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Daniele-Silva A, Lucas Tenório CJ, Roberto da Costa Rodrigues J, Torres-Rêgo M, Cavalcanti FF, de Sousa Ferreira S, Pontes da Silva D, Assunção Ferreira MR, de Freitas Fernandes-Pedrosa M, Lira Soares LA. Anti-inflammatory and antiophidic effects of extract of Hymenaea eriogyne benth and structure-activity relationship prediction of the major markers in silico. JOURNAL OF ETHNOPHARMACOLOGY 2024; 335:118619. [PMID: 39053713 DOI: 10.1016/j.jep.2024.118619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/19/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Hymenaea eriogyne Benth (Fabaceae) is popularly known as "Jatobá". Despite its use in folk medicine to treat inflammatory disorders, there are no descriptions that show its anti-inflammatory potential. AIM OF THE STUDY In this sense, this study aimed to evaluate the anti-inflammatory and antivenom action of bark and leaves extract of H. eriogyne. MATERIALS AND METHODS The in vivo anti-inflammatory activity was conducted by carrageenan-induced paw edema and zymosan-induced air pouch models, evaluating the edematogenic effect, leukocyte migration, protein concentration, levels of pro-inflammatory cytokines, malondialdehyde (MDA) and myeloperoxidase (MPO) activity. The antivenom potential was investigated in vitro on the enzymatic action (proteolytic, phospholipase and hyaluronidase) of Bothrops brazili and B. leucurus venom, as well as in vivo on the paw edema model induced by B. leucurus. Furthermore, the influence of its markers (astilbin and rutin) on MPO activity was investigated in silico. For molecular docking, AutodockVina, Biovia Discovery Studio, and Chimera 1.16 software were used. RESULTS The extracts and bark and leaves of H. eriogyne revealed a high anti-inflammatory effect, with a reduction in all inflammatory parameters evaluated. The bark extract showed superior results when compared to the leaf extract, suggesting the influence of the astilbin concentration, higher in the bark, on the anti-inflammatory action. In addition, only the H. eriogyne bark extract was able to reduce MDA, indicating an associated antioxidant effect. Regarding the in vitro antivenom action, the extracts (bark and leaves) revealed the ability to inhibit the proteolytic, phospholipase and hyaluronidase action of both bothropic venom, with a greater effect against B. leucurus venom. In vivo, extracts from the bark and leaves of H. eriogyne (50-200 mg/kg) showed antiedematogenic activity, reducing the release of MPO and pro-inflammatory cytokines, indicating the presence of bioactive components useful in controlling the inflammatory process induced by the venom. In the in silico assays, astilbin and rutin showed reversible interactions of 9 possible positions and orientations towards MPO, with affinities of -9.5 and -10.4 kcal/mol and interactions with Phe407, Gln91, His95 and Arg239, important active pockets of MPO. Rutin demonstrated more effective types of interactions with MPO. CONCLUSION This approach reveals for the first time the anti-inflammatory action of H. eriogyne bark and leaf extracts in vivo, as well as its antiophidic potential. Moreover, the distinct effect of pharmacogens as antioxidant agents and distinct effect of astilbin and rutin under MPO sheds light on the different anti-inflammatory mechanisms of bioactive compounds present in H. eriogyne extracts, with high potential for the prospection of new pharmacological agents.
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Affiliation(s)
- Alessandra Daniele-Silva
- Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, Brazil; Laboratory of Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Federal University of Rio Grande Do Norte, Brazil
| | - Camylla Janiele Lucas Tenório
- Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, Brazil; Graduate Program of Therapeutic Innovation, Center for Biosciences, Federal University of Pernambuco, Brazil
| | | | - Manoela Torres-Rêgo
- Graduate Program of Chemistry, Chemistry Institute, Federal University of Rio Grande Do Norte, Brazil
| | - Felipe França Cavalcanti
- Graduate Program of Chemistry, Chemistry Institute, Federal University of Rio Grande Do Norte, Brazil
| | - Sarah de Sousa Ferreira
- Laboratory of Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Federal University of Rio Grande Do Norte, Brazil
| | - Diana Pontes da Silva
- Laboratory of Technology and Pharmaceutical Biotechnology, Faculty of Pharmacy, Federal University of Rio Grande Do Norte, Brazil
| | | | | | - Luiz Alberto Lira Soares
- Laboratory of Pharmacognosy, Department of Pharmaceutical Sciences, Federal University of Pernambuco, Recife, Brazil.
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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] [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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Haratipour Z, Foutch D, Blind RD. A novel heuristic of rigid docking scores positively correlates with full-length nuclear receptor LRH-1 regulation. Comput Struct Biotechnol J 2024; 23:3065-3080. [PMID: 39185441 PMCID: PMC11342790 DOI: 10.1016/j.csbj.2024.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/26/2024] [Accepted: 07/26/2024] [Indexed: 08/27/2024] Open
Abstract
The nuclear receptor Liver Receptor Homolog-1 (LRH-1, NR5A2) is a ligand-regulated transcription factor and validated drug target for several human diseases. LRH-1 activation is regulated by small molecule ligands, which bind to the ligand binding domain (LBD) within the full-length LRH-1. We recently identified 57 compounds that bind LRH-1, and unexpectedly found these compounds regulated either the isolated LBD, or the full-length LRH-1 in cells, with little overlap. Here, we correlated compound binding energy from a single rigid-body scoring function with full-length LRH-1 activity in cells. Although docking scores of the 57 hit compounds did not correlate with LRH-1 regulation in wet lab assays, a subset of the compounds had large differences in binding energy docked to the isolated LBD vs. full-length LRH-1, which we used to empirically derive a new metric of the docking scores we call "ΔΔG". Initial regressions, correlations and contingency analyses all suggest compounds with high ΔΔG values more frequently regulated LRH-1 in wet lab assays. We then docked all 57 compounds to 18 separate crystal structures of LRH-1 to obtain averaged ΔΔG values for each compound, which robustly and reproducibly associated with full-length LRH-1 activity in cells. Network analyses on the 18 crystal structures of LRH-1 suggest unique communication paths exist between the subsets of LRH-1 crystal structures that produced high vs. low ΔΔG values, identifying a structural relationship between ΔΔG and the position of Helix 6, a previously established regulatory helix important for LRH-1 regulation. Together, these data suggest rigid-body computational docking can be used to quickly calculate ΔΔG, which positively correlated with the ability of these 57 hit compounds to regulate full-length LRH-1 in cell-based assays. We propose ΔΔG as a novel computational tool that can be applied to LRH-1 drug screens to prioritize compounds for resource-intense secondary screening.
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Affiliation(s)
- Zeinab Haratipour
- Vanderbilt University Medical Center, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Nashville, TN 37232, USA
- Austin Peay State University, Department of Chemistry
| | - David Foutch
- Vanderbilt University Medical Center, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Nashville, TN 37232, USA
| | - Raymond D. Blind
- Vanderbilt University Medical Center, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, Nashville, TN 37232, USA
- Vanderbilt University School of Medicine, Departments of Biochemistry and Pharmacology, Nashville, TN 37232, USA
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Chen J, Ye W. Molecular mechanisms underlying Tao-Hong-Si-Wu decoction treating hyperpigmentation based on network pharmacology, Mendelian randomization analysis, and experimental verification. PHARMACEUTICAL BIOLOGY 2024; 62:296-313. [PMID: 38555860 DOI: 10.1080/13880209.2024.2330609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/02/2024] [Indexed: 04/02/2024]
Abstract
CONTEXT Hyperpigmentation, a common skin condition marked by excessive melanin production, currently has limited effective treatment options. OBJECTIVE This study explores the effects of Tao-Hong-Si-Wu decoction (THSWD) on hyperpigmentation and to elucidate the underlying mechanisms. MATERIALS AND METHODS We employed network pharmacology, Mendelian randomization, and molecular docking to identify THSWD's hub targets and mechanisms against hyperpigmentation. The Cell Counting Kit-8 (CCK-8) assay determined suitable THSWD treatment concentrations for PIG1 cells. These cells were exposed to graded concentrations of THSWD-containing serum (2.5%, 5%, 10%, 15%, 20%, 30%, 40%, and 50%) and treated with α-MSH (100 nM) to induce an in vitro hyperpigmentation model. Assessments included melanin content, tyrosinase activity, and Western blotting. RESULTS ALB, IL6, and MAPK3 emerged as primary targets, while quercetin, apigenin, and luteolin were the core active ingredients. The CCK-8 assay indicated that concentrations between 2.5% and 20% were suitable for PIG1 cells, with a 50% cytotoxicity concentration (CC50) of 32.14%. THSWD treatment significantly reduced melanin content and tyrosinase activity in α-MSH-induced PIG1 cells, along with downregulating MC1R and MITF expression. THSWD increased ALB and p-MAPK3/MAPK3 levels and decreased IL6 expression in the model cells. DISCUSSION AND CONCLUSION THSWD mitigates hyperpigmentation by targeting ALB, IL6, and MAPK3. This study paves the way for clinical applications of THSWD as a novel treatment for hyperpigmentation and offers new targeted therapeutic strategies.
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Affiliation(s)
- Jun Chen
- Department of Geriatrics, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
| | - Wenyi Ye
- Department of Traditional Chinese Internal Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, China
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Bai YR, Yang X, Chen KT, Cuan XD, Zhang YD, Zhou L, Yang L, Liu HM, Yuan S. A comprehensive review of new small molecule drugs approved by the FDA in 2022: Advance and prospect. Eur J Med Chem 2024; 277:116759. [PMID: 39137454 DOI: 10.1016/j.ejmech.2024.116759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024]
Abstract
In 2022, the U.S. Food and Drug Administration approved a total of 16 marketing applications for small molecule drugs, which not only provided dominant scaffolds but also introduced novel mechanisms of action and clinical indications. The successful cases provide valuable information for optimizing efficacy and enhancing pharmacokinetic properties through strategies like macrocyclization, bioequivalent group utilization, prodrug synthesis, and conformation restriction. Therefore, gaining an in-depth understanding of the design principles and strategies underlying these drugs will greatly facilitate the development of new therapeutic agents. This review focuses on the research and development process of these newly approved small molecule drugs including drug design, structural modification, and improvement of pharmacokinetic properties to inspire future research in this field.
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Affiliation(s)
- Yi-Ru Bai
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China
| | - Xin Yang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Ke-Tong Chen
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Xiao-Dan Cuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yao-Dong Zhang
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Li Zhou
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Li Yang
- Department of Obstetrics and Gynecology, Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
| | - Shuo Yuan
- Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Zhengzhou, 450001, China.
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Wang W, Wang H, Luo Y, Li Z, Li J. Discovery of petroleum ether extract of eclipta targeting p53/Fas pathway for the treatment of chemotherapy-induced alopecia: Network pharmacology and experimental validation. JOURNAL OF ETHNOPHARMACOLOGY 2024; 333:118405. [PMID: 38844249 DOI: 10.1016/j.jep.2024.118405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/19/2024] [Accepted: 05/27/2024] [Indexed: 06/15/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ecliptea herba, a traditional Chinese herbal medicine for hair loss, was first recorded in the Tang Dynasty's 'Qian Jin Yue Ling', of which the active ingredients and mechanisms of action in the treatment of chemotherapy-induced hair loss remain poorly investigated. AIM OF THE STUDY To investigate the effects of the petroleum ether extract of Eclipta (PEE) on alopecia and follicle damage and elucidate its potential therapeutic mechanisms using the integration of network pharmacology, bioinformatics, and experimental validation. MATERIALS AND METHODS UPLC-MS was used to analyse the chemical composition of PEE. A network pharmacology approach was employed to establish the 'components-targets-pathways' network of PEE to explore potential therapeutic pathways and targets. Molecular docking was used for validation, and the mechanism of PEE in treating chemotherapy-induced alopecia (CIA) was elucidated using in vitro and in vivo on CIA models. RESULTS UPLC-MS analysis of PEE revealed 185 components, while network pharmacology and molecular docking analyses revealed potential active compounds and their target molecules, suggesting the involvement of core genes, such as TP53, ESR1, AKT1, IL6, TNF, and EGFR. The key components included wedelolactone, dimethyl-wedelolactone, luteoloside, linarin, and hispidulin. In vivo, PEE promoted hair growth, restored the number of hair follicles, and reduced follicle apoptosis. Conversely, in vitro, PEE enhanced cell viability, reduced apoptosis, and protected HaCaT cells from damage induced by 4-hydroperoxycyclophosphamide (4-HC). CONCLUSIONS PEE alleviated hair follicle damage in CIA mice by inhibiting the P53/Fas pathway, which may be associated with inhibiting hair follicle cell apoptosis. This study provides a novel therapeutic strategy for treating cyclophosphamide-induced hair loss.
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Affiliation(s)
- Wuji Wang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China; Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, 563006, China; Department of Pharmacology, School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China.
| | - Honglan Wang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China; Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, 563006, China; Department of Pharmacology, School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China
| | - Yang Luo
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China; Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, 563006, China; Department of Pharmacology, School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China
| | - Zheng Li
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China; Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, 563006, China; Department of Pharmacology, School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China
| | - Jingjie Li
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, 563006, China; Key Laboratory of Basic Pharmacology of Guizhou Province, Zunyi Medical University, Zunyi, 563006, China; Department of Pharmacology, School of Pharmacy, Zunyi Medical University, Zunyi, 563006, China.
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Zhao Y, Zhou Z, Cui X, Yu Y, Yan P, Zhao W. Enhancing insight into ferroptosis mechanisms in sepsis: A genomic and pharmacological approach integrating single-cell sequencing and Mendelian randomization. Int Immunopharmacol 2024; 140:112910. [PMID: 39121604 DOI: 10.1016/j.intimp.2024.112910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
This research investigated the intricate relationship between ferroptosis and sepsis by utilizing advanced genomic and pharmacological methodologies. Specifically, we obtained expression quantitative trait loci (eQTLs) for 435 genes associated with ferroptosis from the eQTLGen Consortium and detected notable cis-eQTLs for 281 of these genes. Next, we conducted a detailed analysis to assess the impact of these eQTLs on susceptibility to sepsis using Mendelian randomization (MR) with data from a cohort of 10,154 sepsis patients and 452,764 controls sourced from the UK Biobank. MR analysis revealed 16 ferroptosis-related genes that exhibited significant associations with sepsis outcomes. To bolster the robustness of these findings, sensitivity analyses were performed to assess pleiotropy and heterogeneity, thus confirming the reliability of the causal inferences. Furthermore, single-cell RNA sequencing data from sepsis patients offered a detailed examination of gene expression profiles, demonstrating varying levels of ferroptosis marker expression across different cell types. Pathway enrichment analysis utilizing gene set enrichment analysis (GSEA) further revealed the key biological pathways involved in the progression of sepsis. Additionally, the use of computational molecular docking facilitated the prediction of interactions between identified genes and potential therapeutic compounds, highlighting novel drug targets. In conclusion, our integrated approach combining genomics and pharmacology offers valuable insights into the involvement of ferroptosis in sepsis, laying the groundwork for potential therapeutic strategies targeting this cell death pathway to enhance sepsis management.
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Affiliation(s)
- Yuanqi Zhao
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Zijian Zhou
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Xiuyu Cui
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Yiwei Yu
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China
| | - Ping Yan
- Department of Gastroenterology, First Affiliated Hospital of Dali University, Dali, China.
| | - Weidong Zhao
- Department of Clinical Laboratory, School of Clinical Medicine, Dali University, Dali, China; Department of Clinical Laboratory, Second Infectious Disease Hospital of Yunnan Province, Dali, China; Immunology Discipline Team, School of Basic Medicine, Dali University, Dali, China.
