Target Protein Localisation and Its Impact on PROTAC-Mediated Degradation

Aim: To investigate and validate the potential target proteins for drug repurposing of newly FDA approved antibacterial drug. Background: Drug repurposing is the process of assigning indications for drugs other than the one(s) that they were initially developed for. Discovery of entirely new indications from already approved drugs is highly lucrative as it minimizes the pipeline of the drug development process by reducing time and cost. In silico driven technologies made it possible to analyze molecules for different target proteins which are not yet explored. Objective: To analyze possible targets proteins for drug repurposing of lefamulin and their validation. Also, in silico prediction of novel scaffolds from lefamulin has been performed for assisting medicinal chemists in future drug design. Methods: A similarity-based prediction tool was employed for predicting target protein and further investigated using docking studies on PDB ID: 2V16. Besides, various in silico tools were employed for prediction of novel scaffolds from lefamulin using scaffold hopping technique followed by evaluation with various in silico parameters viz., ADME, synthetic accessibility and PAINS. Results: Based on the similarity and target prediction studies, renin is found as the most probable target protein for lefamulin. Further, validation studies using docking of lefamulin revealed the significant interactions of lefamulin with the binding pocket of the target protein. Also, three novel scaffolds were predicted using scaffold hopping technique and found to be in the limit to reduce the chances of drug failure in the physiological system during the last stage approval process. Conclusion: To encapsulate the future perspective, lefamulin may assist in the development of the renin inhibitors and, also three possible novel scaffolds with good pharmacokinetic profile can be developed into both as renin inhibitors and for bacterial infections.

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Cation-promoted association of a regulatory and target protein is controlled by protein phosphorylation.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.91.9.3544 ◽

1994 ◽

Vol 91 (9) ◽

pp. 3544-3548 ◽

Cited By ~ 32

Author(s):

M. Feese ◽

D. W. Pettigrew ◽

N. D. Meadow ◽

S. Roseman ◽

S. J. Remington

Keyword(s):

Protein Phosphorylation ◽

Target Protein

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Correlating the Properties of Antibiotics with the Energetics of Partitioning in Colloidal Self-Assemblies and the Effect on the Binding of a Released Drug with a Target Protein

Langmuir ◽

10.1021/acs.langmuir.1c00773 ◽

2021 ◽

Author(s):

Eva Judy ◽

Nand Kishore

Keyword(s):

Target Protein

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The Novel ALG-2 Target Protein CDIP1 Promotes Cell Death by Interacting with ESCRT-I and VAPA/B

International Journal of Molecular Sciences ◽

10.3390/ijms22031175 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1175

Author(s):

Ryuta Inukai ◽

Kanako Mori ◽

Keiko Kuwata ◽

Chihiro Suzuki ◽

Masatoshi Maki ◽

...

Keyword(s):

