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Nascimento ALA, de Oliveira Souza S, Guimarães AS, Figueiredo IM, de Albuquerque Dias T, Gomes FS, Botero WG, Santos JCC. Investigation on humic substance and tetracycline interaction mechanism: biophysical and theoretical studies and assessing their effect on biological activity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:20172-20187. [PMID: 38369661 DOI: 10.1007/s11356-024-32168-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/20/2024] [Indexed: 02/20/2024]
Abstract
Tetracycline (TC) is a widely used antibiotic, and evaluating its interaction with humic substances (HS) that act as a complexing agent in the environment is essential to understanding the availability of this contaminant in the environment. This study evaluated the interaction between HS and TC using different spectroscopic techniques, theoretical studies, and biological assays simulating environmental conditions. TC interacts with HS, preferably by electrostatic forces, with a binding constant of 9.2 × 103 M-1 (30 °C). This process induces conformational changes in the superstructure, preferably in the HS, like protein fraction. Besides, studies using the 8-anilino-1-naphthalene sulfonate (ANS) probe indicated that the antibiotic alters the hydrophobicity degree on HS's surface. Synchronized fluorescence shows that the TC interaction occurs preferentially with the protein-like fraction of soil organic matter (KSV = 26.28 ± 1.03 M-1). The TC epitope was evaluated by 1H NMR and varied according to the pH (4.8 and 9.0) of the medium, as well as the main forces responsible for the stabilization of the HS-TC complex. The molecular docking studies showed that the formation of the HS-TC complex is carried out spontaneously (ΔG = -7.1 kcal mol-1) and is stabilized by hydrogen bonds and electrostatic interactions, as observed in the experimental spectroscopic results. Finally, biological assays indicated that HS influenced the antimicrobial activity of TC. Thus, this study contributed to understanding the dynamics and distribution of TC in the environment and HS's potential in the remediation of antibiotics of this class in natural systems, as these can have adverse effects on ecosystems and human health.
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Affiliation(s)
| | - Shenia de Oliveira Souza
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceio, AL, 57072-900, Brazil
| | - Ari Souza Guimarães
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceio, AL, 57072-900, Brazil
| | - Isis Martins Figueiredo
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceio, AL, 57072-900, Brazil
| | | | - Francis Soares Gomes
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceio, AL, 57072-900, Brazil
| | - Wander Gustavo Botero
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceio, AL, 57072-900, Brazil
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Sousa JN, Queiroz LDRP, de Paula AMB, Guimarães ALS, Lescano CH, Aguilar CM, Pires de Oliveira I, Santos SHS. Gallic acid as a Sestrin (SESN2) activator and potential obesity therapeutic agent: A molecular docking study. Gene 2023; 883:147683. [PMID: 37536400 DOI: 10.1016/j.gene.2023.147683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023]
Abstract
Sestrins (SESNs) are a family of evolutionarily conserved proteins among mammals. They have several body homeostatic functions such as antioxidant, metabolic, and anti-aging, and are required to regenerate hyperoxidized forms of peroxiredoxins and reactive oxygen species. Sestrin 2 has been studied as a therapeutic agent in obesity treatment. Gallic acid (GA) is a triphenolic compound with beneficial biological activities including anti-inflammatory, antidiabetic, antihypertensive, and antioxidant effects. Recent studies demonstrated the GA's ability to reduce body weight gain and improve glycemic parameters. In this sense, the present study aims to investigate the GA activating potential of Sestrin using the molecular docking method. The 3D structure of gallic acid was retrieved from the NCBI PubChem database and the chemical structure of the Sestrin2 protein from the RCSB Protein Data Bank (5DJ4). The docking calculus was performed via UCSF Chimera and AutoDock Vinaprograms. The results showed that amino acids Arg390, Glu451, Trp444, Thr386, Arg448, Thr374, Tyr375, Asn376, Thr377, Leu389, His454, Ser450, His86, and Val455 are very important for GA stabilization, resembling the interactions that permit Leucine to activate SESN2. In this context, the obesity therapeutic property of GA can be understood from a Sestrin activating process through amino acid metabolism.
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Affiliation(s)
- Jaciara Neves Sousa
- Laboratory of Health Science, Postgraduate Program in Health Science, UniversidadeEstadual de Montes Claros (Unimontes), Minas Gerais, Brazil
| | - Lorena Dos Reis Pereira Queiroz
- Laboratory of Health Science, Postgraduate Program in Health Science, UniversidadeEstadual de Montes Claros (Unimontes), Minas Gerais, Brazil
| | - Alfredo Maurício Batista de Paula
- Laboratory of Health Science, Postgraduate Program in Health Science, UniversidadeEstadual de Montes Claros (Unimontes), Minas Gerais, Brazil
| | - André Luiz Sena Guimarães
- Laboratory of Health Science, Postgraduate Program in Health Science, UniversidadeEstadual de Montes Claros (Unimontes), Minas Gerais, Brazil
| | - Caroline Honaiser Lescano
- Institute of Agricultural Sciences (ICA), Food Engineering, Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil
| | - Charles Martins Aguilar
- Institute of Agricultural Sciences (ICA), Food Engineering, Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil
| | - Ivan Pires de Oliveira
- Institute of Agricultural Sciences (ICA), Food Engineering, Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil
| | - Sérgio Henrique Sousa Santos
- Laboratory of Health Science, Postgraduate Program in Health Science, UniversidadeEstadual de Montes Claros (Unimontes), Minas Gerais, Brazil; Institute of Agricultural Sciences (ICA), Food Engineering, Universidade Federal de Minas Gerais (UFMG), Montes Claros, Minas Gerais, Brazil.
