Structure-Guided Discovery and Preclinical Assessment of Novel (Thiophen-3-yl)aminopyrimidine Derivatives as Potent ERK1/2 Inhibitors.

The RAS-RAF-MEK-ERK signaling cascade is abnormally activated in various tumors, playing a crucial role in mediating tumor progression. As the key component at the terminal stage of this cascade, ERK1/2 emerges as a potential antitumor target and offers a promising therapeutic strategy for tumors harboring BRAF or RAS mutations. Here, we identified 36c with a (thiophen-3-yl)aminopyrimidine scaffold as a potent ERK1/2 inhibitor through structure-guided optimization for hit 18. In preclinical studies, 36c showed powerful ERK1/2 inhibitory activities (ERK1/2 IC50 = 0.11/0.08 nM) and potent antitumor efficacy both in vitro and in vivo against triple-negative breast cancer and colorectal cancer models harboring BRAF and RAS mutations. 36c could directly inhibit ERK1/2, significantly block the phosphorylation expression of their downstream substrates p90RSK and c-Myc, and induce cell apoptosis and incomplete autophagy-related cell death. Taken together, this work provides a promising ERK1/2 lead compound for multiple tumor-treatment drug discovery.

Mechanism of antagonist ligand binding to REV-ERBα.

REV-ERBα, a therapeutically promising nuclear hormone receptor, plays a crucial role in regulating various physiological processes such as the circadian clock, inflammation, and metabolism. However, the availability of chemical probes to investigate the pharmacology of this receptor is limited, with SR8278 being the only identified synthetic antagonist. Moreover, no X-ray crystal structures are currently available that demonstrate the binding of REV-ERBα to antagonist ligands. This lack of structural information impedes the development of targeted therapeutics. To address this issue, we employed Gaussian accelerated molecular dynamics (GaMD) simulations to investigate the binding pathway of SR8278 to REV-ERBα. For comparison, we also used GaMD to observe the ligand binding process of STL1267, for which an X-ray structure is available. GaMD simulations successfully captured the binding of both ligands to the receptor's orthosteric site and predicted the ligand binding pathway and important amino acid residues involved in the antagonist SR8278 binding. This study highlights the effectiveness of GaMD in investigating protein-ligand interactions, particularly in the context of drug recognition for nuclear hormone receptors.

Drug delivery via a 3D electro-swellable conjugated polymer hydrogel.

Spatiotemporal controlled drug delivery minimizes side-effects and enables therapies that require specific dosing patterns. Conjugated polymers (CP) can be used for electrically controlled drug delivery; however so far, most demonstrations were limited to molecules up to 500 Da. Larger molecules could be incorporated only during the CP polymerization and thus limited to a single delivery. This work harnesses the record volume changes of a glycolated polythiophene p(g3T2) for controlled drug delivery. p(g3T2) undergoes reversible volumetric changes of up to 300% during electrochemical doping, forming pores in the nm-size range, resulting in a conducting hydrogel. p(g3T2)-coated 3D carbon sponges enable controlled loading and release of molecules spanning molecular weights of 800-6000 Da, from simple dyes up to the hormone insulin. Molecules are loaded as a combination of electrostatic interactions with the charged polymer backbone and physical entrapment in the porous matrix. Smaller molecules leak out of the polymer while larger ones could not be loaded effectively. Finally, this work shows the temporally patterned release of molecules with molecular weight of 1300 Da and multiple reloading and release cycles without affecting the on/off ratio.

Discovery of 2-Amide-3-methylester Thiophenes that Target SARS-CoV-2 Mac1 and Repress Coronavirus Replication, Validating Mac1 as an Antiviral Target.

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus has made it clear that further development of antiviral therapies will be needed. Here, we describe small-molecule inhibitors for SARS-CoV-2 Mac1, which counters ADP-ribosylation-mediated innate immune responses. Three high-throughput screening hits had the same 2-amide-3-methylester thiophene scaffold. We studied the compound binding mode using X-ray crystallography, allowing us to design analogues. Compound 27 (MDOLL-0229) had an IC50 of 2.1 µM and was selective for CoV Mac1 proteins after profiling for activity against a panel of viral and human proteins. The improved potency allowed testing of its effect on virus replication, and indeed, 27 inhibited replication of both murine hepatitis virus (MHV) prototypes CoV and SARS-CoV-2. Sequencing of a drug-resistant MHV identified mutations in Mac1, further demonstrating the specificity of 27. Compound 27 is the first Mac1-targeted small molecule demonstrated to inhibit coronavirus replication in a cell model.

