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Ho WY, Shen ZH, Chen Y, Chen TH, Lu X, Fu YS. Therapeutic implications of quercetin and its derived-products in COVID-19 protection and prophylactic. Heliyon 2024; 10:e30080. [PMID: 38765079 PMCID: PMC11098804 DOI: 10.1016/j.heliyon.2024.e30080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/21/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, which has triggered a global pandemic of the coronavirus infectious disease 2019 (COVID-19). Outbreaks of emerging infectious diseases continue to challenge human health worldwide. The virus conquers human cells through the angiotensin-converting enzyme 2 receptor-driven pathway by mostly targeting the human respiratory tract. Quercetin is a natural flavonoid widely represented in the plant kingdom. Cumulative evidence has demonstrated that quercetin and its derivatives have various pharmacological properties including anti-cancer, anti-hypertension, anti-hyperlipidemia, anti-hyperglycemia, anti-microbial, antiviral, neuroprotective, and cardio-protective effects, because it is a potential treatment for severe inflammation and acute respiratory distress syndrome. Furthermore, it is the main life-threatening condition in patients with COVID-19. This article provides a comprehensive review of the primary literature on the predictable effectiveness of quercetin and its derivatives docked to multi-target of SARS-CoV-2 and host cells via in silico and some of validation through in vitro, in vivo, and clinically to fight SARS-CoV-2 infections, contribute to the reduction of inflammation, which suggests the preventive and therapeutic latency of quercetin and its derived-products against COVID-19 pandemic, multisystem inflammatory syndromes (MIS), and long-COVID.
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Affiliation(s)
- Wan-Yi Ho
- Department of Anatomy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Zi-Han Shen
- Department of Clinical Medicine, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yijing Chen
- Department of Dentisty, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Ting-Hsu Chen
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - XiaoLin Lu
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
| | - Yaw-Syan Fu
- Institute of Respiratory Disease, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
- Anatomy Section, Department of Basic Medical Science, Xiamen Medical College, Xiamen, 361023, Fujian, China
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2
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Spiegel M, Prejanò M, Russo N, Marino T. Primary Antioxidant Power and M pro SARS-CoV-2 Non-Covalent Inhibition Capabilities of Miquelianin. Chem Asian J 2024; 19:e202400079. [PMID: 38415945 DOI: 10.1002/asia.202400079] [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: 01/23/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 02/29/2024]
Abstract
The antioxidant power of quercetin-3-O-glucuronide (miquelianin) has been studied, at the density functional level of theory, in both lipid-like and aqueous environments. In the aqueous phase, the computed pKa equilibria allowed the identification of the neutral and charged species present in solution that can react with the ⋅OOH radical. The Hydrogen Atom Transfer (HAT), Single Electron Transfer (SET) and Radical Adduct Formation (RAF) mechanisms were considered, and the individual, total and fraction corrected rate constants were obtained. Potential non-covalent inhibition of Mpro from SARS-CoV-2 by miquelianin has been also evaluated.
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Affiliation(s)
- Maciej Spiegel
- Department of Organic Chemistry and Pharmaceutical Technology, Wroclaw Medical University, Borowska 211A, 50-556, Wroclaw, Poland
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87136, Rende (CS), Italy
| | - Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87136, Rende (CS), Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87136, Rende (CS), Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, I-87136, Rende (CS), Italy
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3
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Naimi W, Vinnacombe-Willson GA, Saldana S, Ronduen L, Domjan H, Chiang N. Teaching Acid-Base Fundamentals and Introducing pH using Butterfly Pea Flower Tea. JOURNAL OF CHEMICAL EDUCATION 2024; 101:1373-1378. [PMID: 38516052 PMCID: PMC10956649 DOI: 10.1021/acs.jchemed.3c01058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Stimulating interest in science at an early age is important for STEM education. This work details an educational activity utilizing the anthocyanins found in the butterfly pea flower (Clitoria ternatea). This activity was developed for use in official classroom settings, online, and/or at-home with parental or educator guidance. Primary and high school students aged 7 to 14 performed a straightforward extraction of anthocyanin pH indicators from Clitoria ternatea with hot water. Students were able to use this indicator and its vast range of colors to compare the acidity and basicity of different household solutions. Most responses recorded show that students used reasoning from the indicator and a subsequent chemical reaction to correctly differentiate acids from bases and compare their strengths. Overall, this activity's application of non-toxic and easily accessible indicators from the butterfly pea flower assisted in introducing young students to various concepts in acid-base chemistry, including acid/base strength and pH, solute dissolution, neutralization reactions, and qualitative analysis.
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Affiliation(s)
- Wallee Naimi
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Gail A Vinnacombe-Willson
- BioNanoPlasmonics Laboratory, CIC biomaGUNE, Basque Research and Technology Alliance (BRTA), 20014 Donostia-San Sebastián, Spain
| | - Stanley Saldana
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Lionnel Ronduen
- STEM Center, University of Houston, Houston, Texas 77204, United States
| | - Heather Domjan
- STEM Center, University of Houston, Houston, Texas 77204, United States
| | - Naihao Chiang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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Saquib Q, Bakheit AH, Ahmed S, Ansari SM, Al-Salem AM, Al-Khedhairy AA. Identification of Phytochemicals from Arabian Peninsula Medicinal Plants as Strong Binders to SARS-CoV-2 Proteases (3CL Pro and PL Pro) by Molecular Docking and Dynamic Simulation Studies. Molecules 2024; 29:998. [PMID: 38474509 DOI: 10.3390/molecules29050998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/04/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
We provide promising computational (in silico) data on phytochemicals (compounds 1-10) from Arabian Peninsula medicinal plants as strong binders, targeting 3-chymotrypsin-like protease (3CLPro) and papain-like proteases (PLPro) of SARS-CoV-2. Compounds 1-10 followed the Lipinski rules of five (RO5) and ADMET analysis, exhibiting drug-like characters. Non-covalent (reversible) docking of compounds 1-10 demonstrated their binding with the catalytic dyad (CYS145 and HIS41) of 3CLPro and catalytic triad (CYS111, HIS272, and ASP286) of PLPro. Moreover, the implementation of the covalent (irreversible) docking protocol revealed that only compounds 7, 8, and 9 possess covalent warheads, which allowed the formation of the covalent bond with the catalytic dyad (CYS145) in 3CLPro and the catalytic triad (CYS111) in PLPro. Root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and radius of gyration (Rg) analysis from molecular dynamic (MD) simulations revealed that complexation between ligands (compounds 7, 8, and 9) and 3CLPro and PLPro was stable, and there was less deviation of ligands. Overall, the in silico data on the inherent properties of the above phytochemicals unravel the fact that they can act as reversible inhibitors for 3CLPro and PLPro. Moreover, compounds 7, 8, and 9 also showed their novel properties to inhibit dual targets by irreversible inhibition, indicating their effectiveness for possibly developing future drugs against SARS-CoV-2. Nonetheless, to confirm the theoretical findings here, the effectiveness of the above compounds as inhibitors of 3CLPro and PLPro warrants future investigations using suitable in vitro and in vivo tests.
