• Title/Summary/Keyword: FlexX docking

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Molecular Modeling, Synthesis, and Screening of New Bacterial Quorum-sensing Antagonists

  • Kim, Cheol-Jin;Kim, Jae-Eun;Park, Hyung-Yeon;Mclean, Robert J.C.;Kim, Chan-Kyung;Jeon, Jong-Ho;Yi, Song-Se;Kim, Young-Gyu;Lee, Yoon-Sik;Yoon, Je-Yong
    • Journal of Microbiology and Biotechnology
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    • v.17 no.10
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    • pp.1598-1606
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    • 2007
  • A new series comprising 7 analogs of N-(sulfanyl ethanoyl)-L-HSL derivatives, 2 analogs of N-(fluoroalkanoyl)-$_L$-HSL derivatives, N-(fluorosulfonyl)-L-HSL, and 2,2-dimethyl butanoyl HSL were synthesized using a solid-phase organic synthesis method. Each of the 11 synthesized compounds was analyzed using NMR and mass spectroscopies, and molecular modeling studies of the 11 ligands were performed using SYBYL packages. Thereafter, a bacterial test was designed to identify their quorum-sensing inhibition activity and antifouling efficacy. Most of the synthesized compounds were found to be effective as quorum-sensing antagonists, where antagonist screening revealed that 10 among the 11 synthesized ligands were able to antagonize the quorum sensing of A. tumefaciens.

3D-QSAR Studies on Angiotensin-Converting Enzyme (ACE)Inhibitors: a Molecular Design in Hypertensive Agents

  • San Juan, Amor A.;Cho, Seung-Joo
    • Bulletin of the Korean Chemical Society
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    • v.26 no.6
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    • pp.952-958
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    • 2005
  • Angiotensin-converting enzyme (ACE) is known to be primarily responsible for hypertension. Threedimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of 28 ACE inhibitors. The availability of ACE crystal structure (1UZF) provided the plausible biological orientation of inhibitors to ACE active site (C-domain). Alignment for CoMFA obtained by docking ligands to 1UZF protein using FlexX program showed better statistical model as compared to superposition of corresponding atoms. The statistical parameters indicate reasonable models for both CoMFA ($q^2$ = 0.530, $r^2$ = 0.998) and CoMSIA ($q^2$ = 0.518, $r^2$ = 0.990). The 3D-QSAR analyses provide valuable information for the design of ACE inhibitors with potent activity towards C-domain of ACE. The group substitutions involving the phenyl ring and carbon chain at the propionyl and sulfonyl moieties of captopril are essential for better activity against ACE.