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Published on: February 28, 2025
Discovery of a Covalent Small-Molecule eEF1A1 Inhibitor via Structure-Based Virtual Screening
Yangping Deng1, Sizheng Li1, Liang Wang1
1College of Chemistry, State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for New Organic Matter, Nankai University, 94 Weijin Road, Tianjin 300071, China.
Abstract:
Pancreatic cancer remains a formidable health challenge due to its late-stage diagnosis and limited therapeutic options, underscoring the need for novel targets and modalities. Our previous work revealed that the natural product, BE-43547A2, could effectively inhibit the progression of pancreatic cancer by the covalent binding to eukaryotic translation elongation factor 1 α 1 (eEF1A1) at Cys234 (C234). Considering the critical role in protein synthesis and the association with pancreatic cancer progression, eEF1A1 is a novel promising target for pancreatic cancer. However, the rational drug design methods for eEF1A1 are extremely lacking. Herein, using microsecond-scale molecular dynamics (MD) simulations, we identify a suitable eEF1A1 conformation for structure-based virtual screening (SBVS) by targeting the residue of C234. Through a tailored SBVS pipeline, we identified AKOS-04 as a novel small-molecule covalent inhibitor with nanomolar-level potency (IC50 = 28.5 ± 2.86 nM in the PATU8988T cell line). Notably, cellular thermal shift assays (CETSA), with the treatments of dithiothreitol (DTT) and iodoacetamide (IAM), confirmed the covalent Cys-involved interaction of AKOS-04 and eEF1A1. Further structural modification validated the critical contribution of a double bond in the acrylamide group of AKOS-04 for its covalent binding with eEF1A1, manifested by the abolished inhibitory activity of compound 9 with the changed single bond in the acrylamide group. MST experiments confirmed direct binding of the compounds to eEF1A1 protein. AKOS-04 exhibited the strongest binding among the tested compounds, consistent with effective covalent target. Finally, MD simulations and pair-interaction energy analyses highlighted Lys84, Arg218, and Glu230 of eEF1A1 as key residues for driving its binding interactions to AKOS-04. These results reveal that AKOS-04, screened by SBVS against C234 of eEF1A1, represents a promising lead for eEF1A1-targeted pancreatic cancer therapy, highlighting the power of computational approaches in covalent drug discovery.
Insights
Researchers identified AKOS-04, a novel covalent inhibitor targeting eukaryotic translation elongation factor 1 alpha 1 (eEF1A1), showing promise for pancreatic cancer therapy. This discovery highlights computational methods for developing new pancreatic cancer drugs.
Area of Science:
- Biochemistry
- Molecular Biology
- Computational Chemistry
Background:
- Pancreatic cancer presents significant therapeutic challenges due to late diagnosis and limited treatment options.
- Eukaryotic translation elongation factor 1 alpha 1 (eEF1A1) is a promising target for pancreatic cancer therapy, but rational drug design approaches are lacking.
Purpose of the Study:
- To identify novel small-molecule covalent inhibitors of eEF1A1 using structure-based virtual screening (SBVS).
- To validate the efficacy and mechanism of action of identified inhibitors for pancreatic cancer treatment.
Main Methods:
- Microsecond-scale molecular dynamics (MD) simulations to identify suitable eEF1A1 conformations for SBVS.
- Structure-based virtual screening (SBVS) pipeline targeting eEF1A1 Cys234.
- Cellular thermal shift assays (CETSA), dithiothreitol (DTT), and iodoacetamide (IAM) treatments to confirm covalent binding.
- Mutagenesis studies and MicroScale Thermophoresis (MST) to validate compound binding and identify key residues.
Main Results:
- AKOS-04 identified as a potent covalent inhibitor of eEF1A1 with nanomolar potency (IC50 = 28.5 ± 2.86 nM).
- Confirmed covalent interaction between AKOS-04 and eEF1A1 at Cys234.
- Structural modifications confirmed the necessity of the acrylamide double bond for covalent binding.
- MD simulations and energy analyses identified Lys84, Arg218, and Glu230 as key residues for AKOS-04 binding.
Conclusions:
- AKOS-04 is a promising lead compound for eEF1A1-targeted pancreatic cancer therapy.
- SBVS targeting eEF1A1 Cys234 is an effective strategy for covalent drug discovery.
- Computational approaches significantly advance the development of novel pancreatic cancer therapeutics.
