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Elshibani FA, Alamami AD, Mohammed HA, Rasheed RA, El Sabban RM, Yehia MA, Abdel Mageed SS, Majrashi TA, Elkaeed EB, El Hassab MA, Eldehna WM, El-Ashrey MK. A multidisciplinary approach to the antioxidant and hepatoprotective activities of Arbutus pavarii Pampan fruit; in vitro and in Vivo biological evaluations, and in silico investigations. J Enzyme Inhib Med Chem 2024; 39:2293639. [PMID: 38153110 PMCID: PMC10763860 DOI: 10.1080/14756366.2023.2293639] [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: 09/07/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023] Open
Abstract
The Libyan Strawberry, Arbutus pavarii Pampan (ARB), is an endemic Jebel Akhdar plant used for traditional medicine. This study presents the antioxidant and hepatoprotective properties of ARB fruit-extract. ARB phytochemical analysis indicated the presence of 354.54 GAE and 36.2 RE of the phenolics and flavonoids. LC-MS analysis identified 35 compounds belonging to phenolic acids, procyanidins, and flavonoid glycosides. Gallic acid, procyanidin dimer B3, β-type procyanidin trimer C, and quercetin-3-O-glucoside were the major constituents of the plant extract. ARB administration to paracetamol (PAR)-intoxicated rats reduced serum ALT, AST, bilirubin, hepatic tissue MDA and proinflammatory markers; TNF-α and IL-6 with an increase in tissue GSH level and SOD activity. Histological and immunohistochemical studies revealed that ARB restored the liver histology and significantly reduced the tissue expression of caspase 3, IL-1B, and NF-KB in PAR-induced liver damage. Docking analysis disclosed good binding affinities of some compounds with XO, COX-1, 5-LOX, and PI3K.
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Affiliation(s)
- Fatma A. Elshibani
- Department of Pharmacognosy, Faculty of Pharmacy, University of Benghazi, Benghazi, Libya
| | - Abdullah D. Alamami
- Department of Basic Medical Science, Faculty of Pharmacy, University of Benghazi, Benghazi, Libya
| | - Hamdoon A. Mohammed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Qassim, Saudi Arabia
- Department of Pharmacognosy and Medicinal Plants, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Rabab Ahmed Rasheed
- Department of Medical Histology and Cell Biology, Faculty of Medicine, King Salman International University (KSIU), South Sinai, Egypt
| | - Radwa M. El Sabban
- Department of Anatomy, Faculty of Medicine, October 6 University, Giza, Egypt
| | - Mohamed A. Yehia
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, October 6 University, Giza, Egypt
| | - Sherif S. Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, Egypt
| | - Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Mohamed K. El-Ashrey
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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Liu H, Wei G, Wang T, Hou Y, Hou B, Li X, Wang C, Sun M, Su M, Guo Z, Wang L, Kang N, Li M, Jia Z. Angelica keiskei water extract Mitigates Age-Associated Physiological Decline in Mice. Redox Rep 2024; 29:2305036. [PMID: 38390941 PMCID: PMC10896161 DOI: 10.1080/13510002.2024.2305036] [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] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVE Angelica keiskei is a medicinal and edible plant that has been reported to possess potent antioxidant properties in several in vitro models, but its effectiveness on naturally aging organisms is still lacking. This study explores the antioxidant and health-promoting effects of Angelica keiskei in naturally aging mice. METHODS We treated 48-week-old mice with Angelica keiskei water extract (AKWE) 30 days, and measured indicators related to aging and antioxidants. In addition, we conducted network pharmacology analysis, component-target molecular docking, real-time PCR, and MTS assays to investigate relevant factors. RESULTS The results indicated that administration of AKWE to mice led to decrease blood glucose levels, improve muscle fiber structure, muscle strength, gait stability, and increase levels of glutathione and superoxide dismutase in serum. Additionally, it decreased pigmentation of the heart tissues. Angelica keiskei combats oxidative stress by regulating multiple redox signaling pathways, and its ingredients Coumarin and Flavonoids have the potential to bind to SIRT3 and SIRT5. CONCLUSIONS Our findings indicated the potential of Angelica keiskei as a safe and effective dietary supplement to combat aging and revealed the broad prospects of medicinal and edible plants for addressing aging and age-related chronic diseases.
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Affiliation(s)
- Huan Liu
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- Hebei Provincial Key Laboratory of Luobing, Shijiazhuang, People’s Republic of China
| | - Gang Wei
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- Hebei Provincial Key Laboratory of Luobing, Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Tongxing Wang
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Yunlong Hou
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Bin Hou
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
| | - Xiaoyan Li
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
| | - Chao Wang
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
| | - Mingzhe Sun
- College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, People’s Republic of China
| | - Min Su
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- Hebei Provincial Key Laboratory of Luobing, Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Zhifang Guo
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- Hebei Provincial Key Laboratory of Luobing, Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Lu Wang
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- Hebei Provincial Key Laboratory of Luobing, Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Ning Kang
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- Hebei Provincial Key Laboratory of Luobing, Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Mengnan Li
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
| | - Zhenhua Jia
- Key Laboratory of State Administration of TCM (Cardio-Cerebral Vessel Collateral Disease), Shijiazhuang, People’s Republic of China
- National Key Laboratory for Innovation and Transformation of Luobing Theory, Shijiazhuang, People’s Republic of China
- Hebei Academy of Integrated Traditional Chinese and Western Medicine, Shijiazhuang, People’s Republic of China
- High-Level TCM Key Disciplines of National Administration of Traditional Chinese, Shijiazhuang, People's Republic of China
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Wang C, Zhang Y, Yang S, Shi L, Xiu Y, Wu Y, Jiang H. 3-aryl-4-(3,4,5-trimethoxyphenyl)pyridines inhibit tubulin polymerisation and act as anticancer agents. J Enzyme Inhib Med Chem 2024; 39:2286939. [PMID: 38083880 DOI: 10.1080/14756366.2023.2286939] [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: 06/27/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
A series of cis-restricted 3-aryl-4-(3,4,5-trimethoxyphenyl)pyridines as novel tubulin polymerisation inhibitors was designed based on molecular docking. Compound 9p, exhibited potent antiproliferative activity against HeLa, MCF-7, and A549 cell lines. Mechanism studies indicated that 9p potently inhibited tubulin polymerisation and disrupted the microtubule dynamics of tubulin in HeLa cells. Moreover, 9p could cause G2/M phase cell cycle arrest and apoptosis in HeLa cells. In addition, the prediction of physicochemical properties disclosed that 9p conformed well to the Lipinski's rule of five. The initial results suggest that the 3-aryl-4-(3,4,5-trimethoxyphenyl)pyridines could serve as a promising scaffold for the development of novel anticancer drugs.
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Affiliation(s)
- Chao Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Yujing Zhang
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Shanbo Yang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Lingyu Shi
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Yutao Xiu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Yudong Wu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Hongfei Jiang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Qingdao Cancer Institute, Qingdao University, Qingdao, China
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Jiang L, Yang D, Zhang Z, Xu L, Jiang Q, Tong Y, Zheng L. Elucidating the role of Rhodiola rosea L. in sepsis-induced acute lung injury via network pharmacology: emphasis on inflammatory response, oxidative stress, and the PI3K-AKT pathway. Pharm Biol 2024; 62:272-284. [PMID: 38445620 PMCID: PMC10919309 DOI: 10.1080/13880209.2024.2319117] [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: 08/03/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024]
Abstract
CONTEXT Sepsis-induced acute lung injury (ALI) is associated with high morbidity and mortality. Rhodiola rosea L. (Crassulaceae) (RR) and its extracts have shown anti-inflammatory, antioxidant, immunomodulatory, and lung-protective effects. OBJECTIVE This study elucidates the molecular mechanisms of RR against sepsis-induced ALI. MATERIALS AND METHODS The pivotal targets of RR against sepsis-induced ALI and underlying mechanisms were revealed by network pharmacology and molecular docking. Human umbilical vein endothelial cells (HUVECs) were stimulated by 1 μg/mL lipopolysaccharide for 0.5 h and treated with 6.3, 12.5, 25, 50, 100, and 200 μg/mL RR for 24 h. Then, the lipopolysaccharide-stimulated HUVECs were subjected to cell counting kit-8 (CCK-8), enzyme-linked immunosorbent, apoptosis, and Western blot analyses. C57BL/6 mice were divided into sham, model, low-dose (40 mg/kg), mid-dose (80 mg/kg), and high-dose (160 mg/kg) RR groups. The mouse model was constructed through caecal ligation and puncture, and histological, apoptosis, and Western blot analyses were performed for further validation. RESULTS We identified six hub targets (MPO, HRAS, PPARG, FGF2, JUN, and IL6), and the PI3K-AKT pathway was the core pathway. CCK-8 assays showed that RR promoted the viability of the lipopolysaccharide-stimulated HUVECs [median effective dose (ED50) = 18.98 μg/mL]. Furthermore, RR inhibited inflammation, oxidative stress, cell apoptosis, and PI3K-AKT activation in lipopolysaccharide-stimulated HUVECs and ALI mice, which was consistent with the network pharmacology results. DISCUSSION AND CONCLUSION This study provides foundational knowledge of the effective components, potential targets, and molecular mechanisms of RR against ALI, which could be critical for developing targeted therapeutic strategies for sepsis-induced ALI.
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Affiliation(s)
- Lu Jiang
- Department of Emergency, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Dongdong Yang
- Department of Emergency, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Zhuoyi Zhang
- Department of Emergency, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Liying Xu
- Department of Emergency, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Qingyu Jiang
- Department of Emergency, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Yixin Tong
- Department of Emergency, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
| | - Lanzhi Zheng
- Department of Medical Administration, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
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Aly SH, Elissawy AM, El Hassab MA, Majrashi TA, Hassan FE, Elkaeed EB, Eldehna WM, Singab ANB. Comparative metabolic study of the chloroform fraction of three Cystoseira species based on UPLC/ESI/MS analysis and biological activities. J Enzyme Inhib Med Chem 2024; 39:2292482. [PMID: 38086785 DOI: 10.1080/14756366.2023.2292482] [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: 10/07/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
This study aims to investigate the phytoconstituents of the chloroform fraction of three Cystoseira spp. namely C. myrica, C. trinodis, and C. tamariscifolia using UPLC/ESI/MS technique. The results revealed the identification of 19, 20 and 11 metabolites in C. myrica, C. trinodis, and C. tamariscifolia, respectively mainly terpenoids, flavonoids, phenolic acids and fatty acids. Also, an in vitro antioxidant study using FRAP and DPPH assays was conducted where the chloroform fraction of C. trinodis displayed the highest antioxidant activity in both assays, which would be attributed to its highest total phenolics and total flavonoids. Besides, the investigation of COX-1, α-glucosidase and α-amylase inhibitory activities were performed. Regarding C. trinodis, it showed the strongest inhibitory activity towards COX-1. Moreover, it showed potent inhibitory activity towards α-glucosidase and α-amylase enzymes. According to the molecular docking studies, the major compounds characterised showed efficient binding to the active sites of the target enzymes.
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Affiliation(s)
- Shaza H Aly
- Department of Pharmacognosy, Badr University in Cairo (BUC), Badr City, Egypt
| | - Ahmed M Elissawy
- Department of Pharmacognosy, Ain-Shams University, Cairo, Egypt
- Centre of Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt
| | - Mahmoud A El Hassab
- Department of Medicinal Chemistry, King Salman International University (KSIU), South Sinai, Egypt
| | - Taghreed A Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Fatma E Hassan
- Department of Physiology, General Medicine Practice Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Medical Physiology Department, Kasr Alainy, Cairo University, Giza, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Wagdy M Eldehna
- Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Abdel Nasser B Singab
- Department of Pharmacognosy, Ain-Shams University, Cairo, Egypt
- Centre of Drug Discovery Research and Development, Ain Shams University, Cairo, Egypt
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Pan G, Chai L, Chen R, Yuan Q, Song Z, Feng W, Wei J, Yang Z, Zhang Y, Xie G, Yan A, Lv Q, Wang C, Zhao Y, Wang Y. Potential mechanism of Qinggong Shoutao pill alleviating age-associated memory decline based on integration strategy. Pharm Biol 2024; 62:105-119. [PMID: 38145345 PMCID: PMC10763866 DOI: 10.1080/13880209.2023.2291689] [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: 12/30/2022] [Accepted: 11/30/2023] [Indexed: 12/26/2023]
Abstract
CONTEXT Qinggong Shoutao Wan (QGSTW) is a pill used as a traditional medicine to treat age-associated memory decline (AAMI). However, its potential mechanisms are unclear. OBJECTIVE This study elucidates the possible mechanisms of QGSTW in treating AAMI. MATERIALS AND METHODS Network pharmacology and molecular docking approaches were utilized to identify the potential pathway by which QGSTW alleviates AAMI. C57BL/6J mice were divided randomly into control, model, and QGSTW groups. A mouse model of AAMI was established by d-galactose, and the pathways that QGSTW acts on to ameliorate AAMI were determined by ELISA, immunofluorescence staining and Western blotting after treatment with d-gal (100 mg/kg) and QGSTW (20 mL/kg) for 12 weeks. RESULTS Network pharmacology demonstrated that the targets of the active components were significantly enriched in the cAMP signaling pathway. AKT1, FOS, GRIN2B, and GRIN1 were the core target proteins. QGSTW treatment increased the discrimination index from -16.92 ± 7.06 to 23.88 ± 15.94% in the novel location test and from -19.54 ± 5.71 to 17.55 ± 6.73% in the novel object recognition test. ELISA showed that QGSTW could increase the levels of cAMP. Western blot analysis revealed that QGSTW could upregulate the expression of PKA, CREB, c-Fos, GluN1, GluA1, CaMKII-α, and SYN. Immunostaining revealed that the expression of SYN was decreased in the CA1 and DG. DISCUSSION AND CONCLUSIONS This study not only provides new insights into the mechanism of QGSTW in the treatment of AAMI but also provides important information and new research ideas for the discovery of traditional Chinese medicine compounds that can treat AAMI.
