A novel 3-((5-methylpyridin-2-yl)amino)isobenzofuran-1(3H)-one: Molecular structure describe, X-ray diffractions and DFT calculations, antioxidant activity, DNA binding and molecular docking studies

Investigation of the ability of 3-((4-chloro-6-methyl pyrimidin-2-yl)amino) isobenzofuran-1(3H)-one to bind to double-stranded deoxyribonucleic acid

Phthalides represent a notable category of secondary metabolites that are prevalent in various plant species, certain fungi, and liverworts. The significant pharmacological properties of these compounds have led to the synthesis of a novel phthalide derivative. The current study focuses on investigating the binding interactions of a newly synthesized 3-substituted phthalide derivative, specifically 3-((4-chloro-6-methyl pyrimidine-2-yl)amino) isobenzofuran-1(3H)-one (Z11), with double-stranded deoxyribonucleic acid (dsDNA). Research in the pharmaceutical and biological fields aimed at developing more potent DNA-binding agents must take into account the mechanisms by which these newly synthesized compounds interact with DNA. This investigation seeks to explore the binding dynamics between dsDNA and our compound through a variety of analytical techniques, such as electrochemistry, UV spectroscopy, fluorescence spectroscopy, and thermal denaturation. The binding constant (Kb) of Z11 with DNA was determined using both spectroscopic and voltammetric approaches. The research revealed that Z11 employs a groove binding mechanism to associate with dsDNA. To further explore the interactions between Z11 and dsDNA, the study utilized density functional theory (DFT) calculations, molecular docking, and molecular dynamics simulations. These analyses aimed to ascertain the potential for a stable complex formation between Z11 and dsDNA. The results indicate that Z11 is situated within the minor groove of the dsDNA, demonstrating the ability to establish a stable complex. Furthermore, the findings imply that both π-alkyl interactions and hydrogen bonding play significant roles in the stabilization of this complex.

Natural dihydroisobenzofuran derivatives as a template for promising radical scavengers: theoretical insights into structure–activity relationships, thermochemistry and kinetics

Dihydroisobenzofuran heterocycle is a structural motif found in a number of medications with anti-tumour, anti-diabetic, and antibacterial activities. It is also found in a slew of natural substances, most notably fungus metabolites, which have been shown to possess credible radical scavenging activity. Density functional theory studies on three different derivatives were conducted to investigate their electronic structures as well as thermochemical and kinetic behaviour against ·OOH, ·OH, and ·OCH3 in biologically relevant solvents, with the goal of elucidating structure–activity relationships and discussing the potential role of the scaffolds as a template for new semisynthetic antioxidants. The importance of resonance and inductive effects, and also hydrogen bonding, has been underlined, but most importantly, it has been demonstrated that all structures have considerable scavenging potential against all studied radicals, with reactions rates close to the diffusion limit.

Unexpected Formation of 4-[(1-Carbamoyl-3-oxo-1,3-dihydro-2-benzofuran-1-yl)amino]benzoic Acid from 4-[(3-Amino-1-oxo-1H-2-benzopyran-4-yl)amino]benzoic Acid

With the aim of obtaining derivatives belonging to 2′,3′-diphenyl-3H-spiro[[2]benzofuran-1,4′-imidazole]-3,5′(3′H)-dione nucleus, we synthesized 4-[(3-amino-1-oxo-1H-2-benzopyran-4-yl)amino]benzoic acid (a 3,4-diaminoisocoumarine derivative), a known precursor of 4-[(1-carbamoyl-3-oxo-1,3-dihydro-2-benzofuran-1-yl)amino]benzoic acid (a phthalide–carboxamide-bearing system) by a novel methodology that we report here. The reaction conditions were optimized to afford the latter in 62% yield.

Identification of a 3-(5-methyl-2-thiazolylamino)phthalide as a new minor groove agent

A new 3-(5-methyl-2-thiazolylamino)phthalide molecule, 3-((5-methylthiazol-2-yl)amino)isobenzofuran-1(3H)-one, was synthesized and characterized experimentally by FT-IR, NMR, UV-Vis, and single-crystal X-ray analysis and theoretically by quantum chemical calculations. The single-crystal X-ray studies revealed that the compound crystallizes in the monoclinic space group P-2_1/c with unit-cell parameters a = 8.0550(6) Å, b = 6.1386(3) Å, c = 23.3228(18) Å, β = 97.724(6)° and Z = 4. Optimized geometries and the vibrational frequencies were studied at the density functional theory (DFT) level by using the hybrid functional B3LYP with a 6-311 G (d,p) basis set. The title compound was evaluated for its anti-quorum sensing (anti-QS) activity on Chromobacterium violaceum 12472 and additionally for its antibacterial activity against Staphylococcus aureus 29213, Staphylococcus epidermidis 12228, Pseudomonas aeruginosa 27853, Escherichia coli 25922, and Proteus mirabilis 14153. The lowest MIC value was 0.24 μg/mL for S. aureus 29213 and the highest MIC value was 30.75 μg/mL for E. coli 25922. While anti-bacterial activity was observed in those other than the S. epidermidis and P. Mirabilis, anti-QS activity wasn't detected. Investigations on dsDNA binding affinity indicate that the title compound binds to dsDNA via the groove binding mode. Molecular docking calculations and molecular dynamics simulations results showed also that the title compound prefers binding to the minor groove of dsDNA and remains stable in the minor groove throughout the molecular dynamics simulation.Communicated by Ramaswamy H. Sarma.

Depicting the DNA Binding and Cytotoxicity Studies against Human Colorectal Cancer of Aquabis (1-Formyl-2-Naphtholato-k2O,O′) Copper(II): A Biophysical and Molecular Docking Perspective

In this study, we attempted to examine the biological activity of the copper(II)–based small molecule aquabis (1-formyl-2-naphtholato-k2O,O′)copper(II) (1) against colon cancer. The characterization of complex 1 was established by analytical and spectral methods in accordance with the single-crystal X-ray results. A monomeric unit of complex 1 exists in an O4 (H2O) coordination environment with slightly distorted square pyramidal geometry (τ = ~0.1). The interaction of complex 1 with calf thymus DNA (ctDNA) was determined by employing various biophysical techniques, which revealed that complex 1 binds to ctDNA at the minor groove with a binding constant of 2.38 × 105 M–1. The cytotoxicity of complex 1 towards human colorectal cell line (HCT116) was evaluated by the MTT assay, which showed an IC50 value of 11.6 μM after treatment with complex 1 for 24 h. Furthermore, the apoptotic effect induced by complex 1 was validated by DNA fragmentation pattern, which clarified that apoptosis might be regulated through the mitochondrial-mediated production of reactive oxygen species (ROS) causing DNA damage pathway. Additionally, molecular docking was also carried out to confirm the recognition of complex 1 at the minor groove.

DFT study on some polythiophenes containing benzo[d]thiazole and benzo[d]oxazole: structure and band gap

The content of this paper focuses/shed light on the effects of X (X = S in P1 and X = O in P2) in C11H7NSX and R (R = H in P3, R = OCH3 in P4, and R = Cl in P5) in C18H9ON2S2-R on structural features and band gaps of the polythiophenes containing benzo[d]thiazole and benzo[d]oxazole by the Density Function Theory (DFT) method/calculation. The structural features including the electronic structure lattice constant (a), shape, total energy (Etot) per cell, and link length (r), are measured via band gap (Eg) prediction with the package of country density (PDOS) and total country density (DOS) of material studio software. The results obtained showed that the link angle and the link length between atoms were not changed significantly while the Etot was decreased from Etot = - 1904 eV (in P1) to Etot = - 2548 eV (in P2) when replacing O with S; and the Etot of P3 was decreased from Etot = - 3348 eV (in P3) when replacing OCH3, Cl on H of P3 corresponding to Etot = - 3575 eV (P4), - 4264 eV (P5). Similarly, when replacing O in P1 with - S to form P2, the Eg of P1 was dropped from Eg = 0.621 eV to Eg = 0.239 eV for P2. The Eg of P3, P4, and P5 is Eg = 0.006 eV, 0.064 eV, and 0.0645 eV, respectively. When a benzo[d]thiazole was added in P1 (changing into P3), the Eg was extremely strongly decreased, nearly 100 times (from Eg = 0.621 eV to Eg = 0.006 eV). The obtained results serve as a basis for future experimental work and used to fabricate smart electronic device.

Crystal structure, spectral investigations, DFT and antimicrobial activity of brucinium benzilate (BBA)

The unreported brucinium benzilate (BBA) crystal and Hirshfeld surface analysis indicated the influence of intramolecular hydrogen bonding network on the crystal structure. Protonation occurs at the tertiary nitrogen as it is the most basic site. The protonated N-H⁺ proton was observed at 7.08 ppm and the benzilate carbon COO^- at 178.41 ppm. Molecular electrostatic potential (MEP) studies showed the electron-rich and electron-deficient sites in the molecule for understanding BBA interaction with an enzyme. Frontier molecular orbital (FMO) studies indicated that BBA molecule is thermodynamically stable and the HOMO-LUMO energy gap was found to be 4.454 eV. The highest interaction has the energy (322.86 kcal/mol) between tertiary ammonium N(LP) and H⁺. Inhibition tests showed that brucinium benzilate inhibits Bacillus cereus and Salmonella typhimurium bacteria. ADMET properties indicated that BBA has drug characteristics in binding plasma protein.

One-Pot Synthesis of Spiro-isobenzofuran Compounds via the Sequential Condensation/Oxidation Reaction of Ninhydrin with 4-Amino-1,2-naphthoquinones/2-Amino-1,4-naphthoquinones under Mild Conditions

A one-pot route for the synthesis of spiro-isobenzofuran compounds was developed via the condensation reaction of ninhydrin with 4-amino-1,2-naphthoquinones or 2-amino-1,4-naphthoquinones in acetic acid followed by the oxidative cleavage of the corresponding vicinal diols at room temperature. Various derivatives of spiro[benzo[g]indole-2,1'-isobenzofuran]-3,3',4,5(1H) tetraones and spiro[benzo[f]pyrrolo[2,3-h]quinoxaline-2,1'-isobenzofuran]-3,3'(1H)-diones were synthesized in good to high yields. Moreover, further condensation of spiro[benzo[g]indole-2,1'-isobenzofuran]-3,3',4,5(1H)-tetraones with 1,2-diamines resulted in the new spiro-isobenzofuran compounds having phenazine rings in high yields.