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Gato E, Guijarro-Sánchez P, Alonso-García I, Pedraza-Merino R, Conde A, Lence E, Rumbo-Feal S, Peña-Escolano A, Lasarte-Monterrubio C, Blanco-Martín T, Fernández-González A, Fernández-López MDC, Maceiras R, Martínez-Guitián M, Vázquez-Ucha JC, Martínez-Martínez L, González-Bello C, Arca-Suárez J, Beceiro A, Bou G. In vitro development of imipenem/relebactam resistance in KPC-producing Klebsiella pneumoniae involves multiple mutations including OmpK36 disruption and KPC modification. Int J Antimicrob Agents 2023; 62:106935. [PMID: 37541530 DOI: 10.1016/j.ijantimicag.2023.106935] [Citation(s) in RCA: 2] [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: 12/02/2022] [Revised: 05/08/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
OBJECTIVES In order to inform and anticipate potential strategies aimed at combating KPC-producing Klebsiella pneumoniae infections, we analysed imipenem/relebactam and ceftazidime/avibactam single-step mutant frequencies, resistance development trajectories, differentially selected resistance mechanisms and their associated fitness cost using four representative high-risk K. pneumoniae clones. METHODS Mutant frequencies and mutant preventive concentrations were determined using agar plates containing incremental concentrations of β-lactam/β-lactamase inhibitor. Resistance dynamics were determined through incubation for 7 days in 10 mL MH tubes containing incremental concentrations of each antibiotic combination up to their 64 × baseline MIC. Two colonies per strain from each experiment were characterized by antimicrobial susceptibility testing, whole genome sequencing and competitive growth assays (to determine in vitro fitness). KPC variants associated with imipenem/relebactam resistance were characterized by cloning and biochemical experiments, atomic models and molecular dynamics simulation studies. RESULTS Imipenem/relebactam prevented the emergence of single-step resistance mutants at lower concentrations than ceftazidime/avibactam. In three of the four strains evaluated, imipenem/relebactam resistance development emerged more rapidly, and in the ST512/KPC-3 clone reached higher levels compared to baseline MICs than for ceftazidime/avibactam. Lineages evolved in the presence of ceftazidime/avibactam showed KPC substitutions associated with high-level ceftazidime/avibactam resistance, increased imipenem/relebactam susceptibility and low fitness costs. Lineages that evolved in the presence of imipenem/relebactam showed OmpK36 disruption, KPC modifications (S106L, N132S, L167R) and strain-specific substitutions associated with imipenem/relebactam resistance and high fitness costs. Imipenem/relebactam-selected KPC derivatives demonstrated enhanced relebactam resistance through important changes affecting relebactam recognition and positioning. CONCLUSIONS Our findings anticipate potential resistance mechanisms affecting imipenem/relebactam during treatment of KPC-producing K. pneumoniae infections.
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Affiliation(s)
- Eva Gato
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Isaac Alonso-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Rosa Pedraza-Merino
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), España
| | - Adrian Conde
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Soraya Rumbo-Feal
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Andrea Peña-Escolano
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Tania Blanco-Martín
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), España
| | - Ana Fernández-González
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - M Del Carmen Fernández-López
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Romina Maceiras
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain
| | - Marta Martínez-Guitián
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; NANOBIOFAR, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Martínez-Martínez
- Unidad de Microbiología, Hospital Universitario Reina Sofía, Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, e Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), España; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario, Universitario A Coruña, A Coruña, Spain; Ciber de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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2
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Alonso-García I, Vázquez-Ucha JC, Martínez-Guitián M, Lasarte-Monterrubio C, Rodríguez-Pallares S, Camacho-Zamora P, Rumbo-Feal S, Aja-Macaya P, González-Pinto L, Outeda-García M, Maceiras R, Guijarro-Sánchez P, Muíño-Andrade MJ, Fernández-González A, Oviaño M, González-Bello C, Arca-Suárez J, Beceiro A, Bou G. Interplay between OXA-10 β-Lactamase Production and Low Outer-Membrane Permeability in Carbapenem Resistance in Enterobacterales. Antibiotics (Basel) 2023; 12:999. [PMID: 37370318 DOI: 10.3390/antibiotics12060999] [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: 03/10/2023] [Revised: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The OXA-10 class D β-lactamase has been reported to contribute to carbapenem resistance in non-fermenting Gram-negative bacilli; however, its contribution to carbapenem resistance in Enterobacterales is unknown. In this work, minimum inhibitory concentrations (MICs), whole genome sequencing (WGS), cloning experiments, kinetic assays, molecular modelling studies, and biochemical assays for carbapenemase detection were performed to determine the impact of OXA-10 production on carbapenem resistance in two XDR clinical isolates of Escherichia coli with the carbapenem resistance phenotype (ertapenem resistance). WGS identified the two clinical isolates as belonging to ST57 in close genomic proximity to each other. Additionally, the presence of the blaOXA-10 gene was identified in both isolates, as well as relevant mutations in the genes coding for the OmpC and OmpF porins. Cloning of blaOXA-10 in an E. coli HB4 (OmpC and OmpF-deficient) demonstrated the important contribution of OXA-10 to increased carbapenem MICs when associated with porin deficiency. Kinetic analysis showed that OXA-10 has low carbapenem-hydrolysing activity, but molecular models revealed interactions of this β-lactamase with the carbapenems. OXA-10 was not detected with biochemical tests used in clinical laboratories. In conclusion, the β-lactamase OXA-10 limits the activity of carbapenems in Enterobacterales when combined with low permeability and should be monitored in the future.
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Affiliation(s)
- Isaac Alonso-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Martínez-Guitián
- NANOBIOFAR, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Campus Vida Avenida Barcelona s/n, 15782 Santiago de Compostela, Spain
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, Universidade da Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Salud Rodríguez-Pallares
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Camacho-Zamora
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Soraya Rumbo-Feal
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Aja-Macaya
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Lucía González-Pinto
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Michelle Outeda-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Romina Maceiras
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - María José Muíño-Andrade
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Ana Fernández-González
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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3
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Lasarte-Monterrubio C, Guijarro-Sánchez P, Vázquez-Ucha JC, Alonso-Garcia I, Alvarez-Fraga L, Outeda M, Martinez-Guitian M, Peña-Escolano A, Maceiras R, Lence E, González-Bello C, Arca-Suárez J, Bou G, Beceiro A. Antimicrobial Activity of Cefiderocol against the Carbapenemase-Producing Enterobacter cloacae Complex and Characterization of Reduced Susceptibility Associated with Metallo-β-Lactamase VIM-1. Antimicrob Agents Chemother 2023; 67:e0150522. [PMID: 37195077 PMCID: PMC10190674 DOI: 10.1128/aac.01505-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/16/2023] [Indexed: 05/18/2023] Open
Abstract
Emergence of cefiderocol resistance among carbapenemase-producing Enterobacterales, particularly those in the Enterobacter cloacae complex (ECC), is becoming of alarming concern; however, the mechanistic basis of this phenomenon remains poorly understood. We describe the acquisition of VIM-1-mediated reduced cefiderocol susceptibility (MICs 0.5 to 4 mg/L) in a collection of 54 carbapenemase-producing isolates belonging to the ECC. MICs were determined by reference methodologies. Antimicrobial resistance genomic analysis was performed through hybrid WGS. The impact of VIM-1 production on cefiderocol resistance in the ECC background was examined at microbiological, molecular, biochemical, and atomic levels. Antimicrobial susceptibility testing yielded 83.3% susceptible isolates and MIC50/90 values of 1/4 mg/L. Decreased susceptibility to cefiderocol was mainly associated with isolates producing VIM-1, with cefiderocol MICs 2- to 4-fold higher than for isolates carrying other types of carbapenemases. E. cloacae and Escherichia coli VIM-1 transformants displayed significantly enhanced cefiderocol MICs. Biochemical assays with purified VIM-1 protein revealed low but detectable cefiderocol hydrolysis. Simulation studies revealed how cefiderocol is anchored to the VIM-1 active site. Additional molecular assays and WGS data analysis highlighted the implication of SHV-12 coproduction and suggested the inactivation of the FcuA-like siderophore receptor as further contributors to the higher cefiderocol MICs. Our findings warn of the potential of the VIM-1 carbapenemase to at least partly limit the activity of cefiderocol in the ECC. This effect is probably enhanced due to combination with additional mechanisms, such as ESBL production and siderophore inactivation, and indicates the need for active surveillance to extend the life span of this promising cephalosporin.
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Affiliation(s)
- Cristina Lasarte-Monterrubio
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Isaac Alonso-Garcia
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Laura Alvarez-Fraga
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Michelle Outeda
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Marta Martinez-Guitian
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
- NANOBIOFAR, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Peña-Escolano
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Romina Maceiras
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Emilio Lence
- Centre for Research in Biological Chemistry and Molecular Materials (CiQUS), Department of Organic Chemistry, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centre for Research in Biological Chemistry and Molecular Materials (CiQUS), Department of Organic Chemistry, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - German Bou
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
| | - Alejandro Beceiro
- Microbiology Department, A Coruña University Hospital Complex (CHUAC), A Coruña Institute for Biomedical Research (INIBIC), CIBER de Enfermedades Infecciosas (CIBERINFEC), A Coruña, Spain
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Rodríguez D, González-Bello C. Siderophores: Chemical Tools for Precise Antibiotic Delivery. Bioorg Med Chem Lett 2023; 87:129282. [PMID: 37031730 DOI: 10.1016/j.bmcl.2023.129282] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 04/11/2023]
Abstract
The success of precision medicine coupled with the disappointing impact of broad-spectrum antibiotic use on microbiome stability and bacterial resistance, has triggered a shift in antibiotic design strategies toward precision antibiotics. This also includes the implementation of novel vectorization approaches directed to improve the internalization of antibacterial agents into deadly gram-negative pathogens through precise and well-defined mechanisms. The conjugation of antibiotics to siderophores (iron scavengers), which are compounds that are able to afford stable iron-complexes that facilitate the internalization into the cell by using bacterial iron uptake pathways as gateways, is a strategy that has begun to show excellent results with the commercialization of the first antibiotic based on this principle, cefiderocol. This digests review provides an overview of the molecular basis for this antibiotic-siderophore conjugation approach, along with recent successful examples and highlights future challenges facing this booming research area.
