Peichen Pan

Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility

In this study, to accommodate receptor flexibility, based on multiple receptor conformations, a novel ensemble docking protocol was developed by using the naïve Bayesian classification technique, and it was evaluated in terms of the prediction accuracy of docking-based virtual screening (VS) of three important targets in the kinase family: ALK, CDK2, and VEGFR2. First, for each target, the representative crystal structures were selected by structural clustering, and the capability of molecular docking based on each representative structure to discriminate inhibitors from non-inhibitors was examined. Then, for each target, 50 ns molecular dynamics (MD) simulations were carried out to generate an ensemble of the conformations, and multiple representative structures/snapshots were extracted from each MD trajectory by structural clustering. On average, the representative crystal structures outperform the representative structures extracted from MD simulations in terms of the capabilities to separate inhibitors from non-inhibitors. Finally, by using the naïve Bayesian classification technique, an integrated VS strategy was developed to combine the prediction results of molecular docking based on different representative conformations chosen from crystal structures and MD trajectories. It was encouraging to observe that the integrated VS strategy yields better performance than the docking-based VS based on any single rigid conformation. This novel protocol may provide an improvement over existing strategies to search for more diverse and promising active compounds for a target of interest.

Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations

Rho-associated protein kinases (ROCK1 and ROCK2) are promising targets for a number of diseases, including cardiovascular disorders, nervous system diseases, cancers, etc. Recently, we have successfully identified a ROCK1 inhibitor (1) with the triazine core. In order to gain a deeper insight into the microscopic binding of this inhibitor with ROCK1 and design derivatives with improved potency, the interactions between ROCK1 and a series of triazine/pyrimidine-based inhibitors were studied by using an integrated computational protocol that combines molecular docking, molecular dynamics (MD) simulations, binding free energy calculations, and binding energy decomposition analysis. First, three docking protocols, rigid receptor docking, induced fit docking, QM-polarized ligand docking, were used to determine the binding modes of the studied inhibitors in the active site of ROCK1. The results illustrate that rigid receptor docking achieves the best performance to rank the binding affinities of the studied inhibitors. Then, based on the predicted structures from molecular docking, MD simulations and MM/GBSA free energy calculations were employed to determine the dynamic binding process and compare the binding modes of the inhibitors with different activities. The binding free energies predicted by MM/GBSA are in good agreement with the experimental bioactivities, and the analysis of the individual energy terms suggests that the van der Waals interaction is the major driving force for ligand binding. In addition, the residue-inhibitor interaction spectra were obtained by the MM/GBSA free energy decomposition analysis, and the important residues for achieving strong binding were highlighted, which affords important guidance for the rational design of novel ROCK inhibitors. Finally, a variety of derivatives of inhibitor 1 were designed and four of them showed promising potency according to the predictions. We expect that our study can provide significant insight into the development of improved inhibitors of ROCK1.

Advances in the development of Rho-associated protein kinase (ROCK) inhibitors

Rho-associated protein kinases (ROCK1 and ROCK2) belong to the AGC family of serine-threonine kinases, and regulate a wide range of fundamental cell functions. Inhibition of ROCK has been proven to be of potential therapeutic benefit for a variety of diseases. In this review, the structures and therapeutic importance of ROCK are discussed briefly. Then, the recent status of the development of ROCK inhibitors is also summarized. Our review offers a foundation outline from which strategies to design new leads against ROCK can be developed.

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations

How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket of the kinase binding site. Here, by using enhanced sampling simulations (umbrella sampling, US) and two-end-state free energy calculations (MM/GSBA), we systemically studied the dissociation processes of two distinct small molecules escaping from the binding pocket of p38 MAP kinase through the allosteric channel and the ATP channel. The results show that the unbinding pathways along the allosteric channel have much lower PMF depths than those along the ATP channel, suggesting that the allosteric channel is more favorable for the dissociations of the two inhibitors and thereby supporting the general understanding that the largest channel of a target is usually the entry/exit pathway for the binding/dissociation of small molecules. Interestingly, the MM/GBSA approach yielded similar PMF profiles compared with those based on US, a much time consuming approach, indicating that for a general study, such as detecting the important transition state of a ligand binding/unbinding process, MM/GBSA may be a feasible choice.

