In Silico Screening of Some Anti-Cancer Drugs Against the Main Protease of COVID-19 Using Molecular Docking

Abstract:

The SARS‐CoV‐2 pandemic has led to major worldwide health concerns. Design and detection of effective drugs and adjuvant therapies to treat COVID-19 disease in the shortest possible time have become one of the most critical global challenges. In this study, we investigated the effect of some anticancer drugs against the COVID-19 main protease (Mpro / 3CLpro) to detect an effective treatment, using a molecular docking approach as a fast and cost-effective method. Accordingly, 44 anticancer drugs were selected as a target for the virtual screening. The molecular docking study was carried out using AutoDock Tools (ADT), AutoDock Vina, Discovery Studio, and Open Babel software. Tucatinib, selinexor, irinotecan, olaparib, dacomitinib, lapatinib, ibrutinib, and pazopanib were ranked top as COVID-19 inhibitors with the respective binding energy of -10.1, -9.4, -9.2, -8.9, -8.7, -8.7, -8.6, and -8.5 kcal/mol. Among the drugs tested, tucatinib displayed the highest binding affinity and strong interactions with the active site of COVID-19 3CLpro (-10.1 kcal/mol). Pharmacokinetics properties and drug-likeness of the top 8 selected anticancer drugs were evaluated. The results showed that these drugs could be utilized as potential inhibitors against the main protease of COVID-19, which can help control the spread of this disease. However, in vitro, in vivo studies, and clinical trials will help evaluate the efficacy of these drugs against COVID-19.

A Novel Synthetized sulfonylhydrazone coumarin (E)-4-methyl-N'-(1-(3-oxo-3H-benzo[f]chromen-2- yl)ethylidene)benzenesulfonohydrazide Protect against Isoproterenol Induced Myocardial Infarction in Rats by attenuating Oxidative damage, Biological Changes, and Electrocardiogram

Coumarins and their derivatives are becoming a potential source for new drug discovery due to their vast array of biological activities. The present study was designed to investigate the cardioprotective effects of a newly synthesized coumarin, symbolized as 5,6-PhSHC, against cardiac remodeling process in isoproterenol (ISO) induced myocardial infarction (MI) in male Wistar rats by evaluating hematological, biochemical, and cardiac biomarkers. Rats were pre/co-treated with 5,6-PhSHC or clopidogrel (150 μg/kg body weight) daily for a period of 7 days and then MI was induced by injecting ISO (85 mg/kg body weight), at an interval of 24 hours for 2 consecutive days, on 6^th and 7^th days. The in vivo exploration indicated that the injection of 5,6-PhSHC improved the electrocardiographic (ECG) pattern and prevented severe heart damages by reducing leakage of the cardiac injury markers, such as troponin-T (cTn-T), lactate dehydrogenase (LDH), and creatine kinase-MB. The cellular architecture of cardiac sections, altered in the myocardium of infracted rats, was reversed by 5,6-PhSHC treatment. Results showed that injection of 5,6-PhSHC elicited significant cardioprotective effects by prevention of myocardium cell necrosis and inflammatory cells infiltration, along with marked decrease in plasma levels of fibrinogen. In addition, the total cholesterol, triglyceride, LDL-c, and HDL profiles underwent remarkable beneficial changes. It was also interesting to note that 5,6-PhSHC enhanced the antioxidative defense mechanisms by increasing myocardial glutathione (GSH) level, superoxide dismutase (SOD), and catalase (CAT) activities, together with reducing the levels of thiobarbituric-acid-reactive substances (TBARS), when compared with ISO-induced rats. Taken together, these findings suggested a beneficial role for 5,6-PhSHC against ISO-induced MI in rats. Furthermore, in silico analysis showed that 5,6-PhSHC pocess high computational affinities (E-value > - 9.0 kcal/mol) against cyclooxygenase-2 (PDB-ID: 1CX2), vitamin K epoxide reductase (PDB-ID: 3KP9), glycoprotein IIb/IIIa (PDB-ID: 2VDM) and catalase (PDB-ID: 1DGF). Therefore, the present study provided promising data that the newly synthesized coumarin can be useful in the design and synthesis of novel drug against Myocardial infarction. This article is protected by copyright. All rights reserved.

