Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.

Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. PUM is a highly promising lead for antibacterial therapy.

CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses.

Myocardin-related transcription factors (MRTFs) are coactivators of serum response factor (SRF), and thereby regulate cytoskeletal gene expression in response to actin dynamics. MRTFs have also been implicated in transcription of heat shock protein (HSP)-encoding genes in fly ovaries, but the mechanisms remain unclear. Here, we demonstrate that, in mammalian cells, MRTFs are dispensable for gene induction of HSP-encoding genes. However, the widely used small-molecule inhibitors of the MRTF-SRF transcription pathway, derived from CCG-1423, also efficiently inhibit gene transcription of HSP-encoding genes in both fly and mammalian cells in the absence of MRTFs. Quantifying RNA synthesis and RNA polymerase distribution demonstrates that CCG-1423-derived compounds have a genome-wide effect on transcription. Indeed, tracking nascent transcription at nucleotide resolution reveals that CCG-1423-derived compounds reduce RNA polymerase II elongation, and severely dampen the transcriptional response to heat shock. The effects of CCG-1423-derived compounds therefore extend beyond the MRTF-SRF pathway into nascent transcription, opening novel opportunities for their use in transcription research.

A small-molecule allele-selective transcriptional inhibitor of the MIF immune susceptibility locus.

Functional variants of the gene for the cytokine macrophage migration inhibitory factor (MIF) are defined by a 4-nucleotide promoter microsatellite (-794 CATT5-8, rs5844572) and confer risk for autoimmune, infectious, and oncologic diseases. We describe herein the discovery of a prototypic, small molecule inhibitor of MIF transcription with selectivity for high microsatellite repeat number and correspondingly high gene expression. Utilizing a high-throughput luminescent proximity screen, we identify 1-carbomethoxy-5-formyl-4,6,8-trihydroxyphenazine (CMFT) to inhibit the functional interaction between the transcription factor ICBP90 (namely, UHRF1) and the MIF -794 CATT5-8 promoter microsatellite. CMFT inhibits MIF mRNA expression in a -794 CATT5-8 length-dependent manner with an IC50 of 470 nM, and preferentially reduces ICBP90-dependent MIF mRNA and protein expression in high-genotypic versus low-genotypic MIF-expressing macrophages. RNA expression analysis also showed CMFT to downregulate MIF-dependent, inflammatory gene expression with little evidence of off-target metabolic toxicity. These findings provide proof-of-concept for advancing the pharmacogenomic development of precision-based MIF inhibitors for diverse autoimmune and inflammatory conditions.

The therapeutic potential of RNA Polymerase I transcription inhibitor, CX-5461, in uterine leiomyosarcoma.

BACKGROUND: Uterine leiomyosarcoma is a rare aggressive smooth muscle cancer with poor survival rates. RNA Polymerase I (Pol I) activity is elevated in many cancers supporting tumour growth and prior studies in uterine leiomyosarcoma revealed enlarged nucleoli and upregulated Pol I activity-related genes. This study aimed to investigate the anti-tumour potential of CX-5461, a Pol I transcription inhibitor currently being evaluated in clinical trials for several cancers, against the human uterine leiomyosarcoma cell line, SK-UT-1. METHODS: SK-UT-1 was characterised using genome profiling and western blotting. The anti-tumour effects of CX-5461 were investigated using cell proliferation assays, expression analysis using qRT-PCR, and BrdU/PI based cell cycle analysis. RESULTS: Genetic analysis of SK-UT-1 revealed mutations in TP53, RB1, PTEN, APC and TSC1 & 2, all potentially associated with increased Pol I activity. Protein expression analysis showed dysregulated p53, RB1 and c-Myc. CX-5461 treatment resulted in an anti-proliferation response, G2 phase cell-cycle arrest and on-target activity demonstrated by reduced ribosomal DNA transcription. CONCLUSIONS: SK-UT-1 was confirmed as a representative model of uterine leiomyosarcoma and CX-5461 has significant potential as a novel adjuvant for this rare cancer.

Transcription inhibitors prevent amnesia induced by NMDA antagonist-mediated impairment of memory reconsolidation.

Recent studies report that long-term memory retrieval can induce memory reconsolidation, and impairment of this reconsolidation might lead to amnesia. Previously, we found that reconsolidation of a conditioned food aversion memory could be disrupted by translation inhibitors for up to 3 h following a reconsolidation event, thus inducing amnesia. We examined the role of transcription processes in the induction of amnesia in the land snail, Helix lucorum. It received N-methyl-D-aspartate (NMDA) glutamate receptor antagonist and transcription inhibitor 2 days after learning in a neutral context environment; it was then transferred to the learning context followed by reminder with conditioned food stimulus. NMDA receptor blockade, followed by a reminder session, impaired reconsolidation of an aversive memory. Simultaneous administration of an NMDA receptor antagonist and a transcription inhibitor prior to reminder of an aversive event prevented amnesia induction. In contrast, when a transcription inhibitor alone was injected prior to a reminder session, the blockade had no effect on memory. We found that transcription inhibition 0-6 h after amnesia induction suppressed memory loss, but this suppression was lost when inhibitors were administered 9 h after amnesia. Thus, amnesia is likely dependent on transcription processes within a 9-h time window. We can hypothesize that amnesia induction initiates synthesis of specific mRNAs and proteins; furthermore, these events occur within specific time-dependent windows. Our findings could prove useful for the analysis of amnesia formation and for the development of possible ways to prevent memory loss associated with various diseases and injuries in animals and humans.

