Main Protease Enzyme Research Articles

Synthesis, and Characterization and In-Silico Analysis Against SARS CoV-2 of Novel Benzimidazolium Salts

N-heterocyclic carbene molecules are often used as the main scaffold in pharmaceutical chemistry, and one of the most important of these is benzimidazoles. Severe Acute Respiratory Syndrome Coronavirus Disease-2 is the cause of the ongoing pandemic, and a drug should be developed against this virus. Scientists have been investigated the antiviral effects of many not only known molecules but also new molecules. In this study, reactivity and anti-coronavirus disease properties of new benzimidazole derivative molecules were investigated by theoretical methods. Three new benzimidazole derivative molecules were synthesized and fully characterized by FT-IR, 1H NMR and, 13C{1H} NMR spectroscopies for this purpose. Density Functional Theory-based calculation methods were used for optimization and frontier orbitals analysis. Also, the interactions of the molecules were evaluated with coronavirus disease main protease, and severe acute respiratory syndrome coronavirus main peptidase and the results were compared with the results of well-known anti-viral drugs by molecular docking methods. According to the results, 1-allyl-3-(3-chlorobenzyl-5,6-dimethylbenzimidazolium chloride represent the best result against both main protease and main peptidase enzyme with -6.36 kcal/mol and -8.87 kcal/mol, respectively. Additionally, three of the molecules were give better binding results than the well-known anti-viral drugs.

Caffeic acid phenethyl ester: A review on its pharmacological importance, and its association with free radicals, COVID-19, and radiotherapy.

Caffeic acid phenethyl ester (CAPE), a main active component of propolis and a flavonoid, is one of the natural products that has attracted attention in recent years. CAPE, which has many properties such as anti-cancer, anti-inflammatory, antioxidant, antibacterial and anti-fungal, has shown many pharmacological potentials, including protective effects on multiple organs. Interestingly, molecular docking studies showed the possibility of binding of CAPE with replication enzyme. In addition, it was seen that in order to increase the binding security of the replication enzyme and CAPE, modifications can be made at three sites on the CAPE molecule, which leads to the possibility of the compound working more powerfully and usefully to prevent the proliferation of cancer cells and reduce its rate. Also, it was found that CAPE has an inhibitory effect against the main protease enzyme and may be effective in the treatment of SARS-CoV-2. This review covers in detail the importance of CAPE in alternative medicine, its pharmacological value, its potential as a cancer anti-proliferative agent, its dual role in radioprotection and radiosensitization, and its use against coronavirus disease 2019 (COVID-19).

WITHDRAWN: In-Silico Study of Resveratrol as Multi-Edged Potent Inhibitor against SARSCov- 2 and Variants of Concern Using Molecular Dynamic Simulation and PCA Analysis

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Virtual Screening of Artemisia annua Phytochemicals as Potential Inhibitors of SARS-CoV-2 Main Protease Enzyme.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a human coronaviruses that emerged in China at Wuhan city, Hubei province during December 2019. Subsequently, SARS-CoV-2 has spread worldwide and caused millions of deaths around the globe. Several compounds and vaccines have been proposed to tackle this crisis. Novel recommended in silico approaches have been commonly used to screen for specific SARS-CoV-2 inhibitors of different types. Herein, the phytochemicals of Pakistani medicinal plants (especially Artemisia annua) were virtually screened to identify potential inhibitors of the SARS-CoV-2 main protease enzyme. The X-ray crystal structure of the main protease of SARS-CoV-2 with an N3 inhibitor was obtained from the protein data bank while A. annua phytochemicals were retrieved from different drug databases. The docking technique was carried out to assess the binding efficacy of the retrieved phytochemicals; the docking results revealed that several phytochemicals have potential to inhibit the SARS-CoV-2 main protease enzyme. Among the total docked compounds, the top-10 docked complexes were considered for further study and evaluated for their physiochemical and pharmacokinetic properties. The top-3 docked complexes with the best binding energies were as follows: the top-1 docked complex with a -7 kcal/mol binding energy score, the top-2 docked complex with a -6.9 kcal/mol binding energy score, and the top-3 docked complex with a -6.8 kcal/mol binding energy score. These complexes were subjected to a molecular dynamic simulation analysis for further validation to check the dynamic behavior of the selected top-complexes. During the whole simulation time, no major changes were observed in the docked complexes, which indicated complex stability. Additionally, the free binding energies for the selected docked complexes were also estimated via the MM-GB/PBSA approach, and the results revealed that the total delta energies of MMGBSA were -24.23 kcal/mol, -26.38 kcal/mol, and -25 kcal/mol for top-1, top-2, and top-3, respectively. MMPBSA calculated the delta total energy as -17.23 kcal/mol (top-1 complex), -24.75 kcal/mol (top-2 complex), and -24.86 kcal/mol (top-3 complex). This study explored in silico screened phytochemicals against the main protease of the SARS-CoV-2 virus; however, the findings require an experimentally based study to further validate the obtained results.

