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Shah M, Arumugam S. Exploring putative drug properties associated with TNF-alpha inhibition and identification of potential targets in cardiovascular disease using machine learning-assisted QSAR modeling and virtual reverse pharmacology approach. Mol Divers 2024:10.1007/s11030-024-10921-w. [PMID: 38954070 DOI: 10.1007/s11030-024-10921-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Cardiovascular disease is a chronic inflammatory disease with high mortality rates. TNF-alpha is pro-inflammatory and associated with the disease, but current medications have adverse effects. Therefore, efficient inhibitors are urgently needed as alternatives. This study represents a structural-activity relationship investigation of TNF-alpha, curated from the ChEMBL database. Exploratory data analysis was performed to visualize the physicochemical properties of different bioactivity groups. The extracted molecules were subjected to PubChem and SubStructure fingerprints, and a QSAR-based Random Forest (QSAR-RF) model was generated using the WEKA tool. The QSAR random Forest model was built based on the SubStructure fingerprint with a correlation coefficient of 0.992 and 0.716 as the respective tenfold cross-validation scores. The variance important plot (VIP) method was used to extract the important features for TNF-alpha inhibition. The Substructure-based QSAR-RF (SS-QSAR-RF) model was validated using molecules from PubChem and ZINC databases. The generated model also predicts the pIC50 value of the molecules selected from the docking study followed by molecular dynamic simulation with the time step of 100 ns. Through virtual reverse pharmacology, we determined the main drug targets from the top four hit compounds obtained via molecular docking study. Our analysis included an integrated bioinformatics approach to pinpoint crucial targets like EGRF, HSP900A1, STAT3, PSEN1, AKT1, and MDM2. Further, GO and KEGG pathways analysis identified relevant cardiovascular disease-related pathways for the hub gene involved. However, this study provides valuable insights, it is important to note that it lacks experimental application. Future research may benefit from conducting in-vitro and in-vivo studies.
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Affiliation(s)
- Manisha Shah
- Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Sivakumar Arumugam
- Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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Adella Putri AD, Sembiring MH, Tuba S. Phytochemical constituents analysis in laminaria digitata for Alzheimer's disease: molecular docking and in-silico toxicity approach. Commun Integr Biol 2024; 17:2357346. [PMID: 38798825 PMCID: PMC11123516 DOI: 10.1080/19420889.2024.2357346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Alzheimer's disease (AD) is a common brain disease associated with cognitive impairment and dementia. donepezil, an acetylcholinesterase (AChE) inhibitor drug as a commercial AD drug represents a non-cost-effective treatment with the toxic effects reported. As the prevalence of AD increases, the development of effective therapeutic treatments is urgently required. Laminaria digitata is a brown seaweed claimed to be able to prevent and treat neurodegenerative diseases. Therefore, this study measured and compared the binding affinity and toxicity of seven common phytoconstituents in Laminaria digitata against acetylcholinesterase (AChE) with those of donepezil using a molecular docking approach. The binding free energy values of donepezil, dieckol, eckol, fucodiphlorethol G, 7-Phloroecol, laminaran, alginic acid, and fucoidan with acetylcholinesterase (AChE) were -12.3, -13.5, -10.5, -8,7, -9.7, -8.0, -10.3, and -7.4 kcal/mol. All ligands constantly interacted with the AChE amino acid residues, namely Tyr124. Dieckol, with the strongest and most stable interaction, is classified as class IV toxicity, with an LD50 value of 866 mg/kg. It has aryl hydrocarbon receptor (AhR) and mitochondrial membrane potential (MMP) toxicity at certain doses. Theoretically, based on Lipinski's rule, dieckol is likely to have poor absorption and permeation properties; therefore, several considerations during the drug discovery process are needed.
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Affiliation(s)
| | | | - Syahrul Tuba
- Faculty of Military Pharmacy, Indonesia Defense University, Bogor, Indonesia
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Perugino F, Pedroni L, Galaverna G, Dall'Asta C, Dellafiora L. Virtual display of targets: A new level to rise the current understanding of ochratoxin A toxicity from a molecular standpoint. Toxicology 2024; 503:153765. [PMID: 38432407 DOI: 10.1016/j.tox.2024.153765] [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: 01/29/2024] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Ochratoxin A (OTA) is a mycotoxin spread worldwide contaminating several food and feed commodities and rising concerns for humans and animals. OTA toxicity has been thoroughly assessed over the last 60 years revealing a variety of adverse effects, including nephrotoxicity, hepatotoxicity and possible carcinogenicity. However, the underpinning mechanisms of action have yet to be completely displayed and understood. In this framework, we applied a virtual pipeline based on molecular docking, dynamics and umbrella simulations to display new OTA potential targets. The results collected consistently identified OGFOD1, a key player in protein translation, as possibly inhibited by OTA and its 2'R diastereomer. This is consistent with the current knowledge of OTA's molecular toxicology and may fill some gaps from a mechanistic standpoint. This could pave the way for further dedicated analysis focusing their attention on the OTA-OGFOD1 interaction, expanding the current understanding of OTA toxicity at a molecular level.