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Affiliation(s)
- Diana Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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5
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Rodríguez Á, Maneiro M, Lence E, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Quinate-based ligands for irreversible inactivation of the bacterial virulence factor DHQ1 enzyme-A molecular insight. Front Mol Biosci 2023; 10:1111598. [PMID: 36762206 PMCID: PMC9902378 DOI: 10.3389/fmolb.2023.1111598] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Irreversible inhibition of the enzyme type I dehydroquinase (DHQ1), a promising target for anti-virulence drug development, has been explored by enhancing the electrophilicity of specific positions of the ligand towards covalent lysine modification. For ligand design, we made use of the advantages offered by the intrinsic acid-base properties of the amino substituents introduced in the quinate scaffold, namely compounds 6-7 (R configuration at C3), to generate a potential leaving group, as well as the recognition pattern of the enzyme. The reactivity of the C2-C3 bond (Re face) in the scaffold was also explored using compound 8. The results of the present study show that replacement of the C3 hydroxy group of (-)-quinic acid by a hydroxyamino substituent (compound 6) provides a time-dependent irreversible inhibitor, while compound 7, in which the latter functionality was substituted by an amino group, and the introduction of an oxirane ring at C2-C3 bond, compound 8, do not allow covalent modification of the enzyme. These outcomes were supported by resolution of the crystal structures of DHQ1 from Staphylococcus aureus (Sa-DHQ1) and Salmonella typhi (St-DHQ1) chemically modified by 6 at a resolution of 1.65 and 1.90 Å, respectively, and of St-DHQ1 in the complex with 8 (1.55 Å). The combination of these structural studies with extensive molecular dynamics simulation studies allowed us to understand the molecular basis of the type of inhibition observed. This study is a good example of the importance of achieving the correct geometry between the reactive center of the ligand (electrophile) and the enzyme nucleophile (lysine residue) to allow selective covalent modification. The outcomes obtained with the hydroxyamino derivative 6 also open up new possibilities in the design of irreversible inhibitors based on the use of amino substituents.
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Affiliation(s)
- Ángela Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - José M. Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | - Paul Thompson
- Newcastle University Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Alastair R. Hawkins
- Newcastle University Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain,*Correspondence: Concepción González-Bello,
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Garcia-Lainez G, El Ouardi M, Moreno A, Lence E, González-Bello C, Miranda MA, Andreu I. Singlet oxygen and radical-mediated mechanisms in the oxidative cellular damage photosensitized by the protease inhibitor simeprevir. Free Radic Biol Med 2023; 194:42-51. [PMID: 36375737 DOI: 10.1016/j.freeradbiomed.2022.11.006] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/04/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
Hepatitis C, a liver inflammation caused by the hepatitis C virus (HCV), is treated with antiviral drugs. In this context, simeprevir (SIM) is an NS3/4A protease inhibitor used in HCV genotypes 1 and 4. It is orally administered and achieves high virological cure rates. Among adverse reactions associated with SIM treatment, photosensitivity reactions have been reported. In the present work, it is clearly shown that SIM is markedly phototoxic, according to the in vitro NRU assay using BALB/c 3T3 mouse fibroblast. This result sheds light on the nature of the photosensitivity reactions induced by SIM in HCV patients, suggesting that porphyrin elevation in patients treated with SIM may not be the only mechanism responsible for SIM-associated photosensitivity. Moreover, lipid photoperoxidation and protein photooxidation assays, using human skin fibroblasts (FSK) and human serum albumin (HSA), respectively, reveal the capability of this drug to promote photodamage to cellular membranes. Also, DNA photo lesions induced by SIM are noticed through comet assay in FSK cells. Photochemical and photobiological studies on the mechanism of SIM-mediated photodamage to biomolecules indicate that the key transient species generated upon SIM irradiation is the triplet excited state. This species is efficiently quenched by oxygen giving rise to singlet oxygen, which is responsible for the oxidation of lipids and DNA (Type II mechanism). In the presence of HSA, the photobehavior is dominated by binding to site 3 of the protein, to give a stable SIM@HSA complex. Inside the complex, quenching of the triplet excited state is less efficient, which results in a longer triplet lifetime and in a decreased singlet oxygen formation. Hence, SIM-mediated photooxidation of the protein is better explained through a radical (Type I) mechanism.
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Affiliation(s)
- Guillermo Garcia-Lainez
- Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Meryem El Ouardi
- Departamento de Química-Instituto de Tecnología Química UPV-CSIC. Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta de Investigación UPV- IIS La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Alejandro Moreno
- Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Miguel A Miranda
- Departamento de Química-Instituto de Tecnología Química UPV-CSIC. Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta de Investigación UPV- IIS La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain.
| | - Inmaculada Andreu
- Departamento de Química-Instituto de Tecnología Química UPV-CSIC. Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta de Investigación UPV- IIS La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain.
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7
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Pedroso
de Lima F, Lence E, Suárez de Cepeda P, Correia C, Carvalho MA, González-Bello C, Proença MF. Regioselective Synthesis of 2-Aryl-5-cyano-1-(2-hydroxyaryl)-1 H-imidazole-4-carboxamides Self-Assisted by a 2-Hydroxyaryl Group. ACS Omega 2022; 7:23289-23301. [PMID: 35847303 PMCID: PMC9280940 DOI: 10.1021/acsomega.2c01399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The reactivity of the diaminomaleonitrile-based imines containing hydroxyphenyl substituents with diverse aromatic aldehydes has been explored for the synthesis of novel highly substituted nitrogen heterocycles, which are considered privileged scaffolds in drug discovery. We report here a simple and efficient method for the regiocontrolled synthesis of a variety of 2-aryl-5-cyano-1-(2-hydroxyaryl)-1H-imidazole-4-carboxamides from 2-hydroxybenzylidene imines and aromatic aldehydes. Computational studies on the reaction path revealed that the regioselectivity of the reaction toward the formation of imidazole derivatives instead of 1,2-dihydropyrazines, most likely via a diaza-Cope rearrangement, is driven by the 2-hydroxyaryl group in the scaffold. The latter group promotes the intramolecular abstraction and protonation process in the cycloadduct intermediate, triggering the evolution of the reaction toward the formation of imidazole derivatives.
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Affiliation(s)
- Fábio Pedroso
de Lima
- Department
of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Emilio Lence
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Pilar Suárez de Cepeda
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Carla Correia
- Department
of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - M. Alice Carvalho
- Department
of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Concepción González-Bello
- Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - M. Fernanda Proença
- Department
of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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8
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Tamarit L, El Ouardi M, Lence E, Andreu I, González-Bello C, Vayá I, Miranda MA. Switching from ultrafast electron transfer to proton transfer in excited drug–protein complexes upon biotransformation. Chem Sci 2022; 13:9644-9654. [PMID: 36091919 PMCID: PMC9400592 DOI: 10.1039/d2sc03257k] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/10/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Photosensitization by drugs is directly related with the excited species and the photoinduced processes arising from interaction with UVA light. In this context, the ability of gefitinib (GFT), a tyrosine kinase inhibitor (TKI) used for the treatment of a variety of cancers, to induce phototoxicity and photooxidation of proteins has recently been demonstrated. In principle, photodamage can be generated not only by a given drug but also by its photoactive metabolites that maintain the relevant chromophore. In the present work, a complete study of O-desmorpholinopropyl gefitinib (GFT-MB) has been performed by means of fluorescence and ultrafast transient absorption spectroscopies, in addition to molecular dynamics (MD) simulations. The photobehavior of the GFT-MB metabolite in solution is similar to that of GFT. However, when the drug or its metabolite are in a constrained environment, i.e. within a protein, their behavior and the photoinduced processes that arise from their interaction with UVA light are completely different. For GFT in complex with human serum albumin (HSA), locally excited (LE) singlet states are mainly formed; these species undergo photoinduced electron transfer with Tyr and Trp. By contrast, since GFT-MB is a phenol, excited state proton transfer (ESPT) to form phenolate-like excited species might become an alternative deactivation pathway. As a matter of fact, the protein-bound metabolite exhibits higher fluorescence yields and longer emission wavelengths and lifetimes than GFT@HSA. Ultrafast transient absorption measurements support direct ESPT deprotonation of LE states (rather than ICT), to form phenolate-like species. This is explained by MD simulations, which reveal a close interaction between the phenolic OH group of GFT-MB and Val116 within site 3 (subdomain IB) of HSA. The reported findings are relevant to understand the photosensitizing properties of TKIs and the role of biotransformation in this type of adverse side effects. The photoinduced processes from the protein-bound GFT result in electron transfer, while those related with the photoactive metabolite GFT-MB induce excited state proton transfer to form phenolate-like excited species.![]()
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Affiliation(s)
- Lorena Tamarit
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Meryem El Ouardi
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Inmaculada Andreu
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ignacio Vayá
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Miguel A. Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022 València, Spain
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026 Valencia, Spain
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9
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Lence E, González-Bello C. Molecular Basis of Bicyclic Boronate β-Lactamase Inhibitors of Ultrabroad Efficacy - Insights From Molecular Dynamics Simulation Studies. Front Microbiol 2021; 12:721826. [PMID: 34421880 PMCID: PMC8371488 DOI: 10.3389/fmicb.2021.721826] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022] Open
Abstract
β-Lactam antibiotics represent about 70% of all antibacterial agents in clinical use. They are safe and highly effective drugs that have been used for more than 50 years, and, in general, well tolerated by most patients. However, its usefulness has been dramatically reduced with the spread and dissemination worldwide of multi-drug resistant bacteria. These pathogens elude the therapeutic action of these antibiotics by expressing β-lactamase enzymes that catalyze the hydrolysis of their β-lactam ring to give inactive products, which is one of the most relevant resistance mechanisms in deadly pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae. From the drug development point of view, the design of an efficient β-lactamase inhibitor able to block this antibiotic resistance mechanism and restore β-lactam antibiotics efficacy is challenging. This is due to: (1) the huge structural diversity of these enzymes in both the amino acid sequence and architecture of the active site; (2) the distinct hydrolytic capability against different types of substrates; (3) the variety of enzyme mechanisms of action employed, either involving covalent catalyzed processes (serine hydrolases) or non-covalent catalysis (zinc-dependent hydrolases); and (4) the increasing emergence and spread of bacterial pathogens capable of simultaneously producing diverse β-lactamases. Hence, a long-pursued goal has been the development of ultrabroad-spectrum inhibitors able to inhibit both serine- and metallo-β-lactamases. The recent development of taniborbactam (formerly VNRX-5133) and QPX7728, which are bicyclic boronate inhibitors currently under clinical development, represents a huge step forward in this goal. In this article, the molecular basis of the ultrabroad-spectrum of activity of these boron-based inhibitors is analyzed by molecular dynamics simulation studies using the available crystal structures in complex with both inhibitors, or the models constructed from wild-type forms. The efficacy of taniborbactam and QPX7728 is compared with the cyclic boronate inhibitor vaborbactam, which is the first boron-based β-lactamase inhibitor approved by the FDA in combination with meropenem for the treatment of complicated urinary tract infections.
