Article

Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling

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Abstract

Type III phosphatidylinositol 4 kinases (PI4KIIIs) are essential enzymes that relating to the replication of multiple RNA viruses. Understanding the interaction mechanism of molecular compounds with the alpha and beta isoforms of PI4KIII (PI4KIIIα and PI4KIIIβ) is of significance in the development of inhibitors which can bind to these two enzymes selectively. In this work, molecular dynamics (MD) simulations and binding free energy calculations were combined to investigate the binding modes of seven selected compounds to PI4KIIIα and PI4KIIIβ. Analyses based on MD trajectories provide detailed interaction mechanisms of these compounds with PI4KIIIα and PI4KIIIβ at the atomic level, and indicate that the selectivity of these compounds is mainly due to the structural difference of the binding pockets. It is expected that detailed binding information found in this study can provide useful help for the structure-based design of selective inhibitors toward PI4KIIIα and PI4KIIIβ.

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... Overall, combining different non-conflicting protocols into more advanced end-point schemes could be helpful, but the improvements over individual baseline alterations could be marginal. To further explore the space of advanced end-point techniques and search for really usable protocols, we would attempt a series of other modifications (e.g., enhanced sampling [10,[20][21][22]49] and the multi-scale treatment [50,51]) in this WP6 end-point series works. ...
Article
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Host–guest binding, despite the relatively simple structural and chemical features of individual components, still poses a challenge in computational modelling. The extreme underperformance of standard end-point methods in host–guest binding makes them practically useless. In the current work, we explore a potentially promising modification of the three-trajectory realization. The alteration couples the binding-induced structural reorganization into free energy estimation and suffers from dramatic fluctuations in internal energies in protein–ligand situations. Fortunately, the relatively small size of host–guest systems minimizes the magnitude of internal fluctuations and makes the three-trajectory realization practically suitable. Due to the incorporation of intra-molecular interactions in free energy estimation, a strong dependence on the force field parameters could be incurred. Thus, a term-specific investigation of transferable GAFF derivatives is presented, and noticeable differences in many aspects are identified between commonly applied GAFF and GAFF2. These force-field differences lead to different dynamic behaviors of the macrocyclic host, which ultimately would influence the end-point sampling and binding thermodynamics. Therefore, the three-trajectory end-point free energy calculations are performed with both GAFF versions. Additionally, due to the noticeable differences between host dynamics under GAFF and GAFF2, we add additional benchmarks of the single-trajectory end-point calculations. When only the ranks of binding affinities are pursued, the three-trajectory realization performs very well, comparable to and even better than the regressed PBSA_E scoring function and the dielectric constant-variable regime. With the GAFF parameter set, the TIP3P water in explicit solvent sampling and either PB or GB implicit solvent model in free energy estimation, the predictive power of the three-trajectory realization in ranking calculations surpasses all existing end-point methods on this dataset. We further combine the three-trajectory realization with another promising modified end-point regime of varying the interior dielectric constant. The combined regime does not incur sizable improvements for ranks and deviations from experiment exhibit non-monotonic variations.
... Overall, combining different non-conflicting protocols into more advanced end-point schemes could be helpful, but the improvements over individual baseline alterations could be marginal. To further explore the space of advanced end-point techniques and search for really usable protocols, we would attempt a series of other modifications (e.g., enhanced sampling 10, 44-46, 49 and the multi-scale treatment 50,51 ) in this WP6 endpoint series works. ...
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Host-guest binding, despite the relatively simple structural and chemical features of individual components, still poses a challenge in computational modelling. The problems lie in both the accuracy of the employed Hamiltonian (often fixed-charge force fields) and the exhaustiveness of conformational sampling. End-point free energy calculations as fast alternatives to rigorous but costly methods are widely applied in virtual screening in protein-ligand and host-guest systems. However, the extreme underperformance of standard end-point methods makes them practically useless. Modifications of the end-point procedure could bring these methods back to the pool of usable tools, e.g., regression considered in our previous work. In the current work, we explore a potentially promising modification, the three-trajectory realization of the end-point simulation protocol. The alteration couples the binding-induced structural reorganization into free energy estimation and suffers from dramatic fluctuations of internal energies in protein-ligand situations. Fortunately, the relatively small size of host-guest systems minimizes the magnitude of internal fluctuations and makes the three-trajectory realization practically suitable. Due to the incorporation of intra-molecular interactions in free energy estimation, a strong dependence on the force field parameters could be incurred. Thus, a term-specific investigation of transferable GAFF derivatives is presented, and noticeable differences in many aspects are identified between commonly applied GAFF and GAFF2. These force-field differences lead to different dynamic behaviors of the macrocyclic host, which ultimately would influence the end-point sampling and binding thermodynamics. Therefore, the three-trajectory end-point free energy calculations are performed with both GAFF versions to investigate the force-field dependent behavior of computed binding affinities. Also, due to the noticeable differences between host dynamics under GAFF and GAFF2, we add additional benchmarks of the single-trajectory end-point calculations. Numerical results suggest that the single-trajectory realization, regardless of the GAFF version, is still not useful in host-guest binding, although the prediction quality of the GAFF2 parameter set is slightly better than GAFF. As for the three-trajectory realization, the absolute values of computed binding thermodynamics exhibit pronounced force-field-dependent behaviors, which are less significant for ranking information. When only the ranks of binding affinities are pursued, the three-trajectory realization performs very well, comparable to and even better than the regressed PBSA_E scoring function and the dielectric-constant-variable regime. With the GAFF parameter set, the TIP3P water in explicit-solvent sampling and either PB or GB implicit-solvent model in free energy estimation, the predictive power of the three-trajectory realization in ranking calculations surpasses all existing end-point methods on this dataset. We further combine the three-trajectory realization with another promising modified end-point regime of varying the interior dielectric constant. The predicted binding affinities exhibit monotonic responses to the variation of the internal dielectric constant, but the deviations from experiment exhibit non-monotonic variations, which are related to the systematic overestimation of the binding strength under the original three-trajectory realization. By contrast, the combined regime does not incur sizable improvements for ranks, although for most systems the dielectric constant 2 seems to be the best option.
... Methods that are a bit less computationally demanding are end-point free energy methods of MM/PBSA and MM/GBSA [17][18][19]. These end-point techniques are computationally feasible due to their approximated calculation procedure [20][21][22]. The most widely employed end-point scheme uses the singletrajectory approximation and only samples the well-defined bound conformation. ...
Article
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End-point free energy calculations as a powerful tool have been widely applied in protein–ligand and protein–protein interactions. It is often recognized that these end-point techniques serve as an option of intermediate accuracy and computational cost compared with more rigorous statistical mechanic models (e.g., alchemical transformation) and coarser molecular docking. However, it is observed that this intermediate level of accuracy does not hold in relatively simple and prototypical host–guest systems. Specifically, in our previous work investigating a set of carboxylated-pillar[6]arene host–guest complexes, end-point methods provide free energy estimates deviating significantly from the experimental reference, and the rank of binding affinities is also incorrectly computed. These observations suggest the unsuitability and inapplicability of standard end-point free energy techniques in host–guest systems, and alteration and development are required to make them practically usable. In this work, we consider two ways to improve the performance of end-point techniques. The first one is the PBSA_E regression that varies the weights of different free energy terms in the end-point calculation procedure, while the second one is considering the interior dielectric constant as an additional variable in the end-point equation. By detailed investigation of the calculation procedure and the simulation outcome, we prove that these two treatments (i.e., regression and dielectric constant) are manipulating the end-point equation in a somehow similar way, i.e., weakening the electrostatic contribution and strengthening the non-polar terms, although there are still many detailed differences between these two methods. With the trained end-point scheme, the RMSE of the computed affinities is improved from the standard ~ 12 kcal/mol to ~ 2.4 kcal/mol, which is comparable to another altered end-point method (ELIE) trained with system-specific data. By tuning PBSA_E weighting factors with the host-specific data, it is possible to further decrease the prediction error to ~ 2.1 kcal/mol. These observations along with the extremely efficient optimized-structure computation procedure suggest the regression (i.e., PBSA_E as well as its GBSA_E extension) as a practically applicable solution that brings end-point methods back into the library of usable tools for host–guest binding. However, the dielectric-constant-variable scheme cannot effectively minimize the experiment-calculation discrepancy for absolute binding affinities, but is able to improve the calculation of affinity ranks. This phenomenon is somehow different from the protein–ligand case and suggests the difference between host–guest and biomacromolecular (protein–ligand and protein–protein) systems. Therefore, the spectrum of tools usable for protein–ligand complexes could be unsuitable for host–guest binding, and numerical validations are necessary to screen out really workable solutions in these ‘prototypical’ situations.
