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Kasmawati H, Ruslin R, Arfan A, Sida NA, Saputra DI, Halimah E, Mustarichie R. Antibacterial Potency of an Active Compound from Sansevieria trifasciata Prain: An Integrated In Vitro and In Silico Study. Molecules 2023; 28:6096. [PMID: 37630348 PMCID: PMC10457997 DOI: 10.3390/molecules28166096] [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: 06/29/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Sansevieria trifasciata Prain holds great potential as a valuable asset in pharmaceutical development. In this study, our focus is to explore and assess the antibacterial activity of various components derived from this plant, including extracts, fractions, subfractions, and isolates, explicitly targeting two common bacteria: Escherichia coli and Streptococcus aureus. The isolated compound, identified as a derivative pyridone alkaloid (5-methyl-11-(2-oxopyridin-1(2H)-yl)undecaneperoxoicacid), demonstrates notable antibacterial effects. The extracts, fractions, subfractions, and isolates reveal significant bacterial growth reductions (p < 0.05). The minimum inhibitory concentration (MIC) values for Escherichia coli were 1.95 ppm, 3.9 ppm, 15.62 ppm, and 7.81 ppm, respectively, while the MIC values for Streptococcus aureus were 1.95 ppm, 1.95 ppm, 15.62 ppm, and 7.81 ppm, respectively. Computational analysis showed the isolates' interaction with key residues on the active site of β-ketoacyl-ACP synthase from Escherichia coli and TyrRS from Streptococcus aureus. The findings indicate that the isolates exhibit a strong affinity for specific residues, including His333, Cys163, and Phe392 in β-ketoacyl-ACP synthase, as well as Arg88, His117, Glu160, and Gln213 in TyrRS. Comparative energy calculations using MMPBSA demonstrate the isolates' favorable binding energy (-104,101 kJ/mol for β-ketoacyl-ACP synthase and -81,060 kJ/mol for TyrRS) compared to ciprofloxacin. The elucidated antibacterial activity and molecular interactions of the isolates present valuable knowledge for future in vitro studies, facilitating the development of novel antibacterial agents targeting diverse bacterial strains.
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Affiliation(s)
- Henny Kasmawati
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Ruslin Ruslin
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Arfan Arfan
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Nurramadhani A. Sida
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Dimas Isnu Saputra
- Department of Pharmacy, Faculty of Pharmacy, Universitas Halu Oleo, Kendari 93232, Indonesia; (R.R.); (A.A.); (N.A.S.); (D.I.S.)
| | - Eli Halimah
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia;
| | - Resmi Mustarichie
- Department of Analytical Pharmacy and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Bandung 45363, Indonesia
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Emmerich TD, Hayes JM. In Silico-Motivated Discovery of Novel Potent Glycogen Synthase-3 Inhibitors: 1-(Alkyl/arylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione Identified as a Scaffold for Kinase Inhibitor Development. Pharmaceuticals (Basel) 2023; 16:ph16050661. [PMID: 37242443 DOI: 10.3390/ph16050661] [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: 04/02/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) isoforms α and β have diverse roles within cell biology, and have been linked with multiple diseases that include prominent CNS conditions such as Alzheimer's disease and several psychiatric disorders. In this study, motivated by computation, we aimed to identify novel ATP-binding site inhibitors of GSK-3 with CNS-active potential. A ligand screening (docking) protocol against GSK-3β was first optimized, employing an active/decoy benchmarking set, with the final protocol selected based on statistical performance analysis. The optimized protocol involved pre-filtering of ligands using a three-point 3D-pharmacophore, followed by Glide-SP docking applying hinge region hydrogen bonding constraints. Using this approach, the Biogenic subset of the ZINC15 compound database was screened, focused on compounds with potential for CNS-activity. Twelve compounds (generation I) were selected for experimental validation using in vitro GSK-3β binding assays. Two hit compounds, 1 and 2, with 6-amino-7H-benzo[e]perimidin-7-one and 1-(phenylamino)-3H-naphtho[1,2,3-de]quinoline-2,7-dione type scaffolds were identified with IC50 values of 1.63 µM and 20.55 µM, respectively. Ten analogues of 2 (generation II) were selected for structure activity relationship (SAR) analysis and revealed four low micromolar inhibitors (<10 µM), with 19 (IC50 = 4.1 µM)~five times more potent than initial hit compound 2. Selectivity screening of low micromolar inhibitors 14 and 19 (comparing aryl- and alkyl-substituents) against 10 homologous kinases revealed unique selectivity profiles, with both compounds more potent against the GSK-3α isoform (IC50s~2 µM) and, additionally, inhibitors of PKBβ (IC50s < 25 µM). Compound 14 also inhibited ERK2 and 19, PKCγ, but generally good selectivity for GSK-3 isoforms over the other kinases was observed. The compounds had excellent predicted oral bioavailability and CNS-activity profiles, presenting promising candidates for future testing in cellular models of disease.