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Affiliation(s)
- Quaiser Saquib
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed H Bakheit
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sarfaraz Ahmed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Sabiha M Ansari
- Botany & Microbiology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah M Al-Salem
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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5
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Jevtovic V, Alshamari AK, Milenković D, Dimitrić Marković J, Marković Z, Dimić D. The Effect of Metal Ions (Fe, Co, Ni, and Cu) on the Molecular-Structural, Protein Binding, and Cytotoxic Properties of Metal Pyridoxal-Thiosemicarbazone Complexes. Int J Mol Sci 2023; 24:11910. [PMID: 37569285 PMCID: PMC10419307 DOI: 10.3390/ijms241511910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
Thiosemicarbazones and their transition metal complexes are biologically active compounds and anticancer agents with versatile structural properties. In this contribution, the structural features and stability of four pyridoxal-thiosemicarbazone (PLTSC) complexes with Fe, Co, Ni, and Cu were investigated using the density functional theory and natural bond orbital approach. Special emphasis was placed on the analysis of the donor atom-metal interactions. The geometry of compounds and crystallographic structures were further examined by Hirshfeld surface analysis, and the main intermolecular interactions were outlined. It has been shown that the geometry and the number of PLTSC units in the structure determine the type and contribution of the specific interactions. The binding of all four complexes to bovine and human serum albumin was investigated through spectrofluorometric titration. The dependency of the thermodynamic parameters on the present metal ion and geometry was explained by the possible interactions through molecular docking simulations. The binding of complexes to DNA, as one of the possible ways the compounds could induce cell death, was examined by molecular docking. The cytotoxicity was measured towards HCT116, A375, MCF-7, A2780, and MCF5 cell lines, with Cu-PLTSC being the most active, as it had the highest affinity towards DNA and proteins.
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Affiliation(s)
- Violeta Jevtovic
- Department of Chemistry, College of Science, University Ha’il, Ha’il 81451, Saudi Arabia
| | - Asma K. Alshamari
- Department of Chemistry, College of Science, University Ha’il, Ha’il 81451, Saudi Arabia
| | - Dejan Milenković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | | | - Zoran Marković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia
| | - Dušan Dimić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
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Vasić J, Dimić D, Antonijević M, Avdović EH, Milenković D, Nakarada Đ, Dimitrić Marković J, Molnar M, Lončarić M, Bešlo D, Marković Z. The Electronic Effects of 3-Methoxycarbonylcoumarin Substituents on Spectral, Antioxidant, and Protein Binding Properties. Int J Mol Sci 2023; 24:11820. [PMID: 37511579 PMCID: PMC10380446 DOI: 10.3390/ijms241411820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Coumarin derivatives are a class of compounds with pronounced biological activities that depend primarily on the present substituents. Four 3-methoxycarbonylcoumarin derivatives with substituents of different electron-donating/electron-withdrawing abilities (Br, NO2, OH, and OMe) were investigated structurally by NMR, IR, and UV-VIS spectroscopies and density functional theory methods. The appropriate level of theory (B3LYP-D3BJ/6-311++G(d,p) was selected after comparing similar compounds' experimental and theoretical structural parameters. The natural bond orbital and quantum theory of atoms in molecules were employed to investigate the intramolecular interactions governing stability. The electronic effects of substituents mostly affected the aromatic ring that the substituents are directly attached to. The antioxidant properties were investigated by electron paramagnetic resonance spectroscopy towards HO•, and the percentages of reduction were between 13% (6-Br) and 23% (6-OMe). The protein binding properties towards transport proteins were assessed by spectrofluorimetry, molecular docking, and molecular dynamics (MD). The experimentally determined binding energies were well reproduced by molecular docking, showing that the spontaneity of ibuprofen binding was comparable to the investigated compounds. The flexibility of HSA in MD simulations depended on the substituents. These results proved the importance of electronic effects for the protein binding affinities and antioxidant properties of coumarin derivatives.
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Affiliation(s)
- Jelena Vasić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Dušan Dimić
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - Marko Antonijević
- Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia
| | - Edina H Avdović
- Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia
| | - Dejan Milenković
- Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia
| | - Đura Nakarada
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia
| | | | - Maja Molnar
- Department of Applied Chemistry and Ecology, Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Franje Kuhača 18, 31000 Osijek, Croatia
| | - Melita Lončarić
- Department of Applied Chemistry and Ecology, Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Franje Kuhača 18, 31000 Osijek, Croatia
| | - Drago Bešlo
- Department of Agroecology and Environmental Protection, Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimir Prelog 1, 31000 Osijek, Croatia
| | - Zoran Marković
- Institute for Information Technologies Kragujevac, University of Kragujevac, Jovana Cvijica bb, 34000 Kragujevac, Serbia
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Abd El-Lateef HM, Khalaf MM, Kandeel M, Amer AA, Abdelhamid AA, Abdou A. Designing, characterization, biological, DFT, and molecular docking analysis for new FeAZD, NiAZD, and CuAZD complexes incorporating 1-(2-hydroxyphenylazo)- 2-naphthol (H 2AZD). Comput Biol Chem 2023; 105:107908. [PMID: 37352589 DOI: 10.1016/j.compbiolchem.2023.107908] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
Herien, three new Fe(III) (FeAZD), Ni(II) (NiAZD), and Cu(II) (CuAZD) complexes were synthesized and characterized using various physicochemical and spectroscopic approaches. The H2AZD ligand acted as a bi-basic bi-dentate NO ligand in a 1:1 molar ratio. The results revealed that the FeAZD and CuAZD complexes had octahedral geometry, while the NiAZD had a tetrahedral geometry. The optimized geometry, HOMO and LUMO analysis of the ligand and its metal complexes was determined via Density functional theory (DFT) using the B3LYP with 6-311 G(d,p), and LanL2DZ level of theory. The FeAZD, NiAZD and CuAZD had lower energy gap, 7.40, 7.93 and 7.06 eV, respectively, than the free ligand (9.58 eV), which proposed that CuAZD was more active one. The free ligand and its metal complexes were in vitro investigated for their antibacterial and antifungal activity. The results illustrated that the metal complexes had higher antibacterial and antifungal activity than the free ligand. More specifically, the CuAZD demonstrated good antibacterial activity against E. coli, P. aeruginosa, S. aureus, B. cereus, and A. flavus, T. rubrum, and C. albicans, with activity indexes of 72.22%, 65.01%, 77.78%, and 72.22%, 63.16%, 59.09%, and 61.90%, respectively. Also, the metal complexes showed lower MIC (6.25-3.125 ppm) compared to the free ligand (about 50 ppm). Finally, molecular docking was utilized to investigate the ability of the free ligand and its metal complexes to inhibit the growth of E. coli (PDB ID: 5iq9). The results showed that the CuAZD had the highest binding affinity to the receptor, with a more negative docking score of - 7.05 Kcal/mol, and lower inhibition constant (Ki) of 6.90 µM. That is indicating that it may be the most effective at inhibiting the growth of E. coli (PDB ID: 5iq9).
