Inhibition of SARS-CoV2 Replication Regulated by NSP3 through Ayurveda Phytoconstituents of Indian Traditional Medicine

With Covid-19, a significant proportion of the population who are already vaccinated have tested positive. Therefore, there is a need for better medicines that act against the virus rigorously without causing any side effects. We aim to achieve the same through molecular docking and further simulations for bioactive phytochemicals of ayurvedic medicinal plants. The target for this study has been considered the NSP3 protein of the viral RNA that actively takes part in both replication and immune evasion pathways of the virus. Ligand libraries consisting of bioactive phytochemicals of aswasgandha and analogues of curcumin and piperine are curated. The libraries, along with the NSP3 protein moiety are docked onto two active sites. With the best-scored complexes further taken up for molecular dynamics simulation, the study resulted in favourable outcomes for three such ligands (compound ID 5469426, 69501714, ZINC000003874317). © 2023 Bharati Vidyapeeth, New Delhi.

New ventilation design criteria for energy sustainability and indoor air quality in a post Covid-19 scenario.

The Covid-19 outbreak raised great attention to the importance of indoor air quality in buildings. Even if the Covid-19 epidemic is nearing an end, all stakeholders agree that increasing outside air flow rates is beneficial for decreasing the likelihood of contagion, lowering the risk of future pandemics, and enhancing the general safety of the interior environment. Indeed, diverse concerns raised about whether the ventilation standards in place are still adequate. In this context, this research intends to assess the suitability of current ventilation standards in addressing the current pandemic scenario and to offer novel criteria and guidelines for the design and operation of HVAC systems, as well as useful guidance for the creation of future ventilation standards in a post-Covid-19 scenario. To that end, a comprehensive analysis of the ANSI/ASHRAE 62.1 is carried out, with an emphasis on its effectiveness in reducing the risk of infection. Furthermore, the efficacy of various ventilation strategies in reducing the likelihood of contagion has been investigated. Finally, because building ventilation is inextricably linked to energy consumption, the energy and economic implications of the proposed enhancements have been assessed. To carry out the described analysis, a novel method was developed that combines Building Energy Modelling (BEM) and virus contagion risk assessment. The analyses conducted produced interesting insights and criteria for ventilation system design and operation, as well as recommendations for the development of future standards.

In silico identification of the potential natural inhibitors of SARS-CoV-2 Guanine-N7 methyltransferase

Background: The outbreak of the COVID-19 pandemic caused by the SARS-CoV-2 has triggered intense scientific research into the possible therapeutic strategies that can combat the ravaging disease. One of such strategies is the inhibition of an important enzyme that affects an important physiological process of the virus. The enzyme, Guanine-N7 Methyltransferase is responsible for the capping of the SARS-CoV-2 mRNA to conceal it from the host's cellular defense. The aim of the study: This study aims at computationally identifying the potential natural inhibitors of the SARS-CoV-2 Guanine-N7 methyltransferase binding at the active site (Pocket 41). Material(s) and Method(s): A library of small molecules was obtained from edible African plants and was molecularly docked against the SARS-CoV-2 Guanine-N7 methyltransferase (QHD43415_13. pdb) using the Pyrx software. Sinefungin, an approved antiviral drug had a binding score of -7.6 kcal/ mol with the target was chosen as a standard. Using the molecular descriptors of the compounds, virtual screening for oral availability was performed using the Pubchem and SWISSADME web tools. The online servers pkCSM and Molinspiration were used for further screening for the pharmacokinetic properties and bioactivity respectively. The molecular dynamic simulation and analyses of the Apo and Holo proteins were performed using the GROMACS software on the Galaxy webserver. Result(s): With a total RMSD of 77.78, average RMSD of 3.704, total regional (active site) RMSF of 30.61, average regional RMSF of 1.91, gyration of 6.9986, and B factor of 696.14, Crinamidine showed the greatest distortion of the target. Conclusion(s): All the lead compounds performed better than the standard while Crinamidine is predicted to show the greatest inhibitory activity. Further tests are required to further investigate the inhibitory activities of the lead compounds.Copyright © 2022 Belgorod State National Research University. All right reserved.

