Modeling-Enabled Characterization of Novel NLRX1 Ligands

Abstract

Nucleotide-binding domain and leucine-rich repeat containing (NLR) family are intracellular sentinels of cytosolic homeostasis that orchestrate immune and inflammatory responses in infectious and immune-mediated diseases. NLRX1 is a mitochondrial-associated NOD-like receptor involved in the modulation of immune and metabolic responses. This study utilizes molecular docking approaches to investigate the structure of NLRX1 and experimentally assesses binding to naturally occurring compounds from several natural product and lipid databases. Screening of compound libraries predicts targeting of NLRX1 by conjugated trienes, polyketides, prenol lipids, sterol lipids, and coenzyme A-containing fatty acids for activating the NLRX1 pathway. The ligands of NLRX1 were identified by docking punicic acid (PUA), eleostearic acid (ESA), and docosahexaenoic acid (DHA) to the C-terminal fragment of the human NLRX1 (cNLRX1). Their binding and that of positive control RNA to cNLRX1 were experimentally determined by surface plasmon resonance (SPR) spectroscopy. In addition, the ligand binding sites of cNLRX1 were predicted in silico and validated experimentally. Target mutagenesis studies demonstrate that mutation of 4 critical residues ASP677, PHE680, PHE681, and GLU684 to alanine resulted in diminished affinity of PUA, ESA, and DHA to NLRX1. Consistent with the regulatory actions of NLRX1 on the NF-κB pathway, treatment of bone marrow derived macrophages (BMDM)s with PUA and DHA suppressed NF-κB activity in a NLRX1 dependent mechanism. In addition, a series of pre-clinical efficacy studies were performed using a mouse model of dextran sodium sulfate (DSS)-induced colitis. Our findings showed that the regulatory function of PUA on colitis is NLRX1 dependent. Thus, we identified novel small molecules that bind to NLRX1 and exert anti-inflammatory actions.

Fig 1. Binding of punicic acid (PUA) with cNLRX1 wildtype and mutant.

A) Chemical structure of PUA. B) Interactions between PUA and cNLRX1 predicted by molecular docking. PUA is in cyan ball-and-stick representation surrounded by molecular surface of the binding site with coloring by element. The free energy of binding is -6.2 kcal/mol. C) SPR sensograms for the binding of varying concentrations of PUA (40.0, 20.0, 10.0, 5.0, 2.5, 1.25 and 0.0 μM) to immobilized cNLRX1 wildtype (WT) and ASP677, PHE680, PHE681, and GLU684 to alanine mutant (Mutant). The equilibrium constant of dissociation, K_D, of PUA is 1.46 × 10⁻⁵ M for WT and 3.38 × 10⁻⁴ M for Mutant. D) Strength of association plot showing maximum response units for captured cNLRX1 WT or Mutant for a given concentration of PUA

Fig 2. Binding of eleostearic acid (ESA) with cNLRX1 wildtype and mutant.

A) Chemical structure of ESA. B) Interactions between ESA and NLRX1 predicted by molecular docking. ESA is in green ball-and-stick representation surrounded by molecular surface of the binding site with coloring by element. The free energy of binding is -6.2 kcal/mol. C) SPR sensograms for the binding of varying concentrations of ESA (40.0, 20.0, 10.0, 5.0, 2.5, 1.25 and 0.0 μM) to immobilized cNLRX1 (WT) and ASP677, PHE680, PHE681, and GLU684 to alanine mutant (Mutant). The equilibrium constant of dissociation, K_D, of ESA is 1.33 × 10⁻⁵ M for WT and 1.70 × 10⁻⁴ M for Mutant. D) Strength of association plot showing maximum response units for captured cNLRX1 WT or Mutant for a given concentration of ESA.

Fig 3. Binding of docosahexaenoic acid (DHA) with cNLRX1 wildtype and mutant.

A) Chemical structure of DHA. B) Interactions between DHA and cNLRX1 predicted by molecular docking. DHA is in orange ball-and-stick representation surrounded by molecular surface of the binding site with coloring by element. The free energy of binding is -8.0 kcal/mol. C) SPR sensograms for the binding of varying concentrations of DHA (100.0, 50.0, 25.0, 12.5, 6.23, and 3.125 μM) to immobilized cNLRX1 wild-type (WT) and ASP677, PHE680, PHE681, and GLU684 to alanine mutant (Mutant). The equilibrium constant of dissociation, KD, of DHA is 2.3 × 10–6 M for WT and 75.9 × 10–6 M for Mutant. D) Strength of association plot showing maximum response units for captured cNLRX1 WT or Mutant for a given concentration of DHA.

Fig 4. Effect of NLRX1 disruption on NF-κB activation in Bone marrow derived macrophage (BMDM).

BMDMs were isolated from hind legs obtained fromm wild type and Nlrx1-/- in sterile conditions and cultured for 7 days After stimulated with LPS (1μg/ml) for 12 hours, cells were treated with control (medium), 40 μM PUA, and 40 μM DHA for 12 hours. Nuclear extraction was performed on colon homogenates using the Active Motif Nuclear Extraction Kit (Carlsbad, CA). ELISA was performed on both cytoplasmic and nuclear fractions using the Active Motif TransAM^® NF-κB p65 kit according to the manufacturer’s instructions. Letter superscripts indicate significant (P-value < 0.05) differences by ANOVA.

Fig 5. Effect of PUA on WT and Nlrx1-/- mice in DSS-induced colitis (10 mice per group).

A) Average disease activity of treatment groups scored 0–4 daily for six days. B) mRNA expression of TNFα in whole colon on day six of DSS treatment. C) Histopathological assessment of colons by epithelial erosion (EE), leukocytic infiltration (LI), and mucosal thickening (MT). Asterisk indicates P-value < 0.05 by ANOVA.

Fig 6. Expression of fatty acid metabolism related genes altered by absence of NLRX1.

A) RNA-seq expression data was gathered after 7 day exposure to DSS in wild-type and Nlrx1-/- mice. Interactions of genes significantly altered in comparison of Nlrx1-/- treated with DSS to wild-type treated with DSS. Red indicates an up-regulation and green indicates a down-regulation. Image was generated using Ingenuity Pathway Analysis. B) Expression profile of genes encoding for enzymes and transporters in fatty acid metabolism pathways.