Study on the binding mode of a pyrrolotriazin derivative with JAK2 by docking and MD simulation

The pyrrolotriazin derivative 2-(4-(4-((7-(3-(N-methylmethylsulfonamido)phenyl)pyrrolo [2,1-f][1,2,4]triazin-2-yl)amino)phenyl)piperidin-1-yl)acetamide (PPA) is a potential Janus kinase 2 (JAK2) inhibitor. The binding mode between PPA and JAK2 was investigated by using a combined method of docking, molecular dynamics (MD) simulation and binding free-energy calculation. The docking calculations preliminarily indicated that there were two possible binding modes 1 and 2; MD simulations and binding free-energy calculations identified that binding mode 1 was more stable and favourable, with the lower MM-PBSA binding free energy of ?34.00?±?0.17?kcal/mol. Moreover, some valuable binding information is revealed as follows: the inhibitor PPA is suitably located at the ATP-binding site of JAK2 and the hydrophobic interaction plays an essential role. PPA not only interacts with residues Leu855, Val863, Ala880, Tyr931, Leu932 and Leu983 via hydrophobic interaction but also interacts with Ser936 and Asp994 by hydrogen bonds. These two factors are advantageous for PPA to strongly bind to JAK2. These results help to understand the action mechanisms and designing new compounds with a higher affinity to JAK2.     

Intermolecular insights into allosteric inhibition of histone lysine-specific demethylase 1

BackgroundHistone lysine-specific demethylase 1 (LSD1) has become a potential anticancer target for the novel drug discovery. Recent reports have shown that SP2509 and its derivatives strongly inhibit LSD1 as allosteric inhibitors. However, the binding mechanism of these allosteric inhibitors in the allosteric site of LSD1 is not known yet.MethodsThe stability and binding mechanism of allosteric inhibitors in the binding site of LSD1 were evaluated by molecular docking, ligand-based pharmacophore, molecular dynamics (MD) simulations, molecular mechanics generalized born surface area (MM/GBSA) analysis, quantum mechanics/molecular mechanics (QM/MM) calculation and Hirshfeld surface analysis.ResultsThe conformational geometry and the intermolecular interactions of allosteric inhibitors showed high binding affinity towards allosteric site of LSD1 with the neighboring amino acids (Gly358, Cys360, Leu362, Asp375 and Glu379). Meanwhile, MD simulations and MM/GBSA analysis were performed on selected allosteric inhibitors in complex with LSD1 protein, which confirmed the high stability and binding affinity of these inhibitors in the allosteric site of LSD1.ConclusionThe simulation results revealed the crucial factors accounting for allosteric inhibitors of LSD1, including different protein–ligand interactions, the positions and conformations of key residues, and the ligands flexibilities. Meanwhile, a halogen bond interaction between chlorine atom of ligand and key residues Trp531 and His532 was recurrent in our analysis confirming its importance.General significanceOverall, our research analyzed in depth the binding modes of allosteric inhibitors with LSD1 and could provide useful information for the design of novel allosteric inhibitors.     

Identifying the novel inhibitors of lysine-specific demethylase 1 (LSD1) combining pharmacophore-based and structure-based virtual screening

Abstract

Lysine-specific demethylase 1 (LSD1) has been reported to connect with a range of solid tumors. Thus, the exploration of LSD1 inhibitors has emerged as an effective strategy for cancer treatment. In this study, we constructed a pharmacophore model based on a series of flavin adenine dinucleotide (FAD)-competing inhibitors bearing triazole???dithiocarbamate scaffold combining docking, structure–activity relationship (SAR) study, and molecular dynamic (MD) simulation. Meanwhile, another pharmacophore model was also constructed manually, relying on several speculated substrate-competing inhibitors and reported putative vital interactions with LSD1. On the basis of the two pharmacophore models, multi-step virtual screenings (VSs) were performed against substrate-binding pocket and FAD-binding pocket, respectively, combining pharmacophore-based and structure-based strategy to exploit novel LSD1 inhibitors. After bioassay evaluation, four compounds among 21 hits with diverse and novel scaffolds exhibited inhibition activity at the range of 3.63–101.43?μM. Furthermore, substructure-based enrichment was performed, and four compounds with a more potent activity were identified. After that, the time-dependent assay proved that the most potent compound with IC₅₀ 2.21?μM inhibits LSD1 activity in a manner of time-independent. In addition, the compound exhibited a cellular inhibitory effect against LSD1 in MGC-803 cells and may inhibit cell migration and invasion by reversing EMT in cultured gastric cancer cells. Considering the binding mode and SAR of the series of compounds, we could roughly deem that these compounds containing 3-methylxanthine scaffold act through occupying substrate-binding pocket competitively. This study presented a new starting point to develop novel LSD1 inhibitors.     

