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Results for “Molecular Docking Simulation”

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PubMed1995

Modelling the P2Y purinoceptor using rhodopsin as template.

The P2Y1 purinoceptor cloned from chick brain (Webb, T. et al (1993) FEBS Lett., 324, 219-225) is a 362 amino acid, 41 kDa protein. To locate residues tentatively involved in ligand recognition a molecular model of the P2Y purinoceptor has been constructed. The model was based on the primary sequence and structural homology with the G-protein coupled photoreceptor rhodopsin, in analogy to the method proposed by Ballesteros and Weinstein ((1995) Meth. Neurosci. 25, 366-428). Transmembrane helices were constructed from the amino acid sequence, minimized individually, and positioned in a helical bundle. The helical bundle was then minimized using the Amber forcefield in Discover (BIOSYM Technologies) to obtain the final model. Several residues that have been shown to be critical in ligand binding in other GPCRs are conserved in the P2Y1 purinoceptor. According to our model the side chains of these conserved residues are facing the internal cleft in which ligand binding likely occurs. The model also suggests four basic residues (H121 in TM3, H266 and K269 in TM6 and R299 in TM7) near the extracellular surface that might be involved in ligand binding. These basic residues might be essential in coordinating the triphosphate chain of the endogenous ligand adenosine 5'-triphosphate (ATP). Potential binding sites for agonists have been explored by docking several derivatives (including newly synthesized N6-derivatives) into the model. The N6-phenylethyl substituent is tolerated pharmacologically, and in our model this substituent occupies a region predominantly defined by aromatic residues such as F51 (TM1), Y100 (TM2) and F120 (TM3). The dimethylated analogue of ATP, N6,N6-dimethyl-adenosine 5'-triphosphate, is less well tolerated pharmacologically, and our model predicts that the attenuated activity is due to interference with hydrogen bonding capacity to Q296 (TM7).

Amino Acid Sequence↗

PubMed2001

Protein-based alignment in 3D QSAR of 26 indole inhibitors of human pancreatic phospholipase A2.

An automated docking procedure was applied on a series of 26 reversible and competitive indole inhibitors of human pancreatic phospholipase A2 (hp-PLA2). X-ray data of this enzyme are not available and the structure was then reconstructed exploiting its protein sequence and the crystallographic data of a bovine pancreatic source. The docking data were used to build a three-dimensional quantitative structure-activity relationship (3D QSAR) model, established using the comparative molecular field analysis (CoMFA) method. This model, joined to the previous one developed for the indole inhibitors of human non-pancreatic secretory phospholipase A2 (hnps-PLA2), an enzyme involved in inflammation processes, will allow for the selection of new strong anti-inflammatory drugs with negligible side effects, at least at the level of hp-PLA2.

Animals↗

PubMed1999

Crystal structure of the FMN-binding domain of human cytochrome P450 reductase at 1.93 A resolution.

The crystal structure of the FMN-binding domain of human NADPH-cytochrome P450 reductase (P450R-FMN), a key component in the cytochrome P450 monooxygenase system, has been determined to 1.93 A resolution and shown to be very similar both to the global fold in solution (Barsukov I et al., 1997, J Biomol NMR 10:63-75) and to the corresponding domain in the 2.6 A crystal structure of intact rat P450R (Wang M et al., 1997, Proc Nat Acad Sci USA 94:8411-8416). The crystal structure of P450R-FMN reported here confirms the overall similarity of its alpha-beta-alpha architecture to that of the bacterial flavodoxins, but reveals differences in the position, number, and length of the helices relative to the central beta-sheet. The marked similarity between P450R-FMN and flavodoxins in the interactions between the FMN and the protein, indicate a striking evolutionary conservation of the FMN binding site. The P450R-FMN molecule has an unusual surface charge distribution, leading to a very strong dipole, which may be involved in docking cytochrome P450 into place for electron transfer near the FMN. Several acidic residues near the FMN are identified by mutagenesis experiments to be important for electron transfer to P4502D6 and to cytochrome c, a clear indication of the part of the molecular surface that is likely to be involved in substrate binding. Somewhat different parts are found to be involved in binding cytochrome P450 and cytochrome c.

Animals↗

PubMed1996

Active-site-directed 3D database searching: pharmacophore extraction and validation of hits.