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Affiliation(s)
- Thomas D Emmerich
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Joseph M Hayes
- School of Pharmacy & Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
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3
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Hosny S, Ragab MS, Abd El-Baki RF. Synthesis of a new sulfadimidine Schiff base and their nano complexes as potential anti-COVID-19 and anti-cancer activity. Sci Rep 2023; 13:1502. [PMID: 36707628 PMCID: PMC9880939 DOI: 10.1038/s41598-023-28402-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
The primary objective of this study was to describe the cytotoxicity on HEPG-2 cells and to study the COVID‑19 activities of the novel H2L ligand and its Cr and Cu nano-complexes. As well as exploring the chemistry of the prepared nano-complexes. In this paper novel Schiff base, N-(4, 6-dimethyl pyrimidin-2-yl)-4-(((2-hydroxyl naphthalene-1-y l) methylene) amino) benzene-sulfonamidesulfonyl) amide has been synthesized. The novel Schiff base H2L is used to synthesize novel nano and micro-complexes with CrCl2.6H2O and CuCl2.2H2O. The prepared ligand and micro complexes were interpreted by different spectroscopic techniques. The nano-sized Cr and Cu complexes were synthesized in an environmentally friendly manner using Coriandrum sativum (CS) media extract in ethanol. The structure, morphologies and particle size of the nano-sized complexes were determined using FT-IR, TEM, and PXRD. The results showed that the nano-domain complexes are on the Sub-nano scale. Furthermore, using TGA, we studied the effect of heat on the size of newly prepared nano-complexes. Experimental data were supported by DFT calculations. The findings revealed that the metal complexes investigated are more stable than the free ligand H2L. The antitumor activity was examined before and after heating the nano-complexes at 200 °C. The results reveal the Cr nano complex, after heating, exhibited strong antitumor activity with IC50 value (3.349 μg/ml). The tested Cu nano-complex shows good DNA cleavage. The liver cancer and COVID19 proteins were examined using molecular docking to identify the potential binding energy of inhibitors.
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Affiliation(s)
- Shimaa Hosny
- Department of Chemistry, Faculty of Science, New Valley University, Alkharga, 72511, Egypt.
