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Results for “In silico screening”

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PubMedDate not supplied

High-throughput modeling of human G-protein coupled receptors: amino acid sequence alignment, three-dimensional model building, and receptor library screening.

The current study describes the development of a computer package (GPCRmod) aimed at the high-throughput modeling of the therapeutically important family of human G-protein coupled receptors (GPCRs). GPCRmod first proposes a reliable alignment of the seven transmembrane domains (7 TMs) of most druggable human GPCRs based on pattern/motif recognition for each of the 7 TMs that are considered independently. It then converts the alignment into knowledge-based three-dimensional (3-D) models starting from a set of 3-D backbone templates and two separate rotamer libraries for side chain positioning. The 7 TMs of 277 human GPCRs have been accurately aligned, unambiguously clustered in three different classes (rhodopsin-like, secretin-like, metabotropic glutamate-like), and converted into high-quality 3-D models at a remarkable throughput (ca. 3s/model). A 3-D GPCR target library of 277 receptors has consequently been setup. Its utility for "in silico" inverse screening purpose has been demonstrated by recovering among top scorers the receptor of a selective GPCR antagonist as well as the receptors of a promiscuous antagonist. The current GPCR target library thus constitutes a 3-D database of choice to address as soon as possible the "virtual selectivity" profile of any GPCR antagonist or inverse agonist in an early hit optimization process.

Amino Acid Sequence↗

PubMed2003

Synthetic peptides derived from the Wilms' tumor 1 protein sensitize human T lymphocytes to recognize chronic myelogenous leukemia cells.

The Wilms' tumour 1 (WT1) molecule was screened in silico for the presence of 15-mer sequences predicted to bind HLA-DRB1(*)0401 (www.syfpeithi.de). Two peptides with the highest binding scores were synthesized (WT12e, PQQMGSDVRDLNALL and WT331, NKRYFKLSHLQMHSR). In vitro sensitization experiments using PBMC and the 15-mer peptides yielded peptide-specific responses against both WT12e and WT331 from six of seven healthy donors. Moreover, four of four different primary CML cell preparations were directly recognized by five different T cell lines, as assessed by IFN-gamma release. These responses were to a great extent blocked by anti-DR monoclonal antibody. These results suggest that WT1 peptides can be selected that are immunogenic for class II-restricted T-cell responses to native tumor cells, and indicate that they may find application in active immunotherapy of CML.

Adult↗

PubMed2004

Estimating the potential refolding yield of recombinant proteins expressed as inclusion bodies.

Recombinant protein production in bacteria is efficient except that insoluble inclusion bodies form when some gene sequences are expressed. Such proteins must undergo renaturation, which is an inefficient process due to protein aggregation on dilution from concentrated denaturant. In this study, the protein-protein interactions of eight distinct inclusion-body proteins are quantified, in different solution conditions, by measurement of protein second virial coefficients (SVCs). Protein solubility is shown to decrease as the SVC is reduced (i.e., as protein interactions become more attractive). Plots of SVC versus denaturant concentration demonstrate two clear groupings of proteins: a more aggregative group and a group having higher SVC and better solubility. A correlation of the measured SVC with protein molecular weight and hydropathicity, that is able to predict which group each of the eight proteins falls into, is presented. The inclusion of additives known to inhibit aggregation during renaturation improves solubility and increases the SVC of both protein groups. Furthermore, an estimate of maximum refolding yield (or solubility) using high-performance liquid chromatography was obtained for each protein tested, under different environmental conditions, enabling a relationship between "yield" and SVC to be demonstrated. Combined, the results enable an approximate estimation of the maximum refolding yield that is attainable for each of the eight proteins examined, under a selected chemical environment. Although the correlations must be tested with a far larger set of protein sequences, this work represents a significant move beyond empirical approaches for optimizing renaturation conditions. The approach moves toward the ideal of predicting maximum refolding yield using simple bioinformatic metrics that can be estimated from the gene sequence. Such a capability could potentially "screen," in silico, those sequences suitable for expression in bacteria from those that must be expressed in more complex hosts.