TRIM28 in cancer and cancer therapy.

TRIM28 (tripartite motif protein 28) was initially believed to be a transcription inhibitor that plays an important role in DNA damage repair (DDR) and in maintaining cancer cellular stemness. As research has continued to deepen, several studies have found that TRIM28 not only has ubiquitin E3 ligase activity to promote degradation of substrates, but also can promote SUMOylation of substrates. Although TRIM28 is highly expressed in various cancer tissues and has oncogenic effects, there are still a few studies indicating that TRIM28 has certain anticancer effects. Additionally, TRIM28 is subject to complex upstream regulation. In this review, we have elaborated on the structure and regulation of TRIM28. At the same time, highlighting the functional role of TRIM28 in tumor development and emphasizing its impact on cancer treatment provides a new direction for future clinical antitumor treatment.

Highly specific aptamer trap for extremophilic RNA polymerases.

During transcription initiation, the holoenzyme of bacterial RNA polymerase (RNAP) specifically recognizes promoters using a dedicated σ factor. During transcription elongation, the core enzyme of RNAP interacts with nucleic acids mainly nonspecifically, by stably locking the DNA template and RNA transcript inside the main cleft. Here, we present a synthetic DNA aptamer that is specifically recognized by both core and holoenzyme RNAPs from extremophilic bacteria of the Deinococcus-Thermus phylum. The aptamer binds RNAP with subnanomolar affinities, forming extremely stable complexes even at high ionic strength conditions, blocks RNAP interactions with the DNA template and inhibits RNAP activity during transcription elongation. We propose that the aptamer binds at a conserved site within the downstream DNA-binding cleft of RNAP and traps it in an inactive conformation. The aptamer can potentially be used for structural studies to reveal RNAP conformational states, affinity binding of RNAP and associated factors, and screening of transcriptional inhibitors.

RsOBP2a, a member of OBF BINDING PROTEIN transcription factors, inhibits two chlorophyll degradation genes in green radish.

The green radish (Raphanus sativus L.) contains abundant chlorophyll (Chl). DOF-type transcription factor OBF BINDING PROTEIN (OBP) plays crucial functions in plant growth, development, maturation and responses to various abiotic stresses. However, the metabolism by which OBP transcription factors regulate light-induced Chl metabolism in green radish is not well understood. In this study, six OBP genes were identified from the radish genome, distributed unevenly across five chromosomes. Among these genes, RsOBP2a showed significantly higher expression in the green flesh compared to the white flesh of green radish. Analysis of promoter elements suggested that RsOBPs might be involved in stress responses, particularly in light-related processes. Overexpression of RsOBP2a led to increase Chl levels in cotyledons and adventitious roots of radish, while silencing RsOBP2a expression through TYMV-induced gene silencing accelerated leaf senescence. Further investigations revealed that RsOBP2a was localized in the nucleus and served as a transcriptional repressor. RsOBP2a was induced by light and directly suppressed the expression of STAYGREEN (SGR) and RED CHLOROPHYLL CATABOLITE REDUCTASE (RCCR), thereby delaying senescence in radish. Overall, a novel regulatory model involving RsOBP2a, RsSGR, and RsRCCR was proposed to govern Chl metabolism in response to light, offering insights for the enhancement of green radish germplasm.

The Use of Lurbinectedin for the Treatment of Small Cell and Neuroendocrine Carcinoma of the Prostate.

INTRODUCTION: Lurbinectedin is FDA approved for treatment of metastatic small cell lung cancer (SCLC) following progression on or after platinum-based chemotherapy. Prostatic small cell or neuroendocrine carcinoma (SC/NEPC) behaves like SCLC; however, no safety or efficacy data for lurbinectedin in SC/NEPC exists. PATIENTS AND METHODS: All SC/NEPC patients treated with lurbinectedin across 4 academic oncology centers were identified. Baseline patient data and lurbinectedin outcomes including radiographic responses (complete response [CR], partial response [PR], stable disease [SD], progressive disease [PD]), progression free survival (PFS), overall survival (OS), and treatment-related adverse events (trAEs) were described. Clinical benefit rate (CBR) included CR, PR, or SD on imaging. Descriptive statistics were performed. RESULTS: At first lurbinectedin dose, all 18 patients had metastatic disease. Median age was 63.5 (Range: 53-84), number of prior systemic therapies was 4 (Range: 2-7), and lurbinectedin cycles completed was 5 (Range: 1-10). ADT was administered during lurbinectedin treatment in 9/18 patients. CBR was 9/16 (56%). The most common trAEs were fatigue and anemia. Median OS and PFS were 6.01 (0.23-16.69) and 3.35 (0.16-7.79) months. CONCLUSIONS: Lurbinectedin showed modest but significant clinical benefit in some patients with SC/NEPC and demonstrated an acceptable toxicity profile with no hospitalizations from trAEs. SC/NEPC is an aggressive disease with a poor prognosis for which more treatment options are needed. Evidence for subsequent treatments after platinum-based chemotherapy is lacking. Lurbinectedin is an active treatment option for SC/NEPC; however, larger confirmatory studies are needed.

