Recent Advances in Structural Optimization of Quinazoline-Based Protein Kinase Inhibitors for Cancer Therapy (2021-Present).

Cancer is a complicated, multifaceted disease that can impact any organ in the body. Various chemotherapeutic agents have a low selectivity and are very toxic when used alone or in combination with others. Resistance is one of the most important hurdles that develop due to the use of many anticancer therapeutics. As a result, treating cancer requires a target-specific palliative care strategy. Remarkable scientific discoveries have shed light on several of the molecular mechanisms underlying cancer, resulting in the development of various targeted anticancer agents. One of the most important heterocyclic motifs is quinazoline, which has a wide range of biological uses and chemical reactivities. Newer, more sophisticated medications with quinazoline structures have been found in the last few years, and great strides have been made in creating effective protocols for building these pharmacologically active scaffolds. A new class of chemotherapeutic agents known as quinazoline-based derivatives possessing anticancer properties consists of several well-known compounds that block different protein kinases and other molecular targets. This review highlights recent updates (2021-2024) on various quinazoline-based derivatives acting against different protein kinases as anticancer chemotherapeutics. It also provides guidance for the design and synthesis of novel quinazoline analogues that could serve as lead compounds.

Design and Synthesis of Cofacially-Arrayed Polyfluorene Wires for Electron and Energy Transfer Studies.

A study of cofacially arrayed π-systems is of particular importance for the design of functional materials for efficient long-range intra-chain charge transfer through the bulk semiconducting materials in the layers of photovoltaic devices. The effect of π-stacking between a pair of aromatic rings has been mainly studied in the form of cyclophanes, where aromatic rings are forced into a sandwich-like geometry, which extensively deforms the aromatic rings from planarity. The synthetic difficulties associated with the preparation of cyclophane-like structures has prevented the synthesis of many examples of their multi-layered analogues. Moreover, the few available multi-layered cyclophanes are not readily amenable to the structural modification required for the construction of D-spacer-A triads needed to explore mechanisms of electron and energy transfer. In this review, we recount how a detailed experimental and computational analysis of 1,3-diarylalkanes led to the design of a new class of cofacially arrayed polyfluorenes that retain their π-stacked structure. Thus, efficient synthetic strategies have been established for the ready preparation of monodisperse polyfluorenes with up to six π-stacked fluorenes, which afford ready access to D-spacer-A triads by linking donor and acceptor groups to the polyfluorene spacers via single methylenes. Detailed 1H NMR spectroscopy, X-ray crystallography, electrochemistry, and He(I) photoelectron spectroscopy of F2-F6 have confirmed the rigid cofacial stacking of multiple fluorenes in F2-F6, despite the presence of rotatable C-C bonds. These polyfluorenes (F2-F6) form stable cation radicals in which a single hole is delocalized amongst the stacked fluorenes, as judged by the presence of intense charge-resonance transition in their optical spectra. Interestingly, these studies also discern that delocalization of a single cationic charge could occur over multiple fluorene rings in F2-F6, while the exciton is likely localized only onto two fluorenes in F2-F6. Facile synthesis of the D-spacer-A triads allowed us to demonstrate that efficient triplet energy transfer can occur through π-stacked polyfluorenes; the mechanism of energy transfer crosses over from tunneling to hopping with increasing number of fluorenes in the polyfluorene spacer. We suggest that the development of rigidly held π-stacked polyfluorenes, described herein, with well-defined redox and optoelectronic properties provides an ideal scaffold for the study of electron and energy transfer in D-spacer-A triads, where the Fn spacers serve as models for cofacially stacked π-systems.

Design, Synthesis, Electronic Properties, and X-ray Structural Characterization of Various Modified Electron-Rich Calixarene Derivatives and Their Conversion to Stable Cation Radical Salts.

We have designed and synthesized electron-rich calixarene derivatives, which undergo reversible electrochemical oxidation in a well-accessible potential range that allows the ready preparation and isolation of the corresponding cation radicals. Preparation of mono- or tetra-radical cation can be achieved by using stable aromatic cation-radical salts such as MA+•, MB+•, and NAP+• as selective organic oxidants. The cation radicals of calixarenes are stable indefinitely at ambient temperatures and can be readily characterized by UV-vis-NIR spectroscopy. These cation radicals bind a single molecule of nitric oxide within its cavity with remarkable efficiency.

New Quinoxaline-Based Derivatives as PARP-1 Inhibitors: Design, Synthesis, Antiproliferative, and Computational Studies.

