Synthetic library design

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

Drugs produce their therapeutic effects by modulating specific targets, and there are 89 innovative targets of first-in-class drugs approved in 2004–17, each with information about drug clinical trial dated back to 1984. Analysis of the clinical trial timelines of these targets may reveal the trial-speed differentiating features for facilitating target assessment. Here we present a comprehensive analysis of all these 89 targets, following the earlier studies for prospective prediction of clinical success of the targets of clinical trial drugs. Our analysis confirmed the literature-reported common druggability characteristics for clinical success of these innovative targets, exposed trial-speed differentiating features associated to the on-target and off-target collateral effects in humans and further revealed a simple rule for identifying the speedy human targets through clinical trials (from the earliest phase I to the 1st drug approval within 8 years). This simple rule correctly identified 75.0% of the 28 speedy human targets and only unexpectedly misclassified 13.2% of 53 non-speedy human targets. Certain extraordinary circumstances were also discovered to likely contribute to the misclassification of some human targets by this simple rule. Investigation and knowledge of trial-speed differentiating features enable prioritized drug discovery and development.

Screening combinatorial libraries of cyclic peptides using the yeast two-hybrid assay

Peptides are useful reagents for reverse analysis of protein function in a variety of organisms, as they have a dominant mode of action that can inhibit protein interactions or activities. Further, peptides are important tools for validating proteins as therapeutic targets, for determining structure/activity relationships, and for designing small molecules. Genetic selection strategies have been developed for screening combinatorial peptide libraries to rapidly isolate peptides that interact with a given target. In genetic selections and biological assays, linear peptides are not very stable and are rapidly degraded. In contrast, cyclic peptides are more stable and bind with higher affinity. Genetic selections of cyclic peptides are difficult as they are not compatible with most selection technologies. Thus, there has been limited number of applications that use cyclic peptides for the reverse analysis of protein function.Here, we describe a protocol to isolate cyclic peptides that bind proteins in the yeast two-hybrid assay. Cyclic peptides used in the yeast two-hybrid assay are referred to as "lariat" peptides. Lariat peptides are made by blocking the intein-producing cyclic peptide reaction at an intermediate step. They consist of a lactone cyclic peptide or "noose" region connected by an amide bond to a transcription activation domain. Combinatorial libraries of >10(7) lariat peptides can be screened using the yeast two-hybrid assay to isolate lariat peptides for studying the function or validating the therapeutic potential of protein targets.

Design of chemical libraries for screening

IMPORTANCE OF THE FIELD

The ultimate goal of discovery screening is to have a fast and cost-effective strategy to meet the demands of producing high-content lead series with improved prospects for clinical success. While high-throughput screening (HTS) dominates the drug discovery landscape, other processes and technologies have emerged, including high-content screening and fragment-based design to provide alternatives that may be more suitable for certain targets. There has been a growing interest in reducing the number of compounds to be screened to prevent the escalation in the costs, time and resources associated with HTS campaigns. Library design plays a central role in these efforts.

AREAS COVERED IN THIS REVIEW

This opinion provides a survey of some recent developments in the diversity based library design process, but within a historical context. In particular, the importance of chemotyping and substructure analysis and the challenges presented by novel lead discovery technologies that require the design of libraries for screening are discussed.

WHAT THE READER WILL GAIN

Readers will gain an appreciation of some developments in the field of library design and the factors that are driving the development of new library design technologies; specifically, challenges presented for chemoinformatics with the novel screening technologies in diversity based screening and compound filtering.

TAKE HOME MESSAGE

Chemotyping and substrutural analysis are techniques that have been underutilized in the process of library design. However, they offer a direct way to evaluate libraries and have been successfully used to develop predictive methodologies. Tools are available to this end, but the full power of the approach has not been realized yet.

