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  1. Article: Details Matter in Structure-based Drug Design.

    Kuhn, Bernd / Peters, Jens-Uwe / Rudolph, Markus G / Mohr, Peter / Stahl, Martin / Tosstorff, Andreas

    Chimia

    2023  Volume 77, Issue 7-8, Page(s) 489–493

    Abstract: Successful structure-based drug design (SBDD) requires the optimization of interactions with the target protein and the minimization of ligand strain. Both factors are often modulated by small changes in the chemical structure which can lead to profound ... ...

    Abstract Successful structure-based drug design (SBDD) requires the optimization of interactions with the target protein and the minimization of ligand strain. Both factors are often modulated by small changes in the chemical structure which can lead to profound changes in the preferred conformation and interaction preferences of the ligand. We draw from examples of a Roche project targeting phosphodiesterase 10 to highlight that details matter in SBDD. Data mining in crystal structure databases can help to identify these sometimes subtle effects, but it is also a great resource to learn about molecular recognition in general and can be used as part of molecular design tools. We illustrate the use of the Cambridge Structural Database for identifying preferred structural motifs for intramolecular hydrogen bonding and of the Protein Data Bank for deriving propensities for protein-ligand interactions.
    MeSH term(s) Ligands ; Data Mining ; Databases, Factual ; Drug Design ; Learning
    Chemical Substances Ligands
    Language English
    Publishing date 2023-08-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1516-7
    ISSN 0009-4293
    ISSN 0009-4293
    DOI 10.2533/chimia.2023.489
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Structure of reverse gyrase with a minimal latch that supports ATP-dependent positive supercoiling without specific interactions with the topoisomerase domain.

    Mhaindarkar, Vaibhav P / Rasche, René / Kümmel, Daniel / Rudolph, Markus G / Klostermeier, Dagmar

    Acta crystallographica. Section D, Structural biology

    2023  Volume 79, Issue Pt 6, Page(s) 498–507

    Abstract: Reverse gyrase is the only topoisomerase that introduces positive supercoils into DNA in an ATP-dependent reaction. Positive DNA supercoiling becomes possible through the functional cooperation of the N-terminal helicase domain of reverse gyrase with its ...

    Abstract Reverse gyrase is the only topoisomerase that introduces positive supercoils into DNA in an ATP-dependent reaction. Positive DNA supercoiling becomes possible through the functional cooperation of the N-terminal helicase domain of reverse gyrase with its C-terminal type IA topoisomerase domain. This cooperation is mediated by a reverse-gyrase-specific insertion into the helicase domain termed the `latch'. The latch consists of a globular domain inserted at the top of a β-bulge loop that connects this globular part to the helicase domain. While the globular domain shows little conservation in sequence and length and is dispensable for DNA supercoiling, the β-bulge loop is required for supercoiling activity. It has previously been shown that the β-bulge loop constitutes a minimal latch that couples ATP-dependent processes in the helicase domain to DNA processing by the topoisomerase domain. Here, the crystal structure of Thermotoga maritima reverse gyrase with such a β-bulge loop as a minimal latch is reported. It is shown that the β-bulge loop supports ATP-dependent DNA supercoiling of reverse gyrase without engaging in specific interactions with the topoisomerase domain. When only a small latch or no latch is present, a helix in the nearby helicase domain of T. maritima reverse gyrase partially unfolds. Comparison of the sequences and predicted structures of latch regions in other reverse gyrases shows that neither sequence nor structure are decisive factors for latch functionality; instead, the decisive factors are likely to be electrostatics and plain steric bulk.
    MeSH term(s) Protein Structure, Tertiary ; DNA Topoisomerases, Type I/chemistry ; DNA Topoisomerases, Type I/genetics ; DNA Topoisomerases, Type I/metabolism ; DNA Helicases/chemistry ; DNA ; Adenosine Triphosphate
    Chemical Substances DNA reverse gyrase (EC 5.99.1.-) ; DNA Topoisomerases, Type I (EC 5.99.1.2) ; DNA Helicases (EC 3.6.4.-) ; DNA (9007-49-2) ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2023-05-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2968623-4
    ISSN 2059-7983 ; 0907-4449
    ISSN (online) 2059-7983
    ISSN 0907-4449
    DOI 10.1107/S2059798323002565
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Discovery of a Series of Indane-Containing NBTIs with Activity against Multidrug-Resistant Gram-Negative Pathogens.

