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1.
Cell ; 186(16): 3427-3442.e22, 2023 08 03.
Article in English | MEDLINE | ID: mdl-37421949

ABSTRACT

SARS-CoV-2 is associated with broad tissue tropism, a characteristic often determined by the availability of entry receptors on host cells. Here, we show that TMEM106B, a lysosomal transmembrane protein, can serve as an alternative receptor for SARS-CoV-2 entry into angiotensin-converting enzyme 2 (ACE2)-negative cells. Spike substitution E484D increased TMEM106B binding, thereby enhancing TMEM106B-mediated entry. TMEM106B-specific monoclonal antibodies blocked SARS-CoV-2 infection, demonstrating a role of TMEM106B in viral entry. Using X-ray crystallography, cryogenic electron microscopy (cryo-EM), and hydrogen-deuterium exchange mass spectrometry (HDX-MS), we show that the luminal domain (LD) of TMEM106B engages the receptor-binding motif of SARS-CoV-2 spike. Finally, we show that TMEM106B promotes spike-mediated syncytium formation, suggesting a role of TMEM106B in viral fusion. Together, our findings identify an ACE2-independent SARS-CoV-2 infection mechanism that involves cooperative interactions with the receptors heparan sulfate and TMEM106B.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/metabolism , Angiotensin-Converting Enzyme 2/metabolism , Receptors, Virus/metabolism , Virus Internalization , Protein Binding , Membrane Proteins/metabolism , Nerve Tissue Proteins/metabolism
2.
Cell ; 154(3): 651-63, 2013 Aug 01.
Article in English | MEDLINE | ID: mdl-23911327

ABSTRACT

Vessel sprouting by migrating tip and proliferating stalk endothelial cells (ECs) is controlled by genetic signals (such as Notch), but it is unknown whether metabolism also regulates this process. Here, we show that ECs relied on glycolysis rather than on oxidative phosphorylation for ATP production and that loss of the glycolytic activator PFKFB3 in ECs impaired vessel formation. Mechanistically, PFKFB3 not only regulated EC proliferation but also controlled the formation of filopodia/lamellipodia and directional migration, in part by compartmentalizing with F-actin in motile protrusions. Mosaic in vitro and in vivo sprouting assays further revealed that PFKFB3 overexpression overruled the pro-stalk activity of Notch, whereas PFKFB3 deficiency impaired tip cell formation upon Notch blockade, implying that glycolysis regulates vessel branching.


Subject(s)
Endothelial Cells/metabolism , Glycolysis , Neovascularization, Physiologic , Phosphofructokinase-2/metabolism , Animals , Cell Line, Tumor , Cells, Cultured , Endothelial Cells/cytology , Female , Gene Deletion , Gene Silencing , Humans , Male , Mice , Mice, Inbred C57BL , Phosphofructokinase-2/genetics , Pseudopodia/metabolism , Zebrafish
3.
Mol Cell ; 65(6): 1044-1055.e5, 2017 Mar 16.
Article in English | MEDLINE | ID: mdl-28306503

ABSTRACT

Liquid-liquid phase separation (LLPS) of RNA-binding proteins plays an important role in the formation of multiple membrane-less organelles involved in RNA metabolism, including stress granules. Defects in stress granule homeostasis constitute a cornerstone of ALS/FTLD pathogenesis. Polar residues (tyrosine and glutamine) have been previously demonstrated to be critical for phase separation of ALS-linked stress granule proteins. We now identify an active role for arginine-rich domains in these phase separations. Moreover, arginine-rich dipeptide repeats (DPRs) derived from C9orf72 hexanucleotide repeat expansions similarly undergo LLPS and induce phase separation of a large set of proteins involved in RNA and stress granule metabolism. Expression of arginine-rich DPRs in cells induced spontaneous stress granule assembly that required both eIF2α phosphorylation and G3BP. Together with recent reports showing that DPRs affect nucleocytoplasmic transport, our results point to an important role for arginine-rich DPRs in the pathogenesis of C9orf72 ALS/FTLD.


