Protein-ligand Docking Simulation Research Articles

Inhibitory effect of raspberry ketone on α-glucosidase: Docking simulation integrating inhibition kinetics

Inhibition of α-glucosidase is directly associated with treatment of type 2 diabetes. In this regard, we conducted enzyme kinetics integrated with computational docking simulation to assess the inhibitory effect of raspberry ketone (RK) on α-glucosidase. RK bound to the active site of α-glucosidase and interacted with several key residues such as ASP68, TYR71, HIS111, PHE157, PHE158, PHE177, GLN181, ASP214, THR215, ASP349, ASP408, and ARG439, as detected by protein-ligand docking simulation. Subsequently, we confirmed the action of RK on α-glucosidase as the non-competitive type of inhibition in a reversible and rapidly binding manner. The relevant kinetic parameters were IC50=6.17±0.46mM and Ki=7.939±0.211mM. Regarding the structure-activity relationship, the higher concentration of RK induced slight modulation of the shape of the active site as monitored by hydrophobic exposure. The tertiary conformational change was linked to RK inhibition, and mostly involved regional changes of the active site. Our study provides insight into the functional role of RK due to its structural property of a hydroxyphenyl ring that interacts with the active site of α-glucosidase. We suggest that similar hydroxyphenyl ring compounds targeting the key residues of the active site might be potential α-glucosidase inhibitors.

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations.

We performed protein-ligand docking simulations with a ligand T247, which has been reported as a selective inhibitor of a histone deacetylase HDAC3, by the replica-exchange umbrella sampling method in order to estimate the free energy profiles along ligand docking pathways of HDAC3-T247 and HDAC2-T247 systems. The simulation results showed that the docked state of the HDAC3-T247 system is more stable than that of the HDAC2-T247 system although the amino-acid sequences and structures of HDAC3 and HDAC2 are very similar. By comparing structures obtained from the simulations of both systems, we found the difference between structures of hydrophobic residues at the entrance of the catalytic site. Moreover, we performed conventional molecular dynamics simulations of HDAC3 and HDAC2 systems without T247, and the results also showed the same difference of the hydrophobic structures. Therefore, we consider that this hydrophobic structure contributes to the stabilization of the docked state of the HDAC3-T247 system. Furthermore, we show that Tyr209, which is one of the hydrophobic residues in HDAC2, plays a key role in the instability from the simulation results of a mutated-HDAC2 system.

Inhibitory effect of pyrogallol on α-glucosidase: Integrating docking simulations with inhibition kinetics

In this study we conducted serial kinetic studies integrated with computational simulations to judge the inhibitory effect of pyrogallol on α-glucosidase, due to the association between this enzyme and the treatment of type 2 diabetes. As a result, we found that pyrogallol bound to the active site of α-glucosidase, interacting with several key residues, such as ASP68, MET69, TYR71, PHE157, PHE158, PHE177, GLN181, HIS348, ASP349, ASP406, VAL407, ASP408, ARG439, and ARG443, which was predicted by performing a protein-ligand docking simulation. Subsequently, we evaluated the inhibitory effect of pyrogallol on α-glucosidase, and found that it induced a mixed type of inhibition in a reversible and quick-binding manner. The relevant kinetic parameters were evaluated to be: IC50=0.72±0.051mM; Ki=0.37±0.018mM. A tertiary conformational change was synchronized with pyrogallol inhibition and modulation of the shape of the active site was correspondingly observed. Our study provides insight into the functional inhibitory role of pyrogallol, which results from its triple-hydroxyl groups interacting with the active site of α-glucosidase. We suggest that compounds similar to pyrogallol (phenolic hydroxyl compounds) which target the key residues of the active site of α-glucosidase could be potential agents for α-glucosidase inhibition.

Anti-inflammatory effect of avenanthramides via NF-κB pathways in C2C12 skeletal muscle cells.

