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Eberle RJ, Olivier DS, Amaral MS, Pacca CC, Nogueira ML, Arni RK, Willbold D, Coronado MA. Riboflavin, a Potent Neuroprotective Vitamin: Focus on Flavivirus and Alphavirus Proteases. Microorganisms 2022; 10:1331. [PMID: 35889050 PMCID: PMC9315535 DOI: 10.3390/microorganisms10071331] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 12/01/2022] Open
Abstract
Several neurotropic viruses are members of the flavivirus and alphavirus families. Infections caused by these viruses may cause long-term neurological sequelae in humans. The continuous emergence of infections caused by viruses around the world, such as the chikungunya virus (CHIKV) (Alphavirus genus), the zika virus (ZIKV) and the yellow fever virus (YFV) (both of the Flavivirus genus), warrants the development of new strategies to combat them. Our study demonstrates the inhibitory potential of the water-soluble vitamin riboflavin against NS2B/NS3pro of ZIKV and YFV and nsP2pro of CHIKV. Riboflavin presents a competitive inhibition mode with IC50 values in the medium µM range of 79.4 ± 5.0 µM for ZIKV NS2B/NS3pro and 45.7 ± 2.9 μM for YFV NS2B/NS3pro. Against CHIKV nsP2pro, the vitamin showed a very strong effect (93 ± 5.7 nM). The determined dissociation constants (KD) are significantly below the threshold value of 30 µM. The ligand binding increases the thermal stability between 4 °C and 8 °C. Unexpectedly, riboflavin showed inhibiting activity against another viral protein; the molecule was also able to inhibit the viral entry of CHIKV. Molecular dynamics simulations indicated great stability of riboflavin in the protease active site, which validates the repurposing of riboflavin as a promising molecule in drug development against the viruses presented here.
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Affiliation(s)
- Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
| | - Danilo S. Olivier
- Center of Integrated Sciences, Campus Cimba, Federal University of Tocantins, Araguaína 77824-838, TO, Brazil;
| | - Marcos S. Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil;
| | - Carolina C. Pacca
- Instituto Superior de Educação Ceres, FACERES Medical School, São José do Rio Preto 15090-305, SP, Brazil;
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto 15090-000, SP, Brazil;
| | - Mauricio L. Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto 15090-000, SP, Brazil;
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, Department of Physics, IBILCE, São Paulo State University, São Jose do Rio Preto 15054-000, SP, Brazil;
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, 52428 Jülich, Germany
| | - Monika A. Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany;
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Eberle RJ, Olivier DS, Amaral MS, Willbold D, Arni RK, Coronado MA. Promising Natural Compounds against Flavivirus Proteases: Citrus Flavonoids Hesperetin and Hesperidin. Plants (Basel) 2021; 10:plants10102183. [PMID: 34685992 PMCID: PMC8539695 DOI: 10.3390/plants10102183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 05/04/2023]
Abstract
Ubiquitous in citrus plants, Hesperidin and Hesperetin flavanones possess several biological functions, including antiviral activity. Arbovirus infections pose an ever-increasing threat to global healthcare systems. Among the severe arboviral infections currently known are those caused by members of the Flavivirus genus, for example, Dengue Virus-DENV, Yellow Fever Virus-YFV, and West Nile Virus-WNV. In this study, we characterize the inhibitory effect of Hesperidin and Hesperetin against DENV2, YFV, and WNV NS2B/NS3 proteases. We report the noncompetitive inhibition of the NS2B/NS3pro by the two bioflavonoids with half maximal inhibitory concentration (IC50) values <5 µM for HST and <70 µM for HSD. The determined dissociation constants (KD) of both flavonoids is significantly below the threshold value of 30 µM. Our findings demonstrate that a new generation of anti-flavivirus drugs could be developed based on selective optimization of both molecules.
