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1.
Int J Mol Sci ; 23(4)2022 Feb 21.
Article in English | MEDLINE | ID: covidwho-1705083

ABSTRACT

We theoretically investigated the adsorption of two common anti-COVID drugs, favipiravir and chloroquine, on fluorinated C60 fullerene, decorated with metal ions Cr3+, Fe2+, Fe3+, Ni2+. We focused on the effect of fluoridation on the interaction of fullerene with metal ions and drugs in an aqueous solution. We considered three model systems, C60, C60F2 and C60F48, and represented pristine, low-fluorinated and high-fluorinated fullerenes, respectively. Adsorption energies, deformation of fullerene and drug molecules, frontier molecular orbitals and vibrational spectra were investigated in detail. We found that different drugs and different ions interacted differently with fluorinated fullerenes. Cr3+ and Fe2+ ions lead to the defluorination of low-fluorinated fullerenes. Favipiravir also leads to their defluorination with the formation of HF molecules. Therefore, fluorinated fullerenes are not suitable for the delivery of favipiravir and similar drugs molecules. In contrast, we found that fluorine enhances the adsorption of Ni2+ and Fe3+ ions on fullerene and their activity to chloroquine. Ni2+-decorated fluorinated fullerenes were found to be stable and suitable carriers for the loading of chloroquine. Clear shifts of infrared, ultraviolet and visible spectra can provide control over the loading of chloroquine on Ni2+-doped fluorinated fullerenes.


Subject(s)
Amides/chemistry , Antiviral Agents/chemistry , Chloroquine/chemistry , Fullerenes/chemistry , Metals/chemistry , Pyrazines/chemistry , COVID-19 , Density Functional Theory , Drug Carriers/chemistry , Drug Delivery Systems , Halogenation , Models, Molecular , Nickel/chemistry
2.
J Mol Model ; 28(3): 64, 2022 Feb 18.
Article in English | MEDLINE | ID: covidwho-1699453

ABSTRACT

This paper is a summary of research that looks at the potential of fullerene-like (MO)12 nanoclusters (NCs) in drug-carrying systems using density functional theory. Favipiravir/Zn12O12 (- 34.80 kcal/mol), Favipiravir/Mg12O12 (- 34.98 kcal/mol), and Favipiravir/Be12O12 (- 30.22 kcal/mol) were rated in order of drug adsorption degrees. As a result, Favipiravir attachment to (MgO)12 and (ZnO)12 might be simple, increasing Favipiravir loading efficiency. In addition, the quantum theory of atoms in molecules (QTAIM) assessment was utilized to look at the interactions between molecules. The FMO, ESP, NBO, and Eads reactivity patterns were shown to be in excellent agreement with the QTAIM data. The electrostatic properties of the system with the biggest positive charge on the M atom and the largest Eads were shown to be the best. This system was shown to be the best attraction site for nucleophilic agents. The findings show that (MgO)12 and (ZnO)12 have great carrier potential and may be used in medication delivery.


Subject(s)
Amides/administration & dosage , Amides/chemistry , Antiviral Agents/administration & dosage , Drug Delivery Systems/methods , Nanostructures/chemistry , Pyrazines/administration & dosage , Pyrazines/chemistry , Antiviral Agents/chemistry , COVID-19/drug therapy , Density Functional Theory , Fullerenes/chemistry , Humans , Nanostructures/administration & dosage , Quantum Theory , Spectrophotometry, Ultraviolet , Static Electricity
3.
Sci Rep ; 11(1): 23465, 2021 12 06.
Article in English | MEDLINE | ID: covidwho-1556248

