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Alfredo Berzal-Herranz   Dr.  Research Director 
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Alfredo Berzal-Herranz published an article in November 2017.
Research Keywords & Expertise
0 A
0 Gene Silencing
0 SELEX
Top co-authors See all
Wolfgang Nellen

45 shared publications

Universität Kassel

Manuel Espinosa

22 shared publications

Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas, 28040 Madrid, Spain

Georg Sczakiel

19 shared publications

Institut für Molekulare Medizin; Universitätsklinikum Schleswig-Holstein; Universität zu Lübeck; Ratzeburger Allee 160 23538 Lübeck Germany

Thomas Lahlali

3 shared publications

Gerhart Wagner

2 shared publications

66
Publications
70
Reads
17
Downloads
364
Citations
Publication Record
Distribution of Articles published per year 
(1970 - 2018)
Total number of journals
published in
 
36
 
Publications See all
CONFERENCE-ARTICLE 11 Reads 0 Citations <strong>Multivalent Engineered RNA Molecules that Interfere with Hepatitis C Virus Translation and Replication</strong> Cristina Romero-López, Thomas Lahlali, Beatriz Berzal-Herran... Published: 01 November 2017
3rd International Electronic Conference on Medicinal Chemistry, doi: 10.3390/ecmc-3-04654
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The design of novel and efficient compounds fighting against the highly variable RNA viruses, such as hepatitis C virus (HCV), is a major goal. RNA oligonucleotides have gained great interest as specific molecular tools for inhibiting essential viral processes. The combination of different RNA molecules with proven antiviral activity, each with its own activity and specificity, into a single molecule yields the so-called multivalent compounds, which are promising candidates for the development of new therapeutic strategies. These compounds are chimeric entities with enhanced therapeutic properties. In this work, the previously developed chimeric inhibitor RNA HH363-10 was used as archetype for the development of improved anti-HCV inhibitors. HH363-10 consists of a hammerhead ribozyme domain, targeting the essential internal ribosome entry site (IRES) region in the 5’ end of the HCV genome; and an aptamer RNA molecule, directed against the highly conserved IIIf domain of the IRES. As a result of the application of an in vitro selection process to the RNA pool, which results from the partial randomization of the aptamer-domain sequence of the HH363-10 molecule, 10 new multivalent optimized chimeric antiHCV RNA molecules were selected for further analysis. The aptamer RNA domain was evolved to contain two binding sites: the one mapping the IIIf domain, and a newly acquired targeting site, either to the IRES domain IV (which contains the translation start codon) or the essential linker region between the IRES domains I and II. These chimeric molecules efficiently and specifically interfered with HCV IRES-dependent translation in vitro (with IC50 values in the low µM range). They also inhibited both viral translation and replication in cell culture. These findings highlight the feasibility of using in vitro selection strategies for obtaining improved, multivalent RNA molecules with potential clinical applications.

