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Lanka G, Banerjee S, Adhikari N, Ghosh B. Fragment-based discovery of new potential DNMT1 inhibitors integrating multiple pharmacophore modeling, 3D-QSAR, virtual screening, molecular docking, ADME, and molecular dynamics simulation approaches. Mol Divers 2024:10.1007/s11030-024-10837-5. [PMID: 38637479 DOI: 10.1007/s11030-024-10837-5] [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: 11/29/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
DNA methyl transferases (DNMTs) are one of the crucial epigenetic modulators associated with a wide variety of cancer conditions. Among the DNMT isoforms, DNMT1 is correlated with bladder, pancreatic, and breast cancer, as well as acute myeloid leukemia and esophagus squamous cell carcinoma. Therefore, the inhibition of DNMT1 could be an attractive target for combating cancers and other metabolic disorders. The disadvantages of the existing nucleoside and non-nucleoside DNMT1 inhibitors are the main motive for the discovery of novel promising inhibitors. Here, pharmacophore modeling, 3D-QSAR, and e-pharmacophore modeling of DNMT1 inhibitors were performed for the large fragment database screening. The resulting fragments with high dock scores were combined into molecules. The current study revealed several constitutional pharmacophoric features that can be essential for selective DNMT1 inhibition. The fragment docking and virtual screening identified 10 final hit molecules that exhibited good binding affinities in terms of docking score, binding free energies, and acceptable ADME properties. Also, the modified lead molecules (GL1b and GL2b) designed in this study showed effective binding with DNMT1 confirmed by their docking scores, binding free energies, 3D-QSAR predicted activities and acceptable drug-like properties. The MD simulation studies also suggested that leads (GL1b and GL2b) formed stable complexes with DNMT1. Therefore, the findings of this study can provide effective information for the development/identification of novel DNMT1 inhibitors as effective anticancer agents.
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Affiliation(s)
- Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
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Ren J, Ji X, Zhang J, Yu Z, Wang X, Xiong L, Yang N, Tang L, Li Z, Fan Z. Discovery of Trisubstituted N-Phenylpyrazole Containing Diamides with Improved Insecticidal Activity. J Agric Food Chem 2024; 72:8072-8080. [PMID: 38547359 DOI: 10.1021/acs.jafc.3c08759] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
To increase the structural diversity of insecticides and meet the needs of effective integrated insect management, the structure of chlorantraniliprole was modified based on a previously established three-dimensional quantitative structure-activity relationship (3D-QSAR) model. The pyridinyl moiety in the structure of chlorantraniliprole was replaced with a 4-fluorophenyl group. Further modifications of this 4-fluorophenyl group by introducing a halogen atom at position 2 and an electron-withdrawing group (e.g., iodine, cyano, and trifluoromethyl) at position 5 led to 34 compounds with good insecticidal efficacy against Mythimna separata, Plutella xylostella, and Spodoptera frugiperda. Among them, compound IV f against M. separata showed potency comparable to that of chlorantraniliprole. IV p against P. xylostella displayed a 4.5 times higher potency than chlorantraniliprole. In addition, IV d and chlorantraniliprole exhibited comparable potencies against S. frugiperda. Transcriptome analysis showed that the molecular target of compound IV f is the ryanodine receptor. Molecular docking was further performed to verify the mode of action and insecticidal activity against resistant P. xylostella.
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Affiliation(s)
- Jinzhou Ren
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xia Ji
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jin Zhang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhenwu Yu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Xinyuan Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Lixia Xiong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Na Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Liangfu Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhengming Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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Mokgopa KP, Lobb KA, Tshiwawa T. A Computational Study of Green Tea Extracts and their Derivatives as Potential Inhibitors for Squalene Monooxygenase. Med Chem 2024; 20:MC-EPUB-139581. [PMID: 38584555 DOI: 10.2174/0115734064280290240211170037] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/09/2024] [Accepted: 01/24/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND According to the World Health Organisation, cardiovascular complications have been recognized as the leading course of death between 2000 and 2019. Cardiovascular complications are caused by excess LDL cholesterol in the body or arteries that can build up to form a plaque. There are drugs currently in clinical use called statins that target HMGCoA reductase. However, these drugs result in several side effects. This work investigated using computational approaches to lower cholesterol by investigating green tea extracts as an inhibitors for squalene monooxygenase (the second-rate-controlling step in cholesterol synthesis). METHODS Pharmacophore modeling was done to identify possible pharmacophoric sites based on the pIC50 values. The best hypothesis generated by pharmacophore modeling was further validated by atom-based 3D QSAR, where 70% of the data set was treated as the training set. Prior molecular docking ADMET studies were done to investigate the physiochemical properties of these molecules. Glide docking was performed, followed by molecular dynamics to evaluate the protein conformational changes. RESULTS Pharmacophore results suggest that the best molecules to interact with the biological target should have at least one hydrogen acceptor (A5), two hydrogen donors (D9 and D10), and two benzene rings (R14 and R15) for green tea polyphenols and theasinensin A. ADMET result shows that all molecules in this class have low oral adsorption. Molecular docking results showed that some green tea polyphenols have good binding affinities, with most of these structures having a docking score of less than -10 kcal/mol. Molecular dynamics further illustrated that the best-docked ligands perfectly stay within the active site over a 100 ns simulation. CONCLUSION The results obtained from this study suggest that green tea polyphenols have the potential for inhibition of squalene monooxygenase, except for theasinensin A.
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Affiliation(s)
| | - Kevin A Lobb
- Department of Chemistry, Rhodes University, Makhanda, South Africa
- Research Unit in Bioinformatics (RUBi), Rhodes University, Makhanda 6140, South Africa
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Tang Y. Analysis of the binding pattern of NIK inhibitors by computational simulation. J Biomol Struct Dyn 2024; 42:3318-3331. [PMID: 37183664 DOI: 10.1080/07391102.2023.2212782] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
NF-kappaB-Inducing Kinase (NIK) is a key kinase in the activation of the NF-κB non-classical signalling pathway, which has been shown to be over-activated in patients with inflammatory diseases, immune disorders and malignancies and solid tumours inducing activation of the NF-κB non-classical signalling pathway. The design of ATP-competitive small molecule inhibitors against NIK has been a hot topic in the last decade, and many efficient NIK inhibitors have been identified. In this work, I aim to unravel the mechanism of NIK inhibition by different representative NIK type I 1/2 kinase inhibitors, using ADME, molecular docking, molecular dynamics simulation, MM-PBSA analysis and 3D-QSAR analysis. This work contributes to the understanding of the efficiency of NIK inhibitor binding by revealing the basis of the efficiency of NIK inhibitors, the difference in binding modes between different inhibitors and the overall effect on NIK.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yingkai Tang
- Department of Anatomy, School of Basic Medicine, Bengbu Medical University, Bengbu, China
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Liu H, Zhu S, Xia G, Huang Z, Han W, Li Z, Liu C. Effects of 1,4-dihydropyridine derivatives on cell injury and mTOR of HepG2 and 3D-QSAR study. Comput Biol Chem 2024; 109:108010. [PMID: 38232515 DOI: 10.1016/j.compbiolchem.2023.108010] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
1,4-dihydropyridine derivatives (1,4-DHPs) are a class of drugs used to treat cardiovascular diseases, but these drugs can cause liver injury. To reveal the toxicity characteristics of these compounds, we used a series of assays, including cell viability, enzyme activity detection, and western blotting, to investigate the toxicity of seven kinds of 1,4-DHPs (0-100 μM) on HepG2 cells and establish 3D-QSAR model based on relevant toxicity data. After HepG2 cells were treated with 1,4-DHPs for 24 h, high-dose (100 μM) 1,4-DHPs decreased cell viability to varying degrees, while ROS and MDA contents were significantly increased, and ATP content was reduced. Moreover, with the concentration of 100 μM 1,4-DHPs (Nimodipine, Nitrendipine, Cilnidipine, and Manidipine) were markedly inhibited the phosphorylation levels of mTOR protein. The results of the 3D-QSAR model showed that the non-cross validation coefficient (R2) and cross validation coefficient (Q2) of the model were 0.982 and 0.652, respectively. Combined with external validation and the Williams diagram, the model showed good predictability and application domain. Based on the CoMSIA 3D contour map, the introduction of large volume and hydrogen bond receptor groups on the carbonyl oxygen side chains of the 1,4-DHPs ring 3- and 5- was beneficial for reducing the toxicity of 1,4-DHPs. The results of this study could supplement information on the cytotoxicity of 1,4-DHPs, and could provide theoretical support for predicting the toxicity of 1,4-DHPs.
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Affiliation(s)
- Huan Liu
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi 435002, China
| | - Siyu Zhu
- SCAU (Chaozhou) Food Institute Co., Ltd., Chaozhou 521000, China; Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Guiqiong Xia
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhuoquan Huang
- SCAU (Chaozhou) Food Institute Co., Ltd., Chaozhou 521000, China; Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Wenna Han
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhongyi Li
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Chunhong Liu
- SCAU (Chaozhou) Food Institute Co., Ltd., Chaozhou 521000, China; Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
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Li Y, Kowah JAH, Jiang M, Wu Y, Wang L, Yang F. Synthesis, antibacterial activity, and 3D-QASR studies of matrine-indole derivatives as potential antibiotics. Bioorg Med Chem Lett 2024; 102:129671. [PMID: 38387690 DOI: 10.1016/j.bmcl.2024.129671] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Matrine and indole have antibacterial, anticancer, and other biological activities, in order to develop new antibiotics to solve the problem of multi-drug resistant bacteria. In this paper, we synthesized a series of 29 novel matrine derivatives as potential drug candidates by combining indole analogs and matrine. The antibacterial activity of these compounds was evaluated through minimum inhibitory concentration (MIC) assays against five bacterial strains (S. aureus, C. albicans, P. acnes, P. aeruginosa, and E. coli). The obtained results demonstrated promising antibacterial efficacy, particularly for compounds A20 and A18, which exhibited MICs.au values of 0.021 and 0.031 mg/ml, respectively, against S. aureus. Moreover, compounds A20 and A27 displayed remarkable MICc.al values of 2.806 and 4.519 mg/ml, respectively, against C. albicans, surpassing the performance of the clinical antibiotic penicillin G sodium (0.0368 mg/ml) and fluconazole (4.849 mg/ml). These findings underscore the significant bacteriostatic activity of the matrine derivatives. Furthermore, to gain a deeper understanding 3D-QSAR modeling was employed, revealing the critical influence of steric structure, charge distribution, hydrophobic interactions, and hydrogen bonding within the molecular structure on the bacteriostatic activity of the compounds. Additionally, molecular docking simulations shed light on the interaction between compound A20 and bacterial proteins, highlighting the involvement of hydrogen bonding, hydrophobic interactions, and π-π conjugation in the formation of stable complexes that inhibit the normal functioning of the proteins. This comprehensive analysis provided valuable insights into the antibacterial mechanism of the novel matrine derivatives, offering theoretical support for their potential application as antibiotics.
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Affiliation(s)
- Yufang Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China.
| | - Jamal A H Kowah
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Meiyan Jiang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Yaqing Wu
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Lisheng Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China; Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning 530004, China.
| | - Fangfang Yang
- Guangxi - ASEAN Food Inspection and Testing Center, Nanning 530021, China
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Mubarak SJ, Gupta S, Vedagiri H. Scaffold Hopping and Screening for Potent Small Molecule Agonists for GRP94: Implications to Alleviate ER Stress-Associated Pathogenesis. Mol Biotechnol 2024; 66:737-755. [PMID: 36763304 DOI: 10.1007/s12033-023-00685-3] [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: 09/30/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023]
Abstract
Disparity in the activity of Endoplasmic reticulum (ER) leads to degenerative diseases, mainly associated with protein misfolding and aggregation leading to cellular dysfunction and damage, ultimately contributing to ER stress. ER stress activates the complex network of Unfolded Protein Response (UPR) signaling pathways mediated by transmembrane proteins IRE1, ATF6, and PERK. In addition to UPR, many ER chaperones have evolved to optimize the output of properly folded secretory and membrane proteins. Glucose-regulated protein 94 (GRP94), an ER chaperone of heat shock protein HSP90 family, directs protein folding through interaction with other components of the ER protein folding machinery and assists in ER-associated degradation (ERAD). Activation of GRP94 would increase the efficacy of protein folding machinery and regulate the UPR pathway toward homeostasis. The present study aims to screen for novel agonists for GRP94 based on Core hopping, pharmacophore hypothesis, 3D-QSAR, and virtual screening with small-molecule compound libraries in order to improve the efficiency of native protein folding by enhancing GRP94 chaperone activity, therefore to reduce protein misfolding and aggregation. In this study, we have employed the strategy of small molecule-dependent ER programming to enhance the chaperone activity of GRP94 through scaffold hopping-based screening approach to identify specific GRP94 agonists. New scaffolds generated by altering the cores of NECA, the known GRP94 agonist, were validated by employing pharmacophore hypothesis testing, 3D-QSAR modeling, and molecular dynamics simulations. This facilitated the identification of small molecules to improve the efficiency of native protein folding by enhancing GRP94 activity. High-throughput virtual screening of the selected pharmacophore hypothesis against Selleckchem and ZINC databases retrieved a total of 2,27,081 compounds. Further analysis on docking and ADMET properties revealed Epimedin A, Narcissoside, Eriocitrin 1,2,3,4,6-O-Pentagalloylglucose, Secoisolariciresinol diglucoside, ZINC92952357, ZINC67650204, and ZINC72457930 as potential lead molecules. The stability and interaction of these small molecules were far better than the known agonist, NECA indicating their efficacy in selectively alleviating ER stress-associated pathogenesis. These results substantiate the fact that small molecule-dependent ER reprogramming would activate the ER chaperones and therefore reduce the protein misfolding as well as aggregation associated with ER stress in order to restore cellular homeostasis.