Magnetization reversal properties and magnetostatic interactions of disk to rod-shaped FeNi layers separated by ultra-thin Cu layers

From fast magnetic memories with low-power consumption to recording media with high densities, realizing the magnetization reversal and interaction of magnetic layers would allow for manipulating the ultimate properties. Here, we use a pulsed electrochemical deposition technique in porous alumina templates (50 nm in pore diameter) to fabricate arrays of nanowires, consisting of FeNi layers (26-227 nm in thickness) with disk to rod-shaped morphologies separated by ultra-thin (3 nm) Cu layers. By acquiring hysteresis curves and first-order reversal curves (FORCs) of the multilayer nanowire arrays, we comprehensively investigate magnetization reversal properties and magnetostatic interactions of the layers at different field angles (0° ≤θ≤ 90°). These involve the extraction of several parameters, including hysteresis curve coercivity (H_c^Hyst), FORC coercivity (H_c^FORC), interaction field distribution width (ΔH_u), and irreversible fraction of magnetization (IF_m) as a function ofθ. We find relatively constant and continuously decreasing trends ofH_c^Hystwhen 0° ≤θ≤ 45°, and 45° < θ≤ 90°, respectively. Meanwhile, angular dependence ofH_c^FORCandIF_mshows continuously increasing and decreasing trends, irrespective of the FeNi layer morphology. Our FORC results indicate the magnetization reversal properties of the FeNi/Cu nanowires are accompanied with vortex domain wall and single vortex modes, especially at high field angles. The rod-shaped layers also induce maximum ΔH_uduring the reversal process, owing to enhancements in both magnetizing and demagnetizing-type magnetostatic interactions.

Nanoincorporation of Plumbagin in Micelles Increase Its In Vivo Anti-Plasmodial Properties

Background:

The application of plumbagin (PLN), with a wide use in pharmaceutical science, is limited due to its low water solubility and poor bioavailability. Micelles can encapsulate hydrophobic drugs due to their hydrophobic core. The aim of this study was to develop and characterize a polymeric micelle formulation of PLN and evaluate its in vivo anti-plasmodial property.

Methods:

The study was conducted at Zanjan University of Medical Sciences, Zanjan, Iran in 2018. The triblock copolymeric micelles of PLN was prepared by e-caprolactone ring-opening polymerization, by PEG as the macroinitiator and using Sn(Oct)₂ for its catalytic properties. The synthesized nanoparticles were characterized by ¹H NMR, FTIR, GPC, AFM, and DLS. The encapsulation efficiency, drug loading capacity, and drug release were measured by UV-Vis at 520 nm. Also in vivo anti-plasmodial potential of fabricated drug loaded micelle was investigated using the 4-day suppressive test against Plasmodium berghei infection in mice.

Results:

The nanoparticles average diameter was obtained less than 80 nm. The loading capacity and encapsulation efficiencies were 18.9±1.3% and 81±0.78%, respectively. In vitro, PLN release studies showed a sustained-release pattern until 7 days in PLN-loaded micelles (M-PLN) and drug release rate in acidic condition was higher than neutral condition. In vivo, anti-plasmodial results against P. berghei displayed an 8-fold increase in anti-plasmodial activity of M-PLN when compared to free PLN at the tested dosage level on the 7^th day.

Conclusion:

Based on these results, PCL–PEG–PCL micelles have a great potential to be the carrier for PLN for the malaria targeting.