Herein, 2,3-dioxo-1,2,3,4-tetrahydroquinoxaline was used as a bio-isosteric scaffold to the phthalazinone motif of the standard drug Olaparib to design and synthesize new derivatives of potential PARP-1 inhibitory activity using the 6-sulfonohydrazide analog 3 as the key intermediate. Although the new compounds represented the PARP-1 suppression impact of IC50 values in the nanomolar range, compounds 8a, 5 were the most promising suppressors, producing IC50 values of 2.31 and 3.05 nM compared to Olaparib with IC50 of 4.40 nM. Compounds 4, 10b, and 11b showed a mild decrease in the potency of the IC50 range of 6.35-8.73 nM. Furthermore, compounds 4, 5, 8a, 10b, and 11b were evaluated as in vitro antiproliferative agents against the mutant BRCA1 (MDA-MB-436, breast cancer) compared to Olaparib as a positive control. Compound 5 exhibited the most significant potency of IC50; 2.57 µM, whereas the IC50 value of Olaparib was 8.90 µM. In addition, the examined derivatives displayed a promising safety profile against the normal WI-38 cell line. Cell cycle, apoptosis, and autophagy analyses were carried out in the MDA-MB-436 cell line for compound 5, which exhibited cell growth arrest at the G2/M phase, in addition to induction of programmed apoptosis and an increase in the autophagic process. Molecular docking of the compounds 4, 5, 8a, 10b, and 11b into the active site of PARP-1 was carried out to determine their modes of interaction. In addition, an in silico ADMET study was performed. The results evidenced that compound 5 could serve as a new framework for discovering new potent anticancer agents targeting the PARP-1 enzyme.

An Aminoimidazole Radical Intermediate in the Anaerobic Biosynthesis of the 5,6-Dimethylbenzimidazole Ligand to Vitamin B12.

Organisms that perform the de novo biosynthesis of cobalamin (vitamin B12) do so via unique pathways depending on the presence of oxygen in the environment. The anaerobic biosynthesis pathway of 5,6-dimethylbenzimidazole, the so-called "lower ligand" to the cobalt center, has been recently identified. This process begins with the conversion of 5-aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (HBI) by the radical S-adenosyl-l-methionine (SAM) enzyme BzaF, also known as HBI synthase. In this work we report the characterization of a radical intermediate in the reaction of BzaF using electron paramagnetic resonance spectroscopy. Using various isotopologues of AIR, we extracted hyperfine parameters for a number of nuclei, allowing us to propose plausible chemical compositions and structures for this intermediate. Specifically, we find that an aminoimidazole radical is formed in close proximity to a fragment of the ribose ring. These findings induce the revision of past proposed mechanisms and illustrate the ability of radical SAM enzymes to tightly control the radical chemistry that they engender.

A Remarkable Oxidative Cascade That Replaces the Riboflavin C8 Methyl with an Amino Group during Roseoflavin Biosynthesis.

Roseoflavin is a naturally occurring riboflavin analogue with antibiotic properties. It is biosynthesized from riboflavin in a reaction involving replacement of the C8 methyl with a dimethylamino group. Herein we report the identification of a flavin-dependent enzyme that converts flavin mononucleotide (FMN) and glutamate to 8-amino-FMN via the intermediacy of 8-formyl-FMN. A mechanistic proposal for this remarkable transformation is proposed.

From Wires to Cables: Attempted Synthesis of 1,3,5-Trifluorenylcyclohexane as a Platform for Molecular Cables.

Multiple molecular wires braided together in a single assembly, termed as molecular cable, are promising next-generation materials for effective long-range charge transport. As an example of the platform for constructing molecular cables, 1,3,5-trifluorenylcyclohexane (TFC) and its difluorenyl analogues (DFCs) were systematically investigated both experimentally (X-ray crystallography) and theoretically (DFT calculations). Although the syntheses of DFCs were successfully achieved, the synthesis of TFC, which involved a similar intramolecular Friedel-Crafts cyclization as the last step, was unsuccessful. An exhaustive study of the conformational landscape of cyclohexane ring of TFC and DFCs revealed that TFC is a moderately strained molecule (∼17 kcal/mol), and computational studies of the reaction profile show that this steric strain, present in the transition state, is responsible for the unusually high (∼5 years) reaction half-life. A successful synthesis of TFC will require that the steric strain is introduced in multiple steps, and such alternative strategies are being currently explored.

Anaerobic 5-Hydroxybenzimidazole Formation from Aminoimidazole Ribotide: An Unanticipated Intersection of Thiamin and Vitamin B12 Biosynthesis.