Development and Evaluation of an Integrated Virtual Screening Strategy by Combining Molecular Docking and Pharmacophore Searching Based on Multiple Protein Structures

In this study, we developed and evaluated a novel parallel virtual screening strategy by integrating molecular docking and complex-based pharmacophore searching based on multiple protein structures. First, the capacity of molecular docking or pharmacophore searching based on any single structure from nine crystallographic structures of Rho kinase 1 (ROCK1) to distinguish the known ROCK1 inhibitors from noninhibitors was evaluated systematically. Then, the naı̈ve Bayesian classification or recursive partitioning technique was employed to integrate the predictions from molecular docking and complex-based pharmacophore searching based on multiple crystallographic structures of ROCK1, and the integrated protocol yields much better performance than molecular docking or complex-based pharmacophore searching based on any single ROCK1 structure. Finally, the well-validated integrated virtual screening protocol was applied to identify potential inhibitors of ROCK1 from traditional chinese medicine (TCM). The obtained potential active compounds from TCM are structurally novel and diverse compared with the known inhibitors of ROCK1, and they may afford valuable clues for the development of potent ROCK1 inhibitors.

Molecular Principle of Topotecan Resistance by Topoisomerase I Mutations through Molecular Modeling Approaches

Originally isolated from natural products, camptothecin (CPT) has provided extensive playing fields for the development of antitumor drugs. Two of the most successful analogs of CPT, topotecan and irinotecan, have been approved by the FDA for the treatment of colon cancer and ovarian cancer, as well as other cancers. However, the emergence of drug resistance mutations in topoisomerase I is a big challenge for the effective therapy of these drugs. Therefore, in this study, a series of computational approaches from molecular dynamics (MD) simulations to steered molecular dynamics (SMD) simulations and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations were employed to uncover the molecular principle of the topotecan resistance induced by three mutations in DNA topoisomerase I, including E418K, G503S, and D533G. Our results demonstrate a remarkable correlation between the binding free energies predicted by MM/GBSA and the rupture forces computed by SMD, and moreover, the theoretical results given by MM/GBSA and SMD are in excellent agreement with the experimental data for ranking the inhibitory activities: WT > E418K > G503S > D533G. In order to explore the drug resistance mechanism that underlies the loss of the binding affinity of topotecan, the binding modes of topotecan bound to the WT and mutated receptors were presented, and comparisons of the binding geometries and energy contributions on a per residue basis of topotecan between the WT complex and each mutant were also discussed. The results illustrate that the mutations of E418K, G503S, and D533G have great influence on the binding of topotecan to topoisomerase I bound with DNA, and the variations of the polar interactions play critical roles in the development of drug resistance. The information obtained from this study provides useful clues for designing improved topoisomerase I inhibitors for combating drug resistance.

Discovery of a benzofuran derivative (MBPTA) as a novel ROCK inhibitor that protects against MPP⁺-induced oxidative stress and cell death in SH-SY5Y cells.

Parkinson disease (PD) is a neurodegenerative disease with multifactorial etiopathogenesis. The discovery of drug candidates that act on new targets of PD is required to address the varied pathological aspects and modify the disease process. In this study, a small compound, 2-(5-methyl-1-benzofuran-3-yl)-N-(5-propylsulfanyl-1,3,4-thiadiazol-2-yl) acetamide (MBPTA) was identified as a novel Rho-associated protein kinase inhibitor with significant protective effects against 1-methyl-4-phenylpyridinium ion (MPP(+))-induced damage in SH-SY5Y neuroblastoma cells. Further investigation showed that pretreatment of SH-SY5Y cells with MBPTA significantly suppressed MPP(+)-induced cell death by restoring abnormal changes in nuclear morphology, mitochondrial membrane potential, and numerous apoptotic regulators. MBPTA was able to inhibit MPP(+)-induced reactive oxygen species (ROS)/NO generation, overexpression of inducible NO synthase, and activation of NF-κB, indicating the critical role of MBPTA in regulating ROS/NO-mediated cell death. Furthermore, MBPTA was shown to activate PI3K/Akt survival signaling, and its cytoprotective effect was abolished by PI3K and Akt inhibitors. The structural comparison of a series of MBPTA analogs revealed that the benzofuran moiety probably plays a crucial role in the anti-oxidative stress action. Taken together, these results suggest that MBPTA protects against MPP(+)-induced apoptosis in a neuronal cell line through inhibition of ROS/NO generation and activation of PI3K/Akt signaling.