Modified coptisine derivatives as an inhibitor against pathogenic Rhizomucor miehei, Mycolicibacterium smegmatis (Black Fungus), Monkeypox, and Marburg virus by molecular docking and molecular dynamics simulation-based drug design approach.

During the second phase of SARS-CoV-2, an unknown fungal infection, identified as black fungus, was transmitted to numerous people among the hospitalized COVID-19 patients and increased the death rate. The black fungus is associated with the Mycolicibacterium smegmatis, Mucor lusitanicus, and Rhizomucor miehei microorganisms. At the same time, other pathogenic diseases, such as the Monkeypox virus and Marburg virus, impacted global health. Policymakers are concerned about these pathogens due to their severe pathogenic capabilities and rapid spread. However, no standard therapies are available to manage and treat those conditions. Since the coptisine has significant antimicrobial, antiviral, and antifungal properties; therefore, the current investigation has been designed by modifying coptisine to identify an effective drug molecule against Black fungus, Monkeypox, and Marburg virus. After designing the derivatives of coptisine, they have been optimized to get a stable molecular structure. These ligands were then subjected to molecular docking study against two vital proteins obtained from black fungal pathogens: Rhizomucor miehei (PDB ID: 4WTP) and Mycolicibacterium smegmatis (PDB ID 7D6X), and proteins found in Monkeypox virus (PDB ID: 4QWO) and Marburg virus (PDB ID 4OR8). Following molecular docking, other computational investigations, such as ADMET, QSAR, drug-likeness, quantum calculation and molecular dynamics, were also performed to determine their potentiality as antifungal and antiviral inhibitors. The docking score reported that they have strong affinities against Black fungus, Monkeypox virus, and Marburg virus. Then, the molecular dynamic simulation was conducted to determine their stability and durability in the physiological system with water at 100 ns, which documented that the mentioned drugs were stable over the simulated time. Thus, our in silico investigation provides a preliminary report that coptisine derivatives are safe and potentially effective against Black fungus, Monkeypox virus, and Marburg virus. Hence, coptisine derivatives may be a prospective candidate for developing drugs against Black fungus, Monkeypox and Marburg viruses.

Coating of favipiravir (FVP) on silver nanoparticles: First principle study

Silver nanoparticles, thanks to their antiviral and antibacterial properties, have great potential in a variety of applications, such as drug-delivery carriers. The coating properties of silver nanoparticles (size range of 1.6 nm) with a well-known drug, Favipirair, were investigated in this study using quantum mechanical and classical atomistic molecular dynamics simulation in order to use as the drug delivery to treat COVID-19 disease. The drug molecule's optimized structure, frequencies, charge distribution, and electrostatic potential maps were simulated using density functional theory (DFT) at the B3LYP/6–311++g(d,p) level of theory. The coating of AgNP with each of these drugs was then studied using molecular dynamics simulation. The interaction affinity obtained from MD results agrees with the DFT results on drug adsorption on the Ag(1 1 1) slab. © 2023

Measuring the performance of SMEs during the pandemic situation using system dynamic

Purpose: This study aims to create a system dynamics simulation model to forecast the performance of small and medium-sized enterprises (SMEs) if some decision-making is executed to reduce the negative of the coronavirus disease 2019 (COVID-19) pandemic. In particular, this study will focus on SMEs that belong to the furniture industry because the furniture industry is one of the leading industries in Indonesia. Design/methodology/approach: The study develops a system dynamics-based model by using three subsystems, i.e. the "production subsystem,” "demand and revenue subsystem” and "raw material (or wood supply) subsystem.” Findings: The best scenario is the third scenario which increases the capacity to the normal situation and government subsidy during and after the pandemic. This scenario gives the best performance for industry revenue and gross domestic product (GDP). However, for the government, the most significant expenditure occurs in the third scenario. This seems a trade-off for the government whether to save the wooden-based furniture industry by encouraging the industry to continue operating during the pandemic accompanied by high subsidies or limiting the activities of the wooden-based furniture industry to prevent the spread of COVID-19 by providing low subsidies. Research limitations/implications: First, this study does not try to combine the system dynamics (SD) methodology with the other method or use a multi-methodology since SD has several limitations and the other method may have several advantages compared to SD. Second, the models used in this study do not consider the decline in forest area and quality. Third, the demand for wooden-based furniture is obtained from historical data on domestic and foreign sales and fourth, the model does not include the government budget as a constraint to make any subsidy to help the SMEs. Practical implications: This study provides essential insights into implementing the policies in the world pandemic situation when SMEs face lockdown policy. Social implications: The study revealed that relevant policy scenarios could be built after simulating and analyzing each scenario's effect on SMEs' performance during the pandemic. Originality/value: This study will enrich the previous study on the impact of the pandemic on SMEs and the dynamic system modeling on SMEs. The previous study discussed the pandemic's impact on SME performance and the impact's analysis in isolation from the dynamic nature of SME owners' decisions or government policy. In this study, the impact generated from the pandemic situation could be different depending on the decision and policies taken by managers from SMEs and the government. © 2023, Emerald Publishing Limited.

