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  1. Article ; Online: HIV-1 Infection Reduces NAD Capping of Host Cell snRNA and snoRNA.

    Benoni, Barbora / Potužník, Jiří František / Škríba, Anton / Benoni, Roberto / Trylcova, Jana / Tulpa, Matouš / Spustová, Kristína / Grab, Katarzyna / Mititelu, Maria-Bianca / Pačes, Jan / Weber, Jan / Stanek, David / Kowalska, Joanna / Bednarova, Lucie / Keckesova, Zuzana / Vopalensky, Pavel / Gahurova, Lenka / Cahova, Hana

    ACS chemical biology

    2024  

    Abstract: Nicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5' cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capping of RNAs in ... ...

    Abstract Nicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5' cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capping of RNAs in HIV-1-infected cells because HIV-1 is responsible for the depletion of the NAD/NADH cellular pool and causing intracellular pellagra. By applying the NAD captureSeq protocol to HIV-1-infected and uninfected cells, we revealed that four snRNAs (e.g., U1) and four snoRNAs lost their NAD cap when infected with HIV-1. Here, we provide evidence that the presence of the NAD cap decreases the stability of the U1/HIV-1 pre-mRNA duplex. Additionally, we demonstrate that reducing the quantity of NAD-capped RNA by overexpressing the NAD RNA decapping enzyme DXO results in an increase in HIV-1 infectivity. This suggests that NAD capping is unfavorable for HIV-1 and plays a role in its infectivity.
    Language English
    Publishing date 2024-05-15
    Publishing country United States
    Document type Journal Article
    ISSN 1554-8937
    ISSN (online) 1554-8937
    DOI 10.1021/acschembio.4c00151
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Diadenosine Tetraphosphate (Ap

    František Potužník, Jiří / Nešuta, Ondřej / Škríba, Anton / Voleníková, Barbora / Mititelu, Maria-Bianca / Mancini, Flaminia / Serianni, Valentina / Fernandez, Henri / Spustová, Kristína / Trylčová, Jana / Vopalensky, Pavel / Cahová, Hana

    Angewandte Chemie (International ed. in English)

    2023  Volume 63, Issue 6, Page(s) e202314951

    Abstract: The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. ... ...

    Abstract The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. However, the discovery of non-canonical RNA caps in eukaryotes revealed a new niche of previously undetected RNA chemical modifications. We are the first to report the existence of a new non-canonical RNA cap, diadenosine tetraphosphate (Ap
    MeSH term(s) Rats ; Animals ; Humans ; Dinucleoside Phosphates/metabolism ; RNA Caps ; Mammals/metabolism ; Nudix Hydrolases ; Phosphoric Monoester Hydrolases
    Chemical Substances diadenosine tetraphosphate (5542-28-9) ; Dinucleoside Phosphates ; RNA Caps ; NUDT2 protein, human (EC 3.6.1.17) ; Nudix Hydrolases (EC 3.6.1.-) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
    Language English
    Publishing date 2023-11-22
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2011836-3
    ISSN 1521-3773 ; 1433-7851
    ISSN (online) 1521-3773
    ISSN 1433-7851
    DOI 10.1002/anie.202314951
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors.

    Nigam, AkshatKumar / Hurley, Matthew F D / Li, Fengling / Konkoľová, Eva / Klíma, Martin / Trylčová, Jana / Pollice, Robert / Çinaroğlu, Süleyman Selim / Levin-Konigsberg, Roni / Handjaya, Jasemine / Schapira, Matthieu / Chau, Irene / Perveen, Sumera / Ng, Ho-Leung / Ümit Kaniskan, H / Han, Yulin / Singh, Sukrit / Gorgulla, Christoph / Kundaje, Anshul /
    Jin, Jian / Voelz, Vincent A / Weber, Jan / Nencka, Radim / Boura, Evzen / Vedadi, Masoud / Aspuru-Guzik, Alán

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome ...

    Abstract The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 ± 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148 (PDB:8BWU), a potent inhibitor of methyltransferase activity at the nanomolar level (IC
    Language English
    Publishing date 2024-01-13
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.10.03.560722
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Effect of cancer-associated fibroblasts on the migration of glioma cells in vitro.

    Trylcova, Jana / Busek, Petr / Smetana, Karel / Balaziova, Eva / Dvorankova, Barbora / Mifkova, Alzbeta / Sedo, Aleksi

    Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine

    2015  Volume 36, Issue 8, Page(s) 5873–5879

    Abstract: Cancer-associated fibroblasts (CAFs) significantly influence biological properties of many tumors. The role of these mesenchymal cells is also anticipated in human gliomas. To evaluate the putative role of CAFs in glioblastoma, we tested the effect of ... ...

