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Zare F, Ataollahi E, Mardaneh P, Sakhteman A, Keshavarz V, Solhjoo A, Emami L. A combination of virtual screening, molecular dynamics simulation, MM/PBSA, ADMET, and DFT calculations to identify a potential DPP4 inhibitor. Sci Rep 2024; 14:7749. [PMID: 38565703 PMCID: PMC10987597 DOI: 10.1038/s41598-024-58485-x] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/29/2024] [Indexed: 04/04/2024] Open
Abstract
DPP4 inhibitors can control glucose homeostasis by increasing the level of GLP-1 incretins hormone due to dipeptidase mimicking. Despite the potent effects of DPP4 inhibitors, these compounds cause unwanted toxicity attributable to their effect on other enzymes. As a result, it seems essential to find novel and DPP4 selective compounds. In this study, we introduce a potent and selective DPP4 inhibitor via structure-based virtual screening, molecular docking, molecular dynamics simulation, MM/PBSA calculations, DFT analysis, and ADMET profile. The screened compounds based on similarity with FDA-approved DPP4 inhibitors were docked towards the DPP4 enzyme. The compound with the highest docking score, ZINC000003015356, was selected. For further considerations, molecular docking studies were performed on selected ligands and FDA-approved drugs for DPP8 and DPP9 enzymes. Molecular dynamics simulation was run during 200 ns and the analysis of RMSD, RMSF, Rg, PCA, and hydrogen bonding were performed. The MD outputs showed stability of the ligand-protein complex compared to available drugs in the market. The total free binding energy obtained for the proposed DPP4 inhibitor was more negative than its co-crystal ligand (N7F). ZINC000003015356 confirmed the role of the five Lipinski rule and also, have low toxicity parameter according to properties. Finally, DFT calculations indicated that this compound is sufficiently soft.
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Affiliation(s)
- Fateme Zare
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elaheh Ataollahi
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pegah Mardaneh
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), 85354, Freising, Germany
| | - Valiollah Keshavarz
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Quality Control of Drug Products, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Emami L, Zare F, Khabnadideh S, Rezaei Z, Sabahi Z, Zare Gheshlaghi S, Behrouz M, Emami M, Ghobadi Z, Madadelahi Ardekani S, Barzegar F, Ebrahimi A, Sabet R. Synthesis, design, biological evaluation, and computational analysis of some novel uracil-azole derivatives as cytotoxic agents. BMC Chem 2024; 18:3. [PMID: 38173035 PMCID: PMC10765869 DOI: 10.1186/s13065-023-01106-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
The design and synthesis of novel cytotoxic agents is still an interesting topic for medicinal chemistry researchers due to the unwanted side effects of anticancer drugs. In this study, a novel series of uracil-azole hybrids were designed and synthesized. The cytotoxic activity, along with computational studies: molecular docking, molecular dynamic simulation, density functional theory, and ADME properties were also, evaluated. The compounds were synthesized by using 3-methyl-6-chlorouracil as the starting material. Cytotoxicity was determined using MTT assay in the breast carcinoma cell line (MCF-7) and Hepatocellular carcinoma cell line (HEPG-2). These derivatives demonstrated powerful inhibitory activity against breast and hepatocellular carcinoma cell lines in comparison to Cisplatin as positive control. Among these compounds, 4j displayed the best selectivity profile and good activity with IC50 values of 16.18 ± 1.02 and 7.56 ± 5.28 µM against MCF-7 and HEPG-2 cell lines respectively. Structure-activity relationships revealed that the variation in the cytotoxic potency of the synthesized compounds was affected by various substitutions of benzyl moiety. The docking output showed that 4j bind well in the active site of EGFR and formed a stable complex with the EGFR protein. DFT was used to investigate the reactivity descriptors of 4a and 4j. The outputs demonstrated that these uracil-azole hybrids can be considered as potential cytotoxic agents.