Chromatography, High Pressure Liquid↗

PubMed2006

Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling.

Herein we make an overview of the results of our computational experiments aimed at gaining insight into the molecular mechanisms of GPCR functioning either in their normal conditions or when hit by gain-of-function or loss-of-function mutations. Molecular simulations of a number of GPCRs in their wild type and mutated as well as free and ligand-bound forms were instrumental in inferring the structural features, which differentiate the mutation- and ligand-induced active from the inactive states. These features essentially reside in the interaction pattern of the E/DRY arginine and in the degree of solvent exposure of selected cytosolic domains. Indeed, the active states differ from the inactive ones in the weakening of the interactions made by the highly conserved arginine and in the increase in solvent accessibility of the cytosolic interface between helices 3 and 6. Where possible, the structural hallmarks of the active and inactive receptor states are translated into molecular descriptors useful for in silico functional screening of novel receptor mutants or ligands. Computational modeling of the supramolecular organization of GPCRs and their intracellular partners is the current challenge toward a deep understanding of their functioning mechanisms.

Animals↗

PubMed2006

Synthesis of bicyclic molecular scaffolds (BTAa): an investigation towards new selective MMP-12 inhibitors.

Starting from 3-aza-6,8-dioxa-bicyclo[3.2.1]octane scaffold (BTAa) a virtual library of molecules was generated and screened in silico against the crystal structure of the Human Macrophage Metalloelastase (MMP-12). The molecules obtaining high score were synthesized and the affinity for the catalytic domain of MMP-12 was experimentally proved by NMR experiments. A BTAa scaffold 20 having a N-hydroxyurea group in position 3 and a p-phenylbenzylcarboxy amide in position 7 showed a fair inhibition potency (IC50 = 149 microM) for MMP-12 and some selectivity towards five different MMPs. These results, taken together with the X-ray structure of the adduct between MMP-12, the inhibitor 20 and the acetohydroxamic acid (AHA), suggest that bicyclic scaffold derivatives may be exploited for the design of new selective matrix metalloproteinase inhibitors (MMPIs).

Bridged Bicyclo Compounds, Heterocyclic↗

PubMed2004

The design and preparation of metabolically protected new arylpiperazine 5-HT1A ligands.

New arylpiperazines related to buspirone, gepirone and NAN-190 were designed and screened in silico for their 5-HT(1A) affinity and potential sites of metabolism by human cytochrome p450 (CYP3A4). Modifications to these structures were assessed in silico for their influence on both 5HT(1A) affinity and metabolism. Selected new molecules were synthesized and purified in a parallel chemistry approach to determine structure activity relationships (SARs). The resulting molecules were assessed in vitro for their 5HT(1A) affinity and half-life in a heterologously expressed human CYP3A4 assay. Molecular features responsible for 5-HT(1A) affinity and CYP3A4 stability are described.

Cytochrome P-450 CYP3A↗

PubMed2004

Restricted germ cell expression of a gene encoding a novel mammalian HORMA domain-containing protein.

HORMA-domain containing proteins are involved in cell cycle regulation by interactions with chromatin. Through an in silico subtractive screen for mouse genes preferentially expressed in newborn ovaries, we identified a gene that would encode a novel mammalian HORMA domain-containing protein termed Newborn Ovary HORMA protein (Nohma). Reverse transcription polymerase chain reaction and Northern blot analysis have demonstrated a 1.7 kb transcript that is expressed exclusively in germ cells in both male and female mouse gonads. Nohma expression can be detected postnatally in male, and prenatally in female gonads, but shows a sexually dimorphic expression in adult gonads. The Nohma transcript is abundant in the adult testis but limited in the adult ovary. The mouse Nohma gene is comprised of 15 exons and maps to chromosome 3. A human ortholog was also identified. The expression pattern of Nohma suggests that it may be a critical regulatory protein in germ cell meiosis.

Amino Acid Sequence↗

PubMed2003

Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes.

