Flexible Molecular Docking Research Articles

Screening of terpenoids as potential therapeutics against Zaire ebolavirus infection through pharmacophore-based drug design

Backgroud: Ebola virus disease (EVD) has spread to various countries in the world and has caused many deaths. Five different virus species can cause EVD, but the most virulent is Zaire ebolavirus (EBOV). The genome of EBOV includes seven genes that encode proteins playing essential roles in the virus lifecycle. Among these proteins, VP24 plays a vital role in the inhibition of the host cells’ immune system. Therefore, VP24 is a potential target for EVD therapy. In the present study, a potential inhibitor of EBOV VP24 activity was identified through pharmacophore-based drug design. Methods: This research was a in silico study, using pharmacophore based molecular docking simulation to obtain inhibitor candidates. Result: Terpenoids were used as VP24 inhibitor candidates. In particular, 55,979 terpenoids were obtained from the PubChem database. An initial screening based on the toxicity prediction test was performed with DataWarrior software: 3,353 ligands were shown to have a favorable toxicity profile, but only 1,375 among them had suitable pharmacophore features. These ligands were used for pharmacophore-based rigid and flexible molecular docking simulations with PDB ID: 4M0Q, chosen as the crystal structure of EBOV VP24. Six ligands predicted to have strong molecular interactions with EBOV VP24 underwent pharmacological property analysis through various software packages, including DataWarrior, SwissADME, admetSAR, pkCSM, and Toxtree. Conclusions: Taxumairol V was identified as the best candidate for EVD drug therapy via EBOV VP24 inhibition based on its molecular properties, predicted molecular interactions with the target molecule, and predicted pharmacological properties.

Repurposing of FDA-Approved NSAIDs for DPP-4 Inhibition as an Alternative for Diabetes Mellitus Treatment: Computational and in Vitro Study.

A drug repurposing strategy could be a potential approach to overcoming the economic costs for diabetes mellitus (DM) treatment incurred by most countries. DM has emerged as a global epidemic, and an increase in the outbreak has led developing countries like Mexico, India, and China to recommend a prevention method as an alternative proposed by their respective healthcare sectors. Incretin-based therapy has been successful in treating diabetes mellitus, and inhibitors like sitagliptin, vildagliptin, saxagliptin, and alogliptin belong to this category. As of now, drug repurposing strategies have not been used to identify existing therapeutics that can become dipeptidyl peptidase-4 (DPP-4) inhibitors. Hence, this work presents the use of bioinformatics tools like the Activity Atlas model, flexible molecular docking simulations, and three-dimensional reference interaction site model (3D-RISM) calculations to assist in repurposing Food and Drug Administration (FDA)-approved drugs into specific nonsteroidal anti-inflammatory medications such as DPP-4 inhibitors. Initially, the Activity Atlas model was constructed based on the top scoring DPP-4 inhibitors, and then the model was used to understand features of nonsteroidal anti-inflammatory drugs (NSAIDs) as a function of electrostatic, hydrophobic, and active shape features of DPP-4 inhibition. The FlexX algorithm was used to infer protein–ligand interacting residues, and binding energy, to predict potential draggability towards the DPP-4 mechanism of action. 3D-RISM calculations on piroxicam-bound DPP-4 were used to understand the stability of water molecules at the active site. Finally, piroxicam was chosen as the repurposing drug to become a new DPP-4 inhibitor and validated experimentally using fluorescence spectroscopy assay. These findings are novel and provide new insights into the role of piroxicam as a new lead to inhibit DPP-4 and, taking into consideration the biological half-life of piroxicam, it can be proposed as a possible therapeutic strategy for treating diabetes mellitus.

Virtual screening of natural products as an inhibitor of DNA methyltransferase 1 enzyme for breast cancer disease

Breast cancer is the most prevalent cancer in woman worldwide. It has the highest number of new cases which amounted to 40 per 100,000 cases per year, 12.9% of which leads to death. Epigenetic alteration plays a vital role in the process of cancer cell formation and propagation. DNA methylation is one of the most common types of epigenetic alteration which generally leads to breast cancer. The DNA Methylation, a transfer of methyl group from S-adenosyl-methionine (SAM) to cytosine in the CpG dinucleotide, is catalysed by a DNA Methyltransferase-1 (DNMT1) enzyme. In the present study, we performed a virtual screening of natural product compounds as an inhibitor of the DNMT1 enzyme. Virtual screening was conducted on 26,731 natural products obtained from the NCBI PubChem database. Three steps of rigid and one step of flexible molecular docking simulations were performed using MOE 2014.09. Through the simulations, 10 best ligands based on the Gibbs free binding energies ΔGbinding) and the ligand-enzyme complex interactions were identified. The pharmacological test was conducted to observe the physicochemical, toxicity, carcinogenicity-mutagenicity, and bioactivity properties by employing DataWarrior 4.7.2., Toxtree, Molinspiration, admetSAR, and SWISSADME software. The results revealed that three best ligands from the phenolic group were selected due to their exceptional pharmacological characteristics as the drug candidate for breast cancer therapy.