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Affiliation(s)
- Emilio Lence
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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10
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Rubiolo JA, Lence E, González-Bello C, Roel M, Gil-Longo J, Campos-Toimil M, Ternon E, Thomas OP, González-Cantalapiedra A, López-Alonso H, Vieytes MR, Botana LM. Crambescin C1 Acts as A Possible Substrate of iNOS and eNOS Increasing Nitric Oxide Production and Inducing In Vivo Hypotensive Effect. Front Pharmacol 2021; 12:694639. [PMID: 34322022 PMCID: PMC8312399 DOI: 10.3389/fphar.2021.694639] [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: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Crambescins are guanidine alkaloids from the sponge Crambe crambe. Crambescin C1 (CC) induces metallothionein genes and nitric oxide (NO) is one of the triggers. We studied and compared the in vitro, in vivo, and in silico effects of some crambescine A and C analogs. HepG2 gene expression was analyzed using microarrays. Vasodilation was studied in rat aortic rings. In vivo hypotensive effect was directly measured in anesthetized rats. The targets of crambescines were studied in silico. CC and homo-crambescine C1 (HCC), but not crambescine A1 (CA), induced metallothioneins transcripts. CC increased NO production in HepG2 cells. In isolated rat aortic rings, CC and HCC induced an endothelium-dependent relaxation related to eNOS activation and an endothelium-independent relaxation related to iNOS activation, hence both compounds increase NO and reduce vascular tone. In silico analysis also points to eNOS and iNOS as targets of Crambescin C1 and source of NO increment. CC effect is mediated through crambescin binding to the active site of eNOS and iNOS. CC docking studies in iNOS and eNOS active site revealed hydrogen bonding of the hydroxylated chain with residues Glu377 and Glu361, involved in the substrate recognition, and explains its higher binding affinity than CA. The later interaction and the extra polar contacts with its pyrimidine moiety, absent in the endogenous substrate, explain its role as exogenous substrate of NOSs and NO production. Our results suggest that CC serve as a basis to develop new useful drugs when bioavailability of NO is perturbed.
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Affiliation(s)
- Juan A Rubiolo
- Departamento de Zoología, Genética y Antropología Física, Universidad de Santiago de Compostela, Lugo, Spain.,Facultad de Ciencias Bioquímicas y Farmacéuticas-Ministerio de Ciencia, Centro Científico y Tecnológico Acuario del Río Paraná, Tecnología e Innovación Productiva de Santa Fe, Universidad Nacional de Rosario, Rosario, Argentina
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María Roel
- Departamento de Farmacología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - José Gil-Longo
- Departamento de Farmacología, Facultad de Farmacia, Farmacia y Tecnología Farmacéutica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Campos-Toimil
- Departamento de Farmacología, Facultad de Farmacia, Farmacia y Tecnología Farmacéutica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Fisiología y Farmacología de las Enfermedades Crónicas (FIFAEC), CIMUS, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Eva Ternon
- CNRS, OCA, IRD, Géoazur, Université Côte d'Azur, Valbonne, France
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - Antonio González-Cantalapiedra
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Hospital Veterinario Universitario Rof Codina, Facultad de Veterinaria, Universidad de Santiago de Compostel, Lugo, Spain
| | - Henar López-Alonso
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias, Hospital Veterinario Universitario Rof Codina, Facultad de Veterinaria, Universidad de Santiago de Compostel, Lugo, Spain
| | - Mercedes R Vieytes
- Departamento de Fisiología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Luis M Botana
- Departamento de Farmacología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
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11
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Arca-Suárez J, Lasarte-Monterrubio C, Rodiño-Janeiro BK, Cabot G, Vázquez-Ucha JC, Rodríguez-Iglesias M, Galán-Sánchez F, Beceiro A, González-Bello C, Oliver A, Bou G. Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections. J Antimicrob Chemother 2021; 76:91-100. [PMID: 33083833 DOI: 10.1093/jac/dkaa396] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning. OBJECTIVES Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections. METHODS Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes. RESULTS The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold. CONCLUSIONS Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.
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Affiliation(s)
- Jorge Arca-Suárez
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Bruno-Kotska Rodiño-Janeiro
- Prof. Martin Polz Laboratory, University of Vienna, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
| | - Gabriel Cabot
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Manuel Rodríguez-Iglesias
- Servicio de Microbiología and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar; Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
| | - Fátima Galán-Sánchez
- Servicio de Microbiología and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar; Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Germán Bou
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
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12
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Arca-Suárez J, Vázquez-Ucha JC, Fraile-Ribot PA, Lence E, Cabot G, Martínez-Guitián M, Lasarte-Monterrubio C, Rodríguez-Iglesias M, Beceiro A, González-Bello C, Galán-Sánchez F, Oliver A, Bou G. Molecular and biochemical insights into the in vivo evolution of AmpC-mediated resistance to ceftolozane/tazobactam during treatment of an MDR Pseudomonas aeruginosa infection. J Antimicrob Chemother 2021; 75:3209-3217. [PMID: 32728723 DOI: 10.1093/jac/dkaa291] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/03/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Pseudomonas aeruginosa may develop resistance to novel cephalosporin/β-lactamase inhibitor combinations during therapy through the acquisition of structural mutations in AmpC. OBJECTIVES To describe the molecular and biochemical mechanisms involved in the development of resistance to ceftolozane/tazobactam in vivo through the selection and overproduction of a novel AmpC variant, designated PDC-315. METHODS Paired susceptible/resistant isolates obtained before and during ceftolozane/tazobactam treatment were evaluated. MICs were determined by broth microdilution. Mutational changes were investigated through WGS. Characterization of the novel PDC-315 variant was performed through genotypic and biochemical studies. The effects at the molecular level of the Asp245Asn change were analysed by molecular dynamics simulations using Amber. RESULTS WGS identified mutations leading to modification (Asp245Asn) and overproduction of AmpC. Susceptibility testing revealed that PAOΔC producing PDC-315 displayed increased MICs of ceftolozane/tazobactam, decreased MICs of piperacillin/tazobactam and imipenem and similar susceptibility to ceftazidime/avibactam compared with WT PDCs. The catalytic efficiency of PDC-315 for ceftolozane was 10-fold higher in relation to the WT PDCs, but 3.5- and 5-fold lower for piperacillin and imipenem. IC50 values indicated strong inhibition of PDC-315 by avibactam, but resistance to cloxacillin inhibition. Analysis at the atomic level explained that the particular behaviour of PDC-315 is linked to conformational changes in the H10 helix that favour the approximation of key catalytic residues to the active site. CONCLUSIONS We deciphered the precise mechanisms that led to the in vivo emergence of resistance to ceftolozane/tazobactam in P. aeruginosa through the selection of the novel PDC-315 enzyme. The characterization of this new variant expands our knowledge about AmpC-mediated resistance to cephalosporin/β-lactamase inhibitors in P. aeruginosa.
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Affiliation(s)
- Jorge Arca-Suárez
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Pablo Arturo Fraile-Ribot
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gabriel Cabot
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Marta Martínez-Guitián
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Manuel Rodríguez-Iglesias
- Servicio de Microbiología and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar and Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Fátima Galán-Sánchez
- Servicio de Microbiología and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar and Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Germán Bou
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
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13
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Vázquez-Ucha JC, Rodríguez D, Lasarte-Monterrubio C, Lence E, Arca-Suarez J, Maneiro M, Gato E, Perez A, Martínez-Guitián M, Juan C, Oliver A, Bou G, González-Bello C, Beceiro A. 6-Halopyridylmethylidene Penicillin-Based Sulfones Efficiently Inactivate the Natural Resistance of Pseudomonas aeruginosa to β-Lactam Antibiotics. J Med Chem 2021; 64:6310-6328. [PMID: 33913328 DOI: 10.1021/acs.jmedchem.1c00369] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pseudomonas aeruginosa, a major cause of nosocomial infections, is considered a paradigm of antimicrobial resistance, largely due to hyperproduction of chromosomal cephalosporinase AmpC. Here, we explore the ability of 6-pyridylmethylidene penicillin-based sulfones 1-3 to inactivate the AmpC β-lactamase and thus rescue the activity of the antipseudomonal ceftazidime. These compounds increased the susceptibility to ceftazidime in a collection of clinical isolates and PAO1 mutant strains with different ampC expression levels and also improved the inhibition kinetics relative to avibactam, displaying a slow deacylation rate and involving the formation of an indolizine adduct. Bromide 2 was the inhibitor with the lowest KI (15.6 nM) and the highest inhibitory efficiency (kinact/KI). Computational studies using diverse AmpC enzymes revealed that the aromatic moiety in 1-3 targets a tunnel-like site adjacent to the catalytic serine and induces the folding of the H10 helix, indicating the potential value of this not-always-evident pocket in drug design.