Anti-viral drug discovery against monkeypox and smallpox infection by natural curcumin derivatives: A Computational drug design approach.

Background: In the last couple of years, viral infections have been leading the globe, considered one of the most widespread and extremely damaging health problems and one of the leading causes of mortality in the modern period. Although several viral infections are discovered, such as SARS CoV-2, Langya Henipavirus, there have only been a limited number of discoveries of possible antiviral drug, and vaccine that have even received authorization for the protection of human health. Recently, another virial infection is infecting worldwide (Monkeypox, and Smallpox), which concerns pharmacists, biochemists, doctors, and healthcare providers about another epidemic. Also, currently no specific treatment is available against Monkeypox. This research gap encouraged us to develop a new molecule to fight against monkeypox and smallpox disease. So, firstly, fifty different curcumin derivatives were collected from natural sources, which are available in the PubChem database, to determine antiviral capabilities against Monkeypox and Smallpox. Material and method: Preliminarily, the molecular docking experiment of fifty different curcumin derivatives were conducted, and the majority of the substances produced the expected binding affinities. Then, twelve curcumin derivatives were picked up for further analysis based on the maximum docking score. After that, the density functional theory (DFT) was used to determine chemical characterizations such as the highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), softness, and hardness, etc. Results: The mentioned derivatives demonstrated docking scores greater than 6.80 kcal/mol, and the most significant binding affinity was at -8.90 kcal/mol, even though 12 molecules had higher binding scores (-8.00 kcal/mol to -8.9 kcal/mol), and better than the standard medications. The molecular dynamic simulation is described by root mean square deviation (RMSD) and root-mean-square fluctuation (RMSF), demonstrating that all the compounds might be stable in the physiological system. Conclusion: In conclusion, each derivative of curcumin has outstanding absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics. Hence, we recommended the aforementioned curcumin derivatives as potential antiviral agents for the treatment of Monkeypox and Smallpox virus, and more in vivo investigations are warranted to substantiate our findings.

Inhibitory mechanism of clioquinol and its derivatives at the exopeptidase site of human angiotensin-converting enzyme-2 and receptor binding domain of SARS-CoV-2 viral spike.

The outbreak of SARS-CoV-2 infections around the world has prompted scientists to explore different approaches to develop therapeutics against COVID-19. This study focused on investigating the mechanism of inhibition of clioquinol (CLQ) and its derivatives (7-bromo-5-chloro-8-hydroxyquinoline (CLBQ), 5, 7-Dichloro-8-hydroxyquinoline (CLCQ)) against the viral glycoprotein, and human angiotensin-converting enzyme-2 (hACE-2) involved in SARS-CoV-2 entry. The drugs were docked at the exopeptidase site of hACE-2 and receptor binding domain (RBD) sites of SARS-CoV-2 Sgp to calculate the binding affinity of the drugs. To understand and establish the inhibitory characteristics of the drugs, molecular dynamic (MD) simulation of the best fit docking complex performed. Evaluation of the binding energies of the drugs to hACE-2 after 100 ns MD simulations revealed CLQ to have the highest binding energy value of -40.4 kcal/mol close to MLN-7640 (-45.4 kcal/mol), and higher than the exhibited values for its derivatives: CLBQ (-34.5 kcal/mol) and CLCQ (-24.8 kcal/mol). This suggests that CLQ and CLBQ bind more strongly at the exopeptidase site than CLCQ. Nevertheless, the evaluation of binding affinity of the drugs to SARS-CoV-2 Sgp showed the drugs are weakly bound at the RBD site, with CLBQ, CLCQ, CLQ exhibiting relatively low energy values of -16.8 kcal/mol, -16.34 kcal/mol, -12.5 kcal/mol, respectively compared to the reference drug, Bisoxatin (BSX), with a value of -25.8 kcal/mol. The structural analysis further suggests decrease in systems stability and explain the mechanism of inhibition of clioquinol against SARS-CoV-2 as reported in previous in vitro study.Communicated by Ramaswamy H. Sarma.