| | - Mona S Ragab
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Randa F Abd El-Baki
- Department of Chemistry, Faculty of Science, New Valley University, Alkharga, 72511, Egypt
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4
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Husain A, Bhutani M, Parveen S, Khan SA, Ahmad A, Iqbal MA. Design, Synthesis, In Vitro Cytotoxicity, ADME Prediction, and Molecular Docking Study of Benzimidazole-Linked Pyrrolone and N-Benzylpyrrolone Derivatives. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1070428022100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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5
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Sangwan S, Yadav N, Kumar R, Chauhan S, Dhanda V, Walia P, Duhan A. A score years’ update in the synthesis and biological evaluation of medicinally important 2-pyridones. Eur J Med Chem 2022; 232:114199. [DOI: 10.1016/j.ejmech.2022.114199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/06/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022]
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Amer MM, Aziz MA, Shehab WS, Abdellattif MH, Mouneir SM. Recent advances in chemistry and pharmacological aspects of 2-pyridone scaffolds. JOURNAL OF SAUDI CHEMICAL SOCIETY 2021. [DOI: 10.1016/j.jscs.2021.101259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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7
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Abdellattif MH, Abdel-Rahman AAH, Arief MMH, Mouneir SM, Ali A, Hussien MA, Okasha RM, Afifi TH, Hagar M. Novel 2-Hydroselenonicotinonitriles and Selenopheno[2, 3-b]pyridines: Efficient Synthesis, Molecular Docking-DFT Modeling, and Antimicrobial Assessment. Front Chem 2021; 9:672503. [PMID: 34041224 PMCID: PMC8141565 DOI: 10.3389/fchem.2021.672503] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Selenium containing heterocyclic compounds gained great interest as bioactive molecules as of late. This report explores the design, synthesis, characterization, and antimicrobial screening of new pyridine derivatives endowed with selenium moieties. A one-pot multicomponent system with a solvent-free, microwave irradiation environment was employed to afford this series. The spectroscopic techniques were exploited to verify the structures of the synthesized derivatives. Additionally, the agar diffusion method was employed to determine the antimicrobial activity of all the desired compounds. Of all the synthesized molecules, 9b, 12b, 14f, and 16d exhibited well to remarkable antibacterial and antifungal activities. Moreover, derivative 14f demonstrated the most potent antibacterial and antifungal performance. The results were also supported by molecular docking studies, utilizing the MOE (molecular operating environment) which revealed the best binding mode with the highest energy interaction within the binding pocket. Lastly, theoretical DFT calculations were carried out in a gas phase at B3LYP 6-311G (d,p) basis set to predict the molecular geometries and chemical reactivity descriptors. DFT results have been used to illustrate that molecular docking findings and biological activity assessments.
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Affiliation(s)
- Magda H Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | | | | | - Samar M Mouneir
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Amena Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Mostafa A Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Chemistry, Faculty of Science, Port Said University, Port Said, Egypt
| | - Rawda M Okasha
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Tarek H Afifi
- Department of Chemistry, Faculty of Science, Taibah University, Medina, Saudi Arabia
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu, Saudi Arabia.,Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
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8
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Abd-El-Aziz AS, Alsaggaf A, Assirey E, Naqvi A, Okasha RM, Afifi TH, Hagar M. A New Family of Benzo[ h]Chromene Based Azo Dye: Synthesis, In-Silico and DFT Studies with In Vitro Antimicrobial and Antiproliferative Assessment. Int J Mol Sci 2021; 22:2807. [PMID: 33802075 PMCID: PMC7998172 DOI: 10.3390/ijms22062807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/27/2022] Open
Abstract
The high biological activity of the chromene compounds coupled with the intriguing optical features of azo chromophores prompted our desire to construct novel derivatives of chromene incorporating azo moieties 4a-l, which have been prepared via a three-component reaction of 1-naphthalenol-4-[(4-ethoxyphenyl) azo], 1, with the benzaldehyde derivatives and malononitrile. The structural identities of the azo-chromene 4a-l were confirmed on the basis of their spectral data and elemental analysis, and a UV-visible study was performed in a Dimethylformamide (DMF) solution for these molecules. Additionally, the antimicrobial activity was investigated against four human pathogens (Gram-positive and Gram-negative bacteria) and four fungi, employing an agar well diffusion method, with their minimum inhibitory concentrations being reported. Molecules 4a, 4g, and 4h were discovered to be more efficacious against Syncephalastrum racemosum (RCMB 05922) in comparison to the reference drugs, while compounds 4b and 4h demonstrated the highest inhibitory activity against Escherichia coli (E. coli) in evaluation against the reference drugs. Moreover, their cytotoxicity was assessed against three different human cell lines, including human colon carcinoma (HCT-116), human hepatocellular carcinoma (HepG-2), and human breast adenocarcinoma (MCF-7) with a selection of molecules illustrating potency against the HCT-116 and MCF-7 cell lines. Furthermore, the molecular modeling results depicted the binding interactions of the synthesized compounds 3b and 3h in the active site of the E. coli DNA gyrase B enzyme with a clear SAR (structure-activity relationship) analysis. Lastly, the density functional theory's (DFTs) theoretical calculations were performed to quantify the energy levels of the Frontier Molecular Orbitals (FMOs) and their energy gaps, dipole moments, and molecular electrostatic potentials. These data were utilized in the chemical descriptor estimations to confirm the biological activity.
