DR_SEQAN: a PC/Windows-based software to evaluate drug

This article is available from: http://www.biomedcentral.com/1471-2334/6/44[Background] Genotypic assays based on DNA sequencing of part or the whole reverse transcriptase (RT)- and protease (PR)-coding regions of the human immunodeficiency virus type 1 (HIV-1) genome have become part of the routine clinical management of HIV-infected individuals. However, the results are difficult to interpret due to complex interactions between mutations found in viral genes.[Results] DR_SEQAN is a tool to analyze RT and PR sequences. The program output includes a list containing all of the amino acid changes found in the query sequence in comparison with the sequence of a wild-type HIV-1 strain. Translation of codons containing nucleotide mixtures can result in potential ambiguities or heterogeneities in the amino acid sequence. The program identifies all possible combinations of 2 or 3 amino acids that derive from translation of triplets containing nucleotide mixtures. In addition, when ambiguities affect codons relevant for drug resistance, DR_SEQAN allows the user to select the appropriate mutation to be considered by the program's drug resistance interpretation algorithm. Resistance is predicted using a rule-based algorithm, whose efficiency and accuracy has been tested with a large set of drug susceptibility data. Drug resistance predictions given by DR_SEQAN were consistent with phenotypic data and coherent with predictions provided by other publicly available algorithms. In addition, the program output provides two tables showing published drug susceptibility data and references for mutations and combinations of mutations found in the analyzed sequence. These data are retrieved from an integrated relational database, implemented in Microsoft Access, which includes two sets of nonredundant core tables (one for combinations of mutations in the PR and the other for combinations in the RT)[Conclusion] DR_SEQAN is an easy to use off-line application that provides expert advice on HIV genotypic resistance interpretation. It is coded in Visual Basic for use in PC/Windows-based platforms. The program is freely available under the General Public License. The program (including the integrated database), documentation and a sample sequence can be downloaded from http:// www2.cbm.uam.es:8080/lmenendez/DR_SEQAN.zipThis work has been supported in part by the Fundación para la Investigación y Prevención del SIDA en España (FIPSE), through grants 36200/01 and 36460/05. An institutional grant of Fundación Ramón Areces to Centro de Biología Molecular "Severo Ochoa" is also acknowledged.Peer reviewe

Retrotranscriptasas del VIH tipo 1 grupo O, activas a temperaturas elevadas

La presente invención se encuadra dentro del campo de la biotecnología. Más concretamente, se refiere a retrotranscriptasas expresadas y purificadas en bacterias y que tienen la secuencia de aminoácidos de la retrotranscriptasa de un virus de la inmunodeficiencia humana de tipo 1 (VIH-1) del grupo O modificada en las posiciones 358, 359 y 360; y de variantes de esta enzima que contienen cambios adicionales en las posiciones 355 y 357 o en la 478 o en la posición 69 (en este caso acompañada de una inserción de dos aminoácidos). Estas polimerasas presentan mayor actividad que la enzima no mutada, a temperaturas elevadas (superiores a 60ºC). Además retienen capacidad de síntesis de ADN a temperaturas superiores a 70ºC. Por otro lado, la fidelidad de copia de estas enzimas no difiere significativamente de la presentada por la retrotranscriptasa no mutada.Peer reviewedConsejo Superior de Investigaciones CientíficasA1 Solicitud de patente con informe sobre el estado de la técnic

Mutational Patterns Associated with the 69 Insertion Complex in Multi-drug-resistant HIV-1 Reverse Transcriptase that Confer Increased Excision Activity and High-level Resistance to Zidovudine

Human immunodeficiency virus type 1 (HIV-1) strains having dipeptide insertions in the fingers subdomain and other drug resistance-related mutations scattered throughout their reverse transcriptase (RT)-coding region show high-level resistance to zidovudine (AZT) and other nucleoside analogues. Those phenotypic effects have been correlated with their increased ATP-dependent phosphorolytic activity on chain-terminated primers. Mutations T69S and T215Y and a dipeptide insertion (i.e. Ser-Ser) between positions 69 and 70 are required to achieve low-level resistance to thymidine analogues. However, additional amino acid substitutions are necessary to achieve the high-level phenotypic resistance to AZT shown by clinical HIV isolates carrying a dipeptide insertion in their RT-coding region. In order to identify those mutations that contribute to resistance in the sequence context of an insertion-containing RT derived from an HIV clinical isolate (designated as SS RT), we expressed and purified a series of chimeric enzymes containing portions of the wild-type or SS RT sequences. ATP-mediated excision activity measurements using AZT- and stavudine (d4T)-terminated primers and phenotypic assays showed that molecular determinants of high-level resistance to AZT were located in the fingers subdomain of the polymerase. Further studies, using recombinant RTs obtained by site-directed mutagenesis, revealed that M41L, A62V and in a lesser extent K70R, were the key mutations that together with T69S, T215Y and the dipeptide insertion conferred high levels of ATP-dependent phosphorolytic activity on AZT and d4T-terminated primers. Excision activity correlated well with AZT susceptibility measurements, and was consistent with phenotypic resistance to d4T. Structural analysis of the location of the implicated amino acid substitutions revealed a coordinated effect of M41L and A62V on the positioning of the β3–β4 hairpin loop, which plays a key role in the resistance mechanismThis work was supported in part by FIPSE (grant 36523/05) and Fondo de Investigación Sanitaria (through “Red Temática Cooperativa de Investigación en SIDA” G03/173). In addition, work in Madrid was supported by grant BIO2003/01175 (Ministerio de Educación y Ciencia) and an institutional grant from Fundación Ramón Areces. Grant BMC2003/2148 (Ministerio de Educación y Ciencia) (to M. A.M.) is also acknowledgedPeer reviewe

