Acyclic Analogues Research Articles

Structurally Innovative Benzimidazole‐fused Ionic Organoselenium Compounds: Prevalence of Se···N/Se Chalcogen Bonds with the Selenocyanate Receptor

The non‐covalent interactions in molecules play important roles towards their applications in various aspects such as molecular recognition, catalysis, supramolecular chemistry, structural biology, pharmacology etc. Interestingly, among various non‐bonding interactions, chalcogen bonding (ChB) has been extensively studied in different facets of crystal engineering over the last several years. The present study demonstrates the presence of Se···N or Se···Se ChB in the benzimidazole‐fused cyclic selenazonium selenocyanates (6‐8), cyclic selenazinium selenocyanates (9‐10) and the acyclic benzimidazolium analogs having two different types of selenocyanate units (11‐12). The final organoselenium compounds were synthesized from benzimidazole in several steps in reasonably good yields. The single crystal X‐ray structures of the compounds revealed that both the N atom and Se atom of the negatively charged SeCN unit act as ChB acceptors in building the Se···N or Se···Se ChB interactions along with the additional hydrogen bonding (HB) interactions. Moreover, the structural optimization and natural bond orbital (NBO) analyses were carried out using density functional theory (DFT) to calculate the natural charges on different Se centers and the strength of second‐order perturbation energy (E2) for the ChB interactions. Finally, electrostatic potential surface (SEP) of the compounds was developed to visualize the formation of σ‐holes.

Synthesis, anticancer activity, docking and computational studies of new pyridyl-glycosyl hybrids and acyclic analogs.

New pyridine-O-glycosides and their acyclic nucleoside analogues were prepared by heterocyclization and glycosylation. The anticancer activity against HCT-116, HepG2 and MCF-7 human cancer cells and BJ-1 cell revealed that the galacto- and xylopyranosyl glycosides possessing 4-bromophenyl have superior cytotoxic activities against HepG2 cell while glycosides 7-9 resulted in superior cytotoxic activities regarding MCF-7 breast cell. In case of HCT-116 colorectal carcinoma cells, two products and the derived glycosides and acyclic analogues showed potent activities. The most potent compounds were investigated for their possible binding affinities to the active site of CDK2 enzyme via in silico molecular docking simulation in addition to computational studies. The results support the antiproliferative effect and elucidate the interactions of 3a and 8 with catalytic sites.

Mononuclear palladacycles versus acyclic analogues: a structure and reactivity comparison

The metallocyclic ring in mononuclear iminoisoindoline-based palladacycle [(κ2-iminoisoidoline)PdCl(PCy3)] (3) can be ring opened by coordination of phosphine to form the trans bis(phosphine) iminoisoindoline-based palladium(II) complex [(η1-iminoisoidoline)PdCl(PCy3)2] (4) where the η1-iminoisoindoline is coordinated only by an Ar-Pd bond. The ring-opened analogue showed significantly higher coupling activity in Suzuki-Miyaura reactions with aryl chlorides than any iminoisoindoline-based palladacycle studied to date. These results are compared to existing mononuclear palladacycles and reported acyclic analogues.

Structure-Activity Relationship Studies of the Peptide Antibiotic Clovibactin.

Our laboratory reported the chemical synthesis and stereochemical assignment of the recently discovered peptide antibiotic clovibactin. The current paper reports an improved, gram-scale synthesis of the amino acid building block Fmoc-(2R,3R)-3-hydroxyasparagine-OH that enables structure-activity relationship studies of clovibactin. An alanine scan reveals that residues Phe1, d-Leu2, Ser4, Leu7, and Leu8 are important for antibiotic activity. The side-chain amide group of the rare d-Hyn5 residue is not essential to activity and can be replaced with a methyl group with a moderate loss of activity. An acyclic clovibactin analogue reveals that the macrolactone ring is essential to antibiotic activity. The enantiomer of clovibactin is active, albeit somewhat less so than clovibactin. A conformationally constrained clovibactin analogue retains moderate antibiotic activity, while a backbone N-methylated analogue is almost completely inactive. X-ray crystallography of these two analogues reveals that the macrolactone ring adopts a crown-like conformation that binds anions.

