A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections

We present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.     

Identification of Flavonoids as Putative ROS-1 Kinase Inhibitors Using Pharmacophore Modeling for NSCLC Therapeutics

Non-small cell lung cancer (NSCLC) is a lethal non-immunogenic malignancy and proto-oncogene ROS-1 tyrosine kinase is one of its clinically relevant oncogenic markers. The ROS-1 inhibitor, crizotinib, demonstrated resistance due to the Gly2032Arg mutation. To curtail this resistance, researchers developed lorlatinib against the mutated kinase. In the present study, a receptor-ligand pharmacophore model exploiting the key features of lorlatinib binding with ROS-1 was exploited to identify inhibitors against the wild-type (WT) and the mutant (MT) kinase domain. The developed model was utilized to virtually screen the TimTec flavonoids database and the retrieved drug-like hits were subjected for docking with the WT and MT ROS-1 kinase. A total of 10 flavonoids displayed higher docking scores than lorlatinib. Subsequent molecular dynamics simulations of the acquired flavonoids with WT and MT ROS-1 revealed no steric clashes with the Arg2032 (MT ROS-1). The binding free energy calculations computed via molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) demonstrated one flavonoid (Hit) with better energy than lorlatinib in binding with WT and MT ROS-1. The Hit compound was observed to bind in the ROS-1 selectivity pocket comprised of residues from the β-3 sheet and DFG-motif. The identified Hit from this investigation could act as a potent WT and MT ROS-1 inhibitor.     

基于分子动力学模拟和连续介质模型的自由能计算方法*

近些年,基于分子动力学模拟和连续介质模型的自由能计算方法受到了越来越多的关注,其中MM/PBSA就是最具代表性的方法.在MM/PBSA中,体系的焓变采用分子力学(MM)的方法计算得到;溶剂效应中极性部分对自由能的贡献通过解Poisson-Boltzmann(PB)方程的方法计算得到;溶液效应中非极性部分对自由能的贡献则通过分子表面积(SA)计算得到.本文结合我们科研组的工作,就近几年MM/PBSA方法的最新进展做了较为详细的阐述,同时对MM/PBSA的发展前景进行了展望.     

Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA

In the drug discovery process, accurate methods of computing the affinity of small molecules with a biological target are strongly needed. This is particularly true for molecular docking and virtual screening methods, which use approximated scoring functions and struggle in estimating binding energies in correlation with experimental values. Among the various methods, MM‐PBSA and MM‐GBSA are emerging as useful and effective approaches. Although these methods are typically applied to large collections of equilibrated structures of protein‐ligand complexes sampled during molecular dynamics in water, the possibility to reliably estimate ligand affinity using a single energy‐minimized structure and implicit solvation models has not been explored in sufficient detail. Herein, we thoroughly investigate this hypothesis by comparing different methods for the generation of protein‐ligand complexes and diverse methods for free energy prediction for their ability to correlate with experimental values. The methods were tested on a series of structurally diverse inhibitors of Plasmodium falciparum DHFR with known binding mode and measured affinities. The results showed that correlations between MM‐PBSA or MM‐GBSA binding free energies with experimental affinities were in most cases excellent. Importantly, we found that correlations obtained with the use of a single protein‐ligand minimized structure and with implicit solvation models were similar to those obtained after averaging over multiple MD snapshots with explicit water molecules, with consequent save of computing time without loss of accuracy. When applied to a virtual screening experiment, such an approach proved to discriminate between true binders and decoy molecules and yielded significantly better enrichment curves. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Molecular dynamics study of DNA binding by INT‐DBD under a polarized force field

The DNA binding domain of transposon Tn916 integrase (INT‐DBD) binds to DNA target site by positioning the face of a three‐stranded antiparallel β‐sheet within the major groove. As the negatively charged DNA directly interacts with the positively charged residues (such as Arg and Lys) of INT‐DBD, the electrostatic interaction is expected to play an important role in the dynamical stability of the protein–DNA binding complex. In the current work, the combined use of quantum‐based polarized protein‐specific charge (PPC) for protein and polarized nucleic acid‐specific charge (PNC) for DNA were employed in molecular dynamics simulation to study the interaction dynamics between INT‐DBD and DNA. Our study shows that the protein–DNA structure is stabilized by polarization and the calculated protein–DNA binding free energy is in good agreement with the experimental data. Furthermore, our study revealed a positive correlation between the measured binding energy difference in alanine mutation and the occupancy of the corresponding residue's hydrogen bond. This correlation relation directly relates the contribution of a specific residue to protein–DNA binding energy to the strength of the hydrogen bond formed between the specific residue and DNA. © 2013 Wiley Periodicals, Inc.     

