Search

Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic. A multitude of antivirals targeting SARS-CoV-2 have been successfully developed and shown to have clinical benefit in treating COVID-19. However, it has been observed that the virus can escape nearly all of these drugs. Iketani et al. review our current understanding of these resistance mechanisms. [ABSTRACT FROM AUTHOR]

Filamentation is an important virulence factor of the pathogenic fungus Candida albicans. The abolition of Candida albicans hyphal formation by disrupting sterol synthesis is an important concept for the development of antifungal drugs with high safety. Here, we conduct a high-throughput screen using a C. albicans strain expressing green fluorescent protein-labeled Dpp3 to identify anti-hypha agents by interfering with ergosterol synthesis. The antipyrine derivative H55 is characterized to have minimal cytotoxicity and potent inhibition of C. albicans hyphal formation in multiple cultural conditions. H55 monotherapy exhibits therapeutic efficacy in mouse models of azole-resistant candidiasis. H55 treatment increases the accumulation of zymosterol, the substrate of C-24 sterol methyltransferase (Erg6). The results of enzyme assays, photoaffinity labeling, molecular simulation, mutagenesis, and cellular thermal shift assays support H55 as an allosteric inhibitor of Erg6. Collectively, H55, an inhibitor of the fungal-specific enzyme Erg6, holds potential to treat C. albicans infections. [Display omitted] • High-throughput screening for Dpp3 inducers identifies H55, an inhibitor of Erg6 • H55 inhibits adhesion, hyphal growth, and biofilm formation of Candida albicans • H55 exhibits therapeutic efficacy validating Erg6 as a therapeutic target Jin et al. report that the antipyrine derivative H55 is an inhibitor of Erg6 to neutralize the virulence of C. albicans. H55 exhibits therapeutic efficacy in murine candidiasis models and has high biological safety because Erg6 is absent from human cells. [ABSTRACT FROM AUTHOR]

Autotaxin (ATX; ENPP2) produces the lipid mediator lysophosphatidic acid (LPA) that signals through disparate EDG (LPA 1–3) and P2Y (LPA 4–6) G protein-coupled receptors. ATX/LPA promotes several (patho)physiological processes, including in pulmonary fibrosis, thus serving as an attractive drug target. However, it remains unclear if clinical outcome depends on how different types of ATX inhibitors modulate the ATX/LPA signaling axis. Here, we show that the ATX "tunnel" is crucial for conferring key aspects of ATX/LPA signaling and dictates cellular responses independent of ATX catalytic activity, with a preference for activation of P2Y LPA receptors. The efficacy of the ATX/LPA signaling responses are abrogated more efficiently by tunnel-binding inhibitors, such as ziritaxestat (GLPG1690), compared with inhibitors that exclusively target the active site, as shown in primary lung fibroblasts and a murine model of radiation-induced pulmonary fibrosis. Our results uncover a receptor-selective signaling mechanism for ATX, implying clinical benefit for tunnel-targeting ATX inhibitors. [Display omitted] • ATX is a dual-function protein acting as an LPA-producing enzyme and LPA chaperone • Structural integrity of the ATX tunnel is essential to mediate signaling functions • ATX-bound LPA signals preferentially via P2Y-family LPA receptors • Occupancy of the ATX tunnel is crucial for ziritaxestat to exert inhibition in vivo Salgado-Polo et al. report that occupancy of the tunnel of the LPA-producing enzyme ATX regulates signaling outcome, through P2Y-type LPA receptors. Inhibiting this chaperone function of ATX by tunnel-binding inhibitors, such as ziritaxestat, correlates with drug efficacy in a mouse lung fibrosis model. [ABSTRACT FROM AUTHOR]