Thiophene-Based Ligands for Specific Assignment of Distinct Aß Pathologies in Alzheimer's Disease.

Aggregated species of amyloid-ß (Aß) are one of the pathological hallmarks in Alzheimer's disease (AD), and ligands that selectively target different Aß deposits are of great interest. In this study, fluorescent thiophene-based ligands have been used to illustrate the features of different types of Aß deposits found in AD brain tissue. A dual-staining protocol based on two ligands, HS-276 and LL-1, with different photophysical and binding properties, was developed and applied on brain tissue sections from patients affected by sporadic AD or familial AD associated with the PSEN1 A431E mutation. When binding to Aß deposits, the ligands could easily be distinguished for their different fluorescence, and distinct staining patterns were revealed for these two types of AD. In sporadic AD, HS-276 consistently labeled all immunopositive Aß plaques, whereas LL-1 mainly stained cored and neuritic Aß deposits. In the PSEN1 A431E cases, each ligand was binding to specific types of Aß plaques. The ligand-labeled Aß deposits were localized in distinct cortical layers, and a laminar staining pattern could be seen. Biochemical characterization of the Aß aggregates in the individual layers also showed that the variation of ligand binding properties was associated with certain Aß peptide signatures. For the PSEN1 A431E cases, it was concluded that LL-1 was binding to cotton wool plaques, whereas HS-276 mainly stained diffuse Aß deposits. Overall, our findings showed that a combination of ligands was essential to identify distinct aggregated Aß species associated with different forms of AD.

Domino Reaction Protocol to Synthesize Benzothiophene-Derived Chemical Entities as Potential Therapeutic Agents.

An efficient synthesis of 3-amino-2-formyl-functionalized benzothiophenes by a domino reaction protocol and their use to synthesize a library of novel scaffolds have been reported. Reactions of ketones and 1,3-diones with these amino aldehyde derivatives formed a series of benzothieno[3,2-b]pyridine and 3,4-dihydro-2H-benzothiopheno[3,2-b]quinolin-1-one, respectively. A plausible mechanism for the formation of fused pyridine derivatives by the Friedlander reaction has been elucidated by density functional theory (DFT) calculations. Furthermore, hydrazones were obtained by reacting the aldehyde functional group of benzothiophenes with different hydrazine derivatives. Preliminary screening of these compounds against several bacterial strains and cancer cell lines led to the discovery of several hit molecules. Hydrazone and benzothieno[3,2-b]pyridine derivatives are potent cytotoxic and antibacterial agents, respectively. One of the potent compounds effected ∼97% growth inhibition of the LOX IMVI cell line at 10 µM concentration.

N-(Heteroaryl)thiophene sulfonamides as angiotensin AT2 receptor ligands.

Two series of N-(heteroaryl)thiophene sulfonamides, encompassing either a methylene imidazole group or a tert-butylimidazolylacetyl group in the meta position of the benzene ring, have been synthesized. An AT2R selective ligand with a Ki of 42 nM was identified in the first series and in the second series, six AT2R selective ligands with significantly improved binding affinities and Ki values of <5 nM were discovered. The binding modes to AT2R were explored by docking calculations combined with molecular dynamics simulations. Although some of the high affinity ligands exhibited fair stability in human liver microsomes, comparable to that observed with C21 undergoing clinical trials, most ligands displayed a very low metabolic stability with t½ of less than 10 min in human liver microsomes. The most promising ligand, with an AT2R Ki value of 4.9 nM and with intermediate stability in human hepatocytes (t½ = 77 min) caused a concentration-dependent vasorelaxation of pre-contracted mouse aorta.

Discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for treating cancers with microsatellite instability.

