Difference between revisions of "Team:Tuebingen/Attributions"

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       <nav class="Unternavigation-Team">
 
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              <a href="#Introduction">Introduction </a> <br>
 
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              <a href="#Theoretical-Background">Theoretical Background </a> <br>
 
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              <a href="#Practical-Workflow">Practical Workflow </a><br>
 
 
            
 
            
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               <a href="#Results-and-Discussion">Results and Discussion </a><br>
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              <a href="https://2017.igem.org/Team:Tuebingen/Team">Team</a><br>
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              <a href="#Attribution">Attribution</a><br>
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              <a href="#Acknowledgment">Acknowledgment</a><br>
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               <a href="#ReferencesLink">References</a><br>
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                 <h1 id="The-Fourth-Interlab-Study">The fourth InterLab Study</h1>
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                 <h1 id="Attribution" class="anchor"> Attribution</h1>              
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                <h2 id="Introduction" class="anchor">INTRODUCTION</h2>        
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                 <p> This year’s team was led by PD Dr. Bertolt Gust and PD Dr. Elisabeth Fuss. They provided the needed laboratory support and managed      main communication within the university. The student team was coordinated and organized by Brian Weidensee and Nikolas Layer as        student leaders; the original project idea was designed by PD Dr. Bertolt Gust and Nikolas Layer.
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                 <p>How similar can fluorescence measurements be if the same protocol is used all over the world? This question will be answered in the fourth International InterLab Measurement Study for iGEM 2017. For researchers it is important to standardize protocols to produce reproducible data. Fluorescence values measured from GFP and other fluorochromes are usually difficult to compare as different devices and methods give different values in different units. This year's InterLab Study focusses on a comparable measurement of fluorescence by establishing a step by step protocol for plate readers used by all iGEM teams.</p>             
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                <h2 id="Theoretical-Background" class="anchor"> THEORETICAL  BACKGROUND </h2>       
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                <p>Teams are provided with the same protocol to measure GFP fluorescence with a plate reader. Eight different devices were tested which are listed below:</p>
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                  <a href="http://parts.igem.org/Part:BBa_I20270" id="Positive-Control"> ● Positive Control (BBa_I20270)</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_R0040"  id="negative-control"> ● Negative Control (BBa_R0040)</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_J364000" id="Test-Device1">  ● Test Device 1 (BBa_J364000): J23101.BCD2.E0040.B0015</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_J364001" id="Test-Device2">  ● Test Device 2 (BBa_J364001): J23106.BCD2.E0040.B0015</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_J364002" id="Test-Device3">  ● Test Device 3 (BBa_J364002): J23117.BCD2.E0040.B0015</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_J364003" id="Test-Device4">  ● Test Device 4 (BBa_J364003): J23101+I13504</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_J364004" id="Test-Device5">  ● Test Device 5 (BBa_J364004): J23106+I13504</a><br>
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                  <a href="http://parts.igem.org/Part:BBa_J364005" id="Test-Device6">  ● Test Device 6 (BBa_J364005): J23117+I13504</a><br>
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                <p><br> All test devices  are composite parts containing GFP with constitutive promoters,  a negative control without GFP is also included. The vector pSB1C3 has a chloramphenicol resistance. Device 4, 5, and 6 additionally contain a Bicistronic Design Element Number 2 which was designed by Mutalik et al. in a2013 Nature publication. This element should induce precise and reliable gene expression.
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<br><br>  Mutalik, V. K. et al. "Precise and reliable gene expression via standard transcription and translation initiation elements." Nature Methods 10, 354–360 (2013).  
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                    All student members participated in the project development with the special contribution in gene block and part design by Lukas Fuhs and Nikolas Layer. <br>For laboratory execution, we divided the project into three parts: The chemical synthesis was done by Alexandra Haake, Marcel Conrady, Madeleine Heep, and Michael Krummhaar. Lisa Dussling contributed the in-silico analysis and the bioinformatics model while Marcel Conrady, Lukas Fuhs, Madeleine Heep, Mirjam Gneiting, Milena Krach, and Michael Krummhaar were involved in cloning, biochemical analysis, and compound production.  
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                    Milena Krach, Brian Weidensee, and our intern Fan Zhang were responsible for procedure and data submission of the iGEM 2017 interlab study.  
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                    For our this year’s YouTube collaboration project we want to thank all participating iGEM teams and Hannah Brasse for the realization and organization. Hannah Brasse, Lukas Fuhs, Mirjam Gneiting, Madeleine Heep and Milena Krach produced our own video for the channel. All educational projects embedded in our Human Practice project were mainly organized by Vic-Fabienne Schumann and Brian Weidensee with the engagement of the whole student team with special thanks to Marcel Conrady, Madeleine Heep, Milena Krach and Brian Weidensee for supervision of our internship student Fan Zhang.
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                    Our wiki’s structure was mainly designed by Mirjam Gneiting and Alexander Recktenwald; a working code was created and implemented by Alexander Recktenwald.  
  