Avenanthramides (Avns), the polyphenol compounds found only in oats, have been shown to exhibit anti-inflammatory effects mainly by inhibiting nuclear factor (NF)-κB activation in select cell lines. However, the molecular mechanism by which Avns regulate the NF-κB pathway is still unclear. The purpose of this study was to investigate (1) the molecular mechanism by which three main fractions of Avns (AvnA, AvnB and AvnC) interact with IκB Kinase β (IKKβ); and (2) whether this interaction results in reduced inflammatory responses in skeletal muscle cells. The protein-ligand docking and molecular dynamics simulation studies suggest that Avns acted as an allosteric inhibitor for modulating IKKβ's affinity for the NF-κB complex. Thus, Avns reduced IKKβ kinase activity in response to tert-butyl hydroperoxide (tBHP) stimulation and attenuated tBHP-induced TNFα and IL-1β mRNA expression. Furthermore, the three-fold increases in cyclooxygenase-2 (COX-2) protein and luciferase activity with tBHP treatment were reduced by 50% with Avns (P < .01), along with decreased prostaglandin E2 levels (P < .01). These data indicate that Avns are potent inhibitors of NFκB-mediated inflammatory response due to the downregulation of IKKβ activity in C2C12 cells.

Inhibition of human monoamine oxidase A and B by flavonoids isolated from two Algerian medicinal plants

BackgroundMonoamine oxidases (MAOs) are outer mitochondrial membrane flavoenzymes. They catalyze the oxidative deamination of a variety of neurotransmitters. MAO-A and MAO-B may be considered as targets for inhibitors to treat neurodegenerative diseases and depression and for managing symptoms associated with Parkinson's and Alzheimer's diseases. PurposeThe objective was to evaluate the inhibitory effect of Hypericum afrum and Cytisus villosus against MAO-A and B and to isolate the compounds responsible for the MAO-inhibitory activity. MethodsThe inhibitory effect of extracts and purified constituents of H. afrum and C. villosus were investigated in vitro using recombinant human MAO-A and B, and through bioassay-guided fractionation of ethyl acetate fractions of areal parts of the two plants collected in northeastern Algeria. In addition, computational protein-ligand docking and molecular dynamics simulations were carried out to explain the MAO binding at the molecular level. ResultsThe ethyl acetate (EtOAc) fractions of H. afrum and C. villosus showed the highest MAO inhibition activity against MAO A and B with IC50 values of 3.37 µg/ml and 13.50 µg/ml as well as 5.62 and 1.87 µg/ml, respectively. Bioassay-guided fractionation of the EtOAc fractions resulted in the purification and identification of the known flavonoids quercetin, myricetin, genistein and chrysin as the principal MAO-inhibitory constituents. Their structures were established by extensive 1 and 2D NMR studies and mass spectrometry. Quercetin, myricetin and chrysin showed potent inhibitory activity towards MAO-A with IC50 values of 1.52, 9.93 and 0.25 µM, respectively, while genistein more efficiently inhibited MAO-B (IC50 value: 0.65 µM). The kinetics of the inhibition and the study of dialysis dissociation of the complex of quercetin and myricetin and the isoenzyme MAO-A showed competitive and mixed inhibition, respectively. Both compounds showed reversible binding. Molecular docking experiments and molecular dynamics simulations allowed to estimate the binding poses and to identify the most important residues involved in the selective recognition of molecules in the MAOs enzymatic clefts. ConclusionQuercetin and myricetin isolated from H. afrum together with genistein and chrysin isolated from C. villosus have been identified as potent MAO-A and -B inhibitors. H. afrum and C. villosus have properties indicative of potential neuroprotective ability and may be new candidates for selective MAO-A and B inhibitors.

Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose.

Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine. Here we explore their characteristics that could make them prospective leads for known disease-related proteins. High-throughput virtual screening supported by comprehensive multi-software protein-ligand docking simulation and cheminformatics approaches has been applied in investigation of interactions of 1117 proteins with a 169 fullerene nanoparticles decorated with different small molecules. Moreover, obtained docking results were confirmed by the series of unrestricted all-atom molecular dynamics (MD) simulations. Hydrophobicity of fullerene core along with hydrophilic interaction of side chains plays a key role in binding with the studied proteins. We identified a series of nanoparticles that can lead to development of robust drugs for target proteins and another series that can behave as a highly toxic agent. The structure-activity relationship analysis revealed two significant molecular properties responsible for the binding score values. The application of carefully selected computational techniques and described outcome of the study facilitate development of functional fullerene nanoparticles for drug-like and drug delivery applications.