Two new computational tools, PRO_PHARMEX and PRO_SCOPE, for use in active-site-directed searching of 3D databases are described. PRO_PHARMEX is a flexible, graphics-based program facilitating the extraction of pharmacophores from the active site of a target macromolecule. These pharmacophores can then be used to search a variety of databases for novel lead compounds. Such searches can often generate many 'hits' of varying quality. To aid the user in setting priorities for purchase, synthesis or testing, PRO_SCOPE can be used to dock molecules rapidly back into the active site and to assign them a score using an empirical scoring function correlated to the free energy of binding. To illustrate how these tools can add value to existing 3D database software, their use in the design of novel thrombin inhibitors is described.

Binding Sites↗

PubMed2005

Pharmacophore modeling, docking, and principal component analysis based clustering: combined computer-assisted approaches to identify new inhibitors of the human rhinovirus coat protein.

The development and application of a sophisticated virtual screening and selection protocol to identify potential, novel inhibitors of the human rhinovirus coat protein employing various computer-assisted strategies are described. A large commercially available database of compounds was screened using a highly selective, structure-based pharmacophore model generated with the program Catalyst. A docking study and a principal component analysis were carried out within the software package Cerius and served to validate and further refine the obtained results. These combined efforts led to the selection of six candidate structures, for which in vitro anti-rhinoviral activity could be shown in a biological assay.

Antiviral Agents↗

PubMed2005

3,6-disubstituted coumarins as mechanism-based inhibitors of thrombin and factor Xa.

In this work, coumarins were screened on thrombin (THR) and factor Xa (FXa), two of the most promising targets for the development of anticoagulant drugs. This allowed us to highlight compound 30, characterized by a 2,5-dichlorophenyl ester in the 3-position and a chloromethyl moiety in the 6-position, as a very potent THR inhibitor (ki/KI= 37,000 M(-1) s(-1)). Moreover, this compound exhibits good selectivity over FXa (168-fold) and trypsin (54-fold). The mechanism of inactivation was investigated in this series and significantly differs from that previously observed with alpha-chymotrypsin. Indeed, the addition of hydrazine on the THR-inhibitor complex promotes a partial induced THR reactivation. This reactivation, confirmed by LC/MS, showed the resurgence of the native THR and a new dihydrazide complex. Docking experiments were then efficiently used to explain the trends observed in the enzymatic assays as well as to corroborate the postulated inhibition mechanism. Finally, the cell permeability of our derivatives was estimated using a computational approach.

Animals↗

PubMed2002

Binding models of reversible inhibitors to type-B monoamine oxidase.

Interest in the inhibitors of type-B monoamine oxidase has grown in recent years, due to the evidence for multiple roles of one such agent (selegiline) in the pharmacological management of neurodegenerative disorders. A set of 130 reversible and selective inhibitors of MAO-B (including tetrazole, oxadiazolone, and oxadiazinone derivatives) were taken from the literature and subjected to a three-dimensional quantitative structure-activity relationship (3D-QSAR) study, using CoMFA and GOLPE procedures. The steric and lipophilic fields, alone and in combination, provided us with informative models and satisfactory predictions (q2 = 0.73). The validity of these models was checked against the 3D X-ray structure of human MAO-B. Flexible docking calculations, performed by using a new approach which took advantage from QXP and GRID computational tools, showed the diverse inhibitors to interact with MAO-B in a similar binding mode, irrespective of the heterocycle characterizing them. A significant trend of correlation was observed between estimated energies of the complexes and the experimental inhibition data.

Catalytic Domain↗

PubMed2003

In silico structure-based design of a potent, mutation resilient, small peptide inhibitor of HIV-1 reverse transcriptase.

A crucial step in the replication of HIV-1 is the conversion of its single-stranded RNA to double-stranded DNA, which is catalyzed by the virally encoded reverse transcriptase (RT). The latter is therefore a key target for the development of anti-HIV drugs. Currently approved anti-RT drugs fall into two main classes: (i). nucleoside analog inhibitors which are incorporated into the primer strand in their metabolically activated triphosphate forms, causing termination of DNA synthesis due to their 3'-deoxy configuration and (ii). the non-nucleoside inhibitors (NNIs), which are generally specific for HIV-1 RT and bind at an allosteric site approximately 10 A from the active site causing a displacement of the catalytic aspartate residues. The so-called "first generation" NNI drugs are generally susceptible to the effects of single-point mutations within RT, while more recent "second generation" NNIs, such as efavirenz, the carboxanilide UC-781 and certain quinoxalines demonstrate much greater resilience to mutations in RT. The crystal structures of the complexes of wild type and mutant RTs with first and second generation NNIs have shown that, for an inhibitor to be potent as well as mutation resilient, it should (i). make hydrogen bonds with the main chain of RT, (ii). have a large number of interactions with RT and (iii). have the ability to rearrange and adapt to a mutated NNI pocket. Based on the crystal structures of the complexes of wild type RT and Tyr188Cys mutant of RT with UC-781, we have designed a small peptide inhibitor. Docking results on this peptide using AutoDock3.0 and SYBYL 6.8.1 indicate that the peptide has a potency comparable to that of UC-781 with a retention of activity against the Tyr188Cys mutant RT. The proposed, small peptide is seen to possess all the desirable features of a potent and mutation resilient inhibitor and is hence a potential lead compound.

