As a rate-limiting enzyme in the major pathway of l-tryptophan catabolism, indoleamine 2, 3-dioxygenase 1 (IDO1) has been regarded as a potential target for the treatment of a variety of diseases. To identify the key molecular features and extend the structural variety of IDO1 inhibitors, a ferrous binding group (FBG)-based 3D-QSAR pharmacophore model was constructed, validated and used for virtual screening herein. The Specs database was initially filtered based on drug-like rules, and was subsequently screened by the pharmacophore model. Molecular docking simulations and similarity analysis were then followed to prioritize twenty compounds for biological tests. Among them, compound VS-13 exhibited moderate inhibitory activity against IDO1, and could be subjected to further structure-activity relationship studies and structural optimization.
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http://dx.doi.org/10.1016/j.jmgm.2020.107628 | DOI Listing |
Sci Rep
January 2025
Department of Pesticide Chemistry, National Research Centre, Dokki, 12622, Giza, Egypt.
Targeted therapy is preferable over other therapeutics due to its limitation of drawbacks and better pharmaceutical outcomes. VEGF and its receptors have been observed to be hyper-activated in many cancer types and are considered promising targets for assigning anticancer agents. The current study is directed towards synthesis of novel antiproliferative 2-oxoindolin-3-ylidenes incorporating urea function with VEGFR-2 properties.
View Article and Find Full Text PDFCommun Chem
December 2024
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
The PepT transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepT in different states, the molecular basis of peptide recognition and transport by PepT is not fully elucidated. In this study, we used molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepT transporter.
View Article and Find Full Text PDFJ Comput Aided Mol Des
December 2024
Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector-125, Noida, UP, 201313, India.
BMC Biol
December 2024
Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
Background: Molecular interactions between proteins and their ligands are important for drug design. A pharmacophore consists of favorable molecular interactions in a protein binding site and can be utilized for virtual screening. Pharmacophores are easiest to identify from co-crystal structures of a bound protein-ligand complex.
View Article and Find Full Text PDFAsian Pac J Cancer Prev
December 2024
Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
Objective: The study aims to identify potential pharmacophore models for targeting beta-catenin, a crucial protein involved in the development of oral squamous cell carcinoma (OSCC), using a combination of herbal compounds and computational approaches.
Methods: Five natural compounds namely Quercetin, Lycopene, Ovatodiolide, Karsil, and Delphinidin were selected based on their reported activity against beta-catenin. Ligand characteristics were analyzed using SwissADME to evaluate drug-likeness, lipophilicity (logP), and bioavailability.
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