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Affiliation(s)
| | - Surabhi Gupta
- Department of Reproductive Biology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Hemamalini Vedagiri
- Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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Dai P, Jiao J, Li Y, Teng P, Wang Q, Zhu Y, Zhang W. Novel 5-Sulfonyl-1,3,4-thiadiazole-Substituted Flavonoids as Potential Bactericides and Fungicides: Design, Synthesis, Three-Dimensional Quantitative Structure-Activity Relationship Studies. J Agric Food Chem 2024; 72:6672-6683. [PMID: 38481361 DOI: 10.1021/acs.jafc.3c06367] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Flavonoids, ubiquitous natural products, provide sources for drug discovery owing to their structural diversity, broad-spectrum pharmacological activity, and excellent environmental compatibility. To develop antibacterial and antifungal agents with novel mechanisms of action and innovative structures, a series of novel 5-sulfonyl-1,3,4-thiadiazole-substituted flavonoids were designed and synthesized, and their biological activities against seven agriculturally common phytopathogenic microorganisms were evaluated. The results of the antimicrobial bioassay showed that most of the target compounds displayed excellent inhibitory effects against Xanthomonas oryzae, Rhizoctonia solani, and Colletotrichum orbiculare. Compounds 1, 3, 7, 9, 13, and 14 exhibited remarkable antibacterial activity against X. oryzae pv. oryzae with EC50 values below 10 μg/mL, which were superior to bismerthiazol (70.89 μg/mL). Compound 2 (EC50 = 0.41 μg/mL) displayed the most effective inhibitory potency against R. solani in vivo, comparable protective effects with the positive control carbendizam. Preliminary mechanistic studies indicated that compound 2 induced disordered entanglement of hyphae, shrinkage of hyphal surfaces, extravasation of cellular contents, and vacuole swelling and rupture, which disrupted normal hyphal growth. Subsequently, compounds 35-53 with good antifungal activity were designed and synthesized based on reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) models. Compound 49 showed high efficacy and superior antifungal activity against R. solani, with an EC50 value of 0.28 μg/mL and a half-maximal effective concentration of 0.46 μg/mL.
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Affiliation(s)
- Peng Dai
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Jiao
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufei Li
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Teng
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingqing Wang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuchuan Zhu
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weihua Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Dai P, Wang Q, Teng P, Jiao J, Li Y, Xia Q, Zhang W. Design, Synthesis, Antifungal Activity, and 3D-QASR of Novel Oxime Ether-Containing Coumarin Derivatives as Potential Fungicides. J Agric Food Chem 2024; 72:5983-5992. [PMID: 38456397 DOI: 10.1021/acs.jafc.3c06032] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
Structural modification of natural products is an effective approach for improving antifungal activity and has, therefore, been used extensively in the development of new agrochemical products. In this work, a series of novel coumarin derivatives containing oxime ether structures were designed, synthesized, and evaluated for antifungal activity. Some of the designed compounds exhibited promising antifungal activities against tested fungi, and compounds 4a, 4c, 5a, and 6b had EC50 values equivalent to those of commercial fungicides. Compound 6b was the most promising candidate fungicide against Rhizoctonia solani (EC50 = 0.46 μg/mL). In vivo antifungal bioassays suggested that compounds 5a and 6b could serve as novel agricultural antifungals. Furthermore, microscopy demonstrated that compound 6b induced the sprawling growth of hyphae, distorted the outline of cell walls, and reduced mitochondrial numbers. Additionally, the effects of the substituent steric, electrostatic, hydrophobic, and hydrogen-bond fields were elucidated using an accurate and reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) model. The results presented here will guide the discovery of potential novel fungicides for plant disease control in agriculture.
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Affiliation(s)
- Peng Dai
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingqing Wang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Peng Teng
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Jiao
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yufei Li
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qing Xia
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Weihua Zhang
- Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Sun P, Pu J, Lei D, Li J, Ren X, Jin L, Pan L. Novel Aminocoumarin Derivatives against Phytopathogenic Fungi: Design, Synthesis and Structure-Activity Relationships. Chem Biodivers 2024:e202400311. [PMID: 38494946 DOI: 10.1002/cbdv.202400311] [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: 02/05/2024] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 03/19/2024]
Abstract
Phytopathogenic fungi is the most devastating reason for the decrease of the agricultural production and food safety. To develop new fungicidal agents for resistance concerning, a novel series of aminocoumarin derivatives were synthesized and their fungicidal activity were investigated both in vitro and in vivo. Transmission electron microscope (TEM), scanning electron microscope (SEM), RNA-Seq, 3D-QSAR and molecular docking were applied to reveal the underlying anti-fungal mechanisms. Most of the compounds exhibited significant fungicidal activity. Notably, compound 10c had a more extensive fungicidal effect than positive control. TEM indicated that compound 10c could cause abnormal morphology of cell walls, vacuoles and release of cellular contents. Transcriptional analysis data indicated that 895 and 653 out of 1548 differential expressed genes (DEGs) were up-regulated and down-regulated respectively. The Go and KEGG enrichment indicated that the coumarin derivatives could induce significant changes of succinate dehydrogenase (SDH), Acetyl-coenzyme A synthetase (ACCA) and pyruvate dehydrogenase (PDH) genes, which contributed to the disorders of glucolipid metabolism and the dysfunction of mitochondrial. The results demonstrated that aminocoumarins with schiff-base as core moieties could be the promising lead compounds for the discovery of novel fungicides.
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Affiliation(s)
- Pengzhi Sun
- College of Chemistry and Chemical Engineering, Xinjiang Agricultural University, Urumqi, 830052
| | - Jiangping Pu
- College of Chemistry and Chemical Engineering, Xinjiang Agricultural University, Urumqi, 830052
| | - Dongyu Lei
- Department of Physiology, Preclinical School, Xinjiang Medical University, Urumqi, 830011, China
| | - Jiashan Li
- College of Chemistry and Chemical Engineering, Xinjiang Agricultural University, Urumqi, 830052
| | - Xingyu Ren
- College of Chemistry and Chemical Engineering, Xinjiang Agricultural University, Urumqi, 830052
| | - Lu Jin
- College of Chemistry and Chemical Engineering, Xinjiang Agricultural University, Urumqi, 830052
| | - Le Pan
- College of Chemistry and Chemical Engineering, Xinjiang Agricultural University, Urumqi, 830052
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Wen C, Chen H, Tang Y, Lin H, Xu C, Ying Y, Zhu Y, Miao X, Ge RS, Chen C, Chen S. Per- and polyfluoroalkyl substances inhibit human and rat 17β-hydroxysteroid dehydrogenase 1: Quantitative structure-activity relationship and molecular docking analysis. Ecotoxicol Environ Saf 2024; 273:116173. [PMID: 38452703 DOI: 10.1016/j.ecoenv.2024.116173] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/09/2024]
Abstract
Per- and polyfluoroalkyl (PFAS) substances are enduring industrial materials. 17β-Hydroxysteroid dehydrogenase isoform 1 (17β-HSD1) is an estrogen metabolizing enzyme, which transforms estrone into estradiol in human placenta and rat ovary. Whether PFAS inhibit 17β-HSD1 and what the structure-activity relationship (SAR) remains unexplored. We screened 18 PFAS for inhibiting human and rat 17β-HSD1 in microsomes and studied their SAR and mode of action(MOA). Of the 11 perfluorocarboxylic acids (PFCAs), C8-C14 PFCAs at a concentration of 100 μM substantially inhibited human 17β-HSD1, with order of C11 (half-maximal inhibition concentration, IC50, 8.94 μM) > C10 (10.52 μM) > C12 (14.90 μM) > C13 (30.97 μM) > C9 (43.20 μM) > C14 (44.83 μM) > C8 (73.38 μM) > others. Of the 7 per- and poly-fluorosulfonic acids (PFSAs), the potency was C8S (IC50, 14.93 μM) > C7S (80.70 μM) > C6S (177.80 μM) > others. Of the PFCAs, C8-C14 PFCAs at 100 μM markedly reduced rat 17β-HSD1 activity, with order of C11 (IC50, 9.11 μM) > C12 (14.30 μM) > C10 (18.24 μM) > C13 (25.61 μM) > C9 (67.96 μM) > C8 (204.39 μM) > others. Of the PFSAs, the potency was C8S (IC50, 37.19 μM) > C7S (49.38 μM) > others. In contrast to PFOS (C6S), the partially fluorinated compound 6:2 FTS with an equivalent number of carbon atoms demonstrated no inhibition of human and rat 17β-HSD1 activity at a concentration of 100 μM. The inhibition of human and rat enzymes by PFAS followed a V-shaped trend from C4 to C14, with a nadir at C11. Moreover, human 17β-HSD1 was more sensitive than rat enzyme. PFAS inhibited human and rat 17β-HSD1 in a mixed mode. Docking analysis revealed that they bind to the NADPH and steroid binding site of both 17β-HSD1 enzymes. The 3D quantitative SAR (3D-QSAR) showed that hydrophobic region, hydrogen bond acceptor and donor are key factors in binding to 17β-HSD1 active sites. In conclusion, PFAS exhibit inhibitory effects on human and rat 17β-HSD1 depending on factors such as carbon chain length, degree of fluorination, and the presence of carboxylic acid or sulfonic acid groups, with a notable V-shaped shift observed at C11.
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Affiliation(s)
- Chao Wen
- Department of Neonatal Paediatrics, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Huan Chen
- Department of Emergency, the Dingli Clinical College of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Yunbing Tang
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Hang Lin
- Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Pediatric Anesthesiology, Ministry of Education; Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Congcong Xu
- Department of Neonatal Paediatrics, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yingfen Ying
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yang Zhu
- Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, Zhejiang Province 325000, China
| | - Xinjun Miao
- Department of Emergency, the Dingli Clinical College of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Ren-Shan Ge
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Department of Anesthesiology and Perioperative Medicine, the Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Pediatric Anesthesiology, Ministry of Education; Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, Zhejiang Province 325000, China.
| | - Chao Chen
- Department of Neonatal Paediatrics, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
| | - Shangqin Chen
- Department of Neonatal Paediatrics, the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
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12
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Mangala K, Vinayak W, Aasiya C, Chandrakant B, Amol M, Kumar D, Kulkarni R. Reconnoitering imidazopyridazines as anticancer agents based on virtual modelling approach: quantitative structure activity relationship, molecular docking and molecular dynamics. J Biomol Struct Dyn 2024; 42:2392-2409. [PMID: 37160699 DOI: 10.1080/07391102.2023.2204502] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/14/2023] [Indexed: 05/11/2023]
Abstract
Cancer is an unimpeded growth of cells leading to metathesis of cancer and eventually spread throughout the body. PIM kinases are the members of the serine threonine kinase playing role in cancer progression, differentiation and proliferation. Till date there is no single drug targeting PIM-1 kinase in the market, that has made itself a target in limelight for the discover of new anticancer agents. The contemporary research focusses on the development of new inhibitors of PIM-1 kinase by application of ligand-based and structure-based perspective of drug discovery namely 3D-QSAR, molecular docking and dynamics. The following study stated the correlation amid structural and biological activity of the compounds employing 3D-QSAR analysis. Three 3D-QSAR models were generated using 33 molecules from which the excellent model stated an encouraging conventional correlation coefficient (r2) 0.8651, cross validation coefficient (q2) 0.7609. Furthermore, the predicted correlation coefficient (r2 pred) 0.6274, respectively. Molecular docking studies revealed that the most active compound 26 resided in the active pocket of PIM-1 kinase establishing hydrogen bond interactions with Asp186 in the DFG motif; similarly, all other molecules were engaged within the active site of the PIM-1 kinase. Moreover, molecular dynamics simulation study stated the stability of the ligand in the active site of PIM-1 kinase protein by developing two hydrogen bonds throughout the trajectory of 100 ns. In nutshell, the output stated the successful application of ligand and structure-based strategy for the development of novel PIM-1 kinase inhibitors as anticancer agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khandekar Mangala
- Department of Pharmaceutical Chemistry, SVERIs College of Pharmacy, Gopalpur, India
- Department of Pharmaceutical Chemistry, Punyashlok Ahilyadevi Holkar Solapur University, Solapur, India
| | - Walhekar Vinayak
- Department of Pharmaceutical Chemistry, BVDU's Poona College of Pharmacy, Pune, India
| | - Choudhary Aasiya
- Department of Pharmaceutical Chemistry, SVERIs College of Pharmacy, Gopalpur, India
- Department of Pharmaceutical Chemistry, Punyashlok Ahilyadevi Holkar Solapur University, Solapur, India
| | - Bagul Chandrakant
- Department of Pharmaceutical Chemistry, BVDU's Poona College of Pharmacy, Pune, India
| | - Muthal Amol
- Department of Pharmacology, BVDU's Poona College of Pharmacy, Pune, India
| | - Dilip Kumar
- Department of Pharmaceutical Chemistry, BVDU's Poona College of Pharmacy, Pune, India
- Department of Entomology, University of California, Davis, Davis, CA, USA
- UC Davis Comprehensive Cancer Centre, University of California, Davis, Davis, CA, USA
| | - Ravindra Kulkarni
- Department of Pharmaceutical Chemistry, BVDU's Poona College of Pharmacy, Pune, India
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Biharee A, Singh Y, Kulkarni S, Jangid K, Kumar V, Jain AK, Thareja S. An amalgamated molecular dynamic and Gaussian based 3D-QSAR study for the design of 2,4-thiazolidinediones as potential PTP1B inhibitors. J Mol Graph Model 2024; 127:108695. [PMID: 38118354 DOI: 10.1016/j.jmgm.2023.108695] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/22/2023]
Abstract
Overexpression of protein tyrosine phosphatase 1B (PTP1B) is the major cause of various diseases such as diabetes, obesity, and cancer. PTP1B has been identified as a negative regulator of the insulin signaling cascade, thereby causing diabetes. Numerous anti-diabetic medications based on thiazolidinedione have been successfully developed; however, 2,4-thiazolidinedione (2,4-TZD) scaffolds have been reported as potential PTP1B inhibitors for the manifestation of type 2 diabetes mellitus involving insulin resistance. In the present study, we have employed amalgamated approach involving MD-simulation studies (100 ns) as well as Gaussian field-based 3D-QSAR to develop a pharmacophoric model of 2,4-TZD as potent PTP1B inhibitors. MD simulation studies of the most potent compound in the PTP1B (PDB Id: 2QBS) binding pocket revealed that compound 43 was stable in the binding pocket and demonstrated excellent binding efficacy within the active site pocket. MM/GBSA results revealed that compound 43, bearing C-5 arylidine substitution, strongly bound to the target as compared to rosiglitazone with ΔGMM/GBSA difference of -11.13 kcal/mol. PCA, Rg, RMSF, RMSD, and SASA were analyzed from the complex's trajectories to anticipate the simulation outcome. We have suggested a series of 2,4-TZD as possible PTP1B inhibitors based on the results of MD simulation and 3D-QSAR studies.