... Conventional molecular dynamics (cMD) simulations 32-38 and computations of binding free energies (BFEs) [39][40][41][42][43] , including thermodynamics integration 44,45 , FEP 46 , and solvation interaction energy 47,48 , etc., have been essential tools for deciphering ligand-protein and small molecule-solvent interactions; moreover, many works have successfully probed the binding selectivity of inhibitors to homologous proteins with similar structural topology and high sequence identity [49][50][51][52][53][54][55] . However, the conformations sampled by cMD simulations are possibly trapped in the minimal space, which leads to insufficient conformational sampling. ...
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Understanding selectivity-dependent molecular mechanism of inhibitors towards CDK2 over CDK6 is prominent for improving drug design towards the CDK family. Multiple short molecular dynamics (MD) simulations combined with MM-GBSA approach are adopted to investigate molecular mechanism on binding selectivity of inhibitors X64, X3A, and 4 AU to CDK2 and CDK6. The RMSF analysis and calculations of molecular surface areas indicate that local structural and global flexibility of CDK6 are stronger than that of CDK2. Based on dynamics cross-correlation maps (DCCMs), motion modes of CDK2 and CDK6 produce difference due to associations of X64, X3A, and 4 AU. The calculated binding free energies (BFEs) demonstrate that the compensation between binding enthalpy and entropy of X64, X34, and 4 AU is a key force driving selectivity of inhibitors towards CDK2 over CDK6. This work provides valuable information for designing highly selective inhibitors towards CDK2 and CDK6 and further promotes identification of efficient anticancer drugs in the future.
... Subsequently, the generalized Born method (igb =5) and 0.1 M of the salt concentration were executed to strip water and counterions using the MM-GBSA method [35,36] . Analyzing data and graphs were implemented applying GraphPad Prism Version 9.3.1 (GraphPad Software Inc., San Diego, CA; www.graphpad.com). ...
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An accurate prediction of the ligand-receptor binding free energies (ΔG) is a critical step in the early stages of rational drug design. The Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method is a popular approach to estimate ΔG. However, correlations between the predicted and the experimental ΔG are variable. The goal of this study is to investigate various approaches to optimize accuracy of the MM-GBSA method. A molecular dynamic (MD) simulations protocol was applied using penicillopepsin receptor against its inhibitor ligands, repeated 50 times for each complex system. After that, ΔG of the five inhibitors were predicted using MM-GBSA method. Moreover, a diverse ΔG values were calculated from the replicate MD simulations of each system. The results were showed correlations not only between the predicted and the experimental binding affinities of the systems but also between the predicted values and root-mean-square deviation. In addition, statistical analysis was evaluated the sample size.
... For this purpose, we selected a test set (a, b, c, d, e, and f, Figure 5C) of six lipid kinases, PI4KIIIβ inhibitors, whose bioactivities (IC 50 ) are considerably different from each other. 69 For the ligand c, the crystal structure of PI4KIIIβ in complex with c was available (PDB id: 4D0L). 70 As such, the hydrophilicity and hydrophobicity of protein pocket ( Figure 5A) and the interactions of c with the important residues of the binding pocket ( Figure 5B) were analyzed first. ...
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Accurate prediction of protein–ligand binding free energies is important in enzyme engineering and drug discovery. The molecular mechanics/generalized Born surface area (MM/GBSA) approach is widely used to estimate ligand-binding affinities, but its performance heavily relies on the accuracy of its energy components. A hybrid strategy combining MM/GBSA and machine learning (ML) has been developed to predict the binding free energies of protein–ligand systems. Based on the MM/GBSA energy terms and several features associated with protein–ligand interactions, our ML-based scoring function, GXLE, shows much better performance than MM/GBSA without entropy. In particular, the good transferability of the GXLE model is highlighted by its good performance in ranking power for prediction of the binding affinity of different ligands for either the docked structures or crystal structures. The GXLE scoring function and its code are freely available and can be used to correct the binding free energies computed by MM/GBSA.
... Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA) [42,43] are two fast and reliable approaches to measure binding ability of inhibitors to proteins. Moreover, these two methods have obtained great success in insights into ligand-receptor association [43,[65][66][67][68][69]. Hou's group evaluated and compared these two methods, the MM-GBSA method shows a more favourable efficiency than MM-PBSA [70][71][72][73]. ...
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Cyclin-dependent kinase 2 (CDK2) has been regarded as a promising drug target for anti-tumour agents. In this study, molecular dynamics (MD) simulations and principal component (PC) analysis were used to explore binding mechanism of three inhibitors 1PU, CDK, 50Z to CDK2 and influences of their bindings on conformational changes of CDK2. The results show that bindings of inhibitors yield obvious impacts on internal dynamics, movement patterns and conformational changes of CDK2. In addition, molecular mechanics generalized Born surface area (MM-GBSA) was applied to calculate binding free energies between three inhibitors and CDK2 and evaluate their binding ability to CDK2. The results show that CDK has the strongest binding to CDK2 among the current three inhibitors. Residue-based free energy decomposition method was further utilized to decode the contributions of a single residue to binding of inhibitors, and it was found that three inhibitors not only produce hydrogen bonding interactions and hydrophobic interactions with key residues of CDK2, which promotes binding of three inhibitors to CDK2, but also share similar binding modes. This work is expected to be helpful for design of efficient drugs targeting CDK2.
... Compared to a single long cMD simulation, MRMD simulations can be obtain better sampling efficiency. The different works verify that MRMD simulations obtain more rational results in insights into inhibitor-target binding than a single long cMD simulation [17][18][19][20][21]. ...
... One of the widely accepted approaches to compute binding free energies is MM-GBSA method [82][83][84][85][86][87][88][89]. In our study, binding free energies of inhibitors to BRD4(1) were effectively estimated by means of the MM-GBSA method implemented in AMBER18. ...
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It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were integrated together to uncover binding modes of inhibitors 8P9, 8PU, and 8PX to BRD4(1). The results obtained from binding free energy calculations show that van der Waals interactions act as the main regulator in bindings of inhibitors to BRD4(1). The information stemming from PCA reveals that inhibitor associations extremely affect conformational changes, internal dynamics, and movement patterns of BRD4(1). Residue-based free energy decomposition method was wielded to unveil contributions of independent residues to inhibitor bindings and the data signify that hydrogen bonding interactions and hydrophobic interactions are decisive factors affecting bindings of inhibitors to BRD4(1). Meanwhile, eight residues Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asn140, and Ile146 are recognized as the common hot interaction spots of three inhibitors with BRD4(1). The results from this work are expected to provide a meaningfully theoretical guidance for design and development of effective inhibitors inhibiting of the activity of BRD4.
... However, the conformations sampled by CMD simulations cannot surmount some higher energy barriers during the time evolutions and make the sampled conformations be possibly trapped in a locally minimal space, which will result in an insufficient conformational sampling. The previous researches demonstrated that multiple short molecular dynamics (MSMD) simulations were more efficient in the conformation samplings of proteins than those from a single longer simulation [49][50][51][52][53][54][55]. Therefore, a more reliable conformational sampling on the inhibitor-BRD complexes performed by using MSMD simulations may provide significant dynamics information at atomic levels for design of potent inhibitors targeting BRDs. ...
Article
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Emerging evidences indicate bromodomain-containing proteins 2 and 4 (BRD2 and BRD4) play critical roles in cancers, inflammations, cardiovascular diseases and other pathologies. Multiple short molecular dynamics (MSMD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were applied to investigate the binding selectivity of three inhibitors 87D, 88M and 89G towards BRD2 over BRD4. The root-mean-square fluctuation (RMSF) analysis indicates that the structural flexibility of BRD4 is stronger than that of BRD2. Moreover the calculated distances between the Cα atoms in the centres of the ZA_loop and BC_loop of BRD4 are also bigger than that of BRD2. The rank of binding free energies calculated using MM-GBSA method agrees well with that determined by experimental data. The results show that 87D can bind more favourably to BRD2 than BRD4, while 88M has better selectivity on BRD4 over BRD2. Residue-based free-energy decomposition method was utilized to estimate the inhibitor-residue interaction spectrum and the results not only identify the hot interaction spots of inhibitors with BRD2 and BRD4, but also demonstrate that several common residues, including (W370, W374), (P371, P375), (V376, V380) and (L381, L385) belonging to (BRD2, BRD4), generate significant binding difference of inhibitors to BRD2 and BRD4.
... Conventional molecular dynamics (cMD) simulations [34][35][36][37][38][39][40][41][42][43] and binding free energy calculations [44][45][46][47][48][49][50][51][52][53][54] have evolved into universal approaches for investigating the conformational changes and binding mechanisms of proteins; further, certain works have successfully investigated the binding selectivity of inhibitors to homologous proteins with high sequence identity. 47,[55][56][57][58] In fact, these two simulation methods have been used to study the binding modes of inhibitors toward FABPs. For example, Hsu et al. combined cMD simulations and the molecular docking method to investigate the binding mechanisms of SBFI-26 toward FABP5 and FABP7; their results reveal two binding poses of SBFI-26 in its target transporters. ...