Design and Preparation of Copper(II)-Mesalamine Complex Functionalized on Silica-Coated Magnetite Nanoparticles and Study of Its Catalytic Properties for Green and Multicomponent Synthesis of Highly Substituted 4H-Chromenes and Pyridines

In the present study, a green and ecofriendly nanocatalyst was synthesized through functionalization of 2,4,6-trichloro-1,3,5-triazine (TCT) and mesalamine on silica-coated magnetic nanoparticles (MNPs), then coordination with Cu²⁺ without agglomeration, consecutively. The silica-coated MNPs functionalized with the Cu(*II)-mesalamine complex was (Fe₃O₄@SiO₂@NH₂-TCT-mesalamine-Cu(II) MNPs) completely characterized by FT-IR, XRD, EDX, FESEM, TEM, VSM, TGA, and BET analyses. Afterward, the activity of the novel catalyst was investigated in the synthesis of chromene heterocycles, which were an important group of organic compounds. The activity of Fe₃O₄@SiO₂@NH₂-TCT-mesalamine-Cu(II) MNPs as a high-performance heterogeneous nanocatalyst was evaluated for the synthesis of 2-amino-4-aryl-6-(phenylthio)pyridine-3,5-dicarbonitriles and 2-amino-4H-chromenes via aromatic aldehydes, malononitrile, and enolizable C-H acids (resorcinol, 2-hydroxynaphthalene-1,4-dione, and benzenethiol) in ethanol under reflux conditions. Fe₃O₄@SiO₂-TCT-mesalamine-Cu(II) could be quickly separated using an external magnet and reused nine times without a remarkable reduction of its catalytic activity.

Ultrasound-assisted pseudohomogeneous tungstate catalyst for selective oxidation of alcohols to aldehydes

The idea of applying ultrasound (US) as a green activation method in chemical transformations, especially in catalytic alcohol oxidations, technically and ecologically appeals to chemists. In the present work, as an attempt to fulfill the idea of designing an eco-friendly system to oxidize alcoholic substrates into corresponding aldehydes, we developed multifunctional tungstate-decorated CQD base catalyst, A-CQDs/W, and examined its sonooxidation performance in presence of H₂O₂ as a green oxidant in aqua media. By comparing the catalyst performance in oxidize benzyl alcohol as a testing model to benzaldehyde (BeOH) prior and after US irradiation—trace vs 93%- the key role of ultrasonic irradiation in achieving high yield is completely appreciated. Exceptional thermal and compression condition that is created as a result of acoustic waves is in charge of unparalleled yield results in this type of activation method. The immense degree of reagent interaction in this method, ensures the maximum yield in notably low time, which in turn leads to decrease in the number of unreacted reagents and by-products. Meanwhile, the need for using toxic organic solvents and hazardous oxidants, auxiliaries and phase transfer catalyst (PTC) is completely obviated.

Magnetic Silica-Coated Picolylamine Copper Complex [Fe3O4@SiO2@GP/Picolylamine-Cu(II)]-Catalyzed Biginelli Annulation Reaction

An efficient and heterogeneous novel magnetic silica-coated picolylaminecopper complex [Fe₃O₄@SiO₂@GP/Picolylamine-Cu(II)] was synthesized, characterized, and employed as a magnetically recoverable nanocatalyst in Biginelli condensation for the preparation of biologically active 3,4-dihydropyrimidinones. Fe₃O₄@SiO₂@GP/Picolylamine-Cu(II) was synthesized easily using chemical attachment of the picolylaminecompound on Fe₃O₄@SiO₂@GP, followed by treatment with copper salt in ethanol under reflux conditions. Fe₃O₄@SiO₂@GP/Picolylamine-Cu(II) was affirmed by various analyses such as Fourier transform infrared, thermogravimetric analysis, X-ray diffraction, vibrating-sample magnetometry, field-emission scanning electron microscopy, transmission electron microscopy, DLS, inductively coupled plasma, energy-dispersive X-ray spectrometry, X-ray photoelectron spectroscopy, and Brunauer-Emmett-Teller. The resulting catalyst system was successfully used in the Biginelli reaction through a variety of compounds such as aromatic aldehyde, urea, and ethyl acetoacetate under solvent-free conditions or ethylene glycol at 80 °C and yielded the desired products with high conversions with powerful reusability. The current approach was convenient and clean, and only 0.01 g of the catalyst could be used to perform the reaction. The easy work-up procedure, gram-scale synthesis, usage of nontoxic solvent, improved yield, short reaction times, and high durability of the catalyst are several remarkable advantages of the current approach. Also, the Fe₃O₄@SiO₂@GP/Picolylamine-Cu(II) nanocatalyst could be recycled by an external magnet for eight runs with only a significant loss in the product yields.

