Portmann Robert

Bio: Portmann Robert is an academic researcher from Novartis. The author has contributed to research in topics: Carboxamide & Alkyl. The author has an hindex of 7, co-authored 25 publications receiving 454 citations.

Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking.

Abstract: To assess the potential of protein kinase CK2 as a target for developing new antitumor agents, we have undertaken a search for inhibitors of this enzyme. As part of this effort, we report here the discovery of the potent and selective CK2 inhibitor (5-oxo-5,6-dihydroindolo[1,2-a]quinazolin-7-yl)acetic acid. We identified this inhibitor of a novel structural type by high-throughput docking of our corporate compound collection in the ATP binding site of a homology model of human CK2, using an appropriate protocol. The synthesis of the inhibitor as well as that of related analogues whose CK2 inhibitory activities give support to the binding mode proposed by the docking program is described. The results obtained suggest that virtual screening of a 3D database by molecular docking is a useful approach for lead finding provided that adapted postdocking filtering and reranking procedures are applied to the primary hit list.

Naphthalen -1 -yl -(4 -pentyloxynaphthalen -1 -yl)methanone : A potent, orally bioavailable human CB1/CB2 dual agonist with antihyperalgesic properties and restricted central nervous system penetration

Abstract: Selective activation of peripheral cannabinoid CB1 receptors has the potential to become a valuable therapy for chronic pain conditions as long as central nervous system effects are attenuated. A new class of cannabinoid ligands was rationally designed from known aminoalkylindole agonists and showed good binding and functional activities at human CB1 and CB2 receptors. This has led to the discovery of a novel CB1/CB2 dual agonist, naphthalen-1-yl-(4-pentyloxynaphthalen-1-yl)methanone (13), which displays good oral bioavailability, potent antihyperalgesic activity in animal models, and limited brain penetration.

Synthesis of acylaminoalkenylene amides useful as substance p antagonists

Abstract: A process for preparing compounds of formula (I) or a solvate or hydrate thereof, where R, R1, R2, R3 and R5 have the meanings as indicated in the specification. Such compounds are useful in the treatment of a number of conditions associated with substance P and neurokinin.

Notiz zur Synthese Eines Optisch Aktiven Ace‐Hemmers mit Amino‐oxo‐benzazepin‐1‐alkansäure‐Struktur mittels enantiokonvergierender kristallisationsinduzierter Racemat‐Trennung

Abstract: Note on the Synthesis of an Optically Active ACE Inhibitor with Amino-oxo-benzazepine-1-alkanoic-Acid Structure by Means of an Enantioconvergent Crystallization-Based Resolution An enantioselective synthesis of the potent angiotensin-converting enzyme inhibitor (1′S,3S)-3-[(1′-(ethoxy-carbonyl)-3′-phenylpropyl)amino]-2,3,4,5-tetrahydro-2-oxo-1H-1-benzazepine-1-acetic acid hydrochloride (3) is described which user a crystallization-based resolution of a racemic amino intermediate with concomitant racemization of the unwanted enantiomer.

Crystal modification of 1-(2,6-difluorobenzyl)-1h-1,2,3-triazole-4-carboxamide and its use as antiepileptic

Abstract: The invention relates to the novel modifications B and C of the compound 1-(2,6-difluorobenzyl)-1H-1,2,3-triazole-4-carboxamide of formula (I), its use for the treatment of epilepsy and pharmaceutical preparations comprising these crystal modifications.

Docking and scoring in virtual screening for drug discovery: methods and applications.

Abstract: Computational approaches that 'dock' small molecules into the structures of macromolecular targets and 'score' their potential complementarity to binding sites are widely used in hit identification and lead optimization Indeed, there are now a number of drugs whose development was heavily influenced by or based on structure-based design and screening strategies, such as HIV protease inhibitors Nevertheless, there remain significant challenges in the application of these approaches, in particular in relation to current scoring schemes Here, we review key concepts and specific features of small-molecule-protein docking methods, highlight selected applications and discuss recent advances that aim to address the acknowledged limitations of established approaches

The SWISS-MODEL Repository and associated resources

Abstract: SWISS-MODEL Repository (http://swissmodel.expasy.org/repository/) is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models generated by automated homology modelling for all sequences in Swiss-Prot and for relevant models organisms. Regular updates ensure that target coverage is complete, that models are built using the most recent sequence and template structure databases, and that improvements in the underlying modelling pipeline are fully utilised. As of September 2008, the database contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. SWISS-MODEL Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace (http://swissmodel.expasy.org/workspace/). Annotation of models with functional information and cross-linking with other databases such as the Protein Model Portal (http://www.proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources.

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.

Abstract: SWISS-MODEL pioneered the field of automated modeling as the first protein modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper.

A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.

Abstract: A thorough evaluation of some of the most advanced docking and scoring methods currently available is described, and guidelines for the choice of an appropriate protocol for docking and virtual screening are defined. The generation of a large and highly curated test set of pharmaceutically relevant protein-ligand complexes with known binding affinities is described, and three highly regarded docking programs (Glide, GOLD, and ICM) are evaluated on the same set with respect to their ability to reproduce crystallographic binding orientations. Glide correctly identified the crystallographic pose within 2.0 A in 61% of the cases, versus 48% for GOLD and 45% for ICM. In general Glide appears to perform most consistently with respect to diversity of binding sites and ligand flexibility, while the performance of ICM and GOLD is more binding site-dependent and it is significantly poorer when binding is predominantly driven by hydrophobic interactions. The results also show that energy minimization and reranking of the top N poses can be an effective means to overcome some of the limitations of a given docking function. The same docking programs are evaluated in conjunction with three different scoring functions for their ability to discriminate actives from inactives in virtual screening. The evaluation, performed on three different systems (HIV-1 protease, IMPDH, and p38 MAP kinase), confirms that the relative performance of different docking and scoring methods is to some extent binding site-dependent. GlideScore appears to be an effective scoring function for database screening, with consistent performance across several types of binding sites, while ChemScore appears to be most useful in sterically demanding sites since it is more forgiving of repulsive interactions. Energy minimization of docked poses can significantly improve the enrichments in systems with sterically demanding binding sites. Overall Glide appears to be a safe general choice for docking, while the choice of the best scoring tool remains to a larger extent system-dependent and should be evaluated on a case-by-case basis.

Exploring biology with small organic molecules

Abstract: Small organic molecules have proven to be invaluable tools for investigating biological systems, but there is still much to learn from their use. To discover and to use more effectively new chemical tools to understand biology, strategies are needed that allow us to systematically explore ‘biological-activity space’. Such strategies involve analysing both protein binding of, and phenotypic responses to, small organic molecules. The mapping of biological-activity space using small molecules is akin to mapping the stars — uncharted territory is explored using a system of coordinates that describes where each new feature lies.