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Mozibullah M, Eslampanah Seyedi H, Khatun M, Solayman M. Identification and analysis of oncogenic non-synonymous single nucleotide polymorphisms in the human NRAS gene: An exclusive in silico study. J Genet Eng Biotechnol 2024; 22:100378. [PMID: 38797553 PMCID: PMC11087716 DOI: 10.1016/j.jgeb.2024.100378] [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: 12/02/2023] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND N-ras protein is encoded by the NRAS gene and operates as GDP-GTP-controlled on/off switching. N-ras interacts with cellular signaling networks that regulate various cellular activities including cell proliferation and survival. The nonsynonymous single nucleotide polymorphism (nsSNPs)-mediated alteration can substantially disrupt the structure and activity of the corresponding protein. N-ras has been reported to be associated with numerous diseases including cancers due to the nsSNPs. A comprehensive study on the NRAS gene to unveil the potentially damaging and oncogenic nsSNPs is yet to be accomplished. Hence, this extensive in silico study is intended to identify the disease-associated, specifically oncogenic nsSNPs of the NRAS gene. RESULTS Out of 140 missense variants, 7 nsSNPs (I55R, G60E, G60R, Y64D, L79F, D119G, and V152F) were identified to be damaging utilizing 10 computational tools that works based on different algorithms with high accuracy. Among those, G60E, G60R, and D119G variants were further filtered considering their location in the highly conserved region and later identified as oncogenic variants. Interestingly, G60E and G60R variants were revealed to be particularly associated with lung adenocarcinoma, rhabdomyosarcoma, and prostate adenocarcinoma. Therefore, D119G could be subjected to detailed investigation for identifying its association with specific cancer. CONCLUSION This in silico study identified the deleterious and oncogenic missense variants of the human NRAS gene that could be utilized for designing further experimental investigation. The outcomes of this study would be worthwhile in future research for developing personalized medicine.
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Affiliation(s)
- Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | | | - Marina Khatun
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Solayman
- Department of Biochemistry and Molecular Biology, Primeasia University, Bangladesh.
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2
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Liu X, Sun P, Bao X, Cao Y, Wang L, Wang Q. Potential mechanisms of traditional Chinese medicine in treating insomnia: A network pharmacology, GEO validation, and molecular-docking study. Medicine (Baltimore) 2024; 103:e38052. [PMID: 38701256 PMCID: PMC11062677 DOI: 10.1097/md.0000000000038052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
The purpose of this study is to investigate the potential mechanisms of Chinese herbs for the treatment of insomnia using a combination of data mining, network pharmacology, and molecular-docking validation. All the prescriptions for insomnia treated by the academician Qi Wang from 2020 to 2022 were collected. The Ancient and Modern Medical Case Cloud Platform v2.3 was used to identify high-frequency Chinese medicinal herbs and the core prescription. The Traditional Chinese Medicine Systems Pharmacology and UniProt databases were utilized to predict the effective active components and targets of the core herbs. Insomnia-related targets were collected from 4 databases. The intersecting targets were utilized to build a protein-protein interaction network and conduct gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis using the STRING database, Cytoscape software, and clusterProfiler package. Gene chip data (GSE208668) were obtained from the Gene Expression Omnibus database. The limma package was applied to identify differentially expressed genes (DEGs) between insomnia patients and healthy controls. To create a "transcription factor (TF)-miRNA-mRNA" network, the differentially expressed miRNAs were entered into the TransmiR, FunRich, Targetscan, and miRDB databases. Subsequently, the overlapping targets were validated using the DEGs, and further validations were conducted through molecular docking and molecular dynamics simulations. Among the 117 prescriptions, 65 herbs and a core prescription were identified. Network pharmacology and bioinformatics analysis revealed that active components such as β-sitosterol, stigmasterol, and canadine acted on hub targets, including interleukin-6, caspase-3, and hypoxia-inducible factor-1α. In GSE208668, 6417 DEGs and 7 differentially expressed miRNAs were identified. A "TF-miRNA-mRNA" network was constructed by 4 "TF-miRNA" interaction pairs and 66 "miRNA-mRNA" interaction pairs. Downstream mRNAs exert therapeutic effects on insomnia by regulating circadian rhythm. Molecular-docking analyses demonstrated good docking between core components and hub targets. Molecular dynamics simulation displayed the strong stability of the complex formed by small molecule and target. The core prescription by the academician Qi Wang for treating insomnia, which involves multiple components, targets, and pathways, showed the potential to improve sleep, providing a basis for clinical treatment of insomnia.
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Affiliation(s)
- Xing Liu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Pengcheng Sun
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xuejie Bao
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yanqi Cao
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Liying Wang
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Wang
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
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3
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Jin Z, Zhang Y, Luo X, Geng M, Duan W, Xie Z, Zhang H. Design, synthesis, and evaluation of thiazolecarboxamide derivatives as stimulator of interferon gene inhibitors. Mol Divers 2024:10.1007/s11030-024-10860-6. [PMID: 38683489 DOI: 10.1007/s11030-024-10860-6] [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: 03/04/2024] [Accepted: 03/24/2024] [Indexed: 05/01/2024]
Abstract
Stimulator of interferon gene (STING) plays critical roles in the cytoplasmic DNA-sensing pathway and in the induction of inflammatory response. Aberrant cytoplasmic DNA accumulation and STING activation are implicated in numerous inflammatory and autoimmune diseases. Here, we reported the discovery of a series of thiazolecarboxamide-based STING inhibitors through a molecular planarity/symmetry disruption strategy. The privileged compound 15b significantly inhibited STING signaling and suppressed immune-inflammatory cytokine levels in both human and murine cells. In vivo experiments demonstrated 15b effectively ameliorated immune-inflammatory cytokines upregulation in MSA-2-stimulated and Trex1-D18N mice. Furthermore, compound 15b exhibited enhanced efficacy in suppressing interferon-stimulated gene 15 (ISG15), a critical positive feedback regulator of STING. Overall, compound 15b deserves further development for the treatment of STING-associated inflammatory and autoimmune diseases.
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Affiliation(s)
- Zechen Jin
- Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Yan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China
| | - Xin Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xian Lin Road, Nanjing, 210023, China
| | - Meiyu Geng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, 264117, Shandong, China
| | - Wenhu Duan
- Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China
- School of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, 264117, Shandong, China
| | - Zuoquan Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.
| | - Hefeng Zhang
- Small-Molecule Drug Research Center, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, China.
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4
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Özkul Ş, Tunca E, Mert S, Bayrakdar A, Kasımoğulları R. Synthesis, molecular docking analysis, drug-likeness evaluation, and inhibition potency of new pyrazole-3,4-dicarboxamides incorporating sulfonamide moiety as carbonic anhydrase inhibitors. J Biochem Mol Toxicol 2024; 38:e23704. [PMID: 38588035 DOI: 10.1002/jbt.23704] [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: 01/21/2024] [Revised: 03/12/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
A series of novel pyrazole-dicarboxamides were synthesized from pyrazole-3,4-dicarboxylic acid chloride and various primary and secondary sulfonamides. The structures of the new compounds were confirmed by FT-IR, 1H-NMR, 13C-NMR, and HRMS. Then the inhibition effects of newly synthesized molecules on human erythrocyte hCA I and hCA II isoenzymes were investigated. Ki values of the compounds were in the range of 0.024-0.496 µM for hCA I and 0.006-5.441 µM for hCA II. Compounds 7a and 7i showed nanomolar level of inhibition of hCA II, and these compounds exhibited high selectivity for this isoenzyme. Molecular docking studies were performed between the most active compounds 7a, 7b, 7i, and the reference inhibitor AAZ and the hCAI and hCAII to investigate the binding mechanisms between the compounds and the isozymes. These compounds showed better interactions than the AAZ. ADMET and drug-likeness analyses for the compounds have shown that the compounds can be used pharmacologically in living organisms.
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Affiliation(s)
- Şüheda Özkul
- Department of Biochemistry, Faculty of Arts and Sciences, Dumlupınar University, Kütahya, Turkey
| | - Ekrem Tunca
- Department of Biochemistry, Faculty of Arts and Sciences, Dumlupınar University, Kütahya, Turkey
| | - Samet Mert
- Department of Chemistry, Faculty of Arts and Sciences, Dumlupınar University, Kütahya, Turkey
| | - Alpaslan Bayrakdar
- Vocational School of Higher Education for Healthcare Services, Iğdır University, Iğdır, Turkey
| | - Rahmi Kasımoğulları
- Department of Chemistry, Faculty of Arts and Sciences, Dumlupınar University, Kütahya, Turkey
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5
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Liu S, Qin T, Zou F, Dong H, Yu L, Wang H, Zhang L. Pseudolaric acid B exerts an antifungal effect and targets SIRT1 to ameliorate inflammation by regulating Nrf2/NF-κB pathways in fungal keratitis. Inflammopharmacology 2024; 32:1133-1146. [PMID: 38150134 DOI: 10.1007/s10787-023-01408-5] [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: 10/24/2023] [Accepted: 11/30/2023] [Indexed: 12/28/2023]
Abstract
Fungal keratitis (FK) is a vision-threatening infection. We aimed to explore the antifungal and anti-inflammatory effects of pseudolaric acid B (PAB) on FK and the underlying mechanisms involved. Network pharmacology utilized to acquire the potential target genes, and silent information regulator 1 (SIRT1) was consistently downregulated in Gene Expression Omnibus dataset and clinical samples. Molecular docking analysis showed that PAB and SIRT1 had good binding activity. No toxicity was observed in vivo and in vitro with a PAB concentration below 0.3 μM. PAB exerted its antifungal activity by destroying the integrity of hyphae, and alleviated the severity of FK in rats by decreasing clinical scores, fungal burden and inhibiting inflammatory cell infiltration. PAB increased SIRT1 to regulate the crosstalk between nuclear factor erythroid 2-related factor 2 (Nrf2) and nuclear factor kappa-B (NF-κB), decreasing the levels of inflammatory cytokines tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6; and pattern recognition receptors, C-type lectin domain containing 7A (Dectin-1), lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1), toll like receptor (TLR)-2, and TLR4 both in vivo and in vitro. However, this anti-inflammatory effect of PAB was abolished by the SIRT1 inhibitor EX527. This study provides new evidence that PAB has antifungal and anti-inflammatory effects in FK and may provide a novel therapeutic strategy for the treatment of FK.
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Affiliation(s)
- Shuyi Liu
- Dalian Medical University, 9 Lvshun Road South, Dalian, 116044, China
- Department of Ophthalmology, The Third People's Hospital of Dalian, Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Tao Qin
- Dalian Medical University, 9 Lvshun Road South, Dalian, 116044, China
| | - Fengkai Zou
- Dalian Medical University, 9 Lvshun Road South, Dalian, 116044, China
| | - He Dong
- Department of Ophthalmology, The Third People's Hospital of Dalian, Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Liang Yu
- Department of Ophthalmology, The Third People's Hospital of Dalian, Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hai Wang
- Department of Pathology, The Third People's Hospital of Dalian, Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lijun Zhang
- Dalian Medical University, 9 Lvshun Road South, Dalian, 116044, China.
- Department of Ophthalmology, The Third People's Hospital of Dalian, Affiliated Hospital of Dalian Medical University, Dalian, China.
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6
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Majoumo-Mbe F, Sangbong NA, Tadjong Tcho A, Namba-Nzanguim CT, Simoben CV, Eni DB, Alhaji Isa M, Poli ANR, Cassel J, Salvino JM, Montaner LJ, Tietjen I, Ntie-Kang F. 5-chloro-3-(2-(2,4-dinitrophenyl) hydrazono)indolin-2-one: synthesis, characterization, biochemical and computational screening against SARS-CoV-2. CHEMICKE ZVESTI 2024; 78:3431-3441. [PMID: 38685970 PMCID: PMC11055700 DOI: 10.1007/s11696-023-03274-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/04/2023] [Indexed: 05/02/2024]
Abstract
Chemical prototypes with broad-spectrum antiviral activity are important toward developing new therapies that can act on both existing and emerging viruses. Binding of the SARS-CoV-2 spike protein to the host angiotensin-converting enzyme 2 (ACE2) receptor is required for cellular entry of SARS-CoV-2. Toward identifying new chemical leads that can disrupt this interaction, including in the presence of SARS-CoV-2 adaptive mutations found in variants like omicron that can circumvent vaccine, immune, and therapeutic antibody responses, we synthesized 5-chloro-3-(2-(2,4-dinitrophenyl)hydrazono)indolin-2-one (H2L) from the condensation reaction of 5-chloroisatin and 2,4-dinitrophenylhydrazine in good yield. H2L was characterised by elemental and spectral (IR, electronic, Mass) analyses. The NMR spectrum of H2L indicated a keto-enol tautomerism, with the keto form being more abundant in solution. H2L was found to selectively interfere with binding of the SARS-CoV-2 spike receptor-binding domain (RBD) to the host angiotensin-converting enzyme 2 receptor with a 50% inhibitory concentration (IC50) of 0.26 μM, compared to an unrelated PD-1/PD-L1 ligand-receptor-binding pair with an IC50 of 2.06 μM in vitro (Selectivity index = 7.9). Molecular docking studies revealed that the synthesized ligand preferentially binds within the ACE2 receptor-binding site in a region distinct from where spike mutations in SARS-CoV-2 variants occur. Consistent with these models, H2L was able to disrupt ACE2 interactions with the RBDs from beta, delta, lambda, and omicron variants with similar activities. These studies indicate that H2L-derived compounds are potential inhibitors of multiple SARS-CoV-2 variants, including those capable of circumventing vaccine and immune responses. Supplementary Information The online version contains supplementary material available at 10.1007/s11696-023-03274-5.