A novel enzyme based SPR-biosensor to detect bromocriptine as an ergoline derivative drug

In the modern biomedical and therapeutic drug monitoring technology, development of high performance sensing methods for ergoline derivative drug, bromocriptine (BC), is a critical issue due to its plasma low concentration and important function in Parkinson’s disease. The results of the protein-ligand docking simulation consistent with competitive inhibition experimental study strongly support the binding of BC to the laccase active site. Therefore, a new biosensor for direct label-free detection of BC is presented based on surface plasmon resonance (SPR) using laccase from Bacillus sp. HR03 as a recognition element. The biosensor chip surface was constructed by covalent immobilization of the laccase on a SPR carboxymethyl dextran surface. The calculated kinetic affinity (KD) was 5.4nM, which indicated the high affinity between BC and the immobilized laccase. The biosensor could determine BC in a linear detection range from 0.001ng/ml to 1000ng/ml with a lower detection limit of 0.001ng/ml. The biosensor provided acceptable specificity with suitable recovery in simulated blood samples. This new biosensor represents a novel, fast, sensitive, economic cost effective and accurate method for the therapeutic monitoring and detection of the BC.

Using Free Computational Resources To Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted in silico drug design methods, such as molecular geometry optimization, pharmacophore modeling, protein–ligand docking simulations, homology modeling, virtual screening, and pharmacokinetics/toxicity predictions. Freely available software and web servers are selected to compose this pedagogical resource, such that it can be easily implemented in any institution equipped with an Internet connection and Windows OS computers. This material is an illustration of a drug discovery pipeline, starting from the structure of known drugs to obtain novel bioactive compounds, and, therefore, is a valid pedagogical instrument for educating future professionals in the field of drug development.

GANM: A protein–ligand docking approach based on genetic algorithm and normal modes

We describe a new method and a software, called GANM (Genetic Algorithm with Normal Modes), that combines genetic algorithm and normal mode analysis in order to achieve protein–ligand docking simulations that take into account global and local conformational adjustments. The energetical and structural optimization during the ligand binding process is achieved with GA that uses a rotamer library for changing the side chain conformations within and around the binding site. The methodology uses normal modes to account for the global conformational changes of the protein. This software is implemented in distinct versions using different levels of approximations. In this article, we describe the methodology and discuss the results and the performance obtained with the first two versions of GANM. The protein–ligand complexes considered for the test calculations are: (1) Dihydrofolate Reductase (DHFR) and MTX as ligands, (2) HIV-1 Aspartyl Protease with ritonavir, nelfinavir and DMP323 as ligands, and (3) CDK-2 and DT-5 as ligands.

Rotating wall vessel exposure alters protein secretion and global gene expression in Staphylococcus aureus

AbstractStaphylococcus aureus is routinely recovered from air and surface samples taken aboard the International Space Station (ISS) and poses a health threat to crew. As bacteria respond to the low shear forces engendered by continuous rotation conditions in a Rotating Wall Vessel (RWV) and the reduced gravitational field of near-Earth flight by altering gene expression, we examined the effect of low-shear RWV growth on protein secretion and gene expression by three S. aureus isolates. When cultured under 1 g, the total amount of protein secreted by these strains varied up to fourfold; under continuous rotation conditions, protein secretion by all three strains was significantly reduced. Concentrations of individual proteins were differentially reduced and no evidence was found for increased lysis. These data suggest that growth under continuous rotation conditions reduces synthesis or secretion of proteins. A limited number of changes in gene expression under continuous rotation conditions were noted: in all isolates vraX, a gene encoding a polypeptide associated with cell wall stress, was down-regulated. A vraX deletion mutant of S. aureus SH1000 was constructed: no differences were found between SH1000 and ΔvraX with respect to colony phenotype, viability, protein export, antibiotic susceptibility, vancomycin kill kinetics, susceptibility to cold or heat and gene modulation. An ab initio protein–ligand docking simulation suggests a major binding site for β-lactam drugs such as imipenem. If such changes to the bacterial phenotype occur during spaceflight, they will compromise the capacity of staphylococci to cause systemic infection and to circumvent antibacterial chemotherapy.

