithms for the Accurate Prediction of the Impact of Spike Protein Mutations on the Pathogenicity, Stability, and Functionality of the SARS-CoV-2 Virus and Analysis of Potential Therapeutic Targets

Coronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We have used bioinformatics to investigate seventeen mutations in the spike protein of SARS-CoV-2, as this mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapies. Two mutations, H146Y and S221W, were identified as being most pathogenic. Mutations at positions D614G, A829T, and P1263L might also have deleterious effects on protein function. We hypothesized that candidate small molecules may be repurposed to combat viral infection. We investigated changes in binding energies of the ligands and the mutant proteins by assessing molecular docking. For an understanding of cellular function and organization, protein-protein interactions are also critical. Protein-protein docking for naïve and mutated structures of SARS-CoV-2 S protein was evaluated for their binding energy with the angiotensin-converting enzyme 2 (ACE2). These interactions might limit the binding of the SARS-CoV-2 spike protein to the ACE2 receptor or may have a deleterious effect on protein function that may limit infection. These results may have important implications for the transmission of SARS-CoV-2, its pathogenesis, and the potential for drug repurposing and immune therapies.

Identification of Drug Combination Therapies for SARS-CoV-2: A Molecular Dynamics Simulations Approach

Purpose

The development of effective treatments for coronavirus infectious disease 19 (COVID-19) caused by SARS-Coronavirus-2 was hindered by the little data available about this virus at the start of the pandemic. Drug repurposing provides a good strategy to explore approved drugs' possible SARS-CoV-2 antiviral activity. Moreover, drug synergism is essential in antiviral treatment due to improved efficacy and reduced toxicity. In this work, we studied the effect of approved and investigational drugs on one of SARS-CoV-2 essential proteins, the main protease (Mpro), in search of antiviral treatments and/or drug combinations.

Methods

Different possible druggable sites of Mpro were identified and screened against an in-house library of more than 4000 chemical compounds. Molecular dynamics simulations were carried out to explore conformational changes induced by different ligands' binding. Subsequently, the inhibitory effect of the identified compounds and the suggested drug combinations on the Mpro were established using a 3CL protease (SARS-CoV-2) assay kit.

Results

Three potential inhibitors in three different binding sites were identified; favipiravir, cefixime, and carvedilol. Molecular dynamics simulations predicted the synergistic effect of two drug combinations: favipiravir/cefixime, and favipiravir/carvedilol. The in vitro inhibitory effect of the predicted drug combinations was established on this enzyme.

Conclusion

In this work, we could study one of the promising SARS-CoV-2 viral protein targets in searching for treatments for COVID-19. The inhibitory effect of several drugs on Mpro was established in silico and in vitro assays. Molecular dynamics simulations showed promising results in predicting the synergistic effect of drug combinations.