Design, synthesis and evaluation of thieno[3,2-d]pyrimidine derivatives as novel potent CDK7 inhibitors.

The targeting of cyclin-dependent kinase 7 (CDK7) has become a highly desirable therapeutic approach in the field of oncology due to its dual role in regulating essential biological processes, encompassing cell cycle progression and transcriptional control. We have previously identified a highly selective thieno[3,2-d]pyrimidine-based CDK7 inhibitor with demonstrated efficacy and safety in animal model. In this study, we sought to optimize the thieno[3,2-d]pyrimidine core to discover a novel series of CDK7 inhibitors with improved potency and pharmacokinetic (PK) properties. Through extensive structure-activity relationship (SAR) studies, compound 20 has emerged as the lead candidate due to its potent inhibitory activity against CDK7 and remarkable efficacy on MDA-MB-453 cells, a representative triple negative breast cancer (TNBC) cell line. Furthermore, 20 has demonstrated favorable oral bioavailability and exhibited highly desirable pharmacokinetic (PK) properties, making it a promising lead candidate for further structural optimization.

Discovery of novel macrocyclic derivatives as potent and selective cyclin-dependent kinase 2 inhibitors.

Cyclin-dependent kinase 2 (CDK2) is a member of CDK family of kinases (CDKs) that regulate the cell cycle. Its inopportune or over-activation leads to uncontrolled cell cycle progression and drives numerous types of cancers, especially ovarian, uterine, gastric cancer, as well as those associated with amplified CCNE1 gene. However, developing selective lead compound as CDK2 inhibitors remains challenging owing to similarities in the ATP pockets among different CDKs. Herein, we described the optimization of compound 1, a novel macrocyclic inhibitor targeting CDK2/5/7/9, aiming to discover more selective and metabolically stable lead compound as CDK2 inhibitor. Molecular dynamic (MD) simulations were performed for compound 1 and 9 to gain insights into the improved selectivity against CDK5. Further optimization efforts led to compound 22, exhibiting excellent CDK2 inhibitory activity, good selectivity over other CDKs and potent cellular effects. Based on these characterizations, we propose that compound 22 holds great promise as a potential lead candidate for drug development.

Design and Synthesis of Novel Macrocyclic Derivatives as Potent and Selective Cyclin-Dependent Kinase 7 Inhibitors.

The duality of function (cell cycle regulation and gene transcription) of cyclin-dependent kinase 7 (CDK7) makes it an attractive oncology target and the discovery of CDK7 inhibitors has been a long-term pursuit by academia and pharmaceutical companies. However, achieving selective leading compounds is still difficult owing to the similarities among the ATP binding pocket. Herein, we detail the design and synthesis of a series of macrocyclic derivatives with pyrazolo[1,5-a]-1,3,5-triazine core structure as potent and selective CDK7 inhibitors. The diverse manners of macrocyclization led to distinguished selectivity profiles of the CDK family. Molecular dynamics (MD) simulation explained the binding difference between 15- and 16-membered macrocyclic compounds. Further optimization generated compound 37 exhibiting good CDK7 inhibitory activity and high selectivity over other CDKs. This work clearly demonstrated macrocyclization is a versatile method to finely tune the selectivity profile of small molecules and MD simulation can be a valuable tool in prioritizing designs of the macrocycle.

Multivalent Aptamer-Based Lysosome-Targeting Chimeras (LYTACs) Platform for Mono- or Dual-Targeted Proteins Degradation on Cell Surface.

Selective protein degradation platforms have opened novel avenues in therapeutic development and biological inquiry. Antibody-based lysosome-targeting chimeras (LYTACs) have emerged as a promising technology that extends the scope of targeted protein degradation to extracellular targets. Aptamers offer an advantageous alternative owing to their potential for modification and manipulation toward a multivalent state. In this study, a chemically engineered platform of multivalent aptamer-based LYTACs (AptLYTACs) is established for the targeted degradation of either single or dual protein targets. Leveraging the biotin-streptavidin system as a molecular scaffold, this investigation reveals that trivalently mono-targeted AptLYTACs demonstrate optimum efficiency in degrading membrane proteins. The development of this multivalent AptLYTACs platform provides a principle of concept for mono-/dual-targets degradation, expanding the possibilities of targeted protein degradation.

Selective Electrified Propylene-to-Propylene Glycol Oxidation on Activated Rh-Doped Pd.

