Identification of matrix metalloproteinase inhibitors by chemical arrays

Abstract

Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that degrade many extracellular matrix components and that have been implicated in the pathogenesis of various human diseases including cancer metastasis. Here, we screened MMP-9 inhibitors using photo-cross-linked chemical arrays, which can detect small-molecule ligand-protein interactions on a chip in a high-throughput manner. The array slides were probed sequentially with His-MMP-9, anti-His antibody, and a Cy5-labeled secondary antibody and then scanned with a microarray scanner. We obtained 27 hits among 24,275 compounds from the NPDepo library; 2 of the identified compounds (isoxazole compound 1 and naphthofluorescein) inhibited MMP-9 enzyme activity in vitro. We further explored 17 analogs of 1 and found that compound 18 had the strongest inhibitory activity. Compound 18 also inhibited other MMPs, including MMP-2, MMP-12, and MMP-13 and significantly inhibited cell migration in human fibrosarcoma HT1080 cells. These results suggest that 18 is a broad-spectrum MMP inhibitor.

Neurovascular dysfunction and neurodegeneration in dementia and Alzheimer's disease

“…There are several new CypA inhibitors recently developed and investigated for use against hepatitis-C and HIV infections including CPI-431-32 [197], compound 25 [198], SCY-635 [199] and MM284 [200], which all may have a potential to stabilize the BBB in APOE4 carriers. In addition to CypA inhibitors, there are a number of identified MMP-9 inhibitors including minocycline [201], curcumin [202], SB-3CT(2) [203] and compound 18 [204]. For example, minocycline has been demonstrated to reduce hemorrhage frequency and increase endothelial tight junction and basement membrane proteins in aged 5xFAD/ APOE4 transgenic mice [201].…”

Proteomic profiling of small-molecule inhibitors reveals dispensability of MTH1 for cancer cell survival

“…We started the screening of MTH1 inhibitors using chemical array platforms, ultrahigh throughput screening for small-molecule binders of proteins of interest 12 13 14 . Our chemical arrays were used to obtain small-molecule inhibitors of various proteins derived from mammals 15 16 17 18 19 20 21 , fungi 22 , prokaryotes 23 , and viruses 24 25 .…”

Novel diagnosis and therapy for hepatoma targeting HBV-related carcinogenesis through alternative splicing of FIR (PUF60)/FIRΔexon2

“…Small molecular chemical compounds against His-tagged FIR (His-FIR) and His-tagged FIRΔexon2 were screened among 2,3275 chemicals of NPDepo at RIKEN as described previously [35][36][37] . Briefly, His-FIR (645 μg/mL) and FIRΔexon2 (652 μg/mL) proteins were applied to NPDepo array that contains 2,3275 natural chemical compounds.…”

“…Small molecular weight chemical compounds potentially bound to FIRΔexon2 were previously identified [ Figure 1] from the NPDepo at RIKEN, which were a collection of the isolates from natural products, build by Dr Hiroyuki Osada (RIKEN, Japan) and his coworkers [35][36][37] .…”

“…Further, FIR/PUF60 is required for transcriptional and post-transcriptional regulation of HBV pgRNA expression [34] . To develop novel diagnosis and therapy for hepatoma targeting FIR (PUF60)/FIRΔexon2, small molecular chemical compounds against FIRΔexon2 were screened among 2,3275 chemicals by natural product depository (NPDepo) array at RIKEN (Japan) to develop anti-cancer drugs [35][36][37] . Finally, small inhibitory chemicals against FIR/FIRΔexon2 for hepatoma therapy will be discussed.…”