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Affiliation(s)
- Guiyun Pan
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lijuan Chai
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Rui Chen
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qing Yuan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihui Song
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wanying Feng
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jinna Wei
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihua Yang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuhang Zhang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Guinan Xie
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - An Yan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qingbo Lv
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Caijun Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yingqiang Zhao
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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Rajiv Gandhi G, Sharanya CS, Jayanandan A, Haridas M, Edwin Hillary V, Rajiv Gandhi S, Sridharan G, Sivasubramanian R, Silva Vasconcelos AB, Montalvão MM, Antony Ceasar S, Sousa NFD, Scotti L, Scotti MT, Gurgel RQ, Quintans-Júnior LJ. Multitargeted molecular docking and dynamics simulation studies of flavonoids and volatile components from the peel of Citrus sinensis L. (Osbeck) against specific tumor protein markers. J Biomol Struct Dyn 2024; 42:3051-3080. [PMID: 37203996 DOI: 10.1080/07391102.2023.2212062] [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: 10/14/2022] [Accepted: 05/01/2023] [Indexed: 05/20/2023]
Abstract
Citrus sinensis (L.) Osbeck (Rutaceae), commonly known as the sweet orange, is a popular and widely consumed fruit with several medicinal properties. The present study aimed to perform the in silico screening of 18 flavonoids and eight volatile components from the peel of C. sinensis against apoptotic and inflammatory proteins, metalloprotease, and tumor suppressor markers. Flavonoids obtained higher probabilities than volatile components against selected anti-cancer drug targets. Hence, the data from the binding energies against the essential apoptotic and cell proliferation proteins substantiate that they may be promising compounds in developing effective candidates to block cell growth, proliferation, and induced cell death by activating the apoptotic pathway. Further, the binding stability of the selected targets and the corresponding molecules were analyzed by 100 ns molecular dynamics (MD) simulations. Chlorogenic acid has the most binding affinity against the important anti-cancer targets iNOS, MMP-9, and p53. The congruent binding mode to different drug targets focused on cancer shown by chlorogenic acid suggests that it may be a compound with significant therapeutic potential. Moreover, the binding energy predictions indicated that the compound had stable electrostatic and van der Waal energies. Thus, our data reinforce the medicinal importance of flavonoids from C. sinensis and expand the need for more studies, seeking to optimize results and amplify the impacts of further in vitro and in vivo studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gopalsamy Rajiv Gandhi
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Chelankara Suresh Sharanya
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Abhithaj Jayanandan
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Thalassery, Kannur, India
| | - Madathilkovilakath Haridas
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Thalassery, Kannur, India
| | - Varghese Edwin Hillary
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Sathiyabama Rajiv Gandhi
- Laboratory of Neuroscience and Pharmacological Assays (LANEF), Department of Physiology (DFS), Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Gurunagarajan Sridharan
- Department of Biochemistry, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirapalli, India
| | - Rengaraju Sivasubramanian
- Department of Biochemistry, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirapalli, India
| | - Alan Bruno Silva Vasconcelos
- Postgraduate Program of Physiological Sciences (PROCFIS), Federal University of Sergipe (UFS), São Cristóvão, Sergipe, Brazil
| | - Monalisa Martins Montalvão
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Natália Ferreira de Sousa
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Ricardo Queiroz Gurgel
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Lucindo José Quintans-Júnior
- Laboratory of Neuroscience and Pharmacological Assays (LANEF), Department of Physiology (DFS), Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
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8
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Hang NT, Han DK, My TTK, Phuong NV. Investigation of the mechanism of action of chemical constituents of celery seed against gout disease using network pharmacology, molecular docking, and molecular dynamics simulations. J Biomol Struct Dyn 2024; 42:2834-2845. [PMID: 37203990 DOI: 10.1080/07391102.2023.2213337] [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: 12/26/2022] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Abstract
Celery (Apium graveolens L.) has long been considered as a potential herbal medicine for the prevention and treatment of gout. However, the relationship between the chemical constituents and pharmacological activities of this medicinal plant has not been fully investigated yet. Therefore, this study aims to apply network pharmacology, molecular docking and molecular dynamics to explore the relationship between the chemical constituents of celery seed and its biological effects in the treatment of gout. Network pharmacology was built and analyzed based on the data collected from GeneCards, OMIM databases and SwissTargetPrediction web server using Cytoscape 3.9.0 software. The GO and KEGG pathway analysis of the potential targets of celery seed related to gout disease was performed using the ShinyGO v0.75 app. Molecular docking and molecular dynamics were carried out using Autodock vina and NAMD 2.14 software, respectively. The network analysis identified 16 active compounds and thirteen key targets of celery seed in the treatment of gout. The GO analysis and the KEGG pathway enrichment analysis suggested that the mechanism of action of the chemical constituents of celery seed might be involved in several pathways, notably the PI3K-Akt signaling pathway, Ras signaling pathway, and HIF-1 signaling pathway, respectively. Molecular docking and molecular dynamics revealed that apiumetin might be an important chemical that plays a key role in the pharmacological effect of celery seed. These results might be useful to select the Q-markers to control the quality of the products from celery seeds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nguyen Thu Hang
- Department of Pharmacognosy, Faculty of Pharmacognosy and Traditional Medicine, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Do Khai Han
- Department of Pharmacognosy, Faculty of Pharmacognosy and Traditional Medicine, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Than Thi Kieu My
- Department of Pharmacognosy, Faculty of Pharmacognosy and Traditional Medicine, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Nguyen Van Phuong
- Department of Pharmacognosy, Faculty of Pharmacognosy and Traditional Medicine, Hanoi University of Pharmacy, Hanoi, Vietnam
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9
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Canales CSC, Pavan AR, Dos Santos JL, Pavan FR. In silico drug design strategies for discovering novel tuberculosis therapeutics. Expert Opin Drug Discov 2024; 19:471-491. [PMID: 38374606 DOI: 10.1080/17460441.2024.2319042] [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: 11/08/2023] [Accepted: 02/12/2024] [Indexed: 02/21/2024]
Abstract
INTRODUCTION Tuberculosis remains a significant concern in global public health due to its intricate biology and propensity for developing antibiotic resistance. Discovering new drugs is a protracted and expensive endeavor, often spanning over a decade and incurring costs in the billions. However, computer-aided drug design (CADD) has surfaced as a nimbler and more cost-effective alternative. CADD tools enable us to decipher the interactions between therapeutic targets and novel drugs, making them invaluable in the quest for new tuberculosis treatments. AREAS COVERED In this review, the authors explore recent advancements in tuberculosis drug discovery enabled by in silico tools. The main objectives of this review article are to highlight emerging drug candidates identified through in silico methods and to provide an update on the therapeutic targets associated with Mycobacterium tuberculosis. EXPERT OPINION These in silico methods have not only streamlined the drug discovery process but also opened up new horizons for finding novel drug candidates and repositioning existing ones. The continued advancements in these fields hold great promise for more efficient, ethical, and successful drug development in the future.
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Affiliation(s)
- Christian S Carnero Canales
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
- School of Pharmacy, biochemistry and biotechnology, Santa Maria Catholic University, Arequipa, Perú
| | - Aline Renata Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
| | | | - Fernando Rogério Pavan
- School of Pharmaceutical Science, São Paulo State University (UNESP), Araraquara, Brazil
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10
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Ma Y, Song Y, Wang J, Shi X, Yuan Z, Li S, Li H, Chen Z, Li S. Discovery of novel covalent inhibitors of DJ-1 through hybrid virtual screening. Future Med Chem 2024; 16:665-677. [PMID: 38390730 DOI: 10.4155/fmc-2023-0301] [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] [Indexed: 02/24/2024] Open
Abstract
Background: DJ-1 is a ubiquitously expressed protein with multiple functions. Its overexpression has been associated with the occurrence of several cancers, positioning DJ-1 as a promising therapeutic target for cancer treatment. Methods: To find novel inhibitors of DJ-1, we employed a hybrid virtual screening strategy that combines structure-based and ligand-based virtual screening on a comprehensive compound library. Results: In silico study identified six hit compounds as potential DJ-1 inhibitors that were assessed in vitro at the cellular level. Compound 797780-71-3 exhibited antiproliferation activity in ACHN cells with an IC50 value of 12.18 μM and was able to inhibit the Wnt signaling pathway. This study discovers a novel covalent inhibitor for DJ-1 and paves the way for further optimization.
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Affiliation(s)
- Yanyu Ma
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Yidan Song
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Junyi Wang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Xiayu Shi
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Shuang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
- Innovation Center for AI & Drug Discovery, East China Normal University, Shanghai, 200062, China
- Lingang Laboratory, Shanghai, 200031, China
| | - Zhuo Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
- Innovation Center for AI & Drug Discovery, East China Normal University, Shanghai, 200062, China
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11
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Khamlich J, Douiyeh I, Saih A, Moussamih S, Regragui A, Kettani A, Safi A. Molecular docking, pharmacokinetic prediction and molecular dynamics simulations of tankyrase inhibitor compounds with the protein glucokinase, induced in the development of diabetes. J Biomol Struct Dyn 2024; 42:2846-2858. [PMID: 37199320 DOI: 10.1080/07391102.2023.2214217] [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: 01/04/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
GCK is a protein that plays a crucial role in the sensing and regulation of glucose homeostasis, which associates it with disorders of carbohydrate metabolism and the development of several pathologies, including gestational diabetes. This makes GCK an important therapeutic target that has aroused the interest of researchers to discover GKA that are simultaneously effective in the long term and free of side effects. TNKS is a protein that interacts directly with GCK; recent studies have shown that it inhibits GCK action, which affects glucose detection and insulin secretion. This justifies our choice of TNKS inhibitors as ligands to test their effects on the GCK-TNKS complex. For this purpose, we investigated the interaction of the GCK-TNKS complex with 13 compounds (TNKS inhibitors and their analogues) using the molecular docking approach as a first step, after which the compounds that generated the best affinity scores were evaluated for drug similarity and pharmacokinetic properties. Subsequently, we selected the six compounds that generated high affinity and that were in accordance with the parameters of the drug rules as well as pharmacokinetic properties to ensure a molecular dynamics study. The results allowed us to favor the two compounds (XAV939 and IWR-1), knowing that even the tested compounds (TNKS 22, (2215914) and (46824343)) produced good results that can also be exploited. These results are therefore interesting and encouraging, and they can be exploited experimentally to discover a treatment for diabetes, including gestational diabetes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jihane Khamlich
- Laboratory Biochemistry Environment and Agri-food, Department of Biology, Faculty of Science and Technics Mohammedia, Hassan II University Casablanca, Casablanca, Morocco
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences, Ben M'Sik Hassan II University of Casablanca, Casablanca, Morocco
| | - Imane Douiyeh
- Laboratory Biochemistry Environment and Agri-food, Department of Biology, Faculty of Science and Technics Mohammedia, Hassan II University Casablanca, Casablanca, Morocco
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences, Ben M'Sik Hassan II University of Casablanca, Casablanca, Morocco
| | - Asmae Saih
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences, Ben M'Sik Hassan II University of Casablanca, Casablanca, Morocco
| | - Samya Moussamih
- Laboratory of Immunology and Biodiversity, Faculty of Sciences Ain chock, Hassan II University of Casablanca, Casablanca, Morocco
| | - Anas Regragui
- Faculty of Medicine and Pharmacy Casablanca (FMPC), Hassan II University, Casablanca, Morocco
| | - Anass Kettani
- Laboratory of Biology and Health, URAC 34, Faculty of Sciences, Ben M'Sik Hassan II University of Casablanca, Casablanca, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco & Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Amal Safi
- Laboratory Biochemistry Environment and Agri-food, Department of Biology, Faculty of Science and Technics Mohammedia, Hassan II University Casablanca, Casablanca, Morocco
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12
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Lakkadi A, Vuppala S, Nampally V, Kim J, Kim K, Jang J, Tigulla P. Development of novel chromones as antioxidant COX2 inhibitors: in vitro, QSAR, DFT, molecular docking, and molecular dynamics studies. J Biomol Struct Dyn 2024; 42:2793-2808. [PMID: 37184132 DOI: 10.1080/07391102.2023.2212785] [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: 01/19/2023] [Accepted: 04/20/2023] [Indexed: 05/16/2023]
Abstract
The chromone derivatives are playing a prominent role in many plant cycles, for instance, the regulation of growth, stimulation of oxygen uptake in plants, and essential food constituents with valuable pro-health properties. Determination of the antioxidant activity of these compounds is an interesting approach to drug design and development. The antioxidant activity of the novel fifteen chromone compounds was estimated by using a spectrophotometric Dichloro-5,6-dicyano 1,4-benzoquinone (DDQ) assay method and the mechanism of antioxidant activity was discussed based on the Density functional theory (DFT) calculations. The compounds showed significant antioxidant activity which was correlated to their molecular structure by considering various molecular descriptors. Further, by using regression analysis QSAR-modeled equation was proposed and it has shown a high correlation coefficient value (0.946. We perform molecular docking and molecular dynamics simulations against the cyclooxygenase (COX2) enzyme to investigate the molecule's anti-inflammatory activity and stability of protein-ligand complexes. Molecular docking and dynamics simulations revealed the compounds B3 and B8 were interacting with essential residues TYR385, HIS386, ASN382, TRP387, and HIS388 in the binding site that were crucial for optimizing heme and the resultant peroxidase and cyclooxygenase activities. The root mean square displacement and root mean square fluctuation plots revealed the stability of the B3-COX2 and B8-COX2 complexes. Based on our results, B3 and B8 compounds are considered as best antioxidants as well as COX2 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arunapriya Lakkadi
- Department of Chemistry, Bhavan's Vivekananda College of Science, Humanities & Commerce, Sainikpuri, Secunderabad, India
| | - Srimai Vuppala
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
| | | | - Jaeyoung Kim
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
| | - Kiduk Kim
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
| | - Joonkyung Jang
- Department of Nanoenergy Engineering, Pusan National University, Busan, Republic of Korea
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13
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Soylu-Eter Ö, Özsoy N, Karalı N. Synthesis and molecular docking studies of 5-trifluoromethoxy-2-indolinones as cholinesterase dual inhibitors. Future Med Chem 2024; 16:623-645. [PMID: 38470247 DOI: 10.4155/fmc-2023-0281] [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] [Indexed: 03/13/2024] Open
Abstract
Background: In Alzheimer's disease, butyrylcholinesterase (BuChE) activity gradually increases, while acetylcholinesterase (AChE) activity decreases or remains unchanged. Dual inhibitors have important roles in regulation of synaptic acetylcholine levels and progression of Alzheimer's disease. Methods: 1-(Thiomorpholin-4-ylmethyl)/benzyl-5-trifluoromethoxy-2-indolinones (6-7) were synthesized. AChE and BuChE inhibitory effects were investigated with Ellman's method. Molecular docking studies were performed for analyzing the possible binding interactions at active sites. Results: Compound 6g was the strongest inhibitor against both AChE (Ki = 0.35 μM) and BuChE (Ki = 0.53 μM). It showed higher inhibitory effects than both donepezil and galantamine. Moreover, compound 7m had a higher inhibitory effect than galantamine and the effect was comparable to that of donepezil against both AChE (Ki = 0.69 μM) and BuChE (Ki = 0.95 μM). Conclusion: The benzyl substitution compared with 1-(thiomorpholin-4-ylmethyl) group significantly increased both AChE and BuChE inhibitory effects.