ABSTRACT

Human coronavirus NL63 (HCoV-NL63) mainly affects young children and immunocompromised patients, causing morbidity and mortality in a subset of patients. Since no specific treatment is available, this study aims to explore the anti-SARS-CoV-2 agents including favipiravir and remdesivir for treating HCoV-NL63 infection. We first successfully modelled the 3D structure of HCoV-NL63 RNA-dependent RNA polymerase (RdRp) based on the experimentally solved SARS-CoV-2 RdRp structure. Molecular docking indicated that favipiravir has similar binding affinities to SARS-CoV-2 and HCoV-NL63 RdRp with LibDock scores of 75 and 74, respectively. The LibDock scores of remdesivir to SARS-CoV-2 and HCoV-NL63 were 135 and 151, suggesting that remdesivir may have a higher affinity to HCoV-NL63 compared to SARS-CoV-2 RdRp. In cell culture models infected with HCoV-NL63, both favipiravir and remdesivir significantly inhibited viral replication and production of infectious viruses. Overall, remdesivir compared to favipiravir is more potent in inhibiting HCoV-NL63 in cell culture. Importantly, there is no evidence of resistance development upon long-term exposure to remdesivir. Furthermore, combining favipiravir or remdesivir with the clinically used antiviral cytokine interferon-alpha resulted in synergistic effects. These findings provided a proof-of-concept that anti-SARS-CoV-2 drugs, in particular remdesivir, have the potential to be repurposed for treating HCoV-NL63 infection.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Amides/chemistry , Antiviral Agents/chemistry , Coronavirus NL63, Human/enzymology , Pyrazines/chemistry , RNA-Dependent RNA Polymerase/chemistry , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/metabolism , Adenosine Monophosphate/pharmacology , Alanine/chemistry , Alanine/metabolism , Alanine/pharmacology , Amides/metabolism , Amides/pharmacology , Animals , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Binding Sites , Cell Culture Techniques , Cell Line , Coronavirus NL63, Human/physiology , Haplorhini , Humans , Molecular Docking Simulation , Pyrazines/metabolism , Pyrazines/pharmacology , RNA-Dependent RNA Polymerase/metabolism , Virus Replication/drug effects
4.
Mol Cell ; 81(21): 4467-4480.e7, 2021 11 04.
Article in English | MEDLINE | ID: covidwho-1473419

ABSTRACT

Viral RNA-dependent RNA polymerases (RdRps) are a target for broad-spectrum antiviral therapeutic agents. Recently, we demonstrated that incorporation of the T-1106 triphosphate, a pyrazine-carboxamide ribonucleotide, into nascent RNA increases pausing and backtracking by the poliovirus RdRp. Here, by monitoring enterovirus A-71 RdRp dynamics during RNA synthesis using magnetic tweezers, we identify the "backtracked" state as an intermediate used by the RdRp for copy-back RNA synthesis and homologous recombination. Cell-based assays and RNA sequencing (RNA-seq) experiments further demonstrate that the pyrazine-carboxamide ribonucleotide stimulates these processes during infection. These results suggest that pyrazine-carboxamide ribonucleotides do not induce lethal mutagenesis or chain termination but function by promoting template switching and formation of defective viral genomes. We conclude that RdRp-catalyzed intra- and intermolecular template switching can be induced by pyrazine-carboxamide ribonucleotides, defining an additional mechanistic class of antiviral ribonucleotides with potential for broad-spectrum activity.


Subject(s)
Pyrazines/chemistry , RNA Viruses/genetics , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Recombination, Genetic , Ribonucleotides/chemistry , Animals , Antiviral Agents , Catalysis , Cells, Cultured , Genetic Techniques , Genome , Genome, Viral , Homologous Recombination , Humans , Kinetics , Mice , Mice, Transgenic , Molecular Dynamics Simulation , Mutagenesis , Nucleotides/genetics , Protein Conformation , RNA/chemistry , RNA-Dependent RNA Polymerase/metabolism , RNA-Seq , Transgenes , Virulence
5.
Molecules ; 26(13)2021 Jun 28.
Article in English | MEDLINE | ID: covidwho-1383893

ABSTRACT

The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.