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Affiliation(s)
- Hany M Abd El-Lateef
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia; Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt.
| | - Mai M Khalaf
- Department of Chemistry, College of Science, King Faisal University, Al-Ahsa 31982, Saudi Arabia; Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, 31982 Al-Ahsa, Saudi Arabia; Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, 33516 Kafrelsheikh, Egypt
| | - Amer A Amer
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Antar A Abdelhamid
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt; Chemistey Department, Faculty of Science, Al-Baha University, Al-Baha, Saudi Arabia
| | - Aly Abdou
- Department of Chemistry, Faculty of Science, Sohag University, Sohag 82524, Egypt.
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Amić A, Mastiľák Cagardová D. A DFT Study on the Kinetics of HOO •, CH 3OO •, and O 2•- Scavenging by Quercetin and Flavonoid Catecholic Metabolites. Antioxidants (Basel) 2023; 12:1154. [PMID: 37371883 DOI: 10.3390/antiox12061154] [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: 05/01/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Reaction kinetics have been theoretically examined to ascertain the potency of quercetin (Q) and flavonoid catecholic metabolites 1-5 in the inactivation of HOO•, CH3OO•, and O2•- under physiological conditions. In lipidic media, the koverallTST/Eck rate constants for the proton-coupled electron transfer (PCET) mechanism indicate the catecholic moiety of Q and 1-5 as the most important in HOO• and CH3OO• scavenging. 5-(3,4-Dihydroxyphenyl)-γ-valerolactone (1) and alphitonin (5) are the most potent scavengers of HOO• and CH3OO•, respectively. The koverallMf rate constants, representing actual behavior in aqueous media, reveal Q as more potent in the inactivation of HOO• and CH3OO• via single electron transfer (SET). SET from 3-O- phenoxide anion of Q, a structural motif absent in 1-5, represents the most contributing reaction path to overall activity. All studied polyphenolics have a potency of O2•- inactivation via a concerted two-proton-coupled electron transfer (2PCET) mechanism. The obtained results indicate that metabolites with notable radical scavenging potency, and more bioavailability than ingested flavonoids, may contribute to human health-promoting effects ascribed to parent molecules.
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Affiliation(s)
- Ana Amić
- Department of Chemistry, Josip Juraj Strossmayer University of Osijek, Ulica cara Hadrijana 8A, 31000 Osijek, Croatia
| | - Denisa Mastiľák Cagardová
- Institute of Physical Chemistry and Chemical Physics, Department of Chemical Physics, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37 Bratislava, Slovakia
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de Sousa ALM, Rizaldo Pinheiro R, Furtado Araujo J, Mesquita Peixoto R, de Azevedo DAA, Cesar Lima AM, Marques Canuto K, Vasconcelos Ribeiro PR, de Queiroz Souza AS, Rocha Souza SC, de Amorim SL, Paula Amaral G, de Souza V, de Morais SM, Andrioli A, da Silva Teixeira MF. In vitro antiviral effect of ethanolic extracts from Azadirachta indica and Melia azedarach against goat lentivirus in colostrum and milk. Sci Rep 2023; 13:4677. [PMID: 36949145 PMCID: PMC10031174 DOI: 10.1038/s41598-023-31455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/13/2023] [Indexed: 03/24/2023] Open
Abstract
This study aimed to evaluate, in vitro, the use of leaf extracts of Azadirachta indica (A. indica) and Melia azedarach (M. azedarach) as antivirals against caprine lentivirus (CLV) in colostrum and milk of goat nannies. These were collected from eight individuals and infected with the standard strain of CLV. Samples were then subdivided into aliquots and treated with 150 µg/mL of crude extract, and with ethyl acetate and methanol fractions for 30, 60, and 90 min. Next, somatic cells from colostrum and milk were co-cultured with cells from the ovine third eyelid. After this step, viral titers of the supernatants collected from treatments with greater efficacy in co-culture were assessed. The organic ethyl acetate fractions of both plants at 90 min possibly inhibited the viral activity of CLV by up to a thousandfold in colostrum. In milk, this inhibition was up to 800 times for the respective Meliaceae. In conclusion, the ethanolic fraction of ethyl acetate from both plants demonstrated efficacy against CLV in samples from colostrum and milk when subjected to treatment, which was more effective in colostrum.
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Affiliation(s)
- Ana Lidia Madeira de Sousa
- Laboratory of Virology (LABOVIR), State University of Ceará (UECE), Fortaleza, CE, Brazil.
- Faculdade Educar da Ibiapaba, Ípu, CE, Brazil.
| | | | | | - Renato Mesquita Peixoto
- Vale do Salgado University Center (UNIVS), Icó, CE, Brazil
- Terra Nordeste College (FATENE), Caucaia, CE, Brazil
| | | | - Ana Milena Cesar Lima
- Scholarship for Regional Scientific Development of the National Council for Scientific and Technological Development (DCR-CNPq/FUNCAP), Level C, Embrapa Goats and Sheep, Sobral, CE, Brazil
| | - Kirley Marques Canuto
- Multiuser Laboratory of Natural Products Chemistry, Embrapa Tropical Agroindustry, Fortaleza, CE, Brazil
| | | | | | | | - Sara Lucena de Amorim
- Department of Veterinary Medicine, Federal University of Rondônia, Rolim de Moura, RO, Brazil
| | | | - Viviane de Souza
- Laboratory of Microbiology, Embrapa Goats and Sheep, Sobral, CE, Brazil
| | - Selene Maia de Morais
- Laboratory of Chemistry and Natural Products (LQPN), Ceará State University, Fortaleza, CE, Brazil
| | - Alice Andrioli
- Laboratory of Virology, Embrapa Goats and Sheep, Sobral, CE, Brazil
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10
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Ghous F, Shukla S, Singh R, Parveen S, Banerjee M, Bishnoi A. Synthesis, Crystal Structure, Computational Investigation, Molecular Docking Analysis and Anti-lung Cancer Activity of Novel (Z)-3-amino-2-(cyclohexylidenehydrazono)thiazolidin-4-one. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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11
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Spiegel M, Ciardullo G, Marino T, Russo N. Computational investigation on the antioxidant activities and on the M pro SARS-CoV-2 non-covalent inhibition of isorhamnetin. Front Chem 2023; 11:1122880. [PMID: 36762196 PMCID: PMC9902383 DOI: 10.3389/fchem.2023.1122880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023] Open
Abstract
In the present work, we report a computational study on some important chemical properties of the flavonoid isorhamnetin, used in traditional medicine in many countries. In the course of the study we determined the acid-base equilibria in aqueous solution, the possible reaction pathways with the •OOH radical and the corresponding kinetic constants, the complexing capacity of copper ions, and the reduction of these complexes by reducing agents such as superoxide and ascorbic anion by using density functional level of theory Density Functional Theory. Finally, the non-covalent inhibition ability of the SARS-CoV-2 main protease enzyme by isorhamnetin was examined by molecular dynamics (MD) and docking investigation.
