1
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Rojas-Prats E, Martinez-Gonzalez L, Gil C, Ramírez D, Martinez A. Druggable cavities and allosteric modulators of the cell division cycle 7 (CDC7) kinase. J Enzyme Inhib Med Chem 2024; 39:2301767. [PMID: 38205514 PMCID: PMC10786434 DOI: 10.1080/14756366.2024.2301767] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Cell division cycle 7 kinase (CDC7) has been found overexpressed in many cancer cell lines being also one of the kinases involved in the nuclear protein TDP-43 phosphorylation in vivo. Thus, inhibitors of CDC7 are emerging drug candidates for the treatment of oncological and neurodegenerative unmet diseases. All the known CDC7 inhibitors are ATP-competitives, lacking of selectivity enough for success in clinical trials. As allosteric sites are less conserved among kinase proteins, discovery of allosteric modulators of CDC7 is a great challenge and opportunity in this field.Using different computational approaches, we have here identified new druggable cavities on the human CDC7 structure and subsequently selective CDC7 inhibitors with allosteric modulation mainly targeting the pockets where the interaction between this kinase and its activator DBF4 takes place.
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Affiliation(s)
- Elisa Rojas-Prats
- Centro de Investigaciones Biológicas -Margarita Salas-CSIC, Madrid, Spain
| | - Loreto Martinez-Gonzalez
- Centro de Investigaciones Biológicas -Margarita Salas-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de 13 Salud Carlos III, Madrid, Spain
| | - Carmen Gil
- Centro de Investigaciones Biológicas -Margarita Salas-CSIC, Madrid, Spain
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Ana Martinez
- Centro de Investigaciones Biológicas -Margarita Salas-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de 13 Salud Carlos III, Madrid, Spain
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2
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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 DOI: 10.3390/ph17050648] [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] [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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3
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Feijoo-Coronel ML, Mendes B, Ramírez D, Peña-Varas C, de los Monteros-Silva NQE, Proaño-Bolaños C, de Oliveira LC, Lívio DF, da Silva JA, da Silva JMSF, Pereira MGAG, Rodrigues MQRB, Teixeira MM, Granjeiro PA, Patel K, Vaiyapuri S, Almeida JR. Antibacterial and Antiviral Properties of Chenopodin-Derived Synthetic Peptides. Antibiotics (Basel) 2024; 13:78. [PMID: 38247637 PMCID: PMC10812719 DOI: 10.3390/antibiotics13010078] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Antimicrobial peptides have been developed based on plant-derived molecular scaffolds for the treatment of infectious diseases. Chenopodin is an abundant seed storage protein in quinoa, an Andean plant with high nutritional and therapeutic properties. Here, we used computer- and physicochemical-based strategies and designed four peptides derived from the primary structure of Chenopodin. Two peptides reproduce natural fragments of 14 amino acids from Chenopodin, named Chen1 and Chen2, and two engineered peptides of the same length were designed based on the Chen1 sequence. The two amino acids of Chen1 containing amide side chains were replaced by arginine (ChenR) or tryptophan (ChenW) to generate engineered cationic and hydrophobic peptides. The evaluation of these 14-mer peptides on Staphylococcus aureus and Escherichia coli showed that Chen1 does not have antibacterial activity up to 512 µM against these strains, while other peptides exhibited antibacterial effects at lower concentrations. The chemical substitutions of glutamine and asparagine by amino acids with cationic or aromatic side chains significantly favoured their antibacterial effects. These peptides did not show significant hemolytic activity. The fluorescence microscopy analysis highlighted the membranolytic nature of Chenopodin-derived peptides. Using molecular dynamic simulations, we found that a pore is formed when multiple peptides are assembled in the membrane. Whereas, some of them form secondary structures when interacting with the membrane, allowing water translocations during the simulations. Finally, Chen2 and ChenR significantly reduced SARS-CoV-2 infection. These findings demonstrate that Chenopodin is a highly useful template for the design, engineering, and manufacturing of non-toxic, antibacterial, and antiviral peptides.
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Affiliation(s)
- Marcia L. Feijoo-Coronel
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - Bruno Mendes
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Carlos Peña-Varas
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | | | - Carolina Proaño-Bolaños
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
| | - Leonardo Camilo de Oliveira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Diego Fernandes Lívio
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - José Antônio da Silva
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - José Maurício S. F. da Silva
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
| | - Marília Gabriella A. G. Pereira
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
| | - Marina Q. R. B. Rodrigues
- Departamento de Bioquímica, Centro de Ciências Biomédicas, Federal University of Alfenas, Rua Gabriel Monteiro da Silva, 700, Sala E209, Alfenas 37130-001, Brazil
- Departamento de Engenharia de Biossistemas, Campus Dom Bosco, Federal University of São João Del-Rei, Praça Dom Helvécio, 74, Fábricas, São João del-Rei 36301-160, Brazil
| | - Mauro M. Teixeira
- Centro de Pesquisa e Desenvolvimento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Paulo Afonso Granjeiro
- Campus Centro Oeste, Federal University of São João Del-Rei, Rua Sebastião Gonçalves Filho, n 400, Chanadour, Divinópolis 35501-296, Brazil
| | - Ketan Patel
- School of Biological Sciences, University of Reading, Reading RG6 6UB, UK
| | | | - José R. Almeida
- Biomolecules Discovery Group, Universidad Regional Amazónica Ikiam, Km 7 Via Muyuna, Tena 150101, Ecuador
- School of Pharmacy, University of Reading, Reading RG6 6UB, UK
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Martínez-Cifuentes M, Soto-Tapia E, Linares-Pipón C, Bradshaw B, Valenzuela-Hormazabal P, Ramírez D, Muñoz-Torres P, Parra C. Design of β-Keto Esters with Antibacterial Activity: Synthesis, In Vitro Evaluation, and Theoretical Assessment of Their Reactivity and Quorum-Sensing Inhibition Capacity. Pharmaceuticals (Basel) 2023; 16:1339. [PMID: 37895810 PMCID: PMC10610512 DOI: 10.3390/ph16101339] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
This work proposes the design of β-keto esters as antibacterial compounds. The design was based on the structure of the autoinducer of bacterial quorum sensing, N-(3-oxo-hexanoyl)-l-homoserine lactone (3-oxo-C6-HSL). Eight β-keto ester analogues were synthesised with good yields and were spectroscopically characterised, showing that the compounds were only present in their β-keto ester tautomer form. We carried out a computational analysis of the reactivity and ADME (absorption, distribution, metabolism, and excretion) properties of the compounds as well as molecular docking and molecular dynamics calculations with the LasR and LuxS quorum-sensing (QS) proteins, which are involved in bacterial resistance to antibiotics. The results show that all the compounds exhibit reliable ADME properties and that only compound 7 can present electrophile toxicity. The theoretical reactivity study shows that compounds 6 and 8 present a differential local reactivity regarding the rest of the series. Compound 8 presents the most promising potential in terms of its ability to interact with the LasR and LuxS QS proteins efficiently according to its molecular docking and molecular dynamics calculations. An initial in vitro antimicrobial screening was performed against the human pathogenic bacteria Pseudomonas aeruginosa and Staphylococcus aureus as well as the phytopathogenic bacteria Pseudomonas syringae and Agrobacterium tumefaciens. Compounds 6 and 8 exhibit the most promising results in the in vitro antimicrobial screening against the panel of bacteria studied.
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Affiliation(s)
- Maximiliano Martínez-Cifuentes
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile; (E.S.-T.); (C.L.-P.)
| | - Emmanuel Soto-Tapia
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile; (E.S.-T.); (C.L.-P.)
| | - Camila Linares-Pipón
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile; (E.S.-T.); (C.L.-P.)
| | - Ben Bradshaw
- Laboratori de Química Orgánica, Facultat de Farmàcia, IBUB, Universitat de Barcelona, Av. Joan XXIII, s/n, 08028 Barcelona, Spain;
| | - Paulina Valenzuela-Hormazabal
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile; (P.V.-H.); (D.R.)
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile; (P.V.-H.); (D.R.)
| | - Patricio Muñoz-Torres
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile
| | - Claudio Parra
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile; (E.S.-T.); (C.L.-P.)
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5
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Barreto GE, Gonzalez J, Ramírez D. Network pharmacology and topological analysis on tibolone metabolites and their molecular mechanisms in traumatic brain injury. Biomed Pharmacother 2023; 165:115089. [PMID: 37418975 DOI: 10.1016/j.biopha.2023.115089] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023] Open
Abstract
Traumatic brain injury (TBI) is a pathology of great social impact, affecting millions of people worldwide. Despite the scientific advances to improve the management of TBI in recent years, we still do not have a specific treatment that controls the inflammatory process after mechanical trauma. The discovery and implementation of new treatments is a long and expensive process, making the repurpose of approved drugs for other pathologies a clinical interest. Tibolone is a drug in use for the treatment of symptoms associated with menopause and has been shown to have a broad spectrum of actions by regulating estrogen, androgen and progesterone receptors, whose activation exerts potent anti-inflammatory and antioxidant effects. In the present study, we aimed to investigate the therapeutic potential of the tibolone metabolites 3α-Hydroxytibolone, 3β-Hydroxytibolone, and Δ4-Tibolone as a possible therapy in TBI using network pharmacology and network topology analysis. Our results demonstrate that the estrogenic component mediated by the α and β metabolites can regulate synaptic transmission and cell metabolism, while the Δ metabolite may be involved in modulating the post-TBI inflammatory process. We identified several molecular targets, including KDR, ESR2, AR, NR3C1, PPARD, and PPARA, which are known to play critical roles in the pathogenesis of TBI. Tibolone metabolites were predicted to regulate the expression of key genes involved in oxidative stress, inflammation, and apoptosis. Overall, the repurposing of tibolone as a neuroprotective treatment for TBI holds promise for future clinical trials. However, further studies are needed to confirm its efficacy and safety in TBI patients.
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Affiliation(s)
- George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.
| | - Janneth Gonzalez
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá D.C., Colombia
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
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6
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Mancipe JC, Vargas-Pinto P, Rodríguez OE, Borrego-Muñoz P, Castellanos Londoño I, Ramírez D, Piñeros LG, Mejía MC, Pombo LM. Anti-Inflammatory Effect of Izalpinin Derived from Chromolaena leivensis: λ-Carrageenan-Induced Paw Edema and In Silico Model. Molecules 2023; 28:molecules28093722. [PMID: 37175132 PMCID: PMC10179959 DOI: 10.3390/molecules28093722] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The flavonoid izalpinin was isolated from the aerial parts of Chromolaena leivensis. Its structural determination was carried out using MS and NMR spectroscopic techniques (1H, 13C). This compound was evaluated for its anti-inflammatory effect in a rat model on λ-carrageenan-induced plantar edema. Paw inflammation was measured at one-hour intervals for seven hours following the administration of λ-carrageenan. Serum creatine kinase (CK) levels were evaluated, obtaining statistically significant results with the treatments at doses of 10 mg/kg (* p < 0.01) and 20 mg/kg (** p < 0.005). The anti-inflammatory effect of the compound was evaluated by using plethysmography, and the results showed significant differences at the three concentrations (10 mg/kg, 20 mg/kg, 40 mg/kg) in the first and third hours after treatment. * p < 0.05; ** p < 0.001; **** p < 0.0001 vs. the negative control group treated with vehicle (DMSO). Lastly, molecular docking analyses reveal that izalpinin has a strong binding affinity with five target proteins involved in the inflammatory process. The analysis using molecular dynamics allowed demonstrating that the ligand-protein complexes present acceptable stability, with RMSD values within the allowed range.
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Affiliation(s)
- Juan C Mancipe
- Facultad de Ciencias Agropecuarias, Universidad de la Salle, Bogotá 110141, Colombia
| | - Pedro Vargas-Pinto
- Facultad de Ciencias Agropecuarias, Universidad de la Salle, Bogotá 110141, Colombia
| | - Oscar E Rodríguez
- Facultad de Ingeniería, Universidad del Bosque, Bogotá 110121, Colombia
- Escuela de Medicina, Fundación Universitaria Juan N. Corpas, Bogotá 110311, Colombia
| | | | | | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Luis G Piñeros
- Facultad de Ingeniería, Universidad del Bosque, Bogotá 110121, Colombia
| | | | - Luis M Pombo
- Facultad de Ingeniería, Universidad del Bosque, Bogotá 110121, Colombia
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7
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Bonilla-Escribano P, Ramírez D, Baca-García E, Courtet P, Artés-Rodríguez A, López-Castromán J. Multidimensional variability in ecological assessments predicts two clusters of suicidal patients. Sci Rep 2023; 13:3546. [PMID: 36864070 PMCID: PMC9981613 DOI: 10.1038/s41598-023-30085-1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/15/2023] [Indexed: 03/04/2023] Open
Abstract
The variability of suicidal thoughts and other clinical factors during follow-up has emerged as a promising phenotype to identify vulnerable patients through Ecological Momentary Assessment (EMA). In this study, we aimed to (1) identify clusters of clinical variability, and (2) examine the features associated with high variability. We studied a set of 275 adult patients treated for a suicidal crisis in the outpatient and emergency psychiatric departments of five clinical centers across Spain and France. Data included a total of 48,489 answers to 32 EMA questions, as well as baseline and follow-up validated data from clinical assessments. A Gaussian Mixture Model (GMM) was used to cluster the patients according to EMA variability during follow-up along six clinical domains. We then used a random forest algorithm to identify the clinical features that can be used to predict the level of variability. The GMM confirmed that suicidal patients are best clustered in two groups with EMA data: low- and high-variability. The high-variability group showed more instability in all dimensions, particularly in social withdrawal, sleep measures, wish to live, and social support. Both clusters were separated by ten clinical features (AUC = 0.74), including depressive symptoms, cognitive instability, the intensity and frequency of passive suicidal ideation, and the occurrence of clinical events, such as suicide attempts or emergency visits during follow-up. Initiatives to follow up suicidal patients with ecological measures should take into account the existence of a high variability cluster, which could be identified before the follow-up begins.