Spectroscopic details on the molecular structure of pyrimidine‑2‑thiones heterocyclic compounds: computational and antiviral activity against the main protease enzyme of SARS-CoV-2

Computational tools in investigating of spectral heterocyclic compounds ranges based on pyrimidine‑2‑thiones, take some importance in identifying their molecular and electronic behavior. Some charcoal heterocyclic compounds were previously synthesized in our laboratory and their experimental results were compared with the computational evaluation. Computational spectroscopic analytical items (IR, NMR and UV–Vis) were calculated using the more popular DFT methods and the predicted results were compared with the reported experimental ones. Quantum and chemical parameters were calculated and molecular electrostatic surface potential (MEP) was studied which predicted the highly electronic sites around the compounds. Some molecular properties (ionization energy, electron affinity, energy gap, hardness, electronegativity, electrophilicity index, static dipole moment and average linear polarizability) of these Schiff bases which were computed at B3LYP/6-31G(d,p) level in aqueous phase. Benchmark analysis was performed for three ab initio functionals such B3LYP, BPV86 and B3PW91 methods to explain the data resulted from NMR spectra. The docking study of some selected previously synthesized compounds was performed using the viral Mpro enzyme protein in compared to a k36 reference ligand inhibitor. The study indicated the ability of the synthesized compounds to form H-bond and hydrophobic (VDW, π-alkyl and π-sulfur) interactions with Mpro enzyme receptor with high inhibition effect of compound L2.

Identification of Potential Inhibitors for Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2) Angiotensin-converting Enzyme 2 and the Main Protease from Anatolian Traditional Plants

Background: The 2019 novel coronavirus disease (COVID-19) has caused a global health catastrophe by affecting the human population around the globe. Unfortunately, there is no specific medication or treatment currently available for COVID-19. Objective: It is extremely important to find effective drug treatment in order to put an end to this pandemic period and return to normal daily life. In this context and considering the urgency, rather than focusing on the discovery of novel compounds, it is critical to explore the effects of existing herbal agents with proven antiviral properties on the virus. Method: Molecular docking studies were carried out employing three different methods, Glide extra precision (XP) docking, induced fit docking (IFD), and molecular mechanics/generalized born surface area (MM/GBSA), to determine the potential antiviral and antibacterial effects of 58 phytochemicals present in Rosmarinus officinalis, Thymbra spicata, Satureja thymbra, and Stachys lavandulifolia plants against the main protease (Mpro) and angiotensin-converting enzyme 2 (ACE2) enzymes. Results: 7 compounds stood out among all the molecules, showing very high binding affinities. According to our findings, the substances chlorogenic acid, rosmarinic acid, and rosmanol exhibited extremely significant binding affinities for both Mpro and ACE2 enzymes. Furthermore, carnosic acid and alphacadinol showed potent anti-Mpro activity, whereas caffeic acid and carvacrol exhibited promising anti- ACE2 activity. Conclusion: Chlorogenic acid, rosmarinic acid, rosmanol, carnosic acid, alpha-cadinol, caffeic acid, and carvacrol compounds have been shown to be powerful anti-SARS-CoV-2 agents in docking simulations against Mpro and ACE2 enzymes, as well as ADME investigations.