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Affiliation(s)
- Juan C Vázquez-Ucha
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - Diana Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Jorge Arca-Suarez
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Eva Gato
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - Astrid Perez
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - Marta Martínez-Guitián
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - Carlos Juan
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Carretera de Valldemossa, 79, Palma de Mallorca 07120, Spain
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Carretera de Valldemossa, 79, Palma de Mallorca 07120, Spain
| | - German Bou
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología do Complejo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (CICA-INIBIC), Xubias de Arriba, 84, A Coruña 15006, Spain
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14
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Lasarte-Monterrubio C, Vázquez-Ucha JC, Maneiro M, Arca-Suárez J, Alonso I, Guijarro-Sánchez P, Buynak JD, Bou G, González-Bello C, Beceiro A. Activity of Imipenem, Meropenem, Cefepime, and Sulbactam in Combination with the β-Lactamase Inhibitor LN-1-255 against Acinetobacter spp. Antibiotics (Basel) 2021; 10:210. [PMID: 33672671 PMCID: PMC7924334 DOI: 10.3390/antibiotics10020210] [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: 01/27/2021] [Revised: 02/12/2021] [Accepted: 02/14/2021] [Indexed: 11/17/2022] Open
Abstract
Treatment of infections caused by Acinetobacter spp., particularly A. baumannii, is a major clinical problem due to its high rates of antibiotic resistance. New strategies must be developed; therefore, restoration of β-lactam efficacy through the use of β-lactamase inhibitors is paramount. Activities of the antibiotics imipenem, meropenem, cefepime, and sulbactam in combination with the penicillin-sulfone inhibitor LN-1-255 were tested by microdilution against 148 isolates of Acinetobacter spp. collected in 14 hospitals in Spain in 2020. Relevantly, the MIC90 (i.e., minimum concentration at which 90% of isolates were inhibited) of antibiotics in combination with LN-1-255 decreased 4- to 8-fold for all of the Acinetobacter isolates. Considering only the carbapenem-resistant A. baumannii isolates, which produce carbapenem-hydrolyzing class D β-lactamases, the addition of LN-1-255 decreased the resistance rates from 95.1% to 0% for imipenem, from 100% to 9.8% for meropenem, from 70.7% to 7.3% for cefepime, and sulbactam resistance rates from 9.8% to 0% and intermediate susceptibility rates from 53.7% to 2.4%. The inhibitor also decreased the minimum inhibitory concentrations (MICs) when tested against non-carbapenem-resistant Acinetobacter spp. isolates. In conclusion, combining LN-1-255 with imipenem, meropenem, cefepime, and sulbactam to target A. baumannii, and especially carbapenem-resistant isolates, represents an attractive option that should be developed for the treatment of infections caused by this pathogen.
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Affiliation(s)
- Cristina Lasarte-Monterrubio
- Servicio de Microbiología, Instituto de Investigación Biomédica de A Coruña (INIBIC-CICA), Complejo Hospitalario Universitario A Coruña (CHUAC), As Xubias 84, 15006 A Coruña, Spain; (C.L.-M.); (J.C.V.-U.); (P.G.-S.); (G.B.)
| | - Juan C. Vázquez-Ucha
- Servicio de Microbiología, Instituto de Investigación Biomédica de A Coruña (INIBIC-CICA), Complejo Hospitalario Universitario A Coruña (CHUAC), As Xubias 84, 15006 A Coruña, Spain; (C.L.-M.); (J.C.V.-U.); (P.G.-S.); (G.B.)
| | - Maria Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain; (M.M.); (C.G.-B.)
| | - Jorge Arca-Suárez
- Servicio de Microbiología, Instituto de Investigación Biomédica de A Coruña (INIBIC-CICA), Complejo Hospitalario Universitario A Coruña (CHUAC), As Xubias 84, 15006 A Coruña, Spain; (C.L.-M.); (J.C.V.-U.); (P.G.-S.); (G.B.)
| | - Isaac Alonso
- Servicio de Microbiología, Hospital Provincial Pontevedra, Loureiro Crespo 2, 36002 Pontevedra, Spain;
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología, Instituto de Investigación Biomédica de A Coruña (INIBIC-CICA), Complejo Hospitalario Universitario A Coruña (CHUAC), As Xubias 84, 15006 A Coruña, Spain; (C.L.-M.); (J.C.V.-U.); (P.G.-S.); (G.B.)
| | - John D. Buynak
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA;
| | - Germán Bou
- Servicio de Microbiología, Instituto de Investigación Biomédica de A Coruña (INIBIC-CICA), Complejo Hospitalario Universitario A Coruña (CHUAC), As Xubias 84, 15006 A Coruña, Spain; (C.L.-M.); (J.C.V.-U.); (P.G.-S.); (G.B.)
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain; (M.M.); (C.G.-B.)
| | - Alejandro Beceiro
- Servicio de Microbiología, Instituto de Investigación Biomédica de A Coruña (INIBIC-CICA), Complejo Hospitalario Universitario A Coruña (CHUAC), As Xubias 84, 15006 A Coruña, Spain; (C.L.-M.); (J.C.V.-U.); (P.G.-S.); (G.B.)
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15
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Andreu I, Lence E, González-Bello C, Mayorga C, Cuquerella MC, Vayá I, Miranda MA. Protein Binding of Lapatinib and Its N- and O-Dealkylated Metabolites Interrogated by Fluorescence, Ultrafast Spectroscopy and Molecular Dynamics Simulations. Front Pharmacol 2020; 11:576495. [PMID: 33192518 PMCID: PMC7662899 DOI: 10.3389/fphar.2020.576495] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/25/2020] [Indexed: 01/02/2023] Open
Abstract
Lapatinib (LAP) is an anticancer drug generally used to treat breast and lung cancer. It exhibits hypersensitivity reactions in addition to dermatological adverse effects and photosensitivity. Moreover, LAP binds to serum proteins and is readily biotransformed in humans, giving rise to several metabolites, such as N- and O-dealkylated products (N-LAP and O-LAP, respectively). In this context, the aim of the present work is to obtain key information on drug@protein complexation, the first step involved in a number of hypersensitivity reactions, by a combination of fluorescence, femtosecond transient absorption spectroscopy and molecular dynamics (MD) simulations. Following this approach, the behavior of LAP and its metabolites has been investigated in the presence of serum proteins, such as albumins and α1-acid glycoproteins (SAs and AGs, respectively) from human and bovine origin. Fluorescence results pointed to a higher affinity of LAP and its metabolites to human proteins; the highest one was found for LAP@HSA. This is associated to the coplanar orientation adopted by the furan and quinazoline rings of LAP, which favors emission from long-lived (up to the ns time-scale) locally-excited (LE) states, disfavoring population of intramolecular charge transfer (ICT) states. Moreover, the highly constrained environment provided by subdomain IB of HSA resulted in a frozen conformation of the ligand, contributing to fluorescence enhancement. Computational studies were clearly in line with the experimental observations, providing valuable insight into the nature of the binding sites and the conformational arrangement of the ligands inside the protein cavities. Besides, a good correlation was found between the calculated binding energies for each ligand@protein complex and the relative affinities observed in competition experiments.
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Affiliation(s)
- Inmaculada Andreu
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Cristobalina Mayorga
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga and Allergy Research Group, Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain
| | - M Consuelo Cuquerella
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Ignacio Vayá
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Valencia, Spain
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16
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Vayá I, Andreu I, Lence E, González-Bello C, Consuelo Cuquerella M, Navarrete-Miguel M, Roca-Sanjuán D, Miranda MA. Characterization of Locally Excited and Charge-Transfer States of the Anticancer Drug Lapatinib by Ultrafast Spectroscopy and Computational Studies. Chemistry 2020; 26:15922-15930. [PMID: 32585059 DOI: 10.1002/chem.202001336] [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] [Received: 03/17/2020] [Indexed: 12/24/2022]
Abstract
Lapatinib (LAP) is an anticancer drug, which is metabolized to the N- and O-dealkylated products (N-LAP and O-LAP, respectively). In view of the photosensitizing potential of related drugs, a complete experimental and theoretical study has been performed on LAP, N-LAP and O-LAP, both in solution and upon complexation with human serum albumin (HSA). In organic solvents, coplanar locally excited (LE) emissive states are generated; they rapidly evolve towards twisted intramolecular charge-transfer (ICT) states. By contrast, within HSA only LE states are detected. Accordingly, femtosecond transient absorption reveals a very fast switching (ca. 2 ps) from LE (λmax =550 nm) to ICT states (λmax =480 nm) in solution, whereas within HSA the LE species become stabilized and live much longer (up to the ns scale). Interestingly, molecular dynamics simulation studies confirm that the coplanar orientation is preferred for LAP (or to a lesser extent N-LAP) within HSA, explaining the experimental results.