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Affiliation(s)
- Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany;
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
- Correspondence: (R.J.E.); (M.A.C.)
| | - Danilo S. Olivier
- Integrated Sciences Center, Federal University of Tocantins, Araguaína 77824-838, Brazil;
| | - Marcos S. Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, Brazil;
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany;
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, 52428 Jülich, Germany
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Universidade Estadual Paulista (UNESP), São Jose do Rio Preto 15054-000, Brazil;
| | - Monika A. Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany;
- Correspondence: (R.J.E.); (M.A.C.)
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Bhat SK, Joshi MB, Vasishta S, Jagadale RN, Biligiri SG, Coronado MA, Arni RK, Satyamoorthy K. P-I metalloproteinases and L-amino acid oxidases from Bothrops species inhibit angiogenesis. J Venom Anim Toxins Incl Trop Dis 2021; 27:e20200180. [PMID: 34471403 PMCID: PMC8381740 DOI: 10.1590/1678-9199-jvatitd-2020-0180] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Snake venoms are composed of pharmacologically active proteins that are evolutionarily diverse, stable and specific to targets. Hence, venoms have been explored as a source of bioactive molecules in treating numerous diseases. Recent evidences suggest that snake venom proteins may affect the formation of new blood vessels. Excessive angiogenesis has been implicated in several pathologies including tumours, diabetic retinopathy, arthritis, inter alia. In the present study, we have examined the effects of P-I metalloproteinases isolated from Bothrops moojeni (BmMP-1) and Bothrops atrox (BaMP-1) and L-amino acid oxidases (LAAO) isolated from B. moojeni (BmLAAO) and B. atrox (BaLAAO) on biochemical and functional aspects of angiogenesis. METHODS P-I metalloproteinases and LAAO were purified from venom by molecular size exclusion and ion-exchange chromatography and subsequently confirmed using mass spectrometry. The P-I metalloproteinases were characterized by azocaseinolytic, fibrinogenolytic and gelatinase activity and LAAO activity was assessed by enzyme activity on L-amino acids. Influence of these proteins on apoptosis and cell cycle in endothelial cells was analysed by flow cytometry. The angiogenic activity was determined by in vitro 3D spheroid assay, Matrigel tube forming assay, and in vivo agarose plug transformation in mice. RESULTS P-I metalloproteinases exhibited azocaseinolytic activity, cleaved α and partially β chain of fibrinogen, and displayed catalytic activity on gelatin. LAAO showed differential activity on L-amino acids. Flow cytometry analysis indicated that both P-I metalloproteinases and LAAO arrested the cells in G0/G1 phase and further induced both necrosis and apoptosis in endothelial cells. In vitro, P-I metalloproteinases and LAAO exhibited significant anti-angiogenic properties in 3D spheroid and Matrigel models by reducing sprout outgrowth and tube formation. Using agarose plug transplants in mice harbouring P-I metalloproteinases and LAAO we demonstrated a marked disruption of vasculature at the periphery. CONCLUSION Our research suggests that P-I metalloproteinases and LAAO exhibit anti-angiogenic properties in vitro and in vivo.