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Affiliation(s)
- Leila Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fateme Zare
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. of Iran
| | - Soghra Khabnadideh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Rezaei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Sabahi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. of Iran
| | - Saman Zare Gheshlaghi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Marzieh Behrouz
- Department of Chemistry, Shiraz University of Technology, Shiraz, Iran
| | - Mina Emami
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Ghobadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. of Iran
| | | | - Fatemeh Barzegar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Ebrahimi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Razieh Sabet
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, I.R. of Iran.
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Dodonova SA, Zhidkova EM, Kryukov AA, Valiev TT, Kirsanov KI, Kulikov EP, Budunova IV, Yakubovskaya MG, Lesovaya EA. Synephrine and Its Derivative Compound A: Common and Specific Biological Effects. Int J Mol Sci 2023; 24:17537. [PMID: 38139366 PMCID: PMC10744207 DOI: 10.3390/ijms242417537] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
This review is focused on synephrine, the principal phytochemical found in bitter orange and other medicinal plants and widely used as a dietary supplement for weight loss/body fat reduction. We examine different aspects of synephrine biology, delving into its established and potential molecular targets, as well as its mechanisms of action. We present an overview of the origin, chemical composition, receptors, and pharmacological properties of synephrine, including its anti-inflammatory and anti-cancer activity in various in vitro and animal models. Additionally, we conduct a comparative analysis of the molecular targets and effects of synephrine with those of its metabolite, selective glucocorticoid receptor agonist (SEGRA) Compound A (CpdA), which shares a similar chemical structure with synephrine. SEGRAs, including CpdA, have been extensively studied as glucocorticoid receptor activators that have a better benefit/risk profile than glucocorticoids due to their reduced adverse effects. We discuss the potential of synephrine usage as a template for the synthesis of new generation of non-steroidal SEGRAs. The review also provides insights into the safe pharmacological profile of synephrine.
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Affiliation(s)
- Svetlana A. Dodonova
- Research Institute of Experimental Medicine, Department of Pathophysiology, Kursk State Medical University, 305041 Kursk, Russia; (S.A.D.); (A.A.K.)
| | - Ekaterina M. Zhidkova
- Department of Chemical Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (E.M.Z.); (T.T.V.); (K.I.K.); (M.G.Y.)
| | - Alexey A. Kryukov
- Research Institute of Experimental Medicine, Department of Pathophysiology, Kursk State Medical University, 305041 Kursk, Russia; (S.A.D.); (A.A.K.)
| | - Timur T. Valiev
- Department of Chemical Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (E.M.Z.); (T.T.V.); (K.I.K.); (M.G.Y.)
| | - Kirill I. Kirsanov
- Department of Chemical Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (E.M.Z.); (T.T.V.); (K.I.K.); (M.G.Y.)
- Faculty of Oncology, Ryazan State Medical University Named after Academician I.P. Pavlov, 390026 Ryazan, Russia
| | - Evgeny P. Kulikov
- Laboratory of Single Cell Biology, Russian University of People’s Friendship (RUDN) University, 117198 Moscow, Russia;
| | - Irina V. Budunova
- Department of Dermatology, Northwestern University, Chicago, IL 60611, USA;
| | - Marianna G. Yakubovskaya
- Department of Chemical Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (E.M.Z.); (T.T.V.); (K.I.K.); (M.G.Y.)
- Faculty of Oncology, Ryazan State Medical University Named after Academician I.P. Pavlov, 390026 Ryazan, Russia
| | - Ekaterina A. Lesovaya
- Department of Chemical Carcinogenesis, N.N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (E.M.Z.); (T.T.V.); (K.I.K.); (M.G.Y.)
- Faculty of Oncology, Ryazan State Medical University Named after Academician I.P. Pavlov, 390026 Ryazan, Russia
- Laboratory of Single Cell Biology, Russian University of People’s Friendship (RUDN) University, 117198 Moscow, Russia;
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