In a previous search based on the envelope gene, we had identified two related proviral elements that could not be included in identified ERV families. An in silico database screening associated with an in vivo polymerase chain reaction search using primers in the reverse transcriptase domain, now allowed identification of a series of related elements, found at a limited number in simians. A phylogenetic analysis led to their inclusion in a new family of endogenous retroviruses with limited expansion, which we named ERV-Fc, and which is part of the enlarged ERV-F/H family. The human genome comprises only six HERV-Fc, among which two possess full-length coding envelope genes. A complete provirus was identified in the baboon, also disclosing a fully open envelope gene. Cloning of the sites orthologous to the envelope-coding human proviruses demonstrated presence of the integrated proviruses in chimpanzee and gorilla, but not in orangutan. For the baboon element, the orthologous locus was found empty even in the phylogenetically most closely related macaque, again suggesting, together with the complete identity of its LTRs, "recent" integration. The data presented are compatible with an evolutionary scheme in which the ERV-Fc proviruses would be the endogenous traces of an active retroviral element, possibly acting as an infectious retrovirus with low endogeneization potency, with evidence for integrations at two distinct periods of primate evolution.

Amino Acid Sequence↗

PubMed2005

Enhanced phenotyping of complex traits with a circadian clock model.

Models of biological systems are increasingly used to generate and test predictions in silico. This article explores the basic workings of a multifeedback network model of a circadian clock. In a series of in silico experiments, we investigated the influence of the number of feedbacks by adding and removing one or more. We further explore the possibilities of testing in silico models in classic "circadian" protocols. In addition, we performed an in silico mutagenesis screen (by altering parameters throughout the network), creating a library of mutants (based on "phenotype," not "genotype"), and subjected them to a variety of straightforward "circadian" protocols. The results of this mutant "taxonomy" are surprising. While most mutants can be identified (separated) using a limited set of experimental protocols, some resist such a separation, even when "mutations" are at vastly different locations within the complex model. Furthermore, some protocols distinguish similar alleles of the same component, which would be counterproductive. The described taxonomy invites experimental verification, in vivo, and may ultimately streamline genotyping of complex traits, which may have been based previously on imprecise phenotypes.

Circadian Rhythm↗

PubMedDate not supplied

Design of virtual libraries of umami-tasting molecules.

The introduction of molecular tools in food research offers the possibility to the food industry to benefit from the experience gained in the field by pharmaceutical companies. In this work we are showing how in silico virtual screening techniques based on molecular similarity were applied for identifying novel umami-tasting compounds. The results obtained suggest that 5'-ribonucleotides and monosodium glutamate might elicit the fifth basic taste via the same molecular mechanism. New algorithms were developed and used in this work, such as the dimension reduction of data sets by singular value decomposition and the introduction of the correlation dimension as a natural dimension of a chemical space. It is shown that the representations of molecular data sets in chemical spaces possess self-similar properties, characteristic of fractal objects.

Algorithms↗

PubMed2000

Simulations of the estrogen receptor ligand-binding domain: affinity of natural ligands and xenoestrogens.

We have carried out molecular dynamics (MD) simulations and free energy calculations on the alpha-subtype of the human estrogen receptor ligand-binding domain (ERalpha LBD) complexed with a number of known agonists and putative xenoestrogens. Our dynamical simulations of ligand-receptor complexes underscore the highly structured nature of the complex and offer some interesting insights into the structure-activity relationship (SAR) for these ligands. With traditional thermodynamic integration (TI) calculations, we calculate relative binding free energies for three known agonists, in good agreement with experimental values. The sheer number of possible xenoestrogenic compounds makes an approach using traditional free energy calculations unfeasible. Instead, we have made use of a single-step perturbation methodology that allows the calculation of relative free energies for a large number of related polyaromatic hydrocarbons (PAHs) from a single simulation. Our results show good (maximum deviation 3.3 kJ mol(-1)) agreement with experimental data, suggesting the possibility of large-scale xenoestrogen screening in silico to obtain strongly estrogenic compounds for subsequent experimental testing.

Diethylstilbestrol↗

PubMed2004

Computer-assisted design of selective imidazole inhibitors for cytochrome p450 enzymes.

