Should medicinal chemists do molecular modelling?

In this article we discuss the pros and cons of medicinal chemists undertaking three-dimensional (3D) computer-aided drug design (CADD) activities for themselves, from the viewpoint of both medicinal chemists and computational chemists. We describe how best this can be implemented, the potential benefits that can be obtained and the pitfalls that are often encountered.

The discovery of potent and long-acting oral factor Xa inhibitors with tetrahydroisoquinoline and benzazepine P4 motifs.

The discovery and evaluation of potent and long-acting oral sulfonamidopyrrolidin-2-one factor Xa inhibitors with tetrahydroisoquinoline and benzazepine P4 motifs are described. Unexpected selectivity issues versus tissue plasminogen activator in the former series were addressed in the later, delivering a robust candidate for progression towards clinical studies.

Discovery of a potent series of non-steroidal non α-trifluoromethyl carbinol glucocorticoid receptor agonists with reduced lipophilicity.

A novel series of indazole non-steroidal glucocorticoid receptor agonist has been discovered. This series features a sulfonamide central core and meta amides which interact with the extended ligand binding domain. This series has produced some of the most potent and least lipophilic agonists of which we are aware such as 20a (NFκB pIC(50) 8.3 (100%), clogP 1.9). Certain analogues in this series also display evidence for modulated pharmacology.

Synthesis and structure-activity relationships of long-acting beta2 adrenergic receptor agonists incorporating metabolic inactivation: an antedrug approach.

A series of saligenin beta(2) adrenoceptor agonist antedrugs having high clearance were prepared by reacting a protected saligenin oxazolidinone with protected hydroxyethoxyalkoxyalkyl bromides, followed by removal of the hydroxy-protecting group, alkylation, and final deprotection. The compounds were screened for beta(2), beta(1), and beta(3) agonist activity in CHO cells. The onset and duration of action in vitro of selected compounds were assessed on isolated superfused guinea pig trachea. Compound 13f had high potency, selectivity, fast onset, and long duration of action in vitro and was found to have long duration in vivo, low oral bioavailability in the rat, and to be rapidly metabolized. Crystalline salts of 13f (vilanterol) were identified that had suitable properties for inhaled administration. A proposed binding mode for 13f to the beta(2)-receptor is presented.

Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor.

Crystallography and computer modeling have been used to exploit a previously unexplored channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole amides showing excellent complementarity to the channel were designed with the assistance of the computational technique AlleGrow. The accuracy of the design process was demonstrated through crystallographic structural determination of the GR ligand-binding domain-agonist complex of the D-prolinamide derivative 11. The utility of the channel was further exemplified through the design of a potent phenylindazole in which structural motifs, seen to interact with the traditional GR ligand pocket, were abandoned and replaced by interactions within the new channel. Occupation of the channel was confirmed with a second GR crystal structure of this truncated D-alaninamide derivative 13. Compound 11 displays properties compatible with development as an intranasal solution formulation, whereas oral bioavailability has been demonstrated with a related truncated exemplar 14. Data with the pyrrolidinone amide 12 demonstrate the potential for further elaboration within the "meta" channel to deliver compounds with selectivity for the desired transrepressive activity of glucocorticoids. The discovery of these interactions with this important receptor offers significant opportunities for the design of novel GR modulators.

Highly tractable, sub-nanomolar non-steroidal glucocorticoid receptor agonists.

Starting from a non-steroidal glucocorticoid agonist aryl pyrazole derivative, the NFkappaB agonist activity was optimised in an iterative process from pIC(50) 7.5 (for 7), to pIC(50) 10.1 (for 38E1). An explanation for the SAR observed based is presented along with a proposed docking of 38E1 into the active site of the glucocorticoid receptor.

Analysis of neighborhood behavior in lead optimization and array design.

