Tanja Schulz-Gasch

Insight Into Steroid Scaffold Formation from the Structure of Human Oxidosqualene Cyclase

In higher organisms the formation of the steroid scaffold is catalysed exclusively by the membrane-bound oxidosqualene cyclase (OSC; lanosterol synthase). In a highly selective cyclization reaction OSC forms lanosterol with seven chiral centres starting from the linear substrate 2,3-oxidosqualene. Valuable data on the mechanism of the complex cyclization cascade have been collected during the past 50 years using suicide inhibitors, mutagenesis studies and homology modelling. Nevertheless it is still not fully understood how the enzyme catalyses the reaction. Because of the decisive role of OSC in cholesterol biosynthesis it represents a target for the discovery of novel anticholesteraemic drugs that could complement the widely used statins. Here we present two crystal structures of the human membrane protein OSC: the target protein with an inhibitor that showed cholesterol lowering in vivo opens the way for the structure-based design of new OSC inhibitors. The complex with the reaction product lanosterol gives a clear picture of the way in which the enzyme achieves product specificity in this highly exothermic cyclization reaction.

Recore : A fast and versatile method for scaffold hopping based on small molecule crystal structure conformations

Replacing central elements of known active structures is a common procedure to enter new compound classes. Different computational methods have already been developed to help with this task, varying in the description of possible replacements, the query input, and the similarity measure used. In this paper, a novel approach for scaffold replacement and a corresponding software tool, called Recore, is introduced. In contrast to prior methods, our main objective was to combine the following three properties in one tool: to avoid structures with strained conformations, to enable the exploration of large search spaces, and to allow interactive use through short response times. We introduce a new technique employing 3D fragments generated by combinatorial enumeration of cuts. It allows focusing on fragments suitable for scaffold replacement while retaining conformational information of the corresponding crystal structures. Based on this idea, we present an algorithm utilizing a geometric rank searching approach. Given a geometric arrangement of two or three exit vectors and additional pharmacophore features, the algorithm finds fragments fulfilling all these constraints ordered by increasing deviation from the query constraints. For the validation of the approach, three different design scenarios have been used. The results obtained show that our approach is able to propose new valid scaffold topologies.

Scoring functions for protein–ligand interactions: a critical perspective

Scoring functions play an essential role in structure-based virtual screening. They are required to guide the docking of candidate compounds to structures of receptor binding sites, to select probable binding modes, and to discriminate binders from non-binders. Although many scoring functions have successfully been used to identify novel ligands for a wide variety of targets, much work remains to be done to avoid incorrect prediction of binding modes and high numbers of false positives. This review gives an overview of the current state of the field and outlines key issues for the further development of scoring functions.:

Torsion Angle Preferences in Druglike Chemical Space: A Comprehensive Guide

Crystal structure databases offer ample opportunities to derive small molecule conformation preferences, but the derived knowledge is not systematically applied in drug discovery research. We address this gap by a comprehensive and extendable expert system enabling quick assessment of the probability of a given conformation to occur. It is based on a hierarchical system of torsion patterns that cover a large part of druglike chemical space. Each torsion pattern has associated frequency histograms generated from CSD and PDB data and, derived from the histograms, traffic-light rules for frequently observed, rare, and highly unlikely torsion ranges. Structures imported into the corresponding software are annotated according to these rules. We present the concept behind the tree of torsion patterns, the design of an intuitive user interface for the management and usage of the torsion library, and we illustrate how the system helps analyze and understand conformation properties of substructures widely used in medicinal chemistry.

A Real-World Perspective on Molecular Design.

We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.

NAOMI: on the almost trivial task of reading molecules from different file formats.

In most cheminformatics workflows, chemical information is stored in files which provide the necessary data for subsequent calculations. The correct interpretation of the file formats is an important prerequisite to obtain meaningful results. Consistent reading of molecules from files, however, is not an easy task. Each file format implicitly represents an underlying chemical model, which has to be taken into consideration when the input data is processed. Additionally, many data sources contain invalid molecules. These have to be identified and either corrected or discarded. We present the chemical file format converter NAOMI, which provides efficient procedures for reliable handling of molecules from the common chemical file formats SDF, MOL2, and SMILES. These procedures are based on a consistent chemical model which has been designed for the appropriate representation of molecules relevant in the context of drug discovery. NAOMIs functionality is tested by round robin file IO exercises with public data sets, which we believe should become a standard test for every cheminformatics tool.

