Biology subjects

Massirer, K. B.

Publications and source records attributed to Massirer, K. B..

11 recordsLinked to original sources

bioRxiv2026

Bordetella pertussis BctCBA Mediates Citrate-Dependent Zn2+ and Ni2+ binding

Bordetella pertussis, the causative agent of whooping cough, is a reemerging public health threat. While the Tripartite Tricarboxylate Transporter (TTT) system BctCBA was previously implicated solely in citrate uptake, we demonstrate that the solute-binding protein BctC specifically binds citrate chelated with Zn{superscript 2} and Ni{superscript 2}. To elucidate the molecular mechanism of this interaction, we determined the crystal structures of BctC in three states: apo, open, and closed (citrate-zinc-bound), defining the structural determinants for metal-citrate recognition. Comparative analyses suggest that citrate-mediated divalent cation binding is a widespread feature among bacterial TTT homologs. Finally, in silico modeling of the full BctCBA complex predicts an elevator-type transport mechanism. Together, these findings redefine the functional scope of BctCBA, revealing a sophisticated strategy by which B. pertussis exploits organic chelators to acquire essential trace metals during infection.

biochemistry↗

bioRxiv2025

Discovery and characterization of cell-permeable inhibitors of Leishmania mexicana CLK1 using an in-cell target engagement assay

Leishmaniasis is a neglected tropical disease with limited treatment options and significant unmet medical need. Here, we report the development of a bioluminescence resonance energy transfer (BRET)-based target engagement assay in live intact cells to identify and validate cell-permeable, ATP-competitive inhibitors of Leishmania mexicana (Lmx)CLK1. LmxCLK2, a closely related paralogue with an identical protein kinase domain, is also considered in our analysis. Genetic and pharmacological evidence indicates that simultaneous deletion or inhibition of both LmxCLK1/2 is lethal to the parasite. Using our newly developed assay, we screened a library of human kinase inhibitors and identified WZ8040, a third-generation EGFR inhibitor, as a potent LmxCLK1 ligand. WZ8040 demonstrated robust target engagement in both promastigotes and macrophage-internalized amastigotes, with low micromolar EC values for parasite killing and minimal toxicity to host macrophages. Biochemical assays confirmed that WZ8040 covalently binds and inhibits LmxCLK1, with mass spectrometry identifying Cys172 as the primary site of modification. Genetic validation using overexpression and knockout lines supports LmxCLK1 as the primary target of WZ8040. However, the retained activity of WZ8040 in mutant lines with the Cys172Ala substitution suggests that covalent binding is not essential for compound efficacy. Our findings highlight the utility of BRET-based assays for target validation in kinetoplastid parasites and underscore the potential of CLK1 as a druggable kinase in Leishmania. This integrated approach provides a framework for accelerating the discovery of novel anti-leishmanial agents through target engagement-guided strategies. Highlights- A live-cell NanoBRET assay enables in situ target engagement of CLK1 in Leishmania mexicana. - The covalent inhibitor WZ8040 effectively targets LmxCLK1 in both promastigote and intracellular amastigote stages. - CLK1 inhibition by WZ8040 does not depend on covalent modification of a single cysteine residue. - Combined target engagement and phenotypic data support LmxCLK1 as a druggable kinase in Leishmania.

cell biology↗

bioRxiv2025

Fragment Screening by Weak Affinity Chromatography Identifies Ligands for Neisseria gonorrhoeae Undecaprenyl Diphosphate Synthase

The rapid rise of antimicrobial resistance in Neisseria gonorrhoeae underscores the urgent need for new therapeutic strategies. Undecaprenyl diphosphate synthase (UPPS), an essential enzyme in bacterial cell wall biosynthesis, has emerged as a promising antimicrobial target. However, no structural information has been available for the gonococcal enzyme (NgUPPS), and known ligand scaffolds remain limited, hindering structure-based drug discovery efforts. Here, we present a combined weak affinity chromatography-mass spectrometry (WAC-MS) and crystallographic pipeline to identify and structurally characterize fragment binders of NgUPPS. WAC-MS screening of a diverse fragment library identified 23 putative binders, 16 of which were successfully co- crystallized with NgUPPS, primarily via soaking into preformed apo crystals. The resulting high-resolution structures mapped fragment binding across four distinct regions of the enzymes hydrophobic tunnel, encompassing the pyrophosphate- binding pockets and the distal product-binding site. Additionally, we determined the co-crystal structure of NgUPPS with BPH-1100, a known phthalic acid-based UPPS inhibitor, revealing that the enzyme adopts an open, ligand-competent conformation without significant rearrangement. Our results validate NgUPPS as a structurally tractable antibacterial target and provide a strong foundation for fragment-based optimization and the future development of novel inhibitors to combat drug-resistant N. gonorrhoeae.

