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Faya Castillo JE, Zapata Dongo RJ, Wong Chero PA, Infante Varillas SF. Mitoxantrone and abacavir: An ALK protein-targeted in silico proposal for the treatment of non-small cell lung cancer. PLoS One 2024; 19:e0295966. [PMID: 38319906 PMCID: PMC10846704 DOI: 10.1371/journal.pone.0295966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) is a type of lung cancer associated with translocation of the EML4 and ALK genes on the short arm of chromosome 2. This leads to the development of an aberrant protein kinase with a deregulated catalytic domain, the cdALK+. Currently, different ALK inhibitors (iALKs) have been proposed to treat ALK+ NSCLC patients. However, the recent resistance to iALKs stimulates the exploration of new iALKs for NSCLC. Here, we describe an in silico approach to finding FDA-approved drugs that can be used by pharmacological repositioning as iALK. We used homology modelling to obtain a structural model of cdALK+ protein and then performed molecular docking and molecular dynamics of the complex cdALK+-iALKs to generate the pharmacophore model. The pharmacophore was used to identify potential iALKs from FDA-approved drugs library by ligand-based virtual screening. Four pharmacophores with different atomistic characteristics were generated, resulting in six drugs that satisfied the proposed atomistic positions and coupled at the ATP-binding site. Mitoxantrone, riboflavin and abacavir exhibit the best interaction energies with 228.29, 165.40 and 133.48 KJoul/mol respectively. In addition, the special literature proposed these drugs for other types of diseases due to pharmacological repositioning. This study proposes FDA-approved drugs with ALK inhibitory characteristics. Moreover, we identified pharmacophores sites that can be tested with other pharmacological libraries.
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Affiliation(s)
- Juan Enrique Faya Castillo
- Departamento de Ciencias Básicas, Bioética y la Vida Humana, Facultad de Medicina Humana, Universidad de Piura, Lima, Perú
| | - Richard Junior Zapata Dongo
- Departamento de Ciencias Básicas, Bioética y la Vida Humana, Facultad de Medicina Humana, Universidad de Piura, Lima, Perú
| | - Paolo Alberto Wong Chero
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Perú
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El-Saghier AM, Abdou A, Mohamed MAA, Abd El-Lateef HM, Kadry AM. Novel 2-Acetamido-2-ylidene-4-imidazole Derivatives (El-Saghier Reaction): Green Synthesis, Biological Assessment, and Molecular Docking. ACS OMEGA 2023; 8:30519-30531. [PMID: 37636903 PMCID: PMC10448697 DOI: 10.1021/acsomega.3c03767] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023]
Abstract
El-Saghier reaction is the novel, general, and green reaction of various amines with ethyl cyanoacetate and ethyl glycinate hydrochloride. A new series of imidazolidin-4-ones and bis-N-(alkyl/aryl) imidazolidin-4-ones was synthesized in a sequential, one-pot procedure under neat conditions for 2 h at 70 °C. Excellent high yields (90-98%) were achieved in a short period of time while avoiding issues related to the hazardous solvents utilized (cost, safety, and pollution). The spectrum analyses and elemental data of the newly synthesized compounds helped us to clarify their structures. The obtained compounds were tested for antibacterial activity in vitro and compared to the standard antibiotic chloramphenicol as the standard, measuring the inhibition zone (nm) and activity index (%). With an antibacterial percentage value of 80.0 against Escherichia coli, N,N'-(propane-1,3-diyl) bis(2-(4-oxo-4,5-dihydro-1H-imidazole-2-yl) acetamide) proved to be the most effective. Antimicrobial activity was confirmed by a molecular docking investigation to investigate how chemicals bind to the bacterial FabH-CoA complex in E. coli (PDB ID: 1HNJ).