Anti-HIV Agents↗

PubMed2004

[Molecular design and biological activity of BCR-ABL tyrosine kinase inhibitors].

OBJECTIVE: To discover BCR-ABL tyrosine kinase inhibitors through structure based virtual screening. METHODS: Docking screening against the distinctive inactive conformation of the catalytic domain of BCR-ABL tyrosine kinase was performed on 3D database. The MTT assay was performed to assess the viability of the tumor cells treated with selected compounds. The amount and kinase activity of BCR-ABL protein were detected in the presence of compounds by Western blot analysis and immunoprecipitation. RESULTS: From the top 1,000 compounds with the best DOCK energy score, 15 compounds were selected for biological assay. Eight out of 15 compounds showed notable inhibitory activity against Ph+ human K562 cells with IC50 values ranging from 10 to 200 micromol/L. In cell-based assays of ABL tyrosine phosphorylation, the ability of two kinds of novel, structurally diverse, lead compounds to inhibit ABL kinase activity was observed. However, no significant differences in the amount of BCR-ABL protein were noted on the ABL immunoblot in the presence of these lead compounds. CONCLUSIONS: Two promising lead compounds were discovered to inhibit BCR-ABL tyrosine kinase activity. Virtual screening technique has been proven to narrow down the size of screening compound libraries to the most prospective drug candidates with high success rates.

Computer Simulation↗

PubMed2004

Interaction profile-based protein classification of death domain.

BACKGROUND: The increasing number of protein sequences and 3D structure obtained from genomic initiatives is leading many of us to focus on proteomics, and to dedicate our experimental and computational efforts on the creation and analysis of information derived from 3D structure. In particular, the high-throughput generation of protein-protein interaction data from a few organisms makes such an approach very important towards understanding the molecular recognition that make-up the entire protein-protein interaction network. Since the generation of sequences, and experimental protein-protein interactions increases faster than the 3D structure determination of protein complexes, there is tremendous interest in developing in silico methods that generate such structure for prediction and classification purposes. In this study we focused on classifying protein family members based on their protein-protein interaction distinctiveness. Structure-based classification of protein-protein interfaces has been described initially by Ponstingl et al. 1 and more recently by Valdar et al. 2 and Mintseris et al. 3, from complex structures that have been solved experimentally. However, little has been done on protein classification based on the prediction of protein-protein complexes obtained from homology modeling and docking simulation. RESULTS: We have developed an in silico classification system entitled HODOCO (Homology modeling, Docking and Classification Oracle), in which protein Residue Potential Interaction Profiles (RPIPS) are used to summarize protein-protein interaction characteristics. This system applied to a dataset of 64 proteins of the death domain superfamily was used to classify each member into its proper subfamily. Two classification methods were attempted, heuristic and support vector machine learning. Both methods were tested with a 5-fold cross-validation. The heuristic approach yielded a 61% average accuracy, while the machine learning approach yielded an 89% average accuracy. CONCLUSION: We have confirmed the reliability and potential value of classifying proteins via their predicted interactions. Our results are in the same range of accuracy as other studies that classify protein-protein interactions from 3D complex structure obtained experimentally. While our classification scheme does not take directly into account sequence information our results are in agreement with functional and sequence based classification of death domain family members.

Humans↗

PubMed1997

Automated docking of monosaccharide substrates and analogues and methyl alpha-acarviosinide in the glucoamylase active site.

Glucoamylase is an important industrial glucohydrolase with a large specificity range. To investigate its interaction with the monosaccharides D-glucose, D-mannose, and D-galactose and with the substrate analogues 1-deoxynojirimycin, D-glucono-1,5-lactone, and methyl alpha-acarviosinide, MM3(92)-optimized structures were docked into its active site using AutoDock 2.1. The results were compared to structures of glucoamylase complexes obtained by protein crystallography. Charged forms of some substrate analogues were also docked to assess the degree of protonation possessed by glucoamylase inhibitors. Many forms of methyl alpha-acarviosinide were conformationally mapped by using MM3(92), characterizing the conformational pH dependence found for the acarbose family of glucosidase inhibitors. Their significant conformers, representing the most common states of the inhibitor, were used as initial structures for docking. This constitutes a new approach for the exploration of binding modes of carbohydrate chains. Docking results differ slightly from x-ray crystallographic data, the difference being of the order of the crystallographic error. The estimated energetic interactions, even though agreeing in some cases with experimental binding kinetics, are only qualitative due to the large approximations made by AutoDock force field.

