Bettina Hofmann

Bioactivity-guided mapping and navigation of chemical space

The structure- and chemistry-based hierarchical organization of library scaffolds in tree-like arrangements provides a valid, intuitive means to map and navigate chemical space. We demonstrate that scaffold trees built using bioactivity as the key selection criterion for structural simplification during tree construction allow efficient and intuitive mapping, visualization and navigation of the chemical space defined by a given library, which in turn allows correlation of this chemical space with the investigated bioactivity and further compound design. Brachiation along the branches of such trees from structurally complex to simple scaffolds with retained yet varying bioactivity is feasible at high frequency for the five major pharmaceutically relevant target classes and allows for the identification of new inhibitor types for a given target. We provide proof of principle by identifying new active scaffolds for 5-lipoxygenase and the estrogen receptor ERalpha.

Recent Advances in the Search for Novel 5‐Lipoxygenase Inhibitors

5-Lipoxygenase (5-LO) is an important enzyme of the arachidonic acid cascade and catalyses with the help of FLAP, the 5-LO-activating protein, the formation of bioactive leukotrienes (LTs). LTs are inflammatory mediators playing a pathophysiological role in different diseases such as asthma, allergic rhinitis as well as cardiovascular diseases and certain types of cancer. Up to now, only one 5-LO inhibitor is on the market, zileuton for the treatment of asthma. With the rising number of indications for anti-LT therapy, 5-LO inhibitor drug development becomes more and more important. This MiniReview gives an update on 5-LO inhibitors currently under clinical development. Furthermore, the recent advances in the search for novel 5-lipoxygenase inhibitors with a focus on computational methods are summarized. Currently, licofelone is the compound with the highest clinical development status (completed phase III trials). 5-LO inhibitor screening programmes based on computational methods could deliver several promising drug-like new molecules. These activities can be expected to be driven by the newly resolved structure of human 5-LO in the future, enabling structure-based drug design. For the prospective drugs in late-stage clinical development, the future will show their clinical safety and efficacy in the particular diseases.

Identification of human cathepsin G as a functional target of boswellic acids from the anti-inflammatory remedy frankincense.

Frankincense preparations, used in folk medicine to cure inflammatory diseases, showed anti-inflammatory effectiveness in animal models and clinical trials. Boswellic acids (BAs) constitute major pharmacological principles of frankincense, but their targets and the underlying molecular modes of action are still unclear. Using a BA-affinity Sepharose matrix, a 26-kDa protein was selectively precipitated from human neutrophils and identified as the lysosomal protease cathepsin G (catG) by mass spectrometry (MALDI-TOF) and by immunological analysis. In rigid automated molecular docking experiments BAs tightly bound to the active center of catG, occupying the same part of the binding site as the synthetic catG inhibitor JNJ-10311795 (2-[3-{methyl[1-(2-naphthoyl)piperidin-4-yl]amino}carbonyl)-2-naphthyl]-1-(1-naphthyl)-2-oxoethylphosphonic acid). BAs potently suppressed the proteolytic activity of catG (IC50 of ∼600 nM) in a competitive and reversible manner. Related serine proteases were significantly less sensitive against BAs (leukocyte elastase, chymotrypsin, proteinase-3) or not affected (tryptase, chymase). BAs inhibited chemoinvasion but not chemotaxis of challenged neutrophils, and they suppressed Ca2+ mobilization in human platelets induced by isolated catG or by catG released from activated neutrophils. Finally, oral administration of defined frankincense extracts significantly reduced catG activities in human blood ex vivo vs placebo. In conclusion, we show that catG is a functional and pharmacologically relevant target of BAs, and interference with catG could explain some of the anti-inflammatory properties of frankincense.