3D-QSAR (CoMFA,CoMSIA), molecular docking and molecular dynamics simulations study of 6-aryl-5-cyano-pyrimidine derivatives to explore the structure requirements of LSD1 inhibitors

Recently, Histone Lysine Specific Demethylase 1 (LSD1) was regarded as a promising anticancer target for the novel drug discovery. And several small molecules as LSD1 inhibitors in different structures have been reported. In this work, we carried out a molecular modeling study on the 6-aryl-5-cyano-pyrimidine fragment LSD1 inhibitors using three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. The results show that the best CoMFA model has q² = 0.802, r²_ncv = 0.979, and the best CoMSIA model has q² = 0.799, r²_ncv = 0.982. The electrostatic, hydrophobic and H-bond donor fields play important roles in the models. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300 K. All the results can provide us more useful information for our further drug design.     

A computational study of binding between 3-(4-fluorophenyl)-N-((4-fluorophenyl)sulphonyl)acrylamide and tubulin

3-(4-Fluorophenyl)-N-((4-fluorophenyl)sulphonyl)acrylamide (FFSA) is a potential tubulin polymerisation inhibitor. In this article, a theoretical study of the binding between FFSA and tubulin in colchicine site was carried out by molecular docking, molecular dynamics (MD) simulation and binding free energy calculations. The docking calculations preliminarily indicate that there are three possible binding modes 1, 2 and 3; MD simulations and binding free energy calculations identify that binding mode 2 is the most favourable, with the lowest binding free energy of ? 29.54 kcal/mol. Moreover, our valuable results for the binding are as follows: the inhibitor FFSA is suitably located at the colchicine site of tubulin, where it not only interacts with residues Leu248β, Lys254β, Leu255β, Lys352β, Met259β and Val181a by hydrophilic interaction, but also interacts with Val181α and Thr179α by hydrogen bond interaction. These two factors are both essential for FFSA strongly binding to tubulin. These theoretical results help understanding the action mechanism and designing new compounds with higher affinity to tubulin.     

Docking and molecular dynamics study on the inhibitory activity of <Emphasis Type="Italic">N,N</Emphasis>-disubstituted-trifluoro-3-amino-2-propanols-based inhibitors of cholesteryl ester transfer protein

Extensive studies suggest direct links between cholesteryl ester transfer protein (CETP), high-density lipoproteins-cholesterol level and cardiovascular diseases. Many therapeutic approaches are aimed at the CETP. A series of N, N-disubstituted-trifluoro-3-amino-2-propanol analogues are among the most highly potent and selective inhibitors of CETP described to date. For in-depth investigation into the structural and chemical features responsible for exploring the binding pocket of these compounds, as well as for the binding recognition mechanism concerned, we performed a series of automated molecular docking operations. Moreover, the docking results were quite robust as further validated by molecular dynamics. The docking results reveal that the binding site mainly consists of two hydrophobic regions (P1 and P2 site) which are able to accommodate the lipophilic arms of the compounds investigated. Val421 in P1 site and Met194 in P2 site could be considered to be two important residues in forming the two hydrophobic regions. The presence of residues Phe197 and Phe463 in P2 site may be responsible for the binding recognition through π-π stacking interactions. The hydrophobic 3-phenoxy substituent may be important in creating the preferable inhibitive capability for increasing the binding potency. The hydrophobic character of the tetrafluoroethoxybenzyl group at position 3 displays better hydrophobicity than a shorter hydrophobic substituent. An interaction model of CETP-inhibitors is derived that can be successfully used to explain the different biologic activities of these inhibitors. It is anticipated that the findings reported here may provide very useful information or clues for designing effective drugs for the therapeutic treatment of CETP-related cardiovascular diseases.     