2,5-Dimethoxy-benzylidene-rhodanine and its acyclic analogues as selective fluorogenic dyes for lipid droplets of living cells

We report about a series of arylidene-rhodanines and their acyclic analogues. The fluorescent properties of these substances were studied. We showed that the derivatives containing a 2,5-dimethoxybenzylidene fragment or similar groups are characterized by a noticeable variation in the fluorescence quantum yield depending on the properties of the medium. We discovered that two of the synthesized compounds – dimethoxy-benzylidene-rhodanine and dimethoxy-benzylidene-malononitrile – can be used as selective fluorogenic dyes for lipid droplets (adiposomes) of living cells for labeling under fluorescent microscopy conditions.

Fluoro-Crown Ether Phosphate as Efficient Cell-Permeable Drug Carrier by Disrupting Hydration Layer.

Fast and direct permeation of drug molecules is crucial for effective biotherapeutics. Inspired by a recent finding that fluorous compounds disrupt the hydrogen-bonded network of water, we developed fluoro-crown ether phosphate CyclicFP-X. This compound acts as a fast cell-permeating agent, enabling direct delivery of various bioactive cargos (X) into cancer cells without endocytic entrapment. In contrast, its nonfluorinated cyclic analog (CyclicP-X) failed to achieve cellular internalization. Although the acyclic fluorous analog AcyclicFP-X was internalized, this process occurred slowly owing to the involvement of an endocytic trapping pathway. Designed with a high fluorine density, CyclicFP-X exhibits compactness, polarity, and high-water solubility, facilitating lipid vesicle fusion by disrupting their hydration layers. Raman spectroscopy confirmed the generation of dangling -OH bonds upon addition of CyclicFP-OH to water. Furthermore, conjugating CyclicFP-X with fluorouracil (FU, an anticancer drug) via a reductively cleavable disulfide linker (CyclicFP-SS-FU) demonstrated the general utility of fluoro-crown ether phosphate as a potent carrier for biotherapeutics.

Synthesis of acyclic nucleoside analogues through P(NMe2)3-Mediated regioselective N-alkylation

A novel and efficient approach for synthesizing acyclic nucleoside analogues with a side chain length of two carbon atoms has been established. It involves purines reacting with α-keto esters in a P(NMe2)3-mediated deoxygenation process, yielding the products in high yields and regioselectivities (22 examples, up to 93 % yield, up to >20:1 N9/N7 selectivities). This reaction features short reaction times, metal-free catalysis, mild reaction conditions, and broad substrate scope, all of which make it promising for practical applications.

Synthesis of Chiral Acyclic Pyrimidine Nucleoside Analogues from DHAP-Dependent Aldolases.

Dihydroxyacetone phosphate (DHAP)-dependent aldolases catalyze the aldol addition of DHAP to a variety of aldehydes and generate compounds with two stereocenters. This reaction is useful to synthesize chiral acyclic nucleosides, which constitute a well-known class of antiviral drugs currently used. In such compounds, the chirality of the aliphatic chain, which mimics the open pentose residue, is crucial for activity. In this work, three DHAP-dependent aldolases: fructose-1,6-biphosphate aldolase from rabbit muscle, rhanmulose-1-phosphate aldolase from Thermotoga maritima, and fuculose-1-phosphate aldolase from Escherichia coli, were used as biocatalysts. Aldehyde derivatives of thymine and cytosine were used as acceptor substrates, generating new acyclic nucleoside analogues containing two new stereocenters with conversion yields between 70% and 90%. Moreover, structural analyses by molecular docking were carried out to gain insights into the diasteromeric excess observed.

Drug development of paracetamol derivative as antimicrobial activity

Paracetamol derivatives with their N-subsitituted Acyclic Analogues and then subsitituted with a pro drug to enhance its activity by forming cocrystal of Antibacterial & Antifungal and then enhancing the analgesic activity of Paracetamol by attaching it to Dendrimers which enhance it activities against E. Coli & Staphylococcus Auerus and they exhibit high to moderate antimicrobial activity.

