Identification of two novel chemical classes of Autotaxin (ATX) inhibitors using Enalos Asclepios KNIME nodes.

Autor: Stylianaki EA; Biomedical Sciences Research Center 'Alexander Fleming', 16672 Vari, Greece., Mouchlis VD; Department of ChemoInformatics, Novamechanics Ltd., Nicosia 1070, Cyprus; Department of Chemoinformatics, Novamechanics MIKE, Piraeus 18545, Greece; Division of Data Driven Innovation, Entelos Institute, Larnaca 6059, Cyprus., Magkrioti C; Biomedical Sciences Research Center 'Alexander Fleming', 16672 Vari, Greece., Papavasileiou KD; Department of ChemoInformatics, Novamechanics Ltd., Nicosia 1070, Cyprus., Afantitis A; Department of ChemoInformatics, Novamechanics Ltd., Nicosia 1070, Cyprus; Department of Chemoinformatics, Novamechanics MIKE, Piraeus 18545, Greece; Division of Data Driven Innovation, Entelos Institute, Larnaca 6059, Cyprus. Electronic address: afantitis@novamechanics.com., Matralis AN; Biomedical Sciences Research Center 'Alexander Fleming', 16672 Vari, Greece. Electronic address: matralis@fleming.gr., Aidinis V; Biomedical Sciences Research Center 'Alexander Fleming', 16672 Vari, Greece. Electronic address: aidinis@fleming.gr.
Jazyk: angličtina
Zdroj: Bioorganic & medicinal chemistry letters [Bioorg Med Chem Lett] 2024 May 01; Vol. 103, pp. 129690. Date of Electronic Publication: 2024 Mar 05.
DOI: 10.1016/j.bmcl.2024.129690
Abstrakt: Autotaxin is a secreted lysophospholipase D which is a member of the ectonucleotide pyrophosphatase/phosphodiesterase family converting extracellular lysophosphatidylcholine and other non-choline lysophospholipids, such as lysophosphatidylethanolamine and lysophosphatidylserine, to the lipid mediator lysophosphatidic acid. Autotaxin is implicated in various fibroproliferative diseases including interstitial lung diseases, such as idiopathic pulmonary fibrosis and hepatic fibrosis, as well as in cancer. In this study, we present an effort of identifying ATX inhibitors that bind to allosteric ATX binding sites using the Enalos Asclepios KNIME Node. All the available PDB crystal structures of ATX were collected, prepared, and aligned. Visual examination of these structures led to the identification of four crystal structures of human ATX co-crystallized with four known inhibitors. These inhibitors bind to five binding sites with five different binding modes. These five binding sites were thereafter used to virtually screen a compound library of 14,000 compounds to identify molecules that bind to allosteric sites. Based on the binding mode and interactions, the docking score, and the frequency that a compound comes up as a top-ranked among the five binding sites, 24 compounds were selected for in vitro testing. Finally, two compounds emerged with inhibitory activity against ATX in the low micromolar range, while their mode of inhibition and binding pattern were also studied. The two derivatives identified herein can serve as "hits" towards developing novel classes of ATX allosteric inhibitors.
Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Antreas Afantitis reports financial support was provided by EU H2020 project SCENARIOS (grant agreement No. 101037509). Antreas Afantitis reports financial support was provided by EU H2020 project EthnoHERBS (grant agreement No. 823973). Antreas Afantitis reports financial support was provided by Cyclone supercomputer of the High Performance Computing Facility of The Cyprus Institute. Christiana Magkrioti reports financial support was provided by Greek Foundation for Research and Innovation. Antreas Afantitis is affiliated with NovaMechanics Ltd., a drug design company. The other authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper
(Copyright © 2024 Elsevier Ltd. All rights reserved.)
Databáze: MEDLINE
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