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Affiliation(s)
- Alaa S. Abd-El-Aziz
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
| | - Azhaar Alsaggaf
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Eman Assirey
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada; (A.A.); (E.A.)
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Arshi Naqvi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Rawda M. Okasha
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Tarek H. Afifi
- Department of Chemistry, Taibah University, Madinah 30002, Saudi Arabia; (A.N.); (R.M.O.)
| | - Mohamed Hagar
- Department of Chemistry, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia;
- Department of Chemistry, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
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9
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Sulfaguanidine Hybrid with Some New Pyridine-2-One Derivatives: Design, Synthesis, and Antimicrobial Activity against Multidrug-Resistant Bacteria as Dual DNA Gyrase and DHFR Inhibitors. Antibiotics (Basel) 2021; 10:antibiotics10020162. [PMID: 33562582 PMCID: PMC7915026 DOI: 10.3390/antibiotics10020162] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/25/2021] [Accepted: 02/02/2021] [Indexed: 12/18/2022] Open
Abstract
Herein, a series of novel hybrid sulfaguanidine moieties, bearing 2-cyanoacrylamide 2a-d, pyridine-2-one 3-10, and 2-imino-2H-chromene-3-carboxamide 11, 12 derivatives, were synthesized, and their structure confirmed by spectral data and elemental analysis. All the synthesized compounds showed moderate to good antimicrobial activity against eight pathogens. The most promising six derivatives, 2a, 2b, 2d, 3a, 8, and 11, revealed to be best in inhibiting bacterial and fungal growth, thus showing bactericidal and fungicidal activity. These derivatives exhibited moderate to potent inhibition against DNA gyrase and DHFR enzymes, with three derivatives 2d, 3a, and 2a demonstrating inhibition of DNA gyrase, with IC50 values of 18.17-23.87 µM, and of DHFR, with IC50 values of 4.33-5.54 µM; their potency is near to that of the positive controls. Further, the six derivatives exhibited immunomodulatory potential and three derivatives, 2d, 8, and 11, were selected for further study and displayed an increase in spleen and thymus weight and enhanced the activation of CD4+ and CD8+ T lymphocytes. Finally, molecular docking and some AMED studies were performed.
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10
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Mohammed FF, Hagar M, Parveen S, Alnoman RB, Ahmed HA, Ashry ESHE, Rasheed HA. 2-(Alkylthio)-3-(Naphthalen-1-yl)Quinazolin-4(3H)-Ones: Ultrasonic Synthesis, DFT and Molecular Docking Aspects. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1878245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Farrhat F. Mohammed
- Faculty of Science, Chemistry Department, Benghazi University, Bengazhi, Libya
| | - Mohamad Hagar
- Faculty of Science, Chemistry Department, Taibah University, Yanbu, Saudi Arabia
- Faculty of Science, Chemistry Department, Alexandria University, Alexandria, Egypt
| | - Shazia Parveen
- Faculty of Science, Chemistry Department, Taibah University, Yanbu, Saudi Arabia
| | - Rua B. Alnoman
- Faculty of Science, Chemistry Department, Taibah University, Yanbu, Saudi Arabia
| | - Hoda A. Ahmed
- Faculty of Science, Department of Chemistry, Cairo University, Cairo, Egypt
| | - El Sayed H. El Ashry
- Faculty of Science, Chemistry Department, Alexandria University, Alexandria, Egypt
| | - Hanaa A. Rasheed
- Faculty of Science, Chemistry Department, Alexandria University, Alexandria, Egypt
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11
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Parveen S, Alnoman RB, Hagar M, Ahmed HA, Knight JG. Synthesis, Molecular Docking, and DFT Calculation of a Half‐Strapped BODIPY as Potential EGFR Inhibitor**. ChemistrySelect 2020. [DOI: 10.1002/slct.202003621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Shazia Parveen