Impact of Drug Repurposing on SARS-Cov-2 Main Protease

Abstract: The recent emergence of the severe acute respiratory disease caused by a novel coronavirus remains a concern posing many challenges to public health and the global economy. The resolved crystal structure of the main protease of SARS-CoV-2 or SCV2 (Mpro) has led to its identification as an attractive target for designing potent antiviral drugs. Herein, we provide a comparative molecular impact of hydroxychloroquine (HCQ), remdesivir, and β-D-N4-Hydroxycytidine (NHC) binding on SCV2 Mpro using various computational approaches like molecular docking and molecular dynamics (MD) simulation. Data analyses showed that HCQ, remdesivir, and NHC binding to SARS-CoV-2 Mpro decrease the protease loop capacity to fluctuate. These binding influences the drugs' optimum orientation in the conformational space of SCV2 Mpro and produce noticeable steric effects on the interactive residues. An increased hydrogen bond formation was observed in SCV2 Mpro–NHC complex with a decreased receptor residence time during NHC binding. The binding mode of remdesivir to SCV2 Mpro differs from other drugs having van der Waals interaction as the force stabilizing protein–remdesivir complex. Electrostatic interaction dominates in the SCV2 Mpro−HCQ and SCV2 Mpro–NHC. Residue Glu166 was highly involved in the stability of remdesivir and NHC binding at the SCV2 Mpro active site, while Asp187 provides stability for HCQ binding. © 2022, Pleiades Publishing, Ltd.

Electronic, intermolecular, quantum computational investigations, molecular docking and simulation studies of the potent antiviral drug EIDD-2801

In this work, an analysis has been done to describe the molecular structure, spectroscopic, reduced density gradient, topological properties, atomic charges, Lipinski rule, Natural bond orbital analysis, docking and molecular dynamics simulation of the potent antiviral drug EIDD-2801 in the effective treatment against COVID-19. Intramolecular charge distribution is well understood by three schemes such as AIM, Mulliken and NBO analysis and non-covalent interactions have been understood through reduced density gradient. Topological properties, such as charge density and Laplacian of charge density along with the electron localization function, make it easy to obtain comprehensive information about bond strengths and critical points. The details obtained from the calculation of global reactivity descriptors and Lipinski rule are useful for understanding the nature of molecular reactivity and site selectivity. Electrostatic potentials help to identify potential electrophilic and nucleophilic sites for interaction between EIDD-2801 and target proteins. The molecular docking combined with molecular dynamic simulation studies enables us to get better picture about the ligand-protein interaction.Copyright © 2023 Indian Chemical Society

A Tutorial on How to Set Up a System Dynamics Simulation on the Example of Covid-19 Pandemic

The Covid-19 virus has substantially transformed many aspects of life, impacted industries, and revolutionized supply chains all over the world. System dynamics modeling, which incorporates systems thinking to understand and map complex events as well as correlations, can aid in predicting future outcomes of the pandemic and generate key learnings. As system dynamic modeling allows for a deeper understanding of the manifestation and dynamics of disease, it was helpful when examining the implications of the pandemic on the supply chain of semiconductor companies. This tutorial describes how the system dynamics simulation model was constructed for the Covid-19 pandemic using AnyLogic Software. The model serves as a general foundation for further epidemiological simulations and system dynamics modeling. © 2022 IEEE.

