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Daboe M, Parlak C, Direm A, Alver Ö, Ramasami P. Interaction between escitalopram and ibuprofen or paracetamol: DFT and molecular docking on the drug-drug interactions. J Biomol Struct Dyn 2024; 42:672-686. [PMID: 37042928 DOI: 10.1080/07391102.2023.2195004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/17/2023] [Indexed: 04/13/2023]
Abstract
A large number of drugs are introduced each year to treat different diseases. Most of the time, patients suffer from more than one health problem which makes it necessary to take multiple drugs. When drugs are combined, the problem of drug-drug interaction becomes relevant. In this work, we studied the drug-drug interaction between escitalopram and ibuprofen or paracetamol using density functional theory and quantum theory of atoms in molecules. The results suggest that following the interactions, the activity of drugs changes according to site of interaction. Most reactive and most stable interactions would be preferable for the purpose of use. The in silico drug-likeness studies show that escitalopram and paracetamol couple is more bioavailable than escitalopram and ibuprofen couple. Moreover, in order to gain additional insights into the mentioned drugs' interactions, the drugs were docked separately and jointly against the potential targets for antidepressants and NSAIDs, namely 6HIS and 2PXX. The molecular docking results showed a potential improvement of the effectiveness of the drugs after combining by forming hydrogen bonds, hydrophobic contacts and π…π stacking.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Musa Daboe
- Department of Physics, Science Faculty, Ege University, Izmir, Turkey
| | - Cemal Parlak
- Department of Physics, Science Faculty, Ege University, Izmir, Turkey
| | - Amani Direm
- Department of Matter Sciences, Faculty of Sciences and Technology, Abbes Laghrour University, Khenchela, Algeria
- Laboratory of Structures, Properties and Interatomic Interactions LASPI2A, Faculty of Sciences and Technology, Abbes Laghrour University, Khenchela, Algeria
| | - Özgür Alver
- Department of Physics, Science Faculty, Eskişehir Technical University, Eskişehir, Turkey
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, Mauritius
- Department of Chemistry College of Science, Engineering and Technology, University of South Africa, Pretoria, South Africa
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BO2 substituted novel alkyl biphenyl liquid crystalline series: dependence of geometrical and electronic properties on the alkyl chain length. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02956-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Gholami A, Shakerzadeh E, Chigo Anota E, corazon Flores Bautista M. A theoretical perspective on the adsorption performance of pristine and Metal-encapsulated B36N36 fullerenes toward the hydroxyurea and nitrosourea anticancer drugs. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Parlak C, Alver Ö. Paracetamol adsorption on C60 fullerene and its derivatives: In silico insights. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Kadri S, Direm A, Athmani H, El Bali B, Parlak C, Hebbachi R. Dual inhibition of S. aureus TyrRS and S. aureus gyrase by two 4-amino-4′-acetyldiphenyl sulfide-based Schiff bases: Structural features, DFT study, Hirshfeld surface analysis and molecular docking. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Said MA, Riyadh SM, Al-Kaff NS, Nayl AA, Khalil KD, Bräse S, Gomha SM. Synthesis and greener pastures biological study of bis-thiadiazoles as potential Covid-19 drug candidates. ARAB J CHEM 2022; 15:104101. [PMID: 35845755 PMCID: PMC9272579 DOI: 10.1016/j.arabjc.2022.104101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/02/2022] [Indexed: 12/12/2022] Open
Abstract
A novel series of bis- (Abdelhamid et al., 2017, Banerjee et al., 2018, Bharanidharan et al., 2022)thiadiazoles was synthesized from the reaction of precursor dimethyl 2,2'-(1,2-diphenylethane-1,2-diylidene)-bis(hydrazine-1-carbodithioate) and hydrazonyl chlorides in ethanol under ultrasonic irradiation. Spectral tools (IR. NMR, MS, elemental analyses, molecular dynamic simulation, DFT and LUMO and HOMO) were used to elucidate the structure of the isolated products. Molecular docking for the precursor, 3 and ligands 6a-i to two COVID-19 important proteins Mpro and RdRp was compared with two approved drugs, Remdesivir and Ivermectin. The binding affinity varied between the ligands and the drugs. The highest recorded binding affinity of 6c with Mpro was (-9.2 kcal/mol), followed by 6b and 6a, (-8.9 and -8.5 kcal/mol), respectively. The lowest recorded binding affinity was (-7.0 kcal/mol) for 6 g. In comparison, the approved drugs showed binding affinity (-7.4 and -7.7 kcal/mol), for Remdesivir and Ivermectin, respectively, which are within the range of the binding affinity of our ligands. The binding affinity of the approved drug Ivermectin against RdRp recoded the highest (-8.6 kcal/mol), followed by 6a, 6 h, and 6i are the same have (-8.2 kcal/mol). The lowest reading was found for compound 3 ligand (-6.3 kcal/mol). On the other side, the amino acids also differed between the compounds studied in this project for both the viral proteins. The ligand 6a forms three H-bonds with Thr 319(A), Sr 255(A) and Arg 457(A), whereas Ivermectin forms three H-bonds with His 41(A), Gly143(A) and Gln 18(A) for viral Mpro. The RdRp amino acids residues could be divided into four groups based on the amino acids that interact with hydrogen or hydrophobic interactions. The first group contained 6d, 6b, 6 g, and Remdesivir with 1-4 hydrogen bonds and hydrophobic interactions 1 to 10. Group 2 is 6a and 6f exhibited 1 and 3 hydrogen bonds and 15 and 14 hydrophobic interactions. Group 3 has 6e and Ivermectin shows 4 and 3 hydrogen bonds, respectively and 11 hydrophobic interactions for both compounds. The last group contains ligands 3, 6c, 6 h, and 6i gave 1-3 hydrogen bonds and 6c and 3 recorded the highest number of hydrophobic interactions, 14 for both 6c and 6 h. Pro Tox-II estimated compounds' activities as Hepatoxic, Carcinogenic and Mutagenic, revealing that 6f-h were inactive in all five similar to that found with Remdesivir and Ivermectin. The drug-likeness prediction was carried out by studying physicochemical properties, lipophilicity, size, polarity, insolubility, unsaturation, and flexibility. Generally, some properties of the ligands were comparable to that of the standards used in this study, Remdesivir and Ivermectin.
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Affiliation(s)
- Musa A Said
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - Sayed M Riyadh
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Nadia S Al-Kaff
- Department of Biology, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia
| | - A A Nayl
- Department of Chemistry, College of Science, Jouf University, P.O. Box 2014, Sakaka, Aljouf, Saudi Arabia
| | - Khaled D Khalil
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt.,Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Almunawrah, Yanbu 46423, Saudi Arabia
| | - Stefan Bräse
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76133 Karlsruhe, Germany.,Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Director Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sobhi M Gomha
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt.,Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah 42351, Saudi Arabia
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Azo-based Multifunctional Molecules and Their Copper(II) Complexes as Potential Inhibitors Against Alzheimer’s Disease: XRD/Hirshfeld Analysis/ DFT/Molecular Docking/Cytotoxicity. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2022.109535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Parlak C, Alver Ö, Bağlayan Ö, Ramasami P. Theoretical insights of the drug-drug interaction between favipiravir and ibuprofen: a DFT, QTAIM and drug-likeness investigation. J Biomol Struct Dyn 2022:1-8. [DOI: 10.1080/07391102.2022.2066022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Cemal Parlak
- Department of Physics, Science Faculty, Ege University, Izmir, Turkey
| | - Özgür Alver
- Department of Physics, Science Faculty, Eskisehir Technical University, Eskisehir, Turkey
| | - Özge Bağlayan
- Department of Physics, Science Faculty, Eskisehir Technical University, Eskisehir, Turkey
| | - Ponnadurai Ramasami
- Computational Chemistry Group, Department of Chemistry, Faculty of Science, University of Mauritius, Réduit, Mauritius
- Department of Chemistry, College of Science, Engineering and Technology, University of South Africa, Pretoria, South Africa
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COVID-19 Drug Repurposing: A Network-Based Framework for Exploring Biomedical Literature and Clinical Trials for Possible Treatments. Pharmaceutics 2022; 14:pharmaceutics14030567. [PMID: 35335943 PMCID: PMC8955179 DOI: 10.3390/pharmaceutics14030567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/25/2022] [Accepted: 02/25/2022] [Indexed: 12/24/2022] Open
Abstract
Background: With the Coronavirus becoming a new reality of our world, global efforts continue to seek answers to many questions regarding the spread, variants, vaccinations, and medications. Particularly, with the emergence of several strains (e.g., Delta, Omicron), vaccines will need further development to offer complete protection against the new variants. It is critical to identify antiviral treatments while the development of vaccines continues. In this regard, the repurposing of already FDA-approved drugs remains a major effort. In this paper, we investigate the hypothesis that a combination of FDA-approved drugs may be considered as a candidate for COVID-19 treatment if (1) there exists an evidence in the COVID-19 biomedical literature that suggests such a combination, and (2) there is match in the clinical trials space that validates this drug combination. Methods: We present a computational framework that is designed for detecting drug combinations, using the following components (a) a Text-mining module: to extract drug names from the abstract section of the biomedical publications and the intervention/treatment sections of clinical trial records. (b) a network model constructed from the drug names and their associations, (c) a clique similarity algorithm to identify candidate drug treatments. Result and Conclusions: Our framework has identified treatments in the form of two, three, or four drug combinations (e.g., hydroxychloroquine, doxycycline, and azithromycin). The identifications of the various treatment candidates provided sufficient evidence that supports the trustworthiness of our hypothesis.
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Abu-Melha S, Edrees MM, Said MA, Riyadh SM, Al-Kaff NS, Gomha SM. Potential COVID-19 Drug Candidates Based on Diazinyl-Thiazol-Imine Moieties: Synthesis and Greener Pastures Biological Study. Molecules 2022; 27:molecules27020488. [PMID: 35056802 PMCID: PMC8777737 DOI: 10.3390/molecules27020488] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 12/23/2022] Open
Abstract
A novel series of 1-aryl-N-[4-phenyl-5-(arylazo)thiazol-2-yl)methanimines has been synthesized via the condensation of 2-amino-4-phenyl-5-arylazothiazole with various aromatic aldehydes. The synthesized imines were characterized by spectroscopic techniques, namely 1H and 13C-NMR, FTIR, MS, and Elemental Analysis. A molecular comparative docking study for 3a-f was calculated, with reference to two approved drugs, Molnupiravir and Remdesivir, using 7BQY (Mpro; PDB code 7BQY; resolution: 1.7 A°) under identical conditions. The binding scores against 7BQY were in the range of -7.7 to -8.7 kcal/mol for 3a-f. The high scores of the compounds indicated an enhanced binding affinity of the molecules to the receptor. This is due to the hydrophobic interactions and multi-hydrogen bonds between 3a-f ligands and the receptor's active amino acid residues. The main aim of using in silco molecular docking was to rank 3a-f with respect to the approved drugs, Molnupiravir and Remdesivir, using free energy methods as greener pastures. A further interesting comparison presented the laydown of the ligands before and after molecular docking. These results and other supporting statistical analyses suggested that ligands 3a-f deserve further investigation in the context of potential therapeutic agents for COVID-19. Free-cost, PASS, SwissADME, and Way2drug were used in this research paper to determine the possible biological activities and cytotoxicity of 3a-f.
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Affiliation(s)
- Sraa Abu-Melha
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.A.-M.); (M.M.E.)
| | - Mastoura Mohamed Edrees
- Department of Chemistry, Faculty of Science, King Khalid University, Abha 61413, Saudi Arabia; (S.A.-M.); (M.M.E.)
- Department of Organic Chemistry, National Organization for Drug Control and Research (NODCAR), Giza 12311, Egypt
| | - Musa A. Said
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
- Correspondence: (M.A.S.); (S.M.G.)
| | - Sayed M. Riyadh
- Department of Chemistry, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Nadia S. Al-Kaff
- Department of Biology, Faculty of Science, Taibah University, Al-Madinah Al-Munawarah 30002, Saudi Arabia;
| | - Sobhi M. Gomha
- Department of Chemistry, Faculty of Science, Cairo University, Giza 12613, Egypt
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Al-Madinah Al-Munawarah 42351, Saudi Arabia
- Correspondence: (M.A.S.); (S.M.G.)
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