Drug Screening Identifies Sigma-1-Receptor as a Target for the Therapy of VWM Leukodystrophy

Vanishing white matter (VWM) disease is an autosomal genetic leukodystrophy caused by mutations in subunits of eukaryotic translation initiation factor 2B (eIF2B). The clinical symptoms exhibit progressive loss of white matter in both hemispheres of the brain, accompanied by motor functions deterioration, neurological deficits, and early death. To date there is no treatment for VWM disease. The aim of this work was to expedite rational development of a therapeutic opportunity. Our approach was to design a computer-aided strategy for an efficient and reliable screening of drug-like molecules; and to use primary cultures of fibroblasts isolated from the Eif2b5R132H/R132H VWM mouse model for screening. The abnormal mitochondria content phenotype of the mutant cells was chosen as a read-out for a simple cell-based fluorescent assay to assess the effect of the tested compounds. We obtained a hit rate of 0.04% (20 hits out of 50,000 compounds from the selected library). All primary hits decreased mitochondria content and brought it closer to WT levels. Structural similarities between our primary hits and other compounds with known targets allowed the identification of three putative cellular pathways/targets: 11β-hydroxysteroid dehydrogenase type 1, Sonic hedgehog (Shh), and Sigma-1-Receptor (S1R). In addition to initial experimental indication of Shh pathway impairment in VWM mouse brains, the current study provides evidence that S1R is a relevant target for pharmaceutical intervention for potential treatment of the disease. Specifically, we found lower expression level of S1R protein in fibroblasts, astrocytes, and whole brains isolated from Eif2b5R132H/R132H compared to WT mice, and confirmed that one of the hits is a direct binder of S1R, acting as agonist. Furthermore, we provide evidence that treatment of mutant mouse fibroblasts and astrocytes with various S1R agonists corrects the functional impairments of their mitochondria and prevents their need to increase their mitochondria content for compensation purposes. Moreover, S1R activation enhances the survival rate of mutant cells under ER stress conditions, bringing it to WT levels. This study marks S1R as a target for drug development toward treatment of VWM disease. Moreover, it further establishes the important connection between white matter well-being and S1R-mediated proper mitochondria/ER function

Docking Studies on DNA Intercalators

DNA is an important target for the treatment of multiple pathologies, most notably cancer. In particular, DNA intercalators have often been used as anticancer drugs. However, despite their relevance to drug discovery, only a few systematic computational studies were performed on DNA-intercalator complexes. In this work we have analyzed ligand binding sites preferences in 63 high resolution DNA-intercalator complexes available in the PDB and found that ligands bind preferentially between <b>G</b> and <b>C</b> and between the <b>C</b> and <b>A</b> base pairs (70% and 11%, respectively). Next, we examined the ability of AUTODOCK to accurately dock ligands into preformed intercalation sites. Following the optimization of the docking protocol, AUTODOCK was able to generate conformations with RMSD values <2.00 Å with respect to crystal structures in ∼80% of the cases while focusing on the preformed binding site (small grid box) or on the entire DNA structure (large grid box). In addition, a top ranked conformation with an RMSD < 2.00 Å was identified in 75% and 60% of the cases using small and large docking boxes, respectively. Moreover, under the large docking box setting AUTODOCK was able to successfully distinguish between the intercalation site and the minor groove site. However, in all cases the crystal structures and poses tightly clustered around it had a lower score than the best scoring poses suggesting a potential scoring problem with AUTODOCK. A close examination of all cases where the top ranked pose had an RMSD value >2.00 Å suggests that AUTODOCK may overemphasize the hydrogen bonding term. A decision tree was built to identify ligands which are likely to be accurately docked based on their characteristics. This analysis revealed that AUTODOCK performs best for intercalators characterized by a large number of aromatic rings, low flexibility, high molecular weight, and a small number of hydrogen bond acceptors. Finally, for canonical B-DNA structures (where preformed sites are unavailable), we demonstrated that intercalation sites could be formed by inserting an anthracene moiety between the (anticipated) site-flanking base pairs and by relaxing the structure using either energy minimization or preferably molecular dynamics simulations. Such sites were suitable for the docking of different intercalators by AUTODOCK

MOESM1 of A reliable computational workflow for the selection of optimal screening libraries

Additional file 1: Brief description of the evaluated fingerprints. Table S1. Diversity analysis results for the Drug Bank database, Table S2. the CMC database and Table S3. the CHEMBL database, Table S4. similarity analysis results for the six reference active drugs Carbinoxamine, Table S5. Fluocinolone acetonide, Table S6. Lymecycline, Table S7. Haloperidol, Table S8. CHEMBL488890 and Table S9. CHEMBL14759. Table S10. Substructures for promiscuous binders and HTS screening. Table S11. Target classification in the Drug Bank database, Table S12. indication classification in the CMC database, Table S13. target classification in the CHEMBL database. Figure S1. Correlation between experimental and predicted logBB values, Figure S2. full description of the workflow as implemented in Pipeline Pilot, Figure S3. distributions and statistical values of key properties of the Drug Bank, Figure S4. CMC and Figure S5. CHEMBL databases

Highly Potent and Selective Ectonucleotide Pyrophosphatase/Phosphodiesterase I Inhibitors Based on an Adenosine 5′-(α or γ)-Thio-(α,β- or β,γ)-methylenetriphosphate Scaffold

Aberrant nucleotide pyrophosphatase/phosphodiesterase-1 (NPP1) activity is associated with chondrocalcinosis, osteoarthritis, and type 2 diabetes. The potential of NPP1 inhibitors as therapeutic agents, and the scarceness of their structure–activity relationship, encouraged us to develop new NPP1 inhibitors. Specifically, we synthesized ATP-α-thio-β,γ-CH₂ (<b>1</b>), ATP-α-thio-β,γ-CCl₂ (<b>2</b>), ATP-α-CH₂-γ-thio (<b>3</b>), and 8-SH-ATP (<b>4</b>) and established their resistance to hydrolysis by NPP1,3 and NTPDase1,2,3,8 (<5% hydrolysis) (NTPDase = ectonucleoside triphosphate diphosphohydrolase). Analogues <b>1</b>–<b>3</b> at 100 μM inhibited thymidine 5′-monophosphate <i>p</i>-nitrophenyl ester hydrolysis by NPP1 and NPP3 by >90% and 23–43%, respectively, and only slightly affected (0–40%) hydrolysis of ATP by NTPDase1,2,3,8. Analogue <b>3</b> is the most potent NPP1 inhibitor currently known, <i>K</i>_i = 20 nM and IC₅₀ = 0.39 μM. Analogue <b>2a</b> is a selective NPP1 inhibitor with <i>K</i>_i = 685 nM and IC₅₀ = 0.57 μM. Analogues <b>1</b>–<b>3</b> were found mostly to be nonagonists of P2Y₁/P2Y₂/P2Y₁₁ receptors. Docking analogues <b>1</b>–<b>3</b> into the NPP1 model suggested that activity correlates with the number of H-bonds with binding site residues. In conclusion, we propose analogues <b>2a</b> and <b>3</b> as highly promising NPP1 inhibitors