Mechanistic insight into the reaction catalysed by bacterial type II dehydroquinases

DHQ2 (type II dehydroquinase), which is an essential enzyme in Helicobacter pylori and Mycobacterium tuberculosis and does not have any counterpart in humans, is recognized to be an attractive target for the development of new antibacterial agents. Computational and biochemical studies that help understand in atomic detail the catalytic mechanism of these bacterial enzymes are reported in the present paper. A previously unknown key role of certain conserved residues of these enzymes, as well as the structural changes responsible for triggering the release of the product from the active site, were identified. Asp89*/Asp88* from a neighbouring enzyme subunit proved to be the residue responsible for the deprotonation of the essential tyrosine to afford the catalytic tyrosinate, which triggers the enzymatic process. The essentiality of this residue is supported by results from site-directed mutagenesis. For H. pylori DHQ2, this reaction takes place through the assistance of a water molecule, whereas for M. tuberculosis DHQ2, the tyrosine is directly deprotonated by the aspartate residue. The participation of a water molecule in this deprotonation reaction is supported by solvent isotope effects and proton inventory studies. MD simulation studies provide details of the required motions for the catalytic turnover, which provides a complete overview of the catalytic cycle. The product is expelled from the active site by the essential arginine residue and after a large conformational change of a loop containing two conserved arginine residues (Arg109/Arg108 and Arg113/Arg112), which reveals a previously unknown key role for these residues. The present study highlights the key role of the aspartate residue whose blockage could be useful in the rational design of inhibitors and the mechanistic differences between both enzymesFinancial support from the Comunidad de Madrid (S2010-BMD-2457 to F.G.), Xunta de Galicia (10PXIB2200122PR and GRC2010/12 to C.G.-B.) and the Spanish Ministry of Science and Innovation (SAF2009-13914-C02-02 to F.G. and SAF2010-15076 to C.G.-B.) is 5076 to CGB and BFU2008-01588/BMC to MJvR) is gratefully acknowledged. C.C. and A.P. thank the Spanish Ministry of Science and Innovation for their respective FPU fellowshipsS

Synthesis of 3-alkyl enol mimics inhibitors of type II dehydroquinase: factors influencing their inhibition potency

Several 3-alkylaryl mimics of the enol intermediate in the reaction catalyzed by type II dehydroquinase were synthesized to investigate the effect on the inhibition potency of replacing the oxygen atom in the side chain by a carbon atom. The length and the rigidity of the spacer was also studied. The inhibitory properties of the reported compounds against type II dehydroquinase from Mycobacterium tuberculosis and Helicobacter pylori are also reported. The binding modes of these analogs in the active site of both enzymes were studied by molecular docking using GOLD 5.0 and dynamic simulations studiesFinancial support from the Xunta de Galicia (10PXIB2200122PR and GRC2010/12) and the Spanish Ministry of Science and Innovation (SAF2010-15076) is gratefully acknowledged. BB, AS and AP thank the Spanish Ministry of Science and Innovation for FPU fellowshipsS

Exploring the Water-Binding Pocket of the Type II Dehydroquinase Enzyme in the Structure-Based Design of Inhibitors

Structural and computational studies to explore the WAT1 binding pocket in the structure-based design of inhibitors against the type II dehydroquinase (DHQ2) enzyme are reported. The crystal structures of DHQ2 from M. tuberculosis in complex with four of the reported compounds are described. The electrostatic interaction observed between the guanidinium group of the essential arginine and the carboxylate group of one of the inhibitors in the reported crystal structures supports the recently suggested role of this arginine as the residue that triggers the release of the product from the active site. The results of the structural and molecular dynamics simulation studies revealed that the inhibitory potency is favored by promoting interactions with WAT1 and the residues located within this pocket and, more importantly, by avoiding situations where the ligands occupy the WAT1 binding pocket. The new insights can be used to advantage in the structure-based design of inhibitorsFinancial support from the Spanish Ministry of Science and Innovation (Grant SAF2010-15076) and the Xunta de Galicia (Grant GRC2013/041) is gratefully acknowledged. B.B. and A.P. thank the Spanish Ministry of Education for their respective FPU fellowships. A.S. thanks the Spanish Ministry of Economy and Competitiveness for her FPI fellowship. J.M.O. thanks the Xunta de Galicia for a Plan I2C postdoctoral fellowshipS