Microsatellite instability (MSI) is a hypermutable condition caused by DNA mismatch repair system defects, contributing to the development of various cancer types. Recent research has identified Werner syndrome ATP-dependent helicase (WRN) as a promising synthetic lethal target for MSI cancers. Herein, we report the first discovery of thiophen-2-ylmethylene bis-dimedone derivatives as novel WRN inhibitors for MSI cancer therapy. Initial computational analysis and biological evaluation identified a new scaffold for a WRN inhibitor. Subsequent SAR study led to the discovery of a highly potent WRN inhibitor. Furthermore, we demonstrated that the optimal compound induced DNA damage and apoptotic cell death in MSI cancer cells by inhibiting WRN. This study provides a new pharmacophore for WRN inhibitors, emphasizing their therapeutic potential for MSI cancers.

Thienoisoindigo-Based Conjugated Polymers Synthesized by Direct Arylation Polycondensation.

A series of thienoisoindigo (TIG)-based conjugated polymers (CPs) with high molecular weights are synthesized by direct arylation polycondensation (DArP) by using TIG derivatives as CBr monomer and multi-halogenated thiophene derivatives, i.e., (E)-1,2-bis(3,4-difluorothien-2-yl)ethene (4FTVT), (E)-1,2-bis(3,4-dichlorothien-2-yl)ethene (4ClTVT), 3,3',4,4'-tetrafluoro-2,2'-bithiophene (4FBT), and 3,3',4,4'-tetrachloro-2,2'-bithiophene (4ClBT), as CH monomers. Density functional theory (DFT) calculations reveal the high selectivity between α-CH bonds in 4FTVT, 4ClTVT, 4FBT, and 4ClBT and ß-CH bonds in TIG CBr monomer. All four resulting CPs exhibit low optical bandgaps of ca. 1.20 eV and ambipolar transport characteristics with both electron and hole mobility above 0.1 cm2  V-1  s-1 as elaborated with organic thin-film transistors (OTFTs). The polymer TIG-4FTVT delivers the best device performance. With this polymer, n-channel OTFTs with electron mobility up to 1.67 cm2  V-1  s-1 and p-channel OTFTs with hole mobility up to 0.62 cm2  V-1  s-1 are fabricated by modifying source/drain electrodes with polyethylenimine ethoxylated (PEIE) and MoO3 , respectively, to selectively inject electrons and holes.

Correlating Molar Mass, π-Conjugation, and Optical Properties of Narrowly Distributed Anionic Polythiophenes in Aqueous Solutions.

Polythiophene-based conjugated polyelectrolytes (CPE) are attracting increasing attention as sensor or interface materials in chemistry and biology. While cationic polythiophenes are better understood, limited structural information is available on their anionic counterparts. Limited access to well-defined polymers has made the study of structure-property relationships difficult and clear correlations have remained elusive. By combining controlled Kumada catalyst transfer polymerization with a polymer-analog substitution, regioregular and narrowly distributed poly(6-(thiophen-3-yl)hexane-1-sulfonate)s (PTHS) with tailored chain length are prepared. Analysis of their aqueous solution structures by small-angle neutron scattering (SANS) revealed a cylindrical conformation for all polymers tested, with a length close to the contour length of the polymer chains, while the estimated radii remain too small (<1.5 nm) for extensive π-stacking of the chains. The latter is particularly interesting as the longest polymer exhibits a concentration-independent structured absorption typical of crystalline polythiophenes. Increasing the ionic strength of the solution diminishes these features as the Coulomb repulsion between the charged repeat units is shielded, allowing the polymer to adopt a more coiled conformation. The extended π-conjugation, therefore, appears to be a key parameter for these unique optical features, which are not present in the corresponding cationic polythiophenes.

Highly Stretchable Conjugated Polymer/Elastomer Blend Films with Sandwich Structure.

