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Mathada BS, Basha NJ, Javeed M, Karunakar P, Venkatesulu A, Erappa K, Varsha A. Novel pyrimidines as COX-2 selective inhibitors: synthesis, DFT analysis, molecular docking and dynamic simulation studies. J Biomol Struct Dyn 2024; 42:1751-1764. [PMID: 37102863 DOI: 10.1080/07391102.2023.2202248] [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: 10/11/2022] [Accepted: 04/08/2023] [Indexed: 04/28/2023]
Abstract
Pyrimidine and its derivatives are associated with varieties of biological properties. Therefore, we herein reported the synthesis of four novel pyrimidines (2, 3, and 4a, b) derivatives. The structure of these molecules is confirmed by spectroscopic methods such as IR, NMR, and Mass analysis. The electronic behavior of synthesized compounds 4a, b and in silico drug design 4 c, d was explained by Density Functional Theory estimations at the DFT/B3LYP level via 6-31 G++ (d, p) replicates the structure and geometry. All the synthesized compounds were screened for their in vitro COX-1 and COX-2 inhibitory activity compared to standards Celecoxib and Ibuprofen. Compounds 3 and 4a afforded excellent COX-1 and COX-2 inhibitory activities at IC50 = 5.50 and 5.05 μM against COX-1, 0.85 and 0.65 μM against COX-2, respectively. The standard drugs Celecoxib and Ibuprofen showed inhibitory activity at IC50 = 6.34 and 3.1 μM against COX-1, 0.56 and 1.2 μM against COX-2, respectively. Further, these compounds showed high potential docking with SARS-CoV-2 Omicron protease & COX-2 and predicted drug-likeness for the pyrimidine analogs by using Molinspiration. The protein stability, fluctuations of APO-protein, protein-ligand complexes were investigated through Molecular Dynamics simulations studies using Desmond Maestro 11.3 and potential lead molecules were identified.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - N Jeelan Basha
- Department of Chemistry, Indian Academy Degree College-Autonomous, Bengaluru, Karnataka, India
| | - Mohammad Javeed
- P. G. Department and Research Studies in Chemistry, Nrupatunga University, Bengaluru, Karnataka, India
| | - Prashantha Karunakar
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, Karnataka, India
| | - Adavala Venkatesulu
- Department of Post Graduate Studies & Research Centre in Physics, Govt. First Grade College, Hoskote, Karnataka, India
| | - Krishnakanth Erappa
- Department of Post Graduate Studies & Research Centre in Physics, Govt. First Grade College, Hoskote, Karnataka, India
| | - A Varsha
- Department of Biotechnology, PES University, Bengaluru, Karnataka, India
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Elkolli H, Elkolli M, Ataya FS, Salem-Bekhit MM, Zahrani SA, Abdelmageed MWM, Ernst B, Benguerba Y. In Vitro and In Silico Activities of E. radiata and E. cinerea as an Enhancer of Antibacterial, Antioxidant, and Anti-Inflammatory Agents. Molecules 2023; 28:7153. [PMID: 37894631 PMCID: PMC10609132 DOI: 10.3390/molecules28207153] [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: 07/09/2023] [Revised: 08/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Eucalyptus, a therapeutic plant mentioned in the ancient Algerian pharmacopeia, specifically two species belonging to the Myrtaceae family, E. radiata and E. cinerea, were investigated in this study for their antibacterial, antioxidant, and anti-inflammatory properties. The study used aqueous extracts (AE) obtained from these plants, and the extraction yields were found to be different. The in vitro antibacterial activity was evaluated using a disc diffusion assay against three typical bacterial strains. The results showed that the two extracts were effective against all three strains. Both extracts displayed significant antioxidant activity compared to BHT. The anti-inflammatory impact was evaluated using a protein (BSA) inhibition denaturation test. The E. radiata extract was found to inhibit inflammation by 85% at a concentration of 250 µg/mL, significantly higher than the Aspirin. All phytoconstituents present good pharmacokinetic characteristics without toxicity except very slight toxicity of terpineol and cineol and a maximum binding energy of -7.53 kcal/mol for its anti-TyrRS activity in silico. The study suggests that the extracts and their primary phytochemicals could enhance the efficacy of antibiotics, antioxidants, and non-steroidal anti-inflammatory drugs (NSAIDs). As pharmaceutical engineering experts, we believe this research contributes to developing natural-based drugs with potential therapeutic benefits.
