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Sebastiano MR, Hadano S, Cesca F, Iahsp Consortium, Ermondi G. Preclinical alternative drug discovery programs for monogenic rare diseases. The case of hereditary spastic paraplegias. Drug Discov Today 2024:104138. [PMID: 39154774 DOI: 10.1016/j.drudis.2024.104138] [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: 04/09/2024] [Revised: 06/28/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
Patients diagnosed with rare diseases and their and families search desperately to organize drug discovery campaigns. Alternative models that differ from default paradigms offer real opportunities. There are, however, no clear guidelines for the development of such models, which reduces success rates and raises costs. We address the main challenges in making the discovery of new preclinical treatments more accessible, using rare hereditary paraplegia as a paradigmatic case. First, we discuss the necessary expertise, and the patients' clinical and genetic data. Then, we revisit gene therapy, de novo drug development, and drug repurposing, discussing their applicability. Moreover, we explore a pool of recommended in silico tools for pathogenic variant and protein structure prediction, virtual screening, and experimental validation methods, discussing their strengths and weaknesses. Finally, we focus on successful case applications.
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Affiliation(s)
- Matteo Rossi Sebastiano
- University of Torino, Molecular Biotechnology and Health Sciences Department, CASSMedChem, Piazza Nizza, 10138 Torino, Italy
| | - Shinji Hadano
- Molecular Neuropathobiology Laboratory, Department of Physiology, Tokai University School of Medicine, Isehara, Japan
| | - Fabrizia Cesca
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Iahsp Consortium
- University of Torino, Molecular Biotechnology and Health Sciences Department, CASSMedChem, Piazza Nizza, 10138 Torino, Italy; Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy; Department of Medical Sciences, University of Torino, Turin, Italy; Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy; PUXANO, Ottergemsesteenweg Zuid 713, 9000 Gent, Belgium; Department of Developmental Neuroscience, IRCCS Stella Maris, Calambrone, Pisa, Italy; IRCCS Stella Maris Foundation, Molecular Medicine for Neurodegenerative and Neuromuscular Disease Unit, Pisa, Italy; Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Giuseppe Ermondi
- University of Torino, Molecular Biotechnology and Health Sciences Department, CASSMedChem, Piazza Nizza, 10138 Torino, Italy
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Barbaro F, Conza GD, Quartulli FP, Quarantini E, Quarantini M, Zini N, Fabbri C, Mosca S, Caravelli S, Mosca M, Vescovi P, Sprio S, Tampieri A, Toni R. Correlation between tooth decay and insulin resistance in normal weight males prompts a role for myo-inositol as a regenerative factor in dentistry and oral surgery: a feasibility study. Front Bioeng Biotechnol 2024; 12:1374135. [PMID: 39144484 PMCID: PMC11321979 DOI: 10.3389/fbioe.2024.1374135] [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: 01/21/2024] [Accepted: 07/01/2024] [Indexed: 08/16/2024] Open
Abstract
Background In an era of precision and stratified medicine, homogeneity in population-based cohorts, stringent causative entry, and pattern analysis of datasets are key elements to investigate medical treatments. Adhering to these principles, we collected in vivo and in vitro data pointing to an insulin-sensitizing/insulin-mimetic effect of myo-inositol (MYO) relevant to cell regeneration in dentistry and oral surgery. Confirmation of this possibility was obtained by in silico analysis of the relation between in vivo and in vitro results (the so-called bed-to-benchside reverse translational approach). Results Fourteen subjects over the 266 screened were young adult, normal weight, euglycemic, sedentary males having normal appetite, free diet, with a regular three-times-a-day eating schedule, standard dental hygiene, and negligible malocclusion/enamel defects. Occlusal caries were detected by fluorescence videoscanning, whereas body composition and energy balance were estimated with plicometry, predictive equations, and handgrip. Statistically significant correlations (Pearson r coefficient) were found between the number of occlusal caries and anthropometric indexes predicting insulin resistance (IR) in relation to the abdominal/visceral fat mass, fat-free mass, muscular strength, and energy expenditure adjusted to the fat and muscle stores. This indicated a role for IR in affecting dentin reparative processes. Consistently, in vitro administration of MYO to HUVEC and Swiss NIH3T3 cells in concentrations corresponding to those administered in vivo to reduce IR resulted in statistically significant cell replication (ANOVA/Turkey tests), suggesting that MYO has the potential to counteract inhibitory effects of IR on dental vascular and stromal cells turnover. Finally, in in silico experiments, quantitative evaluation (WOE and information value) of a bioinformatic Clinical Outcome Pathway confirmed that in vitro trophic effects of MYO could be transferred in vivo with high predictability, providing robust credence of its efficacy for oral health. Conclusion Our reverse bed-to-benchside data indicate that MYO might antagonize the detrimental effects of IR on tooth decay. This provides feasibility for clinical studies on MYO as a regenerative factor in dentistry and oral surgery, including dysmetabolic/aging conditions, bone reconstruction in oral destructive/necrotic disorders, dental implants, and for empowering the efficacy of a number of tissue engineering methodologies in dentistry and oral surgery.