Subject(s)
Amyotrophic Lateral Sclerosis/metabolism , Arginine/metabolism , Cytoplasmic Granules/metabolism , Dipeptides/metabolism , Intrinsically Disordered Proteins/metabolism , Proteins/metabolism , Amyotrophic Lateral Sclerosis/genetics , Amyotrophic Lateral Sclerosis/pathology , Arginine/chemistry , C9orf72 Protein , Carrier Proteins/genetics , Carrier Proteins/metabolism , Cytoplasmic Granules/pathology , DNA Helicases , Dipeptides/chemistry , Eukaryotic Initiation Factor-2/genetics , Eukaryotic Initiation Factor-2/metabolism , HeLa Cells , Humans , Intrinsically Disordered Proteins/chemistry , Lipid Droplets/metabolism , Phosphorylation , Poly-ADP-Ribose Binding Proteins , Protein Domains , Proteins/chemistry , RNA/metabolism , RNA Helicases , RNA Recognition Motif Proteins , Time Factors , Transfection
4.
Nucleic Acids Res ; 51(4): 1501-1511, 2023 02 28.
Article in English | MEDLINE | ID: mdl-36611237

ABSTRACT

An enzymatic method has been successfully established enabling the generation of partially base-modified RNA (previously named RZA) constructs, in which all G residues were replaced by isomorphic fluorescent thienoguanosine (thG) analogs, as well as fully modified RZA featuring thG, 5-bromocytosine, 7-deazaadenine and 5-chlorouracil. The transcriptional efficiency of emissive fully modified RZA was found to benefit from the use of various T7 RNA polymerase variants. Moreover, dthG could be incorporated into PCR products by Taq DNA polymerase together with the other three base-modified nucleotides. Notably, the obtained RNA products containing thG as well as thG together with 5-bromocytosine could function as effectively as natural sgRNAs in an in vitro CRISPR-Cas9 cleavage assay. N1-Methylpseudouridine was also demonstrated to be a faithful non-canonical substitute of uridine to direct Cas9 nuclease cleavage when incorporated in sgRNA. The Cas9 inactivation by 7-deazapurines indicated the importance of the 7-nitrogen atom of purines in both sgRNA and PAM site for achieving efficient Cas9 cleavage. Additional aspects of this study are discussed in relation to the significance of sgRNA-protein and PAM--protein interactions that were not highlighted by the Cas9-sgRNA-DNA complex crystal structure. These findings could expand the impact and therapeutic value of CRISPR-Cas9 and other RNA-based technologies.


With the advent of CRISPR-Cas9 gene editing, we now have to hand a simple two-component system amendable to silencing and knock-in editing effectively any gene. Yet we must not forget that the implications of immunotoxicity along with the poor stability and specificity of canonical nucleic acids hold enormous challenges for in vivo applications, especially in gene therapy. Our study endorses the feasibility of the enzymatic approach to incorporate nucleobase modifications into the CRISPR-Cas9 system unveiling the tolerance of Cas9 to N1-methylpseudouridine (m1Ψ)- and emissive thienoguanosine (thG)-modified sgRNA as well as thus far uncharted structural requirements for ensuring proper PAM recognition.


Subject(s)
CRISPR-Cas Systems , Nucleic Acids , DNA , Gene Editing/methods , RNA/chemistry , Fluorescence , Guanosine/chemistry
5.
J Virol ; 97(10): e0132523, 2023 10 31.
Article in English | MEDLINE | ID: mdl-37823646

ABSTRACT

IMPORTANCE: Itaconate derivates, as well as the naturally produced metabolite, have been proposed as antivirals against influenza virus. Here, the mechanism behind the antiviral effects of exogenous 4-octyl itaconate (4-OI), a derivative of itaconate, against the influenza A virus replication is demonstrated. The data indicate that 4-OI targets the cysteine at position 528 of the CRM1 protein, resulting in inhibition of the nuclear export of viral ribonucleoprotein complexes in a similar manner as previously described for other selective inhibitors of nuclear export. These results postulate a mechanism not observed before for this immuno-metabolite derivative. This knowledge is helpful for the development of derivatives of 4-OI as potential antiviral and anti-inflammatory therapeutics.


Subject(s)
Antiviral Agents , Exportin 1 Protein , Influenza, Human , Succinates , Virus Replication , Humans , Active Transport, Cell Nucleus , Antiviral Agents/pharmacology , Nuclear Proteins/metabolism , Virus Replication/drug effects , Succinates/pharmacology , Exportin 1 Protein/metabolism
6.
Bioorg Chem ; 147: 107326, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38653153

