A Suite of Biochemical Assays for Screening RNA Methyltransferase BCDIN3D

BCDIN3D is an RNA-methyltransferase that O-methylates the 5′ phosphate of RNA and regulates microRNA maturation. To discover small-molecule inhibitors of BCDIN3D, a suite of biochemical assays was developed. A radiometric methyltransferase assay and fluorescence polarization–based S-adenosylmethionine and RNA displacement assays are described. In addition, differential scanning fluorimetry and surface plasmon resonance were used to characterize binding. These assays provide a comprehensive package for the development of small-molecule modulators of BCDIN3D activity.

Download Full-text

A surface plasmon resonance-based assay for small molecule inhibitors of human cyclophilin A

Analytical Biochemistry ◽

10.1016/j.ab.2005.06.037 ◽

2005 ◽

Vol 345 (2) ◽

pp. 214-226 ◽

Cited By ~ 54

Author(s):

Martin A. Wear ◽

Alan Patterson ◽

Kirk Malone ◽

Colin Dunsmore ◽

Nicholas J. Turner ◽

...

Keyword(s):

Surface Plasmon Resonance ◽

Surface Plasmon ◽

Small Molecule ◽

Plasmon Resonance ◽

Small Molecule Inhibitors ◽

Cyclophilin A

Download Full-text

PD-1-Targeted Discovery of Peptide Inhibitors by Virtual Screening, Molecular Dynamics Simulation, and Surface Plasmon Resonance

Molecules ◽

10.3390/molecules24203784 ◽

2019 ◽

Vol 24 (20) ◽

pp. 3784 ◽

Cited By ~ 2

Author(s):

Yuanqiang Wang ◽

Haiqiong Guo ◽

Zhiwei Feng ◽

Siyi Wang ◽

Yuxuan Wang ◽

...

Keyword(s):

Molecular Dynamics ◽

Cell Death ◽

Surface Plasmon Resonance ◽

Virtual Screening ◽

Programmed Cell Death ◽

Surface Plasmon ◽

Small Molecule ◽

Plasmon Resonance ◽

Small Molecule Inhibitors ◽

Dynamics Simulation

The blockade of the programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) pathway plays a critical role in cancer immunotherapy by reducing the immune escape. Five monoclonal antibodies that antagonized PD-1/PD-L1 interaction have been approved by the Food and Drug Administration (FDA) and marketed as immunotherapy for cancer treatment. However, some weaknesses of antibodies, such as high cost, low stability, poor amenability for oral administration, and immunogenicity, should not be overlooked. To overcome these disadvantages, small-molecule inhibitors targeting PD-L1 were developed. In the present work, we applied in silico and in vitro approaches to develop short peptides targeting PD-1 as chemical probes for the inhibition of PD-1–PD-L1 interaction. We first predicted the potential binding pocket on PD-1/PD-L1 protein–protein interface (PPI). Sequentially, we carried out virtual screening against our in-house peptide library to identify potential ligands. WANG-003, WANG-004, and WANG-005, three of our in-house peptides, were predicted to bind to PD-1 with promising docking scores. Next, we conducted molecular docking and molecular dynamics (MD) simulation for the further analysis of interactions between our peptides and PD-1. Finally, we evaluated the affinity between peptides and PD-1 by surface plasmon resonance (SPR) binding technology. The present study provides a new perspective for the development of PD-1 inhibitors that disrupt PD-1–PD-L1 interactions. These promising peptides have the potential to be utilized as a novel chemical probe for further studies, as well as providing a foundation for further designs of potent small-molecule inhibitors targeting PD-1.

Download Full-text

Kinetic Analysis of Small Molecule Inhibitors Targeting Protein Arginine Methyltransferase-5 (PRMT5) using Surface Plasmon Resonance (SPR)

10.17918/00000234 ◽

2020 ◽

Author(s):

Lynn Kim Baker

Keyword(s):

Surface Plasmon Resonance ◽

Kinetic Analysis ◽

Surface Plasmon ◽

Small Molecule ◽

Plasmon Resonance ◽

Small Molecule Inhibitors ◽

Protein Arginine Methyltransferase ◽

Arginine Methyltransferase ◽

Protein Arginine Methyltransferase 5

Download Full-text

A Surface Plasmon Resonance Spectroscopy Method for Characterizing Small-Molecule Binding to Nerve Growth Factor

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057115607814 ◽

2015 ◽

Vol 21 (1) ◽

pp. 96-100 ◽

Cited By ~ 3

Author(s):

Allison E. Kennedy ◽

Kristen S. Sheffield ◽

Joseph K. Eibl ◽

Michael B. Murphy ◽

Rahul Vohra ◽

...

Keyword(s):

Surface Plasmon Resonance ◽

Nerve Growth Factor ◽

Growth Factor ◽

Surface Plasmon ◽

Small Molecule ◽

Plasmon Resonance ◽

Small Molecule Inhibitors ◽

Resonance Spectroscopy ◽

Nerve Growth ◽

Binding Event

Small-molecule inhibitors have been previously investigated to identify possible therapeutics for the treatment of chronic pain. In the present study, known nerve growth factor (NGF) inhibitors identified by 125I-NGF binding were characterized using affinity and binding evaluations by surface plasmon resonance (SPR) spectroscopy. A novel strategy for characterizing NGF inhibitors was used to determine the binding affinity (KD) and saturation ability of each compound with immobilized NGF. Seventy-four percent of compounds screened demonstrated a positive binding event to NGF. A KD less than 10 μM and a percent saturation greater than 50% were used as thresholds to identify inhibitors that would warrant further investigation. This study details for the first time a methodology that can be used to directly characterize the binding event between small-molecule inhibitors and NGF.

Download Full-text