A modified version of the DOCK program has been used to predict inhibitors for cytochrome P450cam and its L244A mutant. A library of azole compounds was designed in silico and screened for binding to wild-type P450cam. Lead compounds were synthesized and found to inhibit wild-type P450cam. To test our approach to designing ligands that discriminate between closely related sites, the azole library was DOCKed into both the active sites of wild-type P450cam and its L244A mutant. The L244A active site is predicted to be slightly larger than that of wild-type P450cam. Ligands predicted to have a high affinity for the mutant alone were synthesized and assayed with the recombinant enzymes. All of the compounds showed inhibition of the L244A enzyme (IC(50) = 6-40 microM), and the compounds that were predicted to be too large to bind to the wild-type showed poor inhibition (IC(50) > or = 1 mM). The binding mode was shown to be similar to that predicted by our modified version of DOCK by spectroscopic analysis. A discrepancy between the IC(50) values and spectroscopic K(s) values indicates that the spectroscopic binding constants do not accurately estimate inhibitory activity. This study, the first report of computer-assisted ligand (drug) design for P450 enzymes in which the coordination bond between imidazole and the heme is explicitly considered in structural modeling, opens a promising design avenue because azole compounds are widely used as P450 enzyme inhibitors and drugs.

Computer-Aided Design↗

PubMed2006

Identification of novel parasitic cysteine protease inhibitors by use of virtual screening. 2. The available chemical directory.

The incidence of parasitic infections such as malaria, leishmaniasis, and trypanosomiasis has been steadily increasing. Since the existing chemotherapy of these diseases suffers from lack of safe and effective drugs and/or the presence of widespread drug resistance, there is an urgent need for development of potent, mechanism-based antiparasitic agents against these diseases. Cysteine proteases have been established as valid targets for this purpose. The Available Chemical Directory consisting of nearly 355,000 compounds was screened in silico against the homology models of plasmodial cysteine proteases, falcipain-2, and falcipain-3, to identify structurally diverse non-peptide inhibitors. The study led to identification of 22 inhibitors of parasitic cysteine proteases out of which 18 compounds were active against falcipain-2 and falcipain-3. Eight compounds exhibited dual activity against both enzymes. Additionally, four compounds were found to inhibit L. donovani cysteine protease. While one of the cysteine protease inhibitors also exhibited in vitro antiplasmodial activity with an IC50 value of 9.5 microM, others did not show noticeable antiplasmodial activity up to 20 microM. A model identifying important pharmacophoric features common to the structurally diverse falcipain-2 inhibitors has also been developed. Very few potent non-peptide inhibitors of the parasitic cysteine proteases have been reported so far, and identification of these novel and chemically diverse inhibitors should provide leads to be optimized into candidates to treat protozoal infections.

Animals↗

PubMed2006

Calcium channel antagonists discovered by a multidisciplinary approach.

A multidisciplinary project has led to the discovery of novel, structurally diverse, L-type calcium entry blockers (CEBs). The absolute configuration of a recently reported CEB has been determined by vibrational circular dichroism spectroscopy, to assign the stereospecificity of the ligand-channel interaction. Thereafter, a virtual screening procedure was performed with the aim of identifying novel chemotypes for CEBs, starting from a database of purchasable compounds; 340,000 molecules were screened in silico in order to prioritize structures of interest for bioscreening. As a result, 20 compounds were tested in vitro, and functional and binding assays revealed several hits with promising behavior as CEBs.

Animals↗

PubMed2005

Structure-activity models for contact sensitization.

Allergic contact dermatitis (ACD) is a widespread cause of workers' disabilities. Although some substances found in the workplace are rigorously tested, the potential of the vast majority of chemicals to cause skin sensitization remains unknown. At the same time, exhaustive testing of all chemicals in workplaces is costly and raises ethical concerns. New approaches to developing information for risk assessment based on computational (quantitative) structure-activity relationship [(Q)SAR] methods may be complementary to and reduce the need for animal testing. Virtually any number of existing, de novo, and even preconceived compounds can be screened in silico at a fraction of the cost of animal testing. This work investigates the utility of ACD (Q)SAR modeling from the occupational health perspective using two leading software products, DEREK for Windows and TOPKAT, and an original method based on logistic regression methodology. It is found that the correct classification of (Q)SAR predictions for guinea pig data achieves values of 73.3, 82.9, and 87.6% for TOPKAT, DEREK for Windows, and the logistic regression model, respectively. The correct classification using LLNA data equals 73.0 and 83.2% for DEREK for Windows and the logistic regression model, respectively.