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Affiliation(s)
- Fulvio Barbaro
- Department of Medicine and Surgery - DIMEC, Laboratory of Regenerative Morphology and Bioartificial Structures (Re.Mo.Bio.S.), Museum and Historical Library of Biomedicine - BIOMED, University of Parma, Parma, Italy
| | - Giusy Di Conza
- Department of Medicine and Surgery - DIMEC, Laboratory of Regenerative Morphology and Bioartificial Structures (Re.Mo.Bio.S.), Museum and Historical Library of Biomedicine - BIOMED, University of Parma, Parma, Italy
| | - Francesca Pia Quartulli
- Department of Medicine and Surgery - DIMEC, Laboratory of Regenerative Morphology and Bioartificial Structures (Re.Mo.Bio.S.), Museum and Historical Library of Biomedicine - BIOMED, University of Parma, Parma, Italy
| | - Enrico Quarantini
- Odontostomatology Unit, and R&D Center for Artificial Intelligence in Biomedicine and Odontostomatology (A.I.B.O), Galliera Medical Center, San Venanzio di Galliera, Italy
| | - Marco Quarantini
- Odontostomatology Unit, and R&D Center for Artificial Intelligence in Biomedicine and Odontostomatology (A.I.B.O), Galliera Medical Center, San Venanzio di Galliera, Italy
| | - Nicoletta Zini
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, Unit of Bologna, Bologna, Italy
| | - Celine Fabbri
- Course on Odontostomatology, University Vita-Salute San Raffaele, Milan, Italy
| | - Salvatore Mosca
- Course on Disorders of the Locomotor System, Fellow Program in Orthopaedics and Traumatology, University Vita-Salute San Raffaele, Milan, Italy
| | - Silvio Caravelli
- O.U. Orthopedics Bentivoglio, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Massimiliano Mosca
- O.U. Orthopedics Bentivoglio, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Paolo Vescovi
- Department of Medicine and Surgery - DIMEC, Odontostomatology Section, University of Parma, Parma, Italy
| | | | | | - Roberto Toni
- CNR - ISSMC, Faenza, Italy
- Academy of Sciences of the Institute of Bologna, Section IV - Medical Sciences, Bologna, Italy
- Endocrinology, Diabetes, and Nutrition Disorders Outpatient Clinic - OSTEONET (Osteoporosis, Nutrition, Endocrinology, and Innovative Therapies) and R&D Center A.I.B.O, Centro Medico Galliera, San Venanzio di Galliera, Italy
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Tufts Medical Center - Tufts University School of Medicine, Boston, MA, United States
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Liu F, Patt A, Chen C, Huang R, Xu Y, Mathé EA, Zhu Q. Exploring NCATS In-House Biomedical Data for Evidence-based Drug Repurposing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.550045. [PMID: 37546930 PMCID: PMC10401966 DOI: 10.1101/2023.07.21.550045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Drug repurposing is a strategy for identifying new uses of approved or investigational drugs that are outside the scope of the original medical indication. Even though many repurposed drugs have been found serendipitously in the past, the increasing availability of large volumes of biomedical data has enabled more systemic, data-driven approaches for drug candidate identification. At National Center of Advancing Translational Sciences (NCATS), we invent new methods to generate new data and information publicly available to spur innovation and scientific discovery. In this study, we aimed to explore and demonstrate biomedical data generated and collected via two NCATS research programs, the Toxicology in the 21st Century program (Tox21) and the Biomedical Data Translator (Translator) for the application of drug repurposing. These two programs provide complementary types of biomedical data from uncovering underlying biological mechanisms with bioassay screening data from Tox21 for chemical clustering, to enrich clustered chemicals with scientific evidence mined from the Translator towards drug repurposing. 129 chemical clusters have been generated and three of them have been further investigated for drug repurposing candidate identification, which is detailed as case studies.