    Abstract Cancer-associated fibroblasts (CAFs) significantly influence biological properties of many tumors. The role of these mesenchymal cells is also anticipated in human gliomas. To evaluate the putative role of CAFs in glioblastoma, we tested the effect of CAF conditioned media on the proliferation and chemotaxis of glioma cells. The proliferation of glioma cells was stimulated to similar extent by both the normal fibroblasts (NFs) and CAF-conditioned media. Nevertheless, CAF-conditioned media enhanced the chemotactic migration of glioma cells significantly more potently than the media from normal fibroblasts. In order to determine whether CAF-like cells are present in human glioblastomas, immunofluorescence staining was performed on tissue samples from 20 patients using markers typical for CAFs. This analysis revealed regular presence of mesenchymal cells expressing characteristic CAF markers α-smooth muscle actin and TE-7 in human glioblastomas. These observations indicate the potential role of CAF-like cells in glioblastoma biology.
    MeSH term(s) Actins/biosynthesis ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation/genetics ; Culture Media, Conditioned ; Fibroblasts/pathology ; Gene Expression Regulation, Neoplastic ; Glioblastoma/genetics ; Glioblastoma/pathology ; Humans ; Tumor Microenvironment/genetics
    Chemical Substances ACTA2 protein, human ; Actins ; Culture Media, Conditioned
    Language English
    Publishing date 2015-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605825-5
    ISSN 1423-0380 ; 0289-5447 ; 1010-4283
    ISSN (online) 1423-0380
    ISSN 0289-5447 ; 1010-4283
    DOI 10.1007/s13277-015-3259-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: LC/MS analysis and deep sequencing reveal the accurate RNA composition in the HIV-1 virion.

    Šimonová, Anna / Svojanovská, Barbora / Trylčová, Jana / Hubálek, Martin / Moravčík, Ondřej / Zavřel, Martin / Pávová, Marcela / Hodek, Jan / Weber, Jan / Cvačka, Josef / Pačes, Jan / Cahová, Hana

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 8697

    Abstract: The mechanism of action of various viruses has been the primary focus of many studies. Yet, the data on RNA modifications in any type of virus are scarce. Methods for the sensitive analysis of RNA modifications have been developed only recently and they ... ...

    Abstract The mechanism of action of various viruses has been the primary focus of many studies. Yet, the data on RNA modifications in any type of virus are scarce. Methods for the sensitive analysis of RNA modifications have been developed only recently and they have not been applied to viruses. In particular, the RNA composition of HIV-1 virions has never been determined with sufficiently exact methods. Here, we reveal that the RNA of HIV-1 virions contains surprisingly high amount of the 1-methyladenosine. We are the first to use a liquid chromatography-mass spectrometry analysis (LC/MS) of virion RNA, which we combined with m
    MeSH term(s) Adenosine/analogs & derivatives ; Adenosine/metabolism ; Base Sequence ; Cell Line, Tumor ; Chromatography, Liquid/methods ; Genome, Viral/genetics ; HIV-1/genetics ; HIV-1/physiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Mass Spectrometry/methods ; RNA, Small Cytoplasmic/genetics ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Signal Recognition Particle/genetics ; Virion/genetics ; Virion/metabolism ; Virus Assembly/genetics
    Chemical Substances 7SL RNA ; RNA, Small Cytoplasmic ; RNA, Viral ; Signal Recognition Particle ; 1-methyladenosine (15763-06-1) ; RNA, Transfer (9014-25-9) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2019-06-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-45079-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Synthesis and Cytotoxic and Antiviral Activity Profiling of All-Four Isomeric Series of Pyrido-Fused 7-Deazapurine Ribonucleosides.

    Veselovská, Lucia / Kudlová, Natálie / Gurská, Soňa / Lišková, Barbora / Medvedíková, Martina / Hodek, Ondřej / Tloušťová, Eva / Milisavljevic, Nemanja / Tichý, Michal / Perlíková, Pavla / Mertlíková-Kaiserová, Helena / Trylčová, Jana / Pohl, Radek / Klepetářová, Blanka / Džubák, Petr / Hajdúch, Marián / Hocek, Michal

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2020  Volume 26, Issue 57, Page(s) 13002–13015

    Abstract: All four isomeric series of novel 4-substituted pyrido-fused 7-deazapurine ribonucleosides possessing the pyridine nitrogen atom at different positions were designed and synthesized. The total synthesis of each isomeric fused heterocycle through ... ...