Emetine, a potent alkaloid for the treatment of SARS-CoV-2 targeting papain-like protease and non-structural proteins: pharmacokinetics, molecular docking and dynamic studies.

The main objective of this study is to find out the anti-SARS-CoV-2 potential of emetine by using molecular docking and dynamic simulation approaches. Interestingly, molecular docking studies suggest that Emetine showed significant binding affinity toward Nsp15 (-10.8 kcal/mol) followed by Nsp12 (-9.5 kcal/mol), RNA-dependent RNA polymerase, RdRp (-9.5 kcal/mol), Nsp16 (-9.4 kcal/mol), Nsp10 (-9.2 kcal/mol), Papain-like protein (-9.0 kcal/mol), Nsp13 (-9.0 kcal/mol), Nsp14 (-8.9 kcal/mol) and Spike Protein Receptor Domain (-8.8 kcal/mol) and chymotrypsin-like protease, 3CLpro (-8.5 kcal/mol), respectively, which are essential for viral infection and replication. In addition, molecular dynamic simulation (MD) was also performed for 140 ns to explore the stability behavior of the main targets and inhibitor complexes as well as the binding mechanics of the ligand to the target proteins. The obtained MD results followed by absolute binding energy calculation confirm that the binding of emetine at the level of the various receptors is more stable. The complex EmetineNSP15, mechanistically was stabilized as follows: Emetine first binds to the monomer, after, binds to the second inducing the formation of a dimer which in turn leading to the formation of complex that simulation stabilizes it at a value less than 5 Å. Overall, supported by the powerful and good pharmacokinetic data of Emetine, our findings with clinical trials may be helpful to confirm that Emetine could be promoted in the prevention and eradication of COVID-19 by reducing the severity in the infected persons and therefore can open possible new strategies for drug repositioning. Communicated by Ramaswamy H. Sarma.

Study of potentiality of dexamethasone and its derivatives against Covid-19.

In December 2019, COVID-19 epidemic was reported in Wuhan, China, and subsequently the infection has spread all over the world and became pandemic. The death toll associated with the pandemic is increasing day by day in a high rate. Herein, an effort has been made to identify the potentiality of commercially available drugs and also their probable derivatives for creation of better opportunity to make more powerful drugs against coronavirus. This study involves the in-silico interactions of dexamethasone and its derivatives against the multiple proteins of SARS-CoV-2 with the help of various computational methods. Descriptor parameters revealed their non-toxic effect in the human body. Ultimately docking studies and molecular dynamic simulation on those target protein by dexamethasone and its derivatives showed a high binding energy. Dexamethasone showed -9.8 kcal/mol and its derivative D5 showed -12.1 kcal/mol binding energy. Those scores indicate that dexamethasone has more therapeutic effect on SARS CoV-2 than other currently used drugs. Derivatives give the clue for the synthesis of a novel drug to remove SARS CoV-2. Until then, dexamethasone will be used as a potential inhibitor of SARS CoV-2.Communicated by Ramaswamy H. Sarma.

Remdesivir analogs against SARS-CoV-2 RNA-dependent RNA polymerase.

The COVID-19 pandemic has already taken many lives but is still continuing its spread and exerting jeopardizing effects. This study is aimed to find the most potent ligands from 703 analogs of remdesivir against RNA-dependent RNA polymerase (RdRp) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus . RdRp is a major part of a multi-subunit transcription complex of the virus, which is essential for viral replication. In clinical trials, it has been found that remdesivir is effective to inhibit viral replication in Ebola and in primary human lung cell cultures; it effectively impedes replication of a broad-spectrum pre-pandemic bat coronaviruses and epidemic human coronaviruses. After virtual screening, 30 most potent ligands and remdesivir were modified with triphosphate. Quantum mechanics-based quantitative structure-activity relationship envisages the binding energy for ligands applying partial least square (PLS) regression. PLS regression remarkably predicts the binding energy of the effective ligands with an accuracy of 80% compared to the value attained from molecular docking. Two ligands (L4:58059550 and L28:126719083), which have more interactions with the target protein than the other ligands including standard remdesivir triphosphate, were selected for further analysis. Molecular dynamics simulation is done to assess the stability and dynamic nature of the drug-protein complex. Binding-free energy results via PRODIGY server and molecular mechanics/Poisson-Boltzmann surface area method depict that the potential and solvation energies play a crucial role. Considering all computational analysis, we recommend the best remdesivir analogs can be utilized for efficacy test through in vitro and in vivo trials against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

Prospective mode of action of Ivermectin: SARS-CoV-2.

