Development of covalent inhibitors: Principle, design, and application in cancer

Abstract

Covalent inhibitors have been a rapidly growing field in drug discovery due to their therapeutic potential and unique advantages in cancer therapy. As opposed to noncovalent inhibitory drugs, covalent inhibitors reversibly or irreversibly modify proximal nucleophilic amino acid residues on proteins, aiming to selectively recognize and bind to protein targets and addressing some of the challenges faced by noncovalent drugs. Most successful targeted covalent inhibitors depend primarily on binding‐site cysteine residues, but this has limitations for certain protein targets that lack targetable cysteine residues. Recently, the rational design of covalent inhibitors or covalent probes targeting other nucleophilic residues, such as lysine, tyrosine, serine, has turned out to be another promising strategy for cancer therapy. Thus, the development of novel strategies to extend the scope of covalent binding and improve the binding properties is required. This review gives a summary of the development of covalent inhibitors targeting noncysteine from different aspects, including target identification, structure–activity relationships, drug discovery strategies, and binding properties, in the hope of providing a scientific reference for future covalent drug discovery as a means of expanding research in cancer therapy.

Insight into Janus kinases specificity: From molecular architecture to cancer therapeutics

“…Cysteine‐targeting covalent design has achieved great success in the field of kinase inhibitors, 256–258 such as neratinib, 259–261 afatinib, 262–265 dacomitinib, 266–268 osimertinib 269,270 and rociletinib 271 targeting Epidermal Growth Factor Receptor (EGFR‐C797), ibrutinib, 271 acalabrutinib, 272 and poseltinib 273 targeting Bruton's Tyrosine Kinase (BTK‐C481). Moreover, cysteine‐targeting covalent inhibitors have also been extensively studied in other kinases, including Fms‐like tyrosine kinase 3 (FLT3), 274 Extracellular‐regulated kinase 1/2 (ERK1/2), 275 TGF beta‐activated Kinase 1 (TAK1), 276 Phosphoinositide 3‐kinase α (PI3Kα), 277 and others.…”

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

“…A warhead refers to the chemical moiety that forms a covalent bond with the target protein through the classical electrophilic-neutrophilic reaction with nucleophilic amino acids in the protein binding site such as cysteine, lysine etc. Selecting the right warhead or modification is essential since it maximizes the inhibitor's effectiveness, reactivity, and selectivity with the target protein while reducing its off-target effects [49][50][51] . In contrast to small molecules, which might naturally have electrophilic groups in their chemical structures, peptides lack an electrophilic moiety by nature, hence it is necessary to add one in order for a peptide to form a covalent connection with a nucleophilic amino acid, most commonly cysteine and lysine, in the binding site of target protein.…”

Fitting of kinact and KI Values from Endpoint Pre-incubation IC50 Data

“…4,5 These discoveries have led to a resurgence in the interest in TCIs, resulting in many clinical success stories. 3,6,7 However, methods for evaluating the efficiency of irreversible candidates are distinctly different than those traditionally applied to reversible inhibitors, since both binding affinity (K I ) and reactivity (k inact ) must be accounted for by time-dependent evaluation to give a complete picture of efficiency. 8−11 Direct observation of covalent target labeling (e.g., by RapidFire mass spectrometry) 12 or the use of a continuous activity assay in the presence of substrate (also known as Kitz and Wilson conditions), 8,13−15 monitored over time, are two common methods in which time-dependency is directly reflected and kinetic parameters can be calculated from explicit equations using nonlinear regression.…”

“…Targeted covalent inhibitors (TCIs) exploit nucleophilic amino acid side chains in druggable target binding sites through the use of electrophilic “warheads”, resulting in prolonged residence times through a covalent interaction . The key to success is the use of a warhead having attenuated reactivity that only reacts after high affinity equilibrium binding with the desired target. , The scaffold is designed to appropriately position the warhead at the site of reaction in an initial, non-covalent, reversible binding event to promote the subsequent irreversible reaction with the target without requiring the warhead to be highly intrinsically reactive. , These discoveries have led to a resurgence in the interest in TCIs, resulting in many clinical success stories. ,, …”