Molecule Design against JAK-2

Introduction

The design of JAK inhibitors are highlighted

Janus kinases (JAKs) are non-receptor protein tyrosine kinases that catalyze the signaling of a variety of cytokine receptors, including receptors like interleukins, interferon’s, growth hormone, erythropoietin, and leptin. Janus Kinases (JAK) are classified into four category which include JAK1, JAK2, JAK3, and TYK2, are cytoplasmic protein kinases that control cytokine signal transduction by interacting with type I and type II cytokine receptor. When cytokines bind to cognate receptors, causes activation of JAKs, which leads to JAK-mediated tyrosine phosphorylation of STAT proteins and could results transcriptional activation of certain gene sets. JAK1 & 2, and TYK2 are expressed widely in mammalian cells of lymphocytes, whereas JAK3 expression is restricted to leukocytes. Because cytokine receptors are normally functioning as heterodimers, cytokine receptor complexes usually contain more than one kind of JAK kinases.

In general, cytokine binding to the extracellular region of their respective receptors causes receptor dimerization, which facilitates trans-phosphorylation (activation) of the JAKs. The majority of JAKs' have phosphoryl transfer activity which is controlled by the tyrosine kinase domain (JH1). In the kinase activation loop (Tyr1007 and Tyr1008 in JAK2), JH1 catalyzes trans-phosphorylation of two tyrosine residues, which stabilizes the active state. The activation of related Janus kinases, which then mediate the phosphorylation of receptors, occurs when ligands bind to cytokine and hormone receptors. The SH2 domain of STATs (signal transducers and activators of transcription) interacts with receptor, allowing Janus kinases to phosphorylate STAT and activate it (Ihle and Kerr 1995). STAT dimers are translocate to the nucleus, where they play a role in the regulation of hundreds of proteins' expressions (Figure 1).

Autoimmune diseases such as rheumatoid arthritis, ulcerative colitis, and Crohn's disease are caused by JAK-STAT dysfunction. Highly selective TYK2 pseudokinase (JH2) domain is targeted in autoimmune diseases. In psoriasis, pathogenic pathway is IL-23/IL-17 axis, and blocking JAK-STAT pathway is the strategy. BMS-986156 a JAK inhibitor is under phase -III clinical trials. PF-06826647 is in psoriasis phase II clinical trial stage, Brepocitinib is under consideration for oral psoriasis. Tofacinib, is an approved JAK inhibitor for ulcerative colitis. GDC-0214 is currently in clinical trials for asthma. Connective tissue disease (CTD) is another rising disease for JAK as a potential target of first- and second-generation JAK inhibitors (tofacitinib, baricitinib, ruxolitinib, peficitinib, filgotinib, upadacitinib, solcitinib, itacitinib, decernotinib, R333, and pf-06651600) are used for CTDs including RA, systemic lupus erythematosus, dermatomyositis, systemic sclerosis, Sjögren's syndrome, and vasculitis, based on laboratory and clinical research findings. JAK inhibitors have great potential for the treatment of various CTDs by reducing multiple cytokine production and suppressing inflammation, with the advantages of rapid onset in an oral formulation and decreased corticosteroid dependence and the associated adverse events, especially in refractory cases. Recent studies also implied association of JAK in Alopecial areata.

Potent JAK-2 Inhibitors

On the other hand, JAK inhibitors viz., Ruxolitinib and Delgocitinib are used as creams for actopic dermatitis. Dysregulation of JAK-STAT is also linked to the development of myelofibrosis, polycythemiavera, and other myeloproliferative diseases. In 95% of persons with polycythemiavera and a smaller percentage of people with other neoplasms, and activating JAK2 V617F mutation is found. Ruxolitinib is a JAK1/2 inhibitor that is approved by the FDA for the treatment of polycythemiavera and myelofibrosis. JAK have multiple therapeutic applications and could be the potential targets for various types of cancers. The development of new chemical compounds that could be candidates for new medications necessitates the application of hybrid technologies.

To design molecules against JAK-2 we have selected X-ray crystal protein structure of JAK-2 (PDB ID: 3KRR) was downloaded from protein data bank. The cocrystal ligand (NVP-BSK805) was used as reference compound to generate field points and Pharmacophore were generated. The cocrystal ligand interactions with JAK-2 and various field points were represented in below Figure. In this figure, the 3D field points with positive electrostatic potential represented by red color, negative electrostatic potential with cyan color, hydrophobic field points with gold color, Van der Waals field points are represented with yellow.

The binding site interactions of co-crystal ligand against JAK-2 involves the N1 of quinaxoline ring is anchored in the ATP-binding site and forms contact with hinge region involving H-bond interaction with Leu932. The polar pyrazole-piperidinyl moiety extends into hydrophobic region which exhibit pi-H interactions exhibited with Gly935, Leu855, Ala880, Val863, and Leu983 residues. Similarly, the difluorobenzyl-morpholine group extend into the hydrophobic channel of glycine loop.

Recently we have published paper on "Field-Based 3D-QSAR for Tyrosine Protein Kinase Jak- 2 inhibitors" in which we have developed 3D QSAR model and generated a potential ligands from the Natural Database https://doi.org/10.1080/07391102.2023.2226723

Conclusion:

Molecule design against the JAK-2 inhibitor could be performed by using 3D QSAR and pharmacophore approach. Virtual screening was performed based on the Pharmcophore features of cocrystal ligand (PDB ID: 3KRR) and dataset of NPS were selected with RMSD value less than 0.8. Further, developed QSAR model were used to design the ligands and calculate the JAK-2 inhibition activity were predicted (pKi). Thus, statistically robust reported 3D QSAR models could form the basis for design of novel JAK-2 inhibitors.

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