Structural Analysis of a Novel Small Molecule Ligand Bound to the CXCL12 Chemokine

CXCL12 binds to CXCR4, promoting both chemotaxis of lymphocytes and metastasis of cancer cells. We previously identified small molecule ligands that bind CXCL12 and block CXCR4-mediated chemotaxis. We now report a 1.9 Å resolution X-ray structure of CXCL12 bound by such a molecule at a site normally bound by sY21 of CXCR4. The complex structure reveals binding hot spots for future inhibitor design and suggests a new approach to targeting CXCL12–CXCR4 signaling in drug discovery

Additional file 1 of Marinopyrrole derivative MP1 as a novel anti-cancer agent in group 3 MYC-amplified Medulloblastoma

Additional file 1: Supplementary Table 1. The top 50 genes most significantly (p<0.0001) downregulated by the MP1 in HD-MB03 cells. Supplementary Figure S1. Quantification for the expression of key target proteins. Supplementary Figure S2. MP1 modulates target gene sets. Supplementary Figure S3. Top pathways modulated by MP1. Supplementary Figure S4. Effects of MP1 on PROM1 (CD133) and MYC mRNA expression. Supplementary Figure S5. Effect of MP1 on the stability of MYC protein. Supplementary Figure S6. Principal Component Analysis (PCA) between DMSO and MP1 treatment groups. Supplementary Figure S7. MP1 treatment alters energy metabolism in MB. Supplementary Figure S8. Synergy analysis between MP1 and TEM in MYC-amplified MB cells. Supplementary Figure S9. Effects of inhibitors on body weight and histology of the MB xenograft mice

Structure-Based Identification of Novel Ligands Targeting Multiple Sites within a Chemokine–G-Protein-Coupled-Receptor Interface

CXCL12 is a human chemokine that recognizes the CXCR4 receptor and is involved in immune responses and metastatic cancer. Interactions between CXCL12 and CXCR4 are an important drug target but, like other elongated protein–protein interfaces, present challenges for small molecule ligand discovery due to the relatively shallow and featureless binding surfaces. Calculations using an NMR complex structure revealed a binding hot spot on CXCL12 that normally interacts with the I4/I6 residues from CXCR4. Virtual screening was performed against the NMR model, and subsequent testing has verified the specific binding of multiple docking hits to this site. Together with our previous results targeting two other binding pockets that recognize sulfotyrosine residues (sY12 and sY21) of CXCR4, including a new analog against the sY12 binding site reported herein, we demonstrate that protein–protein interfaces can often possess multiple sites for engineering specific small molecule ligands that provide lead compounds for subsequent optimization by fragment based approaches

Fragment-Based and Structure-Guided Discovery and Optimization of Rho Kinase Inhibitors

Using high concentration biochemical assays and fragment-based screening assisted by structure-guided design, we discovered a novel class of Rho-kinase inhibitors. Compound <b>18</b> was equipotent for ROCK1 (IC₅₀ = 650 nM) and ROCK2 (IC₅₀ = 670 nM), whereas compound <b>24</b> was more selective for ROCK2 (IC₅₀ = 100 nM) over ROCK1 (IC₅₀ = 1690 nM). The crystal structure of the compound <b>18</b>–ROCK1 complex revealed that <b>18</b> is a type 1 inhibitor that binds the hinge region in the ATP binding site. Compounds <b>18</b> and <b>24</b> inhibited potently the phosphorylation of the ROCK substrate MLC2 in intact human breast cancer cells