Insights into substrate binding and catalysis in bacterial type I dehydroquinase

Structural, biochemical and computational studies to study substrate binding and the role of the conserved residues of the DHQ1 (type I dehydroquinase) enzyme active site are reported in the present paper. The crystal structure of DHQ1 from Salmonella typhi in complex with (2R)-2-methyl-3-dehydroquinic acid, a substrate analogue, was solved at 1.5 Å. The present study reveals a previously unknown key role for conserved Glu, Phe and Met and Gln, Pro and Ala residues, with the latter three being located in the flexible substrate-covering loop. Glu was shown to be responsible for the folding of this loop and for the dramatic reduction of its flexibility, which triggers active site closure. Glu46 was found to be key in bringing the substrate close to the lysine/histidine catalytic pocket to initiate catalysis. The present study could be useful in the rational design of inhibitors of this challenging and recognized target for the development of novel herbicides and antimicrobial agentsThis work was supported by the Spanish Ministry of Science and Innovation (grant number SAF2010-15076) and via FPU fellowships to M.M. and A.P., the Xunta de Galicia (grant number GRC2013/041) and via postdoctoral fellowships to E.L. and J.M.O., and by the European Regional Development Fund (ERDF)S

Irreversible covalent modification of type I dehydroquinase with a stable Schiff base

The irreversible inhibition of type I dehydroquinase (DHQ1), the third enzyme of the shikimic acid pathway, is investigated by structural, biochemical and computational studies. Two epoxides, which are mimetics of the natural substrate, were designed as irreversible inhibitors of the DHQ1 enzyme and to study the binding requirements of the linkage to the enzyme. The epoxide with the S configuration caused the covalent modification of the protein whereas no reaction was obtained with its epimer. The first crystal structure of DHQ1 from Salmonella typhi covalently modified by the S epoxide, which is reported at 1.4 Å, revealed that the modified ligand is surprisingly covalently attached to the essential Lys170 by the formation of a stable Schiff base. The experimental and molecular dynamics simulation studies reported here highlight the huge importance of the conformation of the C3 carbon of the ligand for covalent linkage to this type of aldolase I enzyme, revealed the key role played by the essential His143 as a Lewis acid in this process and show the need for a neatly closed active site for catalysisFinancial support from the Spanish Ministry of Science and Innovation (SAF2013-42899-R), Xunta de Galicia (GRC2013-041) and the European Regional Development Fund (ERDF) is gratefully acknowledged. LT, AP and MM thank the Spanish Ministry of Education for their respective FPU fellowships. EL and JMO thank and the Xunta de Galicia for their respective postdoctoral fellowshipsS

Natural and anthropogenic processes in La Janda basin (SW Iberia) from the Late Pleistocene to the Mid-Late Holocene

A multiproxy study (pollen, non-pollen palynomorphs, sedimentology, and geochemistry) was carried out in two cores drilled in La Janda basin (SW Iberia) to trace the environmental evolution and human impact on the landscape. An incised fluvial valley existed in the basin during the Late Pleistocene, followed by a transitional environment characterized by the development of saltmarsh vegetation affected by the increased marine influence ca. 10/8.7 ka cal BP. During this period comprising the Upper Palaeolithic and Mesolithic (>∼7.8 ka cal BP), the impact of hunter-gatherer groups on the landscape was rather low according to palynological and geochemical records. A restricted estuary connected to the sea was identified in La Janda between ca. 10/8.7-3.5/3.3 ka cal BP, coinciding with a predominance of saltmarsh vegetation developing on saline shore soils and the punctual presence of foraminifera and dynoflagellate cysts. The anthropogenic pressure was progressively increasing during the Neolithic, especially from ca. 7 ka cal BP, with markers suggesting herding/livestock activities prior to the punctual presence of cereals, which is only confirmed by the archaeological record ca. 6 ka cal BP. Human pressure become more noticeable throughout the Chalcolithic and Bronze Age (∼5-3 ka cal BP), period during which a new transitional phase is recorded in La Janda (ca. 3.5/3.3-1.3 ka cal BP), culminating in the terrestrialization of the area. The predominance of freshwater taxa and decrease of saltmarsh vegetation is observed during this period, and the transformation of the landscape for agricultural activities over the last centuries is reflected in the local presence of cereals and markers of erosive processes.This research was funded by the Deutsche Forschungsgemeinschaft-DFG (project no.57444011 – SFB 806); a “Severo Ochoa” extraordinary grant for excellence IGME, CSIC (AECEX2021); the Consejería de Cultura of the Junta de Andalucía (projects DGBC/IDBC3741 and 4766); the FEDER/MINECO-AGEINVES (HAR2017-8734P); and the Operational Programme and Department of Economy, Knowledge, Business and University of the Regional Government of Andalusia (FEDERUCA18-106917)Peer reviewe

