Structure-based virtual screening identifies a small-molecule inhibitor of the profilin 1–actin interaction

Abstract

Profilin 1 (Pfn1) is an important regulator of the actin cytoskeleton and plays a vital role in many actin-based cellular processes. Therefore, identification of a small-molecule intervention strategy targeted against the Pfn1-actin interaction could have broad utility in cytoskeletal research and further our understanding of the role of Pfn1 in actin-mediated biological processes. Based on an already resolved Pfn1-actin complex crystal structure, we performed structure-based virtual screening of small-molecule libraries to seek inhibitors of the Pfn1-actin interaction. We identified compounds that match the pharmacophore of the key actin residues of Pfn1-actin interaction and therefore have the potential to act as competitive inhibitors of this interaction. Subsequent biochemical assays identified two candidate compounds with nearly identical structures that can mitigate the effect of Pfn1 on actin polymerization As a further proof-of-concept test for cellular effects of these compounds, we performed proximity ligation assays in endothelial cells (ECs) to demonstrate compound-induced inhibition of Pfn1-actin interaction. Consistent with the important role of Pfn1 in regulating actin polymerization and various fundamental actin-based cellular activities (migration and proliferation), treatment of these compounds reduced the overall level of cellular filamentous (F) actin, slowed EC migration and proliferation, and inhibited the angiogenic ability of ECs both and In summary, this study provides the first proof of principle of small-molecule-mediated interference with the Pfn1-actin interaction. Our findings may have potential general utility for perturbing actin-mediated cellular activities and biological processes.

Computational guided identification of novel potent inhibitors of N-terminal domain of nucleocapsid protein of severe acute respiratory syndrome coronavirus 2

“…The final hits from pharmacophore screening were utilized for virtual screening using the crystal structure of NTD-N-protein. Virtual screening, molecular docking and dynamics have been widely used techniques to identify the potent lead molecules and assess the stability of protein-ligand complexes (Dalal et al, 2019;Dhankhar, Dalal, Mahto, et al, 2020;Gau et al, 2018;Meng et al, 2015). Out of the top 50 molecules, three molecules (ZINC000257324845, ZINC000005169973 and ZINC000009913056) were successfully passed the ADMET filters and also having druglike properties, which were analysed by Lipinski's rule of five.…”

3D Convolutional Neural Networks and a CrossDocked Dataset for Structure-Based Drug Design

“…A common approach is to utilize structurebased methods to score potential molecules with respect to the binding site of a given target protein structure to produce a ranked list of hits. [1][2][3][4][5] The scoring function is responsible for evaluating the correctness of the pose of the molecule in the binding site and predicting its binding affinity. Scoring functions fall into one of three categories: force-field based, [6][7][8][9] empirical, 10,11 or knowledge-based.…”

In silico analysis of PFN1 related to amyotrophic lateral sclerosis

“…Interestingly, these mutations were also found in sporadic cases of ALS [8]. The PFN1 gene encodes profilin 1 (PFN1), a 140-residues ubiquitously expressed [9] cytosolic protein [10] that plays key roles in the regulation of actin cytoskeleton [11].…”

“…Moreover, PFN1 is involved in many cellular processes [11] through the interaction with diverse binding partners [14], including structural proteins in neurons, growth factors [9], ribonuclear particles [15] and proteins involved in signaling cascades [9]. PFN1 also plays important roles in membrane trafficking [16], RNA processing and transcription [9], GTPase signaling [17], and neuronal growth and differentiation [16].…”