An efficient in silico screening method based on the protein-compound affinity matrix and its application to the design of a focused library for cytochrome P450 (CYP) ligands

A new method has been developed to design a focused library based on available active compounds using protein-compound docking simulations. This method was applied to the design of a focused library for cytochrome P450 (CYP) ligands, not only to distinguish CYP ligands from other compounds but also to identify the putative ligands for a particular CYP. Principal component analysis (PCA) was applied to the protein-compound affinity matrix, which was obtained by thorough docking calculations between a large set of protein pockets and chemical compounds. Each compound was depicted as a point in the PCA space. Compounds that were close to the known active compounds were selected as candidate hit compounds. A machine-learning technique optimized the docking scores of the protein-compound affinity matrix to maximize the database enrichment of the known active compounds, providing an optimized focused library.     

Screening drugs for metabolic stability using pulsed ultrafiltration mass spectrometry

A pulsed ultrafiltration-mass spectrometric screening method has been developed to evaluate the metabolic stability of drugs. Pooled human liver microsomes containing cytochrome P450 enzymes were trapped by an ultrafiltration membrane in a stirred flow-through chamber, and eight beta-blocker drugs including acebutolol, alprenolol, atenolol, metoprolol, oxprenolol, pindolol, propranolol, and timolol were flow-injected through the chamber along with the cofactor NADPH. The ultrafiltrate was collected, concentrated and analyzed by using liquid chromatography-tandem mass spectrometry (LC-MS-MS) in order to quantitate the unmetabolized fraction of each drug. The metabolic stability of each beta-blocker was determined based on the difference between the corresponding LC-MS-MS peak areas of an experimental incubation and a control without NADPH. A flow-through incubation method, pulsed ultrafiltration metabolic screening minimizes the potential for product feed back inhibition of cytochrome P450 enzymes. The importance of this phenomenon was illustrated by the observation that the metabolic stability of the set of beta-blocker drugs measured using pulsed ultrafiltration more closely resembled the in vivo stability than that determined using a conventional batch incubation with microsomes or an incubation with human hepatocytes. Since a mixture of compounds was analyzed, the relative metabolic stability of each compound could be assessed by comparison to the other compounds in the incubation. This approach might be particularly useful for the ranking of a directed library of drug leads with respect to metabolic stability and then the selection of lead compounds for further drug development.     

Exploratory Study on the RNA‐Binding Structural Motifs by Library Screening Targeting pre‐miRNA‐29 a

The metabolic stream of microRNA (miRNA) production, the so‐called maturation process of miRNAs, became one of important metabolic paths for drug‐targeting to modulate the expression of genes related to a number of diseases. We carried out discovery studies on small molecules binding to the precursor of miR‐29a (pre‐miR‐29a) from a chemical library containing 41 119 compounds (AQ library) by the fluorescent indicator displacement (FID) assay using the xanthone derivative X2SdiMe as a fluorescent indicator. The FID assay provided 1075 compounds, which showed an increase of fluorescence. These compounds were subsequently submitted to a binding analysis in a surface plasmon resonance (SPR) assay on a pre‐miR‐29a immobilized surface. 21 hit compounds were identified with a good reproducibility in the binding. These compounds have not been reported to bind to RNA until now and can be classified into two groups on the basis of the kinetics in the binding. To gain more information on the motif structures that could be necessary for the binding to pre‐miR‐29a, 19 substructures were selected from the hit compounds. The substructure library (SS library) which consisted of 362 compounds was prepared from the AQ library. An SPR assay of the SS library on pre‐miR‐29a‐immobilized surface suggested that five substructures could potentially be important structural motifs to bind to pre‐miR‐29a. These studies demonstrate that the combination of FID‐based screening of chemical library and subsequent SPR assay would be one way for obtaining practical solutions for the discovery of molecules which bind to the target pre‐miRNAs.     

Rational principles of compound selection for combinatorial library design

It is practically impossible in a short period of time to synthesize and test all compounds in any large exhaustive chemical library. We discuss rational approaches to selecting representative subsets of virtual libraries that help direct experimental synthetic efforts for both targeted and diverse library design. For targeted library design, we consider principles based on the similarity to lead molecules. In the case of diverse library design, we discuss algorithms aimed at the selection of both diverse and representative subsets of the entire chemical library space. We illustrate methodologies with several practical examples.     

Modeling the structure of chain-molecule liquids: A computer simulation of the n-alkanes C8–C30

Computer models of a series of liquid n-alkanes were generated, allowing for continuous variation of torsion angles and of atomic positions. Torsional and intramolecular and intermolecular non-bonded potentials were introduced. Calculated fractions of gauche bonds are slightly higher than those calculated from a rotational isomeric state model. Calculated radial distribution functions exhibit peaks in good agreement with experimental data. No directional correlation between chains is found, except at very short distances. Calculated end-to-end distances and radii of gyration indicate random coil conformations. These results are unaffected by extension of the range of interaction to the attractive region and by variations of temperature and density.     

