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Angarita-Rodríguez A, Matiz-González JM, Pinzón A, Aristizabal AF, Ramírez D, Barreto GE, González J. Enzymatic Metabolic Switches of Astrocyte Response to Lipotoxicity as Potential Therapeutic Targets for Nervous System Diseases. Pharmaceuticals (Basel) 2024; 17:648. [PMID: 38794218 PMCID: PMC11124372 DOI: 10.3390/ph17050648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Astrocytes play a pivotal role in maintaining brain homeostasis. Recent research has highlighted the significance of palmitic acid (PA) in triggering pro-inflammatory pathways contributing to neurotoxicity. Furthermore, Genomic-scale metabolic models and control theory have revealed that metabolic switches (MSs) are metabolic pathway regulators by potentially exacerbating neurotoxicity, thereby offering promising therapeutic targets. Herein, we characterized these enzymatic MSs in silico as potential therapeutic targets, employing protein-protein and drug-protein interaction networks alongside structural characterization techniques. Our findings indicate that five MSs (P00558, P04406, Q08426, P09110, and O76062) were functionally linked to nervous system drug targets and may be indirectly regulated by specific neurological drugs, some of which exhibit polypharmacological potential (e.g., Trifluperidol, Trifluoperazine, Disulfiram, and Haloperidol). Furthermore, four MSs (P00558, P04406, Q08426, and P09110) feature ligand-binding or allosteric cavities with druggable potential. Our results advocate for a focused exploration of P00558 (phosphoglycerate kinase 1), P04406 (glyceraldehyde-3-phosphate dehydrogenase), Q08426 (peroxisomal bifunctional enzyme, enoyl-CoA hydratase, and 3-hydroxyacyl CoA dehydrogenase), P09110 (peroxisomal 3-ketoacyl-CoA thiolase), and O76062 (Delta(14)-sterol reductase) as promising targets for the development or repurposing of pharmacological compounds, which could have the potential to modulate lipotoxic-altered metabolic pathways, offering new avenues for the treatment of related human diseases such as neurological diseases.
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Affiliation(s)
- Andrea Angarita-Rodríguez
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - J. Manuel Matiz-González
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá 110121, Colombia
| | - Andrés Pinzón
- Laboratorio de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Andrés Felipe Aristizabal
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - George E. Barreto
- Department of Biological Sciences, University of Limerick, V94 T9PX Limerick, Ireland
- Health Research Institute, University of Limerick, V94 T9PX Limerick, Ireland
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
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2
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Kwofie SK, Adobor C, Quansah E, Bentil J, Ampadu M, Miller WA, Wilson MD. Molecular docking and dynamics simulations studies of OmpATb identifies four potential novel natural product-derived anti-Mycobacterium tuberculosis compounds. Comput Biol Med 2020; 122:103811. [PMID: 32479349 DOI: 10.1016/j.compbiomed.2020.103811] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 11/18/2022]
Abstract
The outer membrane protein A (OmpATb) of Mycobacterium tuberculosis is a virulence factor that neutralizes the host pH to impede the uptake of hydrophilic antitubercular drugs. Identifying natural compounds with the potential to inhibit OmpATb could allow circumvention of the porin-like activities of OmpATb. Four potential leads comprising ZINC000003958185, ZINC000000157405, ZINC000000001392 and ZINC000034268676 were obtained by virtual screening of 6394 diverse natural products. Characterization of the binding interactions of the potential leads with OmpATb revealed nine critical residues comprising ARG86, LEU110, LEU113, LEU114, ALA115, PHE142, SER145, VAL146, and PHE151. Molecular dynamics simulations also revealed very stable protein-lead complexes. Most residues contributed lower binding energies to the overall molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energies of the interactions between the molecules and OmpATb protein. Induced Fit Docking (IFD) of the compounds regenerated poses of the molecular docking using AutoDock Vina. These molecules could be starting templates for designing inhibitors to bypass the pore mediating activities of OmpATb. Based on structural similarity, ZINC000034268676 was suggested as a potential scaffold for designing efflux pump inhibitors of the gate mediating activities of OmpATb and may enhance the uptake of hydrophilic drugs to reduce the duration time of tuberculosis treatment. Furthermore, structurally similar compounds available in the DrugBank database with a similarity threshold of 0.7 have been reported to exhibit antitubercular and anti-mycobacterial activities. These biomolecules can be further characterized experimentally to corroborate their antitubercular activity. Also, the skeletons of the molecules can be adopted as sub-structures for the design of future anti-mycobacterial drugs.