Subject(s)
Coronavirus RNA-Dependent RNA Polymerase/chemistry , Electrons , SARS-CoV-2/enzymology , Algorithms , Amides/chemistry , Antiviral Agents/chemistry , Ligands , Molecular Structure , Protein Binding , Pyrazines/chemistry , Ribonucleosides/chemistry
6.
Virol J ; 18(1): 146, 2021 07 13.
Article in English | MEDLINE | ID: covidwho-1309916

ABSTRACT

BACKGROUND: Favipiravir is used in treatment of Covid-19 patients. We aimed to share of ocular surface fluorescence in a patient after Favipiravir treatment in this case report. CASE PRESENTATION: A 20-year-old male patient declared no known systemic disease prior to Covid-19. He applied to us with blurry vision and blue light reflection after Covid-19 treatment with Favipiravir. We observed bilateral fluorescence on his eyes and fluorescence of his nails. Biomicroscopic examination was insignificant. CONCLUSION: We investigated the fluorescence of favipiravir tablets under ultraviolet light. Drug demonstrated fluorescence. We recorded the favipiravir fluorescence in-vitro. This appears to be a strong evidence in terms of the linkage between the fluorescence of the ocular surface and favipiravir.


Subject(s)
Amides/adverse effects , Antiviral Agents/adverse effects , COVID-19/drug therapy , Eye/chemistry , Pyrazines/adverse effects , Adult , Amides/administration & dosage , Amides/chemistry , Antiviral Agents/administration & dosage , Antiviral Agents/chemistry , COVID-19/virology , Eye/virology , Fluorescence , Humans , Male , Pyrazines/administration & dosage , Pyrazines/chemistry , SARS-CoV-2/physiology
7.
Mol Pharm ; 18(8): 3108-3115, 2021 08 02.
Article in English | MEDLINE | ID: covidwho-1305357

ABSTRACT

Coronavirus disease 2019 (COVID-19) has spread across the world, and no specific antiviral drugs have yet been approved to combat this disease. Favipiravir (FAV) is an antiviral drug that is currently in clinical trials for use against COVID-19. However, the delivery of FAV is challenging because of its limited solubility, and its formulation is difficult with common organic solvents and water. To address these issues, four FAV ionic liquids (FAV-ILs) were synthesized as potent antiviral prodrugs and were fully characterized by nuclear magnetic resonance (NMR) spectroscopy, Fourier-transform infrared (FT-IR) spectrometry, powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), derivative thermogravimetry (DTG), and differential scanning calorimetry (DSC). The aqueous solubility and in vivo pharmacokinetic properties of the FAV-ILs were also evaluated. The FAV-ILs exhibited improved aqueous solubility by 78 to 125 orders of magnitude when compared with that of free FAV. Upon oral dosing in mice, the absolute bioavailability of the ß-alanine ethyl ester FAV formulation was increased 1.9-fold compared with that of the control FAV formulation. The peak blood concentration, elimination half-life, and mean absorption time of FAV were also increased by 1.5-, 2.0-, and 1.5-fold, respectively, compared with the control. Furthermore, the FAV in the FAV-ILs exhibited significantly different biodistribution compared with the control FAV formulation. Interestingly, drug accumulation in the lungs and liver was improved 1.5-fold and 1.3-fold, respectively, compared with the control FAV formulation. These results indicate that the use of ILs exhibits potential as a simple, scalable strategy to improve the solubility and oral absorption of hydrophobic drugs, such as FAV.