Antioxidant activity and molecular docking study of Erythrina × neillii polyphenolics

Species of genus Erythrina have a great contribution in folk medicine; various species are utilized as a tranquilizer, to treat insomnia, inflammation and colic. Besides, Erythrina species have reported antioxidant, hepatoprotective and anxiolytic activities. Erythrina × neillii is a hybrid obtained through a cross between E. herbacea L. and E. humeana Spreng. It has not been well-studied for its chemical or biological profile; therefore it represents an interesting field of study. In this study, seven phenolic compounds; two hydrolysable tannins (1,3), one phenolic acid (2) and four known flavonoids (4–7) were isolated and characterized for the first time in E × neillii and Erythrina genus except for vitexin (7). Isolated compounds were assessed for their antioxidant activities using ORAC assay. 2″-O-galloyl orientin (6) exhibited the highest activity followed by 2″-O-galloyl vitexin (5). Flexible molecular docking on heme oxygenase, an important stress protein that is involved in cellular protection, antioxidant and anti-inflammatory activities, justified the antioxidant activity of the isolated compounds. The best scoring was observed with 2″-O-galloyl orientin forming four binding interactions with residues, Arg 136 (two interactions), Met34 and Gly139. Erythrina × neillii offered powerful and available antioxidant beside significantly active phytoconstituents.

The Topology of the Contacts of Potential Ligands for the UxuR Transcription Factor of Escherichia coli as Revealed by Flexible Molecular Docking

UxuR is a transcription factor that controls the expression of genes involved in hexuronate utilization. Its ability to bind to the promoters of regulated genes is dependent on sugar ligands. Two regions of the preferred interaction with D-glucuronate and D-galacturonate were found on the surface of the UxuR monomer earlier, one of which was located in the flexible linker connecting the N- and C-terminal domains of the protein. Binding of a ligand in this region may change the mutual orientation of the domains, thereby affecting the interaction of UxuR with DNA. The second binding region was found within the pocket of the C-terminal domain from where the regulatory effect may be explained either by conformational changes in the domain, or by influence of sugar ligands on the protein dimerization. Here, a 3D-model of the UxuR dimer was obtained and molecular docking of a range of sugars on its surface was performed. Additional platform for carbohydrate binding was found in the junction of the two C-terminal domains in the UxuR dimer. Interdomain linkers were occupied by different sugars including those that were able to penetrate into the pockets of the C-terminal domains from the side of interdomain space. Potentially, this allows transposing regulatory signal derived from the pocket loading into the conformation transition that changes mutual orientation of the domains.

The use of the docking studies with the purpose of searching Potential Antihypertensive Drugs

Pre-experimental studies in silico successfully used at various stages of the search and optimization of the structures of biologically active compounds. The purpose of present research was the search for perspective anti-hypertensive agents among 160 new synthesized N-R-phenyl-2,3-dihydro-1,3-thiazole-2-imine derivatives containing the morpholine, ethyl(propyl)morpholine, hydroxyethyl, allyl moiety in the structure and 5-substituted derivatives of 2-thio(amino)-1,3,4-thiadiazole using docking studies to two biotargets of angiotensin converting enzyme and angiotensin II receptor. Based on the results of a flexible molecular docking, a promising group of N-R-phenyl-2,3-dihydro-1,3-thiazole-2-imine derivatives containing the morpholine moiety for experimental screening for antihypertensive activity was selected. The high affinity of this series of substances is associated with the formation of bonds between the Oxygen atom of the morpholine cycle and the corresponding amino acid residue in the active site of the angiotensin converting enzyme ??. According to data obtained, different lengths of alkyl chains between the Nitrogen atom of the morpholine cycle and the Nitrogen atom of 1,3-thiazole cycle of the test substances, have a significant impact on the general energy system of complexes formed during interaction of molecules of the substances under research and the enzyme specified.