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Affiliation(s)
- Özge Soylu-Eter
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Istanbul University, 34116, Istanbul, Turkey
- Department of Pharmaceutical Chemistry, Institute of Health Sciences, Istanbul University, 34126, Istanbul, Turkey
| | - Nurten Özsoy
- Department of Biochemistry, Faculty of Pharmacy, Istanbul University, 34116, Istanbul, Turkey
| | - Nilgün Karalı
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Istanbul University, 34116, Istanbul, Turkey
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14
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Parwani K, Patel F, Bhagwat P, Dilip H, Patel D, Thiruvenkatam V, Mandal P. Swertiamarin mitigates nephropathy in high-fat diet/streptozotocin-induced diabetic rats by inhibiting the formation of advanced glycation end products. Arch Physiol Biochem 2024; 130:136-154. [PMID: 34657540 DOI: 10.1080/13813455.2021.1987478] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/15/2022]
Abstract
CONTEXT The molecular mechanism by which Swertiamarin (SM) prevents advanced glycation end products (AGEs) induced diabetic nephropathy (DN) has never been explored. OBJECTIVE To evaluate the effect of SM in preventing the progression of DN in high fat diet-streptozotocin-induced diabetic rats. MATERIALS AND METHODS After 1 week of acclimatisation, the rats were divided randomly into five groups as follows: (1) Control group, which received normal chow diet; (2) High-fat diet (HFD) group which was fed diet comprising of 58.7% fat, 27.5% carbohydrate and 14.4% protein); (3) Aminoguanidine (AG) group which received HFD + 100 mg/k.b.w.AG (intraperitoneal); (4) Metformin (Met) group which received HFD + 70 mg/k.b.w. the oral dose of Met and (5) SM group which was supplemented orally with 50 mg/k.b.w.SM along with HFD. After 12 weeks all HFD fed animals were given a single 35 mg/k.b.w. dose of streptozotocin with continuous HFD feeding for additional 18 weeks. Later, various biochemical assays, urine analyses, histopathological analysis of kidneys, levels of AGEs, expression of various makers, and in-silico analysis were performed. RESULTS The diabetic group demonstrated oxidative stress, increased levels of AGEs, decreased renal function, fibrosis in the renal tissue, higher expression of the receptor for advanced glycation end products (RAGE), which were ameliorated in the SM treated group. In-silico analysis suggests that SM can prevent the binding of AGEs with RAGE. CONCLUSIONS SM ameliorated DN by inhibiting the oxidative stress induced by AGEs.HighlightsSM reduces the levels of hyperglycaemia-induced advanced glycation end products in serum and renal tissue.SM prevents renal fibrosis by inhibiting the EMT in the kidney tissue.The in-silico analysis proves that SM can inhibit the binding of various AGEs with RAGE, thereby inhibiting the AGE-RAGE axis.
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Affiliation(s)
- Kirti Parwani
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science & Technology, Anand, India
| | - Farhin Patel
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science & Technology, Anand, India
| | - Pranav Bhagwat
- Discipline of Chemistry, Indian Institute of Technology, Gandhinagar, India
| | - Haritha Dilip
- Discipline of Chemistry, Indian Institute of Technology, Gandhinagar, India
| | - Dhara Patel
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science & Technology, Anand, India
| | - Vijay Thiruvenkatam
- Discipline of Biological Engineering, Indian Institute of Technology, Gandhinagar, India
| | - Palash Mandal
- Department of Biological Sciences, P. D. Patel Institute of Applied Sciences, Charotar University of Science & Technology, Anand, India
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15
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Alharbi B, Alharethi SH, Al-Soud WA, Ahmed Al-Keridis L, Aljohani AA, Jairajpuri DS, Alshammari N, Adnan M. Exploring the potential of phytochemicals as inhibitors of 3'-phosphoadenosine 5'-phosphosulfate synthase 1 targeting cancer therapy. J Biomol Struct Dyn 2024; 42:3193-3203. [PMID: 37184152 DOI: 10.1080/07391102.2023.2212810] [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: 02/09/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
3'-phosphoadenosine 5'-phosphosulfate synthase 1 (PAPSS1) is an enzyme that critically synthesises the biologically active form of sulfate (PAPS) for all sulfation reactions. The discovery of PAPSS1 as a possible drug target for cancer therapy, specifically in non-small cell lung cancer, has prompted us to investigate potential small-molecule inhibitors of PAPSS1. Here, a structure-based virtual screening method was used to search for phytochemicals in the IMPPAT database to find potential inhibitors of PAPSS1. The primary hits were selected based on their physicochemical, ADMET, and drug-like properties. Then, the binding affinities were calculated and analyzed the interactions to identify safer and more effective hits. The research identified two phytochemicals, Guggulsterone and Corylin, that exhibited significant affinity and specific interaction with the ATP-binding pocket of PAPSS1. Structural observations made by molecular docking were further accompanied by molecular dynamics (MD) simulations and principal component analysis (PCA) to examine the conformational changes and stability of PAPSS1 with the elucidated compounds Guggulsterone and Corylin. MD simulation results suggested that the binding of Guggulsterone and Corylin stabilizes the PAPSS1 structure, leading to fewer conformational changes. This implies that these compounds may be useful in developing PAPSS1 inhibitors for the therapeutic development against non-small cell lung cancer (NSCLC). This study highlights the potential of phytochemicals as PAPSS1 inhibitors and the utility of computational approaches in drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bandar Alharbi
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Lamya Ahmed Al-Keridis
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdullah A Aljohani
- Department of Clinical laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka, Saudi Arabia
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
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Banerjee S, Mahesh Y, Prabhu D, Sekar K, Sen P. Identification of potent anti-fibrinolytic compounds against plasminogen and tissue-type plasminogen activator employing in silico approaches. J Biomol Struct Dyn 2024; 42:3204-3222. [PMID: 37216286 DOI: 10.1080/07391102.2023.2213343] [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: 10/27/2022] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
The zymogen protease Plasminogen (Plg) and its active form plasmin (Plm) carry out important functions in the blood clot disintegration (breakdown of fibrin fibers) process. Inhibition of plasmin effectively reduces fibrinolysis to circumvent heavy bleeding. Currently, available Plm inhibitor tranexamic acid (TXA) used for treating severe hemorrhages is associated with an increased incidence of seizures which in turn were traced to gamma-aminobutyric acid antagonistic activity (GABAa) in addition to having multiple side effects. Fibrinolysis can be suppressed by targeting the three important protein domains: the kringle-2 domain of tissue plasminogen activator, the kringle-1 domain of plasminogen, and the serine protease domain of plasminogen. In the present study, one million molecules were screened from the ZINC database. These ligands were docked to their respective protein targets using Autodock Vina, Schrödinger Glide, and ParDOCK/BAPPL+. Thereafter, the drug-likeness properties of the ligands were evaluated using Discovery Studio 3.5. Subsequently, we subjected the protein-ligand complexes to molecular dynamics simulation of 200 ns in GROMACS. The identified ligands P76(ZINC09970930), C97(ZINC14888376), and U97(ZINC11839443) for each protein target are found to impart higher stability and greater compactness to the protein-ligand complexes. Principal component analysis (PCA) implicates, that the identified ligands occupy smaller phase space, form stable clusters, and provide greater rigidity to the protein-ligand complexes. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis reveals that P76, C97, and U97 exhibit better binding free energy (ΔG) when compared to that of the standard ligands. Thus, our findings can be useful for the development of promising anti-fibrinolytic agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suparna Banerjee
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
| | - Yeshwanth Mahesh
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Dhamodharan Prabhu
- Center for Drug Discovery, Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, India
| | - Prosenjit Sen
- School of Biological Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal, India
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17
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Gul S, Khan AM. Molecular docking studies of isolated marine natural products against α-chymotrypsin. Nat Prod Res 2024; 38:1269-1272. [PMID: 36239528 DOI: 10.1080/14786419.2022.2132501] [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: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 10/17/2022]
Abstract
The α-chymotrypsin is widely present in the digestive system of prokaryotes and eukaryotes that helps in the digestion by the hydrolysis of the peptide bond. It is serine protease enzyme (E.C. 3.4.21.1) and involves in many biological processes as well as in pancreatic disorders. In the previous study, marine red alga namely Jolyna laminariodes was used for the isolation of succinylanthranilic acid ester (2). Further, analogues were synthesised from anthranilic acid by using succinic anhydride, maleic anhydride and glutaric anhydride into corresponding dicarboxylic acids and further into acid ester including succinylanthranilic acid (1), succinylanthranilic acid ester (2), maleinylanthranilic acid (3), maleinylanthranilic acid ester (4), glutarnylanthranilic acid (5) and glutarnylanthranilic acid ester (6). For all natural products analogues percent inhibition against α-chymotrypsin have been calculated. In this study, molecular docking is used to estimate the binding energy of natural product analogues against α-chymotrypsin enzyme. The docking energies are in good agreement with experimental findings.
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Affiliation(s)
- Sana Gul
- Department of Chemistry, Faculty of Science, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Campus, University Road, Karachi-75300, Pakistan
| | - Abdul Majeed Khan
- Department of Chemistry, Faculty of Science, Federal Urdu University of Arts, Science and Technology, Gulshan-e-Iqbal Campus, University Road, Karachi-75300, Pakistan
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Debnath S, Nath M, Sarkar A, Roy G, Chakraborty SK, Debnath B. Phytochemical characterization of Styrax benzoin resin extract, molecular docking, ADME, and antibacterial activity study. Nat Prod Res 2024; 38:1263-1268. [PMID: 36214683 DOI: 10.1080/14786419.2022.2132244] [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: 05/28/2022] [Revised: 09/17/2022] [Accepted: 09/27/2022] [Indexed: 10/17/2022]
Abstract
Styrax benzoin fumes have a spiritual aspect from ancient times, magical essence like a pleasant perfume, and are employed in religious ceremonies in India. This study aims to identify the volatile compounds in S. benzoin extract, their binding affinity to the bacterial target proteins, and study the antibacterial activity of the potential extract. The compounds obtained from GC-MS analysis of S. benzoin extract were subjected to molecular docking studies against DHFR of Staphylococcus aureus, tRNA synthetase of Escherichia coli, DHPS of Mycobacterium tuberculosis. Molecular docking studies revealed that seventeen compounds out of 20 compounds exhibited higher binding affinity than co-ligand (-7.00 kcal/mol) against the Staphylococcus aureus enzyme DHFR. Consequently, the crude extracts were evaluated for antibacterial activity against S. aureus, and the acetone extract showed promising findings. S. benzoin fumes might replace synthetic room fresheners, and promising compounds could be exploited in the cosmetics industry.
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Affiliation(s)
- Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidyalaya, Udaipur, India
| | - Moumita Nath
- Department of Forestry and Biodiversity, Tripura University, Agartala, India
| | - Alekhya Sarkar
- Department of Forestry and Biodiversity, Tripura University, Agartala, India
| | - Gourab Roy
- Department of Zoology, MBB College, Agartala, India
| | | | - Bimal Debnath
- Department of Forestry and Biodiversity, Tripura University, Agartala, India
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19
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Xu Y, Gong H, Zou Y, Mao X. Antihyperuricemic activity and inhibition mechanism of xanthine oxidase inhibitory peptides derived from whey protein by virtual screening. J Dairy Sci 2024; 107:1877-1886. [PMID: 37923199 DOI: 10.3168/jds.2023-24028] [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: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
Xanthine oxidase (XO), a rate-limiting enzyme in uric acid production, is the pivotal therapeutic target for gout and hyperuricemia. In this study, 57 peptides from α-lactalbumin and β-lactoglobulin were obtained via virtual enzymatic hydrolysis, and 10 XO inhibitory peptides were virtually screened using molecular docking. Then toxicity, allergenicity, solubility, and isoelectric point of the obtained 10 novel peptides were evaluated by in silico tools. The XO activity of these synthetic peptides was tested using an in vitro assay by high-performance liquid chromatography. Their inhibitory mechanism was further explored by molecular docking. The results showed that 4 peptides GL, PM, AL, and AM exhibited higher inhibitory activity, and their half maximal inhibitory concentration in vitro was 10.20 ± 0.89, 23.82 ± 0.94, 34.49 ± 0.89, and 40.45 ± 0.92 mM, respectively. The peptides fitted well with XO through hydrogen bond, hydrophobic interaction, and van der Waals forces, and amino acid residues Glu802, Leu873, Arg880, and Pro1076 played an important role in this process. Overall, this study indicated 4 novel peptides GL, PM, AL, and AM from whey protein exhibited XO inhibitory activity, and they might be useful and safe XO inhibitors for hyperuricemia prevention and treatment.