Subject(s)
Amides/administration & dosage , Antiviral Agents/administration & dosage , Ionic Liquids/chemistry , Pyrazines/administration & dosage , Administration, Oral , Amides/chemical synthesis , Amides/chemistry , Amides/pharmacokinetics , Animals , COVID-19/drug therapy , Female , Mice , Mice, Inbred BALB C , Pyrazines/chemical synthesis , Pyrazines/chemistry , Pyrazines/pharmacokinetics , Solubility , Tissue Distribution
8.
Magn Reson Chem ; 59(7): 746-751, 2021 07.
Article in English | MEDLINE | ID: covidwho-1182204

ABSTRACT

Favipiravir is an established antiviral that is currently being assessed as an investigational drug for the treatment of COVID-19. Favipiravir is strikingly similar to two molecules that the World Health Organization (WHO) lists as essential medicines, which also consist of a six-membered aromatic N-heterocycle bearing a carboxamide function: the anti-tuberculosis agent, pyrazinamide, and nicotinamide, also known as vitamin B3 . We demonstrate the utility of 1 H nuclear magnetic resonance (NMR) profiling, an emerging pharmacopoeial tool, for the highly specific identification, selective differentiation of congeners, and subsequent detection of drug falsification or adulteration of these medicines. The straightforward comparison of basic 1-D 1 H NMR spectra, obtained with benchtop or advanced NMR instruments alike, offers a rapid identity assay and works independently of physical reference materials. This approach accelerates and advances pharmaceutical quality control measures under situations of increased drug demand and altered economy, such as during a pandemic.


Subject(s)
Amides/analysis , Antiviral Agents/analysis , Drug Contamination/prevention & control , Niacinamide/analysis , Pyrazinamide/analysis , Pyrazines/analysis , Quality Control , Amides/chemistry , Antiviral Agents/chemistry , Niacinamide/chemistry , Proton Magnetic Resonance Spectroscopy , Pyrazinamide/chemistry , Pyrazines/chemistry , World Health Organization
9.
Anal Chim Acta ; 1159: 338418, 2021 May 15.
Article in English | MEDLINE | ID: covidwho-1172409

ABSTRACT

Favipiravir, a promising antiviral agent, is undergoing clinical trials for the potential treatment of the novel coronavirus disease 2019 (COVID-19). This is the first report for the electrochemical activity of favipiravir and its electroanalytical sensing. For this purpose, the effect of cationic surfactant, CTAB was demonstrated on the enhanced accumulation of favipiravir at the surface of cathodically pretreated boron-doped diamond (CPT-BDD) electrode. At first, the electrochemical properties of favipiravir were investigated in the surfactant-free solutions by the means of cyclic voltammetry. The compound presented a single oxidation step which is irreversible and adsorption controlled. A systematic study of various operational conditions, such as electrode pretreatment, pH of the supporting electrolyte, concentration of CTAB, accumulation variables, and instrumental parameters on the adsorptive stripping response, was examined using square-wave voltammetry. An oxidation signal at around +1.21 V in Britton-Robinson buffer at pH 8.0 containing 6 × 10-4 M CTAB allowed to the adsorptive stripping voltammetric determination of favipiravir (after 60 s accumulation step at open-circuit condition). The process could be used in the concentration range with two linear segments of 0.01-0.1 µg mL-1 (6.4 × 10-8-6.4 × 10-7 M) and 0.1-20.0 µg mL-1 (6.4 × 10-7-1.3 × 10-4 M). The limit of detection values were found to be 0.0028 µg mL-1 (1.8 × 10-8 M), and 0.023 µg mL-1 (1.5 × 10-7 M) for the first and second segments of calibration graph, respectively. The feasibility of developed methodology was tested to the analysis of the commercial tablet formulations and model human urine samples.


Subject(s)
Amides/chemistry , Antiviral Agents/chemistry , Boron , Diamond , Electrodes , Pyrazines/chemistry , Surface-Active Agents/chemistry , Humans , SARS-CoV-2/drug effects
10.
Proc Natl Acad Sci U S A ; 118(7)2021 02 16.
Article in English | MEDLINE | ID: covidwho-1060504

ABSTRACT

The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.