Masitinib analogues with the N-methylpiperazine group replaced – A new hope for the development of anti-COVID-19 drugs

Masitinib is an orally acceptable tyrosine kinase inhibitor that is currently investigated under clinical trials against cancer, asthma, Alzheimer’s disease, multiple sclerosis and amyotrophic lateral sclerosis. A recent study confirmed the anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) activity of masitinib through inhibition of the main protease (Mpro) enzyme, an important pharmacological drug target to block the replication of the coronavirus. However, due to the adverse effects and lower potency of the drug, there are opportunities to design better analogues of masitinib. Herein, we substituted the N-methylpiperazine group of Masitinib with different chemical moieties and evaluated their drug-likeness and toxicities. The filtered analogues were subjected to molecular docking studies which revealed that the analogues with substituents methylamine in M10 (CID10409602), morpholine in M23 (CID59789397) and 4-methylmorpholine in M32 (CID143003625) have a stronger affinity to the drug receptor compared to masitinib. The molecular dynamics (MD) simulation analysis reveals that the identified analogues alter the mobility, structural compactness, accessibility to solvent molecules, and the number of hydrogen bonds in the native target enzyme. These structural alterations can help explain the inhibitory mechanisms of these analogues against the target enzyme. Thus, our studies provide avenues for the design of new masitinib analogues as the SARS-CoV-2 Mpro inhibitors.

POTENSI DAUN TEH HIJAU (Camellia sinensis) SEBAGAI INHIBITOR MAIN PROTEASE (Mpro) COVID-19: SEBUAH STUDI MOLECULAR DOCKING

Green tea is an herbal plant that has active compounds including anti-inflammatory, antioxidant, anti-allergic, and antiviral compounds. A previous study, flavonoid compound in tea leaves has been proven as antiviral. The development of effective antiviral drugs against COVID-19 remains a challenge for researchers across the world. A previous study investigated the role of the main protease enzyme (Mpro) which is useful in the viral life cycle as a promising drug target. This study aims to know the potential compounds of green tea leaves as a COVID-19 Mpro inhibitor using molecular docking. 12 compounds and lopinavir were used. Lipinski analysis was carried out to assess potential compounds as a drug. Docking was carried out by Autodock Tools 1.5.6 and Autodock Vina. The visualization was carried out by Discovery Studio v16. The results showed that all compounds compiled the criteria as a drug based on Lipinski rules. Catechin and epicatechin have the same energy bond as lopinavir with a binding energy of -7.1 kcal/mol. Catechin gallate and epicatechin gallate have the strongest energy bond with a binding energy of -9.0 and -8.2 kcal/mol. All compounds bind in the active site of the COVID-19 Mpro so they are competitive inhibitor. Catechin gallate is the strongest inhibitors.

The Discovery of Small Allosteric and Active Site Inhibitors of the SARS-CoV-2 Main Protease via Structure-Based Virtual Screening and Biological Evaluation.

The main protease enzyme (Mpro) of SARS-CoV-2 is one of the most promising targets for COVID-19 treatment. Accordingly, in this work, a structure-based virtual screening of 3.8 million ligand libraries was carried out. After rigorous filtering, docking, and post screening assessments, 78 compounds were selected for biological evaluation, 3 of which showed promising inhibition of the Mpro enzyme. The obtained hits (CB03, GR04, and GR20) had reasonable potencies with Ki values in the medium to high micromolar range. Interestingly, while our most potent hit, GR20, was suggested to act via a reversible covalent mechanism, GR04 was confirmed as a noncompetitive inhibitor that seems to be one of a kind when compared to the other allosteric inhibitors discovered so far. Moreover, all three compounds have small sizes (~300 Da) with interesting fittings in their relevant binding sites, and they possess lead-like characteristics that can introduce them as very attractive candidates for the future development of COVID-19 treatments.

Recent Development in Small Molecules for SARS-CoV-2 and the Opportunity for Fragment-Based Drug Discovery.