The well-known anti-helminthic drug ivermectin (IVM) has been established as an example of drug repurposing for the management of SARS-CoV-2 infection. Various study has been done to understand the inhibitory mechanism of IVM against SARS-CoV-2 targets. Broadly, IVM has been categorized as a host-directed agent and the proposed mechanism involves inhibition of the IMPα/ß1-mediated nuclear import of viral proteins. In addition, in vitro/in vivo and molecular docking/dynamic simulation studies suggested multitargets mechanism of IVM against SARS-CoV-2. Present manuscript attempts to provide an overview of the detailed mechanism of action based on experimental and computational studies. The knowledge of binding interaction of IVM and SARS-CoV-2 targets will give the direction to developed new and potential anti-COVID agents.

Targeting Olokizumab-Interleukin 6 interaction interface to discover novel IL-6 inhibitors.

The IL-6/IL-6R or IL-6/GP130 protein-protein interactions play a significant role in controlling the development of chronic inflammatory diseases, such as rheumatoid arthritis, Castleman disease, psoriasis, and, most recently, COVID-19. Modulating or antagonizing protein-protein interactions of IL6 binding to its receptors by oral drugs promises similar efficacy to biological therapy in patients, namely monoclonal antibodies. In this study, we used a crystal structure of the Fab part of olokizumab in a complex with IL-6 (PDB ID: 4CNI) to uncover starting points for small molecule IL-6 antagonist discovery. Firstly, a structure­based pharmacophore model of the protein active site cavity was generated to identify possible candidates, followed by virtual screening with a significant database Drugbank. After the docking protocol validation, a virtual screening by molecular docking was carried out and a total of 11 top hits were reported. Detailed analysis of the best scoring molecules was performed with ADME/T analysis and molecular dynamics simulation. Furthermore, the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) technique has been utilized to evaluate the free binding energy. Based on the finding, one newly obtained compound in this study, namely DB15187, may serve as a lead compound for the discovery of IL-6 inhibitors.Communicated by Ramaswamy H. Sarma.

Bacillus species; a potential source of anti-SARS-CoV-2 main protease inhibitors.

The COVID-19 being a preconized global pandemic by the World Health Organization needs persuasive immediate research for possible medications. The present study was carried out with a specific aim to computationally evaluate and identify compounds derived from Bacillus species as the plausible inhibitors against 3-chymotrypsin-like main protease (3CLpro) or main protease (MPro), which is a key enzyme in the life-cycle of coronavirus. The compounds were isolated from the crude extracts of Bacillus species. Among the isolated compounds, novel inhibitory leads were identified using in silico techniques. Molecular docking revealed that stigmasterol (-8.3 kcal/mol), chondrillasterol (-7.9 kcal/mol) and hexadecnoic acid (-6.9 kcal/mol)) among others bind in the substrate-binding pocket and also interacted with the catalytic dyad of the 3-CLpro. Further evaluation using 50 ns molecular dynamic simulation and MMPB-GBSA indicated that among the top three docking hits, hexadecanoic acid was found to be the most promising anti-COVID-19 lead against the main protease. Hexadecanoic acid might serve as a potent anti-SARS-CoV-2 compound to combat COVID-19, however, in vitro and in vivo validation and optimization is needed.Communicated by Ramaswamy H. Sarma.

Screening and identification of potential MERS-CoV papain-like protease (PLpro) inhibitors; Steady-state kinetic and Molecular dynamic studies.