Coactosin-like protein functions as a stabilizing chaperone for 5-lipoxygenase: role of tryptophan 102

The activity of 5-LO (5-lipoxygenase), which catalyses two initial steps in the biosynthesis of pro-inflammatory LTs (leukotrienes), is strictly regulated. One recently discovered factor, CLP (coactosin-like protein), binds 5-LO and promotes LT formation. In the present paper we report that CLP also stabilizes 5-LO and prevents non-turnover inactivation of the enzyme in vitro. Mutagenesis of tryptophan residues in the 5-LO beta-sandwich showed that 5-LO-Trp102 is essential for binding to CLP, and for CLP to support 5-LO activity. In addition, the stabilizing effect also depended on binding between CLP and 5-LO. After mutations which prevent interaction (5-LO-W102A or CLP-K131A), the protective effect of CLP was absent. A calculated 5-LO-CLP docking model indicates that CLP may bind to additional residues in both domains of 5-LO, thus possibly stabilizing the 5-LO structure. To obtain further support for binding between CLP and 5-LO in a living cell, subcellular localization of CLP and 5-LO in the monocytic cell line Mono Mac 6 was determined. In these cells, 5-LO associates with a nuclear fraction only when differentiated cells are primed with phorbol ester and stimulated with ionophore. The same pattern of redistribution was found for CLP, indicating that the two proteins associate with the nucleus in a co-ordinated fashion. The results of the present study support a role for CLP as a chaperoning scaffold factor, influencing both the stability and the activity of 5-LO.

SAR-study on a new class of imidazo[1,2-a]pyridine-based inhibitors of 5-lipoxygenase.

A novel class of 5-lipoxygenase (5-LO) inhibitors characterized by a central imidazo[1,2-a]pyridine scaffold, a cyclohexyl moiety and an aromatic system, is presented. This scaffold was identified in a virtual screening study and exhibits promising inhibitory potential on the 5-LO. Here, we investigate the structure-activity relationships of this compound class. With N-cyclohexyl-6-methyl-2-(4-morpholinophenyl)imidazo[1,2-a]pyridine-3-amine (14), we identified a potent 5-LO inhibitor (IC(50)=0.16μM (intact cells) and 0.1μM (cell-free)), which may possess potential as an effective lead compound intervening with inflammatory diseases and certain types of cancer.

Scaffold-Hopping Cascade Yields Potent Inhibitors of 5-Lipoxygenase

5-lipoxygenase (5-LO) is a validated drug target for the treatment of inflammation and allergic reactions as this enzyme is involved in catalyzing the conversion of arachidonic acid into leukotrienes. Inhibitors with dual activity towards both 5-LO and cyclooxygenase (COX), such as Licofelone, have been described as potent analgesic, anti-inflammatory and antiasthmatic agents lacking the gastrointestinal side effects seen with selective COX inhibitors. More recently, dual 5-LO/COX-2 inhibitors have been suggested as potential anticancer drugs. In this study, ligand-based virtual screening methods were used in an iterative fashion to identify new inhibitors of 5-LO product formation. The study consisted of four subsequent cycles of virtual screening, including 3Dand 2D-based methods and substructure searching, as well as biochemical testing. The iterative steps led to the discovery of a pyridine–imidazole-based lead structure series with nanomolar inhibitory activity in a cellular assay, demonstrating the applicability of advanced virtual screening techniques for designing small, focused, screening libraries that yield high hit rates in cell-based assays. We selected 11 dual 5-LO/COX reference inhibitors from the literature (Supporting Information, figure S1), with the aim to explore the ability of ligand-based virtual screening methods to retrieve isofunctional chemotypes with different backbone architecture (“scaffold-hopping”) from a large compound collection. The first step involved a broad, virtual screening process following the protocol outlined in Figure 1. For each of the 11 queries, two alignment-free similarity searches were performed in the Asinex Gold (November 2005: 231812 compounds) and Platinum (132250 compounds) collections (Asinex Ltd. , Moscow, Russia) using the “Charge3D” and “TripleCharge3D” methods. Briefly, “Charge3D” is an implementation of the correlation vector approach developed by Gasteiger and co-workers. The method compares two molecules based on their three-dimensional distribution of partial atom charges: Euclidian distances of all atom-pair combinations in one molecule are calculated (distances within a certain range are allocated to the same bin), and the charge values of the two atoms that form a pair are multiplied to yield a single value per atom-pair (charge values that were assigned to the same bin were added). Equation (1) describes the autocorrelation vector (CV) calculation used by “Charge3D”, where d is the distance in F, qi and qj are partial atomic charges, A is the number of atoms in a molecule and d defines the Kronecker delta (1 if a given atom pair exist, 0 otherwise). “TripleCharge3D” is an extension of this technique but makes a distinction between atom-pair types according to charge signs (++ , + , ).