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Affiliation(s)
- Avadh Biharee
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Yogesh Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Swanand Kulkarni
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Kailash Jangid
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India
| | - Vinod Kumar
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, Central University of Punjab, Bathinda, Punjab, 151401, India
| | - Akhlesh Kumar Jain
- School of Pharmaceutical Sciences, Guru Ghasidas Central University, Bilaspur, C.G., 495 009, India.
| | - Suresh Thareja
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, Punjab, 151401, India.
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Shafiq N, Zameer R, Attiq N, Moveed A, Farooq A, Imtiaz F, Parveen S, Rashid M, Noor N. Integration of virtual screening of phytoecdysteroids as androgen receptor inhibitors by 3D-QSAR Model, CoMFA, molecular docking and ADMET analysis: An extensive and interactive machine learning. J Steroid Biochem Mol Biol 2024; 237:106427. [PMID: 38008365 DOI: 10.1016/j.jsbmb.2023.106427] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/23/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
Ecdysteroids, a class of naturally isolated polyhydroxylated sterols, stands at a very good place in the pharmaceutical industry from their medicinal point of views like anti-inflammatory, neuroprotective, anti-microbial, anti-diabetic, antioxidant, and anti-tumor effects. Due to their excellent antioxidant and anti-microbial potential, ecdysteroids have extensive use in skin products, especially derma creams. To monitor the best anti-acne phytoecdysteroids, here made use of different computational approaches, by using the rapid, easy, cost-effective and high throughput method to screen and identify ecdysteroids as androgen receptor inhibitors. 3D-QSAR study was carried out on a dataset of ecdysteroids by using comparative molecular field analysis (CoMFA) to determine the factors responsible for the activity of compounds. Statistically a cross-validated (q2) 0.1457 and regression coefficient (r2) 0.9713 indicated the best model. Contour map results showed the influence of steric effect to enhance activity. A molecular docking analysis was done to further find out the binding sites and their anti-acne potential against three crystal structured macromolecules (PDB ID: 2REQ, 2BAC, 4EM0). Docking results were further evaluated by prime MM-GBSA analysis and findings confirmed the accuracy. Toxicity by ADMET assessment was carried out and M2 was found as lead druglike with best anti-acne activity against Propionium acnes GehA lipase bacteria after passing all filters. This research study is novel because it is representing first effort to explore ecdysteroids class for their high therapeutic output as androgen receptor inhibitor by using computational tools and expectedly led to novel scaffold for androgen receptor inhibitor. This is a novel and new approach to investigate the ecdysteroids for first time for their practical applications.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Product Discovery Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan.
| | - Rabia Zameer
- Synthetic and Natural Product Discovery Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Naila Attiq
- Synthetic and Natural Product Discovery Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Aniqa Moveed
- Synthetic and Natural Product Discovery Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Ariba Farooq
- Department of Chemistry, The University of Lahore, Lahore, Pakistan
| | - Fazeelat Imtiaz
- Green Chemistry Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Product Discovery Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Product Discovery Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
| | - Nadia Noor
- Micro-Biology Laboratory, Department of Chemistry, Government College Women University Faisalabad, 38000, Pakistan
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15
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Liu R, Chen X, Li J, Liu X, Shu M. Discovery of novel bromodomain-containing protein 4 (BRD4-BD1) inhibitors combined with 3d-QSAR, molecular docking and molecular dynamics in silico. J Biomol Struct Dyn 2024:1-18. [PMID: 38425011 DOI: 10.1080/07391102.2024.2321249] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
Bromine-containing domain protein 4 (BRD4) plays a crucial role in regulating transcription and genome stability. Selective inhibitors of BRD4-BD1 can specifically target specific bromine domains to affect cell proliferation, apoptosis, and differentiation. In this work, 43 selective benzoazepinone BRD4-BD1 inhibitors were studied using molecular simulations and three-dimensional quantitative conformation relationships (3D-QSAR). A reliable 3D-QSAR model was established based on COMFA (Q2 = 0.532, R2 = 0.981) and COMSIA (S + E + H (Q2 = 0.536, R2 = 0.979) two different analysis methods. Through 3D-QSAR model prediction and quantum chemical analysis, 15 small molecules with stronger inhibitory activity than the template compounds were constructed, and 5 new compounds with higher predictive activity and binding affinity were screened by molecular docking and ADMET methods. According to the molecular dynamics simulation, the key residues that can interact with BRD4-BD1 protein and molecular docking results are consistent, including ASN140, MET132, GLN85, MET105, ASN135 and TYR97. From the MD trajectory, we calculated and analyzed RMSD, RMSF, free binding energy, FECM, DCCM and PCA, the loop region formed by amino acids VAL45∼PRO62 showed α-helix, β-folding and clustering towards the active center with the extension of simulation time. Further optimization of the structure of active candidate compounds A6, A11, A14, and A15 will provide the necessary theoretical basis for the synthesis and activity evaluation of novel BRD4-BD1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rong Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Xiaodie Chen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Jiali Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Xingyun Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
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Hao Y, Feng Y, Dong Y, Ren Y, Huang J, Ma H, Wang C, Jin K, Shang D, Zhang X. Synthesis and Antifungal Properties of 1,2,4-Triazole Schiff Base Agents Based on a 3D-QSAR Model. Chem Biodivers 2024:e202302064. [PMID: 38390665 DOI: 10.1002/cbdv.202302064] [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: 12/27/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 02/24/2024]
Abstract
Based on our previous research, a 3D-QSAR model (q2=0.51, ONC=5, r2=0.982, F=271.887, SEE=0.052) was established to predict the inhibitory effects of triazole Schiff base compounds on Fusarium graminearum, and its predictive ability was also confirmed through the statistical parameters. According to the results of the model design, 30 compounds with superior bioactivity compared to the template molecule 4 were obtained. Seven of these compounds (DES2-6, DES9-10) with improved biological activity and readily available raw materials were successfully synthesized. Their structures were confirmed through HRMS, NMR, and single crystal X-ray diffraction analysis (DES-5). The bioactivity of the final products was investigated through an in vitro antifungal assay. There was little difference in the EC50 values between the experimental and predicted values of the model, demonstrating the reliability of the model. Especially, DES-3 (EC50=9.915 mg/L) and DES-5 (EC50=9.384 mg/L) exhibited better inhibitory effects on Fusarium graminearum compared to the standard drug (SD) triadimenol (EC50=10.820 mg/L). These compounds could serve as potential new fungicides for future research. The interaction between the final products and isocitrate lyase (ICL) was investigated through molecular docking. Compounds with R groups that have a higher electron-donating capacity were found to be biologically active.
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Affiliation(s)
- Yun Hao
- School of Chemical Engineering, Northwest University, Xi'an, 710100, China E-mail: address
| | - Yunrui Feng
- School of Chemical Engineering, Northwest University, Xi'an, 710100, China E-mail: address
| | - Yangming Dong
- School of Chemical Engineering, Northwest University, Xi'an, 710100, China E-mail: address
| | - Yinghui Ren
- School of Chemical Engineering, Northwest University, Xi'an, 710100, China E-mail: address
| | - Jie Huang
- School of Chemical Engineering, Northwest University, Xi'an, 710100, China E-mail: address
| | - Haixia Ma
- School of Chemical Engineering, Northwest University, Xi'an, 710100, China E-mail: address
| | - Cuiling Wang
- School of College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Kangrui Jin
- School of College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Dongyuan Shang
- School of College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiaobin Zhang
- Hospital of Northwest University, Northwest University, Xi'an, 710069, China
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Parveen S, Shehzadi S, Shafiq N, Rashid M, Naz S, Mehmood T, Riaz R, S Almaary K, Nafidi HA, Bourhia M. A discovery of potent kaempferol derivatives as multi-target medicines against diabetes as well as bacterial infections: an in silico approach. J Biomol Struct Dyn 2024:1-23. [PMID: 38334277 DOI: 10.1080/07391102.2024.2308773] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024]
Abstract
Flavonoids demonstrate beneficial effects on human health because flavonoids contain important biological properties. Kaempferol is a flavonol, type of flavonoid found in eatable plants and in plants usually employed in ancient drugs (Moringa oleifera, Tilia spp., fern genus spp. and gingko etc.). Some medicinal studies have shown that the use of foods full of kaempferol decreases the risk of many (cancer, vascular) diseases. All the data of 50 kaempferol derivatives were collected from PubChem database. Through Schrödinger software, 3D-QSAR study was performed for 50 compounds by using method of field base. Conformer of kaempferol derivatives was docked against anti-diabetic, anti-microbial co-crystal structures and protein. To monitor the best anti-diabetic and antibacterial agent, particular kaempferol derivatives were downloaded from PubChem database. Virtual screening by molecular docking provided four lead compounds with four different proteins. These hit compounds were found to be potent inhibitor for diabetic enzymes alpha-amylase and DPP IV and had the potential to suppress DNA gyrase and dihydrofolate reductase synthesis. Molecular dynamic simulation of docked complexes evaluates the value of root mean square fluctuation by iMOD server. Kaempferol 3-O-alpha-L-(2, 3-di-Z-p-coumaroyl) rhamnoside (42) compound used as anti-diabetic and kaempferol 3-O-gentiobioside (3) as antibacterial with good results can be used for drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shagufta Parveen
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Saman Shehzadi
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Nusrat Shafiq
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Sadaf Naz
- Department of Chemistry, The University of Lahore, Lahore, Pakistan
| | - Tahir Mehmood
- Centre for Applied Molecular Biology (CAMB), University of the Punjab, Punjab, Pakistan
| | - Rabia Riaz
- Synthetic and Natural Product Drug Discovery Laboratory, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Khalid S Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec, QC, Canada
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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Kumar V, Jangid K, Kumar N, Kumar V, Kumar V. 3D-QSAR-based pharmacophore modelling of quinazoline derivatives for the identification of acetylcholinesterase inhibitors through virtual screening, molecular docking, molecular dynamics and DFT studies. J Biomol Struct Dyn 2024:1-15. [PMID: 38329085 DOI: 10.1080/07391102.2024.2313157] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/12/2023] [Indexed: 02/09/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurological disorder responsible for the cognitive dysfunction and cognitive impairment in the patients. Acetylcholinesterase inhibitors (AChEIs) are used to treat AD however, these only provided symptomatic relief and more efficient drug molecules are desired for the effective treatment of the disease. In this article, ligand-based drug-designing strategy was used to develop and validate a field-based 3D-QSAR pharmacophore model on quinazoline-based AChEIs reported in the literature. The validated pharmacophore model (AAAHR_1) was used as a prefilter to screen an ASINEX database via virtual screening workflow (VSW). The hits generated were subjected to MM-GBSA to identify potential AChEIs and top three scoring molecules (BAS 05264565, LEG 12727144 and SYN 22339886) were evaluated for thermodynamic stability at the target site using molecular dynamic simulations. Additionally, DFT study was performed to predict the reactivity of lead molecules towards acetylcholinesterase (AChE). Thus, by utilising various computational tools, three molecules were identified as potent AChEIs that can be developed as potential drug candidates for the treatment of AD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vijay Kumar
- Department of Chemistry, Laboratory of Organic and Medicinal Chemistry, Central University of Punjab, Bathinda, India
| | - Kailash Jangid
- Department of Chemistry, Laboratory of Organic and Medicinal Chemistry, Central University of Punjab, Bathinda, India
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, India
| | - Naveen Kumar
- Department of Chemistry, Laboratory of Organic and Medicinal Chemistry, Central University of Punjab, Bathinda, India
| | - Vinay Kumar
- Department of Chemistry, Laboratory of Organic and Medicinal Chemistry, Central University of Punjab, Bathinda, India
| | - Vinod Kumar
- Department of Chemistry, Laboratory of Organic and Medicinal Chemistry, Central University of Punjab, Bathinda, India
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Shafiq N, Shakoor B, Yaqoob N, Parveen S, Brogi S, Mohammad Salamatullah A, Rashid M, Bourhia M. A virtual insight into mushroom secondary metabolites: 3D-QSAR, docking, pharmacophore-based analysis and molecular modeling to analyze their anti-breast cancer potential. J Biomol Struct Dyn 2024:1-22. [PMID: 38299565 DOI: 10.1080/07391102.2024.2304137] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/03/2024] [Indexed: 02/02/2024]
Abstract
Breast cancer is a major issue of investigation in drug discovery due to its rising frequency and global dominance. Plants are significant natural sources for the development of novel medications and therapies. Medicinal mushrooms have many biological response modifiers and are used for the treatment of many physical illnesses. In this research, a database of 89 macro-molecules with anti-breast cancer activity, which were previously isolated from the mushrooms in literature, has been selected for the three-dimensional quantitative structure-activity relationships (3D-QSAR) studies. The 3D-QSAR model was necessarily used in Pharmacopoeia virtual evaluation of the database to develop novel MCF-7 inhibitors. With the known potential targets of breast cancer, the docking studies were achieved. Using molecular dynamics simulations, the targets' stability with the best-chosen natural product molecule was found. Furthermore, the absorption, distribution, metabolism, excretion, and toxicity of three compounds, resulting after the docking study, were predicted. The compound C1 (Pseudonocardian A) showed the features of effective compounds because it has bioavailability from different coral species and is toxicity-free for the prevention of many dermatological illnesses. C1 is chemically active and possesses charge transfer inside the monomer, as seen by the band gaps of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) electrons. The reactivity descriptors ionization potential, electron affinity, chemical potential (μ), hardness (η), softness (S), electronegativity (χ), and electrophilicity index (ω) have been estimated using the energies of frontier molecular orbitals (HOMO-LUMO). Additionally, molecular electrostatic potential maps were created to show that the C1 is reactive.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Bushra Shakoor
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Nazia Yaqoob
- Green Chemistry Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Ahmad Mohammad Salamatullah
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Maryam Rashid
- Synthetic and Natural Products Drug Discovery Lab, Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
- Laboratory of Chemistry-Biochemistry, Environment, Nutrition, and Health, Faculty of Medicine and Pharmacy, University Hassan II, Casablanca, Morocco
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Rezaei H, Zarezade V, Khodadadi I, Tavilani H, Tanzadehpanah H, Karimi J. Unveiling Arformoterol as a potent LSD1 inhibitor for breast cancer treatment: A comprehensive study integrating 3D-QSAR pharmacophore modeling, molecular docking, molecular dynamics simulations and in vitro assays. Int J Biol Macromol 2024; 258:129048. [PMID: 38159701 DOI: 10.1016/j.ijbiomac.2023.129048] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/09/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Lysine Specific Demethylase 1 (LSD1) has been identified as a chromatin-modifying enzyme implicated in various cancer pathogeneses, highlighting the potential for novel epigenetic cancer treatments through the development of effective inhibitors. We employed 3D-QSAR pharmacophore modeling, molecular docking, and molecular dynamics simulations to identify a promising drug candidate for LSD1 inhibition. RMSD, RMSF, H-bond, and DSSP analysis demonstrated that ZINC02599970 (Arformoterol) and ZINC13453966 exhibited the highest LSD1 inhibitory potential. Experimental validation using MCF-7 and MDA-MB-231 cell lines revealed that Arformoterol displayed potent antiproliferative activity with IC50 values of 12.30 ± 1.48 μM and 19.69 ± 1.15 μM respectively. In contrast, the IC50 values obtained for the control (tranylcypromine) in exposure to MCF-7 and MDA-MB-231 cells were 104.6 ± 1.69 μM and 77 ± 0.67 μM, respectively. Arformoterol demonstrated greater LSD1 inhibitory potency in MCF-7 cells compared to MDA-MB-231 cells. Also, the expression of genes involved in chromatin rearrangement (LSD1), angiogenesis (VEGF1), cell migration (RORα), signal transduction (S100A8), apoptosis, and cell cycle (p53) were investigated. Arformoterol enhanced apoptosis and induced cell cycle arrest at the G2/M phase, both in MCF-7 and MDA-MB-231 cancer cells. Based on our findings, we propose that Arformoterol represents a promising candidate for breast cancer treatment, owing to its potent LSD1 inhibitory activity.