Axon degeneration is an early pathological event in many neurological diseases. The identification of the nicotinamide adenine dinucleotide (NAD) hydrolase SARM1 as a central metabolic sensor and axon executioner presents an exciting opportunity to develop novel neuroprotective therapies that can prevent or halt the degenerative process, yet limited progress has been made on advancing efficacious inhibitors. We describe a class of NAD-dependent active-site SARM1 inhibitors that function by intercepting NAD hydrolysis and undergoing covalent conjugation with the reaction product adenosine diphosphate ribose (ADPR). The resulting small-molecule ADPR adducts are highly potent and confer compelling neuroprotection in preclinical models of neurological injury and disease, validating this mode of inhibition as a viable therapeutic strategy. Additionally, we show that the most potent inhibitor of CD38, a related NAD hydrolase, also functions by the same mechanism, further underscoring the broader applicability of this mechanism in developing therapies against this class of enzymes. [Display omitted] • Molecular basis of product-assisted inhibition of the pro-degenerative NADase SARM1 • Inhibitor-ADPR adducts are neuroprotective in mouse models of nerve injury/disease • Mechanism has broad applicability to related NADases like CD38 Bratkowski, Burdett, et al. elucidate the molecular basis of NAD-dependent, active-site inhibition of related NAD hydrolases SARM1 and CD38 by compounds that function by forming covalent adducts with a hydrolysis product, ADPR. They show that the SARM1 inhibitors are neuroprotective in preclinical models of nerve injury and disease. [ABSTRACT FROM AUTHOR]

Notch activation complex kinase (NACK) is a component of the Notch transcriptional machinery critical for the Notch-mediated tumorigenesis. However, the mechanism through which NACK regulates Notch-mediated transcription is not well understood. Here, we demonstrate that NACK binds and hydrolyzes ATP and that only ATP-bound NACK can bind to the Notch ternary complex (NTC). Considering this, we sought to identify inhibitors of this ATP-dependent function and, using computational pipelines, discovered the first small-molecule inhibitor of NACK, Z271-0326, that directly blocks the activity of Notch-mediated transcription and shows potent antineoplastic activity in PDX mouse models. In conclusion, we have discovered the first inhibitor that holds promise for the efficacious treatment of Notch-driven cancers by blocking the Notch activity downstream of the NTC., Competing Interests: A.J.C. is a co-founder of StemSynergy Therapeutics, Inc., which has licensed the Z271-0326 scaffold from the University of Miami. All other authors declare no competing interests., (© 2023 The Author(s).)

Muscle atrophy is debilitating and can be induced by several stressors. Unfortunately, there are no effective pharmacological treatment until now. MicroRNA (miR)-29b is an important target that we identified to be commonly involved in multiple types of muscle atrophy. Although sequence-specific inhibition of miR-29b has been developed, in this study, we report a novel small-molecule miR-29b inhibitor that targets miR-29b hairpin precursor (pre-miR-29b) (Targapremir-29b-066 [TGP-29b-066]) considering both its three-dimensional structure and the thermodynamics of interaction between pre-miR-29b and the small molecule. This novel small-molecule inhibitor has been demonstrated to attenuate muscle atrophy induced by angiotensin II (Ang II), dexamethasone (Dex), and tumor necrosis factor α (TNF-α) in C2C12 myotubes, as evidenced by increase in the diameter of myotube and decrease in the expression of Atrogin-1 and MuRF-1. Moreover, it can also attenuate Ang II-induced muscle atrophy in mice, as evidenced by a similar increase in the diameter of myotube, reduced Atrogin-1 and MuRF-1 expression, AKT-FOXO3A-mTOR signaling activation, and decreased apoptosis and autophagy. In summary, we experimentally identified and demonstrated a novel small-molecule inhibitor of miR-29b that could act as a potential therapeutic agent for muscle atrophy., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)

