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1.
Tropical Journal of Natural Product Research ; 6(8):1336-1342, 2022.
Article in English | EMBASE | ID: covidwho-2033553

ABSTRACT

The COVID-19 pandemic, caused by the SARS-CoV-2, has prompted international concern. This research aims to find bioactive phytocompounds from the traditional herb Icacina trichantha (Oliv) that could be used as a possible SARS-CoV-2 nonstructural protein inhibitor. GC-MS analysis identified fifteen (15) phytocompounds. In silico molecular docking, drug-likeness, toxicity and prediction of these compounds’ substance activity spectra (PASS) were evaluated. The phytocompounds all have good binding energies, according to molecular docking. The phytocompound, 9,12-octadecanoic acid gave the best binding affinity of-24.98 kcal/mole. All of the identified compounds conformed to Lipinski’s Rule of Five (RO5). This showed that the identified I. trichantha (Oliv) compounds would have lower attrition rates during clinical trials and thus have a better chance of being marketed. The current findings suggest that the discovered phytocompounds of I. trichantha (Oliv) could be developed as a novel COVID-19 medication.

2.
Tropical Journal of Natural Product Research ; 6(8):1233-1240, 2022.
Article in English | EMBASE | ID: covidwho-2033551

ABSTRACT

The coronavirus disease 2019 (COVID-19) is caused by the recently discovered coronavirus and affects several countries worldwide. Some medications may alleviate or minimize some of the disease symptoms, but no drug have been proven to prevent or cure it. However, this study was aimed at investigating the role of some medicinal plants as potent inhibitors of COVID-19 main protease (MPro). More than 250 plant extracts with antiviral activity were exploited for their potential SARS-CoV2 medication using molecular docking. The conformational stability of the compounds extracted from the plants with MPro interactions was evaluated using molecular dynamics simulations. Then, the plant extracts with the highest binding energies were used for treatments by administering them to 50 COVID-19 patients, while the other 50 cases received only the drug without the plant extracts. The results of the theoretical analysis revealed high binding energies for seven compounds. Alliin stabilized COVID-19’s MPro while retaining critical connections and remained stable throughout the simulations. Marrubin and thymoquinone are also capable of protein stabilization over the simulated time. The test plants were observed to be effective against the virus in the COVID-19 patients, with a disease symptom improvement response rate of 78-86 and 60-72% for the first and second groups, respectively. Also, the percentage of oxygen increased from the second day after taking the extracts. Ground-glass opacity disappeared from the second group that received the plant extracts. The findings of this study suggest that these compounds have a great potential for therapeutic activity if isolated and administered alone.

3.
Flora ; 27(2):324-334, 2022.
Article in English | EMBASE | ID: covidwho-2033381

ABSTRACT

Introduction: Dipeptidyl peptidase-4 (DPP4) has been shown to be a functional receptor for MERS-CoV. An interaction between the viral spike protein and DPP4 is thought to facilitate viral entry. We aimed to find out whether sitagliptin, a member of DPP4 inhibitors, would have beneficial effects in COVID-19 patients. Materials and Methods: In this single center retrospective study, we evaluated 58 patients of whom 16 were on sitagliptin treatment. Molecular docking studies were performed to identify possible interactions between ACE2 and sitagliptin. Results: Sitagliptin use shortened the time to clinical recovery about 3.5 and fastened viral clearance more than 5 days. Resolution of all symptoms was achieved on a mean±standard error (SE) of 2.50 ± 0.40 days in sitagliptin (+) group and 5.69 ± 0.61 days in sitagliptin (-) group (Log-rank test, p< 0.001). PCR tests for SARS-CoV-2 resulted negative in mean ± SE of 7.50 ± 0.98 days in sitagliptin (+) and 13.17 ± 1.07 days in sitagliptin (-) group (Log-rank test, p= 0.003). Compared to day 0, CRP, ferritin and D-dimer levels on days three, five, and seven were significantly lower whereas lymphocyte count was higher in sitagliptin (+) group. Conclusion: Our results suggest that sitagliptin seems to have a potential to be considered for the treatment of COVID-19.