microbiology↗

bioRxiv2024

Functional characterization of N-acetyltransferase 10 (NAT10) in Leishmania mexicana

Leishmania presents a complex life cycle that involves both invertebrate and vertebrate hosts. By regulating gene expression, protein synthesis, and metabolism, the parasite can adapt to various environmental conditions. This regulation occurs mainly at the post-transcriptional level and may involve epitranscriptomic modifications of RNAs. Recent studies have shown that mRNAs in humans undergo a modification known as N4-acetylcytidine (ac4C) catalyzed by the enzyme N-acetyltransferase (NAT10), impacting mRNAs stability and translation. Here, we characterized the NAT10 homologue of L. mexicana, finding that the enzyme exhibits all the conserved acetyltransferase domains and although failed to functionally complement the Kre33 mutant in Saccharomyces cerevisiae, has in vitro acetyltransferase activity. We also discovered that LmexNAT10 is nuclear, and seems essential, as evidenced by unsuccessful attempts to obtain null mutant parasites. Phenotypic characterization of single-knockout parasites revealed that LmexNAT10 affects the multiplication of procyclic forms and the promastigote-amastigote differentiation. Additionally, in vivo infection studies using the invertebrate vector Lutzomyia longipalpis showed a delay in the parasite differentiation into metacyclics. Finally, we observed changes in the cell cycle progression and protein synthesis in the mutant parasites. Together, these results suggest that LmexNAT10 might be important for parasite differentiation, potentially by regulating ac4C levels.

microbiology↗

bioRxiv2024

PRMT5 is required for full-length HTT expression by repressing multiple proximal intronic polyadenylation sites

Expansion of the CAG trinucleotide repeat tract in exon 1 of the Huntingtin (HTT) gene above a threshold of [~]36 repeats causes Huntingtons disease (HD) through the expression of a polyglutamine-expanded form of the HTT protein. This mutation triggers wide-ranging cellular and biochemical pathologies leading to cognitive, motor, and psychiatric symptoms in HD patients. As accurate splicing is required to produce the full-length HTT protein of [~]348 kDa, targeting HTT splicing with small molecule drugs is a compelling approach to lower HTT protein levels to treat HD, and splice modulators are being tested in the clinic. Here, we identify PRMT5 as a novel regulator of HTT mRNA splicing and alternative polyadenylation. PRMT5 inhibition disrupts the splicing of HTT introns 9 and 10, leading to activation of multiple proximal intronic polyadenylation sites within these introns and promoting premature termination, cleavage and polyadenylation (PCPA) of the HTT mRNA, thus lowering total HTT protein levels. We also detected increasing levels of these truncated, intron-containing HTT transcripts across a series of neuronal differentiation samples which correlated with lower PRMT5 expression. Notably, PRMT5 inhibition in glioblastoma (GBM) stem cells potently induced neuronal differentiation. We posit that PRMT5-mediated regulation of intronic polyadenylation, premature termination and cleavage of the HTT mRNA modulates HTT expression and plays an important role during embryonic development and neuronal differentiation.

neuroscience↗

bioRxiv2023

An experimental target-based platform in yeast for screening Plasmodium vivax deoxyhypusine synthase inhibitors

The enzyme deoxyhypusine synthase (DHS) catalyzes the first step in the post-translational modification of the eukaryotic translation factor 5A (eIF5A). This is the only protein known to contain the amino acid hypusine, which results from this modification. Both eIF5A and DHS are essential for cell viability in eukaryotes, and inhibiting DHS can be a promising strategy for the development of new therapeutic alternatives. The human and parasitic orthologous proteins are different enough to render selective targeting against infectious diseases; however, no DHS inhibitor selective for the parasite ortholog has previously been reported. Here, we established a yeast surrogate genetics platform to identify inhibitors of DHS from Plasmodium vivax, one of the major causative agents of malaria. We constructed genetically modified Saccharomyces cerevisiae strains expressing DHS genes from Homo sapiens (HsDHS) or P. vivax (PvDHS) in place of the endogenous DHS gene from S. cerevisiae. This new strain background was [~]60-fold more sensitive to an inhibitor of human DHS than the one previously used. Initially, a virtual screen using datasets from the ChEMBL-NTD database was performed. Candidate ligands were tested in growth assays using the newly generated yeast strains expressing heterologous DHS genes. Among these, two showed promise by preferentially reducing the growth of the PvDHS-expressing strain. Further, in a robotized assay, we screened 400 compounds from the Pathogen Box library using the same S. cerevisiae strains, and one compound preferentially reduced the growth of the PvDHS-expressing yeast strain. Western blot revealed that these compounds significantly reduced eIF5A hypusination in yeast. Our study demonstrates that this yeast-based platform is suitable for identifying and verifying candidate small molecule DHS inhibitors, selective for the parasite over the human ortholog.