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Affiliation(s)
- Pablo Bonilla-Escribano
- Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - David Ramírez
- Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Enrique Baca-García
- Department of Psychiatry, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid, Spain
- Department of Psychiatry, Hospital Universitario Rey Juan Carlos, Móstoles, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
- Department of Psychiatry, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
- Department of Psychiatry, Hospital Universitario Central de Villalba, Madrid, Spain
- Department of Psychiatry, Hospital Universitario Infanta Elena, Valdemoro, Madrid, Spain
- Universidad Católica del Maude, Talca, Chile
- CIBERSAM, Instituto de Salud Carlos III, Madrid, Spain
| | - Philippe Courtet
- IGF, CNRS-INSERM, Université de Montpellier, Montpellier, France
- Department of Emergency Psychiatry and Acute Care, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Antonio Artés-Rodríguez
- Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBERSAM, Instituto de Salud Carlos III, Madrid, Spain
- Evidence-Based Behavior, Madrid, Spain
| | - Jorge López-Castromán
- Department of Psychiatry, Centre Hospitalier Universitaire de Nîmes, Nîmes, France
- CIBERSAM, Instituto de Salud Carlos III, Madrid, Spain
- IGF, CNRS-INSERM, Université de Montpellier, Montpellier, France
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8
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Arévalo B, Bedoya M, Kiper AK, Vergara F, Ramírez D, Mazola Y, Bustos D, Zúñiga R, Cikutovic R, Cayo A, Rinné S, Ramirez-Apan MT, Sepúlveda FV, Cerda O, López-Collazo E, Decher N, Zúñiga L, Gutierrez M, González W. Selective TASK-1 Inhibitor with a Defined Structure–Activity Relationship Reduces Cancer Cell Proliferation and Viability. J Med Chem 2022; 65:15014-15027. [DOI: 10.1021/acs.jmedchem.1c00378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados−CEAP, Conicyt, Programa Regional R19A10001, Gore Maule, 3460000 Talca, Chile
| | - Mauricio Bedoya
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, 3460000 Talca, Chile
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, 3480094 Talca, Chile
| | - Aytug K. Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 1-2, 35037 Marburg, Germany
| | - Fernando Vergara
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente No. 1141, 3460000 Talca, Chile
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, 4030000 Concepción, Chile
| | - Yuliet Mazola
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente No. 1141, 3460000 Talca, Chile
| | - Daniel Bustos
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, 3460000 Talca, Chile
- Laboratorio de Bioinformática y Química Computacional (LBQC), Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, 3460000 Talca, Chile
| | - Rafael Zúñiga
- Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Casilla, 3460000 Talca, Chile
- Instituto de Investigación Interdisciplinaria, Vicerrectoría Académica, Universidad de Talca, 3460000 Talca, Chile
| | - Rocio Cikutovic
- Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Casilla, 3460000 Talca, Chile
| | - Angel Cayo
- Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Casilla, 3460000 Talca, Chile
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 1-2, 35037 Marburg, Germany
| | - M. Teresa Ramirez-Apan
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510, Coyoacán, 04510 México, DF, México
| | - Francisco V. Sepúlveda
- Centro de Estudios Científicos (CECs), 5110466 Valdivia, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, 5110466 Valdivia, Chile
| | - Oscar Cerda
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas (ICBM), Facultad de Medicina, Universidad de Chile, 8380453 Santiago, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Facultad de Medicina, Universidad de Chile, 8380453 Santiago, Chile
| | - Eduardo López-Collazo
- The Innate Immune Response Group and Tumor Immunology Laboratory, IdiPAZ, La Paz University Hospital, 8046 Madrid, Spain
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 1-2, 35037 Marburg, Germany
- Marburg Center for Mind, Brain and Behavior−MCMBB, Philipps-University Marburg, 35037 Marburg, Germany
| | - Leandro Zúñiga
- Centro de Nanomedicina, Diagnóstico y Desarrollo de Fármacos (ND3), Laboratorio de Fisiología Molecular, Escuela de Medicina, Universidad de Talca, Casilla, 3460000 Talca, Chile
| | - Margarita Gutierrez
- Laboratorio de Síntesis y Actividad Biológica, Instituto de Química de Recursos Naturales, Universidad de Talca, 1 poniente No. 1141, 3460000 Talca, Chile
| | - Wendy González
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, 1 Poniente No. 1141, 3460000 Talca, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 1 Poniente No. 1141, 3460000 Talca, Chile
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9
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Alegría-Arcos M, Barbosa T, Sepúlveda F, Combariza G, González J, Gil C, Martínez A, Ramírez D. Network pharmacology reveals multitarget mechanism of action of drugs to be repurposed for COVID-19. Front Pharmacol 2022; 13:952192. [PMID: 36052135 PMCID: PMC9424758 DOI: 10.3389/fphar.2022.952192] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
The coronavirus disease 2019 pandemic accelerated drug/vaccine development processes, integrating scientists all over the globe to create therapeutic alternatives against this virus. In this work, we have collected information regarding proteins from SARS-CoV-2 and humans and how these proteins interact. We have also collected information from public databases on protein–drug interactions. We represent this data as networks that allow us to gain insights into protein–protein interactions between both organisms. With the collected data, we have obtained statistical metrics of the networks. This data analysis has allowed us to find relevant information on which proteins and drugs are the most relevant from the network pharmacology perspective. This method not only allows us to focus on viral proteins as the main targets for COVID-19 but also reveals that some human proteins could be also important in drug repurposing campaigns. As a result of the analysis of the SARS-CoV-2–human interactome, we have identified some old drugs, such as disulfiram, auranofin, gefitinib, suloctidil, and bromhexine as potential therapies for the treatment of COVID-19 deciphering their potential complex mechanism of action.
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Affiliation(s)
- Melissa Alegría-Arcos
- Facultad de Ingeniería y Negocios, Universidad de Las Américas, Sede Providencia, Santiago, Chile
| | - Tábata Barbosa
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá, Colombia
| | - Felipe Sepúlveda
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
| | - German Combariza
- Universidad Externado de Colombia, Departamento de Matemáticas, Bogotá, Colombia
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Sede Bogotá, Bogotá, Colombia
| | - Carmen Gil
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Ana Martínez
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago, Chile
- *Correspondence: David Ramírez,
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10
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Mazola Y, Márquez Montesinos JCE, Ramírez D, Zúñiga L, Decher N, Ravens U, Yarov-Yarovoy V, González W. Common Structural Pattern for Flecainide Binding in Atrial-Selective Kv1.5 and Nav1.5 Channels: A Computational Approach. Pharmaceutics 2022; 14:pharmaceutics14071356. [PMID: 35890252 PMCID: PMC9318806 DOI: 10.3390/pharmaceutics14071356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 02/04/2023] Open
Abstract
Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its treatment includes antiarrhythmic drugs (AADs) to modulate the function of cardiac ion channels. However, AADs have been limited by proarrhythmic effects, non-cardiovascular toxicities as well as often modest antiarrhythmic efficacy. Theoretical models showed that a combined blockade of Nav1.5 (and its current, INa) and Kv1.5 (and its current, IKur) ion channels yield a synergistic anti-arrhythmic effect without alterations in ventricles. We focused on Kv1.5 and Nav1.5 to search for structural similarities in their binding site (BS) for flecainide (a common blocker and widely prescribed AAD) as a first step for prospective rational multi-target directed ligand (MTDL) design strategies. We present a computational workflow for a flecainide BS comparison in a flecainide-Kv1.5 docking model and a solved structure of the flecainide-Nav1.5 complex. The workflow includes docking, molecular dynamics, BS characterization and pattern matching. We identified a common structural pattern in flecainide BS for these channels. The latter belongs to the central cavity and consists of a hydrophobic patch and a polar region, involving residues from the S6 helix and P-loop. Since the rational MTDL design for AF is still incipient, our findings could advance multi-target atrial-selective strategies for AF treatment.
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Affiliation(s)
- Yuliet Mazola
- Center for Bioinformatics, Simulation and Modeling (CBSM), Universidad de Talca, Talca 3460000, Chile; (Y.M.); (J.C.E.M.M.)
| | - José C. E. Márquez Montesinos
- Center for Bioinformatics, Simulation and Modeling (CBSM), Universidad de Talca, Talca 3460000, Chile; (Y.M.); (J.C.E.M.M.)
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile;
| | - Leandro Zúñiga
- Escuela de Medicina, Centro de Investigaciones Médicas, Universidad de Talca, Talca 3460000, Chile;
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35043 Marburg, Germany;
| | - Ursula Ravens
- Institut für Experimentelle Kardiovaskuläre Medizin, Universitäts-Herzzentrum Freiburg Bad Krotzingen, 79110 Freiburg im Breisgau, Germany;
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA 95616, USA;
| | - Wendy González
- Center for Bioinformatics, Simulation and Modeling (CBSM), Universidad de Talca, Talca 3460000, Chile; (Y.M.); (J.C.E.M.M.)
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Talca 3530000, Chile
- Correspondence:
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11
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Güiza FM, Rodríguez-Núñez YA, Ramírez D, Romero Bohórquez AR, Henao JA, Toro RA, Delgado JM, Díaz de Delgado G. Crystal structure, Hirshfeld surface analysis, and molecular dynamics simulations of two isostructural N-propargyl-4-(2-oxopyrrolidin-1-yl)-1,2,3,4-tetrahydroquinolines. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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12
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McGovern AJ, González J, Ramírez D, Barreto GE. Identification of HMGCR, PPGARG and prohibitin as potential druggable targets of dihydrotestosterone for treatment against traumatic brain injury using system pharmacology. Int Immunopharmacol 2022; 108:108721. [PMID: 35344815 DOI: 10.1016/j.intimp.2022.108721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/03/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Traumatic Brain Injury (TBI) has long-term devastating effects for which there is no accurate and effective treatment for inflammation and chronic oxidative stress. As a disease that affects multiple signalling pathways, the search for a drug with a broader spectrum of pharmacological action is of clinical interest. The fact that endocrine disruption (e.g hypogonadism) has been observed in TBI patients suggests that endogenous therapy with testosterone, or its more androgenic derivative, dihydrotestosterone (DHT), may attenuate, at least in part, the TBI-induced inflammation, but the underlying molecular mechanisms by which this occurs are still not completely clear. AIMS AND METHODS In this study, the main aim was to investigate proteins that may be related to the pathophysiological mechanism of TBI and also be pharmacological targets of DHT in order to explore a possible therapy with this androgen using network pharmacology. RESULTS AND CONCLUSIONS We identified 2.700 proteins related to TBI and 1.567 that are potentially molecular targets of DHT. Functional enrichment analysis showed that steroid (p-value: 2.1-22), lipid metabolism (p-value: 2.8-21) and apoptotic processes (p-value: 5.2-21) are mainly altered in TBI. Furthermore, being mitochondrion an organelle involved on these molecular processes we next identified that out of 32 mitochondrial-related proteins 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase (HMGCR), peroxisome proliferator activated receptor gamma (PPGARG) and prohibitin are those found highly regulated in the network and potential targets of DHT in TBI. In conclusion, the identification of these cellular nodes may prove to be essential as targets of DHT for therapy against post-TBI inflammation.
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Affiliation(s)
- Andrew J McGovern
- Department of Biological Sciences, University of Limerick, Limerick, Ireland
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - David Ramírez
- Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - George E Barreto
- Department of Biological Sciences, University of Limerick, Limerick, Ireland.
