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Article ; Online: Conserved allosteric inhibitory site on the respiratory syncytial virus and human metapneumovirus RNA-dependent RNA polymerases.

Kleiner, Victoria A / O Fischmann, Thierry / Howe, John A / Beshore, Douglas C / Eddins, Michael J / Hou, Yan / Mayhood, Todd / Klein, Daniel / Nahas, Debbie D / Lucas, Bob J / Xi, He / Murray, Edward / Ma, Daphne Y / Getty, Krista / Fearns, Rachel

Communications biology

2023 Volume 6, Issue 1, Page(s) 649

Abstract: Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised ... ...

Abstract	Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults
MeSH term(s)	Infant ; Adult ; Humans ; Aged ; Metapneumovirus/genetics ; Metapneumovirus/metabolism ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; Respiratory Syncytial Virus, Human ; Respiratory Tract Infections ; RNA, Messenger
Chemical Substances	RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; RNA, Messenger
Language	English
Publishing date	2023-06-19
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-04990-0
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural insights into selective small molecule activation of PKG1α.

Metwally, Essam / Mak, Victor / Soriano, Aileen / Zebisch, Matthias / Silvestre, H Leonardo / McEwan, Paul A / Ermakov, Grigori / Beaumont, Maribel / Tawa, Paul / Barker, John J / Yen, Rose / Patel, Akash / Lim, Yeon-Hee / Healy, David / Hanisak, Jennifer / Cheng, Alan C / Greshock, Tom / Fischmann, Thierry O

Communications biology

2023 Volume 6, Issue 1, Page(s) 798

Abstract: cGMP-dependent protein kinase I-α (PKG1α) is a target for pulmonary arterial hypertension due to its role in the regulation of smooth muscle function. While most work has focused on regulation of cGMP turnover, we recently described several small ... ...

Abstract	cGMP-dependent protein kinase I-α (PKG1α) is a target for pulmonary arterial hypertension due to its role in the regulation of smooth muscle function. While most work has focused on regulation of cGMP turnover, we recently described several small molecule tool compounds which were capable of activating PKG1α via a cGMP independent pathway. Selected molecules were crystallized in the presence of PKG1α and were found to bind to an allosteric site proximal to the low-affinity nucleotide binding domain. These molecules act to displace the switch helix and cause activation of PKG1α representing a new mechanism for the activation and control of this critical therapeutic path. The described structures are vital to understanding the function and control of this key regulatory pathway.
MeSH term(s)	Cyclic GMP-Dependent Protein Kinase Type I/metabolism
Chemical Substances	Cyclic GMP-Dependent Protein Kinase Type I (EC 2.7.11.12)
Language	English
Publishing date	2023-07-31
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05095-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Conserved allosteric inhibitory site on the respiratory syncytial virus and human metapneumovirus RNA-dependent RNA polymerases

Victoria A. Kleiner / Thierry O. Fischmann / John A. Howe / Douglas C. Beshore / Michael J. Eddins / Yan Hou / Todd Mayhood / Daniel Klein / Debbie D. Nahas / Bob J. Lucas / He Xi / Edward Murray / Daphne Y. Ma / Krista Getty / Rachel Fearns

Communications Biology, Vol 6, Iss 1, Pp 1-

2023 Volume 12

Abstract: Abstract Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults1–3. Therapeutic small molecule ... ...

Abstract	Abstract Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) are related RNA viruses responsible for severe respiratory infections and resulting disease in infants, elderly, and immunocompromised adults1–3. Therapeutic small molecule inhibitors that bind to the RSV polymerase and inhibit viral replication are being developed, but their binding sites and molecular mechanisms of action remain largely unknown4. Here we report a conserved allosteric inhibitory site identified on the L polymerase proteins of RSV and HMPV that can be targeted by a dual-specificity, non-nucleoside inhibitor, termed MRK-1. Cryo-EM structures of the inhibitor in complexes with truncated RSV and full-length HMPV polymerase proteins provide a structural understanding of how MRK-1 is active against both viruses. Functional analyses indicate that MRK-1 inhibits conformational changes necessary for the polymerase to engage in RNA synthesis initiation and to transition into an elongation mode. Competition studies reveal that the MRK-1 binding pocket is distinct from that of a capping inhibitor with an overlapping resistance profile, suggesting that the polymerase conformation bound by MRK-1 may be distinct from that involved in mRNA capping. These findings should facilitate optimization of dual RSV and HMPV replication inhibitors and provide insights into the molecular mechanisms underlying their polymerase activities.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Pembrolizumab microgravity crystallization experimentation.

Reichert, Paul / Prosise, Winifred / Fischmann, Thierry O / Scapin, Giovanna / Narasimhan, Chakravarthy / Spinale, April / Polniak, Ray / Yang, Xiaoyu / Walsh, Erika / Patel, Daya / Benjamin, Wendy / Welch, Johnathan / Simmons, Denarra / Strickland, Corey

NPJ microgravity

2019 Volume 5, Page(s) 28

Abstract: Crystallization processes have been widely used in the pharmaceutical industry for the manufacture, storage, and delivery of small-molecule and small protein therapeutics. However, the identification of crystallization processes for biologics, ... ...