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Affiliation(s)
- Shreesha K. Bhat
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Manjunath B. Joshi
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sampara Vasishta
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | | | | | - Monika A. Coronado
- Multiuser Center for Biomolecular Innovation, Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, SP, Brazil
| | - Kapaettu Satyamoorthy
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
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Eberle RJ, Olivier DS, Amaral MS, Gering I, Willbold D, Arni RK, Coronado MA. The Repurposed Drugs Suramin and Quinacrine Cooperatively Inhibit SARS-CoV-2 3CL pro In Vitro. Viruses 2021; 13:873. [PMID: 34068686 PMCID: PMC8170883 DOI: 10.3390/v13050873] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 04/02/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Since the first report of a new pneumonia disease in December 2019 (Wuhan, China) the WHO reported more than 148 million confirmed cases and 3.1 million losses globally up to now. The causative agent of COVID-19 (SARS-CoV-2) has spread worldwide, resulting in a pandemic of unprecedented magnitude. To date, several clinically safe and efficient vaccines (e.g., Pfizer-BioNTech, Moderna, Johnson & Johnson, and AstraZeneca COVID-19 vaccines) as well as drugs for emergency use have been approved. However, increasing numbers of SARS-Cov-2 variants make it imminent to identify an alternative way to treat SARS-CoV-2 infections. A well-known strategy to identify molecules with inhibitory potential against SARS-CoV-2 proteins is repurposing clinically developed drugs, e.g., antiparasitic drugs. The results described in this study demonstrated the inhibitory potential of quinacrine and suramin against SARS-CoV-2 main protease (3CLpro). Quinacrine and suramin molecules presented a competitive and noncompetitive inhibition mode, respectively, with IC50 values in the low micromolar range. Surface plasmon resonance (SPR) experiments demonstrated that quinacrine and suramin alone possessed a moderate or weak affinity with SARS-CoV-2 3CLpro but suramin binding increased quinacrine interaction by around a factor of eight. Using docking and molecular dynamics simulations, we identified a possible binding mode and the amino acids involved in these interactions. Our results suggested that suramin, in combination with quinacrine, showed promising synergistic efficacy to inhibit SARS-CoV-2 3CLpro. We suppose that the identification of effective, synergistic drug combinations could lead to the design of better treatments for the COVID-19 disease and repurposable drug candidates offer fast therapeutic breakthroughs, mainly in a pandemic moment.
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Affiliation(s)
- Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (I.G.); (D.W.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
| | - Danilo S. Olivier
- Campus Cimba, Federal University of Tocantins, Araguaína, TO 77824-838, Brazil;
| | - Marcos S. Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS 79070-900, Brazil;
| | - Ian Gering
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (I.G.); (D.W.)
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (I.G.); (D.W.)
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, 40225 Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, 52428 Jülich, Germany
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, IBILCE, Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP 15054-000, Brazil;
| | - Monika A. Coronado
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany; (I.G.); (D.W.)
- Multiuser Center for Biomolecular Innovation, IBILCE, Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP 15054-000, Brazil;
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Eberle RJ, Olivier DS, Pacca CC, Avilla CMS, Nogueira ML, Amaral MS, Willbold D, Arni RK, Coronado MA. In vitro study of Hesperetin and Hesperidin as inhibitors of zika and chikungunya virus proteases. PLoS One 2021; 16:e0246319. [PMID: 33661906 PMCID: PMC7932080 DOI: 10.1371/journal.pone.0246319] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/15/2021] [Indexed: 11/19/2022] Open
Abstract
The potential outcome of flavivirus and alphavirus co-infections is worrisome due to the development of severe diseases. Hundreds of millions of people worldwide live under the risk of infections caused by viruses like chikungunya virus (CHIKV, genus Alphavirus), dengue virus (DENV, genus Flavivirus), and zika virus (ZIKV, genus Flavivirus). So far, neither any drug exists against the infection by a single virus, nor against co-infection. The results described in our study demonstrate the inhibitory potential of two flavonoids derived from citrus plants: Hesperetin (HST) against NS2B/NS3pro of ZIKV and nsP2pro of CHIKV and, Hesperidin (HSD) against nsP2pro of CHIKV. The flavonoids are noncompetitive inhibitors and the determined IC50 values are in low µM range for HST against ZIKV NS2B/NS3pro (12.6 ± 1.3 µM) and against CHIKV nsP2pro (2.5 ± 0.4 µM). The IC50 for HSD against CHIKV nsP2pro was 7.1 ± 1.1 µM. The calculated ligand efficiencies for HST were > 0.3, which reflect its potential to be used as a lead compound. Docking and molecular dynamics simulations display the effect of HST and HSD on the protease 3D models of CHIKV and ZIKV. Conformational changes after ligand binding and their effect on the substrate-binding pocket of the proteases were investigated. Additionally, MTT assays demonstrated a very low cytotoxicity of both the molecules. Based on our results, we assume that HST comprise a chemical structure that serves as a starting point molecule to develop a potent inhibitor to combat CHIKV and ZIKV co-infections by inhibiting the virus proteases.