Article 2 Reads 3 Citations The 5BSL3.2 Functional RNA Domain Connects Distant Regions in the Hepatitis C Virus Genome Cristina Romero-López, Alfredo Berzal-Herranz Published: 31 October 2017
Frontiers in Microbiology, doi: 10.3389/fmicb.2017.02093
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Viral genomes are complexly folded entities that carry all the information required for the infective cycle. The nucleotide sequence of the RNA virus genome encodes proteins and functional information contained in discrete, highly conserved structural units. These so-called functional RNA domains play essential roles in the progression of infection, which requires their preservation from one generation to the next. Numerous functional RNA domains exist in the genome of the hepatitis C virus (HCV). Among them, the 5BSL3.2 domain in the cis-acting replication element (CRE) at the 3′ end of the viral open reading frame has become of particular interest given its role in HCV RNA replication and as a regulator of viral protein synthesis. These functionalities are achieved via the establishment of a complex network of long-distance RNA–RNA contacts involving (at least as known to date) the highly conserved 3′X tail, the apical loop of domain IIId in the internal ribosome entry site, and/or the so-called Alt region upstream of the CRE. Changing contacts promotes the execution of different stages of the viral cycle. The 5BSL3.2 domain thus operates at the core of a system that governs the progression of HCV infection. This review summarizes our knowledge of the long-range RNA–RNA interaction network in the HCV genome, with special attention paid to the structural and functional consequences derived from the establishment of different contacts. The potential implications of such interactions in switching between the different stages of the viral cycle are discussed.
Article 2 Reads 2 Citations Development of Optimized Inhibitor RNAs Allowing Multisite-Targeting of the HCV Genome Cristina Romero-López, Thomas Lahlali, Beatriz Berzal-Herran... Published: 22 May 2017
Molecules, doi: 10.3390/molecules22050861
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Engineered multivalent drugs are promising candidates for fighting infection by highly variable viruses, such as HCV. The combination into a single molecule of more than one inhibitory domain, each with its own target specificity and even a different mechanism of action, results in drugs with potentially enhanced therapeutic properties. In the present work, the anti-HCV chimeric inhibitor RNA HH363-10, which has a hammerhead catalytic domain and an aptamer RNA domain, was subjected to an in vitro selection strategy to isolate ten different optimised chimeric inhibitor RNAs. The catalytic domain was preserved while the aptamer RNA domain was evolved to contain two binding sites, one mapping to the highly conserved IIIf domain of the HCV genome’s internal ribosome entry site (IRES), and the other either to IRES domain IV (which contains the translation start codon) or the essential linker region between domains I and II. These chimeric molecules efficiently and specifically interfered with HCV IRES-dependent translation in vitro (with IC50 values in the low µM range). They also inhibited both viral translation and replication in cell culture. These findings highlight the feasibility of using in vitro selection strategies for obtaining improved RNA molecules with potential clinical applications.
Article 5 Reads 7 Citations Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes Alba Fernández-Sanlés, Pablo Ríos-Marco, Cristina Romero-Lóp... Published: 03 April 2017
Frontiers in Microbiology, doi: 10.3389/fmicb.2017.00546
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The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle. The efficiency of this storage system is attributable to supracoding elements, i.e., discrete, structural units with essential functions. This information storage system overlaps and complements the protein coding sequence and is highly conserved across the genus. It therefore offers interesting potential targets for novel therapeutic strategies. This review summarizes our knowledge of the features of flavivirus genome functional RNA domains. It also provides a brief overview of the main achievements reported in the design of antiviral nucleic acid-based drugs targeting functional genomic RNA elements.
Article 2 Reads 1 Citation Aptamers: Biomedical Interest and Applications Cristina Romero-López, Alfredo Berzal-Herranz Published: 16 March 2017
Pharmaceuticals, doi: 10.3390/ph10010032
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Aptamers are short DNA or RNA oligonucleotides specialized in the specific and efficient binding to a target molecule. They are obtained by in vitro selection or evolution processes. It was in 1990 that two independent research groups described the bases of a new in vitro technology for the identification of RNA molecules able to specifically bind to a target [1,2]. Tuerk and Gold established the principals of the in vitro selection process that was named SELEX (Systematic Evolution of Ligands by Exponential enrichment), which is based on iterative cycles of binding, partitioning, and amplification of oligonucleotides from a pool of variant sequences [2]. Ellington and Szostak coined the term aptamer to define the selected molecules by the application of this method [1]. To date, numerous reports have described the isolation of aptamers directed against a great variety of targets covering a wide diversity of molecules varying in nature, size, and complexity ranging from ions to whole cells, including small molecules (e.g., aminoacids, nucleotides, antibiotics), peptides, proteins, nucleic acids, and viruses, among others (for example, see [3–6]). Modifications and optimization of the SELEX procedure aimed to get newly modified aptamers has also attracted much interest (examples can be found in [7,8]). These advances along with the parallel progresses in the nucleic acids chemistry and cellular delivery fields have allowed for the rise of a new hope in developing aptamers as efficient molecular tools for diagnostics and therapeutics (for recent comprehensive reviews, see [9–11]).
Article 2 Reads 5 Citations The chaperone-like activity of the hepatitis C virus IRES and CRE elements regulates genome dimerization Cristina Romero-López, Alicia Barroso-Deljesus, Alfredo Berz... Published: 24 February 2017
Scientific Reports, doi: 10.1038/srep43415
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The RNA genome of the hepatitis C virus (HCV) establishes a network of long-distance RNA-RNA interactions that direct the progression of the infective cycle. This work shows that the dimerization of the viral genome, which is initiated at the dimer linkage sequence (DLS) within the 3'UTR, is promoted by the CRE region, while the IRES is a negative regulatory partner. Using differential 2'-acylation probing (SHAPE-dif) and molecular interference (HMX) technologies, the CRE activity was found to mainly lie in the critical 5BSL3.2 domain, while the IRES-mediated effect is dependent upon conserved residues within the essential structural elements JIIIabc, JIIIef and PK2. These findings support the idea that, along with the DLS motif, the IRES and CRE are needed to control HCV genome dimerization. They also provide evidences of a novel function for these elements as chaperone-like partners that fine-tune the architecture of distant RNA domains within the HCV genome.
Conference papers
CONFERENCE-ARTICLE 27 Reads 0 Citations Targeting the other genetic information coded by the viral RNA genomes Alfredo Berzal-Herranz, Cristina Romero-López, Beatriz Berza... Published: 31 October 2018
doi: 10.3390/ecmc-4-05577
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In addition of the protein coding information viral RNA genomes code functional information in structurally conserved units termed functional RNA domains. These RNA domains play essential roles in the viral cycle. Members of the Flaviviridae family are responsible of important worldwide human diseases (e.g. hepatitis C, dengue, zika, west Nile fever, among others). Their genome consists in a (+) single stranded RNA molecule, which contains numerous highly structurally conserved RNA domains. They represent a good model to study and characterize the functional roles of RNA domains in the regulation of essential viral processes (e.g. translation, replication). Understanding the molecular mechanisms behind their function is essential to understand the viral infective cycle. Interfering with the function of the genomic RNA domains offers a potential means of developing antiviral strategies. Nucleic acids tools and in particular aptamers are good candidates for targeting structural RNA domains. Besides its potential as therapeutics, aptamers also provides an excellent means for investigating the functionality of RNA domains in viral genomes.

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