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Affiliation(s)
- Hamzeh Rezaei
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Iraj Khodadadi
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Heidar Tavilani
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamid Tanzadehpanah
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshid Karimi
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Mkhayar K, Daoui O, Haloui R, Elkhattabi K, Elabbouchi A, Chtita S, Samadi A, Elkhattabi S. Ligand-Based Design of Novel Quinoline Derivatives as Potential Anticancer Agents: An In-Silico Virtual Screening Approach. Molecules 2024; 29:426. [PMID: 38257339 PMCID: PMC10819159 DOI: 10.3390/molecules29020426] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, using the Comparative Molecular Field Analysis (CoMFA) approach, the structure-activity relationship of 33 small quinoline-based compounds with biological anti-gastric cancer activity in vitro was analyzed in 3D space. Once the 3D geometric and energy structure of the target chemical library has been optimized and their steric and electrostatic molecular field descriptions computed, the ideal 3D-QSAR model is generated and matched using the Partial Least Squares regression (PLS) algorithm. The accuracy, statistical precision, and predictive power of the developed 3D-QSAR model were confirmed by a range of internal and external validations, which were interpreted by robust correlation coefficients (RTrain2=0.931; Qcv2=0.625; RTest2=0.875). After carefully analyzing the contour maps produced by the trained 3D-QSAR model, it was discovered that certain structural characteristics are beneficial for enhancing the anti-gastric cancer properties of Quinoline derivatives. Based on this information, a total of five new quinoline compounds were developed, with their biological activity improved and their drug-like bioavailability measured using POM calculations. To further explore the potential of these compounds, molecular docking and molecular dynamics simulations were performed in an aqueous environment for 100 nanoseconds, specifically targeting serine/threonine protein kinase. Overall, the new findings of this study can serve as a starting point for further experiments with a view to the identification and design of a potential next-generation drug for target therapy against cancer.
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Affiliation(s)
- Khaoula Mkhayar
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez 30000, Morocco; (K.M.); (O.D.); (R.H.)
| | - Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez 30000, Morocco; (K.M.); (O.D.); (R.H.)
| | - Rachid Haloui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez 30000, Morocco; (K.M.); (O.D.); (R.H.)
| | - Kaouakeb Elkhattabi
- Laboratory for Oral Biology and Biotechnology Research, Department of Fundamental Sciences, Faculty of Medicine Dentistry, Mohammed V University, Rabat 10106, Morocco;
| | - Abdelmoula Elabbouchi
- Euromed Research Center, Euromed Faculty of Pharmacy, Euromed University of Fes (UEMF), Meknes Road, Fez 30000, Morocco;
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M’Sik, Hassan II University of Casablanca, Casablanca P.O. Box 7955, Morocco;
| | - Abdelouahid Samadi
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez 30000, Morocco; (K.M.); (O.D.); (R.H.)
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Haloui R, Mkhayar K, Daoui O, El Khattabi K, El Abbouchi A, Chtita S, Elkhattabi S. Design of new small molecules derived from indolin-2-one as potent TRKs inhibitors using a computer-aided drug design approach. J Biomol Struct Dyn 2024:1-18. [PMID: 38217880 DOI: 10.1080/07391102.2024.2302944] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Tropomyosin receptor kinase (TRKs) enzymes are responsible for cancers associated with the neurotrophic tyrosine kinase receptor gene fusion and are identified as effective targets for anticancer drug discovery. A series of small-molecule indolin-2-one derivatives showed remarkable biological activity against TRKs enzymatic activity. These small molecules could have an excellent profile for pharmaceutical application in the treatment of cancers caused by TRKs activity. The aim of this study is to modify the structure of these molecules to obtain new molecules with improved TRK inhibitory activity and pharmacokinetic properties favorable to the design of new drugs. Based on these series, we carried out a 3D-QSAR study. As a result, robust and reliable CoMFA and CoMSIA models are developed and applied to the design of 11 new molecules. These new molecules have a biological activity superior to the most active molecule in the starting series. The eleven designed molecules are screened using drug-likeness, ADMET proprieties, molecular docking, and MM-GBSA filters. The results of this screening identified the T1, T3, and T4 molecules as the best candidates for strong inhibition of TRKs enzymatic activity. In addition, molecular dynamics simulations are performed for TRK free and complexed with ligands T1, T3, and T4 to evaluate the stability of ligand-protein complexes over the simulation time. On the other hand, we proposed experimental synthesis routes for these newly designed molecules. Finally, the designed molecules T1, T2, and T3 have great potential to become reliable candidates for the conception of new drug inhibitors of TRKs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rachid Haloui
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Khaoula Mkhayar
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Ossama Daoui
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
| | - Kaouakeb El Khattabi
- Department of Fundamental Sciences, Faculty of Medicine Dentistry, Mohammed V University of Rabat, Rabat, Morocco
| | - Abdelmoula El Abbouchi
- Euromed Research Center, Euromed Faculty of Pharmacy, Euromed University of Fes (UEMF), Fez, Morocco
| | - Samir Chtita
- Laboratory of Analytical and Molecular Chemistry, Faculty of Sciences Ben M'Sik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Souad Elkhattabi
- Laboratory of Engineering, Systems, and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, Fez, Morocco
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Shi L, Si H. 3D-QSAR Studies on High-affinity Phosphodiestera. Curr Med Chem 2024; 31:CMC-EPUB-137335. [PMID: 38231072 DOI: 10.2174/0109298673275082231220074933] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 01/18/2024]
Abstract
BACKGROUND Recent studies have found that Phosphodiesterase-4 (PDE4) is closely related to the pathogenesis of depression, cognitive impairment and neurological impairment. OBJECTIVE Our objective is to develop potent inhibitors of the high-affinity phosphodiesterase 4D isoform (PDE4D) that can serve as radioligands for Positron Emission Tomography (PET) imaging, thereby advancing research in the field of neurological diseases. METHODS We employed a multi-step approach combining three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, classification techniques, and CoMSIA analysis to investigate the conformational relationship of highaffinity PDE4D inhibitors as PET ligands. ADMET and Drug-likeness predictions were also conducted. By utilizing these methods, our aim was to identify more potent PDE4D inhibitors. RESULTS The results showed that the CoMSIA model with the best principal component scores (n=7) had a cross-validated Q2 value of 0.602 and a non-cross-validated R2 value of 0.976. These results affirmed the excellent predictive capability of the established CoMSIA model. Analysis of the generated 3D-QSAR contour plots highlighted specific regions in the molecular structure of the compounds that can be further optimized and modified. Guided by the contour plots, we designed 100 novel PDE4D inhibitors, and molecular docking was performed for the top 4 compounds with high activity. The molecular docking scores were promising, and ADMET and drug similarity predictions yielded satisfactory results. Taking into consideration these factors, compound 51c was determined to be the optimal compound, laying a solid foundation for further research. CONCLUSION For the continued development of PDE4D PET radioligand, these models and new compounds' developing methodology offer a theoretical foundation and crucial references.
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Affiliation(s)
- Luyang Shi
- College of Life Science, Qingdao University, Qingdao, China
| | - Hongzong Si
- Laboratory of New Fibrous Materials and Modern Textile, The State Key Laboratory, Qingdao University, Qingdao, China
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24
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Fu Y, Zhao S, Ma N, Zhang Y, Cai S. Exploring the Transmembrane Behaviors of Dietary Flavonoids under Intestinal Digestive Products of Different Lipids: Insights into the Structure-Activity Relationship In Vitro. J Agric Food Chem 2024; 72:794-809. [PMID: 38131329 DOI: 10.1021/acs.jafc.3c07239] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This study aimed to investigate the transmembrane transport behavior and structure-activity relationships of various dietary flavonoids in the presence of dietary lipids derived from different sources in vitro. Results revealed that the digestion products of soybean oil (SOED) and lard (LOED) augmented the apparent permeability coefficients of most dietary flavonoids, and SOED exhibited higher transport compared with LOED. The structural properties of flavonoids and the potential interactions between fatty acids in these digestion products and flavonoids may influence the outcomes. 3D quantitative structure-activity relationship analyses revealed that incorporating small-volume groups at position 8 of the A-ring augmented the transmembrane transfer of flavonoids in the LOED system compared with the control group. By contrast, the integration of hydrophobic groups at position 5 of the A-ring and hydrogen bonding acceptor groups at position 6 of the A-ring enhanced the transmembrane transportation of flavonoids in the SOED system. Molecular dynamics simulations revealed that the SOED system may facilitate the interactions with flavonoids to form more stable and compact fatty acid-flavonoid complexes compared to the LOED system. These findings may provide valuable insights into flavonoid absorption to facilitate the development and utilization of functional foods or dietary supplements based on dietary flavonoids.