Dimerization of human 5-lipoxygenase

Abstract Human 5-lipoxygenase (5-LO) can form dimers as shown here via native gel electrophoresis, gel filtration chromatography and LILBID (laser induced liquid bead ion desorption) mass spectrometry. After glutathionylation of 5-LO by diamide/glutathione treatment, dimeric 5-LO was no longer detectable and 5-LO almost exclusively exists in the monomeric form which showed full catalytic activity. Incubation of 5-LO with diamide alone led to a disulfide-bridged dimer and to oligomer formation which displays a strongly reduced catalytic activity. The bioinformatic analysis of the 5-LO surface for putative protein-protein interaction domains and molecular modeling of the dimer interface suggests a head to tail orientation of the dimer which also explains the localization of previously reported ATP binding sites. This interface domain was confirmed by the observation that 5-LO dimer formation and inhibition of activity by diamide was largely prevented when four cysteines (C159S, C300S, C416S, C418S) in this domain were mutated to serines.

Dual-target virtual screening by pharmacophore elucidation and molecular shape filtering.

Dual-target inhibitors gained increased attention in the past years. A novel in silico approach was employed for the discovery of dual 5-lipoxygenase/soluble epoxide hydrolase inhibitors. The ligand-based approach uses excessive pharmacophore elucidation and pharmacophore alignment in conjunction with shape-based scoring. The virtual screening results were verified in vitro, leading to nine novel inhibitors including a dual-target compound.

A Class of 5-Benzylidene-2-phenylthiazolinones with High Potency as Direct 5-Lipoxygenase Inhibitors

A novel class of potent direct 5-lipoxygenase (5-LO) inhibitors bearing a thiazolinone-scaffold identified by virtual screening is presented. A range of substitutions and the importance of the 2-phenyl moiety were evaluated. This series is characterized by high potency in intact polymorphonuclear leukocytes and a cell-free system, exemplified by (Z)-2-(4-chlorophenyl)-5-(4-methoxybenzylidene)-5H-thiazol-4-one (18, IC(50) = 0.28 and 0.09 μM). These disubstituted thiazolinones may possess potential for intervention with inflammatory and allergic diseases and certain cancer types.

5-Lipoxygenase inhibitors: a review of recent patents (2010 – 2012)

Introduction: 5-Lipoxygenase (5-LO) is a crucial enzyme of the arachidonic acid (AA) cascade and catalyzes the formation of bioactive leukotrienes (LTs) with the help of FLAP, the 5-LO-activating protein. LTs are inflammatory mediators playing a pathophysiological role in different diseases like asthma, allergic rhinitis as well as cardiovascular diseases and certain types of cancer. With the rising number of indications for anti-LT therapy, 5-LO inhibitor drug development becomes increasingly important. Areas covered: Here, both recent findings regarding the pathophysiological role of 5-LO and the patents claimed for 5-LO inhibitors are discussed. Focusing on direct inhibitors, several patents disclosing FLAP antagonists are also subject of this review. Novel compounds include 1,5-diarylpyrazoles, indolizines and indoles and several natural product extracts. Expert opinion: Evaluation of the patent activities revealed only quite moderate action. Nevertheless, several auspicious drug-like molecules were disclosed. It seems that in the near future, FLAP inhibitors can be expected to enter the market for the treatment of asthma. With the resolved structure of 5-LO, structure-based drug design is now applicable. Together with the identification of downstream enzyme inhibitors and dual-targeting drugs within the AA cascade, several tools are at hand to cope with 5-LOs increasing pathophysiological roles.