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Article ; Online: Structural analysis of the putative SARS-CoV-2 primase complex.

Konkolova, Eva / Klima, Martin / Nencka, Radim / Boura, Evzen

2020 Volume 211, Issue 2, Page(s) 107548

Abstract: We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the ... ...

Abstract	We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the heterotetramer formed by both nsp7 and nsp8 that is flanked with two symmetry-related nsp8 β-sheet subdomains. It was also revealed that two hydrophobic interfaces one of approx. 1340 Å
MeSH term(s)	Betacoronavirus/chemistry ; Binding Sites ; Coronavirus RNA-Dependent RNA Polymerase ; Crystallography, X-Ray ; DNA Primase/chemistry ; DNA Primase/metabolism ; Models, Molecular ; Multiprotein Complexes ; Protein Conformation ; Protein Multimerization ; RNA/metabolism ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Multiprotein Complexes ; NS8 protein, SARS-CoV-2 ; Viral Nonstructural Proteins ; RNA (63231-63-0) ; DNA Primase (EC 2.7.7.-) ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; NSP7 protein, SARS-CoV-2 (EC 2.7.7.48)
Keywords	covid19
Language	English
Publishing date	2020-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2020.107548
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Article ; Online: Non-Nucleotide RNA-Dependent RNA Polymerase Inhibitor That Blocks SARS-CoV-2 Replication.

Dejmek, Milan / Konkoľová, Eva / Eyer, Luděk / Straková, Petra / Svoboda, Pavel / Šála, Michal / Krejčová, Kateřina / Růžek, Daniel / Boura, Evzen / Nencka, Radim

Viruses

2021 Volume 13, Issue 8

Abstract: SARS-CoV-2 has caused an extensive pandemic of COVID-19 all around the world. Key viral enzymes are suitable molecular targets for the development of new antivirals against SARS-CoV-2 which could represent potential treatments of the corresponding ... ...

Abstract	SARS-CoV-2 has caused an extensive pandemic of COVID-19 all around the world. Key viral enzymes are suitable molecular targets for the development of new antivirals against SARS-CoV-2 which could represent potential treatments of the corresponding disease. With respect to its essential role in the replication of viral RNA, RNA-dependent RNA polymerase (RdRp) is one of the prime targets. HeE1-2Tyr and related derivatives were originally discovered as inhibitors of the RdRp of flaviviruses. Here, we present that these pyridobenzothiazole derivatives also significantly inhibit SARS-CoV-2 RdRp, as demonstrated using both polymerase- and cell-based antiviral assays.
MeSH term(s)	Adenosine Monophosphate/analogs & derivatives ; Adenosine Monophosphate/pharmacology ; Alanine/analogs & derivatives ; Alanine/pharmacology ; Animals ; Antiviral Agents/pharmacology ; Benzothiazoles/pharmacology ; Cell Line ; Cell Survival/drug effects ; Coronavirus RNA-Dependent RNA Polymerase/antagonists & inhibitors ; Dose-Response Relationship, Drug ; Enzyme Inhibitors/pharmacology ; Humans ; Microbial Sensitivity Tests ; Pyridones/pharmacology ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; SARS-CoV-2/physiology ; Virus Replication/drug effects
Chemical Substances	Antiviral Agents ; Benzothiazoles ; Enzyme Inhibitors ; HeE1-2Tyr ; Pyridones ; remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; NSP12 protein, SARS-CoV-2 (EC 2.7.7.48) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2021-08-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13081585
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Article ; Online: Tacrine-Coumarin Derivatives as Topoisomerase Inhibitors with Antitumor Effects on A549 Human Lung Carcinoma Cancer Cell Lines.

Konkoľová, Eva / Hudáčová, Monika / Hamuľaková, Slávka / Jendželovský, Rastislav / Vargová, Jana / Ševc, Juraj / Fedoročko, Peter / Kožurková, Mária

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 4

Abstract: A549 human lung carcinoma cell lines were treated with a series of new drugs with both tacrine and coumarin pharmacophores ( ... ...