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Affiliation(s)
- Felicite Majoumo-Mbe
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Neba Abongwa Sangbong
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Alain Tadjong Tcho
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Cyril T. Namba-Nzanguim
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Conrad V. Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Donatus B. Eni
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
| | - Mustafa Alhaji Isa
- Department of Microbiology, Faculty of Sciences, University of Maiduguri, PMB 1069, Maiduguri, Borno State Nigeria
| | | | - Joel Cassel
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Joseph M. Salvino
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Luis J. Montaner
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Ian Tietjen
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104 USA
| | - Fidele Ntie-Kang
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
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7
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Smith MD, Darryl Quarles L, Demerdash O, Smith JC. Drugging the entire human proteome: Are we there yet? Drug Discov Today 2024; 29:103891. [PMID: 38246414 DOI: 10.1016/j.drudis.2024.103891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Each of the ∼20,000 proteins in the human proteome is a potential target for compounds that bind to it and modify its function. The 3D structures of most of these proteins are now available. Here, we discuss the prospects for using these structures to perform proteome-wide virtual HTS (VHTS). We compare physics-based (docking) and AI VHTS approaches, some of which are now being applied with large databases of compounds to thousands of targets. Although preliminary proteome-wide screens are now within our grasp, further methodological developments are expected to improve the accuracy of the results.
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Affiliation(s)
- Micholas Dean Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN 37830, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - L Darryl Quarles
- Departments of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; ORRxD LLC, 3404 Olney Drive, Durham, NC 27705, USA
| | - Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN 37830, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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Pande S, Patel CA, Dhameliya TM, Beladiya J, Parikh P, Kachhadiya R, Dholakia S. Inhibition of Uridine 5'-diphospho-glucuronosyltransferases A10 and B7 by vitamins: insights from in silico and in vitro studies. In Silico Pharmacol 2024; 12:8. [PMID: 38204437 PMCID: PMC10774253 DOI: 10.1007/s40203-023-00182-0] [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: 08/14/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Uridine 5'-diphospho-glucuronosyltransferases (UGTs) have been considered as a family of enzymes responsible for the glucuronidation process, a crucial phase II detoxification reaction. Among the various UGT isoforms, UGTs A10 and B7 have garnered significant attention due to their broad substrate specificity and involvement in the metabolism of numerous compounds. Recent studies have suggested that certain vitamins may exert inhibitory effects on UGT activity, thereby influencing the metabolism of drugs, environmental toxins, and endogenous substances, ultimately impacting their biological activities. In the present study, the inhibition potential of vitamins (A, B1, B2, B3, B5, B6, B7, B9, D3, E, and C) on UGT1A10 and UGT2B7 was determined using in silico and in vitro approaches. A 3-dimensional model of UGT1A10 and UGT2B7 enzymes was built using Swiss Model, ITASSER, and ROSETTA and verified using Ramachandran plot and SAVES tools. Molecular docking studies revealed that vitamins interact with UGT1A10 and UGT2B7 enzymes by binding within the active site pocket and interacting with residues. Among all vitamins, the highest binding affinity predicted by molecular docking was - 8.61 kcal/mol with vitamin B1. The in vitro studies results demonstrated the inhibition of the glucuronidation activity of UGTs by vitamins A, B1, B2, B6, B9, C, D, and E, with IC50 values of 3.28 ± 1.07 µg/mL, 24.21 ± 1.11 µg/mL, 3.69 ± 1.02 µg/mL, 23.60 ± 1.08 µg/mL, 6.77 ± 1.08 µg/mL, 83.95 ± 1.09 µg/ml, 3.27 ± 1.13 µg/mL and 3.89 ± 1.12 µg/mL, respectively. These studies provided the valuable insights into the mechanisms underlying drug-vitamins interactions and have the potential to guide personalized medicine approaches, optimizing therapeutic outcomes, and ensuring patient safety. Indeed, further research in the area of UGT (UDP-glucuronosyltransferase) inhibition by vitamins is essential to fully understand the clinical relevance and implications of these interactions. UGTs play a crucial role in the metabolism and elimination of various drugs, toxins, and endogenous compounds in the body. Therefore, any factors that can modulate UGT activity, including vitamins, can have implications for drug metabolism, drug-drug interactions, and overall health. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00182-0.
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Affiliation(s)
- Sonal Pande
- Gujarat Technological University, Ahmedabad, India
- Department of Pharmacology, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 India
| | - Chirag A. Patel
- Department of Pharmacology, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 India
| | - Tejas M. Dhameliya
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382 481 India
| | - Jayesh Beladiya
- Department of Pharmacology, L. M. College of Pharmacy, Navrangpura, Ahmedabad, 380009 India
| | - Palak Parikh
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, 38009 India
| | - Radhika Kachhadiya
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, 38009 India
| | - Sandip Dholakia
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, 38009 India
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Liu SJ, Guo BD, Gao QH, Deng YJ, Yan B, Zeng Y, Zhao M, Ren K, Wang F, Guo J. Ursolic acid alleviates chronic prostatitis via regulating NLRP3 inflammasome-mediated Caspase-1/GSDMD pyroptosis pathway. Phytother Res 2024; 38:82-97. [PMID: 37807970 DOI: 10.1002/ptr.8034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/15/2023] [Accepted: 09/26/2023] [Indexed: 10/10/2023]
Abstract
Ursolic acid (UA) is a naturally occurring pentacyclic triterpenoid widely found in fruits and vegetables. It has been reported that UA has anti-inflammatory effects. However, its efficacy and mechanism of action in the treatment of chronic prostatitis (CP) remain unclear. This study aimed to investigate the efficacy of UA treatment in CP and further explore the underlying mechanism. CP rat and pyroptosis cell models were established in vivo and in vitro, respectively. The efficacy of UA in inhibiting CP was evaluated via haematoxylin-eosin (HE) staining and measurement of inflammatory cytokines. RNA sequencing and molecular docking were used to predict the therapeutic targets of UA in CP. The expression of pyroptosis-related proteins was examined using various techniques, including immunohistochemistry, immunofluorescence, and flow cytometry. UA significantly ameliorated pathological damage and reduced the levels of proinflammatory cytokines in the CP model rats. RNA sequencing analysis and molecular docking suggested that NLRP3, Caspase-1, and GSDMD may be key targets. We also found that UA decreased ROS levels, alleviated oxidative stress, and inhibited p-NF-κB protein expression both in vivo and in vitro. UA improved pyroptosis morphology as indicated by electron microscope and inhibited the expression of the pyroptosis-related proteins NLRP3, Caspase-1, ASC, and GSDMD, reversed the levels of IL-1β, IL-18, and lactate dehydrogenase in vivo and in vitro. UA can mitigate CP by regulating the NLRP3 inflammasome-mediated Caspase-1/GSDMD pathway. Therefore, UA may be a potential for the treatment of CP.
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Affiliation(s)
- Sheng-Jing Liu
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Bo-da Guo
- Department of Urology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing-He Gao
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying-Jun Deng
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Bin Yan
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Yin Zeng
- Department of Andrology, Beijing Chinese Medicine Hospital affiliated to Capital Medical University, Beijing, China
| | - Ming Zhao
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Kai Ren
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Fu Wang
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Guo
- Department of Andrology, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing, China
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10
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Zhou X, Tan F, Zhang S, Wang A, Zhang T. A Strategy based on Bioinformatics and Machine Learning Algorithms Reveals Potential Mechanisms of Shelian Capsule against Hepatocellular Carcinoma. Curr Pharm Des 2024; 30:377-405. [PMID: 38310567 DOI: 10.2174/0113816128284465240108071554] [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: 09/27/2023] [Revised: 11/30/2023] [Accepted: 12/11/2023] [Indexed: 02/06/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a prevalent and life-threatening form of cancer, with Shelian Capsule (SLC), a traditional Chinese medicine (TCM) formulation, being recommended for clinical treatment. However, the mechanisms underlying its efficacy remain elusive. This study sought to uncover the potential mechanisms of SLC in HCC treatment using bioinformatics methods. METHODS Bioactive components of SLC were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and HCC-related microarray chip data were sourced from the Gene Expression Omnibus (GEO) database. The selection criteria for components included OB ≧ 30% and DL ≧ 0.18. By integrating the results of differential expression analysis and weighted gene co-expression network analysis (WGCNA), disease-related genes were identified. Therapeutic targets were determined as shared items between candidate targets and disease genes. Protein-protein interaction (PPI) network analysis was conducted for concatenated genes, with core protein clusters identified using the MCODE plugin. Machine learning algorithms were applied to identify signature genes within therapeutic targets. Subsequently, immune cell infiltration analysis, single-cell RNA sequencing (sc-RNA seq) analysis, molecular docking, and ADME analysis were performed for the screened genes. RESULTS A total of 153 SLC ingredients and 170 candidate targets were identified, along with 494 HCCrelated disease genes. Overlapping items between disease genes and drug candidates represented therapeutic genes, and PPI network analysis was conducted using concatenated genes. MCODE1 and MCODE2 cluster genes underwent Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Four signature genes (TOP2A, CYP1A2, CYP2B6, and IGFBP3) were identified from 28 therapeutic genes using 3 machine learning algorithms, with ROC curves plotted. Molecular docking validated the interaction modes and binding abilities between signature genes and corresponding compounds, with free binding energy all <-7 kcal/mol. Finally, ADME analysis revealed similarities between certain SLC components and the clinical drugs Sorafenib and Lenvatinib. CONCLUSION In summary, our study revealed that the mechanism underlying the anti-HCC effects of SLC involves interactions at three levels: components (quercetin, beta-sitosterol, kaempferol, baicalein, stigmasterol, and luteolin), pathways (PI3K-Akt signaling pathway, TNF signaling pathway, and IL-17 signaling pathway), and targets (TOP2A, CYP1A2, CYP2B6, and IGFBP3). This study provides preliminary insights into the potential pharmacological mechanisms of SLC in HCC treatment, aiming to support its clinical application and serve as a reference for future laboratory investigations.
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Affiliation(s)
- Xianqiang Zhou
- Department of Traditional Chinese Medicine, Shanghai Medical College, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai 200040, China
- Department of Pulmonary Diseases, Shanghai Medical College, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai 200072, China
| | - Fang Tan
- Department of Neurology, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei 230031, Anhui Province, China
| | - Suxian Zhang
- Department of Traditional Chinese Medicine, Shanghai Medical College, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - An'an Wang
- Department of Pulmonary Diseases, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Tiansong Zhang
- Department of Traditional Chinese Medicine, Shanghai Medical College, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai 200040, China
- Department of Pulmonary Diseases, Shanghai Medical College, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai 200072, China
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11
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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12
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Zhou X, Tan F, Zhang S, Zhang T. Combining single-cell RNA sequencing data and transcriptomic data to unravel potential mechanisms and signature genes of the progression of idiopathic pulmonary fibrosis to lung adenocarcinoma and predict therapeutic agents. Funct Integr Genomics 2023; 23:346. [PMID: 37996625 DOI: 10.1007/s10142-023-01274-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/29/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Patients with idiopathic pulmonary fibrosis (IPF) have a significantly higher prevalence of lung adenocarcinoma (LUAD) than normal subjects, although the underlying association is unclear. The raw data involved were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis were used to screen for differentially expressed genes (DEGs) and modular signature genes (MSGs). Genes intersecting DEGs and MSGs were considered hub genes for IPF and LUAD. Machine learning algorithms were applied to capture epithelial cell-derived signature genes (EDSGs) shared. External cohort data were exploited to validate the robustness of EDSGs. Immunohistochemical staining and K-M plots were used to denote the prognostic value of EDSGs in LUAD. Based on EDSGs, we constructed a TF-gene-miRNA regulatory network. Molecular docking can validate the strength of action between candidate drugs and EDSGs. Epithelial cells, 650 DEGs, and 1773 MSGs were shared by IPF and LUAD. As for 379 hub genes, we performed pathway and functional enrichment analysis. By analyzing sc-RNA seq data, we identified 1234 marker genes of IPF epithelial cell-derived and 1481 of LUAD. And these genes shared 8 items with 379 hub genes. Through the machine learning algorithms, we further fished TRIM2, S100A14, CYP4B1, LMO7, and SFN. The ROC curves emphasized the significance of EDSGs in predicting the onset of LUAD and IPF. The TF-gene-miRNA network revealed regulatory relationships behind EDSGs. Finally, we predicted appropriate therapeutic agents. Our study preliminarily identified potential mechanisms between IPF and LUAD, which will inform subsequent studies.