Rutaecarpine-inspired scaffold-hopping strategy and Ullmann cross-coupling based synthetic approach: Identification of pyridopyrimidinone-indole based novel anticancer chemotypes

Natural products as starting templates have shown historically major contribution to development of drugs. Inspired by the structure–function of an anticancer natural alkaloid Rutaecarpine, the Scaffold-hopped Acyclic Analogues of Rutaecarpine (SAAR) with ‘N’-atom switch (1°-hop) and ring-opening (2°-hop) were investigated. A new synthetic route was developed for an effective access to the analogues, i.e. 2-indolyl-pyrido[1,2-a]pyrimidinones, which involved preparation of N-Boc-N’-phthaloyltryptamine/mexamine-bromides and pyridopyrmidinon-2-yl triflate, a nickel/palladium-catalysed Ullmann cross-coupling of these bromides and triflate, deprotection of phthalimide followed by N-aroylation, and Boc-deprotection. Fourteen novel SAAR-compounds were prepared, and they showed characteristic antiproliferative activity against various cancer cells. Three most active compounds (11a, 11b, and 11c) exhibited good antiproliferative activity, IC50 7.7–15.8 µM against human breast adenocarcinoma cells (MCF-7), lung cancer cells (A549), and colon cancer cells (HCT-116). The antiproliferative property was also observed in the colony formation assay. The SAAR compound 11b was found to have superior potency than original natural product Rutaecarpine and an anticancer drug 5-FU in antiproliferative activities with relatively lower cytotoxicity towards normal breast epithelial cells (MCF10A) and significantly higher inhibitory effect on cancer cells’ migration. The compound 11b was found to possess favourable in silico physicochemical characteristics (lipophilicity-MLOGP, TPSA, and water solubility-ESOL, and others), bioavailability score, and pharmacokinetic properties (GI absorption, BBB non-permeant, P-gp, and CYP2D6). Interestingly, the compound 11b did not show any medicinal chemistry structural alert of PAINS and Brenk filter. The study represents for the first time the successful discovery of new potent anticancer chemotypes using Rutaecarpine natural alkaloid as starting template and reaffirms the significance of natural product-inspired scaffold-hopping technique in drug discovery research.

Remission of HPV-Related Diseases by Antivirals for Herpesvirus: Clinical Cases and a Literature Review.

Epidemiological studies have shown that HPV-related diseases are the most prevalent sexually transmitted infections. In this context, this report will present various clinical cases demonstrating the effectiveness of Acyclovir (ACV) or its prodrug Valaciclovir (VCV), both acyclic guanosine analogs commonly used for the treatment of HHV-1 and HHV-2, for the treatment of HPV-related diseases. The report shows the remission of five cases of penile condyloma and a case of remission in a woman affected by cervical and vaginal condylomas and a vulvar giant condyloma acuminate of Buschke and Lowenstein. The literature review shows that ACV is effective in treating skin warts when administered orally, topically, and intralesionally, suggesting its therapeutic potential in other diseases associated with HPV. ACV was also used successfully as an adjuvant therapy for juvenile and adult forms of laryngeal papillomatosis, also known as recurrent respiratory papillomatosis, prolonging the patient's symptom-free periods. Although the prevention of HPV infections is certainly achieved with the HPV vaccine, ACV and VCV have shown to be effective even against genotypes not included in the current vaccine and can be helpful for those problematic clinical cases involving unvaccinated individuals, immunocompromised patients, people who live with HIV, or non-responders to the vaccine. We and others concluded that randomized clinical trials are necessary to determine the efficacy of ACV and VCV for HPV-related diseases.

Pharmacogenetics of tenofovir drug transporters in the context of HBV: Is there an impact?

BackgroundCurrent treatments for chronic hepatitis B management include orally administered nucleos(t)ide analogues, such as tenofovir (TDF), which is an acyclic adenine nucleotide analogue used both in HBV and human immune deficiency virus (HIV). The course of HBV infection is mainly dependent on viral factors, such as HBV genotypes, immunological features and host genetic variables, but a few data are available in the context of HBV, in particular for polymorphisms of genes encoding proteins involved in drug metabolism and elimination.Consequently, the aim of this study was to evaluate the potential impact of genetic variants on TDF plasma and urine concentrations in patients with HBV, considering the role of HBV genotypes. MethodsA retrospective cohort study at the Infectious Disease Unit of Amedeo di Savoia Hospital, Torino, Italy, was performed. Pharmacokinetic analyses were performed through liquidi chromatography, whereas pharmacogenetic analyses through real-time PCR. FindingsSixty - eight patients were analyzed: ABCC4 4976 C>T genetic variant showed an impact on urine TDF drug concentrations (p = 0.014). In addition, SLC22A6 453 AA was retained in the final regression multivariate model considering factors predicting plasma concentrations, while ABCC4 4976 TC/CC was the only predictor of urine concentrations in the univariate model. InterpretationIn conclusion, this is the first study showing a potential impact of genetic variants on TDF plasma and urine concentrations in the HBV context, but further studies in different and larger cohorts of patients are required.