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The Fatty acid binding protein 5 and 7 (FABP5 and FABP7) have been regarded as the prospective targets for clinically treating multiple diseases relating with FABPs recently. In this work, multiple short molecular dynamics (MSMD) simulations followed by binding free energy calculations were performed to explore binding selectivity of three inhibitors 65X, 8KS and 5M8 to FABP5 and FABP7. The RMSF analysis suggests that the structural flexibility of FABP5 is stronger than that of FABP7, moreover the calculated molecular surface area of FABP5 are also bigger than that of FABP7. Meanwhile, the results from the cross-correlation analysis show that inhibitor bindings exert different impacts on internal dynamics of FABP5 and FABP7. Binding free energies predicted by molecular mechanics generalized Born surface area (MM-GBSA) method indicate that the increase of the enthalpy changes caused by bindings of inhibitors to FABP7 relative to FABP5 mostly drives binding selectivity of inhibitors toward FABP5 versus FABP7. Hierarchical clustering analysis based on energetic contributions of separate residues and calculations of residue-based free energy decompositions were carried out by using the equilibrated MSMD trajectories. The results not only recognize the hot interaction spots of inhibitors with FABP5 and FABP7, but also display that several common residues, including (T56, T54), (L60, F58), (E75, E73), (A76, A78), (D79, D77), (R81, R79), (R107, R109), (C120, L118) and (R129, R127) belonging to (FABP5, FABP7), generate obvious binding difference of inhibitors to FABP5 and FABP7, suggesting that these residues play significant roles in binding selectivity of inhibitors toward FABP5 and FABP7.
... In this work, to explore effect of binding of zinc ions on conformation changes of SPM-1, three systems, including SPM-1 without zinc ions (free SPM), SPM-1 with single zinc ion and double zinc ions, were chosen to realize our aims. Despite great success of molecular dynamics (MD) simulations in investigating conformational changes of targets caused by ligand bindings (Chen et al., 2019c;De Oliveira dos Santos Soares, Bortot, van der Spoel, & Caliri, 2017;Fischer, van der Spoel, Polêto, & Steuer, 2018;Guo, Han, Luo, & Chen, 2017;Hou, Zhang, Wang, & Wang, 2009;Hu, Ma, & Wang, 2017;Lou, Li, & Han, 2015;Peng et al., 2018;Shi et al., 2018;Song, Luo, & Chen, 2017;Song et al., 2019;Srinivasan & Rajasekaran, 2018;Sun et al., 2014;Tian et al., 2019;Tu et al., 2019;Yang, Zhang, & Han, 2010;Zhang et al., 2017;Zhao, Dong, & Zheng, 2018), conventional MD (cMD) simulations possibly make the simulated conformations fall into local minimum space, which will lead to insufficient conformational sampling. Compared to cMD simulations, replica-exchange molecular dynamics (REMD) simulations, including temperature-replica exchange molecular dynamics (REMD) (Jiang & Roux, 2010;Jiang, Thirman, Jo, & Roux, 2018;Patriksson & van der Spoel, 2008) and replica exchange with solute tempering (REST) (Cole, Tirado-Rives, & Jorgensen, 2014;Huang et al., 2007;Liu, Kim, Friesner, & Berne, 2005;Terakawa, Kameda, & Takada, 2011;Wang, Friesner, & Berne, 2011), can efficiently improve the conformational sampling. ...
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Bromodomain-containing protein 4 (BRD4) plays an important role in mediating gene transcription involved in cancers and non-cancer diseases such as acute heart failure and inflammatory diseases. In this work, multiple short molecular dynamics (MSMD) simulations are integrated with a molecular mechanics generalized Born surface area (MM-GBSA) approach to decipher binding selectivity of three inhibitors 8NS, 82Y, and 837 toward two domains BD1 and BD2 of BRD4. The results demonstrate that the enthalpy effects play critical roles in selectivity identification of inhibitors toward BD1 and BD2, determining that 8NS has better selectivity toward BD2 than BD1, while 82Y and 837 more favorably bind to BD1 than BD2. A residue-based free-energy decomposition method was used to calculate an inhibitor–residue interaction spectrum and unveil contributions of separate residues to binding selectivity. The results identify six common residues, containing (P82, P375), (V87, V380), (L92, L385), (L94, L387), (N140, N433), and (I146, V439) individually belonging to (BD1, BD2) of BRD4, and yield a considerable binding difference of inhibitors to BD1 and BD2, suggesting that these residues play key roles in binding selectivity of inhibitors toward BD1 and BD2 of BRD4. Therefore, these results provide useful dynamics information and a structure affinity relationship for the development of highly selective inhibitors targeting BD1 and BD2 of BRD4.
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Probing molecular mechanism of conformational transformation for two switch domains of H-Ras is of significance for understanding function of H-Ras. Molecular dynamics (MD) simulation, free energy landscapes (FELs) and autocorrelation function were integrated to explore mutation-mediated effect on conformational transformation of two switch domains in the GNP-bound Y137E and Y137F H-Ras. The results suggest that Y137E and Y137F changes free energy profiles of the GNP-associated H-Ras, tune motion correlations between GNP and residues as well as weaken binding of GNP to H-Ras. Thus, point mutations of residues can be used as a possible scheme to tune the activity of H-Ras.
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Recently, bromodomain-containing protein 9 (BRD9) has been a prospective therapeutic target for anticancer drug design. Molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were adopted to explore binding modes of three inhibitors (5SW, 5U2, and 5U6) to BRD9 and identify the hot spot of the inhibitor-BRD9 binding. The results indicate that the inhibitor 5SW has the strongest binding ability to BRD9 among the current three inhibitors. Furthermore, the rank of the binding free energies predicted by MM-GBSA approach agrees with that determined by the experimental values. In addition, inhibitor-residue interactions were computed by using residue-based free-energy decomposition method and the results suggest that residue His42 produces the CH-H interactions, residues Asn100, Ile53 and Val49 produce the CH- π interactions with three inhibitors and Tyr106, Phe45 and Phe44 generate the π-π interactions with inhibitors. Notably, the residue Asn140 forms hydrogen bonding interactions with three inhibitors. This research is expected to provide useful molecular basis and dynamics information at atomic levels for the design of potent inhibitors inhibiting the activity of BRD9.
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It is well known that the interactions of p53 with murine double minute 2 and murine double minute X, namely MDM2 and MDMX, have been significant targets of efficient anti-cancer drug design. In this study, molecular dynamics (MD) simulations, principal component (PC) analysis and binding free energy calculations are combined to recognize binding selectivity of three ligands to MDM2 and MDMX. The binding free energies were estimated by using molecular mechanics generalized Born surface area (MM-GBSA) method and the obtained results display that the increase in the binding enthalpy of three ligands to MDM2 relative to MDMX mainly drives the binding selectivity of them toward MDM2 and MDMX. The information obtained from PC analysis shows that the associations of ligands exert important impacts on internal dynamics of MDM2 and MDMX. Meanwhile, the calculations of residue-based free energy decomposition not only identify the hot interaction spots of ligands with MDM2 and MDMX, but also show the residues (L54, M53), (Y67, Y66), (V93, V92), (H96, P95), (I99, I98) and (Y100, Y99) in (MDM2, MDMX) are responsible for most contributions to the binding selectivity of three ligands toward MDM2 and MDMX. It is believed that this work can provide useful information for design of highly selective and dual inhibitors targeting MDM2 and MDMX. Communicated by Ramaswamy H. Sarma
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ToxIN is a triangular structure formed by three protein toxins (ToxNs) and three specific noncoding RNA antitoxins (ToxIs). To respond to stimuli, ToxI is preferentially degraded, releasing the ToxN. Thus, the dynamic character is essential in the normal function interactions between ToxN and ToxI. Here, equilibrated molecular dynamics (MD) simulations were performed to study the stability of ToxN and ToxI. The results indicate that ToxI adjusts the conformation of 3′ and 5′ termini to bind to ToxN. Steered molecular dynamics (SMD) simulations combined with the recently developed thermodynamic integration in 3nD (TI3nD) method were carried out to investigate ToxN unbinding from the ToxIN complex. The potentials of mean force (PMFs) and atomistic pictures suggest the unbinding mechanism as follows: (1) dissociation of the 5′ terminus from ToxN, (2) missing the interactions involved in the 3′ terminus of ToxI without three nucleotides (G31, A32, and A33), (3) starting to unfold for ToxI, (4) leaving the binding package of ToxN for three nucleotides of ToxI, (5) unfolding of ToxI. This work provides information on the structure-function relationship at the atomistic level, which is helpful for designing new potent antibacterial drugs in the future.
