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Agu PC, Afiukwa CA, Orji OU, Ezeh EM, Ofoke IH, Ogbu CO, Ugwuja EI, Aja PM. Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management. Sci Rep 2023; 13:13398. [PMID: 37592012 PMCID: PMC10435576 DOI: 10.1038/s41598-023-40160-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/05/2023] [Indexed: 08/19/2023] Open
Abstract
Molecular docking is a computational technique that predicts the binding affinity of ligands to receptor proteins. Although it has potential uses in nutraceutical research, it has developed into a formidable tool for drug development. Bioactive substances called nutraceuticals are present in food sources and can be used in the management of diseases. Finding their molecular targets can help in the creation of disease-specific new therapies. The purpose of this review was to explore molecular docking's application to the study of dietary supplements and disease management. First, an overview of the fundamentals of molecular docking and the various software tools available for docking was presented. The limitations and difficulties of using molecular docking in nutraceutical research are also covered, including the reliability of scoring functions and the requirement for experimental validation. Additionally, there was a focus on the identification of molecular targets for nutraceuticals in numerous disease models, including those for sickle cell disease, cancer, cardiovascular, gut, reproductive, and neurodegenerative disorders. We further highlighted biochemistry pathways and models from recent studies that have revealed molecular mechanisms to pinpoint new nutraceuticals' effects on disease pathogenesis. It is convincingly true that molecular docking is a useful tool for identifying the molecular targets of nutraceuticals in the management of diseases. It may offer information about how nutraceuticals work and support the creation of new therapeutics. Therefore, molecular docking has a bright future in nutraceutical research and has a lot of potentials to lead to the creation of brand-new medicines for the treatment of disease.
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Affiliation(s)
- P C Agu
- Department of Biochemistry, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria.
- Department of Science Laboratory Technology (Biochemistry Option), Our Savior Institute of Science, Agriculture, and Technology, Enugu, Nigeria.
| | - C A Afiukwa
- Department of Biotechnology, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria
| | - O U Orji
- Department of Biochemistry, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria
| | - E M Ezeh
- Department of Chemical Engineering, Faculty of Engineering, Caritas University, Amorji-Nike, Enugu, Nigeria
| | - I H Ofoke
- Department of Biochemistry, Faculty of Sciences, Madonna University, Elele, Rivers State, Nigeria
| | - C O Ogbu
- Department of Biochemistry, Federal University of Health Sciences, Otukpo, Benue State, Nigeria
| | - E I Ugwuja
- Department of Biochemistry, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria
| | - P M Aja
- Department of Biochemistry, Faculty of Sciences, Ebonyi State University, Abakaliki, Nigeria.
- Department of Biochemistry, Faculty of Biomedical Sciences, Kampala International University, Ishaka, Uganda.
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Kowalski TW, Feira MF, Lord VO, Gomes JDA, Giudicelli GC, Fraga LR, Sanseverino MTV, Recamonde-Mendoza M, Schuler-Faccini L, Vianna FSL. A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors. Int J Mol Sci 2023; 24:11515. [PMID: 37511270 PMCID: PMC10380514 DOI: 10.3390/ijms241411515] [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: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact the strict transcriptional regulation of the developing embryo. Hence, this study aims to evaluate the TFs altered by IMiDs, prioritizing the ones associated with embryogenesis through transcriptome and systems biology-allied analyses. This study comprises only the experimental data accessed through bioinformatics databases. First, proteins and genes reported in the literature as altered/affected by the IMiDs were annotated. A protein systems biology network was evaluated. TFs beta-catenin (CTNNB1) and SP1 play more central roles: beta-catenin is an essential protein in the network, while SP1 is a putative C2H2 candidate for IMiD-induced degradation. Separately, the differential expressions of the annotated genes were analyzed through 23 publicly available transcriptomes, presenting 8624 differentially expressed genes (2947 in two or more datasets). Seventeen C2H2 TFs were identified as related to embryonic development but not studied for IMiD exposure; these TFs are potential IMiDs degradation neosubstrates. This is the first study to suggest an integration of IMiD molecular mechanisms through C2H2 TF degradation.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Mariléa Furtado Feira
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Vinícius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Julia do Amaral Gomes
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Giovanna Câmara Giudicelli
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Lucas Rosa Fraga
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90010-150, Brazil
| | - Maria Teresa Vieira Sanseverino
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Computer Science, Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
| | - Lavinia Schuler-Faccini
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Fernanda Sales Luiz Vianna
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
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Sciascia QL, Metges CC. Review: Methods and biomarkers to investigate intestinal function and health in pigs. Animal 2023; 17 Suppl 3:100860. [PMID: 37316380 DOI: 10.1016/j.animal.2023.100860] [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: 09/03/2022] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Society is becoming increasingly critical of animal husbandry due to its environmental impact and issues involving animal health and welfare including scientific experiments conducted on farm animals. This opens up two new fields of scientific research, the development of non- or minimally invasive (1) methods and techniques using faeces, urine, breath or saliva sampling to replace existing invasive models, and (2) biomarkers reflecting a disease or malfunction of an organ that may predict the future outcome of a pig's health, performance or sustainability. To date, there is a paucity of non- or minimally invasive methods and biomarkers investigating gastrointestinal function and health in pigs. This review describes recent literature pertaining to parameters that assess gastrointestinal functionality and health, tools currently used to investigate them, and the development or the potential to develop new non- and minimally invasive methods and/or biomarkers in pigs. Methods described within this review are those that characterise gastrointestinal mass such as the citrulline generation test, intestinal protein synthesis rate, first pass splanchnic nutrient uptake and techniques describing intestinal proliferation, barrier function and transit rate, and microbial composition and metabolism. An important consideration is gut health, and several molecules with the potential to act as biomarkers of compromised gut health in pigs are reported. Many of these methods to investigate gut functionality and health are considered 'gold standards' but are invasive. Thus, in pigs, there is a need to develop and validate non-invasive methods and biomarkers that meet the principles of the 3 R guidelines, which aim to reduce and refine animal experimentation and replace animals where possible.