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Oselusi SO, Sibuyi NRS, Meyer M, Madiehe AM. Ehretia Species Phytoconstituents as Potential Lead Compounds against Klebsiella pneumoniae Carbapenemase: A Computational Approach. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8022356. [PMID: 37869630 PMCID: PMC10586912 DOI: 10.1155/2023/8022356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023]
Abstract
The evolution of antibiotic-resistant carbapenemase has negatively impacted the management of critical healthcare-associated infections. K. pneumoniae carbapenemase-2- (KPC-2-) expressing bacteria have developed resistance to conventional therapeutic options, including those used as a last resort for life-threatening diseases. In this study, Ehretia species phytoconstituents were screened for their potential to inhibit KPC-2 protein using in silico approaches. Molecular docking was used to identify strong KPC-2 protein binding phytoconstituents retrieved from the literature. The best-docked conformation of the ligands was selected based on their glide energy and binding interactions. To determine their binding free energies, these hit compounds were subjected to molecular mechanics with generalized born and surface area (MM-GBSA) in the PRIME module. Pharmacological assessments of the ligands were performed to evaluate their drug-likeness. Molecular dynamic (MD) simulations were used to analyze the conformational stability of the selected druglike compounds within the active site of the KPC-2 protein. Overall, a total of 69 phytoconstituents were compiled from the literature. Fourteen of these compounds exhibited a stronger binding affinity for the protein target than the reference drugs. Four of these top hit compounds, DB09, DB12, DB28, and DB66, revealed the highest efficacy in terms of drug-likeness properties. The MD simulation established that among the druglike compounds, DB66 attained stable conformations after 150 ns simulation in the active site of the protein. We concluded that DB66 from Ehretia species could play a significant role in therapeutic efforts against KPC-2-expressing bacteria.
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Affiliation(s)
- Samson O. Oselusi
- Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Nicole R. S. Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Abram M. Madiehe
- Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
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Bello RO, Okunlola ST, Kumar N, Victor O, Jimoh TO, Abdulsalam ZN, Kehinde IO, Umar HI. An integrative computational approach for the identification of dual inhibitors of isocitrate dehydrogenase 1 and 2 from phytocompounds of Phyllantus amarus. J Biomol Struct Dyn 2023:1-17. [PMID: 37559488 DOI: 10.1080/07391102.2023.2245494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023]
Abstract
Genetic alterations of the genes encoding the isocitrate dehydrogenase (IDH) enzymes have been identified in about 20% of acute myeloid leukemia (AML) cases as well as many other forms of cancers. Notable among these alterations are the neomorphic IDH1_R132H and IDH2_R140Q mutations which lead to the production of an oncometabolite. Hence, their inhibition is widely considered a therapeutic strategy in the treatment of many cancers. While many inhibitors of the mutant enzymes have been developed, an inhibitor that is capable of co-inhibiting both enzymes are currently lacking while drug resistance has also limited the clinical usage of previously identified mono inhibitors. Consequently, this study employed molecular modeling approaches, such as molecular docking, molecular mechanics generalized Born Surface area (MM/GBSA), molecular dynamics (MD) simulation, and density functional theory (DFT) analysis to identify potential dual inhibitors of the previously mentioned mutant IDH1/2 from the phytocompounds of Phyllantus amarus. Of the 31 phytocompounds identified, 20 showed good binding affinities for both IDH1 _R132H and IDH2 _R140Q (ranging from -5.2 Kca/mol to -9.6 Kcal/mol) and had desirable pharmacokinetic properties. However, ellagic acid and pinoresinol possessed better pharmacokinetic properties, rendering suitable hits. Investigation of the behavior of the IDH1_R132H and IDH2_R140Q complexes with ellagic acid and pinoresinol via the RMSD, RMSF, and contact map analyses showed that all the complexes-maintained stability throughout the simulation time. Ultimately, ellagic acid and pinoresinol were identified as promising hits for the development of IDH1_R132H and IDH2_R140Q dual inhibitors. However, further experimental studies are needed to confirm their potential as therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ridwan Opeyemi Bello
- Department of Biotechnology, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Salihaat Toyin Okunlola
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Physiology, School of Basic Medical Sciences, Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Neeraj Kumar
- Department of Pharmaceutical Chemistry, Bhupal Nobles' College of Pharmacy, Udaipur, Rajasthan, India
| | - Omoboyede Victor
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Tajudeen O Jimoh
- Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Islamic University in Uganda, Kampala, Uganda
| | - Zainab Naeem Abdulsalam
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
| | - Idayat Oyinkansola Kehinde
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Haruna Isiyaku Umar
- Computer-Aided Therapeutic Discovery and Design Platform (CAT2D), School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
- Department of Biochemistry, School of Life Sciences (SLS), Federal University of Technology Akure, Akure, Ondo State, Nigeria
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Chun CY, Khor SXY, Chia AYY, Tang YQ. In silico study of potential SARS-CoV-2 antagonist from Clitoria ternatea. Int J Health Sci (Qassim) 2023; 17:3-10. [PMID: 37151745 PMCID: PMC10155250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Objectives In this study, we implemented a structure-based virtual screening protocol in search of natural bioactive compounds in Clitoria ternatea that could inhibit the viral Mpro. Methods A library of twelve main bioactive compounds in C. ternatea was created from PubChem database by minimizing ligand structure in PyRx software to increase the ligand flexibility. Molecular docking studies were performed by targeting Mpro (PDB ID: 6lu7) via Discovery Studio Visualiser and PyRx platforms. Top hits compounds were then selected to study their Adsorption, distribution, metabolism, excretion, and toxicity (ADMET) and drug likeness properties through pkCSM pharmacokinetics tool to understand the stability, interaction, conformational changes, and pharmaceutical relevant parameters. Results This investigation found that, in the molecular docking simulation, four bioactive compounds (procyanidin A2 [-9.3 kcal/mol], quercetin-3-rutinoside [-8.9 kcal/mol], delphinidin-3-O-glucoside [-8.3 kcal/mol], and ellagic acid [-7.4 kcal/mol]) showed producing the strongest binding affinity to the Mpro of severe acute respiratory syndrome coronavirus 2, as compared to positive control (N3 inhibitor) (-7.5 kcal/mol). These binding energies were found to be favorable for an efficient docking and resultant. In addition, the stability of quercetin-3-rutinoside and ellagic acid is higher without any unfavorable bond. The ADMET and drug likeness of these two compounds were found that they are considered an effective and safe coronavirus disease 2019 (COVID-19) inhibitors through Lipinski's Rule, absorption, distribution, metabolism, and toxicity properties. Conclusion From these results, it was concluded that C. ternatea possess potential therapeutic properties against COVID-19.
