Discovery, Optimization, and Evaluation of Non-Nucleoside SARS-CoV-2 NSP14 Inhibitors

Journal of Medicinal Chemistry · 2025-09-05 · 1 citations

We recently reported the discovery of TDI-015051, a first-in-class small-molecule inhibitor of the SARS-CoV-2 guanine-N7 methyltransferase nonstructural protein 14 (NSP14). NSP14 plays a critical role in viral RNA cap synthesis and its inhibition represents a novel antiviral approach. Utilizing systematic structure-activity relationship studies, potent non-nucleoside-based inhibitors with single-digit nanomolar cellular activity were identified from an HTS hit lacking cellular activity. Thermal shift assay data and available crystal structures led us to develop a model of the novel inhibitory ternary complex (NSP14, SAH, inhibitor), which was validated with a crystal structure of the complex. The advances described here enabled a successful proof-of-concept study that validated SARS-CoV-2 NSP14 as a novel drug target for COVID-19 and represent the first demonstration of pharmacological inhibition of viral methyltransferases as a viable avenue for an antiviral therapeutic.

Editor’s Note: Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia

Cancer Discovery · 2025-06-03

Discovery of Novel Isofunctional SARS-CoV-2 NSP14 RNA Cap Methyltransferase Inhibitors by Structure-Based Virtual Screening

ACS Medicinal Chemistry Letters · 2025-08-15

In early 2020, SARS-CoV-2 spread into a worldwide pandemic, causing more than 7 million deaths. Direct-acting antivirals (DAAs) complementing vaccines and mitigating severe disease in at-risk populations remain important. Here, we used a structure-based virtual screening (SBVS) workflow to identify new SAH-dependent inhibitors of the SARS-CoV-2 RNA cap methyltransferase NSP14. We virtually screened the Enamine and Sigma in-stock screening collections as well as the 3 orders of magnitude larger Enamine REAL make-on-demand compound library, which produced better docking scores and higher virtual hit rates. While biochemical testing of 145 in-stock library compounds yielded a single NSP14-specific inhibitor, 123 chemically synthesized Enamine REAL SBVS compounds contained 10 hits specifically inhibiting NSP14 with half-maximal inhibitory concentrations (IC50) below 10 μM. The new compounds were chemically distinct in atomic composition from any NSP14 inhibitors previously identified by conventional biochemical high-throughput screening (HTS) and may serve as starting points to develop novel SARS-CoV-2 DAAs.

Addition to “Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation”

Journal of Chemical Information and Modeling · 2024-01-23

ADVERTISEMENT RETURN TO ISSUEPREVAdditions and Correc...Additions and CorrectionsNEXTORIGINAL ARTICLEThis notice is a correctionAddition to "Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation"Shan SunShan SunMore by Shan Sun, Makoto FushimiMakoto FushimiMore by Makoto Fushimi, Thomas RossettiThomas RossettiMore by Thomas Rossettihttps://orcid.org/0000-0003-3457-5390, Navpreet KaurNavpreet KaurMore by Navpreet Kaur, Jacob FerreiraJacob FerreiraMore by Jacob Ferreira, Michael MillerMichael MillerMore by Michael Miller, Jonathan QuastJonathan QuastMore by Jonathan Quast, Joop van den HeuvelJoop van den HeuvelMore by Joop van den Heuvel, Clemens SteegbornClemens SteegbornMore by Clemens Steegbornhttps://orcid.org/0000-0002-0913-1467, Lonny R. LevinLonny R. LevinMore by Lonny R. Levinhttps://orcid.org/0000-0002-5204-6356, Jochen BuckJochen BuckMore by Jochen Buck, Robert W. MyersRobert W. MyersMore by Robert W. Myershttps://orcid.org/0000-0003-2599-1050, Stacia KargmanStacia KargmanMore by Stacia Kargman, Nigel LivertonNigel LivertonMore by Nigel Liverton, Peter T. MeinkePeter T. MeinkeMore by Peter T. Meinkehttps://orcid.org/0000-0002-7548-6215, and David J. Huggins*David J. HugginsMore by David J. Hugginshttps://orcid.org/0000-0003-1579-2496Cite this: J. Chem. Inf. Model. 2024, 64, 3, 1106Publication Date (Web):January 23, 2024Publication History Received12 January 2024Published online23 January 2024Published inissue 12 February 2024https://doi.org/10.1021/acs.jcim.4c00068Copyright © 2024 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views302Altmetric-Citations-LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (753 KB) Get e-AlertscloseSUBJECTS:Free energy,Inhibitors,Optimization,Small molecules,Software Get e-Alerts