    Abstract All four isomeric series of novel 4-substituted pyrido-fused 7-deazapurine ribonucleosides possessing the pyridine nitrogen atom at different positions were designed and synthesized. The total synthesis of each isomeric fused heterocycle through multistep heterocyclization was followed by glycosylation and derivatization at position 4 by cross-coupling reactions or nucleophilic substitutions. All compounds were tested for cytostatic and antiviral activity. The most active were pyrido[4',3':4,5]pyrimidine nucleosides bearing MeO, NH
    MeSH term(s) Antineoplastic Agents/pharmacology ; Antiviral Agents/pharmacology ; Purines/pharmacology ; Ribonucleosides/chemical synthesis ; Ribonucleosides/pharmacology ; Structure-Activity Relationship
    Chemical Substances 7-deazapurine ; Antineoplastic Agents ; Antiviral Agents ; Purines ; Ribonucleosides
    Language English
    Publishing date 2020-09-16
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-X
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.202001124
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Drug Discovery in Low Data Regimes: Leveraging a Computational Pipeline for the Discovery of Novel SARS-CoV-2 Nsp14-MTase Inhibitors

    Nigam, AkshatKumar / Hurley, Matthew F. D. / Li, Fengling / Konkoĺová, Eva / Klíma, Martin / Trylčová, Jana / Pollice, Robert / Çınaroğlu, Süleyman Selim / Levin-Konigsberg, Roni / Handjaya, Jasemine / Schapira, Matthieu / Chau, Irene / Perveen, Sumera / Ng, Ho-Leung / Kaniskan, H. Ümit / Han, Yulin / Singh, Sukrit / Gorgulla, Christoph / Kundaje, Anshul /
    Jin, Jian / Voelz, Vincent A / Weber, Jan / Nencka, Radim / Boura, Evzen / Vedadi, Masoud / Aspuru-Guzik, Alán

    bioRxiv

    Abstract: The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome ...

    Abstract The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has led to significant global morbidity and mortality. A crucial viral protein, the non-structural protein 14 (nsp14), catalyzes the methylation of viral RNA and plays a critical role in viral genome replication and transcription. Due to the low mutation rate in the nsp region among various SARS-CoV-2 variants, nsp14 has emerged as a promising therapeutic target. However, discovering potential inhibitors remains a challenge. In this work, we introduce a computational pipeline for the rapid and efficient identification of potential nsp14 inhibitors by leveraging virtual screening and the NCI open compound collection, which contains 250,000 freely available molecules for researchers worldwide. The introduced pipeline provides a cost-effective and efficient approach for early-stage drug discovery by allowing researchers to evaluate promising molecules without incurring synthesis expenses. Our pipeline successfully identified seven promising candidates after experimentally validating only 40 compounds. Notably, we discovered NSC620333, a compound that exhibits a strong binding affinity to nsp14 with a dissociation constant of 427 ± 84 nM. In addition, we gained new insights into the structure and function of this protein through molecular dynamics simulations. We identified new conformational states of the protein and determined that residues Phe367, Tyr368, and Gln354 within the binding pocket serve as stabilizing residues for novel ligand interactions. We also found that metal coordination complexes are crucial for the overall function of the binding pocket. Lastly, we present the solved crystal structure of the nsp14-MTase complexed with SS148, a potent inhibitor of methyltransferase activity at the nanomolar level (IC50 value of 70 ± 6 nM). Our computational pipeline accurately predicted the binding pose of SS148, demonstrating its effectiveness and potential in accelerating drug discovery efforts against SARS-CoV-2 and other emerging viruses.
    Keywords covid19
    Language English
    Publishing date 2023-10-04
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2023.10.03.560722
    Database COVID19

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  8. Article ; Online: Dipeptidyl peptidase-IV inhibits glioma cell growth independent of its enzymatic activity.

    Busek, Petr / Stremenova, Jarmila / Sromova, Lucie / Hilser, Marek / Balaziova, Eva / Kosek, Dalibor / Trylcova, Jana / Strnad, Hynek / Krepela, Evzen / Sedo, Aleksi

    The international journal of biochemistry & cell biology

    2012  Volume 44, Issue 5, Page(s) 738–747

    Abstract: Malignant gliomas exhibit abnormal expression of proteolytic enzymes that may participate in the uncontrolled cell proliferation and aberrant interactions with the brain extracellular matrix. The multifunctional membrane bound serine aminopeptidase ... ...