Deciphering the crucial molecular properties of a series of Benzothiazole Hydrazone inhibitors that targets anti-apoptotic Bcl-xL protein

The Bcl-2 family proteins are the central regulators of apoptosis. Due to its predominant role in cancer progression, the Bcl-2 family proteins act as attractive therapeutic targets. Recently, molecular series of Benzothiazole Hydrazone (BH) inhibitors that exhibits drug-likeness characteristics, which selectively targets Bcl-xL have been reported. In the present study, docking was used to explore the plausible binding mode of the highly active BH inhibitor with Bcl-xL; and Molecular Dynamics (MD) simulation was applied to investigate the stability of predicted conformation over time. Furthermore, the molecular properties of the series of BH inhibitors were extensively investigated by pharmacophore based 3D-QSAR model. The docking correctly predicted the binding mode of the inhibitor inside the Bcl-xL hydrophobic groove, whereas the MD-based free energy calculation exhibited the binding strength of the complex over the time period. Furthermore, the residue decomposition analysis revealed the major energy contributing residues – F105, L108, L130, N136, and R139 – involved in complex stability. Additionally, a six-featured pharmacophore model – AAADHR.89 – was developed using the series of BH inhibitors that exhibited high survival score. The statistically significant 3D-QSAR model exhibited high correlation co-efficient (R² = .9666) and cross validation co-efficient (Q² = .9015) values obtained from PLS regression analysis. The results obtained from the current investigation might provide valuable insights for rational drug design of Bcl-xL inhibitor synthesis.     

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Designing selective protein kinase B (PKB/Akt) inhibitor is an area of intense research to develop potential anticancer drugs. In the present study, the molecular basis governing PKB-selective inhibition has been investigated using molecular dynamics simulation. The binding free energies calculated by MM/PBSA gave a good correlation with the experimental biological activity and a good explanation of the activity difference of the studied inhibitors. The decomposition of free energies by MM/GBSA indicates that the ethyl group on pyrrolo[2,3-d]pyrimidine ring of inhibitor Lig1 (N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]-methyl}-2,4-difluoro-benzamide) is an important contributor to its PKBα selectivity due to its hydrophobic interaction with the side chain of Thr291 in PKBα. The substituted groups on the pyrrolidine ring of Lig1 also show a strong tendency to mediate protein-ligand interactions through the hydrogen bonds formed between the amino or amide groups of Lig1 and the carboxyl O atoms of Glu234, Glu278, and Asp292 of PKBα. It was reported that there are only three key amino acid differences between PKBα (Thr211, Ala230, Met281) and PKA (Val104, Val123, Leu173) within the clefts of ATP-binding sites. These differences propel a drastic conformational change in PKA, weakening its binding interactions with inhibitor. The impact was also confirmed by MD simulated interaction modes of inhibitor binding to PKBα mutants with the in silico mutations of the three key amino acids, respectively. We expect that the results obtained here could be useful for future rational design of specific ATP-competitive inhibitors of PKBα.     

Design,synthesis and evaluation of γ-turn mimetics as LSD1-selective inhibitors

Lysine-specific demethylase 1 (LSD1) is an attractive molecular target for cancer therapy. We have previously reported potent LSD1-selective inhibitors (i.e., NCD18, NCD38, and their analogs) consisting of trans-2-phenylcyclopropylamine (PCPA) or trans-2-arylcyclopropylamine (ACPA) and a lysine moiety that could form a γ-turn structure in the active site of LSD1. Herein we report the design, synthesis and evaluation of γ-turn mimetic compounds for further improvement of LSD1 inhibitory activity and anticancer activity. Among a series of γ-turn mimetic compounds synthesized by a Mitsunobu-reaction-based amination strategy, we identified 1n as a potent and selective LSD1 inhibitor. Compound 1n induced cell cycle arrest and apoptosis through histone methylation in human lung cancer cells. The γ-turn mimetics approach should offer new insights into drug design for LSD1-selective inhibitors.     

Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies

Abstract

Acetylcholinesterase (AChE) is an important kind of esterase that plays a key biological role in the central and peripheral nervous systems. Recent research has demonstrated that some fullerene derivatives serve as a new nanoscale class of potent inhibitors of AChE, but the specific inhibition mechanism remains unclear. In the present article, several molecular modeling methods, such as molecular docking, molecular dynamics simulations and molecular mechanics/generalized Born surface area calculations, were used for the investigation of the binding mode and inhibition mechanism of fullerene inhibitions for AChE. Results revealed that fullerene inhibitors block the entrance of substrates by binding with the peripheral anionic site (PAS) region. Thus, fullerene derivatives might mainly serve as competitive inhibitors. The interactions of a fullerene backbone with AChE are at the same level in different single side chain systems and seem to be related to the length or aromaticity of the side chain. The inhibitor with multihydroxyl side chains shows an obviously large electrostatic interaction as it forms additional hydrogen bonds with AChE. Moreover, fullerene derivatives might exhibit noncompetitive inhibition partly by affecting some secondary structures around them. Thus, the destructions of these secondary structures can lead to conformational changes in some important regions, such as the catalytic triad and acyl pocket. The investigation is of great importance to the discovery of good fullerene inhibitors.

Communicated by Ramaswamy H. Sarma     

Design,synthesis and in vitro evaluation of stilbene derivatives as novel LSD1 inhibitors for AML therapy

LSD1 is implicated in a number of malignancies and has emerged as an exciting target. As part of our sustained efforts to develop novel reversible LSD1 inhibitors for epigenetic therapy of cancers, in this study, we reported a series of stilbene derivatives and evaluated their LSD1 inhibitory activities, obtaining several compounds as potent LSD1 inhibitors with IC₅₀ values in submicromolar range. Enzyme kinetics studies and SPR assay suggested that compound 8c, the most active LSD1 inhibitor (IC₅₀?=?283?nM), potently inhibited LSD1 in a reversible and FAD competitive manner. Consistent with the kinetics data, molecular docking showed that compound 8c can be well docked into the FAD binding site of LSD1. Flow cytometry analysis showed that compound 8c was capable of up-regulating the expression of the surrogate cellular biomarker CD86 in THP-1 human leukemia cells, suggesting the ability to block LSD1 activity in cells. Compound 8c showed good inhibition against THP-1 and MOLM-13 cells with IC₅₀ values of 5.76 and 8.34?μM, respectively. Moreover, compound 8c significantly inhibited colony formation of THP-1 cells dose dependently.     

Insight into the Enzyme-Inhibitor Interactions of the First Experimentally Determined Human Aromatase

Abstract

Aromatase is an important pharmacological target in the anti-cancer therapy as the intratumoral aromatase is the source of local estrogen production in breast cancer tissues. Suppression of estrogen biosynthesis by aromatase inhibition represents an effective approach for the treatment of hormone-sensitive breast cancer. Because of the membrane-bound character and heme-binding instability, no crystal structure of aromatase was reported for a long time, until recently when crystal structure of human placental aromatase cytochrome P450 in complex with androstenedione was deposited in PDB. The present study is towards understanding the structural and functional characteristics of aromatase to address unsolved mysteries about this enzyme and elucidate the exact mode of binding of aromatase inhibitors. We have performed molecular docking simulation with twelve different inhibitors (ligands), which includes four FDA approved drugs; two flavonoids; three herbal compounds and three compounds having biphenyl motif with known IC₅₀ values into the active site of the human aromatase enzyme. All ligands showed favorable interactions and most of them seemed to interact to hydrophobic amino acids Ile133, Phe134, Phe221, Trp224, Ala306, Val370, Val373, Met374 and Leu477 and hydrophilic Arg115 and neutral Thr310 residues. The elucidation of the actual structure-function relationship of aromatase and the exact binding mode described in this study will be of significant interest as its inhibitors have shown great promise in fighting breast cancer.     