4.
Pharmacognosy Journal ; 14(4):267-272, 2022.
Article in English | EMBASE | ID: covidwho-2033369

ABSTRACT

The global pandemic of COVID-19 has caused disastrous consequences for both humans and the economy. The purpose of this study was to determine the potential of juwet (Syzygium cumini L.) and moringa (Moringa oleifera L.) as inhibitors of RBD spike, helicase, Mpro, and RdRp activity of SARS-CoV-2 with an in-silico approach. Samples were obtained from PubChem and RSCB PDB databases. The drug similarity analysis was determined using Swiss ADME and the Lipinski rule of five. Prediction of antivirus probabilities is carried out with PASS Online. Molecular screening is performed by molecular docking using PyRx. Visualization was used using PyMol and Discovery Studio. The bioactive compounds with the best antiviral potential had the lowest affinity bonds to the target proteins against RBD spike, helicase, Mpro, and RdRp of SARS-CoV-2. Results show that ellagic acid from java plum and myricetin from moringa have the best potential as potential antivirals. However, more research is required to validate the results of these computational predictions.

5.
Results Chem ; 4: 100329, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-2031660

ABSTRACT

This work presented the microwave assisted synthesis of six new 2́-hydroxychalcones and their characterization based on FTIR, UV-Vis, 1H NMR, and mass spectral analysis. Quantum chemical studies confirmed the structures of prepared chalcones. Antioxidant, in vitro antimicrobial and in silico antiviral studies have been performed to evaluate their biological performance. Results of molecular docking of prepared 2́-hydroxychalcones against SARS-CoV-2 (7BQY) main protease disclosed their inhibition which is comparable to standard, remdesivir and better than hydroxychloroquine (HCQ). ADMET prediction revealed them to be non-carcinogenic and relatively safe.

6.
Journal of Ginseng Research ; 2022.
Article in English | ScienceDirect | ID: covidwho-2031450

ABSTRACT

Hypercoagulability is frequently observed in patients with severe coronavirus disease-2019 (COVID-19). Platelets are a favorable target for effectively treating hypercoagulability in COVID-19 patients as platelet hyperactivity has also been observed. It is difficult to develop a treatment for COVID-19 that will be effective against all variants and the use of antivirals may not be fully effective against COVID-19 as activated platelets have been detected in patients with COVID-19. Therefore, patients with less severe side effects often turn toward natural remedies. Numerous phytochemicals are being investigated for their potential to treat a variety of illnesses, including cancer and bacterial and viral infections. Natural products have been used to alleviate COVID-19 symptoms. Panax ginseng has potential for managing cardiovascular diseases and could be a treatment for COVID-19 by targeting the coagulation cascade and platelet activation. Using molecular docking, we analyzed the interactions of bioactive chemicals in P. ginseng with important proteins and receptors involved in platelet activation. Furthermore, the SwissADME online tool was used to calculate the pharmacokinetics and drug-likeness properties of the lead compounds of P. ginseng. Dianthramine, deoxyharrtingtonine, and suchilactone were determined to have favorable pharmacokinetic profiles.

