Late stage assay provider results from the probe development efforts to identify inhibitors of VIM-2 metallo-beta-lactamase (nonselective): Growth inhibition of clinically relevant New Delhi metallo-beta-lactamase-1 (NDM-1)-transformed K. pneumoniae (BAA-2146) in the presence of imipenem (synergy)
Name: Late stage assay provider results from the probe development efforts to identify inhibitors of VIM-2 metallo-beta-lactamase (nonselective): Growth inhibition of clinically relevant New Delhi metallo-beta-lactamase-1 (NDM-1)-transformed K. pneumoniae (BAA-2146) in the presence of imipenem (synergy). ..more
Depositor Specified Assays
Source (MLPCN Center Name): The Scripps Research Institute Molecular Screening Center (SRIMSC)
Center Affiliation: The Scripps Research Institute (TSRI)
Assay Provider: Peter Hodder, TSRI
Network: Molecular Libraries Probe Production Centers Network (MLPCN)
Grant Proposal Number: 1 R21 NS059451-01 Fast Track
Grant Proposal PI: Peter Hodder, TSRI
External Assay ID: NDM-1-KPNEUMONIAE_INH_ABS_0384_SYNERGY MDCSRUN BAA-2146
Name: Late stage assay provider results from the probe development efforts to identify inhibitors of VIM-2 metallo-beta-lactamase (nonselective): Growth inhibition of clinically relevant New Delhi metallo-beta-lactamase-1 (NDM-1)-transformed K. pneumoniae (BAA-2146) in the presence of imipenem (synergy).
The emergence of gram-negative bacteria that exhibit multi-drug resistance, combined with the paucity of new antibiotics, poses a public health challenge (1). The production of bacterial beta-lactamase enzymes, in particular, is a common mechanism of drug resistance (2-4). The beta-lactamases evolved from bacteria with resistance to naturally-occurring beta-lactams or penams (5), agents which inhibit the transpeptidase involved in cell wall biosynthesis (6). Human medicine adapted these agents into synthetic antibiotics such as penicillins, cephalosporins, carbapenems, and monobactams that contain a 2-azetidone ring (5, 7). The metallo-beta-lactamases (MBL) are zinc-dependent class B beta-lactamases that hydrolyze the beta-lactam ring, rendering the antibiotic ineffective (6, 8). Increasingly, nosocomial beta-lactam antibiotic resistance arises in P. aeruginosa, Enterobacteriaceae, and other pathogenic bacteria via gene transfer of B1 MBLs (4, 9), including IMP (active on IMiPenem) (10) and VIM (Verona IMipenemase) (11, 12). For two of these enzymes, VIM-2 and IMP-1, no inhibitors exist for clinical use (6, 9). Thus, the identification of MBL inhibitors would provide useful tools for reducing nosocomial infections and elucidating their mechanism of action (13).
1. Siegel, R.E., Emerging gram-negative antibiotic resistance: daunting challenges, declining sensitivities, and dire consequences. Respir Care, 2008. 53(4): p. 471-9.
2. Gupta, V., An update on newer beta-lactamases. Indian J Med Res, 2007. 126(5): p. 417-27.
3. Bradford, P.A., Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat. Clin Microbiol Rev, 2001. 14(4): p. 933-51, table of contents.
4. Sacha, P., Wieczorek, P., Hauschild, T., Zorawski, M., Olszanska, D., and Tryniszewska, E., Metallo-beta-lactamases of Pseudomonas aeruginosa--a novel mechanism resistance to beta-lactam antibiotics. Folia Histochem Cytobiol, 2008. 46(2): p. 137-42.
5. Koch, A.L., Bacterial wall as target for attack: past, present, and future research. Clin Microbiol Rev, 2003. 16(4): p. 673-87.
6. Jin, W., Arakawa, Y., Yasuzawa, H., Taki, T., Hashiguchi, R., Mitsutani, K., Shoga, A., Yamaguchi, Y., Kurosaki, H., Shibata, N., Ohta, M., and Goto, M., Comparative study of the inhibition of metallo-beta-lactamases (IMP-1 and VIM-2) by thiol compounds that contain a hydrophobic group. Biol Pharm Bull, 2004. 27(6): p. 851-6.
7. Abeylath, S.C. and Turos, E., Drug delivery approaches to overcome bacterial resistance to beta-lactam antibiotics. Expert Opin Drug Deliv, 2008. 5(9): p. 931-49.
8. Wang, Z., Fast, W., Valentine, A.M., and Benkovic, S.J., Metallo-beta-lactamase: structure and mechanism. Curr Opin Chem Biol, 1999. 3(5): p. 614-22.