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Affiliation(s)
- Yaru Xu
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Han Gong
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yang Zou
- Tianjin Haihe Dairy Co. Ltd., Tianjin 300000, China
| | - Xueying Mao
- Key Laboratory of Functional Dairy, Ministry of Education, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
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20
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Su Y, Zhang T, An X, Ma H, Wang M. Design, synthesis, antifungal activity and molecular docking of novel pyrazole-4-carboxamides containing tertiary alcohol and difluoromethyl moiety as potential succinate dehydrogenase inhibitors. Pest Manag Sci 2024; 80:2032-2041. [PMID: 38105405 DOI: 10.1002/ps.7937] [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] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Resistance problems with the long-term and frequent use of existing fungicides, and the lack of structure diversity of traditional pyrazole-4-carboxamide succinate dehydrogenase inhibitors, it is highly required to design and develop new fungicides to address the resistance issue. RESULTS Different from previous pyrazole-4-carboxamide succinate dehydrogenase inhibitors by breaking the norm of difluoromethyl at the C-3 position of pyrazole and introducing a tertiary alcohol group at the C-3 position, 27 novel pyrazole-4-carboxamide derivatives were designed, synthesized and characterized by proton (1 H) nuclear magnetic resonance (NMR), carbon-13 (13 C) NMR, fluorine-19 (19 F) NMR and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). The crystal structures of compounds A14 and C5 were analyzed by single crystal X-ray diffraction. Their in vitro antifungal activities were evaluated against phytopathogen Fusarium graminearum, Botrytis cinerea, Phytophthora capsica, Sclerotinia sclerotiorum, Thanatephorus cucumeris. The results displayed that most of them exhibited significant antifungal activities against S. sclerotiorum at 50 mg/L, the half maximal effective concentration (EC50 ) data of A8 and A14 were 3.96 and 2.52 mg/L, respectively. Their in vivo antifungal activities were evaluated against Pseudoperonospora cubensis, Puccinia sorghi Schw, Colletotrichum gloeosporioides, F. graminearum, Erysiphe graminis, Thanatephorus cucumeris, the control efficacies of A6, B3, C3, and C6 against E. graminis reached 100% at a concentration of 400 mg/L. The molecular docking results showed that the binding mode of the target compounds containing tertiary alcohols were similar to that of fluxapyroxad in succinate dehydrogenase. In addition, tertiary alcohols were involved in the formation of hydrogen bonds. CONCLUSION The excellent in vitro and in vivo inhibitory activities of novel pyrazole-4-carboxamide derivatives against succinate dehydrogenase were reported for the first time, and they could be used as the potential lead compounds. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yanhao Su
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Tingting Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Xinkun An
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Haoyun Ma
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Mingan Wang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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21
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Gnanaselvan S, Yadav SA, Manoharan SP. Structure-based virtual screening of anti-breast cancer compounds from Artemisia absinthium-insights through molecular docking, pharmacokinetics, and molecular dynamic simulations. J Biomol Struct Dyn 2024; 42:3267-3285. [PMID: 37194295 DOI: 10.1080/07391102.2023.2212805] [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: 10/25/2022] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
Breast cancer is the world's second most frequent malignancy, with a significant mortality and morbidity rate. Nowadays, natural breast cancer medicine has piqued attention as disease-curing agent with low side effects. Herein, the leaf powder of Artemisia absinthium was extracted with ethanol, and GC-MS and LC-MS methods were employed to identify the phytocompounds. Using commercial software SeeSAR-9.2 and StarDrop, identified phytocompounds were docked with estrogen and progesterone breast cancer receptors as they promote breast cancer growth to find the binding affinity of the ligands, drugability, and toxicity. Hormone-mediated breast cancer accounts for about 80% of all cases of breast cancer. Cancer cells proliferate when estrogen and progesterone hormones are attached to these receptors. The molecular docking results demonstrated that 3',4',5,7-Tetrahydroxyisoflavanone (THIF) has stronger binding efficacy than standard drugs and other phytocompounds with -28.71 (3 hydrogen bonds) and -24.18 kcal/mol (6 hydrogen bonds) binding energies for estrogen and progesterone receptors, respectively. Pharmacokinetics and toxicity analysis were done to predict the drug-likeness of THIF which results in good drugability and less toxicity. The best fit THIF was subjected to a molecular dynamics simulation analysis by using Gromacs to analyze the conformational changes that occurred during protein-ligand interaction and found that, the structural changes were observed. The results from MD simulation and pharmacokinetic studies suggested that THIF can be expected that in vitro and in vivo research on this compound may lead to the development of a potent anti-breast cancer drug in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suvathika Gnanaselvan
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | | | - Sowmya Priya Manoharan
- Department of Biotechnology, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
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22
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Abhithaj J, Sharanya CS, Arun KG, Jayadevi Variyar E, Sadasivan C. Trypsin is inhibited by phytocompounds liquiritin and terpinen-4-ol from the herb Glycyrrhiza glabra: in vitro and in silico studies. J Biomol Struct Dyn 2024; 42:2957-2964. [PMID: 37184119 DOI: 10.1080/07391102.2023.2212784] [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: 09/28/2022] [Accepted: 04/27/2023] [Indexed: 05/16/2023]
Abstract
Serine proteases are a class of hydrolytic enzymes involved in various physiological functions like digestion, coagulation, fibrinolysis and immunity. The present study evaluates the serine protease inhibitory potential of phytochemicals liquiritin and terpinen-4-ol present in the herb Glycyrrhiza glabra L. using trypsin as the model enzyme. In silico studies showed that both the compounds have a significant binding affinity towards trypsin with a binding energy of -26.66 kcal/mol and -19.79 kcal/mol for liquiritin and terpinen-4-ol, respectively. Their binding affinity was confirmed through in vitro enzyme inhibition assays. The mode of inhibition was found to be uncompetitive. In order to explain the mode of inhibition, docking of the ligands to the enzyme-substrate complex was also done and binding energy was calculated after MD simulation. The energy values showed that the binding affinities of these compounds towards the enzyme substrate complex are more than that towards the enzyme alone. This explains the uncompetitive mode of inhibition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- J Abhithaj
- Department of Biotechnology & Microbiology and Inter University Centre for Bioscience, Kannur University, Kannur, Kerala, India
| | - C S Sharanya
- Department of Biosciences, Rajagiri College of Social Sciences (Autonomous), Cochin, Kerala, India
| | - K G Arun
- Department of Biotechnology & Microbiology and Inter University Centre for Bioscience, Kannur University, Kannur, Kerala, India
| | - E Jayadevi Variyar
- Department of Biotechnology & Microbiology and Inter University Centre for Bioscience, Kannur University, Kannur, Kerala, India
| | - C Sadasivan
- Department of Biotechnology & Microbiology and Inter University Centre for Bioscience, Kannur University, Kannur, Kerala, India
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23
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Iqbal S, Farhanaz, Roohi, Zaheer MR, Shankar K, Hussain MK, Zia Q, Rehman MT, AlAjmi MF, Gupta A. Visible-light promoted catalyst-free (VLCF) multi-component synthesis of spiro indolo-quinazolinone-pyrrolo[3,4-a]pyrrolizine hybrids: evaluation of in vitro anticancer activity, molecular docking, MD simulation and DFT studies. J Biomol Struct Dyn 2024; 42:3145-3165. [PMID: 37227775 DOI: 10.1080/07391102.2023.2214229] [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: 09/23/2022] [Accepted: 05/01/2023] [Indexed: 05/27/2023]
Abstract
A new and highly efficient visible-light-promoted catalyst free (VLCF) strategy for neat and clean synthesis of spiro indolo-quinazolinone-pyrrolo[3,4-a]pyrrolizine hybrids (6a-d) has been introduced. We have performed visible-light triggered 1,3-Dipolar cycloaddition reaction of maleimide (5a-d) with azomethine ylide generated in situ derived from tryptanthrin (3) and L-proline (4) to obtain desired products (6a-d) in good to excellent yield. Authentication and characterization of product was done using various spectroscopic techniques such as IR, 1H NMR, 13C NMR, Mass spectrometry and single crystal XRD analysis. To explain the reaction spontaneity, product stability, reactivity as well as possible mode of the interaction a quantum chemical investigation was performed and depicted through DFT studies. The synthesized compound 6a was also evaluated for anti-proliferative activity against a panel of five cancer cell lines (MCF-7, MDA-MB-231, HeLa, PC-3 and Ishikawa) and normal human embryonic kidney (HEK-293) cell line by using MTT assay. Compound 6a showed very good in vitro anti-proliferative activity (IC50 = 6.58-17.98 μM) against four cancer cell lines and no cytotoxicity against normal HEK-293. In order to evaluate the anticancer potential of compounds 6a-d, molecular docking was performed against wild type and mutant EGFR. The results suggest that all the compounds occupied the active site of both enzymes, with a strong binding energy (-10.2 to -11.5 kcal/mol). These results have been confirmed by molecular dynamics simulation by evaluating root mean square deviation (RMSD) and root mean square fluctuation (RMSF), along with principal component analysis (PCA).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Safia Iqbal
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Farhanaz
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
| | - Roohi
- Protein Research Laboratory, Department of Bioengineering, Integral University, Lucknow, India
| | - Mohd Rehan Zaheer
- Department of Chemistry, R.M.P.S.P. Girls Post Graduate College, Basti, India
| | - Krapa Shankar
- Sun Pharmaceutical industries Ltd, Sarhaul, Sector 18, Gurgaon, India
| | | | - Qamar Zia
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Md Tabish Rehman
- Department of pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Anamika Gupta
- Department of Chemistry, Aligarh Muslim University, Aligarh, India
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24
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Fan Q, Liu X, Zhang Y, Kang W, Si S, Zhang H. Integration of metabolomics and network pharmacology technology to explain the effect mechanisms of Danggui Buxue decoction in vascular dementia. Biomed Chromatogr 2024; 38:e5822. [PMID: 38237172 DOI: 10.1002/bmc.5822] [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: 10/14/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 03/16/2024]
Abstract
Danggui Buxue decoction (DBD) is a traditional Chinese medicine herbal decoction that has a good therapeutic effect on vascular dementia (VaD). However, its pharmacodynamic substances and underlying mechanisms are ambiguous. The work aimed to decipher the pharmacodynamic substances and molecular mechanisms of DBD against VaD rats based on gas chromatography-mass spectrometry metabonomics, network pharmacology, molecular docking, and experimental verification. The results indicated that DBD significantly improved the learning abilities and cognitive impairment in the VaD rat model. Integration analysis of the metabolomics and network pharmacology approach revealed that DBD might primarily affect arachidonic acid (AA) and inositol phosphate metabolic pathways by regulating the platelet activation signaling pathways. Six core targets (TNF [tumor necrosis factor], IL-6 [interleukin 6], PTGS2 [prostaglandin-endoperoxide synthase 2], MAPK1, MAPK3, and TP53) in the platelet activation signaling pathways also had a good affinity to seven main active components (saponins, organic acids, flavonoids, and phthalides) of DBD through the verification of molecular docking. Enzyme-linked immunosorbent assay results (ELISA) showed that the levels of TNF, IL-6, PTGS2, thromboxane B2, and caspase-3 in the platelet activation signaling pathway can be regulated by DBD. Our results indicated that DBD treated VaD mainly by modulating the platelet activation signaling pathway, and AA and inositol phosphate metabolism.
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Affiliation(s)
- Qin Fan
- Gansu University of Chinese Medicine, Lanzhou, China
- Key Laboratory of Chemistry and Quality for Traditional Chinese Medicines of the College of Gansu Province, Lanzhou, China
- Gansu Province Engineering Laboratory for TCM Standardization Technology and Popularization, Lanzhou, China
| | - Xinhong Liu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, China
| | - Yanying Zhang
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Wanrong Kang
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Shanshan Si
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Hongmei Zhang
- Gansu University of Chinese Medicine, Lanzhou, China
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25
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Chen Y, Lu M, Lin M, Gao Q. Network pharmacology and molecular docking to elucidate the common mechanism of hydroxychloroquine treatment in lupus nephritis and IgA nephropathy. Lupus 2024; 33:347-356. [PMID: 38285068 DOI: 10.1177/09612033241230377] [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] [Indexed: 01/30/2024]
Abstract
OBJECTIVE Hydroxychloroquine (HCQ), characterized by a broad effect on immune regulation, has been widely used in the treatment of autoimmune glomerulonephritis such as lupus nephritis (LN) and immunoglobulin A nephropathy (IgAN). The current research investigates whether HCQ plays a role in the treatment of LN and IgAN through common mechanisms since the pathogenesis of both LN and IgAN is closely related to immune complex deposition, complement activation, and ultimately inflammation. METHODS Seventy-two common targets were obtained related to the common mechanism of HCQ treatment of LN and IgAN. Targets associated with LN and IgAN were collected based on DisGeNET, GeneCards, and OMIM databases. Possible HCQ targets were obtained from the PubChem database and PharmMapper databases. The overlapping targets of HCQ ingredients, IgAN, and LN were discovered via the Venn 2.1.0 online platform. Through the DAVID database, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted. Cytoscape (v3.9.1) was used to build a protein-protein interaction (PPI) network. Molecular docking was performed by using AutoDockTools 1.5.6 software and PyMol software to match the binding activity between HCQ and the 10 core targets. RESULTS The results showed that core targets (including MMP 2, PPARG, IL-2, MAPK14, MMP 9, and SRC), three signaling pathways (including the PI3K-Akt, AGE-RAGE, and MAPK), and cell differentiation (including Th1, Th2, and Th17) might be related to the body's immunity and inflammation. These results suggested that HCQ might act on targets and pathways involved in inflammation and immune regulation to exert a common effect on the treatment of LN and IgAN. CONCLUSIONS The current study provided new evidence for the protective mechanism and clinical utility of HCQ against LN and IgAN.
