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El Bakri Y, Ahmad B, Saravanan K, Ahmad I, Bakhite EA, Younis O, Al-Waleedy SAH, Ibrahim OF, Nafady A, Mague JT, Mohamed SK. Insight into crystal structures and identification of potential styrylthieno[2,3- b]pyridine-2-carboxamidederivatives against COVID-19 Mpro through structure-guided modeling and simulation approach. J Biomol Struct Dyn 2024; 42:4325-4343. [PMID: 37318002 DOI: 10.1080/07391102.2023.2220799] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/28/2023] [Indexed: 06/16/2023]
Abstract
Anti-SARS-CoV-2 drugs are urgently needed to prevent the pandemic and for immunization. Their protease inhibitor treatment for COVID-19 has been used in clinical trials. In Calu-3 and THP1 cells, 3CL SARS-CoV-2 Mpro protease is required for viral expression, replication, and the activation of the cytokines IL-1, IL-6, and TNF-. The Mpro structure was chosen for this investigation because of its activity as a chymotrypsin-like enzyme and the presence of a cysteine-containing catalytic domain. Thienopyridine derivatives increase the release of nitric oxide from coronary endothelial cells, which is an important cell signaling molecule with antibacterial activity against bacteria, protozoa, and some viruses. Using DFT calculations, global descriptors are computed from HOMO-LUMO orbitals; the molecular reactivity sites are analyzed from an electrostatic potential map. NLO properties are calculated, and topological analysis is also part of the QTAIM studies. Both compounds 1 and 2 were designed from the precursor molecule pyrimidine and exhibited binding energies (-14.6708 kcal/mol and -16.4521 kcal/mol). The binding mechanisms of molecule 1 towards SARS-COV-2 3CL Mpro exhibited strong hydrogen bonding as well as Vdw interaction. In contrast, derivative 2 was bound to the active site protein's active studied that several residues and positions, including (His41, Cys44, Asp48, Met49, Pro52, Tyr54, Phe140, Leu141, Ser144, His163, Ser144, Cys145, His164, Met165, Glu166, Leu167, Asp187, Gln189, Thr190, and GLn192) are critical for the maintenance of inhibitors inside the active pocket. Molecular docking and 100 ns MD simulation analysis revealed that Both compounds 1 and 2 with higher binding affinity and stability toward the SARS-COV-2 3CL Mpro protein. Binding free energy calculations and other MD parameters support the finding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Youness El Bakri
- Department of Theoretical and Applied Chemistry, South Ural State University, Chelyabinsk, Russian Federation
| | - Basharat Ahmad
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | | | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, Prof. Ravindra Nikam College of Pharmacy, Gondur, Dhule, Maharashtra, India
- Division of Computer Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, Maharashtra, India
| | - Etify A Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Osama Younis
- Chemistry Department, Faculty of Science, the New Valley University, El-Kharja, Egypt
| | | | - Omaima F Ibrahim
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Ayman Nafady
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, LA, USA
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester, England
- Chemistry Department, Faculty of Science, Minia University, El-Minia, Egypt
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Bakhite EA, Abuelhassan S, Gad MA, Abdel-Rahman AE, Ibrahim OF, Marae IS, Mohamed SK, Mague JT, Nafady A. Pyridine Derivatives as Insecticides─Part 4: Synthesis, Crystal Structure, and Insecticidal Activity of Some New Thienylpyridines, Thienylthieno[2,3- b]pyridines, and Related Heterocyclic Derivatives. J Agric Food Chem 2023; 71:17627-17634. [PMID: 37941360 DOI: 10.1021/acs.jafc.3c01202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
The reaction of ethyl 5-cyano-2-methyl-4-(thiophen-2-yl)-6-thioxo-1,6-dihydropyridine-3-carboxylate (1) with 2-chloroacetamide or its N-aryl derivatives gave ethyl 6-((2-amino-2-oxoethyl)thio)-5-cyano-2-methyl-4-(thiophen-2-yl) nicotinate (2a) or its N-aryl derivatives 2b-f, respectively. Cyclization of 2a-f into their isomers 3a-f was carried out by heating in absolute ethanol in the presence of a catalytic amount of sodium ethoxide. The o-aminoamide 3a was reacted with some aryl aldehydes in refluxing ethanol containing a few drops of conc. HCl to afford the corresponding tetrahydropyrimidinones 4a-d. The cyclocondensation reaction of 3a with some cycloalkanones such as cyclopentanone and cyclohexanone gave the corresponding spiro compounds 5a,b. The crystal structures of compounds 2a and 2d were determined by single-crystal X-ray diffraction techniques. All new compounds were evaluated for their insecticidal activity toward nymphs and adults of Aphis gossypi.