7.
Chem Biol Interact ; : 110179, 2022.
Article in English | ScienceDirect | ID: covidwho-2031179

ABSTRACT

Currently, there are no FDA approved antiviral drugs available to treat COVID-19 patients. Also, due to emergence of new SARS-CoV-2 variants, the protective efficacy of vaccines could be reduced, hence it is urgent to have alternative treatments for combating the SARS-CoV-2 infection. Since, there is a long-standing history of herbal medicine in the treatment of respiratory diseases. In the present study, we investigated two polyherbal oil blend viz. Sudarshan AV and Elixir AV (SAV and EAV) in inhibiting SARS-COV-2. From GC-MS analysis of polyherbal oils (SAV and EAV) a total of 11 active compounds were selected, on the basis of their abundance and activity. Further, from the molecular docking studies, we found an inhibitory effect of these compounds on viral envelope and membrane, spike proteins whilst an agonistic effect with human host receptor angiotensin-converting enzyme 2 (ACE2) implicating the crucial role of the individual compound in resistance of SARS-CoV-2. Since, the in-silico results suggest that polyherbal oil (SAV and EAV) contributes in preventing the entry of SARS-CoV-2 into the human body, we further investigated the efficacy of polyherbal formulated essential oil (FEO;SAV & EAV) in prevention and treatment of COVID-19 in hamster model. The male golden Syrian hamsters (n = 23) were divided into 5 groups i.e., Group 1: Control (n = 3);Group 2: Infected (n = 5);Group 3: Infected + Remdesivir (n = 5);Group 4: Infected + FEO (n = 5) and Group 5: Prophylactic FEO + Infected (n = 5). In both treatment and prophylactic groups, the FEO's significantly reduced the lung injury investigated histo-pathologically and viral load expression measured by real time PCR in comparison to infected hamsters. Furthermore, cytokines expression analysis clearly highlighted the efficacy of FEO's due to its anti-inflammatory activity and overall protection in treatment groups. In conclusion, the FEO (SAV & EAV) seem to be potent in both prevention and treatment of COVID-19 and related lung injury.

8.
Biochim Biophys Acta Mol Basis Dis ; : 166551, 2022.
Article in English | ScienceDirect | ID: covidwho-2031146

ABSTRACT

The Spike glycoprotein of SARS-CoV-2, the virus responsible for coronavirus disease 2019, binds to its ACE2 receptor for internalization in the host cells. Elderly individuals or those with subjacent disorders, such as obesity and diabetes, are more susceptible to COVID-19 severity. Additionally, several SARS-CoV-2 variants appear to enhance the Spike-ACE2 interaction, which increases transmissibility and death. Considering that the fruit fly is a robust animal model in metabolic research and has two ACE2 orthologs, Ance and Acer, in this work, we studied the effects of two hypercaloric diets (HFD and HSD) and aging on ACE2 orthologs mRNA expression in Drosophila melanogaster. To complement our work, we analyzed the predicted binding affinity between the Spike protein with Ance and Acer. We show, for the first time, that Ance and Acer genes are differentially regulated and dependent on diet and age in adult flies. At the molecular level, Ance and Acer proteins exhibit the potential to bind to the Spike protein in different regions, as shown by a molecular docking approach. Acer, in particular, interacts with the Spike protein in the same region as in humans. Overall, we suggest that the D. melanogaster is a promising animal model for translational studies on COVID-19 associated risk factors and ACE2.

9.
Arabian Journal of Chemistry ; : 104230, 2022.
Article in English | ScienceDirect | ID: covidwho-2031134

ABSTRACT

Although antimicrobial resistance before the Covid-19 pandemic is a top priority for global public health, research is already ongoing on novel organic compounds with antimicrobial and antiviral properties in changing medical environments in connection with Covid 19. Thanks to the Biginelli reaction, which allows the synthesis of pyrimidine compounds, blockers of calcium channels, antibodies, antiviral, antimicrobial, anti-inflammatory, or antioxidant therapeutic compounds were investigated. In this paper, we aim to present Biginelli's synthesis, its therapeutic properties, and the structural-functional relationship in the test compounds that allows the synthesis of antimicrobial compounds. Both the DFT and TD-DFT computations of spectral data, molecular orbitals (HOMO, LUMO) analysis, and electrostatic potential (MEP) surfaces are carried out as an add-on to synthetic research. Hirshfeld surface analysis was also used to segregate the different intermolecular hydrogen bonds involved in the molecular packing strength. Natural Bond Orbital (NBO) investigation endorses the existence of intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. The dipole moment, linear polarizability, and first hyperpolarizabilities have been explored as molecular parameters. All findings based on DFT exhibit the best consistency with experimental findings, implying that synthesized molecules are highly stable. To better understand the binding mechanism of the SARS-CoV-2 Mpro, we performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations.