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<br><br>  For normalization standard curves were made with the provided measurement kit from iGEM.
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                    All wiki content was created and uploaded by Hannah Brasse, Marcel Conrady, Lisa Dussling, Mirjam Gneiting, Alexandra Haake, Madeleine Heep, Milena Krach, Michael Krummhaar, Nikolas Layer, Vic-Fabienne Schumann, and Brian Weidensee.
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</p>
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                    Without a lot of fundraising, none of our work would have been possible: Hannah Brasse, Alexandra Haake, Madeleine Heep, Milena Krach, Michael Krummhaar, Nikolas Layer, Vic-Fabienne Schumann and Brian Weidensee contributed to this area.  
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                  <br> <br>
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                    We want to especially thank Dr. H. Kalbacher for MALDI-TOF Analysis and crystallization experiments of our chemical compounds. </p>
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                  <h2 id="Practical-Workflow" class="anchor">PRACTICAL WORKFLOW</h2>
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                  <p>Before the actual measurement, calibration was performed for OD600 and a fluorescence standard curve was determined using a clear bottom black 96-well plate in four replicates.</p>
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                  <h5>Table 1: Instrument settings for calibration</h5>
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                  <table style="width:100%">
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  <tr>
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    <th>Instrument Settings</th>
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    <th>OD6000 reference point
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        LUDOX-S40</th>
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    <th>fluorescein fluorescence standard curve</th>
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  </tr>
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  <tr>
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    <td>Positioning delay</td>
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    <td>0.5 s</td>
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    <td>0.2</td>
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  </tr>
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  <tr>
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    <td>Number of flashes per well</td>
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    <td>20</td>
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    <td>25</td>
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  </tr>
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    <td>Orbital/pathlength correction</td>
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    <td>off</td>
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    <td>off</td>
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  </tr>
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  <tr>
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    <td>Optic</td>
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    <td>top</td>
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    <td>top</td>
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    <tr>
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    <td>gain</td>
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    <td></td>
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    <td>700</td>
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  </tr>
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  <tr>
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    <td>Excitation</td>
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    <td></td>
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    <td>485</td>
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  </tr>
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  <tr>
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    <td>Emission</td>
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    <td></td>
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    <td>520</td>
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  </tr>
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  <tr>
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    <td>Orbital/pathlength correction</td>
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    <td>off</td>
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    <td>off</td>
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  </tr>
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</table>
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                  <br><br><br>
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                  <img src="https://static.igem.org/mediawiki/2017/b/b5/T--Tuebingen--Interlabstudy-Fluorescein.png" id="Fluorescin-Standard-Curve">
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                  <h5> Figure 1: Fluorescein standard curve obtained by dilution series of fluorescein in 4 replicates. </h5>
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                  <br>
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                  <p> Subsequently, we performed , the actual measurement of 8 different devices  as shown in figure 2. <br> First, plasmids were transformed in DH5-alpha using the standard transformation protocol from iGEM with the deviation of using LB medium instead of SOC medium. For further information on the used protocol go to "http://parts.igem.org/Help:Protocols/Transformation". <br>
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                  <br> Two colonies were picked for each device and incubated in 5-10 mL LB medium + Chloramphenicol (25 µg/mL). The next day the solution was diluted to an OD of 0.02 and 500 µL of the samples were taken and hold on ice at t=0, 2, 4, 6 h. Absorbance (OD600) and fluorescence were then measured using the FLUOstar OPTIMA from BMG LABTECH.