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Affiliation(s)
- Raphael J. Eberle
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | | | - Carolina C. Pacca
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
- FACERES Medical School, São José do Rio Preto, Brazil
| | - Clarita M. S. Avilla
- Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
| | - Mauricio L. Nogueira
- Faculdade de Medicina de São José do Rio Preto–FAMERP, São José do Rio Preto, Brazil
| | - Marcos S. Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forchungszentrum Jülich, Jülich, Germany
| | - Raghuvir K. Arni
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
| | - Monika A. Coronado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, SP, Brazil
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
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Peinado RDS, Olivier DS, Eberle RJ, de Moraes FR, Amaral MS, Arni RK, Coronado MA. Binding studies of a putative C. pseudotuberculosis target protein from Vitamin B 12 Metabolism. Sci Rep 2019; 9:6350. [PMID: 31015525 PMCID: PMC6478909 DOI: 10.1038/s41598-019-42935-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 05/22/2018] [Accepted: 03/13/2019] [Indexed: 01/20/2023] Open
Abstract
Vitamin B12 acts as a cofactor for various metabolic reactions important in living organisms. The Vitamin B12 biosynthesis is restricted to prokaryotes, which means, all eukaryotic organisms must acquire this molecule through diet. This study presents the investigation of Vitamin B12 metabolism and the characterization of precorrin-4 C(11)-methyltransferase (CobM), an enzyme involved in the biosynthesis of Vitamin B12 in Corynebacterium pseudotuberculosis. The analysis of the C. pseudotuberculosis genome identified two Vitamin B12-dependent pathways, which can be strongly affected by a disrupted vitamin metabolism. Molecular dynamics, circular dichroism, and NMR-STD experiments identified regions in CobM that undergo conformational changes after s-adenosyl-L-methionine binding to promote the interaction of precorrin-4, a Vitamin B12 precursor. The binding of s-adenosyl-L-methionine was examined along with the competitive binding of adenine, dATP, and suramin. Based on fluorescence spectroscopy experiments the dissociation constant for the four ligands and the target protein could be determined; SAM (1.4 ± 0.7 µM), adenine (17.8 ± 1.5 µM), dATP (15.8 ± 2.0 µM), and Suramin (6.3 ± 1.1 µM). The results provide rich information for future investigations of potential drug targets within the C. pseudotuberculosis's Vitamin B12 metabolism and related pathways to reduce the pathogen's virulence in its hosts.
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Affiliation(s)
- Rafaela Dos S Peinado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP, 15054-000, Brazil
| | - Danilo S Olivier
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP, 15054-000, Brazil
| | - Raphael J Eberle
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP, 15054-000, Brazil
| | - Fabio R de Moraes
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP, 15054-000, Brazil
| | - Marcos S Amaral
- Institute of Physics, Federal University of Mato Grosso do Sul, Campo Grande, MS, 79090-700, Brazil
| | - Raghuvir K Arni
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP, 15054-000, Brazil.
| | - Monika A Coronado
- Multiuser Center for Biomolecular Innovation, Departament of Physics, Instituto de Biociências Letras e Ciências Exatas (Ibilce), Universidade Estadual Paulista (UNESP), São Jose do Rio Preto-SP, 15054-000, Brazil.