Renewable-energy-powered electrosynthesis has the potential to contribute to decarbonizing the production of propylene glycol, a chemical that is used currently in the manufacture of polyesters and antifreeze and has a high carbon intensity. Unfortunately, to date, the electrooxidation of propylene under ambient conditions has suffered from a wide product distribution, leading to a low faradic efficiency toward the desired propylene glycol. We undertook mechanistic investigations and found that the reconstruction of Pd to PdO occurs, followed by hydroxide formation under anodic bias. The formation of this metastable hydroxide layer arrests the progressive dissolution of Pd in a locally acidic environment, increases the activity, and steers the reaction pathway toward propylene glycol. Rh-doped Pd further improves propylene glycol selectivity. Density functional theory (DFT) suggests that the Rh dopant lowers the energy associated with the production of the final intermediate in propylene glycol formation and renders the desorption step spontaneous, a concept consistent with experimental studies. We report a 75% faradic efficiency toward propylene glycol maintained over 100 h of operation.

Discovery and optimization of (2-naphthylthio)acetic acid derivative as selective Bfl-1 inhibitor.

Bcl-2 anti-apoptotic protein family suppresses cell death by deploying a surface groove to capture the critical BH3 α-helix of pro-apoptotic members. Bfl-1 is a relatively understudied member of this family, though it has been implicated in the pathogenesis and chemoresistance of a variety of human cancers. Reported small molecular Bfl-1 inhibitors encountered the issue of either lack in potency or poor selectivity against its most homologous member Mcl-1. In order to tackle this issue, compound library was screened and a hit compound UMI-77 was identified. We modified its chemical structure to remove the characteristic of PAINS (pan-assay interference compounds), demonstrated the real binding affinity and achieved selectivity against Mcl-1 under the guidance of computational modeling. After optimization 15 was obtained as leading compound to block Bfl-1/BIM interaction in vitro with more than 10-fold selectivity over Mcl-1. We believe 15 is of great value for the exploration of Bfl-1 biological function and its potential as therapeutic target.

Spatiotemporal Quantification of HER2-targeting Antibody-Drug Conjugate Bystander Activity and Enhancement of Solid Tumor Penetration.

PURPOSE: Antibody-drug conjugate (ADC) has had a transformative effect on the treatment of many solid tumors, yet it remains unclear how ADCs exert bystander activity in the tumor microenvironment. EXPERIMENTAL DESIGN: Here, we directly visualized and spatiotemporally quantified the intratumor biodistribution and pharmacokinetics of different ADC components by developing dual-labeled fluorescent probes. RESULTS: Mechanistically, we found that tumor penetration of ADCs is distinctly affected by their ability to breach the binding site barrier (BSB) in perivascular regions of tumor vasculature, and bystander activity of ADC can only partially breach BSB. Furthermore, bystander activity of ADCs can work in synergy with coadministration of their parental antibodies, leading to fully bypassing BSBs and enhancing tumor penetration via a two-step process. CONCLUSIONS: These promising preclinical data allowed us to initiate a phase I/II clinical study of coadministration of RC48 and trastuzumab in patients with malignant stomach cancer to further evaluate this treatment strategy in humans.

LiBF4-Promoted Aromatic Fluorodetriazenation under Mild Conditions.

An efficient and mild fluorination method through LiBF4-promoted aromatic fluorodetriazenation of 3,3-dimethyl-1-aryltriazenes is developed. The reaction proceeds smoothly and tends to complete within 2 h in the absence of a protic acid or strong Lewis acid. This method tolerates a wide range of functional groups and affords the aryl fluoride products in moderate to excellent yields.

Single-site decorated copper enables energy- and carbon-efficient CO2 methanation in acidic conditions.

Renewable CH4 produced from electrocatalytic CO2 reduction is viewed as a sustainable and versatile energy carrier, compatible with existing infrastructure. However, conventional alkaline and neutral CO2-to-CH4 systems suffer CO2 loss to carbonates, and recovering the lost CO2 requires input energy exceeding the heating value of the produced CH4. Here we pursue CH4-selective electrocatalysis in acidic conditions via a coordination method, stabilizing free Cu ions by bonding Cu with multidentate donor sites. We find that hexadentate donor sites in ethylenediaminetetraacetic acid enable the chelation of Cu ions, regulating Cu cluster size and forming Cu-N/O single sites that achieve high CH4 selectivity in acidic conditions. We report a CH4 Faradaic efficiency of 71% (at 100 mA cm-2) with <3% loss in total input CO2 that results in an overall energy intensity (254 GJ/tonne CH4), half that of existing electroproduction routes.

Structure-Based Design of Y-Shaped Covalent TEAD Inhibitors.