Mechanistic insights into oxidosqualene cyclizations through homology modeling

2,3‐Oxidosqualene cyclases (OSC) are key enzymes in sterol biosynthesis. They catalyze the stereoselective cyclization and skeletal rearrangement of (3S)‐2,3‐oxidosqualene to lanosterol in mammals and fungi and to cycloartenol in algae and higher plants. Sequence information and proposed mechanism of 2,3‐oxidosqualene cyclases are closely related to those of squalene‐hopene cyclases (SHC), which represent functional analogs of OSCs in bacteria. SHCs catalyze the cationic cyclization cascade converting the linear triterpene squalene to fused ring compounds called hopanoids. High stereoselectivity and precision of the skeletal rearrangements has aroused the interest of researchers for nearly half a century, and valuable data on studying mechanistic details in the complex enzyme‐catalyzed cyclization cascade has been collected. Today, interest in cyclases is still unbroken, because OSCs became targets for the development of antifungal and hypocholesterolemic drugs. However, due to the large size and membrane‐bound nature of OSCs, three‐dimensional structural information is still not available, thus preventing a complete understanding of the atomic details of the catalytic mechanism. In this work, we discuss results gained from homology modeling of human OSC based on structural information of SHC from Alicyclobacillus acidocaldarius and propose a structural model of human OSC. The model is in accordance with previously performed experimental studies with mechanism‐based suicide inhibitors and mutagenesis experiments with altered activity and product specificity. Structural insight should strongly stimulate structure‐based design of antifungal or cholesterol‐lowering drugs.

Oxidosqualene Cyclase Second‐Sphere Residues Profoundly Influence the Product Profile

Oxidosqualene cyclases convert oxidosqualene (1) to cyclic triterpene alcohols through cationic cyclization, rearrangement, and deprotonation reactions. These enzymes control the reactivity of carbocations with a precision unrivalled by nonenzymatic catalysts, but how they utilize steric bulk and polar groups to guide carbocation reactivity remains poorly understood. Cycloartenol synthase is an oxidosqualene cyclase that cyclizes oxidosqualene to the protosteryl cation (2), guides rearrangement to the lanosteryl cation (3), and promotes specific deprotonation from C-19 to form cycloartenol (4 ; Scheme 1). Lanosterol synthase is a mechanistically related enzyme that catalyzes the same cyclization and rearrangement reactions, and abstracts a proton from C-8 to form the tetrasubstituted olefin in lanosterol (5). We describe herein mutagenesis experiments and computer modeling that establish that secondsphere oxidosqualene cyclase residues are a critical component of the catalytic distinction between cycloartenol synthase and lanosterol synthase.

Structure-assisted discovery of an aminothiazole derivative as a lead molecule for inhibition of bacterial fatty-acid synthesis

β-Ketoacyl-ACP synthase is a key target for the treatment of infectious diseases. A structure-based biophysical screening approach identified for the first time a synthetic small molecule, 2-phenylamino-4-methyl-5-acetylthiazole, that binds to the active site of the enzyme. Implications for the use of this information in drug discovery are discussed.

CONFECT: Conformations from an Expert Collection of Torsion Patterns

The generation of sets of low‐energy conformations for a given molecule is a central task in drug design. Herein we present a new conformation generator called CONFECT that builds on our previously published library of torsion patterns. Conformations are generated as well as ranked by means of normalized frequency distributions derived from the Cambridge Structural Database (CSD). Following an incremental construction approach, conformations are selected from a systematic enumeration within energetic boundaries. The new tool is benchmarked in several different ways, indicating that it allows the efficient generation of high‐quality conformation ensembles. These ensembles are smaller than those produced by state‐of‐the‐art tools, yet they effectively cover conformational space.