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Affiliation(s)
- Yixuan Chen
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Meiqi Lu
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Mengshu Lin
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Qing Gao
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
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26
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Zhou L, Liu T, Yan T, Yang M, Wang P, Shi L. 'Nine Steaming Nine Sun-drying' processing enhanced properties of Polygonatum kingianum against inflammation, oxidative stress and hyperglycemia. J Sci Food Agric 2024; 104:3123-3138. [PMID: 38072675 DOI: 10.1002/jsfa.13203] [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] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND Polygonatum kingianum Coll. & Hemsl (PK), a prominent medicine and food homology plant, has been consumed as a decoction from boiling water for thousands of years. 'Nine Steaming Nine Sun-drying' processing has been considered an effective method for enriching tonic properties, but studies investigating such impacts on PK and underlying mechanisms are extremely rare. RESULTS We first demonstrated substantial improvements in the anti-oxidative, anti-inflammatory and anti-hyperglycemia effects of the Nine Steaming Nine Sun-drying processed PK water extracts compared with crude PK in cell models (i.e., HepG2 and Raw 264.7 cells). We then integrated foodomics and network pharmacology analysis to uncover the key compounds responsible for the improved benefits. A total of 551 metabolites of PK extracts were identified, including polyphenols, flavonoids, alkaloids, and organic acids. During processing, 204 metabolites were enhanced, and 32 metabolites were recognized as key constituents of processed PK responsible for the improved health-promoting activities, which may affect PI3K-Akt-, MAPK-, and HIF-1 pathways. We further confirmed the high affinity between identified key constituents of processed PK and their predicted acting targets using molecular docking. CONCLUSION Our results provide novel insights into bioactive compounds of processed PK, elaborating the rationality of processing from the perspective of tonic effects. Consuming processed PK could be an efficacious strategy to combat the high prevalence of metabolic diseases that currently affect millions of people worldwide. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Lanqi Zhou
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Tianqi Liu
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Tao Yan
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Minmin Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Wang
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Lin Shi
- School of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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27
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Islam WU, Khan A, Khan F, Ullah S, Waqas M, Khan H, Khan M, Rahman SM, Ali S, Mateen A, Khalid A, Khan A, Al-Harrasi A. Synthesis of novel hydrazide Schiff bases with anti-diabetic and anti-hyperlipidemic effects: in-vitro, in-vivo and in-silico approaches. J Biomol Struct Dyn 2024:1-12. [PMID: 38533896 DOI: 10.1080/07391102.2024.2329296] [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: 12/06/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
The increasing global incidence of non-insulin-dependent diabetes mellitus (NIDDM) necessitates innovative therapeutic solutions. This study focuses on the design, synthesis and biological evaluation of Schiff base derivatives from 2-bromo-2-(2-chlorophenyl) acetic acid, particularly hydrazone compounds 4a and 4b. Both in-vitro and in-vivo assays demonstrate these derivatives' strong antidiabetic and anti-hyperlipidemic properties. In a 15-d experiment, we administered 4a and 4b at doses of 2.5 and 5 mg/kg body weight, which effectively improved symptoms of alloxan-induced diabetes in mice. These symptoms included weight loss, increased water consumption and high blood glucose levels. The compounds also normalized abnormal levels of total cholesterol (TC), triacylglycerol (TG) and low-density lipoprotein cholesterol (LDL-C), while raising the levels of high-density lipoprotein cholesterol (HDLC). Computational analysis showed that these compounds effectively inhibited the α-glucosidase enzyme by interacting with key catalytic residues, specifically Asp214 and Asp349. These computational results were confirmed through in-vitro tests, where 4a and 4b showed strong α-glucosidase inhibitory activity, with IC50 values of 0.70 ± 0.11 and 10.29 ± 0.30 µM, respectively. These compounds were more effective than the standard drug, acarbose, which had an IC50 value of 873.34 ± 1.67 µM. Mechanistic studies further indicated competitive inhibition, reinforcing the therapeutic potential of 4a and 4b for NIDDM treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Waseem Ul Islam
- Department of Pharmacy, University of Swabi, Swabi, Pakistan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Abad Khan
- Department of Pharmacy, University of Swabi, Swabi, Pakistan
| | - Faizullah Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Hammad Khan
- Organic Synthesis and Catalysis Research Laboratory, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Momin Khan
- Department of Chemistry, Abdul Wali Khan Mardan, Mardan, Pakistan
| | - Shaikh Mizanoor Rahman
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Shaukat Ali
- Organic Synthesis and Catalysis Research Laboratory, Institute of Chemical Sciences, University of Peshawar, Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Abdul Mateen
- Department of Pharmacy, University of Swabi, Swabi, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Sultanate of Oman
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Dawbaa S, Türkeş C, Nuha D, Demir Y, Evren AE, Yurttaş L, Beydemir Ş. New N-(1,3,4-thiadiazole-2-yl)acetamide derivatives as human carbonic anhydrase I and II and acetylcholinesterase inhibitors. J Biomol Struct Dyn 2024:1-19. [PMID: 38533902 DOI: 10.1080/07391102.2024.2331085] [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: 09/19/2023] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Various carbonic anhydrase (CA) enzyme isoforms are known today. In addition to the use of CA inhibitors as diuretics, antiepileptics and antiglaucoma agents, the inhibition of other specific isoforms of CA was reported to have clinical benefits in cancers. In this study, two groups of 1,3,4-thiadiazole derivatives were designed and synthesized to act as human CA I and II (hCA I and hCA II) inhibitors. The activities of these compounds were tested in vitro and evaluated in silico studies. The activity of the synthesized compounds was also tested against acetylcholinesterase (AChE) to evaluate the relation of the newly designed structures to the activity against AChE. The synthesized compounds were analyzed by 1H NMR,13C NMR and high-resolution mass spectroscopy (HRMS). The results displayed a better activity of all the synthesized compounds against hCA I than that of the commonly used standard drug, Acetazolamide (AAZ). The compounds also showed better activity against hCA II, except for compounds 5b and 6b. Only compounds 6a and 6c showed superior activity against AChE compared to the standard agent, tacrine (THA). In silico studies, including absorption, distribution, metabolism and excretion (ADME) and drug-likeness evaluation, molecular docking, molecular dynamic simulations (MDSs) and density functional theory (DFT) calculations, were compatible with the in vitro results and presented details regarding the structure-activity relationship.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sam Dawbaa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Department of Doctor of Pharmacy (PharmD), Faculty of Medical Sciences, Thamar University, Dhamar, Yemen
- Department of Pharmacy, Faculty of Medical Sciences, Al-Hikma University, Dhamar, Yemen
| | - Cüneyt Türkeş
- Department of Biochemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan, Turkey
| | - Demokrat Nuha
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Department of Chemistry, Faculty of Science, Eskisehir Technical University, Eskişehir, Turkey
- Faculty of Pharmacy, University for Business and Technology, Prishtina, Kosovo
| | - Yeliz Demir
- Department of Pharmacy Services, Nihat Delibalta Göle Vocational High School, Ardahan University, Ardahan, Turkey
| | - Asaf Evrim Evren
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- Department of Pharmacy Services, Vocational School of Health Services, Bilecik Şeyh Edebali University, Bilecik, Turkey
| | - Leyla Yurttaş
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
| | - Şükrü Beydemir
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, Eskişehir, Turkey
- The Rectorate of Bilecik Seyh Edebali University, Bilecik, Turkey
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Martineau-Côté D, Achouri A, Karboune S, L'Hocine L. Antioxidant and Angiotensin-Converting Enzyme Inhibitory Activity of Faba Bean-Derived Peptides After In Vitro Gastrointestinal Digestion: Insight into Their Mechanism of Action. J Agric Food Chem 2024; 72:6432-6443. [PMID: 38470110 DOI: 10.1021/acs.jafc.4c00829] [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: 03/13/2024]
Abstract
Faba bean flour, after in vitro gastrointestinal digestion, showed important antioxidant and angiotensin-converting enzyme (ACE) inhibitory activities. In the present study, 11 faba bean- derived peptides were synthesized to confirm their bioactivities and provide a deeper understanding of their mechanisms of action. The results revealed that 7 peptides were potent antioxidants, namely, NYDEGSEPR, TETWNPNHPEL, TETWNPNHPE, VIPTEPPH, VIPTEPPHA, VVIPTEPPHA, and VVIPTEPPH. Among them, TETWNPNHPEL had the highest activity in the ABTS (EC50 = 0.5 ± 0.2 mM) and DPPH (EC50 = 2.1 ± 0.1 mM) assays (p < 0.05), whereas TETWNPNHPE had the highest activity (p < 0.05) in the ORAC assay (2.84 ± 0.08 mM Trolox equivalent/mM). Synergistic and/or additive effects were found when selected peptides (TETWNPNHPEL, NYDEGSEPR, and VVIPTEPPHA) were combined. Four peptides were potent ACE inhibitors, where VVIPTEPPH (IC50 = 43 ± 1 μM) and VVIPTEPPHA (IC50 = 50 ± 5 μM) had the highest activity (p < 0.05), followed by VIPTEPPH (IC50 = 90 ± 10 μM) and then VIPTEPPHA (IC50 = 123 ± 5 μM) (p < 0.05). These peptides were noncompetitive inhibitors, as supported by kinetic studies and a molecular docking investigation. This study demonstrated that peptides derived from faba beans have multifunctional bioactivities, making them a promising food-functional and nutraceutical ingredient.
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Affiliation(s)
- Delphine Martineau-Côté
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, Saint-Hyacinthe, Quebec J2S 8E3, Canada
- Department of Food Science and Agricultural Chemistry, Macdonald Campus, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Allaoua Achouri
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, Saint-Hyacinthe, Quebec J2S 8E3, Canada
| | - Salwa Karboune
- Department of Food Science and Agricultural Chemistry, Macdonald Campus, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Lamia L'Hocine
- Agriculture and Agri-Food Canada, Saint-Hyacinthe Research and Development Centre, Saint-Hyacinthe, Quebec J2S 8E3, Canada
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Ma YD, Zhou H, Lin GT, Wu KH, Xu G, Liu X, Xu D. Design, Synthesis, and Fungicidal Activities of Novel N-(Pyrazol-5-yl)benzamide Derivatives Containing a Diphenylamine Moiety. J Agric Food Chem 2024; 72:6691-6701. [PMID: 38498985 DOI: 10.1021/acs.jafc.3c07567] [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: 03/20/2024]
Abstract
To accelerate the development of novel fungicides, a variety of N-(pyrazol-5-yl)benzamide derivatives with a diphenylamine moiety were designed and synthesized using a pharmacophore recombination strategy based on the structure of pyrazol-5-yl-aminophenyl-benzamides. The bioassay results demonstrated that most of the target compounds had excellent in vitro antifungal activities against Sclerotinia sclerotiorum, Valsa mali, and Botrytis cinerea. In particular, compound 5IIIh exhibited remarkable activity against S. sclerotiorum (EC50 = 0.37 mg/L), which was similar to that of fluxapyroxad (EC50 = 0.27 mg/L). In addition, compound 5IIIc (EC50 = 1.32 mg/L) was observed to be more effective against V. mali than fluxapyroxad (EC50 = 12.8 mg/L) and comparable to trifloxystrobin (EC50 = 1.62 mg/L). Furthermore, compound 5IIIh demonstrated remarkable in vivo protective antifungal properties against S. sclerotiorum, with an inhibition rate of 96.8% at 100 mg/L, which was close to that of fluxapyroxad (99.6%). Compounds 5IIIc (66.7%) and 5IIIh (62.9%) exhibited good in vivo antifungal effects against V. mali at 100 mg/L, which were superior to that of fluxapyroxad (11.1%) but lower than that of trifloxystrobin (88.9%). The succinate dehydrogenase (SDH) enzymatic inhibition assay was conducted to confirm the mechanism of action. Molecular docking analysis further revealed that compound 5IIIh has significant hydrogen-bonding, π-π, and p-π conjugation interactions with ARG 43, SER 39, TRP 173, and TYR 58 in the binding site of SDH, and the binding mode was similar to that of the commercial fungicide fluxapyroxad. All of the results suggest that compound 5IIIh could be a potential SDH inhibitor, offering a valuable reference for future studies.
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Affiliation(s)
- Yi-Dan Ma
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Huan Zhou
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Guo-Tai Lin
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Ke-Huan Wu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Gong Xu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Yangling, Shaanxi 712100, People's Republic of China
| | - Xili Liu
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Yangling, Shaanxi 712100, People's Republic of China
| | - Dan Xu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Botanical Pesticide R&D in Shaanxi Province, Yangling, Shaanxi 712100, People's Republic of China
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Abduljalil JM, Elfiky AA, AlKhazindar MM. Tepotinib and tivantinib as potential inhibitors for the serine/threonine kinase of the mpox virus: insights from structural bioinformatics analysis. J Biomol Struct Dyn 2024:1-11. [PMID: 38529847 DOI: 10.1080/07391102.2024.2323699] [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: 12/28/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024]
Abstract
The serine/threonine kinase (STK) plays a central role as the primary kinase in poxviruses, directing phosphoryl transfer reactions. Such reactions are pivotal for the activation of certain proteins during viral replication, assembly, and maturation. Therefore, targeting this key protein is anticipated to impede virus replication. In this work, a structural bioinformatics approach was employed to evaluate the potential of drug-like kinase inhibitors in binding to the ATP-binding pocket on the STK of the Mpox virus. Virtual screening of known kinase inhibitors revealed that the top 10 inhibitors exhibited binding affinities ranging from -8.59 to -12.05 kcal/mol. The rescoring of compounds using the deep-learning default model in GNINA was performed to predict accurate binding poses. Subsequently, the top three inhibitors underwent unbiased molecular dynamics (MD) simulations for 100 ns. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and Principal Component Analysis (PCA) suggested tepotinib as a competitive inhibitor for Mpox virus STK as evidenced by its binding free energy and the induction of similar conformational behavior of the enzyme. Nevertheless, it is sensible to experimentally test all top 10 compounds, as scoring functions and energy calculations may not consistently align with experimental findings. These insights are poised to provide an attempt to identify an effective inhibitor for the Mpox virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen
| | - Abdo A Elfiky
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Maha M AlKhazindar
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
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Li JY, Wang XY, Han MJ, Bai M, Huang XX. Target isolation of diverse sesquiterpenoid from the stems of Daphne genkwa based on molecular networking. J Asian Nat Prod Res 2024:1-12. [PMID: 38529763 DOI: 10.1080/10286020.2024.2325033] [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] [Received: 11/13/2023] [Accepted: 02/25/2024] [Indexed: 03/27/2024]
Abstract
Guiding by LC-MS/MS analysis and the Global Natural Products Social (GNPS) Molecular Networking, three undescribed sesquiterpenoids, stedapgens A-C, and two known analogues were discovered in the barks of Daphne genkwa Sieb. et Zucc. The structures were determined by analysis of their spectroscopic data and quantum-chemical calculations. All the isolated novel compounds were tested for their acetylcholinesterase inhibitory activities with IC50 = 0.754 ± 0.059, 0.696 ± 0.026, and 0.337 ± 0.023 μg/ml. Among them, stedapgen A displayed promising inhibitory activities against AChE, and the binding sites were predicted by molecular docking.
