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Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT. Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme. Chem Biol Drug Des 2014; 82:418-28. [PMID: 23701677 DOI: 10.1111/cbdd.12167] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/06/2013] [Accepted: 05/19/2013] [Indexed: 01/15/2023]
Abstract
Staphylococcus aureus is the leading cause of hospital-acquired infections in the United States. The emergence of multidrug-resistant strains of S. aureus has created an urgent need for new antibiotics. Staphylococcus aureus uses the sortase A enzyme to display surface virulence factors suggesting that compounds that inhibit its activity will function as potent anti-infective agents. Here, we report the identification of several inhibitors of sortase A using virtual screening methods that employ the relaxed complex scheme, an advanced computer-docking methodology that accounts for protein receptor flexibility. Experimental testing validates that several compounds identified in the screen inhibit the activity of sortase A. A lead compound based on the 2-phenyl-2,3-dihydro-1H-perimidine scaffold is particularly promising, and its binding mechanism was further investigated using molecular dynamics simulations and conducting preliminary structure-activity relationship studies.
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Affiliation(s)
- Albert H Chan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Ieong PU, Sørensen J, Vemu PL, Wong CW, Demir Ö, Williams NP, Wang J, Crawl D, Swift RV, Malmstrom RD, Altintas I, Amaro RE. Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations. ACTA ACUST UNITED AC 2014; 29:1745-1755. [PMID: 29399238 DOI: 10.1016/j.procs.2014.05.159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We describe the development of automated workflows that support computed-aided drug discovery (CADD) and molecular dynamics (MD) simulations and are included as part of the National Biomedical Computational Resource (NBCR). The main workflow components include: file-management tasks, ligand force field parameterization, receptor-ligand molecular dynamics (MD) simulations, job submission and monitoring on relevant high-performance computing (HPC) resources, receptor structural clustering, virtual screening (VS), and statistical analyses of the VS results. The workflows aim to standardize simulation and analysis and promote best practices within the molecular simulation and CADD communities. Each component is developed as a stand-alone workflow, which allows easy integration into larger frameworks built to suit user needs, while remaining intuitive and easy to extend.
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Affiliation(s)
- Pek U Ieong
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Jesper Sørensen
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Prasantha L Vemu
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Celia W Wong
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Özlem Demir
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Nadya P Williams
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Jianwu Wang
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Daniel Crawl
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Robert V Swift
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Robert D Malmstrom
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Ilkay Altintas
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA.,National Biomedical Computation Resource, University of California San Diego, 9500 Gilman Drive, MC 0340, La Jolla, CA 92093, USA
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