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Affiliation(s)
- Chian Ying Chun
- School of Health Science, International Medical University, Kuala Lumpur, Malaysia
| | - Sabrina Xin Yi Khor
- School of Biosciences, Faculty of Health and Medical Sciences Taylor’s University, Subang Jaya, Malaysia
| | - Adeline Yoke Yin Chia
- Centre for Drug Discovery and Molecular Pharmacology, Taylor’s University, Subang Jaya, Malaysia
| | - Yin-Quan Tang
- Medical Advancement for Better Quality of Life Impact Lab, Taylor’s University, Subang Jaya, Malaysia
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Gu Y, Liu M, Staker BL, Buchko GW, Quinn RJ. Drug-Repurposing Screening Identifies a Gallic Acid Binding Site on SARS-CoV-2 Non-structural Protein 7. ACS Pharmacol Transl Sci 2023; 6:578-586. [PMID: 37082753 PMCID: PMC10111621 DOI: 10.1021/acsptsci.2c00225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 03/09/2023]
Abstract
SARS-CoV-2 is the agent responsible for acute respiratory disease COVID-19 and the global pandemic initiated in early 2020. While the record-breaking development of vaccines has assisted the control of COVID-19, there is still a pressing global demand for antiviral drugs to halt the destructive impact of this disease. Repurposing clinically approved drugs provides an opportunity to expediate SARS-CoV-2 treatments into the clinic. In an effort to facilitate drug repurposing, an FDA-approved drug library containing 2400 compounds was screened against the SARS-CoV-2 non-structural protein 7 (nsp7) using a native mass spectrometry-based assay. Nsp7 is one of the components of the SARS-CoV-2 replication/transcription complex essential for optimal viral replication, perhaps serving to off-load RNA from nsp8. From this library, gallic acid was identified as a compound that bound tightly to nsp7, with an estimated K d of 15 μM. NMR chemical shift perturbation experiments were used to map the ligand-binding surface of gallic acid on nsp7, indicating that the compound bound to a surface pocket centered on one of the protein's four α-helices (α2). The identification of the gallic acid-binding site on nsp7 may allow development of a SARS-CoV-2 therapeutic via artificial-intelligence-based virtual docking and other strategies.
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Affiliation(s)
- Yushu Gu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Miaomiao Liu
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
| | - Bart L. Staker
- Seattle
Children’s Research Institute, Seattle, Washington 98101, United States
| | - Garry W. Buchko
- Earth
and Biological Sciences Directorate, Pacific
Northwest National Laboratory, Richland, Washington 99354, United States
- School of
Molecular Biosciences, Washington State
University, Pullman, Washington 99164, United States
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Brisbane 4111, Australia
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Edible alginate-based films with anti-SARS-CoV-2 activity. Food Microbiol 2023; 113:104251. [PMID: 37098418 PMCID: PMC9995353 DOI: 10.1016/j.fm.2023.104251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
The viability of SARS-CoV-2 on food surfaces and its propagation through the food chain has been discussed by several stakeholders, as it may represent a serious public health problem, bringing new challenges to the food system. This work shows for the first time that edible films can be used against SARS-CoV-2. Sodium alginate-based films containing gallic acid, geraniol, and green tea extract were evaluated in terms of their antiviral activity against SARS-CoV-2. The results showed that all these films have strong in vitro antiviral activity against this virus. However, a higher concentration of the active compound (1.25%) is needed for the film containing gallic acid to achieve similar results to those obtained for lower concentrations of geraniol and green tea extract (0.313%). Furthermore, critical concentrations of the active compounds in the films were used to evaluate their stability during storage. Results showed that gallic acid-loaded films lose their activity from the second week of storage, while films with geraniol and green tea extract only show a drop in activity after four weeks. These results highlight the possibility of using edible films and coatings as antiviral materials on food surfaces or food contact materials, which may help to reduce the spreading of viruses through the food chain.
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From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440. Int Microbiol 2022; 26:243-255. [PMID: 36357545 PMCID: PMC9649394 DOI: 10.1007/s10123-022-00282-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/18/2022] [Accepted: 10/06/2022] [Indexed: 11/12/2022]
Abstract
Gallic acid is a powerful antioxidant with multiple therapeutic applications, usually obtained from the acidic hydrolysis of tannins produced by many plants. As this process generates a considerable amount of toxic waste, the use of tannases or tannase-producing microorganisms has become a greener alternative over the last years. However, their high costs still impose some barriers for industrial scalability, requiring solutions that could be both greener and cost-effective. Since Pseudomonas putida KT2440 is a powerful degrader of gallic acid, its metabolism offers pathways that can be engineered to produce it from cheap and renewable carbon sources, such as the crude glycerol generated in biodiesel units. In this study, a synthetic operon with the heterologous genes aroG4, quiC and pobA* was developed and expressed in P. putida, based on an in silico analysis of possible metabolic routes, resulting in no production. Then, the sequences pcaHG and galTAPR were deleted from the genome of this strain to avoid the degradation of gallic acid and its main intermediate, the protocatechuic acid. This mutant was transformed with the vector containing the synthetic operon and was finally able to convert glycerol into gallic acid. Production assays in shaker showed a final concentration of 346.7 ± 0.004 mg L-1 gallic acid after 72 h.