The ongoing pandemic of Covid-19 caused by SARS-CoV-2 is a major threat to global public health, drawing attention to develop new therapeutics for treatment. Much research work is focused on identifying or repurposing new small molecules to serve as potential inhibitors by interacting with viral or host-cell molecular targets and understanding the nature of the virus in the host cells. Identifying small molecules as potent inhibitors at an early stage is advantageous in developing a molecule with higher potency and then finding a lead compound for the development of drug discovery. Small molecules can show their inhibition property by targeting either the SARS-CoV-2 main protease (Mpro) enzyme, papain-like protease (PLpro) enzyme, or helicase (Hel), or blocking the spike (S) protein angiotensin-converting enzyme 2 (ACE2) receptor. A very recent outbreak of a new variant (B.1.617.2-termed as Delta variant) of SARS-CoV-2 worldwide posed a greater challenge as it is resistant to clinically undergoing vaccine trials. Thus, the development of new drug molecules is of potential interest to combat SARS-CoV-2 disease, and for that, the fragment-based drug discovery (FBDD) approach could be one of the ways to bring out an effective solution. Two cysteine protease enzymes would be an attractive choice of target for fragment-based drug discovery to tune the molecular structure at an early stage with suitable functionality. In this short review, the recent development in small molecules as inhibitors against Covid-19 is discussed, and the opportunity for FBDD is envisioned optimistically to provide an outlook regarding Covid-19 that may pave the way in the direction of the Covid-19 drug development paradigm.

Efficacy Evaluation of Quercetin and Its Analogues on the Main Protease Enzyme of the COVID-19 Using Molecular Docking Studies

Efficacy Evaluation of Quercetin and Its Analogues on the Main Protease Enzyme of the COVID-19 Using Molecular Docking Studies

Mpro Inhibition: A comparative In silico Therapeutics from Native Indian Plant Species

One of the biggest healthcare threats of this century is COVID – 19, undoubtedly. It has caused millions of deaths and raised alerts in the healthcare domain. This study focuses on the importance of 10 native Indian plant species and the phytochemicals obtained from them as a potential inhibitor to the Main protease enzyme of SARS CoV -2. About 26 phytochemicals were shortlisted for the same from the selected plants. Molecular docking was used to analyze the binding affinity of the phytochemicals in the active pocket of the Main protease enzyme to assess their effectiveness. The docking scores resulted in the selection of four compounds being more favorable than the native inhibitor N3, namely Quercetin, Withaferin A, Sominone, and Nimbin, with their binding energies being -8.42, -9.21, -9.95, -8.88 kcal/mol respectively. Furthermore, these four were further analyzed for their bioavailability scores. The studies showed that Sominone, Withaferin A are more potent inhibitors to Mpro of the SARS CoV-2 in all four. Thus further in Vitro studies can be done accordingly for the same.

Screening, molecular simulation &in silico kinetics of virtually designed covid-19 main protease inhibitors

Coronavirus (covid-19) infection is considered to be deadliest ever pandemic experienced by the human being. It has very badly affected the socio-economic health of human and stuck the scientific community to think and rethink about its complete eradication. But due to no effective treatment or unavailability of vaccine the health professional could not show any significant improvement to control the pandemic. The situation needs newer molecule, vaccine or effective treatment to control covid-19 infection. Different target in viruses has been explored and proteases enzymes were found to be therapeutically effective target for the design of potential anti-covid-19 molecule as it plays the vital role in viral replication and assembly. Structure-based drug design was employed to discover the small molecule of anti-covid-19. Here we considered the small library of naturally occurring polyphenolic compounds and molecular docking, Molecular dynamics (MD) simulations, free binding energy calculation and in-silico ADME calculations to identify the newer HITs. Based upon their score the two molecules were identified as promising candidate. The docking scores were found to be −7.643 and −7.065 for the HIT1 and HIT-2 respectively. In MD simulations study the RMSD values were found to be 4.3 Å & 4.9 Å respectively. To validate these results MM-GBSA was performed and their binding free energies were computationally determined. The prime energy values of identified HITs (−13412.45 & −13441.8 kJ/mole) were found to be very close proximity to reference molecule (−13493.05 kJ/mole). Then in-silico ADME calculations were performed to calculate the drug likeliness identified HITs. BY considering all the values comparative to reference molecule and obtained in-silico pharmacokinetic properties of identified HITs we can suggest that HIT-1 and HIT-2 would be the most promising molecules that can inhibit the main protease enzyme of covid-19. These two molecules would become the potential drug candidate for the treatment of covid-19 infections.

