Molecular modeling study of CP-690550 derivatives as JAK3 kinase inhibitors through combined 3D-QSAR, molecular docking, and dynamics simulation techniques

Finding inhibitors and deciphering inhibitor-induced conformational plasticity in the Janus kinase via multiscale simulations

The Janus kinase (JAK) is a master regulator of the JAK/STAT pathway. Dysregulation of this signalling cascade causes neuroinflammation and autoimmune disorders. Therefore, JAKs have been characterized as an attractive target for developing anti-inflammatory drugs. Nowadays, designing efficient, effective, and specific targeted therapeutics without being cytotoxic has gained interest. We performed the virtual screening of natural products in combination with pharmacological analyses. Subsequently, we performed molecular dynamics simulations to study the stability of the ligand-bound complexes and ligand-induced inactive conformations. Notably, inactive kinases display remarkable conformational plasticity; however, ligand-induced molecular mechanisms of these conformations are still poorly understood. Herein, we performed a free energy landscape analysis to explore the conformational plasticity of the JAK1 kinase. Leonurine, STOCK1N-68642, STOCK1N-82656, and STOCK1N-85809 bound JAK1 exhibited a smooth transition from an active (αC-in) to a completely inactive conformation (αC-out). Ligand binding induces disorders in the αC-helix. Molecular mechanics Poisson Boltzmann surface area (MM/PBSA) calculation suggested three phytochemicals, namely STOCK1N-68642, Epicatechin, and STOCK1N-98615, have higher binding affinity compared to other ligand molecules. The ligand-induced conformational plasticity revealed by our simulations differs significantly from the available crystal structures, which might help in designing allosteric drugs.

Pharmacophore-Based Virtual Screening and Experimental Validation of Pyrazolone-Derived Inhibitors toward Janus Kinases

Janus kinases (JAKs) are nonreceptor protein tyrosine kinases that play a role in a broad range of cell signaling. JAK2 and JAK3 have been involved in the pathogenesis of common lymphoid-derived diseases and leukemia cancer. Thus, inhibition of both JAK2 and JAK3 can be a potent strategy to reduce the risk of these diseases. In the present study, the pharmacophore models built based on the commercial drug tofacitinib and the JAK2/3 proteins derived from molecular dynamics (MD) trajectories were employed to search for a dual potent JAK2/3 inhibitor by a pharmacophore-based virtual screening of 54 synthesized pyrazolone derivatives from an in-house data set. Twelve selected compounds from the virtual screening procedure were then tested for their inhibitory potency against both JAKs in the kinase assay. The in vitro kinase inhibition experiment indicated that compounds 3h, TK4g, and TK4b can inhibit both JAKs in the low nanomolar range. Among them, the compound TK4g showed the highest protein kinase inhibition with the half-maximal inhibitory concentration (IC₅₀) value of 12.61 nM for JAK2 and 15.80 nM for JAK3. From the MD simulations study, it could be found that the sulfonamide group of TK4g can form hydrogen bonds in the hinge region at residues E930 and L932 of JAK2 and E903 and L905 of JAK3, while van der Waals interaction also plays a dominant role in ligand binding. Altogether, TK4g, found by virtual screening and biological tests, could serve as a novel therapeutical lead candidate.

Molecular modelling of quinoline derivatives as telomerase inhibitors through 3D-QSAR, molecular dynamics simulation, and molecular docking techniques