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Affiliation(s)
- Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana; West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana; Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA; Department of Physics and Engineering Science, Coastal Carolina University, Conway, SC, 29528, USA.
| | - Courage Adobor
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana; Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Erasmus Quansah
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Joana Bentil
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Michael Ampadu
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, PMB LG 77, Legon, Accra, Ghana
| | - Whelton A Miller
- Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA; Department of Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael D Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana; Department of Medicine, Loyola University Medical Center, Maywood, IL, 60153, USA
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3
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Monticelli M, Liguori L, Allocca M, Andreotti G, Cubellis MV. β-Glucose-1,6-Bisphosphate Stabilizes Pathological Phophomannomutase2 Mutants In Vitro and Represents a Lead Compound to Develop Pharmacological Chaperones for the Most Common Disorder of Glycosylation, PMM2-CDG. Int J Mol Sci 2019; 20:E4164. [PMID: 31454904 PMCID: PMC6747070 DOI: 10.3390/ijms20174164] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/13/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
A large number of mutations causing PMM2-CDG, which is the most frequent disorder of glycosylation, destabilize phosphomannomutase2. We looked for a pharmacological chaperone to cure PMM2-CDG, starting from the structure of a natural ligand of phosphomannomutase2, α-glucose-1,6-bisphosphate. The compound, β-glucose-1,6-bisphosphate, was synthesized and characterized via 31P-NMR. β-glucose-1,6-bisphosphate binds its target enzyme in silico. The binding induces a large conformational change that was predicted by the program PELE and validated in vitro by limited proteolysis. The ability of the compound to stabilize wild type phosphomannomutase2, as well as frequently encountered pathogenic mutants, was measured using thermal shift assay. β-glucose-1,6-bisphosphate is relatively resistant to the enzyme that specifically hydrolyses natural esose-bisphosphates.
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Affiliation(s)
- Maria Monticelli
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
| | - Ludovica Liguori
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
- Istituto di Chimica Biomolecolare-CNR, 80078 Pozzuoli, Italy
| | - Mariateresa Allocca
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università degli Studi della Campania "Luigi Vanvitelli", 81100 Caserta, Italy
- Istituto di Chimica Biomolecolare-CNR, 80078 Pozzuoli, Italy
| | | | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy
- Istituto di Chimica Biomolecolare-CNR, 80078 Pozzuoli, Italy
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4
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Chitrala KN, Yang X, Busbee B, Singh NP, Bonati L, Xing Y, Nagarkatti P, Nagarkatti M. Computational prediction and in vitro validation of VEGFR1 as a novel protein target for 2,3,7,8-tetrachlorodibenzo-p-dioxin. Sci Rep 2019; 9:6810. [PMID: 31048752 PMCID: PMC6497656 DOI: 10.1038/s41598-019-43232-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
The toxic manifestations of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an environmental contaminant, primarily depend on its ability to activate aryl hydrocarbon receptor (AhR), which is a ligand-dependent transcription factor belonging to the superfamily of basic-helix-loop-helix DNA-binding proteins. In the present study, we aimed to identify novel protein receptor targets for TCDD using computational and in vitro validation experiments. Interestingly, results from computational methods predicted that Vascular Endothelial Growth Factor Receptor 1 (VEGFR1) could be one of the potential targets for TCDD in both mouse and humans. Results from molecular docking studies showed that human VEGFR1 (hVEGFR1) has less affinity towards TCDD compared to the mouse VEGFR1 (mVEGFR1). In vitro validation results showed that TCDD can bind and phosphorylate hVEGFR1. Further, results from molecular dynamic simulation studies showed that hVEGFR1 interaction with TCDD is stable throughout the simulation time. Overall, the present study has identified VEGFR1 as a novel target for TCDD, which provides the basis for further elucidating the role of TCDD in angiogenesis.
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Affiliation(s)
- Kumaraswamy Naidu Chitrala
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
| | - Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
| | - Brandon Busbee
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
| | - Narendra P Singh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
| | - Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Yongna Xing
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, 29208, USA.
