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Diez-Zaera M, Ruiz-Calvo A, Diaz-Hernandez JI, Sebastián-Serrano A, Aivar P, Alvarez-Castelao B, Pintor J, Diaz-Hernandez M, Miras-Portugal MT. Diadenosine pentaphosphate regulates dendrite growth and number in cultured hippocampal neurons. Purinergic Signal 2024; 20:115-125. [PMID: 37246192 PMCID: PMC10997559 DOI: 10.1007/s11302-023-09944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/11/2023] [Indexed: 05/30/2023] Open
Abstract
During the establishment of neuronal circuits, axons and dendrites grow and branch to establish specific synaptic connections. This complex process is highly regulated by positive and negative extracellular cues guiding the axons and dendrites. Our group was pioneer in describing that one of these signals are the extracellular purines. We found that extracellular ATP, through its selective ionotropic P2X7 receptor (P2X7R), negatively regulates axonal growth and branching. Here, we evaluate if other purinergic compounds, such as the diadenosine pentaphosphate (Ap5A), may module the dynamics of dendritic or axonal growth and branching in cultured hippocampal neurons. Our results show that Ap5A negatively modulates the dendrite's growth and number by inducing transient intracellular calcium increases in the dendrites' growth cone. Interestingly, phenol red, commonly used as a pH indicator in culture media, also blocks the P2X1 receptors, avoided the negative modulation of Ap5A on dendrites. Subsequent pharmacological studies using a battery of selective P2X1R antagonists confirmed the involvement of this subunit. In agreement with pharmacological studies, P2X1R overexpression caused a similar reduction in dendritic length and number as that induced by Ap5A. This effect was reverted when neurons were co-transfected with the vector expressing the interference RNA for P2X1R. Despite small hairpin RNAs reverting the reduction in the number of dendrites caused by Ap5A, it did not avoid the dendritic length decrease induced by the polyphosphate, suggesting, therefore, the involvement of a heteromeric P2X receptor. Our results are indicating that Ap5A exerts a negative influence on dendritic growth.
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Affiliation(s)
- M Diez-Zaera
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - A Ruiz-Calvo
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - J I Diaz-Hernandez
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - A Sebastián-Serrano
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - P Aivar
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
- Departamento Ciencia de La Salud, Facultad Ciencias Biomédicas y de La Salud, Universidad Europea de Madrid, 28670, Madrid, Spain
| | - B Alvarez-Castelao
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
| | - J Pintor
- Departamento de Bioquímica y Biología Molecular, Facultad de Óptica y Optometría, Universidad Complutense de Madrid, 28037, Madrid, Spain
| | - M Diaz-Hernandez
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain.
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, IdISSC, Madrid, Spain.
| | - M T Miras-Portugal
- Departamento de Bioquímica y Biología Molecular, Facultad de Veterinaria, Universidad Complutense de Madrid, Avda. Puerta de Hierro S/N, 28040, Madrid, Spain
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Jimenez-Guardeño JM, Ortega-Prieto AM, Menendez Moreno B, Maguire TJA, Richardson A, Diaz-Hernandez JI, Diez Perez J, Zuckerman M, Mercadal Playa A, Cordero Deline C, Malim MH, Martinez-Nunez RT. Drug repurposing based on a quantum-inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2. PLoS Comput Biol 2022; 18:e1010330. [PMID: 35849631 PMCID: PMC9333455 DOI: 10.1371/journal.pcbi.1010330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 07/28/2022] [Accepted: 06/27/2022] [Indexed: 01/18/2023] Open
Abstract
The COVID-19 pandemic has accelerated the need to identify new antiviral therapeutics at pace, including through drug repurposing. We employed a Quadratic Unbounded Binary Optimization (QUBO) model, to search for compounds similar to Remdesivir, the first antiviral against SARS-CoV-2 approved for human use, using a quantum-inspired device. We modelled Remdesivir and compounds present in the DrugBank database as graphs, established the optimal parameters in our algorithm and resolved the Maximum Weighted Independent Set problem within the conflict graph generated. We also employed a traditional Tanimoto fingerprint model. The two methods yielded different lists of lead compounds, with some overlap. While GS-6620 was the top compound predicted by both models, the QUBO model predicted BMS-986094 as second best. The Tanimoto model predicted different forms of cobalamin, also known as vitamin B12. We then determined the half maximal inhibitory concentration (IC50) values in cell culture models of SARS-CoV-2 infection and assessed cytotoxicity. We also demonstrated efficacy against several variants including SARS-CoV-2 Strain England 2 (England 02/2020/407073), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). Lastly, we employed an in vitro polymerization assay to demonstrate that these compounds directly inhibit the RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2. Together, our data reveal that our QUBO model performs accurate comparisons (BMS-986094) that differed from those predicted by Tanimoto (different forms of vitamin B12); all compounds inhibited replication of SARS-CoV-2 via direct action on RdRP, with both models being useful. While Tanimoto may be employed when performing relatively small comparisons, QUBO is also accurate and may be well suited for very complex problems where computational resources may limit the number and/or complexity of possible combinations to evaluate. Our quantum-inspired screening method can therefore be employed in future searches for novel pharmacologic inhibitors, thus providing an approach for accelerating drug deployment.