The physical blending of high-mobility conjugated polymers with ductile elastomers provides a simple way to realize high-performance stretchable films. However, how to control the morphology of the conjugated polymer and elastomer blend film and its response to mechanical fracture processes during stretching are not well understood. Herein, a sandwich structure is constructed in the blend film based on a conjugated polymer poly[(5-fluoro-2,1,3-benzothiadiazole-4,7-diyl)(4,4-dihexadecyl-4H-cyclopenta[2,1-b:3,4-b″]dithiophene-2,6-diyl)(6-fluoro-2,1,3-benzothiadiazole-4,7-diyl)(4,4-dihexadecyl-4H-cyclopenta[2,1-b:3,4-b″]dithiophene-2,6-diyl)] (PCDTFBT) and an elastomer polystyrene-block-poly(ethylene-ran-butylene)-block-polystyrene (SEBS). The sandwich structure is composed of a PCDTFBT:SEBS mixed layer laminated with a PCDTFBT-rich layer at both the top and bottom surfaces. During stretching, the external strain energy can be effectively dissipated by the deformation of the crystalline PCDTFBT domains and amorphous SEBS phases and the recrystallization of the PCDTFBT chains. This endows the blend film with excellent ductility, with a large crack onset strain exceeding 1100%, and minimized the electrical degradation of the blend film at a large strain. This study indicates that the electrical and mechanical performance of conjugated polymer/elastomer blend films can be improved by manipulating their microstructure.

The Effect of Mesoporous Structure of the Support on the Oxidation of Dibenzothiophene.

A source of Brønsted acid centers, generated on the surface of two mesoporous silica supports of different structures (SBA-15 and MCF), was 3-(trihydroxysilyl)-1-propanesufonic acid (TPS). The materials obtained were characterized and applied as catalysts for the oxidative desulfurization of dibenzothiophene (DBT) with hydrogen peroxide as a model ODS (oxidative desulfurization) process. The properties of the materials were examined via nitrogen physisorption, XRD (X-ray Diffraction) and elemental analysis showing the preservation of the support structure after modification with organosilane species. Due to the aggregation of catalyst particles in the reaction mixture, the SBA-15 based catalyst was not very effective in DBT oxidation. Contrary, TPS/MCF catalyst exhibited a very good activity (almost total conversion of DBT after 1 h in optimized reaction conditions) and stability in dibenzothiophene oxidation in mild reaction conditions.

Conjugated Polymers from Direct Arylation Polycondensation of 3,4-Difluorothiophene-Substituted Aryls: Synthesis and Properties.

3,4-Difluorothiophene-substituted aryls, i.e., 1,4-bis(3,4-difluorothiophen-2-yl)-benzene (Ph-2FTh), 1,4-bis(3,4-difluorothiophen-2-yl)-2,5-difluorobenzene (2FPh-2FTh), and 4,7-bis(3,4-difluorothiophen-2-yl)-2,1,3-benzothiadiazole (BTz-2FTh), are synthesized as C─H monomers for the synthesis of conjugated polymers (CPs) via direct arylation polycondensation (DArP) with diketopyrrolopyrrole (DPP) and isoindigo (IID) derivatives as C─Br monomers. The Gibbs free energies of activation for direct arylation (ΔG298 K , kcal mol-1 ) for α─C─H bonds of thiophene moieties as calculated by density functional theory (DFT) are 14.3, 16.5, and 16.4 kcal mol-1 for Ph-2FTh, 2FPh-2FTh and BTz-2FTh, respectively, meaning that inserting an electron-deficient unit in 3,3',4,4'-tetrafluoro-2,2'-bithiophene (4FBT, ΔG298K : 14.6 kcal mol-1 ) may cause a reactivity decrease of the C─H monomers. Photophysical and semiconducting properties of the resulting six CPs (i.e., DPP-Ph, DPP-2FPh, DPP-BTz, 2FIID-Ph, 2FIID-2FPh, and 2FIID-BTz) are characterized in detail. DPP-based CPs show ambipolar transport properties while IID-based ones exhibited n-type behavior owing to the deeper frontier molecular orbital energy levels of IID-based CPs. With source/drain electrodes modified with polyethylenimine ethoxylated, n-channel organic thin-film transistors with maximum electron mobility of 0.40, 0.54, 0.29, 0.05, 0.16, and 0.01 cm2 V-1 s-1 for DPP-Ph, DPP-2FPh, DPP-BTz, 2FIID-Ph, 2FIID-2FPh, and 2FIID-BTz, respectively, are fabricated. DPP-2FPh exhibits the best device performance due to the good film morphology and the highest intermolecular packing order.