Molecular simulation studies on the binding activity and selectivity of 3-amino-phenyl-5-chloro-pyrimidine-2, 4-diamine derivatives in complexes with kinases c-Met and ALK

Receptor tyrosine kinases c-Met and ALK have been demonstrated to be important therapeutic targets for cancer therapy. However, selectivity and drug resistance could hinder the development of their corresponding inhibitors. In this study, three compounds with similar scaffold were examined to study activity and selectivity mechanism towards c-Met or ALK by utilising a combined approach of computational techniques, including flexible dock, molecular electrostatic potential (MESP) calculations, molecular dynamic (MD) simulation, and binding free-energy calculation. Molecular simulation provides us new chemical insights into steric and electronic complementarities of these inhibitors to target binding sites. The computed binding free energies were consistent with the changing trend of experimental affinities on c-Met and ALK. H-bond with Asp169 and hydrophobic interaction with Phe36 of c-Met, respectively, could be crucial for the binding affinity of an inhibitor binding to c-Met. Meanwhile, for inhibitor–ALK complex, both H-bond interactions with Arg28 and Met101 and hydrophobic interactions with Leu30, Val38, and Leu158 could enhance the bioactivity and selectivity. The present work may provide a structural understanding of molecular mechanism expected to be valuable for the guidelines of the development of new potent c-Met or ALK selective inhibitors.     

Exploring the interaction between human focal adhesion kinase and inhibitors: a molecular dynamic simulation and free energy calculations

Focal adhesion kinase is an important target for the treatment of many kinds of cancers. Inhibitors of FAK are proposed to be the anticancer agents for multiple tumors. The interaction characteristic between FAK and its inhibitors is crucial to develop new inhibitors. In the present article, we used Molecular Dynamic (MD) simulation method to explore the characteristic of interaction between FAK and three inhibitors (PHM16, TAE226, and ligand3). The MD simulation results together with MM-GB/SA calculations show that the combinations are enthalpy-driven process. Cys502 and Asp564 are both essential residues due to the hydrogen bond interactions with inhibitors, which was in good agreement with experimental data. Glu500 can form a non-classical hydrogen bond with each inhibitor. Arg426 can form electrostatic interactions with PHM16 and ligand3, while weaker with TAE226. The electronic static potential was employed, and we found that the ortho-position methoxy of TAE226 has a weaker negative charge than the meta-position one in PHM16 or ligand3. Ile428, Val436, Ala452, Val484, Leu501, Glu505, Glu506, Leu553, Gly563 Leu567, Ser568 are all crucial residues in hydrophobic interactions. The key residues in this work will be available for further inhibitor design of FAK and also give assistance to further research of cancer.     

Induced fit docking,free energy calculation and molecular dynamics studies on Mycobacterium tuberculosis alanine racemase inhibitor

Alar, a Pyridoxal 5′-phosphate (PLP)-dependent bacterial enzyme is responsible for the racemisation of L-alanine into D-alanine which is essential for the peptidoglycan biosynthesis in both Gram-positive and Gram-negative bacteria. In the present study, we performed induced fit docking, binding free energy calculation and molecular dynamics simulation to elucidate the Alar inhibition potential of 1,2,4-thiadiazolidine-3,5-dione-based inhibitor 1. The inhibitor binds to the hydrophobic groove of Alar and the binding was found to be stable throughout 20-ns MD simulation. Induced fit docking result showed that Lys42, Tyr46, Tyr175 and Tyr364 residues are primarily responsible for the stabilisation of inhibitor–protein complex. Further, high negative van der Waals binding free energy value of –38.88 kcal/mol, indicated it as the main driving force for the inhibitor binding. Based on the information obtained from this study, we designed few molecules as potent Alar inhibitor. In order to gain structural insight and to validate the stability of complex, we performed 20-ns MD simulation of the designed molecule D1. Results obtained from this study can be used for the design of M. tuberculosis Alar potent inhibitors lacking affinity for the co-factor PLP.     