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                  <a href="https://static.igem.org/mediawiki/2017/8/85/InterLab_2017_Plate_Reader_Protocol.pdf"> (For detailed protocol click here.)</a></p>
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                  <img src="https://static.igem.org/mediawiki/2017/f/fb/T--Tuebingen--Interlabstudy-Workflow.png" id="Workflow-InterLab-Study-2017">
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                  <h5> Figure 2: Workflow InterLab Study 2017 </h5>
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                  <h2 id="Results-and-Discussion" class="anchor"> RESULTS AND DISCUSSION </h2>
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                  <p>The provided protocol by iGEM was easy to implement by providing a step by step guide to perform the experiments. <br><br>
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                      Although our data has a high variance between the devices and between the replicates after normalization, device 1 and 2 showed significant higher fluorescence than device 3. This is in line with the data from the device’s reference in the Registry where device 1 was shown to have the highest absorption followed by device 2 and then device 3.
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                    <h2 id="Acknowledgement" class="anchor"> Acknowledgement</h2>
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                  </p>
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                    <p> AG Prof. Dr. O. Kohlbacher - Hardware and in silico support
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                    Prof. Dr. L.Heide - Clorobiocin Cluster and bacterial strains
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                  <h5>Table 2: Variant RFP with corresponding absorption values</h5>
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                    AG Prof. Dr. D.Schwarzer - chemical synthesis laboratory and support
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                    AG Prof. Dr. S. Grond - Laboratory material support
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                    AG Pr. Dr. Schulze-Osthoff - Laboratory material support
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                    AG Pr. Dr. A. Weber - Laboratory material support for interlab study
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                    Jakob Wendt - Wiki coding support
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                    </p>
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                  <table style="width:100%">
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                    <h2 id="ReferencesLink" class="anchor"> References </h2>
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  <tr>
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                    <div id="References" > <p>
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    <th></th>
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                    Anderle, C., Hennig, S., Kammerer, B., Li, S. M., Wessjohann, L., Gust, B., & Heide, L. (2007). Improved mutasynthetic approaches for the production of modified aminocoumarin antibiotics. Chem Biol, 14(8), 955-967. doi:10.1016/j.chembiol.2007.07.014 <br><br><br>
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    <th>Variant RFP</th>  
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    <th>Absorption / AU oder mAU</th>
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Anderle, C., Stieger, M., Burrell, M., Reinelt, S., Maxwell, A., Page, M., & Heide, L. (2008). Biological activities of novel gyrase inhibitors of the aminocoumarin class. Antimicrob Agents Chemother, 52(6), 1982-1990. doi:10.1128/AAC.01235-07<br><br><br>
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  </tr>
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Bachmann, B. O., Li, R., & Townsend, C. A. (1998). beta-Lactam synthetase: a new biosynthetic enzyme. Proc Natl Acad Sci U S A, 95(16), 9082-9086.<br><br><br>
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  <tr>
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    <td>Device 1</td>
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Beisken, S., Meinl, T., Wiswedel, B., de Figueiredo, L. F., Berthold, M., & Steinbeck, C. (2013). KNIME-CDK: Workflow-driven cheminformatics. BMC Bioinformatics, 14, 257. doi:10.1186/1471-2105-14-257<br><br><br>
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    <td>J23101</td>
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    <td>1791</td>
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Chen, Y., Wendt-Pienkowski, E., Ju, J., Lin, S., Rajski, S. R., & Shen, B. (2010). Characterization of FdmV as an amide synthetase for fredericamycin A biosynthesis in Streptomyces griseus ATCC 43944. J Biol Chem, 285(50), 38853-38860. doi:10.1074/jbc.M110.147744<br><br><br>
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  </tr>
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Fasching, C. E., Tenover, F. C., Slama, T. G., Fisher, L. M., Sreedharan, S., Oram, M., . . . Peterson, L. R. (1991). gyrA mutations in ciprofloxacin-resistant, methicillin-resistant Staphylococcus aureus from Indiana, Minnesota, and Tennessee. J Infect Dis, 164(5), 976-979.<br><br><br>
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  <tr>
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    <td>Device 2</td>
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Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., . . . Shenkin, P. S. (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem, 47(7), 1739-1749. doi:10.1021/jm0306430<br><br><br>
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    <td>J23106</td>
+
 