Synthesis of physically crosslinked PAM/CNT flakes nanocomposite hydrogel films via a destructive approach

Carbon nanotube (CNT)-based hydrogels have recently found a wide variety of applications due to the unique physical and chemical properties of CNTs. CNTs can be used as a nanofiller and/or crosslinker to produce nanocomposite hydrogels with good mechanical and structural properties. In this research, a novel method was reported for producing polyacrylamide (PAM)/oxidized-multiwalled carbon nanotube (O-MWCNT) flakes nanocomposite hydrogel films without using any organic cross-linker or surfactant. Through a mechanism dependent on the reactive oxygen species (ROS), some O-MWCNTs were broken down in situ into small flakes in the aqueous solutions containing acrylamide (AM) and sodium persulfate (NaPS) at the temperature range of 85–90 °C. Simultaneously, in situ polymerization of the AM monomers occurred using free radicals, which resulted in the formation of PAM chains. The flakes acted as crosslinkers by forming hydrogen bonds with PAM chains and formed a hydrogel network after 48 h at room temperature. The hydrogels were characterized by different techniques (FT-IR, Raman, FE-SEM, TEM, TGA, tensile test). The porous structure of the hydrogel films as well as micro-network structures with unique morphologies were observed by SEM. The O-MWCNT flakes and some undegraded O-MWCNTs in the hydrogel network were also observed by TEM. The results showed that PC₂I₂H hydrogel film, as an evolved hydrogel, has excellent swelling performance in aqueous solutions at different pH and temperatures. In addition, this hydrogel showed a tensile strength of 103 MPa in the dry state and an elongation of 703% in the swollen state.

Novel PAM/CNT flakes nanocomposite hydrogel films were synthesized by in situ degradation of the oxidized-MWCNTs into flakes using persulfate activation. The flakes crosslinked the PAM chains via hydrogen bonding to form a hydrogel network.

Design of a Schiff Base Complex of Copper Coated on Epoxy-Modified Core-Shell MNPs as an Environmentally Friendly and Novel Catalyst for the One-Pot Synthesis of Various Chromene-Annulated Heterocycles

An ecofriendly inorganic-organic hybrid and novel Schiff base complex of copper coated on epoxy-modified Fe3O4@SiO2 MNPs was successfully designed and prepared from readily available chemicals. In this method, a Schiff base complex as a linker is utilized to protect copper nanoparticles to the core-shell Fe3O4 exterior without agglomeration. The resulted Schiff base complex of copper coated on epoxy-modified Fe3O4@SiO2 MNPs was characterized and confirmed via different analyses such as FT-IR, TGA, XRD, VSM, FE-SEM, TEM, ICP, EDX, and BET. The novel catalyst was examined for the synthesis of various chromene-annulated heterocycles through the one-pot three component reaction of aromatic aldehydes, various phenols (2-hydroxynaphthalene-1,4-dione/resorcinol/β-naphthol), and malononitrile in ethanol at reflux conditions. This method includes important aspects like no usage of column chromatography, very short reaction times, simplicity of product isolation using ethanol, excellent yields, simple procedures, and magnetic recoverability of the catalyst. All in all, our method makes a novel and significant advancement in the synthesis of various chromene-annulated heterocycles.

