Biology subjects

Chalupska, D.

Publications and source records attributed to Chalupska, D..

6 recordsLinked to original sources

bioRxiv2026

Characterization of the N7 RNA cap methyltransferase from Trichomonas vaginalis and inhibitor discovery

RNA cap formation is essential for eukaryotic gene expression, yet the enzymes responsible for cap methylation remain poorly characterized in many eukaryotic parasites, including Trichomonas vaginalis. Here, we functionally and structurally characterized the RNA guanine-N7 methyltransferases (MTases) from T. vaginalis, TvRNMT1 and TvRNMT2. We determined the crystal structure of TvRNMT1 in complex with S-adenosylhomocysteine (SAH) at 1.6 A resolution and additional structures with the inhibitors sinefungin and OBO101, defining the architecture and ligand-recognition properties of its active site. Screening of SAH analogues identified several inhibitors with submicromolar to low-micromolar activity against both homologues. Molecular docking and modelling of capped RNA binding further delineated the inhibitor- and RNA-binding regions of TvRNMT1 and identified residues that may contribute to cap recognition. These results define the molecular basis of ligand recognition by T. vaginalis RNA cap MTases and establish a structural framework for targeting parasite RNA capping.

molecular biology↗

bioRxiv2026

Branched C7-Substituted 7-Deaza-SAH Analogues Occupy the Entire SAM-Binding Pocket of Mpox Virus VP39 and Dengue Virus NS5 Methyltransferases

Viral RNA-cap MTases are attractive targets for antiviral drug development. We previously identified C7-substituted 7-deaza-SAH analogues as potent inhibitors of the mpox virus 2'-O-MTase VP39. Here, we used structure-guided design to develop branched C7-substituted analogues intended to engage multiple hydrophobic regions of the VP39 SAM-binding pocket. The synthesized compounds were characterized using biochemical and crystallographic approaches. Several analogues effectively inhibited VP39, with the most potent compound displaying an IC50 in the tens-of-nanomolar range. Crystal structures of VP39 in complex with STM1187 and STM1189 confirmed that the branched aromatic substituents extend towards hydrophobic regions adjacent to the SAM binding site. The precise ligand conformations were strongly influenced by linker geometry and the branching groups mode of attachment. STM1078 also inhibited DENV3 NS5 MTase with submicromolar potency, and the complexs structure revealed a conserved binding mode of the SAH-like core accompanied by conformational adaptability of the branched substituent. These results demonstrate how three-dimensional expansion from the 7-deaza position can generate potent inhibitors capable of binding structurally distinct viral MTases.

molecular biology↗

bioRxiv2023

Fluorinated cGAMP analogs, which act as STING agonists and are not cleavable by poxins: structural basis of their function

The Stimulator of Interferon Genes (STING) plays a crucial role in the cGAS-STING pathway of innate immunity, detecting DNA in the cytoplasm and defending against certain cancers, viruses, and bacteria. We designed and synthesized fluorinated carbocyclic cGAMP analogs, MD1203 and MD1202D (MDs), to enhance their stability against nucleases and their affinity for STING. These compounds demonstrated exceptional activity against wild-type STING and all its allelic variations, including the hard-to-target REF isoform. Despite their distinct chemical modifications relative to the canonical CDNs, such as the substitution of guanine with hypoxanthine and the fluorination of the (pseudo)ribose ring, crystallographic analysis revealed a consistent binding mode with STING. Importantly, these compounds were resistant to cleavage by viral poxin nucleases. The crystallographic analysis of poxin/MD complexes unveiled their binding mode at the interface of poxin monomers, with dynamic adenine base orientations. Interestingly, MDs-bound poxin adopted an unliganded-like conformation, distinct from the conformation of cGAMP-bound poxin. Moreover, when MDs were in complex with poxin, they exhibited a different conformation than cGAMP when bound to poxin; in fact, it closely resembled the conformation observed when MDs were bound to STING. In conclusion, the development of MD1203 and MD1202D, showcases their potential as potent STING activators with remarkable stability against poxin-mediated degradation--a crucial characteristic for future development of antivirals.

molecular biology↗

bioRxiv2023

Structural and functional insights in flavivirus NS5 proteins gained by the structure of Ntaya virus polymerase and methyltransferase

Flaviviruses are single-stranded positive-sense RNA (+RNA) viruses that are responsible for several (re)emerging diseases such as Yellow, Dengue or West Nile fevers. The Zika epidemic highlighted their dangerousness when a relatively benign virus known since the 1950s turned into a deadly pathogen. The central protein for their replication is NS5 (non-structural protein 5), which is composed of the N-terminal methyltransferase (MTase) domain and the C-terminal RNA-dependent RNA-polymerase (RdRp) domain. It is responsible for both, RNA replication and installation of the 5 RNA cap. We structurally and biochemically analyzed the Ntaya virus MTase and RdRp domains and we compared their properties to other flaviviral NS5s. The enzymatic centers are well conserved across Flaviviridae, suggesting that the development of drugs targeting all flaviviruses is feasible. However, the enzymatic activities of the isolated proteins were significantly different for the MTase domains.

molecular biology↗

bioRxiv2022

The structure of monkeypox virus 2'-O-ribose methyltransferase VP39 in complex with sinefungin provides the foundation for inhibitor design

Monkeypox is an emerging, rapidly spreading disease with pandemic potential. It is caused by the monkeypox virus (MPXV), a dsDNA virus from the Poxviridae family, that replicates in the cytoplasm and must encode for its own RNA processing machinery including the capping machinery. Here, we present the crystal structure of its 2-O-RNA methyltransferase (MTase) VP39 in complex with the pan-MTase inhibitor sinefungin. A comparison of this 2-O RNA MTase with enzymes from unrelated ssRNA viruses (SARS-CoV-2 and Zika) reveals a surprisingly conserved sinefungin binding mode implicating that a single inhibitor could be used against unrelated viral families.

microbiology↗

bioRxiv2020

Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the Coronavirus disease 2019 (COVID-19) which is currently negatively affecting the population and disrupting the global economy. SARS-CoV-2 belongs to the +RNA virus family that utilize single-stranded positive-sense RNA molecules as genomes. SARS-CoV-2, like other coronaviruses, has an unusually large genome for a +RNA virus that encodes four structural proteins - the matrix (M), small envelope (E), spike (S) and nucleocapsid phosphoprotein (N) - and sixteen nonstructural proteins (nsp1-16) that together ensure replication of the virus in the host cell. The nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Its N-terminal RNA binding domain (N-NTD) captures the RNA genome while the C-terminal domain anchors the ribonucleoprotein complex to the viral membrane via its interaction with the M protein. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD lined with arginine residues suggesting a putative RNA binding site. Next, we performed an NMR titration experiment using an RNA duplex. The observed changes in positions of signals in the N-NTD NMR spectra allowed us to construct a model of the N-NTD in complex with RNA.

biochemistry↗