Neighborhood behavior describes the extent to which small structural changes defined by a molecular descriptor are likely to lead to small property changes. This study evaluates two methods for the quantification of neighborhood behavior: the optimal diagonal method of Patterson et al. and the optimality criterion method of Horvath and Jeandenans. The methods are evaluated using twelve different types of fingerprint (both 2D and 3D) with screening data derived from several lead optimization projects at GlaxoSmithKline. The principal focus of the work is the design of chemical arrays during lead optimization, and the study hence considers not only biological activity but also important drug properties such as metabolic stability, permeability, and lipophilicity. Evidence is provided to suggest that the optimality criterion method may provide a better quantitative description of neighborhood behavior than the optimal diagonal method.

Quantum Isostere Database: a web-based tool using quantum chemical topology to predict bioisosteric replacements for drug design.

This paper introduces the 'Quantum Isostere Database' (QID), a Web-based tool designed to find bioisosteric fragment replacements for lead optimization using stored ab initio data. A wide range of original geometric, electronic, and calculated physical properties are stored for each fragment. Physical descriptors with clear meaning are chosen, such as distribution of electrostatic potential energy values across a fragment surface and geometric parameters to describe fragment conformation and shape from ab initio structures. Further fundamental physical properties are linked to broader chemical characteristics relevant to biological activity, such as H-bond donor and acceptor strengths. Additional properties with less easily interpretable links to biological activity are also stored to allow future development of QSAR/QSPR models for quantities such as pK(a) and solubility. Conformational dependence of the ab initio descriptors is explicitly dealt with by storing properties for a variety of low-energy conformers of each fragment. Capping groups are used in ab initio calculations to represent different chemical environments, based on background research into transferability of electronic descriptors [J. Comput. Chem. 2009, 30, 1300-1318]. The resulting database has a Web interface that allows medicinal chemists to enter a query fragment, select important chemical features, and retrieve a list of suggested replacements with similar chemical characteristics. Examples of known bioisosteric replacements correctly identified by the QID tool are given.

Synthesis and structure-activity relationships of long-acting beta2 adrenergic receptor agonists incorporating arylsulfonamide groups.

A series of saligenin alkoxyalkylphenylsulfonamide beta(2) adrenoceptor agonists were prepared by reacting a protected saligenin oxazolidinone with alkynyloxyalkyl bromides, followed by Sonogashira reaction, hydrogenation, and deprotection. The meta-substituted primary sulfonamide was more potent than the para- and the ortho-analogues. Primary sulfonamides were more potent than the secondary and tertiary analogues. The onset and duration of action in vitro of selected compounds was assessed on isolated superfused guinea pig trachea. Sulfonamide 29b had the best profile of potency, selectivity, onset, and duration of action on both guinea pig trachea and human bronchus. Furthermore, 29b was found to have low oral bioavailability in rat and dog and also to have long duration of action in an in vivo model of bronchodilation. Crystalline salts of 29b were identified that had suitable properties for inhaled administration. A proposed binding mode for 29b to the beta(2)-receptor is presented.

A refined model for prediction of hydrogen bond acidity and basicity parameters from quantum chemical molecular descriptors.

Abraham's H-bonding parameters alpha and beta have been described in terms of a minimal set of readily obtainable molecular descriptors. These parameters are basically equilibrium constants for complexation of acids with a reference base (alpha) or bases with a reference acid (beta) measured in a non-hydrogen bonding solvent such as tetrachloromethane. The models were developed using partial least squares with a diverse dataset recently compiled by Platts et al., encompassing a wide range of hydrogen bond acids and bases in order to give a robust model. Although less accurate than the model of Platts et al. the descriptors used in this work avoid expensive supermolecule calculations, and allow prediction of hydrogen bonding characteristics from the isolated molecular wave function. These descriptors can then be generated for a large number of compounds, making them ideal for storage in a quantum isostere database (QID), the construction of which we initiated. The QID is a web-based tool developed to predict bioisosteric replacements in lead optimisation projects. The current descriptors provide hydrogen bonding characteristics of molecules of interest.

Aryl aminopyrazole benzamides as oral non-steroidal selective glucocorticoid receptor agonists.