Biophysical characterization and ligand-binding properties of the elongation factor Tu from Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb) is the key devastating bacterial pathogen responsible for tuberculosis. Increasing emergence of multi-drug-resistant, extensively drug-resistant, and rifampicin/isoniazid-resistant strains of Mtb makes the discovery of validated drug targets an urgent priority. As a vital translational component of the protein biosynthesis system, elongation factor Tu (EF-Tu) is an important molecular switch responsible for selection and binding of the cognate aminoacyl-tRNA to the acceptor site on the ribosome. In addition, EF-Tu from Mtb (MtbEF-Tu) is involved in the initial step of trans-translation which is an effective system for rescuing the stalled ribosomes from non-stop translation complexes under stress conditions. Given its crucial role in protein biosynthesis, EF-Tu is identified as an excellent molecular target for drug design. Here, we reported the recombinant expression, purification, biophysical characterization, and structural modeling of the MtbEF-Tu protein. Our results demonstrated that prokaryotic expression plasmids of pET28a-MtbEF-Tu could be expressed efficiently in Escherichia coli. We successfully purified the 6× His-tagged proteins with a yield of 16.8 mg from 1 l of Luria Bertani medium. Dynamic light scattering experiments showed that MtbEF-Tu existed in a monomeric form, and circular dichroism experiments indicated that MtbEF-Tu was well structured. Moreover, isothermal titration calorimetry experiments displayed that the purified MtbEF-Tu protein possessed intermediate binding affinities for guanosine-5'-triphosphate (GTP) and GDP. The GTP/GDP-binding sites were predicted by flexible molecular docking approach which reveals that GTP/GDP binds to MtbEF-Tu mainly through hydrogen bonds. Our work lays the essential basis for further structural and functional studies of MtbEF-Tu as well as MtbEF-Tu-related novel drug developments.

IN SILICO DOCKING STUDIES, SYNTHESIS AND CHACTERIZATION OF SOME NOVEL 1,3,4 THIADIAZOLE ANALOGUES OF 4-AMINO HIPPURIC ACID AS POTENT ANTIMICROBIAL AGENTS

The chemistry of heterocyclic compounds has been an interesting field of study for a long time. The heterocyclic nucleus 1,3,4-thiadiazole constitutes an important class of compounds for new drug development. The synthesis of novel thiadiazole derivatives and investigation of their chemical and biological behaviour have gained more importance in recent decades. Molecular docking is a key tool in structural molecular biology and CADD. The goal of the ligand protein is to predict the predominant binding model(s) of ligand with a protein of known 3D structure. In the present work, the motto was to develop new the anti-microbial agents. 1,3,4 Thiadiazole derivative of 4-amino hippuric acid show good anti-microbial activity and greater selectivity with glucosamine - 6 - phosphate synthetase (PDB ID in 2VF5) with flexible molecular docking studies.

Identification and Molecular Docking Study of a Novel Angiotensin-I Converting Enzyme Inhibitory Peptide Derived from Enzymatic Hydrolysates of Cyclina sinensis.

Marine-derived angiotensin-I converting enzyme (ACE) inhibitory peptides have shown potent ACE inhibitory activity with no side effects. In this study, we reported the discovery of a novel ACE-inhibitory peptide derived from trypsin hydrolysates of Cyclina sinensis (CSH). CSH was separated into four different molecular weight (MW) fractions by ultrafiltration. Fraction CSH-I showed the strongest ACE inhibitory activity. A peptide was purified by fast protein liquid chromatography (FPLC) and reversed-phase high-performance liquid chromatography (RP-HPLC) and its sequence was determined to be Trp-Pro-Met-Gly-Phe (WPMGF, 636.75 Da). The Lineweaver-Burk plot showed that WPMGF was a competitive inhibitor of ACE. WPMGF showed a significant degree of stability at varying temperatures, pH, and simulated gastrointestinal environment conditions. We investigated the interaction between this pentapeptide and ACE by means of a flexible molecular docking tool. The results revealed that effective interaction between WPMGF and ACE occurred mainly through hydrogen bonding, hydrophobic interactions, and coordination bonds between WPMGF and Zn(II). In conclusion, our study indicates that a purified extract derived from Cyclina sinensis or the WPMGF peptide could potentially be incorporated in antihypertensive functional foods or dietary supplements.

