The SeeDs approach: integrating fragments into drug discovery

Finding novel compounds as starting points for optimization is a major challenge in drug discovery research. Fragment-based methods have emerged in the past ten years as an effective way to sample chemical diversity with a limited number of low molecular weight compounds. The structures of the fragments(s) binding to the protein can then be used to design new compounds with increased affinity, specificity and novelty. This article describes the Vernalis approach to fragment based drug discovery, called SeeDs (Structural exploitation of experimental Drug startpoints). The approach includes the design of a fragment library, identification of fragments that bind competitively to a target by ligand-based NMR techniques and protein crystal structures to characterize binding. Fragments that bind are then evolved to hits, either by growing the fragment or by combining structural features from a number of compounds. The process is illustrated with examples from recent medicinal chemistry programmes to discover compounds against the oncology targets Hsp90 and PDK1. In addition, we summarise our experience with using molecular docking calculations to predict fragment binding and anecdotes on the selectivity and binding modes for fragments seen against a range of targets.     

SkelGen: a general tool for structure-based de novo ligand design

The recent lapse in productivity in the pharmaceutical industry has facilitated the emergence of experimental and in silico structure-based design methodologies, based on identification of biologically active low molecular weight fragments that can be exploited to produce potential drug candidates with diverse chemistries. SkelGen, an in silico example of this methodology, is reviewed. The ability of this algorithm to identify chemically diverse low molecular weight fragments that would potentially bind to DNA gyrase is recounted, as is the first purely de novo structure-based design of five compounds that show at least micromolar activity against the estrogen receptor. The ability of the algorithm to incorporate partial protein flexibility during its design of compounds to the estrogen receptor is discussed, and an opinion as to the near and long-term futures for de novo design algorithms is expressed.     

High-throughput X-ray crystallography for drug discovery

Knowledge of the three-dimensional structures of protein targets has the potential to greatly accelerate drug discovery, but technical challenges and time constraints have traditionally limited its use to lead optimization. Its application is now being extended beyond structure determination into new approaches for lead discovery. Structure-activity relationships by nuclear magnetic resonance have been widely used to detect ligand binding and to give some indication of the location of the binding site. X-ray crystallography has the advantage of defining ligand-binding sites with greater certainty. High-throughput approaches make this method applicable to screening to identify molecular fragments that bind protein targets, and to defining precisely their binding sites. X-ray crystallography can then be used as a rapid technique to guide the elaboration of the fragments into larger molecular weight compounds that might be useful leads for drug discovery.     

Discovery of β2 Adrenergic Receptor Ligands Using Biosensor Fragment Screening of Tagged Wild-Type Receptor

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Electron density guided fragment-based lead discovery of ketohexokinase inhibitors

A fragment-based drug design paradigm has been successfully applied in the discovery of lead series of ketohexokinase inhibitors. The paradigm consists of three iterations of design, synthesis, and X-ray crystallographic screening to progress low molecular weight fragments to leadlike compounds. Applying electron density of fragments within the protein binding site as defined by X-ray crystallography, one can generate target specific leads without the use of affinity data. Our approach contrasts with most fragment-based drug design methodology where solution activity is a main design guide. Herein we describe the discovery of submicromolar ketohexokinase inhibitors with promising druglike properties.     

NMR fragment screening: tackling protein-protein interaction targets

High-throughput screening of libraries containing compounds of 'drug-like' molecular weight has frequently resulted in no or poor drug candidates, especially when screening against demanding drug targets such as protein-protein interactions. Fragment-based lead discovery and optimization has evolved as a promising solution to this problem by combining the universal adaptability of low-molecular-weight fragments with immediate structural information on fragment binding modes. This review focuses on nuclear magnetic resonance (NMR) fragment screening techniques, which provide a unique combination of medium-throughput, direct binding site information and broad applicability. The utility and exemplary data of chemical shift-detected NMR fragment screening applied to the challenging protein-protein interaction target PDZ domains are summarized.     