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Affiliation(s)
- Yishan Fu
- Faculty of Food Science and Engineering, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, People's Republic of China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, Jiangsu Province, People's Republic of China
| | - Shuai Zhao
- Faculty of Food Science and Engineering, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, People's Republic of China
| | - Nan Ma
- Faculty of Food Science and Engineering, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, People's Republic of China
| | - Yuanyue Zhang
- Faculty of Food Science and Engineering, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, People's Republic of China
| | - Shengbao Cai
- Faculty of Food Science and Engineering, Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming 650500, Yunnan Province, People's Republic of China
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25
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Elbouhi M, Ouabane M, Tabti K, Badaoui H, Abdessadak O, El Alaouy MA, Elkamel K, Lakhlifi T, Sbai A, Ajana MA, Bouachrine M. Computational evaluation of 1,2,3-triazole-based VEGFR-2 inhibitors: anti-angiogenesis potential and pharmacokinetic assessment. J Biomol Struct Dyn 2024:1-11. [PMID: 38193897 DOI: 10.1080/07391102.2023.2301686] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
The vascular endothelial growth factor (VEGF) and its cell surface receptor, as well as the human VEGFR-2 domain kinase, are some of the signaling pathways that have received the most attention in this field. This study aimed to identify novel molecules as VEGFR-2 inhibitors using 3D-QSAR modeling based on 1,2,3-triazole. Docking studies and dynamic simulations were performed to analyze novel interactions with the inhibitors and validate the molecular docking, dynamic simulations, and ADMET analyses. The optimized CoMSIA/SEH model showed good statistical results, and molecular docking and molecular dynamics simulations demonstrated stability of M3 ligand with the receptor and provided insight into ligand-receptor interactions. The newly developed compounds performed well in ADMET evaluations and showed promising results using Lipinski's rule of five, suggesting that the molecule M3 could be a useful anti-angiogenesis agent. In conclusion, this study provides insights into the structure-activity relationship of VEGFR-2 inhibitors and identifies M3 as a potential new anti-angiogenesis drug. The methodology used in this study can be applied to other similar drug targets to discover new and potent inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mhamed Elbouhi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohamed Ouabane
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Kamal Tabti
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Hassan Badaoui
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Oumayma Abdessadak
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Moulay Ahfid El Alaouy
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Khalid Elkamel
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Tahar Lakhlifi
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Abdelouahid Sbai
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Aziz Ajana
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
| | - Mohammed Bouachrine
- Molecular Chemistry and Natural Substances Laboratory (MCNSL), Department of Chemistry, Faculty of Science, Moulay Ismail University, Meknes, Morocco
- Higher School of Technology (EST Khenifra), Sultan Moulay Slimane University, Beni-Mellal, Morocco
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Saha B, Das A, Jangid K, Kumar A, Kumar V, Jaitak V. Identification of coumarin derivatives targeting acetylcholinesterase for Alzheimer's disease by field-based 3D-QSAR, pharmacophore model-based virtual screening, molecular docking, MM/GBSA, ADME and MD Simulation study. Curr Res Struct Biol 2024; 7:100124. [PMID: 38292820 PMCID: PMC10826614 DOI: 10.1016/j.crstbi.2024.100124] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Alzheimer's disease (AD) leads to gradual memory loss including other compromised cognitive abilities. Acetylcholinesterase (AChE), an important biochemical enzyme from the cholinesterase (ChE) family, is recognized as primary pharmacological target for treating AD. Currently marketed drugs for AD treatment are primarily AChE inhibitors and coumarin derivatives comprising a wide variety of pharmacological activities have proved their efficacy towards AChE inhibition. Ensaculin (KA-672 HCl), a compound that belong to the coumarin family, is a clinical trial candidate for AD treatment. Therefore, a ligand library was prepared with 60 reported coumarin derivatives for field-based 3D-QSAR and pharmacophore modelling. The field-based 3D-QSAR model obtained at partial least square (PLS) factor 7, was the best validated model that predicted activity closer to original activity for each ligand introduced. The contour maps demonstrated spatial distribution of favourable and unfavorable steric, hydrophobic, electrostatic and H-bond donor and acceptor contours around coumarin nucleus. The best pharmacophore model, ADHRR_1 exhibited five essential pharmacophoric features of four different traits for optimum AChE inhibition. Virtual screening through ADHRR_1 accompanied with molecular docking and MM/GBSA identified 10 HITs from a 4,00,000 coumarin derivatives from PubChem database. HITs comprised docking scores ranging from -12.096 kcal/mol to -8.271 kcal/mol and compared with the reference drug Donepezil (-8.271 kcal/mol). ADME properties analysis led into detecting two leads (HIT 1 and HIT 2) among these 10 HITs. Molecular Dynamics Simulation indicated thermodynamic stability of the complex of lead compounds with AChE protein. Finally, thorough survey of the experimental results from 3D-QSAR modelling, pharmacophore modelling and molecular docking interactions led us to develop the lead formula I for future advancements in treating AD through AChE inhibitors.
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Affiliation(s)
- Bikram Saha
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, 151401, India
| | - Agnidipta Das
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, 151401, India
| | - Kailash Jangid
- Department of Chemistry, Central University of Punjab, Ghudda, Bathinda, 151401, India
| | - Amit Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, 151401, India
| | - Vinod Kumar
- Department of Chemistry, Central University of Punjab, Ghudda, Bathinda, 151401, India
| | - Vikas Jaitak
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Ghudda, Bathinda, 151401, India
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27
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Li B, Yin X, Cen B, Duan W, Lin G, Wang X, Zou R. High value-added application of natural forest product α-pinene: design, synthesis and 3D-QSAR study of novel α-campholenic aldehyde-based 4-methyl-1,2,4-triazole-thioether compounds with significant herbicidal activity. Nat Prod Res 2024; 38:359-364. [PMID: 36008869 DOI: 10.1080/14786419.2022.2117176] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 10/15/2022]
Abstract
For exploring novel natural product-derived herbicides, 16 novel α-campholenic aldehyde-based 4-methyl-1,2,4-triazole-thioether compounds were designed, synthesized, and characterized by FT-IR, 1H NMR, 13C NMR, ESI-MS and elemental analysis. The preliminary bioassay showed that, at 100 µg/mL, most of the target compounds displayed significant inhibition activity against root-growth of rape(Brassica campestris L.), with inhibition rates of 85.0%~98.2%(A-class activity level), much better than that of the positive control flumioxazin. In addition, an effective and reasonable 3D-QSAR model was established by CoMFA method in SYBYL-X 2.1.1 software. It was found that, the steric field was the major factor towards the herbicidal activity of the target compounds against B. campestris L., and the introduction of bulky groups into m- and p-position of the benzene ring was favourable to increase the herbicidal activity. This kind of title compounds deserved further study as potential leading compounds for the discovery and development of novel herbicidal agents.
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Affiliation(s)
- Baoyu Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
| | - Xianlong Yin
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
| | - Bo Cen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
| | - Wengui Duan
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
| | - Guishan Lin
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
| | - Xiaoyu Wang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
| | - Renxuan Zou
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning, P. R. China
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Song YY, Zhou YZ, Wang YF, Shu TY, Feng Y, Xu M, Su LH, Li HZ. Sesquiterpenoids from aged Artemisia argyi and their 3D-QSAR for anti-HBV activity. Phytochemistry 2024; 217:113912. [PMID: 37918620 DOI: 10.1016/j.phytochem.2023.113912] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Artemisia argyi Levl. Et Vant, commonly known as "Chinese Mugwort," has been utilized in traditional Chinese medicine and cuisine for centuries. Aged Chinese Mugwort has been uncovered to possess superior quality and safety, and its ethyl acetate extract has been found to exhibit anti-hepatitis B virus (HBV) activity. In this study, twenty-five sesquiterpenoids were isolated and characterized from three-year-aged A. argyi. Among them, 14 previously undescribed sesquiterpenoids (1-14), featuring double bond oxidation or ring opening. It is hypothesized that during the aging process, sesquiterpenes undergo oxidative transformation of their double bonds to form alcohols due to external factors and inherent properties. The anti-HBV activity and cytotoxicity of all compounds were assessed in vitro using HepG 2.2.15 cells, and their structure-activity relationships were analyzed through three-dimensional quantitative structure-activity relationship (3D-QASR) techniques. The α-methylene-γ-lactone sesquiterpenoid derivatives were discovered to have potent inhibitory activity against HBV. This research may broaden the potential applications of Chinese Mugwort and offer further guidance for its development and utilization as functional food or traditional Chinese medicine.
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Affiliation(s)
- Yu-Ying Song
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yong-Zhi Zhou
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yun-Fen Wang
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Teng-Yun Shu
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Yang Feng
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Min Xu
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Li-Hua Su
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
| | - Hai-Zhou Li
- Laboratory of Medicinal Chemical Biology, Facaulty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China.
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Liu X, Ma S, Zhang Y, Fu Y, Cai S. Transmembrane behaviors and quantitative structure-activity relationship of dietary flavonoids in the presence of intestinal digestive products from different carbohydrate sources based on in vitro and in silico analysis. Food Chem X 2023; 20:100994. [PMID: 38144778 PMCID: PMC10740061 DOI: 10.1016/j.fochx.2023.100994] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/19/2023] [Accepted: 11/08/2023] [Indexed: 12/26/2023] Open
Abstract
Bioavailability plays a key role for flavonoids to exert their bioactivities. This study investigated the transmembrane transport behavior and structure-activity of dietary flavonoids. Results showed that the apparent permeability coefficients of some flavonoids could be significantly increased when digestion products from rice flour (RD) or wheat flour (WD) are present (p < 0.05), especially in the WD, potentially due to higher reducing sugar (p < 0.05). 3D-QSAR revealed that the hydrogen bond acceptor groups at positions 5 and 6 of ring A, small-volume groups at position 3', hydrophobic groups at position 4', and large-volume groups at position 5' of ring B increased the transmembrane transport of flavonoids in the WD. A hydrogen bond donor group at position 4' of ring B enhanced the transmembrane transport of flavonoid compounds in the RD. These findings contribute to our comprehensive understanding of flavonoid absorption within the context of intestinal carbohydrate digestion.
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Affiliation(s)
- Xiaojing Liu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, People’s Republic of China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, People’s Republic of China
| | - Shuang Ma
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, People’s Republic of China
| | - Yuanyue Zhang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, People’s Republic of China
| | - Yishan Fu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, People’s Republic of China
- Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu Province 214122, People’s Republic of China
| | - Shengbao Cai
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province 650500, People’s Republic of China
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He C, Bai L, Liu D, Liu B. Interaction mechanism of okra ( Abelmoschus esculentus L.) seed protein and flavonoids: Fluorescent and 3D-QSAR studies. Food Chem X 2023; 20:101023. [PMID: 38144792 PMCID: PMC10740111 DOI: 10.1016/j.fochx.2023.101023] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
The binding capacity of 10 flavonoids with okra seed protein (OSP) was studied by fluorescence spectroscopy. The structure of flavonoids had an obvious impact on binding performance. The binding ability of flavanone was lower than that of flavone, isoflavone and dihydrochalcone. The binding capacity of flavonoid glycoside was superior to that of the corresponding flavonoid aglycone. The binding ability was positively correlated with the number of phenolic hydroxyl groups on the B ring. The steric field and electrostatic field model constructed by 3D-QSAR method could well explain the above interaction behavior. Thermodynamic analysis suggested that the quenching mechanism of OSP caused by flavonoids was static quenching, and the binding-site number was 1. In addition, hydrogen bonding and van der Waals force dominated this interaction. The 3D and synchronous fluorescence spectra showed that there was no significant change in the polarity of the environment around tryptophan and tyrosine residues during binding.
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Affiliation(s)
- Chengyun He
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lu Bai
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Daqun Liu
- Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Benguo Liu
- School of Food Science, Henan Institute of Science and Technology, Xinxiang 453003, China
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Faris A, Alnajjar R, Guo J, AL Mughram MH, Aouidate A, Asmari M, Elhallaoui M. Computational 3D Modeling-Based Identification of Inhibitors Targeting Cysteine Covalent Bond Catalysts for JAK3 and CYP3A4 Enzymes in the Treatment of Rheumatoid Arthritis. Molecules 2023; 29:23. [PMID: 38202604 PMCID: PMC10779482 DOI: 10.3390/molecules29010023] [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: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
This work aimed to find new inhibitors of the CYP3A4 and JAK3 enzymes, which are significant players in autoimmune diseases such as rheumatoid arthritis. Advanced computer-aided drug design techniques, such as pharmacophore and 3D-QSAR modeling, were used. Two strong 3D-QSAR models were created, and their predictive power was validated by the strong correlation (R2 values > 80%) between the predicted and experimental activity. With an ROC value of 0.9, a pharmacophore model grounded in the DHRRR hypothesis likewise demonstrated strong predictive ability. Eight possible inhibitors were found, and six new inhibitors were designed in silico using these computational models. The pharmacokinetic and safety characteristics of these candidates were thoroughly assessed. The possible interactions between the inhibitors and the target enzymes were made clear via molecular docking. Furthermore, MM/GBSA computations and molecular dynamics simulations offered insightful information about the stability of the binding between inhibitors and CYP3A4 or JAK3. Through the integration of various computational approaches, this study successfully identified potential inhibitor candidates for additional investigation and efficiently screened compounds. The findings contribute to our knowledge of enzyme-inhibitor interactions and may help us create more effective treatments for autoimmune conditions like rheumatoid arthritis.
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Affiliation(s)
- Abdelmoujoud Faris
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco;
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi 16063, Libya;
- PharmD, Faculty of Pharmacy, Libyan International Medical University, Benghazi 16063, Libya
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Jingjing Guo
- Centre in Artificial Intelligence-Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China;
| | - Mohammed H. AL Mughram
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia; (M.H.A.M.); (M.A.)
| | - Adnane Aouidate
- Laboratory of Organic Chemistry and Physical Chemistry, Team of Molecular Modeling, Materials and Environment, Faculty of Sciences, University Ibn Zohr, Agadir 80060, Morocco;
| | - Mufarreh Asmari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia; (M.H.A.M.); (M.A.)
| | - Menana Elhallaoui
- LIMAS, Department of Chemical Sciences, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco;
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Meng Y, Wei Z, Xue C. Deciphering the interaction mechanism and binding mode between chickpea protein isolate and flavonoids based on experimental studies and molecular simulation. Food Chem 2023; 429:136848. [PMID: 37454615 DOI: 10.1016/j.foodchem.2023.136848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Chickpea protein isolate (CPI) is a promising novel plant protein, and protein-flavonoid system has also been applied in various food products. However, the interaction mechanism between CPI and flavonoids remains to be elucidated. In this paper, the affinity behavior between flavonoids and CPI was explained by constructing the three-dimensional quantitative structure-activity relationship (R2 = 0.988, Q2 = 0.777). Subsequently, four representative flavonoids were selected for further study. Multi-spectroscopy analysis showed that the sequence of affinity for CPI was puerarin > apigenin > naringenin > epigallocatechin gallate. Meanwhile, flavonoids altered the secondary structure and spatial conformation of CPI, leading to the static quenching of CPI. Additionally, thermodynamic analysis indicated that hydrogen bonding and van der Waals forces were the main driving forces for complex binding. Molecular docking and molecular dynamics simulations further explored the binding sites and conformations of complexes. This study provides theoretical guidance for in-depth research on the interaction patterns between biomacromolecules and small molecules in food matrices.