9. Walsh, T.R., Toleman, M.A., Poirel, L., and Nordmann, P., Metallo-beta-lactamases: the quiet before the storm? Clin Microbiol Rev, 2005. 18(2): p. 306-25.
10. Hirakata, Y., Izumikawa, K., Yamaguchi, T., Takemura, H., Tanaka, H., Yoshida, R., Matsuda, J., Nakano, M., Tomono, K., Maesaki, S., Kaku, M., Yamada, Y., Kamihira, S., and Kohno, S., Rapid detection and evaluation of clinical characteristics of emerging multiple-drug-resistant gram-negative rods carrying the metallo-beta-lactamase gene blaIMP. Antimicrob Agents Chemother, 1998. 42(8): p. 2006-11.
11. Lauretti, L., Riccio, M.L., Mazzariol, A., Cornaglia, G., Amicosante, G., Fontana, R., and Rossolini, G.M., Cloning and characterization of blaVIM, a new integron-borne metallo-beta-lactamase gene from a Pseudomonas aeruginosa clinical isolate. Antimicrob Agents Chemother, 1999. 43(7): p. 1584-90.
12. Wang, C.X. and Mi, Z.H., Imipenem-resistant Pseudomonas aeruginosa producing IMP-1 metallo-beta-lactamases and lacking the outer-membrane protein OprD. J Med Microbiol, 2006. 55(Pt 3): p. 353-4.
13. Zuck P, O'Donnell GT, Cassaday J, Chase P, Hodder P, Strulovici B, Ferrer M. Miniaturization of absorbance assays using the fluorescent properties of white microplates. Anal Biochem. 2005 Jul 15;342 (2):254-9.
14. Minond D, Saldanha SA, Subramaniam P, Spaargaren M, Spicer T, Fotsing JR, Weide T, Fokin VV, Sharpless KB, Galleni M, Bebrone C, Lassaux P, Hodder P. Inhibitors of VIM-2 by screening pharmacologically active and click-chemistry compound libraries. Bioorg Med Chem. 2009 Jul 15;17(14):5027-37.
15. Blizzard, T., Chen, H., Kim, S., Wu, J., Young, K., Park, Y.-W., Ogawa, A., Raghoobar, S., Painter, R., Hairston, N., Lee, S., Misura, A., Felcetto, T., Fitzgerald, P., Sharma, N., Lu, J., Ha, S., Hickey, E., Hermes, J., and Hammond, M. Side chain SAR of bicyclic B-lactamase inhibitors (BLIs). 1. Discovery of a class C BLI for combination with imipenem. Bioorganic & Medicinal Chemistry Letters 20 (2010) 918-921.
16. Bonapace, C.R., J.A. Bosso, L.V. Friedrich, and R.L. White, Comparison of methods of interpretation of checkerboard synergy testing. Diagn Microbiol Infect Dis, 2002. 44(4): p. 363-6.
17. Bajaksouzian, S., M.A. Visalli, M.R. Jacobs, and P.C. Appelbaum, Activities of levofloxacin, ofloxacin, and ciprofloxacin, alone and in combination with amikacin, against acinetobacters as determined by checkerboard and time-kill studies. Antimicrob Agents Chemother, 1997. 41(5): p. 1073-6.
18. Wayne, M26-A: Methods for Determining Bactericidal Activity of Antimicrobial Agents; Approved Guideline, E. C. a. L. S. Institute, Editor. 1999, National Committee on Clinical Laboratory Standards
Late stage, powder, synthesized, BAA-2146, NDM-1, carbapenemase, New Delhi metallo-beta-lactamase, New Delhi, NDM, VIM-2, K. pneumoniae, beta-lactamase, metallo beta-lactamase, antibiotic resistance, bacteria, SAR, dose response, kinetic, nonselective, non-selective, inhibitor, inhibit, inhibition, absorbance, checkerboard assay, synergy, potentiation, assay provider, growth, viability, cytotoxicity, minimum inhibitory concentration, MIC, Scripps, Scripps Florida, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Center Network, MLPCN.
