| Literature DB >> 35162960 |
Mariann Kiss1, István Timári1, Teréz Barna2, Zuzana Mészáros3,4, Kristýna Slámová3, Pavla Bojarová3, Vladimír Křen3, Joseph M Hayes5, László Somsák1.
Abstract
Inhibition of the human O-linked β-N-acetylglucosaminidase (hOGA, GH84) enzyme is pharmacologically relevant in several diseases such as neurodegenerative and cardiovascular disorders, type 2 diabetes, and cancer. Human lysosomal hexosaminidases (hHexA and hHexB, GH20) are mechanistically related enzymes; therefore, selective inhibition of these enzymes is crucial in terms of potential applications. In order to extend the structure-activity relationships of OGA inhibitors, a series of 2-acetamido-2-deoxy-d-glucono-1,5-lactone sulfonylhydrazones was prepared from d-glucosamine. The synthetic sequence involved condensation of N-acetyl-3,4,6-tri-O-acetyl-d-glucosamine with arenesulfonylhydrazines, followed by MnO2 oxidation to the corresponding glucono-1,5-lactone sulfonylhydrazones. Removal of the O-acetyl protecting groups by NH3/MeOH furnished the test compounds. Evaluation of these compounds by enzyme kinetic methods against hOGA and hHexB revealed potent nanomolar competitive inhibition of both enzymes, with no significant selectivity towards either. The most efficient inhibitor of hOGA was 2-acetamido-2-deoxy-d-glucono-1,5-lactone 1-naphthalenesulfonylhydrazone (5f, Ki = 27 nM). This compound had a Ki of 6.8 nM towards hHexB. To assess the binding mode of these inhibitors to hOGA, computational studies (Prime protein-ligand refinement and QM/MM optimizations) were performed, which suggested the binding preference of the glucono-1,5-lactone sulfonylhydrazones in an s-cis conformation for all test compounds.Entities:
Keywords: Prime refinement; QM/MM optimization; glyconolactone sulfonylhydrazone; hHexB; hOGA; inhibitor
Mesh:
Substances:
Year: 2022 PMID: 35162960 PMCID: PMC8834866 DOI: 10.3390/ijms23031037
Source DB: PubMed Journal: Int J Mol Sci ISSN: 1422-0067 Impact factor: 5.923
Selected inhibitors of OGA with their activity against HexA/B enzymes and the target compounds of this study.
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| Ar | Ar | ||||
| OGA | HexB | OGA | HexA/B a | ||
| Ph | 46 [ | 36 [ | Ph | 190 [ | 205 [ |
| 4-Me-C6H4- | 28 [ | 21 [ | 4-Me-C6H4- | 155 [ | 332 [ |
| 4-Br-C6H4- | 56 [ | 47 [ | 4-Cl-C6H4- | 83 [ | 170 [ |
| 2-Naphthyl | 36 [ | 47 [ | |||
| Target compounds |
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a This enzyme contains two predominant isozymes, Hex A, a heterodimer, and Hex B, a homodimer.
Synthesis of test compounds 5.
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| Reagents and conditions: | |||||
| Ar | Products and yields (%) | ||||
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| Overall yield of | ||
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| 77 | 69 | 94 | 41 | |
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| 85 | 60 | 83 | 35 | |
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| 86 | 72 | 85 | 44 | |
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| 89 | 77 | 78 | 44 | |
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| 2-naphthyl | 76 | 56 | 75 | 26 |
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| 1-naphthyl | 89 | 66 | 80 | 39 |
Figure 1Nuclear Overhauser effects (NOEs) observed in compound 5d.
Binding affinities of compounds 5 toward hOGA and hHexB enzymes compared to those of some previously known inhibitors.
| Compound | ||||
| hOGA | hHexB | |||
| PUGNAc |
| 46 [ | 36 [ | 0.8 |
| 2-acetamido-2-deoxy- |
| 36 [ | 47 [ | 1.3 |
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| 78 ± 1 | 21 ± 2 | 0.27 |
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| 230 ± 17 | 48 ± 4 | 0.21 |
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| 95 ± 11 | 45 ± 3 | 0.43 |
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| 70 ± 3 | 39 ± 2 | 0.56 |
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| 30 ± 2 | 30 ± 3 | 1 |
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| 27 ± 7 | 6.8 ± 1.8 | 0.25 |
a The ratio defines selectivity towards hOGA.
Energy results for the predicted binding poses of PUGNAc and the six inhibitors 5a–f with hOGA. The atom numbering scheme and the two key potential binding conformations (s-trans and s-cis) around the N1–N2 bond are highlighted.
