Small Molecules as Toll-like Receptor 4 Modulators Drug and In-House Computational Repurposing

The innate immunity toll-like receptor 4 (TLR4) system is a receptor of paramount importance as a therapeutic target. Virtual screening following a “computer-aided drug repurposing” approach was applied to the discovery of novel TLR4 modulators with a non-lipopolysaccharide-like structure. We screened almost 29,000 approved drugs and drug-like molecules from commercial, public, and in-house academia chemical libraries and, after biological assays, identified several compounds with TLR4 antagonist activity. Our computational protocol showed to be a robust approach for the identification of hits with drug-like scaffolds as possible inhibitors of the TLR4 innate immune pathways. Our collaborative work broadens the chemical diversity for inspiration of new classes of TLR4 modulators.This work was financially supported by the Spanish Ministry for Science and Innovation (grants CTQ2014-57141-R, CTQ2017-88353-R, and PID2020-113588RB-I00 for S.M.S.; grants BES-2012-053653 for L.P.R., BES-2015-071588 for J.G.C. and PID2021-124983OB-I00 for J.C.M.), the Spanish Ministry of Economy and Competitiveness and the European Regional Development Fund (MINECO/FEDER; SAF2016-75988-R), and the Community of Madrid (S-2010/BMD-2332) for M.F

Computational approaches to toll-like receptor 4 modulation

24 p.-10 fig.Toll-like receptor 4 (TLR4), along with its accessory protein myeloid differentiation factor 2 (MD-2), builds a heterodimeric complex that specifically recognizes lipopolysaccharides (LPS),which are present on the cell wall of Gram-negative bacteria, activating the innate immune response.Some TLR4 modulators are undergoing preclinical and clinical evaluation for the treatment of sepsis,inflammatory diseases, cancer and rheumatoid arthritis. Since the relatively recent elucidation of the X-ray crystallographic structure of the extracellular domain of TLR4, research around this fascinating receptor has risen to a new level, and thus, new perspectives have been opened. In particular,diverse computational techniques have been applied to decipher some of the basis at the atomic level regarding the mechanism of functioning and the ligand recognition processes involving the TLR4/MD-2 system at the atomic level. This review summarizes the reported molecular modeling and computational studies that have recently provided insights into the mechanism regulating the activation/inactivation of the TLR4/MD-2 system receptor and the key interactions modulating the molecular recognition process by agonist and antagonist ligands. These studies have contributed to the design and the discovery of novel small molecules with promising activity as TLR4 modulators.This work was supported by the Spanish Ministry for Economy and Competitiveness (MINECO) Grant CTQ2014-57141-R and PhD fellowship BES-2015-071588 and by the European Commission granted GLYCOPHARM Marie Curie ITN PITN-GA-2012-317297 (www.glycopharm.eu) and TOLLerant H2020-MSC-ETN-642157 (www.tollerant.eu) projects.Peer reviewe

Molecular insight into the regulation of vimentin by cysteine modifications and zinc binding

23 p.-7 fig.The intermediate filament protein vimentin is involved in essential cellular processes, including cell division and stress responses, as well as in the pathophysiology of cancer, pathogen infection, and autoimmunity. The vimentin network undergoes marked reorganizations in response to oxidative stress, in which modifications of vimentin single cysteine residue, Cys328, play an important role, and is modulated by zinc availability. However, the molecular basis for this regulation is not fully understood. Here, we show that Cys328 displays a low pKa, supporting its reactivity, and is readily alkylated and oxidized in vitro. Moreover, combined oxidation and crosslinking assays and molecular dynamics simulations support that zinc ions interact with Cys328 in its thiolate form, whereas Glu329 and Asp331 stabilize zinc coordination. Vimentin oxidation can induce disulfide crosslinking, implying the close proximity of Cys328 from neighboring dimers in certain vimentin conformations, supported by our computational models. Notably, micromolar zinc concentrations prevent Cys328 alkylation, lipoxidation, and disulfide formation. Moreover, zinc selectively protects vimentin from crosslinking using short-spacer cysteine-reactive but not amine-reactive agents. These effects are not mimicked by magnesium, consistent with a lower number of magnesium ions hosted at the cysteine region, according to molecular dynamics simulations. Importantly, the region surrounding Cys328 is involved in interaction with several drugs targeting vimentin and is conserved in type III intermediate filaments, which include glial fibrillary acidic protein and desmin. Altogether, our results identify this region as a hot spot for zinc binding, which modulates Cys328 reactivity. Moreover, they provide a molecular standpoint for vimentin regulation through the interplay between cysteine modifications and zinc availability.This work was supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 675132 “Masstrplan”, Grants SAF2015-68590-R and RTI2018-097624-B-I00 from Agencia Estatal de Investigación, MICINN/FEDER, Spain, and Instituto de Salud Carlos III/FEDER, RETIC ARADyAL RD16/0006/0021 to DPS; Grant CTQ2017-88353-R from MICINN to SMS; Grant BES-2015-071588 from MICINN to JGC.Peer reviewe