The Baelo Claudia Tsunami Archive (SW Spain)—Archaeological Deposits of High-Energy Events

Over the past decades, substantial progress has been made in tsunami research. Be that as it may, little is still known about tsunami deposits and their related depositional mechanisms in coastal areas in historical and archaeological contexts. In particular, the Phoenician, Greek and Roman trade and military networks along the Mediterranean and Atlantic coasts, with their cities, harbours and additional facilities, are susceptible to serving as archives for extreme wave events. The ruins of the Roman city of Baelo Claudia, located on the Bay of Bolonia Bay (southern Spain), offer a unique environment for studying historical tsunamis in the Gulf of Cadiz. Baelo Claudia suffered at least two earthquakes in Roman times, namely, in the first and fourth centuries CE. The latter, associated with a tsunami, led to the city’s destruction and subsequent decline. Accordingly, three tsunami deposits in Baelo Claudia, dated to ca. 4000 cal BP (2000 BCE), ca. 400 CE and 1755 CE, the last corresponding to the Lisbon tsunami, are described here. The multi-disciplinary research conducted on the sedimentary, archaeological and palaeontological records has revealed event deposits, together with major landscape changes in the environs of the bay after tsunami landfall. Furthermore, the significant archaeoseismic damage detected in recently excavated buildings has been dated to the end of the fourth-century CE. The results presented here serve to supplement the earthquake and tsunami record of coastal Iberia.The authors are grateful to German Science Foundation (DFG grant, RE 1361/28-1) and the MINECO-FEDER Spanish Research Project CGL2015-67169-P (QTECSPAIN-USAL) for their support.Peer reviewe

Tratamientos psicológicos empíricamente apoyados para adultos: Una revisión selectiva

Antecedentes: los tratamientos psicológicos han mostrado su eficacia, efectividad y eficiencia para el abordaje de los trastornos mentales; no obstante, considerando el conocimiento científico generado en los últimos años, no se dispone de trabajos de actualización en español sobre cuáles son los tratamientos psicológicos con respaldo empírico. El objetivo fue realizar una revisión selectiva de los principales tratamientos psicológicos empíricamente apoyados para el abordaje de trastornos mentales en personas adultas. Método: se recogen niveles de evidencia y grados de recomendación en función de los criterios propuestos por el Sistema Nacional de Salud de España (en las Guías de Práctica Clínica) para diferentes trastornos psicológicos. Resultados: los resultados sugieren que los tratamientos psicológicos disponen de apoyo empírico para el abordaje de un amplio elenco de trastornos psicológicos. El grado de apoyo empírico oscila de bajo a alto en función del trastorno psicológico analizado. La revisión sugiere que ciertos campos de intervención necesitan una mayor investigación. Conclusiones: a partir de esta revisión selectiva, los profesionales de la psicología podrán disponer de información rigurosa y actualizada que les permita tomar decisiones informadas a la hora de implementar aquellos procedimientos psicoterapéuticos empíricamente fundamentados en función de las características de las personas que demandan ayuda. Background: Psychological treatments have shown their efficacy, effectiveness, and efficiency in dealing with mental disorders. However, considering the scientific knowledge generated in recent years, in the Spanish context, there are no updating studies about empirically supported psychological treatments. The main goal was to carry out a selective review of the main empirically supported psychological treatments for mental disorders in adults. Method: Levels of evidence and degrees of recommendation were collected based on the criteria proposed by the Spanish National Health System (Clinical Practice Guidelines) for different psychological disorders. Results: The results indicate that psychological treatments have empirical support for the approach to a wide range of psychological disorders. These levels of empirical evidence gathered range from low to high depending on the psychological disorder analysed. The review indicates the existence of certain fields of intervention that need further investigation. Conclusions: Based on this selective review, psychology professionals will be able to have rigorous, up-to-date information that allows them to make informed decisions when implementing empirically based psychotherapeutic procedures based on the characteristics of the people who require help

Representation and biases: Pollen–vegetation relationships and their contribution to the study of fossil pollen records in SW Iberia