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Tang L, Wang D, Chang H, Liu Z, Zhang X, Feng X, Han L. Treating ischemic stroke by improving vascular structure and promoting angiogenesis using Taohong Siwu Decoction: An integrative pharmacology strategy. JOURNAL OF ETHNOPHARMACOLOGY 2024; 332:118372. [PMID: 38777084 DOI: 10.1016/j.jep.2024.118372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Neovessels represent a crucial therapeutic target and strategy for repairing ischemic tissue. Taohong Siwu Decoction (THSWD) exhibits potential in promoting angiogenesis to address ischemic stroke (IS). However, its impact on neovessel structure and function, alongside the underlying molecular mechanisms, remains elusive. AIM OF THE STUDY Our aim is to investigate the protective effects of THSWD on neovessel structure and function, as well as the associated molecular mechanisms, utilizing an integrative pharmacological approach. MATERIALS AND METHODS We initially employed behavioral tests, 2,3,5-triphenyltetrazolium chloride (TTC) staining, Haematoxylin-eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), Laser Doppler flowmetry (LDF), Evans blue staining, and immunofluorescence to evaluate the protective effects of THSWD on neovascular structure and function in middle cerebral artery occlusion/reperfusion (MCAO/R) rats. Subsequently, we utilized network pharmacology, metabolomics, and experimental validation to elucidate the underlying molecular mechanisms of THSWD in enhancing neovascular structure and function. RESULT In addition to significantly reducing neurological deficits and cerebral infarct volume, THSWD mitigated pathological damage, blood-brain barrier (BBB) leakage, and cerebral blood flow disruption. Moreover, it preserved neovascular structure and stimulated angiogenesis. THSWD demonstrated potential in ameliorating cerebral microvascular metabolic disturbances including lipoic acid metabolism, fructose and mannose metabolism, purine metabolism, and ether lipid metabolism. Consequently, it exhibited multifaceted therapeutic effects, encompassing anti-inflammatory, antioxidant, energy metabolism modulation, and antiplatelet aggregation properties. CONCLUSION THSWD exhibited protective effects on cerebral vascular structure and function and facilitated angiogenesis by rectifying cerebral microvascular metabolic disturbances in MCAO/R rats. Furthermore, integrated pharmacology offers a promising approach for studying the intricate traditional Chinese medicine (TCM) system in IS treatment.
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Affiliation(s)
- Linfeng Tang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Dandan Wang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Hao Chang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Zhuqing Liu
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Xueting Zhang
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China
| | - Xuefeng Feng
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, 230031, China
| | - Lan Han
- Department of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China; Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China; MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, 230012, China.
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Li H, Kang L, Dou S, Zhang Y, Zhang Y, Li N, Cao Y, Liu M, Han D, Li K, Feng W. Gleditsiae Sinensis Fructus ingredients and mechanism in anti-asthmatic bronchitis research. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 133:155857. [PMID: 39074420 DOI: 10.1016/j.phymed.2024.155857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 06/04/2024] [Accepted: 07/02/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND Gleditsiae Sinensis Fructus (GSF) is commonly used in traditional medicine to treat respiratory diseases such as bronchial asthma. However, there is a lack of research on the chemical composition of GSF and the pharmacological substance and mechanism of action for GSF in treating bronchial asthma. PURPOSE The chemical constituents of GSF were analyzed using ultrahigh-performance liquid chromatography-quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS). In this study, we combined network pharmacology, molecular docking techniques, and experimental validation to explore the therapeutic efficacy and underlying mechanism of GSF in the treatment of bronchial asthma. METHODS Characterization of the chemical constituents of GSF was conducted using UHPLC-Q-Orbitrap HRMS. The identified chemical components were subjected to screening for active ingredients in the Swiss Absorption, Distribution, Metabolism, and Excretion (ADME) database. Relevant databases were utilized to retrieve target proteins for the active ingredients and targets associated with bronchial asthma disease, and the common targets between the two were selected. Subsequently, the protein-protein interaction (PPI) network was constructed using the String database and Cytoscape software to identify key targets. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using the Metascape database. The "component-common target" network was constructed using Cytoscape to identify the primary active ingredients. Molecular docking validation was conducted using AutoDock software. The bronchial asthma mouse model was established using ovalbumin (OVA), and the lung organ index of the mice was measured. Lung tissue pathological changes were observed using hematoxylin and eosin (HE), Periodic Acid-Schiff (PAS), and Masson staining. The respiratory resistance (Penh) of the mice was assessed using a pulmonary function test instrument. An enzyme-linked immunosorbent assay (ELISA) was used to determine the levels of IgE, IL-4, IL-5, and IL-13 in the mouse serum. Immunofluorescence staining was performed to detect the protein expression levels of AKT and PI3K in the lung tissues. An in vitro experiment was performed to observe the effects of echinocystic acid (EA) on IL-4 stimulated Human ASMCs (hASMCs). Cell viability was measured using a CCK-8 assay to calculate the IC50 value of the EA. A wound healing test was conducted to observe the effect of EA on degree of healing. RT-qPCR was performed to detect the influence of EA on the mRNA expression levels of ALB, SRC, TNF-α, AKT1, and IL6 in the cells. RESULTS A total of 95 chemical constituents were identified from the GSF. Of these, 37 were identified as active ingredients. There were 169 overlapping targets between the active ingredients and the disease targets. A topological analysis of the protein-protein interaction (PPI) network identified the core targets as IL6, TNF, ALB, AKT1, and SRC. An enrichment analysis revealed that the treatment of bronchial asthma with GSF primarily involved the AGE-RAGE signaling pathway and the PI3K-Akt signaling pathway, among others. The primary active ingredients included 13(s)-HOTRE, linolenic acid, and acacetin. The molecular docking results demonstrated a favorable binding activity between the critical components of GSF and the core targets. Animal experimental studies indicated that GSF effectively improved symptoms, lung function, and lung tissue pathological changes in the OVA-induced asthmatic mice, while alleviating inflammatory responses. GSF decreased the fluorescent intensity of the AKT and PI3K proteins. The IC50 value of EA was 30.02μg/ml. EA (30) significantly promoted the proliferation of IL4-stimulated hASMCs cells. EA (30) significantly increased the expression of ALB and SRC mRNA and decreased the expressions of TNF-α, AKT, and IL6 mRNA. CONCLUSION The multiple active ingredients found in GSF exerted their anti-inflammatory effects through multiple targets and pathways. This preliminary study revealed the core target and the mechanism of action underlying its treatment of bronchial asthma. These findings provided valuable insights for further research on the pharmacological substances and quality control of GSF.
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Affiliation(s)
- Hongwei Li
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Research Center for Special Processing Technology of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China
| | - Le Kang
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Research Center for Special Processing Technology of Chinese Medicine, Zhengzhou 450046, China.
| | - Shirong Dou
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China
| | - Yiming Zhang
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China
| | - Yumei Zhang
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China
| | - Ning Li
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China
| | - Yangang Cao
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China
| | - Mengyun Liu
- Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Deen Han
- Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Kai Li
- Henan University of Chinese Medicine, Zhengzhou 450046, China; Henan Research Center for Special Processing Technology of Chinese Medicine, Zhengzhou 450046, China; Collaborative Innovation Center of Research and Development on the Whole Industry Chain of Yu-Yao, Henan Province, Zhengzhou 450046, China.
| | - Weisheng Feng
- Henan University of Chinese Medicine, Zhengzhou 450046, China.
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Abdelfattah MM, El-Hammady MA, Mostafa A, Kutkat O, Abo Shama NM, Nafie MS, El-Ebeedy DA, Abdel Azeiz AZ. Identification of potential antiviral compounds from Egyptian Red Sea soft corals against Middle East respiratory syndrome coronavirus. Nat Prod Res 2024; 38:3353-3359. [PMID: 37589288 DOI: 10.1080/14786419.2023.2247535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023]
Abstract
The ongoing threat of Middle East respiratory syndrome coronavirus (MERS-CoV) underscores the importance of developing effective antiviral treatments. Current research was conducted to identify potential antiviral compounds from soft corals: Sinularia leptoclados, Sarcophyton ehrenbergi, Nephthea sp., Sarcophyton glaucum and Sarcophyton regulare. The antiviral activities of soft corals extracts were evaluated against MERS-CoV. Gas chromatography-mass spectrometry (GC-MS) was used to identify bioactive compounds. The molecular docking was performed to examine the identified compounds for their binding potentials towards three pathogenic factors of MERS-CoV: main protease, spike and non-structural protein 16/10 complex. The methanolic extract of soft coral Sarcophyton regulare exhibited the most promising activity with 50% inhibitory concentration (IC50) of 4.29 µg/ml and selective index (SI) of 112.2. Among the identified compounds in the active fraction, the molecular docking showed that two fatty acid esters: hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester and octadecanoic acid, 2-hydroxy-1 (hydroxymethyl) ethyl ester had promising docking scores.
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Affiliation(s)
- Mariam M Abdelfattah
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th of October City, Egypt
| | | | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Omnia Kutkat
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Noura M Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | | | - Dalia A El-Ebeedy
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th of October City, Egypt
| | - Ahmed Z Abdel Azeiz
- College of Biotechnology, Misr University for Science and Technology (MUST), 6th of October City, Egypt
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Wang Y, Su L, Hu Z, Peng S, Li N, Fu H, Wang B, Wu H. Resveratrol suppresses liver cancer progression by downregulating AKR1C3: targeting HCC with HSA nanomaterial as a carrier to enhance therapeutic efficacy. Apoptosis 2024; 29:1429-1453. [PMID: 39023830 DOI: 10.1007/s10495-024-01995-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
The enzyme AKR1C3 plays a crucial role in hormone and drug metabolism and is associated with abnormal expression in liver cancer, leading to tumor progression and poor prognosis. Nanoparticles modified with HSA can modulate the tumor microenvironment by enhancing photodynamic therapy to induce apoptosis in tumor cells and alleviate hypoxia. Therefore, exploring the potential regulatory mechanisms of resveratrol on AKR1C3 through the construction of HSA-RSV NPs carriers holds significant theoretical and clinical implications for the treatment of liver cancer. The aim of this study is to investigate the targeted regulation of AKR1C3 expression through the loading of resveratrol (RSV) on nanomaterials HSA-RSV NPs (Nanoparticles) in order to alleviate tumor hypoxia and inhibit the progression of hepatocellular carcinoma (HCC), and to explore its molecular mechanism. PubChem database and PharmMapper server were used to screen the target genes of RSV. HCC-related differentially expressed genes (DEGs) were analyzed through the GEO dataset, and relevant genes were retrieved from the GeneCards database, resulting in the intersection of the three to obtain candidate DEGs. GO and KEGG enrichment analyses were performed on the candidate DEGs to analyze the potential cellular functions and molecular signaling pathways affected by the main target genes. The cytohubba plugin was used to screen the top 10 target genes ranked by Degree and further intersected the results of LASSO and Random Forest (RF) to obtain hub genes. The expression analysis of hub genes and the prediction of malignant tumor prognosis were conducted. Furthermore, a pharmacophore model was constructed using PharmMapper. Molecular docking simulations were performed using AutoDockTools 1.5.6 software, and ROC curve analysis was performed to determine the core target. In vitro cell experiments were carried out by selecting appropriate HCC cell lines, treating HCC cells with different concentrations of RSV, or silencing or overexpressing AKR1C3 using lentivirus. CCK-8, clone formation, flow cytometry, scratch experiment, and Transwell were used to measure cancer cell viability, proliferation, migration, invasion, and apoptosis, respectively. Cellular oxygen consumption rate was analyzed using the Seahorse XF24 analyzer. HSA-RSV NPs were prepared, and their characterization and cytotoxicity were evaluated. The biological functional changes of HCC cells after treatment were detected. An HCC subcutaneous xenograft model was established in mice using HepG2 cell lines. HSA-RSV NPs were injected via the tail vein, with a control group set, to observe changes in tumor growth, tumor targeting of NPs, and biological safety. TUNEL, Ki67, and APC-hypoxia probe staining were performed on excised tumor tissue to detect tumor cell proliferation, apoptosis, and hypoxia. Lentivirus was used to silence or overexpress AKR1C3 simultaneously with the injection of HSA-RSV NPs via the tail vein to assess the impact of AKR1C3 on the regulation of HSA-RSV NPs in HCC progression. Bioinformatics analysis revealed that AKR1C3 is an important target gene involved in the regulation of HCC by RSV, which is associated with the prognosis of HCC patients and upregulated in expression. In vitro cell experiments showed that RSV significantly inhibits the respiratory metabolism of HCC cells, suppressing their proliferation, migration, and invasion and promoting apoptosis. Silencing AKR1C3 further enhances the toxicity of RSV towards HCC cells. The characterization and cytotoxicity experiments of nanomaterials demonstrated the successful construction of HSA-RSV NPs, which exhibited stronger inhibitory effects on HCC cells. In vivo, animal experiments further confirmed that targeted downregulation of AKR1C3 by HSA-RSV NPs suppresses the progression of HCC and tumor hypoxia while exhibiting tumor targeting and biological safety. Targeted downregulation of AKR1C3 by HSA-RSV NPs can alleviate HCC tumor hypoxia and inhibit the progression of HCC.
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Affiliation(s)
- Ying Wang
- Operating Room, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, 121001, China
| | - Longxiang Su
- Department of Critical Care Medicine, Peking Union Medical College Hospital, Beijing, 100730, China
| | - Zhansheng Hu
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, Liaoning Province, 121001, China
| | - Shuang Peng
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, Liaoning Province, 121001, China
| | - Na Li
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, Liaoning Province, 121001, China
| | - Haiyan Fu
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, Liaoning Province, 121001, China
| | - Baoquan Wang
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, Liaoning Province, 121001, China
| | - Huiping Wu
- Intensive Care Unit, The First Affiliated Hospital of Jinzhou Medical University, No. 2, Section 5, Renmin Street, Guta District, Jinzhou, Liaoning Province, 121001, China.
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Zhang WQ, Sun JX, Lan ST, Sun XM, Guo YJ, Wen BC, Chen J, Liu G. Regulation of Fuzheng Huayu capsule on inhibiting the fibrosis-associated hepatocellular carcinogenesis. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024; 26:1219-1238. [PMID: 38780602 DOI: 10.1080/10286020.2024.2355132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
In the current study, bioinformatics analysis of the hepatocellular carcinoma (HCC) dataset was conducted with the hepatoprotective effect of the Fuzheng Huayu (FZHY) capsule against the diethylnitrosamine-induced HCC progression analyzed. Eight cell clusters were defined and tanshinone IIA, arachidonic acid, and quercetin, compounds of the FZHY capsule, inhibit HCC progression-related fibrosis by regulating the expression of PLAU and IGFBP3. Combined with the ameliorative effect of the FZHY capsule against liver dysfunctions and expression of PLAU and IGFBP3, our study confirmed the effect of the FZHY capsule on inhibiting the fibrosis-associated HCC progression via regulating the expression of PLAU and IGFBP3.