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    <td>1185</td>
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Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., . . . Mainz, D. T. (2006). Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem, 49(21), 6177-6196. doi:10.1021/jm051256o<br><br><br>
−
  </tr>
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Fu, X. W., Pu, W. C., Zhang, G. L., & Wang, C. (2015). Synthesis of salicylaldehydes from phenols via copper-mediated duff reaction. Research on Chemical Intermediates, 41(11), 8147-8158.<br><br><br>
−
  <tr>
+
 
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    <td>Device 3</td>
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Fujimoto-Nakamura, M., Ito, H., Oyamada, Y., Nishino, T., & Yamagishi, J. (2005). Accumulation of mutations in both gyrB and parE genes is associated with high-level resistance to novobiocin in Staphylococcus aureus. Antimicrob Agents Chemother, 49(9), 3810-3815. doi:10.1128/AAC.49.9.3810-3815.2005<br><br><br>
−
    <td>J23117</td>
+
 
−
    <td>162</td>
+
Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov, 10(5), 449-461. doi:10.1517/17460441.2015.1032936<br><br><br>
−
  </tr>
+
                       
−
                  </table>
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Heide, L. (2014). New aminocoumarin antibiotics as gyrase inhibitors. Int J Med Microbiol, 304(1), 31-36. doi:10.1016/j.ijmm.2013.08.013<br>
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                      <p>Device 4, 5 and 6 with the Bicistronic Design Element Number 2 showed no real difference in comparison to device 1, 2 and 3 where this element was not present. When the data from all teams is compared we will see if there is a bigger influence on gene expression due to the different promoters used.<br>
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                      At time point 2 h the fluorescence signal was the highest despite for the positive control. If the expression of RFP induces stress, one explanation might be that the bacteria induce expression of proteases or reduce the amount of the necessary transcription factors.
+
Holdgate, G. A., Tunnicliffe, A., Ward, W. H., Weston, S. A., Rosenbrock, G., Barth, P. T., . . . Timms, D. (1997). The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Biochemistry, 36(32), 9663-9673. doi:10.1021/bi970294+<br><br><br>
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                      </p>
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Kontoyianni, M. (2017). Docking and Virtual Screening in Drug Discovery. Methods Mol Biol, 1647, 255-266. doi:10.1007/978-1-4939-7201-2_18<br>
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                  <img src=https://static.igem.org/mediawiki/2017/9/9b/T--Tuebingen--Interlabstudy-Data.png id="Results-Fluorescein">
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                  <h5>Figure 3: Results show in µM Fluorescein/OD600 for Devices 1, 2, 3 in comparison  to devices 4, 5, 6. Samples were taken at t = 0, 2, 4, 6 h. Values smaller than 0 were excluded in the graphic. Biological duplicates are represented from each device. BCD2: Bicistronic Design Element Number 2.</h5>
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Lafitte, D., Lamour, V., Tsvetkov, P. O., Makarov, A. A., Klich, M., Deprez, P., . . . Gilli, R. (2002). DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose. Biochemistry, 41(23), 7217-7223.<br>
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 +
Lawson, D. M., & Stevenson, C. E. (2012). Structural and functional dissection of aminocoumarin antibiotic biosynthesis: a review. J Struct Funct Genomics, 13(2), 125-133. doi:10.1007/s10969-012-9138-2<br><br><br>
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Lionta, E., Spyrou, G., Vassilatis, D. K., & Cournia, Z. (2014). Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem, 14(16), 1923-1938.<br><br><br>
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Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev, 46(1-3), 3-26.<br><br><br>
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Luft, T., Li, S. M., Scheible, H., Kammerer, B., & Heide, L. (2005). Overexpression, purification and characterization of SimL, an amide synthetase involved in simocyclinone biosynthesis. Arch Microbiol, 183(4), 277-285. doi:10.1007/s00203-005-0770-0<br><br><br>
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M Lindsay Grayson, S. M. C., James S McCarthy, John Mills, Johan W Mouton, S Ragnar Norrby, David L Paterson, Michael A Pfaller. (2010). Kucers' The Use of Antibiotics Sixth Edition: A Clinical Review of Antibacterial, Antifungal and Antiviral Drugs.<br><br><br>
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Mannhold, R., Poda, G. I., Ostermann, C., & Tetko, I. V. (2009). Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds. J Pharm Sci, 98(3), 861-893. doi:10.1002/jps.21494<br><br><br>
 +
 