Novel Thiazole Carboxylic Acid Derivatives Possessing a “Zinc Binding Feature” as Potential Human Glyoxalase-I Inhibitors

Background: Glyoxalase-I (Glo-I) enzyme is an attractive new target for developing new cancer therapeutics. This enzyme is a dimeric mononuclear zinc coordinating metalloenzyme, and the core zinc ion was utilized in designing potentially active inhibitors possessing a selective zinc binding feature. Objective: A panel of thiazole based carboxylic acid derivatives were designed, synthesized, and evaluated for their in vitro inhibitory activity against Glo-I enzyme based on their chelating potential with the zinc atom at the core of the active site. Methods: Flexible molecular docking was employed in designing the proposed inhibitors. The designed compounds were synthesized, fully characterized, and in vitro assayed against Glo-I enzyme. Results: Compound 14 was identified as the most potent inhibitor of the series with an IC50 of 2.5 µM. Moreover, the in-silico calculated CDocker scores were in excellent agreement with the experimental inhibitory activity of the compounds. Conclusion: The carboxylic acid group was identified as an indispensable chelating functionality in inhibiting Glo-I enzyme. The data obtained in this study indicate that these compounds could be promising anti-cancer candidates and hence warrant further optimization. Keywords: Computer aided drug design, glyoxalase-I, thiazole carboxylic acid, zinc binding feature, CDocker, anticancer.

Prediction of consensus binding mode geometries for related chemical series of positive allosteric modulators of adenosine and muscarinic acetylcholine receptors.

Following insights from recent crystal structures of the muscarinic acetylcholine receptor, binding modes of Positive Allosteric Modulators (PAMs) were predicted under the assumption that PAMs should bind to the extracellular surface of the active state. A series of well-characterized PAMs for adenosine (A1 R, A2A R, A3 R) and muscarinic acetylcholine (M1 R, M5 R) receptors were modeled using both rigid and flexible receptor CHARMM-based molecular docking. Studies of adenosine receptors investigated the molecular basis of the probe-dependence of PAM activity by modeling in complex with specific agonist radioligands. Consensus binding modes map common pharmacophore features of several chemical series to specific binding interactions. These models provide a rationalization of how PAM binding slows agonist radioligand dissociation kinetics. M1 R PAMs were predicted to bind in the analogous M2 R PAM LY2119620 binding site. The M5 R NAM (ML-375) was predicted to bind in the PAM (ML-380) binding site with a unique induced-fit receptor conformation. © 2017 Wiley Periodicals, Inc.

An enantiomer-based virtual screening approach: Discovery of chiral organophosphates as acetyl cholinesterase inhibitors

Chiral organophosphates (OPs) have been used widely around the world, very little is known about binding mechanisms with biological macromolecules. An in-depth understanding of the stereo selectivity of human AChE and discovering bioactive enantiomers of OPs can decrease health risks of these chiral chemicals. In the present study, a flexible molecular docking approach was conducted to investigate different binding modes of twelve phosphorus enantiomers. A pharmacophore model was then developed on basis of the bioactive conformations of these compounds. After virtual screening, twenty-four potential bioactive compounds were found, of which three compounds (Ethyl p-nitrophenyl phenylphosphonate (EPN), 1-naphthaleneacetic anhydride and N,4-dimethyl-N-phenyl-benzenesulfonamide) were tested by use of different in vitro assays. S-isomer of EPN was also found to exhibit greater inhibitory activity towards human AChE than the corresponding R-isomer. These findings affirm that stereochemistry plays a crucial role in virtual screening, and provide a new insight into designing safer organ phosphorus pesticides on human health.

Hexuronates influence the oligomeric form of the Dps structural protein of bacterial nucleoid and its ability to bind to linear DNA fragments

Proteins of the Dps family perform a dual function in bacterial cells. As ferritins, they protect cells from destructive effects of Fe2+ ions, while interacting with DNA they condense the genome in the absence of nutrients. The ability of Dps to self-aggregate is of a great importance. The way of genome remodelling from the condensed state to the active one is not yet known. Here, the effects of two sugar ligands on Dps interaction with DNA have been studied in vitro. For the first time it was demonstrated that D-glucuronate and D-galacturonate, but not D-glucose, can decompose the dodecameric structure of the protein and D-glucuronate stimulated the formation of binary complexes with the linear DNA fragments. As a result of flexible molecular docking, it was found that the molecules of all three sugars potentially can form clusters inside the protein cavity of Dps, but D-glucuronate and D-galacturonate were also bound in the region of intersubunit contacts of oligomer. The consequent destabilization of the intersubunit bonding network can, thus, be the main factor provoking the protein decay to the smaller oligomeric forms. Such a structural rearrangement, leading to a reduction in aggregation, may play a key role in genome decondensation during cell transition to the phase of rapid growth.