Comparative genomics of the bacterial thiamin pyrimidine synthase (thiC) revealed a paralogue of thiC (bzaF) clustered with anaerobic vitamin B12 biosynthetic genes. Here we demonstrate that BzaF is a radical S-adenosylmethionine enzyme that catalyzes the remarkable conversion of aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (5-HBI). We identify the origin of key product atoms and propose a reaction mechanism. These studies represent the first step in solving a long-standing problem in anaerobic vitamin B12 assembly and reveal an unanticipated intersection of thiamin and vitamin B12 biosynthesis.

Molybdopterin biosynthesis-Mechanistic studies on a novel MoaA catalyzed insertion of a purine carbon into the ribose of GTP.

The first step in the biosynthesis of the molybdopterin cofactor involves an unprecedented insertion of the purine C8 carbon between the C2' and C3' carbons of the ribose moiety of GTP. Here we review mechanistic studies on this remarkable transformation. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.

Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase.

Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a ß-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the ß-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.

Radical S-adenosylmethionine (SAM) enzymes in cofactor biosynthesis: a treasure trove of complex organic radical rearrangement reactions.

In this minireview, we describe the radical S-adenosylmethionine enzymes involved in the biosynthesis of thiamin, menaquinone, molybdopterin, coenzyme F420, and heme. Our focus is on the remarkably complex organic rearrangements involved, many of which have no precedent in organic or biological chemistry.

Molybdopterin biosynthesis: trapping of intermediates for the MoaA-catalyzed reaction using 2'-deoxyGTP and 2'-chloroGTP as substrate analogues.

MoaA is a radical S-adenosylmethionine (AdoMet) enzyme that catalyzes a complex rearrangement of guanosine-5'-triphosphate (GTP) in the first step of molybdopterin biosynthesis. In this paper, we provide additional characterization of the MoaA reaction product, describe the use of 2'-chloroGTP to trap the GTP C3' radical, generated by hydrogen atom transfer to the 5'-deoxyadenosyl radical, and the use of 2'-deoxyGTP to block a late step in the reaction sequence. These probes, coupled with the previously reported trapping of an intermediate in which C3' of the ribose is linked to C8 of the purine, allow us to propose a plausible mechanism for the MoaA-catalyzed reaction.

Molybdopterin biosynthesis: trapping an unusual purine ribose adduct in the MoaA-catalyzed reaction.

MoaA/MoaC catalyze a remarkable rearrangement reaction in which guanosine-5'-triphosphate (GTP) is converted to cyclic pyranopterin monophosphate (cPMP). In this reaction, the C8 of GTP is inserted between the C2' and the C3' carbons of the GTP ribose. Previous experiments with GTP isotopomers demonstrated that the ribose C3' hydrogen atom is abstracted by the adenosyl radical. This led to a novel mechanistic proposal involving an intermediate with a bond between the C8 of guanine and C3' of the ribose. This paper describes the use of 2',3'-dideoxyGTP to trap this intermediate.

In vitro reconstitution of the radical S-adenosylmethionine enzyme MqnC involved in the biosynthesis of futalosine-derived menaquinone.

The radical S-adenosylmethionine enzyme MqnC catalyzes conversion of dehypoxanthine futalosine (DHFL) to the unique spiro compound cyclic DHFL in the futalosine pathway for menaquinone biosynthesis. This study describes the in vitro reconstitution of [4Fe-4S] cluster-dependent MqnC activity and identifies the site of abstraction of a hydrogen atom from DHFL by the adenosyl radical.

Catalysis of a new ribose carbon-insertion reaction by the molybdenum cofactor biosynthetic enzyme MoaA.

MoaA, a radical S-adenosylmethionine enzyme, catalyzes the first step in molybdopterin biosynthesis. This reaction involves a complex rearrangement in which C8 of guanosine triphosphate is inserted between C2' and C3' of the ribose. This study identifies the site of initial hydrogen atom abstraction by the adenosyl radical and advances a mechanistic proposal for this unprecedented reaction.

Electrochemistry and electrogenerated chemiluminescence of π-stacked poly(fluorenemethylene) oligomers. Multiple, interacting electron transfers.