Library Design Guided by In-house Developed Computer Tools

In recent years, combinatorial library synthesis for drug discovery begins to migrate from library synthesis solely dictated by chemistry availability to design and synthesis of libraries with more drug-like properties. Lipinski's rule of five has been used to evaluate drug-like properties of individual compound; recently LibProTM, a new computation program has been developed at Pharmacopeia to evaluate durg-like properties of libraries. By using LibPrpTM, chemists at Pharmacopeia are able to obtain information of molecular weight and ClogP distribution of a library, and percentage of library members that violate Lipinski's rule after input structures of synthons for each combinatorial step. Currently, a "virtual library design” approach that is to calculate properties of a library at conceptual phase of the library design has been used to predetermine the value of the library. Also a new computer program used to predict "Absorption” of compounds will also be discussed.     

Ligand design by a combinatorial approach based on modeling and experiment: application to HLA-DR4

Combinatorial synthesis and large scale screening methods are being used increasingly in drug discovery, particularly for finding novel lead compounds. Although these "random" methods sample larger areas of chemical space than traditional synthetic approaches, only a relatively small percentage of all possible compounds are practically accessible. It is therefore helpful to select regions of chemical space that have greater likelihood of yielding useful leads. When three-dimensional structural data are available for the target molecule this can be achieved by applying structure-based computational design methods to focus the combinatorial library. This is advantageous over the standard usage of computational methods to design a small number of specific novel ligands, because here computation is employed as part of the combinatorial design process and so is required only to determine a propensity for binding of certain chemical moieties in regions of the target molecule. This paper describes the application of the Multiple Copy Simultaneous Search (MCSS) method, an active site mapping and de novo structure-based design tool, to design a focused combinatorial library for the class II MHC protein HLA-DR4. Methods for the synthesizing and screening the computationally designed library are presented; evidence is provided to show that binding was achieved. Although the structure of the protein-ligand complex could not be determined, experimental results including cross-exclusion of a known HLA-DR4 peptide ligand (HA) by a compound from the library. Computational model building suggest that at least one of the ligands designed and identified by the methods described binds in a mode similar to that of native peptides.     

Templated synthesis of mesolamellar n-alkylamine borophosphates

A family of lamellar mesostructured n-alkylamine borophosphates, denoted C n A-BPO (BPO stands for inorganic borophosphate layer; n = 9-15, the number of carbon atoms in the n-alkylamine chain) has been prepared hydrothermally at 160 degrees C by using neutral n-alkylamines as templates. Those C n A-BPO compounds were characterized by powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), thermogravimetric measurements, and differential thermal analysis (TG-DTA) as well as chemical analyses. Interestingly, these compounds may form a bilayer, a monolayer, or mixed state of bilayer and monolayer structures depending on the content of n-alkylamine. Linear relationships for both bilayer and monolayer compounds were observed between the interlayer distances and the numbers of carbon atoms in the n-alkylamine chain. The thickness of the inorganic layers, the arrangement of n-alkylamine in the interlayer space, and the composition of the compounds are proposed.     

Discovery of new heterogeneous catalysts for the selective oxidation of propane to acrolein

Combinatorial synthesis and screening technique have been applied to investigate the catalytic activity and selectivity of ternary and quaternary mixed-metal oxide catalysts for the selective oxidation of propane. The catalyst libraries were prepared via a modified sol-gel method using a synthesis robot and library design software, and examined for the catalytic activities in a simple high-throughput reactor system connected to a mass spectrometer for product analysis. Ternary Mo-Cr-Te, V-Cr-Sb, and Mo-V-Cr catalysts have been selected for potential candidate by composition spread approach. In a next generation composition spread library, the composition space of these three ternary compositions was sampled. Screening of this 198-member library provided substantial evidence that each ternary system has its own optimum composition where acrolein formation is highest. In addition, the composition space of the quaternary reference system Mo-V-Te-Nb mixed-oxides has also been prepared and sampled.     

Polyhedral structures with an odd number of vertices: nine-coordinate metal compounds

The stereochemistry of nine-coordinate transition-metal and rare-earth compounds has been studied by means of continuous shape measures (CShM) and related tools. Several reference nine-vertex polyhedra have been defined and their minimal distortion interconversion paths established. A theoretical shape map is presented in which the structures can be placed according to their distances in CShM space to the capped square antiprism and the tricapped trigonal prism, which are the most common polyhedra in nine-coordinate compounds. The structures of almost 2000 metal coordination spheres in molecular and extended solid-state compounds have been analyzed. Clear stereochemical trends can be established for subsets of these compounds grouped according to the nature of their ligands, which include families of compounds spread along the interconversion paths between the capped square antiprism and the capped cube, or between the tricapped trigonal prism and the tridiminished icosahedron.     

