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Book ; Online ; Thesis: A powerful combination of computational methods on the road toward potent non-steroidal inhibitors of steroidogenic enzymes involved in hormone-dependent diseases

Negri, Matthias

2010

Author's details	von Matthias Negri
Language	English
Size	Online-Ressource
Document type	Book ; Online ; Thesis
Thesis / German Habilitation thesis	Saarbrücken, Univ., Diss., 2010
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Article ; Online: Advances in Catchment Science, Hydrochemistry, and Aquatic Ecology Enabled by High-Frequency Water Quality Measurements.

Bieroza, Magdalena / Acharya, Suman / Benisch, Jakob / Ter Borg, Rebecca N / Hallberg, Lukas / Negri, Camilla / Pruitt, Abagael / Pucher, Matthias / Saavedra, Felipe / Staniszewska, Kasia / Van't Veen, Sofie G M / Vincent, Anna / Winter, Carolin / Basu, Nandita B / Jarvie, Helen P / Kirchner, James W

Environmental science & technology

2023 Volume 57, Issue 12, Page(s) 4701–4719

Abstract: High-frequency water quality measurements in streams and rivers have expanded in scope and sophistication during the last two decades. Existing technology ... ...

Abstract	High-frequency water quality measurements in streams and rivers have expanded in scope and sophistication during the last two decades. Existing technology allows
MeSH term(s)	Water Quality ; Hydrobiology ; Rivers ; Forecasting ; Environmental Monitoring
Language	English
Publishing date	2023-03-13
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ISSN	1520-5851
ISSN (online)	1520-5851
DOI	10.1021/acs.est.2c07798
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online ; Thesis: A powerful combination of computational methods on the road toward potent non-steroidal inhibitors of steroidogenic enzymes involved in hormone-dependent diseases

Negri, Matthias [Verfasser]

2010

Author's details	von Matthias Negri
Keywords	Naturwissenschaften ; Science
Subject code	sg500
Language	English
Document type	Book ; Online ; Thesis
Database	Digital theses on the web

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Article ; Online: Homology modeling meets site-directed mutagenesis: An ideal combination to elucidate the topology of 17β-HSD2.

Sager, Christoph P / Weber, Susanne / Negri, Matthias / Banachowicz, Pauline / Möller, Gabriele / Adamski, Jerzy / Hartmann, Rolf W / Marchais-Oberwinkler, Sandrine

The Journal of steroid biochemistry and molecular biology

2020 Volume 206, Page(s) 105790

Abstract: 17β-Hydroxysteroid dehydrogenase type 2 (17β-HSD2) catalyzes the conversion of highly active estrogens and androgens into their less active forms using ... ...

Abstract	17β-Hydroxysteroid dehydrogenase type 2 (17β-HSD2) catalyzes the conversion of highly active estrogens and androgens into their less active forms using NAD
MeSH term(s)	Amino Acids/genetics ; Catalysis ; Enzyme Inhibitors/pharmacology ; Estradiol Dehydrogenases/chemistry ; Estradiol Dehydrogenases/genetics ; Estradiol Dehydrogenases/ultrastructure ; Humans ; Ligands ; Models, Molecular ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Structure-Activity Relationship
Chemical Substances	Amino Acids ; Enzyme Inhibitors ; Ligands ; Estradiol Dehydrogenases (EC 1.1.1.62) ; HSD17B2 protein, human (EC 1.1.1.62)
Language	English
Publishing date	2020-11-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1049188-0
ISSN	1879-1220 ; 0960-0760
ISSN (online)	1879-1220
ISSN	0960-0760
DOI	10.1016/j.jsbmb.2020.105790
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Article ; Online: Novel small molecule inhibitors targeting the "switch region" of bacterial RNAP: structure-based optimization of a virtual screening hit.

Sahner, J Henning / Groh, Matthias / Negri, Matthias / Haupenthal, Jörg / Hartmann, Rolf W

European journal of medicinal chemistry

2013 Volume 65, Page(s) 223–231

Abstract: Rising resistance against current antibiotics necessitates the development of antibacterial agents with alternative targets. The "switch region" of RNA polymerase (RNAP), addressed by the myxopyronins, could be such a novel target site. Based on a hit ... ...