Bio-Guided Isolation of SARS-CoV-2 Main Protease Inhibitors from Medicinal Plants: In Vitro Assay and Molecular Dynamics.

Since the emergence of the pandemic of the coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the discovery of antiviral phytoconstituents from medicinal plants against SARS-CoV-2 has been comprehensively researched. In this study, thirty-three plants belonging to seventeen different families used traditionally in Saudi Arabia were tested in vitro for their ability to inhibit the SARS-CoV-2 main protease (MPRO). Major constituents of the bio-active extracts were isolated and tested for their inhibition potential against this enzyme; in addition, their antiviral activity against the SARS-CoV-2 Egyptian strain was assessed. Further, the thermodynamic stability of the best active compounds was studied through focused comparative insights for the active metabolites regarding ligand–target binding characteristics at the molecular level. Additionally, the obtained computational findings provided useful directions for future drug optimization and development. The results revealed that Psiadia punctulata, Aframomum melegueta, and Nigella sativa extracts showed a high percentage of inhibition of 66.4, 58.7, and 31.5%, against SARS-CoV-2 MPRO, respectively. The major isolated constituents of these plants were identified as gardenins A and B (from P. punctulata), 6-gingerol and 6-paradol (from A. melegueta), and thymoquinone (from N. sativa). These compounds are the first to be tested invitro against SARS-CoV-2 MPRO. Among the isolated compounds, only thymoquinone (THY), gardenin A (GDA), 6-gingerol (GNG), and 6-paradol (PAD) inhibited the SARS-CoV-2 MPRO enzyme with inhibition percentages of 63.21, 73.80, 65.2, and 71.8%, respectively. In vitro assessment of SARS-CoV-2 (hCoV-19/Egypt/NRC-03/2020 (accession number on GSAID: EPI_ISL_430820) revealed a strong-to-low antiviral activity of the isolated compounds. THY showed relatively high cytotoxicity and was anti-SARS-CoV-2, while PAD demonstrated a cytotoxic effect on the tested VERO cells with a selectivity index of CC50/IC50 = 1.33 and CC50/IC50 = 0.6, respectively. Moreover, GNG had moderate activity at non-cytotoxic concentrations in vitro with a selectivity index of CC50/IC50 = 101.3/43.45 = 2.3. Meanwhile, GDA showed weak activity with a selectivity index of CC50/IC50 = 246.5/83.77 = 2.9. The thermodynamic stability of top-active compounds revealed preferential stability and SARS-CoV-2 MPRO binding affinity for PAD through molecular-docking-coupled molecular dynamics simulation. The obtained results suggest the treating potential of these plants and/or their active metabolites for COVID-19. However, further in-vivo and clinical investigations are required to establish the potential preventive and treatment effectiveness of these plants and/or their bio-active compounds in COVID-19.

An in-silico investigation of potential natural polyphenols for the targeting of COVID main protease inhibitor

The deadliest recent pandemic outbreak of COVID-19 disease has severely damaged the socio-economic health of the people globally. Due to unavailability of any effective vaccine or treatment the human beings are still struggling to overcome the pandemic condition. In an attempt to discover anti-COVID molecule, we used in-silico approach and reported 160 natural polyphenols to identify the most promising druggable HITs that can further used for drug discovery process. The co-crystallized structure COVID protease enzyme (PDB id 6LU7) was used. HTVS, MD simulation, binding energy calculations and in-silico ADME calculation were done and analyzed. Depending upon the scores three compounds galangin, nalsudaldain and rhamnezine were identified and the docking score were found to be −7.704, −6.51, −4.212 respectively. These docked complexes were further subjected to MD simulation runs over a 100 ns time and the RMSD and RMSF values were determined. The RMSD values of three compounds were found to be 2.9 Å, 7.6 Å & 9.5 Å respectively and the lowest RMSF values suggested the steady stability of ligand–protein complexes. The binding free energies (ΔG) of compounds with protein were found to be −49.8, −56.45, −62.87 kJ/mole. Moreover, in-silico ADME calculations indicated the drug likeliness properties of these molecules. By considering all these in-silico results the identified HITs would be the most probable anti-COVID drug molecules that can be further taken in wet lab and can act as lead for development of newer inhibitor of COVID-19 main protease enzyme.