SPR-based fragment screening: advantages and applications

Fragment-based screening has recently evolved into a promising strategy in drug discovery, and a range of biophysical methods can be employed for fragment library screening. Relevant approaches, such as X-ray, NMR and tethering are briefly introduced focussing on their suitability for fragment-based drug discovery. In particular the application of surface plasmon resonance (SPR) techniques to the primary screening of large libraries comprising small molecules is discussed in detail. SPR is known to be a powerful tool for studying biomolecular interactions in a sensitive and label-free detection format. Advantages of SPR methods over more traditional assay formats are discussed and the application of available channel and array based SPR systems to biosensing are reviewed. Today, SPR protocols have been applied to secondary screening of compound libraries and hit conformation, but primary screening of large fragment libraries for drug discovery is often hampered by the throughput of available systems. Chemical microarrays, in combination with SPR imaging, can simultaneously generate affinity data for protein targets with up to 9,216 immobilized fragments per array. This approach has proven to be suitable for screening fragment libraries of up to 110,000 compounds in a high throughput fashion. The design of fragment libraries and appropriate immobilization chemistries are discussed, as well as suitable follow-up strategies for fragment hit optimization. Finally, described case studies demonstrate the successful identification of selective low molecular weight inhibitors for pharmacologically relevant drug targets through the SPR screening of fragment libraries.     

Thermodynamics of binding interactions in the rational drug design process

Modern drug discovery usually involves the rapid screening of large numbers of compounds, either individually or in resolvable mixtures. These compounds may be complex and lead-like or may be small fragments representing optimal scaffolds. Several methods are suitable for detecting binding interactions based on a wide range of different physical platforms. However, the use of thermodynamic measurements has a role to play both in the high-throughput identification of binders and also in the fundamental understanding of molecular interaction, which is central to rational drug design. This review describes the benefits and drawbacks of using thermodynamic characterisation of binding interactions at various stages in the rational drug design process and highlights future opportunities for advances in instrumentation and methodology.     

Treatment with dilute alkali-nuclease S1 permits the analysis of DNA damage: cells treated with platinum analogues

We describe here an approach to characterize various lesions induced in DNA by drug treatments, using three parameters: (a) release of single-stranded DNA fragments by cell lysis in dilute alkali, which result from enzymatic strand scission during DNA repair or chemical alterations of DNA; (b) the presence of high molecular weight DNA in cells after lysis in dilute alkali followed by nuclease S1 treatment which, due to drug-induced DNA cross-links and its level is a measure of the amount of DNA-containing cross-links; and (c) the appearance of small double-stranded DNA fragments, when the cell lysis is followed by digestion with nuclease S1 to remove single-stranded DNA. This DNA shows the same characteristics as DNA of untreated cells, but it may contain monoadducts. By following the flow of label through the three parameters, one can characterize both the lesions induced in DNA and how the lesions are repaired. We report here results of three platinum analogues: cis-Pt(II), trans-Pt(II), and cis-FLAP(II). A large proportion of DNA in treated cells appears as fragments (parameter c). The cis- compounds and trans- compounds differ with regard to appearance of high molecular weight DNA (parameter b) and the initial release of fragments (parameter a).     

Fragment-based lead discovery using X-ray crystallography

Fragment screening offers an alternative to traditional screening for discovering new leads in drug discovery programs. This paper describes a fragment screening methodology based on high throughput X-ray crystallography. The method is illustrated against five proteins (p38 MAP kinase, CDK2, thrombin, ribonuclease A, and PTP1B). The fragments identified have weak potency (>100 microM) but are efficient binders relative to their size and may therefore represent suitable starting points for evolution to good quality lead compounds. The examples illustrate that a range of molecular interactions (i.e., lipophilic, charge-charge, neutral hydrogen bonds) can drive fragment binding and also that fragments can induce protein movement. We believe that the method has great potential for the discovery of novel lead compounds against a range of targets, and the companion paper illustrates how lead compounds have been identified for p38 MAP kinase starting from fragments such as those described in this paper.     