 +
Miller, M. T., Bachmann, B. O., Townsend, C. A., & Rosenzweig, A. C. (2001). Structure of beta-lactam synthetase reveals how to synthesize antibiotics instead of asparagine. Nat Struct Biol, 8(8), 684-689. doi:10.1038/90394<br><br><br>
 +
 
 +
Organization, G. W. H. (2017). Prioritization of pathogens to guide discovery, reserach and development of new antibiotics fro drug-resistant bacterial infections, including tuberculosis.<br><br><br>
 +
                       
 +
Paget, M. S., Chamberlin, L., Atrih, A., Foster, S. J., & Buttner, M. J. (1999). Evidence that the extracytoplasmic function sigma factor sigmaE is required for normal cell wall structure in Streptomyces coelicolor A3(2). J Bacteriol, 181(1), 204-211.<br><br><br>
 +
 
 +
Sadiq, A. A., Patel, M. R., Jacobson, B. A., Escobedo, M., Ellis, K., Oppegard, L. M., . . . Kratzke, R. A. (2010). Anti-proliferative effects of simocyclinone D8 (SD8), a novel catalytic inhibitor of topoisomerase II. Invest New Drugs, 28(1), 20-25. doi:10.1007/s10637-008-9209-1<br><br><br>
 +
 
 +
Schimana, J., Fiedler, H. P., Groth, I., Sussmuth, R., Beil, W., Walker, M., & Zeeck, A. (2000). Simocyclinones, novel cytostatic angucyclinone antibiotics produced by Streptomyces antibioticus Tu 6040. I. Taxonomy, fermentation, isolation and biological activities. J Antibiot (Tokyo), 53(8), 779-787.<br><br><br>
 +
                       
 +
Shaikh, S., Fatima, J., Shakil, S., Rizvi, S. M., & Kamal, M. A. (2015). Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J Biol Sci, 22(1), 90-101. doi:10.1016/j.sjbs.2014.08.002<br><br><br>
 +
 
 +
Tetko, I. V., Gasteiger, J., Todeschini, R., Mauri, A., Livingstone, D., Ertl, P., . . . Prokopenko, V. V. (2005). Virtual computational chemistry laboratory--design and description. J Comput Aided Mol Des, 19(6), 453-463. doi:10.1007/s10822-005-8694-y<br><br><br>
 +
 
 +
Tsai, F. T., Singh, O. M., Skarzynski, T., Wonacott, A. J., Weston, S., Tucker, A., . . . Wigley, D. B. (1997). The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins, 28(1), 41-52.<br> </p>
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Revision as of 17:57, 1 November 2017

iGem Tübingen 2017

Team Inspiration Result Human Practice Lab Attribution
TeamBild

Attribution

This year’s team was led by PD Dr. Bertolt Gust and PD Dr. Elisabeth Fuss. They provided the needed laboratory support and managed main communication within the university. The student team was coordinated and organized by Brian Weidensee and Nikolas Layer as student leaders; the original project idea was designed by PD Dr. Bertolt Gust and Nikolas Layer. All student members participated in the project development with the special contribution in gene block and part design by Lukas Fuhs and Nikolas Layer.
For laboratory execution, we divided the project into three parts: The chemical synthesis was done by Alexandra Haake, Marcel Conrady, Madeleine Heep, and Michael Krummhaar. Lisa Dussling contributed the in-silico analysis and the bioinformatics model while Marcel Conrady, Lukas Fuhs, Madeleine Heep, Mirjam Gneiting, Milena Krach, and Michael Krummhaar were involved in cloning, biochemical analysis, and compound production. Milena Krach, Brian Weidensee, and our intern Fan Zhang were responsible for procedure and data submission of the iGEM 2017 interlab study. For our this year’s YouTube collaboration project we want to thank all participating iGEM teams and Hannah Brasse for the realization and organization. Hannah Brasse, Lukas Fuhs, Mirjam Gneiting, Madeleine Heep and Milena Krach produced our own video for the channel. All educational projects embedded in our Human Practice project were mainly organized by Vic-Fabienne Schumann and Brian Weidensee with the engagement of the whole student team with special thanks to Marcel Conrady, Madeleine Heep, Milena Krach and Brian Weidensee for supervision of our internship student Fan Zhang. Our wiki’s structure was mainly designed by Mirjam Gneiting and Alexander Recktenwald; a working code was created and implemented by Alexander Recktenwald. All wiki content was created and uploaded by Hannah Brasse, Marcel Conrady, Lisa Dussling, Mirjam Gneiting, Alexandra Haake, Madeleine Heep, Milena Krach, Michael Krummhaar, Nikolas Layer, Vic-Fabienne Schumann, and Brian Weidensee. Without a lot of fundraising, none of our work would have been possible: Hannah Brasse, Alexandra Haake, Madeleine Heep, Milena Krach, Michael Krummhaar, Nikolas Layer, Vic-Fabienne Schumann and Brian Weidensee contributed to this area. We want to especially thank Dr. H. Kalbacher for MALDI-TOF Analysis and crystallization experiments of our chemical compounds.