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Affiliation(s)
- Wen-Qi Zhang
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Jia-Xin Sun
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Shu-Ting Lan
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Xiao-Mei Sun
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Yi-Jing Guo
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Bi-Chao Wen
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Jie Chen
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
| | - Gang Liu
- Key Laboratory of Medical Cell Biology, Department of Achievement Transformation, Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, China
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Jiang T, Li C, Li Y, Hu W, Guo J, Du X, Meng Q, Zhu X, Song W, Guo J, Su X. Multi-omics and Bioinformatics for the Investigation of Therapeutic Mechanism of Roucongrong Pill against Postmenopausal Osteoporosis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 337:118873. [PMID: 39362330 DOI: 10.1016/j.jep.2024.118873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 09/29/2024] [Accepted: 09/30/2024] [Indexed: 10/05/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The Roucongrong Pill (RCRP), originating from the historical General Medical Collection of Royal Benevolence, is frequently used to treat postmenopausal osteoporosis (PMOP). Despite its prevalent application, the specific anti-osteoporotic mechanisms of RCRP remain to be elucidated. AIM OF THE STUDY This study aims to elucidate the therapeutic mechanism of RCRP in the context of ovariectomy (OVX)-induced PMOP in rats. By employing an integrative approach, the research combines medicinal chemistry, gut microbiota (GM) profiling, metabolomics, MetOrigin traceability, network pharmacology, molecular docking, and molecular dynamics simulations to deliver a comprehensive analysis. MATERIALS AND METHODS Sprague-Dawley (SD) rats underwent bilateral OVX to establish a PMOP model. The therapeutic efficacy of RCRP was evaluated through bone metrics (BMD, bone strength, BV/TV, Tb.Sp), hematoxylin and eosin (H&E) histological assessment, and bone metabolism markers (OPG, BALP, TRACP-5b, β-CTX, RANKL). Fecal metabolomics and 16S rDNA sequencing were employed to assess the influence of RCRP on GM and metabolite profiles. Furthermore, MetOrigin facilitated the traceability analysis of relevant metabolites. Molecular docking identified potential RCRP compounds with anti-PMOP activity, while their stability and protein interactions were assessed through molecular dynamics simulations. Network pharmacology further confirms the targets of action. RESULTS RCRP alleviated PMOP in rats, enhancing bone strength, cortical and trabecular BMD, BV/TV, and serum OPG levels, while reducing Tb.Sp, serum BALP, TRACP-5b, β-CTX, and RANKL concentrations. A total of twenty-six distinct metabolites were identified, of which ten-tribufos, sulfoacetic acid, betamethasone dipropionate, 9-oxooctadeca-10,12,15-trienoic acid, menatetrenone, piperlongumine, maltopentaose, enol-phenylpyruvate, catechol, pentaacetate, and (+)-2-methylpropanoic acid-exhibited correlations with six GM species: Turicibacter, Roseburia, Colidextribacter, Helicobacter, Odoribacter, and Lachnoclostridium, as determined by Spearman's correlation analysis. Notably, MetOrigin revealed the microbial metabolism of taurine and hypotaurine, along with host-specific steroid hormone synthesis. Computational docking studies demonstrated robust interactions between five RCRP-derived steroids (hydroxyecdysone, corticosterone, trilostane, 5α-androstan-3,6,17-trione, and cortisol) and key enzymes (estradiol 17α-dehydrogenase and UDP-glucuronosyltransferase), suggesting a potential enhancement of therapeutic efficacy against PMOP. Furthermore, molecular dynamics simulations indicated stable interactions between hydroxyecdysone and two proteins, with binding free energies of -67.427 kJ/mol and -156.948 kJ/mol, respectively. Through network pharmacology and molecular docking approaches, potential targets of these metabolites were identified, including estrogen receptors ESR1 and ESR2, dual specificity phosphatase 6 (DUSP6), sex hormone-binding globulin (SHBG), prostaglandin E receptor 4 (PTGER4), cannabinoid receptor 2 (CNR2), cathepsin K (CTSK), and androgen receptor (AR). CONCLUSIONS RCRP effectively mitigates OVX-induced bone loss in PMOP rats by modulating GM and associated metabolites, along with their potential targets and key metabolic pathways, including taurine and hypotaurine metabolism, as well as steroid hormone biosynthesis. These findings offer new insights into the therapeutic mechanisms by which RCRP may alleviate PMOP.
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Affiliation(s)
- Tao Jiang
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Chenhao Li
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Yufen Li
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Wanli Hu
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Jiurui Guo
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Xingchen Du
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Qianting Meng
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Xiaojuan Zhu
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Wu Song
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Junpeng Guo
- Changchun University of Chinese Medicine, Changchun 130117, China.
| | - Xin Su
- Changchun University of Chinese Medicine, Changchun 130117, China.
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Gao J, Li D, Feng Z, Zhu X, Yang F, Zhang B, Hu M, Wang Y, Feng H, Yu Y, Xie Q, Chen Z, Li Y. Diterpenoid DGT alleviates atopic dermatitis-like responses in vitro and in vivo via targeting IL-4Rα. Biomed Pharmacother 2024; 179:117321. [PMID: 39191027 DOI: 10.1016/j.biopha.2024.117321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/09/2024] [Accepted: 08/21/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND Atopic dermatitis is a common chronic inflammatory skin disease characterized by relapsing eczema and intense itch. DGT is a novel synthetic heterocyclic diterpenoid derived from plants. Its therapeutic potential and mechanism(s) of action are poorly understood. OBJECTIVES We investigated the potent therapeutic effect of DGT on atopic dermatitis, exploring the underlying mechanisms and determining whether DGT is a safe and well-tolerated topical treatment. METHODS We observed anti-inflammatory effects of DGT on tumor necrosis factor-α/interferon-γ-treated human keratinocytes, and anti-allergic effects on immunoglobulin E-sensitized bone marrow-derived mast cells. In vivo, DGT was topically applied to two experimental mouse models of atopic dermatitis: oxazolone-induced sensitization and topically applied calcipotriol. Then the therapeutic effects of DGT were evaluated physiologically and morphologically. Moreover, we performed nonclinical toxicology and safety pharmacology research, including general toxicity, pharmacokinetics, and safety pharmacology on the cardiovascular, respiratory, and central nervous systems. RESULTS In keratinocytes, DGT reduced the expression of inflammatory factors, promoting the expression of barrier functional proteins and tight junctions and maintaining the steady state of barrier function. DGT also inhibited the activation and degranulation of mast cells induced by immunoglobulin E. Moreover, we found that interleukin-4 receptor-α was the possible target of DGT. Meanwhile, DGT had therapeutic effects on oxazolone/calcipotriol-treated mice. Notably, our pharmacology results demonstrated that DGT was safe and nontoxic in our studies. CONCLUSION DGT's potent anti-inflammatory effects and good safety profile suggest that it is a potential candidate for the treatment of atopic dermatitis.
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Affiliation(s)
- Jingjing Gao
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China; Department of Laboratory Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Dong Li
- Department of Pharmacology, Suzhou Pharmavan Co., Ltd, Suzhou, China
| | - Zhangyang Feng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China
| | - Xiaoqiang Zhu
- Department of Pharmacology, Suzhou Pharmavan Co., Ltd, Suzhou, China
| | - Fei Yang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China; Department of Pharmacology, Suzhou Pharmavan Co., Ltd, Suzhou, China
| | - Biyan Zhang
- Department of Pharmacology, Suzhou Pharmavan Co., Ltd, Suzhou, China
| | - Mingming Hu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China
| | - Yanping Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China
| | - Haimei Feng
- Department of Pharmacology, Suzhou Pharmavan Co., Ltd, Suzhou, China
| | - Yunhui Yu
- Department of Pharmacology, Suzhou Pharmavan Co., Ltd, Suzhou, China
| | - Qing Xie
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China.
| | - Zijun Chen
- College of traditional Chinese medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Yunsen Li
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China.
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Yang M, Mao K, Cao X, Liu H, Mao W, Hao L. Integrated network toxicology, transcriptomics and gut microbiomics reveals hepatotoxicity mechanism induced by benzo[a]pyrene exposure in mice. Toxicol Appl Pharmacol 2024; 491:117050. [PMID: 39111554 DOI: 10.1016/j.taap.2024.117050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/26/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Benzo[a]pyrene (BaP) is a ubiquitous environmental pollutant posing various toxicity effects on organisms. Previous studies demonstrated that BaP could induce hepatotoxicity, while the underlying mechanism remains incompletely elucidated. In this study, a comprehensive strategy including network toxicology, transcriptomics and gut microbiomics was applied to investigate the hepatotoxicity and the associated mechanism of BaP exposure in mice. The results showed that BaP induced liver damage, liver oxidative stress and hepatic lipid metabolism disorder. Mechanistically, BaP may disrupt hepatic lipid metabolism through increasing the uptake of free fatty acid (FFA), promoting the synthesis of FA and triglyceride (TG) in the liver and suppressing lipid synthesis in white adipose tissue. Moreover, integrated network toxicology and hepatic transcriptomics revealed that BaP induced hepatotoxicity by acting on several core targets, such as signal transducer and activator of transcription 1 (STAT1), C-X-C motif chemokine ligand 10 (CXCL10) and toll-like receptor 2 (TLR2). Further analysis suggested that BaP inhibited JAK2-STAT3 signaling pathway, as supported by molecular docking and western blot. The 16S rRNA sequencing showed that BaP changed the composition of gut microbiota which may link to the hepatotoxicity based on the correlation analysis. Taken together, this study demonstrated that BaP caused liver injury, hepatic lipid metabolism disorder and gut microbiota dysbiosis, providing novel insights into the hepatotoxic mechanism induced by BaP exposure.
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Affiliation(s)
- Miao Yang
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kanmin Mao
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Cao
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hongjuan Liu
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weifeng Mao
- China National Center for Food Safety Risk Assessment, No. 37, Guangqu Road, Chaoyang District, Beijing 100022, China.
| | - Liping Hao
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Hubei Key Laboratory of Food Nutrition and Safety, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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16
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Chikhale RV, Prasad RS, de Resende PE, Akojwar NS, Purohit RA, Gurav SS, Sinha SK, Prasad SK. Analysing the impact of eriosematin E from Eriosema chinense Vogel. against different diarrhoeagenic pathovars of Escherichia coli using in silico and in vitro approach. J Biomol Struct Dyn 2024; 42:8493-8504. [PMID: 37599503 DOI: 10.1080/07391102.2023.2246570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Abstract
Since diarrhoea is reportedly the third largest cause of fatality among kids, therefore it is considered to be one of the major areas of concerns among developing nations. The main causative agents of diarrhoea include Escherichia coli, Vibrio cholera, and Shigella spp where E. coli shares the maximum contribution. The roots of the plant Eriosema chinense Vogel. (Fabaceae) are traditionally used by the native tribes of Meghalaya, India to treat diarrhoea. From previous reports, the plant and its marker eriosematin E have been reported to have antidiarrhoeal potential against pathogenic and nonpathogenic diarrhoea. Therefore, the objective of the current investigation was to use in silico studies to determine the efficacy of eriosematin E against different diarrhoeagenic strains of E. coli. Six different pathovars of E. coli i.e. enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohaemorrhagic E. coli (EHEC), enteroaggregative E. coli (EAEC), uropathogenic E. coli (UPEC) and enteroinvasive E. coli (EIEC) were subjected to docking simulation studies utilizing Glide module of Schrodinger Maestro 2018-1 MM Share Version. Based on the obtained binding energy and balance between H-bonding, hydrophobic, and salt bridge interactions eriosematin E was found to be most effective against EPEC followed by EAEC and ETEC, while UPEC and EHEC were moderately affected. The molecular dynamics studies suggested a higher affinity of eriosematin E towards heat-labile enterotoxin b-pentamer from ETEC. The in vitro antibacterial studies against the universal strain S. aureus 12981 and E. coli 10418 revealed the effectiveness of eriosematin E showing MIC values of ≥256 µg/mL.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rupesh V Chikhale
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, UK
| | - Rupali S Prasad
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, Maharashtra, India
| | | | - Natasha S Akojwar
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, Maharashtra, India
| | - Raksha A Purohit
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, Maharashtra, India
| | - Shailendra S Gurav
- Department of Pharmacognosy, Goa College of Pharmacy, Panaji, Goa University, Goa, India
| | - Saurabh K Sinha
- Department of Pharmaceutical Sciences, Mohanlal Sukhadia University, Udaipur, India
| | - Satyendra K Prasad
- Department of Pharmaceutical Sciences, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur, Maharashtra, India
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Zhao Z, Wu Q, Xu Y, Qin Y, Pan R, Meng Q, Li S. Groenlandicine enhances cisplatin sensitivity in cisplatin-resistant osteosarcoma cells through the BAX/Bcl-2/Caspase-9/Caspase-3 pathway. J Bone Oncol 2024; 48:100631. [PMID: 39263651 PMCID: PMC11388767 DOI: 10.1016/j.jbo.2024.100631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/06/2024] [Accepted: 08/19/2024] [Indexed: 09/13/2024] Open
Abstract
Groenlandicine is a protoberberine alkaloid isolated from Coptidis Rhizoma, a widely used traditional Chinese medicine known for its various biological activities. This study aims to validate groenlandicine's effect on both cisplatin-sensitive and cisplatin-resistant osteosarcoma (OS) cells, along with exploring its potential molecular mechanism. The ligand-based virtual screening (LBVS) method and molecular docking were employed to screen drugs. CCK-8 and FCM were used to measure the effect of groenlandicine on the OS cells transfected by lentivirus with over-expression or low-expression of TOP1. Cell scratch assay, CCK-8, FCM, and the EdU assay were utilized to evaluate the effect of groenlandicine on cisplatin-resistant cells. WB, immunofluorescence, and PCR were conducted to measure the levels of TOP1, Bcl-2, BAX, Caspase-9, and Caspase-3. Additionally, a subcutaneous tumor model was established in nude mice to verify the efficacy of groenlandicine. Groenlandicine reduced the migration and proliferation while promoting apoptosis in OS cells, effectively damaging them. Meanwhile, groenlandicine exhibited weak cytotoxicity in 293T cells. Combination with cisplatin enhanced tumor-killing activity, markedly activating BAX, cleaved-Caspase-3, and cleaved-Caspase-9, while inhibiting the Bcl2 pathway in cisplatin-resistant OS cells. Moreover, the level of TOP1, elevated in cisplatin-resistant OS cells, was down-regulated by groenlandicine both in vitro and in vivo. Animal experiments confirmed that groenlandicine combined with cisplatin suppressed OS growth with lower nephrotoxicity. Groenlandicine induces apoptosis and enhances the sensitivity of drug-resistant OS cells to cisplatin via the BAX/Bcl-2/Caspase-9/Caspase-3 pathway. Groenlandicine inhibits OS cells growth by down-regulating TOP1 level.Therefore, groenlandicine holds promise as a potential agent for reversing cisplatin resistance in OS treatment.
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Affiliation(s)
- Zihao Zhao
- Clincal Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Qihong Wu
- The Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, China
| | - Yangyang Xu
- Clincal Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Yuhuan Qin
- Beijing Jinshuitan Hospital Guizhou Hospital, Guiyang, Guizhou Province, China
| | - Runsang Pan
- Basic Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Qingqi Meng
- Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong Province, China
| | - Siming Li
- Clincal Medical College, Guizhou Medical University, Guiyang, Guizhou Province, China
- Guangzhou Red Cross Hospital of Jinan University, Guangzhou, Guangdong Province, China
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18
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Llop-Peiró A, Macip G, Garcia-Vallvé S, Pujadas G. Are protein-ligand docking programs good enough to predict experimental poses of noncovalent ligands bound to the SARS-CoV-2 main protease? Drug Discov Today 2024; 29:104137. [PMID: 39151594 DOI: 10.1016/j.drudis.2024.104137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 08/10/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024]
Abstract
Hundreds of virtual screening (VS) studies have targeted the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) main protease (M-pro) to identify small molecules that inhibit its proteolytic action. Most studies use AutoDock Vina or Glide methodologies [high-throughput VS (HTVS), standard precision (SP), or extra precision (XP)], independently or in a VS workflow. Moreover, the Protein Data Bank (PDB) includes multiple complexes between M-pro and various noncovalent ligands, providing an excellent benchmark for assessing the predictive capabilities of docking programs. Here, we analyze the ability of the three Glide methodologies and AutoDock Vina by using various target structures/preparations to predict the experimental poses of these complexes. Our aims are to optimize target setup and docking methodologies, minimize false positives, and maximize the identification of various chemotypes in a SARS-CoV-2 M-pro noncovalent inhibitor VS campaign.