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13
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Peña-Varas C, Kanstrup C, Vergara-Jaque A, González-Avendaño M, Crocoll C, Mirza O, Dreyer I, Nour-Eldin H, Ramírez D. Structural Insights into the Substrate Transport Mechanisms in GTR Transporters through Ensemble Docking. Int J Mol Sci 2022; 23:ijms23031595. [PMID: 35163519 PMCID: PMC8836200 DOI: 10.3390/ijms23031595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
Glucosinolate transporters (GTRs) are part of the nitrate/peptide transporter (NPF) family, members of which also transport specialized secondary metabolites as substrates. Glucosinolates are defense compounds derived from amino acids. We selected 4-methylthiobutyl (4MTB) and indol-3-ylmethyl (I3M) glucosinolates to study how GTR1 from Arabidopsis thaliana transports these substrates in computational simulation approaches. The designed pipeline reported here includes massive docking of 4MTB and I3M in an ensemble of GTR1 conformations (in both inward and outward conformations) extracted from molecular dynamics simulations, followed by clustered and substrate–protein interactions profiling. The identified key residues were mutated, and their role in substrate transport was tested. We were able to identify key residues that integrate a major binding site of these substrates, which is critical for transport activity. In silico approaches employed here represent a breakthrough in the plant transportomics field, as the identification of key residues usually takes a long time if performed from a purely wet-lab experimental perspective. The inclusion of structural bioinformatics in the analyses of plant transporters significantly speeds up the knowledge-gaining process and optimizes valuable time and resources.
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Affiliation(s)
- Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
| | - Christa Kanstrup
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Mariela González-Avendaño
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Ingo Dreyer
- Center for Bioinformatics, Simulation and Modeling (CBSM), Faculty of Engineering, Campus Talca, Universidad de Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile; (A.V.-J.); (M.G.-A.); (I.D.)
| | - Hussam Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark; (C.K.); (C.C.); (H.N.-E.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-piso 6, Santiago 8900000, Chile;
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago 8900000, Chile
- Correspondence: ; Tel.: +56-(22)-3036667
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14
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Griffon D, Hernandez MJ, Ramírez D. Theoretical Clues for Agroecological Transitions: The Conuco Legacy and the Monoculture Trap. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.529271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The multiple ecological crisis that we are facing forces us to ponder the transition toward sustainable agricultural systems. Two key uncertainties need to be unveiled in addressing this problem; first, we need to identify the general features of alternative models that make them sustainable, and second, we need to explore how to build them from the (flawed) existing systems. In this work we explore these two questions using an ethnoecological and theoretical approach. In the exploration of alternative models, we evaluate an ancestral farming system, the conuco, characterized by, (i) the use of the ecological succession to constantly renew its properties, (ii) the increase of its biodiversity over time (in the horizontal and vertical components), and (iii) the self-regulation of the associated populations. Next, we characterize the topology of ecological networks of agroecosystems along the transition from a monoculture to a conuco-like agroecological system. We use topologies obtained from field information of conventional and agroecological systems as starting and arrival points. To model the dynamics of the systems and numerically simulate the transitions, we use a model based on Generalized Lotka-Volterra equations, where all types of population interactions are represented, with outcomes based on a density-dependent conditionality. The results highlight the relevance of increasing the connectance and diminishing the degree centrality of the conventional systems networks to promote their sustainability. Finally, we propose that the transitions between the monoculture and the agroecological systems could be figuratively interpreted as a cusp catastrophe, where the two systems are understood as alternative stable states and the path from one to the other cannot be reverted by just reversing the values of the control parameter. That is, once a system is in either of these states there is a tendency to stay and a resistance to move away from it. This implies that in the process of transition from a monoculture to a multi-diverse system, it is prudent not to despair if there are no immediate improvements in the performance of the system because once a certain point is reached, the system may experience an abrupt improvement.
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15
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Gallego-Yerga L, Ochoa R, Lans I, Peña-Varas C, Alegría-Arcos M, Cossio P, Ramírez D, Peláez R. Application of ensemble pharmacophore-based virtual screening to the discovery of novel antimitotic tubulin inhibitors. Comput Struct Biotechnol J 2021; 19:4360-4372. [PMID: 34429853 PMCID: PMC8365384 DOI: 10.1016/j.csbj.2021.07.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022] Open
Abstract
Tubulin is a well-validated target for herbicides, fungicides, anti-parasitic, and anti-tumor drugs. Many of the non-cancer tubulin drugs bind to its colchicine site but no colchicine-site anticancer drug is available. The colchicine site is composed of three interconnected sub-pockets that fit their ligands and modify others' preference, making the design of molecular hybrids (that bind to more than one sub-pocket) a difficult task. Taking advantage of the more than eighty published X-ray structures of tubulin in complex with ligands bound to the colchicine site, we generated an ensemble of pharmacophore representations that flexibly sample the interactional space between the ligands and target. We searched the ZINC database for scaffolds able to fit several of the subpockets, such as tetrazoles, sulfonamides and diarylmethanes, selected roughly ~8000 compounds with favorable predicted properties. A Flexi-pharma virtual screening, based on ensemble pharmacophore, was performed by two different methodologies. Combining the scaffolds that best fit the ensemble pharmacophore-representation, we designed a new family of ligands, resulting in a novel tubulin modulator. We synthesized tetrazole 5 and tested it as a tubulin inhibitor in vitro. In good agreement with the design principles, it demonstrated micromolar activity against in vitro tubulin polymerization and nanomolar anti-proliferative effect against human epithelioid carcinoma HeLa cells through microtubule disruption, as shown by immunofluorescence confocal microscopy. The integrative methodology succedes in the design of new scaffolds for flexible proteins with structural coupling between pockets, thus expanding the way in which computational methods can be used as significant tools in the drug design process.
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Affiliation(s)
- Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.,Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
| | - Rodrigo Ochoa
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
| | - Isaías Lans
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia
| | - Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile
| | | | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia.,Center for Computational Mathematics, Flatiron Institute, NY, United States
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.,Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain
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16
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Guzmán L, Parra-Cid C, Guerrero-Muñoz E, Peña-Varas C, Polo-Cuadrado E, Duarte Y, Castro RI, Nerio LS, Araya-Maturana R, Asefa T, Echeverría J, Ramírez D, Forero-Doria O. Antimicrobial properties of novel ionic liquids derived from imidazolium cation with phenolic functional groups. Bioorg Chem 2021; 115:105289. [PMID: 34426154 DOI: 10.1016/j.bioorg.2021.105289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/13/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022]
Abstract
Bacterial infections are nowadays among the major threats to public health worldwide. Thus, there is an urgent and increased need for new antimicrobial agents. As a result, the exploration of the antimicrobial properties of different substances including ionic liquids (ILs) has recently attracted great attention. The present work is aimed at evaluating how the addition of halogens and hydrophobic substituents on alkylimidazolium units of ILs as well as the increase in their chain lengths affects the antimicrobial properties of such ILs. After their synthesis, the antibacterial activities of these compounds against Pseudomona aeruginosa, Escherichia coli, and Staphylococcus aureus are determined by measuring their minimal inhibitory concentrations (MICs). Key features in ILs-membrane interactions are also studied using long-term all-atom molecular dynamics simulations (MDs). The results show that these ILs have good antibacterial activity against S. aureus, E. coli, and P. aeruginosa, with MIC values range from <7.81 to 62.50 μM. The antimicrobial property of tert-butyl N-methylphenolimidazolium salts (denoted as 8b and 8c) is particularly better with MIC values of < 7.81 μM. The antibacterial efficacy is also found to depend on the alkyl chain length and substituents on the phenolic ring. Finally, MDs done for ILs in a phosphatidylcholine (POPC) bilayer show key features in the mechanism of IL-induced membrane disruption, where the ILs are inserted as clusters into one side of the bilayer until saturation is reached. This insertion increases "leaflet strain" up to critical threshold, likely triggering the morphological disruption of the membranes in the microbes.
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Affiliation(s)
- Luis Guzmán
- Departamento de Bioquímica Clínica e Inmunohematología, Facultad de Ciencias de la Salud, Universidad de Talca, P.O. Box 747, Talca 3460000, Chile
| | - Cristóbal Parra-Cid
- Departamento de Bioquímica Clínica e Inmunohematología, Facultad de Ciencias de la Salud, Universidad de Talca, P.O. Box 747, Talca 3460000, Chile
| | - Etiennette Guerrero-Muñoz
- Instituto de Química de Recursos Naturales, Universidad de Talca, P.O. Box 747, Talca 3460000, Chile
| | - Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, El Llano Subercaseaux, 2801-Piso 6, Santiago, Chile
| | - Efraín Polo-Cuadrado
- Instituto de Química de Recursos Naturales, Laboratorio de Síntesis Orgánica, Universidad de Talca, Casilla 747, Talca 3460000, Chile
| | - Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Ricardo I Castro
- Carrera de Ingeniería en Construcción e Instituto de Ciencias Químicas Aplicadas, Multidisciplinary Agroindustry Research Laboratory, Universidad Autónoma de Chile, Talca, Chile
| | - Luz Stella Nerio
- Universidad de la Amazonia, Programa de Química, Calle 17 Diagonal 17 Carrera 3F, Florencia, Colombia
| | - Ramiro Araya-Maturana
- Instituto de Química de Recursos Naturales, Universidad de Talca, P.O. Box 747, Talca 3460000, Chile
| | - Tewodros Asefa
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854, United States; Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854, United States
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad Santiago de Chile, Santiago, Chile
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, El Llano Subercaseaux, 2801-Piso 6, Santiago, Chile
| | - Oscar Forero-Doria
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad Santiago de Chile, Santiago, Chile.
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17
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Nozal V, García‐Rubia A, Cuevas EP, Pérez C, Tosat‐Bitrián C, Bartolomé F, Carro E, Ramírez D, Palomo V, Martínez A. From Kinase Inhibitors to Multitarget Ligands as Powerful Drug Leads for Alzheimer's Disease using Protein-Templated Synthesis. Angew Chem Int Ed Engl 2021; 60:19344-19354. [PMID: 34169618 PMCID: PMC8457121 DOI: 10.1002/anie.202106295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/24/2021] [Indexed: 11/24/2022]
Abstract
Multitarget directed ligands (MTDLs) are arising as promising tools to tackle complex diseases. The main goal of this work is to create powerful modulating agents for neurodegenerative disorders. To achieve this aim, we have combined fragments that inhibit key protein kinases involved in the main pathomolecular pathways of Alzheimer's disease (AD) such as tau aggregation, neuroinflammation and decreased neurogenesis, whilst looking for a third action in beta-secretase (BACE1), responsible of β-amyloid production. We obtained well-balanced MTDLs with in vitro activity in three different relevant targets and efficacy in two cellular models of AD. Furthermore, computational studies confirmed how these compounds accommodate adequately into the long and rather narrow BACE1 catalytic site. Finally, we employed in situ click chemistry using BACE1 as protein template as a versatile synthetic tool that allowed us to obtain further MTDLs.
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Affiliation(s)
- Vanesa Nozal
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
| | - Alfonso García‐Rubia
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Instituto de Salud Carlos III28031MadridSpain
| | - Eva P. Cuevas
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
| | - Concepción Pérez
- Instituto de Química Médica-CSIC)Juan de la Cierva 328006MadridSpain
| | - Carlota Tosat‐Bitrián
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
| | - Fernando Bartolomé
- Hospital Universitario 12 de Octubre Research Institute (imas12)Group of Neurodegenerative DiseasesJuan de la Cierva 328006MadridSpain
| | - Eva Carro
- Hospital Universitario 12 de Octubre Research Institute (imas12)Group of Neurodegenerative DiseasesJuan de la Cierva 328006MadridSpain
| | - David Ramírez
- Instituto de Ciencias BiomédicasUniversidad Autónoma de ChileLlano Subercaseaux2801—piso 6SantiagoChile
| | - Valle Palomo
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Instituto de Salud Carlos III28031MadridSpain
| | - Ana Martínez
- Structural and Chemical Biology DepartmentCentro de Investigaciones Biológicas-CSICRamiro de Maeztu 928040MadridSpain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED)Instituto de Salud Carlos III28031MadridSpain
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18
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Nozal V, García‐Rubia A, Cuevas EP, Pérez C, Tosat‐Bitrián C, Bartolomé F, Carro E, Ramírez D, Palomo V, Martínez A. From Kinase Inhibitors to Multitarget Ligands as Powerful Drug Leads for Alzheimer's Disease using Protein‐Templated Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Vanesa Nozal
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Alfonso García‐Rubia
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) Instituto de Salud Carlos III 28031 Madrid Spain
| | - Eva P. Cuevas
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Concepción Pérez
- Instituto de Química Médica-CSIC) Juan de la Cierva 3 28006 Madrid Spain
| | - Carlota Tosat‐Bitrián
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
| | - Fernando Bartolomé
- Hospital Universitario 12 de Octubre Research Institute (imas12) Group of Neurodegenerative Diseases Juan de la Cierva 3 28006 Madrid Spain
| | - Eva Carro
- Hospital Universitario 12 de Octubre Research Institute (imas12) Group of Neurodegenerative Diseases Juan de la Cierva 3 28006 Madrid Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas Universidad Autónoma de Chile Llano Subercaseaux 2801—piso 6 Santiago Chile
| | - Valle Palomo
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) Instituto de Salud Carlos III 28031 Madrid Spain
| | - Ana Martínez
- Structural and Chemical Biology Department Centro de Investigaciones Biológicas-CSIC Ramiro de Maeztu 9 28040 Madrid Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) Instituto de Salud Carlos III 28031 Madrid Spain
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19
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Ramírez D, Mejia-Gutierrez M, Insuasty B, Rinné S, Kiper AK, Platzk M, Müller T, Decher N, Quiroga J, De-la-Torre P, González W. 5-(Indol-2-yl)pyrazolo[3,4- b]pyridines as a New Family of TASK-3 Channel Blockers: A Pharmacophore-Based Regioselective Synthesis. Molecules 2021; 26:molecules26133897. [PMID: 34202296 PMCID: PMC8271858 DOI: 10.3390/molecules26133897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022] Open
Abstract
TASK channels belong to the two-pore-domain potassium (K2P) channels subfamily. These channels modulate cellular excitability, input resistance, and response to synaptic stimulation. TASK-channel inhibition led to membrane depolarization. TASK-3 is expressed in different cancer cell types and neurons. Thus, the discovery of novel TASK-3 inhibitors makes these bioactive compounds very appealing to explore new cancer and neurological therapies. TASK-3 channel blockers are very limited to date, and only a few heterofused compounds have been reported in the literature. In this article, we combined a pharmacophore hypothesis with molecular docking to address for the first time the rational design, synthesis, and evaluation of 5-(indol-2-yl)pyrazolo[3,4-b]pyridines as a novel family of human TASK-3 channel blockers. Representative compounds of the synthesized library were assessed against TASK-3 using Fluorometric imaging plate reader-Membrane Potential assay (FMP). Inhibitory properties were validated using two-electrode voltage-clamp (TEVC) methods. We identified one active hit compound (MM-3b) with our systematic pipeline, exhibiting an IC50 ≈ 30 μM. Molecular docking models suggest that compound MM-3b binds to TASK-3 at the bottom of the selectivity filter in the central cavity, similar to other described TASK-3 blockers such as A1899 and PK-THPP. Our in silico and experimental studies provide a new tool to predict and design novel TASK-3 channel blockers.