Acknowledgement

AG Prof. Dr. O. Kohlbacher - Hardware and in silico support Prof. Dr. L.Heide - Clorobiocin Cluster and bacterial strains AG Prof. Dr. D.Schwarzer - chemical synthesis laboratory and support AG Prof. Dr. S. Grond - Laboratory material support AG Pr. Dr. Schulze-Osthoff - Laboratory material support AG Pr. Dr. A. Weber - Laboratory material support for interlab study Jakob Wendt - Wiki coding support

Anderle, C., Hennig, S., Kammerer, B., Li, S. M., Wessjohann, L., Gust, B., & Heide, L. (2007). Improved mutasynthetic approaches for the production of modified aminocoumarin antibiotics. Chem Biol, 14(8), 955-967. doi:10.1016/j.chembiol.2007.07.014


Anderle, C., Stieger, M., Burrell, M., Reinelt, S., Maxwell, A., Page, M., & Heide, L. (2008). Biological activities of novel gyrase inhibitors of the aminocoumarin class. Antimicrob Agents Chemother, 52(6), 1982-1990. doi:10.1128/AAC.01235-07


Bachmann, B. O., Li, R., & Townsend, C. A. (1998). beta-Lactam synthetase: a new biosynthetic enzyme. Proc Natl Acad Sci U S A, 95(16), 9082-9086.


Beisken, S., Meinl, T., Wiswedel, B., de Figueiredo, L. F., Berthold, M., & Steinbeck, C. (2013). KNIME-CDK: Workflow-driven cheminformatics. BMC Bioinformatics, 14, 257. doi:10.1186/1471-2105-14-257


Chen, Y., Wendt-Pienkowski, E., Ju, J., Lin, S., Rajski, S. R., & Shen, B. (2010). Characterization of FdmV as an amide synthetase for fredericamycin A biosynthesis in Streptomyces griseus ATCC 43944. J Biol Chem, 285(50), 38853-38860. doi:10.1074/jbc.M110.147744


Fasching, C. E., Tenover, F. C., Slama, T. G., Fisher, L. M., Sreedharan, S., Oram, M., . . . Peterson, L. R. (1991). gyrA mutations in ciprofloxacin-resistant, methicillin-resistant Staphylococcus aureus from Indiana, Minnesota, and Tennessee. J Infect Dis, 164(5), 976-979.


Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., . . . Shenkin, P. S. (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem, 47(7), 1739-1749. doi:10.1021/jm0306430


Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., . . . Mainz, D. T. (2006). Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem, 49(21), 6177-6196. doi:10.1021/jm051256o


Fu, X. W., Pu, W. C., Zhang, G. L., & Wang, C. (2015). Synthesis of salicylaldehydes from phenols via copper-mediated duff reaction. Research on Chemical Intermediates, 41(11), 8147-8158.