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Designing highly selective inhibitors of fatty acid binding proteins 4 and 5 (FABP4 and FABP5) is of importance for treatment of some diseases related with inflammation, metabolism, and tumor growth. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were performed to probe binding selectivity of three inhibitors (5M7, 65X, and 65Z) to FABP4/FABP5 with Ki values of 0.022/0.50 μM, 0.011/0.086 μM, and 0.016/0.12 μM, respectively. The results not only suggest that all inhibitors associate more tightly with FABP4 than FABP5, but also prove that the main forces driving the selective bindings of inhibitors to FABP4 and FABP5 stem from the difference in the van der Waals interactions and polar interactions of inhibitors with two proteins. Meanwhile, a residue-based free energy decomposition method was applied to reveal molecular basis that inhibitors selectively interact with individual residues of two different proteins. The calculated results show that the binding difference of inhibitors to the residues (Phe16, Phe19), (Ala33, Gly36), (Phe57, Leu60), (Ala75, Ala78), (Arg126, Arg129), and (Tyr128, Tyr131) in (FABP4, FABP5) drive the selectivity of inhibitors toward FABP4 and FABP5. This study will provide great help for further design of effective drugs to protect against a series of metabolic diseases, arteriosclerosis, and inflammation.
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Selective modulation of individual bromodomains (BDs) by small molecules represents an important strategy for the treatment of various cancers, considering that the BD-containing proteins share common BD structures and distinct pharmacological functions. Small molecule inhibitors targeting BDs outside of bromodomain and extraterminal domain (BET, including BRD2-4 and BRDT) family are particularly lacking. A small molecule CBP30 exhibited excellent selectivity for the transcriptional coactivators CBP (CREB binding protein) and p300 bromodomains, and provided new opportunity for designing selective non-BET inhibitors. Here, we performed classical molecular dynamics (cMD) and metadynamics simulations to reveal the selective mechanism of CBP30 binding with CBP/p300 and BRD4-BD1/BD2 bromodomains. The cMD simulation combined with binding free energy calculations were performed to compare the overall features of CBP30 binding to CBP/p300 and BRD4-BD1/BD2 bromodomains. Arg1173/1137, as a unique residue for CBP/p300, had strong interactions with the ring B of CBP30, and was responsible for their selective binding via cation-π and hydrogen bond interactions. Metadynamics simulation, together with unbinding free energy profiles, suggested that the dissociation pathways of CBP30 from CBP/p300 and BRD4-BD1/BD2 bromodomains were different, with the unbinding of the former more difficult. These findings will be helpful for novel CBP/p300-inhibitor design and rational structural modification of existing inhibitors to increase their selectivity.
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Phosphatidylinositol 4-kinase IIIβ is a cellular lipid kinase pivotal to pathogenesis of various RNA viruses. These viruses hijack the enzyme in order to modify the structure of intracellular membranes and use them for the construction of functional replication machinery. Selective inhibitors of this enzyme are potential broad-spectrum antiviral agents, as inhibition of this enzyme results in the arrest of replication of PI4K IIIβ-dependent viruses. Herein, we report a detailed study of novel selective inhibitors of PI4K IIIβ, which exert antiviral activity against a panel of single-stranded positive-sense RNA viruses. Our crystallographic data show that the inhibitors occupy the binding site for the adenine ring of the ATP molecule and therefore prevent the phosphorylation reaction.
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How to recruit membrane trafficking machinery PI4KIIIβ is a lipid kinase that underlies Golgi function and is enlisted in biological responses that require rapid delivery of membrane vesicles, such as during the extensive membrane remodeling that occurs at the end of cell division. Burke et al. determined the structure of PI4KIIIβ in a complex with the membrane trafficking GTPase Rab11a. The way in which the proteins interact gives PI4KIIIβ the ability to simultaneously recruit Rab11a and its effectors on specific membranes. Science , this issue p. 1035
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The treatment of chronic hepatitis C virus (HCV) infection has the potential to change significantly over the next few years as therapeutic regimens are rapidly evolving. However, the burden of chronic infection has not been quantified at the global level using the most recent data. Updated estimates of HCV prevalence, viremia and genotypes are critical for developing strategies to manage or eliminate HCV infection. To achieve this, a comprehensive literature search was conducted for anti-HCV prevalence, viraemic prevalence and genotypes for all countries. Studies were included based on how well they could be extrapolated to the general population, sample size and the age of the study. Available country estimates were used to develop regional and global estimates. Eighty-seven countries reported anti-HCV prevalence, while HCV viraemic rates were available for fifty-four countries. Total global viraemic HCV infections were estimated at 80 (64-103) million infections. Genotype distribution was available for ninety-eight countries. Globally, genotype 1 (G1) was the most common (46%), followed by G3 (22%), G2 (13%), and G4 (13%). In conclusion, the total number of HCV infections reported here are lower than previous estimates. The exclusion of data from earlier studies conducted at the peak of the HCV epidemic, along with adjustments for reduced prevalence among children, are likely contributors. The results highlight the need for more robust surveillance studies to quantify the HCV disease burden more accurately.
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Human rhinovirus type C (HRV-C) is a newly discovered enterovirus species frequently associated with exacerbation of asthma and other acute respiratory conditions. Until recently, HRV-C could not be propagated in vitro, hampering in-depth characterization of the virus replication cycle and preventing efficient testing of antiviral agents. Herein we describe several sub-genomic RNA replicon systems and a cell culture infectious model for HRV-C that can be used for antiviral screening. The replicon constructs consist of genome sequences from HRVc15, HRVc11, HRVc24, and HRVc25 strains, with the P1 capsid region replaced by a Renilla luciferase coding sequence. Following the replicon RNA transfection into HeLa cells, the constructs produced time-dependent increases in luciferase signal that can be inhibited in a dose-dependent manner by known inhibitors of HRV replication including the 3C protease inhibitor rupintrivir, nucleoside analog inhibitor MK-0608, and PI4-IIIβ kinase inhibitor PIK93. Furthermore, with the exception of pleconaril and pirodavir, the other tested classes of HRV inhibitors blocked the replication of full length HRVc15 and HRVc11 viruses in human airway epithelial cells (HAEs) differentiated in air liquid interface, exhibiting antiviral activities similar to those observed with HRV-16. In summary, this study is the first comprehensive profiling of multiple classes of antivirals against HRV-C and the set of newly developed quantitative HRV-C antiviral assays represent indispensable tools for the identification and evaluation of novel pan-serotype HRV inhibitors.
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The lipid kinase phosphatidylinositol 4-kinase III alpha (PI4KIIIα) is an essential host factor of hepatitis C virus (HCV) replication. PI4KIIIα catalyzes the synthesis of phosphatidylinositol 4-phosphate (PI4P) accumulating in HCV replicating cells due to enzyme activation resulting from its interaction with nonstructural protein 5A (NS5A). This study describes the interaction between PI4KIIIα and NS5A and its mechanistic role in viral RNA replication. We mapped the NS5A sequence involved in PI4KIIIα interaction to the carboxyterminal end of domain 1 and identified a highly conserved PI4KIIIα functional interaction site (PFIS) encompassing seven amino acids, which are essential for viral RNA replication. Mutations within this region were also impaired in NS5A-PI4KIIIα binding, reduced PI4P levels and altered the morphology of viral replication sites, reminiscent to the phenotype observed by silencing of PI4KIIIα. Interestingly, abrogation of RNA replication caused by mutations in the PFIS correlated with increased levels of hyperphosphorylated NS5A (p58), indicating that PI4KIIIα affects the phosphorylation status of NS5A. RNAi-mediated knockdown of PI4KIIIα or pharmacological ablation of kinase activity led to a relative increase of p58. In contrast, overexpression of enzymatically active PI4KIIIα increased relative abundance of basally phosphorylated NS5A (p56). PI4KIIIα therefore regulates the phosphorylation status of NS5A and viral RNA replication by favoring p56 or repressing p58 synthesis. Replication deficiencies of PFIS mutants in NS5A could not be rescued by increasing PI4P levels, but by supplying functional NS5A, supporting an essential role of PI4KIIIα in HCV replication regulating NS5A phosphorylation, thereby modulating the morphology of viral replication sites. In conclusion, we demonstrate that PI4KIIIα activity affects the NS5A phosphorylation status. Our results highlight the importance of PI4KIIIα in the morphogenesis of viral replication sites and its regulation by facilitating p56 synthesis.