The electrochemistry, spectroscopy, and electrogenerated chemiluminescence (ECL) of a series of π-stacked poly(fluorenemethylene) oligomers (Fn, n = 1-6) were investigated. The pendant cofacially oriented fluorene moieties are essentially in contact with each other by Van der Waals interaction promoting electronic delocalization in these species. All six compounds give successive cyclic voltammetric one-electron (1e) oxidations in 1:1 acetonitrile/benzene (MeCN/Bz), and the multiple 1e transfer properties of all these compounds were confirmed by chronoamperometric experiments with an ultramicroelectrode and digital simulations. The potentials for oxidation of the successive 1e transfers can be explained in terms of electrostatic interactions among the fluorenes. The monomer (F1) shows one irreversible wave, while F2 shows two reversible 1e waves. F3 shows only two reversible 1e oxidation waves, which is consistent with the large energy to remove a third electron because of the greater electrostatic repulsion, so the third wave is shifted toward more positive potentials. Both F4 and F5 show three reversible 1e oxidation waves, while F6 shows four reversible 1e waves. The removal of the first electron from an oligomer becomes easier as n increases. The stability of the radical cations also increases with n. The removal of consecutive electrons from Fn can be correlated with the distance between fluorene moieties. No reduction peaks were observed except for some broad ones at ~-3.2 V vs SCE in THF, which is consitent with the wide highest occupied molecular orbital-lowest unoccupied molecular orbital gap in these compounds (absorbance at about 300 nm). No characteristic annihilation ECL signal was observed for these compounds in 1:1 MeCN/Bz mixed solvent. However, the ECL of F6 in the presence of the coreactant C(2)O(4)(2-) showed a long-wavelength ECL emission that was proposed to be electrolyzed byproduct from the radical cation.

Crossover from single-step tunneling to multistep hopping for molecular triplet energy transfer.

Triplet energy transfer (TT), a key process in molecular and organic electronics, generally occurs by either strongly distance-dependent single-step tunneling or weakly distance-dependent multistep hopping. We have synthesized a series of pi-stacked molecules consisting of a benzophenone donor, one to three fluorene bridges, and a naphthalene acceptor, and studied the rate of TT from benzophenone to naphthalene across the fluorene bridge using femtosecond transient absorption spectroscopy. We show that the dominant TT mechanism switches from tunneling to wire-like hopping between bridge lengths 1 and 2. The crossover observed for TT can be determined by direct observation of the bridge-occupied state.

Intramolecular electron transfer in cofacially pi-stacked fluorenes: evidence of tunneling.

The one-electron reduction of neutral pi-stacked di- and trifluorenes (F-2 and F-3) in HMPA, where ion association is absent, results in the formation of anion radicals in which the odd electron resides predominantly on just one of the external fluorene moieties, as established by EPR spectroscopy. However, in the case of tetrafluorene, introduction of a single electron leads to a kinetically controlled anion radical F-4(int)*- in which the odd electron undergoes rapid exchange between two central fluorene rings, where the anionic charge is partially shielded from solvation due to the presence of external fluorene rings. On a time scale of minutes, anion radical F-4(int)*- converts to a thermodynamically stabilized anion radical F-4(ext)*-, with the electron exhibiting coupling from the protons on an external fluorene moiety. The charge and spin residing on an external moiety allow efficient solvation of the anionic charge. A similar fast exchange of a single electron (probably with the involvement of quantum mechanical tunneling) among three and four internal fluorene moieties is initially observed via EPR spectroscopy in the penta- and hexafluorene derivatives, F-5 and F-6, respectively.

A versatile and conformationally adaptable fluorene-based receptor for efficient binding of silver cation.

We have designed and synthesized a versatile fluorene-based receptor (1) in a one-pot reaction from readily available precursors, which adapts a deltaphane- or pi-prismand-like conformer via a simple C-C bond rotation. Such a conformational adaptability of 1 allows it to bind a single silver cation with remarkable efficiency (K approximately 15 000 M-1) as monitored by 1H NMR or UV-vis spectroscopy and further confirmed by competition experiments with tris[2.2.2]paracyclophane (or pi-prismand 2) as well as a model compound 3 containing only one fluoranyl ring.

Intramolecular C-H/C-D exchange in cofacially stacked polyfluorenes via electron-induced bond activation.

EPR studies in hexamethylphosphoramide, along with DFT studies, reveal that the one-electron reduction of pi-stacked polyfluorenes containing two, three, and four fluorene units leads to the corresponding anion radicals where the odd electron is located exclusively on an outside fluorene moiety. These anion radicals disproportionate to form small concentrations of diamagnetic dianions, wherein there is a nonclassical pz overlap that crosses the C2 axis. The presence of the two extra electrons activates the C-H bonds in the ortho positions, and concomitant overlap of the p-orbitals involving adjacent fluorene moieties results in intramolecular hydrogen exchange at temperatures as low as 90 K.