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Affiliation(s)
- David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801-Piso 5, Santiago 8900000, Chile
- Correspondence: (D.R.); (P.D.-l.-T.); (W.G.)
| | - Melissa Mejia-Gutierrez
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A, Cali 760031, Colombia; (M.M.-G.); (B.I.); (J.Q.)
| | - Braulio Insuasty
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A, Cali 760031, Colombia; (M.M.-G.); (B.I.); (J.Q.)
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Center for Mind, Brain and Behavior (CMBB), Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany; (S.R.); (A.K.K.); (N.D.)
| | - Aytug K. Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Center for Mind, Brain and Behavior (CMBB), Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany; (S.R.); (A.K.K.); (N.D.)
| | - Magdalena Platzk
- Joint Pulmonary Drug Discovery Lab Bayer-MGH, Boston, MA 02114, USA;
| | - Thomas Müller
- Bayer AG, Research & Development, Pharmaceuticals, D-42096 Wuppertal, Germany;
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Center for Mind, Brain and Behavior (CMBB), Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany; (S.R.); (A.K.K.); (N.D.)
| | - Jairo Quiroga
- Heterocyclic Compounds Research Group, Department of Chemistry, Universidad del Valle, A.A, Cali 760031, Colombia; (M.M.-G.); (B.I.); (J.Q.)
| | - Pedro De-la-Torre
- Department of Otolaryngology, Harvard Medical School and Massachusetts Eye and Ear, 243 Charles St, Boston, MA 02114, USA
- Caribe Therapeutics, Vía 40 No. 69-111, Oficina 804 A, Barranquilla 080002, Colombia
- Correspondence: (D.R.); (P.D.-l.-T.); (W.G.)
| | - Wendy González
- Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Poniente No. 1141, Talca 3460000, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca 3460000, Chile
- Correspondence: (D.R.); (P.D.-l.-T.); (W.G.)
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20
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Kiper AK, Bedoya M, Stalke S, Marzian S, Ramírez D, de la Cruz A, Peraza DA, Vera-Zambrano A, Márquez Montesinos JCE, Arévalo Ramos BA, Rinné S, Gonzalez T, Valenzuela C, Gonzalez W, Decher N. Identification of a critical binding site for local anaesthetics in the side pockets of K v 1 channels. Br J Pharmacol 2021; 178:3034-3048. [PMID: 33817777 DOI: 10.1111/bph.15480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/31/2020] [Revised: 02/24/2021] [Accepted: 03/10/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND AND PURPOSE Local anaesthetics block sodium and a variety of potassium channels. Although previous studies identified a residue in the pore signature sequence together with three residues in the S6 segment as a putative binding site, the precise molecular basis of inhibition of Kv channels by local anaesthetics remained unknown. Crystal structures of Kv channels predict that some of these residues point away from the central cavity and face into a drug binding site called side pockets. Thus, the question arises whether the binding site of local anaesthetics is exclusively located in the central cavity or also involves the side pockets. EXPERIMENTAL APPROACH A systematic functional alanine mutagenesis approach, scanning 58 mutants, together with in silico docking experiments and molecular dynamics simulations was utilized to elucidate the binding site of bupivacaine and ropivacaine. KEY RESULTS Inhibition of Kv 1.5 channels by local anaesthetics requires binding to the central cavity and the side pockets, and the latter requires interactions with residues of the S5 and the back of the S6 segments. Mutations in the side pockets remove stereoselectivity of inhibition of Kv 1.5 channels by bupivacaine. Although binding to the side pockets is conserved for different local anaesthetics, the binding mode in the central cavity and the side pockets shows considerable variations. CONCLUSION AND IMPLICATIONS Local anaesthetics bind to the central cavity and the side pockets, which provide a crucial key to the molecular understanding of their Kv channel affinity and stereoselectivity, as well as their spectrum of side effects.
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Affiliation(s)
- Aytug K Kiper
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Sarah Stalke
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - Stefanie Marzian
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Alicia de la Cruz
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Diego A Peraza
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Alba Vera-Zambrano
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Biochemistry Department, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | | | | | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
| | - Teresa Gonzalez
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain.,Biochemistry Department, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Valenzuela
- Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) and Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Spanish Network for Biomedical Research in Cardiovascular Research (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Wendy Gonzalez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Philipps-University Marburg, Marburg, Germany
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21
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Vargas-Sanchez K, Losada-Barragán M, Mogilevskaya M, Novoa-Herrán S, Medina Y, Buendía-Atencio C, Lorett-Velásquez V, Martínez-Bernal J, Gonzalez-Reyes RE, Ramírez D, Petry KG. Screening for Interacting Proteins with Peptide Biomarker of Blood-Brain Barrier Alteration under Inflammatory Conditions. Int J Mol Sci 2021; 22:ijms22094725. [PMID: 33946948 PMCID: PMC8124558 DOI: 10.3390/ijms22094725] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases are characterized by increased permeability of the blood-brain barrier (BBB) due to alterations in cellular and structural components of the neurovascular unit, particularly in association with neuroinflammation. A previous screening study of peptide ligands to identify molecular alterations of the BBB in neuroinflammation by phage-display, revealed that phage clone 88 presented specific binding affinity to endothelial cells under inflammatory conditions in vivo and in vitro. Here, we aimed to identify the possible target receptor of the peptide ligand 88 expressed under inflammatory conditions. A cross-link test between phage-peptide-88 with IL-1β-stimulated human hCMEC cells, followed by mass spectrometry analysis, was used to identify the target of peptide-88. We modeled the epitope-receptor molecular interaction between peptide-88 and its target by using docking simulations. Three proteins were selected as potential target candidates and tested in enzyme-linked immunosorbent assays with peptide-88: fibronectin, laminin subunit α5 and laminin subunit β-1. Among them, only laminin subunit β-1 presented measurable interaction with peptide-88. Peptide-88 showed specific interaction with laminin subunit β-1, highlighting its importance as a potential biomarker of the laminin changes that may occur at the BBB endothelial cells under pathological inflammation conditions.
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Affiliation(s)
- Karina Vargas-Sanchez
- Grupo de Neurociencia Translacional, Facultad de Medicina, Universidad de los Andes, Bogotá 111711, Colombia
- Correspondence: ; Tel.: +57-13102405706
| | - Monica Losada-Barragán
- Grupo de Biología Celular y Funcional e Ingeniería de Moléculas, Departamento de Biología, Universidad Antonio Nariño, Bogotá 110231, Colombia; (M.L.-B.); (Y.M.)
| | - Maria Mogilevskaya
- Grupo de Investigación GINIC-HUS, Universidad ECCI, Bogotá 111311, Colombia;
| | - Susana Novoa-Herrán
- Grupo de Investigación en Hormonas (Hormone Research Laboratory), Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia; or
- Grupo de Fisiología Molecular, Subdirección de Investigación Científica y Tecnológica, Instituto Nacional de Salud, Bogotá 111321, Colombia
| | - Yehidi Medina
- Grupo de Biología Celular y Funcional e Ingeniería de Moléculas, Departamento de Biología, Universidad Antonio Nariño, Bogotá 110231, Colombia; (M.L.-B.); (Y.M.)
| | - Cristian Buendía-Atencio
- Grupo de Investigación en Modelado y Computación Científica, Departamento de Química, Universidad Antonio Nariño, Bogotá 110231, Colombia;
| | - Vaneza Lorett-Velásquez
- Facultad de Medicina y Ciencias de la Salud, Universidad Militar Nueva Granada, Bogotá 110231, Colombia; (V.L.-V.); (J.M.-B.)
| | - Jessica Martínez-Bernal
- Facultad de Medicina y Ciencias de la Salud, Universidad Militar Nueva Granada, Bogotá 110231, Colombia; (V.L.-V.); (J.M.-B.)
| | - Rodrigo E. Gonzalez-Reyes
- Grupo de Investigación en Neurociencias (NeURos), Centro de Neurociencia Neurovitae-UR, Escuela de Medicina y Ciencias de la Salud, Universidad del Rosario, Bogotá 111711, Colombia;
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, El llano Subercaseaux 2801, Santiago 8900000, Chile;
| | - Klaus G. Petry
- INSERM U1049 and U1029 Neuroinflammation and Angiogenesis Group, Bordeaux University, F33000 Bordeaux, France;
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22
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Ginex T, Garaigorta U, Ramírez D, Castro V, Nozal V, Maestro I, García-Cárceles J, Campillo NE, Martinez A, Gastaminza P, Gil C. Host-Directed FDA-Approved Drugs with Antiviral Activity against SARS-CoV-2 Identified by Hierarchical In Silico/In Vitro Screening Methods. Pharmaceuticals (Basel) 2021; 14:ph14040332. [PMID: 33917313 PMCID: PMC8067418 DOI: 10.3390/ph14040332] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/01/2021] [Accepted: 04/03/2021] [Indexed: 12/13/2022] Open
Abstract
The unprecedent situation generated by the COVID-19 global emergency has prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the treatment of COVID-19 patients. In the attempt to proceed toward a proper rationalization of the search for new antivirals among approved drugs, we carried out a hierarchical in silico/in vitro protocol which successfully combines virtual and biological screening to speed up the identification of host-directed therapies against COVID-19 in an effective way. To this end a multi-target virtual screening approach focused on host-based targets related to viral entry, followed by the experimental evaluation of the antiviral activity of selected compounds, has been carried out. As a result, five different potentially repurposable drugs interfering with viral entry—cepharantine, clofazimine, metergoline, imatinib and efloxate—have been identified.
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Affiliation(s)
- Tiziana Ginex
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
| | - Urtzi Garaigorta
- Centro Nacional de Biotecnología-CSIC, Calle Darwin 3, 28049 Madrid, Spain; (U.G.); (V.C.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Llano Subercaseaux 2801—piso 6, Santiago 7500912, Chile;
| | - Victoria Castro
- Centro Nacional de Biotecnología-CSIC, Calle Darwin 3, 28049 Madrid, Spain; (U.G.); (V.C.)
| | - Vanesa Nozal
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
| | - Inés Maestro
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
| | - Javier García-Cárceles
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
| | - Nuria E. Campillo
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
| | - Ana Martinez
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
| | - Pablo Gastaminza
- Centro Nacional de Biotecnología-CSIC, Calle Darwin 3, 28049 Madrid, Spain; (U.G.); (V.C.)
- Correspondence: (P.G.); (C.G.)
| | - Carmen Gil
- Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (T.G.); (V.N.); (I.M.); (J.G.-C.); (N.E.C.); (A.M.)
- Correspondence: (P.G.); (C.G.)
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23
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Valdés-Jiménez A, Peña-Varas C, Borrego-Muñoz P, Arrue L, Alegría-Arcos M, Nour-Eldin H, Dreyer I, Nuñez-Vivanco G, Ramírez D. PSC-db: A Structured and Searchable 3D-Database for Plant Secondary Compounds. Molecules 2021; 26:1124. [PMID: 33672700 PMCID: PMC7924326 DOI: 10.3390/molecules26041124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
Plants synthesize a large number of natural products, many of which are bioactive and have practical values as well as commercial potential. To explore this vast structural diversity, we present PSC-db, a unique plant metabolite database aimed to categorize the diverse phytochemical space by providing 3D-structural information along with physicochemical and pharmaceutical properties of the most relevant natural products. PSC-db may be utilized, for example, in qualitative estimation of biological activities (Quantitative Structure-Activity Relationship, QSAR) or massive docking campaigns to identify new bioactive compounds, as well as potential binding sites in target proteins. PSC-db has been implemented using the open-source PostgreSQL database platform where all compounds with their complementary and calculated information (classification, redundant names, unique IDs, physicochemical properties, etc.) were hierarchically organized. The source organism for each compound, as well as its biological activities against protein targets, cell lines and different organism were also included. PSC-db is freely available for public use and is hosted at the Universidad de Talca.