Abstract	A549 human lung carcinoma cell lines were treated with a series of new drugs with both tacrine and coumarin pharmacophores (derivatives
MeSH term(s)	A549 Cells ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Cell Proliferation/drug effects ; Coumarins/chemistry ; Coumarins/pharmacology ; DNA Topoisomerases, Type I/metabolism ; DNA Topoisomerases, Type II/metabolism ; Drug Screening Assays, Antitumor ; Humans ; Molecular Structure ; Poly-ADP-Ribose Binding Proteins/antagonists & inhibitors ; Poly-ADP-Ribose Binding Proteins/metabolism ; Tacrine/chemistry ; Tacrine/pharmacology ; Topoisomerase I Inhibitors/chemistry ; Topoisomerase I Inhibitors/pharmacology ; Topoisomerase II Inhibitors/chemistry ; Topoisomerase II Inhibitors/pharmacology ; Tumor Cells, Cultured
Chemical Substances	Antineoplastic Agents ; Coumarins ; Poly-ADP-Ribose Binding Proteins ; Topoisomerase I Inhibitors ; Topoisomerase II Inhibitors ; Tacrine (4VX7YNB537) ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; TOP1 protein, human (EC 5.99.1.2) ; DNA Topoisomerases, Type II (EC 5.99.1.3) ; TOP2A protein, human (EC 5.99.1.3)
Language	English
Publishing date	2021-02-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26041133
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Article ; Online: Guanine quadruplexes in the RNA genome of the tick-borne encephalitis virus: their role as a new antiviral target and in virus biology.

Holoubek, Jiří / Bednářová, Klára / Haviernik, Jan / Huvarová, Ivana / Dvořáková, Zuzana / Černý, Jiří / Outlá, Martina / Salát, Jiří / Konkol'ová, Eva / Boura, Evzen / Růžek, Daniel / Vorlíčková, Michaela / Eyer, Luděk / Renčiuk, Daniel

Nucleic acids research

2022 Volume 50, Issue 8, Page(s) 4574–4600

Abstract: We have identified seven putative guanine quadruplexes (G4) in the RNA genome of tick-borne encephalitis virus (TBEV), a flavivirus causing thousands of human infections and numerous deaths every year. The formation of G4s was confirmed by biophysical ... ...

Abstract	We have identified seven putative guanine quadruplexes (G4) in the RNA genome of tick-borne encephalitis virus (TBEV), a flavivirus causing thousands of human infections and numerous deaths every year. The formation of G4s was confirmed by biophysical methods on synthetic oligonucleotides derived from the predicted TBEV sequences. TBEV-5, located at the NS4b/NS5 boundary and conserved among all known flaviviruses, was tested along with its mutated variants for interactions with a panel of known G4 ligands, for the ability to affect RNA synthesis by the flaviviral RNA-dependent RNA polymerase (RdRp) and for effects on TBEV replication fitness in cells. G4-stabilizing TBEV-5 mutations strongly inhibited RdRp RNA synthesis and exhibited substantially reduced replication fitness, different plaque morphology and increased sensitivity to G4-binding ligands in cell-based systems. In contrast, strongly destabilizing TBEV-5 G4 mutations caused rapid reversion to the wild-type genotype. Our results suggest that there is a threshold of stability for G4 sequences in the TBEV genome, with any deviation resulting in either dramatic changes in viral phenotype or a rapid return to this optimal level of G4 stability. The data indicate that G4s are critical elements for efficient TBEV replication and are suitable targets to tackle TBEV infection.
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Encephalitis Viruses, Tick-Borne/drug effects ; Encephalitis Viruses, Tick-Borne/genetics ; Encephalitis, Tick-Borne/drug therapy ; Encephalitis, Tick-Borne/genetics ; G-Quadruplexes ; Humans ; Ligands ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics
Chemical Substances	Antiviral Agents ; Ligands ; RNA, Viral ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2022-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac225
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Zs.A 1067: Show issues