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Eberle RJ, Kawai LA, de Moraes FR, Olivier D, do Amaral MS, Tasic L, Arni RK, Coronado MA. Inhibition of thioredoxin A1 from Corynebacterium pseudotuberculosis by polyanions and flavonoids. Int J Biol Macromol 2018; 117:1066-1073. [DOI: 10.1016/j.ijbiomac.2018.06.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 11/17/2022]
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Eberle RJ, Kawai LA, de Moraes FR, Tasic L, Arni RK, Coronado MA. Biochemical and biophysical characterization of a mycoredoxin protein glutaredoxin A1 from Corynebacterium pseudotuberculosis. Int J Biol Macromol 2018; 107:1999-2007. [DOI: 10.1016/j.ijbiomac.2017.10.063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 10/06/2017] [Accepted: 10/11/2017] [Indexed: 11/29/2022]
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Caruso IP, Panwalkar V, Coronado MA, Dingley AJ, Cornélio ML, Willbold D, Arni RK, Eberle RJ. Structure and interaction of Corynebacterium pseudotuberculosis cold shock protein A with Y-box single-stranded DNA fragment. FEBS J 2017; 285:372-390. [PMID: 29197185 DOI: 10.1111/febs.14350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 08/01/2017] [Revised: 11/07/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
Abstract
Cold shock proteins (Csps) function to preserve cell viability at low temperatures by binding to nucleic acids and consequently control gene expression. The mesophilic bacterium Corynebacterium pseudotuberculosis is the causative agent of caseous lymphadenitis in animals, and infection in livestock is a considerable economic burden worldwide. In this report, the structure of cold shock protein A from Cp (Cp-CspA) and biochemical analysis of its temperature-dependent interaction with a Y-box ssDNA motif is presented. The Cp-CspA structure contains five β-strands making up a β-barrel fold with 11 hydrophobic core residues and two salt bridges that confers it with a melting temperature of ~ 54 °C that is similar to mesophilic Bs-CspB. Chemical shift perturbations analysis revealed that residues in the nucleic acid-binding motifs (RNP 1 and 2) and loop 3 are involved in binding to the Y-box fragment either by direct interaction or by conformational rearrangements remote from the binding region. Fluorescence quenching experiments of Cp-CspA showed that the dissociation constants for Y-box ssDNA binding is nanomolar and the binding affinity decreased as the temperature increased, indicating that the interaction is enthalpically driven and the hydrogen bonds and van der Waals forces are important contributions for complex stabilization. The Y31 of Cp-CspA is a particular occurrence among Csps from mesophilic bacteria that provide a possible explanation for the higher binding affinity to ssDNA than that observed for Bs-CspB. Anisotropy measurements indicated that the reduction in molecular mobility of Cp-CspA upon Y-box binding is characterized by a cooperative process. DATABASE Resonance assignment and structural data are available in the Biological Magnetic Resonance Data Bank and Protein Data Bank under accession number 26802 and 5O6F, respectively.
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Affiliation(s)
- Icaro P Caruso
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Vineet Panwalkar
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Monika A Coronado
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Andrew J Dingley
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Marinônio L Cornélio
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Dieter Willbold
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Raghuvir K Arni
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
| | - Raphael J Eberle
- Department of Physics, Multiuser Center for Biomolecular Innovation (CMIB), IBILCE/UNESP, São José do Rio Preto, São Paulo, Brazil
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Coronado MA, Caruso IP, Oliveira VMD, Contessoto VG, Leite VBP, Kawai LA, Arni RK, Eberle RJ. Cold Shock Protein A from Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure. Protein Pept Lett 2017; 24:358-367. [PMID: 28176661 DOI: 10.2174/0929866524666170207153808] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 11/30/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 11/22/2022]
Abstract
The conformational stability of the Cold shock protein A (CspA) from C. pseudotuberculosis (Cp), a nucleic acid binding protein in function of pH and salt concentration was examined by using differential scanning calorimetry and CD spectroscopy in combination with computational analysis to identify the specify amino acids undergoing change. Our approach identified a sodiumbinding site in CpCspA and at pH 8.0 a significant reduction in the β-sheet content was observed which resulted in a decrease of the protein thermal stability. The computational analyses identified His30 and His65 as the amino acids with the largest charge shifts at different pHs. His30/His65 are part of the extensive hydrogen bonding network and along with the ion-binding site are essential for the conformational stability of CspA.