1-Deoxynojirimycin↗

PubMed2006

Arylthiopyrrole (AThP) derivatives as non-nucleoside HIV-1 reverse transcriptase inhibitors: synthesis, structure-activity relationships, and docking studies (part 1).

Novel arylthio isopropyl pyridinylmethylpyrrolemethanol (AThP) derivatives 3-5, which are related to capravirine (S-1153), were synthesized and tested for their ability to block the replication cycle of HIV-1 in infected cells. The newly synthesized AThPs are active in the concentration range of 0.008-53 microM. Even if compounds 3-5 are generally less potent than S-1153, their SI values are in some cases similar to that of the reference drug. In fact, the cytotoxicities of AThPs are generally lower than that of S-1153. Compound 4e was the most active derivative of this series in cell-based assays; its potency is similar to that of S-1153 (EC(50)=8 and 3 nM, respectively), as is its selectivity index (SI=6250 and 7000, respectively). AThP derivatives were proven to target HIV-1 RT. In fact, compounds 3-5 generally inhibited the viral enzyme at concentrations similar to those observed in cell-based assays. A selected number of AThPs (4k and 5a,e) were tested against clinically relevant drug-resistant forms of recombinant reverse transcriptase (rRT) carrying the K103N and Y181I mutations. Carbamate 5e showed an approximate 240-fold decrease in activity against Y181I, but only a 10-fold loss in potency against the K103N rRT form. Docking calculations were also performed to investigate the binding mode of compounds 2, 4e, 4j, 4k and 5e into the non-nucleoside binding site of HIV-1 RT and to rationalize some structure-activity relationships and resistance data.

Binding Sites↗

PubMed2006

Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum alpha-(1-->2)-mannosidase I to elucidate the pathway to the substrate transition state.

Alpha-(1-->2)-mannosidase I from the endoplasmic reticulum (ERManI), a Family 47 glycoside hydrolase, is a key enzyme in the N-glycan synthesis pathway. Catalytic-domain crystal structures of yeast and human ERMan1s have been determined, the former with a hydrolytic product and the latter without ligands, with the inhibitors 1-deoxymannojirimycin and kifunensine, and with a thiodisaccharide substrate analog. Both inhibitors were bound at the base of the funnel-shaped active site as the unusual 1C4 conformer, while the substrate analog glycon is a 3S1 conformer. In the current study, AutoDock was used to dock alpha-D-mannopyranosyl-(1-->2)-alpha-D-mannopyranose with its glycon in chair (1C4,4C1), half-chair (3H2,3H4,4H3), skew-boat (OS2,3S1,5S1), boat (2,5B,3,OB,B1,4,B2,5), and envelope (3E,4E,E3,E4) conformations into the yeast ERManI active site. Both docked energies and forces on docked ligand atoms were calculated to determine how the ligand distorts to the transition state. From these, we can conclude that (1) both 1C4 and OS2 can be the starting conformers; (2) the most likely binding pathway is 1C4-->3H2-->OS2-->3,OB-->3S1-->3E; (3) the transition state is likely to be close to a 3E conformation.

Binding Sites↗

PubMed1997

Meeting review: the Second meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996.

In most fields of scientific endeavor, the outcomes of important experiments are not always known before the experiments are performed. But in protein structure prediction, algorithms are usually developed and tested in situations where the answers are known. In December 1996, the Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2) was held in Asilomar, California to rectify this situation: protein sequences were provided in advance for which the experimental structure had not yet been published. Over 70 research groups provided bona fide predictions on 42 targets in four categories: comparative or 'homology' modeling, fold recognition or 'threading', ab initio structure predictions, and docking predictions. Since the previous CASP meeting in 1994, the role of fold recognition in structure prediction has increased enormously with the largest number of groups participating in this category. In this review, we highlight some of the important developments and give at least a qualitative sense of what kind of methods produced some of the better predictions.

Computer Simulation↗

PubMed2005

Optimal clustering for detecting near-native conformations in protein docking.