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Affiliation(s)
- Maciej Spiegel
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy,Department of Pharmacognosy and Herbal Medicines, Wroclaw Medical University, Wroclaw, Poland
| | - Giada Ciardullo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Rende, Cosenza, Italy,*Correspondence: Nino Russo,
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12
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Çelik F, Süleymanoğlu N, Ustabaş R, Türkan F, Güler Hİ, Ünver Y, Kahriman N. New chalcone derivative, ethyl 2-(4-(3-(benzo[ b]thiophen-2-yl)acryloyl)phenoxy)acetate: synthesis, characterization, DFT study, enzyme inhibition activities and docking study. J Biomol Struct Dyn 2022; 40:12260-12267. [PMID: 34445923 DOI: 10.1080/07391102.2021.1969287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Chalcone derivative, ethyl 2-(4-(3-(benzo[b]thiophen-2yl)acryloyl)phenoxy)acetate (I), was synthesized. Compound I was characterized by proton and carbon-13 nuclear magnetic resonance (1H- and 13C- NMR), fourier transform infrared (FTIR) and mass (LC-ESI-MS/MS) spectroscopic methods. Density Functional Theory (DFT) calculations for compound I were performed at B3LYP/6-311++G(d,p) level. Optimized geometry, frontier molecular orbitals (HOMO; highest occupied molecular orbital; LUMO: lowest unoccupied molecular orbital), IR and NMR parameters of compound I were obtained. The evaluations reveal that the calculation results support the experimental results. The inhibition effects of compound I on cholinesterases and GST enzyme were investigated. Ki and inhibition concentration (IC50) values were calculated separately. Ki values of compound I were found for GST 14.19 ± 2.15, for AChE 11.13 ± 1.22 and for BChE 8.74 ± 0.76 recpectively. The docking analysis of compound I supported the enzym inhibition activity exhibiting high inhibition constant and binding energy for three receptors. Compound I is strongly bound to AChE, huBChE and Glutathione S-transferase with binding energies -11.24, -8.56 and -10.39 kcal/mol, respectively.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatih Çelik
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey
| | - Nevin Süleymanoğlu
- Vocational School of Technical Sciences, Gazi University, Ostim, Ankara, Turkey
| | - Reşat Ustabaş
- Department of Mathematics and Science Education, Educational Faculty, Ondokuz Mayıs University, Kurupelit, Samsun, Turkey
| | - Fikret Türkan
- Health Services Vocational School, Iğdır University, Iğdır, Turkey
| | - Halil İbrahim Güler
- Department of Molecular Biology and Genetics, Karadeniz Technical University Faculty of Science, Trabzon, Turkey
| | - Yasemin Ünver
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey
| | - Nuran Kahriman
- Department of Chemistry, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey
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13
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Priscilla J, Dhas DA, Joe IH, Balachandran S. Spectroscopic (FT-IR, FT-Raman) investigation, topological (QTAIM, RDG, ELF) analysis, drug-likeness and anti-inflammatory activity study on 2-methylaminobenzoic acid alkaloid. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Manhas FM, Fatima A, Verma I, Siddiqui N, Muthu S, AlSalem HS, Savita S, Singh M, Javed S. Quantum computational, spectroscopic (FT-IR, NMR and UV–Vis) profiling, Hirshfeld surface, molecular docking and dynamics simulation studies on pyridine-2,6-dicarbonyl dichloride. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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15
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Ünver Y, Süleymanoğlu N, Ustabaş R, Güler Hİ, Bektaş E, Bektaş Kİ, Çelik F. New carbazol derivatives containing 1,2,4-triazole: Synthesis, characterization, DFT study, acetylcholinesterase activity and docking study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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16
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Yorur Goreci C. Synthesis and comparative spectroscopic studies, HOMO–LUMO analysis and molecular docking studies of 3,3′-(1,4-phenylene)bis[2-(6-chloropyridin-3-yl)prop‑2-enenitrile] based on DFT. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Spectroscopic, quantum chemical and molecular docking studies on friedelin, the major triterpenoid isolated from Garcinia imberti. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Synthesis, crystal structure, DFT and molecular docking studies of N-acetyl-2,4-[diaryl-3-azabicyclo[3.3.1]nonan-9-yl]-9-spiro-4'-acetyl-2'-(acetylamino)-4',9-dihydro-[1',3',4']-thiadiazoles: A potential SARS-nCoV-2 Mpro (COVID-19) inhibitor. J Mol Struct 2022; 1259:132747. [PMID: 35250091 PMCID: PMC8888462 DOI: 10.1016/j.molstruc.2022.132747] [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: 01/07/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 11/21/2022]
Abstract
In this paper, we describe the synthesis and crystal structure analysis of N-acetyl-2,4-[diphenyl-3-azabicyclo[3.3.1]nonan-9-yl]-9-spiro-4′-acetyl-2′-(acetylamino)-4′,9-dihydro-[1′,3′,4′]-thiadiazole (3a) and N-acetyl- 2,4-[bis(p-methoxyphenyl)-3-azabicyclo[3.3.1]nonan-9-yl]-9-spiro-4′-acetyl-2′-(acetylamino)-4′,9-dihydro-[1′,3′,4′]-thiadiazole (3b). The title compounds 3a and 3b are characterized by 1D NMR and single crystal x-ray diffraction analysis. Non-covalent interactions in a molecule were identified by Hirshfeld surface (dnorm contacts and 2D fingerprint plot) analysis. In addition, the existence of chalcogen bond (S•••O bond) in the molecular structures (3a and 3b) are described by NCI-RDG and QTAIM analysis. NBO analysis is employed to describe the orbital interactions and electron transfer between sulfur and oxygen atoms. Molecular docking is carried out for compounds 3a and 3b with COVID-19 viral protein SARS-nCoV-2 Mpro (PDB ID: 6LU7).