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Affiliation(s)
- Monika A Coronado
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Icaro P Caruso
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Vinicius M de Oliveira
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Vinícius G Contessoto
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Vitor B P Leite
- Department of Physics, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Liege A Kawai
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Raghuvir K Arni
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Sao Jose do Rio Preto-SP, 15054-000. Brazil
| | - Raphael J Eberle
- Multiuser Center for Biomolecular Innovation, Universidade Estadual Paulista (UNESP), Rua Cristovao Colombo 2265, Sao Jose do Rio Preto-SP, 15054-000. Brazil
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11
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Georgieva D, Hildebrand D, Simas R, Coronado MA, Kwiatkowski M, Schlüter H, Arni R, Spencer P, Betzel C. Protein Profile Analysis of Two Australian Snake Venoms by One- Dimensional Gel Electrophoresis and MS/MS Experiments. Curr Med Chem 2017; 24:1892-1908. [PMID: 28571558 DOI: 10.2174/0929867324666170601073148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/03/2017] [Revised: 05/15/2017] [Accepted: 05/22/2017] [Indexed: 11/22/2022]
Abstract
The Pseudechis colletti and Pseudechis butleri venoms were analyzed by 1-D gel electrophoresis, followed by mass spectrometric analysis of tryptic peptides obtained from the protein bands. Both venoms contain highly potent pharmacologically active components, which were assigned to the following protein families: basic and acidic phospholipases A2 (PLA2s), L-amino acid oxidases (LAAOs), P-III metalloproteinases (P-III SVMPs), 5'- nucleotidases (5'-NTDs), cysteine-rich secretory proteins (CRISPs), venom nerve growth factors (VNGFs) and post-synaptic neurotoxins. Considerable predominance of PLA2s over other toxins is a characteristic feature of both venoms. The major differences in the venom compositions are the higher concentration of SVMPs and CRISPs in the P. butleri venom, as well as the presence of post-synaptic neurotoxins. Furthermore, the analysis revealed a high concentration of proteins with myotoxic, coagulopathic and apoptotic activities. PLA2s are responsible for the myotoxic and anticoagulant effects observed in patients after envenomation (4). The other protein families, encountered in the two venoms, probably contribute to the major symptoms described for these venoms. These results explain the observed clinical effects of the black snake envenomation. The analyzed venoms contain group P-III metalloproteinases of medical importance with the potency to be used for diagnostic purposes of von Willebrand factor (vWF) disease, for regulation of vWF in thrombosis and haemostasis, for studying the function of the complement system in host defense and in the pathogenesis of diseases. Comparison of venomic data showed similarities in the major venom components of snakes from the genus Pseudechis, resulting in common clinical effects of envenomation, and demonstrating close relationships between venom toxins of Elapidae snakes.
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Affiliation(s)
- Dessislava Georgieva
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Diana Hildebrand
- Institute of Clinical Chemistry, University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
| | - Rodrigo Simas
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestrasse 85, 22603 Hamburg, Germany
| | - Monika A Coronado
- Multiuser Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, R. Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - Marcel Kwiatkowski
- Institute of Clinical Chemistry, University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry, University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
| | - Raghuvir Arni
- Multiuser Center for Biomolecular Innovation, Department of Physics, IBILCE/UNESP, R. Cristóvão Colombo 2265, São José do Rio Preto 15054-000, SP, Brazil
| | - Patrick Spencer
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, Avenue Lineu Prestes 2242, São Paulo 05508-000, SP, Brazil
| | - Christian Betzel
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestrasse 85, 22603 Hamburg, Germany
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12