Aryl aminopyrazole amides capped with N-alkylbenzamides 13-16 are selective glucocorticoid receptor agonists. 2,6-Disubstituted benzamides have prednisolone-like potency or better in vitro. Good oral exposure was demonstrated in the rat, with compounds with lower lipophilicity, for example N-hydroxyethyl benzamides (e.g., 16e).

Toward an ab initio fragment database for bioisosterism: dependence of QCT properties on level of theory, conformation, and chemical environment.

The goal of this work is to assess the scope and suitability of atomic and bond properties for use in a bioisostere fragment database. This database will contain fragment descriptors that can be used to represent portions of larger molecules and similarity in properties between fragments, which will then be used to find bioisosteric replacements in future work. Seventeen common organic fragments relevant to drug design featured as "linker groups" that were capped by two terminal groups. Each terminal group could be one of the set of 12 possible sets: 10 aromatic heterocycles, a phenyl ring, or an ethyl. This enabled a systematic investigation of the chemical environment, enriched with conformational flexibility within the linker group, for a total of 307 different atoms. Five different levels of theory were investigated. This work paves the way to the construction of a quantum mechanical bioisosteric fragment database, for which transferability of stored fragment properties is of fundamental importance.

X-ray crystal structure of the novel enhanced-affinity glucocorticoid agonist fluticasone furoate in the glucocorticoid receptor-ligand binding domain.

An X-ray crystal structure is reported for the novel enhanced-affinity glucocorticoid agonist fluticasone furoate (FF) in the ligand binding domain of the glucocorticoid receptor. Comparison of this structure with those of dexamethasone and fluticasone propionate shows the 17 alpha furoate ester to occupy more fully the lipophilic 17 alpha pocket on the receptor, which may account for the enhanced glucocorticoid receptor binding of FF.

Nonsteroidal glucocorticoid agonists: tetrahydronaphthalenes with alternative steroidal A-ring mimetics possessing dissociated (transrepression/transactivation) efficacy selectivity.

The synthesis and biological activity of tetrahydronaphthalene derivatives coupled to various heterocycles are described. These compounds are potent glucocorticoid receptor agonists with efficacy selectivity in an NFkappaB glucocorticoid receptor (GR) agonist assay (representing transrepression effects) over an MMTV GR agonist assay (representing transactivation effects). Quinolones, indoles, and C- and N-linked quinolines are some of the heterocycles that provide efficacy selectivity. For example, the isoquinoline 49D1E2 has NFkappaB agonism with pIC50 of 8.66 (89%) and reduced efficacy in MMTV agonism (6%), and the quinoline 55D1E1 has NFkappaB agonism with pIC50 of 9.30 (101%) and reduced efficacy in MMTV agonism with pEC50 of 8.02 (47%). A description of how a compound from each class is modeled in the active site of the receptor is given.

Non-steroidal glucocorticoid agonists: the discovery of aryl pyrazoles as A-ring mimetics.

Starting from an established series of non-steroidal glucocorticoid receptor (GR) agonists, a large array was designed where a metabolically labile benzoxazinone moiety was replaced. Initial hits bound to GR but lacked agonist activity. Following two further iterations, potent GR agonists were discovered with 20D1E1 having NFkappaB agonism pIC(50) 8.8 (103%). Other analogues such as 23D1E1 display a dissociated profile (NFkappaB pIC(50) 8.1 (103%), MMTV pEC(50) 7.02 (36%)). The tetrahydronaphthalene moiety can also be replaced with substituted aryls such as 24E1 and 25E1.

Dissociated nonsteroidal glucocorticoid receptor modulators; discovery of the agonist trigger in a tetrahydronaphthalene-benzoxazine series.