La actividad RNasa H de la retrotranscriptasa del VIH como diana terapéutica

La infección por el virus de la inmunodeficiencia humana (VIH) es un gran problema de salud a nivel mundial. Actualmente se dispone de fármacos antirretrovirales que controlan la infección, pero su efectividad a largo plazo está comprometida por su toxicidad y la aparición de resistencias. Por ello es importante identificar y explotar nuevas dianas terapéuticas. En este trabajo se han examinado varios compuestos conocidos por afectar a la actividad ribonucleasa H (RNasa H) de la retrotranscriptasa (RT) viral, pues es una diana no explotada y que ofrece la posibilidad de desarrollar inhibidores que actúen sobre múltiples dianas, dada la similitud de su sitio activo con el de la integrasa viral y por su localización próxima al dominio DNA polimerasa de la RT. Se han realizado diferentes ensayos enzimáticos con oligonucleótidos marcados que han permitido confirmar la inhibición de la actividad RNasa H por distintos compuestos y evaluar sus efectos sobre la DNA polimerasa e integrasa virales. Todos ellos mostraron eficacia a nivel micro- y submicromolar en la inhibición de la actividad RNasa H, mientras que para las otras dos actividades sus efectos fueron más modestos. Solo uno de los compuestos (WX-II-25) ha mostrado ser un buen inhibidor dual, con potencias similares para las actividades RNasa H e integrasa (IC50 de 0,72 y 1 μM respectivamente), mientras que el compuesto SL-6h ha mostrado capacidad de inhibir las tres actividades enzimáticas, aunque con potencias peores (IC50 de 1,85 μM para la actividad RNasa H y superior a 10 μM para las otras dos). Aun así, estos compuestos representan buenos candidatos para continuar con su investigación. En el futuro sería conveniente confirmar su capacidad inhibitoria en ensayos celulares y evaluar en detalle su unión a los enzimas, lo cual permitirá utilizarlos como referencia para el desarrollo de inhibidores múltiples potentes que puedan llegar a la clínic

DR_SEQAN: a PC/Windows-based software to evaluate drug resistance using human immunodeficiency virus type 1 genotypes

BACKGROUND: Genotypic assays based on DNA sequencing of part or the whole reverse transcriptase (RT)- and protease (PR)-coding regions of the human immunodeficiency virus type 1 (HIV-1) genome have become part of the routine clinical management of HIV-infected individuals. However, the results are difficult to interpret due to complex interactions between mutations found in viral genes. RESULTS: DR_SEQAN is a tool to analyze RT and PR sequences. The program output includes a list containing all of the amino acid changes found in the query sequence in comparison with the sequence of a wild-type HIV-1 strain. Translation of codons containing nucleotide mixtures can result in potential ambiguities or heterogeneities in the amino acid sequence. The program identifies all possible combinations of 2 or 3 amino acids that derive from translation of triplets containing nucleotide mixtures. In addition, when ambiguities affect codons relevant for drug resistance, DR_SEQAN allows the user to select the appropriate mutation to be considered by the program's drug resistance interpretation algorithm. Resistance is predicted using a rule-based algorithm, whose efficiency and accuracy has been tested with a large set of drug susceptibility data. Drug resistance predictions given by DR_SEQAN were consistent with phenotypic data and coherent with predictions provided by other publicly available algorithms. In addition, the program output provides two tables showing published drug susceptibility data and references for mutations and combinations of mutations found in the analyzed sequence. These data are retrieved from an integrated relational database, implemented in Microsoft Access, which includes two sets of non-redundant core tables (one for combinations of mutations in the PR and the other for combinations in the RT). CONCLUSION: DR_SEQAN is an easy to use off-line application that provides expert advice on HIV genotypic resistance interpretation. It is coded in Visual Basic for use in PC/Windows-based platforms. The program is freely available under the General Public License. The program (including the integrated database), documentation and a sample sequence can be downloaded fro

