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Rational Design of Benzylidenehydrazinyl-Substituted Thiazole Derivatives as Potent Inhibitors of Human Dihydroorotate Dehydrogenase with in Vivo Anti-arthritic Activity.

Li S, Luan G, Ren X, Song W, Xu L, Xu M, Zhu J, Dong D, Diao Y, Liu X, Zhu L, Wang R, Zhao Z, Xu Y, Li H - Sci Rep (2015)

Bottom Line: Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range.Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo.Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.

ABSTRACT
Human dihydroorotate dehydrogenase (hDHODH) is an attractive therapeutic target for the treatment of rheumatoid arthritis, transplant rejection and other autoimmune diseases. Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range. Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo. Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold. This work not only elucidates promising scaffolds targeting hDHODH for the treatment of rheumatoid arthritis, but also demonstrates that the water-mediated hydrogen bond interaction is an important factor in molecular design and optimization.

No MeSH data available.


Related in: MedlinePlus

X-ray structure determination of hDHODH in complex with 19 (PDB ID: 4LS1) and 27 (PDB ID: 4LS2).(A) 2Fo-Fc electron density (blue) for 19 contoured at 1σ. Critical residues are represented as thin green sticks. (B) Specific binding information of the tunnel-like binding site of 4LS1. The surface of the binding site is colored purple. Compound 19 is displayed as cyan sticks and important residues are represented as gray lines. (C) 2Fo-Fc electron density (blue) for 27 contoured at 1σ. (D) Specific binding information of the tunnel-like binding site of 4LS2. Compound 27 (cyan) and acetate molecule (green) are displayed in stick mode. Water molecules are displayed as red balls and hydrogen bonds are shown as yellow dashed lines.
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f3: X-ray structure determination of hDHODH in complex with 19 (PDB ID: 4LS1) and 27 (PDB ID: 4LS2).(A) 2Fo-Fc electron density (blue) for 19 contoured at 1σ. Critical residues are represented as thin green sticks. (B) Specific binding information of the tunnel-like binding site of 4LS1. The surface of the binding site is colored purple. Compound 19 is displayed as cyan sticks and important residues are represented as gray lines. (C) 2Fo-Fc electron density (blue) for 27 contoured at 1σ. (D) Specific binding information of the tunnel-like binding site of 4LS2. Compound 27 (cyan) and acetate molecule (green) are displayed in stick mode. Water molecules are displayed as red balls and hydrogen bonds are shown as yellow dashed lines.

Mentions: Using our established X-ray crystallographic protocols (see Experimental Section), we obtained a 2.20 Å X-ray structure of compound 19 in complex with hDHODH. The coordinates of the complex structure have been deposited in the Protein Data Bank as the entry 4LS1. The binding mode of compound 19 is presented in Fig. 3A,B. A similar water-bridging hydrogen bond network was observed around the benzylidenehydrazinyl-substituted thiazole portion of inhibitor 19. Crystallographic water molecules (W592, W620, and W659) were observed at nearly the same location and function in the same way as those depicted in Fig. 2. W659 mediates the interaction between Gln47, Thr360 and the carboxyl group. W620 is also tetra-coordinated with the ligand and the protein by simultaneously forming two hydrogen bonds with the receptor and another two with compound 19. A 1.1-Å deviation is apparent between W592 and W661 in Fig. 2. Compared to W661, W592 is closer to Ala55 and slightly further from the hydrazine moiety. However, the bridging functions of W592 are unaffected, and W592 is involved in three hydrogen bonds with the nitrogen atom of the thiazole group, the secondary amine of the hydrazine moiety and the carbonyl oxygen atom of residue Ala55. The novel binding modes of W592 and W620, coupled with the typical binding pattern of W659, result in the formation of a complicated hydrogen bond network that contributes to the stability of the bioactive conformation of the flexible scaffold provided by the benzylidenehydrazinyl-substituted thiazole moiety, which enables favorable polar interactions with hDHODH. Moreover, in subsite S2 of the ubiquinone-binding site, the carboxyl of the benzoic acid moiety forms a nearly perfectly oriented salt bridge with the side chain of Arg136. The combination of this favorable salt bridge and the strong water-bridging hydrogen bond network increase the potency of compound 19 compared to compound 18.


Rational Design of Benzylidenehydrazinyl-Substituted Thiazole Derivatives as Potent Inhibitors of Human Dihydroorotate Dehydrogenase with in Vivo Anti-arthritic Activity.