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Affiliation(s)
- Ahmed M. El-Saghier
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Aly Abdou
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | | | - Hany M. Abd El-Lateef
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
- Department
of Chemistry, College of Science, King Faisal
University, Al-Ahsa 31982, Saudi Arabia
| | - Asmaa M. Kadry
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
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Abd El-Lateef HM, Khalaf MM, Amer AA, Kandeel M, Abdelhamid AA, Abdou A. Synthesis, Characterization, Antimicrobial, Density Functional Theory, and Molecular Docking Studies of Novel Mn(II), Fe(III), and Cr(III) Complexes Incorporating 4-(2-Hydroxyphenyl azo)-1-naphthol (Az). ACS OMEGA 2023; 8:25877-25891. [PMID: 37521661 PMCID: PMC10373178 DOI: 10.1021/acsomega.3c01413] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023]
Abstract
This work synthesized three new CrAz2, MnAz2, and FeAz2 complexes and investigated them using IR, mass, UV spectroscopy, elemental analysis, conductivity and magnetic tests, and thermogravimetric analysis. The azo-ligand, 4-(2-hydroxyphenylAzo)-1-naphthol (Az), couples with metal ions via its nitrogen (in -N=N- bonds) and oxygen (in hydroxyl group) atoms, according to the IR spectra of these complexes. Through thermal examination (TG/TGA), the number and location of water in the complexes were also determined. Density functional theory (DFT) theory is applied to ameliorate the structures of the ligand (Az) and metal complexes and analyze the quantum chemical characteristics of these complexes. The antifungal and antibacterial activity of the ligand and its complexes opposed to several hazardous bacteria and fungi was investigated in vitro. Metal complexes were discovered to have a higher inhibitory impact on some organisms than the free ligand. The MnAz2 complex exhibited the best activity among the studied materials, whereas the CrAz2 complex had the lowest. The compounds' binding affinity to the E. coli (PDB ID: 1hnj) structure was predicted using molecular docking. Binding energies were calculated by analyzing protein-substrate interactions. These encouraging findings imply that these chemicals may have physiological effects and may be valuable for a variety of medical uses in the future.
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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
- Chemistry
Department, 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
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | - Amer A. Amer
- Chemistry
Department, 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
| | - Antar A. Abdelhamid
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
- Chemistry
Department, Faculty of Science, Albaha University, Albaha 1988, Saudi Arabia
| | - Aly Abdou
- Chemistry
Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
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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: 12] [Impact Index Per Article: 12.0] [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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Shaaban S, Abdou A, Alhamzani AG, Abou-Krisha MM, Al-Qudah MA, Alaasar M, Youssef I, Yousef TA. Synthesis and in Silico Investigation of Organoselenium-Clubbed Schiff Bases as Potential Mpro Inhibitors for the SARS-CoV-2 Replication. Life (Basel) 2023; 13:life13040912. [PMID: 37109441 PMCID: PMC10141725 DOI: 10.3390/life13040912] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Since the first report of the organoselenium compound, ebselen, as a potent inhibitor of the SARS-CoV-2 Mpro main protease by Z. Jin et al. (Nature, 2020), different OSe analogs have been developed and evaluated for their anti-COVID-19 activities. Herein, organoselenium-clubbed Schiff bases were synthesized in good yields (up to 87%) and characterized using different spectroscopic techniques. Their geometries were studied by DFT using the B3LYP/6–311 (d, p) approach. Ten FDA-approved drugs targeting COVID-19 were used as model pharmacophores to interpret the binding requirements of COVID-19 inhibitors. The antiviral efficiency of the novel organoselenium compounds was assessed by molecular docking against the 6LU7 protein to investigate their possible interactions. Our results showed that the COVID-19 primary protease bound to organoselenium ligands with high binding energy scores ranging from −8.19 to −7.33 Kcal/mol for 4c and 4a to −6.10 to −6.20 Kcal/mol for 6b and 6a. Furthermore, the docking data showed that 4c and 4a are good Mpro inhibitors. Moreover, the drug-likeness studies, including Lipinski’s rule and ADMET properties, were also assessed. Interestingly, the organoselenium candidates manifested solid pharmacokinetic qualities in the ADMET studies. Overall, the results demonstrated that the organoselenium-based Schiff bases might serve as possible drugs for the COVID-19 epidemic.
