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Cytotoxic Evaluation, Molecular Docking, and 2D-QSAR Studies of Dihydropyrimidinone Derivatives as Potential Anticancer Agents. JOURNAL OF ONCOLOGY 2022; 2022:7715689. [PMID: 35509846 PMCID: PMC9061032 DOI: 10.1155/2022/7715689] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022]
Abstract
The diverse pharmacological role of dihydropyrimidinone scaffold has made it to be an interesting drug target. Because of the high incidence and mortality rate of breast cancer, there is a dire need of discovering new pharmacotherapeutic agents in managing this disease. A series of twenty-two derivatives of 6-(chloromethyl)-4-(4-hydroxyphenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (3a-3k) and ethyl 6-(chloromethyl)-4-(2-hydroxyphenyl)-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate (4a-4k) synthesized in a previous study were evaluated for their anticancer potential against breast cancer cell line. Molecular docking studies were performed to analyze the binding mode and interaction pattern of these compounds against nine breast cancer target proteins. The in vitro cell proliferation assay was performed against the breast cancer cell line MCF-7. The structure activity relationship of these compounds was further studied using QSARINS. Among nine proteins, the docking analysis revealed efficient binding of compounds 4f, 4e, 3e, 4g, and 4h against all target proteins. The in vitro cytotoxic assay revealed significant anticancer activity of compound 4f having
of 2.15 μM. The compounds 4e, 3e, 4g, and 4h also showed anticancer activities with
of 2.401, 2.41, 2.47 and 2.33 μM, respectively. The standard tamoxifen showed
1.88 μM. The 2D qualitative structure-activity relationship (QSAR) analysis was also carried out to identify potential breast cancer targets through QSARINS. The final QSAR equation revealed good predictivity and statistical validation
and
values for the model obtained from QSARINS was 0.98 and 0.97, respectively. The active compounds showed very good anticancer activities, and the binding analysis has revealed stable hydrogen bonding of these compounds with the target proteins. Moreover, the QSAR analysis has predicted useful information on the structural requirement of these compounds as anticancer agents with the importance of topological and autocorrelated descriptors in effecting the cancer activities.
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Flavone-based hydrazones as new tyrosinase inhibitors: Synthetic imines with emerging biological potential, SAR, molecular docking and drug-likeness studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131933] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Ashraf J, Mughal EU, Alsantali RI, Obaid RJ, Sadiq A, Naeem N, Ali A, Massadaq A, Javed Q, Javid A, Sumrra SH, Zafar MN, Ahmed SA. Structure-based designing and synthesis of 2-phenylchromone derivatives as potent tyrosinase inhibitors: In vitro and in silico studies. Bioorg Med Chem 2021; 35:116057. [DOI: 10.1016/j.bmc.2021.116057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/13/2022]
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Design and synthesis of new flavonols as dual ɑ-amylase and ɑ-glucosidase inhibitors: Structure-activity relationship, drug-likeness, in vitro and in silico studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128458] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Chopra V, Sangarappillai RM, Romero‐Canelón I, Jones AM. Lysyl Oxidase Like‐2 (LOXL2): An Emerging Oncology Target. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.201900119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Vriddhi Chopra
- School of PharmacyUniversity of Birmingham Birmingham B15 2TT UK
| | | | | | - Alan M. Jones
- School of PharmacyUniversity of Birmingham Birmingham B15 2TT UK
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Lysyl oxidases: from enzyme activity to extracellular matrix cross-links. Essays Biochem 2019; 63:349-364. [DOI: 10.1042/ebc20180050] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022]
Abstract
AbstractThe lysyl oxidase family comprises five members in mammals, lysyl oxidase (LOX) and four lysyl oxidase like proteins (LOXL1-4). They are copper amine oxidases with a highly conserved catalytic domain, a lysine tyrosylquinone cofactor, and a conserved copper-binding site. They catalyze the first step of the covalent cross-linking of the extracellular matrix (ECM) proteins collagens and elastin, which contribute to ECM stiffness and mechanical properties. The role of LOX and LOXL2 in fibrosis, tumorigenesis, and metastasis, including changes in their expression level and their regulation of cell signaling pathways, have been extensively reviewed, and both enzymes have been identified as therapeutic targets. We review here the molecular features and three-dimensional structure/models of LOX and LOXLs, their role in ECM cross-linking, and the regulation of their cross-linking activity by ECM proteins, proteoglycans, and by inhibitors. We also make an overview of the major ECM cross-links, because they are the ultimate molecular readouts of LOX/LOXL activity in tissues. The recent 3D model of LOX, which recapitulates its known structural and biochemical features, will be useful to decipher the molecular mechanisms of LOX interaction with its various substrates, and to design substrate-specific inhibitors, which are potential antifibrotic and antitumor drugs.
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Hajdú I, Kardos J, Major B, Fabó G, Lőrincz Z, Cseh S, Dormán G. Inhibition of the LOX enzyme family members with old and new ligands. Selectivity analysis revisited. Bioorg Med Chem Lett 2018; 28:3113-3118. [PMID: 30098867 DOI: 10.1016/j.bmcl.2018.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 01/08/2023]
Abstract
Lysyl oxidase (LOX) enzymes as potential drug targets maintain constant attention in the therapy of fibrosis, cancer and metastasis. In order to measure the inhibitory activity of small molecules on the LOX enzyme family members a fluorometric activity screening method was developed. During assay validation, previously reported non-selective small inhibitor molecules (BAPN, MCP-1, thiram, disulfiram) were investigated on all of the major LOX enzymes. We confirmed that MCP-1, thiram, disulfiram are in fact pan-inhibitors, while BAPN inhibits only LOX-like enzymes (preferably LOX-like-protein-2, LOXL2) in contrast to the previous reports. We measured the LOX inhibitory profile of a small targeted library generated by 2D ligand-based chemoinformatics methods. Ten hits (10.4% hit rate) were identified, and the compounds showed distinct activity profiles. Potential inhibitors were also identified for LOX-like-protein-3 (LOXL3) and LOX-like-protein-4 (LOXL4), that are considered as emerging drug targets in the therapy of melanoma and gastric cancer.