Inhibition of main protease enzyme (Mpro) by active compounds in cabya (Piper retrofractum Vahl.) for covid-19 treatment via in silico experiment

Covid-19 is caused by aetiological agent for SARS-CoV-2. The disease has caused pandemic responsible for deaths and economic loss worldwide. Therefore, novel drugs of covid-19 primarily using herbs are urgently needed. Cabya (Piper retrofractum Vahl.) is a popular spice and also traditionally applied for herbal medicines. This study conducted an in silico experiment to screen methanolic active compounds in cabya and test their inhibitory activities against main protease enzyme (Mpro) as receptor of SARS-CoV-2. The in silico approach complied with molecular docking protocols enabling to evaluate performance of the compounds to inhibit Mpro. Two common drugs were used as control, i.e. chloroquine and ivermectin. As the results, molecular docking showed a promising inhibition by active compounds in cabya; in this regard, beta-sitosterol demonstrated the strongest inhibition against Mpro with binding affinity -7,5 kcal/mol, which is better than chloroquine (-4.8 kcal/mol) and close to ivermectin (-8,5 kcal/mol). The interaction resulted from two hydrogen bonds with amino acids ARG A131 and ASP A289 at distance of 15Å and 2,49 Å, respectively. The inhibition site of beta-sitosterol was similar to that of ivermectin. This research revealed the potential use of cabya for covid-19 treatment through restriction of molecular binding between virus and receptor.

In Silico Studies of Synthetic Sulfatide as a Potential Drug Candidate Against Covid-19

Sulfatides play various roles in many biological processes such as cancer metastasis, viral infections and regulation in nerve cells. The sulfatide molecules are related with hypertension diseases in which ACE2 (Angiotensin converting enzyme) is important for regulating blood pressure. ACE2 is also a key receptor for Covid-19 and highly expressed many different tissue types. Understanding the interaction between the sulfatides and ACE2 might be a key factor to develop potential novel treatments against Covid-19. Here we studied the interaction of main protease enzyme (6LU7) of Covid-19 with native sulfatide(A), chitosan based synthetic sulfatide(B) and inhibitor N3, through in silico studies such as molecular docking, molecular dynamics, ADMET prediction and target selection analysis. The compounds A, B and N3 bind the virus protease enzyme with docking score of -5.420, -6.009, -6.161 kcal/mol respectively indicates synthetic sulfatide binds better than native sulfatide and comparable to N3. Besides, molecular dynamics studies were carried out to reveal the stability of the complexes of interest. ADMET and target prediction studies carried out to reveal pharmacological properties and toxicity of the complexes and synthetic sulfatide found to be a drug-like molecule. We anticipate that computational investigation of virus interaction mechanisms will be an important starting point for experimental research in drug development efforts against Covid-19.

Identification of Natural Compounds with Anti-SARS-CoV-2 Activity using Machine Learning, Molecular Docking and Molecular Dynamics Simulation Studies