Pharmacophore generation,atom-based 3D-QSAR,molecular docking and molecular dynamics simulation studies on benzamide analogues as FtsZ inhibitors

FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant bacterial pathogens. Pharmacophore modelling, molecular docking and molecular dynamics (MD) simulation studies were performed on a series of three-substituted benzamide derivatives. In the present study a five-featured pharmacophore model with one hydrogen bond acceptors, one hydrogen bond donors, one hydrophobic and two aromatic rings was developed using 97 molecules having MIC values ranging from .07 to 957 μM. A statistically significant 3D-QSAR model was obtained using this pharmacophore hypothesis with a good correlation coefficient (R² = .8319), cross validated coefficient (Q² = .6213) and a high Fisher ratio (F = 103.9) with three component PLS factor. A good correlation between experimental and predicted activity of the training (R² = .83) and test set (R² = .67) molecules were displayed by ADHRR.1682 model. The generated model was further validated by enrichment studies using the decoy test and MAE-based criteria to measure the efficiency of the model. The docking studies of all selected inhibitors in the active site of FtsZ protein showed crucial hydrogen bond interactions with Val 207, Asn 263, Leu 209, Gly 205 and Asn-299 residues. The binding free energies of these inhibitors were calculated by the molecular mechanics/generalized born surface area VSGB 2.0 method. Finally, a 15 ns MD simulation was done to confirm the stability of the 4DXD–ligand complex. On a wider scope, the prospect of present work provides insight in designing molecules with better selective FtsZ inhibitory potential.     

New thiopyrimidine-benzenesulfonamide conjugates as selective carbonic anhydrase II inhibitors: synthesis,in vitro biological evaluation,and molecular docking studies

In the present work, a new series of thiopyrimidine-benzenesulfonamide conjugates was designed, synthesized and tested as carbonic anhydrase (CA, EC 4.2.1.1) inhibitors. Our design strategy was based on the molecular hybridization of the benzenesulfonamide moiety as a zinc binding group (ZBG), an alkylated thiopyrimidine moiety as a spacer and (un)substituted phenyl moieties with various electronic and hydrophobic environments as a tail. The designed and synthesized compounds were evaluated against four human (h) CA isoforms hCA I, hCA II, hCA IX and hCA XII. Series 6 showed promising activity and selectivity toward the cytosolic isoforms hCA I and hCA II versus the membrane bound isoforms hCA IX and hCA XII. Compounds 6e and 6f showed K_i of 0.04 µM against hCA II with a selectivity of 15.8- to 980-fold towards hCA II over hCA I, hCA IX, hCA XII isoforms. Molecular docking in the hCA II active site attributed the promising inhibitory activity of series 6 to the interaction of their sulfonamide moiety with the active site Zn²⁺ ion as well as its hydrogen bonding with the key amino acids Thr199 and Thr200. Through hydrophobic interaction, the benzenesulfonamide and the thiopyrimidine moieties interact with the hydrophobic side chains of the amino acids Val121/Leu198 and Ile91/Phe131, respectively. These results indicated that the designed and synthesized series is an interesting scaffold that can be further optimized for the development of selective antiglaucoma drugs.     

Structure prediction and R115866 binding study of human CYP26A1: homology modelling,fold recognition,molecular docking and MD simulations

Two three-dimensional (3D) models of human cytochrome P450 26A1 (CYP26A1) were constructed using the programs Modeller and Sybyl-GeneFold, respectively. After refinement by molecular mechanics and molecular dynamics (MD) simulations, the two models were validated by structure analysis-validation online server. Subsequently, a flexible docking study was performed on the model constructed by GeneFold with the potent and specific inhibitor R115866 to examine the enzyme–inhibitor interactions. From the docking results, we can see R115866 interacts with amino acid residues at the active site by multiple hydrophobic interactions including the side chains of His111, Trp112, Ser115, Val116, Leu125, Ser126, Leu221, Phe222, Glu296, Phe299, Gly300, Glu303, Thr304, Pro371 and the cofactor heme. Trp112 and Thr304 form hydrogen bonds with R115866 and play important roles in stabilising the complex. This constructed CYP26A1 model may provide an opportunity to understand the action mode of the enzyme and could be useful in designing novel retinoic acid metabolism blocking agents (RAMBAs).