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Epi-absorbance-based dose response biochemical high throughput screening assay for selective inhibitors of VIM-2 metallo-beta-lactamase

PubChem AID
1919
External ID
VIM2NITRO_INH_EPIABS_1536_3XIC50
BioAssay Type
Confirmatory
Tested Substances
Version
Status
Live
Dates
  • Deposit:
    2009-09-03
  • Modify:
    2013-01-04
Description
This bioassay record (AID 1919) is associated with a total of 39 additional BioAssay records in PubChem, which includes several assay projects. Chemical probes ML121, CID 53362017, and ML302 were developed for the target metallo beta-lactamase [Pseudomonas aeruginosa] and reported in AID 1854, AID 624079, AID 624081, AID 624083, AID 624084, AID 624085, AID 624096, and AID 624097.

1 Description

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: VIM2NITRO_INH_EPIABS_1536_3XIC50

Name: Epi-absorbance-based dose response biochemical high throughput screening assay for selective inhibitors of VIM-2 metallo-beta-lactamase.

Description:

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).

References:

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.

Keywords:

VIM-2, beta-lactamase, antibiotic resistance, bacteria, dose response, HTS, high throughput screen, 1536, selective, inhibitor, epi-absorbance, fluorescence, Scripps, Scripps Florida, The Scripps Research Institute Molecular Screening Center, SRIMSC, Molecular Libraries Probe Production Center Network, MLPCN.

2 Protocol

Assay Overview:

The purpose of this assay is to determine dose response curves for compounds identified as active in a set of previous experiments entitled, "Primary biochemical high throughput screening assay to identify inhibitors of VIM-2 metallo-beta-lactamase," (AID 1527), and inactive in a set of experiments entitled, "Epi-absorbance primary biochemical high throughput screening assay to identify inhibitors of IMP-1 metallo-beta-lactamase," (AID 1556). This biochemical epi-absorbance-format assay employs the cephalosporin nitrocefin as the VIM-2 substrate, and takes advantage of the fluorescent properties of white microtiter plates (13). Nitrocefin is a yellow chromogenic substrate (Imax = 395 nm) that is hydrolyzed by beta-lactamases to yield a red product with increased absorbance properties (Imax = 495 nm) that quenches plate fluorescence by absorbing the plate's emission light (13). In this assay, test compounds are incubated with purified VIM-2 enzyme and nitrocefin in detergent-containing buffer at room temperature. The reaction is stopped by the addition of EDTA, followed by measurement of well fluorescence. As designed, compounds that inhibit VIM-2 will inhibit nitrocefin hydrolysis, inhibit generation of red product, and inhibit quenching of plate fluorescence, resulting in an increase in well fluorescence. Compounds were tested in triplicate using a dilution series starting at a nominal test concentration of 60 uM.

Protocol Summary:

Prior to the start of the assay, 2.5 uL of Assay Buffer (5 0mM HEPES, 50 uM ZnSO4, 0.05% Brij 35, pH 7.1) containing 0.13 nM VIM-2 protein were dispensed into a 1536 microtiter plate. Next, 30 nL of test compound in DMSO or DMSO alone (0.45% final concentration) were added to the appropriate wells. The plates were then incubated for 15 minutes at 25 C.

The assay was started by dispensing 2.5 uL of 120 uM nitrocefin solution in Assay Buffer into all wells. After 25 minutes of incubation at 25 C, 5.0 uL of 500 mM EDTA were added to each well to stop the reaction. Next, the plates were centrifuged briefly and well fluorescence was read on a Viewlux microplate reader (PerkinElmer, Turku, Finland) (excitation = 480 nm, emission = 530 nm).

The Optical Density (OD) for each well was calculated according to the following equation:

OD = -log( RFU_SampleWell / RFU_BlankWell )

Where:

RFU_SampleWell is defined as the raw fluorescence value obtained from test compound wells,

RFU_BlankWell is defined as the raw fluorescence value obtained from wells containing Assay Buffer.

The percent inhibition for each compound was calculated as follows:

%_Inhibition = 100 * ( 1 - ( Test_Compound - Median_Positive_Control ) / ( Median_Negative_Control - Median_ Positive _Control ) )

Where:

Test_Compound is defined as wells containing VIM-2 in the presence of test compound,

Negative_Control is defined as wells containing VIM-2 in the presence of DMSO,

Positive_Control is defined as wells containing DMSO alone.

PubChem Activity Outcome and Score:

For each test compound, percent inhibition was plotted against compound concentration. A four parameter equation describing a sigmoidal dose-response curve was then fitted with adjustable baseline using Assay Explorer software (MDL Information Systems). The reported IC50 values were generated from fitted curves by solving for the X-intercept value at the 50% inhibition level of the Y-intercept value. In cases where the highest concentration tested (i.e. 60 uM) did not result in greater than 50% inhibition, the IC50 was determined manually as greater than 60 uM.

Compounds with an IC50 greater than 10 uM were considered inactive. Compounds with an IC50 equal to or less than 10 uM were considered active.

Any compound with a percent inhibition value <50% at all test concentrations was assigned an activity score of zero. Any compound with a percent inhibition value >50% at any test concentration was assigned an activity score greater than zero. Activity score was then ranked by the potency, with the most potent compounds assigned the highest activity scores.

The activity score range for active compounds is 100-72, for inactive 71-0.

List of Reagents:

Recombinant VIM-2 (supplied by Assay Provider)

Nitrocefin (BD Diagnostic Systems, part 296289)

1536-well plates (Greiner, part 789173)

HEPES (Invitrogen, part 15630)

Brij 35 (Sigma-Aldrich, part B4184)

Zinc Sulfate (Sigma-Aldrich, part 204986)

3 Comment

Due to the increasing size of the MLPCN compound library, 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, compounds that modulate well fluorescence. All test compound concentrations reported above and below are nominal; the specific test concentration(s) for a particular compound may vary based upon the actual sample provided by the MLSMR. The MLSMR was not able to provide all compounds selected for testing in this AID.

4 Result Definitions

5 Data Table

6 Target

9 Identity

9.1 BioAssay Name

Epi-absorbance-based dose response biochemical high throughput screening assay for selective inhibitors of VIM-2 metallo-beta-lactamase

9.2 Source

9.3 External ID

VIM2NITRO_INH_EPIABS_1536_3XIC50

9.4 Project Category

NIH Molecular Libraries Probe Production Network

9.5 BioAssay Type

Confirmatory

9.6 Deposit Date

2009-09-03

9.7 Modify Date

Version 1.1
Version 1.2
2013-01-04 (currently shown)

9.8 Grant Number

1 R21 NS059451-01

9.9 Status

Live

10 Same-Project BioAssays

11 BioAssay Annotations

1 of 2
Assay Format
biochemical format
Assay Type
direct enzyme activity assay
Detection Method
fluorescence intensity
2 of 2
Assay Type
Binding

12 Classification

12.1 CDD Tree

13 Information Sources

CONTENTS