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Affiliation(s)
- Ariadna Llop-Peiró
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, 43007 Tarragona, Catalonia, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, 43007 Tarragona, Catalonia, Spain; CELLEX Research Laboratories, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias. 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Catalonia, Spain; Pulmonology Department, Hospital Clínic, 08036 Barcelona, Catalonia, Spain
| | - Santiago Garcia-Vallvé
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, 43007 Tarragona, Catalonia, Spain.
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Research group in Cheminformatics & Nutrition, 43007 Tarragona, Catalonia, Spain.
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Shen Y, You Z, Li L, Tang X, Shan X. The interaction of PRDX1 with Cofilin promotes oral squamous cell carcinoma metastasis. Int J Cancer 2024; 155:1290-1302. [PMID: 38738971 DOI: 10.1002/ijc.34999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/14/2024]
Abstract
Peroxiredoxin 1 (PRDX1) is an important member of the peroxiredoxin family (PRDX) and is upregulated in a variety of tumors. Previous studies have found that high PRDX1 expression is closely related to the metastasis of oral squamous cell carcinoma (OSCC), but the specific molecular mechanism is elusive. To elucidate the role of PRDX1 in the metastasis process of OSCC, we evaluated the expression of PRDX1 in OSCC clinical specimens and its impact on the prognosis of OSCC patients. Then, the effect of PRDX1 on OSCC metastasis and cytoskeletal reconstruction was explored in vitro and in nude mouse tongue cancer models, and the molecular mechanisms were also investigated. PRDX1 can directly interact with the actin-binding protein Cofilin, inhibiting the phosphorylation of its Ser3 site, accelerating the depolymerization and turnover of actin, promoting OSCC cell movement, and aggravating the invasion and metastasis of OSCC. In clinical samples and mouse tongue cancer models, PRDX1 also increased lymph node metastasis of OSCC and was negatively correlated with the phosphorylation of Cofilin; PRDX1 also reduced the overall survival rate of OSCC patients. In summary, our study identified that PRDX1 may be a potential therapeutic target to inhibit OSCC metastasis.
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Affiliation(s)
- Yajun Shen
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices& Beijing Key Laboratory of Digital Stomatology & NHC Key Laboratory of Digital Stomatology & NMPA Key Laboratory for Dental Materials, Beijing, China
| | - Zixuan You
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices& Beijing Key Laboratory of Digital Stomatology & NHC Key Laboratory of Digital Stomatology & NMPA Key Laboratory for Dental Materials, Beijing, China
| | - Lingyu Li
- Department of Oral Pathology, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing, China
| | - Xiaofei Tang
- Division of Oral Pathology, Beijing Institute of Dental Research, Beijing Stomatological Hospital & School of Stomatology, Capital Medical University, Beijing, China
| | - Xiaofeng Shan
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center for Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices& Beijing Key Laboratory of Digital Stomatology & NHC Key Laboratory of Digital Stomatology & NMPA Key Laboratory for Dental Materials, Beijing, China
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20
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Zeng P, Huang H, Li D. Combining bioinformatics, network pharmacology, and artificial intelligence to predict the mechanism of resveratrol in the treatment of rheumatoid arthritis. Heliyon 2024; 10:e37371. [PMID: 39309832 PMCID: PMC11416256 DOI: 10.1016/j.heliyon.2024.e37371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/07/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
Background Rheumatoid arthritis (RA) is a chronic autoimmune disorder that causes joint inflammation and destruction, resulting in significant physical and economic burdens. Finding effective and targeted therapy for RA remains a top priority. Resveratrol is a potential candidate with anti-inflammatory and immunomodulatory properties for RA treatment. This study aims to determine the therapeutic targets and signaling pathways of resveratrol in the treatment of RA. Methods The GSE205962 dataset downloaded from The Gene Expression Omnibus (GEO) database was used to obtain the differentially expressed genes (DEGs) in blood samples from the patients and the healthy. PharmMapper database and Cytoscape (v3.9.1) were applied to construct the resveratrol pharmacophore target network. Gene functional enrichment analysis, including the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, was based on the BiNGo plug-in of Cytoscape and David's online tool. The intersection of the target genes of resveratrol and the DEGs were considered potential therapeutic genes (PT-genes). The Protein-Protein Interaction (PPI) network of PT-genes was constructed using the STRING tool, and the key therapeutic genes (KT-genes) were determined using the cytoHubba plug-in based on the Maximal Clique Centrality (MCC) algorithms. Molecular docking validation of resveratrol and therapeutic targets was performed based on the protein structure of KT-genes predicted by AlphaFold. Results A total of 2202 DEGs and 47PT-genes were identified. GO analysis showed that the three groups of genes, the DEGs, the resveratrol target genes, and the PT-genes, have similar results for the top-five gene functional enrichment. PT-genes were closely related to the pathways of metabolic pathways, pathways in cancer, proteoglycans in cancer, insulin signaling pathway, and chemokine signaling pathway. The common pathway enriched by KEGG for the DEGs, and the resveratrol target genes was up to 36 %. The nine KT-genes were ABL1, ANXA5, CASP3, HSP90AA1, LCK, MAP2K1, MAPK1, PIK3R1, and RAC1, and the lowest free energy indicating the resveratrol/protein affinity were -8.4, -7.4, -6.4, -6.7, -8.0, -7.9, -7.4, -6.7, and -7.9, respectively. Conclusion Nine KT-genes were identified and validated as the most potential therapeutic targets in the treatment of RA with resveratrol, which provide new insights into therapeutic mechanisms and may improve the efficiency of drug development.
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Affiliation(s)
- Piaoqi Zeng
- Department of Rheumatology, Ganzhou People's Hospital, Hongqi Avenue, Zhanggong District, Ganzhou City, 341000, Jiangxi Province, China
| | - Haohan Huang
- Department of Orthopaedics, Gongli Hospital of Shanghai Pudong New Area, 219 Miaopu Rd, Shanghai 200011, China
| | - Dongsheng Li
- Department of Rheumatology, Ganzhou People's Hospital, Hongqi Avenue, Zhanggong District, Ganzhou City, 341000, Jiangxi Province, China
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21
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Liu S, Zhou X, Zhang L, Luo W. Network pharmacology and bioinformatics approach to unravel the mechanism of Xiao-chai-hu-tang herbal formula in tinnitus treatment. Heliyon 2024; 10:e37584. [PMID: 39315211 PMCID: PMC11417242 DOI: 10.1016/j.heliyon.2024.e37584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/21/2024] [Accepted: 09/05/2024] [Indexed: 09/25/2024] Open
Abstract
Background Tinnitus treatment remains a global challenge, and current therapeutic approaches are still controversial. This study aims to elucidate the potential mechanisms of Xiao-Chai-Hu-Tang (XCHT) in treating tinnitus through the analysis of network pharmacology, mendelian randomization and molecular docking, and molecular dynamics simulation analysis. We hope to contribute to the research on the target of action of traditional Chinese medicine and exploration of the mechanism of tinnitus. Methods We utilized network pharmacology to screen potential targets of action of XCHT on tinnitus. Mendelian randomization was employed to determine the causal relationship between potential targets of action and tinnitus. Finally, molecular docking and molecular dynamics simulation with clear targets and the combination of the active ingredient in effectiveness. Results Through network pharmacology, we identified 38 potential targets of action. Mendelian randomization analysis revealed that HIF1A (OR [95 % CI] = 0.78 [0.65, 0.94], P = 0.008) and CCND1 (OR [95 % CI] = 1.22 [1.00, 1.49], P = 0.04) exhibited significant results with tinnitus. Molecular docking and molecular dynamics simulation of HIF1A and active ingredients demonstrated good binding efficacy. Conclusion HIF1A may play a key role in the treatment of tinnitus by XCHT, which may play a certain protective role in tinnitus patients and may inhibit the occurrence and development of tinnitus. However, the specific mechanism and effect need to be further studied and verified.
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Affiliation(s)
- Shihan Liu
- Department of Otorhinolaryngology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xintong Zhou
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lingli Zhang
- Department of Otorhinolaryngology, Central Hospital Affiliated to Chongqing University of Technology, Chongqing, China
| | - Wenlong Luo
- Department of Otorhinolaryngology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Ji T, Dong X, Wei L, Xue Y, Wang X, Cai K, Zhou H, Wang Z, Xu B, Xu F. Decoding of the saltiness enhancement taste peptides from Jinhua ham and its molecular mechanism of interaction with ENaC/TMC4 receptors. Food Chem 2024; 463:141455. [PMID: 39362094 DOI: 10.1016/j.foodchem.2024.141455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/13/2024] [Accepted: 09/26/2024] [Indexed: 10/05/2024]
Abstract
This study focused on unlocking the potential of Jinhua ham-derived peptides (JHP) for enhancing saltiness. JHP (<3 kDa) was obtained through ultrafiltration and desalting, reducing the salt content by 96 %. Four peptide fractions (JHP-P1/P2/P3/P4) were isolated using Sephadex G-25 gel filtration and anion-exchange chromatography. Sensory evaluation and electronic tongue analysis revealed that JHP-P2 (0.5 mg/mL) exhibited the highest saltiness which could replace four-fold NaCl salinity. Three peptides (DL, FMSALF, and HVRRK) identified by UPLC-QTOF-MS/MS were simulated with salty taste receptors ENaC/TMC4. Results indicated that Ser84 and Phe89 of ENaC and Asn404 and Lys567 of TMC4 are crucial for peptide docking related to salty taste. Molecular dynamics simulations showed that the three peptides bind to the TMC4 and ENaC through van der Waals forces, electrostatic interactions, and hydrogen bonds. These findings establish a robust theoretical foundation for salt reduction strategies and provide novel insights into the potential applications of Jinhua ham.
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Affiliation(s)
- Tong Ji
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Xinran Dong
- Mondelez Suzhou Food Co., Ltd, Suzhou 215000, China
| | - Lei Wei
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Yuanyuan Xue
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Xuefeng Wang
- College of Food Science and Technology, Yunnan Agriculture University, Kunming 650000, China
| | - Kezhou Cai
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Hui Zhou
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Zhaoming Wang
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Baocai Xu
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China
| | - Feiran Xu
- School of Food and Biological Engineering, Key Laboratory of Animal Source of Anhui Province, Hefei University of Technology, Hefei 230601, China; Shandong Delisi Food Co., Ltd, Weifang 262200, China.
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Lin LQ, Chen YH, Tian YF, Chen YS, Zheng ZY, Wu JX, Hu F, Wu C, Xie LH. Study on the cross-resistance of Aedes albopictus (Skuse) (Diptera: Culicidae) to deltamethrin and pyriproxyfen. Parasit Vectors 2024; 17:403. [PMID: 39334398 PMCID: PMC11438187 DOI: 10.1186/s13071-024-06485-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 09/03/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Insecticide resistance poses a significant challenge in the implementation of vector-borne disease control strategies. We have assessed the resistance levels of Aedes albopictus to deltamethrin and pyriproxyfen (PPF) in Fujian Province (China) and investigated the correlation between these resistance levels and mutations in the voltage-gated sodium channel (VGSC). METHODS The WHO bioassay protocol was used to evaluate the resistance coefficient of Ae. albopictus to deltamethrin and PPF, comparing a susceptible population from the Foshan (FS) area with wild populations from the Sanming (SM), Quanzhou (QZ), Zhangzhou (ZZ), Putian (PT) and Fuzhou (FZ) areas in Fujian Province. Genomic DNA was analyzed by PCR and sequencing to detect knockdown resistance (kdr) in the VGSC, specifically at the pyrethroid resistance alleles V1016V, I1532I and F1534F. Molecular docking was also performed to analyze the binding interactions of PPF and its metabolite 4'-OH-PPF to cytochrome P450 (CYP) 2C19, 2C9 and 3A4 and Ae. albopictus methoprene-tolerant receptors (AeMet), respectively. RESULTS The analysis of resistance to deltamethrin and PPF among Ae. albopictus populations from the various regions revealed that except for the sensitive population in FS and the SM population, the remaining four regional populations demonstrated resistance levels ranging from 4.31- to 18.87-fold for deltamethrin and from 2.85- to 3.62-fold for PPF. Specifically, the FZ and PT populations exhibited high resistance to deltamethrin, whereas the ZZ and QZ populations approached moderate resistance levels. Also, the resistance of the FZ, PT and ZZ populations to PPF increased slowly but consistently with the increasing trend of deltamethrin resistance. Genomic analysis identified multiple non-synonymous mutations within the VGSC gene; the F1534S and F1534L mutations showed significant resistance to deltamethrin in Ae. albopictus. Molecular docking results revealed that PPF and its metabolite 4'-OH-PPF bind to the Ae. albopictus AeMet receptor and CYP2C19. CONCLUSIONS The wild Ae. albopictus populations of Fujian Province showed varying degrees of resistance to deltamethrin and PPF and a trend of cross-resistance to deltamethrin and PPF. Increased vigilance is needed for potential higher levels of cross-resistance, especially in the PT and FZ regions.
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Affiliation(s)
- Ling-Qun Lin
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Ya-Hui Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Yi-Fan Tian
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Yu-Sen Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Zhao-Yang Zheng
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Jing-Xin Wu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China
| | - Fen Hu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China.
| | - Cheng Wu
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China.
| | - Li-Hua Xie
- Department of Pathogenic Biology, School of Basic Medical Sciences, Fujian Medical University, No. 1 Xuefu North Road, Fuzhou, 350122, Fujian, China.
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Borges KCM, Costa VAF, Neves B, Kipnis A, Junqueira-Kipnis AP. New antibacterial candidates against Acinetobacter baumannii discovered by in silico-driven chemogenomics repurposing. PLoS One 2024; 19:e0307913. [PMID: 39325805 PMCID: PMC11426455 DOI: 10.1371/journal.pone.0307913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/14/2024] [Indexed: 09/28/2024] Open
Abstract
Acinetobacter baumannii is a worldwide Gram-negative bacterium with a high resistance rate, responsible for a broad spectrum of hospital-acquired infections. A computational chemogenomics framework was applied to investigate the repurposing of approved drugs to target A. baumannii. This comprehensive approach involved compiling and preparing proteomic data, identifying homologous proteins in drug-target databases, evaluating the evolutionary conservation of targets, and conducting molecular docking studies and in vitro assays. Seven drugs were selected for experimental assays. Among them, tavaborole exhibited the most promising antimicrobial activity with a minimum inhibitory concentration (MIC) value of 2 μg/ml, potent activity against several clinically relevant strains, and robust efficacy against biofilms from multidrug-resistant strains at a concentration of 16 μg/ml. Molecular docking studies elucidated the binding modes of tavaborole in the editing and active domains of leucyl-tRNA synthetase, providing insights into its structural basis for antimicrobial activity. Tavaborole shows promise as an antimicrobial agent for combating A. baumannii infections and warrants further investigation in preclinical studies.
