Research Highlights

New Drug Effective Against methicillin-resistant Staphylococcus aureus (MRSA)

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Figure 1: A subset of the new compounds identified which could be effective against MRSA. Compound No. 16 is identified through in silico screening, so was another potent compound No. 17 (not shown). The compounds are shown in crystal complex with E. coli UPPS. The IC50 values that indicate the potency of the compounds are shown for E. coli (Ec) and S. aureus (Sa).

Millions of people die each year from bacterial infections in tuberculosis or pneumonia. The bacterium, Staphlococcus aureus, while usually harmless, may lead to ear infection, sinusitis, pneumonia, meningitis, toxic shock syndrome and a number of postsurgical infections. Typically patients are prescribed antibiotics, which inhibit the bacterial cell wall formation to kill the bacteria. However, since the discovery of penicillin by Sir Alexander Fleming that inhibits S. aureus growth, many pathogenic bacteria have become resistant after acquiring an enzyme, β-lactamase, that breaks down penicillin. For example, met(h)icillin was developed in 1959 to treat S. aureus but is no longer used due to the emergence of methicillin-resistant S. aureus (MRSA). Since then, MRSA is still commonly used to describe S. aureus strains resistant to all penicillins. 

Prof. Eric Oldfield and his team of researchers at University of Illinois, Urbana-Champaign (UIUC), have been studying the bacterial cell wall biosynthetic pathway, and trying to identify other points of intervention to deal with antibiotic resistance bacteria. “There’s an urgent need for more antibiotics because of drug resistance,” Oldfield said. “There are, for example, completely drug-resistant strains of tuberculosis. None of the drugs work against these strains of tuberculosis, and so, if you get it, you die.” 

“And Staph itself actually kills more people in the U.S. than does HIV/AIDS.” Oldfield continued. One enzyme that has drawn their interest is the undecaprenyl diphosphate synthase (UPPS), which is an essential bacterial protein not used by humans. The enzyme acts upstream from the site of penicillin action, and represents a new opportunity to treat MRSA. Together with Prof. Andy McCammon’s group at University of California, San Diego (UC San Diego), the two teams have collaborated for more than two years on the computer aided drug discovery for new antibiotics. The research team had previously applied the relaxed complex scheme, developed at the National Biomedical Computation Resource, in a virtual screening experiment using the National Cancer Institute Diversity Set (NCIDS) compound library to identify inhibitors to farnesyl diphosphate synthase (FPPS), another upstream enzyme in the bacterial cell wall biosynthesis. The results were published in a 2011 article in Chemical Biology and Drug Design journal [1]. Interestingly, several of the top hits exhibited potent activities against UPPS. In their latest finding published in the 2013 Proceedings of the National Academy of Sciences (PNAS), the team has reported that derivatives of the UPPS inhibitors previously identified exhibit potent activities and are protective in a mouse infection model [2]. 

In this study, William Sinko, a graduate student, and Drs. Steffen Lindert and Cesar Oliveira, postdoctoral fellows in Prof. McCammon’s group, predicted compound 16 to be an FPPS inhibitor. This was found to be the case but also, the compound inhibited UPPS. Wei Zhu, a graduate student, in the Oldfield lab then used a computational technical technique called compound similarity search to find even better leads. Wei Zhu and Yonghui Zhang, a research scientist, in the Oldfield group, tested these compounds in UPPS inhibition assays and also determined how they bind to UPPS by using x-ray crystallography. Finally, the Oldfield lab derived and tested new analogs of the compounds that worked very well against UPPS. “And we found one (Compound 17) that was about 1,000 times more active than the first hit we had against FPPS,” Oldfield said.

One of the most intriguing outcomes of this series of studies is that many of the inhibitors (non-bisphosphonate inhibitors) do not bind to the active site but to a distant site. Additional computational analyses by the McCammon group suggest the distant binding site may be more favorable for inhibitor binding because it introduces less perturbation on the enzyme conformation. The ability of the virtual screening technique to identify active compounds using the distant site as a target gave the best selectivity compared with other sites, each tested against 1000 dummy compounds using the Schrodinger docking software Glide.

Illinois chemistry and Institute for Genomic Biology professor Douglas Mitchell and Dr. Victor Nizet at UC San Diego tested compound 17 in cell culture and mice, respectively. “Twenty out of 20 animals survived if they were treated with this drug lead and zero survived if they weren’t treated,” Oldfield said. While it may still take years before these new drug leads could be optimized and tested for safety and efficacy through clinical trials, this study demonstrated the power of the tools developed by NBCR, and the synergy exhibited by these collaborating teams.

This research highlight was based on the original story by University of Illinois [3]. Nature Reviews Drug Discovery also featured this work in a recent Research Highlight [4].

References: 

  1. Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E and McCammon JA (2011) Non-bisphosphonate inhibitors of isoprenoid biosynthesis identified via computer-aided drug design. Chem Biol Drug Des 78:323-32. doi: 10.1111/j.1747-0285.2011.01164.x
  2. Zhu W, Zhang Y, Sinko W, Hensler ME, Olson J, Molohon KJ, Lindert S, Cao R, Li K, Wang K, Wang Y, Liu YL, Sankovsky A, de Oliveira CA, Mitchell DA, Nizet V, McCammon JA and Oldfield E (2013) Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A 110:123-8. doi: 10.1073/pnas.1219899110
  3. New compound overcomes drug-resistant Staph infection in mice
  4. Crunkhorn S (2013) Antibacterial drugs: New antibiotics on the horizon? Nat Rev Drug Discov 12:99. doi: 10.1038/nrd3940

Researchers: NBCR: J. Andrew McCammon, Ph.D., Core lead; William Sinko, Ph.D., Cesar de Oliveira, Ph.D., Stephen Lindert, Ph.D. Collaborators: Victor Nizet, Ph.D (UCSD).; Eric Oldfield, Ph.D., and Douglas Mitchell, Ph.D. (U Illinois) Collaborative Project Lead

Figure 1: A subset of the new compounds identified which could be effective against MRSA.