Subject(s)
Amides/pharmacology , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Enzyme Inhibitors/pharmacology , Pyrazines/pharmacology , SARS-CoV-2/ultrastructure , Amides/chemistry , Coronavirus RNA-Dependent RNA Polymerase/antagonists & inhibitors , Coronavirus RNA-Dependent RNA Polymerase/chemistry , Cryoelectron Microscopy/methods , Enzyme Inhibitors/chemistry , Pyrazines/chemistry , Ribonucleotides/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/enzymology , Single Molecule Imaging/methods
11.
Spectrochim Acta A Mol Biomol Spectrosc ; 247: 119082, 2021 Feb 15.
Article in English | MEDLINE | ID: covidwho-1023740

ABSTRACT

With the global epidemic of the COVID-19 virus, extensive and rapid research on drug therapy is underway around the world. In this regard, one of the most widely studied drugs is Favipiravir. Our aim in this paper is to conduct comprehensive research based on the Density Functional Theory (DFT) on the potential of metallofullerenes as suitable drug carriers. The surface interaction of Favipiravir with organometallic compound resulted by doping of the five transition metals of the first row of the periodic table (Ti, Cr, Cr, Fe, Ni, and Zn) was examined in depth to select the most suitable metallofullerenes. First, the adsorption geometries of Favipiravir drug onto each metallofullerene were deeply investigated. It was found that Cr-, Fe-, and Ni-doped fullerenes provide the excellent adsorbent property with adsorption energies of -148.2, -149.6, and -146.6 kJ/mol, respectively. The Infrared spectroscopy (IR) study was conducted to survey the stretching vibration of bonds involving in the systems, specialty the CO in the drug, CM in the metallofullerene, and MO in the metallofullerene-drug complex. Finally, the UV-vis analysis showed that the absorption spectra for the studied systems may be attributed to the transition from π-π* and/or n-π*.


Subject(s)
Amides/chemistry , COVID-19/epidemiology , Fullerenes/chemistry , Pandemics , Pyrazines/chemistry , SARS-CoV-2/chemistry , Amides/therapeutic use , COVID-19/drug therapy , Fullerenes/therapeutic use , Humans , Molecular Structure , Pyrazines/therapeutic use , Spectrophotometry, Infrared
12.
Molecules ; 25(23)2020 Dec 03.
Article in English | MEDLINE | ID: covidwho-963646

ABSTRACT

The RNA-dependent RNA polymerase (RdRp) is an essential enzyme for the viral replication process, catalyzing the viral RNA synthesis using a metal ion-dependent mechanism. In recent years, RdRp has emerged as an optimal target for the development of antiviral drugs, as demonstrated by recent approvals of sofosbuvir and remdesivir against Hepatitis C virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respectively. In this work, we overview the main sequence and structural features of the RdRp of emerging RNA viruses such as Coronaviruses, Flaviviruses, and HCV, as well as inhibition strategies implemented so far. While analyzing the structural information available on the RdRp of emerging RNA viruses, we provide examples of success stories such as for HCV and SARS-CoV-2. In contrast, Flaviviruses' story has raised attention about how the lack of structural details on catalytically-competent or ligand-bound RdRp strongly hampers the application of structure-based drug design, either in repurposing and conventional approaches.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , RNA Viruses/enzymology , RNA-Dependent RNA Polymerase/chemistry , Amides/chemistry , Amides/pharmacology , Coronavirus/drug effects , Coronavirus/enzymology , Coronavirus/genetics , Drug Design , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Flavivirus/drug effects , Flavivirus/enzymology , Flavivirus/genetics , Hepacivirus/drug effects , Hepacivirus/enzymology , Hepacivirus/genetics , Humans , Pyrazines/chemistry , Pyrazines/pharmacology , RNA Virus Infections/epidemiology , RNA Viruses/drug effects , RNA-Dependent RNA Polymerase/antagonists & inhibitors , RNA-Dependent RNA Polymerase/metabolism , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology
13.
BMC Res Notes ; 13(1): 527, 2020 Nov 11.
Article in English | MEDLINE | ID: covidwho-917943