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Affiliation(s)
- Yuan Meng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China
| | - Zihao Wei
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao 266404, China; Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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Li K, Hong S, Yu Z, Hong Z, Sun Y, Cheng J, Tang L, Wang Y, Qi X, Fan Z. Computation-Directed Molecular Design, Synthesis, and Fungicidal Activity of Succinate Dehydrogenase Inhibitors. J Agric Food Chem 2023; 71:19372-19384. [PMID: 38049388 DOI: 10.1021/acs.jafc.3c05232] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Succinate dehydrogenase inhibitors (SDHIs) are a class of fungicides targeting the pathogenic fungi mitochondrial SDH. Here, molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR), and molecular dynamics (MD) simulations were used to guide SDHI innovation. Molecular docking was performed to explore the binding modes of SDH and its inhibitors. 3D-QSAR models were carried out on 33 compounds with activity against Rhizoctonia cerealis (R. cerealis); their structure-activity relationships were analyzed using comparative molecular field analysis and comparative molecular similarity indices analysis. MD simulations were used to assess the stability of the complexes under physiological conditions, and the results were consistent with molecular docking. Binding free energy was calculated through the molecular mechanics generalized born surface area method, and the binding free energy was decomposed. The results are consistent with the activity of bioassay and indicate that van der Waals and lipophilic interactions contribute the most in the molecular binding process. Afterward, we designed and synthesized 12 compounds under the guidance of the above-mentioned analyses, bioassay found that F9 was active against R. cerealis with the EC50 value of 9.43 μg/mL, and F4, F5, and F9 were active against Botrytis cinerea with an EC50 values of 5.80, 3.17, and 1.63 μg/mL, respectively. They all showed good activity between positive controls of pydiflumetofen and thifluzamide. Our study provides new considerations for effective SDHIs discovery.
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Affiliation(s)
- Kun Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Shuang Hong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zhenwu Yu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Zeyu Hong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yaru Sun
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Liangfu Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
| | - Yong Wang
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300112, P. R. China
| | - Xin Qi
- Institute of Germplasm Resources and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300112, P. R. China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, P. R. China
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Raju B, Sapra B, Silakari O. 3D-QSAR assisted identification of selective CYP1B1 inhibitors: an effective bioisosteric replacement/molecular docking/electrostatic complementarity analysis. Mol Divers 2023; 27:2673-2693. [PMID: 36441444 DOI: 10.1007/s11030-022-10574-7] [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: 10/08/2021] [Accepted: 11/20/2022] [Indexed: 11/29/2022]
Abstract
Cytochrome P450-1B1 is a majorly overexpressed drug-metabolizing enzyme in tumors and is responsible for inactivation and subsequent resistance to a variety of anti-cancer drugs, i.e., docetaxel, tamoxifen, and cisplatin. In the present study, a 3D quantitative structure-activity relationship (3D-QSAR) model has been constructed for the identification, design, and optimization of novel CYP1B1 inhibitors. The model has been built using a set of 148 selective CYP1B1 inhibitors. The developed model was evaluated based on certain statistical parameters including q2 and r2 which showed the acceptable predictive and descriptive capability of the generated model. The developed 3D-QSAR model assisted in understanding the key molecular fields which were firmly related to the selective CYP1B1 inhibition. A theoretic approach for the generation of new lead compounds with optimized CYP1B1 receptor affinity has been performed utilizing bioisosteric replacement analysis. These generated molecules were subjected to a developed 3D-QSAR model to predict the inhibitory activity potentials. Furthermore, these compounds were scrutinized through the activity atlas model, molecular docking, electrostatic complementarity, molecular dynamics, and waterswap analysis. The final hits might act as selective CYP1B1 inhibitors which could address the issue of resistance. This 3D-QSAR includes several chemically diverse selective CYP1B1 receptor ligands and well accounts for the individual ligand's inhibition affinities. These features of the developed 3D-QSAR model will ensure future prospective applications of the model to speed up the identification of new potent and selective CYP1B1 receptor ligands.
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Affiliation(s)
- Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Bharti Sapra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India.
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Desai SP, Mohite S, Alobid S, Saralaya M, Patil AS, Das K, Almadani ME, Arif Hussain S, Hussain Alamer B, Abdulrahman Jibreel E, Ibrahim Almoteer A, Mohammed Basheeruddin Asdaq S. 3D QSAR study on substituted 1, 2, 4 triazole derivatives as anticancer agents by kNN MFA approach. Saudi Pharm J 2023; 31:101836. [PMID: 38028224 PMCID: PMC10661185 DOI: 10.1016/j.jsps.2023.101836] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Background and objectives Researchers have recently focused on the biological and synthetic effects of 1, 2, and 4-triazole fused heterocyclic molecules because they have tremendous medicinal value. The objective of the present study was to carry out the 3D QSAR evaluation on the substituted 1,2, and 4 triazole derivatives for anticancer potential using k-Nearest Neighbor-Molecular Field Analysis (kNN-MFA) method. Methods Using the molecular design suite, a three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis was undertaken on a series of 4-amino-5-(pyridin3yl)-4H-1, 2, and 4-triazole-3-thiol anticancer drugs (Vlife MDS). This study used a genetic algorithm and a manual selection approach on 20 substituted 1, 2, and 4-triazole derivatives. Based on the genetic algorithm (GA), the 3D-QSAR model was generated. Statistical significance and predictive capacity were evaluated using internal and external validation. Results The most significant model has a correlation coefficient of 0.9334 (squared correlation coefficient r2 = 0.8713), showing that biological activity and descriptors have a strong relationship. The model exhibited internal predictivity of 74.45 percent (q2 = 0.2129), external predictivity of 81.09 percent (pred r2 = 0.8417), and the smallest error term for the predictive correlation coefficient (pred r2se = 0.1255). The model revealed steric (S 1047--0.0780--0.0451S 927) and electrostatic (E 1002) data points that contribute remarkably to anticancer activity. A molecular field study demonstrates a link between the structural features of substituted triazole derivatives and their activities. Conclusion The good-to-moderate anticancer potential of compounds confirms the significant pharmacological role of 1,2,4-triazole derivatives. These results could lead to the identification of potential chemical compounds with optimal anticancer activity and minimal side effects.
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Affiliation(s)
- Shailaja P. Desai
- Annasaheb Dange College of Pharmacy, Ashta, Maharashtra, Walwa, Sangli 416301, India
| | - S.K. Mohite
- Department of Pharmaceutical Chemistry, Rajarambapu College of Pharmacy, Kasegaon, Sangli, Maharashtra 415409, India
| | - Saad Alobid
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - M.G. Saralaya
- Annasaheb Dange College of Pharmacy, Ashta, Maharashtra, Walwa, Sangli 416301, India
| | - Ashwini S Patil
- Annasaheb Dange College of Pharmacy, Ashta, Maharashtra, Walwa, Sangli 416301, India
| | - Kuntal Das
- Department of Pharmacognosy, Mallige College of Pharmacy, #71 Silvepura Chikkabanavara Post, Bangalore 90, India
| | - Moneer E. Almadani
- Department of Clinical Medicine, College of Medicine, AlMaarefa University, Dariyah, Riyadh 13713, Saudi Arabia
| | - Syed Arif Hussain
- Respiratory Care Department, College of Applied Sciences, AlMaarefa University, Dariyah 13713, Riyadh, Saudi Arabia
| | - Bader Hussain Alamer
- Department of Emergency Medical Services, College of Applied Sciences, AlMaarefa University, Riyadh, Saudi Arabia
| | - Ebtesam Abdulrahman Jibreel
- Department of Nursing, College of Applied Sciences, AlMaarefa University, Dariyah 13713, Riyadh, Saudi Arabia
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Wang F, Wen M, Zhou B. Exploring details about structure requirements based on antioxidant tripeptide derived from β-Lactoglobulin by in silico approaches. Amino Acids 2023; 55:1909-1922. [PMID: 37917178 DOI: 10.1007/s00726-023-03350-w] [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: 05/23/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023]
Abstract
β-Lactoglobulin is one of the proteins in milk possessing antioxidant activity. The peptides derived from β-Lactoglobulin exhibit higher antioxidant activities than the most commonly used antioxidant. Furthermore, the detailed structure-activity relationship of these antioxidant peptides has not been elucidated. Therefore, in the present work, two-dimensional quantitative structure-activity relationship (2D-QSAR) and three-dimensional quantitative structure-activity relationship (3D-QSAR) models were constructed to investigate the structural factors affecting activities and gave information for the rational design of novel antioxidant peptides. After calculation and screening of molecular descriptors, linear and nonlinear models were developed by multiple linear regression (MLR), partial least squares regression (PLSR) and support vector machines (SVM) approaches. The statistical parameters are as follows: R2 = 0.643, Q2 = 0.553/MLR, R2 = 0.612, Q2 = 0.5278/PLSR, R2 = 0.7085, Q2 = 0.6887/SVM, indicating that the SVM model is superior to the MLR and PLSR models. In addition, in the 3D-QSAR models, the Dragon-CoMFA (R2cv = 0.537, R2pred = 0.5201) and Dragon-CoMSIA (R2cv = 0.665, R2pred = 0.6489) methods were conducted to predict the antioxidant activities. Comparison of statistical parameters illustrates that the suitability of Dragon-CoMSIA is superior to the Dragon-CoMFA model. The results show the robustness and excellent prediction of the proposed models, and would be applied for modifying and designing novel and potent antioxidant peptides.
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Affiliation(s)
- Fangfang Wang
- School of Life Science, Linyi University, Linyi, 276000, China.
| | - Menghao Wen
- School of Life Science, Linyi University, Linyi, 276000, China
| | - Bo Zhou
- State Key Laboratory of Functions and Applications of Medicinal Plants, College of Basic Medical, Guizhou Medical University, Guizhou, 550004, China
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Zhang Z, Luo Z, Sun Y, Deng D, Su K, Li J, Yan Z, Wang X, Cao J, Zheng W, Ang S, Feng Y, Zhang K, Ma H, Wu P. Discovery of novel cannabidiol derivatives with augmented antibacterial agents against methicillin-resistant Staphylococcus aureus. Bioorg Chem 2023; 141:106911. [PMID: 37832223 DOI: 10.1016/j.bioorg.2023.106911] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023]
Abstract
Drug-resistant bacterium infections are a severe threat to public health and novel antimicrobial agents combating drug-resistant bacteria are an unmet medical need. Although cannabidiol (CBD) has been reported to show antibacterial effects, whether its antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) can be improved remains unclear. Herein, a series of novel CBD derivatives were designed and synthesized using various chemical approaches including amidation, Friedel-Crafts alkylation, and Negishi cross-coupling reaction for the modifications at the C-7, C-2', C-4', and C-6' positions of CBD skeleton. Derivative 21f showed augmented antibacterial activity against MRSA with a minimum inhibitory concentration of 4 μM without cytotoxic effect in microglia BV2 cells. Further mechanistic studies suggested that 21f inhibited the formation of biofilms, induced excess reactive oxygen species, and reduced bacterial metabolism, which collectively led to the acceleration of bacterial death. Findings from this study expand the understanding of CBD derivatives as promising antibacterial agents, which provides useful information for the development of cannabinoid-based antibacterial agents.
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Affiliation(s)
- Zhen Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Zhujun Luo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Ying Sun
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Duanyu Deng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Kaize Su
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Jinxuan Li
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Zhenping Yan
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Xu Wang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Jifan Cao
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Wende Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Song Ang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Yanxian Feng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China.
| | - Hang Ma
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, USA; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China.
| | - Panpan Wu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China; International Healthcare Innovation Institute (Jiangmen), Jiangmen 529040, PR China; Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, PR China.
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Jalali Z, Nejad Ebrahimi S, Rezadoost H. Identifying natural products for gastric cancer treatment through pharmacophore creation, 3D QSAR, virtual screening, and molecular dynamics studies. Daru 2023; 31:243-258. [PMID: 37733194 PMCID: PMC10624797 DOI: 10.1007/s40199-023-00480-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Gastric cancer (GC) is known as the fourth leading cause of cancer-related death and the fifth major cancer in the world, and this is a serious threat to general health all over the world. The lack of early detection markers results in a belated diagnosis, i.e. the final stages, which could be associated with the ineffectiveness of the treatment strategies, and naturally, it leads to poor prognosis. Even though a variety of treatments have been developed, there is a trend of studying traditional medicinal plants, due to the worrying side effect of drugs available in the market. METHODS In this study, pharmacophore generation and 3D-QSAR model were created using 50 compounds with anti-gastric cancer activity (with IC50 had been reported in the previous studies). RESULTS Based on three of the best pharmacophoric hypotheses, virtual screening was performed to discover the top anti-gastric cancer compounds from a database of 183,885 compounds. The selected compounds were used for molecular docking with three protein receptors 7BKG, 4F5B, and 4ZT1 to investigate the intermolecular interactions between these ligands and receptors. Finally, 21 lead compounds with the highest amount of docking score ranging from - 13.366 to -6.404 kcal/mol were selected, and then the ADME/Tox properties of these compounds were calculated. All these compounds have a fitness score above 1.8, a molecular weight of less than 500 g/mol, hydrogen bond donors up to 3, hydrogen bond acceptors up to 8.50, and logP of 1.013 to 4.174. Finally, molecular dynamic simulations for top-scoring ligand-receptor complexes were investigated. CONCLUSION These selected lead compounds have the most anti-gastric cancer effects among the 183,885 compounds in the database. Therefore, lead compounds might be considered for gastric cancer therapy in future studies.