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Ozkan G, Franco P, De Marco I, Capanoglu E, Esatbeyoglu T. Investigating the effects of supercritical antisolvent process and food models on antioxidant capacity, bioaccessibility and transepithelial transport of quercetin and rutin. Food Funct 2022; 13:4469-4477. [PMID: 35343983 DOI: 10.1039/d1fo04091j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the present study, the effects of the Supercritical Anti-Solvent (SAS) process and food models on the antioxidant capacity, bioaccessibility and transport dynamics of flavonol-loaded polyvinylpyrrolidone (PVP) based microparticles were investigated using a combined in vitro gastrointestinal digestion/Caco-2 cell culture model. SAS-processed and unprocessed flavonols were supplied in two different food models: 10% ethanol for an aqueous hydrophilic food simulant and 3% acetic acid for an acidic food simulant. The SAS processing of quercetin and rutin resulted in a much higher recovery of these bioactives as well as greater retention of antioxidant capacity after gastrointestinal digestion in both hydrophilic and acidic food models. The present study also demonstrates that SAS coprecipitation has a positive effect on the stability and transport of bioactives across the epithelial cell layer. It can be deduced from the results that the SAS process can be a useful method in pharmaceutical and nutraceutical applications with high stability, bioaccessibility, bioavailability and thus enhanced nutritional value.
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Affiliation(s)
- Gulay Ozkan
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey. .,Institute of Food Science and Human Nutrition, Gottfried Wilhelm Leibniz University Hannover, Am Kleinen Felde 30, 30167 Hannover, Germany.
| | - Paola Franco
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Iolanda De Marco
- Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Esra Capanoglu
- Department of Food Engineering, Faculty of Chemical and Metallurgical Engineering, Istanbul Technical University, 34469 Maslak, Istanbul, Turkey.
| | - Tuba Esatbeyoglu
- Institute of Food Science and Human Nutrition, Gottfried Wilhelm Leibniz University Hannover, Am Kleinen Felde 30, 30167 Hannover, Germany.
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20
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Pastwińska J, Karaś K, Sałkowska A, Karwaciak I, Chałaśkiewicz K, Wojtczak BA, Bachorz RA, Ratajewski M. Identification of Corosolic and Oleanolic Acids as Molecules Antagonizing the Human RORγT Nuclear Receptor Using the Calculated Fingerprints of the Molecular Similarity. Int J Mol Sci 2022; 23:ijms23031906. [PMID: 35163824 PMCID: PMC8837092 DOI: 10.3390/ijms23031906] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023] Open
Abstract
RORγT is a protein product of the RORC gene belonging to the nuclear receptor subfamily of retinoic-acid-receptor-related orphan receptors (RORs). RORγT is preferentially expressed in Th17 lymphocytes and drives their differentiation from naive CD4+ cells and is involved in the regulation of the expression of numerous Th17-specific cytokines, such as IL-17. Because Th17 cells are implicated in the pathology of autoimmune diseases (e.g., psoriasis, inflammatory bowel disease, multiple sclerosis), RORγT, whose activity is regulated by ligands, has been recognized as a drug target in potential therapies against these diseases. The identification of such ligands is time-consuming and usually requires the screening of chemical libraries. Herein, using a Tanimoto similarity search, we found corosolic acid and other pentacyclic tritepenes in the library we previously screened as compounds highly similar to the RORγT inverse agonist ursolic acid. Furthermore, using gene reporter assays and Th17 lymphocytes, we distinguished compounds that exert stronger biological effects (ursolic, corosolic, and oleanolic acid) from those that are ineffective (asiatic and maslinic acids), providing evidence that such combinatorial methodology (in silico and experimental) might help wet screenings to achieve more accurate results, eliminating false negatives.
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Affiliation(s)
- Joanna Pastwińska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Kaja Karaś
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Anna Sałkowska
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Iwona Karwaciak
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Katarzyna Chałaśkiewicz
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
| | - Błażej A. Wojtczak
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland;
| | - Rafał A. Bachorz
- Laboratory of Molecular Modeling, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland;
| | - Marcin Ratajewski
- Laboratory of Epigenetics, Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.P.); (K.K.); (A.S.); (I.K.); (K.C.)
- Correspondence: ; Tel.: +48-42-209-33-89
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21
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Palanisamy K, Rubavathy SME, Prakash M, Thilagavathi R, Hosseini-Zare MS, Selvam C. Antiviral activities of natural compounds and ionic liquids to inhibit the Mpro of SARS-CoV-2: a computational approach. RSC Adv 2022; 12:3687-3695. [PMID: 35425367 PMCID: PMC8979281 DOI: 10.1039/d1ra08604a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 12/14/2022] Open
Abstract
The recalcitrant spread of the COVID-19 pandemic produced by the novel coronavirus SARS-CoV-2 is one of the most destructive occurrences in history. Despite the availability of several effective vaccinations and their widespread use, this line of immunization often faces questions about its long-term efficacy. Since coronaviruses rapidly change, and multiple SARS-CoV-2 variants have emerged around the world. Therefore, finding a new target-based medication became a priority to prevent and control COVID-19 infections. The main protease (Mpro) is a salient enzyme in coronaviruses that plays a vital role in viral replication, making it a fascinating therapeutic target for SARS-CoV-2. We screened 0.2 million natural products against the Mpro of SARS-CoV-2 using the Universal Natural Product Database (UNPD). As well, we studied the role of ionic liquids (ILs) on the structural stabilization of Mpro. Cholinium-based ILs are biocompatible and used for a variety of biomedical applications. Molecular docking was employed for the initial screening of natural products and ILs against Mpro. To predict the drug-likeness features of lead compounds, we calculated the ADMET properties. We performed MD simulations for the selected complexes based on the docking outcomes. Using MM/PBSA approaches, we conclude that compounds NP-Hit2 (-25.6 kcal mol-1) and NP-Hit3 (-25.3 kcal mol-1) show stronger binding affinity with Mpro. The hotspot residues of Thr25, Leu27, His41, Met49, Cys145, Met165, and Gln189 strongly interacted with the natural compounds. Furthermore, naproxenate, ketoprofenate, and geranate, cholinium-based ILs strongly interact with Mpro and these ILs have antimicrobial properties. Our findings will aid in the development of effective Mpro inhibitors.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology Kattankulathur-603203 Chennai Tamil Nadu India