Rising mortality due to cancer has led to the development and identification of newer targets and molecules to cure the disease. Telomerase is one of the attractive targets for design of many chemotherapeutic drugs. This research highlights the designing of novel telomerase inhibitors using ligand-based (3D-QSAR) and structure-based (molecular docking and molecular dynamics simulation) approaches. For the development of the 3D-QSAR model, 37 synthetic molecules reported earlier as telomerase inhibitors were selected from diversified literature. Three different alignment methods were explored; among them, distill alignment was found to be the best method with good statistical results and was used for the generation of QSAR model. Statistically significant CoMSIA model with a correlation coefficient (r²_ncv) value of 0.974, leave one out (q²) value of 0.662 and predicted correlation coefficient (r²_pred) value of 0.560 was used for the analysis of QSAR. For the MDS study, A-chain of telomerase was stabilised for 50 ns with respect to 1-atm pressure, with an average temperature of 299.98 k and with potential energy of 1,145,336 kJ/m converged in 997 steps. Furthermore, the behaviour study of variants towards the target revealed that active variable gave better affinity without affecting amino acid sequences and dimensions of protein which was accomplished through RMSD, RMSF and Rg analysis. Results of molecular docking study supported the outcomes of QSAR contour maps as ligand showed similar interactions with surrounded amino acids which were identified in contour map analysis. The results of the comprehensive study might be proved valuable for the development of potent telomerase inhibitors.

Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases

Janus kinases (JAKs) are enzymes involved in signaling pathways that affect hematopoiesis and immune cell functions. JAK1, JAK2, and JAK3 play different roles in numerous diseases of the immune system and have also been considered as potential targets for cancer therapy. In the present study, the susceptibility of the oral JAK inhibitor tofacitinib against these three JAKs was elucidated using the 500-ns molecular dynamics (MD) simulations and free energy calculations based on MM-PB(GB)SA, QM/MM-GBSA (PM3 and SCC-DFTB), and SIE methods. The obtained results revealed that tofacitinib could interact with all JAKs at the ATP-binding site via electrostatic attraction, hydrogen bond formation, and in particular van der Waals interaction. The conserved glutamate and leucine residues (E957 and L959 of JAK1, E930 and L932 of JAK2, and E903 and L905 of JAK3) located in the hinge region stabilized tofacitinib binding through strongly formed hydrogen bonds. Complexation with the incoming tofacitinib led to a closed conformation of the ATP-binding site and a decreased protein fluctuation at the glycine loop of the JAK protein. The binding affinities of tofacitinib/JAKs were ranked in the order of JAK3 > JAK2 ∼ JAK1, which are in line with the reported experimental data.

Construction of Quantitative Structure Activity Relationship (QSAR) Models to Predict Potency of Structurally Diversed Janus Kinase 2 Inhibitors

Janus kinase 2 (JAK2) inhibitors represent a promising therapeutic class of anticancer agents against many myeloproliferative disorders. Bioactivity data on pIC50 of 2229 JAK2 inhibitors were employed in the construction of quantitative structure-activity relationship (QSAR) models. The models were built from 100 data splits using decision tree (DT), support vector machine (SVM), deep neural network (DNN) and random forest (RF). The predictive power of RF models were assessed via 10-fold cross validation, which afforded excellent predictive performance with R2 and RMSE of 0.74 ± 0.05 and 0.63 ± 0.05, respectively. Moreover, test set has excellent performance of R2 (0.75 ± 0.03) and RMSE (0.62 ± 0.04). In addition, Y-scrambling was utilized to evaluate the possibility of chance correlation of the predictive model. A thorough analysis of the substructure fingerprint count was conducted to provide insights on the inhibitory properties of JAK2 inhibitors. Molecular cluster analysis revealed that pyrazine scaffolds have nanomolar potency against JAK2.