Immunosuppressive effects of new thiophene-based KV1.3 inhibitors.

Voltage-gated potassium channel KV1.3 inhibitors have been shown to be effective in preventing T-cell proliferation and activation by affecting intracellular Ca2+ homeostasis. Here, we present the structure-activity relationship, KV1.3 inhibition, and immunosuppressive effects of new thiophene-based KV1.3 inhibitors with nanomolar potency on K+ current in T-lymphocytes and KV1.3 inhibition on Ltk- cells. The new KV1.3 inhibitor trans-18 inhibited KV1.3 -mediated current in phytohemagglutinin (PHA)-activated T-lymphocytes with an IC50 value of 26.1 nM and in mammalian Ltk- cells with an IC50 value of 230 nM. The KV1.3 inhibitor trans-18 also had nanomolar potency against KV1.3 in Xenopus laevis oocytes (IC50 = 136 nM). The novel thiophene-based KV1.3 inhibitors impaired intracellular Ca2+ signaling as well as T-cell activation, proliferation, and colony formation.

Building Block Engineering toward Realizing High-Performance Electrochromic Materials and Glucose Biosensing Platform.

The molecular engineering of conjugated systems has proven to be an effective method for understanding structure-property relationships toward the advancement of optoelectronic properties and biosensing characteristics. Herein, a series of three thieno[3,4-c]pyrrole-4,6-dione (TPD)-based conjugated monomers, modified with electron-rich selenophene, 3,4-ethylenedioxythiophene (EDOT), or both building blocks (Se-TPD, EDOT-TPD, and EDOT-Se-TPD), were synthesized using Stille cross-coupling and electrochemically polymerized, and their electrochromic properties and applications in a glucose biosensing platform were explored. The influence of structural modification on electrochemical, electronic, optical, and biosensing properties was systematically investigated. The results showed that the cyclic voltammograms of EDOT-containing materials displayed a high charge capacity over a wide range of scan rates representing a quick charge propagation, making them appropriate materials for high-performance supercapacitor devices. UV-Vis studies revealed that EDOT-based materials presented wide-range absorptions, and thus low optical band gaps. These two EDOT-modified materials also exhibited superior optical contrasts and fast switching times, and further displayed multi-color properties in their neutral and fully oxidized states, enabling them to be promising materials for constructing advanced electrochromic devices. In the context of biosensing applications, a selenophene-containing polymer showed markedly lower performance, specifically in signal intensity and stability, which was attributed to the improper localization of biomolecules on the polymer surface. Overall, we demonstrated that relatively small changes in the structure had a significant impact on both optoelectronic and biosensing properties for TPD-based donor-acceptor polymers.

Synthesis, Spectral, Redox and Theoretical Studies of Stable Nonaromatic Dicarba Dithia Hexaphyrin(2.0.1.1.1.0)s with Two Inverted Thiophenes.

A series of dicarba dithia hexaphyrin(2.0.1.1.1.0)s containing two p-phenylene rings, two thiophene rings, and two pyrrole rings connected via five meso carbons were synthesized by condensing the key precursor, hexapyrrane, which was prepared over a sequence of steps, with the appropriate aromatic aldehyde under acid catalytic conditions followed by alumina chromatographic purification. Detailed one-dimensional (1D) and two-dimensional (2D) NMR studies revealed that the two thiophene rings were inverted and facing outward from the macrocyclic core. Interestingly, one of the inverted thiophene rings adopts a normal orientation in the protonated derivatives of macrocycles generated by addition of trifluoroacetic acid to the appropriate macrocyclic solution. The spectroscopic studies support the non-aromatic nature of macrocycles, and the macrocycles exhibit a distinct sharp band at ∼425 nm along with a broad band in the range of 550-1000 nm, which experienced a red shift with a clear color change in the protonated derivatives. The redox studies showed lower oxidation potentials, indicating their electron-rich nature. The density functional theoretical (DFT) studies showed that the hexaphyrins adopt oval-shaped structures, and time-dependent-DFT (TD-DFT) studies parallelly matched the experimental observations of macrocycles.