    Cumming, John G / Kreis, Lukas / Kühne, Holger / Wermuth, Roger / Vercruysse, Maarten / Kramer, Christian / Rudolph, Markus G / Xu, Zhiheng

    ACS medicinal chemistry letters

    2023  Volume 14, Issue 7, Page(s) 993–998

    Abstract: The rise of multidrug-resistant (MDR) Gram-negative bacteria is a major global health problem necessitating the discovery of new classes of antibiotics. Novel bacterial topoisomerase inhibitors (NBTIs) target the clinically validated bacterial type II ... ...

    Abstract The rise of multidrug-resistant (MDR) Gram-negative bacteria is a major global health problem necessitating the discovery of new classes of antibiotics. Novel bacterial topoisomerase inhibitors (NBTIs) target the clinically validated bacterial type II topoisomerases with a distinct binding site and mechanism of action to fluoroquinolone antibiotics, thus avoiding cross-resistance to this drug class. Here we report the discovery of a series of NBTIs incorporating a novel indane DNA binding moiety. X-ray cocrystal structures of compounds
    Language English
    Publishing date 2023-06-22
    Publishing country United States
    Document type Journal Article
    ISSN 1948-5875
    ISSN 1948-5875
    DOI 10.1021/acsmedchemlett.3c00187
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A high quality, industrial data set for binding affinity prediction: performance comparison in different early drug discovery scenarios.

    Tosstorff, Andreas / Rudolph, Markus G / Cole, Jason C / Reutlinger, Michael / Kramer, Christian / Schaffhauser, Hervé / Nilly, Agnès / Flohr, Alexander / Kuhn, Bernd

    Journal of computer-aided molecular design

    2022  Volume 36, Issue 10, Page(s) 753–765

    Abstract: We release a new, high quality data set of 1162 PDE10A inhibitors with experimentally determined binding affinities together with 77 PDE10A X-ray co-crystal structures from a Roche legacy project. This data set is used to compare the performance of ... ...

    Abstract We release a new, high quality data set of 1162 PDE10A inhibitors with experimentally determined binding affinities together with 77 PDE10A X-ray co-crystal structures from a Roche legacy project. This data set is used to compare the performance of different 2D- and 3D-machine learning (ML) as well as empirical scoring functions for predicting binding affinities with high throughput. We simulate use cases that are relevant in the lead optimization phase of early drug discovery. ML methods perform well at interpolation, but poorly in extrapolation scenarios-which are most relevant to a real-world application. Moreover, we find that investing into the docking workflow for binding pose generation using multi-template docking is rewarded with an improved scoring performance. A combination of 2D-ML and 3D scoring using a modified piecewise linear potential shows best overall performance, combining information on the protein environment with learning from existing SAR data.
    MeSH term(s) Ligands ; Protein Binding ; Drug Discovery ; Proteins/chemistry ; Machine Learning ; Molecular Docking Simulation
    Chemical Substances Ligands ; Proteins
    Language English
    Publishing date 2022-09-25
    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/s10822-022-00478-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding.

    Rudolph, Markus G / Klostermeier, Dagmar

    Biological chemistry

    2015  Volume 396, Issue 8, Page(s) 849–865

    Abstract: DEAD-box helicases catalyze RNA duplex unwinding in an ATP-dependent reaction. Members of the DEAD-box helicase family consist of a common helicase core formed by two RecA-like domains. According to the current mechanistic model for DEAD-box mediated RNA ...

    Abstract DEAD-box helicases catalyze RNA duplex unwinding in an ATP-dependent reaction. Members of the DEAD-box helicase family consist of a common helicase core formed by two RecA-like domains. According to the current mechanistic model for DEAD-box mediated RNA unwinding, binding of RNA and ATP triggers a conformational change of the helicase core, and leads to formation of a compact, closed state. In the closed conformation, the two parts of the active site for ATP hydrolysis and of the RNA binding site, residing on the two RecA domains, become aligned. Closing of the helicase core is coupled to a deformation of the RNA backbone and destabilization of the RNA duplex, allowing for dissociation of one of the strands. The second strand remains bound to the helicase core until ATP hydrolysis and product release lead to re-opening of the core. The concomitant disruption of the RNA binding site causes dissociation of the second strand. The activity of the helicase core can be modulated by interaction partners, and by flanking N- and C-terminal domains. A number of C-terminal flanking regions have been implicated in RNA binding: RNA recognition motifs (RRM) typically mediate sequence-specific RNA binding, whereas positively charged, unstructured regions provide binding sites for structured RNA, without sequence-specificity. Interaction partners modulate RNA binding to the core, or bind to RNA regions emanating from the core. The functional interplay of the helicase core and ancillary domains or interaction partners in RNA binding and unwinding is not entirely understood. This review summarizes our current knowledge on RNA binding to the DEAD-box helicase core and the roles of ancillary domains and interaction partners in RNA binding and unwinding by DEAD-box proteins.
    MeSH term(s) Adenosine Triphosphate/metabolism ; Binding Sites ; DEAD-box RNA Helicases/metabolism ; Hydrolysis ; Nucleic Acid Conformation ; Protein Binding ; Protein Structure, Tertiary ; RNA/chemistry ; RNA/metabolism
    Chemical Substances RNA (63231-63-0) ; Adenosine Triphosphate (8L70Q75FXE) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2015-08
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1334659-3
    ISSN 1437-4315 ; 1431-6730 ; 1432-0355
    ISSN (online) 1437-4315
    ISSN 1431-6730 ; 1432-0355
    DOI 10.1515/hsz-2014-0277
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Mapping the spectrum of conformational states of the DNA- and C-gates in Bacillus subtilis gyrase.

    Rudolph, Markus G / Klostermeier, Dagmar

    Journal of molecular biology

    2013  Volume 425, Issue 15, Page(s) 2632–2640

    Abstract: Type II DNA topoisomerases alter the supercoiling state of DNA in an ATP-dependent fashion that requires large conformational changes. The directionality of DNA strand transfer is controlled by three transient protein interfaces, termed the N-gate, DNA- ... ...

    Abstract Type II DNA topoisomerases alter the supercoiling state of DNA in an ATP-dependent fashion that requires large conformational changes. The directionality of DNA strand transfer is controlled by three transient protein interfaces, termed the N-gate, DNA-gate, and C-gate. Bacterial gyrase is a type II DNA topoisomerase of A2B2 composition. The N-gate is formed by the two GyrB subunits and the GyrA subunits form the DNA- and C-gates. In structures of type II topoisomerase fragments, the DNA- and C-gates delimit a cavity for DNA and can be open or closed. However, the conformational space accessible has not yet been mapped. Here, we describe the crystal structure of the Bacillus subtilis DNA gyrase A subunit lacking the C-terminal DNA-wrapping domains. Five dimeric states of the GyrA N-terminal domain are observed, with their DNA- and C-gates either closed, or open to different extents. All of these conformations can in principle accommodate double-stranded DNA in the central cavity but only one conformation has its DNA-gate open wide enough for DNA to enter. The structure thus reflects the lower limit of DNA-gate opening that must occur during gyrase catalysis. The DNA-gate is formed by two flat surfaces, with few interactions. In contrast, the C-gate exhibits a highly undulated surface and forms a large number of interactions. None of the dimers in the crystal structures display an open C-gate that would allow DNA passage, in agreement with a transient opening of this gate during the catalytic cycle of DNA supercoiling.
    MeSH term(s) Bacillus subtilis/chemistry ; Bacillus subtilis/enzymology ; Crystallography, X-Ray ; DNA Gyrase/chemistry ; DNA Gyrase/metabolism ; Models, Molecular ; Protein Conformation ; Protein Multimerization
    Chemical Substances DNA Gyrase (EC 5.99.1.3)
    Language English
    Publishing date 2013-08-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2013.04.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Mapping the Spectrum of Conformational States of the DNA- and C-Gates in Bacillus subtilis Gyrase

    Rudolph, Markus G / Klostermeier, Dagmar

    Journal of molecular biology. 2013 Aug. 9, v. 425, no. 15

    2013  

    Abstract: Type II DNA topoisomerases alter the supercoiling state of DNA in an ATP-dependent fashion that requires large conformational changes. The directionality of DNA strand transfer is controlled by three transient protein interfaces, termed the N-gate, DNA- ... ...

    Abstract Type II DNA topoisomerases alter the supercoiling state of DNA in an ATP-dependent fashion that requires large conformational changes. The directionality of DNA strand transfer is controlled by three transient protein interfaces, termed the N-gate, DNA-gate, and C-gate. Bacterial gyrase is a type II DNA topoisomerase of A₂B₂ composition. The N-gate is formed by the two GyrB subunits and the GyrA subunits form the DNA- and C-gates. In structures of type II topoisomerase fragments, the DNA- and C-gates delimit a cavity for DNA and can be open or closed. However, the conformational space accessible has not yet been mapped. Here, we describe the crystal structure of the Bacillus subtilis DNA gyrase A subunit lacking the C-terminal DNA-wrapping domains. Five dimeric states of the GyrA N-terminal domain are observed, with their DNA- and C-gates either closed, or open to different extents. All of these conformations can in principle accommodate double-stranded DNA in the central cavity but only one conformation has its DNA-gate open wide enough for DNA to enter. The structure thus reflects the lower limit of DNA-gate opening that must occur during gyrase catalysis. The DNA-gate is formed by two flat surfaces, with few interactions. In contrast, the C-gate exhibits a highly undulated surface and forms a large number of interactions. None of the dimers in the crystal structures display an open C-gate that would allow DNA passage, in agreement with a transient opening of this gate during the catalytic cycle of DNA supercoiling.
    Keywords Bacillus subtilis ; DNA ; DNA topoisomerase (ATP-hydrolysing) ; catalytic activity ; crystal structure
    Language English
    Dates of publication 2013-0809
    Size p. 2632-2640.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2013.04.010
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: Domain swap in the C-terminal ubiquitin-like domain of human doublecortin.

    Rufer, Arne C / Kusznir, Eric / Burger, Dominique / Stihle, Martine / Ruf, Armin / Rudolph, Markus G

    Acta crystallographica. Section D, Structural biology

    2018  Volume 74, Issue Pt 5, Page(s) 450–462

    Abstract: Doublecortin, a microtubule-associated protein that is only produced during neurogenesis, cooperatively binds to microtubules and stimulates microtubule polymerization and cross-linking by unknown mechanisms. A domain swap is observed in the crystal ... ...

    Abstract Doublecortin, a microtubule-associated protein that is only produced during neurogenesis, cooperatively binds to microtubules and stimulates microtubule polymerization and cross-linking by unknown mechanisms. A domain swap is observed in the crystal structure of the C-terminal domain of doublecortin. As determined by analytical ultracentrifugation, an open conformation is also present in solution. At higher concentrations, higher-order oligomers of the domain are formed. The domain swap and additional interfaces observed in the crystal lattice can explain the formation of doublecortin tetramers or multimers, in line with the analytical ultracentrifugation data. Taken together, the domain swap offers a mechanism for the observed cooperative binding of doublecortin to microtubules. Doublecortin-induced cross-linking of microtubules can be explained by the same mechanism. The effect of several mutations leading to lissencephaly and double-cortex syndrome can be traced to the domain swap and the proposed self-association of doublecortin.
    MeSH term(s) Crystallography, X-Ray ; Humans ; Lissencephaly/genetics ; Microtubule-Associated Proteins/chemistry ; Microtubule-Associated Proteins/genetics ; Microtubule-Associated Proteins/metabolism ; Microtubules/metabolism ; Mutation ; Neuropeptides/chemistry ; Neuropeptides/genetics ; Neuropeptides/metabolism ; Protein Conformation ; Protein Domains ; Protein Multimerization ; Ubiquitin/chemistry ; Ultracentrifugation
    Chemical Substances Microtubule-Associated Proteins ; Neuropeptides ; Ubiquitin ; doublecortin protein
    Language English
    Publishing date 2018-04-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2020492-9
    ISSN 2059-7983 ; 1399-0047 ; 0907-4449
    ISSN (online) 2059-7983 ; 1399-0047
    ISSN 0907-4449
    DOI 10.1107/S2059798318004813
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Synthesis, Characterization, and

    Hunziker, Daniel / Reinehr, Sabrina / Palmhof, Marina / Wagner, Natalie / Biniasch, Thomas / Stute, Gesa / Mattei, Patrizio / Schmitz, Petra / DiGiorgio, Patrick / Hert, Jérôme / Rudolph, Markus G / Benz, Joerg / Stihle, Martine / Gsell, Bernard / Müller, Stephan / Gasser, Rodolfo / Schonhoven, Nina / Ullmer, Christoph / Joachim, Stephanie C

    Frontiers in pharmacology

    2022  Volume 12, Page(s) 699535

    Abstract: The autotaxin-lysophosphatidic acid (ATX-LPA) signaling pathway plays a role in a variety of autoimmune diseases, such as rheumatoid arthritis or neurodegeneration. A link to the pathogenesis of glaucoma is suggested by an overactive ATX-LPA axis in ... ...

    Abstract The autotaxin-lysophosphatidic acid (ATX-LPA) signaling pathway plays a role in a variety of autoimmune diseases, such as rheumatoid arthritis or neurodegeneration. A link to the pathogenesis of glaucoma is suggested by an overactive ATX-LPA axis in aqueous humor samples of glaucoma patients. Analysis of such samples suggests that the ATX-LPA axis contributes to the fibrogenic activity and resistance to aqueous humor outflow through the trabecular meshwork. In order to inhibit or modulate this pathway, we developed a new series of ATX-inhibitors containing novel bicyclic and spirocyclic structural motifs. A potent lead compound (IC
    Language English
    Publishing date 2022-01-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2021.699535
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core.

    Rudolph, Markus G / Klostermeier, Dagmar

    RNA (New York, N.Y.)

    2009  Volume 15, Issue 11, Page(s) 1993–2001

    Abstract: DEAD box family helicases consist of a helicase core that is formed by two flexibly linked RecA-like domains. The helicase activity can be regulated by N- or C-terminal extensions flanking the core. Thermus thermophilus heat resistant RNA-dependent ... ...

    Abstract DEAD box family helicases consist of a helicase core that is formed by two flexibly linked RecA-like domains. The helicase activity can be regulated by N- or C-terminal extensions flanking the core. Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) is the first DEAD box helicase that forms a dimer using a unique dimerization domain. In addition to the dimerization domain, Hera contains a C-terminal RNA binding domain (RBD) that shares sequence homology only to uncharacterized proteins of the Deinococcus/Thermus group. The crystal structure of Hera_RBD reveals the fold of an altered RNA recognition motif (RRM) with limited structural homology to the RBD of the DEAD box helicase YxiN from Bacillus subtilis. Comparison with RRM/RNA complexes shows that a RNA binding mode different than that suggested for YxiN, but similar to U1A, can be inferred for Hera. The orientation of the RBD relative to the helicase core was defined in a second crystal structure of a Hera fragment including the C-terminal RecA domain, the dimerization domain, and the RBD. The structures allow construction of a model for the entire Hera helicase dimer. A likely binding surface for large RNA substrates that spans both RecA-like domains and the RBD is identified.
    MeSH term(s) Amino Acid Sequence ; Crystallography, X-Ray ; DEAD-box RNA Helicases/chemistry ; DEAD-box RNA Helicases/metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Binding ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; RNA/chemistry ; RNA/metabolism ; Sequence Alignment ; Structural Homology, Protein ; Substrate Specificity ; Thermus thermophilus/enzymology
    Chemical Substances RNA (63231-63-0) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2009-08-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.1820009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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