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Affiliation(s)
- Jia-Yi Li
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xin-Yi Wang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Mei-Juan Han
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Ming Bai
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug Research & Development, Liaoning Province; Engineering Research Center of Natural Medicine Active Molecule Research & Development, Liaoning Province; Key Laboratory of Natural Bioactive Compounds Discovery & Modification, Shenyang; School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China
- Basic Science Research Center Base (Pharmaceutical Science), Shandong Province, Yantai University, Yantai 264005, China
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Riadi Y, Afzal O, Kumar S, Varadharajan V, Geesi MH. Synthesis of novel ( R)-carvone-tagged thiazolidinone as anticancer leads: characterization, in vitro antiproliferative evaluation and in silico studies. J Biomol Struct Dyn 2024:1-14. [PMID: 38523573 DOI: 10.1080/07391102.2024.2331095] [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: 01/04/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
This work describes the successful synthesis of a series of three novel thiazolidinone-carvone-O-alkyl hybrids through a two-step approach involving heterocyclization and O-alkylation reactions. Comprehensive structural characterization of the obtained products was achieved using NMR and HRMS spectroscopic techniques. This study assessed in vitro antiproliferative activity of synthesized thiazolidinone-carvone-O-alkyl hybrids (5a-c) against various human cancer cell lines, viz. HT-1080 (fibrosarcoma), A-549 (lung cancer), MCF-7 (breast cancer) and MDA-MB-231 (breast cancer). MTT assay revealed promising results for compounds 5b and 5c, demonstrating good antiproliferative activity against A-549 and MCF-7 cell lines comparable to the positive control, Doxorubicin. Compound 5a, harbouring an O-acetoxy group, displayed limited anticancer activity against MCF-7 and MDA-MB-231 cells, with IC50 values of 69.33 ± 0.42 µM and >100 µM, respectively. Docking results confirmed that the compounds 5a-c binds at the active site of p21 with docking scores -2.0, -4.8, and -7.0 kcal/mol, respectively. Compound 5a-c also showed good binding potential against Bcl2 protein with docking score of -4.9, -6.0, -5.5 kcal/mol, respectively. Furthermore, binding energy analysis and dynamics simulation studies of compounds towards p21 and Bcl2 yielded promising results. In PAK4 assay, compound 5c showed comparable potency (IC50 6.76 µM) with the standard control UC2288 (IC50 6.40 µM), while in BCL-2 TR-FRET assay, 5c exhibited good inhibition (IC50 1.78 µM) as compared to Venetoclax (IC50 0.016 µM). In conclusion, compounds 5a-c could be used as a structural framework for the discovery of novel therapeutics to combat different types of cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yassine Riadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | | | - Mohammed H Geesi
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Song P, Wang S, Han R, Wang H, Hu B, Luan J, Zhang H, Wang Z, Ma C, Wang J. Insights into the selective mechanism of PDE2/9a inhibitors from silico aspects. J Biomol Struct Dyn 2024:1-18. [PMID: 38525932 DOI: 10.1080/07391102.2024.2331098] [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: 01/17/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024]
Abstract
The selective design of competitive enzyme inhibitors is an extremely difficult task but necessary work for certain types of systems, such as the phosphodiesterase (PDE) system addressed in this article. In the PDE family, PDE2A and PDE9 respectively target the central nervous system and heart failure, and share many conserved amino acids at their binding sites. Therefore, gaining a deep understanding of the selective mechanisms of PDE2A/9A is crucial for designing highly selective drugs. In this study, various computer-aided drug design (CADD) methods, including molecular docking, molecular dynamics simulations (MD), and binding free energy calculations, are employed to explore the selective mechanisms of PDE2A/9A. Overall, our research results indicate a selective design strategy for PDE2A, which involves incorporating hydrophobic or aromatic moieties into the molecular structure to better accommodate the hydrophobic pocket of PDE2A. Additionally, it is recommended to introduce functional groups capable of forming connections with selective residues, such as Phe830 and Gln812 for PDE2A, or Ala452 and Tyr424 for PDE9A, to enhance the selectivity of inhibitors targeting PDE2A/9A. This achievement is anticipated to pave the way for the development of innovative and selective small molecules targeting PDE2A/9A.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pengfei Song
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Shizhun Wang
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Ruiheng Han
- Pharmaceutical department, Avanc Pharmaceutical Co., Ltd., China
| | - Hanxun Wang
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Baichun Hu
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Jiasi Luan
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Medical Devices, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Haoyu Zhang
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Zhijian Wang
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Chao Ma
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design &Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University, Shenyang, China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, People's Republic of China
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Ettitaou A, Kabdy H, Oubella K, Raoui K, Oubahmane M, Aboufatima R, Elyazouli L, Garzoli S, Chait A. Molecular docking of quercetin: a promising approach for the development of new anti-inflammatory and analgesic drugs. Nat Prod Res 2024:1-10. [PMID: 38520257 DOI: 10.1080/14786419.2024.2333053] [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: 02/02/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024]
Abstract
The aim of this study is to investigate the antinociceptive, anti-inflammatory and antipyretic effects of quercetin. Additionally, molecular docking studies were conducted to evaluate potential interactions between quercetin and various molecular targets. Animal models were used to conduct a comprehensive pharmacological investigation of quercetin. Evaluation of analgesic activity revealed a reduction in the number of abdominal cramps during the twisting test and inhibition of pain during the second phase of the formaldehyde test. Additionally, evaluation of its anti-inflammatory activity showed a reduction in ear oedema. However, it is important to note that quercetin administration has not been shown to significantly reduce yeast-induced hyperthermia. The docking study revealed the high inhibitory potential of quercetin against the COX-2 receptor.
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Affiliation(s)
- Amina Ettitaou
- Laboratory of Pharmacology, Neurobiology, Anthropology and Environment, Department of Biology, Faculty of Sciences Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Hamid Kabdy
- Laboratory of Pharmacology, Neurobiology, Anthropology and Environment, Department of Biology, Faculty of Sciences Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Khadija Oubella
- Laboratory of Pharmacology, Neurobiology, Anthropology and Environment, Department of Biology, Faculty of Sciences Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Karima Raoui
- Laboratory of Pharmacology, Neurobiology, Anthropology and Environment, Department of Biology, Faculty of Sciences Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Mehdi Oubahmane
- Laboratory of Molecular Chemistry, Department of Chemistry, Faculty of Sciences Semlalia, Cadi Ayyad University, Marrakech, Morocco
| | - Rachida Aboufatima
- Laboratory of Genie Biologic, Faculty of Sciences and Technics, Sultan Moulay Slimane University, Beni Mellal, Morocco
| | - Loubna Elyazouli
- Laboratory of Pharmacology, Neurobiology, Anthropology and Environment, Department of Biology, Faculty of Sciences Semlalia, University Cadi Ayyad, Marrakech, Morocco
| | - Stefania Garzoli
- Department of Chemistry and Technologies of Drug, Sapienza University, Rome, Italy
| | - Abderrahman Chait
- Laboratory of Pharmacology, Neurobiology, Anthropology and Environment, Department of Biology, Faculty of Sciences Semlalia, University Cadi Ayyad, Marrakech, Morocco
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Forid MS, Patil RB, Roney M, Huq AKMM, Mohd Nasir MHB, Mohd Aluwi MFF, Azuri MS, Wan Ishak WMB. Identification of β-cycloidal-derived mono-carbonyl curcumin analogs as potential interleukin-6 inhibitor to treat wound healing through QSAR, molecular docking, MD simulation, MM-GBSA calculation. J Biomol Struct Dyn 2024:1-12. [PMID: 38520169 DOI: 10.1080/07391102.2024.2331089] [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: 12/20/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Interleukin-6 (IL-6) is a cytokine that involved in the different phases of wound healing. It is responsible for promoting inflammation, regulating tissue repair scar formation, stimulating the production of extracellular matrix components and recruiting immune cells to the wound site. Therefore, suppressing IL-6 is beneficial for wound healing. However, no small molecules are currently available in the market against the IL-6. As a result, this research gap motivates us to find a potential inhibitor. This study aimed to investigate the wound healing potential of novel β-cycloidal-derived mono-carbonyl curcumin analogs reported in the literature through screening a series of computational studies. The calculated pIC50 value of 18 compounds (below 10) showed that all compounds may have potential therapeutic efficacy. Molecular docking studies revealed that compound C12 (-45.6044 kcal/mol) bound most strongly in the active site of IL-6 compared to the FDA-approved drug clindamycin (-42.3223). The Molecular Dynamic (MD) simulation displayed that lead compound C12 had the highest stability in the active site of IL-6 compared to the reference drug clindamycin. Furthermore, MMGBSA results indicated that C12 (-20.28 kcal/mol) had the highest binding energy compared to clindamycin (-8.36 kcal/mol). The ADMET analysis predicted that C12 are favourable for drug candidates. This study recommended compound C12 as a lead IL-6 inhibitor for future testing and development as therapeutics for wound healing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Shaekh Forid
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - Rajesh B Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Societys, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Miah Roney
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - A K M Moyeenul Huq
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Bin Mohd Nasir
- Department of Biotechnology, Kulliyyah of Science, International Islamic University of Malaysia (IIUM) Kuantan Campus, Jalan Sultan Ahmad Shah, Kuantan, Pahang Darul Makmur, Malaysia
| | - Mohd Fadhlizil Fasihi Mohd Aluwi
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
- Bio Aromatic Research Centre, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - Muhammad Saupi Azuri
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
| | - Wan Maznah Binti Wan Ishak
- Faculty of Chemical and Process Engineering Technology, Universiti Malaysia Pahang Al-Sultan Abdullah, Lebuhraya Persiaran Tun Khalil Yaakob, Kuantan, Pahang, Malaysia
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Orozco-Ugarriza ME, Arrieta Caldera NP, Olivo-Martínez Y. Antimicrobial phytoconstituents from Azadirachta indica (neem) with potential inhibitor against FtsZ protein of Pseudomonas aeruginosa. Nat Prod Res 2024:1-6. [PMID: 38516734 DOI: 10.1080/14786419.2024.2332946] [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: 10/20/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
Pseudomonas aeruginosa is a well-known pathogen for its rapid development of multi-drug antibiotic resistance. This pathogen is responsible for numerous human diseases, particularly affecting immunocompromised and elderly patients. Hence, discovering novel therapeutics has become necessary in the fight against antimicrobial resistance. This study is focused on evaluating the potential inhibitory activity of eleven phytocompounds from Azadirachta indica against the nucleotide-binding site of the FtsZ protein of P. aeruginosa through a cheminformatics approach. FtsZ is an indispensable and highly conserved protein in prokaryotic cell division. Docking studies revealed favourable binding energies (ΔG= - 8.3 to - 5.4 kcal/mol) for all selected phytoconstituents. Finally, we selected Nimbiol (CID 11119228), as a lead compound, exhibiting a binding energy (ΔG= -7.8 kcal/mol) for the target. Based on our findings, Nimbiol shows potential as an anti-FtsZ compound, making it a promising candidate for further in vitro and in vivo investigations to assess its antimicrobial activity.
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Affiliation(s)
- Mauricio E Orozco-Ugarriza
- Grupo de investigación en Microbiología y Ambiente (GIMA), Universidad de San Buenaventura, Cartagena, Colombia
- Grupo de investigación traslacional en Biomedicina y Biotecnología (GITB&B), Corporación para el desarrollo de la Investigación en Biomedicina & Biotecnología, Cartagena, Colombia
| | | | - Yenifer Olivo-Martínez
- Grupo de investigación en Microbiología y Ambiente (GIMA), Universidad de San Buenaventura, Cartagena, Colombia
- Biochemistry and Diseases Research Group, Facultad de Medicina, Universidad de Cartagena, Cartagena, Colombia
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Dhawale SA, Mahajan S, Pandit M, Gawale S, Ghodke M, Tapadiya G. Molecular docking and molecular dynamic simulation-based phytoconstituents against SARS-CoV-2 with dual inhibition of the primary protease targets. Nat Prod Res 2024:1-6. [PMID: 38517217 DOI: 10.1080/14786419.2024.2330526] [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: 05/12/2023] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
A novel coronavirus has caused major health problems and is spreading globally. The main protease enzyme plays a significant role in the number of copies of ss-RNA produced during the proteolytic cleavage of polypeptides. This work aims to find possible dual inhibitors of the 3-Chymotrypsin-like proteases PDB-6W63 and 6LU7 which increase efficiency and faster inhibition activity. By using an in-silico technique, polyphenols are molecularly docked against these targets to inhibit protease enzymes. Some polyphenols, such as pelargonidin and naringin, have significant dual inhibition characteristics with remarkable binding affinities with active scaffolds of both proteins, which have important ADMET parameters. These organic molecules are strongly bonded with amino acids of protein via mostly hydrogen bonding. These polyphenols also have outstanding docking scores and MMGBSA energies. The validity of the docking score was evaluated using a molecular dynamics simulation that assessed the stability of the complex. With the aid of computer-aided drug design, we hypothesise that the dual inhibition of compounds pelargonidin and naringin could effectively and potentially oppose SARS-CoV-2.
