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24 September 2007

ENDSTATE OF PROJECT: Targeted Delivery of Antibiotics using Nanoparticles (specifically, how will the binding of nanoparticles to antibiotics' receptor sites allow for a longer half life of the drug?)

Questions to be answered: 1. How does the antibiotic work? How does the antibiotic’s structure affect its function? Where does it affect the function of the bacteria?

[Hey Andy, if you put an asterisk * at the start of a line the wiki will make it a bulleted item. Two asterisks will make an indented item, etc. Eg,

  • Bullet 1
  • Bullet 2
    • Sub-bullet
  • Bullet 3
    • Sub
    • Sub, etc.

Joe 10:42, 6 October 2007 (EDT)]

Cefamondole nafate (formate ester form of cefamandole) • Broad spectrum cephalosporin • Disrupt synthesis of peptidoglycan layer of bacterial wall • Key ring structure is the beta lactam (four member ring - 3 carbons and one nitrogen) • Drug Resistance:

      o	BACTERIA (1 point) Popularity lead to beta – lactamase (breaks beta lactam ring), 
      o	HUMANS (1 point) Clavulanic acid, beta – lactamase inhibitor
      o	BACTERIA (1 point) Changed the structure of penicillin binding proteins (PBP) sites – involved in the final  
               stages of peptidoglycan synthesis 

• ?? Structure of PBP binding site

Rifampin • DNA –dependent RNA polymerase inhibitor by best subunit binding • Lipophilic nature – good for meningitis form of tuberculosis (b/c requires distribution to CNS and penetration of blood-brain barrier)

2. Based on structure of antibiotic, is nanoparticle binding possible? What kind of nanoparticle? How will they bind? Is it even worth it?

3. NEXT STEP Additional article and research:

  • Targeted delivery of antibiotics using liposomes and nanoparticles: research and applications

International Journal of Antimicrobial Agents, Vol. 13, Issue 3, January 2000, pp 155-168

  • PBP structure in action www.bio.com/redirectors/lindredirect5_28.jhtml?link=6


1 October 2007 7 October 2007

1. NEXT STEP

  • Run and Interpret Gaussian IOT verify reactive center of beta lactam (amide bond "ruptures" IOT for covalent bond with serine residue at the PBP's receptorWHAT KIND OF A REACTION WOULD THIS BE? SERINE WITH THE BETA LACTAM RING?

NOTES: Gaussian shows beta lactam ring as LUMO and would expect interaction with HOMO of PBP enzyme binding site. Must examine specific PBP's receptor site and postulate where electron density may exist.

  • Find structure of PBP's receptor site
  • Understand what about the R groups allow for effective antibiotic attack on Gram positive and negative membranes. What are gram positive and negative membranes? Maybe run a gram positive and gram negative effective antibiotic on Gaussian.[WHAT WOULD THIS TELL YOU?]

NOTES: Gaussian showed HOMO of antibiotic on a benzene ring R group. Interesting. Leads me to believe that the R group as a larger effect on the drug's efficicy than just the obvious beta lactam ring. So, the R group changes must alter the effect of drug on gram +/- membranes but still how? Need to research their possible interactions.

  • Find through interlibrary loan: "Targeted delivery of antibiotics using liposomes and nanoparticles: research and applications" International Journal of Antimicrobial Agents, Vol. 13, Issue 3, January 2000, pp 155-168
  • Start research on what nanoparticles will be likely candidates for antibiotic binding (chemical properties and physical properties, like shape, buckeyballs, nanotubes, etc.) Maybe Zinc Oxide?
  • Outline structure of Mid Term Report:

Background of Penicillin based antibiotics (structure, PBP, HOMO/LUMO) Run HOMO/LUMO for different R groups and their effect on gram positive/negative membranes ...

SOME GENERAL IDEAS ON WHAT NANOPARTICLES ARE AND OTHER APPLICATIONS WOULD HELP TO PUT THIS IN PERSPECTIVE. YOU WANT TO KNOW SPECIFICALLY HOW THE ANTIBIOTIC BINDS AND TO WHAT [AS WE DISCUSSED, THE ENZYME OR A SITE ON THE CELL WALL]

24 October 2007

Next Step

  • Start research on what nanoparticles will be likely candidates for antibiotic binding (chemical properties and physical properties, like shape, buckeyballs, nanotubes, etc.) Maybe Zinc Oxide?
  • Metallic nanoparticle research
    • Characteristics of specific metals and their susceptibility to binding with CN
    • Recent studies of metallic nanoparticle research and their antibiotic effects
    • Would characteristically antibacterial nanoparticles assist in antibiotic effects of drug?
  • Current research has focused on drug carriers of a nanoparticle size. What research is there for elemental nanoparticles?
  • Continue to explore structure of PBP's receptor site, or extrapolate the structure
  • Understand what about the R groups allow for effective antibiotic attack on Gram positive and negative membranes. Maybe run a gram positive and gram negative effective antibiotic on Gaussian.
  • Preliminary design of experiment (conditions, reactants, hypothesis, etc)

Notes from 31 October 2007 Meeting with Pan Bo, Post Doctorate Student at UMASS Amherst Plant and Soil Sciences Laboratory

Refine Experimental Question: Targeted Delivery of Antibiotics using Nanoparticles (specifically, how will the binding of nanoparticles to antibiotics' receptor sites allow for a longer half life of the drug?) Furthermore: How will adsorption/desorption of historically antibacterial nanoparticles to antibiotics contribute to the overall efficacy?

Available Nanoparticles used in UMASS Lab Oxides: Ti , Zn, Al, C nanotubes, Si (?) Criteria in Selection for my project: Cost, Safety

Experimental Design Tools: UV Spec HPLC (UMASS) http://en.wikipedia.org/wiki/HPLC http://www.pharm.uky.edu/ASRG/HPLC/hplcmytry.html http://www.waters.com/watersdivision/ContentD.asp?watersit=JDRS-5LTGBH3

Step 1: Adsorption a. Differing Penicillin Concentrations w/ same concentration of Nanoparticles [NP] Differing Penicillin Concentrations w/o Nanoparticles b. Shake and allow for binding for 5 days c. Centrifuge down the nanoparticles, measure weight and compare to starting [NP] d. Remove supernatant (presumably antibiotic and bound nanoparticle e. Measure saturation point of antibiotic with NP

Step 2: Desorption Targeted Delivery Can I mimic organ (or other targeted area) environment IOT measure desorption of nanoparticle in these conditions? By changing dissolved organic matter content (DOM), pH, Ion availability (Na, Al, K), or temperature in solution?

Examine kinetics of desorption: How fast it occurs? How much is desorbed into solution?

Step 3: Discussion Connect adsorption/desorption to medically related field. What conclusions can I draw from the results of Step 1/2?

Step 4: Antibacterial Effect of Nanoparticle Binding How can I accurately measure the antibacterial effects of the antibioitics + nanoparticles? Biological petri dish method may not be a good quantitative method.