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Affiliation(s)
- Kellen Christina Malheiros Borges
- Molecular Bacteriology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
- Microbiology Laboratory, Department of Biology, Academic Areas, Federal Institute of Goiás, Anápolis, Goiás, Brazil
| | | | - Bruno Neves
- Laboratory of Cheminformatics, Faculty of Pharmacy, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - André Kipnis
- Molecular Bacteriology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Ana Paula Junqueira-Kipnis
- Molecular Bacteriology Laboratory, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
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Garisetti V, Varughese RE, Anandamurthy A, Haribabu J, Allard Garrote C, Dasararaju G. Virtual screening, molecular docking and dynamics simulation studies to identify potential agonists of orphan receptor GPR78 targeting CNS disorders. J Recept Signal Transduct Res 2024:1-15. [PMID: 39314078 DOI: 10.1080/10799893.2024.2405488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 09/04/2024] [Accepted: 09/11/2024] [Indexed: 09/25/2024]
Abstract
G protein-coupled receptors (GPCRs) are important targets in drug discovery because of their roles in physiological and pathological processes. Orphan GPCRs are GPCR proteins for which endogenous ligands have not yet been identified and they present interesting avenues for therapeutic intervention. This study focuses on GPR78, an orphan GPCR that is expressed in the central nervous system and linked to neurological disorders. GPR78 has no reported crystal structure and there is limited research. In this study, we have predicted the three dimensional model of GPR78 and its probable binding pocket. Structure-based virtual screening was carried out using the ChemDiv and Enamine REAL databases, followed by induced-fit docking studies to identify potential lead compounds with favorable interactions. These lead compounds were then embedded into a POPC lipid bilayer for a 200 ns molecular dynamics simulation. Free energy landscapes and MM-PBSA analyses were performed to assess the binding energies and conformational dynamics. The results highlight the dynamic nature of GPR78 in the presence of lead compounds and show favorable binding interactions. This study aims to predict a reliable three dimensional model of GPR78 and identify novel lead compounds through a comprehensive in silico approach. The identification of these potential GPR78 agonists represents a significant step in the development of new therapeutics for neurological disorders, highlighting the therapeutic potential of orphan GPR78 in CNS disorders.
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Affiliation(s)
- Vasavi Garisetti
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Roslin Elsa Varughese
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Arthikasree Anandamurthy
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
| | - Jebiti Haribabu
- Facultad de Medicina, Universidad de Atacama, Copiapo, Chile
- Chennai Institute of Technology (CIT), Chennai, India
| | - Claudio Allard Garrote
- Departamento de Química y Biología, Facultad de Ciencias Naturales, Universidad de Atacama, Copiapo, Chile
| | - Gayathri Dasararaju
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, India
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Zhao Y, Yin N, Yang R, Faiola F. Recent advances in environmental toxicology: Exploring gene editing, organ-on-a-chip, chimeric animals, and in silico models. Food Chem Toxicol 2024; 193:115022. [PMID: 39326696 DOI: 10.1016/j.fct.2024.115022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 09/05/2024] [Accepted: 09/22/2024] [Indexed: 09/28/2024]
Abstract
In our daily life, we are exposed to various environmental pollutants in multiple ways. At present, we mainly rely on animal models and two-dimensional cell culture models to evaluate the toxicity of environmental pollutants. Nevertheless, results in animal models do not always apply to humans because of differences between species, while two-dimensional cell culture models cannot replicate the in vivo microenvironments, making it difficult to predict the true toxic response of environmental pollutants in humans. The development of various high-end technologies in recent years has provided new opportunities for environmental toxicology research. The application of these high-end technologies in environmental toxicology can complement the limitations of traditional environmental toxicology screening and more accurately predict the toxicity of environmental pollutants. In this review, we first introduce the advantages and disadvantages of traditional environmental toxicology methods, then review the principles and development of four high-end technologies, such as gene editing, organ-on-a-chip, chimeric animals, and in silico models, summarize their application in toxicity testing, and finally emphasize their importance/potential in environmental toxicology.
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Affiliation(s)
- Yanyi Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nuoya Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Renjun Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Francesco Faiola
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
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Lam HYI, Guan JS, Ong XE, Pincket R, Mu Y. Protein language models are performant in structure-free virtual screening. Brief Bioinform 2024; 25:bbae480. [PMID: 39327890 PMCID: PMC11427677 DOI: 10.1093/bib/bbae480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/17/2024] [Accepted: 09/12/2024] [Indexed: 09/28/2024] Open
Abstract
Hitherto virtual screening (VS) has been typically performed using a structure-based drug design paradigm. Such methods typically require the use of molecular docking on high-resolution three-dimensional structures of a target protein-a computationally-intensive and time-consuming exercise. This work demonstrates that by employing protein language models and molecular graphs as inputs to a novel graph-to-transformer cross-attention mechanism, a screening power comparable to state-of-the-art structure-based models can be achieved. The implications thereof include highly expedited VS due to the greatly reduced compute required to run this model, and the ability to perform early stages of computer-aided drug design in the complete absence of 3D protein structures.
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Affiliation(s)
- Hilbert Yuen In Lam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore, Republic of Singapore
- MagMol Pte. Ltd., 68 Circular Road, #02-01, Singapore 049422, Singapore, Republic of Singapore
| | - Jia Sheng Guan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore, Republic of Singapore
| | - Xing Er Ong
- MagMol Pte. Ltd., 68 Circular Road, #02-01, Singapore 049422, Singapore, Republic of Singapore
| | - Robbe Pincket
- Heliovision, Asstraat 5, 3000 Leuven, Leuven, Kingdom of Belgium
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore, Republic of Singapore
- MagMol Pte. Ltd., 68 Circular Road, #02-01, Singapore 049422, Singapore, Republic of Singapore
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Okpako IO, Ng'ong'a FA, Kyama CM, Njeru SN. Network pharmacology, molecular docking, and in vitro study on Aspilia pluriseta against prostate cancer. BMC Complement Med Ther 2024; 24:338. [PMID: 39304868 DOI: 10.1186/s12906-024-04642-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Current prostate cancer treatments are associated with life-threatening side effects, prompting the search for effective and safer alternatives. Aspilia pluriseta Schweinf. ex Engl. has previously shown anticancer activity in lung and liver cancer cell lines. This study investigated its potential for prostate cancer. METHODS A crude extract of A. pluriseta root was prepared using dichloromethane/methanol (1:1 v/v) and partitioned into hexane, ethyl acetate, and water fractions. The MTT assay was used to assess the antiproliferative activity of the fractions. The active fractions were tested at 6.25-200 µg/ml on human prostate cancer DU-145 cells and non-cancerous Vero E6 cells. Qualitative phytochemical and gas chromatography-mass spectrometry (GC-MS) analyses were conducted to identify chemical compounds. Network pharmacology was employed to predict molecular targets and modes of action of the identified chemical compounds, with subsequent validation through molecular docking and real-time PCR. RESULTS Active extracts included crude dichloromethane/methanol, hexane, and ethyl acetate fractions, inhibiting DU-145 cell proliferation with IC50 values of 16.94, 20.06, and 24.14 µg/ml, respectively. Selectivity indices were determined to be 6.04 (crude), 3.62 (hexane), and 6.68 (ethyl acetate). Identified phytochemicals comprised phenols, terpenoids, flavonoids, tannins, sterols, and saponins. GC-MS analysis revealed seventy-nine (79) compounds, with seven (7) meeting ideal drug candidate parameters; their hub gene targets included MAPK3, MAPK1, IL6, TP53, ESR1, PTGS2, MMP9, MDM2, AR, and MAP2K1, implicating regulation of PI3K/Akt, MAPK, and p53 signaling pathways as potential modes of action. Core compounds such as 1-heneicosanol, lanosterol, andrographolide, and retinoic acid exhibited strong binding activities, particularly lanosterol with MAPK21 (-9.7 kcal/mol), ESR1 (-8.9 kcal/mol), and MAPK3 (-8.8 kcal/mol). Treatment with A. pluriseta downregulated AR expression and upregulated p53, while also downregulating CDK1 and BCL-2 and upregulating caspase-3. CONCLUSIONS A. pluriseta extracts inhibited DU-145 cell growth without causing cellular toxicity, suggesting great potential for development as an anti-prostate cancer agent. However, further in vitro and in vivo experiments are recommended.
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Affiliation(s)
- Innocent Oluwaseun Okpako
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation, Nairobi, Kenya.
| | - Florence Atieno Ng'ong'a
- Department of Biochemistry, School of Biomedical Sciences, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Cleophas Mutinda Kyama
- Department of Medical Laboratory Sciences, School of Biomedical Sciences, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Sospeter Ngoci Njeru
- Centre for Traditional Medicine and Drug Research and Centre for Community Driven Research, Kenya Medical Research Institute, Nairobi, Kenya.
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Zhang H, Yu J, Yang Z, Guo Z, Liu R, Qin Q, Sun Y, Liu N, Gao Z, Zhao D, Cheng M. Structure-based virtual screening discovers novel PKMYT1 inhibitors. RSC Med Chem 2024; 15:3114-3124. [PMID: 39309356 PMCID: PMC11411631 DOI: 10.1039/d4md00389f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 07/21/2024] [Indexed: 09/25/2024] Open
Abstract
PKMYT1, a member of the WEE family, plays a crucial role in the cell cycle by specifically phosphorylating CDK1-CyclinB at Tyr15 and Thr14. Recent investigations have revealed that the amplification of CCNE1 and the inhibition of PKMYT1 kinase collectively result in synthetic lethality, further indicating that PKMYT1 is promising as an effective target for tumor therapy. Existing PKMYT1 inhibitors are mostly derivatives of RP-6306 or pan-inhibitors, limiting their further development. Herein, we conducted virtual screening of a natural product library, and in vitro enzyme experiments demonstrated that EGCG, GCG, and luteolin exhibited potent inhibitory activities with IC50 values of 0.137 μM, 0.159 μM, and 1.5 μM, respectively. Subsequently, analysis of the hit compounds and RP-6306, using different molecular simulation methods, revealed that stable hydrogen bonds with Asp251 and Glu157 in the DFG region were vital for binding to PKMYT1, more so than hydrogen bonds in the hinge and loop regions.
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Affiliation(s)
- Haoyu Zhang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Jinyu Yu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Ziheng Yang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Zhiqiang Guo
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Rui Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Qiaohua Qin
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Yixiang Sun
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Nian Liu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Zixuan Gao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University Shenyang 110016 China
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University Shenyang 110016 China
- Key Laboratory of Intelligent Drug Design and New Drug Discovery of Liaoning Province, Shenyang Pharmaceutical University Shenyang 110016 China
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30
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Xi Y, Zheng P, Xi W, Fu T. Exploring the impact of estrogenic endocrine disruptors on cervical cancer progression: A transcriptome analysis and prognostic model development. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 285:117025. [PMID: 39303635 DOI: 10.1016/j.ecoenv.2024.117025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/31/2024] [Accepted: 09/07/2024] [Indexed: 09/22/2024]
Abstract
Cervical cancer is the fourth most common cancer among women globally. The detrimental health effects of estrogenic endocrine disruptors (EED), such as bisphenol A (BPA) and phthalates, are recognized, but their role in cervical cancer progression remains unclear. To investigate this, a transcriptome analysis using bioinformatics was conducted. The Comparative Toxicogenomics Database (CTD) identified estrogen-responsive genes (ERGs) associated with EED. Cervical cancer expression and clinical data were sourced from The Cancer Genome Atlas (TCGA). The limma package identified differentially expressed ERGs (DERGs), which were further analyzed for molecular mechanisms through enrichment analysis. LASSO regression developed a prognostic risk score model, and COX analysis identified prognostic biomarkers. ssGSEA assessed immune tumor infiltration, and Autodock performed molecular docking. A total of 217 DERGs were linked to endocrine resistance, estrogen signaling, and the cell cycle. The prognostic risk score and nomogram based on DERGs were highly predictive of cervical cancer prognosis and could serve as independent risk factors. The risk score influenced the tumor immune microenvironment by affecting immune cell presence. SCARA3 and FASN emerged as independent prognostic factors, with molecular docking confirming strong binding between EED and FASN. DERGs can aid in creating a reliable prognostic model and predicting overall survival in cervical cancer patients, offering new insights into the impact of EED on cancer progression and highlighting environmental factors related to cancer risks and development.
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Affiliation(s)
- Yanni Xi
- Yulin Hospital of the First Affiliated Hospital of Xi'an Jiaotong University, China
| | - Pengsheng Zheng
- Department of Reproductive Medicine, The First Affiliated Hospital of the Medical College, Xi'an Jiaotong University, China.
| | - Wenjin Xi
- Department of Immunology, Air Force Medical, China
| | - Ting Fu
- Yulin Hospital of the First Affiliated Hospital of Xi'an Jiaotong University, China
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Zhai Y, Zhang F, Zhou J, Qiao C, Jin Z, Zhang J, Wu C, Shi R, Huang J, Gao Y, Guo S, Wang H, Chai K, Zhang X, Wang T, Sheng X, Liu X, Wu J. Mechanism of norcantharidin intervention in gastric cancer: analysis based on antitumor proprietary Chinese medicine database, network pharmacology, and transcriptomics. Chin Med 2024; 19:129. [PMID: 39289763 PMCID: PMC11406961 DOI: 10.1186/s13020-024-01000-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 09/06/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND Combining antitumor proprietary Chinese medicine (pCm) with radiotherapy and chemotherapy can effectively improve tumor cure rates and enhance patients' quality of life. Gastric cancer (GC) severely endangers public health. Despite satisfactory therapeutic effects achieved by using antitumor pCm to treat GC, its underlying mechanism remains unclear. OBJECTIVE To integrate existing research data, construct a database of antitumor pCm, and study the intervention mechanisms in GC by focusing on their monomer components. METHODS We constructed an antitumor pCm database based on China's medical insurance catalog, and employed network pharmacology, molecular docking methods, cell experiments, transcriptomics, and bioinformatics to investigate the intervention mechanisms of effective pCm components for GC. RESULTS The study built an antitumor pCm database including 55 pCms, 171 Chinese herbal medicines, 1955 chemical components, 2104 targets, and 32 disease information. Network pharmacology and molecular docking technology identified norcantharidin as an effective component of antitumor pCm. In vitro experiments showed that norcantharidin effectively inhibited GC cell proliferation, migration, and invasion; blocked the G2/M cell cycle phase; and induced GC cell apoptosis. Transcriptomic results revealed that norcantharidin affected biological processes, such as cell adhesion, migration, and inflammatory responses by influencing PI3K-AKT, NF-κB, JAK-STAT, TNF-α signaling pathways, and EMT-related pathways. Core molecules of norcantharidin involved in GC intervention include SERPINE1, SHOX2, SOX4, PRDM1, TGFR3, TOX, PAX9, IL2RB, LAG3, and IL15RA. Additionally, the key target SERPINE1 was identified using bioinformatics methods. CONCLUSION Norcantharidin, as an effective component of anti-tumor pCm, exerts its therapeutic effects on GC by influencing biological processes such as cell adhesion, migration, and inflammation. This study provides a foundation and research strategy for the post-marketing re-evaluation of antitumor pCms.
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Affiliation(s)
- Yiyan Zhai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Fanqin Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiying Zhou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chuanqi Qiao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Zhengsen Jin
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jingyuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Chao Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Rui Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Jiaqi Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Yifei Gao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Siyu Guo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Haojia Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Keyan Chai
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaomeng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Tieshan Wang
- Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xiaoguang Sheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Xinkui Liu
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, Shandong, China.
| | - Jiarui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, 100029, China.