ABSTRACT

OBJECTIVES: The aim of this study was to use Ligand-based pharmacophore modelling approach for four established antiviral drugs, namely remdesivir, lopinavir, ritonavir and hydroxychloroquine for COVID-19 inhibitors as training sets. In this study Twenty vanillin derivatives together with monolaurin and tetrodotoxin were used as test sets to evaluate as potential SARS-CoV-2 inhibitors. The Structure-based pharmacophore modelling approach was also performed using 5RE6, 5REX and 5RFZ in order to analyse the binding site and ligand-protein complex interactions. RESULTS: The pharmacophore modelling mode of 5RE6 displayed two Hydrogen Bond Acceptors (HBA) and one Hydrophobic (HY) interaction. Besides, the pharmacophore model of 5REX showed two HBA and two HY interactions. Finally, the pharmacophore model of 5RFZ showed three HBA and one HY interaction. Based on ligand-based approach, 20 Schiff-based vanillin derivatives, showed strong MPro inhibition activity. This was due to their good alignment and common features to PDB-5RE6. Similarly, monolaurin and tetrodotoxin displayed some significant activity against SARS-CoV-2. From structure-based approach, vanillin derivatives (1) to (12) displayed some potent MPro inhibition against SARS-CoV-2. Favipiravir, chloroquine and hydroxychloroquine also showed some significant MPro inhibition.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Chloroquine/pharmacology , Cysteine Proteinase Inhibitors/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Amides/chemistry , Amides/pharmacology , Antiviral Agents/chemistry , Benzaldehydes/chemistry , Chloroquine/chemistry , Computer Simulation , Coronavirus 3C Proteases , Cysteine Endopeptidases , Cysteine Proteinase Inhibitors/chemistry , Humans , Hydroxychloroquine/chemistry , Hydroxychloroquine/pharmacology , Laurates/chemistry , Laurates/pharmacology , Microbial Sensitivity Tests , Models, Molecular , Monoglycerides/chemistry , Monoglycerides/pharmacology , Pyrazines/chemistry , Pyrazines/pharmacology , SARS-CoV-2 , Structure-Activity Relationship , Tetrodotoxin/chemistry , Tetrodotoxin/pharmacology
14.
Sci Rep ; 10(1): 14290, 2020 08 31.
Article in English | MEDLINE | ID: covidwho-738236

ABSTRACT

Several drug candidates have been proposed and tested as the latest clinical treatment for coronavirus pneumonia (COVID-19). Chloroquine, hydroxychloroquine, ritonavir/lopinavir, and favipiravir are under trials for the treatment of this disease. The hyperpolarization technique has the ability to further provide a better understanding of the roles of these drugs at the molecular scale and in different applications in the field of nuclear magnetic resonance/magnetic resonance imaging. This technique may provide new opportunities in diagnosis and research of COVID-19. Signal amplification by reversible exchange-based hyperpolarization studies on large-sized drug candidates were carried out. We observed hyperpolarized proton signals from whole structures, due to the unprecedented long-distance polarization transfer by para-hydrogen. We also found that the optimal magnetic field for the maximum polarization transfer yield was dependent on the molecular structure. We can expect further research on the hyperpolarization of other important large molecules, isotope labeling, as well as polarization transfer on nuclei with a long spin relaxation time. A clinical perspective of these features on drug molecules can broaden the application of hyperpolarization techniques for therapeutic studies.