In order to provide a better framework for the interpretation of fossil pollen records, a set of 49 modern pollen samples collected across different habitats of SW Iberia, categorised by context and sample type (soil vs moss), were selected to explore pollen–vegetation relationships by multivariate analysis and identify possible biases in pollen representativeness. The distribution of both samples and pollen taxa in the plots is successfully explained according to specific environmental variables in some clusters (A, B and E) in which plant communities depend on certain environmental conditions. On the other hand, other clusters (C, D and F) are better explained by opposition to some variables and suggest a wider range of adaptability of their floristic communities. The classification of samples by context consistently explains their differences in vegetal and environmental terms. However, some discrepancies seem to be better explained by sample type (soil vs moss), which raises some questions on how taphonomic factors may cause biases in both modern and fossil pollen samples.This research was funded by the Deutsche Forschungsgemeinschaft-DFG (project no. 57444011 – SFB 806) and a “Severo Ochoa” extraordinary grant for excellence IGME-CSIC (AECEX2021)Peer reviewe

Nutrition and cataract in low-income Mexicans: experience in an Eye Camp

Surgical Eye-camps for cataract treatment of low-income adult Mexicans have been undertaken over the last 10 years. Despite the high prevalence of cataracts among these subjects, no assessment of their nutritional or health status has ever been made. We compare the results obtained for 81 adults (44 men and 37 women) who received treatment in May 1997 with those for a "control" group of age and sex-matched but affluent individuals in Mexico City. a-Tocopherol and b-carotene were assessed and analysed by HPLC and colorimetric procedures, respectively. The plasma tocopherol to cholesterol ratio did not reveal deficiencies of this vitamin, and only 5 patients (2 men and 3 women) had low b-carotene plasma levels. The patients had high BMI values, with 32% of men and 30% of women overweight, and 2% and 14%, respectively, obese, with higher glucose, cholesterol and triglyceride values reflecting enhanced insulin resistance and lipid abnormalities. The alkaline phosphatase values were elevated ,suggesting that many of these blind patients are osteomalacic because they now remain indoors. Although it has been suggested that an adequate intake of carotenes and tocopherol are associated with absence of cataract, this appears not to be the case in our study population. Surveys in Mexico have revealed, however, a highly prevalent deficiency of other vitamins such as niacin and riboflavin, both of which have been proved to be protective against cataract. It appears that nutritional deficiencies, obesity, incipient diabetes and lipid disorders co-exist in modern Mexico. We have identified a need for research to aid the design of preventive nutritional approaches at the population level that could be applied in parallel with ongoing surgical treatmentNutrición y catarata en mexicanos de bajo ingreso: experiencia en un campamento de cirugía de ojos. Durante los últimos 10 años se han llevado a cabo en México Campamentos Quirúrgicos para el tratamiento de catarata en sujetos de escasos recursos. A pesar de la alta prevalencia de catarata, nunca se ha valorado el estado de nutrición ni de salud de éstas poblaciones. En este estudio comparamos los resultados obtenidos en 81 adultos (44 hombres y 37 mujeres) que recibieron tratamiento en Mayo de 1977, con los de un grupo "control" de sujetos de mayor afluencia, pareados para edad y sexo. Se valoraron los niveles de a-tocoferol y b-carotenos los cuales se analizaron con HPLC y colorimetría respectivamente. La relación tocoferol:colesterol en plasma no reveló deficiencia de ésta vitamina, y se encontraron niveles plasmáticos bajos de b-carotenos en solo 5 sujetos (2 hombres y 3 mujeres). Los IMC se encontraron elevados: 32% de hombres y 30% de las mujeres con sobrepeso y 2% y 14% obesos respectivamente. Los valores de glucosa, colesterol y triglicéridos fueron altos lo que refleja un aumento en la resistencia a la insulina y anormalidades en los lípidos. Los valores de fosfatasa alcalina se encontraron elevados lo que sugiere que muchos de estos pacientes ciegos padecen osteomalacia ya que permanecen confinados a su hogar. Aunque se ha sugerido que una ingesta adecuada de carotenos y tocoferol están asociadas a ausencia de catarata, ese no fue el caso en la población estudiada. Estudios en el país revelan, sin embargo, la deficiencia altamente prevalente de otras vitaminas tales como la niacina y la riboflavina cuyos efectos protectores en catarata han sido comprobados. En el México moderno por lo tanto, coexisten las deficiencias nutricias, la obesidad, la diabetes incipiente y las alteraciones en los lípidos. Hemos identificado la necesidad de que se inicien investigaciones que apoyen programas preventivos de nutrición a nivel poblacional que pudieran ser implementados paralelamente al tratamiento quirúrgic