Abstract	Rising resistance against current antibiotics necessitates the development of antibacterial agents with alternative targets. The "switch region" of RNA polymerase (RNAP), addressed by the myxopyronins, could be such a novel target site. Based on a hit candidate discovered by virtual screening, a small library of 5-phenyl-3-ureidothiophene-2-carboxylic acids was synthesized resulting in compounds with increased RNAP inhibition. Hansch analysis revealed π (lipophilicity constant) and σ (Hammet substituent constant) of the substituents at the 5-phenyl moiety to be crucial for activity. The binding mode was proven by the targeted introduction of a moiety mimicking the enecarbamate side chain of myxopyronin into the hit compound, accompanied by enhanced RNAP inhibitory potency. The new compounds displayed good antibacterial activities against Gram positive bacteria and Gram negative Escherichia coli TolC and a reduced resistance frequency compared to the established antibiotic rifampicin.
MeSH term(s)	Anti-Bacterial Agents/chemical synthesis ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Carboxylic Acids/chemical synthesis ; Carboxylic Acids/chemistry ; Carboxylic Acids/pharmacology ; DNA-Directed RNA Polymerases/antagonists & inhibitors ; DNA-Directed RNA Polymerases/metabolism ; Dose-Response Relationship, Drug ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Escherichia coli/drug effects ; Escherichia coli/enzymology ; High-Throughput Screening Assays ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Structure ; Small Molecule Libraries/chemical synthesis ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Structure-Activity Relationship ; Thiophenes/chemical synthesis ; Thiophenes/chemistry ; Thiophenes/pharmacology
Chemical Substances	5-phenyl-3-ureidothiophene-2-carboxylic acid ; Anti-Bacterial Agents ; Carboxylic Acids ; Enzyme Inhibitors ; Small Molecule Libraries ; Thiophenes ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2013-07
Publishing country	France
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2013.04.060
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Article ; Online: Discovery of novel bacterial RNA polymerase inhibitors: pharmacophore-based virtual screening and hit optimization.

Hinsberger, Stefan / Hüsecken, Kristina / Groh, Matthias / Negri, Matthias / Haupenthal, Jörg / Hartmann, Rolf W

Journal of medicinal chemistry

2013 Volume 56, Issue 21, Page(s) 8332–8338

Abstract: The bacterial RNA polymerase (RNAP) is a validated target for broad spectrum antibiotics. However, the efficiency of drugs is reduced by resistance. To discover novel RNAP inhibitors, a pharmacophore based on the alignment of described inhibitors was ... ...

Abstract	The bacterial RNA polymerase (RNAP) is a validated target for broad spectrum antibiotics. However, the efficiency of drugs is reduced by resistance. To discover novel RNAP inhibitors, a pharmacophore based on the alignment of described inhibitors was used for virtual screening. In an optimization process of hit compounds, novel derivatives with improved in vitro potency were discovered. Investigations concerning the molecular mechanism of RNAP inhibition reveal that they prevent the protein-protein interaction (PPI) between σ(70) and the RNAP core enzyme. Besides of reducing RNA formation, the inhibitors were shown to interfere with bacterial lipid biosynthesis. The compounds were active against Gram-positive pathogens and revealed significantly lower resistance frequencies compared to clinically used rifampicin.
MeSH term(s)	Anti-Bacterial Agents/chemical synthesis ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Bacillus subtilis/drug effects ; DNA-Directed RNA Polymerases/antagonists & inhibitors ; DNA-Directed RNA Polymerases/metabolism ; Dose-Response Relationship, Drug ; Drug Discovery ; Enzyme Inhibitors/chemical synthesis ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Escherichia coli/drug effects ; Escherichia coli/enzymology ; High-Throughput Screening Assays ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Structure ; Pseudomonas aeruginosa/drug effects ; Staphylococcus aureus/drug effects ; Structure-Activity Relationship
Chemical Substances	Anti-Bacterial Agents ; Enzyme Inhibitors ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2013-11-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/jm400485e
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Article ; Online: Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17β-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps.

Negri, Matthias / Recanatini, Maurizio / Hartmann, Rolf W

Journal of computer-aided molecular design

2011 Volume 25, Issue 9, Page(s) 795–811

Abstract: 17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of ... ...