Cell Death ◽

Essential Gene ◽

Susceptibility Gene ◽

Target Protein ◽

Hek293 Cells ◽

Dependent Manner ◽

Gene Encoding ◽

Endosomal Sorting ◽

Cell Death Pathways ◽

Apoptotic Protein

Apoptosis-linked gene 2 (ALG-2, also known as PDCD6) is a member of the penta-EF-hand (PEF) family of Ca2+-binding proteins. The murine gene encoding ALG-2 was originally reported to be an essential gene for apoptosis. However, the role of ALG-2 in cell death pathways has remained elusive. In the present study, we found that cell death-inducing p53 target protein 1 (CDIP1), a pro-apoptotic protein, interacts with ALG-2 in a Ca2+-dependent manner. Co-immunoprecipitation analysis of GFP-fused CDIP1 (GFP-CDIP1) revealed that GFP-CDIP1 associates with tumor susceptibility gene 101 (TSG101), a known target of ALG-2 and a subunit of endosomal sorting complex required for transport-I (ESCRT-I). ESCRT-I is a heterotetrameric complex composed of TSG101, VPS28, VPS37 and MVB12/UBAP1. Of diverse ESCRT-I species originating from four VPS37 isoforms (A, B, C, and D), CDIP1 preferentially associates with ESCRT-I containing VPS37B or VPS37C in part through the adaptor function of ALG-2. Overexpression of GFP-CDIP1 in HEK293 cells caused caspase-3/7-mediated cell death. In addition, the cell death was enhanced by co-expression of ALG-2 and ESCRT-I, indicating that ALG-2 likely promotes CDIP1-induced cell death by promoting the association between CDIP1 and ESCRT-I. We also found that CDIP1 binds to vesicle-associated membrane protein-associated protein (VAP)A and VAPB through the two phenylalanines in an acidic tract (FFAT)-like motif in the C-terminal region of CDIP1, mutations of which resulted in reduction of CDIP1-induced cell death. Therefore, our findings suggest that different expression levels of ALG-2, ESCRT-I subunits, VAPA and VAPB may have an impact on sensitivity of anticancer drugs associated with CDIP1 expression.

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The 3D-Screen Technology, an Innovative Cell-based Assay to Identify Modulators that Alter Target Protein Conformation: Example with HCV

Antiviral Research ◽

10.1016/j.antiviral.2011.03.167 ◽

2011 ◽

Vol 90 (2) ◽

pp. A77

Author(s):

Isabelle Valarche ◽

Amaya Berecibar ◽

Mehdi Lahmar ◽

Luc Batard ◽

Aurelie Martin ◽

...

Keyword(s):

Protein Conformation ◽

Target Protein

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Random and combinatorial mutagenesis for improved total production of secretory target protein in Escherichia coli

Scientific Reports ◽

10.1038/s41598-021-84859-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

David Gonzalez-Perez ◽

James Ratcliffe ◽

Shu Khan Tan ◽

Mary Chen May Wong ◽

Yi Pei Yee ◽

...

Keyword(s):

Escherichia Coli ◽

Protein Secretion ◽

Protein Production ◽

Secretory Protein ◽

Target Protein ◽

Carrier Protein ◽

Signal Peptides ◽

Carrier Proteins ◽

E Coli ◽

Combinatorial Mutagenesis

AbstractSignal peptides and secretory carrier proteins are commonly used to secrete heterologous recombinant protein in Gram-negative bacteria. The Escherichia coli osmotically-inducible protein Y (OsmY) is a carrier protein that secretes a target protein extracellularly, and we have previously applied it in the Bacterial Extracellular Protein Secretion System (BENNY) to accelerate directed evolution. In this study, we reported the first application of random and combinatorial mutagenesis on a carrier protein to enhance total secretory target protein production. After one round of random mutagenesis followed by combining the mutations found, OsmY(M3) (L6P, V43A, S154R, V191E) was identified as the best carrier protein. OsmY(M3) produced 3.1 ± 0.3 fold and 2.9 ± 0.8 fold more secretory Tfu0937 β-glucosidase than its wildtype counterpart in E. coli strains BL21(DE3) and C41(DE3), respectively. OsmY(M3) also produced more secretory Tfu0937 at different cultivation temperatures (37 °C, 30 °C and 25 °C) compared to the wildtype. Subcellular fractionation of the expressed protein confirmed the essential role of OsmY in protein secretion. Up to 80.8 ± 12.2% of total soluble protein was secreted after 15 h of cultivation. When fused to a red fluorescent protein or a lipase from Bacillus subtillis, OsmY(M3) also produced more secretory protein compared to the wildtype. In this study, OsmY(M3) variant improved the extracellular production of three proteins originating from diverse organisms and with diverse properties, clearly demonstrating its wide-ranging applications. The use of random and combinatorial mutagenesis on the carrier protein demonstrated in this work can also be further extended to evolve other signal peptides or carrier proteins for secretory protein production in E. coli.

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