1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Al-Waleedy SAH, Mohamed SK, Mague JT, Akkurt M, Abbady MS, Bakhite EA. Crystal structure and Hirshfeld surface analysis of ethyl 2-({5-acetyl-3-cyano-6-methyl-4-[( E)-2-phenyl-ethen-yl]pyridin-2-yl}sulfan-yl)acetate. Acta Crystallogr E Crystallogr Commun 2021; 77:730-733. [PMID: 34513020 PMCID: PMC8382064 DOI: 10.1107/s2056989021005600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
In the title mol-ecule, C21H20N2O3S, the styryl and ester substituents are displaced to opposite sides of the plane of the pyridine ring. In the crystal, C-H⋯O hydrogen bonds form chains extending parallel to the a-axis direction, which pack with partial inter-calation of the styryl and ester substituents. A Hirshfeld surface analysis indicates that the most significant contributions to the crystal packing are from H⋯H (43.6%), C⋯H/H⋯C (15.6%), O⋯H/H⋯O (14.9%) and N⋯H/H⋯N (11.2%) contacts.
Collapse
Affiliation(s)
| | - 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, LA 70118, USA
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey
| | - Mohamed S. Abbady
- Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Etify A. Bakhite
- Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| |
Collapse
|
4
|
Sayed EM, Hassanien R, Mohamed SK, Mague JT, Akkurt M, Farhan N, Bakhite EA, Al-Waleedy SAH. Crystal structure and Hirshfeld surface analysis of 2-{[7-acetyl-4-cyano-6-hy-droxy-8-(4-meth-oxy-phen-yl)-1,6-dimethyl-5,6,7,8-tetra-hydro-iso-quino-lin-3-yl]sulfan-yl}- N-phenyl-acetamide. Acta Crystallogr E Crystallogr Commun 2021; 77:663-667. [PMID: 34164148 PMCID: PMC8183441 DOI: 10.1107/s2056989021005430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 11/21/2022]
Abstract
The title mol-ecule, C29H29N3O4S, adopts a conformation with the two phenyl substituents disposed on opposite sides of the mean plane of the iso-quinoline unit. In the crystal, corrugated layers of mol-ecules are formed by N-H⋯O, C-H⋯N and C-H⋯S hydrogen bonds together with C-H⋯π(ring) inter-actions. These layers are connected by C-H⋯O contacts. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (45.2%), C⋯H/H⋯C (20.2%), O⋯H/H⋯O (15.8%) and N⋯H/H⋯N (11.0%) inter-actions.
Collapse
Affiliation(s)
- Eman M. Sayed
- Chemistry Department, Faculty of Science, New Valley University, 72511 El-Kharja, Egypt
| | - Reda Hassanien
- Chemistry Department, Faculty of Science, New Valley University, 72511 El-Kharja, 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, LA 70118, USA
| | - Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey
| | - Nasser Farhan
- Chemistry Department, Faculty of Science, New Valley University, 72511 El-Kharja, Egypt
| | - Etify A. Bakhite
- Chemistry Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | | |
Collapse
|
5
|
Akkurt M, Marae IS, Mague JT, Mohamed SK, Bakhite EA, Al-Waleedy SAH. Crystal structure and Hirshfeld surface analysis of 2-{[7-acetyl-8-(4-chloro-phen-yl)-4-cyano-6-hy-droxy-1,6-dimethyl-5,6,7,8-tetra-hydro-isoquinolin-3-yl]sulfan-yl}- N-(4-chloro-phen-yl)acetamide. Acta Crystallogr E Crystallogr Commun 2021; 77:527-531. [PMID: 34026258 PMCID: PMC8100273 DOI: 10.1107/s2056989021003674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/06/2021] [Indexed: 11/11/2022]
Abstract
In the title mol-ecule, C28H25Cl2N3O3S, the heterocyclic portion of the tetra-hydro-iso-quinoline unit is planar while the cyclo-hexene ring adopts a twist-boat conformation. The two 4-chloro-phenyl groups extend away from one side of this unit while the hydroxyl and acetyl groups extend away from the opposite side and form an intra-molecular O-H⋯O hydrogen bond. The crystal packing consists of layers parallel to the bc plane. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (37.3%), Cl⋯H/H⋯Cl (17.6%), O⋯H/H⋯O (11.1%), C⋯H/H⋯C (10.9%) and N⋯H/H⋯N (9.7%) inter-actions.
Collapse
Affiliation(s)
- Mehmet Akkurt
- Department of Physics, Faculty of Sciences, Erciyes University, 38039 Kayseri, Turkey
| | - Islam S. Marae
- Chemistry Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | - Joel T. Mague
- Department of Chemistry, Tulane University, New Orleans, LA 70118, USA
| | - 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
| | - Etify A. Bakhite
- Chemistry Department, Faculty of Science, Assiut University, 71516 Assiut, Egypt
| | | |
Collapse
|
6
|
Al-Taifi EA, Al-Waleedy SAH, Abbady MS, Abdu-Allah HHM, Marae IS, Abuelhassan S, Bakhite EA. Synthesis and characterization of some new S-substituted sulfanylpyridines, thieno[2,3-b]pyridines and related heterocycles. ARKIVOC 2020. [DOI: 10.24820/ark.5550190.p011.295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|