MERS-CoV belongs to the coronavirus group. Recent years have seen a rash of coronavirus epidemics. In June 2012, MERS-CoV was discovered in the Kingdom of Saudi Arabia, with 2,591 MERSA cases confirmed by lab tests by the end of August 2022 and 894 deaths at a case-fatality ratio (CFR) of 34.5% documented worldwide. Saudi Arabia reported the majority of these cases, with 2,184 cases and 813 deaths (CFR: 37.2%), necessitating a thorough understanding of the molecular machinery of MERS-CoV. To develop antiviral medicines, illustrative investigation of the protein in coronavirus subunits are required to increase our understanding of the subject. In this study, recombinant expression and purification of MERS-CoV (PLpro), a primary goal for the development of 22 new inhibitors, were completed using a high throughput screening methodology that employed fragment-based libraries in conjunction with structure-based virtual screening. Compounds 2, 7, and 20, showed significant biological activity. Moreover, a docking analysis revealed that the three compounds had favorable binding mood and binding free energy. Molecular dynamic simulation demonstrated the stability of compound 2 (2-((Benzimidazol-2-yl) thio)-1-arylethan-1-ones) the strongest inhibitory activity against the PLpro enzyme. In addition, disubstitutions at the meta and para locations are the only substitutions that may boost the inhibitory action against PLpro. Compound 2 was chosen as a MERS-CoV PLpro inhibitor after passing absorption, distribution, metabolism, and excretion studies; however, further investigations are required.

Euphorbia neriifolia L. phytochemical lead compounds discovered using pharmacoinformatic methods as possible SARS CoV-2 main protease inhibitors

The corona virus (CoV) family's emerging SARS-CoV-2 strain potentially causes one of the most catastrophic COVID-19 pandemics in mankind. Other than vaccines for preventing SARS-CoV-2 infection, no selective drugs are available to treat the disease caused by the SARS-CoV-2. The main protease (Mpro) of SARS-CoV-2 plays a critical role in viral replication, and inhibiting the protease can hamper the virus's replication and infection process. Thus, we aimed to identify SARS-CoV-2 main protease (Mpro) inhibitors from Euphorbia neriifolia. Primarily, a total of 31 compounds were selected through wide literature study and the Indian Medicinal Plants, Phytochemistry and Therapeutics (IMPPAT) server. Current advances in computer-aided drug discovery includes molecular docking, pharmacokinetics, drug properties, toxicity analysis and molecular dynamic (MD) simulation were applied in characterization and identification of possible lead compounds in E. neriifolia. The compound's screening through molecular docking resulted in four phytochemicals, viz., CID: 5316673, CID: 102316539, CID: 101257, and CID: 9547213 exhibiting higher binding affinity of-8.461,-7.355,-6.404, and-6.382 kcal/mol, respectively, to the active site of the target Mpro. Subsequently, these four phytochemicals exhibited good pharmacokinetics and drug properties without toxicity. A MD simulation confirmed the binding stability of four phytochemicals to the Mpro. Our study identified four phytochemicals (CID: 5316673, CID: 102316539, CID: 101257, and CID: 9547213) can be developed as treatment option for SARS-CoV-2 disease related complications. Further in vitro and in vivo screening of the anti-SARS-CoV-2 effectiveness of E. neriifolia, as well as future clinical studies, are encouraged. © 2023 Marmara University Press.

In silico investigation of the interactions of certain drugs proposed for the treatment of Covid-19 with the paraoxonase-1.

Coronavirus disease 2019 (Covid-19) has caused one of the biggest pandemics of modern times, infected over 240 million people and killed over 4.9 million people, and continues to do so. Although many drugs are widely recommended in the treatment of this disease, the interactions of these drugs with an anti-atherosclerotic enzyme, paraoxonase-1 (PON1), are not well known. In our study, we investigated the interactions of 18 different drugs, which are claimed to be effective against covid-19, with the PON1 enzyme and its genetics variants L55M and Q192R with molecular docking, molecular dynamics simulation and free energy calculation method MM/PBSA. We found that ruxolitinib, dexamethasone, colchicine; dexamethasone, sitagliptin, baricitinib and galidesivir, ruxolitinib, hydroxychloroquine were the most effective compounds in binding PON1-w, PON1L55M and PON1Q192R respectively. Mainly, sitagliptin, galidesivir and hydroxychloroquine have attracted attention by showing very high affinity (<-300 kJ/mol) according to the MM/PBSA method. We concluded that the drug interactions should be considered and more attention should be paid in the use of these drugs.Communicated by Ramaswamy H. Sarma.