The coronavirus pandemic of 2019 (COVID-19) has adversely affected public health and the socioeconomic situation worldwide. Although there is no therapeutic drug to treat COVID, several treatment options are being considered to alleviate symptoms. Hence, researches on prophylactic treatment for COVID are being encouraged. Searching natural products is a rational strategy since it has served as a valuable source of lead compounds in drug discovery. In this study, three machine learning approaches, including Support Vector Machine (SVM), Random Forest (RF) and Gradient Boosting Machine (GBM), have been used to develop the classification model. The molecular docking was performed on AutoDock vina. Further, molecular dynamics (MD) simulation of the potential inhibitors was conducted using the AmberTools package. The accuracy for SVM, RF and GBM was found to be 60.45 %, 63.43 % and 64.93 %, respectively. Further, the model has demonstrated specificity range of 41.67 % to 50.00 % and sensitivity range of 74.32 % to 79.73 %. Application of the model on the NuBBE database, a repository of natural compounds, led us to identify 322 unique natural compounds, likely possessing anti-SARSCoV- 2activity. Further, molecular docking study has yielded three flavonoids and one lignoid compounds with comparable binding affinities to the standard compound. In addition, MD showed that these compounds form stable complexes with different magnitude of binding energy. The in silico investigations suggest that these four compounds likely demonstrate their anti-SARS-CoV-2activity by inhibiting the main protease enzyme. Our developed and validated in silico high-throughput investigations may assist in identifying and developing antiviral drug-like compounds from natural sources. Dhaka Univ. J. Pharm. Sci. 21(1): 1-13, 2022 (June)

Synthesis, crystal structure, and a molecular modeling approach to identify effective antiviral hydrazide derivative against the main protease of SARS-CoV-2

In the fall of 2019, a new type of coronavirus took place in Wuhan city, China, and rapidly spread across the world and urges the scientific community to develop antiviral therapeutic agents. In our effort we have synthesized a new hydrazide derivative, (E)-N'-(1-(4-bromophenyl)ethylidene)-2-(6-methoxynaphthalen-2-yl)propanehydrazide for this purpose because of its potential inhibitory proprieties. The asymmetric unit of the title molecule consists of two independent molecules differing noticeably in conformation. In the crystal, the independent molecules are linked by N—H···O and C—H···O hydrogen bonds and C—H···π(ring) interactions into helical chains extending along the b-axis direction. The chains are further joined by additional C—H···π(ring) interactions into the full 3-D structure. To obtain a structure-activity relationship, the DFT-NBO analysis is performed to study the intrinsic electronic properties of the title compound. Molecular modeling studies were also conducted to examine the binding affinity of the compound for the SARS-CoV-2 main protease enzyme and to determine intermolecular binding interactions. The compound revealed a stable binding mode at the enzyme active pocket with a binding energy value of -8.1 kcal/mol. Further, stable dynamics were revealed for the enzyme-compound complex and reported highly favorable binding energies. The net MMGBSA binding energy of the complex is -37.41 kcal/mol while the net MMPBSA binding energy is -40.5 kcal/mol. Overall, the compound disclosed the strongest bond of ing the main protease enzyme and might be a good lead for further structural optimization.

Immunomodulatory and Anti-Inflammatory Effects of Berberine in Lung Tissue and its Potential Application in Prophylaxis and Treatment of COVID-19.

Natural products with known safety profiles are a promising source for the discovery of new drug leads. Berberine presents an example of one such phytochemical that has been extensively studied for its anti-inflammatory and immunomodulatory properties against myriads of diseases, ranging from respiratory disorders to viral infections. A growing body of research supports the pluripotent therapeutic role berberine may play against the dreaded disease COVID-19. The exact pathophysiological features of COVID-19 are yet to be elucidated. However, compelling evidence suggests inflammation and immune dysregulations as major features of this disease. Being a potent immunomodulatory and anti-inflammatory agent, berberine may prove to be useful for the prevention and treatment of COVID-19. This review aims to revisit the pharmacological anti-inflammatory and immunomodulatory benefits of berberine on a multitude of respiratory infections, which like COVID-19, are known to adversely affect the airways and lungs. We speculate that berberine may help alleviate COVID-19 via preventing cytokine storm, restoring Th1/Th2 balance, and enhancing cell-mediated immunity. Furthermore, the role this promising phytochemical plays on other important inflammatory mediators involved in respiratory disorders will be underscored. We further highlight the role of berberine against COVID-19 by underscoring direct evidence from in silico, in vitro, and in vivo studies suggesting the inhibitory potential berberine may play against three critical SARS-CoV-2 targets, namely main protease, spike protein, and angiotensin-converting enzyme 2 receptor. Further preclinical and clinical trials are certainly required to further substantiate the efficacy and potency of berberine against COVID-19 in humans.