Full-atom model of the agonist LPS-bound toll-like receptor 4 dimer in a membrane environment

21 p.-14 fig. In Memoriam Prof. Kilian Muñiz (R.I.P.). Excellent person, great heart.The innate immunity TLR4/MD-2 system is a membrane receptor of paramount importance as therapeutic target. Its assembly, upon binding of Gram-negative bacteria lipopolysaccharide (LPS), and also dependent on the membrane composition, finally triggers the immune response cascade. We here combine ab-initio calculations, molecular docking, all-atom molecular dynamics simulations, and thermodynamics calculations to provide the most realistic and complete 3D models of the active full TLR4 complex embedded into a realistic membrane to date. Our studies reveal functional and structural insights into the transmembrane domain behavior in different membrane environments, the ectodomain bouncing movement, and the dimerization patterns of the intracellular TIR domain. Our work provides TLR4 models as reasonable 3D structures for the (TLR4/MD-2/LPS) 2 architecture accounting for the active (agonist) state of the TLR4, and pointing to a signal transduction mechanism across cell membrane. These observations unveil relevant molecular aspects involved in the TLR4 innate immune pathways and will promote the discovery of new TLR4 modulators.This work was financially supported by the Spanish Ministry for Science and Innovation (grants CTQ2014-57141-R, CTQ2017-88353-R, and PID2020-113588RB-I00; grants BES-2012-053653 for L.P.R., BES-2015-071588 for J.G.C. and PRE2018-086249 for A.M.R.), and the European Commission Marie Sklodowska-Curie actions (H2020-MSCA-ITN 642157 “TOLLerant”).Peer reviewe

Pairing Bacteroides vulgatus LPS structure with its immunomodulatory effects on human cellular models

15 p.-5 fig.-1 tab.-1 graph abst. This paper is dedicated to Prof. Jesús Jiménez-Barbero for his 60th birthday.The gut microbiota guide the development of the host immune system by setting a systemic threshold for immune activation. Lipopolysaccharides (LPSs) from gut bacteria are able to trigger systemic and local proinflammatory and immunomodulatory responses, and this capability strongly relies on their fine structures. Up to now, only a few LPS structures from gut commensals have been elucidated; therefore, the molecular motifs that may be important for LPS–mammalian cell interactions at the gut level are still obscure. Here, we report on the full structure of the LPS isolated from one of the prominent species of the genus Bacteroides, Bacteroides vulgatus. The LPS turned out to consist of a particular chemical structure based on hypoacylated and mono-phosphorylated lipid A and with a galactofuranose-containing core oligosaccharide and an O-antigen built up of mannose and rhamnose. The evaluation of the immunological properties of this LPS on human in vitro models revealed a very interesting capability to produce anti-inflammatory cytokines and to induce a synergistic action of MD-2/TLR4- and TLR2-mediated signaling pathways.F.D.L. acknowledges Progetto STAR 2018 Linea 1 grant E66C18001330003. S.M.S. acknowledges Spanish Ministry of Science (ref. CTQ2017-88353-R). A.M., F.D.L., and A.S.acknowledge H2020 Marie Skłodowska-Curie ITN 2018 “SweetCrossTalk” grant 814102. A.M. acknowledges progetto POR SATIN POR-FESR 2014−2 0 2 0 g r a n t B61C17000070007 (OR3) and Progetto POR Campania Oncoterapia 2014−2020 grant B61G18000470007. A.S. acknowledges PRIN-MIUR 2017 Glytunes project. A.S. and F.C. acknowledge COST (European Cooperation in Science and Technology) Action CA18103 (INNOGLY). F.C. was financially supported by the NWO Spinoza award of Y.K.Peer reviewe