- Faculty of Science Chemistry Department Taibah University 46423 Yanbu Saudi Arabia
| | - Rua B. Alnoman
- Faculty of Science Chemistry Department Taibah University 46423 Yanbu Saudi Arabia
| | - Mohamad Hagar
- Faculty of Science Chemistry Department Taibah University 46423 Yanbu Saudi Arabia
- Faculty of Science Chemistry Department Alexandria University Alexandria Egypt
| | - Hoda A. Ahmed
- Faculty of Science Chemistry Department Taibah University 46423 Yanbu Saudi Arabia
- Faculty of Science Department of Chemistry Cairo University Cairo Egypt
| | - Julian G. Knight
- School of Chemistry Bedson Building Newcastle University Newcastle upon Tyne NE1 7RU UK
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12
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Al-Janabi ASM, Elzupir AO, Yousef TA. Synthesis, anti-bacterial evaluation, DFT study and molecular docking as a potential 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2 inhibitors of a novel Schiff bases. J Mol Struct 2020; 1228:129454. [PMID: 33100378 PMCID: PMC7568132 DOI: 10.1016/j.molstruc.2020.129454] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/03/2020] [Accepted: 10/13/2020] [Indexed: 02/09/2023]
Abstract
New Schiff bases {N'-(phenyl(pyridin-2-yl)methylene) isonicotinohydrazide (L1H), N1 -(naphthalen-1-yl)-N2 -(phenyl(pyridin-2-yl) methylidene) ethane-1,2-diamine (L2H), N-(6-chlorobenzo[d]thiazol-2-yl)-1-phenyl-1-(pyridin-2-yl) methanimine (L3H)}were synthesized by reaction of 2-benzoylpyridine with different amines (2-amino-6-chlorobenzothiazole, isonicotinohydrazide and N 1-(naphthalen-1-yl)ethane-1,2-diamine) and characterized by 1H-NMR, 13C-NMR, IR mass spectroscopy and elemental analysis. The compounds were assayed by the disc diffusion method for anti-bacterial against five pathogenic bacteria species (Staphylococcus aureus, Micrococcus luteus, Staphylococcus pyogenes, Bacillus subtilis, and E. coli). All prepared Schiff bases showed good activity compared to positive control (streptomycin), Moreover the L3H showed the highest activity against S. aureus, and M. luteus than the other compounds and streptomycin. In additional molecular docking studies with 3-chymotrypsin-like protease (3CLpro), the essential enzyme for SARS-CoV-2 proliferation. The rest of compounds have shown promising results as 3CLpro inhibitors interacting with the active sites of the enzymes. Finally, DFT 's estimated electrostatic molecular potential results were used to illustrate the molecular docking findings. The DFT calculations showed that L3H has the highest dipole moment and electrophilicity index. Interestingly, L2H of the largest energy gap ∆E = 2.49 eV, there are several hydrophilic interactions that could facilitate the binding with the receptors. All of these parameters could be shared to significantly affect the protein sites of binding affinity with different extent.
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Affiliation(s)
- Ahmed S M Al-Janabi
- Department of Biochemistry, College of Veterinary Medicine, Tikrit University, Tikrit, Iraq
| | - Amin O Elzupir
- Imam Mohammad Ibn Saud Islamic University (IMSIU), College of Science, Deanship of Scientific Research, Riyadh, KSA
| | - Tarek A Yousef
- Department of Chemistry, Science College, Imam Mohammad Ibn Saud Islamic University, (IMSIU), Riyadh, KSA, P.O. Box 90950, Riyadh 11623, Saudi Arabia.,Toxic and Narcotic drug, Forensic Medicine Department, Mansoura Laboratory, Medicolegal organization, Ministry of Justice, Egypt
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13
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Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations. Int J Mol Sci 2020; 21:ijms21113922. [PMID: 32486229 PMCID: PMC7312990 DOI: 10.3390/ijms21113922] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2'-Fluoro-2'-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.