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Du P, Xu L, Wang Y, Jiao T, Cheng J, Zhang C, Tapu MSR, Dai J, Li J. Astragaloside IV ameliorates pressure overload-induced heart failure by enhancing angiogenesis through HSF1/VEGF pathway. Heliyon 2024; 10:e37019. [PMID: 39296120 PMCID: PMC11408759 DOI: 10.1016/j.heliyon.2024.e37019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/24/2024] [Accepted: 08/26/2024] [Indexed: 09/21/2024] Open
Abstract
Astragaloside IV(AS-IV), the main active ingredient of Astragalus, has been used as a treatment for heart failure with favorable effects, but its molecular mechanism has not been fully elucidated. Network pharmacological analysis and molecular docking revealed that Heat shock transcription factor 1 (HSF1) is a potential target of AS-IV. We designed cellular and animal experiments to investigate the role and intrinsic molecular mechanisms of AS-IV in ameliorating pressure overload-induced heart failure. In cellular experiments, Myocardial microvascular endothelial cells (MMVECs) were cultured in isolation and stimulated by adding high and low concentrations of AS-IV, and a cell model with down-regulation of HSF1 expression was constructed by using siRNA technology. Changes in the expression of key molecules of HSF1/VEGF signaling pathway and differences in tube-forming ability were detected in different groups of cells using PCR, WB and tube-forming assay. In animal experiments, TAC technology was applied to establish a pressure overload-induced heart failure model in C57 mice, postoperative mice were ingested AS-IV by gavage, and adenoviral transfection technology was applied to construct a mouse model with down-regulation of HSF1 expression.Small animal ultrasound for cardiac function assessment, MASSON staining, CD31 immunohistochemistry, and Western blotting (WB) were performed on the mice. The results showed that AS-IV could promote the expression of key molecules of HSF1/VEGF signaling pathway, enhance the tube-forming ability of MMVECs, increase the density of myocardial capillaries, reduce myocardial fibrosis, and improve the cardiac function of mice with TAC.AS-IV could modulate the HSF1/VEGF signaling pathway to promote the angiogenesis and improve the pressure overload-induced heart failure.
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Affiliation(s)
- Peizhao Du
- Department of Cardiology, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai University of Traditional Chinese Medicine, Shanghai, 201999, China
| | - Linghao Xu
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China
- Department of Cardiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yuanqi Wang
- Department of Cardiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Tiantian Jiao
- Department of Cardiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jing Cheng
- Department of Cardiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chunsheng Zhang
- Department of Cardiology, East Hospital of Clinical Medical College, Nanjing Medical University, Nanjing, 211166, China
| | - Md Sakibur Rahman Tapu
- Department of Cardiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jian Dai
- Department of Cardiology, Baoshan District Hospital of Integrated Traditional Chinese and Western Medicine of Shanghai, Shanghai University of Traditional Chinese Medicine, Shanghai, 201999, China
| | - Jiming Li
- Department of Cardiology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
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Cao Z, Ma N, Shan M, Wang S, Du J, Cheng J, Sun P, Sun N, Jin L, Fan K, Yin W, Li H, Yin C, Sun Y. Baicalin Inhibits FIPV Infection In Vitro by Modulating the PI3K-AKT Pathway and Apoptosis Pathway. Int J Mol Sci 2024; 25:9930. [PMID: 39337417 PMCID: PMC11431997 DOI: 10.3390/ijms25189930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Feline infectious peritonitis (FIP), a serious infectious disease in cats, has become a challenging problem for pet owners and the industry due to the lack of effective vaccinations and medications for prevention and treatment. Currently, most natural compounds have been proven to have good antiviral activity. Hence, it is essential to develop efficacious novel natural compounds that inhibit FIPV infection. Our study aimed to screen compounds with in vitro anti-FIPV effects from nine natural compounds that have been proven to have antiviral activity and preliminarily investigate their mechanisms of action. In this study, the CCK-8 method was used to determine the maximum noncytotoxic concentration (MNTC), 50% cytotoxic concentration (CC50), and 50% effective concentration (EC50) of natural compounds on CRFK cells and the maximum inhibition ratio (MIR) of the compounds inhibit FIPV. The effect of natural compounds on FIPV-induced apoptosis was detected via Annexin V-FITC/PI assay. Network pharmacology (NP), molecular docking (MD), and 4D label-free quantitative (4D-LFQ) proteomic techniques were used in the joint analysis the mechanism of action of the screened natural compounds against FIPV infection. Finally, Western blotting was used to validate the analysis results. Among the nine natural compounds, baicalin had good antiviral effects, with an MIR > 50% and an SI > 3. Baicalin inhibited FIPV-induced apoptosis. NP and MD analyses showed that AKT1 was the best target of baicalin for inhibiting FIPV infection. 4D-LFQ proteomics analysis showed that baicalin might inhibit FIPV infection by modulating the PI3K-AKT pathway and the apoptosis pathway. The WB results showed that baicalin promoted the expression of EGFR, PI3K, and Bcl-2 and inhibited the expression of cleaved caspase 9 and Bax. This study found that baicalin regulated the PI3K-AKT pathway and the apoptosis pathway in vitro and inhibited FIPV-induced apoptosis, thus exerting anti-FIPV effects.
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Affiliation(s)
- Zhongda Cao
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
- China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Nannan Ma
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Maoyang Shan
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Shiyan Wang
- China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Jige Du
- China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Jia Cheng
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Panpan Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Na Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Lin Jin
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Kuohai Fan
- Laboratory Animal Center, Shanxi Agricultural University, Jinzhong 030801, China
| | - Wei Yin
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Hongquan Li
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Chunsheng Yin
- China Institute of Veterinary Drug Control, Beijing 100081, China
| | - Yaogui Sun
- Shanxi Key Laboratory for Modernization of TCVM, College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
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Chang J, Wang J, Li X, Zhong Y. Predicting prospective therapeutic targets of Bombyx batryticatus for managing diabetic kidney disease through network pharmacology analysis. Medicine (Baltimore) 2024; 103:e39598. [PMID: 39287308 PMCID: PMC11404872 DOI: 10.1097/md.0000000000039598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
We conducted network pharmacology and molecular docking analyses, and executed in vitro experiments to assess the mechanisms and prospective targets associated with the bioactive components of Bombyx batryticatus in the treatment of diabetic kidney disease (DKD). The bioactive components and potential targets of B batryticatus were sourced from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. Using 5 disease databases, we conducted a comprehensive screening of potential disease targets specifically associated with DKD. Common targets shared between the bioactive components and disease targets were identified through the use of the R package, and subsequently, a protein-protein interaction network was established using data from the STRING database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses pertaining to the identified common targets were conducted using the Database for Annotation, Visualization, and Integrated Discovery. Molecular docking simulations involving the bioactive components and their corresponding targets were modeled through AutoDock Vina and Pymol. Finally, to corroborate and validate these findings, experimental assays at the cellular level were conducted. Six bioactive compounds and 142 associated targets were identified for B batryticatus. Among the 796 disease targets associated with DKD, 56 targets were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed the involvement of these shared targets in diverse biological processes and signaling pathways, notably the PI3K-Akt signaling pathway. Molecular docking analyses indicated a favorable binding interaction between quercetin, the principal bioactive compound in B batryticatus, and RAC-alpha serine/threonine-protein kinase. Subsequently, in vitro experiments substantiated the inhibitory effect of quercetin on the phosphorylation level of PI3K and Akt. The present study provides theoretical evidence for a comprehensive exploration of the mechanisms and molecular targets by which B batryticatus imparts protective effects against DKD.
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Affiliation(s)
- Jingsheng Chang
- Department of Nephrology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jue Wang
- Department of Nephrology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xueling Li
- Department of Nephrology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifei Zhong
- Department of Nephrology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Pang L, Zhao Y, Xu Y, Gao C, Wang C, Yu X, Wang F, He K. Mechanisms Underlying the Therapeutic Effects of JianPiYiFei II Granules in Treating COPD Based on GEO Datasets, Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulations. BIOLOGY 2024; 13:711. [PMID: 39336138 PMCID: PMC11428342 DOI: 10.3390/biology13090711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/30/2024]
Abstract
BACKGROUND JianPiYiFei (JPYF) II granules are a Chinese medicine for the treatment of chronic obstructive pulmonary disease (COPD). However, the main components and underlying mechanisms of JPYF II granules are not well understood. This study aimed to elucidate the potential mechanism of JPYF II granules in the treatment of COPD using network pharmacology, molecular docking, and molecular dynamics simulation techniques. METHODS The active compounds and corresponding protein targets of the JPYF II granules were found using the TCMSP, ETCM, and Uniport databases, and a compound-target network was constructed using Cytoscape3.9.1. The COPD targets were searched for in GEO datasets and the OMIM and GeneCards databases. The intersection between the effective compound-related targets and disease-related targets was obtained, PPI networks were constructed, and GO and KEGG enrichment analyses were performed. Then, molecular docking analysis verified the results obtained using network pharmacology. Finally, the protein-compound complexes obtained from the molecular docking analysis were simulated using molecular dynamics (MD) simulations. RESULTS The network pharmacological results showed that quercetin, kaempferol, and stigmasterol are the main active compounds in JPYF II granules, and AKT1, IL-6, and TNF are key target proteins. The PI3K/AKT signaling pathway is a potential pathway through which the JPYF II granules affect COPD. The results of the molecular docking analysis suggested that quercetin, kaempferol, and stigmasterol have a good binding affinity with AKT1, IL-6, and TNF. The MD simulation results showed that TNF has a good binding affinity with the compounds. CONCLUSIONS This study identified the effective compounds, targets, and related underlying molecular mechanisms of JPYF II granules in the treatment of COPD through network pharmacology, molecular docking, and MD simulation techniques, which provides a reference for subsequent research on the treatment of COPD.
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Affiliation(s)
- Liyuan Pang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Yongjuan Zhao
- Department of Pulmonary and Critical Care Medicine, China-Japan Union Hospital of Jilin University, Changchun 130021, China
| | - Yang Xu
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Chencheng Gao
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Chao Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Xiao Yu
- Department of Histology & Embryology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Fang Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Kan He
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
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Funari A, Fiscon G, Paci P. Network medicine and systems pharmacology approaches to predicting adverse drug effects. Br J Pharmacol 2024. [PMID: 39262113 DOI: 10.1111/bph.17330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 09/13/2024] Open
Abstract
Identifying and understanding the relationships between drug intake and adverse effects that can occur due to inadvertent molecular interactions between drugs and targets is a difficult task, especially considering the numerous variables that can influence the onset of such events. The ability to predict these side effects in advance would help physicians develop strategies to avoid or counteract them. In this article, we review the main computational methods for predicting side effects caused by drug molecules, highlighting their performance, limitations and application cases. Furthermore, we provide an overall view of resources, such as databases and tools, useful for building side effect prediction analyses.
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Affiliation(s)
- Alessio Funari
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- Department of Computer, Control and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
- Department of Computer, Control and Management Engineering "Antonio Ruberti", Sapienza University of Rome, Rome, Italy
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Comajuncosa-Creus A, Jorba G, Barril X, Aloy P. Comprehensive detection and characterization of human druggable pockets through binding site descriptors. Nat Commun 2024; 15:7917. [PMID: 39256431 PMCID: PMC11387482 DOI: 10.1038/s41467-024-52146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/27/2024] [Indexed: 09/12/2024] Open
Abstract
Druggable pockets are protein regions that have the ability to bind organic small molecules, and their characterization is essential in target-based drug discovery. However, deriving pocket descriptors is challenging and existing strategies are often limited in applicability. We introduce PocketVec, an approach to generate pocket descriptors via inverse virtual screening of lead-like molecules. PocketVec performs comparably to leading methodologies while addressing key limitations. Additionally, we systematically search for druggable pockets in the human proteome, using experimentally determined structures and AlphaFold2 models, identifying over 32,000 binding sites across 20,000 protein domains. We then generate PocketVec descriptors for each site and conduct an extensive similarity search, exploring over 1.2 billion pairwise comparisons. Our results reveal druggable pocket similarities not detected by structure- or sequence-based methods, uncovering clusters of similar pockets in proteins lacking crystallized inhibitors and opening the door to strategies for prioritizing chemical probe development to explore the druggable space.
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Affiliation(s)
- Arnau Comajuncosa-Creus
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Guillem Jorba
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Xavier Barril
- Facultat de Farmàcia and Institut de Biomedicina, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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Gong Y, Wang J, Pan M, Zhao Y, Zhang H, Zhang F, Liu J, Yang J, Hu J. Harmine inhibits pulmonary fibrosis through regulating DNA damage repair-related genes and activation of TP53-Gadd45α pathway. Int Immunopharmacol 2024; 138:112542. [PMID: 38924867 DOI: 10.1016/j.intimp.2024.112542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/15/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Harmine has many pharmacological activities and has been found to significantly inhibit the fibrosis of keloid fibroblasts. DNA damage repair (DDR) is essential to prevent fibrosis. This study aimed to investigate the effects of harmine on pulmonary fibrosis and its underlying mechanisms. METHODS Bleomycin and TGF-β1 were used to construct pulmonary fibrosis models in vivo and in vitro, then treated with harmine to explore harmine's effects in treating experimental pulmonary fibrosis and its related mechanisms. Then, RNA sequencing was applied to investigate further the crucial DDR-related genes and drug targets of harmine against pulmonary fibrosis. Finally, the expression levels of DDR-related genes were verified by real-time quantitative PCR (RT-qPCR) and western blot. RESULTS Our in vivo experiments showed that harmine treatment could improve weight loss and lung function and reduce tissue fibrosis in mice with pulmonary fibrosis. The results confirmed that harmine could inhibit the viability and migration of TGF-β1-induced MRC-5 cells, induce their apoptosis, and suppress the F-actin expression, suggesting that harmine could suppress the phenotypic transition from lung fibroblasts to lung myoblasts. In addition, RNA sequencing identified 1692 differential expressed genes (DEGs), and 10 DDR-related genes were screened as critical DDR-related genes. RT-qPCR and western blotting showed that harmine could down-regulate the expression of CHEK1, ERCC1, ERCC4, POLD1, RAD51, RPA1, TOP1, and TP53, while up-regulate FEN1, H2AX and GADD45α expression. CONCLUSIONS Harmine may inhibit pulmonary fibrosis by regulating DDR-related genes and activating the TP53-Gadd45α pathway.
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Affiliation(s)
- Yuehong Gong
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China; Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, Xinjiang 830011, China
| | - Jie Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China; Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, Xinjiang 830011, China
| | - Meichi Pan
- Department of Pharmacognosy, School of Pharmacy, Xinjiang Medical University, Urumqi 830017, China
| | - Yicong Zhao
- Department of Pharmacognosy, School of Pharmacy, Xinjiang Medical University, Urumqi 830017, China
| | - Haibo Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China; Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, Xinjiang 830011, China
| | - Fei Zhang
- Department of Medicine, School of Pharmacy, Xinjiang Medical University, Urumqi 830017, China
| | - Jiangyun Liu
- Soochow Univ, College of Pharmaceutic Science, Suzhou 215123, China
| | - Jianhua Yang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Xinjiang Medical University, First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China; Department of Pharmacy, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Key Laboratory of Clinical Drug Research, Urumqi, Xinjiang 830011, China.
| | - Junping Hu
- Department of Pharmacognosy, School of Pharmacy, Xinjiang Medical University, Urumqi 830017, China.