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RNA viruses can rapidly mutate and acquire resistance to drugs that directly target viral enzymes, which poses serious problems in a clinical context. Therefore, there is a growing interest in the development of antiviral drugs that target host factors critical for viral replication, since they are unlikely to mutate in response to therapy. We recently demonstrated that phosphatidylinositol-4-kinase IIIβ (PI4KIIIβ) and its product phosphatidylinositol-4-phosphate (PI4P) are essential for replication of enteroviruses, a group of medically important RNA viruses including poliovirus (PV), coxsackievirus, rhinovirus, and enterovirus 71. Here, we show that enviroxime and GW5074 decreased PI4P levels at the Golgi complex by directly inhibiting PI4KIIIβ. Coxsackievirus mutants resistant to these inhibitors harbor single point mutations in the non-structural protein 3A. These 3A mutations did not confer compound-resistance by restoring the activity of PI4KIIIβ in the presence of the compounds. Instead, replication of the mutant viruses no longer depended on PI4KIIIβ, since their replication was insensitive to siRNA-mediated depletion of PI4KIIIβ. The mutant viruses also did not rely on other isoforms of PI4K. Consistently, no high level of PI4P could be detected at the replication sites induced by the mutant viruses in the presence of the compounds. Collectively, these findings indicate that through specific single point mutations in 3A, CVB3 can bypass an essential host factor and lipid for its propagation, which is a new example of RNA viruses acquiring resistance against antiviral compounds, even when they directly target host factors.Cell Research advance online publication 4 September 2012; doi:10.1038/cr.2012.129.
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Type III phosphatidylinositol-4-kinase beta (PI4KIIIβ) was previously implicated in hepatitis C virus (HCV) replication by small interfering RNA (siRNA) depletion and was therefore proposed as a novel cellular target for the treatment of hepatitis C. Medicinal chemistry efforts identified highly selective PI4KIIIβ inhibitors that potently inhibited the replication of genotype 1a and 1b HCV replicons and genotype 2a virus in vitro. Replicon cells required more than 5 weeks to reach low levels of 3- to 5-fold resistance, suggesting a high resistance barrier to these cellular targets. Extensive in vitro profiling of the compounds revealed a role of PI4KIIIβ in lymphocyte proliferation. Previously proposed functions of PI4KIIIβ in insulin secretion and the regulation of several ion channels were not perturbed with these inhibitors. Moreover, PI4KIIIβ inhibitors were not generally cytotoxic as demonstrated across hundreds of cell lines and primary cells. However, an unexpected antiproliferative effect in lymphocytes precluded their further development for the treatment of hepatitis C.
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A numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated. The relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration. The method is applied to a molecular dynamics simulation of a liquid of 64 n-butane molecules and compared to a simulation using generalized coordinates. The method should be useful for molecular dynamics calculations on large molecules with internal degrees of freedom.
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The activity of phosphatidylinositol 4-kinase class III beta (PI4KIIIβ) has been shown to be required for the replication of multiple picornaviruses; however, it is unclear whether a physical association between PI4KIIIβ and the viral replication machinery exists and, if it does, whether association is necessary. We examined the ability of the 3A protein from 18 different picornaviruses to form a complex with PI4KIIIβ by affinity purification of Strep-Tagged transiently transfected constructs followed by mass spectrometry and Western blotting for putative interacting targets. We found that the 3A proteins of Aichi virus, bovine kobuvirus, poliovirus, coxsackievirus B3, and human rhinovirus 14 all copurify with PI4KIIIβ. Furthermore, we found that multiple picornavirus 3A proteins copurify with the Golgi adaptor protein acyl coenzyme A (acyl-CoA) binding domain protein 3 (ACBD3/GPC60), including those from Aichi virus, bovine kobuvirus, human rhinovirus 14, poliovirus, and coxsackievirus B2, B3, and B5. Affinity purification of ACBD3 confirmed interaction with multiple picornaviral 3A proteins and revealed the ability to bind PI4KIIIβ in the absence of 3A. Mass-spectrometric analysis of transiently expressed Aichi virus, bovine kobuvirus, and human klassevirus 3A proteins demonstrated that the N-terminal glycines of these 3A proteins are myristoylated. Alanine-scanning mutagenesis along the entire length of Aichi virus 3A followed by transient expression and affinity purification revealed that copurification of PI4KIIIβ could be eliminated by mutation of specific residues, with little or no effect on recruitment of ACBD3. One mutation at the N terminus, I5A, significantly reduced copurification of both ACBD3 and PI4KIIIβ. The dependence of Aichi virus replication on the activity of PI4KIIIβ was confirmed by both chemical and genetic inhibition. Knockdown of ACBD3 by small interfering RNA (siRNA) also prevented replication of both Aichi virus and poliovirus. Point mutations in 3A that eliminate PI4KIIIβ association sensitized Aichi virus to PIK93, suggesting that disruption of the 3A/ACBD3/PI4KIIIβ complex may represent a novel target for therapeutic intervention that would be complementary to the inhibition of the kinase activity itself.
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4-anilino quinazolines have been identified as inhibitors of HCV replication. The target of this class of compounds was proposed to be the viral protein NS5A, although unequivocal proof has never been presented. A 4-anilino quinazoline moiety is often found in kinase inhibitors, leading us to formulate the hypothesis that the anti-HCV activity displayed by these compounds might be due to inhibition of a cellular kinase. Type III phosphatidylinositol 4-kinase α (PI4KIIIα) has recently been identified as a host factor for HCV replication. We therefore evaluated AL-9, a compound prototypical of the 4-anilino quinazoline class, on selected phosphatidylinositol kinases. AL-9 inhibited purified PI4KIIIα and, to a lesser extent, PI4KIIIβ. In Huh7.5 cells, PI4KIIIα is responsible for the phosphatidylinositol-4 phosphate (PI4P) pool present in the plasma membrane. Accordingly, we observed a gradual decrease of PI4P in the plasma membrane upon incubation with AL-9, indicating that this agent inhibits PI4KIIIα also in living cells. Conversely, AL-9 did not affect the level of PI4P in the Golgi membrane, suggesting that the PI4KIIIβ isoform was not significantly inhibited under our experimental conditions. Incubation of cells expressing HCV proteins with AL-9 induced abnormally large clusters of NS5A, a phenomenon previously observed upon silencing PI4KIIIα by RNA interference. In light of our findings, we propose that the antiviral effect of 4-anilino quinazoline compounds is mediated by the inhibition of PI4KIIIα and the consequent depletion of PI4P required for the HCV membranous web. In addition, we noted that HCV has a profound effect on cellular PI4P distribution, causing significant enrichment of PI4P in the HCV-membranous web and a concomitant depletion of PI4P in the plasma membrane. This observation implies that HCV--by recruiting PI4KIIIα in the RNA replication complex--hijacks PI4P metabolism, ultimately resulting in a markedly altered subcellular distribution of the PI4KIIIα product.
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Enviroxime is an antienterovirus compound that targets viral protein 3A and/or 3AB and suppresses a step in enterovirus replication by unknown mechanism. To date, four antienterovirus compounds, i.e., GW5074, Flt3 inhibitor II, TTP-8307, and AN-12-H5, are known to have similar mutations in the 3A protein-encoding region causing resistance to enviroxime (a G5318A [3A-Ala70Thr] mutation in poliovirus [PV]) and are considered enviroxime-like compounds. Recently, antienterovirus activity of a phosphatidylinositol 4-kinase III beta (PI4KB) inhibitor, PIK93, was reported, suggesting that PI4KB is an important host factor targetable by antienterovirus compounds (N. Y. Hsu et al., Cell 141:799-811, 2010). In this study, we analyzed the inhibitory effects of previously identified enviroxime-like compounds (GW5074 and AN-12-H5) and a newly identified antienterovirus compound, T-00127-HEV1, on phosphoinositide (PI) kinases. We found that T-00127-HEV1 inhibited PI4KB activity with a higher specificity for than other PI kinases, in contrast to GW5074, which had a broad specificity for PI kinases. In contrast, AN-12-H5 showed no inhibitory effect on PI4KB activity and only moderate inhibitory effects on PI 3-kinase activity. Small interfering RNA (siRNA) screening targeting PI kinases identified PI4KB is a target of GW5074 and T-00127-HEV1, but not of AN-12-H5, for anti-PV activity. Interestingly, T-00127-HEV1 and GW5074 did not inhibit hepatitis C virus (HCV) replication, in contrast to a strong inhibitory effect of AN-12-H5. These results suggested that PI4KB is an enterovirus-specific host factor required for the replication process and targeted by some enviroxime-like compounds (T-00127-HEV1 and GW5074) and that enviroxime-like compounds may have targets other than PI kinases for their antiviral effect.