Abstract 1231: First-in-class AR-V7/AR-fl small molecule molecular glue degrader for prostate cancer treatment

Cancer Research · 2024-03-22 · 1 citations

Abstract Metastatic castration resistance prostate cancer (mCRPC) is a lethal disease due to the development of treatment to androgen receptor (AR) signaling inhibitors (ARSi) and taxane chemotherapy. Treatment resistance occurs partly due to the expression of AR splice variants that lack the ligand binding domain (LBD) and are constitutively active in the nucleus. AR-V7 is the most prevalent variant conferring clinical resistance to both ARSi and taxanes. Currently, there is no selective AR-V7 inhibitor leaving patients with limited therapeutic options. Thus, the development of selective AR-V7 inhibitors is a high priority, clinically unmet need. To identify AR-V7 pharmacologic inhibitors, we performed a high throughput small molecule phenotypic screen using enzymatic complementation and nuclear AR-V7 as the assay endpoint. Our primary screen of ~170K compounds (z score = 0.8), followed by a cell-toxicity counter screen and a secondary GFP screen identified hit compound 7907, as a dual AR-V7/AR-fl protein degrader, with unique chemotype compared to all known AR modulators. Hit to lead optimization by medicinal chemistry/SAR studies identified lead compound 15, with increased potency compared to 7907. Mechanistically, we showed that compound 15 shortened AR-V7 protein half-life by activating the ubiquitin-proteasome pathway and inducing proteasomal degradation of both AR-V7/AR-fl, without affecting their transcription. Importantly, compound 15 induced degradation occurred within 3hr of treatment and was blocked by the clinically approved proteasome inhibitor, bortezomib. TurboID proximity ligation assay identified distinct E3 ligases, uniquely interacting with AR-V7 or AR-fl. Using AR-V7/AR-fl deletion mutants we further showed that compound 15 activity is mediated by the N-terminal domain of AR, present in both proteins. Remarkably, compound 15 sensitized LNCaP95 cells (endogenous AR-V7/AR-fl expression) to enzalutamide suggesting potential therapeutic synergism and ability to reverse enzalutamide resistance. Ongoing studies aim to narrow down the binding site of compound 15 as well as identify the E3 ligases mediating its activity. Together, these data support a molecular glue degrader mechanism of action, consistent with published studies showing that molecular glue degraders are ideal for targeting classically “undruggable” proteins lacking an LBD or containing intrinsically disordered domains, as is the case for AR-V7. Currently, all AR-directed therapies target the LBD of AR-fl, inhibiting AR signaling. AR-V7 expression is a direct outcome of this inhibition, leading to AR-fl and AR-V7 co-expression in patient tumors. We posit that our drug candidate, by offering dual AR-V7/AR-fl inhibition in a single treatment, has the potential to not only benefit patients with mCRPC but also patients with hormone-sensitive disease, and delay AR-V7 expression. Citation Format: CheukMan C. Au, Catrina Estrella, Prerna Vatsa, Michelle Naidoo, Michael Miller, Peter T. Meinke, David M. Nanus, Paraskevi Giannakakou. First-in-class AR-V7/AR-fl small molecule molecular glue degrader for prostate cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1231.