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Affiliation(s)
- Q L Sciascia
- Research Institute for Farm Animal Biology, Institute of Nutritional Physiology "Oskar Kellner", Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - C C Metges
- Research Institute for Farm Animal Biology, Institute of Nutritional Physiology "Oskar Kellner", Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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Morrison JI, Petrovic A, Metzendorf NG, Rofo F, Yilmaz CU, Stenler S, Laudon H, Hultqvist G. Standardized Preclinical In Vitro Blood-Brain Barrier Mouse Assay Validates Endocytosis-Dependent Antibody Transcytosis Using Transferrin-Receptor-Mediated Pathways. Mol Pharm 2023; 20:1564-1576. [PMID: 36808999 PMCID: PMC9997753 DOI: 10.1021/acs.molpharmaceut.2c00768] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The presence of the blood-brain barrier (BBB) creates a nigh-on impenetrable obstacle for large macromolecular therapeutics that need to be delivered to the brain milieu to treat neurological disorders. To overcome this, one of the strategies used is to bypass the barrier with what is referred to as a "Trojan Horse" strategy, where therapeutics are designed to use endogenous receptor-mediated pathways to piggyback their way through the BBB. Even though in vivo methodologies are commonly used to test the efficacy of BBB-penetrating biologics, comparable in vitro BBB models are in high demand, as they benefit from being an isolated cellular system devoid of physiological factors that can on occasion mask the processes behind BBB transport via transcytosis. We have developed an in vitro BBB model (In-Cell BBB-Trans assay) based on the murine cEND cells that help delineate the ability of modified large bivalent IgG antibodies conjugated to the transferrin receptor binder scFv8D3 to cross an endothelial monolayer grown on porous cell culture inserts (PCIs). Following the administration of bivalent antibodies into the endothelial monolayer, a highly sensitive enzyme-linked immunosorbent assay (ELISA) is used to determine the concentration in the apical (blood) and basolateral (brain) chambers of the PCI system, allowing for the evaluation of apical recycling and basolateral transcytosis, respectively. Our results show that antibodies conjugated to scFv8D3 transcytose at considerably higher levels compared to unconjugated antibodies in the In-Cell BBB-Trans assay. Interestingly, we are able to show that these results mimic in vivo brain uptake studies using identical antibodies. In addition, we are able to transversely section PCI cultured cells, allowing for the identification of receptors and proteins that are likely involved in the transcytosis of the antibodies. Furthermore, studies using the In-Cell BBB-Trans assay revealed that transcytosis of the transferrin-receptor-targeting antibodies is dependent on endocytosis. In conclusion, we have designed a simple, reproducible In-Cell BBB-Trans assay based on murine cells that can be used to rapidly determine the BBB-penetrating capabilities of transferrin-receptor-targeting antibodies. We believe that the In-Cell BBB-Trans assay can be used as a powerful, preclinical screening platform for therapeutic neurological pathologies.
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Affiliation(s)
- Jamie I Morrison
- Institutionen för Farmaci, Uppsala Universitet, Uppsala 752 37, Sweden
| | - Alex Petrovic
- Institutionen för Farmaci, Uppsala Universitet, Uppsala 752 37, Sweden
| | | | - Fadi Rofo
- Institutionen för Farmaci, Uppsala Universitet, Uppsala 752 37, Sweden
| | - Canan U Yilmaz
- Institutionen för Farmaci, Uppsala Universitet, Uppsala 752 37, Sweden
| | - Sofia Stenler
- Institutionen för Farmaci, Uppsala Universitet, Uppsala 752 37, Sweden
| | | | - Greta Hultqvist
- Institutionen för Farmaci, Uppsala Universitet, Uppsala 752 37, Sweden
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In vitro cultivation methods for coccidian parasite research. Int J Parasitol 2022:S0020-7519(22)00153-9. [DOI: 10.1016/j.ijpara.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/29/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022]
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Fanizza F, Campanile M, Forloni G, Giordano C, Albani D. Induced pluripotent stem cell-based organ-on-a-chip as personalized drug screening tools: A focus on neurodegenerative disorders. J Tissue Eng 2022; 13:20417314221095339. [PMID: 35570845 PMCID: PMC9092580 DOI: 10.1177/20417314221095339] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/04/2022] [Indexed: 01/15/2023] Open
Abstract
The Organ-on-a-Chip (OoC) technology shows great potential to revolutionize the
drugs development pipeline by mimicking the physiological environment and
functions of human organs. The translational value of OoC is further enhanced
when combined with patient-specific induced pluripotent stem cells (iPSCs) to
develop more realistic disease models, paving the way for the development of a
new generation of patient-on-a-chip devices. iPSCs differentiation capacity
leads to invaluable improvements in personalized medicine. Moreover, the
connection of single-OoC into multi-OoC or body-on-a-chip allows to investigate
drug pharmacodynamic and pharmacokinetics through the study of multi-organs
cross-talks. The need of a breakthrough thanks to this technology is
particularly relevant within the field of neurodegenerative diseases, where the
number of patients is increasing and the successful rate in drug discovery is
worryingly low. In this review we discuss current iPSC-based OoC as drug
screening models and their implication in development of new therapies for
neurodegenerative disorders.
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Affiliation(s)
- Francesca Fanizza
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Marzia Campanile
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Gianluigi Forloni
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta,” Politecnico di Milano, Milan, Italy
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
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