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Affiliation(s)
- Sachin A Dhawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Sadhana Mahajan
- Department of Pharmaceutical Chemistry, K.B.H.S.S Trusts Institute of Pharmacy, Nashik, Maharashtra, India
| | - Madhuri Pandit
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Sachin Gawale
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Mangesh Ghodke
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
| | - Ganesh Tapadiya
- Department of Pharmaceutical Chemistry, Shreeyash Institute of Pharmaceutical Education and Research, Aurangabad, Maharashtra, India
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Jin X, Hu X, Chen J, Shan L, Hao D, Zhang R. Electric field induced the changes in structure and function of human transforming growth factor beta receptor type I: from molecular dynamics to docking. J Biomol Struct Dyn 2024:1-12. [PMID: 38516997 DOI: 10.1080/07391102.2024.2329288] [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: 11/18/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
The transforming growth factor beta (TGF-β) signaling pathway is believed to play essential roles in several physiological activities, including cancer. TGF-β receptor type I (TBR-I) is a key membrane receptor protein in the TGF-β signaling pathway, which relates to many intracellular biological effects. In recent years, cold atmospheric plasma (CAP) has been found to have promising prospects in selective anticancer therapy and has confirmed its essential role in the TGF-β signaling pathway. However, the ambiguous effect of CAP-induced electric field (EF) on TBR-I still limits the application of CAP in clinical therapy. Molecular dynamics is applied to assess the effect of EF on the structure of the extracellular domain of TBR-I using a series of indicators and methods, and then we discuss the ligand binding ability of TBR-I. Results show that moderate EF intensities' structural restraints may contribute to the structural stability and ligand-binding ability of TBR-I, but an EF higher than 0.1 V/nm will be harmful. What's more, EF induces a change in the docking interface of TBR-I, showing the conformation and position of special sequences of residues decide the ligand binding surface. The relevant results suggest that CAP-induced EF plays a crucial role in receptor-receptor interaction and provides significant guidelines for EF-related anticancer therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xinrui Jin
- School of Energy and Electrical Engineering, Chang'an University, Xi'an, China
| | - Xiaochuan Hu
- School of Energy and Electrical Engineering, Chang'an University, Xi'an, China
| | - Jiayu Chen
- School of Energy and Electrical Engineering, Chang'an University, Xi'an, China
| | - Lequn Shan
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Dingjun Hao
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Rui Zhang
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
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Chen W, Liu Q, Gao X, Geng Y, Kan H. Observational study on the potential mechanism of Sanao decoction in the treatment of asthma based on network pharmacology and molecular docking. Medicine (Baltimore) 2024; 103:e37592. [PMID: 38518018 PMCID: PMC10957020 DOI: 10.1097/md.0000000000037592] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 02/22/2024] [Indexed: 03/24/2024] Open
Abstract
Bronchial asthma (BA) is a chronic respiratory disease closely related to immune system dysregulation. Traditional Chinese medicine has long adopted the strategy of Sanao decoction in the treatment of bronchial asthma. However, due to the multi-target and multi-pathway characteristics of Chinese herbal medicine, we are still unclear about the specific mechanism of Sanao decoction in treating bronchial asthma. To investigate the mechanism of action of Sanao decoction in the treatment of BA using a network pharmacology approach and preliminary validation by molecular docking technology. Traditional Chinese medicine systems pharmacology database and analysis platform and UniProt databases were used to search the active ingredients and targets of Sanao decoction, and BA-related targets were screened according to GeneCards and online Mendelian inheritance in man database databases. The intersection targets were imported into the STRING database to construct a protein-protein interaction network, and Cytoscape 3.9.1 software was used to screen out hub genes. This study also constructed a "drug-ingredient-target" visual network diagram. Gene Ontology and Kyoto Encyclopedia of Genomes enrichment analysis was performed on targets in the protein-protein interaction network using the ClusterProfiler package in R, with a P value < .05. Autodock software was used for molecular docking to complete the preliminary verification of core components and targets. A total of 73 active compounds and 308 targets of Sanao decoction, including 1640 BA-related disease targets, were retrieved from mainstream databases. Gene Ontology analysis and Kyoto encyclopedia of genes and genomes enrichment analysis suggested that Sanao decoction plays a role in the treatment of BA through signaling pathways such as PI3K-Akt, MAPK, and IL-17 signaling pathway. The 9 core goals represent the main elements related to Sanao decoction in the treatment of BA. Subsequently, the molecular docking results showed that most of the active compounds of Sanao decoction have strong binding efficiency with the hub gene. Sanao decoction has a key impact on BA through multiple channels. In summary, this intricate network reflects the potential of Sanao decoction in treating BA, a multifactorial disease. In addition, this study laid the foundation for further in vivo and in vitro experimental research and expanded the clinical application of Sanao decoction.
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Affiliation(s)
- Wenpei Chen
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Qiwei Liu
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Xuyan Gao
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
| | - Yingbao Geng
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
- Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, China
| | - Hongxing Kan
- School of Medical Informatics Engineering, Anhui University of Chinese Medicine, Hefei, China
- Anhui Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei, China
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Ben Romdhane O, Baccari W, Saidi I, Flamini G, Ascrizzi R, Chaieb I, Harrath AH, Ben Jannet H. Chemical Composition, Repellent, and Phytotoxic Potentials of the Fractionated Resin Essential Oil from Araucaria heterophylla Growing in Tunisia. Chem Biodivers 2024:e202400185. [PMID: 38513004 DOI: 10.1002/cbdv.202400185] [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: 01/22/2024] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
The resin essential oil (REO) of Araucaria heterophylla trunk bark was investigated for its chemical composition. Then, it was evaluated for its insecticidal and allelopathic activities. The REO was obtained by hydrodistillation for 9 h (yield of 4.2% w/w). Moreover, fractional hydrodistillation was carried out at 3-hour intervals, resulting in 3 fractions (R1-R3). GC/MS analysis of the obtained samples allowed the identification of 25 compounds, representing between 91.2 and 96.3% of their total constituents, which consisted predominantly of sesquiterpene hydrocarbons, oxygenated sesquiterpenes and diterpene hydrocarbons. α-Copaene (1), γ-muurolene (4), α-copaen-11-ol (7), spathulenol (9), 15-copaenol (10), ylangenal (21), dehydrosaussurea lactone (22), and sandaracopimaradiene (23) were identified as major compounds. The second part aimed to assess the impact of the A. heterophylla EO and its three fractions for their insecticidal and repellent activity against Tribolium castaneum (Herbst), of which a strong repellent activity was noted. In addition, the studied samples showed high phytotoxic effects against Lactuca sativa. The main compounds of the studied samples were docked into the active pocket of protoporphyrinogen IX oxidase (PDB: 1SEZ), a key enzyme in chlorophyll biosynthesis. Thus, it is recommended to use the REO of A. heterophylla as a natural herbicide.
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Affiliation(s)
- Oumayma Ben Romdhane
- University of Monastir, Chemistry, Avenue de l'environnement, Monastir, Monastir, 5019, Monastir, TUNISIA
| | - Wiem Baccari
- University of Monastir, Chemistry, Avenue de l'environnement, Monastir, Monastir, 5019, Monastir, TUNISIA
| | - Ilyes Saidi
- University of Monastir, Chemistry, Avenue de l'environnement, Monastir, Monastir, 5019, Monastir, TUNISIA
| | - Guido Flamini
- University of Pisa, di Farmacia, Via Bonanno 6, 56126 Pisa, Italy, Pisa, ITALY
| | - Roberta Ascrizzi
- University of Pisa, di Farmacia, Via Bonanno 6, 56126 Pisa, Italy, Pisa, ITALY
| | - Ikbal Chaieb
- University of Sousse, Regional Centre of Research on Horticulture and Organic Agriculture, 57, Chott Mariem, TN-4042 Sousse, Sousse, TUNISIA
| | - Abdel Halim Harrath
- King Saud University, Department of Zoology, Riyad 11451, Saudi Arabia, Riyad, SAUDI ARABIA
| | - Hichem Ben Jannet
- Faculty of sciences of Monastir, Chemistry, Avenue of environment, Monastir, 5019, Monastir, TUNISIA
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Yang X, Li F, Shi Y, Wu Y, Yang R, Liu X, Zhang Y, Zhang G, Ma M, Luo Z, Han X, Xie Y, Liu S. Integrated network pharmacology and experimental verification to explore the potential mechanism of San Ying decoction for treating triple-negative breast cancer. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38516703 DOI: 10.3724/abbs.2024015] [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] [Indexed: 03/23/2024] Open
Abstract
Traditional Chinese medicine (TCM) has been used to treat triple-negative breast cancer (TNBC), a breast cancer subtype with poor prognosis. Clinical studies have verified that the Sanyingfang formula (SYF), a TCM prescription, has obvious effects on inhibiting breast cancer recurrence and metastasis, prolonging patient survival, and reducing clinical symptoms. However, its active ingredients and molecular mechanisms are still unclear. In this study, the active ingredients of each herbal medicine composing SYF and their target proteins are obtained from the Traditional Chinese Medicine Systems Pharmacology database. Breast cancer-related genes are obtained from the GeneCards database. Major targets and pathways related to SYF treatment in breast cancer are identified by analyzing the above data. By conducting molecular docking analysis, we find that the active ingredients quercetin and luteolin bind well to the key targets KDR1, PPARG, SOD1, and VCAM1. In vitro experiments verify that SYF can reduce the proliferation, migration, and invasion ability of TNBC cells. Using a TNBC xenograft mouse model, we show that SYF could delay tumor growth and effectively inhibit the occurrence of breast cancer lung metastasis in vivo. PPARG, SOD1, KDR1, and VCAM1 are all regulated by SYF and may play important roles in SYF-mediated inhibition of TNBC recurrence and metastasis.
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Affiliation(s)
- Xiaojuan Yang
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Feifei Li
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Youyang Shi
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yuanyuan Wu
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Rui Yang
- Department of Breast Surgery, Shanxi Provincial Cancer Hospital, Taiyuan 030013, China
| | - Xiaofei Liu
- Department of Breast Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yang Zhang
- Department of Breast Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guangtao Zhang
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Mei Ma
- Institute of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Zhanyang Luo
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xianghui Han
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Ying Xie
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Sheng Liu
- Institute of Traditional Chinese Medicine Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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Xian M, Xu J, Zheng Y, Zhang L, Zhao J, Chen J, Li S, Lin L, Zhong Y, Yang Z, Xie T, Huang L, Ding Y. Network Pharmacology and Experimental Verification Reveal the Regulatory Mechanism of Chuanbeimu in Treating Chronic Obstructive Pulmonary Disease. Int J Chron Obstruct Pulmon Dis 2024; 19:799-813. [PMID: 38529478 PMCID: PMC10962663 DOI: 10.2147/copd.s442191] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/15/2024] [Indexed: 03/27/2024] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a common respiratory disorder in pulmonology. Chuanbeimu (CBM) is a traditional Chinese medicinal herb for treating COPD and has been widely utilized in clinical practice. However, the mechanism of CBM in the treatment of COPD remains incompletely understood. This study aims to investigate the underlying therapeutic mechanism of CBM for COPD using network pharmacology and experimental approaches. Methods Active ingredients and their targets were obtained from the Traditional Chinese Medicine Systems Pharmacology database. COPD-associated targets were retrieved from the GeneCards database. The common targets for CBM and COPD were identified through Venn diagram analysis. Protein-protein interaction (PPI) networks and disease-herb-ingredient-target networks were constructed. Subsequently, the results of the network pharmacology were validated by molecular docking and in vitro experiments. Results Seven active ingredients and 32 potential targets for CBM were identified as closely associated with COPD. The results of the disease-herb-ingredient-target network and PPI network showed that peimisine emerged as the core ingredient, and SRC, ADRB2, MMP2, and NOS3 were the potential targets for CBM in treating COPD. Molecular docking analysis confirmed that peimisine exhibited high binding affinity with SRC, ADRB2, MMP2, and NOS3. In vitro experiments demonstrated that peimisine significantly upregulated the expression of ADRB2 and NOS3 and downregulated the expression of SRC and MMP2. Conclusion These findings indicate that CBM may modulate the expression of SRC, ADRB2, MMP2, and NOS3, thereby exerting a protective effect against COPD.
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Affiliation(s)
- Meilan Xian
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China
- Department of General Diseases, Hainan Chengmei Hospital, Haikou, Hainan, 570300, People’s Republic of China
| | - Jiaoyuan Xu
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China
- Department of General Clinic, Longbo Health Hospital, Lingao County, Hainan, 571800, People’s Republic of China
| | - Yamei Zheng
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Lei Zhang
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Jie Zhao
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Jie Chen
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China
| | - Siguang Li
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China
| | - Lingsang Lin
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China
| | - Yi Zhong
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Zehua Yang
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Tian Xie
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Linhui Huang
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
| | - Yipeng Ding
- Department of General Practice, Hainan Affiliated Hospital of Hainan Medical University, Hainan General Hospital, Haikou, Hainan, 570311, People’s Republic of China
- Department of Pulmonary and Critical Care Medicine, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570311, People’s Republic of China
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Wu Z, Zhang C, Huang Y, Tao N, Wang T, Cai X, Wang Z, Li X. Tryptanthrin Derivative B1 Binds Viral Genome-Linked Protein (VPg) of Potato Virus Y. J Agric Food Chem 2024; 72:5699-5709. [PMID: 38462724 DOI: 10.1021/acs.jafc.4c01306] [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: 03/12/2024]
Abstract
Potato virus Y (PVY) is a plant virus that is known to be responsible for substantial economic losses in agriculture. Within the PVY genome, viral genome-linked protein (VPg) plays a pivotal role in the viral translation process. In this study, VPg was used as a potential target for analyzing the antiviral activity of tryptanthrin derivatives. In vitro, the dissociation constants of B1 with PVY VPg were 0.69 μmol/L (measured by microscale thermophoresis) and 4.01 μmol/L (measured via isothermal titration calorimetry). B1 also strongly bound to VPg proteins from three other Potyviruses. Moreover, in vivo experiments demonstrated that B1 effectively suppressed the expression of the PVY gene. Molecular docking experiments revealed that B1 formed a hydrogen bond with N121 and that no specific binding occurred between B1 and the PVY VPgN121A mutant. Therefore, N121 is a key amino acid residue in PVY VPg involved in B1 binding. These results highlight the potential of PVY VPg as a potential target for the development of antiviral agents.