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5
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Kana O, Brylinski M. Elucidating the druggability of the human proteome with eFindSite. J Comput Aided Mol Des 2019; 33:509-519. [PMID: 30888556 PMCID: PMC6516084 DOI: 10.1007/s10822-019-00197-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/12/2019] [Indexed: 01/12/2023]
Abstract
Identifying the viability of protein targets is one of the preliminary steps of drug discovery. Determining the ability of a protein to bind drugs in order to modulate its function, termed the druggability, requires a non-trivial amount of time and resources. Inability to properly measure druggability has accounted for a significant portion of failures in drug discovery. This problem is only further exacerbated by the large sample space of proteins involved in human diseases. With these barriers, the druggability space within the human proteome remains unexplored and has made it difficult to develop drugs for numerous diseases. Hence, we present a new feature developed in eFindSite that employs supervised machine learning to predict the druggability of a given protein. Benchmarking calculations against the Non-Redundant data set of Druggable and Less Druggable binding sites demonstrate that an AUC for druggability prediction with eFindSite is as high as 0.88. With eFindSite, we elucidated the human druggability space to be 10,191 proteins. Considering the disease space from the Open Targets Platform and excluding already known targets from the predicted data set reveal 2731 potentially novel therapeutic targets. eFindSite is freely available as a stand-alone software at https://github.com/michal-brylinski/efindsite .
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Affiliation(s)
- Omar Kana
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
- Center for Computation & Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
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6
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The Analysis of Variants in the General Population Reveals That PMM2 Is Extremely Tolerant to Missense Mutations and That Diagnosis of PMM2-CDG Can Benefit from the Identification of Modifiers. Int J Mol Sci 2018; 19:ijms19082218. [PMID: 30061496 PMCID: PMC6121245 DOI: 10.3390/ijms19082218] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/19/2018] [Accepted: 07/26/2018] [Indexed: 12/11/2022] Open
Abstract
Type I disorders of glycosylation (CDG), the most frequent of which is phosphomannomutase 2 (PMM2-CDG), are a group of diseases causing the incomplete N-glycosylation of proteins. PMM2-CDG is an autosomal recessive disease with a large phenotypic spectrum, and is associated with mutations in the PMM2 gene. The biochemical analysis of mutants does not allow a precise genotype⁻phenotype correlation for PMM2-CDG. PMM2 is very tolerant to missense and loss of function mutations, suggesting that a partial deficiency of activity might be beneficial under certain circumstances. The patient phenotype might be influenced by variants in other genes associated with the type I disorders of glycosylation in the general population.
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7
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Computational Modeling of the Staphylococcal Enterotoxins and Their Interaction with Natural Antitoxin Compounds. Int J Mol Sci 2018; 19:ijms19010133. [PMID: 29301344 PMCID: PMC5796082 DOI: 10.3390/ijms19010133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 01/08/2023] Open
Abstract
Staphylococcus aureus is an opportunistic bacterium that produces various types of toxins, resulting in serious food poisoning. Staphylococcal enterotoxins (SEs) are heat-stable and resistant to hydrolysis by digestive enzymes, representing a potential hazard for consumers worldwide. In the present study, we used amino-acid sequences encoding SEA and SEB-like to identify their respective template structure and build the three-dimensional (3-D) models using homology modeling method. Two natural compounds, Betulin and 28-Norolean-12-en-3-one, were selected for docking study on the basis of the criteria that they satisfied the Lipinski’s Rule-of-Five. A total of 14 and 13 amino-acid residues were present in the best binding site predicted in the SEA and SEB-like, respectively, using the Computer Atlas of Surface Topology of Proteins (CASTp). Among these residues, the docking study with natural compounds Betulin and 28-Norolean-12-en-3-one revealed that GLN43 and GLY227 in the binding site of the SEA, each formed a hydrogen-bond interaction with 28-Norolean-12-en-3-one; while GLY227 residue established a hydrogen bond with Betulin. In the case of SEB-like, the docking study demonstrated that ASN87 and TYR88 residues in its binding site formed hydrogen bonds with Betulin; whereas HIS59 in the binding site formed a hydrogen-bond interaction with 28-Norolean-12-en-3-one. Our results demonstrate that the toxic effects of these two SEs can be effectively treated with antitoxins like Betulin and 28-Norolean-12-en-3-one, which could provide an effective drug therapy for this pathogen.
