Indoloxytriazines as binding molecules for the JAK2 JH2 pseudokinase domain and its V617F variant

Newton, Ana S.; Liosi, Maria-Elena; Henry, Sean P.; Deiana, Luca; Faver, John C.; Krimmer, S.G.; Puleo, D.E.; Schlessinger, Joseph; Jorgensen, William L.

doi:10.1016/j.tetlet.2021.153248

Cited by 8 publications

(31 citation statements)

References 18 publications

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“…This core could then be attached to a phenyl group via an ether linkage instead to better mimic the triazine series. Since the indole hydrogen is hydrogen-bonded to Asn678 in this series, 25 we also sought to attach an amino group to the phenyl group (Figure 1, green). This resultant aniline could then provide a synthetic handle to connect the terminal carboxylic acid through various linkers, completing the redesign of JAK198 into a new series.…”

Section: T H Imentioning

confidence: 99%

“…Replacement of the sulfonamide by an amide yielded significant improvement; analogue 5 has a K d of 18.8 ± 0.2 μM, comparable to those of previously reported triazines. 25 Curiously, the extension of the alkyl chain of 5 by a single methylene unit to give 6 significantly reduced the binding to JAK2 JH2. Furthermore, conversion of the amides 5 and 6 to the corresponding ureas 7 and 8 gave equivalent binding.…”

Section: T H Imentioning

confidence: 99%

“…As expected, the pyrrolopyrimidine subunit is hydrogen-bonded with the hinge region of the JAK2 JH2 domain (Figure 3A) in similar fashion to our previously reported triazine and triazole analogues. 22,25 There is a tight cation−π interaction between the phenoxy ring and Lys581. Interestingly, the urea moiety, while initially installed to mimic the hydrogen bonding found with the planar indole, possesses a dihedral angle of 55.7°in the crystal, out-ofplane with the attached phenolic ether (Figure 3B); however, it is also hydrogen-bonded to Asn678 as for the indole.…”

Section: T H Imentioning

confidence: 99%

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Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies

Henry

Liosi

Ippolito

et al. 2022

ACS Med. Chem. Lett.

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The Janus kinase 2 (JAK2) pseudokinase domain (JH2) is an ATP-binding domain that regulates the activity of the catalytic tyrosine kinase domain (JH1). Dysregulation of JAK2 JH1 signaling caused by the V617F mutation in JH2 is implicated in various myeloproliferative neoplasms. To explore if JAK2 activity can be modulated by a small molecule binding to the ATP site in JH2, we have developed several ligand series aimed at selectively targeting the JAK2 JH2 domain. We report here the evolution of a false virtual screen hit into a new JAK2 JH2 series. Optimization guided by computational modeling has yielded analogues with nanomolar affinity for the JAK2 JH2 domain and >100-fold selectivity for the JH2 domain over the JH1 domain. A crystal structure for one of the potent compounds bound to JAK2 JH2 clarifies the origins of the strong binding and selectivity. The compounds expand the platform for seeking molecules to regulate JAK2 signaling, including V617F JAK2 hyperactivation.

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Section: T H Imentioning

confidence: 99%

Section: T H Imentioning

confidence: 99%

Section: T H Imentioning

confidence: 99%

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Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies

Henry

Liosi

Ippolito

et al. 2022

ACS Med. Chem. Lett.

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“…Along these lines, we endeavored to identify small molecules that could selectively bind the JH2 over the JH1 domain and aim to use them as chemical probes to test this hypothesis. These efforts have led to the development of several series of novel JAK2 JH2 binders: indoloxytriazines, diaminotriazoles, and pyrrolopyrimidines (Figure ). , …”

Section: Introductionmentioning

confidence: 99%

Insights on JAK2 Modulation by Potent, Selective, and Cell-Permeable Pseudokinase-Domain Ligands

et al. 2022

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JAK2 is a non-receptor tyrosine kinase that regulates hematopoiesis through the JAK-STAT pathway. The pseudokinase domain (JH2) is an important regulator of the activity of the kinase domain (JH1). V617F mutation in JH2 has been associated with the pathogenesis of various myeloproliferative neoplasms, but JAK2 JH2 has been poorly explored as a pharmacological target. In light of this, we aimed to develop JAK2 JH2 binders that could selectively target JH2 over JH1 and test their capacity to modulate JAK2 activity in cells. Toward this goal, we optimized a diaminotriazole lead compound into potent, selective, and cell-permeable JH2 binders leveraging computational design, synthesis, binding affinity measurements for the JH1, JH2 WT, and JH2 V617F domains, permeability measurements, crystallography, and cell assays. Optimized diaminotriazoles are capable of inhibiting STAT5 phosphorylation in both WT and V617F JAK2 in cells.

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“…Computational approaches to hit discovery and lead refinement can be broadly classified as either screening-based − or hypothesis-driven. − Available methods are covered in a number of excellent reviews. − Structure-based screening approaches generally rely on a (possibly dynamic) library of compounds or fragments and a mechanism to score ligands or otherwise discriminate predicted binders from nonbinders . Since library screening readily scales to large numbers of compounds (10 8 in a recent example) and can be conducted without human intuition, − it is frequently employed as a high-throughput approach. , Hypothesis-directed approaches are varied but may start by obtaining structural information about the macromolecular target alone or in complex with a drug lead , or cognate ligand .…”

Section: Introductionmentioning

confidence: 99%

Drug Discovery by Automated Adaptation of Chemical Structure and Identity

Patel

Chau

Debesai

et al. 2022

J. Chem. Theory Comput.

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Computer-aided drug design offers the potential to dramatically reduce the cost and effort required for drug discovery. While screening-based methods are valuable in the early stages of hit identification, they are frequently succeeded by iterative, hypothesis-driven computations that require recurrent investment of human time and intuition. To increase automation, we introduce a computational method for lead refinement that combines concerted dynamics of the ligand/protein complex via molecular dynamics simulations with integrated Monte Carlo-based changes in the chemical formula of the ligand. This approach, which we refer to as ligand-exchange Monte Carlo molecular dynamics, accounts for solvent- and entropy-based contributions to competitive binding free energies by coupling the energetics of bound and unbound states during the ligand-exchange attempt. Quantitative comparison of relative binding free energies to reference values from free energy perturbation, conducted in vacuum, indicates that ligand-exchange Monte Carlo molecular dynamics simulations sample relevant conformational ensembles and are capable of identifying strongly binding compounds. Additional simulations demonstrate the use of an implicit solvent model. We speculate that the use of chemical graphs in which exchanges are only permitted between ligands with sufficient similarity may enable an automated search to capture some of the benefits provided by human intuition during hypothesis-guided lead refinement.

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Indoloxytriazines as binding molecules for the JAK2 JH2 pseudokinase domain and its V617F variant

Cited by 8 publications

References 18 publications

Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies

Conversion of a False Virtual Screen Hit into Selective JAK2 JH2 Domain Binders Using Convergent Design Strategies

Insights on JAK2 Modulation by Potent, Selective, and Cell-Permeable Pseudokinase-Domain Ligands

Drug Discovery by Automated Adaptation of Chemical Structure and Identity

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