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Affiliation(s)
- Zeinab Jalali
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, 1983963113, Tehran, Iran
| | - Samad Nejad Ebrahimi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, 1983963113, Tehran, Iran.
| | - Hassan Rezadoost
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Evin, 1983963113, Tehran, Iran
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Huang BB, Gao MW, Li G, Ouyang MA, Chen QJ. Design, Synthesis, Structure-Activity Relationship, and Three-Dimensional Quantitative Structure-Activity Relationship of Fusarium Acid Derivatives and Analogues as Potential Fungicides. J Agric Food Chem 2023; 71:18566-18577. [PMID: 37971433 DOI: 10.1021/acs.jafc.3c04720] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
In research related to fungicides, the development of compounds from natural products with high antifungal activity has attracted considerable attention. Fusaric acid (FA), an alkaloid isolated from the metabolites of Fusarium oxysporum, is an important precursor for developing pharmacologically active herbicides. In our previous work, we reported that FA has a wide range of inhibitory activities against 14 plant pathogenic fungi. In particular, it exhibited excellent antifugal effects on Colletotrichum higginsianum (EC50 = 31.7 μg/mL). Herein, to explore the practical application in the agricultural field, the design and synthesis of three series of FA derivatives and their inhibitory activities against plant pathogenic fungi were examined. Results demonstrated that the optimized FA derivatives had excellent inhibitory activities against C. higginsianum, Helminthosporium (Harpophora maydis), and Pyricularia grisea. In particular, the inhibitory activities were considerably improved when the 5-butyl groups of FA were substituted. The EC50 of C. higginsianum and P. grisea was only 1.2 and 12.0 μg/mL when 5-butylalkyl groups were substituted with 5-([1,1'-biphenyl]-4-yl) and 5-phenyl, respectively. Moreover, the safety index of target compounds, which was obtained from the treatment index of medicines, on rice seeds was evaluated. Finally, 16 leading compounds (H4, H22-H24, H27, H29, H30-H34, H37, H45, H50, H52, and H53) were obtained; they had considerable potential for additional modification and optimization as agricultural fungicides. Moreover, three-dimensional quantitative structure-activity relationship models were developed for obtaining a systematic structure-activity relationship profile to explore the possibility of more potent FA derivatives as novel fungicides.
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Affiliation(s)
- Bin Bin Huang
- Key Laboratory of Biopesticide and Chemical Biology (Ministry of Education), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Ming Wei Gao
- Key Laboratory of Biopesticide and Chemical Biology (Ministry of Education), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Guo Li
- Key Laboratory of Biopesticide and Chemical Biology (Ministry of Education), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Ming-An Ouyang
- Key Laboratory of Biopesticide and Chemical Biology (Ministry of Education), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
| | - Qi-Jian Chen
- Key Laboratory of Biopesticide and Chemical Biology (Ministry of Education), Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, People's Republic of China
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Lian Z, Su K, Lu H, Qu C, Ma X. Combining Mendelian Randomization Analysis and 3D-QSAR to Investigate the Effectiveness of a New Series of Hydroxyquinolines in Osteoarthritis. Curr Med Chem 2023; 31:CMC-EPUB-136319. [PMID: 38385247 DOI: 10.2174/0109298673287134231121050158] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/04/2023] [Accepted: 11/12/2023] [Indexed: 02/23/2024]
Abstract
BACKGROUND Osteoarthritis (OA) represents a persistent degenerative joint ailment. As OA advances, profound joint pain coupled with diminished joint function inflicts substantial physical distress and psychological strain on patients. Presently, pharmacological solutions for arthritis remain limited, primarily encompassing analgesics and joint replacement surgical procedures. Hence, non-operative strategies to mitigate osteoarthritis progression have captured significant attention in orthopedic research. OBJECTIVE This study aims to discern a definitive causal linkage between ADAMTS-4/5 and osteoarthritis through Mendelian randomization analysis. Moreover, it seeks to anticipate the therapeutic efficacy of a suite of emergent hydroxyquinolines for osteoarthritis using the Quantitative Structure-Activity Relationship (QSAR) methodology. METHODS Within this study, genetic variants specific to knee osteoarthritis were procured as exposure variables from a genome-wide association study (GWAS). Genetic variant data for ADAMTS-4/5 served as the endpoint to evaluate the causal nexus employing univariate Mendelian randomization. This analysis underpins the hypothesis that ADAMTS-4/5 presents a promising therapeutic target for osteoarthritis management. The suppressive properties of novel hydroxyquinolines against ADAMTS-4/5 were subsequently examined through conformational analyses, underscoring the potential of these compounds as therapeutic candidates for osteoarthritis. RESULTS IVW outcomes from the Mendelian randomization revealed a significant association of KOA (OR: 1.1675, 95% CI: 1.0003-1.3627, P = 0.0495) with ADAMTS-5. However, KOA (OR: 1.0801, 95% CI: 0.9256-1.2604, P = 0.3278) displayed no evident connection with ADAMTS-4. Notably, the instrumental variables manifested neither heterogeneity nor horizontal pleiotropy. In this research endeavor, 16 pharmacological models were formulated via the CoMSIA method within 3D conformational relationship evaluations. A synergistic interplay of hydrophobic, spatial, and hydrogen-bonded receptor domains emerged as the most predictively potent. The cross-validation coefficient q2 for the optimum model stood at 0.716, with a principal component score of 5, a regression coefficient r2 of 0.971, a standard estimation error of 0.351, and an f-value of 156.951. Such metrics intimate the commendable predictive prowess of our devised CoMSIA models. CONCLUSION The research unearthed a robust causal interrelation between ADAMTS-5 and osteoarthritis via Mendelian randomization. Furthermore, a credible drug model targeting ADAMTS-5 was constructed. Collectively, these findings illuminate a path forward in the pursuit of target-specific drugs for osteoarthritis management in subsequent investigations.
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Affiliation(s)
- Zheng Lian
- Affiliated Hospital of Qingdao University orthopedic surgery Qingdao China
| | - Kunpeng Su
- Affiliated Hospital of Qingdao University orthopedic surgery Qingdao China
| | - Hui Lu
- Affiliated Hospital of Qingdao University orthopedic surgery Qingdao China
| | - Changpeng Qu
- Affiliated Hospital of Qingdao University orthopedic surgery Qingdao China
| | - Xuexiao Ma
- Affiliated Hospital of Qingdao University orthopedic surgery Qingdao China
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González Y, Mojica-Flores R, Moreno-Labrador D, Pecchio M, Rao KSJ, Ahumedo-Monterrosa M, Fernández PL, Larionov OV, Lakey-Beitia J. Tetrahydrocurcumin Derivatives Enhanced the Anti-Inflammatory Activity of Curcumin: Synthesis, Biological Evaluation, and Structure-Activity Relationship Analysis. Molecules 2023; 28:7787. [PMID: 38067518 PMCID: PMC10708537 DOI: 10.3390/molecules28237787] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Tetrahydrocurcumin, the most abundant curcumin transformation product in biological systems, can potentially be a new alternative therapeutic agent with improved anti-inflammatory activity and higher bioavailability than curcumin. In this article, we describe the synthesis and evaluation of the anti-inflammatory activities of tetrahydrocurcumin derivatives. Eleven tetrahydrocurcumin derivatives were synthesized via Steglich esterification on both sides of the phenolic rings of tetrahydrocurcumin with the aim of improving the anti-inflammatory activity of this compound. We showed that tetrahydrocurcumin (2) inhibited TNF-α and IL-6 production but not PGE2 production. Three tetrahydrocurcumin derivatives inhibited TNF-α production, five inhibited IL-6 production, and three inhibited PGE2 production. The structure-activity relationship analysis suggested that two factors could contribute to the biological activities of these compounds: the presence or absence of planarity and their structural differences. Among the tetrahydrocurcumin derivatives, cyclic compound 13 was the most active in terms of TNF-α production, showing even better activity than tetrahydrocurcumin. Acyclic compound 11 was the most effective in terms of IL-6 production and retained the same effect as tetrahydrocurcumin. Moreover, acyclic compound 12 was the most active in terms of PGE2 production, displaying better inhibition than tetrahydrocurcumin. A 3D-QSAR analysis suggested that the anti-inflammatory activities of tetrahydrocurcumin derivatives could be increased by adding bulky groups at the ends of compounds 2, 11, and 12.
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Affiliation(s)
- Yisett González
- Center for Molecular and Cellular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama City 0843-01103, Panama; (Y.G.); (D.M.-L.); (P.L.F.)
- Sistema Nacional de Investigación (SNI), SENACYT, Panama City 0816-02852, Panama
| | - Randy Mojica-Flores
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama City 0843-01103, Panama;
| | - Dilan Moreno-Labrador
- Center for Molecular and Cellular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama City 0843-01103, Panama; (Y.G.); (D.M.-L.); (P.L.F.)
| | - Marisín Pecchio
- Center for Academic Affairs and Collaboration, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama City 0843-01103, Panama;
| | - K. S. Jagannatha Rao
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation (KLEF) Deemed to be University, Vaddeswaram 522 302, India;
| | - Maicol Ahumedo-Monterrosa
- Natural Products Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, Cartagena 130015, Colombia;
| | - Patricia L. Fernández
- Center for Molecular and Cellular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama City 0843-01103, Panama; (Y.G.); (D.M.-L.); (P.L.F.)
- Sistema Nacional de Investigación (SNI), SENACYT, Panama City 0816-02852, Panama
| | - Oleg V. Larionov
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Johant Lakey-Beitia
- Sistema Nacional de Investigación (SNI), SENACYT, Panama City 0816-02852, Panama
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Clayton, City of Knowledge, Panama City 0843-01103, Panama;
- Department of Chemistry, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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Andrades-Lagos J, Campanini-Salinas J, Sabadini G, Andrade V, Mella J, Vásquez-Velásquez D. QSAR Studies, Synthesis, and Biological Evaluation of New Pyrimido-Isoquinolin-Quinone Derivatives against Methicillin-Resistant Staphylococcus aureus. Pharmaceuticals (Basel) 2023; 16:1621. [PMID: 38004487 PMCID: PMC10675065 DOI: 10.3390/ph16111621] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
According to the WHO, antimicrobial resistance is among the top 10 threats to global health. Due to increased resistance rates, an increase in the mortality and morbidity of patients has been observed, with projections of more than 10 million deaths associated with infections caused by antibacterial resistant microorganisms. Our research group has developed a new family of pyrimido-isoquinolin-quinones showing antibacterial activities against multidrug-resistant Staphylococcus aureus. We have developed 3D-QSAR CoMFA and CoMSIA studies (r2 = 0.938; 0.895), from which 13 new derivatives were designed and synthesized. The compounds were tested in antibacterial assays against methicillin-resistant Staphylococcus aureus and other bacterial pathogens. There were 12 synthesized compounds active against Gram-positive pathogens in concentrations ranging from 2 to 32 µg/mL. The antibacterial activity of the derivatives is explained by the steric, electronic, and hydrogen-bond acceptor properties of the compounds.
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Affiliation(s)
- Juan Andrades-Lagos
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile;
- Drug Development Laboratory, Faculty of Chemical and Pharmaceutical, Sciences, Universidad de Chile, Santiago 8380492, Chile
| | - Javier Campanini-Salinas
- Drug Development Laboratory, Faculty of Chemical and Pharmaceutical, Sciences, Universidad de Chile, Santiago 8380492, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Puerto Montt 5501842, Chile
| | - Gianfranco Sabadini
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile;
- Centro de Investigación Farmacopea Chilena, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2360102, Chile
| | - Victor Andrade
- Laboratory of Neuroscience and Functional Medicine, International Center for Biomedicine, Faculty of Sciences, University of Chile, Santiago 7800003, Chile;
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Cologne, 50923 Köln, Germany
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany
| | - Jaime Mella
- Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Av. Gran Bretaña 1111, Valparaíso 2360102, Chile;
- Centro de Investigación Farmacopea Chilena, Facultad de Farmacia, Universidad de Valparaíso, Av. Gran Bretaña 1093, Valparaíso 2360102, Chile
| | - David Vásquez-Velásquez
- Drug Development Laboratory, Faculty of Chemical and Pharmaceutical, Sciences, Universidad de Chile, Santiago 8380492, Chile
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Abd El-Karim SS, Anwar MM, Ahmed NS, Syam YM, Elseginy SA, Aly HF, Younis EA, Khalil WKB, Ahmed KA, Mohammed FF, Rizk M. Discovery of novel benzofuran-based derivatives as acetylcholinesterase inhibitors for the treatment of Alzheimer's disease: Design, synthesis, biological evaluation, molecular docking and 3D-QSAR investigation. Eur J Med Chem 2023; 260:115766. [PMID: 37678141 DOI: 10.1016/j.ejmech.2023.115766] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
A series of novel benzofuran-based compounds 7a-s were designed, synthesized, and investigated in vitro as acetylcholinesterase inhibitors (AChEIs). Compounds 7c and 7e displayed promising inhibitory activity with IC50 values of 0.058 and 0.086 μM in comparison to donepezil with an IC50 value of 0.049 μM. The new molecules' antioxidant evaluation revealed that 7c, 7e, 7j, 7n, and 7q produced the strongest DPPH scavenging activity when compared to vitamin C. As it was the most promising AChEI, compound 7c was selected for further biological evaluation. Acute and chronic toxicity studies exhibited that 7c showed no signs of toxicity or adverse events, no significant differences in the blood profile, and an insignificant difference in hepatic enzymes, glucose, urea, creatinine, and albumin levels in the experimental rat group. Furthermore, 7c did not produce histopathological damage to normal liver, kidney, heart, and brain tissues, ameliorated tissue malonaldehyde (MDA) and glutathione (GSH) levels and reduced the expression levels of the APP and Tau genes in AD rats. Molecular docking results of compounds 7c and 7e showed good binding modes in the active site of the acetylcholinesterase enzyme, which are similar to the native ligand donepezil. 3D-QSAR analysis revealed the importance of the alkyl group in positions 2 and 3 of the phenyl moiety for the activity. Overall, these findings suggested that compound 7c could be deemed a promising candidate for the management of Alzheimer's disease.