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Velázquez-Enríquez JM, Santos-Álvarez JC, Ramírez-Hernández AA, Reyes-Jiménez E, Pérez-Campos Mayoral L, Romero-Tlalolini MDLÁ, Jiménez-Martínez C, Arellanes-Robledo J, Villa-Treviño S, Vásquez-Garzón VR, Baltiérrez-Hoyos R. Chlorogenic acid attenuates idiopathic pulmonary fibrosis: An integrated analysis of network pharmacology, molecular docking, and experimental validation. Biochem Biophys Res Commun 2024; 734:150672. [PMID: 39260206 DOI: 10.1016/j.bbrc.2024.150672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 08/26/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024]
Abstract
AIMS Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung condition, the cause of which remains unknown and for which no effective therapeutic treatment is currently available. Chlorogenic acid (CGA), a natural polyphenolic compound found in different plants and foods, has emerged as a promising agent due to its anti-inflammatory, antioxidant, and antifibrotic properties. However, the molecular mechanisms underlying the therapeutic effect of CGA in IPF remain unclear. The purpose of this study was to analyze the pharmacological impact and underlying mechanisms of CGA in IPF. MAIN METHODS Using network pharmacology analysis, genes associated with IPF and potential molecular targets of CGA were identified through specialized databases, and a protein-protein interaction (PPI) network was constructed. Molecular docking was performed to accurately select potential therapeutic targets. To investigate the effects of CGA on lung histology and key gene expression, a murine model of bleomycin-induced lung fibrosis was used. KEY FINDINGS Network pharmacology analysis identified 384 were overlapped between CGA and IPF. Key targets including AKT1, TP53, JUN, CASP3, BCL2, MMP9, NFKB1, EGFR, HIF1A, and IL1B were identified. Pathway analysis suggested the involvement of cancer, atherosclerosis, and inflammatory processes. Molecular docking confirmed the stable binding between CGA and targets. CGA regulated the expression mRNA of EGFR, MMP9, AKT1, BCL2 and IL1B and attenuated pulmonary fibrosis in the mouse model. SIGNIFICANCE CGA is a promising multi-target therapeutic agent for IPF, which is supported by its efficacy in reducing fibrosis through the modulation of key pathways. This evidence provides a basis to further investigate CGA as an IPF potential treatment.
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Affiliation(s)
- Juan Manuel Velázquez-Enríquez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico.
| | - Jovito Cesar Santos-Álvarez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico
| | - Alma Aurora Ramírez-Hernández
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico
| | - Edilburga Reyes-Jiménez
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico
| | - Laura Pérez-Campos Mayoral
- Facultad Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico
| | - María de Los Ángeles Romero-Tlalolini
- CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico
| | - Cristian Jiménez-Martínez
- Departamento de Ingeniería Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Profesional Adolfo López Mateos, Zacatenco, Av. Wilfrido Massieu Esq. Cda. Miguel Stampa S/N, Alcaldía Gustavo A. Madero, Mexico City, 07738, Mexico
| | - Jaime Arellanes-Robledo
- Laboratorio de Enfermedades Hepáticas, Instituto Nacional de Medicina Genómica - INMEGEN, México City, 14610, Mexico; Dirección Adjunta de Investigación Humanística y Científica, Consejo Nacional de Humanidades, Ciencias y Tecnologías - CONAHCYT, México City, 03940, Mexico
| | - Saúl Villa-Treviño
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, C.P. 07360, Mexico
| | - Verónica Rocío Vásquez-Garzón
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico; CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico
| | - Rafael Baltiérrez-Hoyos
- Laboratorio de Fibrosis y Cáncer, Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico; CONAHCYT-Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Ex Hacienda de Aguilera S/N, Sur, San Felipe del Agua, Oaxaca, C.P. 68020, Mexico.
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Zhai P, Ouyang XH, Yang ML, Lin L, Li JY, Li YM, Cheng X, Zhu R, Hu DS. Luteolin protects against myocardial ischemia/reperfusion injury by reducing oxidative stress and apoptosis through the p53 pathway. JOURNAL OF INTEGRATIVE MEDICINE 2024:S2095-4964(24)00388-1. [PMID: 39343710 DOI: 10.1016/j.joim.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 08/13/2024] [Indexed: 10/01/2024]
Abstract
OBJECTIVE Myocardial ischemia/reperfusion injury (MIRI) is an obstacle to the success of cardiac reperfusion therapy. This study explores whether luteolin can mitigate MIRI by regulating the p53 signaling pathway. METHODS Model mice were subjected to a temporary surgical ligation of the left anterior descending coronary artery, and administered luteolin. The myocardial infarct size, myocardial enzyme levels, and cardiac function were measured. Latent targets and signaling pathways were screened using network pharmacology and molecular docking. Then, proteins related to the p53 signaling pathway, apoptosis and oxidative stress were measured. Hypoxia/reoxygenation (HR)-incubated HL1 cells were used to validate the effects of luteolin in vitro. In addition, a p53 agonist and an inhibitor were used to investigate the mechanism. RESULTS Luteolin reduced the myocardial infarcted size and myocardial enzymes, and restored cardiac function in MIRI mice. Network pharmacology identified p53 as a hub target. The bioinformatic analyses showed that luteolin had anti-apoptotic and anti-oxidative properties. Additionally, luteolin halted the activation of p53, and prevented both apoptosis and oxidative stress in myocardial tissue in vivo. Furthermore, luteolin inhibited cell apoptosis, JC-1 monomer formation, and reactive oxygen species elevation in HR-incubated HL1 cells in vitro. Finally, the p53 agonist NSC319726 downregulated the protective attributes of luteolin in the MIRI mouse model, and both luteolin and the p53 inhibitor pifithrin-α demonstrated a similar therapeutic effect in the MIRI mice. CONCLUSION Luteolin effectively treats MIRI and may ameliorate myocardial damage by regulating apoptosis and oxidative stress through its targeting of the p53 signaling pathway. Please cite this article as: Zhai P, Ouyang XH, Yang ML, Lin L, Li JY, Li YM, Cheng X, Zhu R, Hu DS. Luteolin protects against myocardial ischemia/reperfusion injury by reducing oxidative stress and apoptosis through the p53 pathway. J Integr Med. 2024; Epub ahead of print.Please cite this article as: Zhai P, Ouyang XH, Yang ML, Lin L, Li JY, Li YM, Cheng X, Zhu R, Hu DS. Luteolin protects against myocardial ischemia/reperfusion injury by reducing oxidative stress and apoptosis through the p53 pathway. J Integr Med. 2024; Epub ahead of print.
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Affiliation(s)
- Pan Zhai
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Xiao-Hu Ouyang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Meng-Ling Yang
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Lan Lin
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Jun-Yi Li
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Yi-Ming Li
- Department of Critical Care Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xiang Cheng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China; Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China
| | - Rui Zhu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China.
| | - De-Sheng Hu
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China; Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China; China-Russia Medical Research Center for Stress Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, Hubei Province, China.
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Liu M, Wang Y, Deng W, Xie J, He Y, Wang L, Zhang J, Cui M. Combining network pharmacology, machine learning, molecular docking and molecular dynamic to explore the mechanism of Chufeng Qingpi decoction in treating schistosomiasis. Front Cell Infect Microbiol 2024; 14:1453529. [PMID: 39310787 PMCID: PMC11413488 DOI: 10.3389/fcimb.2024.1453529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Accepted: 08/05/2024] [Indexed: 09/25/2024] Open
Abstract
Background Although the Chufeng Qingpi Decoction (CQD) has demonstrated clinical effectiveness in the treatment of schistosomiasis, the precise active components and the underlying mechanisms of its therapeutic action remain elusive. To achieve a profound comprehension, we incorporate network pharmacology, bioinformatics analysis, molecular docking, and molecular dynamics simulations as investigative methodologies within our research framework. Method Utilizing TCMSP and UniProt, we identified formula components and targets. Cytoscape 3.10.0 was used to construct an herb-target interaction network. Genecards, DisGeNET, and OMIM databases were examined for disease-related objectives. A Venn diagram identified the intersection of compound and disease targets. Using Draw Venn, overlapping targets populated STRING for PPI network. CytoNCA identified schistosomiasis treatment targets. GO & KEGG enrichment analysis followed High-scoring genes in PPI were analyzed by LASSO, RF, SVM-RFE. Molecular docking & simulations investigated target-compound interactions. Result The component's target network encompassed 379 nodes, 1629 edges, highlighting compounds such as wogonin, kaempferol, luteolin, and quercetin. Amongst the proteins within the PPI network, PTGS2, TNF, TGFB1, BCL2, TP53, IL10, JUN, MMP2, IL1B, and MYC stood out as the most prevalent entities. GO and KEGG revealed that mainly involved the responses to UV, positive regulation of cell migration and motility. The signal pathways encompassed Pathways in cancer, Lipid and atherosclerosis, Fluid shear stress and atherosclerosis, as well as the AGE-RAGE. Bioinformatics analysis indicated TP53 was the core gene. Ultimately, the molecular docking revealed that wogonin, kaempferol, luteolin, and quercetin each exhibited significant affinity in their respective interactions with TP53. Notably, kaempferol exhibited the lowest binding energy, indicating a highly stable interaction with TP53. Lastly, we validated the stability of the binding interaction between the four small molecules and the TP53 through molecular dynamics simulations. The molecular dynamics simulation further validated the strongest binding between TP53 and kaempferol. In essence, our research groundbreaking in its nature elucidates for the first time the underlying molecular mechanism of CQD in the therapeutic management of schistosomiasis, thereby providing valuable insights and guidance for the treatment of this disease. Conclusion This study uncovered the efficacious components and underlying molecular mechanisms of the Chufeng Qingpi Decoction in the management of schistosomiasis, thereby offering valuable insights for future fundamental research endeavors.
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Affiliation(s)
- Minglu Liu
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yuxin Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Wen Deng
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Jiahao Xie
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yanyao He
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Liang Wang
- Research and Teaching Department of Comparative Medicine, Dalian Medical University, Dalian, Liaoning, China
| | - Jianbin Zhang
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning, China
| | - Ming Cui
- Emergency Department, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
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Zhao SL, Liu D, Ding LQ, Liu GK, Yao T, Wu LL, Li G, Cao SJ, Qiu F, Kang N. Schisandra chinensis lignans improve insulin resistance by targeting TLR4 and activating IRS-1/PI3K/AKT and NF-κB signaling pathways. Int Immunopharmacol 2024; 142:113069. [PMID: 39241520 DOI: 10.1016/j.intimp.2024.113069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/14/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
Schisandra chinensis, a traditional Chinese medicine, has been widely applied in China to treat diabetes and its complications. The aim of this study was to discover the active compounds and explain related molecular mechanism contributing to the anti-diabetic effect of Schisandra chinensis. Herein, the therapeutic effects of Schisandra chinensis extracts on type 2 diabetes mellitus (T2DM) were firstly confirmed in vivo. Subsequently, various lignans were isolated from Schisandra chinensis and tested for hypoglycemic activity in palmitic acid-induced insulin-resistant HepG2 (IR-HepG2) cells. Among these lignans, R-biar-(7S,8R)-6,7,8,9-tetrahydro-1,2,3,12,13,14-hexamethoxy-7,8-dimethyl-7-dibenzo [a, c] cyclooctenol (compound 2) and Gomisin A (compound 4) were identified significantly increased the glucose consumption in IR-HepG2 cells. Meanwhile, compounds 2 and 4 activated the insulin receptor substrate-1 (IRS-1)/phosphoinositide 3-kinase (PI3K)/Ak strain transforming (AKT) pathway, which regulates glucose transporter 2 (GLUT2) and glucose-6-phosphatase (G6Pase), essential for gluconeogenesis and glucose uptake. These compounds also inhibited the nuclear factor-κB (NF-κB) signaling pathway, reducing interleukin-6 (IL-6) levels. Importantly, the hypoglycemic effects of compounds 2 and 4 were diminished after Toll-like receptor 4 (TLR4) knockdown. Cellular thermal shift assays confirmed increased TLR4 protein stability upon treatment with these compounds, indicating direct binding to TLR4. Furthermore, TLR4 knockdown reversed the effects of compounds 2 and 4 on the NF-κB and IRS-1/PI3K/AKT pathways. Taken together, compounds 2 and 4 alleviate IR by targeting TLR4, thereby modulating the NF-κB and IRS-1/PI3K/AKT pathways. These findings suggest that compounds 2 and 4 could be developed as therapeutic agents for T2DM.
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Key Words
- Gomisin A
- IRS-1/PI3K/AKT pathway
- Insulin resistance (IR)
- NF-κB pathway
- R-biar-(7S,8R)-6,7,8,9-tetrahydro-1,2,3,12,13,14-hexamethoxy-7,8- dimethyl-7-dibenzo[a,c]cyclooctenol
- Toll like receptor 4 (TLR4)
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Affiliation(s)
- Shao-Li Zhao
- School of Medical Technology, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Da Liu
- School of Medical Technology, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Li-Qin Ding
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Guan-Ke Liu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Tie Yao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin-Lin Wu
- School of Medical Technology, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Gen Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shi-Jie Cao
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Feng Qiu
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Ning Kang
- School of Medical Technology, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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Raguraman V, Chauhan L, Gehlot P, Kongkham B, Hariprasad P. Computational insights into the role of structurally diverse plant secondary metabolites as inhibitors against Imidazole Glycerol Phosphate Dehydratase of Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:8159-8171. [PMID: 37578041 DOI: 10.1080/07391102.2023.2245486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
Mycobacterium tuberculosis (Mtb) is one of the major causes of death worldwide and there is a pressing need for the development of novel drug leads. The Imidazole Glycerol Phosphate Dehydratase (IGPD) of Mtb is one of the key enzymes in the histidine biosynthesis pathway and has been recognized as the potentially underexploited drug target for anti-tuberculosis treatment. In the present study, 6063 structurally diverse plant secondary metabolites (PSM) were screened for their efficiency in inhibiting the catalytic activity of IGPD through molecular docking. The top 150 PSMs with the lowest binding energy represent the chemical classes, including Tannins (34%), Flavonoid Glycosides (14%), Terpene Glycosides (10%), Steroid Lactones (9.3%), Flavonoids (6.6%), Steroidal Glycosides (4.6%), etc. Bismahanine, Ashwagandhanolide, and Daurisoline form stable IGPD-inhibitor complexes with binding free energies of -291.3 ± 16.5, -279.0 ± 25.0, and -279.8 ± 17.6 KJ/mol, respectively, as determined by molecular dynamics simulations. These PSM demonstrated strong H-bond interactions with the amino acid residues Ile279, Arg281, and Lys276 in the catalytic region of IGPD, as revealed by structural snapshots. On the basis of our findings, these three PSM could be considered as possible leads against IGPD and should be explored in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasantharaja Raguraman
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Leena Chauhan
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Priyanka Gehlot
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - Bhani Kongkham
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
| | - P Hariprasad
- Environmental Biotechnology Laboratory, Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
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Yang C, Li J, Luo M, Zhou W, Xing J, Yang Y, Wang L, Rao W, Tao W. Unveiling the molecular mechanisms of Dendrobium officinale polysaccharides on intestinal immunity: An integrated study of network pharmacology, molecular dynamics and in vivo experiments. Int J Biol Macromol 2024; 276:133859. [PMID: 39009260 DOI: 10.1016/j.ijbiomac.2024.133859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/13/2024] [Accepted: 07/11/2024] [Indexed: 07/17/2024]
Abstract
Intestinal immunity plays a pivotal role in overall immunological defenses, constructing mechanisms against pathogens while maintaining balance with commensal microbial communities. Existing therapeutic interventions may lead to drug resistance and potential toxicity when immune capacity is compromised. Dendrobium officinale, a traditional Chinese medicine, contains components identified to bolster immunity. Employing network pharmacology strategies, this study identified constituents of Dendrobium officinale and their action targets in the TCMSP and Swiss Target Prediction databases, and compared them with intestinal immunity-related targets. Protein-protein interaction networks revealed the core targets of Dendrobium officinale polysaccharides, encompassing key pathways such as cell proliferation, inflammatory response, and immune reactions, particularly in association with the Toll-like receptor 4. Molecular docking and molecular dynamics simulation further confirmed the high affinity and stability between Dendrobium officinale polysaccharides and Toll-like receptor 4. In vivo experiments demonstrated that Dendrobium officinale polysaccharides modulates the expression of Toll-like receptor 4 and its downstream key proteins in the colonic mucosa of mice. Consequently, these findings suggest that Dendrobium officinale polysaccharides may serve as a potential modulator for intestinal immune functions, with its mechanism potentially related to the Toll-like receptor 4.
