Computational Approaches Towards the Rational
Design of Drug-like Compound Libraries Pp. 453-475
Hans Matter, Karl-Heinz Baringhaus, Thorsten Naumann, Thomas Klabunde, Bernard Pirard
Prediction of Intestinal Absorption and Blood-Brain Barrier Penetration by Computational Methods Pp. 477-496
David E.
Clark
Genotype-Phenotype Linkage for Directed
Evolution and Screening of Combinatorial Protein Libraries Pp. 497-509
N. Doi and H.
Yanagawa
High Throughput Log D Determination Using
Liquid Chromatography-Mass Spectrometry Pp. 511-519
Dean M.
Wilson, Xiaoli Wang, Erin Walsh, and Robyn A. Rourick
Solid-phase Bromination and Suzuki Coupling
of 2-Carboxyindoles Pp.
521-524
J. Tois , R.
Franzén , O. Aitio , I. Laakso, J. Huuskonen and J.Taskinen
Identifying Substrates for Endothelium-Specific
Tie-2 Receptor Tyrosine Kinase from Phage-Displayed Peptide Libraries for High
Throughput Screening Pp.
525-533
Su-Jun Deng,
Wei Liu, Catherine A. Simmons, John T. Moore and Gaochao Tian
[Back
to top] Computational Approaches Towards
the Rational Design of Drug-like Compound Libraries
Hans
Matter, Karl-Heinz Baringhaus, Thorsten Naumann, Thomas Klabunde, Bernard
Pirard
During the practice of combinatorial chemistry, it has been realized that molecular diversity is not the only essential feature in a synthetically feasible library. In addition, it is of utmost importance to enrich potential libraries with those molecules which could be converted to viable drug candidates. Given the enormous number of potentially synthesizable compounds, there is a need to design a subset of true “drug-like” compounds. In addition, a paradigm shift in drug discovery has resulted in the integration of pharmacokinetic and drug development activities into early stages of lead discovery. In particular, in silico filters are being developed and used to help identify and screen out compounds that are unlikely to become drugs. This paper highlights recent computational approaches towards the design of drug-like compound libraries, in particular, the prediction of drug-likeness in a more general sense as well as intestinal absorption through passive transport, the permeation of the blood-brain barrier and recent developments towards identification of potentially metabolically unstable molecules. Current computational tools for library design allow the incorporation of medicinal chemistry knowledge into library planning by a variety of methods, ranging from the use of privileged building blocks and simple counting of structural properties (e.g. number of hydrogen bonding partners) to relatively complex regression or neural network-based models to explain oral bioavailability and other pharmacokinetic properties by structural features. These tools are being incorporated more frequently into drug design according to the “rule-of-five” which refers to simple descriptors correlated to oral drug absorption. Combining experimental knowledge with effective computational filtering and prediction of various aspects of drug-likeness thus facilitates the rapid and cost-effective elimination of poor candidates prior to synthesis and helps focus attention on interesting molecules.
[Back to top] Prediction of Intestinal Absorption and Blood-Brain Barrier Penetration by Computational Methods
David
E. Clark
This review surveys the computational methods that have been developed with the aim of identifying drug candidates likely to fail later on the road to market. The specifications for such computational methods are outlined, including factors such as speed, interpretability, robustness and accuracy. Then, computational filters aimed at predicting “drug-likeness” in a general sense are discussed before methods for the prediction of more specific properties - intestinal absorption and blood-brain barrier penetration - are reviewed. Directions for future research are discussed and, in concluding, the impact of these methods on the drug discovery process, both now and in the future, is briefly considered.
[Back to top] Genotype-Phenotype Linkage for Directed
Evolution and Screening of Combinatorial Protein Libraries
N.
Doi and H. Yanagawa
The technologies for screening peptide and protein libraries for studies in the fields of directed protein evolution and functional genomics have advanced with astonishing speed. For screening of functional proteins, three technologies are required: (i) the construction of a gene library (genotype), (ii) the establish-ment of a linkage between each protein (phenotype) and its encoding gene (genotype), and (iii) the selection of desired proteins (phenotype) from the library. This review highlights the genotype-phenotype linkage technologies, which can be classified into three types; that is, cell-type linkage, virus-type linkage, and array-type linkage methods. These methods are summarized, and their advantages and disadvantages are discussed.
[Back
to top] High Throughput Log D Determination Using
Liquid Chromatography-Mass Spectrometry
Dean M. Wilson, Xiaoli Wang, Erin Walsh, and Robyn A. Rourick
A method has been developed which allows direct measurement of partition coefficients (log D, log P) using liquid chromatography-mass spectrometry (LC-MS). The high throughput, microtiter plate based protocol uses small quantities of 10 mM analyte in DMSO solution (5 mL) and is therefore amenable to standard archive and screening formats. Single Ion Monitoring (SIM) mass spectrometry is used to achieve optimal sensitivity. Experimental log D values for 34 known drugs have been determined, with partition coefficients ranging from –2 to 5, giving data very similar to literature values. In these analyses, deviations from known values average less than 0.3 log units. The sample handling and data processing have been significantly automated, and the protocol has been applied to over 800 in-house lead molecules to date. In its format, sensitivity, throughput, and amenability to automation, it represents significant progress in the direct measurement of partitioning behavior [1].
[Back
to top]
Solid-phase Bromination and Suzuki Coupling of 2-Carboxyindoles
J.
Tois , R. Franzén , O. Aitio , I. Laakso, J. Huuskonen and J.Taskinen
As part of an ongoing lead discovery project we have developed a convenient method for the modification and substitution of indole moieties at the 3-position. Selective bromination of three different 2-carboxyindoles was followed by Suzuki cross-coupling with aryl and heteroaryl boronic acids on a Merrifield resin solid-phase. After column chromatography, yields of the 3- substituted indoles ranged from 42-98%,
[Back
to top] Identifying Substrates for Endothelium-Specific Tie-2 Receptor Tyrosine
Kinase from Phage-Displayed Peptide Libraries for High Throughput Screening
The peptide substrate specificity of Tie-2 was probed using the phage display method in order to identify efficient substrate for high throughput screening. Two random peptide libraries, pGWX3YX4 and pGWX4YX4, were constructed, in which all twenty amino acid residues were represented at the X positions flanking the fixed tyrosine residue Y. A fusion protein of GST and the catalytic domain of human Tie-2 was used to perform the phage phosphorylation. The phosphorylated phage particles were enriched by panning over immobilized anti-phosphotyrosine antibody pY20 for a total of 5 rounds. Four phage clones (3T61, 3T68, C1-90 and D1-15) that express a peptide sequence that can be phosphorylated by the recombinant catalytic domain of human Tie-2 were identified. Synthetic peptides made according to the sequences of the 4 selected clones from the two libraries, which had widely different sequences, were active substrates of Tie-2. Kinetic analysis revealed that D1-15 had the best catalytic efficiency with a kcat/Km of 5.9x104 M-1 s-1. Three high throughput screening assay formats, dissociation-enhanced lanthanide fluoroimmunoassay (DELFIA), radioactive plate binding (RPB) and time-resolved fluorescent resonance energy transfer (TR-FRET) were developed to assess the suitability of these phage display selected peptides in screening Tie-2 inhibitors. Three out of four peptides were functional in the DELFIA assay and D1-15 was functional in the TR-FRET assay.