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Affiliation(s)
- Jose M. Jimenez-Guardeño
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ana Maria Ortega-Prieto
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - Thomas J. A. Maguire
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Adam Richardson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | | | - Javier Diez Perez
- Fujitsu Technology Solutions S.A., Pozuelo de Alarcón, Madrid, Spain
| | - Mark Zuckerman
- South London Virology Centre, King’s College Hospital, London, United Kingdom
| | | | | | - Michael H. Malim
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Rocio Teresa Martinez-Nunez
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
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Jimenez-Guardeño JM, Ortega-Prieto AM, Moreno BM, Maguire TJ, Richardson A, Diaz-Hernandez JI, Diez Perez J, Zuckerman M, Playa AM, Deline CC, Malim MH, Martinez-Nunez RT. Drug repurposing based on a Quantum-Inspired method versus classical fingerprinting uncovers potential antivirals against SARS-CoV-2 including vitamin B12. bioRxiv 2021:2021.06.25.449609. [PMID: 34401881 PMCID: PMC8366797 DOI: 10.1101/2021.06.25.449609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic has accelerated the need to identify new therapeutics at pace, including through drug repurposing. We employed a Quadratic Unbounded Binary Optimization (QUBO) model, to search for compounds similar to Remdesivir (RDV), the only antiviral against SARS-CoV-2 currently approved for human use, using a quantum-inspired device. We modelled RDV and compounds present in the DrugBank database as graphs, established the optimal parameters in our algorithm and resolved the Maximum Weighted Independent Set problem within the conflict graph generated. We also employed a traditional Tanimoto fingerprint model. The two methods yielded different lists of compounds, with some overlap. While GS-6620 was the top compound predicted by both models, the QUBO model predicted BMS-986094 as second best. The Tanimoto model predicted different forms of cobalamin, also known as vitamin B12. We then determined the half maximal inhibitory concentration (IC 50 ) values in cell culture models of SARS-CoV-2 infection and assessed cytotoxicity. Lastly, we demonstrated efficacy against several variants including SARS-CoV-2 Strain England 2 (England 02/2020/407073), B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). Our data reveal that BMS-986094 and different forms of vitamin B12 are effective at inhibiting replication of all these variants of SARS-CoV-2. While BMS-986094 can cause secondary effects in humans as established by phase II trials, these findings suggest that vitamin B12 deserves consideration as a SARS-CoV-2 antiviral, particularly given its extended use and lack of toxicity in humans, and its availability and affordability. Our screening method can be employed in future searches for novel pharmacologic inhibitors, thus providing an approach for accelerating drug deployment.