Targeting programmed cell death 4 (PDCD4) with biogenic compounds in ARDS by Gaussian process‐based QSAR virtual screening

The programmed cell death 4 (PDCD4) has recently been recognized as a new and attractive target of acute respiratory distress syndrome. Here, we attempted to discover new and potent PDCD4 mediator ligands from biogenic compounds using a synthetic strategy of statistical virtual screening and experimental affinity assay. In the procedure, a Gaussian process‐based quantitative structure‐activity relationship regression predictor was developed and validated statistically based on a curated panel of structure‐based protein‐ligand affinity data. The predictor was integrated with pharmacokinetics analysis, chemical redundancy reduction, and flexible molecular docking to perform high‐throughput virtual screening against a distinct library of chemically diverse, drug‐like biogenic compounds. Consequently, 6 hits with top scores were selected, and their binding affinities to the recumbent protein of human PDCD4 were identified, 3 out of which were determined to have high or moderate affinity with Kd at micromolar level. Structural analysis of protein‐ligand complexes revealed that hydrophobic interactions and van der Waals contacts are the primary chemical forces to stabilize the complex architecture of PDCD4 with these mediator ligands, while few hydrogen bonds, salt bridges, and/or π‐π stacking at the complex interfaces confer selectivity and specificity for the protein‐ligand recognition. It is suggested that the statistical Gaussian process‐based quantitative structure‐activity relationship screening strategy can be successfully applied to rational discovery of biologically active compounds. The newly identified molecular entities targeting PDCD4 are considered as promising lead scaffolds to develop novel chemical therapeutics for acute respiratory distress syndrome.

Computational approaches to find the active binding sites of biological targets against busulfan

Determination of electrophilic and nucleophilic sites of a molecule is the primary task to find the active sites of the lead molecule. In the present study, the active sites of busulfan have been predicted by molecular electrostatic potential surface and Fukui function analysis with the help of dispersion corrected density functional theory. Similarly, the identification of active binding sites of the proteins against lead compound plays a vital role in the field of drug discovery. Rigid and flexible molecular docking approaches are used for this purpose. For rigid docking, Hex 8.0.0 software employing fast Fourier transform (FFT) algorithm has been used. The partial flexible blind docking simulations have been performed with AutoDock 4.2 software; where a Lamarckian genetic algorithm is employed. The results showed that the most electrophilic atoms of busulfan bind with the targets. It is clear from the docking studies that busulfan has inhibition capability toward the targets 12CA and 1BZM. Graphical Abstract Docking of ligand and protein.

HQSAR and molecular docking studies of furanyl derivatives as adenosine A2A receptor antagonists

Structure- and ligand-based computational design strategies were used to understand the molecular requirements of furanyl derivatives 2-(furan-2-yl)-[1,2,4]triazolo[1,5-f]pyrimidin-5-amines (TfPAs), 2-(furan-2-yl)-[1,2,4]triazolo[1,5-a]pyrazin-8-amine (TaPAs), and 2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-7-amines (TTAs) as adenosine A2A receptor (A2AR) antagonists. First, we studied the structure–activity relationship of the selected compounds using hologram quantitative structure–activity relationship (HQSAR) methodology. The best model (training set included 67 compounds) included fragment parameters such as atoms (A), bonds (B), connections (C), and donors/acceptors groups (DA) and had a good q2 value of 0.776 including size fragments of 7–10 and the hologram length of 199. It also predicted adequately the compounds contained in the test set (10 compounds). In addition, we studied the binding orientations of the higher and less active compounds using flexible molecular docking. We found orientations that are in agreement with previous reports.

Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach.