Phosphatase PPM1F is a regulator of cell adhesion by fine-tuning integrin activity and actin cytoskeleton structures. Elevated expression of this enzyme in human tumors is associated with high invasiveness, enhanced metastasis, and poor prognosis. Thus, PPM1F is a target for pharmacological intervention, yet inhibitors of this enzyme are lacking. Here, we use high-throughput screening to identify Lockdown, a reversible and non-competitive PPM1F inhibitor. Lockdown is selective for PPM1F, because this compound does not inhibit other protein phosphatases in vitro and does not induce additional phenotypes in PPM1F knockout cells. Importantly, Lockdown-treated glioblastoma cells fully re-capitulate the phenotype of PPM1F-deficient cells as assessed by increased phosphorylation of PPM1F substrates and corruption of integrin-dependent cellular processes. Ester modification yields LockdownPro with increased membrane permeability and prodrug-like properties. LockdownPro suppresses tissue invasion by PPM1F-overexpressing human cancer cells, validating PPM1F as a therapeutic target and providing an access point to control tumor cell dissemination. [Display omitted] • High-throughput screen identifies Lockdown, an inhibitor of the phosphatase PPM1F • Lockdown acts in a dose-dependent, allosteric manner with high selectivity for PPM1F • Ester-modified Lockdown blocks PPM1F-mediated effects on integrin β1 and PAK in cells • Lockdown inhibits migration of tumor cells validating PPM1F as a therapeutic target The Ser/Thr phosphatase PPM1F regulates integrin-mediated cell adhesion and actin cytoskeleton dynamics. In this study, Grimm et al. identify and optimize a potent and cell-active PPM1F inhibitor, which allows selective blockade of PPM1F activity, thereby suppressing invasive motility of tumor cells in vitro and in vivo. [ABSTRACT FROM AUTHOR]

Deubiquitinating enzymes (DUBs) are a class of isopeptidases that regulate ubiquitin dynamics through catalytic cleavage of ubiquitin from protein substrates and ubiquitin precursors. Despite growing interest in DUB biological function and potential as therapeutic targets, few selective small-molecule inhibitors and no approved drugs currently exist. To identify chemical scaffolds targeting specific DUBs and establish a broader framework for future inhibitor development across the gene family, we performed high-throughput screening of a chemically diverse small-molecule library against eight different DUBs, spanning three well-characterized DUB families. Promising hit compounds were validated in a series of counter-screens and orthogonal assays, as well as further assessed for selectivity across expanded panels of DUBs. Through these efforts, we have identified multiple highly selective DUB inhibitors and developed a roadmap for rapidly identifying and validating selective inhibitors of related enzymes. [Display omitted] • High-throughput screen of ∼50k compound library against 8 deubiquitinases • Identification and validation of selective inhibitors for individual DUBs • Study demonstrates importance of validation experiments as part of hit triage • Generation of robust dataset of compound activities against selected DUBs Deubiquitinases (DUBs) have emerged as therapeutically interesting targets due to their involvement in protein turnover in cells. Varca et al. describe a multi-DUB high-throughput screen and orthogonal validation campaign to identify new tool compounds for elucidating DUB function and provide a roadmap for future DUB inhibitor screens. [ABSTRACT FROM AUTHOR]