ABSTRACT

Continuing our research into the anticancer properties of acrylonitriles, we present a study involving the design, synthesis, computational analysis, and biological assessment of novel acrylonitriles derived from methoxy, hydroxy, and N-substituted benzazole. Our aim was to examine how varying the number of methoxy and hydroxy groups, as well as the N-substituents on the benzimidazole core, influences their biological activity. The newly synthesized acrylonitriles exhibited strong and selective antiproliferative effects against the Capan-1 pancreatic adenocarcinoma cell line, with IC50 values ranging from 1.2 to 5.3 µM. Consequently, these compounds were further evaluated in three other pancreatic adenocarcinoma cell lines, while their impact on normal PBMC cells was also investigated to determine selectivity. Among these compounds, the monohydroxy-substituted benzimidazole derivative 27 emerged with the most profound and broad-spectrum anticancer antiproliferative activity being emerged as a promising lead candidate. Moreover, a majority of the acrylonitriles in this series exhibited significant antioxidative activity, surpassing that of the reference molecule BHT, as demonstrated by the FRAP assay (ranging from 3200 to 5235 mmolFe2+/mmolC). Computational analysis highlighted the prevalence of electron ionization in conferring antioxidant properties, with computed ionization energies correlating well with observed activities.


Subject(s)
Acrylonitrile , Antineoplastic Agents , Antioxidants , Cell Proliferation , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Pancreatic Neoplasms , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Antineoplastic Agents/chemical synthesis , Cell Proliferation/drug effects , Humans , Acrylonitrile/chemistry , Acrylonitrile/pharmacology , Acrylonitrile/analogs & derivatives , Acrylonitrile/chemical synthesis , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/pathology , Structure-Activity Relationship , Molecular Structure , Antioxidants/pharmacology , Antioxidants/chemistry , Antioxidants/chemical synthesis , Adenocarcinoma/drug therapy , Adenocarcinoma/pathology , Cell Line, Tumor , Benzimidazoles/chemistry , Benzimidazoles/pharmacology , Benzimidazoles/chemical synthesis
7.
PLoS Genet ; 17(2): e1009387, 2021 02.
Article in English | MEDLINE | ID: mdl-33577603

ABSTRACT

Cholesterol-dependent cytolysins (CDCs), of which intermedilysin (ILY) is an archetypal member, are a group of pore-forming toxins secreted by a large variety of pathogenic bacteria. These toxins, secreted as soluble monomers, oligomerize upon interaction with cholesterol in the target membrane and transect it as pores of diameters of up to 100 to 300 Å. These pores disrupt cell membranes and result in cell lysis. The immune receptor CD59 is a well-established cellular factor required for intermedilysin pore formation. In this study, we applied genome-wide CRISPR-Cas9 knock-out screening to reveal additional cellular co-factors essential for ILY-mediated cell lysis. We discovered a plethora of genes previously not associated with ILY, many of which are important for membrane constitution. We show that heparan sulfates facilitate ILY activity, which can be inhibited by heparin. Furthermore, we identified hits in both protein and lipid glycosylation pathways and show a role for glucosylceramide, demonstrating that membrane organization is important for ILY activity. We also cross-validated identified genes with vaginolysin and pneumolysin and found that pneumolysin's cytolytic activity strongly depends on the asymmetric distribution of membrane phospholipids. This study shows that membrane-targeting toxins combined with genetic screening can identify genes involved in biological membrane composition and metabolism.


Subject(s)
Bacterial Proteins/metabolism , Bacteriocins/metabolism , Cell Membrane/metabolism , Cholesterol/metabolism , Cytotoxins/metabolism , Heparitin Sulfate/metabolism , Bacterial Proteins/genetics , Bacteriocins/genetics , CD59 Antigens/metabolism , CRISPR-Cas Systems , Cell Line, Tumor , Cytotoxins/genetics , HEK293 Cells , Humans , Porosity
8.
Int J Mol Sci ; 25(4)2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38396966

ABSTRACT

Newly designed pentacyclic benzimidazole derivatives featuring amino or amido side chains were synthesized to assess their in vitro antiproliferative activity. Additionally, we investigated their direct interaction with nucleic acids, aiming to uncover potential mechanisms of biological action. These compounds were prepared using conventional organic synthesis methodologies alongside photochemical and microwave-assisted reactions. Upon synthesis, the newly derived compounds underwent in vitro testing for their antiproliferative effects on various human cancer cell lines. Notably, derivatives 6 and 9 exhibited significant antiproliferative activity within the submicromolar concentration range. The biological activity was strongly influenced by the N atom's position on the quinoline moiety and the position and nature of the side chain on the pentacyclic skeleton. Findings from fluorescence, circular dichroism spectroscopy, and thermal melting assays pointed toward a mixed binding mode-comprising intercalation and the binding of aggregated compounds along the polynucleotide backbone-of these pentacyclic benzimidazoles with DNA and RNA.