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Affiliation(s)
- Alejandro Valdés-Jiménez
- Center for Bioinformatics, Simulations, and Modeling (CBSM), Faculty of Engineering, University of Talca, Talca 3460000, Chile; (A.V.-J.); (I.D.); (G.N.-V.)
| | - Carlos Peña-Varas
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile; (C.P.-V.); (L.A.); (M.A.-A.)
| | - Paola Borrego-Muñoz
- Bioorganic Chemistry Laboratory, Facultad de Ciencias Básicas y Aplicadas, Campus Nueva Granada, Universidad Militar Nueva Granada, Cajicá 250247, Colombia;
| | - Lily Arrue
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile; (C.P.-V.); (L.A.); (M.A.-A.)
| | - Melissa Alegría-Arcos
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile; (C.P.-V.); (L.A.); (M.A.-A.)
| | - Hussam Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, 1017 Copenhagen, Denmark;
| | - Ingo Dreyer
- Center for Bioinformatics, Simulations, and Modeling (CBSM), Faculty of Engineering, University of Talca, Talca 3460000, Chile; (A.V.-J.); (I.D.); (G.N.-V.)
| | - Gabriel Nuñez-Vivanco
- Center for Bioinformatics, Simulations, and Modeling (CBSM), Faculty of Engineering, University of Talca, Talca 3460000, Chile; (A.V.-J.); (I.D.); (G.N.-V.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8900000, Chile; (C.P.-V.); (L.A.); (M.A.-A.)
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24
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Gonzalez W, Nuñez-Vivanco G, Ramírez D, Kiper AK, Rinne S, Bedoya M, Arévalo B, Márquez-Montesinos J, Reyes-Parada M, Yarov-Yarovoy V, Decher N. A “Receptophore Model” for Local Anesthetics Binding Site in Cardiac Ion Channels. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.1616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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25
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Gil C, Ginex T, Maestro I, Nozal V, Barrado-Gil L, Cuesta-Geijo MÁ, Urquiza J, Ramírez D, Alonso C, Campillo NE, Martinez A. COVID-19: Drug Targets and Potential Treatments. J Med Chem 2020; 63:12359-12386. [PMID: 32511912 PMCID: PMC7323060 DOI: 10.1021/acs.jmedchem.0c00606] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Currently, humans are immersed in a pandemic caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which threatens public health worldwide. To date, no drug or vaccine has been approved to treat the severe disease caused by this coronavirus, COVID-19. In this paper, we will focus on the main virus-based and host-based targets that can guide efforts in medicinal chemistry to discover new drugs for this devastating disease. In principle, all CoV enzymes and proteins involved in viral replication and the control of host cellular machineries are potentially druggable targets in the search for therapeutic options for SARS-CoV-2. This Perspective provides an overview of the main targets from a structural point of view, together with reported therapeutic compounds with activity against SARS-CoV-2 and/or other CoVs. Also, the role of innate immune response to coronavirus infection and the related therapeutic options will be presented.
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Affiliation(s)
- Carmen Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Tiziana Ginex
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Inés Maestro
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Vanesa Nozal
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Lucía Barrado-Gil
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Miguel Ángel Cuesta-Geijo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Urquiza
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - David Ramírez
- Instituto de Ciencias Biomédicas,
Universidad Autónoma de Chile,
Llano Subercaseaux 2801- piso 6, 7500912 Santiago,
Chile
| | - Covadonga Alonso
- Department of Biotechnology,
Instituto Nacional de Investigación y
Tecnología Agraria y Alimentaria (INIA),
Ctra. de la Coruña km 7.5, 28040 Madrid,
Spain
| | - Nuria E. Campillo
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones
Biológicas Margarita Salas (CSIC), Ramiro
de Maeztu 9, 28040 Madrid, Spain
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26
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Pérez-Reytor D, Pavón A, Lopez-Joven C, Ramírez-Araya S, Peña-Varas C, Plaza N, Alegría-Arcos M, Corsini G, Jaña V, Pavez L, Del Pozo T, Bastías R, Blondel CJ, Ramírez D, García K. Analysis of the Zonula occludens Toxin Found in the Genome of the Chilean Non-toxigenic Vibrio parahaemolyticus Strain PMC53.7. Front Cell Infect Microbiol 2020; 10:482. [PMID: 33072618 PMCID: PMC7541967 DOI: 10.3389/fcimb.2020.00482] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Vibrio parahaemolyticus non-toxigenic strains are responsible for about 10% of acute gastroenteritis associated with this species, suggesting they harbor unique virulence factors. Zonula occludens toxin (Zot), firstly described in Vibrio cholerae, is a secreted toxin that increases intestinal permeability. Recently, we identified Zot-encoding genes in the genomes of highly cytotoxic Chilean V. parahaemolyticus strains, including the non-toxigenic clinical strain PMC53.7. To gain insights into a possible role of Zot in V. parahaemolyticus, we analyzed whether it could be responsible for cytotoxicity. However, we observed a barely positive correlation between Caco-2 cell membrane damage and Zot mRNA expression during PMC53.7 infection and non-cytotoxicity induction in response to purified PMC53.7-Zot. Unusually, we observed a particular actin disturbance on cells infected with PMC53.7. Based on this observation, we decided to compare the sequence of PMC53.7-Zot with Zot of human pathogenic species such as V. cholerae, Campylobacter concisus, Neisseria meningitidis, and other V. parahaemolyticus strains, using computational tools. The PMC53.7-Zot was compared with other toxins and identified as an endotoxin with conserved motifs in the N-terminus and a variable C-terminal region and without FCIGRL peptide. Notably, the C-terminal diversity among Zots meant that not all of them could be identified as toxins. Structurally, PMC53.7-Zot was modeled as a transmembrane protein. Our results suggested that it has partial 3D structure similarity with V. cholerae-Zot. Probably, the PMC53.7-Zot would affect the actin cytoskeletal, but, in the absence of FCIGRL, the mechanisms of actions must be elucidated.
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Affiliation(s)
- Diliana Pérez-Reytor
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Alequis Pavón
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Carmen Lopez-Joven
- Facultad de Ciencias Veterinarias, Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Valdivia, Chile
| | - Sebastián Ramírez-Araya
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Carlos Peña-Varas
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Nicolás Plaza
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Melissa Alegría-Arcos
- Facultad de Ciencias, Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
| | - Gino Corsini
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Víctor Jaña
- Facultad de Medicina Veterinaria y Agronomía, Universidad de las Américas, Santiago, Chile
| | - Leonardo Pavez
- Departamento de Ciencias Químicas y Biológicas, Universidad Bernardo O'Higgins, Santiago, Chile.,Instituto de Ciencias Naturales, Universidad de Las Américas, Santiago, Chile
| | - Talia Del Pozo
- Centro Tecnológico de Recursos Vegetales, Escuela de Agronomía, Universidad Mayor, Huechuraba, Chile
| | - Roberto Bastías
- Laboratorio de Microbiología, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Carlos J Blondel
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile.,Facultad de Medicina y Facultad de Ciencias de la Vida, Instituto de Ciencias Biomédicas, Universidad Andrés Bello, Santiago, Chile
| | - David Ramírez
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Katherine García
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
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27
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Becerra GP, Rojas-Rodríguez F, Ramírez D, Loaiza AE, Tobar-Tosse F, Mejía SM, González J. Structural and functional computational analysis of nicotine analogs as potential neuroprotective compounds in Parkinson disease. Comput Biol Chem 2020; 86:107266. [PMID: 32388154 DOI: 10.1016/j.compbiolchem.2020.107266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/13/2020] [Indexed: 11/27/2022]
Abstract
As the mechanism of interaction between nicotinic receptors with nicotine analogs is not yet fully understood, information at molecular level obtained from computational calculations is needed. In this sense, this work is a computational study of eight nicotine analogs, all with pyrrolidine ring modifications over a nicotine-based backbone optimized with B3LYP-D3/aug-cc-pVDZ. A molecular characterization was performed focusing on geometrical parameters such as pseudo-rotation angles, atomic charges, HOMO and LUMO orbitals, reactivity indexes and intermolecular interactions. Three analogs, A2 (3-(1,3-dimethyl-4,5-dihydro-1h-pirazole-5-yl) pyridine), A3 (3-(3-methyl-4,5-dihydro-1H-pyrazol-5-yl)-pyridine) and A8 (5-methyl-3-(pyridine-3-yl)-4,5-dihydroisoxazole), were filtered suggesting putative neuroprotective activity taking into account different reactivity values, such as their lowest hardness: 2.37 eV (A8), 2.43 eV (A2) and 2.56 eV (A3), compared to the highest hardness value found: 2.71 eV for A5 (3-((2S,4R)-4-(fluoromethyl)-1-methylpyrrolidine-2-il) pyridine), similar to the value of nicotine (2.70 eV). Additionally, molecular docking of all 8 nicotine analogs with the α 7 nicotinic acetylcholine receptor (α 7 nAChR) was performed. High values of interaction between the receptor and the three nicotine analogs were obtained: A3 (-7.1 kcal/mol), A2 (-6.9 kcal/mol) and A8 (-6.8 kcal/mol); whereas the affinity energy of nicotine was -6.4 kcal/mol. Leu116 and Trp145 are key residues in the binding site of α 7 nAChR interacting with nicotine analogs. Therefore, based upon these results, possible application of these nicotine analogs as neuroprotective compounds and potential implication at the design of novel Parkinson's treatments is evidenced.
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Affiliation(s)
- Gina Paola Becerra
- Laboratorio de Bioquímica Computacional Estructural y Bioinformática, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia; Laboratorio de Química Computacional, Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Felipe Rojas-Rodríguez
- Laboratorio de Bioquímica Computacional Estructural y Bioinformática, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, El Llano Subercaseaux 2801-Piso 5, 8900000, Santiago, Chile
| | - Alix E Loaiza
- Laboratorio de Síntesis Orgánica, Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Fabian Tobar-Tosse
- Departamento de Ciencias Básicas de la Salud, Facultad de Ciencias de la Salud, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Sol M Mejía
- Laboratorio de Química Computacional, Departamento de Química, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - Janneth González
- Laboratorio de Bioquímica Computacional Estructural y Bioinformática, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
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28
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Garcia-Rodriguez J, Fernandez-Gomez J, Cozar J, Miñana B, Gomez-Veiga F, Rodriguez-Antolin A, Pórtela P, Blanco E, González J, Baena V, Morales P, Villavicencio H, Palou J, Loizaga A, Ciudin A, Mihai D, Martínez Jabaloyas J, Castelló A, Díez N, Romero F, Subirá J, Chávez A, Capapé V, Mata M, Elizalde J, Lobato J, Jiménez J, Pérez Llorca L, Tenza J, Herranz F, Husillos A, López E, Ramírez D, Blaha I, Izquierdo E, Reina L, Passas J, Díez L, Hevia M, Castells M, Concepción Masip T, Plata A, Asuar Aydillo S, Alonso J, Mateos J, Carballido J, Martínez C, Areche J, Rodríguez R, Hevia V, Álvarez S, Requena M, Prieto R, Carazo J, Márquez J, Gómez E, García J, Amón J, Cepeda M, Álvarez L, Rodríguez V, de la Cruz B, Rivero A, Sánchez J, Mainez J, Medina R, Conde M, Castiñeiras J, González Baena A, Sánchez E, Campanario R, Saiz R, Romero E, Morote J, Raventós C, Celma A, Vázquez F, Gómez A, Buendía E, García N. Androgen deprivation therapy in patients with localized disease: Comparison with curative intent treatments and time to castration resistance. Results of the Spanish Prostate Cancer Registry. Actas Urol Esp 2020; 44:156-163. [PMID: 32113829 DOI: 10.1016/j.acuro.2019.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 03/26/2019] [Accepted: 06/09/2019] [Indexed: 10/24/2022]
Abstract
BACKGROUND The effect of primary androgen deprivation therapy (ADT) in patients with localized prostate cancer (PCa) has not been well documented. The objective of the present study was to analyze the outcome of tumors treated with ADT as primary therapy in the Spanish Prostate Cancer Registry (19.4% of the series). PATIENTS AND METHODS Patients were classified in three groups: 1) with low/intermediate risk clinically localized tumors; 2) with high risk and locally advanced (T3-4) tumors; 3) with metastatic tumors. Time to castration resistance and overall cancer-specific survival were analyzed. In non-metastatic tumors, survivals in patients treated with ADT were compared with data from patients who underwent local treatments from the Spanish Prostate Cancer Registry. RESULTS 703 cases were analyzed. There were significant differences in the time to castration resistance, which was lower in the group of metastatic tumors. During follow-up, there were 179 deaths (25.5%) of which 89 (12.6%) were due to PCa. After 3 years of ADT, only 14.6% of patients in group 1 had died (1% due to PCa), 20.5% in group 2 and 46.8% in group 3 (9.2% and 31.3% due to PCa, respectively). Cancer-specific survival was significantly worse in group 1 using ADT than radical prostatectomy or radiotherapy. In high-risk and locally advanced tumors, ADT also had a lower cancer-specific survival than local treatments. CONCLUSION A longer time until the castration resistance was observed in patients with well- and intermediate-risk localized tumors treated with ADT. Patients with metastatic tumors showed the shortest time to castration resistance.