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Affiliation(s)
- István Hajdú
- TargetEx Ltd., Madách Imre utca 31/2, H-2120 Dunakeszi, Hungary; Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - József Kardos
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Balázs Major
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - Gabriella Fabó
- TargetEx Ltd., Madách Imre utca 31/2, H-2120 Dunakeszi, Hungary
| | - Zsolt Lőrincz
- TargetEx Ltd., Madách Imre utca 31/2, H-2120 Dunakeszi, Hungary
| | - Sándor Cseh
- TargetEx Ltd., Madách Imre utca 31/2, H-2120 Dunakeszi, Hungary
| | - György Dormán
- TargetEx Ltd., Madách Imre utca 31/2, H-2120 Dunakeszi, Hungary.
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Sajjadi SM, Rahimi H, Mohammadi S, Faranoush M, Mirzahoseini H, Toogeh G. In silico designing of a new cysteine analogue of hirudin variant 3 for site specific PEGylation. Res Pharm Sci 2017; 12:60-66. [PMID: 28255315 PMCID: PMC5333481 DOI: 10.4103/1735-5362.199048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hirudin is an anticoagulant agent of the salivary glands of the medicinal leech. Recombinant hirudin (r-Hir) displays certain drawbacks including bleeding and immunogenicity. To solve these problems, cysteine-specific PEGylation has been proposed as a successful technique. However, proper selection of the appropriate cysteine residue for substitution is a critical step. This study has, for the first time, used a computational approach aimed at identifying a single potential PEGylation site for replacement by cysteine residue in the hirudin variant 3 (HV3). Homology modeling (HM) was performed using MODELLER. All non-cysteine residues of the HV3 were replaced with the cysteine. The best model was selected based on the results of discrete optimized protein energy score, PROCHECK software, and Verify3D. The receptor binding was investigated using protein-protein docking by ClusPro web tool which was then visualized using LigPlot+ software and PyMOL. Finally, multiple sequence alignment (MSA) using ClustalW software and disulfide bond prediction were performed. According to the results of HM and docking, Q33C, which was located on the surface of the protein, was the best site for PEGylation. Furthermore, MSA showed that Q33 was not a conserved residue and LigPlot+ software showed that it is not involved in the hirudin-thrombin binding pocket. Moreover, prediction softwares established that it is not involved in disulfide bond formation. In this study, for the first time, the utility of the in silico approach for creating a cysteine analogue of HV3 was introduced. Our study demonstrated that the substitution of Q33 by cysteine probably has no effect on the biological activity of the HV3. However, experimental analyses are required to confirm the results.
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Affiliation(s)
- Seyed Mehdi Sajjadi
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, I.R. Iran
| | - Hamzeh Rahimi
- Molecular Medicine Group, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - Saeed Mohammadi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, I.R. Iran
| | - Mohammad Faranoush
- Rasoul Akram Medical Center, Iran University of Medical Sciences, Tehran, I.R. Iran
| | - Hasan Mirzahoseini
- Biotechnology Group, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - Gholamreza Toogeh
- Thrombosis and Homeostasis Research Center, Imam Khomeni Hospital Complex, Tehran University of Medical Sciences, Tehran, I.R. Iran
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Raees MA, Hussain H, Al-Rawahi A, Csuk R, Muhammad SA, Khan HY, Rehman NU, Abbas G, Al-Broumi MA, Green IR, Elyassi A, Mahmood T, Al-Harrasi A. Anti-proliferative and computational studies of two new pregnane glycosides from Desmidorchis flava. Bioorg Chem 2016; 67:95-104. [DOI: 10.1016/j.bioorg.2016.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 05/24/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
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Muhammad SA, Fatima N. In silico analysis and molecular docking studies of potential angiotensin-converting enzyme inhibitor using quercetin glycosides. Pharmacogn Mag 2015; 11:S123-6. [PMID: 26109757 PMCID: PMC4461951 DOI: 10.4103/0973-1296.157712] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/26/2014] [Accepted: 05/27/2015] [Indexed: 11/04/2022] Open
Abstract
The purpose of this study was to analyze the inhibitory action of quercetin glycosides by computational docking studies. For this, natural metabolite quercetin glycosides isolated from buckwheat and onions were used as ligand for molecular interaction. The crystallographic structure of molecular target angiotensin-converting enzyme (ACE) (peptidyl-dipeptidase A) was obtained from PDB database (PDB ID: 1O86). Enalapril, a well-known brand of ACE inhibitor was taken as the standard for comparative analysis. Computational docking analysis was performed using PyRx, AutoDock Vina option based on scoring functions. The quercetin showed optimum binding affinity with a molecular target (angiotensin-converting-enzyme) with the binding energy of -8.5 kcal/mol as compared to the standard (-7.0 kcal/mol). These results indicated that quercetin glycosides could be one of the potential ligands to treat hypertension, myocardial infarction, and congestive heart failure.
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Affiliation(s)
- Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Nighat Fatima
- Department of Pharmacy, COMSATS Institute of Information Technology, Abbottabad, Pakistan
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