High throughput microsomal stability assay for insoluble compounds

High throughput metabolic stability assays are widely implemented in drug discovery to guide structural modification, predict in vivo performance, develop structure-metabolic stability relationships, and triage compounds for in vivo animal studies. However, these methods are often developed and validated using commercial drugs. Many drug discovery compounds differ from commercial drugs, with many having high lipophilicity, high molecular weight and low solubility. The impact of very low solubility on metabolic stability assay results was explored. Two metabolic stability assays, the 'aqueous dilution method' and the 'cosolvent method, were compared. For commercial drugs and most discovery compounds having reasonable drug-like properties, the two methods gave comparable results. For highly lipophilic, insoluble drug discovery compounds, the 'aqueous dilution method' gave artificially higher stability results. The cosolvent method performs compound dilutions in solutions with higher organic solvent content and adds solutions directly to microsomes to assist with solubilization, minimize precipitation and reduce non-specific binding to plastics. This method is more applicable in drug discovery where compounds of a wide range of solubility are studied.     

Non-stoichiometric inhibition in integrated lead finding – a literature review

ABSTRACT

Introduction: Non-stoichiometric inhibition summarizes different mechanisms by which low-molecular weight compounds can reproducibly inhibit high-throughput screening (HTS) and other lead finding assays without binding to a structurally defined site on their molecular target. This disqualifies such molecules from optimization by medicinal chemistry, and therefore their rapid elimination from screening hit lists is essential for productive and effective drug discovery.

Areas covered: This review covers recent literature that either investigates the various mechanisms behind non-stoichiometric inhibition or suggests assays and readouts to identify them. In addition, combination of the various methods to distill promising molecules out of raw primary hit lists step-by-step is considered. Emerging technologies to demonstrate target engagement in cells are also discussed.

Expert opinion: Over the last few years, awareness of non-stoichiometric inhibitors within screening libraries and HTS hit lists has considerably increased, not only in the pharmaceutical industry but also in the academic drug discovery community. This has resulted in a variety of methods to detect and handle such compounds. These range from in silico approaches to flag suspicious compounds, and counterassays to measure non-stoichiometric inhibition, to biophysical methods that positively demonstrate stoichiometric binding. In addition, novel technologies to verify target engagement within cells are becoming available. While still a time- and resource-consuming nuisance, non-stoichiometric inhibitors therefore do not fundamentally jeopardize the discovery of low molecular weight lead and drug candidates. Rather, they should be viewed as a manageable issue that with appropriate expertise can be overcome through integration of the above-mentioned approaches.     

Fragment-based QSAR strategies in drug design

Recently, fragment-based drug design has been established as a crucial strategy for hit identification and lead generation, which has strongly encouraged the development of approaches to specifically recognize and evaluate molecular fragments or structural scaffolds that preferentially interact with particular sites of important biological targets. In this context, fragment-based quantitative structure-activity relationship (FB-QSAR) has emerged as a versatile tool to explore the chemical and biological space of data sets of compounds. FB-QSAR approaches have evolved from a classical use in the generation of standard QSAR models into advanced drug design tools for database mining, pharmacokinetic property prediction and optimization of multiple parameters. This paper provides a brief perspective on the evolution and current status of FB-QSAR, highlighting new opportunities in drug design.     

Fragment-based QSAR strategies in drug design

Recently, fragment-based drug design has been established as a crucial strategy for hit identification and lead generation, which has strongly encouraged the development of approaches to specifically recognize and evaluate molecular fragments or structural scaffolds that preferentially interact with particular sites of important biological targets. In this context, fragment-based quantitative structure–activity relationship (FB-QSAR) has emerged as a versatile tool to explore the chemical and biological space of data sets of compounds. FB-QSAR approaches have evolved from a classical use in the generation of standard QSAR models into advanced drug design tools for database mining, pharmacokinetic property prediction and optimization of multiple parameters. This paper provides a brief perspective on the evolution and current status of FB-QSAR, highlighting new opportunities in drug design.     

The depolymerization of chitosan: effects on physicochemical and biological properties

Chitosan has been extensively used as an absorption enhancer for macromolecules and as gene delivery vehicle. Both properties are molecular weight (MW) dependent. Here, we investigate factors affecting the oxidative depolymerization of chitosan and physicochemical properties of the resulting polymer fractions including their cytotoxicity. The molecular weight of the depolymerized chitosan was influenced by the initial concentration and the source of chitosan. At constant initial concentrations, the molecular weight decreased linearly with the chitosan/NaNO2 ratio and was a function of logarithm of the reaction time. Chitosan with larger molecular weight was more sensitive to depolymerization. No structural change was observed during the depolymerization process by infrared and proton nuclear magnetic resonance spectroscopy. In addition, thermal properties of chitosan fragments were studied by thermal gravimetric analysis and it was found that the decomposition temperature was molecular weight dependent. Furthermore, the solubility of different molecular weight chitosan was assayed as a function of pH and it increased with decreasing molecular weight. The cytotoxicity of chitosan was concentration dependent but almost molecular weight independent according to MTT assay using L929 cell line recommended by USP26. In summary, low molecular weight fractions of chitosan may potentially useful for the design of drug delivery systems due to the improved solubility properties.     