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29
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Pimentel J, Arias A, Ramírez D, Molina A, Chomat AM, Cockcroft A, Andersson N. Game-Based Learning Interventions to Foster Cross-Cultural Care Training: A Scoping Review. Games Health J 2020; 9:164-181. [PMID: 32027184 DOI: 10.1089/g4h.2019.0078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Objective: Differences in cultural background between health providers and patients can reduce effective access to health services in multicultural settings. Health sciences educators have recently suggested that game-based learning may be effective for cross-cultural care training. This scoping review maps published knowledge on educational games intended to foster cross-cultural care training and highlights the research gaps for future research. Materials and Methods: A scoping review searched PubMed, Eric, Embase, Lilacs, PsycINFO, and Google Scholar for theoretical and empirical research, using terms relevant to cross-cultural care and game-based learning. A participatory research framework engaged senior medical students and participatory research experts in conducting and evaluating the review. Results: Forty-one documents met the inclusion criteria, all from developed countries. The most common source of publication was nursing and medicine (39%; 16/41) and used the cultural competence approach (44%; 18/41). Around one-half of the publications (51%; 21/41) were theoretical and 39% (16/41) were empirical. Empirical studies most commonly used mixed methods (44%; 7/16), followed by strictly quantitative (31%; 5/16) or qualitative (25%; 4/16) approaches. There were no randomized controlled trials and only one study engaged end-users in the design. Empirical studies most frequently assessed role-play-related games (44%; 7/16) and used game evaluation-related outcomes or learning-related outcomes. None used patient-oriented outcomes. Findings suggest that educational games are an effective and engaging educational intervention for cross-cultural care training. Conclusions: The paucity of studies on educational games and cross-cultural care training precludes a systematic review. Future empirical studies should focus on randomized counterfactual designs and patient-related outcomes. We encourage involving end-users in developing content for educational games.
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Affiliation(s)
- Juan Pimentel
- CIET-PRAM, Department of Family Medicine, McGill University, Montreal, Canada.,Departamento de Medicina Familiar y Salud Pública, Facultad de Medicina, Universidad de La Sabana, Chia, Colombia.,Grupo de Estudios en Sistemas Tradicionales de Salud, Universidad del Rosario, Bogota, Colombia
| | - Alexandra Arias
- Departamento de Medicina Familiar y Salud Pública, Facultad de Medicina, Universidad de La Sabana, Chia, Colombia
| | - David Ramírez
- Departamento de Medicina Familiar y Salud Pública, Facultad de Medicina, Universidad de La Sabana, Chia, Colombia
| | - Adriana Molina
- Departamento de Medicina Familiar y Salud Pública, Facultad de Medicina, Universidad de La Sabana, Chia, Colombia
| | - Anne-Marie Chomat
- CIET-PRAM, Department of Family Medicine, McGill University, Montreal, Canada
| | - Anne Cockcroft
- CIET-PRAM, Department of Family Medicine, McGill University, Montreal, Canada
| | - Neil Andersson
- CIET-PRAM, Department of Family Medicine, McGill University, Montreal, Canada.,Centro de Investigación de Enfermedades Tropicales (CIET), Universidad Autónoma de Guerrero, Acapulco, Mexico
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30
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Bustos D, Bedoya M, Ramírez D, Concha G, Zúñiga L, Decher N, Hernández-Rodríguez EW, Sepúlveda FV, Martínez L, González W. Elucidating the Structural Basis of the Intracellular pH Sensing Mechanism of TASK-2 K 2P Channels. Int J Mol Sci 2020; 21:ijms21020532. [PMID: 31947679 PMCID: PMC7013731 DOI: 10.3390/ijms21020532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/25/2019] [Accepted: 01/08/2020] [Indexed: 11/23/2022] Open
Abstract
Two-pore domain potassium (K2P) channels maintain the cell’s background conductance by stabilizing the resting membrane potential. They assemble as dimers possessing four transmembrane helices in each subunit. K2P channels were crystallized in “up” and “down” states. The movements of the pore-lining transmembrane TM4 helix produce the aperture or closure of side fenestrations that connect the lipid membrane with the central cavity. When the TM4 helix is in the up-state, the fenestrations are closed, while they are open in the down-state. It is thought that the fenestration states are related to the activity of K2P channels and the opening of the channels preferentially occurs from the up-state. TASK-2, a member of the TALK subfamily of K2P channels, is opened by intracellular alkalization leading the deprotonation of the K245 residue at the end of the TM4 helix. This charge neutralization of K245 could be sensitive or coupled to the fenestration state. Here, we describe the relationship between the states of the intramembrane fenestrations and K245 residue in TASK-2 channel. By using molecular modeling and simulations, we show that the protonated state of K245 (K245+) favors the open fenestration state and, symmetrically, that the open fenestration state favors the protonated state of the lysine residue. We show that the channel can be completely blocked by Prozac, which is known to induce fenestration opening in TREK-2. K245 protonation and fenestration aperture have an additive effect on the conductance of the channel. The opening of the fenestrations with K245+ increases the entrance of lipids into the selectivity filter, blocking the channel. At the same time, the protonation of K245 introduces electrostatic potential energy barriers to ion entrance. We computed the free energy profiles of ion penetration into the channel in different fenestration and K245 protonation states, to show that the effects of the two transformations are summed up, leading to maximum channel blocking. Estimated rates of ion transport are in qualitative agreement with experimental results and support the hypothesis that the most important barrier for ion transport under K245+ and open fenestration conditions is the entrance of the ions into the channel.
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Affiliation(s)
- Daniel Bustos
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca 3460000, Chile; (D.B.); (M.B.)
- Departamento de Computación e Industrias, Facultad de Ciencias de la Ingeniería, Universidad Católica del Maule, Talca 3460000, Chile
| | - Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca 3460000, Chile; (D.B.); (M.B.)
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago 8380453, Chile;
| | - Guierdy Concha
- Centro de Investigaciones Médicas, Escuela de Medicina, Universidad de Talca, Talca 3460000, Chile; (G.C.); (L.Z.)
- Magíster en Gestión de Operaciones, Facultad de Ingeniería (Campus Los Niches), Universidad de Talca, Talca 3460000, Chile
| | - Leandro Zúñiga
- Centro de Investigaciones Médicas, Escuela de Medicina, Universidad de Talca, Talca 3460000, Chile; (G.C.); (L.Z.)
- Programa de Investigación Asociativa en Cáncer Gástrico (PIA-CG), Universidad de Talca, Talca 3460000, Chile
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, D-35037 Marburg, Germany;
| | | | - Francisco V. Sepúlveda
- Centro de Estudios Científicos (CECs), Avenida Arturo Prat 514, Valdivia 5110466, Chile
- Correspondence: (F.V.S.); (L.M.); (W.G.)
| | - Leandro Martínez
- Institute of Chemistry and Center for Computing in Engineering & Science, University of Campinas, Campinas 13083-861 SP, Brazil
- Correspondence: (F.V.S.); (L.M.); (W.G.)
| | - Wendy González
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca 3460000, Chile; (D.B.); (M.B.)
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca 3460000, Chile
- Correspondence: (F.V.S.); (L.M.); (W.G.)
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Abstract
Rational drug design targeting ion channels is an exciting and always evolving research field. New medicinal chemistry strategies are being implemented to explore the wild chemical space and unravel the molecular basis of the ion channels modulators binding mechanisms. TASK channels belong to the two-pore domain potassium channel family and are modulated by extracellular acidosis. They are extensively distributed along the cardiovascular and central nervous systems, and their expression is up- and downregulated in different cancer types, which makes them an attractive therapeutic target. However, TASK channels remain unexplored, and drugs designed to target these channels are poorly selective. Here, we review TASK channels properties and their known blockers and activators, considering the new challenges in ion channels drug design and focusing on the implementation of computational methodologies in the drug discovery process.
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Affiliation(s)
- Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular (CBSM) , Universidad de Talca , 1 Poniente No. 1141 , 3460000 Talca , Chile
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior, MCMBB , Philipps-University of Marburg , Deutschhausstraße 2 , Marburg 35037 , Germany
| | - Aytug K Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior, MCMBB , Philipps-University of Marburg , Deutschhausstraße 2 , Marburg 35037 , Germany
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior, MCMBB , Philipps-University of Marburg , Deutschhausstraße 2 , Marburg 35037 , Germany
| | - Wendy González
- Centro de Bioinformática y Simulación Molecular (CBSM) , Universidad de Talca , 1 Poniente No. 1141 , 3460000 Talca , Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD) , Universidad de Talca , 1 Poniente No. 1141 , 3460000 Talca , Chile
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud , Universidad Autónoma de Chile , El Llano Subercaseaux 2801, Piso 6 , 8900000 Santiago , Chile
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Ramírez D, Bedoya M, Kiper AK, Rinné S, Morales-Navarro S, Hernández-Rodríguez EW, Sepúlveda FV, Decher N, González W. Structure/Activity Analysis of TASK-3 Channel Antagonists Based on a 5,6,7,8 tetrahydropyrido[4,3-d]pyrimidine. Int J Mol Sci 2019; 20:ijms20092252. [PMID: 31067753 PMCID: PMC6539479 DOI: 10.3390/ijms20092252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 11/16/2022] Open
Abstract
TASK-3 potassium (K+) channels are highly expressed in the central nervous system, regulating the membrane potential of excitable cells. TASK-3 is involved in neurotransmitter action and has been identified as an oncogenic K+ channel. For this reason, the understanding of the action mechanism of pharmacological modulators of these channels is essential to obtain new therapeutic strategies. In this study we describe the binding mode of the potent antagonist PK-THPP into the TASK-3 channel. PK-THPP blocks TASK-1, the closest relative channel of TASK-3, with almost nine-times less potency. Our results confirm that the binding is influenced by the fenestrations state of TASK-3 channels and occurs when they are open. The binding is mainly governed by hydrophobic contacts between the blocker and the residues of the binding site. These interactions occur not only for PK-THPP, but also for the antagonist series based on 5,6,7,8 tetrahydropyrido[4,3-d]pyrimidine scaffold (THPP series). However, the marked difference in the potency of THPP series compounds such as 20b, 21, 22 and 23 (PK-THPP) respect to compounds such as 17b, inhibiting TASK-3 channels in the micromolar range is due to the presence of a hydrogen bond acceptor group that can establish interactions with the threonines of the selectivity filter.
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Affiliation(s)
- David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile. El Llano Subercaseaux 2801-Piso 6, 7500912 Santiago, Chile.
| | - Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
| | - Aytug K Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany.
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany.
| | - Samuel Morales-Navarro
- Bachillerato en Ciencias, Facultad de Ciencias, Universidad Santo Tomás, Av. Circunvalación Poniente #1855, 3460000 Talca, Chile.
| | - Erix W Hernández-Rodríguez
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
- Escuela de Química y Farmacia. Facultad de Medicina. Universidad Católica del Maule, 3460000 Talca, Chile.
| | | | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany.
| | - Wendy González
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile.
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Rodríguez V, Pineda H, Ardila N, Insuasty D, Cárdenas K, Román J, Urrea M, Ramírez D, Fierro R, Rivera Z, García J. Efficient Fmoc Group Removal Using Diluted 4-Methylpiperidine: An Alternative for a Less-Polluting SPPS-Fmoc/tBu Protocol. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09865-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Jørgensen ME, Xu D, Crocoll C, Ernst HA, Ramírez D, Motawia MS, Olsen CE, Mirza O, Nour-Eldin HH, Halkier BA. Correction: Origin and evolution of transporter substrate specificity within the NPF family. eLife 2019; 8:46989. [PMID: 30938287 PMCID: PMC6445569 DOI: 10.7554/elife.46989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Delsouc MB, Ghersa F, Ramírez D, Della Vedova MC, Gil RA, Vallcaneras SS, Casais M. Endometriosis progression in tumor necrosis factor receptor p55-deficient mice: Impact on oxidative/nitrosative stress and metallomic profile. J Trace Elem Med Biol 2019; 52:157-165. [PMID: 30732877 DOI: 10.1016/j.jtemb.2018.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/07/2018] [Accepted: 12/29/2018] [Indexed: 01/01/2023]
Abstract
The present study was conducted to investigate whether the deficiency of tumor necrosis factor receptor p55 (TNFRp55) modulates oxidative/nitrosative stress and metallomic profile into the peritoneal cavity during the experimental endometriosis progression in mice. Female C57BL/6 mice, wild-type (WT) and TNFRp55 knockout (KO) of two months were used. Endometriosis was induced experimentally by autotransplanting three pieces of the right uterine horn to the intestinal mesentery. After four weeks, endometriotic-like lesions and peritoneal lavage fluid were collected. The obtained peritoneal fluid was analyzed for nitrite levels using the Griess method and trace elements concentrations by ICP-MS. Both endometriotic-like lesions and cells isolated from peritoneal lavage were analyzed for the following oxidative/nitrosative stress markers: inducible nitric oxide synthase (iNOS) expression by Western Blot; total antioxidant capacity (TAC), the activity of two antioxidant enzymes (CAT and GPX) and thiobarbituric acid-reactive substances (TBARS) concentration, by spectrophotometric method; and protein carbonyl content and nitrotyrosine presence by ELISA. In comparison to WT group, KO mice exhibited larger lesion volume; higher levels of nitrite, copper (Cu) and strontium (Sr) in the peritoneal fluid; increased TAC, CAT, and GPX in peritoneal lavage cells; decreased concentration of TBARS in lesions and protein carbonyl in peritoneal lavage cells. Significant positive correlations between Cu and lesion volume, Sr and lesion volume, and Cu and Sr were obtained. Our results suggest that the TNFRp55 deficiency increases antioxidant protection and promotes high Cu-Sr concentrations in the peritoneal cavity, which favors the progression of experimental endometriosis.