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Affiliation(s)
- Florinda Perugino
- Department of Food and Drug, University of Parma, Parma, Italy; Department of Biology, University of Naples Federico II, Naples, Italy
| | - Lorenzo Pedroni
- Department of Food and Drug, University of Parma, Parma, Italy
| | | | | | - Luca Dellafiora
- Department of Food and Drug, University of Parma, Parma, Italy.
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Castillo-García EL, Cossio-Ramírez AL, Córdoba-Méndez ÓA, Loza-Mejía MA, Salazar JR, Chávez-Gutiérrez E, Bautista-Poblet G, Castillo-Mendieta NT, Moreno DA, García-Viguera C, Pinto-Almazán R, Almanza-Pérez JC, Gallardo JM, Guerra-Araiza C. In Silico and In Vivo Evaluation of the Maqui Berry ( Aristotelia chilensis (Mol.) Stuntz) on Biochemical Parameters and Oxidative Stress Markers in a Metabolic Syndrome Model. Metabolites 2023; 13:1189. [PMID: 38132871 PMCID: PMC10744843 DOI: 10.3390/metabo13121189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/25/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Metabolic syndrome (MetS) is a complex disease that includes metabolic and physiological alterations in various organs such as the heart, pancreas, liver, and brain. Reports indicate that blackberry consumption, such as maqui berry, has a beneficial effect on chronic diseases such as cardiovascular disease, obesity, and diabetes. In the present study, in vivo and in silico studies have been performed to evaluate the molecular mechanisms implied to improve the metabolic parameters of MetS. Fourteen-day administration of maqui berry reduces weight gain, blood fasting glucose, total blood cholesterol, triacylglycerides, insulin resistance, and blood pressure impairment in the diet-induced MetS model in male and female rats. In addition, in the serum of male and female rats, the administration of maqui berry (MB) improved the concentration of MDA, the activity of SOD, and the formation of carbonyls in the group subjected to the diet-induced MetS model. In silico studies revealed that delphinidin and its glycosylated derivatives could be ligands of some metabolic targets such as α-glucosidase, PPAR-α, and PPAR-γ, which are related to MetS parameters. The experimental results obtained in the study suggest that even at low systemic concentrations, anthocyanin glycosides and aglycones could simultaneously act on different targets related to MetS. Therefore, these molecules could be used as coadjuvants in pharmacological interventions or as templates for designing new multitarget molecules to manage patients with MetS.
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Affiliation(s)
- Emily Leonela Castillo-García
- Unidad de Investigación Médica en Farmacología, Hospital de Especialidades Dr. Bernardo Sepúlveda, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (E.L.C.-G.); (G.B.-P.)
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City 52919, Mexico
| | - Ana Lizzet Cossio-Ramírez
- Maestría en Ciencias de la Salud, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Óscar Arturo Córdoba-Méndez
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (Ó.A.C.-M.); (M.A.L.-M.); (J.R.S.)
| | - Marco A. Loza-Mejía
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (Ó.A.C.-M.); (M.A.L.-M.); (J.R.S.)
| | - Juan Rodrigo Salazar
- Design, Isolation, and Synthesis of Bioactive Molecules Research Group, Chemical Sciences School, Universidad La Salle-México, Benjamín Franklin 45, Mexico City 06140, Mexico; (Ó.A.C.-M.); (M.A.L.-M.); (J.R.S.)
| | - Edwin Chávez-Gutiérrez
- Doctorado en Ciencias en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación Manuel Carpio y Plan de Ayala s/n, Mexico City 11340, Mexico;
| | - Guadalupe Bautista-Poblet
- Unidad de Investigación Médica en Farmacología, Hospital de Especialidades Dr. Bernardo Sepúlveda, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (E.L.C.-G.); (G.B.-P.)
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City 52919, Mexico
| | - Nadia Tzayaka Castillo-Mendieta
- Postdoctorate-Conacyt-Unidad de Investigación Médica en Enfermedades Neurologicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330 Col. Doctores, Mexico City 06725, Mexico;
| | - Diego A. Moreno
- Laboratorio de Fitoquímica y Alimentos Saludables (LabFAS), CEBAS, CSIC. Campus Universitario de Espinardo-25, E-30100 Murcia, Spain; (D.A.M.); (C.G.-V.)
| | - Cristina García-Viguera
- Laboratorio de Fitoquímica y Alimentos Saludables (LabFAS), CEBAS, CSIC. Campus Universitario de Espinardo-25, E-30100 Murcia, Spain; (D.A.M.); (C.G.-V.)
| | - Rodolfo Pinto-Almazán
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Mexico City 11340, Mexico
| | - Julio César Almanza-Pérez
- Laboratorio de Farmacologia, Departamento de Ciencias de la Salud, DCBS, UAM-I, Mexico City 09310, Mexico;
| | - Juan Manuel Gallardo
- Unidad de Investigación Médica en Enfermedades Nefrológicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - Christian Guerra-Araiza
- Unidad de Investigación Médica en Farmacología, Hospital de Especialidades Dr. Bernardo Sepúlveda, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico; (E.L.C.-G.); (G.B.-P.)
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