Identification of putative sugar binding sites in phage proteins


De novo identification of substrates for enzymes is typically done experimentally. However, the approach takes time and requires a recombinant protein to test the predictions. While for many proteins it is a routine, for others it becomes problematic due to expression problems, solubility/aggregation of the purified biomolecule and time constraints. Therefore, in silico approaches which offer a chance to bypass the tedium are very desired. In the recent work by Swietnicki and Brzozowska https://doi.org/10.1016/j.jmgm.2019.07.002, the authors used computational tools to identify putative binding site for a sugar substrate. A closely related carbohydrate was not the substrate and the in silico tools were used to differentiate between the 2 molecules. Analysis of binding energies and retention on the molecule during molecular dynamics simulation showed that the difference between molecules was most likely attributed to the residence time of carbohydrates on the protein. The authors went a step further and analyzed the binding site of the enzyme to predict putative preferences for the enzyme and elucidate its catalytic mechanism.

The methodology used by the authors has been in use in the commercial sector for many years for a different work. Application of the approach to bacteriophages may have a future as an alternative to experimental screening of bacteria against a panel of phages. If the pre-screening is performed in silico based on DNA sequence of a pathogen and a constructed in silico library of bacteriophage proteins, selection of phages could be substantially shortened. One could also imagine a personalized bacteriophage therapy for infectious, and not only, diseases in humans as a future medical approach to treating bacterial infections. For the drug-resistant pathogens, bacteriophage therapy could be personalized as any other branch of medicine.

The work was performed at the Institute of Immunology and Experimental Therapy of the the Polish Academy of Science in Wroclaw, PL and guided by Dr. Swietnicki. Computational resources were from the on-site IT Department and the software was purchased from Schrodinger LLC (www.schrodinger.com).

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Bad science for money


 

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New blockers of Pseudomonas aeruginosa virulence


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In the recent work by Swietnicki et al. (BBRC, https://doi.org/10.1016/j.bbrc.2019.04.055), the group showed how to block bacterial transport system in Pseudomonas aeruginosa responsible for secretion of the most potent toxin by the pathogen. The study demonstrated a proof-of-concept how to do it safely, selectively and without killing the pathogen. The strategy relied on disabling the offensive weaponry of pathogen normally used to destroy human cells. Since the pathogen is on the list of ESKAPE pathogens and responsible for severe complications in hospital intensive care units (ICUs) in patients undergoing organ transplants, chemotherapy and receiving antiviral drugs (HIV/AIDS), the strategy may offer an alternative to antibiotics in the future.

The work was performed at the Institute of Immunology and Experimental Therapy of the Polish Academy of Science in Wroclaw, PL and guided by Dr. Swietnicki. Contributing experiments were performed by the group guided by Prof. Krzysztof Marycz at the Wroclaw University of Environmental Life Sciences and students from the Silesian Medical University and Wroclaw Technical University.

New antibiotics for P. mirabilis and S. aureus


I am organizing a fundraiser to finance development of new antibiotics against Proteus mirabilis. Goal is to collect 900,000 PLN (1 USD=3.38 PLN) towards basic research. Please visit https://lnkd.in/d4N89bW if you want to donate.

Paper describing a proof-of-concept technology approach and the results for Proteus mirabilis and Staphylococcus aureus is available online at https://doi.org/10.1016/j.bbrc.2018.10.189. Compounds are novel and could be used for further development into a new class of antibiotics.

Technology used to come to that point is described under Technology heading.