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Article ; Online: Structural analysis of the putative SARS-CoV-2 primase complex

Konkolova, Eva / Klima, Martin / Nencka, Radim / Boura, Evzen

Journal of Structural Biology

2020 Volume 211, Issue 2, Page(s) 107548

Keywords	Structural Biology ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2020.107548
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Article: Structural analysis of the putative SARS-CoV-2 primase complex

Konkolova, Eva / Klima, Martin / Nencka, Radim / Boura, Evzen

J Struct Biol

Abstract	We report the crystal structure of the SARS-CoV-2 putative primase composed of the nsp7 and nsp8 proteins. We observed a dimer of dimers (2:2 nsp7-nsp8) in the crystallographic asymmetric unit. The structure revealed a fold with a helical core of the heterotetramer formed by both nsp7 and nsp8 that is flanked with two symmetry-related nsp8 ß-sheet subdomains. It was also revealed that two hydrophobic interfaces one of approx. 1340 Å2 connects the nsp7 to nsp8 and a second one of approx. 950 Å2 connects the dimers and form the observed heterotetramer. Interestingly, analysis of the surface electrostatic potential revealed a putative RNA binding site that is formed only within the heterotetramer.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #593332
Database	COVID19

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Article ; Online: Tacrine-Coumarin Derivatives as Topoisomerase Inhibitors with Antitumor Effects on A549 Human Lung Carcinoma Cancer Cell Lines

Eva Konkoľová / Monika Hudáčová / Slávka Hamuľaková / Rastislav Jendželovský / Jana Vargová / Juraj Ševc / Peter Fedoročko / Mária Kožurková

Molecules, Vol 26, Iss 4, p

2021 Volume 1133

Abstract: A549 human lung carcinoma cell lines were treated with a series of new drugs with both tacrine and coumarin pharmacophores (derivatives 1a – 2c ) in order to test the compounds’ ability to inhibit both cancer cell growth and topoisomerase I and II ... ...

Abstract	A549 human lung carcinoma cell lines were treated with a series of new drugs with both tacrine and coumarin pharmacophores (derivatives 1a – 2c ) in order to test the compounds’ ability to inhibit both cancer cell growth and topoisomerase I and II activity. The ability of human topoisomerase I ( h TOPI) and II to relax supercoiled plasmid DNA in the presence of various concentrations of the tacrine-coumarin hybrid molecules was studied with agarose gel electrophoresis. The biological activities of the derivatives were studied using MTT assays, clonogenic assays, cell cycle analysis and quantification of cell number and viability. The content and localization of the derivatives in the cells were analysed using flow cytometry and confocal microscopy. All of the studied compounds were found to have inhibited topoisomerase I activity completely. The effect of the tacrine-coumarin hybrid compounds on cancer cells is likely to be dependent on the length of the chain between the tacrine and coumarin moieties ( 1c , 1d = tacrine-(CH 2 ) 8–9 -coumarin). The most active of the tested compounds, derivatives 1c and 1d , both display longer chains.
Keywords	tacrine-coumarin derivatives ; DNA ; topoisomerases I ; II ; cytotoxicity ; lung carcinoma cells ; A549 ; Organic chemistry ; QD241-441
Subject code	540
Language	English
Publishing date	2021-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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
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Article ; Online: Antiviral Activity of 7-Substituted 7-Deazapurine Ribonucleosides, Monophosphate Prodrugs, and Triphoshates against Emerging RNA Viruses.