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Affiliation(s)
- Ignacio Vayá
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS), La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Inmaculada Andreu
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS), La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago, de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago, de Compostela, Spain
| | - M Consuelo Cuquerella
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS), La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Miriam Navarrete-Miguel
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071, València, Spain
| | - Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, P.O. Box 22085, 46071, València, Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, València, Spain.,Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS), La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
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17
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Rodríguez D, Maneiro M, Vázquez-Ucha JC, Beceiro A, González-Bello C. 6-Arylmethylidene Penicillin-Based Sulfone Inhibitors for Repurposing Antibiotic Efficiency in Priority Pathogens. J Med Chem 2020; 63:3737-3755. [PMID: 32196336 DOI: 10.1021/acs.jmedchem.0c00127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The ability of 6-(aryl)methylidene penicillin-based sulfones 1-7 to repurpose β-lactam antibiotics activity with bacterial species that carry carbapenem-hydrolyzing class D β-lactamases (OXA-23, OXA-24/40 and OXA-48), as well as with class A (TEM-1, CTX-M-2) and class C (CMY-2, DHA-1) enzymes, is reported. The combinations imipenem/3 and imipenem/4 restored almost completely the antibiotic efficacy in OXA-23 and OXA-24/40 carbapenemase-producing A. baumannii strains (1 μg mL-1) and also provided good results for OXA-48 carbapenemase-producing K. pneumoniae strains (4 μg mL-1). Compounds 2-6 in combinations with ceftazidime and ampicillin were also efficient in restoring antibiotic efficacy in E. coli strains carrying class C (CMY-2 and DHA-1) and class A (TEM-1 and CTX-M-2) β-lactamase enzymes, respectively. Kinetic and inhibition studies with the OXA-24/40 enzyme, protein mass spectrometry analysis and docking studies allowed us to gain an insight into the inhibition mechanism and the experimentally observed differences between the ligands.
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Affiliation(s)
- Diana Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C Vázquez-Ucha
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Xubias de Arriba, 84, 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología do Complexo Hospitalario Universitario da Coruña (CHUAC), Instituto de Investigación Biomédica da Coruña (INIBIC), Xubias de Arriba, 84, 15006 A Coruña, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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18
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Limones-Herrero D, Palumbo F, Vendrell-Criado V, Andreu I, Lence E, González-Bello C, Miranda MA, Jiménez MC. Investigation of metabolite-protein interactions by transient absorption spectroscopy and in silico methods. Spectrochim Acta A Mol Biomol Spectrosc 2020; 226:117652. [PMID: 31654902 DOI: 10.1016/j.saa.2019.117652] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/23/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Transient absorption spectroscopy in combination with in silico methods has been employed to study the interactions between human serum albumin (HSA) and the anti-psychotic agent chlorpromazine (CPZ) as well as its two demethylated metabolites (MCPZ and DCPZ). Thus, solutions containing CPZ, MCPZ or DCPZ and HSA (molar ligand:protein ratios between 1:0 and 1:3) were submitted to laser flash photolysis and the ΔAmax value at λ = 470 nm, corresponding to the triplet excited state, was monitored. In all cases, the protein-bound ligand exhibited higher ΔAmax values measured after the laser pulse and were also considerably longer-lived than the non-complexed forms. This is in agreement with an enhanced hydrophilicity of the metabolites, due to the replacement of methyl groups with H that led to a lower extent of protein binding. For the three compounds, laser flash photolysis displacement experiments using warfarin or ibuprofen indicated Sudlow site I as the main binding site. Docking and molecular dynamics simulation studies revealed that the binding mode of the two demethylated ligands with HSA would be remarkable different from CPZ, specially for DCPZ, which appears to come from the different ability of their terminal ammonium groups to stablish hydrogen bonding interactions with the negatively charged residues within the protein pocket (Glu153, Glu292) as well as to allocate the methyl groups in an apolar environment. DCPZ would be rotated 180° in relation to CPZ locating the aromatic ring away from the Sudlow site I of HSA.
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Affiliation(s)
- Daniel Limones-Herrero
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Fabrizio Palumbo
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Victoria Vendrell-Criado
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Inmaculada Andreu
- Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - M Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain; Unidad Mixta de Investigación UPV-Instituto de Investigación Sanitaria (IIS) La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain.
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González-Bello C, Rodríguez D, Pernas M, Rodríguez Á, Colchón E. β-Lactamase Inhibitors To Restore the Efficacy of Antibiotics against Superbugs. J Med Chem 2019; 63:1859-1881. [PMID: 31663735 DOI: 10.1021/acs.jmedchem.9b01279] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Infections caused by resistant bacteria are nowadays too common, and some pathogens have even become resistant to multiple types of antibiotics, in which case few or even no treatments are available. In recent years, the most successful strategy in anti-infective drug discovery for the treatment of such problematic infections is the combination therapy "antibiotic + inhibitor of resistance". These inhibitors allow the repurposing of antibiotics that have already proven to be safe and effective for clinical use. Three main types of compounds have been developed to block the principal bacterial resistance mechanisms: (i) β-lactamase inhibitors; (ii) outer membrane permeabilizers; (iii) efflux pump inhibitors. This Perspective is focused on β-lactamase inhibitors that disable the most prevalent cause of antibiotic resistance in Gram-negative bacteria, i.e., the deactivation of the most widely used antibiotics, β-lactams (penicillins, cephalosporines, carbapenems, and monobactams), by the production of β-lactamases. An overview of the most recently identified β-lactamase inhibitors and of combination therapy is provided. The article also covers the mechanism of action of the different types of β-lactamase enzymes as a basis for inhibitor design and target inactivation.
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Diana Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Marina Pernas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Ángela Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Esther Colchón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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20
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González-Bello C. Recently developed synthetic compounds with anti-infective activity. Curr Opin Pharmacol 2019; 48:17-23. [DOI: 10.1016/j.coph.2019.03.004] [Citation(s) in RCA: 7] [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: 02/12/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
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21
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Molins-Molina O, Pérez-Ruiz R, Lence E, González-Bello C, Miranda MA, Jiménez MC. Photobinding of Triflusal to Human Serum Albumin Investigated by Fluorescence, Proteomic Analysis, and Computational Studies. Front Pharmacol 2019; 10:1028. [PMID: 31616294 PMCID: PMC6764118 DOI: 10.3389/fphar.2019.01028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/10/2019] [Accepted: 08/12/2019] [Indexed: 11/13/2022] Open
Abstract
Triflusal is a platelet antiaggregant employed for the treatment and prevention of thromboembolic diseases. After administration, it is biotransformed into its active metabolite, the 2-hydroxy-4-trifluoromethylbenzoic acid (HTB). We present here an investigation on HTB photobinding to human serum albumin (HSA), the most abundant protein in plasma, using an approach that combines fluorescence, MS/MS, and peptide fingerprint analysis as well as theoretical calculations (docking and molecular dynamics simulation studies). The proteomic analysis of HTB/HSA photolysates shows that HTB addition takes place at the ε-amino groups of the Lys137, Lys199, Lys205, Lys351, Lys432, Lys525, Lys541 and Lys545 residues and involves replacement of the trifluoromethyl moiety of HTB with a new amide function. Only Lys199 is located in an internal pocket of the protein, and the remaining modified residues are placed in the external part. Docking and molecular dynamic simulation studies reveal that HTB supramolecular binding to HSA occurs in the "V-cleft" region and that the process is assisted by the presence of Glu/Asp residues in the neighborhood of the external Lys, in agreement with the experimentally observed modifications. In principle, photobinding can occur with other trifluoroaromatic compounds and may be responsible for the appearance of undesired photoallergic side effects.
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Affiliation(s)
- Oscar Molins-Molina
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politécnica de València, Valencia, Spain
| | - Raúl Pérez-Ruiz
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politécnica de València, Valencia, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politécnica de València, Valencia, Spain
| | - M Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politécnica de València, Valencia, Spain
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22
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Maneiro M, Lence E, Sanz-Gaitero M, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Hydroxylammonium derivatives for selective active-site lysine modification in the anti-virulence bacterial target DHQ1 enzyme. Org Chem Front 2019. [DOI: 10.1039/c9qo00453j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first example of a hydroxylammonium derivative that causes a specific covalent modification of the active-site lysine residue of an aldolase enzyme, which is a promising target for anti-bacterial drug discovery, is reported.
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Affiliation(s)
- María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Marta Sanz-Gaitero
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - José M. Otero
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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Pernas M, Blanco B, Lence E, Thompson P, Hawkins AR, González-Bello C. Synthesis of rigidified shikimic acid derivatives by ring-closing metathesis to imprint inhibitor efficacy against shikimate kinase enzyme. Org Chem Front 2019. [DOI: 10.1039/c9qo00562e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rigidification of the high-energy conformation of shikimic acid was used to enhance inhibitor efficacy against shikimate kinase enzyme, an attractive target for antibiotic drug discovery.
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Affiliation(s)
- Marina Pernas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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24
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Molins-Molina O, Lence E, Limones-Herrero D, González-Bello C, Miranda MA, Jiménez MC. Identification of a common recognition center for a photoactive non-steroidal antiinflammatory drug in serum albumins of different species. Org Chem Front 2019. [DOI: 10.1039/c8qo01045e] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoreactivity, proteomic and molecular dynamic simulation studies demonstrate the existence of a common recognition center for carprofen in serum albumins of different species, in the interface between subdomains IB and IIIA.