| | - S M Esther Rubavathy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology Kattankulathur-603203 Chennai Tamil Nadu India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology Kattankulathur-603203 Chennai Tamil Nadu India
| | - Ramasamy Thilagavathi
- Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education Coimbatore India
| | - Maryam S Hosseini-Zare
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA
| | - Chelliah Selvam
- Department of Pharmaceutical and Environmental Health Sciences, College of Pharmacy and Health Sciences, Texas Southern University Houston TX-77004 USA
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22
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Defant A, Dosi F, Innocenti N, Mancini I. Synthesis of Nucleoside-like Molecules from a Pyrolysis Product of Cellulose and Their Computational Prediction as Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors. Int J Mol Sci 2022; 23:518. [PMID: 35008944 PMCID: PMC8745730 DOI: 10.3390/ijms23010518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/01/2023] Open
Abstract
(1R,5S)-1-Hydroxy-3,6-dioxa-bicyclo[3.2.1]octan-2-one, available by an efficient catalytic pyrolysis of cellulose, has been applied as a chiral building block in the synthesis of seven new nucleoside analogues, with structural modifications on the nucleobase moiety and on the carboxyl- derived unit. The inverted configuration by Mitsunobu reaction used in their synthesis was verified by 2D-NOESY correlations, supported by the optimized structure employing the DFT methods. An in silico screening of these compounds as inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase has been carried out in comparison with both remdesivir, a mono-phosphoramidate prodrug recently approved for COVID-19 treatment, and its ribonucleoside metabolite GS-441524. Drug-likeness prediction and data by docking calculation indicated compound 6 [=(3S,5S)-methyl 5-(hydroxymethyl)-3-(6-(4-methylpiperazin-1-yl)-9H-purin-9-yl)tetrahydrofuran-3-carboxylate] as the best candidate. Furthermore, molecular dynamics simulation showed a stable interaction of structure 6 in RNA-dependent RNA polymerase (RdRp) complex and a lower average atomic fluctuation than GS-441524, suggesting a well accommodation in the RdRp binding pocket.
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Affiliation(s)
- Andrea Defant
- Laboratorio di Chimica Bioorganica, Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento, Italy; (F.D.); (N.I.)
| | | | | | - Ines Mancini
- Laboratorio di Chimica Bioorganica, Dipartimento di Fisica, Università di Trento, Via Sommarive 14, 38123 Trento, Italy; (F.D.); (N.I.)
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23
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Moradi S, Shareghi B, Saboury AA, Farhadian S. The influence of Cadaverine on the structure, stability, and activity of acid phosphatase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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24
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25
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Albutti A. Rescuing the Host Immune System by Targeting the Immune Evasion Complex ORF8-IRF3 in SARS-CoV-2 Infection with Natural Products Using Molecular Modeling Approaches. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:112. [PMID: 35010372 PMCID: PMC8750414 DOI: 10.3390/ijerph19010112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022]
Abstract
The perennial emergence of SARS-CoV-2 and its new variants causing upper respiratory complexities since December 2019 has aggravated the pandemic situation around the world. SARS-CoV-2 encodes several proteins among which ORF8 is a novel factor that is unique to SARS-CoV-2 only and is reported to help the virus in disease severity and immune evasion. ORF8-IRF3 complex induces endoplasmic reticulum stress, thus helps in the evasion of immune response. Consequently, targeting the ORF8-IRF3 complex is considered as a prime target for the discovery of novel drugs against SARS-CoV-2. In this regard, computational methods are of great interest to fast track the identification and development of novel drugs. Virtual screening of South African Natural Compounds Database (SANCDB), followed by docking and molecular dynamics (MD) simulation analysis, were performed to determine novel natural compounds. Computational molecular search and rescoring of the SANCDB database followed by induced-fit docking (IFD) protocol identified Quercetin 3-O-(6″-galloyl)-beta-D-galactopyranoside (SANC00850), Tribuloside (SANC01050), and Rutin (SANC00867) are the best scoring compounds. Structural-dynamic properties assessment revealed that these three compounds have stable dynamics, compactness, and a higher number of hydrogen bonds. For validation, we used MM/GBSA, in silico bioactivity estimation and dissociation constant (KD) approaches, which revealed that these compounds are the more potent inhibitors of the ORF8-IRF3 complex and would rescue the host immune system potentially. These compounds need further in vitro and in vivo validations to be used as therapeutics against SARS-CoV-2 to rescue the host immune system during COVID-19 infection.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia
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26
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Cao J, Lian G, Qi X, Jin G. Design synthesis and photophysical properties of a novel antitumor fluorescence agents. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Di Petrillo A, Orrù G, Fais A, Fantini MC. Quercetin and its derivates as antiviral potentials: A comprehensive review. Phytother Res 2021; 36:266-278. [PMID: 34709675 PMCID: PMC8662201 DOI: 10.1002/ptr.7309] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/08/2021] [Accepted: 10/02/2021] [Indexed: 01/21/2023]
Abstract
Quercetin, widely distributed in fruits and vegetables, is a flavonoid known for its antioxidant, antiviral, antimicrobial, and antiinflammatory properties. Several studies highlight the potential use of quercetin as an antiviral, due to its ability to inhibit the initial stages of virus infection, to be able to interact with proteases important for viral replication, and to reduce inflammation caused by infection. Quercetin could also be useful in combination with other drugs to potentially enhance the effects or synergistically interact with them, in order to reduce their side effects and related toxicity. Since there is no comprehensive compilation about antiviral activities of quercetin and derivates, the aim of this review is providing a summary of their antiviral activities on a set of human viral infections along with mechanisms of action. Thus, the following family of viruses are examined: Flaviviridae, Herpesviridae, Orthomyxoviridae, Coronaviridae, Hepadnaviridae, Retroviridae, Picornaviridae, Pneumoviridae, and Filoviridae.