10.
Mini Rev Med Chem ; 2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-2029879

ABSTRACT

Widely consumed worldwide, Nigella sativa (NS) is a medicinal herb commonly used in various alternative medicine systems such as Unani and Tibb, Ayurveda, and Siddha. Recommended for regular use in Tibb-e-Nabwi (Prophetic Medicine), NS is considered one of the most notable forms of healing medicine in Islamic literature. Thymoquinone (TQ), the main component of the essential oil of NS, has been reported to have many properties such as antioxidant, anti-inflammatory, antiviral, and antineoplastic. Its chemical structure indicates antiviral potential against many viruses, including the hepatitis C virus, human immunodeficiency virus, and other coronavirus diseases. Interestingly, molecular docking studies have demonstrated that TQ can potentially inhibit the development of the coronavirus disease 2019 (COVID-19) by binding to the receptor site on the transmembrane serine proteinase 2 (the activator enzyme that attaches the virus to the cell). In addition, TQ has been shown to be effective against cancer cells due to its inhibitory effect by binding to the different regions of MDM2, according to the proposed molecular docking study. Detailed in this review is the origin of TQ, its significance in alternative medicine, pharmacological value, potential as a cancer anti-proliferative agent, use against the coronavirus disease 2019 (COVID-19), and treatment of other diseases.

11.
Indian Journal of Biochemistry and Biophysics ; 59(9):879-891, 2022.
Article in English | Scopus | ID: covidwho-2030669

ABSTRACT

Drug repurposing is a major approach used by researchers to tackle the COVID-19 pandemic which has been worsened by the current surge of delta variant in many countries. Though drugs like Remdesivir and Hydroxychloroquine have been repurposed, studies prove these drugs have insignificant effect in treatment. So, in this study, we use the already FDA approved database of 1615 drugs to apply semi-flexible and flexible molecular docking methods to calculate the docking scores and identify the best 20 potential inhibitors for our modelled delta variant spike protein RBD. Then, we calculate 2325 1-D and 2-D molecular descriptors and use machine-learning algorithms like K-Nearest Neighbor, Random Forest, Support Vector Machine and ensemble stacking method to build regression-based prediction models. We identify 15 best descriptors for the dataset all of which were found to be inversely correlated with ligand binding. With only these few descriptors, the models performed excellently with an area under curve (AUC) value of 0.952 in Regression Error Characteristic curve for ensemble stacking. Therefore, we comment that these 15 descriptors are the most important features for the binding of inhibitors to the spike protein and hence these should be studied properly in terms of drug repurposing and drug discovery. © 2022, National Institute of Science Communication and Policy Research. All rights reserved.

12.
J Biomol Struct Dyn ; : 1-11, 2022.
Article in English | PubMed | ID: covidwho-2028811

ABSTRACT

A two-layer ONIOM(B3LYP/6-31G*:PM7) method is used to model the binding of several drug/drug-like molecules (L) at the SARS-CoV-2 S-protein: human ACE2 protein interface cavity. The selected molecules include a set of thirty-five ligands from the study of Smith and Smith which showed a high docking score in the range of -7.0 to -7.7 kcal/mol and another set of seven repurposing drugs, viz. favipiravir, remdesivir, EIDD, galidesivir, triazavirin, ruxolitinib, and baricitinib. The ONIOM model of the cavity (M) showed a highly polarized electron distribution along its top-to-bottom direction while Ls with lengths in the range 1.0 - 1.5 nm fitted well inside the cavity in a head-to-tail fashion to yield ML complexes. The ligands showed a large variation in the ONIOM-level binding energy (E(b)), in the range -2.7 to -85.4 kcal/mol. The E(b) of ML complexes better than -40.0 kcal/mol is observed for myricetin, fidarestat, protirelin, m-digallic acid, glucogallin, benserazide hydrochlorideseradie, remdesivir, tazobactum, sapropterin, nitrofurantoin, quinonoid, pyruvic acid calcium isoniazid, and aspartame, and among them the highest E(b) -85.4 kcal/mol is observed for myricetin. A hydroxy substitution is suggested for the phenyl ring of aspartame to improve its binding behavior at the cavity, and the resulting ligand 43 showed the best E(b) -84.5 kcal/mol. The ONIOM-level study is found to be effective for the interpretation of the noncovalent interactions resulting from residues such as arginine, histidine, tyrosine, lysine, carboxylate, and amide moieties in the active site and suggests rational design strategies for COVID-19 drug development. Communicated by Ramaswamy H. Sarma.