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Affiliation(s)
- Zilin Wu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Chun Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Yuanqin Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Na Tao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Tao Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Xiaobo Cai
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Zhenchao Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
- College of Pharmacy, Guizhou University, Guiyang 550025, China
| | - Xiangyang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
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Chen S, Yi J, Kang Q, Song M, Raubenheimer D, Lu J. Identification of a Novel Peptide with Alcohol Dehydrogenase Activating Ability from Ethanol-Induced Lactococcus lactis: A Combined In Silico Prediction and In Vivo Validation. J Agric Food Chem 2024; 72:5746-5756. [PMID: 38450489 DOI: 10.1021/acs.jafc.3c07632] [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: 03/08/2024]
Abstract
Alcohol dehydrogenase (ADH) is a crucial rate-limiting enzyme in alcohol metabolism. Our previous research found that ethanol-induced intracellular extracts of Lactococcus lactis (L. lactis) could enhance alcohol metabolism in mice, but the responsible compounds remain unidentified. The study aimed to screen potential ADH-activating peptides from ethanol-induced L. lactis using virtual screening and molecular docking calculation. Among them, the pentapeptide FAPEG might bind to ADH through hydrophobic interaction and hydrogen bonds, then enhancing ADH activity. Spectroscopy analysis further investigated the peptide-enzyme interaction between FAPEG and ADH, including changes in the amino acid residue microenvironment and secondary structural alterations. Furthermore, FAPEG could protect against alcoholic liver injury (ALI) in mice by reducing blood alcohol concentration, enhancing the activity of antioxidant and alcohol metabolism enzymes, and attenuating alcohol-induced hepatotoxicity, which was related to the activation of the Nrf2/keap1/HO-1 signaling pathway. The study provided preliminary evidence that the generation of ADH-activating peptides in ethanol-induced L. lactis has the potential in preventing ALI in mice using in silico prediction and in vivo validation approaches.
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Affiliation(s)
- Sisi Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Physical Education College, Zhengzhou University, Zhengzhou 450001, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
| | - Juanjuan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Mo Song
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - David Raubenheimer
- Charles Perkins Centre, University of Sydney, Sydney 2006, New South Wales, Australia
| | - Jike Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
- Food Laboratory of Zhongyuan, Luohe 462300, China
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Zhu Z, Zhang W, Li Z, Zhao W, Liu C, Zhu B, He P, Tang S, Wu Y, Yang J, Yang Q. Rethinking Sweetener Discovering: Multiparameter Modeling of Molecular Docking Results between the T1R2-T1R3 Receptor and Compounds with Different Tastes. J Agric Food Chem 2024. [PMID: 38508871 DOI: 10.1021/acs.jafc.4c00407] [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: 03/22/2024]
Abstract
Molecular docking has been widely applied in the discovery of new sweeteners, yet the interpretation of computational results sometimes remains difficult. Here, the interaction between the T1R2-T1R3 sweet taste receptor and 66 tasting compounds, including 26 sweet, 19 bitter, and 21 sour substances was investigated by batch molecular docking processes. Statistical analysis of the docking results generated two novel methods of interpreting taste properties. Quantitative correlation between relative sweetness (RS) and docking results created a multiparameter model to predict sweetness intensity, whose correlation coefficient r = 0.74 is much higher than r = 0.17 for the linear correlation model between sweetness and binding energy. The improved correlation indicated that docking results besides binding energy contain undiscovered information about the ligand-protein interaction. Qualitative discriminant analysis of different tasting molecules generated an uncorrelated linear discriminant analysis (UDLA) model, which achieved an overall 93.1% accuracy in discriminating the taste of molecules, with specific accuracy for verifying sweet, bitter, and sour compounds reaching 88.0%, 92.1%, and 100%. These unprecedented models provide a unique perspective for interpreting computational results and may inspire future research on sweetener discovery.
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Affiliation(s)
- Zhiyang Zhu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Wei Zhang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Zhenjie Li
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Wei Zhao
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Chunbo Liu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Baokun Zhu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Pei He
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Shiyun Tang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Yiqin Wu
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Ji Yang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
| | - Qianxu Yang
- R&D Center, China Tobacco Yunnan Industrial Co., Ltd., Hongjin Road 367, Kunming 650224, China
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Zhao LX, Chen KY, Luo K, He XL, Gao S, Fu Y, Zou YL, Ye F. Design, Synthesis, and Biological Activity of Novel Phenyltriazolinone PPO Inhibitors Containing Five-Membered Heterocycles. J Agric Food Chem 2024; 72:5625-5635. [PMID: 38447070 DOI: 10.1021/acs.jafc.3c07411] [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: 03/08/2024]
Abstract
Protoporphyrinogen oxidase (PPO, EC 1.3.3.4) catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX, which is a key step in the synthesis of porphyrins in vivo. PPO inhibitors use protoporphyrinogen oxidase as the target and block the biosynthesis process of porphyrin by inhibiting the activity of the enzyme, eventually leading to plant death. In this paper, phenyl triazolinone was used as the parent structure, and the five-membered heterocycle with good herbicidal activity was introduced by using the principle of substructure splicing. According to the principle of bioisosterism, the sulfur atoms on the thiophene ring were replaced with oxygen atoms. Finally, 33 phenyl triazolinones and their derivatives were designed and synthesized, and their characterizations and biological activities were investigated. The in vitro PPO inhibitory activity and greenhouse herbicidal activity of 33 target compounds were determined, and compound D4 with better activity was screened out. The crop safety determination, field weeding effect determination, weeding spectrum determination, and crop metabolism study were carried out. The results showed that compound D4 showed good safety to corn, soybean, wheat, and peanut but poor selectivity to cotton. The field weeding effect of this compound is comparable to that of the commercial herbicide sulfentrazone. The herbicidal spectrum experiment showed that compound D4 had a wide herbicidal spectrum and a good growth inhibition effect on dicotyledonous weeds. Molecular docking results showed that compound D4 forms a hydrogen bond with amino acid residue Arg-98 in the tobacco mitochondria (mtPPO)-active pocket and forms two π-π stacking interactions with Phe-392. This indicates that compound D4 has stronger PPO inhibitory activity. This indicates that compound D4 has wide prospects for development.
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Affiliation(s)
- Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Kun-Yu Chen
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Kai Luo
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Xiao-Li He
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Yue-Li Zou
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin 150030, China
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Zhang K, Tang Y, Yu H, Yang J, Tao L, Xiang P. Discovery of lupus nephritis targeted inhibitors based on De novo molecular design: comprehensive application of vinardo scoring, ADMET analysis, and molecular dynamics simulation. J Biomol Struct Dyn 2024:1-14. [PMID: 38501728 DOI: 10.1080/07391102.2024.2329293] [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: 12/09/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Lupus Nephritis (LN) is an autoimmune disease affecting the kidneys, and conventional drug studies have limitations due to its imprecise and complex pathogenesis. Therefore, the aim of this study was to design a novel Lupus Nephritis-targeted drug with good clinical due potential, high potency and selectivity by computer-assisted approach.NIK belongs to the serine/threonine protein kinase, which is gaining attention as a drug target for Lupus Nephritis. we used bioinformatics, homology modelling and sequence comparison analysis, small molecule ab initio design, ADMET analysis, molecular docking, molecular dynamics simulation, and MM/PBSA analysis to design and explore the selectivity and efficiency of a novel Lupus Nephritis-targeting drug, ClImYnib, and a classical NIK inhibitor, NIK SMI1. We used bioinformatics techniques to determine the correlation between lupus nephritis and the NF-κB signaling pathway. De novo drugs design was used to create a NIK-targeted inhibitor, ClImYnib, with lower toxicity, after which we used molecular dynamics to simulate NIK SMI1 against ClImYnib, and the simulation results showed that ClImYnib had better selectivity and efficiency. Our research delves into the molecular mechanism of protein ligands, and we have designed and validated an excellent NIK inhibitor using multiple computational simulation methods. More importantly, it provides an idea of target designing small molecules.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kaiyuan Zhang
- School of Clinical Medicine, Bengbu Medical College, China
| | - Yingkai Tang
- Department of Anatomy, School of basic Medicine, Bengbu Medical College, China
| | - Haiyue Yu
- School of Clinical Medicine, Bengbu Medical College, China
| | - Jingtao Yang
- School of Clinical Medicine, Bengbu Medical College, China
| | - Lu Tao
- Central Laboratory, The Frist Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Ping Xiang
- Central Laboratory, The Frist Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
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Tabassum A, Nadeem H, Azeem F, Siddique MH, Zubair M, Kanwal A, Rasul I. An integrated network pharmacology approach to discover therapeutic mechanisms of Commiphora wightii for the treatment of Bell's palsy. J Biomol Struct Dyn 2024:1-18. [PMID: 38502688 DOI: 10.1080/07391102.2024.2326196] [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: 02/27/2024] [Indexed: 03/21/2024]
Abstract
Bell's palsy (BP) can result in facial paralysis. Inflammation or injury to the cranial nerves that regulate the facial muscles is primarily responsible for that disease. Commiphora wightii remains recognized as a cure for a few human ailments. This study focused on therapeutic phenomena of C. wightii for the treatment of Bell's palsy, utilizing the network drug discovery and molecular docking techniques. Active biological constituents of C. wightii were retrieved from literature and independent databases. Potential therapeutic targets (431) of 13 bioactive phytochemicals were fetched via SwissTargetPrediction tool. Putative intersecting targets (855) of Bell's palsy were computed through the DisGeNET and GeneCards datasets. Subsequently, by the analysis of potential shared targets (87) of C. wightii and Bell's palsy, a Venn diagram was drawn. DAVID database was used to evaluate gene functional annotations and enriched pathways that are involved in Bell's palsy. STRING database was used for generating the protein-protein relationship complex. Visual presentations of the interactions of potential targets to active chemical constituents were done by the Cytoscape. Whereas, the conformational research sorted out 10 key targets through the protein-protein interactions network. Moreover, the capacity of therapeutic ingredients to interact with a target inhibiting Bell's palsy was confirmed by molecular docking, which might ratify the findings of network pharmacology. In the molecular complex of AKT1-cholesterol, a 100-ns simulation unveiled a graceful stability, with a minimal 0.167 Å ligand shift and resilient hydrogen bonds (ASN54 and SER205). The final 20 ns showcased a P1 motif pirouette, gracefully forming aromatic bonds with H165 and W186, underscoring the complex's dynamic finesse. This study evaluated compound-target interactions and their impact on disease-related genes. It revealed that five genes (AKT1, TNF, MAPK3, EGFR and SRC) of C. wightii might be useful therapeutic targets for the treatment of Bell's palsy, as well as helping in lowering down the blood pressure.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ayesha Tabassum
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Habibullah Nadeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Hussnain Siddique
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Zubair
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Aqsa Kanwal
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Ijaz Rasul
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
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50
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Seyfi S, Salarinejad S, Moghimi S, Toolabi M, Sadeghian N, Tüzün B, Firoozpour L, Ketabforoosh SHME, Taslimi P, Foroumadi A. Synthesis, biological activities, and molecular docking studies of triazolo[4,3-b]triazine derivatives as a novel class of α-glucosidase and α-amylase inhibitors. Arch Pharm (Weinheim) 2024:e2300628. [PMID: 38501879 DOI: 10.1002/ardp.202300628] [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: 10/29/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/20/2024]
Abstract
In diabetes mellitus, amylase and glucosidase enzymes are the primary triggers. The main function of these enzymes is to break macromolecules into simple sugar units, which directly affect blood sugar levels by increasing blood permeability. To overcome this metabolic effect, there is a need for a potent and effective inhibitor capable of suppressing the enzymatic conversion of sugar macromolecules into their smaller units. Herein, we reported the discovery of a series of substituted triazolo[4,3-b][1,2,4]triazine derivatives as α-glucosidase and α-amylase inhibitors. All target compounds demonstrated significant inhibitory activities against α-glucosidase and α-amylase enzymes compared with acarbose as the positive control. The most potent compound 10k, 2-[(6-phenyl-[1,2,4]triazolo[4,3-b][1,2,4]triazin-3-yl)thio]-N-[4-(trifluoromethyl)phenyl]acetamide, demonstrated IC50 values of 31.87 and 24.64 nM against α-glucosidase and α-amylase enzymes, respectively. To study their mechanism of action, kinetic studies were also done, which determined the mode of inhibition of both enzymes. Molecular docking was used to confirm the binding interactions of the most active compounds.
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Affiliation(s)
- Soheila Seyfi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Salarinejad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Setareh Moghimi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Toolabi
- Department of Medicinal Chemistry, School of Pharmacy, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nastaran Sadeghian
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Burak Tüzün
- Plant and Animal Production Department, Technical Sciences Vocational School of Sivas, Sivas Cumhuriyet University, Sivas, Turkey
| | - Loghman Firoozpour
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima H M E Ketabforoosh
- Department of Medicinal Chemistry, School of Pharmacy, Alborz University of Medical Science, Karaj, Iran
| | - Parham Taslimi
- Department of Biotechnology, Faculty of Science, Bartin University, Bartin, Turkey
| | - Alireza Foroumadi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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