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14
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Al-Mutabagani LA, Alshabanah LA, Ahmed HA, Hagar M, Al-Ola KAA. New Symmetrical U- and Wavy-Shaped Supramolecular H-Bonded Systems; Geometrical and Mesomorphic Approaches. Molecules 2020; 25:E1420. [PMID: 32245001 PMCID: PMC7144929 DOI: 10.3390/molecules25061420] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 01/28/2023] Open
Abstract
New mesomorphic symmetrical 2:1 supramolecular H-bonded complexes of seven phenyl rings were prepared between 4-n-alkoxyphenylazobenzoic acids and 4-(2-(pyridin-3-yl)diazenyl)phenyl nicotinate. Mesomorphic studies of the prepared complexes were investigated using differential scanning calorimetry (DSC) and polarizing optical microscopy (POM). Fermi bands of the formed H-bonded interactions were confirmed by FT-IR spectroscopy. Geometrical parameters for all complexes were performed using the density functional theory (DFT) calculations method. Theoretical results revealed that the prepared H-bonded complexes are in non-linear geometry with U-shaped and wavy-shaped geometrical structures; however, the greater linearity of the wavy-shaped compounds could be the reason for their stability with respect to the U-shaped conformer. Moreover, the stable, wavy shape of supramolecular H-bonded complexes (SMHBCs) has been used to illustrate mesomeric behavior in terms of the molecular interaction. The experimental mesomorphic investigations revealed that all complexes possess enantiotropic smectic C phase. Phases were confirmed by miscibility with a standard smectic C (SmC) compound. A comparison was constructed to investigate the effect of incorporating azophenyl moiety into the mesomeric behavior of the corresponding five-membered complexes. It was found that the addition of the extra phenylazo group to the acid moiety has a great increment of the mesophase stability (TC) values with respect to the monotropic SmC phase of the five aromatic systems to the high stable enantiotropic SmC mesophase.
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Affiliation(s)
- Laila A. Al-Mutabagani
- College of Science, Chemistry Department, Riyadh, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia; (L.A.A.-M); (L.A.A.)
| | - Latifah Abdullah Alshabanah
- College of Science, Chemistry Department, Riyadh, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia; (L.A.A.-M); (L.A.A.)
| | - Hoda A. Ahmed
- Faculty of Science, Department of Chemistry, Cairo University, Cairo 12613, Egypt
- Chemistry Department, College of Sciences, Yanbu, Taibah University, Yanbu 30799, Saudi Arabia
| | - Mohamed Hagar
- Chemistry Department, College of Sciences, Yanbu, Taibah University, Yanbu 30799, Saudi Arabia
- Faculty of Science, Chemistry Department, Alexandria University, Alexandria 21321, Egypt
| | - Khulood A. Abu Al-Ola
- Chemistry Department, College of Sciences, Al-Madina Al-Munawarah, Taibah University, Al-Madina 30002, Saudi Arabia;
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15
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Alhaddad OA, Ahmed HA, Hagar M. Experimental and Theoretical Approaches of New Nematogenic Chair Architectures of Supramolecular H-Bonded Liquid Crystals. Molecules 2020; 25:E365. [PMID: 31963165 PMCID: PMC7024265 DOI: 10.3390/molecules25020365] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/10/2020] [Accepted: 01/10/2020] [Indexed: 01/21/2023] Open
Abstract
New four isomeric chair architectures of 1:1 H-bonded supramolecular complexes were prepared through intermolecular interactions between 4-(2-(pyridin-4-yl)diazenyl-(2-(or 3-)chlorophenyl) 4-alkoxybenzoates and 4-n-alkoxybenzoic acids. The H-bond formation of all complexes was confirmed by differential scanning calorimetry (DSC) and Fourier-transform infrared spectroscopy (FTIR). Mesomorphic characterization was carried by DSC and polarized optical microscopy (POM). It was found that all prepared laterally chloro-substituted supramolecular complexes were nematogenic, and exhibited nematic phase and low melting temperature. The thermal stability of the nematic mesophase observed depends upon the location and spatial orientation of the lateral Cl- atom in as well as the length of terminal chains. Theoretical calculations were carried out within the paradigm of the density functional theory (DFT) in order to establish the molecular conformation for the formed complexes and estimate their thermal parameters. The results of the computational calculations revealed that the H-bonded complexes were in a chair form molecular geometry. Additionally, out of the acquired data, it was possible to designate the influence of the position and orientation of the lateral group as well as the alkoxy chain length on the stability of the nematic phase.