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Affiliation(s)
- Xianqiang Zhou
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China
- Department of Pulmonary Diseases, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai, 200072, China
| | - Fang Tan
- Department of Neurology, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, 230031, Anhui Province, China
| | - Suxian Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Tiansong Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China.
- Department of Pulmonary Diseases, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai, 200072, China.
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13
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Lyu F, Wang L, Jia Y, Wang Y, Qi H, Dai Z, Zhou X, Zhu H, Li B, Xu Y, Liu J. Analysis of Zinc and Stromal Immunity in Disuse Osteoporosis: Mendelian Randomization and Transcriptomic Analysis. Orthop Surg 2023; 15:2947-2959. [PMID: 37752822 PMCID: PMC10622276 DOI: 10.1111/os.13840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/22/2023] [Accepted: 06/30/2023] [Indexed: 09/28/2023] Open
Abstract
OBJECTIVE Disuse osteoporosis is known to be primarily caused by a lack of exercise. However, the causal relationships between zinc and immunity and disuse osteoporosis remain unknown. This study investigated these relationships and their potential mechanisms. METHODS This study was an integrative study combining genome-wide association studies and transcriptomics. Two-sample Mendelian randomization analysis (MR) was used to analyze the causal relationships between exposures (zinc, immunity, physical activity) and the outcome (osteoporosis) with the aid of single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs). Four models, MR-Egger, inverse variance weighted, weighted median and MR-Pleiotrophy RESidual Sum and Outlier (MRPRESSO), were used to calculate odds ratio values. Sensitivity and heterogeneity analyses were also performed using MRPRESSO and MR-Egger methods. The mRNA transcriptomic analysis was subsequently conducted. Zinc metabolism scores were acquired through single-sample Gene Set Enrichment Analysis algorithms. Stromal scores were obtained using the R Package "estimate" algorithms. Important Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathways were also derived through gene set variation analysis. Cytoscape software helped construct the transcription factor (TF)-mRNA-microRNA (miRNA) network. Virtual screening and molecular docking were performed. Polymerase chain reaction validation was also carried out in vivo. RESULTS Causal relationships were demonstrated between zinc and exercise (95% confidence interval [CI] = 1.30-2.95, p = 0.001), exercise and immunity (95% CI = 0.36-0.80, p = 0.002), exercise and osteoporosis (95% CI = 0.97-0.99, p = 0.0007), and immunity disorder and osteoporosis (95% CI = 1.30-2.03, p = 0.00002). One hundred and seventy-nine mRNAs in important modules were screened. Combining the differential expressional genes (DEGs) and the Boruta selection, six DEGs were screened (AHNAK, CSF2, ADAMTS12, SRA1, RUNX2, and SLC39A14). TF HOXC10 and miRNA hsa-miR-204 were predicted. Then, the TF-mRNA-miRNA network was successfully constructed. RUNX2 and SLC39A14 were identified as hub mRNAs in the TF-mRNA-miRNA network. Eventually, the novel small drug C6O4NH5 was designed according to the pharmacophore structure of SLC39A14. The docking energy for the novel drug was -5.83 kcal/mol. SLC39A14 and RUNX2 were downregulated (of statistical significance p-value < 0.05) in our animal experiment. CONCLUSION This study revealed that zinc had a protective causal relationship with disuse osteoporosis by promoting exercise and immunity. SLC39A14 and RUNX2 mRNA participated in this zinc-related mechanism.
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Affiliation(s)
- Fei Lyu
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
- Orthopedic Center (Sports Medicine Center)Inner Mongolia People's HospitalHohhotChina
| | - Li Wang
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Yiming Jia
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
- Department of OrthopedicsChifeng Municipal HospitalChifengChina
| | - Yuanlin Wang
- Department of Joint SurgeryTianjin HospitalTianjinChina
- Tianjin Institute of AnesthesiologyTianjin Medical UniversityTianjinChina
| | - Haolan Qi
- School of MedicineNankai UniversityTianjinChina
| | - Zhengxu Dai
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Xuyang Zhou
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Haoran Zhu
- School of MedicineXi'an Jiaotong UniversityXianChina
| | - Bing Li
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
| | - Yujing Xu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of PharmacyTianjin Medical UniversityTianjinChina
| | - Jun Liu
- College of OrthopedicsTianjin Medical UniversityTianjinChina
- Department of Joint SurgeryTianjin HospitalTianjinChina
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14
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Zheng J, Zhang Z, An J, Xue Y, Yu B. Adaptive laboratory evolution of Rhodococcus rhodochrous DSM6263 for chlorophenol degradation under hypersaline condition. Microb Cell Fact 2023; 22:220. [PMID: 37880695 PMCID: PMC10601206 DOI: 10.1186/s12934-023-02227-7] [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: 08/29/2023] [Accepted: 10/08/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Normally, a salt amount greater than 3.5% (w/v) is defined as hypersaline. Large amounts of hypersaline wastewater containing organic pollutants need to be treated before it can be discharged into the environment. The most critical aspect of the biological treatment of saline wastewater is the inhibitory/toxic effect exerted on bacterial metabolism by high salt concentrations. Although efforts have been dedicated to improving the performance through the use of salt-tolerant or halophilic bacteria, the diversities of the strains and the range of substrate spectrum remain limited, especially in chlorophenol wastewater treatment. RESULTS In this study, a salt-tolerant chlorophenol-degrading strain was generated from Rhodococcus rhodochrous DSM6263, an original aniline degrader, by adaptive laboratory evolution. The evolved strain R. rhodochrous CP-8 could tolerant 8% NaCl with 4-chlorophenol degradation capacity. The synonymous mutation in phosphodiesterase of strain CP-8 may retard the hydrolysis of cyclic adenosine monophosphate (cAMP), which is a key factor reported in the osmoregulation. The experimentally verified up-regulation of intracellular cAMP level in the evolved strain CP-8 contributes to the improvement of growth phenotype under high osmotic condition. Additionally, a point mutant of the catechol 1,2-dioxygenase, CatAN211S, was revealed to show the 1.9-fold increment on activity, which the mechanism was well explained by molecular docking analysis. CONCLUSIONS This study developed one chlorophenol-degrading strain with extraordinary capacity of salt tolerance, which showed great application potential in hypersaline chlorophenol wastewater treatment. The synonymous mutation in phosphodiesterase resulted in the change of intracellular cAMP concentration and then increase the osmotic tolerance in the evolved strain. The catechol 1,2-dioxygenase mutant with improved activity also facilitated chlorophenol removal since it is the key enzyme in the degradation pathway.
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Affiliation(s)
- Jie Zheng
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhengzhi Zhang
- Linyi Municipal Ecology and Environment Bureau, 276000, Linyi, China
| | - Juan An
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yubin Xue
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
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15
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Shi M, Zheng X, Zhou Y, Yin Y, Lu Z, Zou Z, Hu Y, Liang Y, Chen T, Yang Y, Jing M, Lei D, Yang P, Li X. Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:33658-33674. [PMID: 37744850 PMCID: PMC10515184 DOI: 10.1021/acsomega.3c03935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Bromodomain and extra-terminal domain (BET) proteins play an important role in epigenetic regulation and are linked to several diseases; therefore, they are interesting targets. BET has two bromodomains: bromodomain 1 (BD1) and BD2. Selective targeting of BD1 or BD2 may produce different activities and greater effects than pan-BD inhibitors. However, the selective mechanism of the specific core must be studied at the atomic level. This study determined the effectiveness of pyrrolopyridone analogues to selectively inhibit BD2 using a pan-BD inhibitor (ABBV-075) and a selective-BD2 inhibitor (ABBV-744). Molecular dynamics simulations and calculations of binding free energies were used to systematically study the selectivity of BD2 inhibition by the pyrrolopyridone analogues. Overall, the pyrrolopyridone analogue inhibitors targeting BD2 interacted mainly with the following amino acid pairs between bromodomain-containing protein 4 (BRD4)-BD1 and BRD4-BD2 complexes: I146/V439, N140/N433, D144/H437, P82/P375, V87/V380, D88/D381, and Y139/Y432. The pyrrolopyridone analogues targeting BRD4-BD2 were divided into five regions based on selectivity mechanism. These results suggest that the R3 and R5 regions of pyrrolopyridone analogues can be modified to improve the selectivity between BRD4-BD1 and BRD4-BD2. The selectivity of BD2 inhibition by pyrrolopyridone analogues can be used to design novel BD2 inhibitors based on a pyrrolopyridone core.
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Affiliation(s)
- Mingsong Shi
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
- Innovation
Center of Nursing Research, Nursing Key Laboratory of Sichuan Province,
West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xueting Zheng
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Zhou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuan Yin
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhou Lu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhiyan Zou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Hu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuanyuan Liang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Tingting Chen
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuhan Yang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Meng Jing
- Department
of Pathology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Dan Lei
- School
of Life Science and Engineering, Southwest
University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Pei Yang
- Department
of Hepatobiliary Surgery, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Xiaoan Li
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
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16
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Li X, Wang W, Wang X, Wang H. Differential immunotoxicity effects of triclosan and triclocarban on larval zebrafish based on RNA-Seq and bioinformatics analysis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 262:106665. [PMID: 37611455 DOI: 10.1016/j.aquatox.2023.106665] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 08/25/2023]
Abstract
Herein, we demonstrated that sublethal-dose exposure to triclosan (TCS) and triclocarban (TCC) triggered larval zebrafish immunotoxicity. Acute exposure to TCS induced significant increases in larval neutrophils and macrophages and a prominent decrease in thymic T cells. In contrast, three kinds of cells (neutrophils, macrophages, and thymic T cells) were significantly reduced under TCC exposure, suggesting that both TCS and TCC suppress thymus development and mature T-cell differentiation. TCC was confirmed to have more severe immunotoxicity than TCS. Using Illumina RNA-Seq, 581 and 738 differentially expressed genes (DEGs) were identified in the TCS and TCC treatments, respectively. GO function and KEGG pathway enrichment analyses revealed that the DEGs were not identical in terms of biological processes, cellular components and molecular functions, but were primarily involved in immune response. KEGG analysis showed that approximately 47% and 11% of DEGs were mainly enriched in the immune system of the TCC and TCS treatments, respectively. Protein-protein interaction (PPI) network analysis confirmed that the hub genes enriched in the immune-related pathways differed between TCS and TCC exposure. The hub genes were fynb, mapk12b, scarb1, pik3r2, prkg3, srfa, arhgef2, cldn15la, and cldn15lb in the TCS treatment, and plg, serping1, masp2, fgg, vtnb, mmp9, serpine1, il1b, sb:cb37 and stat3 in the TCC treatment. Molecular docking simulation demonstrated that both TCS and TCC were stably docked with their target hub genes, and that their target molecules for inducing immunotoxicity were different. The differential target molecules and action pathways induced by TCS and TCC exposure provide us with diagnostic targets and toxicological endpoints.
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Affiliation(s)
- Xin Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Weiwei Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xuedong Wang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Huili Wang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China; School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China.
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17
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Xie Y, Liu L, Zheng J, Shi K, Ai W, Zhang X, Wang P, Lan Z, Chen L. Polygoni Multiflori Radix Praeparata and Acori Tatarinowii Rhizoma ameliorate scopolamine-induced cognitive impairment by regulating the cholinergic and synaptic associated proteins. JOURNAL OF ETHNOPHARMACOLOGY 2023; 311:116400. [PMID: 37003402 DOI: 10.1016/j.jep.2023.116400] [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: 02/19/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The combination of Polygoni Multiflori Radix Praeparata (PMRP) and Acori Tatarinowii Rhizoma (ATR) is often used in traditional Chinese medicine to prevent and treat Alzheimer's disease (AD). However, it is not clear whether the effects and mechanisms of the decoction prepared by traditional decocting method (PA) is different from that prepared by modern decocting method (P + A). AIM OF THE STUDY The present study aimed to investigate the differences in the protective effects of PA and P + A on scopolamine induced cognitive impairment, and to explore its potential mechanism. MATERIALS AND METHODS To assess the protective effect of PA and P + A on cognitive dysfunction, the mice were orally administrated with PA (1.56, 6.24 g kg-1•day-1) and P + A (1.56, 6.24 g kg-1•day-1) for 26 days before co-treatment with scopolamine (4 mg kg-1•day-1, i.p.). The learning and memory abilities of mice were examined by Morris water maze test, and the expressions of proteins related to cholinergic system and synaptic function were detected by the methods of ELISA, real-time PCR and Western blotting. Then, molecular docking technique was used to verify the effect of active compounds in plasma after PA administration on Acetylcholinesterase (AChE) protein. Finally, the Ellman method was used to evaluate the effects of different concentrations of PA, P + A (1 μg/mL-100 mg/mL) and the compounds (1-100 μM) on AChE activity in vitro. RESULTS On one hand, in the scopolamine-induced cognitive impairment mouse model, both of PA and P + A could improve the cognitive impairment, while the effect of PA on cognitive amelioration was better than that of P + A. Moreover, PA regulated the cholinergic and synaptic functions by enhancing the concentration of acetylcholine (ACh), the mRNA levels of CHT1, Syn, GAP-43 and PSD-95, and the related proteins (CHT1, VACHT, Syn, GAP-43 and PSD-95), and significantly inhibiting the expression of AChE protein. Meanwhile, P + A only up-regulated the mRNA levels of GAP-43 and PSD-95, increased the expressions of CHT1, VACHT, Syn, GAP-43 and PSD-95 proteins, and inhibited the expression of AChE protein. On the other hand, the in vitro study showed that some compounds including emodin-8-o-β-d-Glucopyranoside, THSG and α-Asarone inhibited AChE protein activity with the IC50 values 3.65 μM, 5.42 μM and 9.43 μM, respectively. CONCLUSIONS These findings demonstrate that both of PA and P + A can ameliorate the cognitive deficits by enhancing cholinergic and synaptic related proteins, while PA has the stronger improvement effect on the cholinergic function, which may be attributed to the compounds including THSG, emodin, emodin-8-O-β-D-glucopyranoside and α-asarone. The present study indicated that PA has more therapeutic potential in the treatment of neurodegenerative diseases such as AD. The results provide the experimental basis for the clinical use of PA.