synthetic biology↗

bioRxiv2022

UHMK1 is a novel splicing regulatory kinase

The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif (UHM), a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3 splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors in vitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology (GO) analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome, but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 200 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on gene expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Finally, the functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration of the cells. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.

molecular biology↗

bioRxiv2019

The C-terminal domains SnRK2-box and ABA-box have a role in sugarcane SnRK2s auto-activation and activity

Resistance to drought stress is fundamental to plant survival and development. Abscisic acid (ABA) is one of the major hormones involved in different types of abiotic and biotic stress responses. ABA intracellular signaling has been extensively explored in Arabidopsis thaliana and occurs via a phosphorylation cascade mediated by three related protein kinases, denominated SnRK2s (SNF1-related protein kinases). However, the role of ABA signaling and the biochemistry of SnRK2 in crop plants remains underexplored. Considering the importance of the ABA hormone in abiotic stress tolerance, here we investigated the regulatory mechanism of sugarcane SnRK2s - known as SAPKs (Stress/ABA-activated Protein Kinases). The crystal structure of ScSAPK10 revealed the characteristic SnRK2 family architecture, in which the regulatory SnRK2-box interacts with the kinase domain C helix. To study sugarcane SnRK2 regulation, we produced a series of mutants for the protein regulatory domains SnRK2-box and ABA-box. Surprisingly, mutations in the SnRK2-box did not drastically affect sugarcane SnRK2 activity, in contrast to previous observations for the homologous proteins in Arabidopsis. Also, we found that the ABA-box might have a role in SnRK2 activation in the absence of PP2C phosphatase. Taken together, our results demonstrate that both C-terminal domains of sugarcane SnRK2 proteins play a fundamental role in protein activation and activity.

plant biology↗

bioRxiv2019

Structural and binding studies of human CAMKK2 kinase domain bound to small molecule ligands

Calcium/Calmodulin-dependent Protein Kinase Kinase 2 (CAMKK2) acts as a signaling hub, receiving signals from various regulatory pathways and decoding them via phosphorylation of downstream protein kinases - such as AMPK (AMP-activated protein kinase) and CAMK types I and IV. CAMKK2 relevance is highlighted by its constitutive activity being implicated in several human pathologies. However, at present, there are no specific small-molecule inhibitors available for this protein kinase. Moreover, CAMKK2 and its closest human homologue, CAMKK1, are thought to have overlapping biological roles. Here we present six novel co-structures of CAMKK2 bound to potent ligands identified from a library of ATP-competitive kinase inhibitors. Isothermal titration calorimetry (ITC) revealed that binding to some of these molecules is enthalpy driven. We expect our results to further advance current efforts to discover small molecule kinase inhibitors specific to each human CAMKK.

biochemistry↗

bioRxiv2018

BioFeatureFinder: Flexible, unbiased analysis of biological characteristics associated with genomic regions

BioFeatureFinder is a novel algorithm which allows analyses of many biological genomic landmarks (including alternatively spliced exons, DNA/RNA-binding protein binding sites, and gene/transcript functional elements, nucleotide content, conservation, k-mers, secondary structure) to identify distinguishing features. BFF uses a flexible underlying model that combines classical statistical tests with Big Data machine-learning strategies. The model is created using thousands of biological characteristics (features) that are used to build a feature map and interpret category labels in genomic ranges. Our results show that BFF is a reliable platform for analyzing large-scale datasets. We evaluated the RNA binding feature map of 110 eCLIP-seq datasets and were able to recover several well-known features from the literature for RNA-binding proteins; we were also able to uncover novel associations. BioFeatureFinder is available at https://github.com/kbmlab/BioFeatureFinder/.

bioinformatics↗

bioRxiv2017

Structural characterization of human Vaccinia-Related Kinases (VRK) bound to small-molecule inhibitors identifies different P-loop conformations

The human genome encodes two active Vaccinia-related protein kinases (VRK), VRK1 and VRK2. These proteins have been implicated in a number of cellular processes and linked to a variety of tumors. However, understanding the cellular role of VRKs and establishing their potential use as targets for therapeutic intervention has been limited by the lack of tool compounds that can specifically modulate the activity of these kinases in cells. Here we identified BI-D1870, a dihydropteridine inhibitor of RSK kinases, as a promising starting point for the development of chemical probes targeting the active VRKs. We solved co-crystal structures of both VRK1 and VRK2 bound to BI-D1870 and of VRK1 bound to two broad-spectrum inhibitors. These structures revealed that both VRKs can adopt a P-loop folded conformation, which is stabilized by different mechanisms on each protein. Based on these structures, we suggest modifications to the dihydropteridine scaffold that can be explored to produce potent and specific inhibitors towards VRK1 and VRK2.

biochemistry↗