Allergens↗

PubMed2005

Design principles of chemical penetration enhancers for transdermal drug delivery.

Chemical penetration enhancers (CPEs) are present in a large number of transdermal, dermatological, and cosmetic products to aid dermal absorption of curatives and aesthetics. This wide spectrum of use is based on only a handful of molecules, the majority of which belong to three to four typical chemical functionalities, sporadically introduced as CPEs in the last 50 years. Using >100 CPEs representing several chemical functionalities, we report on the fundamental mechanisms that determine the barrier disruption potential of CPEs and skin safety in their presence. Fourier transform infrared spectroscopy studies revealed that regardless of their chemical make-up, CPEs perturb the skin barrier via extraction or fluidization of lipid bilayers. Irritation response of CPEs, on the other hand, correlated with the denaturation of stratum corneum proteins, making it feasible to use protein conformation changes to map CPE safety in vitro. Most interestingly, the understanding of underlying molecular forces responsible for CPE safety and potency reveals inherent constraints that limit CPE performance. Reengineering this knowledge back into molecular structure, we designed >300 potential CPEs. These molecules were screened in silico and subsequently tested in vitro for molecular delivery. These molecules significantly broaden the repertoire of CPEs that can aid the design of optimized transdermal, dermatological, and cosmetic formulations in the future.

Administration, Cutaneous↗

PubMed2006

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

The National Microbial Pathogen Data Resource (NMPDR) (http://www.nmpdr.org) is a National Institute of Allergy and Infections Disease (NIAID)-funded Bioinformatics Resource Center that supports research in selected Category B pathogens. NMPDR contains the complete genomes of approximately 50 strains of pathogenic bacteria that are the focus of our curators, as well as >400 other genomes that provide a broad context for comparative analysis across the three phylogenetic Domains. NMPDR integrates complete, public genomes with expertly curated biological subsystems to provide the most consistent genome annotations. Subsystems are sets of functional roles related by a biologically meaningful organizing principle, which are built over large collections of genomes; they provide researchers with consistent functional assignments in a biologically structured context. Investigators can browse subsystems and reactions to develop accurate reconstructions of the metabolic networks of any sequenced organism. NMPDR provides a comprehensive bioinformatics platform, with tools and viewers for genome analysis. Results of precomputed gene clustering analyses can be retrieved in tabular or graphic format with one-click tools. NMPDR tools include Signature Genes, which finds the set of genes in common or that differentiates two groups of organisms. Essentiality data collated from genome-wide studies have been curated. Drug target identification and high-throughput, in silico, compound screening are in development.

Bacteria↗

PubMed2004

BAC resources for the rat genome project.

Two 11-fold redundant bacterial artificial chromosome (BAC) libraries (RPCI-32 and CHORI-230) have been constructed to support the rat genome project. The first library was constructed using a male Brown Norway (BN/SsNHsd) rat as a DNA source long before plans for rat genome sequencing had been launched. The second library was prepared from a highly inbred female (BN/SsNHsd/MCW) rat in support of the rat genome sequencing project. The use of an inbred rat strain is essential to avoid problems with genome assembly resulting from the difficulty of distinguishing haplotype variation from variation among duplicons. We have demonstrated the suitability of the library by using a detailed quality assessment of large insert sizes, narrow size distribution, consistent redundancy for many markers, and long-range continuity of BAC contig maps. The widespread use of the two libraries as an integral part of the rat genome project has led to the database annotations for many clones, providing rat researchers with a rich resource of BAC clones that can be screened in silico for genes of interest.

Animals↗