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Affiliation(s)
- Yuman Xie
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Li Liu
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Junzuo Zheng
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Kun Shi
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Wenqi Ai
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Xuesong Zhang
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Ping Wang
- School of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, PR China
| | - Zhou Lan
- School of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, PR China.
| | - Lvyi Chen
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, 430074, PR China.
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Li JX, Han ZX, Cheng X, Zhang FL, Zhang JY, Su ZJ, Li BP, Jiang ZR, Li RZ, Xie Y, Yan PY, Tang L, Yang JS. Combinational study with network pharmacology, molecular docking and preliminary experiments on exploring common mechanisms underlying the effects of weijing decoction on various pulmonary diseases. Heliyon 2023; 9:e15631. [PMID: 37153415 PMCID: PMC10160751 DOI: 10.1016/j.heliyon.2023.e15631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/09/2023] Open
Abstract
Objective 'Homotherapy for heteropathy' is a theory by which different diseases with similar pathogenesis can be treated with one Chinese formula. We aimed to explore the key components and core targets of Weijing decoction (WJD) in treating various lung diseases, namely, pneumonia, chronic obstructive pulmonary disease (COPD), acute lung injury (ALI), pulmonary fibrosis, pulmonary tuberculosis and non-small cell lung cancer (NSCLC), via network pharmacology, molecular docking and some experiments. Significance This is the first study on the mechanism of WJD in treating various lung diseases by 'homotherapy for heteropathy'. This study is helpful for the transformation of TCM formula and development of new drugs. Methods Active components and therapeutic targets of WJD were obtained via TCMSP and UniProt databases. Targets of the six pulmonary diseases were harvested from the GeneCards TTD, DisGeNet, UniProt and OMIM databases. Drug-disease intersection targets, corresponding Venn diagrams, herb-component-target networks and protein-protein interaction networks were established. Furthermore, GO biological function and KEGG enrichment analysis were completed. Moreover, the binding activity between main compounds and core targets was measured through molecular docking. Finally, the xenograft NSCLC mouse model was established. Immune responses were evaluated by flow cytometry and mRNA expression levels of critical targets were measured by real-time PCR. Results JUN, CASP3 and PTGS2 were the most critical targets in six pulmonary diseases. The active compounds beta-sitosterol, tricin and stigmasterol stably bound to many active sites on target proteins. WJD had extensive pharmacological regulation, involving pathways related to cancer, inflammation, infection, hypoxia, immunity and so on. Conclusions Effects of WJD against various lung diseases involve lots of compounds, targets and pathways. These findings will facilitate further research as well as clinical application of WJD.
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Affiliation(s)
- Jia-Xin Li
- Macau University of Science and Technology, Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macao, China
| | - Zhong-Xiao Han
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Xin Cheng
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Feng-Lin Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jing-Yi Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zi-Jie Su
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Biao-Ping Li
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Zhi-Rui Jiang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Run-Ze Li
- Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou 510006, China
| | - Ying Xie
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, Guangdong Province, China
| | - Pei-Yu Yan
- Macau University of Science and Technology, Faculty of Chinese Medicine, State Key Laboratory of Quality Research in Chinese Medicines, Macao, China
- Corresponding author.
| | - Ling Tang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
- Corresponding author.
| | - Jia-Shun Yang
- Department of Rehabilitation Medicine, The Seventh Affiliated Hospital of Southern Medical University, Foshan 528244, China
- Corresponding author.
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Agnihotri P, Deka H, Chakraborty D, Monu, Saquib M, Kumar U, Biswas S. Anti-inflammatory potential of selective small compounds by targeting TNF-α & NF-kB signaling: a comprehensive molecular docking and simulation study. J Biomol Struct Dyn 2023; 41:13815-13828. [PMID: 37013999 DOI: 10.1080/07391102.2023.2196692] [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: 10/15/2022] [Accepted: 02/11/2023] [Indexed: 04/05/2023]
Abstract
Tumor necrosis factor alpha (TNF-α) is the major cause of inflammation in autoimmune diseases like rheumatoid arthritis (RA). It's mechanisms of signal transduction through nuclear factor kappa B (NF-kB) pathway via small molecules such as metabolite crosstalk are still elusive. In this study, we have targeted TNF-α and NF-kB through metabolites of RA, to inhibit TNF-α activity and deter NF-kB signaling pathways, thereby mitigating the disease severity of RA. TNF-α and NF-kB structure was obtained from PDB database and metabolites of RA were selected from literature survey. In-silico studies were carried out by molecular docking using AutoDock Vina software and further, known TNF-α and NF-kB inhibitors were compared and revealed metabolite's capacity to targets the respective proteins. Most suitable metabolite was then validated by MD simulation to verify its efficiency against TNF-α. Total 56 known differential metabolites of RA were docked with TNF-α and NF-kB compared to their corresponding inhibitor compounds. Four metabolites such as Chenodeoxycholic acid, 2-Hydroxyestrone, 2-Hydroxyestradiol (2-OHE2), and 16-Hydroxyestradiol were identified as a common TNF-α inhibitor's having binding energies ranging from -8.3 to -8.6 kcal/mol, followed by docking with NF-kB. Further, 2-OHE2 was selected because of having binding energy -8.5 kcal/mol, found to inhibit inflammation and the effectiveness was validated by root mean square fluctuation, radius of gyration and molecular mechanics with generalized born and surface area solvation against TNF-α. Thus 2-OHE2, an estrogen metabolite was identified as the potential inhibitor, attenuated inflammatory activation and can be utilized as a therapeutic target to disseminate severity of RA.
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Affiliation(s)
- Prachi Agnihotri
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemchandra Deka
- Gauhati University Institute of Science and Technology, Guwahati University, Guwahati, India
| | - Debolina Chakraborty
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Monu
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mohd Saquib
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Uma Kumar
- All India Institute of Medical Sciences, New Delhi, India
| | - Sagarika Biswas
- Council of Scientific & Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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20
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Designing of thiazolidinones against chicken pox, monkey pox, and hepatitis viruses: A computational approach. Comput Biol Chem 2023; 103:107827. [PMID: 36805155 PMCID: PMC9922439 DOI: 10.1016/j.compbiolchem.2023.107827] [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: 12/17/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/14/2023]
Abstract
Computational designing of four different series (D-G) of thiazolidinone was done starting from different amines which was further condensed with various aldehydes. These underwent in silico molecular investigations for density functional theory (DFT), molecular docking, and absorption, distribution metabolism, excretion, and toxicity (ADMET) studies. The different electrochemical parameters of the compounds are predicted using quantum mechanical modeling approach with Gaussian. The docking software was used to dock the compounds against choosing PDB file for chickenpox, human immunodeficiency, hepatitis, and monkeypox virus as 1OSN, 1VZV, 6VLK, 1RTD, 3I7H, 3TYV, 4JU3, and 4QWO, respectively. The molecular interactions were visualized with discovery studio and maximum binding affinity was observed with D8 compounds against 4QWO (-13.383 kcal/mol) while for compound D5 against 1VZV which was -12.713 kcal/mol. Swiss ADME web tool was used to assess the drug-likeness of the designed compounds under consideration, and it is concluded that these molecules had a drug-like structure with almost zero violations.
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21
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Cao T, Wu H, Ji T. Bioinformatics-based construction of prognosis-related methylation prediction model for pancreatic cancer patients and its application value. Front Pharmacol 2023; 14:1086309. [PMID: 36969862 PMCID: PMC10034005 DOI: 10.3389/fphar.2023.1086309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/06/2023] [Indexed: 03/12/2023] Open
Abstract
Objective: Pancreatic adenocarcinoma (PAAD) is a highly malignant gastrointestinal tumor with almost similar morbidity and mortality. In this study, based on bioinformatics, we investigated the role of gene methylation in PAAD, evaluated relevant factors affecting patient prognosis, screened potential anti-cancer small molecule drugs, and constructed a prediction model to assess the prognosis of PAAD.Methods: Clinical and genomic data of PAAD were collected from the Tumor Genome Atlas Project (TCGA) database and gene expression profiles were obtained from the GTEX database. Analysis of differentially methylated genes (DMGs) and significantly differentially expressed genes (DEGs) was performed on tumorous samples with KRAS wild-type and normal samples using the “limma” package and combined analysis. We selected factors significantly associated with survival from the significantly differentially methylated and expressed genes (DMEGs), and their fitting into a relatively streamlined prognostic model was validated separately from the internal training and test sets and the external ICGC database to show the robustness of the model.Results: In the TCGA database, 2,630 DMGs were identified, with the largest gap between DMGs in the gene body and TSS200 region. 318 DEGs were screened, and the enrichment analysis of DMGs and DEGs was taken to intersect DMEGs, showing that the DMEGs were mainly related to Olfactory transduction, natural killer cell mediated cytotoxicity pathway, and Cytokine -cytokine receptor interaction. DMEGs were able to distinguish well between PAAD and paraneoplastic tissues. Through techniques such as drug database and molecular docking, we screened a total of 10 potential oncogenic small molecule compounds, among which felbamate was the most likely target drug for PAAD. We constructed a risk model through combining three DMEGs (S100P, LY6D, and WFDC13) with clinical factors significantly associated with prognosis, and confirmed the model robustness using external and internal validation.Conclusion: The classification model based on DMEGs was able to accurately separate normal samples from tumor samples and find potential anti-PAAD drugs by performing gene-drug interactions on DrugBank.
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Affiliation(s)
| | | | - Tengfei Ji
- *Correspondence: Tiansheng Cao, ; Tengfei Ji,
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22
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Prednisone acetate modulates Th1/Th2 and Th17/Treg cell homeostasis in experimental autoimmune uveitis via orchestrating the Notch signaling pathway. Int Immunopharmacol 2023; 116:109809. [PMID: 36753985 DOI: 10.1016/j.intimp.2023.109809] [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: 09/22/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/09/2023]
Abstract
Uveitis is an immune eye disease that can seriously impair vision. Glucocorticoids (GCS) have been extensively used to treat uveitis, though the mechanisms have not been fully elucidated. In this study, we investigated the regulatory effects of prednisone acetate (PA) on the Th1/Th2 and Th17/Treg balance in experimental autoimmune uveitis (EAU) through modulating the Notch signaling pathway. Briefly, Lewis rats were randomly divided into the normal control (NC), EAU, and EAU + PA groups. Rats in EAU and EAU + PA groups were induced EAU, while those in the EAU + PA group were treated with PA. Clinical and histopathological scores were employed to assess the progression of EAU. The expression levels of Notch signaling-related molecules (Notch1, Notch2, Dll3, Dll4, and Rbpj) and Th-associated cytokines (IFN-γ, IL-4, IL-10, and IL-17) were assessed via quantitative PCR (qPCR) and enzyme-linked immunosorbent assay (ELISA). In addition, the frequencies of Th1, Th2, Th17 and Treg cells were detected by flow cytometry. These experimental results indicated that activation of the Notch signaling pathway occurred in EAU rats and resulted in a severe imbalance of the Th17/Treg and Th1/Th2 ratios. PA treatment significantly alleviated ocular inflammation, inhibited activation of the Notch signaling pathway, and declined Th1, and Th17 cell differentiation, thereby restoring the Th1/Th2 and Th17/Treg balance. Collectively, PA can positively enhance the systemic immune response and improve the intraocular microenvironmental homeostasis by inhibiting activation of the Notch signaling pathway and by restoring Th1/Th2 and Th17/Treg balance, thus achieving the goal of treating uveitis.
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23
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Chaurasiya A, Shome A, Chawla PA. Molecular docking analysis of peptide-based antiviral agents against SARS-CoV-2 main protease: an approach towards drug repurposing. EXPLORATION OF MEDICINE 2023. [DOI: 10.37349/emed.2023.00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Aim:
Utilizing the therapeutic potentials of previously approved medications against a new target or pharmacological response is known as drug repurposing. The health and scientific communities are under continual pressure to discover new compounds with antiviral potential due to the rising reports of viral resistance and the occurrence and re-emergence of viral outbreaks. The use of antiviral peptides has emerged as an intriguing option in this search. Here, this article includes the current United States Food and Drug Administration (FDA)-approved antiviral peptides that might be enforced for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and carried out docking study of the viral protease inhibitors.