Identification of Chinese Herbal Compounds with Potential as JAK3 Inhibitors

The Janus kinases (JAKs) consist of four similar tyrosine kinases and function as key hubs in the signaling pathways that are implicated in both innate and adaptive immunity. Among the four members, JAK3 is probably the more attractive target for treatment of inflammatory diseases because its inhibition demonstrates the greatest immunosuppression and most profound effect in the treatment of such disorders. Although many JAK3 inhibitors are already available, certain shortcomings have been identified, mostly acquired drug resistance or unwanted side effects. To discover and identify new promising lead candidates, in this study, the structure of JAK3 (3LXK) was obtained from the Protein Data Bank and used for simulation modeling and protein-ligand interaction analysis. The ~36,000 Chinese herbal compounds obtained from TCM Database@Taiwan were virtually screened by AutoDock Vina docking program and filtered with Lipinski's Rules and ADME/T virtual predictions. Because of high occurrence of fake hits during docking, we selected 12 phytochemicals which have demonstrated modulating JAKs expressions among the top 50 chemicals from docking results. To validate whether these compounds are able to directly mediate JAK3 kinase, we have investigated the inhibitory activity using enzymatic activity assays, western blot, and HEK 293 cell STAT5 transactivity assays. The molecular analysis included docking and molecular dynamics (MD) simulations in order to investigate structural conformations and to explore the key amino acids in the interaction between JAK3 kinase and its putative ligands. The results demonstrated that Cryptotanshinone, Icaritin, and Indirubin exhibited substantial inhibitory activity against JAK3 kinase in vitro. The results also provide binding models of the protein-ligand interaction, detailing the interacting amino acid residues at the active ATP-binding domains of JAK3 kinase. In conclusion, our work discovered 3 potential natural inhibitors of JAK3 kinase and could provide new possibilities and stimulate new insights for the treatment of JAK3-targeted diseases.

Understanding the structural features of JAK2 inhibitors: a combined 3D-QSAR, DFT and molecular dynamics study

JAK2 plays a critical role in JAK/STAT signaling pathway and in patho-mechanism of myeloproliferative disorders and autoimmune diseases. Thus, effective JAK2 inhibitors provide a promising opportunity for the pharmaceutical intervention of many diseases. In this work, 3D-QSAR study was performed on a series of 1-amino-5H-pyrido-indole-4-carboxamide derivatives as JAK2 inhibitors to obtain reliable comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) models with three different alignment methods. Among the different alignment methods, ligand-based (CoMFA: q² = 0.676, r² = 0.979; CoMSIA: q² = 0.700, r² = 0.953) and pharmacophore-based alignment (CoMFA: q² = 0.710, r² = 0.982; CoMSIA: q² = 0.686, r² = 0.960) has produced better statistical results when compared to receptor-based alignment (CoMFA: q² = 0.507, r² = 0.979; CoMSIA: q² = 0.544, r² = 0.917). Statistical parameters indicated that data are well fitted and have high predictive ability. The presence of electrostatic and hydrophobic field is highly desirable for potent inhibitory activity, and the steric field plays a minor role in modulating the activity. The contour analysis indicates ARG980, ASN981, ASP939 and LEU937 have more possibility of interacting with bulky, hydrophobic groups in pyrido and positive and negative groups in pyrazole ring. Based on our findings, we have designed sixteen molecules and predicted its activity and drug-like properties. Subsequently, molecular docking, molecular dynamics and DFT calculations were performed to evaluate its potency.

The antityrosinase and antioxidant activities of flavonoids dominated by the number and location of phenolic hydroxyl groups

Background

Compounds with the ability to scavenge reactive oxygen species (ROS) and inhibit tyrosinase may be useful for the treatment and prevention from ROS-related diseases. The number and location of phenolic hydroxyl of the flavonoids will significantly influence the inhibition of tyrosinase activity. Phenolic hydroxyl is indispensable to the antioxidant activity of flavonoids. Isoeugenol, shikonin, baicalein, rosmarinic acid, and dihydromyricetin have respectively one, two, three, four, or five phenolic hydroxyls. The different molecular structures with the similar structure to l-3,4-dihydroxyphenylalanine (l-DOPA) were expected to the different antityrosinase and antioxidant activities.

Methods

This investigation tested the antityrosinase activity, the inhibition constant, and inhibition type of isoeugenol, shikonin, baicalein, rosmarinic acid, and dihydromyricetin. Molecular docking was examined by the Discovery Studio 2.5 (CDOCKER Dock, Dassault Systemes BIOVIA, USA). This experiment also examined the antioxidant effects of the five compounds on supercoiled pBR322 plasmid DNA, lipid peroxidation in rat liver mitochondria in vitro, and DPPH, ABTS, hydroxyl, or superoxide free radical scavenging activity in vitro.