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Jack KS, Asaruddin MRB, Bhawani SA. Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2. CHEMICAL AND BIOLOGICAL TECHNOLOGIES IN AGRICULTURE 2022; 9:73. [PMID: 37520584 PMCID: PMC9579622 DOI: 10.1186/s40538-022-00340-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/27/2022] [Indexed: 05/30/2023]
Abstract
Background Virgin coconut oil is mostly made up of saturated fatty acids in which approximately 72% are medium chain triglycerides. Medium chain triglycerides can be digested into medium chain fatty acids and medium chain monoglycerides which are bioactive components. Therefore, it is very important to study the in-silico ability of some Virgin coconut oil derivatives, namely, medium chain fatty acids and medium chain monoglycerides to inhibit Cyclooxygenase 2 (COX-2) protein for prevention of excessive inflammatory response. Results Pharmacophore study displayed monolaurin with two hydrogen bond donor, three hydrogen bond acceptor and five hydrophobic interactions, while lauric acid presented two hydrogen bond acceptor, five hydrophobic interactions and a negative ion interaction. Molecular docking underlined the ability of monolaurin in the inhibition of COX-2 protein which causes inflammatory action with a decent result of energy binding affinity of - 7.58 kcal/mol and 15 interactions out of which 3 are strong hydrogen bond with TYR385 (3.00 Å), PHE529 (2.77 Å), and GLY533 (3.10 Å) residues of the protein. Monolaurin was employed as hydrogen bond acceptor to the side of residue TYR385 of COX-2 protein with an occupancy of 67.03% and was observed to be long-living during the entire 1000 frames of the molecular dynamic simulation. The analysis of RMSD score of the Monolaurin-COX-2 complex backbone was calculated to be low (1.137 ± 0.153 Å) and was in a stable range of 0.480 to 1.520 Å. Redocking of this complex still maintained a strong hydrogen bond (2.87 Å) with the main residue TYR385. AMDET results where promising for medium chain fatty acids and medium chain monoglycerides with good physicochemical drug scores. Conclusions This can be concluded from the results obtained that the monolaurin has strong interactions with COX-2 protein to disrupt its function due to significant hydrogen bonds and hydrophobic interactions with amino acid residues present in the target protein's active site. These results displayed a very significant anti-inflammatory potential of monolaurin and a new promising drug candidates as anti-inflammatory agent. Graphical Abstract
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Affiliation(s)
- Kho Swen Jack
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak Malaysia
| | - Mohd Razip Bin Asaruddin
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak Malaysia
| | - Showkat Ahmad Bhawani
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak Malaysia
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Lin S, Wang X, Tang RWL, Lee HC, Chan HH, Choi SSA, Dong TTX, Leung KW, Webb SE, Miller AL, Tsim KWK. The Extracts of Polygonum cuspidatum Root and Rhizome Block the Entry of SARS-CoV-2 Wild-Type and Omicron Pseudotyped Viruses via Inhibition of the S-Protein and 3CL Protease. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123806. [PMID: 35744929 PMCID: PMC9231230 DOI: 10.3390/molecules27123806] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 12/24/2022]
Abstract
COVID-19, resulting from infection by the SARS-CoV-2 virus, caused a contagious pandemic. Even with the current vaccines, there is still an urgent need to develop effective pharmacological treatments against this deadly disease. Here, we show that the water and ethanol extracts of the root and rhizome of Polygonum cuspidatum (Polygoni Cuspidati Rhizoma et Radix), a common Chinese herbal medicine, blocked the entry of wild-type and the omicron variant of the SARS-CoV-2 pseudotyped virus into fibroblasts or zebrafish larvae, with IC50 values ranging from 0.015 to 0.04 mg/mL. The extracts were shown to inhibit various aspects of the pseudovirus entry, including the interaction between the spike protein (S-protein) and the angiotensin-converting enzyme II (ACE2) receptor, and the 3CL protease activity. Out of the chemical compounds tested in this report, gallic acid, a phytochemical in P. cuspidatum, was shown to have a significant anti-viral effect. Therefore, this might be responsible, at least in part, for the anti-viral efficacy of the herbal extract. Together, our data suggest that the extracts of P. cuspidatum inhibit the entry of wild-type and the omicron variant of SARS-CoV-2, and so they could be considered as potent treatments against COVID-19.
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Affiliation(s)
- Shengying Lin
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Xiaoyang Wang
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Roy Wai-Lun Tang
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Hung Chun Lee
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Ho Hin Chan
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Sheyne S. A. Choi
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Tina Ting-Xia Dong
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Ka Wing Leung
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Sarah E. Webb
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Andrew L. Miller
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
| | - Karl Wah-Keung Tsim
- Division of Life Science and Centre for Chinese Medicine, The Hong Kong University of Science and Technology, Hong Kong, China; (S.L.); (X.W.); (R.W.-L.T.); (H.C.L.); (T.T.-X.D.); (K.W.L.)
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong, China; (H.H.C.); (S.S.A.C.); (S.E.W.); (A.L.M.)
- Correspondence: ; Tel.: +852-2358-7332
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11
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Czech B, Krzyszczak A, Boguszewska-Czubara A, Opielak G, Jośko I, Hojamberdiev M. Revealing the toxicity of lopinavir- and ritonavir-containing water and wastewater treated by photo-induced processes to Danio rerio and Allivibrio fischeri. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 824:153967. [PMID: 35182634 PMCID: PMC8849850 DOI: 10.1016/j.scitotenv.2022.153967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 05/30/2023]
Abstract
In coronavirus disease 2019 (COVID-19), among many protocols, lopinavir and ritonavir in individual or combined forms with other drugs have been used, causing an increase in the concentration of antiviral drugs in the wastewater and hospital effluents. In conventional wastewater treatment plants, the removal efficiency of various antiviral drugs is estimated to be low (<20%). The high values of predicted no-effect concentration (PNEC) for lopinavir and ritonavir (in ng∙L-1) reveal their high chronic toxicity to aquatic organisms. This indicates that lopinavir and ritonavir are current priority antiviral drugs that need to be thoroughly monitored and effectively removed from any water and wastewater samples. In this study, we attempt to explore the impacts of two photo-induced processes (photolysis and photocatalysis) on the toxicity of treated water and wastewater samples containing lopinavir and ritonavir to zebrafish (Danio rerio) and marine bacteria (Allivibrio fischeri). The obtained results reveal that traces of lopinavir in water under photo-induced processes may cause severe problems for Danio rerio, including pericardial edema and shortening of the tail, affecting its behavior, and for Allivibrio fischeri as a result of the oxygen-depleted environment, inflammation, and oxidative stress. Hence, lopinavir must be removed from water and wastewater before being in contact with light. In contrast, the photo-induced processes of ritonavir-containing water and wastewater reduce the toxicity significantly. This shows that even if the physicochemical parameters of water and wastewater are within the standard requirements/limits, the presence of traces of antiviral drugs and their intermediates can affect the survival and behavior of Danio rerio and Allivibrio fischeri. Therefore, the photo-induced processes and additional treatment of water and wastewater containing ritonavir can minimize its toxic effect.
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Affiliation(s)
- Bożena Czech
- Department of Radiochemistry and Environmental Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 3 Maria Curie-Skłodowska Sq., 20-031 Lublin, Poland.
| | - Agnieszka Krzyszczak
- Department of Radiochemistry and Environmental Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 3 Maria Curie-Skłodowska Sq., 20-031 Lublin, Poland
| | - Anna Boguszewska-Czubara
- Department of Medical Chemistry, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland
| | - Grzegorz Opielak
- Chair and Department of Human Physiology, Medical University of Lublin, ul. Radziwillowska 11, 20-080 Lublin, Poland
| | - Izabela Jośko
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka Street 15, 20-950 Lublin, Poland
| | - Mirabbos Hojamberdiev
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany.