Methods:
In silico techniques like molecular docking was carried out using Autodock Vina software.
Results:
The molecular docking studies of peptide-based antiviral agents against SARS-CoV-2 [Protein Data Bank (PDB) ID: 7P35] using docking software AutoDockTools 1.5.6. Among all the docked ligands, compound velpatasvir showed interaction with residues ILE213, GLN256, LEU141, GLN189, GLU166, HIS41, CYS145, and ASN142, and displayed the highest docking score of –8.2 kcal/mol. This medication could be a novel treatment lead or candidate for treating SARS-CoV-2.
Conclusions:
To conclude, a docking study of peptide based antiviral compounds for their binding mode in the catalytic domain of SARS-CoV-2 receptor is reported. On molecular docking, the compounds have showed remarkable binding affinity with the amino acids of receptor chain A. The compounds occupied the same binding cavity as the reference compound maintaining the interactions with conserved amino acid residues essential for significant inhibitory potential, especially for compound velpatasvir with binding score of –8.2 kcal/mol.
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Affiliation(s)
- Abhishek Chaurasiya
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| | - Abhimannu Shome
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
| | - Pooja A. Chawla
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga 142001, India
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24
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da Silva DF, de Souza JL, da Costa DM, Costa DB, Moreira POL, Fonseca ALD, Varotti FDP, Cruz JN, Dos Santos CBR, Alves CQ, Leite FHA, Brandão HN. Antiplasmodial activity of coumarins isolated from Polygala boliviensis: in vitro and in silico studies. J Biomol Struct Dyn 2023; 41:13383-13403. [PMID: 36744465 DOI: 10.1080/07391102.2023.2173295] [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: 09/10/2021] [Accepted: 01/21/2023] [Indexed: 02/07/2023]
Abstract
Polygala boliviensis is found in the Brazilian semiarid region. This specie is little chemically and biologically studied. Polygala spp. have different metabolites, especially coumarins. Studies indicate that coumarins have antimalarial potential, denoting the importance of researching new active compounds from plants, since the resistance of Plasmodium strains to conventional therapy has increased. The present study aimed to evaluate the antiplasmodial activity of auraptene and poligalen against a chloroquine-resistant strain of Plasmodium falciparum. Coumarins were isolated from P. boliviensis by open column chromatography and identified by Nuclear Magnetic Resonance Spectroscopy. A cytotoxicity assay was carried out using MTT test, and the in vitro antiplasmodial activity was evaluated using the W2 strain. The antiplasmodial activity results found were IC50=0.171 ± 0.016 for auraptene and 0.164 ± 0.012 for poligalen; the selectivity indexes were 78.71 and 609.76, respectively. Inverse virtual screening in the BRAMMT database by OCTOPUS 1.2 was applied to coumarins to find potential P. falciparum targets and showed higher affinity energy of auraptene for purine nucleoside phosphorylase (PfPNP) and of poligalen for dihydroorotate dehydrogenase (PfDHODH). Molecular Dynamics studies (MD and MM-GBSA) approach were applied to calculate binding energies against selected P. falciparum targets and showed that all coumarins were stable at the binding site during simulations. Furthermore, energies were favorable for complexation. This is the first report of auraptene in P. boliviensis species and of in vitro antiplasmodial activity of auraptene and poligalen. In silico studies indicated that the mechanism of action of coumarins is the inhibition of PfPNP and PfDHODH.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Danielle Figuerêdo da Silva
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Jéssica Lima de Souza
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Diego Mota da Costa
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - David Bacelar Costa
- Departamento de Saúde, Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Paulo Otávio Lourenço Moreira
- Centro de Ciências da Saúde, Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Amanda Luisa da Fonseca
- Centro de Ciências da Saúde, Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Fernando de Pilla Varotti
- Centro de Ciências da Saúde, Laboratório de Bioquímica Medicinal, Universidade Federal de São João Del-Rei, Divinópolis, Minas Gerais, Brazil
| | - Jorddy Neves Cruz
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Modelagem e Química Computacional, Universidade Federal do Amapá, Macapá, Amapá, Brazil
| | - Cleydson Breno Rodrigues Dos Santos
- Departamento de Ciências Biológicas e da Saúde, Laboratório de Modelagem e Química Computacional, Universidade Federal do Amapá, Macapá, Amapá, Brazil
| | - Clayton Queiroz Alves
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Franco Henrique Andrade Leite
- Departamento de Saúde, Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | - Hugo Neves Brandão
- Departamento de Saúde, Laboratório de Bioprospecção Vegetal, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
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Network pharmacology study of the mechanism underlying the therapeutic effect of Zhujing pill and its main component oleanolic acid against diabetic retinopathy. Biosci Rep 2023; 43:232265. [PMID: 36714956 PMCID: PMC9894013 DOI: 10.1042/bsr20220893] [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: 04/26/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 01/31/2023] Open
Abstract
Diabetic retinopathy (DR) is the leading cause of blindness in the working population worldwide, with few effective drugs available for its treatment in the early stages. The Zhujing pill (ZJP) is well-established to enhance the early symptoms of DR, but the mechanism underlying its therapeutic effect remains unclear. In the present study, we used systems biology and multidirectional pharmacology to screen the main active ingredients of ZJP and retrieved DrugBank and Genecards databases to obtain 'drug-disease' common targets. Using bioinformatics analysis, we obtained the core targets, and potential mechanisms of action of ZJP and its main components for the treatment of DR. Molecular docking was used to predict the binding sites and the binding affinity of the main active ingredients to the core targets. The predicted mechanism was verified in animal experiments. We found that the main active ingredient of ZJP was oleanolic acid, and 63 common 'drug-disease' targets were identified. Topological analysis and cluster analysis based on the protein-protein interaction network of the Metascape database screened the core targets as PRKCA, etc. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these core targets were significantly enriched in the pro-angiogenic pathway of the VEGF signaling pathway. Molecular docking and surface plasmon resonance revealed that ZJP and its main active component, oleanolic acid had the highest binding affinity with PKC-α, the core target of the VEGF signaling pathway. Animal experiments validated that ZJP and oleanolic acid could improve DR.
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Dorahy G, Chen JZ, Balle T. Computer-Aided Drug Design towards New Psychotropic and Neurological Drugs. Molecules 2023; 28:molecules28031324. [PMID: 36770990 PMCID: PMC9921936 DOI: 10.3390/molecules28031324] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Central nervous system (CNS) disorders are a therapeutic area in drug discovery where demand for new treatments greatly exceeds approved treatment options. This is complicated by the high failure rate in late-stage clinical trials, resulting in exorbitant costs associated with bringing new CNS drugs to market. Computer-aided drug design (CADD) techniques minimise the time and cost burdens associated with drug research and development by ensuring an advantageous starting point for pre-clinical and clinical assessments. The key elements of CADD are divided into ligand-based and structure-based methods. Ligand-based methods encompass techniques including pharmacophore modelling and quantitative structure activity relationships (QSARs), which use the relationship between biological activity and chemical structure to ascertain suitable lead molecules. In contrast, structure-based methods use information about the binding site architecture from an established protein structure to select suitable molecules for further investigation. In recent years, deep learning techniques have been applied in drug design and present an exciting addition to CADD workflows. Despite the difficulties associated with CNS drug discovery, advances towards new pharmaceutical treatments continue to be made, and CADD has supported these findings. This review explores various CADD techniques and discusses applications in CNS drug discovery from 2018 to November 2022.
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Affiliation(s)
- Georgia Dorahy
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Jake Zheng Chen
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Thomas Balle
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW 2050, Australia
- Correspondence:
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Duran-Frigola M, Cigler M, Winter GE. Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence. J Am Chem Soc 2023; 145:2711-2732. [PMID: 36706315 PMCID: PMC9912273 DOI: 10.1021/jacs.2c11098] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
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Affiliation(s)
- Miquel Duran-Frigola
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,Ersilia
Open Source Initiative, 28 Belgrave Road, CB1 3DE, Cambridge, United Kingdom,
| | - Marko Cigler
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,
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28
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Shanmugam A, Venkattappan A, Gromiha MM. Structure based Drug Designing Approaches in SARS-CoV-2 Spike Inhibitor Design. Curr Top Med Chem 2023; 22:2396-2409. [PMID: 36330617 DOI: 10.2174/1568026623666221103091658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The COVID-19 outbreak and the pandemic situation have hastened the research community to design a novel drug and vaccine against its causative organism, the SARS-CoV-2. The spike glycoprotein present on the surface of this pathogenic organism plays an immense role in viral entry and antigenicity. Hence, it is considered an important drug target in COVID-19 drug design. Several three-dimensional crystal structures of this SARS-CoV-2 spike protein have been identified and deposited in the Protein DataBank during the pandemic period. This accelerated the research in computer- aided drug designing, especially in the field of structure-based drug designing. This review summarizes various structure-based drug design approaches applied to this SARS-CoV-2 spike protein and its findings. Specifically, it is focused on different structure-based approaches such as molecular docking, high-throughput virtual screening, molecular dynamics simulation, drug repurposing, and target-based pharmacophore modelling and screening. These structural approaches have been applied to different ligands and datasets such as FDA-approved drugs, small molecular chemical compounds, chemical libraries, chemical databases, structural analogs, and natural compounds, which resulted in the prediction of spike inhibitors, spike-ACE-2 interface inhibitors, and allosteric inhibitors.
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Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem, 636308, Tamil Nadu, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology ,Madras, Chennai, 600036, Tamil Nadu, India
| | - Anbazhagan Venkattappan
- Department of Chemistry, Vinayaka Mission's Kirupananda Variyar Arts and Science College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem, 636308, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology ,Madras, Chennai, 600036, Tamil Nadu, India
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Liu Y, Wei F, Xu R, Cheng T, Ma Y. Insights into the Binding Interaction of Catechol 1,2-Dioxygenase with Catechol in Achromobacter xylosoxidans DN002. Appl Biochem Biotechnol 2023; 195:298-313. [PMID: 36074236 DOI: 10.1007/s12010-022-04129-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 01/13/2023]
Abstract
Microbial remediation has become one of the promising ways to eliminate polycyclic aromatic hydrocarbons (PAHs) pollution due to its efficient enzyme metabolism system. Catechol 1,2-dioxygenase (C12O) is a crucial rate-limiting enzyme in the degradation pathway of PAHs in Achromobacter xylosoxidans DN002 that opens the benzene ring through the ortho-cleavage pathway. However, little attention has been given to explore the interaction mechanism of relevant enzyme-substrate. This study aims to investigate the binding interaction between C12O of strain DN002 and catechol by means of a molecular biological approach combined with homology modeling, molecular docking, and multiple spectroscopies. The removal rate of catechol in the mutant strain of cat A deletion was only 12.03%, compared to the wild-type strain (54.21%). A Ramachandran plot of active site regions of the primary amino acid sequences in the native enzyme showed that 93.5% sequences were in the most favored regions on account of the results of homology modeling, while an additional 6.2% amino acid sequences were found in conditionally allowed regions, and 0.4% in generously allowed regions. The binding pocket of C12O with catechol was analyzed to obtain that the catalytic trimeric group of Tyr164-His224-His226 was proven to be great vital for the ring-opening reaction of catechol by molecular docking. In the native enzyme, binding complexes were spontaneously formed by hydrophobic interactions. Binding constants and thermodynamic potentials from fluorescence spectra indicated that catechol effectively quenched the intrinsic fluorescence of C12O in the C12O/catechol complex via conventional static and dynamic quenching mechanisms of C12O. The results of ultraviolet and visible (UV) spectra, synchronous fluorescence, and circular dichroism (CD) spectra revealed conspicuous changes in the local conformation, and site-directed mutagenesis confirmed the role of predicted key residues during catalysis, wherein His226 had a significant effect on catechol utilization by C12O. This is the first report to reveal interactions of C12O with substrate from the molecular docking results, providing the mechanistic understanding of representative dioxygenases involved in aromatic compound degradation, and a solid foundation for further site modifications as well as strategies for the directed evolution of this enzyme.
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Affiliation(s)
- Yani Liu
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, 229 Taibai North Rd, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Fengdan Wei
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, 229 Taibai North Rd, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Rui Xu
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, 229 Taibai North Rd, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Tao Cheng
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, 229 Taibai North Rd, Xi'an, Shaanxi, 710069, People's Republic of China
| | - Yanling Ma
- Shaanxi Provincial Key Laboratory of Biotechnology, Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, 229 Taibai North Rd, Xi'an, Shaanxi, 710069, People's Republic of China.
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Childers MC, Daggett V. Molecular Dynamics Methods for Antibody Design. Methods Mol Biol 2023; 2552:109-124. [PMID: 36346588 DOI: 10.1007/978-1-0716-2609-2_5] [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] [Indexed: 06/16/2023]
Abstract
Complex and coordinated dynamics are closely connected with protein functions, including the binding of antibodies to antigens. Knowledge of such dynamics could improve the design of antibodies. Molecular dynamics (MD) simulations provide a "computational microscope" that can resolve atomic motions and inform antibody design efforts.