Ganciclovir (GCV) is the first-line therapy against human cytomegalovirus (HCMV), a widespread infection that is particularly dangerous for immunodeficient individuals. Closely resembling deoxyguanosine triphosphate, the tri-phosphorylated metabolite of GCV (GCV-TP) is preferentially incorporated by the viral DNA polymerase, thereby terminating chain extension and, eventually, viral replication. However, the treatment outcome of GCV varies greatly among individuals, therefore warranting better understanding of its metabolism. Here we show that NUDT15, a Nudix hydrolase known to metabolize thiopurine triphosphates, can similarly hydrolyze GCV-TP through biochemical studies and co-crystallization of the NUDT15/GCV-TP complex. More critically, GCV efficacy was potentiated in HCMV-infected cells following NUDT15 depletion by RNAi or inhibition by an in-house-developed, nanomolar NUDT15 inhibitor, TH8321, suggesting that pharmacological targeting of NUDT15 is a possible avenue to improve existing anti-HCMV regimens. Collectively, the data further implicate NUDT15 as a broad-spectrum metabolic regulator of nucleoside analog therapeutics, such as thiopurines and GCV. [Display omitted] • NUDT15 hydrolyzes the active metabolites of antiherpes ganciclovir • Depletion of NUDT15 via RNAi potentiates the anti-HCMV efficacy of ganciclovir • Nanomolar NUDT15 inhibitor TH8321 demonstrates submicromolar cellular activity • Application of TH8321 potentiates the anti-HCMV efficacy of ganciclovir Zhang et al. show that the hydrolyase NUDT15 dephosphorylates the active metabolite of antiherpes ganciclovir and thereby limits its efficacy. NUDT15 inhibition via an in-house-developed nanomolar inhibitor TH8321 significantly potentiates ganciclovir, recapitulating NUDT15 depletion. Overall, this suggests that targeting NUDT15 is a potential avenue to improve the current antiherpes therapy. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has been disastrous to society and effective drugs are urgently needed. The papain-like protease domain (PLpro) of SARS-CoV-2 (SCoV2) is indispensable for viral replication and represents a putative target for pharmacological intervention. In this work, we describe the development of a potent and selective SCoV2 PLpro inhibitor, 19. The inhibitor not only effectively blocks substrate cleavage and immunosuppressive function imparted by PLpro, but also markedly mitigates SCoV2 replication in human cells, with a submicromolar IC 50. We further present a convenient and sensitive activity probe, 7 , and complementary assays to readily evaluate SCoV2 PLpro inhibitors in vitro or in cells. In addition, we disclose the co-crystal structure of SCoV2 PLpro in complex with a prototype inhibitor, which illuminates their detailed binding mode. Overall, these findings provide promising leads and important tools for drug discovery aiming to target SCoV2 PLpro. [Display omitted] • Development of a sensitive and affordable PLpro activity probe • Identification of potential SCoV2 PLpro inhibitors through HTS • Co-crystal structure determination and lead optimization • Characterization of a submicromolar inhibitor of SCoV2 PLpro represents a putative druggable target for SCoV2. Utilizing multiple approaches, including fluorogenic activity probes, HTS, co-crystallization, structure-based design, and other optimized cellular assays, Shan et al. successfully develop a potent and selective inhibitor of SCoV2 PLpro. [ABSTRACT FROM AUTHOR]

PARP7 is a monoPARP that catalyzes the transfer of single units of ADP-ribose onto substrates to change their function. Here, we identify PARP7 as a negative regulator of nucleic acid sensing in tumor cells. Inhibition of PARP7 restores type I interferon (IFN) signaling responses to nucleic acids in tumor models. Restored signaling can directly inhibit cell proliferation and activate the immune system, both of which contribute to tumor regression. Oral dosing of the PARP7 small-molecule inhibitor, RBN-2397, results in complete tumor regression in a lung cancer xenograft and induces tumor-specific adaptive immune memory in an immunocompetent mouse cancer model, dependent on inducing type I IFN signaling in tumor cells. PARP7 is a therapeutic target whose inhibition induces both cancer cell-autonomous and immune stimulatory effects via enhanced IFN signaling. These data support the targeting of a monoPARP in cancer and introduce a potent and selective PARP7 inhibitor to enter clinical development., Competing Interests: Declaration of interests J.M.G., M.M.V., R.P.A., K.K., K.G.K.-B., B.G., A.Z.L., J.R. Molina, E.M., K.K.S., T.J.W., D.J.B., C.R.M., Y.R., M.N., Z.A.V., S.P.N., E.B., J.-R. Mo, W.D.C., A.S.A.M., J.S., L.U., K.W.K., V.M.R., and H.K. are all employees and shareholders of Ribon Therapeutics at the time of data collection. P.E.R. served as a consultant to Ribon Therapeutics, and T.J.M. is a founder and shareholder in Ribon Therapeutics. M.M.V., K.K.S., and K.W.K. are inventors on US Patent Nos. 10550105, 10870641, and 11014913, which are related to RBN-2397 and assigned to Ribon Therapeutics., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene that compromise its chloride channel activity. Here, we present a therapeutic strategy to ameliorate RNA splicing deficiency of CFTR with a small molecule. The 3,849 + 10 kb C>T is the most common splicing mutation in CF, creating a pseudo exon with premature stop codon. We reveal that the 3,849 + 10 kb C>T-induced CFTR pseudo exon is regulated by phosphorylation of serine/arginine-rich splicing factors, and their functional inhibition by a CDC-like kinase inhibitor restores normal splicing of CFTR. Subsequent screening of our focused chemical library identified CaNDY as a rectifier of the aberrant splicing. CaNDY treatment restored normal splicing of CFTR with the 3,849 + 10 kb C>T in CF patient cells and functional CFTR protein expression in the CF model cells. Our findings open the door for mechanism-based personalized medicine for pseudo-exon-type genetic diseases. • Mechanism of 3,849 + 10 kb C>T-induced CFTR pseudo exon inclusion is unveiled • SRSFs activated by CLK are required for the CFTR pseudo exon recognition • CLK inhibitor CaNDY was identified as a potent suppressor of CFTR pseudo exon • CaNDY treatment rescues defective CFTR channel activity due to 3,849 + 10 kb C>T Shibata et al. propose a mechanism-oriented precision medicine treatment for cystic fibrosis that ameliorates aberrant splicing caused by 3,849 + 10 kb C>T mutation of CFTR. They reveal that CFTR pseudo exon recognition depends on function of CLK and SRSF. Administration of the CLK inhibitor CaNDY restored normal splicing of CFTR and rescued CFTR channel activity. [ABSTRACT FROM AUTHOR]

