Molecular Diversity

, 15:989 | Cite as

Potent antimicrobial small molecules screened as inhibitors of tyrosine recombinases and Holliday junction-resolving enzymes

  • Marc C. Rideout
  • Jeffrey L. Boldt
  • Gabriel Vahi-Ferguson
  • Peter Salamon
  • Adel Nefzi
  • John M. Ostresh
  • Marc Giulianotti
  • Clemencia Pinilla
  • Anca M. Segall
Full-Length Paper


Holliday junctions (HJs) are critical intermediates in many recombination-dependent DNA repair pathways. Our lab has previously identified several hexameric peptides that target HJ intermediates formed in DNA recombination reactions. One of the most potent peptides, WRWYCR, is active as a homodimer and has shown bactericidal activity partly because of its ability to interfere with DNA repair proteins that act upon HJs. To increase the possibility of developing a therapeutic targeting DNA repair, we searched for small molecule inhibitors that were functional surrogates of the peptides. Initial screens of heterocyclic small molecule libraries resulted in the identification of several N-methyl aminocyclic thiourea inhibitors. Like the peptides, these inhibitors trapped HJs formed during recombination reactions in vitro, but were less potent than the peptides in biochemical assays and had little antibacterial activity. In this study, we describe the screening of a second set of libraries containing somewhat larger and more symmetrical scaffolds in an effort to mimic the symmetry of a WRWYCR homodimer and its target. From this screen, we identified several pyrrolidine bis-cyclic guanidine inhibitors that also interfere with processing of HJs in vitro and are potent inhibitors of Gram-negative and especially Gram-positive bacterial growth. These molecules are proof-of-principle of a class of compounds with novel activities, which may in the future be developed into a new class of antibiotics that will expand the available choices for therapy against drug-resistant bacteria.


Site-specific recombination λ-Integrase Holliday junction Combinatorial libraries DNA repair 

Supplementary material

11030_2011_9333_MOESM1_ESM.pdf (2.4 mb)
ESM 1 (PDF 2437 kb)


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Marc C. Rideout
    • 1
  • Jeffrey L. Boldt
    • 1
    • 2
  • Gabriel Vahi-Ferguson
    • 1
    • 3
  • Peter Salamon
    • 3
  • Adel Nefzi
    • 4
  • John M. Ostresh
    • 5
  • Marc Giulianotti
    • 4
  • Clemencia Pinilla
    • 5
  • Anca M. Segall
    • 1
  1. 1.Department of Biology and Center for Microbial SciencesSan Diego State UniversitySan DiegoUSA
  2. 2.Genomatica, Inc.San DiegoUSA
  3. 3.Department of Mathematics and StatisticsSan Diego State UniversitySan DiegoUSA
  4. 4.Torrey Pines Institute for Molecular StudiesPort St. LucieUSA
  5. 5.Torrey Pines Institute for Molecular StudiesSan DiegoUSA

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