Capecitabine, a fluoropyrimidine prodrug, has been a frequently chosen ligand for the last one and half decades to inhibit thymidylate synthase (TYMS) for treatment of colorectal cancer. TYMS is a key enzyme for de novo synthesis of deoxythymidine monophosphate and subsequent synthesis of DNA. Recent years have also seen the trait of modifying ligands using halogens and trifluoromethyl (–CF3) group to ensure enhanced drug performance. In this study, in silico modification of capecitabine with Cl, Br, I atoms and –CF3 group has been performed. Density functional theory has been employed to optimize the drug molecules and elucidate their thermodynamic and electrical properties such as Gibbs free energy, enthalpy, electronic energy, dipole moment and frontier orbital features (HOMO–LUMO gap, hardness and softness). Flexible and rigid molecular docking have been implemented between drugs and the receptor TYMS. Both inter- and intra-molecular non-covalent interactions involving the amino acid residues of TYMS and the drug molecules are explored in details. The drugs were superimposed on the resolved crystal structure (at 1.9 Å) of ZD1694/dUMP/TYMS system to shed light on similarity of the binding of capecitabine, and its modifiers, to that of ZD1694. Together, these results may provide more insights prior to synthesizing halogen-directed derivatives of capecitabine for anticancer treatment.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-1844-y) contains supplementary material, which is available to authorized users.

Faster Binding Free-Energy Landscape Calculation by Virtual-State Coupled Adaptive Umbrella Sampling

Accurate calculations of binding free-energy landscapes provide useful thermodynamic quantities to understand a given biological process. Adaptive umbrella sampling (AUS) aims to calculate such binding free-energy landscape along a given reaction coordinate. Typically, AUS requires a biasing force, which is defined from a canonical probability distribution of the reaction coordinate; and the distribution is updated iteratively until the system randomly walks along the reaction coordinate. However, convergence of the above iterative process may require enormous sampling, and hence computationally expensive. We established a novel method “virtual-state coupled adaptive umbrella sampling” (V-AUS) by enhancing the sampling along a virtual degree of freedom. The V-AUS quickly estimates free-energy landscape compared to AUS. We applied this method successfully to obtain the free-energy landscape for flexible binding between two Aβ-peptides in explicit water at room temperature (J. Comput. Chem. vol. 36, p1489, 2015). To further improve the V-AUS ensuring even faster convergence to uniform sampling we designed a set of methods on top of V-AUS. We define grids around a receptor in which its ligand is placed to obtain a better initial set of conformations. Secondly, sampling errors from the estimated canonical probability distribution due to inadequate sampling are removed by Markov state modeling. Thirdly, we introduce a set of novel fitting schemes to parameterize the biasing force in terms of reaction coordinate. These set of methods to improve V-AUS are tested for Ala-pentapeptide dimerization. We conclude that by using such advanced set of methods faster free-energy calculation of flexible molecular docking is possible. Currently a study for larger biological system is ongoing.

Structural modeling of the ExuR and UxuR transcription factors of E. coli: search for the ligands affecting their regulatory properties

Gammaproteobacteria get energy for their growth from different carbon sources using either glycolysis or alternative metabolic pathways induced in stress conditions. These metabolic switches are coordinated by complex interplay of regulatory proteins sensing concentrations of available metabolites by mechanisms yet to be understood. Here, we use two transcriptional regulators, ExuR and UxuR, controlling d-galacturonate (d-gal) and d-glucuronate metabolism in Escherichia coli, as the targets for computational search of low-molecular compounds capable to bind their ligand-binding domains. Using a flexible molecular docking, we modeled the interactions of these proteins with substrates and intermediates of glycolysis, Ashwell and Entner–Doudoroff pathways. For UxuR, the two preferred sites of ligand binding were found: one is located within the C-terminal domain, while another occupies the interdomain space. For ExuR, the only one preferred site was detected in the interdomain area. Availability of this area to different ligands suggests that, similar to the Lac repressor, the DNA-binding properties of UxuR and ExuR may be changed by repositioning of their domains. Experimental assays confirmed the ability of ligands with highest affinities to bind the regulatory proteins and affect their interaction with DNA. d-gal that is carried into the cell by the ExuT transporter appeared to be the best ligand for repressor of the exuT transcription, ExuR. For UxuR, the highest affinity was found for d-fructuronate transported by GntP, which biosynthesis is repressed by UxuR. Providing a feedback loop to balance the concentrations of different nutrients, such ligand-mediated modulation can also coordinate switching between different metabolic pathways in bacteria.

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.

A novel enhanced conformational sampling method, virtual-system-coupled adaptive umbrella sampling (V-AUS), was proposed to compute 300-K free-energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V-AUS was applied to complex formation of two disordered amyloid-β (Aβ30-35 ) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300-K free-energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β-sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V-AUS converged to uniform distribution more effectively than conventional AUS sampling did.