13.
Research on Chemical Intermediates ; : 1-23, 2022.
Article in English | Academic Search Complete | ID: covidwho-2027604

ABSTRACT

Pyrazoline and its derivatives have numerous prominent pharmacological effects. Focusing on its anti-viral property, we have designed and synthesized three novel pyrazoline derivatives (A1–A3) through one-pot three components and characterized them using different spectroscopic techniques (FT-IR, 1H NMR, 13C NMR, and UV). These compounds were evaluated against SARS-CoV-2 main protease utilizing in-silico molecular docking studies. The docking results displayed good inhibitory activity of the synthesized compounds. Among them, compound A2 was the most active against targeted protein. The drug-likeness and ADMET properties were predicted to have varied profiles but could still be developed, especially A2. DFT/TD-DFT calculations through B3LYP/6-311G++ level of theory were applied to provide comparable theoretical data along with MEP map and electronic energy gap of HOMO → LUMO. [ FROM AUTHOR] Copyright of Research on Chemical Intermediates is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

14.
Annals of Phytomedicine-an International Journal ; 10:S77-S85, 2021.
Article in English | Web of Science | ID: covidwho-2026890

ABSTRACT

Viral mutations can become more common as a result of natural selection, random genetic drift or recent epidemiological trends. Even more difficult is to determine whether a single mutation will affect the fate of an illness or a pandemic. World Health Organization designated the latest strain of SARS-CoV-2, the Omicron, as a "variant of concern" as more countries are reporting cases, and it contains a unique mix of mutations that might help it spread faster. Mutations in the SARS-CoV-2 strains at the high rates lead to the in effectiveness of vaccines and developed drugs. As the mutations occur only on the spike proteins of the viral particles, targeting other vital enzymes, i.e., proteases for drug discovery paves way for potential drug candidate irrespective of the mutations. So, the present study focuses on identifying the phytocompounds from Datura metal L. inhibiting the SARS-CoV-2 proteases. The druglikeness, PASS predictions and ADMET properties of the selected compounds were performed. 31 compounds were identified from the KNApSAck database and subjected to molecular docking studies. From the analysis, 7 compounds. Withametelin I, Withametelin J, Withametelin K, Withametelin L, Withametelin M, Withametelin N and Withametelin O showed significant binding energies and ADMET values. Therefore, these compounds can be further utilized for development of novel drugs for treatment of SARS-CoV-2 infections.

15.
Journal of Chemistry and Technologies ; 30(2):151-158, 2022.
Article in English | Scopus | ID: covidwho-2025783

ABSTRACT

Five previously known anthraquinones with amino derivatives and synthesized new triazene (1-[(1E)-3,3-bis(2-hydroxyethyl)triaz-1-en-1-ol]-4-[(2-hydroxyethyl)amino]anthracene-9,10-dione) were evaluated in-silico as inhibitors of COVID-19 main protease. Preliminary screening has shown that the presence of a sulfo group in the second position of the anthraquinone ring reduces activity, probably due to the inability of the molecule to cross the hydrophilic-lipophilic barrier. Therefore, the desulfation reaction of 4-substituted anthraquinone was carried out and triazene was synthesized on its basis, which due to the presence of a triazene bridge showed good activity. The structures of the synthesized compound were confirmed by IR, 1H, 13C NMR, and LC-MS spectral studies. Chemo-informatics study showed that the compound obeyed the Lipinski's rule. Computational docking analysis was performed using PyRx, AutoDock Vina option based on scoring functions. In-silico molecular docking study results demonstrated greater binding energy and affinity to the active binding site of the N3 Coronavirus primary protease. © 2022 Oles Honchar Dnipro National University;