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Affiliation(s)
- Chenchen Yang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jingrui Li
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mengfan Luo
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Wanyi Zhou
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianrong Xing
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ying Yang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Lu Wang
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Wenjia Rao
- School of Sciences, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Wenyang Tao
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
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Li J, Wang D, Hao X, Li Y, Gao H, Fan Y, Fang B, Guo Y. Exploring the high-quality ingredients and mechanisms of Da Chuanxiong Formula in the treatment of neuropathic pain based on network pharmacology, molecular docking, and molecular dynamics simulation. Biomed Pharmacother 2024; 178:117195. [PMID: 39068852 DOI: 10.1016/j.biopha.2024.117195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/10/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024] Open
Abstract
Da Chuanxiong Formula (DCXF) is a traditional herbal prescription used for pain management. It consists of Chuanxiong Rhizoma (CR) and Gastrodiae Rhizoma (GR). Despite its long history of use, the underlying therapeutic mechanism of DCXF remains insufficiently understood. Therefore, in this study, key target genes were obtained through network pharmacology research methods and molecular docking techniques, including transient receptor potential vanilloid 1 (TRPV1), adenosine A2a receptor (ADORA2A), nuclear receptor subfamily 3 group C member 1 (NR3C1), and protein kinase C beta (PRKCB). Molecular dynamics simulations demonstrated the favorable binding between all four key genes and their corresponding compounds. Notably, chronic constriction injury (CCI) treatment resulted in a significant decrease in mechanical threshold and thermal latency period for rat foot contraction, which was ameliorated upon administration of DCXF. Furthermore, real-time quantitative reverse transcription PCR (RT-qPCR) and western blot (WB) analyses indicated an upregulation of TRPV1, ADORA2A, NR3C1, and PRKCB expression in the rat dorsal root ganglion following CCI, which was attenuated by treatment with DCXF. The expressions of inflammatory factors, including tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1β), and interleukin 6 (IL-6), in the rat dorsal root ganglion were assessed using ELISA, confirming consistent trends with the aforementioned findings. The results of this study offer a promising theoretical foundation for the utilization of DCXF in the treatment of neuropathic pain (NP).
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Affiliation(s)
- Jinshi Li
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Dongxu Wang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Xiaotong Hao
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Yuan Li
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Hairong Gao
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Yiting Fan
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Bo Fang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China.
| | - Yang Guo
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, China.
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Pyne N, Ray R, Paul S. Computational and experimental approaches manifest the leishmanicidal potential of α-mangostin resourced from Garcinia cowa. Acta Trop 2024; 257:107291. [PMID: 38889863 DOI: 10.1016/j.actatropica.2024.107291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/11/2024] [Accepted: 06/15/2024] [Indexed: 06/20/2024]
Abstract
Owing to the persistent number of parasitic deaths, Visceral leishmaniasis continues to haunt several economically weaker sections of India. The disease causes over 30,000 deaths and threatens millions annually on a global scale. The standard pentavalent antimonials, on the other hand, are associated with health adversities and disease relapse. The current study is focused on the search for the most potential natural bioactive phytocompound from the bark extract of the Northeastern Indian plant, Garcinia cowa, that shows potent anti-leishmanial properties. The High Resonance Liquid Chromatography followed by Mass Spectrometry (HR-LCMS) study followed by an in silico molecular docking using computational tools revealed that α-mangostin might potentially possess antiparasitic activity. To validate the anti-leishmanial efficacy of the compound, a cell viability assay was performed, which demonstrated the parasite-specific inhibitory activity of α-mangostin; with IC50 values ranging from 4.95 - 7.37 µM against the different forms of Leishmania donovani parasite. The flow cytometric analysis of the phytocompound treated parasites indicated an oxidative and nitrosative stress-mediated apoptotic cell death in the parasites, by the suggestive surge in nuclear fragmentation and mitochondrial dysfunction. Simultaneously, a cytokine profiling study suggested approximate two-to-three-fold upregulated levels of pro-inflammatory cytokines post-compound treatment, which is predicted to actively contribute to parasite-killing. α-mangostin was also found to reduce the chances of parasite survival by inhibiting arginase enzyme activity, which in favorable conditions facilitates its sustenance. This study thereby substantiates that α-mangostin significantly possesses anti-leishmanial potentiality that can be developed into a cure for this infectious disease.
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Affiliation(s)
- Nibedita Pyne
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, Kolkata 700019, India
| | - Ribhu Ray
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, Kolkata 700019, India
| | - Santanu Paul
- Laboratory of Cell and Molecular Biology, Department of Botany, Centre of Advanced Study, University of Calcutta, Kolkata 700019, India.
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Jain P, Parikh S, Patel P, Shah S, Patel K. Comprehensive insights into herbal P-glycoprotein inhibitors and nanoformulations for improving anti-retroviral therapy efficacy. J Drug Target 2024; 32:884-908. [PMID: 38748868 DOI: 10.1080/1061186x.2024.2356751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/28/2024] [Accepted: 05/10/2024] [Indexed: 05/28/2024]
Abstract
The worldwide HIV cases were 39.0 million (33.1-45.7 million) in 2022. Due to genetic variations, HIV-1 is more easily transmitted than HIV-2 and favours CD4 + T cells and macrophages, producing AIDS. Conventional HIV drug therapy has many drawbacks, including adherence issues leading to resistance, side effects that lower life quality, drug interactions, high costs limiting global access, inability to eliminate viral reservoirs, chronicity requiring lifelong treatment, emerging toxicities, and a focus on managing infections. Conventional dosage forms have bioavailability issues due to intestinal P-glycoprotein (P-gp) efflux, which can reduce anti-retroviral drug efficacy and lead to resistance. Use of phyto-constituents with P-gp regulating actions has great benefits for semi-synthetic modification to create formulations with greater bioavailability and reduced toxicity, which improves drug effectiveness. Lipid-based nanocarriers, solid lipid nanoparticles, nanostructured lipid carriers, polymer-based nanocarriers, and inorganic nanoparticles may inhibit P-gp efflux. Employing potent P-gp inhibitors within nanocarriers as a Trojan horse approach can enhance the intracellular accumulation of anti-retroviral drugs (ARDs), which are substrates for efflux transporters. This technique increases oral bioavailability and offers lower-dose options, boosting HIV patient compliance and lowering costs. Molecular docking of the inhibitor with P-gp may anticipate optimum binding and function, allowing drug efflux to be minimised.
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Affiliation(s)
- Prexa Jain
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad, India
| | - Shreni Parikh
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad, India
| | - Paresh Patel
- Department of Pharmaceutical Chemistry, L. J. Institute of Pharmacy, L J University, Ahmedabad, India
| | - Shreeraj Shah
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad, India
| | - Kaushika Patel
- Department of Pharmaceutical Technology, L. J. Institute of Pharmacy, L J University, Ahmedabad, India
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Vikram A, Patel SK, Singh A, Pathania D, Ray RS, Upadhyay AK, Dwivedi A. Natural autophagy activators: A promising strategy for combating photoaging. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155508. [PMID: 38901286 DOI: 10.1016/j.phymed.2024.155508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Photodamage to the skin stands out as one of the most widespread epidermal challenges globally. Prolonged exposure to sunlight containing ultraviolet radiation (UVR) instigates stress, thereby compromising the skin's functionality and culminating in photoaging. Recent investigations have shed light on the importance of autophagy in shielding the skin from photodamage. Despite the acknowledgment of numerous phytochemicals possessing photoprotective attributes, their potential to induce autophagy remains relatively unexplored. PURPOSE Diminished autophagy activity in photoaged skin underscores the potential benefits of restoring autophagy through natural compounds to enhance photoprotection. Consequently, this study aims to highlight the role of natural compounds in safeguarding against photodamage and to assess their potential to induce autophagy via an in-silico approach. METHODS A thorough search of the literature was done using several databases, including PUBMED, Science Direct, and Google Scholar, to gather relevant studies. Several keywords such as Phytochemical, Photoprotection, mTOR, Ultraviolet Radiation, Reactive oxygen species, Photoaging, and Autophagy were utilized to ensure thorough exploration. To assess the autophagy potential of phytochemicals through virtual screening, computational methodologies such as molecular docking were employed, utilizing tools like AutoDock Vina. Receptor preparation for docking was facilitated using MGLTools. RESULTS The initiation of structural and functional deterioration in the skin due to ultraviolet radiation (UVR) or sunlight-induced reactive oxygen species/reactive nitrogen species (ROS/RNS) involves the modulation of various pathways. Natural compounds like phenolics, flavonoids, flavones, and anthocyanins, among others, possess chromophores capable of absorbing light, thereby offering photoprotection by modulating these pathways. In our molecular docking study, these phytochemicals have shown binding affinity with mTOR, a negative regulator of autophagy, indicating their potential as autophagy modulators. CONCLUSION This integrated review underscores the photoprotective characteristics of natural compounds, while the in-silico analysis reveals their potential to modulate autophagy, which could significantly contribute to their anti-photoaging properties. The findings of this study hold promise for the advancement of cosmeceuticals and therapeutics containing natural compounds aimed at addressing photoaging and various skin-related diseases. By leveraging their dual benefits of photoprotection and autophagy modulation, these natural compounds offer a multifaceted approach to combatting skin aging and related conditions.
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Affiliation(s)
- Apeksha Vikram
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Sunil Kumar Patel
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Arshwinder Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala-147004 Punjab, India
| | - Diksha Pathania
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Ratan Singh Ray
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India
| | - Atul Kumar Upadhyay
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala-147004 Punjab, India.
| | - Ashish Dwivedi
- Photobiology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan 31, Mahatma Gandhi Marg, Lucknow-226001 Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002 Uttar Pradesh, India.
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He J, Zhu X, Xu K, Li Y, Zhou J. Network toxicological and molecular docking to investigate the mechanisms of toxicity of agricultural chemical Thiabendazole. CHEMOSPHERE 2024; 363:142711. [PMID: 38964723 DOI: 10.1016/j.chemosphere.2024.142711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/11/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Abstract
Food safety is closely linked to human health. Thiabendazole is widely used as a fungicide and deodorant on agricultural products like vegetables and fruits to prevent fungal infections during transport and storage. This study aims to investigate the toxicity and potential mechanisms of Thiabendazole using novel network toxicology and molecular docking techniques. First, the ADMETlab2.0 and ADMETsar databases, along with literature, predicted Thiabendazole's potential to induce cancer and liver damage. Disease target libraries were constructed using GeneCards and TCMIP databases, while Thiabendazole target libraries were constructed using Swiss Target Prediction and TCMIP databases. The Venn database identified potential targets associated with Thiabendazole-induced cancer and liver injury. Protein-protein interaction (PPI) networks were derived from the STRING database, and gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways were obtained from the DAVID database. Molecular docking assessed the binding affinity between Thiabendazole and core targets. The study revealed 29 potential targets for Thiabendazole-induced cancer and 30 potential targets for liver injury. PPI identified 5 core targets for Thiabendazole-induced cancers and 4 core targets for induced liver injury. KEGG analysis indicated that Thiabendazole might induce gastric and prostate cancer via cyclin-dependent kinase 2 (CDK2) and epidermal growth factor receptor (EGFR) targets, and liver injury through the same targets, with the p53 signaling pathway being central. GO analysis indicated that Thiabendazole-induced cancers and liver injuries were related to mitotic cell cycle G2/M transition and DNA replication. Molecular docking showed stable binding of Thiabendazole with core targets including CDK1, CDK2, EGFR, and checkpoint kinase 1 (CHEK1). These findings suggest Thiabendazole may affect the G2/M transition of the mitotic cell cycle through the p53 signaling pathway, potentially inducing cancer and liver injury. This study provides a theoretical basis for understanding the potential molecular mechanisms underlying Thiabendazole toxicity, aiding in the prevention and treatment of related diseases. Additionally, the network toxicology approach accelerates the elucidation of toxic pathways for uncharacterized agricultural chemicals.
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Affiliation(s)
- Junhui He
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products/Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530006, China; Department of Pharmacology, Guangxi Key Laboratory of Traditional Chinese Medicine Quality Standards, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Naning, 530022, China.
| | - Xiufang Zhu
- School of Material Science and Engineering, Hubei University of Automotive Technology, Shiyan, 442000, China
| | - Kaimeng Xu
- Yunnan Provincial Key Laboratory of Wood Adhesives and Glued Products, International Joint Research Center for Biomass Materials, Southwest Forestry University, Kunming, 650224, China
| | - Ye Li
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN, USA
| | - Juying Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products/Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Guangxi Minzu University, Nanning, 530006, China.
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50
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Ezzemani W, Altawalah H, Windisch M, Ouladlahsen A, Saile R, Kettani A, Ezzikouri S. Identification of Zika virus NS2B-NS3 protease and NS5 polymerase inhibitors by structure-based virtual screening of FDA-approved drugs. J Biomol Struct Dyn 2024; 42:8073-8088. [PMID: 37528667 DOI: 10.1080/07391102.2023.2242963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/26/2023] [Indexed: 08/03/2023]
Abstract
Zika virus (ZIKV) is a mosquito-borne human flavivirus responsible that causing emergency outbreaks in Brazil. ZIKV is suspected of causing Guillain-Barre syndrome in adults and microcephaly. The NS2B-NS3 protease and NS5 RNA-dependent RNA polymerase (RdRp), central to ZIKV multiplication, have been identified as attractive molecular targets for drugs. We performed a structure-based virtual screening of 2,659 FDA-approved small molecule drugs in the DrugBank database using AutoDock Vina in PyRx v0.8. Accordingly, 15 potential drugs were selected as ZIKV inhibitors because of their high values (binding affinity - binding energy) and we analyzed the molecular interactions between the active site amino acids and the compounds. Among these drugs, tamsulosin was found to interact most efficiently with NS2B/NS3 protease, as indicated by the lowest binding energy value (-8.27 kJ/mol), the highest binding affinity (-5.7 Kcal/mol), and formed H-bonds with amino acid residues TYRB130, SERB135, TYRB150. Furthermore, biotin was found to interact most efficiently with NS5 RdRp with a binding energy of -150.624 kJ/mol, a binding affinity of -5.6 Kcal/mol, and formed H-bonds with the amino acid residues ASPA665 and ASPA540. In vitro, in vivo, and clinical studies are needed to demonstrate anti-ZIKV safety and the efficacy of these FDA-approved drug candidates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait
| | - Marc Windisch
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Ahd Ouladlahsen
- Faculté de médecine et de pharmacie, Université Hassan II, Casablanca, Morocco
- Service des maladies Infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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