Papers by Tanja Schulz-Gasch
Small Molecule — Protein Interactions, 2003
Journal of the American Chemical Society, 2005
Efforts to modify the catalytic specificity of enzymes consistently show that it is easier to bro... more Efforts to modify the catalytic specificity of enzymes consistently show that it is easier to broaden the substrate or product specificity of an accurate enzyme than to restrict the selectivity of one that is promiscuous. Described herein are experiments in which cycloartenol synthase was redesigned to become a highly accurate lanosterol synthase. Several single mutants have been described that modify the catalytic specificity of cycloartenol to form some lanosterol. Modeling studies were undertaken to identify combinations of mutations that cooperate to decrease the formation of products other than lanosterol. A double mutant was constructed and characterized and was shown to cyclize oxidosqualene accurately to lanosterol (99%). This catalytic change entailed both relocating polarity with a His477Asn mutation and modifying steric constraints with an Ile481Val mutation.
Journal of Medicinal Chemistry, 2005
The MM-PBSA approach has become a popular method for calculating binding affinities of biomolecul... more The MM-PBSA approach has become a popular method for calculating binding affinities of biomolecular complexes. Published application examples focus on small test sets and few proteins and, hence, are of limited relevance in assessing the general validity of this method. To further characterize MM-PBSA, we report on a more extensive study involving a large number of ligands and eight different proteins. Our results show that applying the MM-PBSA energy function to a single, relaxed complex structure is an adequate and sometimes more accurate approach than the standard free energy averaging over molecular dynamics snapshots. The use of MM-PBSA on a single structure is shown to be valuable (a) as a postdocking filter in further enriching virtual screening results, (b) as a helpful tool to prioritize de novo design solutions, and (c) for distinguishing between good and weak binders (∆pIC 50 g 2-3), but rarely to reproduce smaller free energy differences.
Journal of Medicinal Chemistry, 2013
Crystal structure databases offer ample opportunities to derive small molecule conformation prefe... more 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.
Journal of Chemical Information and Modeling, 2007
Replacing central elements of known active structures is a common procedure to enter new compound... more 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.
CHIMIA International Journal for Chemistry, 2005
Abstract: Novel inhibitors of oxidosqualene cyclase (OSC) for the treatment of dyslipidemia are r... more Abstract: Novel inhibitors of oxidosqualene cyclase (OSC) for the treatment of dyslipidemia are reported. Starting point for the chemistry program was a set of compounds derived from a fungicide project which, in addition to high affinity for OSC from Candida albicans, also showed ...
ChemBioChem, 2004
Oxidosqualene cyclases convert oxidosqualene (1) to cyclic triterpene alcohols through cationic c... more Oxidosqualene cyclases convert oxidosqualene (1) to cyclic triterpene alcohols through cationic cyclization, rearrangement, and deprotonation reactions. [1] 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.
Bioorganic & Medicinal Chemistry Letters, 2013
A series of highly potent &am... more A series of highly potent & selective adamantane derived CB2 agonists was identified in a high-throughput screen. A SAR was established and physicochemical properties were significantly improved. This was accompanied by potency of the compounds on the Q63R variant and varying β-arrestin data which will support the insight into their relevance for the in vivo situation.
ACS Medicinal Chemistry Letters, 2014
3-Amido-3-aryl-piperidines were discovered as a novel structural class of GlyT1 inhibitors. The s... more 3-Amido-3-aryl-piperidines were discovered as a novel structural class of GlyT1 inhibitors. The structure-activity relationship, which was developed, led to the identification of highly potent compounds exhibiting excellent selectivity against the GlyT2 isoform, drug-like properties, and in vivo activity after oral administration.
Drug Discovery Today: Technologies, 2004
Scoring functions play an essential role in structure-based virtual screening. They are required ... more 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.:
Acta crystallographica. Section D, Biological crystallography, 2007
Fatty-acid synthesis in bacteria is of great interest as a target for the discovery of antibacter... more Fatty-acid synthesis in bacteria is of great interest as a target for the discovery of antibacterial compounds. The addition of a new acetyl moiety to the growing fatty-acid chain, an essential step in this process, is catalyzed by beta-ketoacyl-ACP synthase (KAS). It is inhibited by natural antibiotics such as cerulenin and thiolactomycin; however, these lack the requirements for optimal drug development. Structure-based biophysical screening revealed a novel synthetic small molecule, 2-phenylamino-4-methyl-5-acetylthiazole, that binds to Escherichia coli KAS I with a binding constant of 25 microM as determined by fluorescence titration. A 1.35 A crystal structure of its complex with its target reveals noncovalent interactions with the active-site Cys163 and hydrophobic residues of the fatty-acid binding pocket. The active site is accessible through an open conformation of the Phe392 side chain and no conformational changes are induced at the active site upon ligand binding. This r...