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12
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Jalaleddine N, Hachim M, Al-Hroub H, Saheb Sharif-Askari N, Senok A, Elmoselhi A, Mahboub B, Samuel Kurien NM, Kandasamy RK, Semreen MH, Halwani R, Soares NC, Al Heialy S. N6-Acetyl-L-Lysine and p-Cresol as Key Metabolites in the Pathogenesis of COVID-19 in Obese Patients. Front Immunol 2022; 13:827603. [PMID: 35663953 PMCID: PMC9161728 DOI: 10.3389/fimmu.2022.827603] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Despite the growing number of the vaccinated population, COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global health burden. Obesity, a metabolic syndrome affecting one-third of the population, has proven to be a major risk factor for COVID-19 severe complications. Several studies have identified metabolic signatures and disrupted metabolic pathways associated with COVID-19, however there are no reports evaluating the role of obesity in the COVID-19 metabolic regulation. In this study we highlight the involvement of obesity metabolically in affecting SARS-CoV-2 infection and the consequent health complications, mainly cardiovascular disease. We measured one hundred and forty-four (144) metabolites using ultra high-performance liquid chromatography-quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) to identify metabolic changes in response to SARS-CoV-2 infection, in lean and obese COVID-19 positive (n=82) and COVID-19 negative (n=24) patients. The identified metabolites are found to be mainly correlating with glucose, energy and steroid metabolisms. Further data analysis indicated twelve (12) significantly yet differentially abundant metabolites associated with viral infection and health complications, in COVID-19 obese patients. Two of the detected metabolites, n6-acetyl-l-lysine and p-cresol, are detected only among the COVID-19 cohort, exhibiting significantly higher levels in COVID-19 obese patients when compared to COVID-19 lean patients. These metabolites have important roles in viral entry and could explain the increased susceptibility of obese patients. On the same note, a set of six metabolites associated with antiviral and anti-inflammatory functions displayed significantly lower abundance in COVID-19 obese patients. In conclusion, this report highlights the plasma metabolome of COVID-19 obese patients as a metabolic feature and signature to help improve clinical outcomes. We propose n6-acetyl-l-lysine and p-cresol as potential metabolic markers which warrant further investigations to better understand their involvement in different metabolic pathways in COVID-19.
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Affiliation(s)
- Nour Jalaleddine
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Mahmood Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Hamza Al-Hroub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Adel Elmoselhi
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Bassam Mahboub
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Pulmonary Medicine and Allergy and Sleep Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Nimmi Moni Samuel Kurien
- Department of Pulmonary Medicine and Allergy and Sleep Medicine, Rashid Hospital, Dubai Health Authority, Dubai, United Arab Emirates
| | - Richard K Kandasamy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, Trondheim, Norway
| | - Mohammad H Semreen
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Rabih Halwani
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Prince Abdullah Ben Khaled Celiac Disease Research Chair, Department of Pediatrics, Faculty of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Nelson C Soares
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.,Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
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13
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Mahmoudi S, Dehkordi MM, Asgarshamsi MH. The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects. Biophys Chem 2022; 288:106824. [PMID: 35728510 PMCID: PMC9095071 DOI: 10.1016/j.bpc.2022.106824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 05/07/2022] [Indexed: 02/07/2023]
Abstract
The novel coronavirus that caused COVID-19 pandemic is SARS-CoV-2. Although various vaccines are currently being used to prevent the disease's severe consequences, there is still a need for medications for those who become infected. The SARS-CoV-2 has a variety of proteins that have been studied extensively since the virus's advent. In this review article, we looked at chemical to molecular aspects of the various structures studied that have pharmaceutical activity and attempted to find a link between drug activity and compound structure. For example, designing of the compounds which bind to the allosteric site and modify hydrogen bonds or the salt bridges can disrupt SARS-CoV2 RBD–ACE2 complex. It seems that quaternary ammonium moiety and quinolin-1-ium structure could act as a negative allosteric modulator to reduce the tendency between spike-ACE2. Pharmaceutical structures with amino heads and hydrophobic tails can block envelope protein to prevent making mature SARS-CoV-2. Also, structures based on naphthalene pharmacophores or isosteres can form a strong bond with the PLpro and form a π-π and the Mpro's active site can be occupied by octapeptide compounds or linear compounds with a similar fitting ability to octapeptide compounds. And for protein RdRp, it is critical to consider pH and pKa so that pKa regulation of compounds to comply with patients is very effective, thus, the presence of tetrazole, phenylpyrazole groups, and analogs of pyrophosphate in the designed drugs increase the likelihood of the RdRp active site inhibition. Finally, it can be deduced that designing hybrid drug molecules along with considering the aforementioned characteristics would be a suitable approach for developing medicines in order to accurate targeting and complete inhibition this virus.
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Affiliation(s)
- Samira Mahmoudi
- Department of Microbial Biotechnology, School of Biological Sciences, Islamic Azad University Tehran North Branch, Tehran, Iran.
| | - Mehrdad Mohammadpour Dehkordi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mohammad Hossein Asgarshamsi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
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14
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Identification of secondary metabolites from Crescentia cujete as promising antibacterial therapeutics targeting type 2A topoisomerases through molecular dynamics simulation. Comput Biol Med 2022; 145:105432. [PMID: 35344868 DOI: 10.1016/j.compbiomed.2022.105432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/18/2022] [Accepted: 03/20/2022] [Indexed: 12/14/2022]
Abstract
The potential of fluoroquinolones as remarkable antibacterial agents evolved from their ability to generate 'poison' complexes between type IIA topoisomerases [topo2As (DNA gyrases and topoisomerases IV)] and DNA. However, the overuse of fluoroquinolones coupled with chromosomal mutations in topo2As has increased incidence of resistance and consequently undermined the application of the currently available fluoroquinolones in clinical practice. In this study, the molecular mechanism of interaction between the secondary metabolites of Crescentia cujete (an underutilized plant with proven anti-bacterial activity) and topo2As was investigated using computational methods. Through molecular docking, the top five compounds with the best affinity for each topo2A were identified and subjected to molecular dynamics simulation over a period of 100 ns. The results revealed that the identified compounds had higher binding energy values than the reference standards against the topo2As except for topoisomerase IV ParC, and this was consistent with the results of the structural stability and compactness of the resulting complexes. Specifically, cistanoside D (-49.18 kcal/mol), chlorogenic acid (-55.55 kcal/mol), xylocaine (-33.08 kcal/mol), and naringenin (-35.48 kcal/mol) had the best affinity for DNA gyrase A, DNA gyrase B, topoisomerase IV ParC, and topoisomerase IV ParE, respectively. Of the constituents of C. cujete evaluated, only apigenin and luteolin had affinity for all the four targets. These observations are indicative of the identified compounds as potential inhibitors of topo2As as evidenced from the molecular interactions including hydrogen bonds established with the active site amino acids of the respective targets. This is the first in silico report on the antibacterial effect of C. cujete and the findings would guide structural modification of the identified compounds as novel inhibitors of topo2As for further in vitro and in vivo assessments.