Farnesyltransferase and geranylgeranyltransferase I: structures, mechanism, inhibitors and molecular modeling

Farnesyltransferase (FTase) and geranylgeranyltransferase type I (GGTase-I) have crucial roles in the post-translational modifications of Ras proteins and, therefore, they are promising therapeutic targets for the treatment of various Ras-induced cancers and several other kinds of diseases. In this review, we provide an overview of the structures and biological functions of FTase and GGTase-I. Then, we summarize the typical inhibitors of FTase and GGTase-I, and highlight the drug candidates in clinical trials. In addition, we survey some recent advances in computer-aided drug design (CADD) and molecular modeling studies of FTase and GGTase-I.

The competitive binding between inhibitors and substrates of HCV NS3/4A protease: A general mechanism of drug resistance

Hepatitis C virus (HCV) infection is a serious public health problem throughout the world. Great success has been achieved in developing inhibitors targeting the HCV NS3/4A protease over the past decade, but the rapid emergence of drug resistant mutations greatly compromises the efficacy of antiviral drugs or drug candidates. According to the substrate envelope hypothesis (Romano et al., 2010), severe drug resistant mutations would always occur where the inhibitors protrude from the substrate envelope, defined as a consensus volume occupied by the viral substrates in the active site of the NS3/4A protease. However, the substrate envelope hypothesis just qualitatively assesses the impact of mutations to a specific inhibitor, but no quantitative data is obtained. To remedy the weakness, the dynamic binding patterns of HCV NS3/4A protease inhibitors or substrates were investigated by molecular dynamics (MD) simulations and continuum solvation binding affinity predictions in this study. By comparing the quantitative binding profiles between the substrates and inhibitors, derived from the free energy decomposition analysis, we observed most residues involved in drug resistance form stronger interactions with the inhibitors than with the substrates, which is roughly coincident with the substrate envelope hypothesis and supports the general mechanism of drug resistance: the critical resistant mutations impair more to the binding of inhibitors than that of substrates. Furthermore, our predictions illustrate that the natural substrates of NS3/4A form balanced interactions with the strands 135-139 and 154-160 whereas the inhibitors cannot. Therefore, to overcome drug resistance, it may be necessary to restore the interaction balance between the two strands and the drug candidates. To our disappointment, the underlying resistant mechanisms of some mutations could not be well captured by just comparing the binding profiles of inhibitors and substrates, and more studies should be proceeded to propose a general drug resistance mechanism.

Pathway-Dependent Inhibition of Paclitaxel Hydroxylation by Kinase Inhibitors and Assessment of Drug–Drug Interaction Potentials

Paclitaxel is often used in combination with small molecule kinase inhibitors to enhance antitumor efficacy against various malignancies. Because paclitaxel is metabolized by CYP2C8 and CYP3A4, the possibility of drug–drug interactions mediated by enzyme inhibition may exist between the combining agents. In the present study, a total of 12 kinase inhibitors were evaluated for inhibitory potency in human liver microsomes by monitoring the formation of CYP2C8 and CYP3A4 metabolites simultaneously. For reversible inhibition, nilotinib was found to be the most potent inhibitor against both CYP2C8 and CYP3A4, and the inhibition potency could be explained by strong hydrogen binding based on molecular docking simulations and type II binding based on spectral analysis. Comparison of Ki values revealed that the CYP2C8 pathway was more sensitive toward some kinase inhibitors (such as axitinib), while the CYP3A4 pathway was preferentially inhibited by others (such as bosutinib). Pathway-dependent inactivation (time-dependent inhibition) was also observed for a number of kinase inhibitors against CYP3A4 but not CYP2C8. Further studies showed that axitinib had a KI of 0.93 μM and kinact of 0.0137 min−1, and the observed inactivation toward CYP3A4 was probably due to the formation of reactive intermediate(s). Using a static model, a reasonably accurate prediction of drug–drug interactions was achieved by incorporating parallel pathways and hepatic extraction ratio. The present results suggest that potent and pathway-dependent inhibition of CYP2C8 and/or CYP3A4 pathways by kinase inhibitors may alter the ratio of paclitaxel metabolites in vivo, and that such changes can be clinically relevant as differential metabolism has been linked to paclitaxel-induced neurotoxicity in cancer patients.