Metalla-Carbaporphyrinoids Consisting of an Acyclic N-Confused Tetrapyrrole Analogue Served as Stable Near-Infrared-II Dyes.

We present herein the synthesis of novel pseudo-metalla-carbaporphyrinoid species (1M: M=Pd and Pt) achieved through the inner coordination of palladium(II) and platinum(II) with an acyclic N-confused tetrapyrrin analogue. Despite their tetrapyrrole frameworks being small, akin to well-known porphyrins, these species exhibit an unusually narrow HOMO-LUMO gap, resulting in an unprecedentedly low-energy absorption in the second near-infrared (NIR-II) region. Density functional theory (DFT) calculations revealed unique dπ-pπ-conjugated electronic structures involving the metal dπ-ligand pπ hybridized molecular orbitals of 1M. Magnetic circular dichroism (MCD) spectroscopy confirmed distinct electronic structures. Remarkably, the complexes feature an open-metal coordination site in the peripheral NN dipyrrin site, forming hetero-metal complexes (1Pd-BF2 and 1Pt-BF2) through boron difluoride complexation. The resulting hetero metalla-carbaporphyrinoid species displayed further redshifted NIR-II absorption, highly efficient photothermal conversion efficiencies (η; 62-65 %), and exceptional photostability. Despite the challenges associated with the theoretical and experimental assessment of dπ-pπ-conjugated metalla-aromaticity in relatively larger (more than 18π electrons) polycyclic ring systems, these organometallic planar tetrapyrrole systems could serve as potential molecular platforms for aromaticity-relevant NIR-II dyes.

Arylidene-imidazolones and their acyclic analogue as fluorescent sensors of metal ions

We report about a series of methylene-imidazolones with complexing groups. The fluorescent properties of these compounds were studied in various solvents as well as in the presence of different salts. We discovered that two of the synthesized substances – hydroxyquinolinidene-imidazolone and difluorobenzimidazolidene-imidazolone – can be used as selective fluorescent sensors for cadmium and zinc ions and potentially as markers for monitoring intracellular processes.

Chiral Bis-phosphate Macrocycles for Catalytic, Efficient, and Enantioselective Electrophilic Fluorination.

Incorporation of privileged catalytic scaffolds into a macrocyclic skeleton represents an attractive strategy to furnish supramolecular catalysis systems with enzyme-mimetic cavity and multi-site cooperation. Herein we reported the synthesis, structure, binding properties and catalytic application of a series of chiral bis-phosphate macrocycles toward the challenging asymmetric electrophilic fluorination. With a large, integrated chiral cavity and two cooperative phosphate sites, these macrocycles exhibited good inclusion toward 1,4-diazabicyclo[2.2.2]octane (DABCO) dicationic ammoniums through complementary ion-pair and C-H⋅⋅⋅O interactions, as confirmed by crystallographic and solution binding studies. In fluorocyclization of tryptamines with Selectfluor reagent which has a similar DABCO-based dicationic structure, only 2 mol% macrocycle catalyst afforded the desired pyrroloindoline products in moderate yields and up to 91 % ee. For comparison, the acyclic mono-phosphate analogue gave obviously lower reactivity and enantioselectivity (<20 % ee), suggesting a remarkable macrocyclic effect. The high catalytic efficiency and superior stereocontrol were ascribed to the tight ion-pair binding and cavity-directed noncovalent interaction cooperation.