Subject(s)
Antineoplastic Agents , Humans , Structure-Activity Relationship , Cell Line, Tumor , Drug Screening Assays, Antitumor , Antineoplastic Agents/chemistry , Benzimidazoles/chemistry , Cell Proliferation , Molecular Structure
9.
Alzheimers Dement ; 19(4): 1245-1259, 2023 04.
Article in English | MEDLINE | ID: mdl-35993441

ABSTRACT

INTRODUCTION: The most common genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are hexanucleotide repeats in chromosome 9 open reading frame 72 (C9orf72). These repeats produce dipeptide repeat proteins with poly(PR) being the most toxic one. METHODS: We performed a kinome-wide CRISPR/Cas9 knock-out screen in human induced pluripotent stem cell (iPSC) -derived cortical neurons to identify modifiers of poly(PR) toxicity, and validated the role of candidate modifiers using in vitro, in vivo, and ex-vivo studies. RESULTS: Knock-down of NIMA-related kinase 6 (NEK6) prevented neuronal toxicity caused by poly(PR). Knock-down of nek6 also ameliorated the poly(PR)-induced axonopathy in zebrafish and NEK6 was aberrantly expressed in C9orf72 patients. Suppression of NEK6 expression and NEK6 activity inhibition rescued axonal transport defects in cortical neurons from C9orf72 patient iPSCs, at least partially by reversing p53-related DNA damage. DISCUSSION: We identified NEK6, which regulates poly(PR)-mediated p53-related DNA damage, as a novel therapeutic target for C9orf72 FTD/ALS.


Subject(s)
Amyotrophic Lateral Sclerosis , Frontotemporal Dementia , Induced Pluripotent Stem Cells , Animals , Humans , Amyotrophic Lateral Sclerosis/genetics , Frontotemporal Dementia/genetics , Induced Pluripotent Stem Cells/metabolism , C9orf72 Protein/genetics , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , CRISPR-Cas Systems , Zebrafish/genetics , Zebrafish/metabolism , Neurons/metabolism , DNA Repeat Expansion/genetics , NIMA-Related Kinases/genetics , NIMA-Related Kinases/metabolism
10.
Molecules ; 28(20)2023 Oct 21.
Article in English | MEDLINE | ID: mdl-37894686

ABSTRACT

A series of novel 2,6-diphenyl substituted imidazo[4,5-b]pyridines was designed and synthesized using optimized Suzuki cross coupling to evaluate their biological activity in vitro. The conditions of the Suzuki coupling were evaluated and optimized using a model reaction. To study the influence of the substituents on the biological activity, we prepared N-unsubstituted and N-methyl substituted imidazo[4,5-b]pyridines with different substituents at the para position on the phenyl ring placed at position 6 on the heterocyclic scaffold. Antiproliferative activity was determined on diverse human cancer cell lines, and the selectivity of compounds with promising antiproliferative activity was determined on normal peripheral blood mononuclear cells (PBMC). Pronounced antiproliferative activity was observed for p-hydroxy substituted derivatives 13 and 19, both displaying strong activity against most of the tested cell lines (IC50 1.45-4.25 µM). The unsubstituted N-methyl derivative 19 proved to be the most active derivative. There was a dose-dependent accumulation of G2/M arrested cells in several cancer cell lines after exposure to compound 19, implying a cell cycle-phase-specific mechanism of action. Additionally, the novel series of derivatives was evaluated for antiviral activity against a broad panel of viruses, yet the majority of tested compounds did not show antiviral activity.


Subject(s)
Antineoplastic Agents , Leukocytes, Mononuclear , Humans , Antineoplastic Agents/pharmacology , Pyridines/pharmacology , Cell Line, Tumor , Antiviral Agents/pharmacology , Cell Proliferation , Structure-Activity Relationship , Molecular Structure , Drug Screening Assays, Antitumor
11.
Molecules ; 28(9)2023 Apr 25.
Article in English | MEDLINE | ID: mdl-37175129

ABSTRACT

Herein, we present the design and synthesis of novel N-substituted benzimidazole-derived Schiff bases, and the evaluation of their antiviral, antibacterial, and antiproliferative activity. The impact on the biological activity of substituents placed at the N atom of the benzimidazole nuclei and the type of substituents attached at the phenyl ring were examined. All of the synthesized Schiff bases were evaluated in vitro for their antiviral activity against different viruses, antibacterial activity against a panel of bacterial strains, and antiproliferative activity on several human cancer cell lines, thus enabling the study of the structure-activity relationships. Some mild antiviral effects were noted, although at higher concentrations in comparison with the included reference drugs. Additionally, some derivatives showed a moderate antibacterial activity, with precursor 23 being broadly active against most of the tested bacterial strains. Lastly, Schiff base 40, a 4-N,N-diethylamino-2-hydroxy-substituted derivative bearing a phenyl ring at the N atom on the benzimidazole nuclei, displayed a strong antiproliferative activity against several cancer cell lines (IC50 1.1-4.4 µM). The strongest antitumoral effect was observed towards acute myeloid leukemia (HL-60).