Milisavljevic, Nemanja / Konkolová, Eva / Kozák, Jaroslav / Hodek, Jan / Veselovská, Lucia / Sýkorová, Veronika / Čížek, Karel / Pohl, Radek / Eyer, Luděk / Svoboda, Pavel / Růžek, Daniel / Weber, Jan / Nencka, Radim / Bouřa, Evžen / Hocek, Michal

ACS infectious diseases

2021 Volume 7, Issue 2, Page(s) 471–478

Abstract: A series of 7-deazaadenine ribonucleosides bearing alkyl, alkenyl, alkynyl, aryl, or hetaryl groups at position 7 as well as their 5'- ...

Abstract	A series of 7-deazaadenine ribonucleosides bearing alkyl, alkenyl, alkynyl, aryl, or hetaryl groups at position 7 as well as their 5'-
MeSH term(s)	Antiviral Agents/pharmacology ; COVID-19/drug therapy ; COVID-19/virology ; Cell Line, Tumor ; Dengue Virus/drug effects ; Encephalitis Viruses, Tick-Borne/drug effects ; Humans ; Phosphates/pharmacology ; Prodrugs/pharmacology ; Purine Nucleosides ; Purines/pharmacology ; RNA Viruses/drug effects ; RNA-Dependent RNA Polymerase/metabolism ; Ribonucleosides/pharmacology ; SARS-CoV-2/drug effects ; West Nile virus/drug effects ; Zika Virus/drug effects
Chemical Substances	7-deazapurine ; Antiviral Agents ; Phosphates ; Prodrugs ; Purine Nucleosides ; Purines ; Ribonucleosides ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Language	English
Publishing date	2021-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2373-8227
ISSN (online)	2373-8227
DOI	10.1021/acsinfecdis.0c00829
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Article ; Online: Remdesivir triphosphate can efficiently inhibit the RNA-dependent RNA polymerase from various flaviviruses.

Konkolova, Eva / Dejmek, Milan / Hřebabecký, Hubert / Šála, Michal / Böserle, Jiří / Nencka, Radim / Boura, Evzen

Antiviral research

2020 Volume 182, Page(s) 104899

Abstract: Remdesivir was shown to inhibit RNA-dependent RNA-polymerases (RdRp) from distinct viral families such as from Filoviridae (Ebola) and Coronaviridae (SARS-CoV, SARS-CoV-2, MERS). In this study, we tested the ability of remdesivir to inhibit RdRps from ... ...

Abstract	Remdesivir was shown to inhibit RNA-dependent RNA-polymerases (RdRp) from distinct viral families such as from Filoviridae (Ebola) and Coronaviridae (SARS-CoV, SARS-CoV-2, MERS). In this study, we tested the ability of remdesivir to inhibit RdRps from the Flaviviridae family. Instead of remdesivir, we used the active species that is produced in cells from remdesivir, the appropriate triphosphate, which could be directly tested in vitro using recombinant flaviviral polymerases. Our results show that remdesivir can efficiently inhibit RdRps from viruses causing severe illnesses such as Yellow fever, West Nile fever, Japanese and Tick-borne encephalitis, Zika and Dengue. Taken together, this study demonstrates that remdesivir or its derivatives have the potential to become a broad-spectrum antiviral agent effective against many RNA viruses.
MeSH term(s)	Adenosine Triphosphate/analogs & derivatives ; Adenosine Triphosphate/chemistry ; Adenosine Triphosphate/pharmacology ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; COVID-19 ; Coronavirus Infections/drug therapy ; Coronavirus Infections/virology ; Flavivirus/drug effects ; Flavivirus/enzymology ; Humans ; Inhibitory Concentration 50 ; Pandemics ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/virology ; RNA Viruses/drug effects ; RNA Viruses/enzymology ; RNA-Dependent RNA Polymerase/antagonists & inhibitors ; RNA-Dependent RNA Polymerase/metabolism ; SARS-CoV-2
Chemical Substances	Antiviral Agents ; Adenosine Triphosphate (8L70Q75FXE) ; GS-441524 triphosphate (AEL0YED4SU) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48)
Keywords	covid19
Language	English
Publishing date	2020-08-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2020.104899
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