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Generalized Born (GB) models provide a computationally efficient means of representing the electrostatic effects of solvent and are widely used, especially in molecular dynamics (MD). A class of particularly fast GB models is based on integration over an interior volume approximated as a pairwise union of atom spheres-effectively, the interior is defined by a van der Waals rather than Lee-Richards molecular surface. The approximation is computationally efficient, but if uncorrected, allows for high dielectric (water) regions smaller than a water molecule between atoms, leading to decreased accuracy. Here, an earlier pairwise GB model is extended by a simple analytic correction term that largely alleviates the problem by correctly describing the solvent-excluded volume of each pair of atoms. The correction term introduces a free energy barrier to the separation of non-bonded atoms. This free energy barrier is seen in explicit solvent and Lee-Richards molecular surface implicit solvent calculations, but has been absent from earlier pairwise GB models. When used in MD, the correction term yields protein hydrogen bond length distributions and polypeptide conformational ensembles that are in better agreement with explicit solvent results than earlier pairwise models. The robustness and simplicity of the correction preserves the efficiency of the pairwise GB models while making them a better approximation to reality.
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I84V mutation in HIV-1 protease (PR) has produced drug resistance on multiple inhibitors. Thermodynamic integration (TI), solvated interaction energy (SIE) and dynamic analysis were applied to comparatively probe drug-resistant mechanisms of I84V mutation toward four inhibitors. Dynamic analysis suggests that in the I84V mutants the flaps of PR are more flexible and domains near the flaps of PR and residues 84/84′ also change obviously. Binding free energy predictions show I84V mutation mainly drive the decrease in van der Waals interactions of inhibitors with PR. This study is expected to provide theoretical helps for designs of potent inhibitors targeting HIV-1 protease.
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In this work, we developed a computational protocol that employs multiple molecular docking experiments, followed by pose clustering, molecular dynamic simulations (10ns), and energy rescoring to produce reliable 3D models of antibody-carbohydrate complexes. The protocol was applied to 10 carbohydrate-antibody co-complexes and 3 unliganded (apo) antibodies. Pose clustering significantly reduced the number of potential poses. For each system 15 or fewer clusters, out of 100 initial poses, were generated and chosen for further analysis. MD simulations allowed the docked poses to either converge or disperse, and rescoring increased the likelihood that the best-ranked pose was an acceptable pose. This approach is amenable to automation, and can be a valuable aid in determining the structure of antibody-carbohydrate complexes provided there is no major side chain rearrangement or backbone conformational change in the H3 loop of the CDR regions. Further, the basic protocol of docking a small ligand to a known binding site, clustering the results, and performing MD with a suitable force field is applicable to any protein ligand system.
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Significance Phosphoinositide lipids, produced by phosphorylation of the membrane lipid phosphatidylinositol, play essential roles throughout the cell in defining organelle membrane identity and in initiating and mediating cellular signaling processes. Plasma membrane (PM) phosphoinositides, which reside at the interface between the intracellular and extracellular environments, play especially critical roles. The synthesis of all PM phosphoinositides begins with the conversion of phosphatidylinositol to phosphatidylinositol-4-phosphate by the heterotrimeric PI4KIIIα complex. This study reports the high-resolution structure of the PI4KIIIα complex, revealing a large, intricately structured superassembly whose complexity positions it as a major regulatory junction for PM phosphoinositide synthesis. The structure now provides a framework to guide further efforts to understand its regulation.
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The hydrolysis of a β-lactam core ring caused by new Delphi metallo-β-lactamase 1 (NDM-1) with the help of two zinc cofactors induces significant resistance toward β-lactam antibiotics. Molecular dynamics (MD) simulations and the umbrella sampling method are integrated to study the conformational change mechanism of NDM-1 mediated by zinc ion binding. The statistical analyses of interaction contacts of the antibiotic ampicillin (AMP) with residues based on MD trajectories suggest that two Zn ions are essential for maintaining the binding of AMP with NDM-1. Umbrella sampling simulations further reveal that double-Zn coordination exerts strong restriction on the motions of loop L10 relative to loops L3 and L4. Principal component (PC) analysis also demonstrates that zinc ion binding totally inhibits the motion extent of NDM-1 and changes internal motion modes in NDM-1. We expect that the current study can provide significant dynamical information involving conformational changes of NDM-1 for the development of efficient inhibitors to decrease drug resistance of NDM-1 toward antibiotics.
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Phosphatidylinositol 4-kinase IIIβ (PI4KB) is indispensable for the replication of various positive-sense single stranded RNA viruses, which hijack this cellular enzyme to remodel intracellular membranes of infected cells to set up the functional replication machinery. Therefore, the inhibition of this PI4K isoform leads to the arrest of viral replication. Here, we report on the synthesis of novel PI4KB inhibitors, which were rationally designed based on two distinct structural types of inhibitors that bind in the ATP binding side of PI4KB. These “hybrids” excel not only in outstanding inhibitory activity but they also show high selectivity to PI4KB compared to other kinases. Thus, these compounds exert selective nanomolar or even subnanomolar activity against PI4KB as well as profound antiviral effect against hepatitis C virus, human rhinovirus and coxsackievirus B3. Our crystallographic analysis unveiled the exact position of the side chains and explains their extensive contribution to the inhibitory activity.
Article
Protein–protein interactions (PPIs) are fundamental to all biological processes. Recently, the CK2β-derived cyclic peptide (Pc) has been demonstrated to antagonize efficiently CK2α/CK2β interaction and strongly affect the phosphorylation of CK2β-dependent CK2 substrate specificity. The binding affinity of Pc to CK2α is destroyed to different extents by two single-point mutations of Tyr188 to Ala (Y188A) and Phe190 to Ala (F190A), which exert negative effects on the inhibitory activity (IC50) of Pc against CK2α/CK2β interaction from 3.0 μM to 54.0 μM and >>100 μM, respectively. However, the structural influences of Y188A and F190A mutations on the CK2α–Pc complex remain unclear. In this study, comparative molecular dynamic simulations(MD), principal component analysis (PCA), domain cross-correlation map (DCCM) and energy calculations were performed on wild type (WT), Y188A mutant, and F190A mutant systems. Results revealed that the order communications between hydrophobic and polar interactions were essential for CK2α-Pc binding in WT system. In addition to the loss of the hydrogen bond between Gln36 of CK2α and Gly189 of Pc in two mutants, the improper recognition mechanisms occurred through different pathways. These pathways included the weakened hydrophobic interactions in Y188A mutant as well as decreased polar and hydrophobic interactions in F190A mutant. Energy analytical results qualitatively elucidated the instability of two mutants and energetic contributions of the key residues. This study not only revealed the structural mechanisms for the decreased binding affinity of Y188A and F190A mutant CK2α–Pc complexes, but also provided valuable clues for the rational design of CK2α/CK2β subunit interaction inhibitors with high affinity and specificity.
Article
Type III Phosphatidylinositol 4-kinase (PI4KIIIβ) is an essential enzyme in mediating membrane trafficking, and is implicated in a variety of pathogenic processes. It is a key host factor mediating replication of RNA viruses. The design of potent and specific inhibitors of this enzyme will be essential to define its cellular roles, and may lead to novel anti-viral therapeutics. We previously reported the PI4K inhibitor PIK93, and this compound has defined key functions of PI4KIIIβ. However, this compound showed high cross reactivity with class I and III PI3Ks. Using structure-based drug design we have designed novel potent and selective (>1000 fold over class I and class III PI3Ks) PI4KIIIβ inhibitors. These compounds showed anti-viral activity against Hepatitis C Virus. The co-crystal structure of PI4KIIIβ bound to one of the most potent compounds reveals the molecular basis of specificity. This work will be vital in the design of novel PI4KIIIβ inhibitors, which may play significant roles as anti-viral therapeutics.
Article
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
Article
Synthesis and SAR of 2-alkyloxazoles as class III phosphatidylinositol-4-kinase beta (PI4KIIIβ) inhibitors is described. These compounds demonstrate that inhibition of PI4KIIIβ leads to potent inhibition of HCV replication as observed in genotype (GT) 1a and 1b replicon and GT2a JFH1 virus assays in vitro.
Article
The generalized Born (GB) model is one of the fastest implicit solvent models, and it has become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with trade-offs, and many reports in the literature have pointed out weaknesses with GB models. Because the quality of a GB model is heavily affected by empirical parameters used in calculating solvation energy, in this work we have refit these parameters for GB-Neck, a recently developed GB model, in order to improve the accuracy of both the solvation energy and effective radii calculations. The data sets used for fitting are significantly larger than those used in the past. Comparing to other pairwise GB models like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2) has better agreement with Poisson–Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins. Secondary structure preferences are also in much better agreement with those obtained from explicit solvent MD simulations. We also obtain near-quantitative reproduction of experimental structure and thermal stability profiles for several model peptides with varying secondary structure motifs. Extension to nonprotein systems will be explored in the future.