Computational chemistry approaches to drug discovery in signal transduction

The advent of therapeutic strategies aimed at targeting specific macromolecular components of deregulated signaling pathways associated with particular disease states has given rise to the idea that it should be possible to design ligands as drug candidates to these targets from first principles. This concept has been beckoning for a long time but structure-based ligand design only became feasible once it was possible to determine the 3-D structures of molecular targets at atomic resolution. However, structure-based design turned out to be difficult, chiefly because under physiological conditions both receptors and ligands are not static but they behave dynamically. While it is possible to design ligands with high steric and electronic complementarity to a receptor site, it is always uncertain how biologically relevant the assumed conformations of both ligand and receptor actually are. The fact that it remains beyond our current abilities to predict with sufficient accuracy the affinity between hypothetical ligand and receptor poses is in part connected with this problem and continues to confound the reliable prediction of drug-like ligands for therapeutic targets. Nevertheless, significant progress has been made and so-called virtual screening methods that use computational methods to dock candidate ligands into receptor sites and to score the resulting complexes are now used routinely as one of the components in drug discovery screening campaigns. Here an overview is given of the underlying principles, implementations, and applications of structure-guided computational design technologies. Although the emphasis is on receptor-based strategies, mention will also be made of some of the more established ligand-based approaches, such as similarity analyses and quantitative structure-activity relationship methods.

Blood-brain barrier permeability considerations for CNS-targeted compound library design

A further refinement of the concept of drug-likeness is required for compound libraries intended for central nervous system (CNS) targets to account for the limitations imposed by blood-brain barrier permeability. This review describes criteria and processes that can be applied in the de novo design and assembly of libraries to increase the odds of compounds residing within CNS-accessible chemical space. A number of published examples where CNS activity and/or penetration characteristics have been a factor in library design are discussed.

Structure-directed combinatorial library design

In recent years pharmaceutical companies have utilized structure-based drug design and combinatorial library design techniques to speed up their drug discovery efforts. Both approaches are routinely used in the lead discovery and lead optimization stages of the drug discovery process. Fragment-based drug design, a new power tool in the drug design toolbox, is also gaining acceptance across the pharmaceutical industry. This review will focus on the interplay between these three design techniques and recent developments in computational methodologies that enhance their integration. Examples of successful synergistic applications of these three techniques will be highlighted. Opinion regarding possible future directions of the field will be given.

Split-intein mediated circular ligation used in the synthesis of cyclic peptide libraries in E. coli

Recent advances in chemical biology and the advantages presented by in vivo screening have highlighted the need for a robust and flexible biologically synthesized small-molecule library. Herein we describe a method for the biosynthesis of cyclic peptide libraries of up to 10(8) members in Escherichia coli using split-intein circular ligation of peptides and proteins (SICLOPPS). The method utilizes split-intein chemistry to cyclize randomized peptide sequences. The cyclic peptide library can potentially be of any size and the peptide itself may contain unlimited random residues. However, the library size is limited by the transformation efficiency of E. coli and random residues are generally limited to five, but additional amino acids can be used in the cyclic peptide backbone, varying the structure and ring size of the cyclic peptide. SICLOPPS libraries have been combined with a bacterial reverse two-hybrid system in our labs and used in the identification of inhibitors of several protein-protein interactions. This protocol is expected to take around 3-4 weeks to implement.

Hybrid molecules with a dual mode of action: dream or reality?

The drug market is still dominated by small molecules, and more than 80% of the clinical development of drug candidates in the top 20 pharmaceutical firms is still based on small molecules. The high cost of developing and manufacturing "biological drugs" will contribute to leaving an open space for drugs based on cheap small molecules. Four main routes can be explored to design affordable and efficient drugs: (i) a drastic reduction of the production costs of biological drugs, (ii) a real improvement of drug discovery via "computer-assisted combinatorial methods", (iii) going back to an extensive exploration of natural products as drug sources, and (iv) drug discovery by rational drug design and bio-inspired design that hopefully includes serendipity and human inspiration. At the border between bio-inspired design and rational design, one can imagine preparation of hybrid molecules with a dual mode of action to create efficient new drugs. In this Account, hybrid molecules are defined as chemical entities with two or more structural domains having different biological functions and dual activity, indicating that a hybrid molecule acts as two distinct pharmacophores. In order to obtain new antimalarial drugs that are affordable and able to avoid the emergence of resistant strains, we developed hybrid molecules with a dual mode of action (a "double-edged sword") able to kill multiresistant strains by oral administration. These hybrid molecules, named trioxaquines, with two pharmacophores able to interact with the heme target are made with a trioxane motif covalently linked to an aminoquinoline entity. More than 100 trioxaquines have been prepared by Palumed over a period of 4 years, and in collaboration with Sanofi-Aventis, the trioxaquine PA1103-SAR116242 has been selected in January 2007 as candidate for preclinical development.