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Affiliation(s)
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
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Abdusalam AAA. In-silico identification of novel inhibitors for human Aurora kinase B form the ZINC database using molecular docking-based virtual screening. RESEARCH RESULTS IN PHARMACOLOGY 2022. [DOI: 10.3897/rrpharmacology.8.82977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Introduction: Aurora kinase enzymes play critical functions in mammals. Aurora kinases are mitotic regulators that are involved in a variety of processes during cell division. The overexpression of these enzymes is associated with tumour formation and is symptomatic of clinical circumstances in cancer patients who have been diagnosed.
Materials and methods: The current study reports an in-silico virtual screening (VS) and molecular docking analysis of 2500 compounds retrieved from the ZINC database and five current clinical trial compounds against Aurora Kinase B using AutoDock Vina to identify potential inhibitors.
Results and discussion: The top six compounds that resulted from the screening were ZINC00190959, ZINC07889110, ZINC0088285, ZINC01404326, ZINC00882846 and ZINC08813187, which showed lower free energy of binding (FEB) against the target protein binding pocket. The FEB were as follows: -11.92, -11.85, -11.46, -11.33, -11.21 and -11.1 kcal/mol, using AutoDock, and -11.7, -11.5, -11.2, -11.0, -10.8 and -10.6 kcal/mol for AutoDock Vina, respectively. These findings were superior to those obtained with the co-crystallized ligand VX-680, with a -7.5 kcal/mol and the current clinical trial drug. Finally, using a VS and molecular docking approach, novel Aurora kinase B inhibitors were effectively identified from the ZINC database fulfilling the Lipinski rule of five with low FEB and functional molecular interactions with the target protein.
Conclusion: The findings suggest that the six compounds could be used as a potential agent for cancer treatments.
Graphical abstract
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Wang X, Jiang Y, Zhou P, Lin L, Yang Y, Yang Q, Zhang J, Zhu D. Effective natural inhibitors targeting granzyme B in rheumatoid arthritis by computational study. Front Med (Lausanne) 2022; 9:1052792. [PMID: 36582296 PMCID: PMC9792495 DOI: 10.3389/fmed.2022.1052792] [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: 09/28/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is an autoimmune disease characterized by erosive arthritis, and current treatments for RA fall short of the outcomes expected by clinicians and patients. Objectives This study aimed to identify novel therapeutic and prognostic targets in RA at the genomic level and to screen desirable compounds with potential inhibitory effects on GZMB. Methods We performed differential gene analysis on GSE55235 and GSE55457 from Gene Expression Omnibus (GEO) and then obtained the intersection of the two differentially expressed genes (DEGs) lists by drawing Venn diagrams. Then we performed protein-protein interaction (PPI) network analysis, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis on the DEGs of the intersection. Next, we downloaded the crystal structure of Granzyme B (GZMB). Molecular docking technology was used to screen potential inhibitors of GZMB in subsequent experiments, and we then analyzed the toxicity and water solubility of these potential inhibitors for future drug experiments. Finally, whether the docking of these small molecules with GZMB is stable is tested by molecular dynamics. Results A total of 352 mutual DEGs were identified. Twenty hub genes were obtained according to PPI network analysis, among which the GZMB gene attracted the attention of our research. Three potent natural compounds, ZINC000004557101, ZINC000012495776, and ZINC000038143593, bound to GZMB, show better binding affinity. Furthermore, they are predicted to own low Ames mutagenicity, developmental toxicity potential, rodent carcinogenicity, and high tolerance to cytochrome P4502D6. Molecular dynamics simulations show that ZINC000004557101 and GZMB have more advantageous potential energy and can exist stably in a natural environment. Moreover, we finally verified the inhibitory effect of ZINC000004557101 on granzyme B by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and Western blotting experiment. Conclusion RA patients showed increased GZMB expression. ZINC000004557101 is a potential drug targeting GZMB for treating RA.
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Cardona‐Galeano W, Yepes AF, Quintero‐Saumeth J, Robledo SM, Alzate F, Rojano B. A Biologically Active Chromone from
Bomarea setacea
(
alstroemeriaceae
): Leishmanicidal, Antioxidant and Multilevel Computational Studies. ChemistrySelect 2022. [DOI: 10.1002/slct.202203852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Wilson Cardona‐Galeano
- Chemistry of Colombian Plants, Institute of Chemistry Faculty of Exact and Natural Sciences University of Antioquia-UdeA Calle 70 No. 52-21 A.A 1226 Medellín Colombia
| | - Andres F. Yepes
- Chemistry of Colombian Plants, Institute of Chemistry Faculty of Exact and Natural Sciences University of Antioquia-UdeA Calle 70 No. 52-21 A.A 1226 Medellín Colombia
| | - Jorge Quintero‐Saumeth
- Chemistry of Colombian Plants, Institute of Chemistry Faculty of Exact and Natural Sciences University of Antioquia-UdeA Calle 70 No. 52-21 A.A 1226 Medellín Colombia
| | - Sara M. Robledo
- PECET-Medical Research Institute Faculty of Medicine University of Antioquia-UdeA Calle 70 No. 52-21 A.A 1226 Medellín Colombia
| | - Fernando Alzate
- Group of Botanical Studies Institute of Biology Natural and Exact Sciencies Faculty University of Antioquia-UdeA Calle 70 No. 52-21 A.A 1226 Medellín Colombia
| | - Benjamín Rojano
- School of Chemistry Faculty of Science National University of Colombia, Sede Medellín Calle 59 A Número 63-20 A.A 0534 Medellín Colombia
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Xu H, Qu J, Wang J, Han K, Li Q, Bi W, Liu R. Discovery of pulmonary fibrosis inhibitor targeting TGF-β RI in Polygonum cuspidatum by high resolution mass spectrometry with in silico strategy. J Pharm Anal 2022; 12:860-868. [PMID: 36605575 PMCID: PMC9805938 DOI: 10.1016/j.jpha.2020.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/27/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
Pulmonary fibrosis (PF) is an irreversible lung disease that is characterized by excessive scar tissue with a poor median survival rate of 2-3 years. The inhibition of transforming growth factor-β receptor type-I (TGF-β RI) by an appropriate drug may provide a promising strategy for the treatment of this disease. Polygonum cuspidatum (PC) is a well-known traditional Chinese herbal medicine which has an anti-PF effect. Accordingly, a combination of high resolution mass spectrometry with an in silico strategy was developed as a new method to search for potential chemical ingredients of PC that target the TGF-β RI. Based on this strategy, a total of 24 ingredients were identified. Then, absorption, distribution, metabolism, and excretion (ADME)-related properties were subsequently predicted to exclude compounds with potentially undesirable pharmacokinetics behaviour. Molecular docking studies on TGF-β RI were adopted to discover new PF inhibitors. Eventually, a compound that exists in PC known as resveratrol was proven to have excellent biological activity on TGF-β RI, with an IC50 of 2.211 μM in vitro. Furthermore, the complex formed through molecular docking was tested via molecular dynamics simulations, which revealed that resveratrol had strong interactions with residues of TGF-β RI. This study revealed that resveratrol has significant potential as a treatment for PF due to its ability to target TGF-β RI. In addition, this research demonstrated the exploration of natural products with excellent biological activities toward specific targets via high resolution mass spectrometry in combination with in silico technology is a promising strategy for the discovery of novel drugs.
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Affiliation(s)
- Huarong Xu
- National and Local Joint Engineering Laboratory for Key Technology of Chinese Material Medica Quality Control, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiameng Qu
- National and Local Joint Engineering Laboratory for Key Technology of Chinese Material Medica Quality Control, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Traditional Chinese Material Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Kefei Han
- National and Local Joint Engineering Laboratory for Key Technology of Chinese Material Medica Quality Control, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
- School of Traditional Chinese Material Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Qing Li
- National and Local Joint Engineering Laboratory for Key Technology of Chinese Material Medica Quality Control, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Wenchuan Bi
- Health Science Center Department of Pharmacy, Shenzhen University, Shenzhen, Guangdong, 518118, China
- Corresponding author.
| | - Ran Liu
- National and Local Joint Engineering Laboratory for Key Technology of Chinese Material Medica Quality Control, School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, 110016, China
- Corresponding author.
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Chen S, Tan X, Tang S, Xu M, Xu X, Ren F, Yang Z. Discovery of novel 5′-methylthioadenosine nucleosidase inhibitors by virtual screening and bioassays. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Liu J, Xie X, Qin K, Xu L, Peng J, Li X, Li X, Liu Z. Dexamethasone and potassium canrenoate alleviate hyperalgesia by competitively regulating IL-6/JAK2/STAT3 signaling pathway during inflammatory pain in vivo and in vitro. Immun Inflamm Dis 2022; 10:e721. [PMID: 36301041 PMCID: PMC9597488 DOI: 10.1002/iid3.721] [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: 05/29/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Background Dexamethasone (Dexa) and potassium canrenoate (Cane) modulate nociceptive behavior via glucocorticoid receptor (GR) and mineralocorticoid receptor (MR) by two mechanisms (genomic and nongenomic pathways). This study was designed to investigate the Dexa‐ or Cane‐mediated nongenomic and genomic effects on mechanical nociception and inflammation‐induced changes in interleukin‐6 (IL‐6) mediated signaling pathway in rats. Methods Freund's complete adjuvant (FCA) was used to trigger an inflammation of the right hind paw in male Sprague–Dawley rats. First, the mechanical nociceptive behavioral changes were examined following intraplantar administration of GR agonist Dexa and/or MR antagonist Cane in vivo. Subsequently, the protein levels of IL‐6, IL‐6Rα, JAK2, pJAK2, STAT3, pSTAT3Ser727, migration inhibitory factor, and cyclooxygenase‐2 were assessed by Western blot following intraplantar injection of Dexa or Cane or the combination. Moreover, the molecular docking studies determined the interaction between Dexa, Cane, and IL‐6. The competition binding assay was carried out using enzyme‐linked immunosorbent assays (ELISA). Results Administration of Dexa and Cane dose‐dependently attenuated FCA‐induced inflammatory pain. The sub‐additive effect of Dexa/Cane combination was elucidated by isobologram analysis, accompanied by decrease in the spinal levels of IL‐6, pJAK2, and pSTAT3Ser727. The molecular docking study demonstrated that both Dexa and Cane displayed a firm interaction with THR138 binding site of IL‐6 via a strong hydrogen bond. ELISA revealed that Dexa has a higher affinity to IL‐6 than Cane. Conclusions There was no additive or negative effect of Dexa and Cane, and they modulate the IL‐6/JAK2/STAT3 signaling pathway through competitive binding with IL‐6 and relieves hypersensitivity during inflammatory pain.
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Affiliation(s)
- Jie Liu
- Department of AnesthesiologyThe Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdongChina
| | - Xiaolan Xie
- Department of AnesthesiologyThe Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdongChina
| | - Kai Qin
- Department of AnesthesiologyThe Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdongChina
| | - Le Xu
- Department of AnesthesiologyThe Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdongChina
| | - Juxiang Peng
- Department of AnesthesiologyThe Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdongChina
| | - Xiangyu Li
- Department of AnesthesiologyThe Second Affiliated Hospital of Guangzhou University of Chinese MedicineGuangzhouGuangdongChina
| | - Xiongjuan Li
- Department of Anesthesiology, Shenzhen Second People's HospitalThe First Affiliated Hospital of Shenzhen University, Health Science CenterShenzhenGuangdongChina
| | - Zhiheng Liu
- Department of Anesthesiology, Shenzhen Second People's HospitalThe First Affiliated Hospital of Shenzhen University, Health Science CenterShenzhenGuangdongChina
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Huang J, Lin S, Zhu F, Xu L. Exploring the underlying mechanism of oleanolic acid treating glioma by transcriptome and molecular docking. Biomed Pharmacother 2022; 154:113586. [PMID: 36007277 DOI: 10.1016/j.biopha.2022.113586] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/02/2022] Open
Abstract
OBJECTIVE Oleanolic acid is a promising drug for treating gliomas, but its underlying mechanism is unclear. This study aimed to determine the potential effect of oleanolic acid on glioma and its mechanism. METHODS Firstly, the effects of oleanolic acid on the proliferation, invasion, and apoptosis of glioma U251 cells were detected by in vitro experiments such as MTT assay, cell cloning, and flow cytometry. The transcriptome data of U251 cells treated with oleanolic acid and untreated were sequenced by mRNA, and then the differentially expressed genes were analyzed by gene ontology (GO), genomic encyclopedia (KEGG) pathway enrichment analysis, and protein interaction topology analysis. The underlying mechanism of oleanolic acid was predicted, and the related protein interaction network was constructed. Finally, Western blotting and molecular docking techniques verified the mRNA sequencing results. RESULTS Oleanolic acid could effectively inhibit the proliferation, colony formation, and invasion of U251 cells and induce apoptosis. A total of 446 differentially expressed genes were detected by mRNA sequencing, of which 96 genes were up-regulated and 350 down-regulated. Oleanolic acid induces the TNF signal pathway and NOD-like receptor signal pathway at the intracellular level. In addition, OAS2, OASL, IFIT3, RSAD2, and IRF1 may be the core targets of oleanolic acid in treating glioma. CONCLUSION Transcriptome combined with molecular docking technique is used to predict the possible mechanism of oleanolic acid in the treatment of glioma, which provides new ideas and insights for developing and researching antitumor drugs.