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Ke Z, Fan X, Di Y, Chen F, Han X, Yang K, Li B. A Comprehensive Investigation into the Crystallology, Molecule, and Quantum Chemistry Properties of Two New Hydrous Long-Chain Dibasic Ammonium Salts CnH2n+8N2O6 (n = 35 and 37). Int J Mol Sci 2023; 24:ijms24065467. [PMID: 36982543 PMCID: PMC10052139 DOI: 10.3390/ijms24065467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/01/2023] [Accepted: 03/05/2023] [Indexed: 03/18/2023] Open
Abstract
Through the salification reaction of carboxylation, successful attachment of the long-chain alkanoic acid to the two ends of 1,3-propanediamine was realized, which enabled the doubling of the long-chain alkanoic acid carbon chain. Hydrous 1,3-propanediamine dihexadecanoate (abbreviated as 3C16) and 1,3-propanediamine diheptadecanoate (abbreviated as 3C17) were synthesized afterward, and their crystal structures were characterized by the X-ray single crystal diffraction technique. By analyzing their molecular and crystal structure, their composition, spatial structure, and coordination mode were determined. Two water molecules played important roles in stabilizing the framework of both compounds. Hirshfeld surface analysis revealed the intermolecular interactions between the two molecules. The 3D energy framework map presented the intermolecular interactions more intuitively and digitally, in which dispersion energy plays a dominant role. DFT calculations were performed to analyze the frontier molecular orbitals (HOMO–LUMO). The energy difference between the HOMO–LUMO is 0.2858 eV and 0.2855 eV for 3C16 and 3C17, respectively. DOS diagrams further confirmed the distribution of the frontier molecular orbitals of 3C16 and 3C17. The charge distributions in the compounds were visualized using a molecular electrostatic potential (ESP) surface. ESP maps indicated that the electrophilic sites are localized around the oxygen atom. The crystallographic data and parameters of quantum chemical calculation in this paper will provide data and theoretical support for the development and application of such materials.
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Affiliation(s)
- Zengbo Ke
- School of Materials Science and Chemical Engineering, Xi’an Technological University, Xi’an 710021, China
- College of Chemical Engineering and Modern Materials, Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, Shangluo University, Shangluo 726000, China
| | - Xinhui Fan
- School of Materials Science and Chemical Engineering, Xi’an Technological University, Xi’an 710021, China
- Correspondence: (X.F.); (Y.D.)
| | - Youying Di
- College of Chemical Engineering and Modern Materials, Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, Shangluo University, Shangluo 726000, China
- Correspondence: (X.F.); (Y.D.)
| | - Fengying Chen
- College of Chemical Engineering and Modern Materials, Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, Shangluo University, Shangluo 726000, China
| | - Xi Han
- College of Chemical Engineering and Modern Materials, Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, Shangluo University, Shangluo 726000, China
| | - Ke Yang
- School of Materials Science and Chemical Engineering, Xi’an Technological University, Xi’an 710021, China
| | - Bing Li
- School of Materials Science and Chemical Engineering, Xi’an Technological University, Xi’an 710021, China
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A novel colorimetric chemosensor based on 2-[(carbamothioylhydrazono) methyl]phenyl 4-methylbenzenesulfonate (CHMPMBS) for the detection of Cu(II) in aqueous medium. RESEARCH ON CHEMICAL INTERMEDIATES 2022. [DOI: 10.1007/s11164-022-04905-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Hossain MS, Khushy KA, Latif MA, Hossen MF, Asraf MA, Kudrat-E-Zahan M, Abdou A. Co(II), Ni(II), and Cu(II) Complexes Containing Isatin-Based Schiff Base Ligand: Synthesis, Physicochemical Characterization, DFT Calculations, Antibacterial Activity, and Molecular Docking Analysis. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222120222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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