    Abstract Malignant gliomas exhibit abnormal expression of proteolytic enzymes that may participate in the uncontrolled cell proliferation and aberrant interactions with the brain extracellular matrix. The multifunctional membrane bound serine aminopeptidase dipeptidyl peptidase (DPP)-IV has been linked to the development and progression of several malignancies, possibly both through the enzymatic and nonenzymatic mechanisms. In this report we demonstrate the expression of DPP-IV and homologous proteases fibroblast activation protein, DPP8 and DPP9 in primary cell cultures derived from high-grade gliomas, and show that the DPP-IV-like enzymatic activity is negatively associated with their in vitro growth. More importantly, the DPP-IV positive subpopulation isolated from the primary cell cultures using immunomagnetic separation exhibited slower proliferation. Forced expression of the wild as well as the enzymatically inactive mutant DPP-IV in glioma cell lines resulted in their reduced growth, migration and adhesion in vitro, as well as suppressed glioma growth in an orthotopic xenotransplantation mouse model. Microarray analysis of glioma cells with forced DPP-IV expression revealed differential expression of several candidate genes not linked to the tumor suppressive effects of DPP-IV in previous studies. Gene set enrichment analysis of the differentially expressed genes showed overrepresentation of gene ontology terms associated with cell proliferation, cell adhesion and migration. In conclusion, our data show that DPP-IV may interfere with several aspects of the malignant phenotype of glioma cells in great part independent of its enzymatic activity.
    MeSH term(s) Animals ; Cell Adhesion ; Cell Cycle ; Cell Movement ; Cell Proliferation ; Dipeptidases/genetics ; Dipeptidases/metabolism ; Dipeptidyl Peptidase 4/genetics ; Dipeptidyl Peptidase 4/metabolism ; Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/genetics ; Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Glioma/enzymology ; Glioma/genetics ; Humans ; Immunomagnetic Separation ; Male ; Mice ; Mutation ; Primary Cell Culture ; Signal Transduction/genetics ; Transfection ; Tumor Cells, Cultured ; Xenograft Model Antitumor Assays
    Chemical Substances Dipeptidases (EC 3.4.13.-) ; DPP9 protein, human (EC 3.4.14.-) ; Dipeptidyl-Peptidases and Tripeptidyl-Peptidases (EC 3.4.14.-) ; DPP4 protein, human (EC 3.4.14.5) ; DPP8 protein, human (EC 3.4.14.5) ; Dipeptidyl Peptidase 4 (EC 3.4.14.5)
    Language English
    Publishing date 2012-05
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1228429-4
    ISSN 1878-5875 ; 1357-2725
    ISSN (online) 1878-5875
    ISSN 1357-2725
    DOI 10.1016/j.biocel.2012.01.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Dipeptidyl peptidase-IV inhibits glioma cell growth independent of its enzymatic activity

    Busek, Petr / Stremenova, Jarmila / Sromova, Lucie / Hilser, Marek / Balaziova, Eva / Kosek, Dalibor / Trylcova, Jana / Strnad, Hynek / Krepela, Evzen / Sedo, Aleksi

    international journal of biochemistry & cell biology

    Volume v. 44,, Issue no. 5

    Abstract: Malignant gliomas exhibit abnormal expression of proteolytic enzymes that may participate in the uncontrolled cell proliferation and aberrant interactions with the brain extracellular matrix. The multifunctional membrane bound serine aminopeptidase ... ...

    Abstract Malignant gliomas exhibit abnormal expression of proteolytic enzymes that may participate in the uncontrolled cell proliferation and aberrant interactions with the brain extracellular matrix. The multifunctional membrane bound serine aminopeptidase dipeptidyl peptidase (DPP)-IV has been linked to the development and progression of several malignancies, possibly both through the enzymatic and nonenzymatic mechanisms. In this report we demonstrate the expression of DPP-IV and homologous proteases fibroblast activation protein, DPP8 and DPP9 in primary cell cultures derived from high-grade gliomas, and show that the DPP-IV-like enzymatic activity is negatively associated with their in vitro growth. More importantly, the DPP-IV positive subpopulation isolated from the primary cell cultures using immunomagnetic separation exhibited slower proliferation. Forced expression of the wild as well as the enzymatically inactive mutant DPP-IV in glioma cell lines resulted in their reduced growth, migration and adhesion in vitro, as well as suppressed glioma growth in an orthotopic xenotransplantation mouse model. Microarray analysis of glioma cells with forced DPP-IV expression revealed differential expression of several candidate genes not linked to the tumor suppressive effects of DPP-IV in previous studies. Gene set enrichment analysis of the differentially expressed genes showed overrepresentation of gene ontology terms associated with cell proliferation, cell adhesion and migration. In conclusion, our data show that DPP-IV may interfere with several aspects of the malignant phenotype of glioma cells in great part independent of its enzymatic activity.
    Keywords cell culture ; xenotransplantation ; proteinases ; genes ; immunomagnetic separation ; animal models ; phenotype ; proteolysis ; gene expression regulation ; mutants ; cell proliferation ; extracellular matrix ; microarray technology ; fibroblasts ; enzyme activity ; gene expression ; cell adhesion ; cell growth ; brain
    Language English
    Document type Article
    ISSN 1357-2725
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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