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Citro V, Cimmaruta C, Liguori L, Viscido G, Cubellis MV, Andreotti G. A mutant of phosphomannomutase1 retains full enzymatic activity, but is not activated by IMP: Possible implications for the disease PMM2-CDG. PLoS One 2017; 12:e0189629. [PMID: 29261720 PMCID: PMC5736207 DOI: 10.1371/journal.pone.0189629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/29/2017] [Indexed: 11/18/2022] Open
Abstract
The most frequent disorder of glycosylation, PMM2-CDG, is caused by a deficiency of phosphomannomutase activity. In humans two paralogous enzymes exist, both of them require mannose 1,6-bis-phosphate or glucose 1,6-bis-phosphate as activators, but only phospho-mannomutase1 hydrolyzes bis-phosphate hexoses. Mutations in the gene encoding phosphomannomutase2 are responsible for PMM2-CDG. Although not directly causative of the disease, the role of the paralogous enzyme in the disease should be clarified. Phosphomannomutase1 could have a beneficial effect, contributing to mannose 6-phosphate isomerization, or a detrimental effect, hydrolyzing the bis-phosphate hexose activator. A pivotal role in regulating mannose-1phosphate production and ultimately protein glycosylation might be played by inosine monophosphate that enhances the phosphatase activity of phosphomannomutase1. In this paper we analyzed human phosphomannomutases by conventional enzymatic assays as well as by novel techniques such as 31P-NMR and thermal shift assay. We characterized a triple mutant of phospomannomutase1 that retains mutase and phosphatase activity, but is unable to bind inosine monophosphate.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
| | | | - Ludovica Liguori
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, Italy
- Dipartimento di scienze e tecnologie ambientali, biologiche e farmaceutiche, Università della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Gaetano Viscido
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, Italy
- * E-mail:
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E-Learning for Rare Diseases: An Example Using Fabry Disease. Int J Mol Sci 2017; 18:ijms18102049. [PMID: 28946642 PMCID: PMC5666731 DOI: 10.3390/ijms18102049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 12/23/2022] Open
Abstract
Background: Rare diseases represent a challenge for physicians because patients are rarely seen, and they can manifest with symptoms similar to those of common diseases. In this work, genetic confirmation of diagnosis is derived from DNA sequencing. We present a tutorial for the molecular analysis of a rare disease using Fabry disease as an example. Methods: An exonic sequence derived from a hypothetical male patient was matched against human reference data using a genome browser. The missense mutation was identified by running BlastX, and information on the affected protein was retrieved from the database UniProt. The pathogenic nature of the mutation was assessed with PolyPhen-2. Disease-specific databases were used to assess whether the missense mutation led to a severe phenotype, and whether pharmacological therapy was an option. Results: An inexpensive bioinformatics approach is presented to get the reader acquainted with the diagnosis of Fabry disease. The reader is introduced to the field of pharmacological chaperones, a therapeutic approach that can be applied only to certain Fabry genotypes. Conclusion: The principle underlying the analysis of exome sequencing can be explained in simple terms using web applications and databases which facilitate diagnosis and therapeutic choices.
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Citro V, Cammisa M, Liguori L, Cimmaruta C, Lukas J, Cubellis MV, Andreotti G. The Large Phenotypic Spectrum of Fabry Disease Requires Graduated Diagnosis and Personalized Therapy: A Meta-Analysis Can Help to Differentiate Missense Mutations. Int J Mol Sci 2016; 17:ijms17122010. [PMID: 27916943 PMCID: PMC5187810 DOI: 10.3390/ijms17122010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/23/2016] [Accepted: 11/24/2016] [Indexed: 12/28/2022] Open
Abstract
Fabry disease is caused by mutations in the GLA gene and is characterized by a large genotypic and phenotypic spectrum. Missense mutations pose a special problem for graduating diagnosis and choosing a cost-effective therapy. Some mutants retain enzymatic activity, but are less stable than the wild type protein. These mutants can be stabilized by small molecules which are defined as pharmacological chaperones. The first chaperone to reach clinical trial is 1-deoxygalactonojirimycin, but others have been tested in vitro. Residual activity of GLA mutants has been measured in the presence or absence of pharmacological chaperones by several authors. Data obtained from transfected cells correlate with those obtained in cells derived from patients, regardless of whether 1-deoxygalactonojirimycin was present or not. The extent to which missense mutations respond to 1-deoxygalactonojirimycin is variable and a reference table of the results obtained by independent groups that is provided with this paper can facilitate the choice of eligible patients. A review of other pharmacological chaperones is provided as well. Frequent mutations can have residual activity as low as one-fourth of normal enzyme in vitro. The reference table with residual activity of the mutants facilitates the identification of non-pathological variants.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy.
| | - Marco Cammisa
- Istituto di Genetica e Biofisica 'A. Buzzati-Traverso', CNR, 80131 Napoli, Italy.
| | | | - Chiara Cimmaruta
- Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy.