3D-QSAR,docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors

Janus kinase 3 (JAK3) is a promising drug target for the treatment of inflammatory diseases, autoimmune disorders, organ transplant rejection and various cancers. In the present study, 3D-QSAR, docking, MD simulation and MM/PBSA studies were performed on a series of pyrimidine-based JAK3 inhibitors. A reliable COMSIA (q² = 0.717 and r² = 0.986) model was developed and validated using external validation test set, bootstrapping, progressive scrambling and r_m² metrics analyses. Structural requirements identified through contour maps of the model were strategically utilized to computationally design 170 novel JAK3 inhibitors with improved potency. Docking studies were performed on the selected data set and newly designed compounds to show their binding mode and to identify important interacting residues inside the active site of JAK3. In addition, docking results of the selected designed compounds inside the active sites of JAK1, JAK2 and TYK2 indicated their JAK3 selectivity. MD simulation (100 ns) on the docked complex of compound 28 (one of highly active compounds of the data set) assisted in the further exploration of the binding interactions. Some crucial residues like Lys830 (glycine-rich loop), Val836, Ala853, Leu905 (hinge region), Cys909, Asn954, Leu956 and Ala966 were identified. Hydrogen bond interactions with hinge residue Leu905 were critical for the binding of JAK3 inhibitors. Additionally, MM/PBSA calculation provided the binding free energy of the compound 28. Newly designed molecules showed promising results in the preliminary in silico ADMET evaluations. Outcomes of the study can further be exploited to develop potent JAK3 inhibitors.     

Exploring the interaction between 3-D structure of TLR 9 and prostaglandin analogues

Toll-like receptor 9 (TLR9) is a class of pattern recognition receptors (PRRs) approved to have an essential role with the development of autoimmune illnesses such as psoriasis and arthritis. TRL9 is predominantly expressed on dendritic cells (DCs) and macrophages, and it mediates antigen presentation to T cells. In this regard, interfering with this interaction by inhibiting TLR9 could be an effective immunotherapy strategy for certain diseases. Based on previous research (Degraaf et al.2014, Farrugia et al., 2017) indicating that prostaglandins play a significant role in regulating or reducing the expression of TLRs, their function against intracellular TLRs such as TLR9 may involve direct inhibition of these receptors. The 3D structure of the human-TLR9 is modelled and described molecularly and then prepared to be docked by prostaglandin analogues, followed by molecular dynamic (MD) simulation, MM/PBSA analysis, and PCA analysis. The study uncovered significant direct interactions between TLR9 and prostaglandin analogues, specifically with the FDA-approved Bimatoprost (BI), which demonstrates the highest binding affinity (calculated as an estimated affinity) and an interesting MM/PBSA score and should be the primary focus of future research into the treatment of autoimmune diseases. In addition, the modelled structure of human-TLR9 and its binding site described in this study could serve as a useful starting point for the development of additional inhibitors.     

Computational alanine scanning mutagenesis--an improved methodological approach

Alanine scanning mutagenesis of protein-protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot-spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild-type and alanine mutated complexes (DeltaDeltaG(binding)). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm- and hot-spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein-protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations.     

Synergistic effect of polylactic acid(PLA) and Poly(butylene succinate-co-adipate) (PBSA) based sustainable,reactive, super toughened eco-composite blown films for flexible packaging applications

Polylactic acid (PLA)/poly (butylene succinate-co-adipate) (PBSA) based blend films at variable compositions and fixed weight percentage of Epoxy functionalized styrene acrylate (ESA) were prepared using a single step blending process, followed by blown film extrusion process. The morphological studies revealed proper interaction between polymers by the interaction of chain extender (ESA) subsequently improved the mechanical properties of the prepared blown films. Similarly, the blend films showed a decrease in oxygen transmission rate (OTR) and water vapor transmission rate (WVTR) in the order of 60% and 14% as compared with VPLA film. The optical and antislip properties of the blend films also increased considerably. The thermal analysis of the blend films depicted marginal enhancement in the stability of PLA along with heterogeneous nucleation effect in PLA matrix due to the presence of ESA and PBSA.     

Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N

Complexes of two Cyanovirin-N (CVN) mutants, m4-CVN and P51G-m4-CVN, with deoxy di-mannose analogs were employed as models to generate conformational ensembles using explicit water Molecular Dynamics (MD) simulations in solution and in crystal environment. The results were utilized for evaluation of binding free energies with the molecular mechanics Poisson-Boltzmann (or Generalized Born) surface area, MM/PB(GB)SA, methods. The calculations provided the ranking of deoxy di-mannose ligands affinity in agreement with available qualitative experimental evidences. This confirms the importance of the hydrogen-bond network between di-mannose 3'- and 4'-hydroxyl groups and the protein binding site B(M) as a basis of the CVN activity as an effective HIV fusion inhibitor. Comparison of binding free energies averaged over snapshots from the solution and crystal simulations showed high promises in the use of the crystal matrix for acceleration of the conformational ensemble generation, the most time consuming step in MM/PB(GB)SA approach. Correlation between energy values based on solution versus crystal ensembles is 0.95 for both MM/PBSA and MM/GBSA methods.