Asparagusic Acid - A Unique Approach toward Effective Cellular Uptake of Therapeutics: Application, Biological Targets, and Chemical Properties.

The synthetic approaches towards unique asparagusic acid and its analogues as well as its chemical use, the breadth of its biological properties and their relevant applications have been explored. The significance of the 1,2-dithiolane ring tension in dithiol-mediated uptake and its use for the intracellular transport of molecular cargoes is discussed alongside some of the challenges that arise from the fast thiolate-disulfide interchange. The short overview with the indication of the available literature on natural 1,2-dithiolanes synthesis and biological activities is also included. The general review structure is based on the time-line perspective of the application of asparagusic acid moiety as well as its primitive derivatives (4-amino-1,2-dithiolane-4-carboxylic acid and 4-methyl-1,2-dithiolane-4-carboxilic acid) used in clinics/cosmetics, focusing on the recent research in this area and including international patents applications.

In Silico-Guided Rational Drug Design and Synthesis of Novel 4-(Thiophen-2-yl)butanamides as Potent and Selective TRPV1 Agonists.

We describe an in silico-guided rational drug design and the synthesis of the suggested ligands, aimed at improving the TRPV1-ligand binding properties and the potency of N-(4-hydroxy-3-methoxybenzyl)-4-(thiophen-2-yl) butanamide I, a previously identified TRPV1 agonist. The docking experiments followed by molecular dynamics simulations and thermodynamic analysis led the drug design toward both the introduction of a lipophilic iodine and a flat pyridine/benzene at position 5 of the thiophene nucleus. Most of the synthesized compounds showed high TRPV1 efficacy and potency as well as selectivity. The molecular modeling analysis highlighted crucial hydrophobic interactions between Leu547 and the iodo-thiophene nucleus, as in amide 2a, or between Phe543 and the pyridinyl moiety, as in 3a. In the biological evaluation, both compounds showed protective properties against oxidative stress-induced ROS formation in human keratinocytes. Additionally, while 2a showed neuroprotective effects in both neurons and rat brain slices, 3a exhibited potent antinociceptive effect in vivo..

Tuning of Heterocyclic Ring in Para-Benzi Heterosapphyrins.

Three examples of moderately aromatic p-benzi dithiasapphyrin and p-benzi tellurathiasapphyrins have been synthesized by condensing p-benzithiophene diol with 16-thia/telluratripyrrane under acid-catalyzed reaction conditions. The X-ray structural analysis showed that the thiophene ring in p-benzi dithiasapphyrin was inverted, whereas the tellurophene ring in p-benzi tellurathiasapphyrins was normal conformation with respect to the macrocyclic core. However, NMR studies revealed that the thiophene ring in protonated p-benzi dithiasapphyrin flips to normal, whereas the tellurophene ring in p-benzi tellurathiasapphyrins flips to inverted orientation.

Design, Synthesis and Aromaticity of an Alternating Cyclo[4]Thiophene[4]Furan.

A new class of conjugated macrocycle, the cyclo[4]thiophene[4]furan hexyl ester (C4TE4FE), is reported. This cycle consists of alternating α-linked thiophene-3-ester and furan-3-ester repeat units, and was prepared in a single step using Suzuki-Miyaura cross-coupling of a 2-(thiophen-2-yl)furan monomer. The ester side groups help promote a syn conformation of the heterocycles, which enables formation of the macrocycle. Cyclic voltammetry studies revealed that C4TE4FE could undergo multiple oxidations, so treatment with SbCl5 resulted in formation of the [C4TE4FE]2+ dication. Computational work, paired with 1 H NMR spectroscopy of the dication, revealed that the cycle becomes globally aromatic upon 2e- oxidation, as the annulene pathway along the outer ring becomes Hückel aromatic. The change in ring current for the cycle upon oxidation was clear from 1 H NMR spectroscopy, as the protons of the thiophene and furan rings shifted downfield by nearly 6 ppm. This work highlights the potential of sequence control in furan-based macrocycles to tune electronic properties.