Experiences in fragment-based drug discovery

Fragment-based drug discovery (FBDD) has become established in both industry and academia as an alternative approach to high-throughput screening for the generation of chemical leads for drug targets. In FBDD, specialised detection methods are used to identify small chemical compounds (fragments) that bind to the drug target, and structural biology is usually employed to establish their binding mode and to facilitate their optimisation. In this article, we present three recent and successful case histories in FBDD. We then re-examine the key concepts and challenges of FBDD with particular emphasis on recent literature and our own experience from a substantial number of FBDD applications. Our opinion is that careful application of FBDD is living up to its promise of delivering high quality leads with good physical properties and that in future many drug molecules will be derived from fragment-based approaches.     

Two‐ and Three‐dimensional Rings in Drugs

Using small, flat aromatic rings as components of fragments or molecules is a common practice in fragment‐based drug discovery and lead optimization. With an increasing focus on the exploration of novel biological and chemical space, and their improved synthetic accessibility, 3D fragments are attracting increasing interest. This study presents a detailed analysis of 3D and 2D ring fragments in marketed drugs. Several measures of properties were used, such as the type of ring assemblies and molecular shapes. The study also took into account the relationship between protein classes targeted by each ring fragment, providing target‐specific information. The analysis shows the high structural and shape diversity of 3D ring systems and their importance in bioactive compounds. Major differences in 2D and 3D fragments are apparent in ligands that bind to the major drug targets such as GPCRs, ion channels, and enzymes.     

Interdependent chemical-electrochemical steps in retrometabolism-based drug and safer chemical design

An extension of the retrometabolic based drug (chemical) design concept, specifically the soft drug approach, to the family of nitrone compounds is presented. Nitrones oppose oxidative challenges by virtue of their ability to very rapidly trap free radical species that are more stable and biochemically less harmful than the original molecular fragments. Moreover, the spin adducts may undergo further transformations including reaction with a second radical and decomposition (hydrolysis) to hydroxylamines and carbonyl compounds. Nitrones and their spin adducts may generate nitric oxide in vivo, which, like nitrones themselves, exerts a number of diverse activities in phylogenetically distant species as well as opposing effects in related biological systems. It was described as a major messenger in the cardiovascular, immune, and nervous systems, in which it plays regulatory, signaling, cytoprotective, and cytotoxic effects. Nitrones play an important role in the synthesis of drugs belonging to chemically and pharmacologically very different classes. A combined chemical-electrochemical synthesis of nitrones has been elaborated. These compounds may be obtained from aldehydes or ketones and N-substituted hydroxylamines. These reactions were performed directly, in situ in the electrochemical cell, where phenylhydroxylamine obtained by electroreduction of nitrobenzene derivatives reacts with the carbonyl compound introduced in the cell. The kinetic and thermodynamic parameters of the processes were determined by analyzing the adequate polarographic curves. Differences between purely chemical and mixed chemical-electrochemical methods are discussed. Analysis of the experimental data permits optimization of the investigated process from a preparative point of view. Effects of structural factors were systematically evaluated. The proposed method may be useful for combinatorial chemistry as well.     

MOLECULAR WEIGHT OF B. SUBTILIS ALPHA-AMYLASE DERIVED FROM CHEMICAL STUDIES

Bacillus subtilis α-amylase was cleaved with cyanogen bromide and the amino terminal sequences of the purified products were determined. The molecular weights of the cyanogen bromide fragments were ascertained on an agarose column equilibrated with 6m guanidine hydrochloride. The molecular weights of these fragments were also calculated from their amino acid compositions. The data obtained by these methods concurred and established the molecular weight of the enzyme monomer as 48,000.