Subject(s)
Antineoplastic Agents , Humans , Antineoplastic Agents/pharmacology , Schiff Bases/pharmacology , Cell Proliferation , Structure-Activity Relationship , Benzimidazoles/pharmacology , Antiviral Agents/pharmacology
12.
Angew Chem Int Ed Engl ; 62(34): e202304476, 2023 08 21.
Article in English | MEDLINE | ID: mdl-37218580

ABSTRACT

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are modular megaenzymes that employ unusual catalytic domains to assemble diverse bioactive natural products. One such PKS is responsible for the biosynthesis of the oximidine anticancer agents, oxime-substituted benzolactone enamides that inhibit vacuolar H+ -ATPases. Here, we describe the identification of the oximidine gene cluster in Pseudomonas baetica and the characterization of four novel oximidine variants, including a structurally simpler intermediate that retains potent anticancer activity. Using a combination of in vivo, in vitro and computational approaches, we experimentally elucidate the oximidine biosynthetic pathway and reveal an unprecedented mechanism for O-methyloxime formation. We show that this process involves a specialized monooxygenase and methyltransferase domain and provide insight into their activity, mechanism and specificity. Our findings expand the catalytic capabilities of trans-AT PKSs and identify potential strategies for the production of novel oximidine analogues.


Subject(s)
Antineoplastic Agents , Polyketides , Polyketide Synthases/genetics , Polyketide Synthases/metabolism , Antineoplastic Agents/pharmacology , Antineoplastic Agents/metabolism , Bacteria , Secondary Metabolism , Polyketides/metabolism
13.
J Neuroinflammation ; 19(1): 293, 2022 Dec 08.
Article in English | MEDLINE | ID: mdl-36482436

ABSTRACT

BACKGROUND: HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP) is an incapacitating neuroinflammatory disorder for which no disease-modifying therapy is available, but corticosteroids provide some clinical benefit. Although HAM/TSP pathogenesis is not fully elucidated, older age, female sex and higher proviral load are established risk factors. We investigated systemic cytokines and a novel chronic inflammatory marker, GlycA, as possible biomarkers of immunopathogenesis and therapeutic response in HAM/TSP, and examined their interaction with established risk factors. PATIENTS AND METHODS: We recruited 110 People living with HTLV-1 (PLHTLV-1, 67 asymptomatic individuals and 43 HAM/TSP patients) with a total of 946 person-years of clinical follow-up. Plasma cytokine levels (IL-2, IL-4, IL-6, IL-10, IL-17A, IFN-γ, TNF) and GlycA were quantified by Cytometric Bead Array and 1NMR, respectively. Cytokine signaling and prednisolone response were validated in an independent cohort by nCounter digital transcriptomics. We used multivariable regression, machine learning algorithms and Bayesian network learning for biomarker identification. RESULTS: We found that systemic IL-6 was positively correlated with both age (r = 0.50, p < 0.001) and GlycA (r = 0.45, p = 0.00049) in asymptomatics, revealing an 'inflammaging" signature which was absent in HAM/TSP. GlycA levels were higher in women (p = 0.0069), but cytokine levels did not differ between the sexes. IFN-γ (p = 0.007) and IL-17A (p = 0.0001) levels were increased in untreated HAM/TSP Multivariable logistic regression identified IL-17A and proviral load as independent determinants of clinical status, resulting in modest accuracy of predicting HAM/TSP status (64.1%), while a machine learning-derived decision tree classified HAM/TSP patients with 90.7% accuracy. Pre-treatment GlycA and TNF levels significantly predicted clinical worsening (measured by Osame Motor Disability Scale), independent of proviral load. In addition, a poor prednisolone response was significantly correlated with higher post-treatment IFN-γ levels. Likewise, a transcriptomic IFN signaling score, significantly correlated with previously proposed HAM/TSP biomarkers (CASP5/CXCL10/FCGR1A/STAT1), was efficiently blunted by in vitro prednisolone treatment of PBMC from PLHTLV-1 and incident HAM/TSP. CONCLUSIONS: An age-related increase in systemic IL-6/GlycA levels reveals inflammaging in PLHTLV-1, in the absence of neurological disease. IFN-γ and IL-17A are biomarkers of untreated HAM/TSP, while pre-treatment GlycA and TNF predict therapeutic response to prednisolone pulse therapy, paving the way for a precision medicine approach in HAM/TSP.