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Affiliation(s)
- Somaia S Abd El-Karim
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt.
| | - Manal M Anwar
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt.
| | - Nesreen S Ahmed
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Yasmin M Syam
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Samia A Elseginy
- Green Chemistry Department, Chemical Industries Research Division, National Research Centre, P. O. Box 12622, El-Bohouth St, Dokki, Cairo, Egypt
| | - Hanan F Aly
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Eman A Younis
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
| | - Wagdy K B Khalil
- Department of Cell Biology, National Research Centre, P.O. Box 12262 El-Bohouth St, Dokki, Cairo, Egypt
| | - Kawkab A Ahmed
- Pathology Departments, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Faten F Mohammed
- Pathology Departments, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Maha Rizk
- Department of Therapeutic Chemistry, National Research Centre, P.O. Box 12262 El-Bohouth St, Cairo, Egypt
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Trigui E, Ben Hassen H, Zaghden H, Trigui M, Achour S. A Bioinformatic Study on the Potential Anti-Vitiligo Activity of a Carpobrotus edulis Compound. Molecules 2023; 28:7545. [PMID: 38005266 PMCID: PMC10673461 DOI: 10.3390/molecules28227545] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
The plant Carpobrotus edulis has traditionally been known for its wide applications in diseases, especially vitiligo, which is characterized by patches and white macules caused by the loss of melanocytes. One of the chemical treatments for vitiligo consists mainly of skin repigmentation and usually leads to a non-durable effect by inhibiting the Janus kinase (JAK) signal transduction (STAT pathway). JAK inhibitors generally block multiple JAK tyrosine kinases, which leads to secondary effects. In this study, natural molecules from Carpobrotus edulis were extracted and tested using a structure-based drug-design approach and pharmacophore modeling. The best-fit candidate from the extracted molecules was compared to the chemical molecules used. The results indicated a similarity between the chemical and natural ligands which suggested the potential use of the natural product against vitiligo. The main finding of this research work was the discovery of a new molecule extracted from a natural plant and the detection of its anti-vitiligo activity using an in-silico approach. This method can significantly reduce the cost of searching for potential medicinal molecules.
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Affiliation(s)
- Emna Trigui
- Laboratory of Bioressources, Integrative Biology & Valorisation (BIOLIVAL), Higher Institute of Biotechnology of Monastir, Monastir University, Monastir 5000, Tunisia; (E.T.); (M.T.); (S.A.)
| | - Hanen Ben Hassen
- Laboratory of Probabilities and Statistics, Faculty of Sciences of Sfax, Sfax University, Sfax 3000, Tunisia
| | - Hatem Zaghden
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj-Cédria, Hammam-Lif 2050, Tunisia
| | - Maher Trigui
- Laboratory of Bioressources, Integrative Biology & Valorisation (BIOLIVAL), Higher Institute of Biotechnology of Monastir, Monastir University, Monastir 5000, Tunisia; (E.T.); (M.T.); (S.A.)
| | - Sami Achour
- Laboratory of Bioressources, Integrative Biology & Valorisation (BIOLIVAL), Higher Institute of Biotechnology of Monastir, Monastir University, Monastir 5000, Tunisia; (E.T.); (M.T.); (S.A.)
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Wu J, Li P, Chen X, Liu R, Mu Y, Shen Y, Cheng X, Shu M, Bai Y. Structural optimization of pyrrolopyrimidine BTK inhibitors based on molecular simulation. J Mol Model 2023; 29:367. [PMID: 37950076 DOI: 10.1007/s00894-023-05744-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT BTK is a critical regulator involved in the proliferation, differentiation, and apoptosis of B cells. BTK inhibitors can effectively alleviate various diseases such as tumors, leukemia, and asthma. During this study, a range of novel BTK inhibitors were designed using 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation. METHODS We selected 41 pyrrolopyrimidine derivatives as BTK inhibitors to structure a 3D-QSAR model. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were adopted to research the connection between the pharmacological activities and chemical structures of the compounds. The CoMFA model (q2 = 0.519, R2 = 0.971), CoMSIA model (q2 = 0.512, R2 = 0.990), and external validation demonstrated excellent predictive performance and reliability of the 3D-QSAR model. We designed eight novel molecules with higher inhibitory activities according to the three-dimensional equipotential fields and explored the interactions between the compounds and BTK by molecular docking, which showed that the novel molecules had higher binding affinities with BTK than the template molecule 18. Then, the results of molecular docking were further verified by MD simulation, which showed that amino acid residues such as Leu528, Val416, and Met477 played vital parts in the interaction, and the binding free energy analysis showed that the novel molecules had higher stability with BTK. Finally, the ADME/T properties were predicted for all of the novel compounds, and the results showed that the majority of them had favorable pharmacokinetic properties. Therefore, this study provides strong support for the development of novel BTK inhibitors.
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Affiliation(s)
- Jinping Wu
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China
| | - Peng Li
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China
| | - Xiaodie Chen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Rong Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Yucheng Mu
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Xilan Cheng
- Pharmacy Department, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Yixiao Bai
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China.
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Yu Z, Huang Y, Cheng J, Li K, Hong Z, Ren J, Yuan H, Tang L, Wang Z, Fan Z. 3D-QSAR Combination with Molecular Dynamics Simulations to Effectively Design the Active Ryanodine Receptor Agonists against Spodoptera frugiperda. J Agric Food Chem 2023; 71:16504-16520. [PMID: 37902622 DOI: 10.1021/acs.jafc.3c05223] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Computer-aided molecular modeling was applied to design a series of Spodoptera frugiperda RyR agonists. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. MD simulations in the complex with S. frugiperda native, mutant RyR, and mammalian RyR1 under physiological conditions were used to validate the detailed binding mechanism. Binding free energy calculation by molecular mechanics generalized surface area (MM-GBSA) explained the role of key amino acid residues in ligand-receptor binding. Therefore, 14 new compounds were effectively designed and synthesized, and a bioassay indicated that compounds A-2 and A-3 showed comparable activity to that of chloranthraniliprole with LC50 values of 0.27, 0.18, and 0.20 mg L-1, respectively, against S. frugiperda. Most target compounds also displayed good activity against Mythinma separata at 0.1 mg L-1. Molecular docking and MM-GBSA calculations demonstrated that A-3 had a better binding capacity with native and mutant S. frugiperda RyRs.
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Affiliation(s)
- Zhenwu Yu
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Yuting Huang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, People's Republic of China
| | - Kun Li
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Zeyu Hong
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Jinzhou Ren
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Haolin Yuan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Liangfu Tang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Zhihong Wang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
- Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, People's Republic of China
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Kammari K, Devaraya K, Swain S, Kondapi AK. The topoisomerase II β -kinase associated with HIV-1 is a potential target for pyridine-bischalcones' anti-HIV-1 activity. Eur J Med Chem 2023; 259:115623. [PMID: 37473689 DOI: 10.1016/j.ejmech.2023.115623] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
Topoisomerase II (TopoII) is a critical component of HIV-1 integration, proviral DNA synthesis, and reverse transcription. During HIV-1 infection, the TopoIIβkinase (TopoIIβKHIV-1) phosphorylates TopoIIβ. Our earlier research demonstrated that the pyridine scaffold has potent anti-HIV-1 activity by specifically inhibiting TopoIIβKHIV-1 activity. 3D QSAR results showed the presence of molecular features for interaction with TopoIIβKHIV-1 requiring chemically induced proximity for potential interaction. In this study, the chalcone and methyl groups were added to the pyridine scaffold's core to achieve the desired proximity length between the pyridine scaffold and charged centers, which resulted in an inhibitory activity against TopoIIβKHIV-1 and viral replication. According to the findings, the TopoIIβKHIV-1activity was inhibited by the inclusion of the pyridine scaffold with the chalcone group, leading to better anti-HIV-1 activity. The water-soluble methylated pyridinium chalcones' showed significant TopoIIβKHIV-1 antagonism, anti-HIV-1 activity (from IC50 > 500 nM to ID50 25 nM), and reduced cytotoxicity (CC50 = 2 mM). These activities could be associated with the charge on the pyridine and extended proximity. Therefore, it is clear that within the scope of this work, altering the proximity length and charge centers of pyridine molecules are critical for the design and development of effective anti-HIV-1 leads, specifically targeting TopoIIβKHIV-1.
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Affiliation(s)
- Kurumurthy Kammari
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, India
| | - Kiran Devaraya
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, India
| | - Sarita Swain
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, India
| | - Anand K Kondapi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, India.
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Chen S, Wang S, Zheng J, Lu H, Chen H, Tang Y, Wang N, Zhu Y, Wang Y, Duan P, Ge RS. Bisphenol analogues inhibit human and rat 17β-hydroxysteroid dehydrogenase 1: 3D-quantitative structure-activity relationship ( 3D-QSAR) and in silico docking analysis. Food Chem Toxicol 2023; 181:114052. [PMID: 37758047 DOI: 10.1016/j.fct.2023.114052] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 10/02/2023]
Abstract
Bisphenols, estrogenic endocrine-disrupting chemicals, disrupt at least one of three endocrine pathways (estrogen, androgen, and thyroid). 17β-Hydroxysteroid dehydrogenase 1 (17β-HSD1) is a steroidogenic enzyme that catalyzes the activation of estradiol from estrone in human placenta and rat ovary. However, whether bisphenols inhibit 17β-HSD1 and the mode of action remains unclear. This study we screened 17 bisphenols for inhibiting human 17β-HSD1 in placental microsomes and rat 17β-HSD1 in ovarian microsomes and determined 3D-quantitative structure-activity relationship (3D-QSAR) and mode of action. We observed some bisphenols with substituents were found to significantly inhibit both human and rat 17β-HSD1 with the most potent inhibition on human enzyme by bisphenol H (IC50 = 0.90 μM) when compared to bisphenol A (IC50 = 113.38 μM). Rat enzyme was less sensitive to the inhibition of bisphenols than human enzyme with bisphenol H (IC50 = 32.94 μM) for rat enzyme. We observed an inverse correlation between IC50 and hydrophobicity (expressed as Log P). Docking analysis showed that they bound steroid-binding site of 17β-HSD1. The 3D-QSAR models demonstrated that hydrophobic region, hydrophobic aromatic, ring aromatic, and hydrogen bond acceptor are key factors for the inhibition of steroid synthesis activity of 17β-HSD1.
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Affiliation(s)
- Sailing Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Shaowei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Jingyi Zheng
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Han Lu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Huiqian Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Yunbing Tang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Nan Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Yang Zhu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Yiyan Wang
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Ping Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
| | - Ren-Shan Ge
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China; Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital and Yuying Children's Hospital, Key Laboratory of Pediatric Anesthesiology, Ministry of Education, Key Laboratory of Anesthesiology of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province and Key Laboratory of Male Health and Environment of Wenzhou, 325000, Zhejiang Province, China.
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49
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Hadni H, Elhallaoui M. Discovery of anti-colon cancer agents targeting wild-type and mutant p53 using computer-aided drug design. J Biomol Struct Dyn 2023; 41:10171-10189. [PMID: 36533393 DOI: 10.1080/07391102.2022.2153919] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Mutations in the p53 gene are common and occur in over 50% of all cancers, as it is involved in DNA damage repair, cell cycle regulation and apoptosis. Moreover, the p53 gene is mutated in 70% of colon cancers. Therefore, the development of drugs to combat this mutation requires urgent attention. With this in mind, in silico drug design approaches were applied on quinoline derivatives with anticancer activity. In 3D-QSAR study, steric, electrostatic, hydrophobic and H-bond acceptor fields (SEHA) play an important role in prediction and design of new colon cancer compounds. Indeed, the two best CoMSIA/SEHA models with (Q2 = 0.737, R2 = 0.914, R pred 2 = 0.720) and (Q2 = 0.738, R2 = 0.919, R pred 2 = 0.739) show good prediction of human colon carcinoma HCT 116 (p53+/+) and (p53-/-) activities, respectively. Furthermore, the predictive ability and robustness of these models were tested by several validation methods. Molecular docking analyses reveal crucial interactions with the active sites of the p53 protein in both wild type and mutant. Based on these theoretical studies, we designed 10 new compounds with good anticancer activity potential, which were evaluated using ADMET properties. Molecular dynamics simulations were performed to confirm the detailed binding mode of the docking results. Finally, the MM-GBSA based on molecular dynamics simulation confirmed that the designed compounds were able to form stable hydrogen bonding interactions with the crucial residues, which are essential to overcome the p53 mutation in colon cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hanine Hadni
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Menana Elhallaoui
- LIMAS, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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50
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Gautam P, Bisht P, Gautam A, Gupta GD, Singh R, Verma SK. A comprehension on structure guided alignment dependent 3D-QSAR modelling, and molecular dynamics simulation on 2,4-thiazolidinediones as aldose reductase inhibitors for the management of diabetic complications. J Biomol Struct Dyn 2023:1-20. [PMID: 37904329 DOI: 10.1080/07391102.2023.2275190] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023]
Abstract
Aldose reductase is an oxo-reductase enzyme belonging to the aldo-keto reductase class. Compounds having thiazolidine-2,4-dione scaffold are reported as potential aldose reductase inhibitors for diabetic complications. The present work uses structure-guided alignment-dependent Gaussian field- and atom-based 3D-QSAR on a dataset of 84 molecules. 3D-QSAR studies on two sets of dataset alignment have been carried out to understand the favourable and unfavourable structural features influencing the affinity of these inhibitors towards the enzyme. Using common pharmacophore hypotheses, the five-point pharmacophores for aldose reductase favourable features were generated. The molecular dynamics simulations (up to 100 ns) were performed for the potent molecule from each alignment set (compounds 24 and 65) compared to reference standard tolrestat and epalrestat to study target-ligand complexes' binding energy and stability. Compound 65 was most stable with better interactions in the aldose reductase binding pocket than tolrestat. The MM-PBSA study suggests compound 65 possessed better binding energy than reference standard tolrestat, i.e. -87.437 ± 19.728 and -73.424 ± 12.502 kJ/mol, respectively. The generated 3D-QSAR models provide information about structure-activity relationships and ligand-target binding energy. Target-specific stability data from MD simulation would be helpful for rational compound design with better aldose reductase activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyadarshi Gautam
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Priya Bisht
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | | | - Rajveer Singh
- Department of Pharmacognosy, ISF College of Pharmacy, Moga, India
| | - Sant Kumar Verma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
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