Abstract	17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of estrogen-dependent diseases like breast cancer and endometriosis. 17β-HSD1 belongs to the bisubstrate enzymes and exists as an ensemble of conformations. These principally differ in the region of the βFαG'-loop, suggesting a prominent role in substrate and inhibitor binding. Although several classes of potent non-steroidal 17β-HSD1 inhibitors currently exist, their binding mode is still unclear. We aimed to elucidate the binding mode of bis(hydroxyphenyl)arenes, a highly potent class of 17β-HSD1 inhibitors, and to rank these compounds correctly with respect to their inhibitory potency, two essential aspects in drug design. Ensemble docking experiments resulted in a steroidal binding mode for the closed enzyme conformations and in an alternative mode for the opened and occluded conformers with the inhibitors placed below the NADPH interacting with it synergically via π-π stacking and H-bond formation. Both binding modes were investigated by MD simulations and MM-PBSA binding free energy estimations using as representative member for this class compound 1 (50 nM). Notably, only the alternative binding mode proved stable and was energetically more favorable, while when simulated in the steroidal binding mode compound 1 was displaced from the active site. In parallel, ab initio studies of small NADPH-inhibitor complexes were performed, which supported the importance of the synergistic interaction between inhibitors and cofactor.
MeSH term(s)	17-Hydroxysteroid Dehydrogenases/antagonists & inhibitors ; 17-Hydroxysteroid Dehydrogenases/chemistry ; 17-Hydroxysteroid Dehydrogenases/metabolism ; Binding Sites ; Drug Design ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Molecular Dynamics Simulation ; Protein Binding ; Static Electricity ; Thermodynamics
Chemical Substances	Enzyme Inhibitors ; 17-Hydroxysteroid Dehydrogenases (EC 1.1.-) ; 3 (or 17)-beta-hydroxysteroid dehydrogenase (EC 1.1.1.51)
Language	English
Publishing date	2011-08-06
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	808166-9
ISSN	1573-4951 ; 0920-654X
ISSN (online)	1573-4951
ISSN	0920-654X
DOI	10.1007/s10822-011-9464-7
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Article ; Online: Structural basis for species specific inhibition of 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1): computational study and biological validation.

Klein, Tobias / Henn, Claudia / Negri, Matthias / Frotscher, Martin

PloS one

2011 Volume 6, Issue 8, Page(s) e22990

Abstract: 17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the reduction of estrone to estradiol, which is the most potent estrogen in humans. Inhibition of 17β-HSD1 and thereby reducing the intracellular estradiol concentration is thus a promising ... ...

Abstract	17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the reduction of estrone to estradiol, which is the most potent estrogen in humans. Inhibition of 17β-HSD1 and thereby reducing the intracellular estradiol concentration is thus a promising approach for the treatment of estrogen dependent diseases. In the past, several steroidal and non-steroidal inhibitors of 17β-HSD1 have been described but so far there is no cocrystal structure of the latter in complex with 17β-HSD1. However, a distinct knowledge of active site topologies and protein-ligand interactions is a prerequisite for structure-based drug design and optimization. An elegant strategy to enhance this knowledge is to compare inhibition values obtained for one compound toward ortholog proteins from various species, which are highly conserved in sequence and differ only in few residues. In this study the inhibitory potencies of selected members of different non-steroidal inhibitor classes toward marmoset 17β-HSD1 were determined and the data were compared with the values obtained for the human enzyme. A species specific inhibition profile was observed in the class of the (hydroxyphenyl)naphthols. Using a combination of computational methods, including homology modelling, molecular docking, MD simulation, and binding energy calculation, a reasonable model of the three-dimensional structure of marmoset 17β-HSD1 was developed and inhibition data were rationalized on the structural basis. In marmoset 17β-HSD1, residues 190 to 196 form a small α-helix, which induces conformational changes compared to the human enzyme. The docking poses suggest these conformational changes as determinants for species specificity and energy decomposition analysis highlighted the outstanding role of Asn152 as interaction partner for inhibitor binding. In summary, this strategy of comparing the biological activities of inhibitors toward highly conserved ortholog proteins might be an alternative to laborious x-ray or site-directed mutagenesis experiments in certain cases. Additionally, it facilitates inhibitor design and optimization by offering new information on protein-ligand interactions.
MeSH term(s)	Amino Acid Sequence ; Amino Acids/chemistry ; Amino Acids/genetics ; Amino Acids/metabolism ; Animals ; Binding Sites/genetics ; Callithrix ; Computer Simulation ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Estradiol Dehydrogenases/antagonists & inhibitors ; Estradiol Dehydrogenases/chemistry ; Estradiol Dehydrogenases/metabolism ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Binding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Species Specificity ; Structure-Activity Relationship ; Substrate Specificity
Chemical Substances	Amino Acids ; Enzyme Inhibitors ; Estradiol Dehydrogenases (EC 1.1.1.62) ; HSD17B1 protein, human (EC 1.1.1.62) ; HSD17B2 protein, human (EC 1.1.1.62)
Language	English
Publishing date	2011-08-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0022990
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Article ; Online: Advances in Catchment Science, Hydrochemistry, and Aquatic Ecology Enabled by High-Frequency Water Quality Measurements

Bieroza, Magdalena / Acharya, Suman / Benisch, Jakob / ter Borg, Rebecca N. / Hallberg, Lukas / Negri, Camilla / Pruitt, Abagael / Pucher, Matthias / Saavedra, Felipe / Staniszewska, Kasia / van't Veen, Sofie G.M. / Vincent, Anna / Winter, Carolin / Basu, Nandita B. / Jarvie, Helen P. / Kirchner, James W. / id_orcid:0 000-0001-6577-3619

Environmental Science & Technology, 57 (12)

2023

Abstract: High-frequency water quality measurements in streams and rivers have expanded in scope and sophistication during the last two decades. Existing technology allows in situ automated measurements of water quality constituents, including both solutes and ... ...

Abstract	High-frequency water quality measurements in streams and rivers have expanded in scope and sophistication during the last two decades. Existing technology allows in situ automated measurements of water quality constituents, including both solutes and particulates, at unprecedented frequencies from seconds to subdaily sampling intervals. This detailed chemical information can be combined with measurements of hydrological and biogeochemical processes, bringing new insights into the sources, transport pathways, and transformation processes of solutes and particulates in complex catchments and along the aquatic continuum. Here, we summarize established and emerging high-frequency water quality technologies, outline key high-frequency hydrochemical data sets, and review scientific advances in key focus areas enabled by the rapid development of high-frequency water quality measurements in streams and rivers. Finally, we discuss future directions and challenges for using high-frequency water quality measurements to bridge scientific and management gaps by promoting a holistic understanding of freshwater systems and catchment status, health, and function. ISSN:0013-936X ISSN:1520-5851
Keywords	Catchment science ; stream hydrochemistry ; aquatic ecology ; high-frequency ; water quality monitoring ; optical sensors
Subject code	550
Language	English
Publishing date	2023-03-28
Publisher	American Chemical Society
Publishing country	ch
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Insights in 17beta-HSD1 enzyme kinetics and ligand binding by dynamic motion investigation.

Negri, Matthias / Recanatini, Maurizio / Hartmann, Rolf W

PloS one

2010 Volume 5, Issue 8, Page(s) e12026

Abstract: Background: Bisubstrate enzymes, such as 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), exist in solution as an ensemble of conformations. 17beta-HSD1 catalyzes the last step of the biosynthesis of estradiol and, thus, it is a potentially ... ...

Abstract	Background: Bisubstrate enzymes, such as 17beta-hydroxysteroid dehydrogenase type 1 (17beta-HSD1), exist in solution as an ensemble of conformations. 17beta-HSD1 catalyzes the last step of the biosynthesis of estradiol and, thus, it is a potentially attractive target for breast cancer treatment. Methodology/principal findings: To elucidate the conformational transitions of its catalytic cycle, a structural analysis of all available crystal structures was performed and representative conformations were assigned to each step of the putative kinetic mechanism. To cover most of the conformational space, all-atom molecular dynamic simulations were performed using the four crystallographic structures best describing apoform, opened, occluded and closed state of 17beta-HSD1 as starting structures. With three of them, binary and ternary complexes were built with NADPH and NADPH-estrone, respectively, while two were investigated as apoform. Free energy calculations were performed in order to judge more accurately which of the MD complexes describes a specific kinetic step. Conclusions/significance: Remarkably, the analysis of the eight long range trajectories resulting from this multi-trajectory/-complex approach revealed an essential role played by the backbone and side chain motions, especially of the betaF alphaG'-loop, in cofactor and substrate binding. Thus, a selected-fit mechanism is suggested for 17beta-HSD1, where ligand-binding induced concerted motions of the FG-segment and the C-terminal part guide the enzyme along its preferred catalytic pathway. Overall, we could assign different enzyme conformations to the five steps of the random bi-bi kinetic cycle of 17beta-HSD1 and we could postulate a preferred pathway for it. This study lays the basis for more-targeted biochemical studies on 17beta-HSD1, as well as for the design of specific inhibitors of this enzyme. Moreover, it provides a useful guideline for other enzymes, also characterized by a rigid core and a flexible region directing their catalysis.
MeSH term(s)	17-Hydroxysteroid Dehydrogenases/chemistry ; 17-Hydroxysteroid Dehydrogenases/metabolism ; Biocatalysis ; Crystallography, X-Ray ; Enzyme Assays ; Estrone/metabolism ; Humans ; Kinetics ; Ligands ; Molecular Dynamics Simulation ; Movement ; NADP/metabolism ; Protein Binding ; Protein Structure, Secondary ; Reproducibility of Results ; Thermodynamics
Chemical Substances	Ligands ; Estrone (2DI9HA706A) ; NADP (53-59-8) ; 17-Hydroxysteroid Dehydrogenases (EC 1.1.-) ; 3 (or 17)-beta-hydroxysteroid dehydrogenase (EC 1.1.1.51)
Language	English
Publishing date	2010-08-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0012026
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