Subject(s)
HTLV-I Infections , Motor Disorders , Neuroinflammatory Diseases , Female , Humans , Bayes Theorem , Cytokines , Human T-lymphotropic virus 1 , Interleukin-17 , Interleukin-6 , Leukocytes, Mononuclear , Motor Disorders/virology , Neuroinflammatory Diseases/virology , HTLV-I Infections/complications
14.
Bioorg Chem ; 127: 106032, 2022 10.
Article in English | MEDLINE | ID: mdl-35872398

ABSTRACT

Imidazo[4,5-b]pyridine derived acrylonitriles were synthesized and explored for their in vitro antiproliferative effect on a diverse human cancer cell line panel. Three compounds, 20, 21 and 33, showed strong activity in the submicromolar range (IC50 0.2-0.6 µM), and were chosen for further biological experiments. Immunofluorescence staining and tubulin polymerization assays confirmed tubulin as the main target, but excluded its colchicine-binding site as a potential interacting unit. This was supported by the computational analysis, which revealed that the most potent ligands act on the extended colchicine site on the surface between interacting tubulin subunits, where they interfere with their polymerization and reveal pronounced antitumor properties. In addition, lead molecule 21 potently inhibited cancer cell migration, while it did not affect the viability of normal cells even at the highest concentration tested (100 µM).


Subject(s)
Antineoplastic Agents , Neoplasms , Antineoplastic Agents/chemistry , Cell Line, Tumor , Cell Proliferation , Colchicine/pharmacology , Drug Screening Assays, Antitumor , Humans , Molecular Structure , Polymerization , Pyridines/chemistry , Structure-Activity Relationship , Tubulin/metabolism , Tubulin Modulators
15.
Nature ; 538(7623): 114-117, 2016 Oct 06.
Article in English | MEDLINE | ID: mdl-27680702

ABSTRACT

The common participation of oncogenic KRAS proteins in many of the most lethal human cancers, together with the ease of detecting somatic KRAS mutant alleles in patient samples, has spurred persistent and intensive efforts to develop drugs that inhibit KRAS activity. However, advances have been hindered by the pervasive inter- and intra-lineage diversity in the targetable mechanisms that underlie KRAS-driven cancers, limited pharmacological accessibility of many candidate synthetic-lethal interactions and the swift emergence of unanticipated resistance mechanisms to otherwise effective targeted therapies. Here we demonstrate the acute and specific cell-autonomous addiction of KRAS-mutant non-small-cell lung cancer cells to receptor-dependent nuclear export. A multi-genomic, data-driven approach, utilizing 106 human non-small-cell lung cancer cell lines, was used to interrogate 4,725 biological processes with 39,760 short interfering RNA pools for those selectively required for the survival of KRAS-mutant cells that harbour a broad spectrum of phenotypic variation. Nuclear transport machinery was the sole process-level discriminator of statistical significance. Chemical perturbation of the nuclear export receptor XPO1 (also known as CRM1), with a clinically available drug, revealed a robust synthetic-lethal interaction with native or engineered oncogenic KRAS both in vitro and in vivo. The primary mechanism underpinning XPO1 inhibitor sensitivity was intolerance to the accumulation of nuclear IκBα (also known as NFKBIA), with consequent inhibition of NFκB transcription factor activity. Intrinsic resistance associated with concurrent FSTL5 mutations was detected and determined to be a consequence of YAP1 activation via a previously unappreciated FSTL5-Hippo pathway regulatory axis. This occurs in approximately 17% of KRAS-mutant lung cancers, and can be overcome with the co-administration of a YAP1-TEAD inhibitor. These findings indicate that clinically available XPO1 inhibitors are a promising therapeutic strategy for a considerable cohort of patients with lung cancer when coupled to genomics-guided patient selection and observation.