Li S, Luan G, Ren X, Song W, Xu L, Xu M, Zhu J, Dong D, Diao Y, Liu X, Zhu L, Wang R, Zhao Z, Xu Y, Li H - Sci Rep (2015)

X-ray structure determination of hDHODH in complex with 19 (PDB ID: 4LS1) and 27 (PDB ID: 4LS2).(A) 2Fo-Fc electron density (blue) for 19 contoured at 1σ. Critical residues are represented as thin green sticks. (B) Specific binding information of the tunnel-like binding site of 4LS1. The surface of the binding site is colored purple. Compound 19 is displayed as cyan sticks and important residues are represented as gray lines. (C) 2Fo-Fc electron density (blue) for 27 contoured at 1σ. (D) Specific binding information of the tunnel-like binding site of 4LS2. Compound 27 (cyan) and acetate molecule (green) are displayed in stick mode. Water molecules are displayed as red balls and hydrogen bonds are shown as yellow dashed lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595849&req=5

f3: X-ray structure determination of hDHODH in complex with 19 (PDB ID: 4LS1) and 27 (PDB ID: 4LS2).(A) 2Fo-Fc electron density (blue) for 19 contoured at 1σ. Critical residues are represented as thin green sticks. (B) Specific binding information of the tunnel-like binding site of 4LS1. The surface of the binding site is colored purple. Compound 19 is displayed as cyan sticks and important residues are represented as gray lines. (C) 2Fo-Fc electron density (blue) for 27 contoured at 1σ. (D) Specific binding information of the tunnel-like binding site of 4LS2. Compound 27 (cyan) and acetate molecule (green) are displayed in stick mode. Water molecules are displayed as red balls and hydrogen bonds are shown as yellow dashed lines.
Mentions: Using our established X-ray crystallographic protocols (see Experimental Section), we obtained a 2.20 Å X-ray structure of compound 19 in complex with hDHODH. The coordinates of the complex structure have been deposited in the Protein Data Bank as the entry 4LS1. The binding mode of compound 19 is presented in Fig. 3A,B. A similar water-bridging hydrogen bond network was observed around the benzylidenehydrazinyl-substituted thiazole portion of inhibitor 19. Crystallographic water molecules (W592, W620, and W659) were observed at nearly the same location and function in the same way as those depicted in Fig. 2. W659 mediates the interaction between Gln47, Thr360 and the carboxyl group. W620 is also tetra-coordinated with the ligand and the protein by simultaneously forming two hydrogen bonds with the receptor and another two with compound 19. A 1.1-Å deviation is apparent between W592 and W661 in Fig. 2. Compared to W661, W592 is closer to Ala55 and slightly further from the hydrazine moiety. However, the bridging functions of W592 are unaffected, and W592 is involved in three hydrogen bonds with the nitrogen atom of the thiazole group, the secondary amine of the hydrazine moiety and the carbonyl oxygen atom of residue Ala55. The novel binding modes of W592 and W620, coupled with the typical binding pattern of W659, result in the formation of a complicated hydrogen bond network that contributes to the stability of the bioactive conformation of the flexible scaffold provided by the benzylidenehydrazinyl-substituted thiazole moiety, which enables favorable polar interactions with hDHODH. Moreover, in subsite S2 of the ubiquinone-binding site, the carboxyl of the benzoic acid moiety forms a nearly perfectly oriented salt bridge with the side chain of Arg136. The combination of this favorable salt bridge and the strong water-bridging hydrogen bond network increase the potency of compound 19 compared to compound 18.

Bottom Line: Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range.Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo.Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.

ABSTRACT
Human dihydroorotate dehydrogenase (hDHODH) is an attractive therapeutic target for the treatment of rheumatoid arthritis, transplant rejection and other autoimmune diseases. Based on the X-ray structure of hDHODH in complex with lead compound 7, a series of benzylidenehydrazinyl-substituted thiazole derivatives as potent inhibitors of hDHODH were designed and synthesized, of which 19 and 30 were the most potent with IC50 values in the double-digit nanomolar range. Moreover, compound 19 displayed significant anti-arthritic effects and favorable pharmacokinetic profiles in vivo. Further X-ray structure and SAR analyses revealed that the potencies of the designed inhibitors were partly attributable to additional water-mediated hydrogen bond networks formed by an unexpected buried water between hDHODH and the 2-(2-methylenehydrazinyl)thiazole scaffold. This work not only elucidates promising scaffolds targeting hDHODH for the treatment of rheumatoid arthritis, but also demonstrates that the water-mediated hydrogen bond interaction is an important factor in molecular design and optimization.

No MeSH data available.


Related in: MedlinePlus