The CDY (chromodomain on the Y) proteins play an essential role in normal spermatogenesis and brain development. Dysregulation of their expression has been linked to male infertility and various neurological diseases. Like the chromodomains of HP1 and Polycomb, the CDY chromodomains also recognize the lysine-methylated ARKS motif embedded in histone and non-histone proteins. Interestingly, the CDY chromodomains exhibit different binding preferences for the lysine-methylated ARKS motif in different sequence contexts. Here, we present the structural basis for selective binding of CDY1 to H3K9me3 and preferential binding of CDYL2 to H3tK27me3 over H3K27me3. In addition, we use a CDYL1/2-selective compound, UNC4850, to gain further insight into the molecular mechanisms underlying CDYL2 binding specificity. Our work also provides critical implications that CDYL1b's role in the regulation of neural development is dependent on its recognition of the lysine-methylated ARKS motif. • CDY1 is a specific reader of H3K9me3 • CDYL1b and CDYL2 are preferential binders of H3K9me3 and H3tK27me3 over H3K27me3 • UNC4850 is a specific small-molecule inhibitor toward CDYL1/2 CDY (chromodomain on the Y) proteins are able to recognize the lysine-methylated ARKS motif through their chromodomains. Dong et al. elucidate the binding selectivity of the CDY chromodomains using a combination of structural, chemical, and biochemical approaches. [ABSTRACT FROM AUTHOR]

Cyclin-dependent kinase 7 (CDK7) regulates both cell cycle and transcription, but its precise role remains elusive. We previously described THZ1, a CDK7 inhibitor, which dramatically inhibits superenhancer-associated gene expression. However, potent CDK12/13 off-target activity obscured CDK7s contribution to this phenotype. Here, we describe the discovery of a highly selective covalent CDK7 inhibitor. YKL-5-124 causes arrest at the G 1 /S transition and inhibition of E2F-driven gene expression; these effects are rescued by a CDK7 mutant unable to covalently engage YKL-5-124, demonstrating on-target specificity. Unlike THZ1, treatment with YKL-5-124 resulted in no change to RNA polymerase II C-terminal domain phosphorylation; however, inhibition could be reconstituted by combining YKL-5-124 and THZ531, a selective CDK12/13 inhibitor, revealing potential redundancies in CDK control of gene transcription. These findings highlight the importance of CDK7/12/13 polypharmacology for anti-cancer activity of THZ1 and posit that selective inhibition of CDK7 may be useful for treatment of cancers marked by E2F misregulation. • Development of YKL-5-124 a potent, selective and covalent CDK7 inhibitor • Selective CDK7 inhibition results in cell-cycle inhibition rather than apoptosis • YKL-5-124 exhibited little effect on RNA polymerase II phosphorylation status Olson et al. describe the development and characterization of YKL-5-124, a potent, selective, and covalent CDK7 inhibitor. YKL-5-124 displays biochemical and cellular selectivity for CDK7 over CDK12/13, structurally related kinases. CDK7 inhibition by YKL-5-124 induces a strong cell-cycle arrest and a surprisingly weak effect on RNA Pol II phosphorylation. [ABSTRACT FROM AUTHOR]

