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, 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 (


Bad science for money




Poor quality or bad science is becoming more visible. If you think it is an isolated case, you are dead wrong. There is one company, at least, which prides itself on paying money for inclusion of their work in your citation. There is a message from a sucker from such an enterprise:

Dear XXX,

How are you?

My name is Zhang, I am from China. I am a businessman, my business is about Citing for Money.

Please let me introduce the nature of this business:

As you know, the IF(Impact Factor)of a journal is very important, if a journal has a high Impact Factor, the journal will be very significant and famous. So many journals published in English ask my company to improve their Impact Factors. And the only way to improve the Impact Factors is to cite papers from the journals.

So now I invite you to cooperate into this business, the cooperation method is as follows:

1.The price is : 50 USD for each citation, that is, if you cite 1 paper in one of your papers, you will get 50USD, and if you cite 8 papers in one of your papers, you will get 400 USD;

2.Payment method: 

      A, Chinese bank account(I will send RMB to your Chinese bank account according to the latest exchange rate); 

      B, Western union company(the banks in your city can do western union payment, you can call the banks to ask); 

      C, if you are from Iran, considering Iran sanction, now there is an Iranian in my team, he can send money to your Iran bank account in Rials according to the latest exchange rate;

      D, alipay account; 

      E, wechat;

      if you want to know the details, please reply this email to

3.You reply this email to  so I will know that you would like to cooperate with my company;

4.I will send the citation regulation and journal list to you, many journals in different research fields ask my company to improve their Impact Factors, you will find some journals that are relevant to your research;

5.You will cite some papers from the journals in your paper, before you cite them, you should tell me which papers you are going to cite;

6.As soon as the paper is accepted, you should tell me the information of the accepted paper, and I will make budgeting for you;

7.As soon as the paper is published onine, you should tell me and send the paper link to me, and I will send money to you;

8.In fact, now there are many professors in different countries cooperating with my company, they cite papers from the journals, and I send money to them. Please reply this email to   I will send the “money payment list” to you, so you will see that I have really sent much money to professors in different countries.
If you would like to cooperate with my company in citing for money, please reply this email to  and we will talk about the details.

Thank you very much!
Yours sincerely,

Looking forward to your feedback.

New blockers of Pseudomonas aeruginosa virulence

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In the recent work by Swietnicki et al. (BBRC,, 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 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 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.