Ligand-based virtual screening by novelty detection with self-organizing maps

We describe a novel method for ligand-based virtual screening, based on utilizing Self-Organizing Maps (SOM) as a novelty detection device. Novelty detection (or one-class classification) refers to the attempt of identifying patterns that do not belong to the space covered by a given data set. In ligand-based virtual screening, chemical structures perceived as novel lie outside the known activity space and can therefore be discarded from further investigation. In this context, the concept of "novel structure" refers to a compound, which is unlikely to share the activity of the query structures. Compounds not perceived as "novel" are suspected to share the activity of the query structures. Nowadays, various databases contain active structures but access to compounds which have been found to be inactive in a biological assay is limited. This work addresses this problem via novelty detection, which does not require proven inactive compounds. The structures are described by spatial autocorrelation functions weighted by atomic physicochemical properties. Different methods for selecting a subset of targets from a larger set are discussed. A comparison with similarity search based on Daylight fingerprints followed by data fusion is presented. The two methods complement each other to a large extent. In a retrospective screening of the WOMBAT database novelty detection with SOM gave enrichment factors between 105 and 462-an improvement over the similarity search based on Daylight fingerprints between 25% and 100%, when the 100 top ranked structures were considered. Novelty detection with SOM is applicable (1) to improve the retrieval of potentially active compounds also in concert with other virtual screening methods; (2) as a library design tool for discarding a large number of compounds, which are unlikely to possess a given biological activity; and (3) for selecting a small number of potentially active compounds from a large data set.     

Geometric structure of X(AuPH3)4+ (X = N, P, As, Sb): Td or C4v?

The geometric structures of X(AuPH3)4+ (X = N, P, As, Sb) compounds have been determined by DFT and ab-initio methods. In agreement with experiment, N(AuPH3)4+ is Td and As(AuPH3)4+ is C4v with an apical As atom. Calculated molecular and experimental crystal structure parameters are compared. The structures of X(AuPH3)4+ (X = P, Sb) are predicted. P(AuPH3)4+ favors Td, as confirmed by CC2. The closed-shell interaction distances of Au...Au from Xalpha are consistent with the experimental values. The electronic structures and chemical deformation densities are analyzed.     

Use of catalyst pharmacophore models for screening of large combinatorial libraries

Using a data set comprised of literature compounds and structure-activity data for cyclin dependent kinase 2, several pharmacophore hypotheses were generated using Catalyst and evaluated using several criteria. The two best were used in retrospective searches of 10 three-dimensional databases containing over 1,000,000 proprietary compounds. The results were then analyzed for the efficiency with which the hypotheses performed in the areas of compound prioritization, library prioritization, and library design. First as a test of their compound prioritization capabilities, the pharmacophore models were used to search combinatorial libraries that were known to contain CDK active compounds to see if the pharmacophore models could selectively choose the active compounds over the inactive compounds. Second as a test of their utility in library design again the pharmacophore models were used to search the active combinatorial libraries to see if the key synthons were over represented in the hits from the pharmacophore searches. Finally as a test of their ability to prioritize combinatorial libraries, several inactive libraries were searched in addition to the active libraries in order to see if the active libraries produced significantly more hits than the inactive libraries. For this study the pharmacophore models showed potential in all three areas. For compound prioritization, one of the models selected active compounds at a rate nearly 11 times that of random compound selection though in other cases models missed the active compounds entirely. For library design, most of the key fragments were over represented in the hits from at least one of the searches though again some key fragments were missed. Finally, for library prioritization, the two active libraries both produced a significant number of hits with both pharmacophore models, whereas none of the eight inactive libraries produced a significant number of hits for both models.     

Combinatorial library-based design with Basis Products

Uncovering useful lead compounds from a vast virtual library of synthesizable compounds continues to be of tremendous interest to pharmaceutical researchers. Here we present the concept of Basis Products (BPs), a new and broadly applicable method for achieving efficient selections from a combinatorial library. By definition, Basis Products are a strategically selected subset of compounds from a potentially very large combinatorial library, and any compound in a combinatorial library can represented by its BPs. In this article we will show how to use BP docking scores to find the top compounds of a combinatorial library. Compared with the brute-force docking of an entire virtual library, docking with BPs are much more efficient because of the substantial size reduction, saving both time and resources. We will also demonstrate how BPs can be used for property-based combinatorial library designs. Furthermore, BPs can also be considered as fragments carrying chemistry knowledge, hence they can potentially be used in combination with any fragment-based design method. Therefore, BPs can be used to integrate combinatorial design with structure-based design and/or fragment-based design. Other potential applications of BPs include lead hopping and consensus core building, which we will describe briefly as well in this report.