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Affiliation(s)
- Jinxiang Huang
- Department of Neurosurgery, Shanghai Institute of Neurosurgery, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China.
| | - Shengnan Lin
- Department of Clinical Pharmacy, Sanming First Hospital, Affiliated Hospital of Fujian Medical University, Sanming City, Fujian Province, China.
| | - Feng Zhu
- Department of Neurosurgery, Sanming First Hospital, Affiliated Hospital of Fujian Medical University, Sanming City, Fujian Province, China.
| | - Luning Xu
- Department of Clinical Pharmacy, Sanming First Hospital, Affiliated Hospital of Fujian Medical University, Sanming City, Fujian Province, China.
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Zheng L, Ji YY, Dai YC, Wen XL, Wu SC. Network pharmacology and molecular docking reveal zedoary turmeric-trisomes in Inflammatory bowel disease with intestinal fibrosis. World J Clin Cases 2022; 10:7674-7685. [PMID: 36158488 PMCID: PMC9372848 DOI: 10.12998/wjcc.v10.i22.7674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/05/2022] [Accepted: 06/30/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a complex chronic IBD that is closely associated with risk factors such as environment, diet, medications and lifestyle that may influence the host microbiome or immune response to antigens. At present, with the increasing incidence of IBD worldwide, it is of great significance to further study the pathogenesis of IBD and seek new therapeutic targets. Traditional Chinese medicine (TCM) treatment of diseases is characterized by multiple approaches and multiple targets and has a long history of clinical application in China. The mechanism underlying the effect of zedoary turmeric-trisomes on inducing mucosal healing in IBD is not clear.
AIM To explore the effective components and potential mechanism of zedoary turmeric-trisomes in the treatment of IBD with intestinal fibrosis using network pharmacology and molecular docking techniques.
METHODS The chemical constituents and targets of Rhizoma zedoary and Rhizoma sanarum were screened using the TCMSP database. The GeneCards database was searched to identify targets associated with intestinal fibrosis in IBD. The intersection of chemical component targets and disease targets was obtained using the Venny 2.1 online analysis platform, and the common targets were imported into the STRING 11.0 database to construct a protein interaction regulatory network. A “zedoary turmeric-trisomes-chemical composition-target-disease” network diagram was subsequently constructed using Cytoscape 3.7.2 software, and the topological properties of the network were analyzed using the “Network Analysis” plug-in. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the common targets were performed using the DAVID 6.8 database to elucidate the mechanism of zedoary turmeric-trisomes in the treatment of IBD. Subsequently, molecular docking of the compounds and targets with the highest intermediate values in the “zedoary turmeric-trisomes-chemical composition-target-disease” network was performed using Sybyl-x 2.1.1 software.
RESULTS A total of 5 chemical components with 60 targets were identified, as well as 3153 targets related to IBD and 44 common targets. The protein-protein interaction network showed that the core therapeutic targets included JUN, MAPK14, CASP3, AR, and PTGS2. The GO enrichment analysis identified 759 items, and the KEGG enrichment analysis yielded 52 items, including the cancer pathway, neuroactive ligand-receptor interaction, hepatitis B, and the calcium signaling pathway, reflecting the complex biological processes of the multicomponent, multitarget and multipathway treatment of diseases with zedoary turmeric-trisomes. Molecular docking showed that the compound bonded with the target through hydrogen bond interactions and exhibited good docking activity.
CONCLUSION This study identified the potential mechanism of action of zedoary turmeric-trisomes in the treatment of inflammatory bowel fibrosis using network pharmacology and molecular docking technology, providing a scientific basis for further expansion of their clinical use.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 730000, Shaanxi Province, China
| | - Yong-Yi Ji
- Department of Neurology, Xi’an Hospital of Traditional Chinese Medicine, Xi’an 710021, Shaanxi Province, China
| | - Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
| | - Xin-Li Wen
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Xi’an 710003, Shaanxi Province, China
| | - Shi-Cheng Wu
- Department of Proctology, Gansu Academy of Traditional Chinese Medicine, GanSu Hospital of Traditional Chinese Medicine, Lanzhou 730050, Gansu Province, China
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Zhang B, Liu G, Wang X, Hu X. Identification of Molecular Targets and Potential Mechanisms of Yinchen Wuling San Against Head and Neck Squamous Cell Carcinoma by Network Pharmacology and Molecular Docking. Front Genet 2022; 13:914646. [PMID: 35873484 PMCID: PMC9306494 DOI: 10.3389/fgene.2022.914646] [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: 04/07/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) represents one of the most malignant and heterogeneous tumors, and the patients have low 5-year survival. Traditional Chinese medicine (TCM) has been demonstrated as an effective complementary and/or alternative therapy for advanced malignancies including HNSCC. It has been noted that several herbs that are used for preparing Yinchen Wuling San (YWLS) have anti-tumor activities, whereas their mechanisms of action remain elusive. In this study, network pharmacology and molecular docking studies were employed to explore the underlying mechanisms of action of YWLS against HNSCC. The 58 active ingredients from six herbs used for YWLS and their 506 potential targets were screened from the traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP) and SwissTargetPrediction database. A total of 2,173 targets associated with HNSCC were mainly identified from the DisGeNET and GeneCards databases. An active components-targets-disease network was constructed in the Cytoscape. Top 20 hub targets, such as AKT1, EGFR, TNF, ESR1, SRC, HSP90AA1, MAPK3, ERBB2, and CCND1, were identified by a degree in the protein–protein interaction (PPI) network. Gene functional enrichment analysis showed that PI3K-AKT, MAPK, Ras, TNF, and EGFR were the main signaling pathways of YWLS in treating HNSCC. There were 48 intersected targets such as EGFR, AKT1, and TNF that were associated with patients’ outcomes by the univariate Cox analysis, and most of them had increased expression in the tumor as compared to normal tissues. The area under curves of receiver operating characteristic indicated their diagnostic potential. Inhibition of these survival-related targets and/or combination with EGFR or AKT inhibitors were promising therapeutic options in HNSCC. The partial active components of YWLS exhibited good binding with the hub targets, and ADME analysis further evaluated the drug-likeness of the active components. These compounds and targets identified in this study might provide novel treatment strategies for HNSCC patients, and the subsequent work is essential to verify the underlying mechanisms of YWLS against HNSCC.
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Affiliation(s)
- Biyu Zhang
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Genyan Liu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Xin Wang
- School of Medicine, Jiujiang University, Jiujiang, China
| | - Xuelei Hu
- Key Laboratory of Green Chemical Engineering Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
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Zhou B, Qian Z, Li Q, Gao Y, Li M. Assessment of pulmonary infectious disease treatment with Mongolian medicine formulae based on data mining, network pharmacology and molecular docking. CHINESE HERBAL MEDICINES 2022; 14:432-448. [PMID: 36118001 PMCID: PMC9476772 DOI: 10.1016/j.chmed.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/21/2022] [Accepted: 03/19/2022] [Indexed: 11/19/2022] Open
Abstract
Objective Methods Results Conclusion
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Affiliation(s)
- Baochang Zhou
- College of Traditional Chinese Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Zhanhong Qian
- College of Traditional Chinese Medicine, Inner Mongolia Medical University, Hohhot 010110, China
| | - Qinyu Li
- Department of Pharmacy, Baotou Medical College, Baotou 014040, China
| | - Yuan Gao
- Inner Mongolia Autonomous Region Hospital of Traditional Chinese Medicine (Inner Mongolia Medical University of Clinical College of Traditional Chinese Medicine), Hohhot 010020, China
- Corresponding authors.
| | - Minhui Li
- College of Traditional Chinese Medicine, Inner Mongolia Medical University, Hohhot 010110, China
- Department of Pharmacy, Baotou Medical College, Baotou 014040, China
- Inner Mongolia Institute of Traditional Chinese and Mongolian Medicine, Hohhot 010010, China
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou 014040, China
- Corresponding authors.
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Wang T, Zhou Y, Wang K, Jiang X, Wang J, Chen J. Prediction and validation of potential molecular targets for the combination of Astragalus membranaceus and Angelica sinensis in the treatment of atherosclerosis based on network pharmacology. Medicine (Baltimore) 2022; 101:e29762. [PMID: 35776988 PMCID: PMC9239660 DOI: 10.1097/md.0000000000029762] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Since the 20th century, mortality rate due to cardiovascular diseases has increased, posing a substantial economic burden on society. Atherosclerosis is a common cardiovascular disease that requires urgent and careful attention. This study was conducted to predict and validate the potential molecular targets and pathways of Astragalus membranaceus and Angelica sinensis (A&A) in the treatment of atherosclerosis using network pharmacology. The active ingredients of A&A were obtained using the TCMSP database, while the target genes of atherosclerosis were acquired using 2 databases, namely GeneCards and DrugBank. The disease-target-component model map and the core network were obtained using Cytoscape 3.8.2 and MCODE plug-in, respectively. The core network was then imported into the STRING database to obtain the protein-protein interaction (PPI) network diagram. Moreover, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were performed using the HIPLOT online website. Finally, the small molecules related to key signaling pathways were molecularly docked and visualized. Under the screening conditions of oral bioavailability ≥ 30% and drug-likeness ≥ 0.18, 22 active ingredients were identified from A&A, and 174 relevant targets were obtained. Additionally, 54 active ingredients were found in the extracted core network. Interleukin (IL)-17 signaling pathway, tumor necrosis factor (TNF) signaling pathway, and Toll-like receptor (TLR) signaling pathway were selected as the main subjects through KEGG enrichment analysis. Core targets (RELA, IKBKB, CHUK, and MMP3) and active ingredients (kaempferol, quercetin, and isorhamnetin) were selected and validated using molecular docking. This study identified multiple molecular targets and pathways for A&A in the treatment of atherosclerosis. A&A has the potential to treat atherosclerosis through an antiinflammatory approach.
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Affiliation(s)
- Tianyue Wang
- The 2nd Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | | | - Kaina Wang
- The 1st Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xinyu Jiang
- The 1st Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jingbo Wang
- Library, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jing Chen
- School of life science, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Jing Chen, School of life science, Zhejiang Chinese Medical University, No. 548, Binwen Road, Binjiang District, Hangzhou City 310053, Zhejiang Province, China (e-mail: )
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Taldaev A, Terekhov R, Nikitin I, Zhevlakova A, Selivanova I. Insights into the Pharmacological Effects of Flavonoids: The Systematic Review of Computer Modeling. Int J Mol Sci 2022; 23:6023. [PMID: 35682702 PMCID: PMC9181432 DOI: 10.3390/ijms23116023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022] Open
Abstract
Computer modeling is a method that is widely used in scientific investigations to predict the biological activity, toxicity, pharmacokinetics, and synthesis strategy of compounds based on the structure of the molecule. This work is a systematic review of articles performed in accordance with the recommendations of PRISMA and contains information on computer modeling of the interaction of classical flavonoids with different biological targets. The review of used computational approaches is presented. Furthermore, the affinities of flavonoids to different targets that are associated with the infection, cardiovascular, and oncological diseases are discussed. Additionally, the methodology of bias risks in molecular docking research based on principles of evidentiary medicine was suggested and discussed. Based on this data, the most active groups of flavonoids and lead compounds for different targets were determined. It was concluded that flavonoids are a promising object for drug development and further research of pharmacology by in vitro, ex vivo, and in vivo models is required.
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Affiliation(s)
- Amir Taldaev
- Laboratoty of Nanobiotechnology, Institute of Biomedical Chemistry, Pogodinskaya Str. 10/8, 119121 Moscow, Russia
- Department of Chemistry, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (R.T.); (I.N.); (A.Z.); (I.S.)
| | - Roman Terekhov
- Department of Chemistry, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (R.T.); (I.N.); (A.Z.); (I.S.)
| | - Ilya Nikitin
- Department of Chemistry, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (R.T.); (I.N.); (A.Z.); (I.S.)
| | - Anastasiya Zhevlakova
- Department of Chemistry, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (R.T.); (I.N.); (A.Z.); (I.S.)
| | - Irina Selivanova
- Department of Chemistry, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (R.T.); (I.N.); (A.Z.); (I.S.)