Subject(s)
Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Coronavirus Infections/virology , Drug Discovery , Pneumonia, Viral/virology , Amides/chemistry , Amides/pharmacology , Antiviral Agents/chemistry , COVID-19 , Chloroquine/chemistry , Chloroquine/pharmacology , Coronavirus Infections/diagnosis , Drug Discovery/methods , Humans , Lopinavir/chemistry , Lopinavir/pharmacology , Molecular Structure , Nuclear Magnetic Resonance, Biomolecular , Pandemics , Pneumonia, Viral/diagnosis , Pyrazines/chemistry , Pyrazines/pharmacology , Ritonavir/chemistry , Ritonavir/pharmacology , SARS-CoV-2
15.
J Nanosci Nanotechnol ; 20(12): 7311-7323, 2020 12 01.
Article in English | MEDLINE | ID: covidwho-680345

ABSTRACT

We started a study on the molecular docking of six potential pharmacologically active inhibitors compounds that can be used clinically against the COVID-19 virus, in this case, remdesivir, ribavirin, favipiravir, galidesivir, hydroxychloroquine and chloroquine interacting with the main COVID-19 protease in complex with a COVID-19 N3 protease inhibitor. The highest values of affinity energy found in order from highest to lowest were chloroquine (CHL), hydroxychloroquine (HYC), favipiravir (FAV), galidesivir (GAL), remdesivir (REM) and ribavirin (RIB). The possible formation of hydrogen bonds, associations through London forces and permanent electric dipole were analyzed. The values of affinity energy obtained for the hydroxychloroquine ligands was -9.9 kcal/mol and for the chloroquine of -10.8 kcal/mol which indicate that the coupling contributes to an effective improvement of the affinity energies with the protease. Indicating that, the position chosen to make the substitutions may be a pharmacophoric group, and cause changes in the protease.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Betacoronavirus/drug effects , Betacoronavirus/enzymology , Coronavirus Infections/drug therapy , Coronavirus Infections/virology , Cysteine Endopeptidases/chemistry , Pneumonia, Viral/drug therapy , Pneumonia, Viral/virology , Protease Inhibitors/chemistry , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/chemistry , Adenine/administration & dosage , Adenine/analogs & derivatives , Adenine/chemistry , Adenine/pharmacology , Adenosine/analogs & derivatives , Adenosine Monophosphate/administration & dosage , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/pharmacology , Alanine/administration & dosage , Alanine/analogs & derivatives , Alanine/chemistry , Alanine/pharmacology , Amides/administration & dosage , Amides/chemistry , Amides/pharmacology , Antiviral Agents/administration & dosage , Binding Sites , COVID-19 , Chloroquine/administration & dosage , Chloroquine/chemistry , Chloroquine/pharmacology , Coronavirus 3C Proteases , Drug Interactions , Humans , Hydrogen Bonding , Hydroxychloroquine/administration & dosage , Hydroxychloroquine/chemistry , Hydroxychloroquine/pharmacology , Ligands , Molecular Docking Simulation , Nanotechnology , Pandemics , Protease Inhibitors/administration & dosage , Pyrazines/administration & dosage , Pyrazines/chemistry , Pyrazines/pharmacology , Pyrrolidines/administration & dosage , Pyrrolidines/chemistry , Pyrrolidines/pharmacology , Ribavirin/administration & dosage , Ribavirin/chemistry , Ribavirin/pharmacology , SARS-CoV-2 , Static Electricity
16.
SLAS Discov ; 25(10): 1141-1151, 2020 12.
Article in English | MEDLINE | ID: covidwho-654127

ABSTRACT

COVID-19 respiratory disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has rapidly become a global health issue since it emerged in December 2019. While great global efforts are underway to develop vaccines and to discover or repurpose therapeutic agents for this disease, as of this writing only the nucleoside drug remdesivir has been approved under Emergency Use Authorization to treat COVID-19. The RNA-dependent RNA polymerase (RdRP), a viral enzyme for viral RNA replication in host cells, is one of the most intriguing and promising drug targets for SARS-CoV-2 drug development. Because RdRP is a viral enzyme with no host cell homologs, selective SARS-CoV-2 RdRP inhibitors can be developed that have improved potency and fewer off-target effects against human host proteins and thus are safer and more effective therapeutics for treating COVID-19. This review focuses on biochemical enzyme and cell-based assays for RdRPs that could be used in high-throughput screening to discover new and repurposed drugs against SARS-CoV-2.


Subject(s)
Antiviral Agents/pharmacology , COVID-19/drug therapy , Enzyme Inhibitors/pharmacology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Viral Proteins/antagonists & inhibitors , Adenosine Monophosphate/analogs & derivatives , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/pharmacology , Alanine/analogs & derivatives , Alanine/chemistry , Alanine/pharmacology , Amides/chemistry , Amides/pharmacology , Antiviral Agents/chemistry , Drug Discovery , Enzyme Inhibitors/chemistry , High-Throughput Screening Assays/methods , Humans , Middle East Respiratory Syndrome Coronavirus/chemistry , Middle East Respiratory Syndrome Coronavirus/drug effects , Pyrazines/chemistry , Pyrazines/pharmacology , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , Viral Proteins/chemistry , Viral Proteins/metabolism , Virus Replication/drug effects
17.
Int J Mol Sci ; 21(11)2020 May 30.
Article in English | MEDLINE | ID: covidwho-437471

ABSTRACT

The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2'-Fluoro-2'-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.


Subject(s)
Antiviral Agents/pharmacology , Cysteine Endopeptidases/chemistry , Molecular Docking Simulation , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/chemistry , Amides/chemistry , Amides/pharmacology , Amodiaquine/chemistry , Amodiaquine/pharmacology , Antiviral Agents/chemistry , Binding Sites , Coronavirus 3C Proteases , Cysteine Endopeptidases/metabolism , Protease Inhibitors/chemistry , Protein Binding , Pyrazines/chemistry , Pyrazines/pharmacology , Ribavirin/chemistry , Ribavirin/pharmacology , Viral Nonstructural Proteins/metabolism
18.
J Phys Chem Lett ; 11(11): 4430-4435, 2020 Jun 04.
Article in English | MEDLINE | ID: covidwho-233085

ABSTRACT

The pandemic outbreak of a new coronavirus (CoV), SARS-CoV-2, has captured the world's attention, demonstrating that CoVs represent a continuous global threat. As this is a highly contagious virus, it is imperative to understand RNA-dependent-RNA-polymerase (RdRp), the key component in virus replication. Although the SARS-CoV-2 genome shares 80% sequence identity with severe acute respiratory syndrome SARS-CoV, their RdRps and nucleotidyl-transferases (NiRAN) share 98.1% and 93.2% identity, respectively. Sequence alignment of six coronaviruses demonstrated higher identity among their RdRps (60.9%-98.1%) and lower identity among their Spike proteins (27%-77%). Thus, a 3D structural model of RdRp, NiRAN, non-structural protein 7 (nsp7), and nsp8 of SARS-CoV-2 was generated by modeling starting from the SARS counterpart structures. Furthermore, we demonstrate the binding poses of three viral RdRp inhibitors (Galidesivir, Favipiravir, and Penciclovir), which were recently reported to have clinical significance for SARS-CoV-2. The network of interactions established by these drug molecules affirms their efficacy to inhibit viral RNA replication and provides an insight into their structure-based rational optimization for SARS-CoV-2 inhibition.


Subject(s)
Betacoronavirus/enzymology , Nucleotidyltransferases/chemistry , RNA-Dependent RNA Polymerase/chemistry , Adenine/analogs & derivatives , Adenine/chemistry , Adenine/metabolism , Adenosine/analogs & derivatives , Amides/chemistry , Amides/metabolism , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Betacoronavirus/isolation & purification , Binding Sites , COVID-19 , Coronavirus Infections/epidemiology , Coronavirus Infections/pathology , Coronavirus Infections/virology , Humans , Molecular Docking Simulation , Nucleotidyltransferases/metabolism , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Protein Structure, Tertiary , Pyrazines/chemistry , Pyrazines/metabolism , Pyrrolidines/chemistry , Pyrrolidines/metabolism , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2
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