Intrinsic relative preference profile of pan-kinase inhibitor drug staurosporine towards the clinically occurring gatekeeper mutations in Protein Tyrosine Kinases. (October 2021)

• Record Type: Journal Article
• Authors: Ren, Zheng; Li, Qian; Shen, Yiwen; Meng, Ling
• Is Part Of: Computational biology and chemistry. Volume 94(2021)
• Publication Date: 2021-10
• Subjects: Protein tyrosine kinase -- Pan-kinase inhibitor -- Staurosporine -- Gatekeeper mutation -- Kinase context -- Relative preference; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2021.107562
• Languages: English
• ISSNs: 1476-9271

Abstract

Abstract: Protein tyrosine kinases (PTKs) have been recognized as the attractive druggable targets of various diseases including cancer. However, many PTKs are clinically observed to establish a gatekeeper mutation in the peripheral hinge section of active site, which plays a primary role in development of acquired drug resistance to kinase inhibitors. The natural product Staurosporine, an ATP-competitive reversible pan-kinase inhibitor, has been found to exhibit wild type-sparing selectivity for some PTK gatekeeper mutants. In this study, totally 23 acquired drug-resistant gatekeeper mutations harbored on 17 PTKs involved in diverse cancers were curated, from which only five amino acid types, namely Thr, Met, Val, Leu and Ile, were observed at both wild-type and mutant residues of these clinically occurring gatekeeper sites. Here, an integrative strategy that combined molecular modeling and kinase assay was described to systematically investigate the relative preference of Staurosporine towards the five gatekeeper amino acid types in real kinase context and in a psendokinase model. A kinase-free, intrinsic relative preference profile of Staurosporine to gatekeeper amino acids was created: (dispreferred) Thr ⊳ Val ⊳ Ile ⊳ Leu ⊳ Met (preferred). It is found that kinase context has no essential effect on the profile; different kinases and even psendokinase can obtain a consistent conclusion for the preference order. Theoretically, we can use the profile to predict Staurosporine response to any gatekeeper mutation between the five amino acid types in any PTK. Structural and energetic analyses revealed that the multiple-aromatic ring system of Staurosporine can form multiple noncovalent interactions with the weakly polar side chain of Met and can pack tightly or moderately against the nonpolar side chains of Val, Ile and Leu, thus stabilizing the kinase–inhibitor system (Δ U < 0), whereas the polar side chain of Thr may cause unfavorable electronegative and solvent effects with the aromatic electrons of Staurosporine, thus destabilizing the system (Δ U > 0). Graphical Abstract: ga1 Highlights: Staurosporine response to clinically occurring kinase gatekeeper mutations is analyzed systematically. A kinase-free, intrinsic relative preference profile of Staurosporine to gatekeeper amino acids is created. Methionine is identified as the most favorable gatekeeper amino acid for Staurosporine. Kinase context has no essential effect on Staurosporine response to gatekeeper mutations.