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Mariutti RB, Chaves-Moreira D, Vuitika L, Caruso ÍP, Coronado MA, Azevedo VA, Murakami MT, Veiga SS, Arni RK. Bacterial and Arachnid Sphingomyelinases D: Comparison of Biophysical and Pathological Activities. J Cell Biochem 2017; 118:2053-2063. [PMID: 27808444 DOI: 10.1002/jcb.25781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/01/2016] [Indexed: 01/29/2023]
Abstract
Sphingomyelinases D have only been identified in arachnid venoms, Corynebacteria, Arcanobacterium, Photobacterium and in the fungi Aspergillus and Coccidioides. The arachnid and bacterial enzymes share very low sequence identity and do not contain the HKD sequence motif characteristic of the phospholipase D superfamily, however, molecular modeling and circular dichroism of SMases D from Loxosceles intermedia and Corynebacterium pseudotuberculosis indicate similar folds. The phospholipase, hemolytic and necrotic activities and mice vessel permeabilities were compared and both enzymes possess the ability to hydrolyze phospholipids and also promote similar pathological reactions in the host suggesting the existence of a common underlying mechanism in tissue disruption. J. Cell. Biochem. 118:2053-2063, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ricardo Barros Mariutti
- Department of Physics, Multiuser Center for Biomolecular Innovation, UNESP, São José do Rio Preto, SP, Brazil
| | | | | | - Ícaro Putinhon Caruso
- Department of Physics, Multiuser Center for Biomolecular Innovation, UNESP, São José do Rio Preto, SP, Brazil
| | - Monika A Coronado
- Department of Physics, Multiuser Center for Biomolecular Innovation, UNESP, São José do Rio Preto, SP, Brazil
| | - Vasco A Azevedo
- Institute of Biological Sciences, UFMG, Belo Horizonte, MG, Brazil
| | - Mario T Murakami
- Brazilian Biosciences National Laboratory, LNBio, Campinas, SP, Brazil
| | | | - Raghuvir K Arni
- Department of Physics, Multiuser Center for Biomolecular Innovation, UNESP, São José do Rio Preto, SP, Brazil
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13
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Lindae A, Eberle RJ, Caruso IP, Coronado MA, de Moraes FR, Azevedo V, Arni RK. Expression, purification and characterization of cold shock protein A of Corynebacterium pseudotuberculosis. Protein Expr Purif 2015; 112:15-20. [DOI: 10.1016/j.pep.2015.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 10/23/2022]
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14
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Okamoto DN, Kondo MY, Oliveira LCG, Honorato RV, Zanphorlin LM, Coronado MA, Araújo MS, da Motta G, Veronez CL, Andrade SS, Oliveira PSL, Arni RK, Cintra ACO, Sampaio SV, Juliano MA, Juliano L, Murakami MT, Gouvea IE. P-I class metalloproteinase from Bothrops moojeni venom is a post-proline cleaving peptidase with kininogenase activity: insights into substrate selectivity and kinetic behavior. Biochim Biophys Acta 2013; 1844:545-52. [PMID: 24373874 DOI: 10.1016/j.bbapap.2013.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 11/29/2022]
Abstract
Snake venom metalloproteinases (SVMPs) belonging to P-I class are able to hydrolyze extracellular matrix proteins and coagulation factors triggering local and systemic reactions by multiple molecular mechanisms that are not fully understood. BmooMPα-I, a P-I class SMVP from Bothrops moojeni venom, was active upon neuro- and vaso-active peptides including angiotensin I, bradykinin, neurotensin, oxytocin and substance P. Interestingly, BmooMPα-I showed a strong bias towards hydrolysis after proline residues, which is unusual for most of characterized peptidases. Moreover, the enzyme showed kininogenase activity similar to that observed in plasma and cells by kallikrein. FRET peptide assays indicated a relative promiscuity at its S2-S'2 subsites, with proline determining the scissile bond. This unusual post-proline cleaving activity was confirmed by the efficient hydrolysis of the synthetic combinatorial library MCA-GXXPXXQ-EDDnp, described as resistant for canonical peptidases, only after Pro residues. Structural analysis of the tripeptide LPL complexed with BmooMPα-I, generated by molecular dynamics simulations, assisted in defining the subsites and provided the structural basis for subsite preferences such as the restriction of basic residues at the S2 subsite due to repulsive electrostatic effects and the steric impediment for large aliphatic or aromatic side chains at the S1 subsite. These new functional and structural findings provided a further understanding of the molecular mechanisms governing the physiological effects of this important class of enzymes in envenomation process.