Transcriptional enhanced associate domain (TEAD) proteins together with their transcriptional coactivator yes-associated protein (YAP) and transcriptional coactivator with the PDZ-binding motif (TAZ) are important transcription factors and cofactors that regulate gene expression in the Hippo pathway. In mammals, the TEAD families have four homologues: TEAD1 (TEF-1), TEAD2 (TEF-4), TEAD3 (TEF-5), and TEAD4 (TEF-3). Aberrant expression and hyperactivation of TEAD/YAP signaling have been implicated in a variety of malignancies. Recently, TEADs were recognized as being palmitoylated in cells, and the lipophilic palmitate pocket has been successfully targeted by both covalent and noncovalent ligands. In this report, we present the medicinal chemistry effort to develop MYF-03-176 (compound 22) as a selective, cysteine-covalent TEAD inhibitor. MYF-03-176 (compound 22) significantly inhibits TEAD-regulated gene expression and proliferation of the cell lines with TEAD dependence including those derived from mesothelioma and liposarcoma.

Depletion of creatine phosphagen energetics with a covalent creatine kinase inhibitor.

Creatine kinases (CKs) provide local ATP production in periods of elevated energetic demand, such as during rapid anabolism and growth. Thus, creatine energetics has emerged as a major metabolic liability in many rapidly proliferating cancers. Whether CKs can be targeted therapeutically is unknown because no potent or selective CK inhibitors have been developed. Here we leverage an active site cysteine present in all CK isoforms to develop a selective covalent inhibitor of creatine phosphagen energetics, CKi. Using deep chemoproteomics, we discover that CKi selectively engages the active site cysteine of CKs in cells. A co-crystal structure of CKi with creatine kinase B indicates active site inhibition that prevents bidirectional phosphotransfer. In cells, CKi and its analogs rapidly and selectively deplete creatine phosphate, and drive toxicity selectively in CK-dependent acute myeloid leukemia. Finally, we use CKi to uncover an essential role for CKs in the regulation of proinflammatory cytokine production in macrophages.

Covalent disruptor of YAP-TEAD association suppresses defective Hippo signaling.

The transcription factor TEAD, together with its coactivator YAP/TAZ, is a key transcriptional modulator of the Hippo pathway. Activation of TEAD transcription by YAP has been implicated in a number of malignancies, and this complex represents a promising target for drug discovery. However, both YAP and its extensive binding interfaces to TEAD have been difficult to address using small molecules, mainly due to a lack of druggable pockets. TEAD is post-translationally modified by palmitoylation that targets a conserved cysteine at a central pocket, which provides an opportunity to develop cysteine-directed covalent small molecules for TEAD inhibition. Here, we employed covalent fragment screening approach followed by structure-based design to develop an irreversible TEAD inhibitor MYF-03-69. Using a range of in vitro and cell-based assays we demonstrated that through a covalent binding with TEAD palmitate pocket, MYF-03-69 disrupts YAP-TEAD association, suppresses TEAD transcriptional activity and inhibits cell growth of Hippo signaling defective malignant pleural mesothelioma (MPM). Further, a cell viability screening with a panel of 903 cancer cell lines indicated a high correlation between TEAD-YAP dependency and the sensitivity to MYF-03-69. Transcription profiling identified the upregulation of proapoptotic BMF gene in cancer cells that are sensitive to TEAD inhibition. Further optimization of MYF-03-69 led to an in vivo compatible compound MYF-03-176, which shows strong antitumor efficacy in MPM mouse xenograft model via oral administration. Taken together, we disclosed a story of the development of covalent TEAD inhibitors and its high therapeutic potential for clinic treatment for the cancers that are driven by TEAD-YAP alteration.

Achieving high selectivity towards electro-conversion of CO2 using In-doped Bi derived from metal-organic frameworks.

Metal-organic frameworks (MOFs) and their derivatives have shown great potential as electrocatalysts, in virtue of their ease of functionalization and abundance of active sites. Here, we report a series of indium-doped bismuth MOF-derived composites (BiInX-Y@C) for the direct conversion of carbon dioxide (CO2) to hydrocarbon derivatives. Amongst the catalysts studied, BiIn5-500@C demonstrated high selectivity for the production of formate and intrinsic activity in a wide potential window, ranging from - 1.16 to - 0.76 V vs. RHE (VRHE). At - 0.86 VRHE, the Faradaic efficiency and total current density were determined as 97.5% and - 13.5 mA cm-2, respectively. In addition, a 15-h stability test shows no obvious signs of deactivation. Complementary density functional theory (DFT) calculations revealed that the In-doped Bi2O3 are the predominant active centers for HCOOH production in the reduction of CO2 under the action of the BiInX-Y@C catalyst. This work provides new detailed insights into reaction mechanism, and selectivity for reduction of CO2via MOFs, which are expected to inspire and guide the design of novel, selective and efficient catalysts.

Partitioning of cancer therapeutics in nuclear condensates.