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15
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Ghazi I, Zefzoufi M, Siniti M, Fdil R, Elattari H. Corrosion Inhibition of Carob Pod Pulp ( Ceratonia siliqua L .) on Carbon Steel Surface C38 in Hydrochloric Acid. JOURNAL OF BIO- AND TRIBO-CORROSION 2022; 8:31. [PMID: 35043082 PMCID: PMC8756756 DOI: 10.1007/s40735-022-00630-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 01/19/2023]
Abstract
The effect of C. siliqua pulp corrosion inhibition on carbon steel has been studied by gravimetric testing and electrochemical methods. In this study, two raw extracts were prepared from the pod pulp of C. siliqua: the first is methanolic and the second is aqueous. The UHPLC/DAD analysis indicated gallic acid's presence in the extracts (methanolic and aqueous) of C. siliqua as a major compound. The inhibition results achieved revealed that the aqueous extract with gallic acid had a good anticorrosion activity with an inhibition rate of 91.32% at 3 g/l for a temperature of 323 K. Potentiodynamic polarization was performed in 1 M HCl without and with different concentrations of C. siliqua extracts clearly proves that inhibitor extracts behave as mixed type. Adsorption of this inhibitor for different extracts studied on the surface of the carbon steel obeys Langmuir adsorption with negative values of Δ G ads ∘ , suggesting a stable and spontaneous inhibition process.
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Affiliation(s)
- I. Ghazi
- Research Team “Thermodynamic Catalysis and Surfaces”, Department of Chemistry, Faculty of Science, University of Chouaib Doukkali, BP: 20, 24000 El Jadida, Morocco
- Laboratory of Coordination and Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Chouaib Doukkali, BP: 20, 24000 El Jadida, Morocco
| | - M. Zefzoufi
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Science, University of Chouaib Doukkali, BP: 20, 24000 El Jadida, Morocco
| | - M. Siniti
- Research Team “Thermodynamic Catalysis and Surfaces”, Department of Chemistry, Faculty of Science, University of Chouaib Doukkali, BP: 20, 24000 El Jadida, Morocco
| | - R. Fdil
- Laboratory of Bioorganic Chemistry, Department of Chemistry, Faculty of Science, University of Chouaib Doukkali, BP: 20, 24000 El Jadida, Morocco
| | - H. Elattari
- Laboratory of Coordination and Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Chouaib Doukkali, BP: 20, 24000 El Jadida, Morocco
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16
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Abstract
RNA viruses cause many routine illnesses, such as the common cold and the flu. Recently, more deadly diseases have emerged from this family of viruses. The hepatitis C virus has had a devastating impact worldwide. Despite the cures developed in the U.S. and Europe, economically disadvantaged countries remain afflicted by HCV infection due to the high cost of these medications. More recently, COVID-19 has swept across the world, killing millions and disrupting economies and lifestyles; the virus responsible for this pandemic is a coronavirus. Our understanding of HCV and SARS CoV-2 replication is still in its infancy. Helicases play a critical role in the replication, transcription and translation of viruses. These key enzymes need extensive study not only as an essential player in the viral lifecycle, but also as targets for antiviral therapeutics. In this review, we highlight the current knowledge for RNA helicases of high importance to human health.
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Affiliation(s)
- John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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17
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Saliu TP, Umar HI, Ogunsile OJ, Okpara MO, Yanaka N, Elekofehinti OO. Molecular docking and pharmacokinetic studies of phytocompounds from Nigerian Medicinal Plants as promising inhibitory agents against SARS-CoV-2 methyltransferase (nsp16). J Genet Eng Biotechnol 2021; 19:172. [PMID: 34751829 PMCID: PMC8576800 DOI: 10.1186/s43141-021-00273-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/26/2021] [Indexed: 02/01/2023]
Abstract
Background Since the index case was reported in China, COVID-19 has led to the death of at least 4 million people globally. Although there are some vaccine cocktails in circulation, the emergence of more virulent variants of SARS-CoV-2 may make the eradication of COVID-19 more difficult. Nsp16 is an S-adenosyl-L-Methionine-dependent methyltransferase that plays an important role in SARS-CoV-2 viral RNA cap formation—a crucial process that confers viral stability and prevents virus detection by cell innate immunity mechanisms. This unique property makes nsp16 a promising molecular target for COVID-19 drug design. Thus, this study aimed to identify potent phytocompounds that can effectively inhibit SARS-CoV-2 nsp16. We performed in silico pharmacokinetic screening and molecular docking studies using 100 phytocompounds—isolated from fourteen Nigerian plants—as ligands and nsp16 (PDB: 6YZ1) as the target. Results We found that only 59 phytocompounds passed the drug-likeness analysis test. However, after the docking analysis, only six phytocompounds (oxopowelline, andrographolide, deacetylbowdensine, 11, 12-dimethyl sageone, sageone, and quercetin) isolated from four Nigerian plants (Crinum jagus, Andrographis paniculata, Sage plants (Salvia officinalis L.), and Anacardium occidentale) showed good binding affinity with nsp16 at its active site with docking score ranging from − 7.9 to − 8.4 kcal/mol. Conclusions Our findings suggest that the six phytocompounds could serve as therapeutic agents to prevent viral survival and replication in cells. However, further studies on the in vitro and in vivo inhibitory activities of these 6 hit phytocompounds against SARS-CoV-2 nsp16 are needed to confirm their efficacy and dose. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-021-00273-5.