Article
Two series of inhibitors of type III phosphatidylinositol-4-kinase were identified by high throughput screening and optimised to derive probe compounds that independently and selectively inhibit the α- and the β-isoforms with no significant activity towards related kinases in the pathway. In a cellular environment, inhibition of the α- but not the β-subtype led to a reduction in phosphatidylinositol-4-phosphate and phosphatidylinositol-4,5-bisphosphate concentration, causing inhibition of inositol-1-phosphate formation and inhibition of proliferation in a panel of cancer cell lines.
Article
Abstract Phosphatidylinositol lipids are signaling molecules involved in nearly all aspects of cellular regulation. Production of phosphatidylinositol 4-phosphate (PI4P) has long been recognized as one of the first steps in generating poly-phosphatidylinositol phosphates involved in actin organization, cell migration, and signal transduction. In addition, progress over the last decade has brought to light independent roles for PI4P in membrane trafficking and lipid homeostasis. Here, we describe recent advances that reveal the breadth of processes regulated by PI4P, the spectrum of PI4P effectors, and the mechanisms of spatiotemporal control that coordinate crosstalk between PI4P and cellular signaling pathways.
Article
Cytochrome P450 (CYP) 17A1 is a dual-function monooxygenase with a critical role in the synthesis of many human steroid hormones. The enzyme is an important target for the treatment of breast and prostate cancers that proliferate in response to oestrogens and androgens. Despite the ample experimental mutagenesis data, the molecular origin and the structural motifs for the enzymatic activities deficiencies have not been rationalized at the atomic resolution. To this end, we have investigated the effects on structural characteristics and tunnel geometry upon single point mutations in CYP17A1. The MD simulation results combined with PMF calculations and MM-GBSA calculations render an "access mechanism" which encapsulates the effects of mutations on the changes in both structural flexibility and tunnel dynamics, bridging the gap between the theory and the experimentally observed results of enzymatic activity decrease. The underlying molecular mechanism of the heterogeneities in open/closed conformational changes, as well as the wider opening of their respective major tunnels between wt17A1 and two mutants, may be attributed to the closer distances of hydrophobic residues or the disruption of a hydrophobic core. The knowledge of ligand binding characteristics and key residues contributions could guide future experimental and computational work on CYPs so that desirable changes in their enzymatic activities may be achieved. The present study provides important insights into the structure-function relationships of CYP17A1 protein, which could contribute to further understanding about 17-hydroxylase deficiencies and may also improve the understanding of polycystic ovary disease.
Article
Hepatitis C virus (HCV) assembles many host cellular proteins into unique membranous replication structures as a prerequisite for viral replication, and PI4KIIIα is an essential component of these replication organelles. RNA interference of PI4KIIIα results in a breakdown of this replication complex and cessation of HCV replication in Huh-7 cells. PI4KIIIα is a lipid kinase that interacts with the HCV nonstructural 5A protein (NS5A) and enriches the HCV replication complex with its product, phosphoinositol 4-phosphate (PI4P). Elevated levels of PI4P at the endoplasmic reticulum have been linked to HCV infection in the liver of HCV infected patients.1 We investigated if small molecule inhibitors of PI4KIIIα could inhibit HCV replication in vitro. The synthesis and structure-activity relationships associated with the biological inhibition of PI4KIIIα and HCV replication are described. These efforts led directly to identification of quinazolinone 28 that displays high selectivity for PI4KIIIα and potently inhibits HCV replication in vitro.
Article
The pairwise descreening approximation provides a rapid computational algorithm for the evaluation of solute shape effects on electrostatic contributions to solvation energies. In this article we show that solvation models based on this algorithm are useful for predicting free energies of solvation across a wide range of solute functionalities, and we present six new general parametrizations of aqueous free energies of solvation based on this approach. The first new model is based on SM2-type atomic surface tensions, the AM1 model for the solute, and Mulliken charges. The next two new models are based on SM5-type surface tensions, either the AM1 or the PM3 model for the solute, and Mulliken charges. The final three models are based on SM5-type atomic surface tensions and are parametrized using the AM1 or the PM3 model for the solute and CM1 charges. The parametrizations are based on experimental data for a set of 219 neutral solute molecules containing a wide range of organic functional groups and the atom types H, C, N, O, F, P, S, Cl, Br, and I and on data for 42 ions containing the same elements. The average errors relative to experiment are slightly better than previous methods, butsmore significantlysthe computational cost is reduced for large molecules, and the methods are well suited to using analytic derivatives.
Article
An N·log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation of the resulting convolutions using fast Fourier transforms. Timings and accuracies are presented for three large crystalline ionic systems. The Journal of Chemical Physics is copyrighted by The American Institute of Physics.
Article
Analytic expressions for mean squared positions and velocities of a harmonic oscillator are derived for Langevin dynamics algorithms valid in the high and low friction limits, and for the Verlet algorithm. For typical values of the parameters, errors in the positions are small. However, if the velocity is defined by the usual Verlet form, kinetic energies (and therefore calculated temperatures) can be in error by several per cent for the Langevin algorithms. If the Bunger-Brooks-Karplus algorithm is used to calculate positions, a simple redefinition of the velocity results greatly in improved kinetic energies. In addition, due to cancellation of errors in the velocities and the positions, the correct virial is obtained. The effect of including the force derivative in diffusive algorithms is examined. Positional and velocity averages are calculated for the Verlet algorithm for arbitrary initial conditions, and errors in the total energy and virial are analysed. Connection is made with the Langevin algorithms, and it is shown for harmonic oscillators that different definitions of the velocity are required to optimally calculate the temperature, pressure, and total energy, respectively.
Article
The small GTPase ADP-ribosylation factor (ARF) regulates the structure and function of the Golgi complex through mechanisms that are understood only in part, and which include an ability to control the assembly of coat complexes and phospholipase D (PLD). Here we describe a new property of ARF, the ability to recruit phosphatidylinositol-4-OH kinase- and a still unidentified phosphatidylinositol-4-phosphate-5-OH kinase to the Golgi complex, resulting in a potent stimulation of synthesis of phosphatidylinositol-4-phosphate and phosphatidylinositol-4,5-bisphosphate; this ability is independent of its activities on coat proteins and PLD. Phosphatidylinositol-4-OH kinase- is required for the structural integrity of the Golgi complex: transfection of a dominant-negative mutant of the kinase markedly alters the organization of the organelle.
Article
Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.
Article
Because of their wide use in molecular modeling, methods to compute molecular surfaces have received a lot of interest in recent years. However, most of the proposed algorithms compute the analytical representation of only the solvent-accessible surface. There are a few programs that compute the analytical representation of the solvent-excluded surface, but they often have problems handling singular cases of self-intersecting surfaces and tend to fail on large molecules (more than 10,000 atoms). We describe here a program called MSMS, which is shown to be fast and reliable in computing molecular surfaces. It relies on the use of the reduced surface that is briefly defined here and from which the solvent-accessible and solvent-excluded surfaces are computed. The four algorithms composing MSMS are described and their complexity is analyzed. Special attention is given to the handling of self-intersecting parts of the solvent-excluded surface called singularities. The program has been compared with Connolly's program PQMS [M. L. Connolly (1993) Journal of Molecular Graphics, Vol. 11, pp. 139–141] on a set of 709 molecules taken from the Brookhaven Data Base. MSMS was able to compute topologically correct surfaces for each molecule in the set. Moreover, the actual time spent to compute surfaces is in agreement with the theoretical complexity of the program, which is shown to be O[n log(n)] for n atoms. On a Hewlett-Packard 9000/735 workstation, MSMS takes 0.73 s to produce a triangulated solvent-excluded surface for crambin (1crn, 46 residues, 327 atoms, 4772 triangles), 4.6 s for thermolysin (3tln, 316 residues, 2437 atoms, 26462 triangles), and 104.53 s for glutamine synthetase (2gls, 5676 residues, 43632 atoms, 476665 triangles). © 1996 John Wiley & Sons, Inc.
Article
Several RNA viruses have recently been shown to hijack members of the host phosphatidylinositol (PtdIns) 4-kinase (PI4K) family of enzymes. They use PI4K to generate membranes enriched in phosphatidylinositide 4-phosphate (PtdIns4P or PI4P) lipids, which can be used as replication platforms. Viral replication machinery is assembled on these platforms as a supramolecular complex and PtdIns4P lipids regulate viral RNA synthesis. This article highlights these recent studies on the regulation of viral RNA synthesis by PtdIns4P lipids. It explores the potential mechanisms by which PtdIns4P lipids can contribute to viral replication and discusses the therapeutic potential of developing antiviral molecules that target host PI4Ks as a form of panviral therapy.
