Theoretical and experimental investigations into structural, electronic, molecular and biological properties of 4-(3-chlorophenyl)-1-(3-chloropropyl) piperazin-1-ium chloride

Advances in structure-based drug design targeting membrane protein markers in prostate cancer

Prostate cancer (PCa) is one of the leading cancers in men and the lack of suitable biomarkers or their modulators results in poor prognosis. Membrane proteins (MPs) have a crucial role in the development and progression of PCa and can be attractive therapeutic targets. However, experimental limitations in targeting MPs hinder effective biomarker and inhibitor discovery. To overcome this barrier, computational methods can yield structural insights and screen large libraries of compounds, accelerating lead identification and optimization. In this review, we examine current breakthroughs in computer-aided drug design (CADD), with emphasis on structure-based approaches targeting the most relevant membrane-bound PCa biomarkers.

A Highly Fluorescent Pyrene-Based Sensor for Selective Detection Of Fe3+ Ion in Aqueous Medium: Computational Investigations

In this work, we introduce a highly selective and sensitive fluorescent sensor based on pyrene derivative for Fe(III) ion sensing in DMSO/water media. 2-(pyrene-2-yl)-1-(pyrene-2-ylmethyl)-1H-benzo[d]imidazole (PEBD) receptor was synthesized via simple condensation reaction and confirmed by spectroscopic techniques. The receptor exhibits fluorescence quenching in the presence of Fe(III) ions at 440 nm. ESI-MS and Job's method were used to confirm the 1:1 molar binding ratio of the receptor PEBD to Fe(III) ions. Using the Benesi-Hildebrand equation the binding constant value was determined as 8.485 × 10³ M^-1. Furthermore, the limit of detection (LOD, 3σ/K) value was found to be 1.81 µM in DMSO/water (95/5, v/v) media. According to the Environmental Protection Agency (EPA) of the United States, it is lower than the acceptable value of Fe³⁺ in drinking water (0.3 mg/L). The presence of 14 other metal ions such Co²⁺, Cr³⁺, Cu²⁺, Fe²⁺, Hg²⁺, Pb²⁺, K⁺, Ni²⁺, Mg²⁺, Cd²⁺, Ca²⁺, Mn²⁺, Al³⁺, and Zn²⁺ did not interfere with the detection of Fe(III) ions. The fluorescence life-time of the receptor PEBD with and without Fe³⁺ ion was found to be 1.097 × 10^-9 s and 0.9202 × 10^-9 s respectively. Similarly, the quantum yield of the receptor PEBD with Fe³⁺ and without Fe³⁺ ion was calculated, and found as 0.05 and 0.25 respectively. Computational studies of the receptor PEBD were carried out with density functional theory (DFT) using B3LYP/ 6-311G (d, p), LANL2DZ level of theory.

Distance Effects of Phenylpiperazine-Containing Methacrylic Polymers on Optical and Structural Properties

New materials based on methacrylic polymers modified with 1-(4-nitrophenyl)piperazine side chains, differing in the distance of the chromophore from the polymer main chain and/or the separation between the chromophoric units in the chain, are obtained and characterized in terms of their potential applications in optoelectronic devices. The surface, structural, and optical properties of the investigated materials are determined using atomic force microscopy, spectroscopic ellipsometry combined with transmission measurements, Raman and Fourier transform infrared spectroscopy, as well as cyclic voltammetry. The relevant model systems are additionally analyzed with quantum chemical density functional theory calculations in order to enable the generalization of the structure-photophysical property relationships for the optimization of the material features. It is found that the structural modification of the material, relying on the transit of the piperazine moiety away from the main polymer chain, leads to the hypsochromic shift of the absorption spectrum. Moreover, the lowest refractive index values are obtained for the polymer with a distant ethylene group in the side-chains and increased separation between the piperazine units. It was shown that the optical energy band gaps of the investigated piperazine-containing polymers are in the range from 2.73 to 2.81 eV, which reveals their promising potential for the advances in photovoltaics, field effect transistors, or electrochromic devices as an alternative for other widely applied polymer materials.

Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review

Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.

Substituent effects on the ultraviolet absorption properties of stilbene compounds-Models for molecular cores of absorbents

The effects of substituent X and Y on ultraviolet (UV) absorption properties of stilbene compounds XPhCHCHPhY (XSBY) were studied both experimentally and computationally from the viewpoint of UV maximum absorption wavelength (λ_max) and the corresponding energy (υ_max). In the studies, the contribution of substituents on υ_max shift was explored. The results show that with increase of electron withdrawing or electron donating ability of X or Y, there is an enhanced electron delocalization of XSBY that leads to bathochromic shift. Computational analyses based on density functional theory were conducted to elucidate the phenomena. It is disclosed that the υ_max values are significantly affected by the excited state, though the electronic effect of ground state cannot be ignored. Finally, on the basis of the respective influences of X and Y, a quantitative model, which was proved reliable by the leave-one-out method, was developed to scale the effects of terminal substituents on υ_max. According to the model, the effects of substituents X or Y exhibit almost the same action on υ_max owing to the symmetric skeleton of the XSBY compounds. The findings provide deep insight into the effects of terminal substituents on UV absorption properties of stilbene compounds, and the derived model enables practical expression of the relationship between substituents and UV absorption.