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Affiliation(s)
- Tolulope Peter Saliu
- Computational and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, P.M.B 704, Akure, Ondo State, Nigeria. .,Graduate School of Integrated Sciences for Life, Hiroshima University, 4-4 Kagamiyama 1-chome, Higashi-Hiroshima, 739-8528, Japan.
| | - Haruna I Umar
- Computational and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, P.M.B 704, Akure, Ondo State, Nigeria
| | - Olawale Johnson Ogunsile
- Computational and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, P.M.B 704, Akure, Ondo State, Nigeria
| | - Micheal O Okpara
- Computational and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, P.M.B 704, Akure, Ondo State, Nigeria
| | - Noriyuki Yanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 4-4 Kagamiyama 1-chome, Higashi-Hiroshima, 739-8528, Japan
| | - Olusola Olalekan Elekofehinti
- Computational and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, P.M.B 704, Akure, Ondo State, Nigeria
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18
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Li H, Xu F, Liu C, Cai A, Dain JA, Li D, Seeram NP, Cho BP, Ma H. Inhibitory Effects and Surface Plasmon Resonance-Based Binding Affinities of Dietary Hydrolyzable Tannins and Their Gut Microbial Metabolites on SARS-CoV-2 Main Protease. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12197-12208. [PMID: 34586788 PMCID: PMC8491554 DOI: 10.1021/acs.jafc.1c03521] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 05/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (Mpro) inhibitors are considered as potential treatments for coronavirus disease 2019, and dietary polyphenols show promise in SARS-CoV-2 Mpro inhibition based on in silico studies. In the present study, we utilize a combination of biochemical-, surface plasmon resonance-, and docking-based assays to evaluate the inhibition and binding affinities of a series of tannins and their gut microbial metabolites on SARS-CoV-2 Mpro. The tested compounds (2-50 μM) were hydrolyzable tannins, including ellagitannins (punicalagin and ellagic acid) and gallotannins (tannic acid, pentagalloyl glucose, ginnalin A, and gallic acid), and their gut microbial metabolites, urolithins and pyrogallol, respectively. They inhibited SARS-CoV-2 Mpro (by 6.6-100.0% at 50 μM) and bound directly to the Mpro protein (with dissociation constants from 1.1 × 10-6 to 5.3 × 10-5 M). This study sheds light on the inhibitory effects of tannins and their metabolites on SARS-CoV-2 Mpro.
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Affiliation(s)
- Huifang Li
- School of Biotechnology and Health Sciences, Wuyi University; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529020, China
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Feng Xu
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550001, China
| | - Chang Liu
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Ang Cai
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, USA
| | - Joel A. Dain
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, USA
| | - Dongli Li
- Department of Chemistry, University of Rhode Island, Kingston, RI 02881, USA
| | - Navindra P. Seeram
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Bongsup P. Cho
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Hang Ma
- School of Biotechnology and Health Sciences, Wuyi University; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529020, China
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
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19
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Fighting coronaviruses with natural polyphenols. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021; 37:102179. [PMID: 34630764 PMCID: PMC8491928 DOI: 10.1016/j.bcab.2021.102179] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 08/11/2021] [Accepted: 09/28/2021] [Indexed: 02/06/2023]
Abstract
Few licensed drugs and vaccines are available concerning COVID-19, a disease caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2). Furthermore, numerous recent SARS-COV-2 variants of have arisen globally, demonstrating the need to develop broadly protective interventions for different coronavirus strains. Polyphenols are the largest class of natural bioactive compounds, categorized as flavonoids (catechins, quercetin and kaempferol) and non-flavonoids (gallic acid and resveratrol), and these compounds have been described as effective antiviral agents. This is because they can inhibit coronavirus enzymes, blocking replication and infection. The present short manuscript aimed to summarize and report the current evidence from well-known powerful flavonoid (catechin, quercetin, and kaempferol) and non-flavonoid (gallic acid and resveratrol) polyphenols obtained from plant extracts that inhibit coronavirus strains in in vitro models or by computer modeling. The knowledge of strategies beyond conventional treatments may be helpful in the development of new coronavirus drugs, treatments/medicines, or formulations.
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20
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Novel Molecules derived from 3-O-(6-galloylglucoside) inhibit Main Protease of SARS-CoV 2 In Silico. ACTA ACUST UNITED AC 2021; 76:785-796. [PMID: 34629698 PMCID: PMC8490610 DOI: 10.1007/s11696-021-01899-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/21/2021] [Indexed: 11/04/2022]
Abstract
The ongoing pandemic caused by the severe acute respiratory syndrome 2 (SARS-CoV 2) has led to more than 168 million confirmed cases with 3.5 million deaths as at 28th May, 2021 across 218 countries. The virus has a cysteine protease called main protease (Mpro) which is significant to it life cycle, tagged as a suitable target for novel antivirals. In this computer-assisted study, we designed 100 novel molecules through an artificial neural network-driven platform called LigDream (https://playmolecule.org/LigDream/) using 3-O-(6-galloylglucoside) as parent molecule for design. Druglikeness screening of the molecules through five (5) different rules was carried out, followed by a virtual screening of those molecules without a single violation of the druglike rules using AutoDock Vina against Mpro. The in silico pharmacokinetic features were predicted and finally, quantum mechanics/molecular mechanics (QM/MM) study was carried out using Molecular Orbital Package 2016 (MOPAC2016) on the overall hit compound with controls to determine the stability and reactivity of the lead molecule. The findings showed that eight (8) novel molecules violated none of the druglikeness rules of which three (3) novel molecules (C33, C35 and C54) showed the utmost binding affinity of −8.3 kcal/mol against Mpro; C33 showed a good in silico pharmacokinetic features with acceptable level of stability and reactively better than our controls based on the quantum chemical descriptors analysis. However, there is an urgent need to carry out more research on these novel molecules for the fight against the disease.
