3. the activity of [T315I]Abl oncogene. The gene encodes persistently high levels of cytoplasmic and constitutively active BCR-ABL tyrosine kinase, which is usually detected in >90% of CML patients and 25% of adult patients with acute lymphocytic leukemia (ALL)3. Animal studies also provide evidence to support BCR-ABL Derazantinib (ARQ-087) as the oncogenic cause of CML as it was shown to induce a myeloproliferative syndrome that closely resembles the chronic phase of human CML4. Philadelphia chromosome-positive (Ph+) patients in chronic phase of CML rely on sustained administration of small-molecule tyrosine kinase inhibitors (TKIs). The first-line therapy is usually imatinib mesylate (IM, also known as STI-571 or Gleevec?), a TKI that binds to the ATP cleft of the inactive form of BCR-ABL and prevents the conformational change required for kinase activation5. Clinical resistance to TKI therapy is usually a significant issue in the treatment of CML patients in the advanced stage of the disease1,6, primarily because the induction of point mutations in the BCR-ABL kinase domain name impair the conversation between IM and the ATP binding cleft7. Two second generation TKIs, dasatinib8,9 and nilotinib9, and one third generation TKI, bosutinib10,11,12, were developed to overcome IM-resistant BCR-ABL mutants; however, none have shown significant activity against T315Ithe most problematic of the mutants due to its resistance to multiple TKIs. In 2012, ponatinib13 (AP24534, Iclusig?) was approved by the Food and Drug Administration (FDA) as a therapeutic for CML or ALL Ph+ patients carrying the T315I mutation. Although ponatinib has shown potent inhibition against all clinically important BCR-ABL single mutants including T315I, compound mutants harboring the T315I mutation are highly resistant to this TKI13,14,15. Therefore, overcoming BCR-ABL-dependent resistance to current CML therapies remains a major challenge in drug design. In addition to the ATP cleft, the catalytic domain of BCR-ABL (Fig. 1a) includes a second distinct site: a substrate-binding site. Kinase substrates have larger contact area with the kinase domain than ATP, and the substrate-binding site is specific to each kinase, suggesting that inhibitors targeting this site would be less affected by mutations compared to TKIs16. Thus, peptide inhibitors targeting the substrate-binding site are an alternative strategy that can be used to inhibit BCR-ABL with higher specificity than the small molecule TKIs. Open in a separate window Figure 1 Three-dimensional structures of Abl kinase and MCoTI-II, and amino acid sequences of MCoTI-II variants considered in this study.(a) Abl kinase with substrate-ATP conjugate bound to the catalytic site (PDB ID: 2g2f). The substrate (abltide, in magenta) binds in the cleft between the N- and C-lobes; the phosphorylation site is oriented towards the ATP binding pocket in the N-lobe. (b) Three-dimensional structure and amino acid Derazantinib (ARQ-087) sequence of native MCoTI-II (PDB ID: lib9). The cysteine-rich peptide has a unique cyclic cystine knot (CCK) motif, comprising a cyclic backbone and three interlocking disulfides (shown in yellow). The starting point of the peptide sequence (G1) is connected KLF8 antibody to the corresponding position on its ribbon structure with a dashed line. The six cysteine residues partition the backbone into six loops. Loops 1 and 6, which were replaced with foreign sequences in this study, are highlighted in red and blue, respectively. (c) Sequence alignment of native MCoTI-II and MTAbl peptides. The six cysteines are highlighted in yellow and numbered using Roman numerals (ICVI). Foreign sequences containing the recognition motif of Abl kinase inserted into loops 1 or 6 are colored in red and blue, respectively. The phosphorylatable tyrosines are in Derazantinib (ARQ-087) bold font and the phosphorylated tyrosine residues are labeled with an asterisk. The Cys ICIV, IICV and IIICVI disulfide linkages are shown using dark gray lines. MCoTI-II and all the MTAbl peptides are head-to-tail cyclized, indicated by a light gray line. The affinity of MTAbl00 and MTAbl08 to Abl kinase was evaluated using molecular modeling only (labeled with a superscript M). Substrate-based kinase inhibitors are typically designed using knowledge on a range of peptide substrates17,18. A large study of kinase specificity using 2.5 billion synthetic peptides and nine tyrosine kinases19,20 led to the identification of the consensus motif Ile/Val/Leu-Tyr-Xaa-Xaa-Pro/Phe (where Xaa is any amino acid) required for substrate recognition by Abl kinase. As Abl kinase shares the same feature of the catalytic domain of BCR-ABL that is crucial for its oncogenetic activities, abltide (EAIYAAPFAKKK), the optimal substrate of Abl kinase containing the consensus motif, can be used as a starting point for a rational design of a substrate-based inhibitor of the oncogenic BCR-ABL. Although peptides have high target specificity and low toxicity profiles, their development as therapeutics is hampered by their low stability and limited access to intracellular space21. The discovery of cyclotides, peptides.