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Affiliation(s)
- Oscar Molins-Molina
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC
- Universitat Politècnica de València
- 46071 Valencia
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Daniel Limones-Herrero
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC
- Universitat Politècnica de València
- 46071 Valencia
- Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- Departamento de Química Orgánica
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Miguel A. Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC
- Universitat Politècnica de València
- 46071 Valencia
- Spain
| | - M. Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC
- Universitat Politècnica de València
- 46071 Valencia
- Spain
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25
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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26
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Pérez-Ruiz R, Molins-Molina O, Lence E, González-Bello C, Miranda MA, Jiménez MC. Photogeneration of Quinone Methides as Latent Electrophiles for Lysine Targeting. J Org Chem 2018; 83:13019-13029. [PMID: 30274513 DOI: 10.1021/acs.joc.8b01559] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Latent electrophiles are nowadays very attractive chemical entities for drug discovery, as they are unreactive unless activated upon binding with the specific target. In this work, the utility of 4-trifluoromethyl phenols as precursors of latent electrophiles, quinone methides (QM), for lysine-targeting is demonstrated. These Michael acceptors were photogenerated for specific covalent modification of lysine residues using human serum albumin (HSA) as a model target. The reactive QM-type intermediates I or II, generated upon irradiation of 4-trifluoromethyl-1-naphthol (1)@HSA or 4-(4-trifluorometylphenyl)phenol (2)@HSA complexes, exhibited chemoselective reactivity toward lysine residues leading to amide adducts, which was confirmed by proteomic analysis. For ligand 1, the covalent modification of residues Lys106 and Lys414 (located in subdomains IA and IIIA, respectively) was observed, whereas for ligand 2, the modification of Lys195 (in subdomain IIA) took place. Docking and molecular dynamics simulation studies provided an insight into the molecular basis of the selectivity of 1 and 2 for these HSA subdomains and the covalent modification mechanism. These studies open the opportunity of performing protein silencing by generating reactive ligands under very mild conditions (irradiation) for specific covalent modification of hidden lysine residues.
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Affiliation(s)
- Raúl Pérez-Ruiz
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain.,Photoactivated Processes Unit , IMDEA Energy Institute , Av. Ramón de la Sagra 3 , 28935 Móstoles, Madrid , Spain
| | - Oscar Molins-Molina
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica , Universidade de Santiago de Compostela , Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica , Universidade de Santiago de Compostela , Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Miguel A Miranda
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain
| | - M Consuelo Jiménez
- Departamento de Química, Instituto de Tecnología Química UPV-CSIC , Universitat Politécnica de València , Camino de Vera s/n , 46071 Valencia , Spain
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27
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Lence E, van der Kamp MW, González-Bello C, Mulholland AJ. QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes. Org Biomol Chem 2018; 16:4443-4455. [PMID: 29767194 PMCID: PMC6011038 DOI: 10.1039/c8ob00066b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/18/2018] [Indexed: 11/29/2022]
Abstract
Type II dehydroquinase enzymes (DHQ2), recognized targets for antibiotic drug discovery, show significantly different activities dependent on the species: DHQ2 from Mycobacterium tuberculosis (MtDHQ2) and Helicobacter pylori (HpDHQ2) show a 50-fold difference in catalytic efficiency. Revealing the determinants of this activity difference is important for our understanding of biological catalysis and further offers the potential to contribute to tailoring specificity in drug design. Molecular dynamics simulations using a quantum mechanics/molecular mechanics potential, with correlated ab initio single point corrections, identify and quantify the subtle determinants of the experimentally observed difference in efficiency. The rate-determining step involves the formation of an enolate intermediate: more efficient stabilization of the enolate and transition state of the key step in MtDHQ2, mainly by the essential residues Tyr24 and Arg19, makes it more efficient than HpDHQ2. Further, a water molecule, which is absent in MtDHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in HpDHQ2, was found to destabilize both the transition state and the enolate intermediate. The quantification of the contribution of key residues and water molecules in the rate-determining step of the mechanism also leads to improved understanding of higher potencies and specificity of known inhibitors, which should aid ongoing inhibitor design.
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Affiliation(s)
- Emilio Lence
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
Jenaro de la Fuente s/n
, 15782 Santiago de Compostela
, Spain
.
; Tel: +34 881 815726
| | - Marc W. van der Kamp
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
- School of Biochemistry
, University of Bristol
, University Walk
,
BS8 1TD Bristol
, UK
.
; Tel: +44 (0)117 3312147
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
Jenaro de la Fuente s/n
, 15782 Santiago de Compostela
, Spain
.
; Tel: +34 881 815726
| | - Adrian J. Mulholland
- Centre for Computational Chemistry
, School of Chemistry
, University of Bristol
,
Cantock's Close
, BS8 1TS Bristol
, UK
.
; Tel: +44 (0)117 9289097
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28
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Vendrell-Criado V, González-Bello C, Miranda MA, Jiménez MC. A combined photophysical and computational study on the binding of mycophenolate mofetil and its major metabolite to transport proteins. Spectrochim Acta A Mol Biomol Spectrosc 2018; 199:308-314. [PMID: 29627615 DOI: 10.1016/j.saa.2018.03.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/06/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
Binding of the immunosuppressive agent mycophenolate mofetil (MMP) and its pharmacologically active metabolite mycophenolic acid (MPA) to human serum albumin (HSA) and α1-acid glycoprotein (HAAG) has been investigated by means of an integrated approach involving selective excitation of the drug fluorophore, following their UV-A triggered fluorescence and docking studies. The formation of the protein/ligand complexes was evidenced by a dramatic enhancement of the fluorescence intensity and a hypsochromic shift of the emission band. In HSA, competitive studies using oleic acid as site I probe revealed site I as the main binding site of the ligands. Binding constants revealed that the affinity of the active metabolite by HSA is four-fold higher than its proactive form. Moreover, the affinity of MMP by HSA is three-fold higher than by HAAG. Docking studies revealed significant molecular binding differences in the binding of MMP and MPA to sub-domain IIA of HSA (site 1). For MPA, the aromatic moiety would be in close contact to Trp214 with the flexible chain pointing to the other end of the sub-domain; on the contrary, for MMP, the carboxylate group of the chain would be fixed nearby Trp214 through electrostatic interactions with residues Arg218 and Arg222.
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Affiliation(s)
- Victoria Vendrell-Criado
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
| | - M Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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29
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Peón A, Robles A, Blanco B, Convertino M, Thompson P, Hawkins AR, Caflisch A, González-Bello C. Reducing the Flexibility of Type II Dehydroquinase for Inhibition: A Fragment-Based Approach and Molecular Dynamics Study. ChemMedChem 2017; 12:1512-1524. [DOI: 10.1002/cmdc.201700396] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/01/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Adrián Robles
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Beatriz Blanco
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Marino Convertino
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
- Current address: Department of Biochemistry and Biophysics; University of North Carolina, School of Medicine; Chapel Hill NC 27599 USA
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne; Catherine Cookson Building, Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Amedeo Caflisch
- Department of Biochemistry; University of Zurich; 8057 Zurich Switzerland
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, CIQUS, and Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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Pérez-Ruíz R, Lence E, Andreu I, Limones-Herrero D, González-Bello C, Miranda MA, Jiménez MC. A New Pathway for Protein Haptenation by β-Lactams. Chemistry 2017; 23:13986-13994. [PMID: 28791745 DOI: 10.1002/chem.201702643] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 06/08/2017] [Indexed: 11/09/2022]
Abstract
The covalent binding of β-lactams to proteins upon photochemical activation has been demonstrated by using an integrated approach that combines photochemical, proteomic and computational studies, selecting human serum albumin (HSA) as a target protein and ezetimibe (1) as a probe. The results have revealed a novel protein haptenation pathway for this family of drugs that is an alternative to the known nucleophilic ring opening of β-lactams by the free amino group of lysine residues. Thus, photochemical ring splitting of the β-lactam ring, following a formal retro-Staudinger reaction, gives a highly reactive ketene intermediate that is trapped by the neighbouring lysine residues, leading to an amide adduct. For the investigated 1/HSA system, covalent modification of residues Lys414 and Lys525, which are located in sub-domains IIIA and IIIB, respectively, occurs. The observed photobinding may constitute the key step in the sequence of events leading to photoallergy. Docking and molecular dynamics simulation studies provide an insight into the molecular basis of the selectivity of 1 for these HSA sub-domains and the covalent modification mechanism. Computational studies also reveal positive cooperative binding of sub-domain IIIB that explains the experimentally observed modification of Lys414, which is located in a barely accessible pocket (sub-domain IIIA).
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Affiliation(s)
- Raúl Pérez-Ruíz
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de Valencia, Camino de Vera s/n, 46071, Valencia, Spain.,Present address: Instituto Imdea Energía, Parque Tecnológico de Móstoles, Av. Ramón de la Sagra, 3., 28935, Móstoles, Madrid, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Inmaculada Andreu
- Instituto de Investigación Sanitaria La Fe, Hospital Universitari i Politècnic La Fe, Avenida de Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Daniel Limones-Herrero
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de Valencia, Camino de Vera s/n, 46071, Valencia, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de Valencia, Camino de Vera s/n, 46071, Valencia, Spain
| | - M Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC, Universitat Politècnica de Valencia, Camino de Vera s/n, 46071, Valencia, Spain
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González-Bello C. Antibiotic adjuvants - A strategy to unlock bacterial resistance to antibiotics. Bioorg Med Chem Lett 2017; 27:4221-4228. [PMID: 28827113 DOI: 10.1016/j.bmcl.2017.08.027] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [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: 06/23/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 12/11/2022]
Abstract
Resistance to available antibiotics in pathogenic bacteria is currently a global challenge since the number of strains that are resistant to multiple types of antibiotics has increased dramatically each year and has spread worldwide. To unlock this problem, the use of an 'antibiotic adjuvant' in combination with an antibiotic is now being exploited. This approach enables us to prolong the lifespan of these life-saving drugs. This digests review provides an overview of the main types of antibiotic adjuvants, the basis of their operation and the remaining issues to be tackled in this field. Particular emphasis is placed on those compounds that are already in clinical development, namely β-lactamase inhibitors.