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do Bomfim MR, Barbosa DB, de Carvalho PB, da Silva AM, de Oliveira TA, Taranto AG, Leite FHA. Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics. J Biomol Struct Dyn 2022:1-15. [DOI: 10.1080/07391102.2022.2069155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mayra Ramos do Bomfim
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | - Deyse Brito Barbosa
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
| | | | - Alisson Marques da Silva
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
| | - Tiago Alves de Oliveira
- Departamento de Informática, Gestão e Design, Centro Federal de Educação Tecnológica de Minas Gerais, Divinópolis, Brazil
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Alex Gutterres Taranto
- Departamento de Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei, Brazil
- Faculty of Computing, University of Latvia (UL), Riga, Latvia
| | - Franco Henrique Andrade Leite
- Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Feira de Santana, Brazil
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Zhang ZY, Mao ZJ, Ruan YP, Zhang X. Computational identification of Shenshao Ningxin Yin as an effective treatment for novel coronavirus infection (COVID-19) with myocarditis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:5772-5792. [PMID: 35603378 DOI: 10.3934/mbe.2022270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND The newly identified betacoronavirus SARS-CoV-2 is the causative pathogen of the 2019 coronavirus disease (COVID-19), which has killed more than 4.5 million people. SARS-CoV-2 causes severe respiratory distress syndrome by targeting the lungs and also induces myocardial damage. Shenshao Ningxin Yin (SNY) has been used for more than 700 years to treat influenza. Previous randomized controlled trials (RCTs) have demonstrated that SNY can improve the clinical symptoms of viral myocarditis, reverse arrhythmia, and reduce the level of myocardial damage markers. METHODS This work uses a rational computational strategy to identify existing drug molecules that target host pathways for the treatment of COVID-19 with myocarditis. Disease and drug targets were input into the STRING database to construct proteinɃprotein interaction networks. The Metascape database was used for GO and KEGG enrichment analysis. RESULTS SNY signaling modulated the pathways of coronavirus disease, including COVID-19, Ras signaling, viral myocarditis, and TNF signaling pathways. Tumor necrosis factor (TNF), cellular tumor antigen p53 (TP53), mitogen-activated protein kinase 1 (MAPK1), and the signal transducer and activator of transcription 3 (STAT3) were the pivotal targets of SNY. The components of SNY bound well with the pivotal targets, indicating there were potential biological activities. CONCLUSION Our findings reveal the pharmacological role and molecular mechanism of SNY for the treatment of COVID-19 with myocarditis. We also, for the first time, demonstrate that SNY displays multi-component, multi-target, and multi-pathway characteristics with a complex mechanism of action.
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Affiliation(s)
- Ze-Yu Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Zhu-Jun Mao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
- Chinese Medicine Plant Essential Oil Zhejiang Engineering Research Center, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Ye-Ping Ruan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
- Chinese Medicine Plant Essential Oil Zhejiang Engineering Research Center, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xin Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China
- Chinese Medicine Plant Essential Oil Zhejiang Engineering Research Center, Zhejiang Chinese Medical University, Hangzhou 310053, China
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Martinelli DD. Generative machine learning for de novo drug discovery: A systematic review. Comput Biol Med 2022; 145:105403. [PMID: 35339849 DOI: 10.1016/j.compbiomed.2022.105403] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/08/2023]
Abstract
Recent research on artificial intelligence indicates that machine learning algorithms can auto-generate novel drug-like molecules. Generative models have revolutionized de novo drug discovery, rendering the explorative process more efficient. Several model frameworks and input formats have been proposed to enhance the performance of intelligent algorithms in generative molecular design. In this systematic literature review of experimental articles and reviews over the last five years, machine learning models, challenges associated with computational molecule design along with proposed solutions, and molecular encoding methods are discussed. A query-based search of the PubMed, ScienceDirect, Springer, Wiley Online Library, arXiv, MDPI, bioRxiv, and IEEE Xplore databases yielded 87 studies. Twelve additional studies were identified via citation searching. Of the articles in which machine learning was implemented, six prominent algorithms were identified: long short-term memory recurrent neural networks (LSTM-RNNs), variational autoencoders (VAEs), generative adversarial networks (GANs), adversarial autoencoders (AAEs), evolutionary algorithms, and gated recurrent unit (GRU-RNNs). Furthermore, eight central challenges were designated: homogeneity of generated molecular libraries, deficient synthesizability, limited assay data, model interpretability, incapacity for multi-property optimization, incomparability, restricted molecule size, and uncertainty in model evaluation. Molecules were encoded either as strings, which were occasionally augmented using randomization, as 2D graphs, or as 3D graphs. Statistical analysis and visualization are performed to illustrate how approaches to machine learning in de novo drug design have evolved over the past five years. Finally, future opportunities and reservations are discussed.
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Arjmand B, Hamidpour SK, Alavi-Moghadam S, Yavari H, Shahbazbadr A, Tavirani MR, Gilany K, Larijani B. Molecular Docking as a Therapeutic Approach for Targeting Cancer Stem Cell Metabolic Processes. Front Pharmacol 2022; 13:768556. [PMID: 35264950 PMCID: PMC8899123 DOI: 10.3389/fphar.2022.768556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Cancer stem cells (CSCs) are subpopulation of cells which have been demonstrated in a variety of cancer models and involved in cancer initiation, progression, and development. Indeed, CSCs which seem to form a small percentage of tumor cells, display resembling characteristics to natural stem cells such as self-renewal, survival, differentiation, proliferation, and quiescence. Moreover, they have some characteristics that eventually can demonstrate the heterogeneity of cancer cells and tumor progression. On the other hand, another aspect of CSCs that has been recognized as a central concern facing cancer patients is resistance to mainstays of cancer treatment such as chemotherapy and radiation. Owing to these details and the stated stemness capabilities, these immature progenitors of cancerous cells can constantly persist after different therapies and cause tumor regrowth or metastasis. Further, in both normal development and malignancy, cellular metabolism and stemness are intricately linked and CSCs dominant metabolic phenotype changes across tumor entities, patients, and tumor subclones. Hence, CSCs can be determined as one of the factors that correlate to the failure of common therapeutic approaches in cancer treatment. In this context, researchers are searching out new alternative or complementary therapies such as targeted methods to fight against cancer. Molecular docking is one of the computational modeling methods that has a new promise in cancer cell targeting through drug designing and discovering programs. In a simple definition, molecular docking methods are used to determine the metabolic interaction between two molecules and find the best orientation of a ligand to its molecular target with minimal free energy in the formation of a stable complex. As a comprehensive approach, this computational drug design method can be thought more cost-effective and time-saving compare to other conventional methods in cancer treatment. In addition, increasing productivity and quality in pharmaceutical research can be another advantage of this molecular modeling method. Therefore, in recent years, it can be concluded that molecular docking can be considered as one of the novel strategies at the forefront of the cancer battle via targeting cancer stem cell metabolic processes.
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Affiliation(s)
- Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Babak Arjmand, ; Bagher Larijani,
| | - Shayesteh Kokabi Hamidpour
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hanieh Yavari
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ainaz Shahbazbadr
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Babak Arjmand, ; Bagher Larijani,
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Qin L, Kuai J, Yang F, Yang L, Sun P, Zhang L, Li G. Selected by bioinformatics and molecular docking analysis, Dhea and 2–14,15-Eg are effective against cholangiocarcinoma. PLoS One 2022; 17:e0260180. [PMID: 35113866 PMCID: PMC8812988 DOI: 10.1371/journal.pone.0260180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/03/2021] [Indexed: 12/04/2022] Open
Abstract
Object To identify novel targets for the diagnosis, treatment and prognosis of cholangiocarcinoma, we screen ideal lead compounds and preclinical drug candidates with MYC inhibitory effect from the ZINC database, and verify the therapeutic effect of Dhea and 2–14,15-Eg on cholangiocarcinoma. Methods The gene expression profiles of GSE132305, GSE89749, and GSE45001 were obtained respectively from the Gene Expression Omnibus database. The DEGs were identified by comparing the gene expression profiles of cholangiocarcinoma and normal tissues. GO, KEGG analysis and PPI network analyses were performed. LibDock, ADME and toxicity prediction, molecular docking and molecular dynamics simulations were used to identify potential inhibitors of MYC. Moreover, in vitro, MTT assay, colony-forming assay, the scratch assay and Western blotting were performed to verify the therapeutic effect of Dhea and 2–14,15-Eg. Results PPI network analysis showed that ALB, MYC, APOB, IGF1 and KNG1 were hub genes, of which MYC was mainly studied in this study. A battery of computer-aided virtual techniques showed that Dhea and 2–14,15-Eg have lower rodent carcinogenicity, Ames mutagenicity, developmental toxicity potential, and high tolerance to cytochrome P4502D6, as well as could exist stably in natural circumstances. In vitro assays showed that Dhea and 2–14,15-Eg inhibited cholangiocarcinoma cellular viability, proliferation, and migration inhibiting expression of MYC. Conclusion This study suggested that Dhea and 2–14,15-Eg were novel potential inhibitors of MYC targeting, as well as are a promising drug in dealing with cholangiocarcinoma and have a perspective application.
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Affiliation(s)
- Lei Qin
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Jun Kuai
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Fang Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Lu Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Peisheng Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Lanfang Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
| | - Guangpeng Li
- Department of Emergency, The First Affiliated Hospital of Xinxiang Medical College, Xin Xiang, China
- * E-mail:
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Yang C, Zhao H, Sun Y, Wang C, Geng X, Wang R, Tang L, Han D, Liu J, Tan W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3083-3095. [PMID: 35293579 PMCID: PMC8989545 DOI: 10.1093/nar/gkac156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/24/2022] [Accepted: 02/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Cheng Wang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xinyao Geng
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ruowen Wang
- To whom correspondence should be addressed. Tel: +86 02168385698; Fax:+86 02168385698;
| | - Lumin Tang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianjun Liu
- Correspondence may also be addressed to Jianjun Liu.
| | - Weihong Tan
- Correspondence may also be addressed to Weihong Tan.
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Yao L, Ban F, Peng S, Xu D, Li H, Mo H, Hu L, Zhou X. Exogenous Iron Induces NADPH Oxidases-Dependent Ferroptosis in the Conidia of Aspergillus flavus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13608-13617. [PMID: 34747604 DOI: 10.1021/acs.jafc.1c04411] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Aspergillus flavus is saprophytic soil fungus that contaminates seed crops with the carcinogenic secondary metabolite aflatoxin, posing a significant threat to humans and animals. Ferrous sulfate is a common iron supplement that is used to the treatment of iron-deficiency anemia. Here, we identified an unexpected inhibitory role of ferrous sulfate on A. flavus. With specific fluorescent dyes, we detected several conidial ferroptosis hallmarks in conidia under the treatment of 1 mM Fe2+, including nonapoptosis necrosis, iron-dependent, lipid peroxide accumulation, and ROS burst. However, unlike traditional ferroptosis in mammals, Fe2+ triggered conidial ferroptosis in A. flavus was regulated by NADPH oxidase (NOXs) activation instead of Fenton reaction. Transcriptomic and some other bioinformatics analyses showed that NoxA in A. flavus might be a potential target of Fe2+, and thus led to the occurrence of conidial ferroptosis. Furthermore, noxA deletion mutant was constructed, and both ROS generation and conidial ferroptosis in ΔnoxA was reduced when exposed to Fe2+. Taken together, our study revealed an exogenous Fe2+-triggered conidial ferroptosis pathway mediated by NoxA of A. flavus, which greatly contributes to the development of an alternative strategy to control this pathogen.
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Affiliation(s)
- Lishan Yao
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Fangfang Ban
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Shurui Peng
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Dan Xu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Hongbo Li
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Haizhen Mo
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Liangbin Hu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
| | - Xiaohui Zhou
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, Connecticut 06269, United States
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Evaluation of Effects of Ractopamine on Cardiovascular, Respiratory, and Locomotory Physiology in Animal Model Zebrafish Larvae. Cells 2021; 10:cells10092449. [PMID: 34572098 PMCID: PMC8466814 DOI: 10.3390/cells10092449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 12/31/2022] Open
Abstract
Ractopamine (RAC) is a beta-adrenoceptor agonist that is used to promote lean and increased food conversion efficiency in livestock. This compound has been considered to be causing behavioral and physiological alterations in livestock like pig. Few studies have addressed the potential non-target effect of RAC in aquatic animals. In this study, we aimed to explore the potential physiological response after acute RAC exposure in zebrafish by evaluating multiple endpoints like locomotor activity, oxygen consumption, and cardiovascular performance. Zebrafish larvae were subjected to waterborne RAC exposure at 0.1, 1, 2, 4, or 8 ppm for 24 h, and the corresponding cardiovascular, respiratory, and locomotion activities were monitored and quantified. In addition, we also performed in silico molecular docking for RAC with 10 zebrafish endogenous β-adrenergic receptors to elucidate the potential acting mechanism of RAC. Results show RAC administration can significantly boost locomotor activity, cardiac performance, oxygen consumption, and blood flow rate, but without affecting the cardiac rhythm regularity in zebrafish embryos. Based on structure-based flexible molecular docking, RAC display similar binding affinity to all ten subtypes of endogenous β-adrenergic receptors, from adra1aa to adra2db, which are equivalent to the human one. This result suggests RAC might act as high potency and broad spectrum β-adrenergic receptors agonist on boosting the locomotor activity, cardiac performance, and oxygen consumption in zebrafish. To validate our results, we co-incubated a well-known β-blocker of propranolol (PROP) with RAC. PROP exposure tends to minimize the locomotor hyperactivity, high oxygen consumption, and cardiac rate in zebrafish larvae. In silico structure-based molecular simulation and binding affinity tests show PROP has an overall lower binding affinity than RAC. Taken together, our studies provide solid in vivo evidence to support that RAC plays crucial roles on modulating cardiovascular, respiratory, and locomotory physiology in zebrafish for the first time. In addition, the versatile functions of RAC as β-agonist possibly mediated via receptor competition with PROP as β-antagonist.
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