The precise control of CRISPR-Cas9 activity is required for a number of genome engineering technologies. Here, we report a generalizable platform that provided the first synthetic small-molecule inhibitors of Streptococcus pyogenes Cas9 (SpCas9) that weigh <500 Da and are cell permeable, reversible, and stable under physiological conditions. We developed a suite of high-throughput assays for SpCas9 functions, including a primary screening assay for SpCas9 binding to the protospacer adjacent motif, and used these assays to screen a structurally diverse collection of natural-product-like small molecules to ultimately identify compounds that disrupt the SpCas9-DNA interaction. Using these synthetic anti-CRISPR small molecules, we demonstrated dose and temporal control of SpCas9 and catalytically impaired SpCas9 technologies, including transcription activation, and identified a pharmacophore for SpCas9 inhibition using structure-activity relationships. These studies establish a platform for rapidly identifying synthetic, miniature, cell-permeable, and reversible inhibitors against both SpCas9 and next-generation CRISPR-associated nucleases., (Published by Elsevier Inc.)

Cancer cells can avoid and suppress immune responses through activation of inhibitory immune checkpoint proteins, such as PD-1, PD-L1, and CTLA-4. Blocking the activities of these proteins with monoclonal antibodies, and thus restoring T cell function, has delivered breakthrough therapies against cancer. In this review, we describe the latest work on structural characterization of the checkpoint proteins, their interactions with cognate ligands and with therapeutic antibodies. Structures of the extracellular portions of these proteins reveal that they all have a similar modular structure, composed of small domains similar in topology to the domains found in antibodies. Structural basis for blocking the PD-1/PD-L1 interaction by small molecules is illustrated with the compound BMS-202 that binds to and induces dimerization of PD-L1., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The androgen receptor (AR) is critical for the progression of prostate cancer to a castration-resistant (CRPC) state. AR antagonists are ineffective due to their inability to repress the expression of AR or its splice variant, AR-V7. Here, we report that the tyrosine kinase ACK1 (TNK2) phosphorylates histone H4 at tyrosine 88 upstream of the AR transcription start site. The WDR5/MLL2 complex reads the H4-Y88-phosphorylation marks and deposits the transcriptionally activating H3K4-trimethyl marks promoting AR transcription. Reversal of the pY88-H4 epigenetic marks by the ACK1 inhibitor (R)-9bMS-sensitized naive and enzalutamide-resistant prostate cancer cells and reduced AR and AR-V7 levels to mitigate CRPC tumor growth. Thus, a feedforward ACK1/pY88-H4/WDR5/MLL2/AR epigenetic circuit drives CRPC and is necessary for maintenance of the malignant state., (Copyright © 2017 Elsevier Inc. All rights reserved.)

Oncogenic Ras plays a key role in cancer initiation but also contributes to malignant phenotypes by stimulating nutrient uptake and promoting invasive migration. Because these latter cellular responses require Rac-mediated remodeling of the actin cytoskeleton, we hypothesized that molecules involved in Rac activation may be valuable targets for cancer therapy. We report that genetic inactivation of the Rac-specific guanine nucleotide exchange factor DOCK1 ablates both macropinocytosis-dependent nutrient uptake and cellular invasion in Ras-transformed cells. By screening chemical libraries, we have identified 1-(2-(3'-(trifluoromethyl)-[1,1'-biphenyl]-4-yl)-2-oxoethyl)-5-pyrrolidinylsulfonyl-2(1H)-pyridone (TBOPP) as a selective inhibitor of DOCK1. TBOPP dampened DOCK1-mediated invasion, macropinocytosis, and survival under the condition of glutamine deprivation without impairing the biological functions of the closely related DOCK2 and DOCK5 proteins. Furthermore, TBOPP treatment suppressed cancer metastasis and growth in vivo in mice. Our results demonstrate that selective pharmacological inhibition of DOCK1 could be a therapeutic approach to target cancer cell survival and invasion., (Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.)