Article
The Golgi complex is a ribbon-like organelle composed of stacks of flat cisternae interconnected by tubular junctions. It occupies a central position in the endomembrane system as proteins and lipids that are synthesized in the endoplasmic reticulum (ER) pass through the Golgi complex to undergo biosynthetic modification (mainly glycosylation) and to be sorted to their final destinations. In addition the Golgi complex possesses a number of activities, apparently not directly connected with its main role in trafficking and sorting, which have been recently reviewed in Wilson et al. 2011. In spite of the constant massive flux of material the Golgi complex maintains its identity and phosphoinositides (PIs), among other factors, play a central role in this process. The active metabolism of PIs at the Golgi is necessary for the proper functioning of the organelle both in terms of membrane trafficking/sorting and its manifold metabolic and signalling activities. Phosphatidylinositol 4-phosphate (PtdIns4P), in particular, is responsible for the recruitment of numerous cytosolic proteins that recognise and bind PtdIns4P via specific lipid-binding domains. In this chapter we will summarize the findings that have contributed to our current understanding of the role of PIs in the biology of the Golgi complex in terms of the regulation of PI metabolism and the functional roles and regulation of PtdIns4P effectors.
Article
Parmscan is an automatic engine for force-field parameterization. In this work, we applied both systematic search (SS) and a genetic algorithm (GA) to optimize the force-field parameters (bond length, bond angle, as well as torsional angle terms) to reproduce the relative energies of conformational pairs as well as other molecular properties such as vibrational frequencies. We present an example of how to apply Parmscan to reproduce the relative energies of 11 hydrocarbons by optimizing the torsional parameter of Csp3-Csp3-Csp3-Csp3 using both systematic search and the genetic algorithm. Both of the two methods successfully found the lowest RMS error, which is 0.51 kcal/mol (the unsigned mean error is 0.37 kcal/mol). The Cornell et al. model (Parm94, ref. 21) achieves an RMS error of 0.78 kcal/mol. A second example is the application of the genetic algorithm to optimize the torsional parameter Csp3-O-Csp3-O and bond angle parameter O-Csp3-O simultaneously for 11 dioxanes, to reproduce the experimental relative energies. After 300-400 iterations of GA optimizations, the RMS deviation is reduced to 0.56-0.57 kcal/mol, slightly better than that of Parm99 (ref.22) and much better than that of the Cornell et al. model. In further applications, the bond length and bond angle parameters of hydrocarbons and benzene were optimized to reproduce the experimental vibrational frequencies. Encouraging results were obtained compared to the Cornell et al. force field: for the low vibrational frequencies of ethane, propane, and butane, the new model achieves an unsigned mean error of 19 cm-1, compared to 30 cm-1 of the Cornell et al. model; for 20 vibrational frequencies of benzene, the new model can also give much smaller unsigned mean error (29 vs. 53 cm-1). It seems that after appropriate parameterizations, a simple harmonic molecular model, such as employed in AMBER, can also reproduce lower vibrational frequencies of molecules quite well.
Article
The AM1-BCC method quickly and efficiently generates high-quality atomic charges for use in condensed-phase simulations. The underlying features of the electron distribution including formal charge and delocalization are first captured by AM1 atomic charges for the individual molecule. Bond charge corrections (BCCs), which have been parameterized against the HF/6-31G* electrostatic potential (ESP) of a training set of compounds containing relevant functional groups, are then added using a formalism identical to the consensus BCI (bond charge increment) approach. As a proof of the concept, we fit BCCs simultaneously to 45 compounds including O-, N-, and S-containing functionalities, aromatics, and heteroaromatics, using only 41 BCC parameters. AM1-BCC yields charge sets of comparable quality to HF/6-31G* ESP-derived charges in a fraction of the time while reducing instabilities in the atomic charges compared to direct ESP-fit methods. We then apply the BCC parameters to a small “test set” consisting of aspirin, d-glucose, and eryodictyol; the AM1-BCC model again provides atomic charges of quality comparable with HF/6-31G* RESP charges, as judged by an increase of only 0.01 to 0.02 atomic units in the root-mean-square (RMS) error in ESP. Based on these encouraging results, we intend to parameterize the AM1-BCC model to provide a consistent charge model for any organic or biological molecule. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 132–146, 2000
Article
We describe the development, current features, and some directions for future development of the AMBER package of computer programs. This package has evolved from a program that was constructed to do Assisted Model Building and Energy Refinement to a group of programs embodying a number of the powerful tools of modern computational chemistry-molecular dynamics and free energy calculations.
Article
The phosphoinositides (PIs) are membrane phospholipids that actively operate at membrane-cytosol interfaces through the recruitment of a number of effector proteins. In this context, each of the seven different PI species represents a topological determinant that can establish the nature and the function of the membrane where it is located. Phosphatidylinositol 4-phosphate (PtdIns(4)P) is the most abundant of the monophosphorylated inositol phospholipids in mammalian cells, and it is produced by D-4 phosphorylation of the inositol ring of PtdIns. PtdIns(4)P can be further phosphorylated to PtdIns(4,5)P(2) by PtdIns(4)P 5-kinases and, indeed, PtdIns(4)P has for many years been considered to be just the precursor of PtdIns(4,5)P(2). Over the last decade, however, a large body of evidence has accumulated that shows that PtdIns(4)P is, in its own right, a direct regulator of important cell functions. The subcellular localisation of the PtdIns(4)P effectors initially led to the assumption that the bulk of this lipid is present in the membranes of the Golgi complex. However, the existence and physiological relevance of ;non-Golgi pools' of PtdIns(4)P have now begun to be addressed. The aim of this Commentary is to describe our present knowledge of PtdIns(4)P metabolism and the molecular machineries that are directly regulated by PtdIns(4)P within and outside of the Golgi complex.
Article
Phosphatidylinositol 4-kinases (PI 4-kinases) catalyze the conversion of phosphatidylinositol to phosphatidylinositol 4-phosphate (PtdIns4P). The four known mammalian PI 4-kinases, PI4KA, PI4KB, PI4K2A, and PI4K2B have roles in intracellular lipid and protein trafficking. PI4KA and PI4KB also assist in the replication of several positive-sense RNA viruses. The identification of selective inhibitors of these kinases would be facilitated by assays suitable for high-throughput screening. We describe a homogeneous and nonisotopic assay for PI 4-kinase activity based on the bioluminescent detection of the ADP produced by kinase reactions. We have evaluated this assay with known nonselective inhibitors of PI 4-kinases and show that it performs similar to radiometric assay formats previously described in the literature. In addition, this assay generates Z-factor values of >0.7 for PI4KA in a 384-well format, demonstrating its suitability for high-throughput screening applications.
Article
Hepatitis C virus (HCV) is a major causative agent of chronic liver disease in humans. To gain insight into host factor requirements for HCV replication, we performed a siRNA screen of the human kinome and identified 13 different kinases, including phosphatidylinositol-4 kinase III alpha (PI4KIIIα), as being required for HCV replication. Consistent with elevated levels of the PI4KIIIα product phosphatidylinositol-4-phosphate (PI4P) detected in HCV-infected cultured hepatocytes and liver tissue from chronic hepatitis C patients, the enzymatic activity of PI4KIIIα was critical for HCV replication. Viral nonstructural protein 5A (NS5A) was found to interact with PI4KIIIα and stimulate its kinase activity. The absence of PI4KIIIα activity induced a dramatic change in the ultrastructural morphology of the membranous HCV replication complex. Our analysis suggests that the direct activation of a lipid kinase by HCV NS5A contributes critically to the integrity of the membranous viral replication complex.
Article
The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) and the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods calculate binding free energies for macromolecules by combining molecular mechanics calculations and continuum solvation models. To systematically evaluate the performance of these methods, we report here an extensive study of 59 ligands interacting with six different proteins. First, we explored the effects of the length of the molecular dynamics (MD) simulation, ranging from 400 to 4800 ps, and the solute dielectric constant (1, 2, or 4) on the binding free energies predicted by MM/PBSA. The following three important conclusions could be observed: (1) MD simulation length has an obvious impact on the predictions, and longer MD simulation is not always necessary to achieve better predictions. (2) The predictions are quite sensitive to the solute dielectric constant, and this parameter should be carefully determined according to the characteristics of the protein/ligand binding interface. (3) Conformational entropy often show large fluctuations in MD trajectories, and a large number of snapshots are necessary to achieve stable predictions. Next, we evaluated the accuracy of the binding free energies calculated by three Generalized Born (GB) models. We found that the GB model developed by Onufriev and Case was the most successful model in ranking the binding affinities of the studied inhibitors. Finally, we evaluated the performance of MM/GBSA and MM/PBSA in predicting binding free energies. Our results showed that MM/PBSA performed better in calculating absolute, but not necessarily relative, binding free energies than MM/GBSA. Considering its computational efficiency, MM/GBSA can serve as a powerful tool in drug design, where correct ranking of inhibitors is often emphasized.