Atención e inhibición en el Deterioro Cognitivo Leve y Enfermedad de Alzheimer

Mild cognitive impairment is understood as a cognitive deficit of insufficient severity to fulfil the criteria for Alzheimer’s disease. Many studies have attempted to identify which cognitive functions are most affected by this type of impairment and which is the most sensitive neuropsychological test for early detection. This study investigated sustained and selective attention, processing speed, and the inhibition process using a sample of people divided into three groups mild cognitive impairment, Alzheimer disease and cognitively healthy controls selected and grouped based on their scores in the Mini Mental State Examination and Cambridge Cognitive Examination-revised. Three tests from the Cambridge Neuropsychological Test Automated Battery (Motor Screening Task, Stop Signal Task and Reaction time) were used as well as the d2 attention test. The results show that that participants with mild cognitive impairment and Alzheimer disease showed lower levels of concentration compared with the cognitively healthy controls group in the d2 test and longer reaction times in the Cambridge Neuropsychological Test Automated Battery, although the differences were not marked in the latter test. The impairments in basic cognitive processes, such as reaction time and sustained attention, indicate the need to take these functions into account in the test protocols when discriminating between normal aging and early and preclinical dementia processes.El Deterioro Cognitivo Leve es entendido como un déficit cognitivo de curso insuficiente para cumplir criterios de demencia o Enfermedad de Alzheimer. Muchos estudios tratan de averiguar cuáles son las funciones cognitivas más afectadas en este tipo de deterioro, así como las pruebas neuropsicológicas más sensibles a la hora de detectarlos tempranamente. Este estudio tratará de estudiar la atención sostenida y selectiva, velocidad de procesamiento, así como el factor de inhibición, en una muestra de sujetos divididos en tres grupos (Deterioro Cognitivo leve, Demencia de Alzheimer y sujetos cognitivamente sanos), mediante el Mini Mental State Examination y la batería Cambridge Cognitive Examination-revised. Para ello utilizaremos las pruebas Cambridge Neuropsychological Test Automated Battery (Motor Screening Task, Stop Signal Task, Reaction Time) así como el test de atención d2. Los resultados muestran que aquellos sujetos con Deterioro Cognitivo Leve y Demencia de Alzheimer obtienen índices menores de concentración en comparación con los sujetos cognitivamente sanos en el test d2, así como mayores tiempos de reacción en las pruebas del Cambridge Neuropsychological Test Automated Battery, aunque estos no muestran diferencias tan marcadas. Este deterioro en los procesos cognitivos básicos, tales como el tiempo de reacción o la atención sostenida, nos indica la necesidad de tener en cuenta estas funciones en los protocolos de evaluación a la hora de discriminar entre el envejecimiento normal y los procesos tempranos de demencia

VAPC, an human endogenous inhibitor for hepatitis C virus (HCV) infection, is intrinsically unstructured but forms a "fuzzy complex" with HCV NS5B

10.1371/journal.pone.0040341PLoS ONE77

2019 meeting of the global virus network

The Global Virus Network (GVN) was established in 2011 to strengthen research and responses to emerging viral causes of human disease and to prepare against new viral pandemics. There are now 52 GVN Centers of Excellence and 9 Affiliate laboratories in 32 countries. The 11th International GVN meeting was held from June 9–11, 2019 in Barcelona, Spain and was jointly organized with the Spanish Society of Virology. A common theme throughout the meeting was globalization and climate change. This report highlights the recent accomplishments of GVN researchers in several important areas of medical virology, including severe virus epidemics, anticipation and preparedness for changing disease dynamics, host-pathogen interactions, zoonotic virus infections, ethical preparedness for epidemics and pandemics, one health and antivirals.info:eu-repo/semantics/submittedVersio

Recent advances in the molecular design and applications of proteolysis targeting chimera-based multi-specific antiviral modality

Viral infections represent a major threat to human health and the global economy; however, most of the currently available antiviral drugs are not fully effective in restricting viral replication and selecting for drug-resistant variants. Targeted protein degradation technologies are promising strategies to avoid or delay the emergence of drug resistance. Among the protein degradation-based multi-specific approaches, proteolysis targeting chimera (PROTAC) is the main strategy applied in the antiviral field. In this review we will introduce the elements and mechanisms of action used by PROTAC technology, as well as the advantages of PROTACs over available antiviral drugs. We also summarize the latest progress in the application of PROTACs in antiviral research, discuss existing challenges and look into future opportunities for antiviral drug discovery

Catalytic activity of iridium NHC complexes covalently bonded to carbon nanotubes and graphene oxide

Trabajo presentado a la Annual World Conference on Carbon, celebrada en Dresden (Alemania) del 12 al 17 de julio de 2015.Carbon nanotubes and graphene have been extensively applied as proactive supports to generate heterogeneous catalysts. Both exhibit a carbon structure composed by carbon atoms with sp2 hybridization and both are used in similar applications, as in catalysis. However, the role of each particular substrate, determined by its structural peculiarities, can be differentvshould be studied for each particular catalytic reaction and in their structure.The aim of this work is to study the differences between oxidized carbon nanotubes (CNT) and graphene oxides (GO) as proactive supports of iridium Nheterocyclic carbene (NHC) catalyst. The effect of their inherent structure in the catalytic activity in hydrogen transfer reactions was studied in detail.The authors thank MINECO/MECD (Projects CONSOLIDER INGENIO 2010 CSD2009-00050, CTQ 2010-15221, Ramón y Cajal contract of P. Alvarez and fellowship of M. Blanco) and the Diputación General de Aragón (E07) for their financial support.Peer Reviewe