16.
J Genet Eng Biotechnol ; 20: 88, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2021376

ABSTRACT

Background: In seek of potent and non-toxic iminoguanidine derivatives formerly assessed as active Pseudomonas aeruginosa inhibitors, a combined mathematical approach of quantitative structure-activity relationship (QSAR), homology modeling, docking simulation, ADMET, and molecular dynamics simulations were executed on iminoguanidine derivatives. Results: The QSAR method was employed to statistically analyze the structure-activity relationships (SAR) and had conceded good statistical significance for eminent predictive model; (GA-MLR: Q2 LOO = 0.8027; R 2 = 0.8735; R 2 ext = 0.7536). Thorough scrutiny of the predictive models disclosed that the Centered Broto-Moreau autocorrelation - lag 1/weighted by I-state and 3D topological distance-based autocorrelation-lag 9/weighted by I-state oversee the biological activity and rendered much useful information to realize the properties required to develop new potent Pseudomonas aeruginosa inhibitors. The next mathematical model work accomplished here emphasizes finding a potential drug that could aid in curing Pseudomonas aeruginosa and SARS-CoV-2 as the drug targets Pseudomonas aeruginosa. This involves homology modeling of RNA polymerase-binding transcription factor DksA and COVID-19 main protease receptors, docking simulations, and pharmacokinetic screening studies of hits compounds against the receptor to identify potential inhibitors that can serve to regulate the modeled enzymes. The modeled protein exhibits the most favorable regions more than 90% with a minimum disallowed region less than 5% and is simulated under a hydrophilic environment. The docking simulations of all the series to the binding pocket of the built protein model were done to demonstrate their binding style and to recognize critical interacting residues inside the binding site. Their binding constancy for the modeled receptors has been assessed through RMSD, RMSF, and SASA analysis from 1-ns molecular dynamics simulations (MDS) run. Conclusion: Our acknowledged drugs could be a proficient cure for SARS-CoV-2 and Pseudomonas aeruginosa drug discovery, having said that extra testing (in vitro and in vivo) is essential to explain their latent as novel drugs and manner of action. Supplementary Information: The online version contains supplementary material available at 10.1186/s43141-022-00362-z.

17.
Applied Sciences ; 12(16):8361, 2022.
Article in English | ProQuest Central | ID: covidwho-2023103

ABSTRACT

In the current market, there is a growing interest in traditional herbal nutraceuticals. Therefore, herbal formulations have re-emerged as products with sought-after nutraceutical and disease-preventing properties. The health-promoting effects of herbal bioactives are attributed to the active phytoconstituents of these plants. Thus, the aim of the present study was to evaluate the putative nutraceutical effectiveness of the preparations of ten herbs (chamomile, purple coneflower, lemon verbena, pennyroyal, spearmint, oregano, marjoram, headed savory, sea buckthorn, and St. John’s wort) by combining in silico techniques and LC-MS/MS analysis. The binding potential of the selected phenolic compounds, according to literature and web databases, was investigated by using molecular target prediction tools. Aldose reductase (AR), an enzyme of polyol pathway which is related to hyperglycemic-induced pathologies, emerged as the most promising molecular target. The molecular docking results showed that rosmarinic acid, caftaric acid, naringenin, and quercetin presented the highest binding affinity. In a further step, the phytochemical profile of the examined infusions, obtained by LC-MS/MS analysis, revealed that the abovementioned compounds were present, mainly in the herbs of the Lamiaceae family, designating headed savory as the herbal infusion with possible significant inhibitory activity against AR.

