Discovery of a Covalent Small-Molecule eEF1A1 Inhibitor via Structure-Based Virtual Screening.

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.