Subject(s)
Active Transport, Cell Nucleus/drug effects , Cell Nucleus/metabolism , Karyopherins/antagonists & inhibitors , Karyopherins/metabolism , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Proto-Oncogene Proteins p21(ras)/genetics , Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors , Receptors, Cytoplasmic and Nuclear/metabolism , Adaptor Proteins, Signal Transducing/antagonists & inhibitors , Adaptor Proteins, Signal Transducing/metabolism , Animals , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/metabolism , Carcinoma, Non-Small-Cell Lung/pathology , Cell Line, Tumor , Cell Nucleus/drug effects , Cell Proliferation/drug effects , Cell Survival/drug effects , Cell Survival/genetics , DNA-Binding Proteins/antagonists & inhibitors , DNA-Binding Proteins/metabolism , Female , Follistatin-Related Proteins/genetics , Genes, Lethal/genetics , Hippo Signaling Pathway , Humans , Lung Neoplasms/drug therapy , Lung Neoplasms/pathology , Mice , Mutation , NF-KappaB Inhibitor alpha/metabolism , NF-kappa B/antagonists & inhibitors , NF-kappa B/metabolism , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/metabolism , Phosphoproteins/antagonists & inhibitors , Phosphoproteins/metabolism , Porphyrins/pharmacology , Protein Serine-Threonine Kinases/metabolism , RNA Interference , RNA, Small Interfering , Signal Transduction , TEA Domain Transcription Factors , Transcription Factors/antagonists & inhibitors , Transcription Factors/metabolism , Verteporfin , Xenograft Model Antitumor Assays , YAP-Signaling Proteins , Exportin 1 Protein
16.
Mol Ther ; 29(1): 208-224, 2021 01 06.
Article in English | MEDLINE | ID: mdl-33002419

ABSTRACT

While drug resistance mutations provide the gold standard proof for drug target engagement, target deconvolution of inhibitors identified from a phenotypic screen remains challenging. Genetic screening for functional in-frame drug resistance mutations by tiling CRISPR-Cas nucleases across protein coding sequences is a method for identifying a drug's target and binding site. However, the applicability of this approach is constrained by the availability of nuclease target sites across genetic regions that mediate drug resistance upon mutation. In this study, we show that an enhanced AsCas12a variant (enAsCas12a), which harbors an expanded targeting range, facilitates screening for drug resistance mutations with increased activity and resolution in regions that are not accessible to other CRISPR nucleases, including the prototypical SpCas9. Utilizing enAsCas12a, we uncover new drug resistance mutations against inhibitors of NAMPT and KIF11. These findings demonstrate that enAsCas12a is a promising new addition to the CRISPR screening toolbox and allows targeting sites not readily accessible to SpCas9.


Subject(s)
CRISPR-Cas Systems , Clustered Regularly Interspaced Short Palindromic Repeats , Drug Resistance/genetics , Endonucleases/metabolism , Genetic Testing/methods , Mutation , Binding Sites , Protein Binding
17.
Mol Divers ; 26(5): 2595-2612, 2022 Oct.
Article in English | MEDLINE | ID: mdl-34997441

ABSTRACT

In the present study, we report the design and synthesis of novel amide-type hybrid molecules based on anthranilic acid and quinoline or ß-carboline heterocyclic scaffolds. Three types of biological screenings were performed: (i) in vitro antiproliferative screening against a panel of solid tumor and leukemia cell lines, (ii) antiviral screening against several RNA viruses, and (iii) anti-quorum sensing screening using gram-negative Chromobacterium violaceum as the reporter strain. Antiproliferative screening revealed a high activity of several compounds. Anthranilamides 12 and 13 with chloroquine core and halogenated anthranilic acid were the most active agents toward diverse cancer cell lines such as glioblastoma, pancreatic adenocarcinoma, colorectal carcinoma, lung carcinoma, acute lymphoblastic, acute myeloid, chronic myeloid leukemia, and non-Hodgkin lymphoma, but also against noncancerous cell lines. Boc-protected analogs 2 and 3 showed moderate activities against the tested cancer cells without toxic effects against noncancerous cells. A nonhalogenated quinoline derivative 10 with N-benzylanthranilic acid residue was equally active as 12 and 13 and selective toward tumor cells. Chloroquine and quinoline anthranilamides 10-13 exerted pronounced antiviral effect against human coronaviruses 229E and OC43, whereas 12 and 13 against coronavirus OC43 (EC50 values in low micromolar range; selectivity indices from 4.6 to > 10.4). Anthranilamides 14 and 16 with PQ core inhibited HIV-1 with EC50 values of 9.3 and 14.1 µM, respectively. Compound 13 displayed significant anti-quorum/biofilm effect against the quorum sensing reporter strain (IC50 of 3.7 µM) with no apparent bactericidal effect.


