Distinguishing the optimal binding mechanism of an E3 ubiquitin ligase: Covalent versus noncovalent inhibition

Abstract

The development of covalent drugs, specifically in cancer therapeutics, has recently sparked interest among the pharmaceutical research community.While representing a significant fraction of the drugs in the market, very few have been deliberately designed to interact covalently with their biological target. One of the enzymes that have been both covalently and noncovalently targeted is the Neural Precursor Cell Expressed Developmentally Downregulated gene 4-1 (Nedd4-1). This enzyme has been found to have multiple physiological implications, including its involvement in cancer invasion. A critical gap still remains in the molecular understanding of the structural mechanism upon the covalent and noncovalent binding to Nedd4-1. In this study, we explore the most optimal binding mechanism in the inhibition of the catalytic site of the Nedd4-1. Our results exhibited a greater stability in the covalent complex compared with the noncovalent complex. This was supported by the secondary structure elements that were more dominant in the covalently inhibited complex. This complex disclosed an optimal free binding energy landscape, induced by the catalytic site energy contributions that showed to be more favorable. The insights demonstrating the above binding mechanism of Nedd4-1 establishes covalent inhibition as the preferred method of inhibition of the enzyme. This investigation aids in the understanding of the structural mechanism of Nedd4-1 inhibition and would assist in the design of more potent covalent inhibitors at the catalytic site of Nedd4-1. K E Y W O R D Scovalent inhibition, MD simulation, Nedd4-1, noncovalent inhibition

Nanodrug delivery systems for regulating microglial polarization in ischemic stroke treatment: A review

“…In membrane engineering, both covalent and non-covalent modifications present their respective advantages and disadvantages, respectively sacrificing the protective role on membrane protein activity and the firmness of the connection. 105 The primary approach for determining the success of membrane modification is through assessing membrane potential, particle size, morphology, and other factors. 106 However, the reliability of these methods is heavily dependent on experimental conditions and subjective factors.…”

Cell Membrane-Coated Mimics: A Methodological Approach for Fabrication, Characterization for Therapeutic Applications, and Challenges for Clinical Translation

“…For example, noncovalent modifications protect the membrane protein functionality, but the interactions are weaker in linkage strength. 415 Conversely, covalent bonding with a template is robust, but there is a risk of altering the natural membrane functionality and compromising the protein profiles. Changes in the ζ potential only primary measure the membrane modification, 333 creating a necessitous gap in qualitative and quantitative evaluation techniques.…”

“…Optimizing protocols to selectively retain proteins of interest and remove unwanted proteins from the cell membrane can enhance the CMC performance and remains to explore. Surface modification of cell membrane: Numerous membrane modification strategies are known, but not all of them offer proper orientation, linkage strength, and conserve membrane protein functionality. For example, noncovalent modifications protect the membrane protein functionality, but the interactions are weaker in linkage strength . Conversely, covalent bonding with a template is robust, but there is a risk of altering the natural membrane functionality and compromising the protein profiles.…”

Membrane engineering of cell membrane biomimetic nanoparticles for nanoscale therapeutics

“…Each modification method has its inherent benefits and drawbacks. The noncovalent modification offers preferable protection of membrane protein activity, while the noncovalent interaction is not firm enough compared with covalent bonds 100 . Covalent bonds anchor functional molecules on the membranes solidly, but it is easy to compromise the membrane protein profile and sacrifice the natural function of cytomembrane due to the conventional chemical reaction.…”

“…The noncovalent modification offers preferable protection of membrane protein activity, while the noncovalent interaction is not firm enough compared with covalent bonds. 100 Covalent bonds anchor functional molecules on the membranes solidly, but it is easy to compromise the membrane protein profile and sacrifice the natural function of cytomembrane due to the conventional chemical reaction. Limited by the technology of production, separation, and purification, enzyme-involved modification is difficult to be applied to the optimization of CM-NP.…”