Clustering is one of the most powerful tools in computational biology. The conventional wisdom is that events that occur in clusters are probably not random. In protein docking, the underlying principle is that clustering occurs because long-range electrostatic and/or desolvation forces steer the proteins to a low free-energy attractor at the binding region. Something similar occurs in the docking of small molecules, although in this case shorter-range van der Waals forces play a more critical role. Based on the above, we have developed two different clustering strategies to predict docked conformations based on the clustering properties of a uniform sampling of low free-energy protein-protein and protein-small molecule complexes. We report on significant improvements in the automated prediction and discrimination of docked conformations by using the cluster size and consensus as a ranking criterion. We show that the success of clustering depends on identifying the appropriate clustering radius of the system. The clustering radius for protein-protein complexes is consistent with the range of the electrostatics and desolvation free energies (i.e., between 4 and 9 Angstroms); for protein-small molecule docking, the radius is set by van der Waals interactions (i.e., at approximately 2 Angstroms). Without any a priori information, a simple analysis of the histogram of distance separations between the set of docked conformations can evaluate the clustering properties of the data set. Clustering is observed when the histogram is bimodal. Data clustering is optimal if one chooses the clustering radius to be the minimum after the first peak of the bimodal distribution. We show that using this optimal radius further improves the discrimination of near-native complex structures.

Amino Acid Sequence↗

PubMed2001

Discovery of a novel serine protease inhibitor utilizing a structure-based and experimental selection of fragments technique.

We report a set of strategies to develop novel ligands (Structure Based and Experimental Selection of Fragments: SbE-SF). First, a docking simulation utilizing DOCK3.5 is performed in order to screen the fragment database, which was generated with the in-house program FRAGMENT++ specifically for docking simulation purposes. Although the affinity of these small molecules (fragments) is expected to be low, the affinity of fragments selected by computation is assayed by experiment to determine which ones can be potent inhibitors. After determining such key fragments. additional fragments are attached to the key ones in order to increase the binding affinity,taking into account the binding modes predicted by computation. This method has been applied to a thrombin inhibitor study, resulting in the discovery of a novel inhibitor exhibiting pIC50 = 7.9.

Drug Design↗

PubMed1994

Computer modeling of adsorption on an activated charcoal surface.

The molecular modeling program SYBYL was used to simulate the adsorption of various barbiturates by an activated charcoal surface. The compounds barbituric acid (BA), barbital (B), phenobarbital (PB), mephobarbital (M), and primidone (Pr) were modeled, and their structures were energetically minimized. These structures agreed with literature reports for the conformations of these molecules in dimethyl sulfoxide-d6, methanol-d4, and chloroform-d. The activated charcoal surface was modeled using graphitic crystallites which had either no oxygen-containing functional group, a C-OH functional group, or a C = O functional group. The presence of the C-O (presumably C-OH) and C = O functional states on activated charcoal surfaces had been previously determined by X-ray photoelectron spectroscopy. It was assumed that the crystallite was locally flat. Upon docking, conformational changes were observed for barbital, phenobarbital, mephobarbital, and primidone. Estimates for the heat of adsorption ranged from -62.3 kJ/mol for barbituric acid to -91.1 kJ/mol for mephobarbital on the hydroxylated surface. Allowance for the heat of desorption of the required number of water molecules from the surface, also determined by SYBYL, gave heat of displacement values of -19.4 kJ/mol for barbituric acid and -32.6 kJ/mol for mephobarbital. These values compared well to the heat of displacement values obtained by isoperibol calorimetry, which were -20.3 kJ/mol for barbituric acid and -31.6 kJ/mol for mephobarbital. Previous laboratory studies had demonstrated the greater importance of the C-O functional state for barbiturate adsorption compared to the C = O functional state. The computer-modeled system predicted the same result.

Adsorption↗

PubMed2003

Helix-turn-helix motifs in unsolvated peptides.

The conformations of unsolvated Ac-A14KG3A14K + 2H+ (Ac = acetyl, A = alanine, K = lysine, G = glycine) have been examined by ion mobility measurements and molecular dynamics simulations. This peptide was designed as a model helix-turn-helix motif. It was found to adopt three distinct geometries which were assigned to an extended helical conformation which is only stable at low temperatures (<230 K), a relatively high energy but metastable structure with exchanged lysines, and a coiled-coil. The coiled coil (which consists of an antiparallel arrangement of two helical alanine sections linked by a flexible glycine loop) is the dominant conformation. For temperatures >350 K, the experimental results indicate the helices uncouple and the loop randomizes. From equilibrium constants determined for this helix coupling right arrow over left arrow uncoupling transition, we found DeltaH degrees = -45 kJ mol-1 and DeltaS degrees = 114 J K-1 mol-1. -DeltaH degrees is essentially the enthalpy change for docking the two helices together while DeltaS degrees is essentially the entropy change for freeing up the glycine loop.

Glycine↗