Karl Edman

Novel Prostaglandin D Synthase Inhibitors Generated by Fragment-Based Drug Design.

We describe the discovery of novel inhibitors of prostaglandin D2 synthase (PGDS) through fragment-based lead generation and structure-based drug design. A library of 2500 low-molecular-weight compounds was screened using 2D nuclear magnetic resonance (NMR), leading to the identification of 24 primary hits. Structure determination of protein-ligand complexes with the hits enabled a hit optimization process, whereby we harvested increasingly more potent inhibitors out of our corporate compound collection. Two iterative cycles were carried out, comprising NMR screening, molecular modeling, X-ray crystallography, and in vitro biochemical testing. Six novel high-resolution PGDS complex structures were determined, and 300 hit analogues were tested. This rational drug design procedure culminated in the discovery of 24 compounds with an IC 50 below 1 microM in the in vitro assay. The best inhibitor (IC 50 = 21 nM) is one of the most potent inhibitors of PGDS to date. As such, it may enable new functional in vivo studies of PGDS and the prostaglandin metabolism pathway.

Ligand binding mechanism in steroid receptors; from conserved plasticity to differential evolutionary constraints

Steroid receptor drugs have been available for more than half a century, but details of the ligand binding mechanism have remained elusive. We solved X-ray structures of the glucocorticoid and mineralocorticoid receptors to identify a conserved plasticity at the helix 6-7 region that extends the ligand binding pocket toward the receptor surface. Since none of the endogenous ligands exploit this region, we hypothesized that it constitutes an integral part of the binding event. Extensive all-atom unbiased ligand exit and entrance simulations corroborate a ligand binding pathway that gives the observed structural plasticity a key functional role. Kinetic measurements reveal that the receptor residence time correlates with structural rearrangements observed in both structures and simulations. Ultimately, our findings reveal why nature has conserved the capacity to open up this region, and highlight how differences in the details of the ligand entry process result in differential evolutionary constraints across the steroid receptors.

The Discovery of Potent and Selective Non-Steroidal Glucocorticoid Receptor Modulators, Suitable for Inhalation.

We report the discovery of highly potent and selective non-steroidal glucocorticoid receptor modulators with PK properties suitable for inhalation. A high throughput screen of the AstraZeneca compound collection identified sulfonamide 3 as a potent non-steroidal glucocorticoid receptor ligand. Further optimization of this lead generated indazoles 30 and 48 that were progressed to characterization in in vivo models. X-ray crystallography was used to gain further insight into the binding mode of selected ligands.

Cathepsin C Inhibitors: Property Optimization and Identification of a Clinical Candidate

A lead generation and optimization program delivered the highly selective and potent CatC inhibitor 10 as an in vivo tool compound and potential development candidate. Structural studies were undertaken to generate SAR understanding.

Discovery of 9-(1-phenoxyethyl)-2-morpholino-4-oxo-pyrido[1,2-a]pyrimidine-7-carboxamides as oral PI3Kβ inhibitors, useful as antiplatelet agents.

Optimization of AZD6482 (2), the first antiplatelet PI3Kβ inhibitor evaluated in man, focused on improving the pharmacokinetic profile to a level compatible with once daily oral dosing as well as achieving adequate selectivity towards PI3Kα to minimize the risk for insulin resistance. Structure-based design and optimization of DMPK properties resulted in (R)-16, a novel, orally bioavailable PI3Kβ inhibitor with potent in vivo anti-thrombotic effect with excellent separation to bleeding risk and insulin resistance.

Non-covalent inhibitors of rhinovirus 3C protease

The first known non-covalent inhibitors of rhinovirus 3C protease (3CP) have been identified through fragment based screening and hit identification activities.

Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design

Computer-aided drug design plays an important role in medicinal chemistry to obtain insights into molecular mechanisms and to prioritize design strategies. Although significant improvement has been made in structure based design, it still remains a key challenge to accurately model and predict induced fit mechanisms. Most of the current available techniques either do not provide sufficient protein conformational sampling or are too computationally demanding to fit an industrial setting. The current study presents a systematic and exhaustive investigation of predicting binding modes for a range of systems using PELE (Protein Energy Landscape Exploration), an efficient and fast protein-ligand sampling algorithm. The systems analyzed (cytochrome P, kinase, protease, and nuclear hormone receptor) exhibit different complexities of ligand induced fit mechanisms and protein dynamics. The results are compared with results from classical molecular dynamics simulations and (induced fit) docking. This study shows that ligand induced side chain rearrangements and smaller to medium backbone movements are captured well in PELE. Large secondary structure rearrangements, however, remain challenging for all employed techniques. Relevant binding modes (ligand heavy atom RMSD < 1.0 Å) can be obtained by the PELE method within a few hours of simulation, positioning PELE as a tool applicable for rapid drug design cycles.

The Discovery of Mmp7 Inhibitors Exploiting a Novel Selectivity Trigger.

Matrilysin or matrix metalloproteinase 7 (MMP7) is a member of a class of zinc-dependent endopeptidases (MMPs) capable of degrading extracellular matrix proteins and thought to play an important role in tissue remodeling associated with various physiological and pathological processes. It has broad specificity and cleaves a number of matrix substances, including proteoglycans and collagen III/IV/V/IX/X/XI, which underlies a potential role for MMP7 inhibitors in the treatment of disease associated with tissue degradation/remodeling. In addition, MMP7 has been reported to have a potential role in tumor metastasis and inflammatory processes. It has also been reported to be expressed in osteoarthritic cartilage, where it is colocalized with the tetraspanin, CD151, which has been implicated in its pericellular activation. As a class, MMPs have been the subject of intense study within the pharmaceutical industry over the last decade, and inhibitors have been described for many of the individual MMPs. However, MMP selectivity remains a significant hurdle for most MMP inhibitors due to a reliance on zinc chelation to provide a significant component of the binding energy. Despite high therapeutic value, there has been a consistent lack of success with such inhibitors in the clinic, and this can largely be attributed to several factors: poor selectivity, poor target validation for the targeted therapy, and poorly defined predictive preclinical animal models for safety and efficacy. The selectivity problem is particularly true with compounds bearing groups that chelate strongly to zinc (e.g. , hydroxamate, reverse hydroxamate) because a large component of the binding energy is derived from a feature common to all MMPs. With this in mind, we initiated a program to identify selective MMP7 inhibitors employing a high-throughput screening approach, with MMP selectivity assessment very early in the screening process. To provide an initial indication of selectivity, actives were screened against MMP1 and MMP14. Compounds showing good selectivity against these two MMPs were then screened against MMP2, MMP12 and MMP13 to give an indication of wider MMP selectivity. As anticipated, potent hydroxamate and reverse hydroxamate inhibitors were identified but none of them showed selectivity over other MMPs. In fact, without exception, hydroxamate, reverse hydroxamate and also hydantoin inhibitors proved more active against many of the other MMPs than against MMP7. One active hit that emerged from these initial selectivity screens was the carboxylic acid compound I. The compound has low potency against MMP7, but there was no indication of activity against any of the other MMPs tested. The low potency limited a true assessment of selectivity but, nonetheless, this initial lead was pursued further, driven largely by two factors: ease of synthesis and crystallization. Firstly, we were able to successfully crystallize this compound within the MMP7 protein and determine the complex structure to enable an understanding of the binding mode. Secondly, the compound was relatively simple and amenable to parallel synthesis from commercial sulfonyl chlorides and amino acids, which would facilitate a rapid initial exploration of structure–activity relationships. Furthermore, the library design for this parallel chemistry could be directed by virtual docking experiments using the X-ray data generated from compound I. We also crystallized one of the nonselective reverse hydroxamate MMP7 inhibitors (compound II) to assess the binding mode of compounds possessing a large S1’ substituent. MMP7 is unusual in the MMP family in the sense that it possesses a very shallow S1’ selectivity pocket, and compound II was expected to provide a poor fit. What was seen from X-ray data is that this compound expands the S1’ pocket to accommodate the large side chain. Using this information, we were able to employ both the open and closed MMP7 binding sites for virtual docking experiments. The structural work carried out around compounds I and II (Figure 1) is described below. The results give some insight into the basis of the selectivity seen with compound I. Also described are the initial results from the library design based on the structural data to increase MMP7 potency whilst retaining selectivity over other MMPs. MMP7 is the smallest member of the MMP family, with the mature enzyme consisting of the catalytic domain alone. The MMP7 structure confirmed the open-faced a-b-sandwich fold (Figure 2), characteristic for most zinc-dependant endopeptidases. The active site is located in a groove adjacent to the central helix B and the antiparallel b-sheet, and it is delineated by the typical HEXGHXXGXXH sequence motif. Upon binding, the scissile peptide bond is positioned with the carbonyl oxygen towards the catalytic zinc ion, which is coordinated by the three histidine residues. The nearby glutamate acts as a general base, promoting nucleophilic attack by a catalytic water molecule and subsequently stabilizes the tetrahedral intermediate. In addition to the catalytic zinc, the structure contains two calcium ions and one additional zinc ion, important for maintaining the structural integrity of the b-sheet. [a] Dr. K. Edman, C. Johansson, Dr. J. Petersen, Dr. A. Tervo, L. Wissler Global Structural Chemistry, AstraZeneca Mçlndal Pepparedsleden 1, 43183 Mçlndal (Sweden) Fax: (+ 46) 31-776-3700 Karl.Edman@astrazeneca.com [b] Dr. M. Furber, P. Hemsley, Dr. G. Pairaudeau, Dr. M. Stocks, Dr. A. Ward, Dr. E. Wells Departments of Medicinal Chemistry and BioSciences AstraZeneca Charnwood Bakewell Road, Loughborough, Leicestershire LE11 5RH (UK) Supporting information for this article is available on the WWW under http://dx.doi.org/10.1002/cmdc.201000550.