Docking Simulation and Competitive Experiments Validate the Interaction Between the 2,5-Xylidine Inhibitor and Rigidoporus lignosus Laccase

Laccases are polyphenol oxidases which oxidize a broad range of reducing substrates, preferably phenolic compounds, and their use in biotechnological applications is increasing. Recently, the first X-ray structure of active laccase from white rot fungus Rigidoporus lignosus has been reported containing a full complement of copper ions. Comparison among selected fungal laccases of known 3D structure has shown that the Rigidoporus lignosus laccase has a very high similarity with the Trametes versicolor laccase that, being co-crystallized with 2,5-xylidine, shows a well defined binding pocket for the substrate. Global sequence alignment between Rigidoporus lignosus and Trametes versicolor laccases shows 73% of identity but, surprisingly, there is no identity and neither conservative substitutions between the residues composing the loops directly contacting the 2,5-xylidine. Moreover the structural alignment of these two enzymes identifies in these loops a striking structural similarity proposing the question if 2,5-xylidine may bind in same enzyme pocket. Here we report the protein-ligand docking simulation of 3D structure of Rigidoporus lignosus laccase and 2,5-xylidine. Docking simulation analyses show that spatial conformation of the two 2,5-xylidine binding pockets, despite differences in the residues directly contacting the ligand, may arrange a similar pocket that allows a comparable accommodation of the inhibitor. To validate these results the binding of 2,5-xylidine in the substrate cavity has been confirmed by kinetic competitive experiments.

Exploring sequence space: Profile analysis and protein‐ligand docking to screen ω‐aminotransferases with expanded substrate specificity

omega-Aminotransferase (omegaAT) is an interesting biocatalyst for the preparation of chiral amines, which are widely used as building blocks for pharmaceuticals, agrochemicals and fine chemicals. With the assumption that substrate and sequence spaces are in the process of co-evolution, we explored sequences space to screen the enzymes showing activity to new target compounds. Bacterial genome sequences (n=527) were analyzed by the profiles of subgroups in aminotransferase group II including ornithine aminotransferase (orAT), acetylornithine aminotransferase (aoAT), omegaAT, gamma-aminobutyrate aminotransferase (GABAAT) and 7,8-diaminopelargonate aminotransferase (DAPAAT). We selected the sequences having a Z score of 0-1.8 to guarantee the omegaAT reaction and to avoid the typical omegaAT sequences. Among the selected sequences, we filtered out the sequences with very low Z scores for the rest of four subgroups in aminotransferase group II to consider the diversity. For the selected sequences, we performed protein-ligand docking simulations to predict the docking pose of amino acceptor. Throughout all the analysis procedures, several candidate aminotransferase sequences for the asymmetric synthesis of chiral amines were obtained. An efficient procedure for virtual screening of novel enzymes was demonstrated.

Prenylflavonoids as Nonsteroidal Phytoestrogens and Related Structure–Activity Relationships

In the search for estrogen receptor (ER) modulators, a series of prenylflavonoids were found to be widely distributed amongst tonic herbal medicines and to possess estrogen-like activity in MCF-7/BOS cells, as evaluated by an estrogen-screening assay. Cell-cycle analysis revealed that the stimulatory effects of these compounds toward cell proliferation were elicited at the G1-S checkpoint and could significantly increase the S-phase population of MCF-7 cells under hormone-free conditions. ER-responsive gene (PS2, PgR) and protein (PgR) expression was also detected; mRNA and protein-expression levels for PS2 and PgR were up-regulated by the compounds in a dose-dependent manner. These effects could be inhibited by the pure ER antagonist ICI 182,780 ((7alpha-[9-{4,4,5,5,5-pentafluoropentyl}sulfinyl]nonyl)estra-1,3,5(10)-triene-3,17beta-diol). It was therefore concluded that the estrogen-like effects of these prenylflavonoids were mediated primarily through ERs. Furthermore, to explore the structure-activity relationship based on the estrogen receptor and detailed molecular mechanisms among the prenylflavonoids, protein-ligand docking simulations were carried out by using the DS-MODELING software package. The binding affinity of each prenylflavonoid toward ERalpha was scored, and the receptor-ligand interaction was also analyzed to provide the simulation characteristics of virtual molecular recognition mechanisms.