Small-molecule inhibition of SARS-CoV-2 NSP14 RNA cap methyltransferase

Nature · 2024-12-11 · 40 citations

Lead Optimization of Small Molecule ENL YEATS Inhibitors to Enable <i>In Vivo</i> Studies: Discovery of TDI-11055

ACS Medicinal Chemistry Letters · 2024-03-12 · 8 citations

Eleven-nineteen leukemia (ENL) is an epigenetic reader protein that drives oncogenic transcriptional programs in acute myeloid leukemia (AML). AML is one of the deadliest hematopoietic malignancies, with an overall 5-year survival rate of 27%. The epigenetic reader activity of ENL is mediated by its YEATS domain that binds to acetyl and crotonyl marks on histone tails and colocalizes with promoters of actively transcribed genes that are essential for leukemia. Prior to the discovery of TDI-11055, existing inhibitors of ENL YEATS showed in vitro potency, but had not shown efficacy in in vivo animal models. During the course of the medicinal chemistry campaign described here, we identified ENL YEATS inhibitor TDI-11055 that has an improved pharmacokinetic profile and is appropriate for in vivo evaluation of the ENL YEATS inhibition mechanism in AML.

Indazole to 2‐Cyanoindole Scaffold Progression for Mycobacterial Lipoamide Dehydrogenase Inhibitors Achieves Extended Target Residence Time and Improved Antibacterial Activity

Angewandte Chemie · 2024-07-13 · 2 citations

Abstract Tuberculosis remains a leading cause of death from a single infection worldwide. Drug resistance to existing and even new antimycobacterials calls for research into novel targets and unexplored mechanisms of action. Recently we reported on the development of tight‐binding inhibitors of Mycobacterium tuberculosis (Mtb) lipoamide dehydrogenase (Lpd), which selectively inhibit the bacterial but not the human enzyme based on a differential modality of inhibitor interaction with these targets. Here we report on the striking improvement in inhibitor residence time on the Mtb enzyme associated with scaffold progression from an indazole to 2‐cyanoindole. Cryo‐EM of Lpd with the bound 2‐cyanoindole inhibitor 19 confirmed displacement of the buried water molecule deep in the binding channel with a cyano group. The ensuing hours‐long improvement in on‐target residence time is associated with enhanced antibacterial activity in axenic culture and in primary mouse macrophages. Resistance to 2‐cyanoindole inhibitors involves mutations within the inhibitor binding site that have little effect on inhibitor affinity but change the modality of inhibitor‐target interaction, resulting in fast dissociation from Lpd. These findings underscore that on‐target residence time is a major determinant of antibacterial activity and in vivo efficacy.

Indazole to 2‐Cyanoindole Scaffold Progression for Mycobacterial Lipoamide Dehydrogenase Inhibitors Achieves Extended Target Residence Time and Improved Antibacterial Activity

Angewandte Chemie International Edition · 2024-07-13 · 4 citations

Tuberculosis remains a leading cause of death from a single infection worldwide. Drug resistance to existing and even new antimycobacterials calls for research into novel targets and unexplored mechanisms of action. Recently we reported on the development of tight-binding inhibitors of Mycobacterium tuberculosis (Mtb) lipoamide dehydrogenase (Lpd), which selectively inhibit the bacterial but not the human enzyme based on a differential modality of inhibitor interaction with these targets. Here we report on the striking improvement in inhibitor residence time on the Mtb enzyme associated with scaffold progression from an indazole to 2-cyanoindole. Cryo-EM of Lpd with the bound 2-cyanoindole inhibitor 19 confirmed displacement of the buried water molecule deep in the binding channel with a cyano group. The ensuing hours-long improvement in on-target residence time is associated with enhanced antibacterial activity in axenic culture and in primary mouse macrophages. Resistance to 2-cyanoindole inhibitors involves mutations within the inhibitor binding site that have little effect on inhibitor affinity but change the modality of inhibitor-target interaction, resulting in fast dissociation from Lpd. These findings underscore that on-target residence time is a major determinant of antibacterial activity and in vivo efficacy.

Supplementary Data from Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia

2023-04-04

Supplementary Data from Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia