DFT and molecular simulation validation of the binding activity of PDEδ inhibitors for repression of oncogenic k-Ras

The development of effective drugs targeting the K-Ras oncogene product is a significant focus in anticancer drug development. Despite the lack of successful Ras signaling inhibitors, recent research has identified PDEδ, a KRAS transporter, as a potential target for inhibiting the oncogenic KRAS signaling pathway. This study aims to investigate the interactions between eight K-Ras inhibitors (deltarazine, deltaflexin 1 and 2, and its analogues) and PDEδ to understand their binding modes. The research will utilize computational techniques such as density functional theory (DFT) and molecular electrostatic surface potential (MESP), molecular docking, binding site analyses, molecular dynamic (MD) simulations, electronic structure computations, and predictions of the binding free energy. Molecular dynamic simulations (MD) will be used to predict the binding conformations and pharmacophoric features in the active site of PDEδ for the examined structures. The binding free energies determined using the MMPB(GB)SA method will be compared with the observed potency values of the tested compounds. This computational approach aims to enhance understanding of the PDEδ selective mechanism, which could contribute to the development of novel selective inhibitors for K-Ras signaling.

Antibacterial Activity of Quinoline-Based Derivatives against Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa: Design, Synthesis, DFT and Molecular Dynamic Simulations

Bacterial virulence becomes a significant challenge for clinical treatments, particularly those characterized as Multi-Drug-Resistant (MDR) strains. Therefore, the preparation of new compounds with active moieties could be a successful approach for eradication of MDR strains. For this purpose, newly synthesized quinoline compounds were prepared and tested for their antimicrobial activity against Methicillin-Resistant Staphylococcus Aureus (MRSA) and Pseudomonas Aeruginosa (PA). Among the synthesized derivatives, compounds 1-(quinolin-2-ylamino)pyrrolidine-2,5-dione (8) and 2-(2-((5-methylfuran-2-yl)methylene)hydrazinyl)quinoline (12) were shown to possess the highest antimicrobial activity with the minimum inhibitory concentration with the values of 5±2.2 and10±1.5 μg/mL towards Pseudomonas aeruginosa without any activity towards MRSA. Interestingly, compounds 2-(2-((1H-indol-3-yl)methylene)hydrazinyl)quinoline (13) and 2-(4-bromophenyl)-3-(quinolin-2-ylamino)thiazolidin-4-one (16c) showed significant inhibition activity against Staphylococcus aureus MRSA and Pseudomonas aeruginosa. Compound 13 (with indole moiety) particularly displayed excellent bactericidal activity with low MIC values 20±3.3 and 10±1.5 μg/mL against Staphylococcus aureus MRSA and Pseudomonas aeruginosa, respectively. Effects molecular modelling was used to determine the mode of action for the antimicrobial effect. The stability of complexes formed by docking and target-ligand pairing was evaluated using molecular dynamics simulations. The compounds were also tested for binding affinity to the target protein using MM-PBSA. Density-functional theory (DFT) calculations were also used to investigate the electrochemical properties of various compounds.

Discovery of Novel Coumarin-Schiff Base Hybrids as Potential Acetylcholinesterase Inhibitors: Design, Synthesis, Enzyme Inhibition, and Computational Studies

To discover anti-acetylcholinesterase agents for the treatment of Alzheimer's disease (AD), a series of novel Schiff base-coumarin hybrids was rationally designed, synthesized successfully, and structurally characterized using Fourier transform infrared (FTIR), Nuclear magnetic resonance (NMR), and High-Resolution Mass Spectrometry (HRMS) analyses. These hybrids were evaluated for their potential inhibitory effect on acetylcholinesterase (AChE). All of them exhibited excellent inhibitory activity against AChE. The IC₅₀ values ranged from 87.84 to 515.59 μg/mL; hybrids 13c and 13d with IC₅₀ values of 0.232 ± 0.011 and 0.190 ± 0.004 µM, respectively, showed the most potent activity as acetylcholinesterase inhibitors (AChEIs). The reference drug, Galantamine, yielded an IC₅₀ of 1.142 ± 0.027 µM. Reactivity descriptors, including chemical potential (μ), chemical hardness (η), electrophilicity (ω), condensed Fukui function, and dual descriptors are calculated at wB97XD/6-311++ G (d,p) to identify reactivity changes of the designed compounds. An in-depth investigation of the natural charge pattern of the studied compounds led to a deep understanding of the important interaction centers between these compounds and the biological receptors of AChE. The molecular electrostatic surface potential (MESP) of the most active site in these derivatives was determined using high-quality information and visualization. Molecular docking analysis was performed to predict binding sites and binding energies. The structure-activity-property relationship studies indicated that the proposed compounds exhibit good oral bioavailability properties. To explore the stability and dynamic behavior of the ligand-receptor complexes, molecular dynamics simulations (MDS) were performed for 100 ns on the two best docked derivatives, 13c and 13d, with the AChE (4EY7) receptor. A popular method for determining the free binding energies (MM/GBSA) is performed using snapshots taken from the systems' trajectories at 100 ns. These results revealed that the complex system of compound 13d acquired a relatively more stable conformation and exhibited better descriptors than the complex system of compound 13c and the Galantamine drug, suggesting its potential as an effective inhibiting drug. The binding free energy analysis revealed that the 13d-4EY7 complex exhibited greater stability with AChE receptors compared to other complexes.

Synthesis, spectral characterization, DFT calculations, pharmacological studies, CT-DNA binding and molecular docking of potential N, O-multidentate chelating ligand and its VO(II), Zn(II) and ZrO(II) chelates

The pharmacological efficacy of the variety tetradentate ligands encouraged us to design attractive compounds through effective synthetic procedure. The prepared Schiff base ligand 6,6'-((1E,1'E)-((4-chloro-1,2-phenylene)bis(azaneylylidene))bis(methaneylylidene))bis(2-ethoxy phenol (H₂L), which derived from 4-chloro-o-phenylenediamine and 3-ethoxy-salicylaldehyde and its VO(II), Zn(II) and ZrO(II) metal chelates, have been synthesized and characterized with aim of that it may struggle the invasion of drug resistance. The chemical structural of studied compounds were discussed by TGA, elemental analysis, UV-Vis., ¹H NMR, ¹³C NMR, FTIR, mass spectral, PXRD, molar conductance, magnetic susceptibility measurements and density functional theory. The results assigned square pyramid geometries for [VOL] and [ZrOL].2H₂O chelates and an octahedral geometry for [ZnL(H₂O)₂].2H₂O chelate. Powder XRD data showed that the complexes are monoclinic with polycrystalline nature. The results of CT-DNA interaction with the titled chelates showed that the binding between CT-DNA and the metal complexes occurs through intercalation mode. Their CT-DNA binding efficiency estimated in terms of their binding constants (K_b), which gave the order: VOL (6.9 × 10⁵) > ZrOL (6.3 × 10⁵) > ZnL(H₂O)₂ (5.5 × 10⁵). The antimicrobial activities of the synthesized compounds were tested against selected fungal and bacterial strains using well diffusion technique. The obtained chelates showed higher antifungal and antibacterial activities than their corresponding ligand. Furthermore, the M-complexes showed higher potent cytotoxic effect toward HEK-293, human colorectal HepG-2, HCT-116 and MCF-7 adenocarcinoma cell lines compared to the free H₂L ligand. Investigation of antioxidant property represented that all the prepared complexes have better radical scavenging potencies against DPPH radicals than the free H₂L ligand. To study the molecular docking of proposed compounds versus Tyrosine kinases receptor (TKR), we used AutoDock1.5.6rc3® suite. The current compounds (H₂L, VOL, ZrOL and ZnL(H₂O)₂) and STI were found to bind with C-kit of TKR with HBs at ILE789.A, ILE808.A, ASP810.A, GLU640.A and TYR846 amino acid residue and the binding energies were - 8.9, -8.93, -8.83, -1.48 and -10.39 kcal/mol respectively.

Density Functional Theory, Chemical Reactivity, Pharmacological Potential and Molecular Docking of Dihydrothiouracil-Indenopyridopyrimidines with Human-DNA Topoisomerase II

In this work, three computational methods (Hatree-Fock (HF), Møller-Plesset 2 (MP2), and Density Functional Theory (DFT)) using a variety of basis sets are used to determine the atomic and molecular properties of dihydrothiouracil-based indenopyridopyrimidine (TUDHIPP) derivatives. Reactivity descriptors of this system, including chemical potential (µ), chemical hardness (η), electrophilicity (ω), condensed Fukui function and dual descriptors are calculated at B3LYP/6-311++ G (d,p) to identify reactivity changes of these molecules in both gas and aqueous phases. We determined the molecular electrostatic surface potential (MESP) to determine the most active site in these molecules. Molecular docking study of TUDHIPP with topoisomerase II α and β is performed, predicting binding sites and binding energies with amino acids of both proteins. Docking studies of TUDHIPP versus etoposide suggest their potential as antitumor candidates. We have applied Lipinski, Veber's rules and analysis of the Golden triangle and structure activity/property relationship for a series of TUDHIPP derivatives indicate that the proposed compounds exhibit good oral bioavailability. The comparison of the drug likeness descriptors of TUDHIPP with those of etoposide, which is known to be an antitumor drug, indicates that TUDHIPP can be considered as an antitumor drug. The overall study indicates that TUDHIPP has comparable and even better descriptors than etoposide proposing that it can be as effective antitumor drug, especially 2H, 6H and 7H compounds.