Structure-Based Drug Design of Mineralocorticoid Receptor Antagonists to Explore Oxosteroid Receptor Selectivity.

The mineralocorticoid receptor (MR) is a nuclear hormone receptor involved in the regulation of body fluid and electrolyte homeostasis. In this study we explore selectivity triggers for a series of nonsteroidal MR antagonists to improve selectivity over other members of the oxosteroid receptor family. A biaryl sulfonamide compound was identified in a high‐throughput screening (HTS) campaign. The compound bound to MR with pKi=6.6, but displayed poor selectivity over the glucocorticoid receptor (GR) and the progesterone receptor (PR). Following X‐ray crystallography of MR in complex with the HTS hit, a compound library was designed that explored an induced‐fit hypothesis that required movement of the Met852 side chain. An improvement in MR selectivity of 11‐ to 79‐fold over PR and 23‐ to 234‐fold over GR was obtained. Given the U‐shaped binding conformation, macrocyclizations were explored, yielding a macrocycle that bound to MR with pKi=7.3. Two protein–ligand X‐ray structures were determined, confirming the hypothesized binding mode for the designed compounds.

Discovery of indazole ethers as novel, potent, non-steroidal glucocorticoid receptor modulators.

A structure-based design approach led to the identification of a novel class of indazole ether based, non-steroidal glucocorticoid receptor (GR) modulators. Several examples were identified that displayed cell potency in the picomolar range, inhibiting LPS-induced TNF-α release by primary peripheral blood mononuclear cells (PBMCs). Additionally, an improved steroid hormone receptor binding selectivity profile, compared to classical steroidal GR agonists, was demonstrated. The indazole ether core tolerated a broad range of substituents allowing for modulation of the physiochemical parameters. A small sub-set of indazole ethers, with pharmacokinetic properties suitable for oral administration, was investigated in a rat antigen-induced joint inflammation model and demonstrated excellent anti-inflammatory efficacy.