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Affiliation(s)
- Amalia Di Petrillo
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Germano Orrù
- Department of Surgical Science, University of Cagliari, Cagliari, Italy
| | - Antonella Fais
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Massimo C Fantini
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
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El Gizawy HA, Boshra SA, Mostafa A, Mahmoud SH, Ismail MI, Alsfouk AA, Taher AT, Al-Karmalawy AA. Pimenta dioica (L.) Merr. Bioactive Constituents Exert Anti-SARS-CoV-2 and Anti-Inflammatory Activities: Molecular Docking and Dynamics, In Vitro, and In Vivo Studies. Molecules 2021; 26:5844. [PMID: 34641388 PMCID: PMC8510437 DOI: 10.3390/molecules26195844] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
In response to the urgent need to control Coronavirus disease 19 (COVID-19), this study aims to explore potential anti-SARS-CoV-2 agents from natural sources. Moreover, cytokine immunological responses to the viral infection could lead to acute respiratory distress which is considered a critical and life-threatening complication associated with the infection. Therefore, the anti-viral and anti-inflammatory agents can be key to the management of patients with COVID-19. Four bioactive compounds, namely ferulic acid 1, rutin 2, gallic acid 3, and chlorogenic acid 4 were isolated from the leaves of Pimenta dioica (L.) Merr (ethyl acetate extract) and identified using spectroscopic evidence. Furthermore, molecular docking and dynamics simulations were performed for the isolated and identified compounds (1-4) against SARS-CoV-2 main protease (Mpro) as a proposed mechanism of action. Furthermore, all compounds were tested for their half-maximal cytotoxicity (CC50) and SARS-CoV-2 inhibitory concentrations (IC50). Additionally, lung toxicity was induced in rats by mercuric chloride and the effects of treatment with P. dioca aqueous extract, ferulic acid 1, rutin 2, gallic acid 3, and chlorogenic acid 4 were recorded through measuring TNF-α, IL-1β, IL-2, IL-10, G-CSF, and genetic expression of miRNA 21-3P and miRNA-155 levels to assess their anti-inflammatory effects essential for COVID-19 patients. Interestingly, rutin 2, gallic acid 3, and chlorogenic acid 4 showed remarkable anti-SARS-CoV-2 activities with IC50 values of 31 µg/mL, 108 μg/mL, and 360 µg/mL, respectively. Moreover, the anti-inflammatory effects were found to be better in ferulic acid 1 and rutin 2 treatments. Our results could be promising for more advanced preclinical and clinical studies especially on rutin 2 either alone or in combination with other isolates for COVID-19 management.
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Affiliation(s)
- Heba A El Gizawy
- Department of Pharmacognosy, Faculty of Pharmacy, October 6 University (O6U), October 6 City, Giza 12585, Egypt
| | - Sylvia A Boshra
- Department of Biochemistry, Faculty of Pharmacy, October 6 University (O6U), October 6 City, Giza 12585, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Dokki, Giza 12622, Egypt
| | - Sara H Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Dokki, Giza 12622, Egypt
| | - Muhammad I Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The British University in Egypt, Al-Sherouk City, Cairo-Suez Desert Road, Cairo 11837, Egypt
| | - Aisha A Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 84428, Saudi Arabia
| | - Azza T Taher
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, October 6 University (O6U), October 6 City, Giza 12585, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
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Jovanović JĐ, Antonijević M, El‐Emam AA, Marković Z. Comparative MD Study of Inhibitory Activity of Opaganib and Adamantane-Isothiourea Derivatives toward COVID-19 Main Protease M pro. ChemistrySelect 2021; 6:8603-8610. [PMID: 34909459 PMCID: PMC8662094 DOI: 10.1002/slct.202101898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/18/2021] [Indexed: 12/16/2022]
Abstract
In this study, the inhibitory potency of four adamantly- isothiourea derivatives (compounds 1 [4-bromobenzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 2 [3,5-bis(trifluoromethyl)benzyl (Z)-N'-(adamantan-1-yl)-4-phenylpiperazine-1-carbothioimidate], 3 [4-bromobenzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate] and 4 [3,5-bis(trifluoromethyl)benzyl (Z)-N-(adamantan-1-yl)morpholine-4-carbothioimidate]) was evaluated against SARS-CoV-2 targeted proteins. The investigated compounds 1-4 possess a similar structure to opaganib, which is used in studies like a potential drug for COVID-19 treatment. Since examined adamantly-isothiourea derivatives (1-4) shown broad-spectrum of antibacterial activity and significant in vitro cytotoxic effects against five human tumor cell lines and shown similarity in structure with opaganib, it was of interest to study their inhibitory potency toward some SARS-CoV-2 proteins such as SARS-CoV-2 main protease Mpro and mutation of SARS-CoV-2 Spike (S) Protein D614G. The inhibitory potency of studied compounds is examined using molecular docking and molecular dynamic simulations. The results of molecular docking simulations indicate compound 1 as the most prominent candidate of inhibition of SARS-CoV-2 main protease Mpro (▵Gbind=11.24 kcal/mol), while almost the same inhibition potency of all studied compounds is exhibited toward D614G. Regarding the results obtained by molecular dynamic simulations, compounds 1 and 4 possess similar inhibitory potency toward SARS-CoV-2 main protease Mpro as opaganib (▵Gbind ≈ 40 kcal/mol).
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Affiliation(s)
- Jelena Đorović Jovanović
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| | - Marko Antonijević
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
| | - Ali A. El‐Emam
- Department of Medicinal ChemistryFaculty of PharmacyMansoura UniversityMansoura35516Egypt
| | - Zoran Marković
- Department of ScienceInstitute for Information TechnologiesUniversity of Kragujevac, Jovana Cvijića bb34000Kragujevac, Republic ofSerbia
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Bektaş E, Sahin H, Beldüz AO, Güler Hİ. HIV-1-RT inhibition activity of Satureja spicigera (C.KOCH) BOISS. Aqueous extract and docking studies of phenolic compounds identified by RP-HPLC-DAD. J Food Biochem 2021; 46:e13921. [PMID: 34477237 DOI: 10.1111/jfbc.13921] [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: 06/25/2021] [Revised: 08/09/2021] [Accepted: 08/25/2021] [Indexed: 11/30/2022]
Abstract
AIDS is a global disease caused by HIV, affecting millions of people and causing death. The current limitations of antiretroviral therapy used in the therapy of HIV/AIDS have led to the need to search for new and effective drugs from natural products, especially plants. Herewith, using the present study, the detection of HIV-1-RT inhibition of aqueous extract of Satureja spicigera (C.KOCH) BOISS. was performed for the first time. Besides, total phenolic content (TPC), analysis of phenolic constituents by RP-HPLC-DAD and antioxidant capacity by DPPH and Ferric reducing antioxidant power (FRAP) methods were determined for the first time. In addition, molecular docking studies were carried out between HIV-1-RT and phenolic substances, the presence of which was determined in the aqueous extract, for the determination of the phenolics that may be responsible for HIV-1-RT activity. HIV-1-RT inhibition was defined as IC50 : 22.83 μg/ml. Benzoic acid, vanillin, rutin, and chlorogenic acid were present as main phenolics in quantities of 621.96, 505.87, 349.33, and 323.23 µg phenolic/g extract, respectively. Further, TPC, DPPH, and FRAP were calculated as in the order of 151.69 mg GAE/g extract, 23.77 µg/ml, and 445.7 µmol TE/g extract. Chlorogenic acid (-8.48 kcal/mol) was found to be the most effective ligand in docking studies, with a value close to positive standard nevirapine (-9.35 kcal/mol). Hereby, although the aqueous extract of S. spicigera can be used as a natural antioxidant, the crude extract or its phenolics have the potential to be used in the treatment of AIDS due to its high HIV-1-RT activity. PRACTICAL APPLICATIONS: In this study, anti-HIV-1-RT and antioxidant activity and total phenolic content of Satureja spicigera aqueous extract were determined. In addition, HPLC analysis of some phytochemicals and the activities of these phytochemicals against HIV-1-RT enzyme was determined by molecular docking studies. The results showed that the aqueous extract of S. spicigera and some of the phytochemicals it contains have the potential to be used as a natural product against HIV infection or in the treatment of AIDS.