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| Inhibitor/pose | Prime Hierarchical | Prime Local | QM/MM | ||||
| Prime | Relative | Prime | Relative | Absolute | Relative | Dihedral a (°) | |
| PUGNAc | |||||||
| Pose 1 | −34,316.1 | 0.0 | −34,320.1 | 0.6 | −1328.97031 | 1.2 | - |
| Pose 2 | −34,315.9 | 0.2 | −34,320.7 | 0.0 | −1328.96987 | 1.5 | - |
| Pose 3 | −34,315.8 | 0.3 | −34,320.1 | 0.6 | −1328.97033 | 1.2 | - |
| Pose 4 | −34,315.6 | 0.5 | −34,319.9 | 0.8 | −1328.97226 | 0.0 | - |
| Pose 5 | −34,315.6 | 0.5 | −34,320.5 | 0.2 | −1328.97227 | 0.0 | - |
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| Pose 1 | −34,317.1 | 0.0 | −34,320.7 | 0.9 | −1728.25188 | 8.8 | −14.9 |
| Pose 2 | −34,315.8 | 1.3 | −34,318.0 | 3.6 | −1728.26592 | 0.0 | −172.2 |
| Pose 3 | −34,315.2 | 1.9 | −34,320.2 | 1.4 | −1728.25192 | 8.8 | −15.1 |
| Pose 4 | −34,315.1 | 2.0 | −34,318.6 | 3.0 | −1728.26597 | 0.0 | −171.8 |
| Pose 5 | −34,314.8 | 2.3 | −34,321.6 | 0.0 | −1728.25203 | 8.7 | −15.1 |
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| Pose 1 | −34,303.5 | 0.0 | −34,310.8 | 0.0 | −2025.91547 | 13.3 | 8.1 |
| Pose 2 | −34,302.4 | 1.1 | −34,304.6 | 6.2 | −2025.93662 | 0.0 | −168.0 |
| Pose 3 | −34,302.0 | 1.5 | −34,305.1 | 5.7 | −2025.92286 | 8.6 | −22.0 |
| Pose 4 | −34,301.5 | 2.0 | −34,305.0 | 5.8 | −2025.92249 | 8.9 | −21.4 |
| Pose 5 | −34,301.5 | 2.0 | −34,305.2 | 5.6 | −2025.92290 | 8.6 | −22.0 |
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| Pose 1 | −34,318.0 | 0.0 | −34,322.8 | 0.3 | −1788.16899 | 8.7 | −17.9 |
| Pose 2 | −34,317.5 | 0.5 | −34,323.1 | 0.0 | −1788.16894 | 8.8 | −17.5 |
| Pose 3 | −34,317.4 | 0.6 | −34,322.3 | 0.8 | −1788.18292 | 0.0 | −170.7 |
| Pose 4 | −34,317.3 | 0.7 | −34,321.8 | 1.3 | −1788.18290 | 0.0 | −170.6 |
| Pose 5 | −34,316.8 | 1.2 | −34,319.1 | 4.0 | −1788.18236 | 0.4 | −149.3 |
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| Pose 1 | −34,318.3 | 0.0 | −34,320.1 | 0.2 | −2148.53075 | 9.0 | −19.6 |
| Pose 2 | −34,316.6 | 1.7 | −34,320.3 | 0.0 | −2148.53084 | 8.9 | −19.7 |
| Pose 3 | −34,315.9 | 2.4 | −34,319.4 | 0.9 | −2148.53121 | 8.7 | −20.5 |
| Pose 4 | −34,315.8 | 2.5 | −34,319.1 | 1.2 | −2148.53073 | 9.0 | −19.3 |
| Pose 5 | −34,315.1 | 3.2 | −34,319.5 | 0.8 | −2148.54505 | 0.0 | −169.2 |
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| Pose 1 | −34,303.0 | 0.0 | −34,308.7 | 0.0 | −1842.54825 | 8.6 | −11.8 |
| Pose 2 | −34,302.9 | 0.1 | −34,306.0 | 2.7 | −1842.56165 | 0.2 | −169.3 |
| Pose 3 | −34,300.8 | 2.2 | −34,306.6 | 2.1 | −1842.56197 | 0.0 | −169.6 |
| Pose 4 | −34,300.6 | 2.4 | −34,306.9 | 1.8 | −1842.56199 | 0.0 | −169.5 |
| Pose 5 | −34,300.3 | 2.7 | −34,306.7 | 2.0 | −1842.56189 | 0.1 | −169.7 |
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| Pose 1 | −34,308.4 | 0.0 | −34,311.4 | 1.5 | −1842.54544 | 4.7 | −0.8 |
| Pose 2 | −34,304.6 | 3.8 | −34,309.9 | 3.0 | −1842.54384 | 5.7 | 3.6 |
| Pose 3 | −34,303.2 | 5.2 | −34,312.9 | 0.0 | −1842.53822 | 9.2 | −2.1 |
| Pose 4 | −34,302.0 | 6.4 | −34,305.5 | 7.4 | −1842.54411 | 5.6 | −169.9 |
| Pose 5 | −34,301.4 | 7.0 | −34,308.7 | 4.2 | −1842.55296 | 0.0 | −154.1 |
a Dihedral angles close to 0° correspond to s-trans and those close to ±180° to s-cis conformations.
Figure 2Predicted model complexes of the phenyl-substituted analogs 5a–d following QM/MM optimizations of complexes from Prime hierarchical optimization mode protein–ligand refinements. Shown are the relative positions of the inhibitors following enzyme backbone superimposition; the protein from the predicted hOGA-5a complex only is displayed for clarity. Fluorine ligand atoms are shown as cyan and chlorine as orange.
Figure 3Predicted models of hOGA-5e (A) and hOGA-5f (B) following QM/MM optimizations of complexes from Prime hierarchical optimization mode enzyme–inhibitor refinements.