- Istituto di Chimica Biomolecolare, CNR, 80078 Pozzuoli, Italy.
| | - Jan Lukas
- Albrecht-Kossel-Institute for Neuroregeneration, University Rostock Medical Center, 18147 Rostock, Germany.
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11
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Citro V, Peña-García J, den-Haan H, Pérez-Sánchez H, Del Prete R, Liguori L, Cimmaruta C, Lukas J, Cubellis MV, Andreotti G. Identification of an Allosteric Binding Site on Human Lysosomal Alpha-Galactosidase Opens the Way to New Pharmacological Chaperones for Fabry Disease. PLoS One 2016; 11:e0165463. [PMID: 27788225 PMCID: PMC5082870 DOI: 10.1371/journal.pone.0165463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 10/12/2016] [Indexed: 12/19/2022] Open
Abstract
Personalized therapies are required for Fabry disease due to its large phenotypic spectrum and numerous different genotypes. In principle, missense mutations that do not affect the active site could be rescued with pharmacological chaperones. At present pharmacological chaperones for Fabry disease bind the active site and couple a stabilizing effect, which is required, to an inhibitory effect, which is deleterious. By in silico docking we identified an allosteric hot-spot for ligand binding where a drug-like compound, 2,6-dithiopurine, binds preferentially. 2,6-dithiopurine stabilizes lysosomal alpha-galactosidase in vitro and rescues a mutant that is not responsive to a mono-therapy with previously described pharmacological chaperones, 1-deoxygalactonojirimycin and galactose in a cell based assay.
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Affiliation(s)
- Valentina Citro
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
| | - Jorge Peña-García
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Spain
| | - Helena den-Haan
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Spain
| | - Horacio Pérez-Sánchez
- Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica San Antonio de Murcia (UCAM), Spain
- * E-mail: (MVC); (HPS)
| | - Rosita Del Prete
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
| | - Ludovica Liguori
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, 80078, Italy
| | - Chiara Cimmaruta
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
- Istituto di Chimica Biomolecolare–CNR, Pozzuoli, 80078, Italy
| | - Jan Lukas
- Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, Napoli, 80126, Italy
- * E-mail: (MVC); (HPS)
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12
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Abstract
Many mutations responsible of Fabry disease destabilize lysosomal alpha-galactosidase, but retain the enzymatic activity. These mutations are associated to a milder phenotype and are potentially curable with a pharmacological therapy either with chaperones or with drugs that modulate proteostasis. We demonstrate the effectiveness of molecular dynamics simulations to correlate the genotype to the severity of the disease. We studied the relation between protein flexibility and residual enzymatic activity of pathological missense mutants in the cell. We found that mutations occurring at flexible sites are likely to retain activity in vivo. The usefulness of molecular dynamics for diagnostic purposes is not limited to lysosomal galactosidase because destabilizing mutations are widely encountered in other proteins, too, and represent a large share of all the ones associated to human diseases. Residual alpha-galactosidase activity may relate to mild phenotype in Fabry disease. Molecular dynamics identifies flexible residues in lysosomal alpha-galactosidase. Mutations at flexible sites tend to maintain residual alpha-galactosidase activity.