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Affiliation(s)
- Jose M. Jimenez-Guardeño
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Ana Maria Ortega-Prieto
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Borja Menendez Moreno
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Thomas J.A. Maguire
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Adam Richardson
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Juan Ignacio Diaz-Hernandez
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Javier Diez Perez
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Mark Zuckerman
- South London Virology Centre, King’s College Hospital, London (UK)
| | - Albert Mercadal Playa
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Carlos Cordero Deline
- Fujitsu Technology Solutions S.A., Camino del Cerro de los Gamos, 1, 28224, Pozuelo de Alarcón, Madrid (Spain)
| | - Michael H. Malim
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
| | - Rocio T Martinez-Nunez
- Dept Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London (UK)
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Fakhry M, Roszkowska M, Briolay A, Bougault C, Guignandon A, Diaz-Hernandez JI, Diaz-Hernandez M, Pikula S, Buchet R, Hamade E, Badran B, Bessueille L, Magne D. TNAP stimulates vascular smooth muscle cell trans-differentiation into chondrocytes through calcium deposition and BMP-2 activation: Possible implication in atherosclerotic plaque stability. Biochim Biophys Acta Mol Basis Dis 2016; 1863:643-653. [PMID: 27932058 DOI: 10.1016/j.bbadis.2016.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/12/2016] [Accepted: 12/04/2016] [Indexed: 01/15/2023]
Abstract
Atherosclerotic plaque calcification varies from early, diffuse microcalcifications to a bone-like tissue formed by endochondral ossification. Recently, a paradigm has emerged suggesting that if the bone metaplasia stabilizes the plaques, microcalcifications are harmful. Tissue-nonspecific alkaline phosphatase (TNAP), an ectoenzyme necessary for mineralization by its ability to hydrolyze inorganic pyrophosphate (PPi), is stimulated by inflammation in vascular smooth muscle cells (VSMCs). Our objective was to determine the role of TNAP in trans-differentiation of VSMCs and calcification. In rodent MOVAS and A7R5 VSMCs, addition of exogenous alkaline phosphatase (AP) or TNAP overexpression was sufficient to stimulate the expression of several chondrocyte markers and induce mineralization. Addition of exogenous AP to human mesenchymal stem cells cultured in pellets also stimulated chondrogenesis. Moreover, TNAP inhibition with levamisole in mouse primary chondrocytes dropped mineralization as well as the expression of chondrocyte markers. VSMCs trans-differentiated into chondrocyte-like cells, as well as primary chondrocytes, used TNAP to hydrolyze PPi, and PPi provoked the same effects as TNAP inhibition in primary chondrocytes. Interestingly, apatite crystals, associated or not to collagen, mimicked the effects of TNAP on VSMC trans-differentiation. AP and apatite crystals increased the expression of BMP-2 in VSMCs, and TNAP inhibition reduced BMP-2 levels in chondrocytes. Finally, the BMP-2 inhibitor noggin blocked the rise in aggrecan induced by AP in VSMCs, suggesting that TNAP induction in VSMCs triggers calcification, which stimulates chondrogenesis through BMP-2. Endochondral ossification in atherosclerotic plaques may therefore be induced by crystals, probably to confer stability to plaques with microcalcifications.
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Affiliation(s)
- Maya Fakhry
- Univ Lyon, University Lyon 1, ICBMS, UMR CNRS 5246, F-69622 Lyon, France; Lebanese University, Laboratory of Cancer Biology and Molecular Immunology, EDST-PRASE, Hadath-Beirut, Lebanon
| | - Monika Roszkowska
- Univ Lyon, University Lyon 1, ICBMS, UMR CNRS 5246, F-69622 Lyon, France; Laboratory of Biochemistry of Lipids, Department of Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - Anne Briolay
- Univ Lyon, University Lyon 1, ICBMS, UMR CNRS 5246, F-69622 Lyon, France
| | - Carole Bougault
- Univ Lyon, University Lyon 1, ICBMS, UMR CNRS 5246, F-69622 Lyon, France
| | - Alain Guignandon
- Univ Lyon, Université Jean Monnet Saint-Etienne, LBTO, UMR INSERM 1059, F-42023 Saint-Etienne, France
| | - Juan Ignacio Diaz-Hernandez
- Universidad Complutense de Madrid, Facultad de Veterinaria, Dpt. Bioquimica y Biologia Molecular IV, Madrid, Spain
| | - Miguel Diaz-Hernandez
- Universidad Complutense de Madrid, Facultad de Veterinaria, Dpt. Bioquimica y Biologia Molecular IV, Madrid, Spain
| | - Slawomir Pikula
- Laboratory of Biochemistry of Lipids, Department of Biochemistry, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | - René Buchet
- Univ Lyon, University Lyon 1, ICBMS, UMR CNRS 5246, F-69622 Lyon, France
| | - Eva Hamade
- Lebanese University, Laboratory of Cancer Biology and Molecular Immunology, EDST-PRASE, Hadath-Beirut, Lebanon
| | - Bassam Badran
- Lebanese University, Laboratory of Cancer Biology and Molecular Immunology, EDST-PRASE, Hadath-Beirut, Lebanon
| | | | - David Magne
- Univ Lyon, University Lyon 1, ICBMS, UMR CNRS 5246, F-69622 Lyon, France.