JAK out of the Box; The Rationale behind Janus Kinase Inhibitors in the COVID-19 setting, and their potential in obese and diabetic populations.

The adaptive use of Janus kinase (JAK)-inhibitors has been suggested by rheumatology experts in the management of COVID-19. We recount the rationale behind their use in this setting, and the current evidence for and against their use in this review. JAK-inhibitors role in COVID-19 infection appears to be multifaceted, including preventing viral endocytosis and dampening the effect of excessive chemokines. This drug class may be able to achieve these effects at already preapproved dosages. Concerns arise regarding reactivation of latent viral infections and the feasibility of their use in those with severe disease. Most interestingly, JAK-Inhibitors may also have an additional advantage for diabetic and obese populations, where the dysregulation of JAK-signal transducer and activator of transcription pathway may be responsible for their increased risk of poor outcomes. Targeting this pathway may provide a therapeutic advantage for these patient groups.

Lurbinectedin: an FDA-approved inducer of immunogenic cell death for the treatment of small-cell lung cancer.

Lurbinectedin is a DNA-binding inhibitor of transcription that potently induces immunogenic cell death (ICD). In June 2020, the Federal Drug Administration (FDA) approved lurbinectedin for the salvage treatment of small-cell lung cancer that has relapsed from platinum compound-based first-line chemotherapy. Thus, the clinical activity of lurbinectedin may originate, at least in part, from the induction of ICD.

Kinase inhibitors tyrphostin 9 and rottlerin block early steps of rabies virus cycle.

Rabies virus (RABV) is a neurotropic virus that causes fatal encephalitis in humans and animals and still kills up to 59,000 people worldwide every year. To date, only preventive or post-exposure vaccination protects against the disease but therapeutics are missing. After screening a library of 80 kinases inhibitors, we identified two compounds as potent inhibitors of RABV infection: tyrphostin 9 and rottlerin. Mechanism of action studies show that both inhibitors interfere with an early step of viral cycle and can prevent viral replication. In presence of tyrphostin 9, the viral entry through endocytosis is disturbed leading to improper delivery of viral particles in cytoplasm, whereas rottlerin is inhibiting the transcription, most likely by decreasing intracellular ATP concentration, and therefore the replication of the viral genome.

Selective inhibition of HIV-1 replication by the CDK9 inhibitor FIT-039.

FIT-039 has recently been identified as a novel cyclin-dependent kinase 9 inhibitor with potent antiviral activity against a broad spectrum of DNA viruses, such as herpes simplex virus type 1 (HSV-1) and human cytomegaloviruses. In this study, FIT-039 was examined for its inhibitory effect on human immunodeficiency virus type 1 (HIV-1) replication in chronically infected cells. Its 50% effective concentration was 1.4-2.1µM, irrespective of the cells used for antiviral assays, while its 50% cytotoxic concentration was >20µM, indicating that FIT-039 is a selective inhibitor of HIV-1 replication. FIT-039 also inhibited HIV-1 RNA expression in a dose-dependent fashion. Since previous studies demonstrated that FIT-039 exhibited antiviral efficacy without noticeable adverse effects in HSV-1-infected mice, the compound should be further investigated for its clinical potential against HIV-1 infection.

Identification and characterization of a novel FstK-like protein from spotted knifejaw iridovirus (genus Megalocytivirus).

Prokaryotes contain many DNA binding proteins with large molecular weights and multiple domains. DNA binding proteins are involved in DNA replication, transcription, and other physiological processes. In this study, a DNA binding protein, containing an Ftsk-like protein (FLP) domain, was cloned and characterized from SKIV-ZJ07, a member of the RSIV-type megalocytivirus, using bioinformatics and molecular biology approaches. SKIV-FLP is 3,762 base pairs long, encodes a viral protein of 1253 amino acid residuals, and contains an Ftsk (or EBV-NA3) and a Grx-2 domain. Virion localization indicated that SKIV-FLP is a major viral structural protein located below the major capsid protein. Laser confocal microscopy showed that SKIV-FLP is a cytoplasm-/nuclear-localized protein. However, the reconstruction experiments demonstrated that SKIV-FLP may contain three nuclear localization signals, each present in FLP-NT (1-380 aa), FtsK domain (380-880 aa), and Grx-2 domain (880-1253 aa). When SKIV-FLP was fused to the Gal-4 DNA-binding domain and co-transfected with L8G5-Luc, SKIV-FLP suppressed L8G5-Luc transcription. As a transcription inhibitor, SKIV-FLP also inhibited the transcription of NF-κB and IFN-γ (a type II IFN) promoter in HEK293T cells, suggesting that SKIV-FLP has a role in evading host immunity.