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain.
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Limones-Herrero D, Pérez-Ruiz R, Lence E, González-Bello C, Miranda MA, Jiménez MC. Mapping a protein recognition centre with chiral photoactive ligands. An integrated approach combining photophysics, reactivity, proteomics and molecular dynamics simulation studies. Chem Sci 2017; 8:2621-2628. [PMID: 28553497 PMCID: PMC5431658 DOI: 10.1039/c6sc04900a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 11/04/2016] [Accepted: 12/30/2016] [Indexed: 01/10/2023] Open
Abstract
A multidisciplinary strategy to obtain structural information on the intraprotein region is described here. As probe ligands, (S)- and (R)-CPFMe (the methyl esters of the chiral drug carprofen) have been selected, while bovine α1-acid glycoprotein (BAAG) has been chosen as a biological host. The procedure involves the separate irradiation of the BAAG/(S)-CPFMe and BAAG/(R)-CPFMe complexes, coupled with fluorescence spectroscopy, laser flash photolysis, proteomic analysis, docking and molecular dynamics simulations. Thus, irradiation of the BAAG/CPFMe complexes at λ = 320 nm was followed by fluorescence spectroscopy. The intensity of the emission band obtained after irradiation indicated photodehalogenation, whereas its structureless shape suggested covalent binding of the resulting radical CBZMe˙ to the biopolymer. After gel filtration chromatography, the spectra still displayed emission, in agreement with covalent attachment of CBZMe˙ to BAAG. Stereodifferentiation was observed in this process. After trypsin digestion and ESI-MS/MS, the incorporation of CBZMe was detected at Phe68. Docking and molecular dynamics simulation studies, which were carried out using a homology model of BAAG, reveal that the closer proximity of the aromatic moiety of the (S)-enantiomer to the phenyl group of Phe68 would be responsible for the experimentally observed, more effective chemical modification of the protein. The proposed tridimensional structure of BAAG covalently modified by the two enantiomers is also provided. In principle, this approach can be extended to a variety of protein/ligand complexes.
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Affiliation(s)
- Daniel Limones-Herrero
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
| | - Raúl Pérez-Ruiz
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , C/ Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) , Departamento de Química Orgánica , Universidade de Santiago de Compostela , C/ Jenaro de la Fuente s/n , 15782 Santiago de Compostela , Spain
| | - Miguel A Miranda
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
| | - M Consuelo Jiménez
- Departamento de Química/Instituto de Tecnología Química UPV-CSIC , Universitat Politècnica de València , Camino de Vera s/n , 46022 , Valencia , Spain . ;
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Prado V, Lence E, Thompson P, Hawkins AR, González-Bello C. Frontispiece: Freezing the Dynamic Gap for Selectivity: Motion-Based Design of Inhibitors of the Shikimate Kinase Enzyme. Chemistry 2016. [DOI: 10.1002/chem.201685062] [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)
- Verónica Prado
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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Prado V, Lence E, Thompson P, Hawkins AR, González-Bello C. Freezing the Dynamic Gap for Selectivity: Motion-Based Design of Inhibitors of the Shikimate Kinase Enzyme. Chemistry 2016; 22:17988-18000. [DOI: 10.1002/chem.201602923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences, Medical School; University of Newcastle upon Tyne, Catherine Cookson Building; Framlington Place Newcastle upon Tyne NE2 4HH UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Departamento de Química Orgánica; Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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Prado V, Lence E, Maneiro M, Vázquez-Ucha JC, Beceiro A, Thompson P, Hawkins AR, González-Bello C. Targeting the Motion of Shikimate Kinase: Development of Competitive Inhibitors that Stabilize an Inactive Open Conformation of the Enzyme. J Med Chem 2016; 59:5471-87. [DOI: 10.1021/acs.jmedchem.6b00483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - María Maneiro
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Juan C. Vázquez-Ucha
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences,
Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences,
Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
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Vallejo JA, Martínez-Guitián M, Vázquez-Ucha JC, González-Bello C, Poza M, Buynak JD, Bethel CR, Bonomo RA, Bou G, Beceiro A. LN-1-255, a penicillanic acid sulfone able to inhibit the class D carbapenemase OXA-48. J Antimicrob Chemother 2016; 71:2171-80. [PMID: 27125555 DOI: 10.1093/jac/dkw105] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/04/2016] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES Carbapenemases are the most important mechanism responsible for carbapenem resistance in Enterobacteriaceae. Among carbapenemases, OXA-48 presents unique challenges as it is resistant to β-lactam inhibitors. Here, we test the capacity of the compound LN-1-255, a 6-alkylidene-2'-substituted penicillanic acid sulfone, to inhibit the activity of the carbapenemase OXA-48. METHODS The OXA-48 gene was cloned and expressed in Klebsiella pneumoniae and Escherichia coli in order to obtain MICs in the presence of inhibitors (clavulanic acid, tazobactam and sulbactam) and LN-1-255. OXA-48 was purified and steady-state kinetics was performed with LN-1-255 and tazobactam. The covalent binding mode of LN-1-255 with OXA-48 was studied by docking assays. RESULTS Both OXA-48-producing clinical and transformant strains displayed increased susceptibility to carbapenem antibiotics in the presence of 4 mg/L LN-1-255 (2-32-fold increased susceptibility) and 16 mg/L LN-1-255 (4-64-fold increased susceptibility). Kinetic assays demonstrated that LN-1-255 is able to inhibit OXA-48 with an acylation efficiency (k2/K) of 10 ± 1 × 10(4) M(-1) s(-1) and a slow deacylation rate (koff) of 7 ± 1 × 10(-4) s(-1). IC50 was 3 nM for LN-1-255 and 1.5 μM for tazobactam. Lastly, kcat/kinact was 500-fold lower for LN-1-255 than for tazobactam. CONCLUSIONS In these studies, carbapenem antibiotics used in combination with LN-1-255 are effective against the carbapenemase OXA-48, an important emerging mechanism of antibiotic resistance. This provides an incentive for further investigations to maximize the efficacy of penicillin sulfone inhibition of class D plasmid-carried Enterobacteriaceae carbapenemases.
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Affiliation(s)
- Juan A Vallejo
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), 15006 A Coruña, Spain
| | - Marta Martínez-Guitián
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), 15006 A Coruña, Spain
| | - Juan C Vázquez-Ucha
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), 15006 A Coruña, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Margarita Poza
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), 15006 A Coruña, Spain
| | - John D Buynak
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275, USA
| | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, OH 44106, USA Departments of Biochemistry, Molecular Biology and Microbiology, Pharmacology and Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - German Bou
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), 15006 A Coruña, Spain
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Prado V, Lence E, Vallejo JA, Beceiro A, Thompson P, Hawkins AR, González-Bello C. Study of the Phosphoryl-Transfer Mechanism of Shikimate Kinase by NMR Spectroscopy. Chemistry 2016; 22:2758-68. [PMID: 26797764 DOI: 10.1002/chem.201504438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 01/16/2023]
Abstract
The phosphoryl-transfer mechanism of shikimate kinase from Mycobacterium tuberculosis and Helicobacter pylori, which is an attractive target for antibiotic drug discovery, has been studied by 1D (1)H and (31)P NMR spectroscopy. Metaphosphoric acid proved to be a good mimetic of the metaphosphate intermediate and facilitated the ready and rapid evaluation by NMR spectroscopic analysis of a dissociative mechanism. The required closed form of the active site for catalysis was achieved by the use of ADP (product) or two synthetic ADP analogues (AMPNP, AMPCP). Molecular dynamics simulation studies reported here also revealed that the essential arginine (Arg116/Arg117 in H. pylori and M. tuberculosis, respectively), which activates the γ-phosphate group of ATP for catalysis and triggers the release of the product for turnover, would also be involved in the stabilisation of the metaphosphate intermediate during catalysis. We believe that the studies reported here will be helpful for future structure-based design of inhibitors of this attractive target. The approach is also expected be useful for studies on the possible dissociative mechanism of other kinase enzymes.
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Affiliation(s)
- Verónica Prado
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain
| | - Juan A Vallejo
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), Hospital Teresa Herrera, As Xubias, 84, 15006 A, Coruña, Spain
| | - Alejandro Beceiro
- Servicio de Microbioloxía-INIBIC, Complexo Hospitalario Universitario A Coruña (CHUAC), Hospital Teresa Herrera, As Xubias, 84, 15006 A, Coruña, Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Alastair R Hawkins
- Institute of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Catherine Cookson Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, calle Jenaro de la Fuente s/n, 15782, Santiago de Compostela, Spain.