Fujimoto-Nakamura, M., Ito, H., Oyamada, Y., Nishino, T., & Yamagishi, J. (2005). Accumulation of mutations in both gyrB and parE genes is associated with high-level resistance to novobiocin in Staphylococcus aureus. Antimicrob Agents Chemother, 49(9), 3810-3815. doi:10.1128/AAC.49.9.3810-3815.2005


Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov, 10(5), 449-461. doi:10.1517/17460441.2015.1032936


Heide, L. (2014). New aminocoumarin antibiotics as gyrase inhibitors. Int J Med Microbiol, 304(1), 31-36. doi:10.1016/j.ijmm.2013.08.013
Holdgate, G. A., Tunnicliffe, A., Ward, W. H., Weston, S. A., Rosenbrock, G., Barth, P. T., . . . Timms, D. (1997). The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Biochemistry, 36(32), 9663-9673. doi:10.1021/bi970294+


Kontoyianni, M. (2017). Docking and Virtual Screening in Drug Discovery. Methods Mol Biol, 1647, 255-266. doi:10.1007/978-1-4939-7201-2_18
Lafitte, D., Lamour, V., Tsvetkov, P. O., Makarov, A. A., Klich, M., Deprez, P., . . . Gilli, R. (2002). DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose. Biochemistry, 41(23), 7217-7223.
Lawson, D. M., & Stevenson, C. E. (2012). Structural and functional dissection of aminocoumarin antibiotic biosynthesis: a review. J Struct Funct Genomics, 13(2), 125-133. doi:10.1007/s10969-012-9138-2


Lionta, E., Spyrou, G., Vassilatis, D. K., & Cournia, Z. (2014). Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem, 14(16), 1923-1938.


Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev, 46(1-3), 3-26.


Luft, T., Li, S. M., Scheible, H., Kammerer, B., & Heide, L. (2005). Overexpression, purification and characterization of SimL, an amide synthetase involved in simocyclinone biosynthesis. Arch Microbiol, 183(4), 277-285. doi:10.1007/s00203-005-0770-0


M Lindsay Grayson, S. M. C., James S McCarthy, John Mills, Johan W Mouton, S Ragnar Norrby, David L Paterson, Michael A Pfaller. (2010). Kucers' The Use of Antibiotics Sixth Edition: A Clinical Review of Antibacterial, Antifungal and Antiviral Drugs.


Mannhold, R., Poda, G. I., Ostermann, C., & Tetko, I. V. (2009). Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds. J Pharm Sci, 98(3), 861-893. doi:10.1002/jps.21494


Miller, M. T., Bachmann, B. O., Townsend, C. A., & Rosenzweig, A. C. (2001). Structure of beta-lactam synthetase reveals how to synthesize antibiotics instead of asparagine. Nat Struct Biol, 8(8), 684-689. doi:10.1038/90394


Organization, G. W. H. (2017). Prioritization of pathogens to guide discovery, reserach and development of new antibiotics fro drug-resistant bacterial infections, including tuberculosis.


Paget, M. S., Chamberlin, L., Atrih, A., Foster, S. J., & Buttner, M. J. (1999). Evidence that the extracytoplasmic function sigma factor sigmaE is required for normal cell wall structure in Streptomyces coelicolor A3(2). J Bacteriol, 181(1), 204-211.


Sadiq, A. A., Patel, M. R., Jacobson, B. A., Escobedo, M., Ellis, K., Oppegard, L. M., . . . Kratzke, R. A. (2010). Anti-proliferative effects of simocyclinone D8 (SD8), a novel catalytic inhibitor of topoisomerase II. Invest New Drugs, 28(1), 20-25. doi:10.1007/s10637-008-9209-1


Schimana, J., Fiedler, H. P., Groth, I., Sussmuth, R., Beil, W., Walker, M., & Zeeck, A. (2000). Simocyclinones, novel cytostatic angucyclinone antibiotics produced by Streptomyces antibioticus Tu 6040. I. Taxonomy, fermentation, isolation and biological activities. J Antibiot (Tokyo), 53(8), 779-787.


Shaikh, S., Fatima, J., Shakil, S., Rizvi, S. M., & Kamal, M. A. (2015). Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J Biol Sci, 22(1), 90-101. doi:10.1016/j.sjbs.2014.08.002


Tetko, I. V., Gasteiger, J., Todeschini, R., Mauri, A., Livingstone, D., Ertl, P., . . . Prokopenko, V. V. (2005). Virtual computational chemistry laboratory--design and description. J Comput Aided Mol Des, 19(6), 453-463. doi:10.1007/s10822-005-8694-y


Tsai, F. T., Singh, O. M., Skarzynski, T., Wonacott, A. J., Weston, S., Tucker, A., . . . Wigley, D. B. (1997). The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins, 28(1), 41-52.