Subject(s)
Adenocarcinoma , Pancreatic Neoplasms , Quinolines , Amides , Anti-Bacterial Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Carbolines/pharmacology , Chloroquine , Humans , Quinolines/chemistry , Quinolines/pharmacology , ortho-Aminobenzoates
18.
Mol Divers ; 26(3): 1357-1371, 2022 Jun.
Article in English | MEDLINE | ID: mdl-34165689

ABSTRACT

A new series of ( ±)-(3-(3,5-dimethyl-1H-pyrazol-1-yl)-6-phenyl-6,7-dihydro-5H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-7-yl)(phenyl)methanones were efficiently synthesized starting from 4-amino-5-hydrazinyl-4H-1,2,4-triazole-3-thiol 1, acetyl acetone 2, various aromatic and heterocyclic aldehydes 3 and phenacyl bromides 4. All the newly synthesized compounds were tested for their antiviral and antitumoral activity. It was shown that subtle structural variations on the phenyl moiety allowed to tune biological properties toward antiviral or antitumoral activity. Mode-of-action studies revealed that the antitumoral activity was due to inhibition of tubulin polymerization.


Subject(s)
Thiadiazines , Antiviral Agents/pharmacology , Thiadiazines/chemistry , Triazoles/chemistry
19.
Int J Mol Sci ; 23(3)2022 Jan 29.
Article in English | MEDLINE | ID: mdl-35163481

ABSTRACT

Several key functions of the androgen receptor (AR) such as hormone recognition and co-regulator recruitment converge in the ligand binding domain (LBD). Loss- or gain-of-function of the AR contributes to pathologies such as the androgen insensitivity syndrome and prostate cancer. Here, we describe a gain-of-function mutation of the surface-exposed threonine at position 850, located at the amino-terminus of Helix 10 (H10) in the AR LBD. Since T850 phosphorylation was reported to affect AR function, we created the phosphomimetic mutation T850D. The AR T850D variant has a 1.5- to 2-fold increased transcriptional activity with no effect on ligand affinity. In the androgen responsive LNCaP cell line grown in medium with low androgen levels, we observed a growth advantage for cells in which the endogenous AR was replaced by AR T850D. Despite the distance to the AF2 site, the AR T850D LBD displayed an increased affinity for coactivator peptides as well as the 23FQNLF27 motif of AR itself. Molecular Dynamics simulations confirm allosteric transmission of the T850D mutation towards the AF2 site via extended hydrogen bond formation between coactivator peptide and AF2 site. This mechanistic study thus confirms the gain-of-function character of T850D and T850 phosphorylation for AR activity and reveals details of the allosteric communications within the LBD.


Subject(s)
Mutation/genetics , Receptors, Androgen/chemistry , Receptors, Androgen/genetics , Cell Line, Tumor , Cell Nucleus/metabolism , Gain of Function Mutation/genetics , Humans , Kinetics , Ligands , Lysine/metabolism , Male , Models, Molecular , Phosphorylation , Protein Binding , Protein Multimerization , Protein Structure, Tertiary , Protein Transport , Ubiquitination
20.
Molecules ; 28(1)2022 Dec 21.
Article in English | MEDLINE | ID: mdl-36615231

ABSTRACT

A series of cyano- and amidino-substituted imidazo[4,5-b]pyridines were synthesized using standard methods of organic synthesis, and their biological activity was evaluated. Biological evaluation included in vitro assessment of antiproliferative effects on a diverse selection of human cancer cell lines, antibacterial activity against chosen Gram-positive and Gram-negative bacterial strains, and antiviral activity on a broad panel of DNA and RNA viruses. The most pronounced antiproliferative activity was observed for compound 10, which contained an unsubstituted amidino group, and compound 14, which contained a 2-imidazolinyl amidino group; both displayed selective and strong activity in sub-micromolar inhibitory concentration range against colon carcinoma (IC50 0.4 and 0.7 µM, respectively). All tested compounds lacked antibacterial activity, with the exception of compound 14, which showed moderate activity against E. coli (MIC 32 µM). Bromo-substituted derivative 7, which contained an unsubstituted phenyl ring (EC50 21 µM), and para-cyano-substituted derivative 17 (EC50 58 µM) showed selective but moderate activity against respiratory syncytial virus (RSV).


Subject(s)
Antineoplastic Agents , Pyridines , Humans , Cell Line, Tumor , Pyridines/pharmacology , Escherichia coli , Antineoplastic Agents/pharmacology , Anti-Bacterial Agents/pharmacology , Structure-Activity Relationship , Cell Proliferation
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