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Andreotti G, Cabeza de Vaca I, Poziello A, Monti MC, Guallar V, Cubellis MV. Conformational response to ligand binding in phosphomannomutase2: insights into inborn glycosylation disorder. J Biol Chem 2014; 289:34900-10. [PMID: 25324542 PMCID: PMC4263888 DOI: 10.1074/jbc.m114.586362] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The most common glycosylation disorder is caused by mutations in the gene encoding phosphomannomutase2, producing a disease still without a cure. Phosphomannomutase2, a homodimer in which each chain is composed of two domains, requires a bisphosphate sugar (either mannose or glucose) as activator, opening a possible drug design path for therapeutic purposes. The crystal structure of human phosphomannomutase2, however, lacks bound substrate and a key active site loop. To speed up drug discovery, we present here the first structural model of a bisphosphate substrate bound to human phosphomannomutase2. Taking advantage of recent developments in all-atom simulation techniques in combination with limited and site-directed proteolysis, we demonstrated that α-glucose 1,6-bisphosphate can adopt two low energy orientations as required for catalysis. Upon ligand binding, the two domains come close, making the protein more compact, in analogy to the enzyme in the crystals from Leishmania mexicana. Moreover, proteolysis was also carried out on two common mutants, R141H and F119L. It was an unexpected finding that the mutant most frequently found in patients, R141H, although inactive, does bind α-glucose 1,6-bisphosphate and changes conformation.
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Affiliation(s)
- Giuseppina Andreotti
- From the Istituto di Chimica Biomolecolare-Consiglio Nazionale Delle Ricerche, 80078 Pozzuoli, Italy
| | - Israel Cabeza de Vaca
- Joint Barcelona Supercomputing Center-Center for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain
| | - Angelita Poziello
- From the Istituto di Chimica Biomolecolare-Consiglio Nazionale Delle Ricerche, 80078 Pozzuoli, Italy, Dipartimento di Biologia, Università Federico II, 80126 Naples, Italy
| | - Maria Chiara Monti
- Dipartimento di Farmacia, Università degli Studi di Salerno, 84084 Fisciano, Italy
| | - Victor Guallar
- Joint Barcelona Supercomputing Center-Center for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29, 08034 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08010 Barcelona, Spain, and
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Azzollini J, Rovina D, Gervasini C, Parenti I, Fratoni A, Cubellis MV, Cerri A, Pietrogrande L, Larizza L. Functional characterisation of a novel mutation affecting the catalytic domain of MMP2 in siblings with multicentric osteolysis, nodulosis and arthropathy. J Hum Genet 2014; 59:631-7. [PMID: 25273674 DOI: 10.1038/jhg.2014.84] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 01/16/2023]
Abstract
Multicentric osteolysis, nodulosis and arthropathy (MONA) is a rare autosomal recessive disorder. To date, 13 mutations of the matrix metalloproteinase 2 (MMP2) gene have been detected in 26 patients with MONA and other osteolytic syndromes. Here, we describe the molecular and functional analysis of a novel MMP2 mutation in two adult Italian siblings with MONA. Both siblings displayed palmar-plantar subcutaneous nodules, tendon retractions, limb arthropathies, osteolysis in the toes and pigmented fibrous skin lesions. Molecular analysis identified a homozygous MMP2 missense mutation in exon 8 c.1228G>C (p.G410R), not detected in 260 controls and predicted by several bioinformatic tools to be pathogenic. By protein modelling, the mutant residue was predicted to affect the main chain conformation of the catalytic domain. Gelatin zymography, the gold standard test for MMP2 function, of serum-free conditioned medium from G410R-MMP2-expressing human embryonic kidney (HEK) cells, showed a complete loss of gelatinolytic activity. The novel mutation is located in the catalytic domain, as are 3 (p.E404K, p.V400del and p.G406D) of the other 13 MMP2 mutations described to date; however, p.G410R underlies a phenotype that is only partially overlapping that of other MMP2 exon 8 mutation carriers. Our results further delineate the complexity of genotype-phenotype correlations in MONA, broaden the repertoire of reported MMP2 mutation and enhance the comprehension of the protein motifs crucial for MMP2 catalytic activity.