2,5-Dimethoxy-Benzylidene-Rhodanine and Its Acyclic Analogues as Selective Fluorogenic Dyes for Lipid Droplets of Living Cells

2,5-Dimethoxy-Benzylidene-Rhodanine and Its Acyclic Analogues as Selective Fluorogenic Dyes for Lipid Droplets of Living Cells

Atroposelective Construction of Tetrasubstituted Axially Chiral Alkene Frameworks

AbstractThe construction of axially chiral alkene frameworks is currently one of hottest topics in the field of organic synthetic chemistry. Compared to traditional axially chiral molecules, such as biaryls, heterobiaryls, and anilides, the synthesis of axially chiral alkenes is far more challenging, especially for acyclic tetrasubstituted alkene analogues. In this review, we summarized the development of strategies for the synthesis of tetrasubstituted axially chiral alkene analogues, including asymmetric difunctionalization, C–H functionalization, cross-coupling, (dynamic) kinetic resolution, and asymmetric allylic substitution-isomerization.1 Introduction2 Synthesis of Cyclic Tetrasubstituted Axially Chiral Alkenes3 Synthesis of Acyclic Tetrasubstituted Axially Chiral Alkenes4 Summary and Outlook

Exploiting the Mechanical Bond Effect for Enhanced Molecular Recognition and Sensing.

The ubiquity of charged species in biological and industrial processes has resulted in ever-increasing interest in their selective recognition, detection, and environmental remediation. Building on the established coordination chemistry principles of the chelate and macrocyclic effects, and host preorganization, supramolecular chemists seek to construct specific 3D binding cavities reminiscent of biotic systems to enhance host-guest binding affinity and selectivity. Mechanically interlocked molecules (MIMs) present a wholly unique platform for synthetic host design, wherein topologies afforded by the mechanical bond enable the decoration of 3D cavities for non-covalent interactions with a range of target guest geometries. Notably, MIM host systems exhibit mechanical bond effect augmented affinities and selectivities for a variety of charged guest species, compared to non-interlocked acyclic and macrocycle host analogs. Furthermore, the modular nature of MIM synthesis facilitates incorporation of optical and electrochemical reporter groups, enabling fabrication of highly sensitive and specific molecular sensors. This review discusses the development of recognition and sensing MIMs, from the first reports in the late 20th century through to the present day, delineating how their topologically preorganized and dynamic host cavities enhance charged guest recognition and sensing, demonstrating the mechanical bond effect as a potent tool in future chemosensing materials.

Nucleos(t)ide analogs for hepatitis B virus infection differentially regulate the growth factor signaling in hepatocytes.

Recent clinical studies have suggested that the risk of developing HCC might be lower in patients with chronic hepatitis B receiving tenofovir disoproxil fumarate than in patients receiving entecavir, although there is no difference in biochemical and virological remission between the 2 drugs. The effects of nucleoside analogs (NsAs; lamivudine and entecavir) or nucleotide analogs (NtAs; adefovir disoproxil, tenofovir disoproxil fumarate, and tenofovir alafenamide) on cell growth and the expression of growth signaling molecules in hepatoma cell lines and PXB cells were investigated in vitro. The tumor inhibitory effects of NsAs or NtAs were evaluated using a mouse xenograft model, and protein phosphorylation profiles were investigated. The binding of NsAs or NtAs to the insulin receptor (INSR) was investigated by thermal shift assays. NtAs, but not NsAs, showed direct growth inhibitory effects on hepatoma cell lines in vitro and a mouse model in vivo. A phosphoprotein array revealed that INSR signaling was impaired and the levels of phosphorylated (p)-INSRβ and downstream molecules phosphorylated (p)-IRS1, p-AKT, p-Gab1, and p-SHP2 were substantially reduced by NtAs. In addition, p-epidermal growth factor receptor and p-AKT levels were substantially reduced by NtAs. Similar findings were also found in PXB cells and nontumor lesions of liver tissues from patients with chronic hepatitis B. Prodrug NtAs, but not their metabolites (adefovir, adefovir monophosphate, adefovir diphosphate, tenofovir, tenofovir monophosphate, and tenofovir diphosphate), had such effects. A thermal shift assay showed the binding of NtAs to INSRβ. NtAs (adefovir disoproxil, tenofovir disoproxil fumarate, and tenofovir alafenamide), which are adenine derivative acyclic nucleotide analogs, potentially bind to the ATP-binding site of growth factor receptors and inhibit their autophosphorylation, which might reduce the risk of HCC in patients with chronic hepatitis B.

Synthesis of acyclic analogues of adenosine sulfonamides and their activity against RNA cap guanine N7-methyltransferase of SARS-CoV-2

Original N-arylsulfonamide acyclic analogues of adenosine as bisubstrates of RNA cap guanine N7-methyltransferase nsp14 of SARS-CoV-2 were prepared and some of them were barely active at 50 μM against this RNA cap methylation enzyme.