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Affiliation(s)
- M B Delsouc
- Laboratorio de Biología de la Reproducción (LABIR), Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina
| | - F Ghersa
- Laboratorio de Biología de la Reproducción (LABIR), Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina
| | - D Ramírez
- Laboratorio de Medicina Experimental & Traduccional (LME&T), Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina
| | - M C Della Vedova
- Instituto de Química de San Luis (INQUISAL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina
| | - R A Gil
- Instituto de Química de San Luis (INQUISAL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina
| | - S S Vallcaneras
- Laboratorio de Biología de la Reproducción (LABIR), Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina
| | - M Casais
- Laboratorio de Biología de la Reproducción (LABIR), Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis (IMIBIO-SL), CONICET, Ejército de Los Andes 950, CP D5700HHW, San Luis, Argentina.
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Rinné S, Kiper AK, Vowinkel KS, Ramírez D, Schewe M, Bedoya M, Aser D, Gensler I, Netter MF, Stansfeld PJ, Baukrowitz T, Gonzalez W, Decher N. The molecular basis for an allosteric inhibition of K +-flux gating in K 2P channels. eLife 2019; 8:39476. [PMID: 30803485 PMCID: PMC6391080 DOI: 10.7554/elife.39476] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 02/06/2019] [Indexed: 01/05/2023] Open
Abstract
Two-pore-domain potassium (K2P) channels are key regulators of many physiological and pathophysiological processes and thus emerged as promising drug targets. As for other potassium channels, there is a lack of selective blockers, since drugs preferentially bind to a conserved binding site located in the central cavity. Thus, there is a high medical need to identify novel drug-binding sites outside the conserved lipophilic central cavity and to identify new allosteric mechanisms of channel inhibition. Here, we identified a novel binding site and allosteric inhibition mechanism, disrupting the recently proposed K+-flux gating mechanism of K2P channels, which results in an unusual voltage-dependent block of leak channels belonging to the TASK subfamily. The new binding site and allosteric mechanism of inhibition provide structural and mechanistic insights into the gating of TASK channels and the basis for the drug design of a new class of potent blockers targeting specific types of K2P channels.
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Affiliation(s)
- Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Aytug K Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Kirsty S Vowinkel
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - David Ramírez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Talca, Chile
| | - Marcus Schewe
- Institute of Physiology, University of Kiel, Kiel, Germany
| | - Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile
| | - Diana Aser
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Isabella Gensler
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Michael F Netter
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
| | - Phillip J Stansfeld
- Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | - Wendy Gonzalez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, Talca, Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, Marburg, Germany
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Novoa-Aponte L, Ramírez D, Argüello JM. The interplay of the metallosensor CueR with two distinct CopZ chaperones defines copper homeostasis in Pseudomonas aeruginosa. J Biol Chem 2019; 294:4934-4945. [PMID: 30718281 DOI: 10.1074/jbc.ra118.006316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 10/17/2018] [Revised: 01/31/2019] [Indexed: 12/27/2022] Open
Abstract
Copper homeostasis in pathogenic bacteria is critical for cuproprotein assembly and virulence. However, in vivo biochemical analyses of these processes are challenging, which has prevented defining and quantifying the homeostatic interplay between Cu+-sensing transcriptional regulators, chaperones, and sequestering molecules. The cytoplasm of Pseudomonas aeruginosa contains a Cu+-sensing transcriptional regulator, CueR, and two homologous metal chaperones, CopZ1 and CopZ2, forming a unique system for studying Cu+ homeostasis. We found here that both chaperones exchange Cu+, albeit at a slow rate, reaching equilibrium after 3 h, a time much longer than P. aeruginosa duplication time. Therefore, they appeared as two separate cellular Cu+ pools. Although both chaperones transferred Cu+ to CueR in vitro, experiments in vivo indicated that CopZ1 metallates CueR, eliciting the translation of Cu+ efflux transporters involved in metal tolerance. Although this observation was consistent with the relative Cu+ affinities of the three proteins (CopZ1 < CueR < CopZ2), in vitro and in silico analyses also indicated a stronger interaction between CopZ1 and CueR that was independent of Cu+ In contrast, CopZ2 function was defined by its distinctly high abundance during Cu2+ stress. Under resting conditions, CopZ2 remained largely in its apo form. Metal stress quickly induced CopZ2 expression, and its holo form predominated, reaching levels commensurate with the cytoplasmic Cu+ levels. In summary, these results show that CopZ1 acts as chaperone delivering Cu+ to the CueR sensor, whereas CopZ2 functions as a fast-response Cu+-sequestering storage protein. We propose that equivalent proteins likely play similar roles in most bacterial systems.
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Affiliation(s)
- Lorena Novoa-Aponte
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01605
| | - David Ramírez
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01605
| | - José M Argüello
- From the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01605
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Berrouiguet S, Ramírez D, Barrigón ML, Moreno-Muñoz P, Carmona Camacho R, Baca-García E, Artés-Rodríguez A. Combining Continuous Smartphone Native Sensors Data Capture and Unsupervised Data Mining Techniques for Behavioral Changes Detection: A Case Series of the Evidence-Based Behavior (eB2) Study. JMIR Mhealth Uhealth 2018; 6:e197. [PMID: 30530465 PMCID: PMC6305880 DOI: 10.2196/mhealth.9472] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 05/18/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The emergence of smartphones, wearable sensor technologies, and smart homes allows the nonintrusive collection of activity data. Thus, health-related events, such as activities of daily living (ADLs; eg, mobility patterns, feeding, sleeping, ...) can be captured without patients' active participation. We designed a system to detect changes in the mobility patterns based on the smartphone's native sensors and advanced machine learning and signal processing techniques. OBJECTIVE The principal objective of this work is to assess the feasibility of detecting mobility pattern changes in a sample of outpatients with depression using the smartphone's sensors. The proposed method processed the data acquired by the smartphone using an unsupervised detection technique. METHODS In this study, 38 outpatients from the Hospital Fundación Jiménez Díaz Psychiatry Department (Madrid, Spain) participated. The Evidence-Based Behavior (eB2) app was downloaded by patients on the day of recruitment and configured with the assistance of a physician. The app captured the following data: inertial sensors, physical activity, phone calls and message logs, app usage, nearby Bluetooth and Wi-Fi connections, and location. We applied a change-point detection technique to location data on a sample of 9 outpatients recruited between April 6, 2017 and December 14, 2017. The change-point detection was based only on location information, but the eB2 platform allowed for an easy integration of additional data. The app remained running in the background on patients' smartphone during the study participation. RESULTS The principal outcome measure was the identification of mobility pattern changes based on an unsupervised detection technique applied to the smartphone's native sensors data. Here, results from 5 patients' records are presented as a case series. The eB2 system detected specific mobility pattern changes according to the patients' activity, which may be used as indicators of behavioral and clinical state changes. CONCLUSIONS The proposed technique could automatically detect changes in the mobility patterns of outpatients who took part in this study. Assuming these mobility pattern changes correlated with behavioral changes, we have developed a technique that may identify possible relapses or clinical changes. Nevertheless, it is important to point out that the detected changes are not always related to relapses and that some clinical changes cannot be detected by the proposed method.
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Affiliation(s)
- Sofian Berrouiguet
- Department of Psychiatry and Emergency, Brest Medical University Hospital, Brest, France.,IMT Atlantique, Lab-STICC, F-29238, Brest, France.,SPURBO EA 7479, Université de Bretagne Occidentale (UBO), Brest, France.,CHRU Cavale Blanche University Hospital of Brest, Brest, France
| | - David Ramírez
- Universidad Carlos III de Madrid, Leganés, Spain.,Gregorio Marañón Health Research Institute, Madrid, Spain
| | - María Luisa Barrigón
- Department of Psychiatry, Fundación Jiménez Díaz Hospital, Madrid, Spain.,Department of Psychiatry, Autónoma University, Madrid, Spain
| | - Pablo Moreno-Muñoz
- Universidad Carlos III de Madrid, Leganés, Spain.,Gregorio Marañón Health Research Institute, Madrid, Spain
| | | | - Enrique Baca-García
- Department of Psychiatry, Fundación Jiménez Díaz Hospital, Madrid, Spain.,Department of Psychiatry, Autónoma University, Madrid, Spain.,Centro de Investigación en Salud Mental, Carlos III Institute of Health, Madrid, Spain
| | - Antonio Artés-Rodríguez
- Universidad Carlos III de Madrid, Leganés, Spain.,Gregorio Marañón Health Research Institute, Madrid, Spain.,Centro de Investigación en Salud Mental, Carlos III Institute of Health, Madrid, Spain
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Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P. An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Mol Microbiol 2018; 110:357-369. [PMID: 30047562 PMCID: PMC6207460 DOI: 10.1111/mmi.14086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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] [Accepted: 07/18/2018] [Indexed: 02/04/2023]
Abstract
Biological systems require precise copper homeostasis enabling metallation of cuproproteins while preventing metal toxicity. In bacteria, sensing, transport, and storage molecules act in coordination to fulfill these roles. However, there is not yet a kinetic schema explaining the system integration. Here, we report a model emerging from experimental and computational approaches that describes the dynamics of copper distribution in Pseudomonas aeruginosa. Based on copper uptake experiments, a minimal kinetic model describes well the copper distribution in the wild-type bacteria but is unable to explain the behavior of the mutant strain lacking CopA1, a key Cu+ efflux ATPase. The model was expanded through an iterative hypothesis-driven approach, arriving to a mechanism that considers the induction of compartmental pools and the parallel function of CopA and Cus efflux systems. Model simulations support the presence of a periplasmic copper storage with a crucial role under dyshomeostasis conditions in P. aeruginosa. Importantly, the model predicts not only the interplay of periplasmic and cytoplasmic pools but also the existence of a threshold in the concentration of external copper beyond which cells lose their ability to control copper levels.
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Affiliation(s)
- Jignesh H Parmar
- Center for Quantitative Medicine and Department of Cell Biology, University of Connecticut School of Medicine, 263 Farmington Av, Farmington, CT, 06030, USA
| | - Julia Quintana
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - David Ramírez
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Reinhard Laubenbacher
- Center for Quantitative Medicine and Department of Cell Biology, University of Connecticut School of Medicine, 263 Farmington Av, Farmington, CT, 06030, USA
- Jackson Laboratory for Genomic Medicine, 10 Discovery Dr, Farmington, CT, 06032, USA
| | - José M Argüello
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA, 01609, USA
| | - Pedro Mendes
- Center for Quantitative Medicine and Department of Cell Biology, University of Connecticut School of Medicine, 263 Farmington Av, Farmington, CT, 06030, USA
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Galvis V, Berrospi R, Tello A, Ramírez D, Villarreal D. Mycotic keratitis caused by Scedosporium apiospermum in an immunocompetent patient. ACTA ACUST UNITED AC 2018; 93:613-616. [PMID: 30017419 DOI: 10.1016/j.oftal.2018.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/01/2018] [Revised: 05/20/2018] [Accepted: 05/29/2018] [Indexed: 11/26/2022]
Abstract
CLINICAL CASE A 51 year-old immunocompetent male was referred due to presenting with a large corneal ulcer with hypopyon in the right eye. Topical amphotericin B, fluconazole and moxifloxacin, as well as oral itraconazole were initially indicated. Following the report of mycotic structures on staining, topical natamycin was started. The result of the culture was reported two weeks later as, Scedosporium apiospermum (S. apiospermum), and topical voriconazole was then added. The response to treatment was very slow, and took five weeks after receiving triple therapy (natamycin, voriconazole and fluconazole) and one dose of intrastromal voriconazole, for the hypopyon to disappear. The final outcome was successful, achieving healing of the ulcer. The patient is waiting for a corneal transplant. DISCUSSION A microbiological study is essential in patients in whom fungal keratitis is suspected. The treatment of choice against S. apiospermum is with voriconazole, but the combination of various antifungal agents may be required.