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Hassan AR, Sanad IM, Allam AE, Abouelela ME, Sayed AM, Emam SS, El-Kousy SM, Shimizu K. Chemical constituents from Limonium tubiflorum and their in silico evaluation as potential antiviral agents against SARS-CoV-2. RSC Adv 2021; 11:32346-32357. [PMID: 35495487 PMCID: PMC9042241 DOI: 10.1039/d1ra05927k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/25/2021] [Indexed: 11/21/2022] Open
Abstract
Wild plants growing in the Egyptian deserts are facing abiotic stress, which can lead to interesting & safe natural products possessing potential chemical profiles. Consequently, our study was designed to assess the phytochemical composition of the aerial parts of Limonium tubiflorum (family Plumbaginaceae) growing wild in Egypt for the first time. In addition, in silico screening and molecular dynamic simulation of all isolated phytoconstituents were run against the main protease (Mpro) and spike glycoprotein SARS-CoV-2 targets which displayed a crucial role in the replication of this virus. Our findings showed that the phytochemical investigation of 70% ethanol extract of L. tubiflorum aerial parts afforded six known flavonoids; myricetin 3-O-(2′′-galloyl)-β-d-galactopyranoside (1), myricetin 3-O-(2′′-galloyl)-α-l-rhamnopyranoside (2), myricetin 3-O-(3′′-galloyl)-α-l-rhamnopyranoside (3), myricetin 3-O-β-d-galactopyranoside (5), apigenin (6), myricetin (7), along with two known phenolic acid derivatives; gallic acid (4) and ethyl gallate (8). Docking studies revealed that compounds (1) & (2) were the most effective compounds with binding energies of −17.9664 & −18.6652 kcal mol−1 against main protease and −18.9244 & −18.9272 kcal mol−1 towards spike glycoprotein receptors, respectively. The molecular dynamics simulation experiment agreed with the docking study and reported stability of compounds (1) and (2) against the selected targets which was proved by low RMSD for the tested components. Moreover, the structure–activity relationship revealed that the presence of the galloyl moiety is necessary for enhancement of the activity. Overall, the galloyl substructure of myricetin 3-O-glycoside derivatives (1 and 2) isolated from L. tubiflorum may be a possible lead for developing COVID-19 drugs. Further, in vitro and in vivo assays are recommended to support our in silico studies. Wild plants growing in the Egyptian deserts are facing abiotic stress, which can lead to interesting & safe natural products possessing potential chemical profiles.![]()
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Affiliation(s)
- Ahmed R Hassan
- Medicinal and Aromatic Plants Department, Desert Research Center El-Matariya 11753 Cairo Egypt
| | - Ibrahim M Sanad
- Medicinal and Aromatic Plants Department, Desert Research Center El-Matariya 11753 Cairo Egypt
| | - Ahmed E Allam
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut 71524 Egypt
| | - Mohamed E Abouelela
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University Assiut 71524 Egypt
| | - Ahmed M Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University Beni-Suef 62513 Egypt
| | - Shalabia S Emam
- Medicinal and Aromatic Plants Department, Desert Research Center El-Matariya 11753 Cairo Egypt
| | - Salah M El-Kousy
- Chemistry Department, Menoufia University Shebin El-Kom 32861 El-Menoufia Egypt
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
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22
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Liskova A, Koklesova L, Samec M, Abdellatif B, Zhai K, Siddiqui M, Šudomová M, Hassan ST, Kudela E, Biringer K, Giordano FA, Büsselberg D, Golubnitschaja O, Kubatka P. Targeting phytoprotection in the COVID-19-induced lung damage and associated systemic effects-the evidence-based 3PM proposition to mitigate individual risks. EPMA J 2021; 12:325-347. [PMID: 34367380 PMCID: PMC8329620 DOI: 10.1007/s13167-021-00249-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 02/06/2023]
Abstract
The risks related to the COVID-19 are multi-faceted including but by far not restricted to the following: direct health risks by poorly understood effects of COVID-19 infection, overloaded capacities of healthcare units, restricted and slowed down care of patients with non-communicable disorders such as cancer, neurologic and cardiovascular pathologies, among others; social risks-restricted and broken social contacts, isolation, professional disruption, explosion of aggression in the society, violence in the familial environment; mental risks-loneliness, helplessness, defenceless, depressions; and economic risks-slowed down industrial productivity, broken delivery chains, unemployment, bankrupted SMEs, inflation, decreased capacity of the state to perform socially important programs and to support socio-economically weak subgroups in the population. Directly or indirectly, the above listed risks will get reflected in a healthcare occupation and workload which is a tremendous long-term challenge for the healthcare capacity and robustness. The article does not pretend to provide solutions for all kind of health risks. However, it aims to present the scientific evidence of great clinical utility for primary, secondary, and tertiary care to protect affected individuals in a cost-effective manner. To this end, due to pronounced antimicrobial, antioxidant, anti-inflammatory, and antiviral properties, naturally occurring plant substances are capable to protect affected individuals against COVID-19-associated life-threatening complications such as lung damage. Furthermore, they can be highly effective, if being applied to secondary and tertiary care of noncommunicable diseases under pandemic condition. Thus, the stratification of patients evaluating specific health conditions such as sleep quality, periodontitis, smoking, chronic inflammation and diseases, metabolic disorders and obesity, vascular dysfunction, and cancers would enable effective managemenet of COVID-19-associated complications in primary, secondary, and tertiary care in the context of predictive, preventive, and personalized medicine (3PM).
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Affiliation(s)
- Alena Liskova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Lenka Koklesova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Marek Samec
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Basma Abdellatif
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144 Qatar
| | - Kevin Zhai
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144 Qatar
| | - Manaal Siddiqui
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144 Qatar
| | - Miroslava Šudomová
- Museum of Literature in Moravia, Klášter 1, 66461, Rajhrad, Czech Republic
| | - Sherif T.S. Hassan
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Erik Kudela
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Kamil Biringer
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Frank A. Giordano
- Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, 24144 Qatar
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
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23
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Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Int J Biol Sci 2021; 17:1547-1554. [PMID: 33907518 PMCID: PMC8071772 DOI: 10.7150/ijbs.59943] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Suppression of type I interferon (IFN) response is one pathological outcome of the infection of highly pathogenic human coronaviruses. To effect this, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 encode multiple IFN antagonists. In this study, we reported on the IFN antagonism of SARS-CoV-2 main protease NSP5. NSP5 proteins of both SARS-CoV and SARS-CoV-2 counteracted Sendai virus-induced IFN production. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. The suppressive effect of NSP5 on IFN-β gene transcription induced by RIG-I, MAVS, TBK1 and IKKϵ suggested that NSP5 likely acts at a step downstream of IRF3 phosphorylation in the cytoplasm. NSP5 did not influence steady-state expression or phosphorylation of IRF3, suggesting that IRF3, regardless of its phosphorylation state, might not be the substrate of NSP5 protease. However, nuclear translocation of phosphorylated IRF3 was severely compromised in NSP5-expressing cells. Taken together, our work revealed a new mechanism by which NSP5 proteins encoded by SARS-CoV and SARS-CoV-2 antagonize IFN production by retaining phosphorylated IRF3 in the cytoplasm. Our findings have implications in rational design and development of antiviral agents against SARS-CoV-2.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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