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Miras-Portugal MT, Gomez-Villafuertes R, Gualix J, Diaz-Hernandez JI, Artalejo AR, Ortega F, Delicado EG, Perez-Sen R. Nucleotides in neuroregeneration and neuroprotection. Neuropharmacology 2015; 104:243-54. [PMID: 26359530 DOI: 10.1016/j.neuropharm.2015.09.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 02/03/2023]
Abstract
Brain injury generates the release of a multitude of factors including extracellular nucleotides, which exhibit bi-functional properties and contribute to both detrimental actions in the acute phase and also protective and reparative actions in the later recovery phase to allow neuroregeneration. A promising strategy toward restoration of neuronal function is based on activation of endogenous adult neural stem/progenitor cells. The implication of purinergic signaling in stem cell biology, including regulation of proliferation, differentiation, and cell death has become evident in the last decade. In this regard, current strategies of acute transplantation of ependymal stem/progenitor cells after spinal cord injury restore altered expression of P2X4 and P2X7 receptors and improve functional locomotor recovery. The expression of both receptors is transcriptionally regulated by Sp1 factor, which plays a key role in the startup of the transcription machinery to induce regeneration-associated genes expression. Finally, general signaling pathways triggered by nucleotide receptors in neuronal populations converge on several intracellular kinases, such as PI3K/Akt, GSK3 and ERK1,2, as well as the Nrf-2/heme oxigenase-1 axis, which specifically link them to neuroprotection. In this regard, regulation of dual specificity protein phosphatases can become novel mechanism of actions for nucleotide receptors that associate them to cell homeostasis regulation. This article is part of the Special Issue entitled 'Purines in Neurodegeneration and Neuroregeneration'.
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Affiliation(s)
- M Teresa Miras-Portugal
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
| | - Rosa Gomez-Villafuertes
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain.
| | - Javier Gualix
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
| | - Juan Ignacio Diaz-Hernandez
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
| | - Antonio R Artalejo
- Department of Toxicology and Pharmacology, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
| | - Felipe Ortega
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
| | - Esmerilda G Delicado
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
| | - Raquel Perez-Sen
- Department of Biochemistry and Molecular Biology IV, Veterinary School, Universidad Complutense of Madrid, 28040 Madrid, Spain
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Diaz-Hernandez JI, Moncada S, Bolaños JP, Almeida A. Poly(ADP-ribose) polymerase-1 protects neurons against apoptosis induced by oxidative stress. Cell Death Differ 2007; 14:1211-21. [PMID: 17347665 DOI: 10.1038/sj.cdd.4402117] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In neurons, DNA is prone to free radical damage, although repair mechanisms preserve the genomic integrity. However, activation of the DNA repair system, poly(ADP-ribose) polymerase (PARP-1), is thought to cause neuronal death through NAD+ depletion and mitochondrial membrane potential (delta psi(m)) depolarization. Here, we show that abolishing PARP-1 activity in primary cortical neurons can either enhance or prevent apoptotic death, depending on the intensity of an oxidative stress. Only in severe oxidative stress does PARP-1 activation result in NAD+ and ATP depletion and neuronal death. To investigate the role of PARP-1 in an endogenous model of oxidative stress, we used an RNA interference (RNAi) strategy to specifically knock down glutamate-cysteine ligase (GCL), the rate-limiting enzyme of glutathione biosynthesis. GCL RNAi spontaneously elicited a mild type of oxidative stress that was enough to stimulate PARP-1 in a Ca2+-calmodulin kinase II-dependent manner. GCL RNAi-mediated PARP-1 activation facilitated DNA repair, although neurons underwent delta psi(m) loss followed by some apoptotic death. PARP-1 inhibition did not prevent delta psi(m) loss, but enhanced the vulnerability of neurons to apoptosis upon GCL silencing. Conversely, mild expression of PARP-1 partially prevented to GCL RNAi-dependent apoptosis. Thus, in the mild progressive damage likely occur in neurodegenerative diseases, PARP-1 activation plays a neuroprotective role that should be taken into account when considering therapeutic strategies.
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Affiliation(s)
- J I Diaz-Hernandez
- Unidad de Investigación, Hospital Universitario de Salamanca-Instituto de Estudios Ciencias de la Salud de Castilla y León, Salamanca, Spain
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