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Design and Drug Screening of Targeted Proteins Inhibitor

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 1396

Special Issue Editors


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Guest Editor
College of Chemistry & Pharmacy, Northwest Agriculture and Forestry University, Xianyang, China
Interests: structure-based drug design; protein inhibitor; antibacterial activity; antifungal activity; insecticidal activity; anti-inflammatory

E-Mail Website
Guest Editor
College of Chemistry & Pharmacy, Northwest Agriculture and Forestry University, Xianyang, China
Interests: organic synthesis; pharmaceutical synthesis; natural product synthesis; drug discovery; biological activity research

Special Issue Information

Dear Colleagues,

In the drug discovery process, the development of novel drugs with potential interactions with therapeutic protein targets is of central importance. However, it is well-known that bringing a new drug into the market is a costly process in terms of money, manpower, and time. Thus, it is important to overcome limitations of the conventional drug discovery methods with efficient, low-cost, and broad-spectrum computational alternatives. To this end, the employment of rational drug design techniques by top pharmaceutical companies and other research groups has become essential for the preliminary stage of drug discovery to expedite the drug development process in a more cost-efficient way and to minimize failures in the final stage.

In the entire drug discovery paradigm, lots of different design strategies are employed. For example, the combination of two different bioactive units to generate a single bioactive scaffold (molecular hybridization) is a popular design strategy for medicinal chemists and is also known as scaffold hopping strategy. Structure-based drug design (SBDD) is a more specific, efficient, and rapid process for lead discovery and optimization because it deals with the 3D structure of a target protein and knowledge about the disease at the molecular level. Current SBDD methods consider the key features of the binding cavity of the therapeutic target to design efficient ligands. Computational resources serve as an efficient technology for accelerating the drug discovery process, which includes various screening procedures, combinatorial chemistry, and calculations of properties such as absorption, distribution, metabolism, excretion and toxicity (ADMET).

Dr. Ding Li
Dr. Zhigang Liu
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • rational drug design
  • computer-aided drug discovery
  • structure-based drug design
  • fragment-based drug discovery
  • ligand-based drug design
  • bioisosterism
  • scaffold hoping

Published Papers (2 papers)

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Research

16 pages, 4504 KiB  
Article
Study on the Mechanism of Lipid Peroxidation Induced by Carbonate Radicals
by Heng Cao, Sheng-Feng Xiong, Li-Long Dong and Zhou-Tong Dai
Molecules 2024, 29(5), 1125; https://doi.org/10.3390/molecules29051125 - 02 Mar 2024
Viewed by 547
Abstract
Based on the reported research, hydroxyl radicals can be rapidly transformed into carbonate radicals in the carbonate–bicarbonate buffering system in vivo. Many of the processes considered to be initiated by hydroxyl radicals may be caused by carbonate radicals, which indicates that lipid peroxidation [...] Read more.
Based on the reported research, hydroxyl radicals can be rapidly transformed into carbonate radicals in the carbonate–bicarbonate buffering system in vivo. Many of the processes considered to be initiated by hydroxyl radicals may be caused by carbonate radicals, which indicates that lipid peroxidation initiated by hydroxyl radicals can also be caused by carbonate radicals. To date, theoretical research on reactions of hydrogen abstraction from and radical addition to polyunsaturated fatty acids (PUFAs) of carbonate radicals has not been carried out systematically. This paper employs (3Z,6Z)-nona-3,6-diene (NDE) as a model for polyunsaturated fatty acids (PUFAs). Density functional theory (DFT) with the CAM-B3LYP method at the 6-311+g(d,p) level was used to calculate the differences in reactivity of carbonate radicals abstracting hydrogen from different positions of NDE and their addition to the double bonds of NDE under lipid solvent conditions with a dielectric constant of 4.0 (CPCM model). Grimme’s empirical dispersion correction was taken into account through the D3 scheme. The energy barrier, reaction rate constants, internal energy, enthalpy and Gibbs free energy changes in these reactions were calculated With zero-point vibrational energy (ZPVE) corrections. The results indicated that carbonate radicals initiate lipid peroxidation primarily through hydrogen abstraction from diallyl carbon atoms. The reaction of hydrogen abstraction from diallyl carbon atoms exhibits the highest reaction rate, with a reaction rate constant approximately 43-fold greater than the second-ranked hydrogen abstraction from allyl carbon atoms. This process has the lowest energy barrier, internal energy, enthalpy, and Gibbs free energy changes, indicating that it is also the most spontaneous process. Full article
(This article belongs to the Special Issue Design and Drug Screening of Targeted Proteins Inhibitor)
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13 pages, 4888 KiB  
Article
Novel Scaffold Agonists of the α2A Adrenergic Receptor Identified via Ensemble-Based Strategy
by Shiyang Sun, Pengyun Li, Jiaqi Wang, Dongsheng Zhao, Tingting Yang, Peilan Zhou, Ruibin Su, Zhibing Zheng and Song Li
Molecules 2024, 29(5), 1097; https://doi.org/10.3390/molecules29051097 - 29 Feb 2024
Viewed by 602
Abstract
The α2A adrenergic receptor (α2A-AR) serves as a critical molecular target for sedatives and analgesics. However, α2A-AR ligands with an imidazole ring also interact with an imidazoline receptor as well as other proteins and lead to undesirable effects, [...] Read more.
The α2A adrenergic receptor (α2A-AR) serves as a critical molecular target for sedatives and analgesics. However, α2A-AR ligands with an imidazole ring also interact with an imidazoline receptor as well as other proteins and lead to undesirable effects, motivating us to develop more novel scaffold α2A-AR ligands. For this purpose, we employed an ensemble-based ligand discovery strategy, integrating long-term molecular dynamics (MD) simulations and virtual screening, to identify new potential α2A-AR agonists with novel scaffold. Our results showed that compounds SY-15 and SY-17 exhibited significant biological effects in the preliminary evaluation of protein kinase A (PKA) redistribution assays. They also reduced levels of intracellular cyclic adenosine monophosphate (cAMP) in a dose-dependent manner. Upon treatment of the cells with 100 μM concentrations of SY-15 and SY-17, there was a respective decrease in the intracellular cAMP levels by 63.43% and 53.83%. Subsequent computational analysis was conducted to elucidate the binding interactions of SY-15 and SY-17 with the α2A-AR. The binding free energies of SY-15 and SY-17 calculated by MD simulations were −45.93 and −71.97 kcal/mol. MD simulations also revealed that both compounds act as bitopic agonists, occupying the orthosteric site and a novel exosite of the receptor simultaneously. Our findings of integrative computational and experimental approaches could offer the potential to enhance ligand affinity and selectivity through dual-site occupancy and provide a novel direction for the rational design of sedatives and analgesics. Full article
(This article belongs to the Special Issue Design and Drug Screening of Targeted Proteins Inhibitor)
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