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Affiliation(s)
- Débora N Okamoto
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Marcia Y Kondo
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Lilian C G Oliveira
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Rodrigo V Honorato
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, 13083-100 Campinas, SP, Brazil
| | - Leticia M Zanphorlin
- Departamento de Orgânica, Instituto de Química, UNICAMP, 13083-970 Campinas, Brazil
| | - Monika A Coronado
- Departamento de Física, IBILCE, UNESP, 15054-000 São José do Rio Preto, Brazil
| | - Mariana S Araújo
- Departamento de Bioquímica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Guacyara da Motta
- Departamento de Bioquímica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Camila L Veronez
- Departamento de Bioquímica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Sheila S Andrade
- Departamento de Ginecologia, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Paulo S L Oliveira
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, 13083-100 Campinas, SP, Brazil
| | - Raghuvir K Arni
- Departamento de Física, IBILCE, UNESP, 15054-000 São José do Rio Preto, Brazil
| | - Adelia C O Cintra
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, 14040-903 Ribeirão Preto, SP, Brazil
| | - Suely V Sampaio
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-USP, 14040-903 Ribeirão Preto, SP, Brazil
| | - Maria A Juliano
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Luiz Juliano
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil
| | - Mário T Murakami
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisas em Energia e Materiais, 13083-100 Campinas, SP, Brazil.
| | - Iuri E Gouvea
- Departamento de Biofísica, Universidade Federal de São Paulo, 04044-020 São Paulo, SP, Brazil.
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15
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Coronado MA, Gabdulkhakov A, Georgieva D, Sankaran B, Murakami MT, Arni RK, Betzel C. Structure of the polypeptide crotamine from the Brazilian rattlesnake Crotalus durissus terrificus. Acta Crystallogr D Biol Crystallogr 2013; 69:1958-64. [PMID: 24100315 PMCID: PMC3792641 DOI: 10.1107/s0907444913018003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/29/2013] [Indexed: 11/10/2022]
Abstract
The crystal structure of the myotoxic, cell-penetrating, basic polypeptide crotamine isolated from the venom of Crotalus durissus terrificus has been determined by single-wavelength anomalous dispersion techniques and refined at 1.7 Å resolution. The structure reveals distinct cationic and hydrophobic surface regions that are located on opposite sides of the molecule. This surface-charge distribution indicates its possible mode of interaction with negatively charged phospholipids and other molecular targets to account for its diverse pharmacological activities. Although the sequence identity between crotamine and human β-defensins is low, the three-dimensional structures of these functionally related peptides are similar. Since crotamine is a leading member of a large family of myotoxic peptides, its structure will provide a basis for the design of novel cell-penetrating molecules.
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Affiliation(s)
- Monika A. Coronado
- Multi User Center for Biomolecular Innovation, Department of Physics, São Paulo State University, UNESP/IBILCE, C. Postal 136, 15054-000 São José do Rio Preto-SP, Brazil
- Institute of Biochemistry and Molecular Biology, Hamburg University, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
| | - Azat Gabdulkhakov
- Institute of Protein Research, RAS, Pushchino, Moscow Region 142290, Russian Federation
| | - Dessislava Georgieva
- Institute of Biochemistry and Molecular Biology, Hamburg University, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
| | - Banumathi Sankaran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94702, USA
| | - Mario T. Murakami
- Biosciences National Laboratory, National Center for Energy and Materials Research, Giuseppe Maximo Scolfaro 10000, 13083-970 Campinas-SP, Brazil
| | - Raghuvir K. Arni
- Multi User Center for Biomolecular Innovation, Department of Physics, São Paulo State University, UNESP/IBILCE, C. Postal 136, 15054-000 São José do Rio Preto-SP, Brazil
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Hamburg University, Martin-Luther-King Platz 6, 20146 Hamburg, Germany
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