Biology subjects

Nencka, R.

Publications and source records attributed to Nencka, R..

9 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↗

bioRxiv2024

Mechanistic Insights into Alcohol-Induced DNA Crosslink Repair by the Fanconi Anemia Nuclease Slx4-Xpf-Ercc1

During cell division, DNA replication stalls upon alcohol-derived interstrand crosslink, employing DNA repair pathways. Acetaldehyde, a toxic metabolite of alcohol, can induce DNA crosslinks between complementary DNA strands, causing significant genomic instability. The repair of acetaldehyde DNA crosslinks (AA-ICLs) is vital for maintaining genome integrity and preventing mutagenic events. The Fanconi anemia (FA) repair pathways involvement in fixing the AA-ICLs is crucial, ensuring cellular homeostasis and safeguarding genomic stability. Dysregulation of the FA pathway has been linked to Fanconi anemia, a rare genetic disorder characterized by hypersensitivity to DNA-damaging agents, including acetaldehyde. However, the precise mechanism of the repair and incision of AA-ICLs is unknown. Here, we demonstrate the role of the FA pathway nuclease SLX4-XPF-ERCC1 (SXE) in the repair of AA-ICL. We have generated site-specific AA-ICL within the replication fork, and we found SXE to excise the crosslink from the replication fork, bringing evidence of its role in the repair of alcohol-induced DNA lesions. This nuclease complex performs two precise incisions around the lesion. We also demonstrate that the SXE nuclease excises an abasic site interstrand crosslink in a similar manner. Given the evidence in conjunction with previous repair studies that have been conducted, our work suggests that SXE is a versatile nuclease complex.

biochemistry↗

bioRxiv2023

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

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 (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.

biochemistry↗

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↗

bioRxiv2021

Bispecific antibody prevents SARS-CoV-2 escape and protects mice from disease

Neutralizing antibodies targeting the receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) are among the most promising approaches against coronavirus disease 2019 (COVID-19)1,2. We developed a bispecific, IgG1-like molecule (CoV-X2) based on two antibodies derived from COVID-19 convalescent donors, C121 and C1353. CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable S binding to Angiotensin-Converting Enzyme 2 (ACE2), the virus cellular receptor. Furthermore, CoV-X2 neutralizes SARS-CoV-2 and its variants of concern, as well as the escape mutants generated by the parental monoclonals. In a novel animal model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, combining into a single molecule the advantages of antibody cocktails.

immunology↗

bioRxiv2020

High-throughput fluorescent assay for inhibitor screening of proteases from RNA viruses

Spanish flu and other influenza outbreaks, the recent Zika epidemics, and the ongoing COVID-19 pandemic are the most profound examples of severe widespread diseases that are caused by RNA viruses. Perhaps less well known yet dangerous RNA viruses cause deadly diseases such as polio, Ebola, measles, rubella, yellow fever, dengue fever and many others. To combat a particular viral disease by diminishing its spread and number of fatal cases, effective vaccines and antivirals are indispensable. Therefore, quick access to the means of discovery of new treatments for any epidemic outbreak is of great interest and in vitro biochemical assays are the basis of drug discovery. The recent outbreak of the coronavirus pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) demands an affordable and reliable assay for testing antivirals. Here, we developed a quick and inexpensive high-throughput fluorescent assay to test inhibitors of viral proteases. Accordingly, we employed this assay to sample inhibitors for papain-like protease from SARS-CoV-2. In addition, we validated this assay for screening inhibitors of flaviviral protease from the tick-borne encephalitis virus to emphasize a broad range of applications of our approach. This fluorescent high-throughput assay is based on fluorescent energy transfer (FRET) between two distinct fluorescent proteins (eGFP and mCherry) connected via a substrate polypeptide. When the substrate is cleaved, FRET is abolished and the change in fluorescence corresponds to reaction progress. Our data show that this assay can be used for testing the inhibitors in the 96 or 384 well plates format with robust and reproducible outcomes.

biochemistry↗

bioRxiv2020

Structural analysis of the SARS-CoV-2 methyltransferase complex involved in coronaviral RNA cap creation

COVID-19 pandemic is caused by the SARS-CoV-2 virus that has several enzymes that could be targeted by antivirals including a 2-O RNA methyltransferase (MTase) that is involved in the viral RNA cap formation; an essential process for RNA stability. This MTase is composed of two nonstructural proteins, the nsp16 catalytic subunit and the activating nsp10 protein. We have solved the crystal structure of the nsp10-nsp16 complex bound to the pan-MTase inhibitor sinefungin in the active site. Based on the structural data we built a model of the MTase in complex with RNA that illustrates the catalytic reaction. A structural comparison to the Zika MTase revealed low conservation of the catalytic site between these two RNA viruses suggesting preparation of inhibitors targeting both these viruses will be very difficult. Together, our data will provide the information needed for structure-based drug design.

molecular biology↗

bioRxiv2018

Viral RNA-dependent RNA polymerase inhibitor 7-deaza-2′-C-methyladenosine prevents death in a mouse model of West Nile virus infection

West Nile virus (WNV) is a medically important emerging arbovirus causing serious neuroinfections in humans against which no approved antiviral therapy is currently available. In this study, we demonstrate that 2'-C- methyl- or 4'-azido-modified nucleosides are highly effective inhibitors of WNV replication, showing nanomolar or low micromolar anti-WNV activity and negligible cytotoxicity in cell culture. One representative of C2'-methylated nucleosides, 7-deaza-2'-C- methyladenosine, significantly protected WNV-infected mice from disease progression and mortality. Twice daily treatment at 25 mg/kg starting at the time of infection resulted in 100% survival of the mice. This compound was highly effective, even if the treatment was initiated 3 days post-infection, at the time of a peak of viremia, which resulted in a 90% survival rate. However, the antiviral effect of 7-deaza-2'-C- methyladenosine was absent or negligible when the treatment was started 8 days post-infection (i.e., at the time of extensive brain infection). The 4'-azido moiety appears to be another important determinant for highly efficient inhibition of WNV replication in vitro. However, the strong anti-WNV effect of 4'-azidocytidine and 4'-azido-aracytidine was cell type-dependent and observed predominantly in PS cells. The effect was much less pronounced in Vero cells. Our results indicate that 2'-C- methylated or 4'-azidated nucleosides merit further investigation as potential therapeutic agents for treating WNV infections, as well as infections caused by other medically important flaviviruses.

microbiology↗