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Affiliation(s)
- Etify A Bakhite
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Suzan Abuelhassan
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Mohamed A Gad
- Research Institute of Plant Protection, Agriculture Research Center, Giza 12112, Egypt
| | - Abdu E Abdel-Rahman
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Omaima F Ibrahim
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Islam S Marae
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Shaaban K Mohamed
- Chemistry and Environmental Division, Manchester Metropolitan University, Manchester M1 5GD, England
- Chemistry Department, Faculty of Science, Minia University, 61519 El-Minia, Egypt
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Ayman Nafady
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Elham A. Al-Taifi, Al-Aghbari SAZ, El-Ossaily YA, Yeap GY, Marae IS, Ibrahim OF, Bakhite EA. Synthesis, Characterization, and Antimicrobial Activity of Some New Thiophene Derivatives and Crystal Structure of Ethyl [4-(2-Thienylmethylene)Aminophenoxy]Acetate. Russ J Bioorg Chem 2022. [DOI: 10.1134/s1068162022020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Marae IS, Ibrahim OF, Abdel‐Hafez SH, Mohamed SK, Mague JT, Bakhite EA. Synthesis, characterization and crystal structure of some novel partially hydrogenated isoquinolines and their fused heterocyclic systems. J Heterocycl Chem 2022. [DOI: 10.1002/jhet.4462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Islam S. Marae
- Department of Chemistry, Faculty of science Assiut University Assiut Egypt
| | - Omaima F. Ibrahim
- Department of Chemistry, Faculty of science Assiut University Assiut Egypt
| | - Shams H. Abdel‐Hafez
- Department of Chemistry College of Science, Taif University, P.O. Box 11099 Taif Saudi Arabia
| | - Shaaban K. Mohamed
- Chemistry and Environmental Division Manchester Metropolitan University, Manchester M1 5GD UK
- Chemistry Department, Faculty of Science Minia University, 61519 El‐Minia Egypt
| | - Joel T. Mague
- Department of Chemistry Tulane University New Orleans Louisiana USA
| | - Etify A. Bakhite
- Department of Chemistry, Faculty of science Assiut University Assiut Egypt
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Mohamed SK, Bakhite EA, Çelikesir ST, Abdu-Allah HHM, Akkurt M, Ibrahim OF, Mague JT, Al-Waleedy SAH. Crystal structure and Hirshfeld surface analysis of 5-acetyl-3-amino-6-methyl-N-phenyl-4-[(E)-2-phenylethenyl]thieno[2,3-b]pyridine-2-carboxamide. Acta Crystallogr E Cryst Commun 2022; 78:225-230. [PMID: 35145756 PMCID: PMC8819448 DOI: 10.1107/s2056989022000743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022]
Abstract
The asymmetric unit of the title molecule consists of four molecules that differ primarily in the orientations of the styryl and the N-phenylcarboxamido groups. The asymmetric unit of the title compound, C25H21N3O2S, comprises four molecules. Their conformations differ primarily in the orientations of the styryl and the N-phenylcarboxamido groups. In the crystal, intermolecular N—H⋯N, C—H⋯O and C—H⋯S hydrogen-bonding contacts as well a C—H⋯π(ring) interactions lead to the formation of a layer structure parallel to (010). Hirshfeld surface analysis revealed that H⋯H interactions represent the main contributions to the crystal packing.
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