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Affiliation(s)
- Fang Liu
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD
| | - Andrew Patt
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
| | - Chloe Chen
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD
| | - Ruili Huang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
| | - Yanji Xu
- Division of Rare Diseases Research Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD
| | - Ewy A Mathé
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
| | - Qian Zhu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD
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Integrated approach to elucidate metal-implant related adverse outcome pathways. Regul Toxicol Pharmacol 2022; 136:105277. [DOI: 10.1016/j.yrtph.2022.105277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
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Clerbaux LA, Albertini MC, Amigó N, Beronius A, Bezemer GFG, Coecke S, Daskalopoulos EP, del Giudice G, Greco D, Grenga L, Mantovani A, Muñoz A, Omeragic E, Parissis N, Petrillo M, Saarimäki LA, Soares H, Sullivan K, Landesmann B. Factors Modulating COVID-19: A Mechanistic Understanding Based on the Adverse Outcome Pathway Framework. J Clin Med 2022; 11:4464. [PMID: 35956081 PMCID: PMC9369763 DOI: 10.3390/jcm11154464] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 12/10/2022] Open
Abstract
Addressing factors modulating COVID-19 is crucial since abundant clinical evidence shows that outcomes are markedly heterogeneous between patients. This requires identifying the factors and understanding how they mechanistically influence COVID-19. Here, we describe how eleven selected factors (age, sex, genetic factors, lipid disorders, heart failure, gut dysbiosis, diet, vitamin D deficiency, air pollution and exposure to chemicals) influence COVID-19 by applying the Adverse Outcome Pathway (AOP), which is well-established in regulatory toxicology. This framework aims to model the sequence of events leading to an adverse health outcome. Several linear AOPs depicting pathways from the binding of the virus to ACE2 up to clinical outcomes observed in COVID-19 have been developed and integrated into a network offering a unique overview of the mechanisms underlying the disease. As SARS-CoV-2 infectibility and ACE2 activity are the major starting points and inflammatory response is central in the development of COVID-19, we evaluated how those eleven intrinsic and extrinsic factors modulate those processes impacting clinical outcomes. Applying this AOP-aligned approach enables the identification of current knowledge gaps orientating for further research and allows to propose biomarkers to identify of high-risk patients. This approach also facilitates expertise synergy from different disciplines to address public health issues.
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Affiliation(s)
- Laure-Alix Clerbaux
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | | | - Núria Amigó
- Biosfer Teslab SL., 43204 Reus, Spain;
- Department of Basic Medical Sciences, Universitat Rovira i Virgili (URV), 23204 Reus, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Anna Beronius
- Institute of Environmental Medicine, Karolinska Institutet, 17177 Stockholm, Sweden;
| | - Gillina F. G. Bezemer
- Impact Station, 1223 JR Hilversum, The Netherlands;
- Department of Pharmaceutical Sciences, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sandra Coecke
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Evangelos P. Daskalopoulos
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Giusy del Giudice
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Dario Greco
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Lucia Grenga
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, F-30200 Bagnols-sur-Ceze, France;
| | - Alberto Mantovani
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Amalia Muñoz
- European Commission, Joint Research Centre (JRC), 2440 Geel, Belgium;
| | - Elma Omeragic
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Nikolaos Parissis
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
| | - Laura A. Saarimäki
- Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE), Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (G.d.G.); (D.G.); (L.A.S.)
| | - Helena Soares
- Laboratory of Immunobiology and Pathogenesis, Chronic Diseases Research Centre, Faculdade de Ciências Médicas Medical School, University of Lisbon, 1649-004 Lisbon, Portugal;
| | - Kristie Sullivan
- Physicians Committee for Responsible Medicine, Washington, DC 20016, USA;
| | - Brigitte Landesmann
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (S.C.); (E.P.D.); (N.P.); (M.P.); (B.L.)
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