18.
Front Pharmacol ; 13:961154, 2022.
Article in English | PubMed | ID: covidwho-2022838

ABSTRACT

Background: Due to the constant mutation of virus and the lack of specific therapeutic drugs, the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still poses a huge threat to the health of people, especially those with underlying diseases. Therefore, drug discovery against the SARS-CoV-2 remains of great significance. Methods: With the main protease of virus as the inhibitor target, 9,614 genistein derivatives were virtually screened by LeDock and AutoDock Vina, and the top 20 compounds with highest normalized scores were obtained. Molecular dynamics simulations were carried out for studying interactions between these 20 compounds and the target protein. The drug-like properties, activity, and ADMET of these compounds were also evaluated by DruLiTo software or online server. Results: Twenty compounds, including compound 11, were screened by normalized molecular docking, which could bind to the target through multiple non-bonding interactions. Molecular dynamics simulation results showed that compounds 2, 4, 5, 11, 13, 14, 17, and 18 had the best binding force with the target protein of SARS-CoV-2, and the absolute values of binding free energies all exceeded 50 kJ/mol. The drug-likeness properties indicated that a variety of compounds including compound 11 were worthy of further study. The results of bioactivity score prediction found that compounds 11 and 12 had high inhibitory activities against protease, which indicated that these two compounds had the potential to be further developed as COVID-19 inhibitors. Finally, compound 11 showed excellent predictive ADMET properties including high absorption and low toxicity. Conclusion: These in silico work results show that the preferred compound 11 (ZINC000111282222), which exhibited strong binding to SARS-CoV-2 main protease, acceptable drug-like properties, protease inhibitory activity and ADMET properties, has great promise for further research as a potential therapeutic agent against COVID-19.

19.
Frontiers in Immunology ; 13, 2022.
Article in English | Web of Science | ID: covidwho-2022758

ABSTRACT

Coronavirus disease 2019 (COVID-19) is a severe pandemic that has posed an unprecedented challenge to public health worldwide. Hepatocellular carcinoma (HCC) is a common digestive system malignancy, with high aggressiveness and poor prognosis. HCC patients may be vulnerable to COVID-19. Since the anti-inflammatory, immunomodulatory and antiviral effects of vitamin D, we aimed to investigate the possible therapeutic effects and underlying action mechanisms of vitamin D in COVID-19 and HCC in this study. By using a range of bioinformatics and network pharmacology analyses, we identified many COVID-19/HCC target genes and analyzed their prognostic significance in HCC patients. Further, a risk score model with good predictive performance was developed to evaluate the prognosis of HCC patients with COVID-19 based on these target genes. Moreover, we identified seven possible pharmacological targets of vitamin D against COVID-19/HCC, including HMOX1, MB, TLR4, ALB, TTR, ACTA1 and RBP4. And we revealed the biological functions, signaling pathways and TF-miRNA coregulatory network of vitamin D in COVID-19/HCC. The enrichment analysis revealed that vitamin D could help in treating COVID-19/HCC effects through regulation of immune response, epithelial structure maintenance, regulation of chemokine and cytokine production involved in immune response and anti-inflammatory action. Finally, the molecular docking analyses were performed and showed that vitamin D possessed effective binding activity in COVID-19. Overall, we revealed the possible molecular mechanisms and pharmacological targets of vitamin D for treating COVID-19/HCC for the first time. But these findings need to be further validated in actual HCC patients with COVID-19 and need further investigation to confirm.

20.
Struct Chem ; : 1-21, 2022 Jul 04.
Article in English | MEDLINE | ID: covidwho-2014346

ABSTRACT

COVID-19 disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) has resulted in tremendous loss of lives across the world and is continuing to do so. Extensive work is under progress to develop inhibitors which can prevent the disease by arresting the virus in its life cycle. One such way is by targeting the main protease of the virus which is crucial for the cleavage and conversion of polyproteins into functional units of polypeptides. In this endeavor, our effort was to identify hit molecule inhibitors for SARS-CoV2 main protease using fragment-based drug discovery (FBDD), based on the available crystal structure of chromene-based inhibitor (PDB_ID: 6M2N). The designed molecules were validated by molecular docking and molecular dynamics simulations. The stability of the complexes was further assessed by calculating their binding free energies, normal mode analysis, mechanical stiffness, and principal component analysis. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-01995-z.

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