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Affiliation(s)
- Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS); Universidade de Santiago de Compostela; calle Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
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Fondo M, Doejo J, García-Deibe AM, Sanmartín J, González-Bello C, Vicente R. Hydrolysis of imidazolidine ligands mediated by CuII: Mononuclear, tetranuclear and 1D CuII-amine complexes. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.07.028] [Citation(s) in RCA: 2] [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] [Indexed: 11/28/2022]
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González-Bello C, Tizón L, Lence E, Otero JM, van Raaij MJ, Martinez-Guitian M, Beceiro A, Thompson P, Hawkins AR. Chemical Modification of a Dehydratase Enzyme Involved in Bacterial Virulence by an Ammonium Derivative: Evidence of its Active Site Covalent Adduct. J Am Chem Soc 2015; 137:9333-43. [DOI: 10.1021/jacs.5b04080] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | - Mark J. van Raaij
- Departamento
de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Marta Martinez-Guitian
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Alejandro Beceiro
- Servicio
de Microbiología-INIBIC, Complejo Hospitalario Universitario A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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Costas C, López-Puente V, Bodelón G, González-Bello C, Pérez-Juste J, Pastoriza-Santos I, Liz-Marzán LM. Using surface enhanced Raman scattering to analyze the interactions of protein receptors with bacterial quorum sensing modulators. ACS Nano 2015; 9:5567-76. [PMID: 25927541 PMCID: PMC4446724 DOI: 10.1021/acsnano.5b01800] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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] [Indexed: 05/13/2023]
Abstract
Many members of the LuxR family of quorum sensing (QS) transcriptional activators, including LasR of Pseudomonas aeruginosa, are believed to require appropriate acyl-homoserine lactone (acyl-HSL) ligands to fold into an active conformation. The failure to purify ligand-free LuxR homologues in nonaggregated form at the high concentrations required for their structural characterization has limited the understanding of the mechanisms by which QS receptors are activated. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can be applied to study proteins at extremely low concentrations in their active state. The high sensitivity of SERS has allowed us to detect molecular interactions between the ligand-binding domain of LasR (LasRLBD) as a soluble apoprotein and modulators of P. aeruginosa QS. We found that QS activators and inhibitors produce differential SERS fingerprints in LasRLBD, and in combination with molecular docking analysis provide insight into the relevant interaction mechanism. This study reveals signal-specific structural changes in LasR upon ligand binding, thereby confirming the applicability of SERS to analyze ligand-induced conformational changes in proteins.
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Affiliation(s)
- Celina Costas
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
| | | | - Gustavo Bodelón
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
- Address correspondence to ,
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jorge Pérez-Juste
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
| | | | - Luis M. Liz-Marzán
- Departamento de Química Física, Universidade de Vigo, 36301 Vigo, Spain
- Bionanoplasmonics Laboratory, CIC biomaGUNE, Paseo de Miramón 182, 20009 Donostia-San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
- Address correspondence to ,
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Tizón L, Maneiro M, Peón A, Otero JM, Lence E, Poza S, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Irreversible covalent modification of type I dehydroquinase with a stable Schiff base. Org Biomol Chem 2015; 13:706-16. [DOI: 10.1039/c4ob01782j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structural and computational studies carried out with two epoxides provide insight into the irreversible inhibition of type I dehydroquinase.
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Affiliation(s)
- Lorena Tizón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - María Maneiro
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - José M. Otero
- Departamento de Bioquímica y Biología Molecular and CIQUS
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Emilio Lence
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Sergio Poza
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mark J. van Raaij
- Departamento de Estructura de Macromoléculas
- Centro Nacional de Biotecnología (CSIC)
- 28049 Madrid
- Spain
| | - Paul Thompson
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Alastair R. Hawkins
- Institute of Cell and Molecular Biosciences
- Medical School
- University of Newcastle upon Tyne
- Newcastle upon Tyne NE2 4HH
- UK
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares (CIQUS)
- Universidad de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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43
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Blanco B, Sedes A, Peón A, Otero JM, van Raaij MJ, Thompson P, Hawkins AR, González-Bello C. Exploring the Water-Binding Pocket of the Type II Dehydroquinase Enzyme in the Structure-Based Design of Inhibitors. J Med Chem 2014; 57:3494-510. [DOI: 10.1021/jm500175z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Beatriz Blanco
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antía Sedes
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio Peón
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José M. Otero
- Departamento
de Bioquímica y Biología Molecular, Centro Singular
de Investigación en Química Biológica y Materiales
Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mark J. van Raaij
- Departamento
de Estructura de Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Paul Thompson
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute
of Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Concepción González-Bello
- Centro
Singular de Investigación en Química Biológica
y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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44
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González-Bello C. Irreversible covalent modification of type I dehydroquinase: Structure-based design and simulation studies. Med Chem 2014. [DOI: 10.4172/2161-0444.s1.010] [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: 11/09/2022]
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45
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Blanco B, Prado V, Lence E, Otero JM, Garcia-Doval C, van Raaij MJ, Llamas-Saiz AL, Lamb H, Hawkins AR, González-Bello C. Mycobacterium tuberculosis shikimate kinase inhibitors: design and simulation studies of the catalytic turnover. J Am Chem Soc 2013; 135:12366-76. [PMID: 23889343 DOI: 10.1021/ja405853p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shikimate kinase (SK) is an essential enzyme in several pathogenic bacteria and does not have any counterpart in human cells, thus making it an attractive target for the development of new antibiotics. The key interactions of the substrate and product binding and the enzyme movements that are essential for catalytic turnover of the Mycobacterium tuberculosis shikimate kinase enzyme (Mt-SK) have been investigated by structural and computational studies. Based on these studies several substrate analogs were designed and assayed. The crystal structure of Mt-SK in complex with ADP and one of the most potent inhibitors has been solved at 2.15 Å. These studies reveal that the fixation of the diaxial conformation of the C4 and C5 hydroxyl groups recognized by the enzyme or the replacement of the C3 hydroxyl group in the natural substrate by an amino group is a promising strategy for inhibition because it causes a dramatic reduction of the flexibility of the LID and shikimic acid binding domains. Molecular dynamics simulation studies showed that the product is expelled from the active site by three arginines (Arg117, Arg136, and Arg58). This finding represents a previously unknown key role of these conserved residues. These studies highlight the key role of the shikimic acid binding domain in the catalysis and provide guidance for future inhibitor designs.
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Affiliation(s)
- Beatriz Blanco
- Centro Singular de Investigación en Química Biológica y Materiales Moleculares, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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46
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Lence E, Tizón L, Otero JM, Peón A, Prazeres VFV, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, González-Bello C. Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids. ACS Chem Biol 2013. [PMID: 23198883 DOI: 10.1021/cb300493s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural changes caused by the substitution of the aromatic moiety in (2S)-2-benzyl-3-dehydroquinic acids and its epimers in C2 by electron-withdrawing or electron-donating groups in type II dehydroquinase enzyme from M. tuberculosis and H. pylori has been investigated by structural and computational studies. Both compounds are reversible competitive inhibitors of this enzyme, which is essential in these pathogenic bacteria. The crystal structures of M. tuberculosis and H. pylori in complex with (2S)-2-(4-methoxy)benzyl- and (2S)-2-perfluorobenzyl-3-dehydroquinic acids have been solved at 2.0, 2.3, 2.0, and 1.9 Å, respectively. The crystal structure of M. tuberculosis in complex with (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid is also reported at 1.55 Å. These crystal structures reveal key differences in the conformation of the flexible loop of the two enzymes, a difference that depends on the presence of electron-withdrawing or electron-donating groups in the aromatic moiety of the inhibitors. This loop closes over the active site after substrate binding, and its flexibility is essential for the function of the enzyme. These differences have also been investigated by molecular dynamics simulations in an effort to understand the significant inhibition potency differences observed between some of these compounds and also to obtain more information about the possible movements of the loop. These computational studies have also allowed us to identify key structural factors of the H. pylori loop that could explain its reduced flexibility in comparison to the M. tuberculosis loop, specifically by the formation of a key salt bridge between the side chains of residues Asp18 and Arg20.
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Affiliation(s)
| | | | | | | | | | | | - Gavin C. Fox
- Proxima 2, Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin, F-91192
Gif-sur-Yvette, France
| | - Mark J. van Raaij
- Departamento de Estructura de
Macromoléculas, Centro Nacional de Biotecnología (CSIC), Campus Cantoblanco, 28049 Madrid, Spain
| | - Heather Lamb
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
| | - Alastair R. Hawkins
- Institute of Cell and Molecular
Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, U.K
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47
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Peón A, Coderch C, Gago F, González-Bello C. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors. ChemMedChem 2013; 8:740-7. [PMID: 23450741 DOI: 10.1002/cmdc.201300013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Indexed: 11/08/2022]
Abstract
Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.
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Affiliation(s)
- Antonio Peón
- Centro Singular de Investigación en Química Biológica y Materiales, Moleculares CIQUS, Universidad de Santiago de Compostela calle Jenaro de la Fuente s/n, 15782 Santiago de Compostela Spain
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48
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García-Deibe AM, Sanmartín-Matalobos J, González-Bello C, Lence E, Portela-García C, Martínez-Rodríguez L, Fondo M. Metal-Assisted Ring-Closing/Opening Process of a Chiral Tetrahydroquinazoline. Inorg Chem 2012; 51:1278-93. [DOI: 10.1021/ic2017038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ana M. García-Deibe
- Departamento de Química
Inorgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela,
Spain
| | - Jesús Sanmartín-Matalobos
- Departamento de Química
Inorgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela,
Spain
| | - Concepción González-Bello
- Centro Singular de
Investigación
en Química Biológica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Emilio Lence
- Centro Singular de
Investigación
en Química Biológica y Materiales Moleculares (CIQUS), Universidad de Santiago de Compostela, 15782 Santiago
de Compostela, Spain
| | - Cristina Portela-García
- Departamento de Química
Inorgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela,
Spain
| | - Luis Martínez-Rodríguez
- Departamento de Química
Inorgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela,
Spain
| | - Matilde Fondo
- Departamento de Química
Inorgánica, Facultad de Química, Universidad de Santiago de Compostela, 15782 Santiago de Compostela,
Spain
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Blanco B, Sedes A, Peón A, Lamb H, Hawkins AR, Castedo L, González-Bello C. Synthesis of 3-alkyl enol mimics inhibitors of type II dehydroquinase: factors influencing their inhibition potency. Org Biomol Chem 2012; 10:3662-76. [DOI: 10.1039/c2ob07081b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Sanmartín-Matalobos J, Portela-García C, Martínez-Rodríguez L, González-Bello C, Lence E, García-Deibe AM, Fondo M. Structural variety of zinc and copper complexes based on a 2,3-disubstituted 1,2,3,4-tetrahydroquinazoline ligand. Dalton Trans 2012; 41:6998-7004. [DOI: 10.1039/c2dt30550j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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