The tetrahydronaphthalene-benzoxazine glucocorticoid receptor (GR) partial agonist 4b was optimized to produce potent full agonists of GR. Aromatic ring substitution of the tetrahydronaphthalene leads to weak GR antagonists. Discovery of an "agonist trigger" substituent on the saturated ring of the tetrahydronaphthalene leads to increased potency and efficacious GR agonism. These compounds are efficacy selective in an NFkB GR agonist assay (representing transrepression effects) over an MMTV GR agonist assay (representing transactivation effects). 52 and 60 have NFkB pIC(50) = 8.92 (105%) and 8.69 (92%) and MMTV pEC(50) = 8.20 (47%) and 7.75 (39%), respectively. The impact of the trigger substituent on agonism is modeled within GR and discussed. 36, 52, and 60 have anti-inflammatory activity in a mouse model of inflammation after topical dosing with 52 and 60, having an effect similar to that of dexamethasone. The original lead was discovered by a manual agreement docking method, and automation of this method is also described.

Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring functions.

A new method for the postprocessing of docking outputs has been developed, based on encoding putative 3D binding modes (docking solutions) as ligand-protein interactions into simple bit strings, a method analogous to the structural interaction fingerprint. Instead of employing traditional scoring functions, the method uses a series of new, knowledge-based scores derived from the similarity of the bit strings for each docking solution to that of a known reference binding mode. A GOLD docking study was carried out using the Bissantz estrogen receptor antagonist set along with the new scoring method. Superior recovery rates, with up to 2-fold enrichments, were observed when the new knowledge-based scoring was compared to the GOLD fitness score. In addition, top ranking sets of molecules (actives and potential actives or decoys) were structurally diverse with low molecular weights and structural complexities. Principal component analysis and clustering of the fingerprints permits the easy separation of active from inactive binding modes and the visualization of diverse binding modes.

Retrospective docking study of PDE4B ligands and an analysis of the behavior of selected scoring functions.

Scoring forms a major obstacle to the success of any docking study. In general, fast scoring functions perform poorly when used to determine the relative affinity of ligands for their receptors. In this study, the objective was not to rank compounds with confidence but simply to identify a scoring method which could provide a 4-fold hit enrichment in a screening sample over random selection. To this end, LigandFit, a fast shape matching docking algorithm, was used to dock a variety of known inhibitors of type 4 phosphodiesterase (PDE4B) into its binding site determined crystallographically for a series of pyrazolopyridine inhibitors. The success of identifying good poses with this technique was explored through RMSD comparisons with 19 known inhibitors for which crystallographic structures were available. The effectiveness of five scoring functions (PMF, JAIN, PLP2, LigScore2, and DockScore) was then evaluated through consideration of the success in enriching the top ranked fractions of nine artificial databases, constructed by seeding 1980 inactive ligands (pIC50 < 5) with 20 randomly selected inhibitors (pIC50 > 6.5). PMF and JAIN showed high average enrichment factors (greater than 4 times) in the top 5-10% of the ranked databases. Rank-based consensus scoring was then investigated, and the rational combination of 3 scoring functions resulted in more robust scoring schemes with (cScore)-DPmJ (consensus score of DockScore, PMF, and JAIN) and (cScore)-PPmJ (PLP2, PMF, and JAIN) yielding particularly good results. These cScores are believed to be of greater general application. Finally, the analysis of the behavior of the scoring functions across different chemotypes uncovered the inherent bias of the docking and scoring toward compounds in the same structural family as that employed for the crystal structure, suggesting the need to use multiple versions of the binding site for more successful virtual screening strategies.

Design and synthesis of new nonsteroidal glucocorticoid modulators through application of an "agreement docking" method.

Structurally related glucocorticoid receptor (GR) binders were docked into the GR active site to select the binding mode closest to the true docking mode. This process, termed an "agreement docking method", led to the design of tetrahydronaphthalene 9. The method was validated by the syntheses of 9 and related analogues, which are potent binders of GR. 15a is a partial agonist while 9e and 15a are micromolar antagonists in a mouse mammary tumor virus transactivation assay.

Drug rings database with web interface. A tool for identifying alternative chemical rings in lead discovery programs.

This paper describes the development of a drug rings database and Web-based search tools. The database contains ring structures from both corporate and commercial databases, along with characteristic descriptors including frequency of occurrence as an indicator of synthetic accessibility and calculated property and geometric parameters. Analysis of the rings in several major databases is described, with illustrations of applications of the database in lead discovery programs where bioisosteres and geometric isosteres are sought.