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Affiliation(s)
- V Galvis
- Centro oftalmológico Virgilio Galvis, Floridablanca, Colombia; Fundación Oftalmológica de Santander, FOSCAL, Floridablanca, Colombia; Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia
| | - R Berrospi
- Centro oftalmológico Virgilio Galvis, Floridablanca, Colombia; Fundación Oftalmológica de Santander, FOSCAL, Floridablanca, Colombia
| | - A Tello
- Centro oftalmológico Virgilio Galvis, Floridablanca, Colombia; Fundación Oftalmológica de Santander, FOSCAL, Floridablanca, Colombia; Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia.
| | - D Ramírez
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Autónoma de Bucaramanga, Bucaramanga, Colombia; Facultad de Ciencias de la Salud, Medicina, Universidad El Bosque, Bogotá, Colombia
| | - D Villarreal
- Laboratorio Clínico Higuera Escalante-Centro de Diagnóstico ocular (OCULAB), Floridablanca, Colombia
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Ramírez D, Caballero J. Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data? Molecules 2018; 23:molecules23051038. [PMID: 29710787 PMCID: PMC6102569 DOI: 10.3390/molecules23051038] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/21/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022] Open
Abstract
Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor binding site. However, the selection of the “best” solution is not a trivial task, despite the widely accepted selection criterion that the best pose corresponds to the best energy score. Here, several rigid-target docking methods were evaluated on the same dataset with respect to their ability to reproduce crystallographic binding orientations, to test if the best energy score is a reliable criterion for selecting the best solution. For this, two experiments were performed: (A) to reconstruct the ligand-receptor complex by performing docking of the ligand in its own crystal structure receptor (defined as self-docking), and (B) to reconstruct the ligand-receptor complex by performing docking of the ligand in a crystal structure receptor that contains other ligand (defined as cross-docking). Root-mean square deviation (RMSD) was used to evaluate how different the obtained docking orientation is from the corresponding co-crystallized pose of the same ligand molecule. We found that docking score function is capable of predicting crystallographic binding orientations, but the best ranked solution according to the docking energy is not always the pose that reproduces the experimental binding orientation. This happened when self-docking was achieved, but it was critical in cross-docking. Taking into account that docking is typically used with predictive purposes, during cross-docking experiments, our results indicate that the best energy score is not a reliable criterion to select the best solution in common docking applications. It is strongly recommended to choose the best docking solution according to the scoring function along with additional structural criteria described for analogue ligands to assure the selection of a correct docking solution.
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Affiliation(s)
- David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, 5 Poniente No. 1670, 3460000 Talca, Chile.
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
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Ramírez D, Naranjo B, Duchicela J. Estimulación de germinación y colonización radicular de Diversispora trimulares por flavonoides de exudados radiculares de Nicotiana glauca. Rev U D C A Act & Div Cient 2017. [DOI: 10.31910/rudca.v20.n2.2017.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Ojeda PG, Ramírez D, Alzate-Morales J, Caballero J, Kaas Q, González W. Computational Studies of Snake Venom Toxins. Toxins (Basel) 2017; 10:E8. [PMID: 29271884 PMCID: PMC5793095 DOI: 10.3390/toxins10010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Most snake venom toxins are proteins, and participate to envenomation through a diverse array of bioactivities, such as bleeding, inflammation, and pain, cytotoxic, cardiotoxic or neurotoxic effects. The venom of a single snake species contains hundreds of toxins, and the venoms of the 725 species of venomous snakes represent a large pool of potentially bioactive proteins. Despite considerable discovery efforts, most of the snake venom toxins are still uncharacterized. Modern bioinformatics tools have been recently developed to mine snake venoms, helping focus experimental research on the most potentially interesting toxins. Some computational techniques predict toxin molecular targets, and the binding mode to these targets. This review gives an overview of current knowledge on the ~2200 sequences, and more than 400 three-dimensional structures of snake toxins deposited in public repositories, as well as of molecular modeling studies of the interaction between these toxins and their molecular targets. We also describe how modern bioinformatics have been used to study the snake venom protein phospholipase A2, the small basic myotoxin Crotamine, and the three-finger peptide Mambalgin.
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Affiliation(s)
- Paola G Ojeda
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - David Ramírez
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomedicas, Universidad Autonoma de Chile, 3460000 Talca, Chile.
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, 3460000 Talca, Chile.
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3460000 Talca, Chile.
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Ramírez D, Arévalo B, Martínez G, Rinné S, Sepúlveda FV, Decher N, González W. Side Fenestrations Provide an "Anchor" for a Stable Binding of A1899 to the Pore of TASK-1 Potassium Channels. Mol Pharm 2017; 14:2197-2208. [PMID: 28494157 DOI: 10.1021/acs.molpharmaceut.7b00005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A1899 is a potent and selective inhibitor of the two-pore domain potassium (K2P) channel TASK-1. It was previously reported that A1899 acts as an open-channel blocker and binds to residues of the P1 and P2 regions, the M2 and M4 segments, and the halothane response element. The recently described crystal structures of K2P channels together with the newly identified side fenestrations indicate that residues relevant for TASK-1 inhibition are not purely facing the central cavity as initially proposed. Accordingly, the TASK-1 binding site and the mechanism of inhibition might need a re-evaluation. We have used TASK-1 homology models based on recently crystallized K2P channels and molecular dynamics simulation to demonstrate that the highly potent TASK-1 blocker A1899 requires binding to residues located in the side fenestrations. Unexpectedly, most of the previously described residues that interfere with TASK-1 blockade by A1899 project their side chains toward the fenestration lumina, underlining the relevance of these structures for drug binding in K2P channels. Despite its hydrophobicity, A1899 does not seem to use the fenestrations to gain access to the central cavity from the lipid bilayer. In contrast, binding of A1899 to residues of the side fenestrations might provide a physical "anchor", reflecting an energetically favorable binding mode that after pore occlusion stabilizes the closed state of the channels.
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Affiliation(s)
- David Ramírez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca , 1 poniente No. 1141, 3460000 Talca, Chile.,Instituto de Ciencias Biomédicas, Universidad Autonoma de Chile , 5 Poniente No. 1670, 3460000 Talca, Chile
| | - Bárbara Arévalo
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca , 1 poniente No. 1141, 3460000 Talca, Chile
| | - Gonzalo Martínez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca , 1 poniente No. 1141, 3460000 Talca, Chile
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology Group, University of Marburg , 35037 Marburg, Germany
| | | | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology Group, University of Marburg , 35037 Marburg, Germany
| | - Wendy González
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca , 1 poniente No. 1141, 3460000 Talca, Chile
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45
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Jørgensen ME, Xu D, Crocoll C, Ernst HA, Ramírez D, Motawia MS, Olsen CE, Mirza O, Nour-Eldin HH, Halkier BA. Origin and evolution of transporter substrate specificity within the NPF family. eLife 2017; 6:e19466. [PMID: 28257001 PMCID: PMC5336358 DOI: 10.7554/elife.19466] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/06/2017] [Indexed: 02/06/2023] Open
Abstract
Despite vast diversity in metabolites and the matching substrate specificity of their transporters, little is known about how evolution of transporter substrate specificities is linked to emergence of substrates via evolution of biosynthetic pathways. Transporter specificity towards the recently evolved glucosinolates characteristic of Brassicales is shown to evolve prior to emergence of glucosinolate biosynthesis. Furthermore, we show that glucosinolate transporters belonging to the ubiquitous NRT1/PTR FAMILY (NPF) likely evolved from transporters of the ancestral cyanogenic glucosides found across more than 2500 species outside of the Brassicales. Biochemical characterization of orthologs along the phylogenetic lineage from cassava to A. thaliana, suggests that alterations in the electrogenicity of the transporters accompanied changes in substrate specificity. Linking the evolutionary path of transporter substrate specificities to that of the biosynthetic pathways, exemplify how transporter substrate specificities originate and evolve as new biosynthesis pathways emerge.
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Affiliation(s)
- Morten Egevang Jørgensen
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Deyang Xu
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Heidi Asschenfeldt Ernst
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - David Ramírez
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de TalcaTalcaChile
- Instituto de Innovación Basada en Ciencia, Universidad de TalcaTalcaChile
| | - Mohammed Saddik Motawia
- Center for Plant Plasticity, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Carl Erik Olsen
- Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Osman Mirza
- Department of Drug Design and Pharmacology, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Hussam Hassan Nour-Eldin
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of ScienceUniversity of CopenhagenFrederiksbergDenmark
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46
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Resende L, Almeida J, Schezaro-Ramos R, Collaço R, Simioni L, Ramírez D, González W, Soares A, Calderon L, Marangoni S, da Silva S. Exploring and understanding the functional role, and biochemical and structural characteristics of an acidic phospholipase A2, AplTx-I, purified from Agkistrodon piscivorus leucostoma snake venom. Toxicon 2017; 127:22-36. [DOI: 10.1016/j.toxicon.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/28/2016] [Accepted: 01/03/2017] [Indexed: 12/15/2022]
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47
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Ramírez D, Caballero J, Zúñiga L, Arévalo B, Kiper A, Rinne S, Decher N, Gonzalez W. Structure-Based Discovery of Potential Two-Pore-Domain Potassium Channel Task-3 (K 2P 9.1) Modulators. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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48
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Almeida J, Lancellotti M, Soares A, Calderon L, Ramírez D, González W, Marangoni S, Da Silva S. CoaTx-II, a new dimeric Lys49 phospholipase A2 from Crotalus oreganus abyssus snake venom with bactericidal potential: Insights into its structure and biological roles. Toxicon 2016; 120:147-58. [DOI: 10.1016/j.toxicon.2016.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 01/01/2023]
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49
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Rodríguez YA, Gutiérrez M, Ramírez D, Alzate-Morales J, Bernal CC, Güiza FM, Romero Bohórquez AR. Novel N-allyl/propargyl tetrahydroquinolines: Synthesis via Three-component Cationic Imino Diels-Alder Reaction, Binding Prediction, and Evaluation as Cholinesterase Inhibitors. Chem Biol Drug Des 2016; 88:498-510. [PMID: 27085663 PMCID: PMC5053295 DOI: 10.1111/cbdd.12773] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/10/2016] [Accepted: 04/05/2016] [Indexed: 01/11/2023]
Abstract
New N‐allyl/propargyl 4‐substituted 1,2,3,4‐tetrahydroquinolines derivatives were efficiently synthesized using acid‐catalyzed three components cationic imino Diels–Alder reaction (70–95%). All compounds were tested in vitro as dual acetylcholinesterase and butyryl‐cholinesterase inhibitors and their potential binding modes, and affinity, were predicted by molecular docking and binding free energy calculations (∆G) respectively. The compound 4af (IC50 = 72 μm) presented the most effective inhibition against acetylcholinesterase despite its poor selectivity (SI = 2), while the best inhibitory activity on butyryl‐cholinesterase was exhibited by compound 4ae (IC50 = 25.58 μm) with considerable selectivity (SI = 0.15). Molecular docking studies indicated that the most active compounds fit in the reported acetylcholinesterase and butyryl‐cholinesterase active sites. Moreover, our computational data indicated a high correlation between the calculated ∆G and the experimental activity values in both targets.
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Affiliation(s)
- Yeray A Rodríguez
- Laboratorio Síntesis Orgánica, Instituto de Química de Recursos Naturales, Universidad de Talca, Casilla 747, Talca, 3460000, Chile
| | - Margarita Gutiérrez
- Laboratorio Síntesis Orgánica, Instituto de Química de Recursos Naturales, Universidad de Talca, Casilla 747, Talca, 3460000, Chile.
| | - David Ramírez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, 3460000, Chile
| | - Jans Alzate-Morales
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, 3460000, Chile
| | - Cristian C Bernal
- Grupo de Investigación de Compuestos Orgánicos de Interés Medicinal (CODEIM), Parque Tecnológico Guatiguará, Universidad Industrial de Santander, A.A. 678, Piedecuesta, Colombia
| | - Fausto M Güiza
- Grupo de Investigación de Compuestos Orgánicos de Interés Medicinal (CODEIM), Parque Tecnológico Guatiguará, Universidad Industrial de Santander, A.A. 678, Piedecuesta, Colombia
| | - Arnold R Romero Bohórquez
- Grupo de Investigación de Compuestos Orgánicos de Interés Medicinal (CODEIM), Parque Tecnológico Guatiguará, Universidad Industrial de Santander, A.A. 678, Piedecuesta, Colombia.
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50
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Abstract
Due
to the synergic relationship between medical chemistry, bioinformatics and
molecular simulation, the development of new accurate computational tools for
small molecules drug design has been rising over the last years. The main result
is the increased number of publications where computational techniques such as
molecular docking, de novo design as well as virtual screening have been
used to estimate the binding mode, site and energy of novel small molecules. In
this work I review some tools, which enable the study of biological systems at
the atomistic level, providing relevant information and thereby, enhancing the
process of rational drug design.
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Affiliation(s)
- David Ramírez
- Centro de Bioinformática y Simulación Molecular, Universidad de Talca, 2 Norte 685, Casilla, Talca, Chile
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