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Affiliation(s)
- Jacopo Azzollini
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Ilaria Parenti
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | - Alessia Fratoni
- Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy
| | | | - Amilcare Cerri
- Dermatologic Unit, Department of Health Sciences, San Paolo Hospital, University of Milan, Milan, Italy
| | - Luca Pietrogrande
- Operative Unit of Orthopaedics and Traumatology, Department of Health Sciences, San Paolo Hospital, University of Milan, Milan, Italy
| | - Lidia Larizza
- 1] Medical Genetics, Department of Health Sciences, University of Milan, Milan, Italy [2] Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Milan, Italy
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Andreotti G, Citro V, Correra A, Cubellis MV. A thermodynamic assay to test pharmacological chaperones for Fabry disease. Biochim Biophys Acta Gen Subj 2013; 1840:1214-24. [PMID: 24361605 PMCID: PMC3909460 DOI: 10.1016/j.bbagen.2013.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 12/04/2013] [Accepted: 12/11/2013] [Indexed: 12/29/2022]
Abstract
Background The majority of the disease-causing mutations affect protein stability, but not functional sites and are amenable, in principle, to be treated with pharmacological chaperones. These drugs enhance the thermodynamic stability of their targets. Fabry disease, a disorder caused by mutations in the gene encoding lysosomal alpha-galactosidase, represents an excellent model system to develop experimental protocols to test the efficiency of such drugs. Methods The stability of lysosomal alpha-galactosidase under different conditions was studied by urea-induced unfolding followed by limited proteolysis and Western blotting. Results We measured the concentration of urea needed to obtain half-maximal unfolding because this parameter represents an objective indicator of protein stability. Conclusions Urea-induced unfolding is a versatile technique that can be adapted to cell extracts containing tiny amounts of wild-type or mutant proteins. It allows testing of protein stability as a function of pH, in the presence or in the absence of drugs. Results are not influenced by the method used to express the protein in transfected cells. General significance Scarce and dispersed populations pose a problem for the clinical trial of drugs for rare diseases. This is particularly true for pharmacological chaperones that must be tested on each mutation associated with a given disease. Diverse in vitro tests are needed. We used a method based on chemically induced unfolding as a tool to assess whether a particular Fabry mutation is responsive to pharmacological chaperones, but, by no means is our protocol limited to this disease. Pharmacological chaperones stabilize the folded state of proteins. Only some Fabry mutations can be treated with pharmacological chaperones. Urea-induced unfolding represents a novel assay to test the efficiency of drugs. The test with urea can be applied to a tiny amount of mutants in raw extracts. Responsiveness of Fabry mutations to drugs can be tested with urea-induced unfolding.
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Affiliation(s)
| | - Valentina Citro
- Istituto di Genetica e Biofisica 'A. Buzzati Traverso,' CNR, Napoli, Italy.
| | - Antonella Correra
- Istituto di Genetica e Biofisica 'A. Buzzati Traverso,' CNR, Napoli, Italy; Dipartimento di Biologia, Università Federico II, Napoli, Italy.
| | - Maria Vittoria Cubellis
- Dipartimento di Biologia, Università Federico II, Napoli, Italy; Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy.
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Cammisa M, Correra A, Andreotti G, Cubellis MV. Fabry_CEP: a tool to identify Fabry mutations responsive to pharmacological chaperones. Orphanet J Rare Dis 2013; 8:111. [PMID: 23883437 PMCID: PMC3729670 DOI: 10.1186/1750-1172-8-111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Accepted: 06/20/2013] [Indexed: 01/12/2023] Open
Abstract
Fabry_CEP is a user-friendly web-application designed to help clinicians Choose Eligible Patients for the therapy with pharmacological chaperones. It provides a database and a predictive tool to evaluate the responsiveness of lysosomal alpha-galactosidase mutants to a small molecule drug, namely 1-Deoxy-galactonojirimycin. The user can introduce any missense/nonsense mutation in the coding sequence, learn whether it is has been tested and gain access to appropriate reference literature. In the absence of experimental data structural, functional and evolutionary analysis provides a prediction and the probability that a given mutation is responsive to the drug.
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Affiliation(s)
- Marco Cammisa
- Dipartimento di Biologia, Università Federico II, Napoli, Italy
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Gissi C, Romano P, Ferro A, Giugno R, Pulvirenti A, Facchiano A, Helmer-Citterich M. Bioinformatics in Italy: BITS2012, the ninth annual meeting of the Italian Society of Bioinformatics. BMC Bioinformatics 2013; 14 Suppl 7:S1. [PMID: 23815154 PMCID: PMC3633006 DOI: 10.1186/1471-2105-14-s7-s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The BITS2012 meeting, held in Catania on May 2-4, 2012, brought together almost 100 Italian researchers working in the field of Bioinformatics, as well as students in the same or related disciplines. About 90 original research works were presented either as oral communication or as posters, representing a landscape of Italian current research in bioinformatics. This preface provides a brief overview of the meeting and introduces the manuscripts that were accepted for publication in this supplement, after a strict and careful peer-review by an International board of referees.
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