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Affiliation(s)
- Ersan Bektaş
- Espiye Vocational School, Giresun University, Giresun, Turkey
| | - Huseyin Sahin
- Espiye Vocational School, Giresun University, Giresun, Turkey
| | - Ali Osman Beldüz
- Faculty of Science, Department of Biology, Karadeniz Technical University, Trabzon, Turkey
| | - Halil İbrahim Güler
- Faculty of Science, Department of Molecular Biology and Genetics, Karadeniz Technical University, Trabzon, Turkey
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Olanlokun JO, Okoro PO, Lawal OS, Bodede O, Olotu F, Idowu TO, Prinsloo G, Soliman ME, Olorunsogo OO. Betulinic acid purified from Alstonia boonei inhibits folate biosynthesis in malarial Plasmodium, enhances mitochondrial pore opening and F1F0 ATPase in mice. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Antonijević MR, Simijonović DM, Avdović EH, Ćirić A, Petrović ZD, Marković JD, Stepanić V, Marković ZS. Green One-Pot Synthesis of Coumarin-Hydroxybenzohydrazide Hybrids and Their Antioxidant Potency. Antioxidants (Basel) 2021; 10:1106. [PMID: 34356339 PMCID: PMC8301024 DOI: 10.3390/antiox10071106] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Compounds from the plant world that possess antioxidant abilities are of special importance for the food and pharmaceutical industry. Coumarins are a large, widely distributed group of natural compounds, usually found in plants, often with good antioxidant capacity. The coumarin-hydroxybenzohydrazide derivatives were synthesized using a green, one-pot protocol. This procedure includes the use of an environmentally benign mixture (vinegar and ethanol) as a catalyst and solvent, as well as very easy isolation of the desired products. The obtained compounds were structurally characterized by IR and NMR spectroscopy. The purity of all compounds was determined by HPLC and by elemental microanalysis. In addition, these compounds were evaluated for their in vitro antioxidant activity. Mechanisms of antioxidative activity were theoretically investigated by the density functional theory approach and the calculated values of various thermodynamic parameters, such as bond dissociation enthalpy, proton affinity, frontier molecular orbitals, and ionization potential. In silico calculations indicated that hydrogen atom transfer and sequential proton loss-electron transfer reaction mechanisms are probable, in non-polar and polar solvents respectively. Additionally, it was found that the single-electron transfer followed by proton transfer was not an operative mechanism in either solvent. The conducted tests indicate the excellent antioxidant activity, as well as the low potential toxicity, of the investigated compounds, which makes them good candidates for potential use in food chemistry.
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Affiliation(s)
- Marko R. Antonijević
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (M.R.A.); (D.M.S.)
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (A.Ć.); (Z.D.P.)
| | - Dušica M. Simijonović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (M.R.A.); (D.M.S.)
| | - Edina H. Avdović
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (M.R.A.); (D.M.S.)
| | - Andrija Ćirić
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (A.Ć.); (Z.D.P.)
| | - Zorica D. Petrović
- Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia; (A.Ć.); (Z.D.P.)
| | - Jasmina Dimitrić Marković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11000 Belgrade, Serbia;
| | - Višnja Stepanić
- Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Zoran S. Marković
- Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia; (M.R.A.); (D.M.S.)
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Adımcılar V, Çeşme M, Şenel P, Danış İ, Ünal D, Gölcü A. Comparative study of cytotoxic activities, DNA binding and molecular docking interactions of anticancer agent epirubicin and its novel copper complex. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Elseginy SA, Anwar MM. In silico analysis of SARS-CoV-2 papain-like protease potential inhibitors. RSC Adv 2021; 11:38616-38631. [PMID: 35493238 PMCID: PMC9044241 DOI: 10.1039/d1ra07845c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/23/2021] [Indexed: 01/08/2023] Open
Abstract
The emergent outbreak caused by severe acute respiratory syndrome coronavirus 2 continues spreading and causing huge social and economic disruption. Papain-like protease (PLpro) has a crucial role in the cleavage of viral polyproteins, and disruption of host responses. PLpro is considered an important goal for the development of SARS-CoV-2 inhibitors. ZINC101291108 (lead 1) and ZINC16449029 (lead 2) were identified as potent SARS-CoV-2 PLpro inhibitors with IC50 values of 0.085 μM and 0.063 μM, respectively. Molecular dynamics simulations (MD) were carried out for lead 1, 2 and several reported SARS-CoV-2 inhibitors. Analysis results of the simulations confirmed the stability of both compounds and showed that they adopted two confirmations along the simulation period. The per-residue decomposition results revealed that the key residues involved in inhibitor binding were E167, P247, P248, Y264, Y268 and Q269. H-bond analyses showed H-bonds with G266 and N267 and salt bridges with G209 and Y273, which are essential for strengthening the substrate-binding pocket. Both inhibitors showed hydrophobic interactions with the S4 site and BL2 loop residues. The RMSD of the BL2 loop with the two inhibitors was investigated, and the results showed that the Y268 and Q269 BL2 loop residues moved outward to accommodate the large size of lead 2. The van der Waals interaction was the main energy contribution that stabilized lead 2, while van der Waals and electrostatic interactions were the main energy contributions stabilizing lead 1. Rational design strategies were suggested to replace the 2-(2-hydroxybenzylidene) hydrazine moiety with naphthalene or nitrobenzene at the P4 position of lead 2 and introduce polar substituents as aniline and benzoate groups at position P1 to enhance hydrophobic interactions and H-bonds, respectively. The emergent outbreak caused by severe acute respiratory syndrome coronavirus 2 continues spreading and causing huge social and economic disruption.![]()
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Affiliation(s)
- Samia A. Elseginy
- Green Chemistry Department, Chemical Industries Research Division, National Research Centre, P.O. Box 12622, Egypt
| | - Manal M. Anwar
- Therapeutical Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt
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