The purpose of this assay is to determine if powder samples of a compounds identified as VIM-2 nonselective inhibitor probe candidates can reduce the growth of K. pneumoniae (BAA-2146) transformed withNDM-1. NDM-1 is the gene found in some bacteria which codes for the carbapenemase enzyme, resulting in the ability of bacteria to neutralize antibiotics such as Imipenem which contain the beta-lactam carbapenen. There are currently no NDM-1 inhibitors. Synergy assays were conducted using two-fold serial broth dilution method as recommended by Clinical and Laboratory Standards Institute (CLSI). All testing was performed in 384 well plates in 0.06 mL final volume. Imipenem or test compound was titrated in Cation Adjusted Mueller-Hinton Broth (CAMHB) immediately prior to testing. Imipenem and inhibitor were diluted down columns and across rows respectively. K. pneumoniae previously grown in CAMHB to log phase OD600 of 0.5 - 0.7 was used to inoculate each well with 0.03 mL of bacterial inoculums of 1 x 10^6 CFU/mL. The plates were incubated for at least 18 hours at 37 C under aerobic conditions. The results of synergy testing were determined in manners previously reported (14-17).Turbidity was determined using OD590 and Minimum Inhibitory Concentrations (MIC) were determined per CLSI methods (18). As designed, compounds with antibacterial activity will inhibit bacterial growth, leading to reduced well absorbance. Synergy between the antibiotic and test compound is reported as the minimum concentration of test compound required to restore or enhance imipenem susceptibility (14).
Prior to the start of the assay, compounds or imipenem was titrated as described above, in separate plates, in 15 uL of CAMHB in a 384 well microtiter plate. Next, these titrations were combined into one assay plate for a total volume of 30 uL yielding unique combinations of test compounds and imipenem. Next, 30 uL of CAMHB inoculated with BAA-2146 /NDM-1 K. pneumoniae at 1 x 10^6 CFU/mL was added to wells. Next, the plates were centrifuged briefly and were incubated for 18 hours at 37 C in a humidified environment. Absorbance (OD590) was read on a Tecan Spectraflour Plus plate reader (Tecan U.S., Inc.) using 4 reads per well. The percent inhibition for each compound was calculated as follows:
%_Inhibition = 100 * ( ( Test_Compound - Median_Low_Control ) / ( Median_High_Control - Median_Low_Control ) )
High_Control is defined as wells containing media only (no bacteria).
Low_Control is defined as wells containing NDM-1-transformed BAA-2146 K. pneumoniae.
Test_Compound is defined as wells containing NDM-1-transformed BAA-2146 K. pneumoniae in the presence of test compound.
A mathematical algorithm was used to determine the MIC of compounds. Two values were calculated: (1) the average percent inhibition of all high control wells, and (2) three times their standard deviation. The sum of these two values was used as a cutoff parameter. The reported MIC values were generated by identifying the lowest concentration of inhibitor that yields a value that is less than the cutoff value; i.e. no bacterial growth. In cases where the highest concentration tested (i.e. 100 uM) did not result in a value that was less than the cutoff, the MIC was determined as greater than the highest concentration tested.
PubChem Activity Outcome and Score:
Compounds with a four fold reduction in MIC value greater than 10 uM were considered inactive. Compounds with an four fold reduction in MIC value equal to or less than 10 uM were considered active.
Activity score was then ranked by the potency of the compounds, with the most potent compounds assigned the highest activity scores.
The PubChem Activity Score range for inactive compounds is 0-0. There are no active compounds.
List of Reagents:
384 well plates (Corning, part 3701)
Imipenem antibiotic (USP, Rockville MD, part 1337809)
NDM-1-transformed K. pneumoniae (BAA-2146, ATCC)
Mueller Hinton II Broth Cation-Adjusted (CAMHB; Becton Dickinson, part 297963)
This assay was performed by the assay provider. This assay may have been run as two or more separate campaigns, each campaign testing a unique set of compounds. All data reported were normalized on a per-plate basis. Possible artifacts of this assay can include, but are not limited to: dust or lint located in or on wells of the microtiter plate, and compounds that modulate well absorbance. All test compound concentrations reported are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided.
BAO: version: 1.4b1090
BAO: bioassay specification: assay stage: confirmatory
BAO: bioassay specification: assay biosafety level: bsl1
BAO: assay format: cell-based format
BAO: bioassay specification: assay measurement type: kinetic assay
BAO: bioassay specification: assay readout content: assay readout method: regular screening
BAO: bioassay specification: assay readout content: content readout type: single readout
BAO: meta target: molecular target: protein target: enzyme: protease
BAO: meta target: biological process target: cell death
BAO: meta target detail: binding reporter specification: interaction: protein-small molecule
BAO: assay design: viability reporter: atp content
BAO: detection technology: spectrophotometry: absorbance
BAO: bioassay specification: bioassay type: functional: viability
BAO: bioassay specification: assay footprint: microplate: 384 well plate
BAO: bioassay specification: assay measurement throughput quality: concentration response multiple replicates
* Activity Concentration.
Data Table (Concise)