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Affiliation(s)
- O. A. Alhaddad
- Chemistry Department, College of Sciences, Taibah University, Madina Monawara 30002, Saudi Arabia;
| | - H. A. Ahmed
- Chemistry Department, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia
- Department of Chemistry, Faculty of Science, Cairo University, Cairo 12613, Egypt
| | - M. Hagar
- Chemistry Department, College of Sciences, Taibah University, Yanbu 30799, Saudi Arabia
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt
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16
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Alnoman RB, Parveen S, Hagar M, Ahmed HA, Knight JG. A new chiral boron-dipyrromethene (BODIPY)-based fluorescent probe: molecular docking, DFT, antibacterial and antioxidant approaches. J Biomol Struct Dyn 2019; 38:5429-5442. [PMID: 31809642 DOI: 10.1080/07391102.2019.1701555] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A new chiral BODIPY-based fluorescent compound, 5-bromo-4,4-difluoro-3(S)-1-phenylethyl)amino) BODIPY, 4 was synthesized for biomedical applications. Optical, antimicrobial, antioxidant properties of the compound 4 are investigated. The partition coefficient suggested that the compound 4 has the potential to be developed as an active antibacterial and antioxidant candidate. In this context, antibacterial assay was carried out for compound 4 against various bacterial strains, revealing maximum inhibition zone (24 ± 2.19 mm) in Escherichia coli. Moreover, results of antioxidant activity of compound 4 revealed IC50 values to be greater than ascorbic acid. Molecular docking has given brief insight about the binding of the compound 4, suggesting that it has a strong potential to inhibit bacterial target enzymes viz., DNA gyrase, enzymes in the type II fatty acid synthesis and Ddl (d-alanine: d-alanine ligase) in peptidoglycan synthesis. The molecular geometry and electrostatic potential of compound 4, was established by DFT (Density Functional Theory) calculations.AbbreviationsBBBblood‒brain barrierBDEbond dissociation energyBODIPYboron-dipyrromethaneDdlD-alanine:D-alanine ligaseDDQ2,3-dichloro-5,6-dicyano-1,4-benzoquinoneDFTdensity functional theoryDNAdeoxyribonucleic acidDPPH1,1‒diphenyl‒2‒picrylhydrazylNBSN-bromo succinimideROSreactive oxygen speciesUV-visultraviolet-visibleFMOfrontier molecular orbitalsHOMOhighest occupied molecular orbitalLUMOlowest unoccupied molecular orbitalCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rua B Alnoman
- Department of Chemistry, Faculty of Science, Taibah University, Yanbu, Yanbu, Saudi Arabia
| | - Shazia Parveen
- Department of Chemistry, Faculty of Science, Taibah University, Yanbu, Yanbu, Saudi Arabia
| | - Mohamad Hagar
- Department of Chemistry, Faculty of Science, Taibah University, Yanbu, Yanbu, Saudi Arabia.,Department of Chemistry, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Hoda A Ahmed
- Department of Chemistry, Faculty of Science, Taibah University, Yanbu, Yanbu, Saudi Arabia.,Department of Chemistry, Faculty of Science, Cairo University, Cairo, Egypt
| | - Julian G Knight
- School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, UK
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