Journal of computational chemistry, Jan 30, 2003
2,3-Oxidosqualene cyclases (OSC) are key enzymes in sterol biosynthesis. They catalyze the stereo... more 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 ...
Journal of molecular modeling, 2003
Two new docking programs FRED (OpenEye Scientific Software) and Glide (Schrödinger, Inc.) in comb... more Two new docking programs FRED (OpenEye Scientific Software) and Glide (Schrödinger, Inc.) in combination with various scoring functions implemented in these programs have been evaluated against a variety of seven protein targets (cyclooxygenase-2, estrogen receptor, p38 MAP kinase, gyrase B, thrombin, gelatinase A, neuraminidase) in order to assess their accuracy in virtual screening. Sets of known inhibitors were added to and ranked relative to a random library of drug-like compounds. Performance was compared in terms of enrichment factors and CPU time consumption. Results and specific features of the two new tools are discussed and compared to previously published results using FlexX (Tripos, Inc.) as a docking engine. In addition, general criteria for the selection of docking algorithms and scoring functions based on binding-site characteristics of specific protein targets are proposed. Figure Enrichment factors obtained with FlexX, Glide and FRED docking engines in combination w...
Most available tools for conformer generation, like OMEGA [1], ROTATE [2], and MIMUMBA , divide t... more Most available tools for conformer generation, like OMEGA [1], ROTATE [2], and MIMUMBA , divide the conformational space into quantized degrees of freedom, i.e. torsion angles, which are treated independently. The independence of torsions is however not valid for all fragments . There are pairs of mutually dependent degrees of freedom e.g. two consecutive torsion angles in aryl-X-aryl systems. The fact that two torsions are dependent implies that if one of the torsions is set to a specific angle, the set of possible angles for the other torsion is limited. This knowledge could be used to significantly narrow down the conformational space in deterministic rule-based conformation generators.
FEBS Open Bio, 2013
Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabol... more Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated the thermodynamics of binding of four inhibitors directed against either the CoA or the acylcarnitine binding sites using isothermal titration calorimetry (ITC). CPT-2 is a monotopic membrane protein and was solubilized by β-octylglucoside (β-OG) above its critical micellar concentration (CMC) to perform inhibitor titrations in solutions containing detergent micelles. The CMC of β-OG in the presence of inhibitors was measured with ITC and small variations were observed. The inhibitors bound to rat CPT-2 (rCPT-2) with 1:1 stoichiometry and the dissociation constants were in the range of K D = 2-20 μM. New X-ray structures and docking models of rCPT-2 in complex with inhibitors enable an analysis of the thermodynamic data in the context of the interaction observed for the individual binding sites of the ligands. For all ligands the binding enthalpy was exothermic, and enthalpy as well as entropy contributed to the binding reaction, with the exception of ST1326 for which binding was solely enthalpy-driven. The substrate analog ST1326 binds to the acylcarnitine binding site and a heat capacity change close to zero suggests a balance of electrostatic and hydrophobic interactions. An excellent correlation of the thermodynamic (ITC) and structural (X-ray crystallography, models) data was observed suggesting that ITC measurements provide valuable information for optimizing inhibitor binding in drug discovery.
Journal of Computer-Aided Molecular Design, 2011
De novo ligand design supports the search for novel molecular scaffolds in medicinal chemistry pr... more De novo ligand design supports the search for novel molecular scaffolds in medicinal chemistry projects. This search can either be based on structural information of the targeted active site (structure-based approach) or on similarity to known binders (ligand-based approach). In the absence of structural information on the target, pharmacophores provide a way to find topologically novel scaffolds. Fragment spaces have proven to be a valuable source for molecular structures in de novo design that are both diverse and synthetically accessible. They also offer a simple way to formulate custom chemical spaces. We have implemented a new method which stochastically constructs new molecules from fragment spaces under consideration of a three dimensional pharmacophore. The program has been tested on several published pharmacophores and is shown to be able to reproduce scaffold hops from the literature, which resulted in new chemical entities.
Journal of Chemical Information and Modeling, 2011
In most cheminformatics workflows, chemical information is stored in files which provide the nece... more 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. NAOMI's 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.
Journal of Chemical Information and Modeling, 2004
We describe the application of ensemble methods to binary classification problems on two pharmace... more We describe the application of ensemble methods to binary classification problems on two pharmaceutical compound data sets. Several variants of single and ensembles models of k-nearest neighbors classifiers, support vector machines (SVMs), and single ridge regression models are compared. All methods exhibit robust classification even when more features are given than observations. On two data sets dealing with specific properties of drug-like substances (cytochrome P450 inhibition and "Frequent Hitters", i.e., unspecific protein inhibition), we achieve classification rates above 90%. We are able to reduce the cross-validated misclassification rate for the Frequent Hitters problem by a factor of 2 compared to previous results obtained for the same data set with different modeling techniques.
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Papers by Tanja Schulz-Gasch