Results

The compounds exhibited good antityrosinase activities. Molecular docking results implied that the compounds could interact with the amino acid residues in the active site center of antityrosinase. These compounds also exhibited antioxidant effects on DPPH, ABTS, hydroxyl, or superoxide free radical scavenging activity in vitro, lipid peroxidation in rat liver mitochondria induced by Fe²⁺/vitamin C system in vitro, and supercoiled pBR322 plasmid DNA. The activity order is isoeugenol < shikonin < baicalein < rosmarinic acid < dihydromyricetin. The results showed the compounds with more phenolic hydroxyls have more antioxidant and antityrosinase activities.

Conclusion

This was the first study of molecular docking for modeling the antityrosinase activity of compounds. This was also the first study of the protective effects of compounds on supercoiled pBR322 plasmid DNA, the lipid peroxidation inhibition activity in liver mitochondria. These results suggest that the compounds exhibited antityrosinase and antioxidant activities may be useful in skin pigmentation and food additives.

Electronic supplementary material

The online version of this article (10.1186/s13020-018-0206-9) contains supplementary material, which is available to authorized users.

In silico exploration of aryl sulfonamide analogs as voltage-gated sodium channel 1.7 inhibitors by using 3D-QSAR, molecular docking study, and molecular dynamics simulations

It has been demonstrated by human genetics that the voltage-gated sodium channel Nav1.7 is currently a promising target for the treatment of pain. In this research, we performed molecular simulation works on a series of classic aryl sulfonamide Nav1.7 inhibitors using three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for the first time to explore the correlation between their structures and activities. The results of the relevant statistical parameters of comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analyses (CoMSIA) had been verified to be reasonable, and the deep relationship between the structures and activities of these inhibitors was obtained by analyzing the contour maps. The generated 3D-QSAR model showed a good predictive ability and provided valuable clues for the rational modification of molecules. The interactions between compounds and proteins were modeled by molecular docking studies. Finally, accuracy of the docking results and stability of the complexes were verified by 100 ns MD simulations. Detailed information on the key residues at the binding site and the types of interactions they participate in involved was obtained. The van der Waals energy contributed the most in the molecular binding process according to the calculation of binding free energy. All research results provided a good basis for further research on novel and effective Nav1.7 inhibitors.

Discovery of FIXa inhibitors by combination of pharmacophore modeling, molecular docking, and 3D-QSAR modeling

Human Coagulation Factor IXa (FIXa), specifically inhibited at the initiation stage of the blood coagulation cascade, is an excellent target for developing selective and safe anticoagulants. To explore this inhibitory mechanism, 86 FIXa inhibitors were selected to generate pharmacophore models and subsequently SAR models. Both best pharmacophore model and ROC curve were built through the Receptor-Ligand Pharmacophore Generation module. CoMFA model based on molecular docking and PLS factor analysis methods were developed. Model propagations values are q² = 0.709, r² = 0.949, and r²_pred = 0.905. The satisfactory q² value of 0.609, r² value of 0.962, and r²_pred value of 0.819 for CoMSIA indicated that the CoMFA and CoMSIA models are both available to predict the inhibitory activity on FIXa. On the basis of pharmacophore modeling, molecular docking, and 3D-QSAR modeling screening, six molecules are screened as potential FIXa inhibitors.

Recent Developments and Applications of the MMPBSA Method

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.

The role of JAK-STAT signaling pathway and its regulators in the fate of T helper cells

The Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway plays critical roles in orchestrating of immune system, especially cytokine receptors and they can modulate the polarization of T helper cells. This pathway is regulated by an array of regulator proteins, including Suppressors of Cytokine Signaling (SOCS), Protein Inhibitors of Activated STATs (PIAS) and Protein Tyrosine Phosphatases (PTPs) determining the initiation, duration and termination of the signaling cascades. Dysregulation of the JAK-STAT pathway in T helper cells may result in various immune disorders. In this review, we represent how the JAK-STAT pathway is generally regulated and then in Th cell subsets in more detail. Finally, we introduce novel targeted strategies as promising therapeutic approaches in the treatment of immune disorders. Studies are ongoing for identifying the other regulators of the JAK-STAT pathway and designing innovative therapeutic strategies. Therefore, further investigation is needed.