The nucleus contains diverse phase-separated condensates that compartmentalize and concentrate biomolecules with distinct physicochemical properties. Here, we investigated whether condensates concentrate small-molecule cancer therapeutics such that their pharmacodynamic properties are altered. We found that antineoplastic drugs become concentrated in specific protein condensates in vitro and that this occurs through physicochemical properties independent of the drug target. This behavior was also observed in tumor cells, where drug partitioning influenced drug activity. Altering the properties of the condensate was found to affect the concentration and activity of drugs. These results suggest that selective partitioning and concentration of small molecules within condensates contributes to drug pharmacodynamics and that further understanding of this phenomenon may facilitate advances in disease therapy.

Treatment-Induced Tumor Dormancy through YAP-Mediated Transcriptional Reprogramming of the Apoptotic Pathway.

Eradicating tumor dormancy that develops following epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) treatment of EGFR-mutant non-small cell lung cancer, is an attractive therapeutic strategy but the mechanisms governing this process are poorly understood. Blockade of ERK1/2 reactivation following EGFR TKI treatment by combined EGFR/MEK inhibition uncovers cells that survive by entering a senescence-like dormant state characterized by high YAP/TEAD activity. YAP/TEAD engage the epithelial-to-mesenchymal transition transcription factor SLUG to directly repress pro-apoptotic BMF, limiting drug-induced apoptosis. Pharmacological co-inhibition of YAP and TEAD, or genetic deletion of YAP1, all deplete dormant cells by enhancing EGFR/MEK inhibition-induced apoptosis. Enhancing the initial efficacy of targeted therapies could ultimately lead to prolonged treatment responses in cancer patients.

Total Synthesis of Lapidilectine B Enabled by Manganese(III)-Mediated Oxidative Cyclization of Indoles.

A novel manganese(III)-mediated oxidative cyclization of readily accessible 1,2,3-trisubstituted indoles is described. This unprecedented method enabled the efficient construction of a complex polycyclic scaffold bearing a spiro-indoline motif and a lactone moiety in one step. Its synthetic utility was demonstrated in the total synthesis of lapidilectine B (in 18 steps) by employing a strategic regioselective ring-expansion and a silver-promoted allenic amine cyclization as the additional key elements.

Copper-Catalyzed Diaryl Ether Formation from (Hetero)aryl Halides at Low Catalytic Loadings.

Diaryl formation is achieved by coupling phenols and (hetero)aryl halides under the catalysis of CuI/N,N'-bis(2-phenylphenyl) oxalamide (BPPO) or CuI/N-(2-phenylphenyl)-N'-benzyl oxalamide (PPBO) at 90 °C using DMF or MeCN as the solvent. Only 0.2-2 mol % CuI and ligand are required for complete conversion, which represents the lowest catalytic loadings for a general Cu/ligand-catalyzed diaryl ether formation.

CuI/Oxalamide Catalyzed Couplings of (Hetero)aryl Chlorides and Phenols for Diaryl Ether Formation.

Couplings between (hetero)aryl chlorides and phenols can be effectively promoted by CuI in combination with an N-aryl-N'-alkyl-substituted oxalamide ligand to proceed smoothly at 120 °C. For this process, N-aryl-N'-alkyl-substituted oxalamides are more effective ligands than bis(N-aryl)-substituted oxalamides. A wide range of electron-rich and electron-poor aryl and heteroaryl chlorides gave the corresponding coupling products in good yields. Satisfactory conversions were achieved with electron-rich phenols as well as a limited range of electron-poor phenols. Catalyst and ligand loadings as low as 1.5 mol % are sufficient for the scaled-up variants of some of these reactions.

Assembly of Primary (Hetero)Arylamines via CuI/Oxalic Diamide-Catalyzed Coupling of Aryl Chlorides and Ammonia.

A general and practical catalytic system for aryl amination of aryl chlorides with aqueous or gaseous ammonia has been developed, with CuI as the catalyst and bisaryl oxalic diamides as the ligands. The reaction proceeds at 105-120 °C to provide a diverse set of primary (hetero)aryl amines in high yields with various functional groups.

CuI/Oxalic Diamide Catalyzed Coupling Reaction of (Hetero)Aryl Chlorides and Amines.

A class of oxalic diamides are found to be effective ligands for promoting CuI-catalyzed aryl amination with less reactive (hetero)aryl chlorides. The reaction proceeds at 120 °C with K3PO4 as the base in DMSO to afford a wide range of (hetero)aryl amines in good to excellent yields. The bis(N-aryl) substituted oxalamides are superior ligands to N-aryl-N'-alkyl substituted or bis(N-alkyl) substituted oxalamides. Both the electronic nature and the steric property of the aromatic rings in ligands are important for their efficiency.