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Affiliation(s)
- Hayet Elkolli
- Laboratory of Multiphasic Polymeric Materials, Départment of Process Engineering, Faculty of Technology, University Ferhat Abbas of Setif 1, Setif 19000, Algeria;
| | - Meriem Elkolli
- Laboratory of Applied Microbiology, Faculty of Natural and Life Sciences, University of Ferhat Abbas Setif 1, Setif 19000, Algeria;
| | - Farid S. Ataya
- Biochemistry Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mounir M. Salem-Bekhit
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Sami Al Zahrani
- Kayyali Chair for Pharmaceutical Industries, Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Mostafa W. M. Abdelmageed
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia;
| | - Barbara Ernst
- Laboratory of Molecular Recognition and Separation Processes (RePSeM), CNRS, IPHC UMR 7178, University of Strasbourg, ECPM 25 Becquerel Road, F-67000 Strasbourg, France
| | - Yacine Benguerba
- Laboratory of Biopharmacy and Pharmacotechnics (LPBT), University of Ferhat Abbas Setif 1, Setif 19000, Algeria
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Nabi SA, Ramzan F, Lone MS, Nainwal LM, Hamid A, Batool F, Husain M, Samim M, Shafi S, Sharma K, Bano S, Javed K. Halogen substituted aurones as potential apoptotic agents: synthesis, anticancer evaluation, molecular docking, ADMET and DFT study. J Biomol Struct Dyn 2023:1-18. [PMID: 37517055 DOI: 10.1080/07391102.2023.2240897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023]
Abstract
A series of halogen-substituted aurone derivatives (2a-k) were synthesized and evaluated for an anti-proliferative study against NCI 60 cancer cell line panel and showed that most of the compounds predominantly exhibited promising activity against MCF-7. Compound 2e exhibited promising anticancer activity against the MCF-7 cancer cell line with 84.98% percentage growth inhibition in a single dose assay of 10 μM with an IC50 value of 8.157 ± 0.713 μM. In apoptotic assay, the effect of compound 2e on the cell cycle progression indicated that exposure of MCF-7 cells to compound 2e induced a significant disruption in the cell cycle profile including a time-dependent decrease in the cell population at G0/G1 and G2/M phase and arrests the cell cycle at the S phase. In silico, molecular docking ADME and toxicity studies of all compounds were also carried out. The docking study revealed that all the aurone derivatives displayed good docking scores ranging from -7.066 to -8.573. The results of Molecular Electrostatic Potential Mapping (MESP) and Density Functional Theory (DFT) studies of the most active compound 2e and least active compound 2k also favoured the experimental results.
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Affiliation(s)
- Syed Ayaz Nabi
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Farhat Ramzan
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Mehak Saba Lone
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Lalit Mohan Nainwal
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, New Delhi, India
- Department of Pharmacy, School of Medical & Allied Sciences, G. D. Goenka University, Gurugram, Haryana, India
| | - Aabid Hamid
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Pilani, Rajasthan, India
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India
| | | | | | - Mohammed Samim
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Syed Shafi
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
| | - Kalicharan Sharma
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Sameena Bano
- Department of Computer Science and Engineering, School of Engineering Sciences and Technology, Jamia Hamdard (Hamdard University), New Delhi, India
| | - Kalim Javed
- Department of Chemistry, School of Chemical and Life Sciences, New Delhi, India
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Li RJ, Xu JY, Wang X, Liao LJ, Wei X, Xie P, Xu WY, Xu ZY, Xie SH, Jiang YY, Huang L, Wang LY, Huang GR, Huang YQ. Therapeutic effect of demethylated hydroxylated phillygenin derivative on Helicobacter pylori infection. Front Microbiol 2023; 14:1071603. [PMID: 37275170 PMCID: PMC10235509 DOI: 10.3389/fmicb.2023.1071603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
Modifying and transforming natural antibacterial products is a novel idea for developing new efficacious compounds. Phillygenin has an inhibitory effect on H. pylori. The aim of the present study was to prepare a phillygenin derivative (PHI-Der) through demethylation and hydroxylation. The minimum inhibitory concentration of 18 strains of H. pylori from different sources was 8-32 μg/mL in vitro, and the activity increased 2-8 times than that of phillygenin. PHI-Der could significantly inhibit the colonization of H. pylori in vivo, reduce the inflammatory response, and promote the repair of inflammatory damage. Further, we used SwissTargetPrediction to predict that its main targets are ALOX5, MCL1, and SLC6A4, and find that it can inhibit bacterial biofilm formation and reduce bacterial infection of cells. It can enhance the intracellular oxidative capacity of H. pylori to inhibit H. pylori growth. Further, it could prevent the oxidation of H. pylori-infected cells and reduce the inflammatory response, which plays a role in protection. In conclusion, compared to phillygenin, PHI-Der had better antibacterial activity and was more effective in treating H. pylori infection. It has characteristics of high safety, specificity, resistance to drug resistance and better antibacterial activity than phillygenin, it's a good antioxidant for host cells.
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Affiliation(s)
- Ru-Jia Li
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
- Clinical Laboratory of 980 Hospital of PLA Joint Logistics Support Force (Bethune International Peace Hospital), Shijiazhuang, Hebei, China
| | - Jia-yin Xu
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Xue Wang
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Li-juan Liao
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Xian Wei
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Ping Xie
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Wen-yan Xu
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Zhen-yi Xu
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Shuo-hua Xie
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Yu-ying Jiang
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Liang Huang
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Lu-yao Wang
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Gan-rong Huang
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
| | - Yan-Qiang Huang
- Key Laboratory of the Prevention and Treatment of Drug Resistant Microbial Infecting (Youjiang Medical University for Nationalities), Education Department of Guangxi Zhuang Autonomous Region, Baise, China
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Sahu P, Jena AB, Barik S, Kisan HK, Isab AA, Dandapat J, Dinda J. Gold(III) assisted C-N bond dissociation; Synthesis, structure, photoluminescence, and pharmacokinetic studies of 1,10/- phenanthroline-gold(III)-N-heterocyclic carbene. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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6
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Antioxidant activity of new synthesized imine and its corresponding α-aminophosphonic acid: Experimental and theoretical evaluation. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Synthesis, biological activities, molecular docking, theoretical calculations of some 1,3,4-oxadiazoles, 1,2,4-triazoles, and 1,2,4-triazolo[3,4-b]-1,3,4-thiadiazines derivatives. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Badran AS, Ibrahim MA. Synthesis, spectral characterization, DFT and in silico ADME studies of the novel pyrido[1,2-a]benzimidazoles and pyrazolo[3,4-b]pyridines. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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9
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New aromatic hydrazones: Synthesis, structural analysis, DFT study, biological activity, ADME-T properties and in silico evaluation of their inhibition of SAS-CoV-2 main protease. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.134997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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10
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Sumi M, Nevaditha N, Sindhu Kumari B. Synthesis, spectroscopic investigation and bioactivities of metal complexes from curcuma longa derivative. Inorganica Chim Acta 2023. [DOI: 10.1016/j.ica.2023.121397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Al-GHULIKAH H, IBRAHIM S, GHABI A, MTIRAOUI H, JEANNEAU E, MSADDEK M. Novel isoxazole linked 1,5- benzodiazepine derivatives: Design, synthesis, molecular docking and antimicrobial evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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