Magnetic Nanoparticles Functionalized with Copper Hydroxyproline Complexes as an Efficient, Recoverable, and Recyclable Nanocatalyst: Synthesis and Its Catalytic Application in a Tandem Knoevenagel-Michael Cyclocondensation Reaction

A novel catalyst has been afforded by attaching of a Cu(proline)₂ complex to magnetic nanoparticles through cheap, simple, and readily available chemicals. This catalyst was characterized by Fourier transform infrared, energy-dispersive X-ray, X-ray diffraction, vibrating-sample magnetometry, transmission electron microscopy, scanning electron microscopy, and inductively coupled plasma analyses. The catalytic activity of the Fe₃O₄@NH₂@TCT@HProCu nanocatalyst was investigated in a green and effective synthesis of pyran derivatives in high yields by applying three-component reactions of malononitrile, dimedone, and aldehydes in ethanol. Conversion was high under optimal conditions. The obtained nanocatalyst could be easily separated from the mixture of the reaction and was recyclable nine times via a simple magnet without considerable reduction of its catalytic efficiency. Operational simplicity, high product yields, environmental friendliness, ecofriendliness, economical processing, and easy workup are the features of this methodology.

Repositioning therapeutics for COVID-19: virtual screening of the potent synthetic and natural compounds as SARS-CoV-2 3CLpro inhibitors

The widespread transmission of SARS-CoV-2 has sparked alarm worldwide. Attaining the best drugs to treat COVID-19 at the shortest possible time is one of the most critical issues in this urgent situation. Molecular docking investigation of the therapeutic potential of marketed drugs is a fast and cost-effective approach to provide a solution to this problem. The recent research efforts have led to the resolving of the 3CLpro structure as a key protease in the lifecycle of coronavirus, which could facilitate in silico evaluation of drug candidates. Herein, the similarity between the SARS-CoV-2-3CL main protease and the other SARS-CoV receptors was evaluated via multiple sequence alignment and phylogenetic tree. The reported structure of the 3CLpro was considered as a target to identify potential inhibitors for treating COVID-19 using molecular docking based virtual screening protocol. Accordingly, a database of 50 synthetic compounds with various pharmacological usage such as antiviral, anti-inflammatory, anti-human immunodeficiency viruses, antimalarial, antibacterial, anticancer, and antioxidant including approved drugs and those undergoing clinical trials, and 40 natural compounds particularly those employed in traditional Iranian medicine was constructed. The output of multiple sequence alignment analysis showed that SARS-CoV-2 main protease shares a similarity of 96% with SARS-CoV. Also, the docking results indicated that the licofelone acyl glucuronide as an anti-inflammatory drug and delta-bilirubin as an antioxidant and anti-inflammatory agent as well as kappa-carrageenan conformer, beta-D-galactopyranosyl and calycosin 7-O-glucoside as natural compounds with minimal side-effects, according to in vitro studies, are good candidates to block the enzymatic activity of SARS-CoV-2 3CLpro. Moreover, the compound 1 with the highest negative binding energy is a chemical compound that due to its favorable interactions with the 3CLpro can be identified as a representative potential drug candidate for COVID-19.

A review on the syntheses of Dronabinol and Epidiolex as classical cannabinoids with various biological activities including those against SARS-COV2

The very important psychoactive phytocannabinoid from Cannabis Δ⁹ tetrahydrocannabinol (Δ⁹-THC) and its non-psychotropic member is cannabidiol (CBD). These compounds have a variety of pharmacological activities. THC has been approved for the treatment of nausea caused by chemotherapy, multiple sclerosis and chronic and neuropathic pain and research is underway to use it to treat stimulation of dementia, anorexia nervous and Tourette’s syndrome. CBD has therapeutic benefits in Epilepsy, neuroprotective, cancer, inflammatory and anxiety. Recognizing candidate drugs efficiently in the new SARS-CoV2 disease 2019 (Covid-19) is crucial. Cannabidiol and Δ⁹-tetrahydrocannabinol have immunomodulatory and anti-inflammatory effects. They can reduce the uncontrolled cytokine production of acute lung injury. Although THD and CBD can be extracted from natural sources due to the disadvantages of this method such as difficulty in purification, cultivation, etc. It has been proven that chemical-synthesis methods of these two compounds can solve these problems. This review briefly summarizes the chemical-synthetic strategies of Dronabinol and Epidiolex from THC and CBD.

