Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling

Abstract

The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties available in virtual libraries. Therefore, we opted to divide an existing covalent Nedd4-1 inhibitor into two parts: a non-covalent binding group and a pre-selected α, β-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on molecular interactions at the binding site. The pharmacophore was then subjected to virtual screening to identify structurally similar hit compounds. Multiple filtrations were implemented prior to selecting four hits, which were validated with a covalent conjugation and later assessed by molecular dynamic simulations. The results showed that, of the four hit molecules, Zinc00937975 exhibited advantageous molecular groups, allowing for favourable interactions with one of the characteristic cysteine residues. Predictive pharmacokinetic analysis further justified the compound as a potential lead molecule, prompting its recommendation for confirmatory biological evaluation. Our inhouse, refined, pharmacophore model approach serves as a robust method that will encourage screening for novel covalent inhibitors in drug discovery.

Weak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124

“…The catalytic SER124 is in-between the a 3 -helix and the b 5 -strand in the active site. The approach of irreversible covalent inhibition of biological targets using covalent compounds to cure pathogenic diseases has remained promising in the drug design area (Bjij et al, 2019), and the dynamic perspectives in this study corroborated with the experimental protocol reported on the putative covalent inhibition of the Ag85C role through the interaction of SER124 residue with the phosphorus oxygen atom of the Cis (b-isomer)monocyclic enolphosphorus Cycliphostin (CyC 8b ) compounds.…”

The design and development of covalent protein-protein interaction inhibitors for cancer treatment

“…Aided by recent advancements in structural biology and chemistry, covalent inhibitors have emerged as a potentially effective approach towards PPI inhibition [37,38]. Studies have indicated that covalent drugs are less likely to promote resistance [39], which could be important for diseases such as cancer and infectious diseases where drug resistance is a major challenge. Covalent inhibitors are generally comprised of a specificity group to recognize the target protein and a functional "warhead" that forms a covalent linkage with the protein.…”

Covalent Flexible Peptide Docking in Drug Discovery: Current Challenges and Potential Interventions

“…Although significant efforts have been made to aid the modelling and design of noncovalent peptides, the molecular simulations of covalent peptide interactions remain a challenging task, especially with the lack of peptide-specific validated protocol that takes into account covalent binding between the peptide and the receptor [18,[20][21][22] . Along with our earlier reports on covalent docking [23][24][25][26][27][28][29] , The current report will concentrate on covalent peptide docking, its challenges, and provide potential solutions including technical guidance to useful tools and approaches to assist with the rational design of covalent peptide inhibitors.…”

“…We have previously discussed covalent docking in detail, including its uses and applications, available tools, advantages and disadvantages [25][26][27] . To avoid repetition of information, the primary objective of this review is the covalent docking technique specifically related to peptidebased molecules.…”