Metabolomics approach to study in vivo toxicity of graphene oxide nanosheets

Although graphene oxide (GO) nanosheets are widely used in different fields, the mechanism of their toxicity remains relatively unknown. NMR-based metabolomics was used to study in vivo time and dose-dependent toxicity of GO nanosheets in mice. Sixty serum samples from mice in four different time intervals including 24 and 72 h and 7 and 21 days after injection of 0-, 1-, and 10-mg/kg b.w. were analyzed based on ¹ HNMR spectra of each sample and multivariate methods. In comparison with the control group, 12 changed metabolites were identified in GO nanosheet-treated mice groups. These metabolites are involved in steroid hormone biosynthesis and steroid biosynthesis pathways. It was seen that the time factor is more important than the dose factor and the groups were separated in a time direction, completely. We found that GO nanosheets has toxicity and can affect steroidal hormones. However, this study shows that after 21 days, the treated groups regardless of their GO nanosheet dose are very close to the control group. This means that in one step exposure to GO nanosheets, their toxicity diminished after 21 days.

In silico evaluation of COVID-19 main protease interactions with honeybee natural products for discovery of high potential antiviral compounds

This research investigates antiviral potential of extracted honeybee products against COVID-19 main protease (Mpro) by computational methods. The crystal structure of COVID-19 Mpro was obtained from the protein data bank. Six synthetic drugs with antiviral properties were used as control samples in order to compare the results with those of natural ligands. The six honeybee components, namely 3,4,5-Tricaffeoylquinic acid, Kaempferol-3-O-glucoside, (E)-2'-Geranyl-3',4',7-Trihydroxyflavanone, 6-Cinnamylchrysin, (+)-Pinoresinol, and (24E)-3-Oxo-27,28-dihydroxycycloart-24-en-26-oic acid, have represented the lowest binding energies of -9.0, -8.5, -8.2, -7.8, -7.7, -7.3 and -6.7 Kcal/mol, respectively. These natural inhibitors were then picked for further investigations on their pharmacokinetic features. Also a 150 ns of Molecular dynamics simulations were carried out in order to evaluate their effects on protein structure and dynamics. The 3, 4, 5-Tricaffeoylquinic acid is hopefully proposed for COVID-19 Mpro inhibition if further in vitro, in vivo, and clinical trial studies will approve its effectiveness against COVID-19.

Highly Sensitive Colorimetric Naked-Eye Detection of HgII Using a Sacrificial Metal-Organic Framework

This study has developed a specific, easy, and novel approach to designing a sacrificial metal-organic framework (MOF) that can detect and measure the amount of Hg²⁺ in aqueous and nonaqueous solutions using the naked eye. The functionalized [Zn(oba)(RL3)_0.5]_n·1.5DMF (TMU-59) provides the ability of simple visual assessment or colorimetric readout without sophisticated analytical equipment. Because of the special interaction with Hg²⁺, degradation of the structure of this unique MOF causes the solution to change color from colorless to a pink that is easily recognizable to the naked eye. The presence of a methyl group plays a major role in naked-eye detection by a qualitative sensor. Furthermore, this qualitative sensor data for the production of a simple, instant, and portable red, green, and blue (RGB)-based quantitative sensor were used to determine the concentration of Hg²⁺ in different specimens. As a turn-off fluorescence sensor, this unique structure is also capable of detecting Hg²⁺ at very low concentrations (the limit of detection is 0.16 ppb). To the best of our knowledge, TMU-59 is the first MOF-based naked-eye sensor that can successfully and specifically display the presence of Hg²⁺ through a major color change.