Abstract	Crystallization processes have been widely used in the pharmaceutical industry for the manufacture, storage, and delivery of small-molecule and small protein therapeutics. However, the identification of crystallization processes for biologics, particularly monoclonal antibodies, has been prohibitive due to the size and the flexibility of their overall structure. There remains a challenge and an opportunity to utilize the benefits of crystallization of biologics. The research laboratories of Merck Sharp & Dome Corp. (MSD) in collaboration with the International Space Station (ISS) National Laboratory performed crystallization experiments with pembrolizumab (Keytruda
Language	English
Publishing date	2019-12-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2823626-9
ISSN	2373-8065
ISSN	2373-8065
DOI	10.1038/s41526-019-0090-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch.

Howe, John A / Xiao, Li / Fischmann, Thierry O / Wang, Hao / Tang, Haifeng / Villafania, Artjohn / Zhang, Rumin / Barbieri, Christopher M / Roemer, Terry

RNA biology

2016 Volume 13, Issue 10, Page(s) 946–954

Abstract: Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, ...

Abstract	Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil is structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.
Language	English
Publishing date	2016-10-02
Publishing country	United States
Document type	Journal Article
ISSN	1555-8584
ISSN (online)	1555-8584
DOI	10.1080/15476286.2016.1216304
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Preclinical characterization and clinical translation of pharmacodynamic markers for MK-5890: a human CD27 activating antibody for cancer immunotherapy.

Guelen, Lars / Fischmann, Thierry O / Wong, Jerelyn / Mauze, Smita / Guadagnoli, Marco / Bąbała, Nikolina / Wagenaars, Jozef / Juan, Veronica / Rosen, David / Prosise, Winnie / Habraken, Maurice / Lodewijks, Imke / Gu, Danling / Stammen-Vogelzangs, Judith / Yu, Ying / Baker, Jeanne / Lutje Hulsik, David / Driessen-Engels, Lilian / Malashock, Dan /

Kreijtz, Joost / Bertens, Astrid / de Vries, Evert / Bovens, Astrid / Bramer, Arne / Zhang, Yiwei / Wnek, Richard / Troth, Sean / Chartash, Elliot / Dobrenkov, Konstantin / Sadekova, Svetlana / van Elsas, Andrea / Cheung, Jason K / Fayadat-Dilman, Laurence / Borst, Jannie / Beebe, Amy M / Van Eenennaam, Hans

Journal for immunotherapy of cancer

2022 Volume 10, Issue 9

Abstract: Background: Immune checkpoint inhibitors (ICI) have radically changed cancer therapy, but most patients with cancer are unresponsive or relapse after treatment. MK-5890 is a CD27 agonist antibody intended to complement ICI therapy. CD27 is a member of ... ...

Abstract	Background: Immune checkpoint inhibitors (ICI) have radically changed cancer therapy, but most patients with cancer are unresponsive or relapse after treatment. MK-5890 is a CD27 agonist antibody intended to complement ICI therapy. CD27 is a member of the tumor necrosis factor receptor superfamily that plays a critical role in promoting responses of T cells, B cells and NK cells. Methods: Anti-CD27 antibodies were generated and selected for agonist activity using NF-кB luciferase reporter assays. Antibodies were humanized and characterized for agonism using in vitro T-cell proliferation assays. The epitope recognized on CD27 by MK-5890 was established by X-ray crystallography. Anti-tumor activity was evaluated in a human CD27 knock-in mouse. Preclinical safety was tested in rhesus monkeys. Pharmacodynamic properties were examined in mouse, rhesus monkeys and a phase 1 dose escalation clinical study in patients with cancer. Results: Humanized anti-CD27 antibody MK-5890 (hIgG1) was shown to bind human CD27 on the cell surface with sub-nanomolar potency and to partially block binding to its ligand, CD70. Crystallization studies revealed that MK-5890 binds to a unique epitope in the cysteine-rich domain 1 (CRD1). MK-5890 activated CD27 expressed on 293T NF-κB luciferase reporter cells and, conditional on CD3 stimulation, in purified CD8+ T cells without the requirement of crosslinking. Functional Fc-receptor interaction was required to activate CD8+ T cells in an ex vivo tumor explant system and to induce antitumor efficacy in syngeneic murine subcutaneous tumor models. MK-5890 had monotherapy efficacy in these models and enhanced efficacy of PD-1 blockade. MK-5890 reduced in an isotype-dependent and dose-dependent manner circulating, but not tumor-infiltrating T-cell numbers in these mouse models. In rhesus monkey and human patients, reduction in circulating T cells was transient and less pronounced than in mouse. MK-5890 induced transient elevation of chemokines MCP-1, MIP-1α, and MIP-1β in the serum of mice, rhesus monkeys and patients with cancer. MK-5890 was well tolerated in rhesus monkeys and systemic exposure to MK-5890 was associated with CD27 occupancy at all doses. Conclusions: MK-5890 is a novel CD27 agonistic antibody with the potential to complement the activity of PD-1 checkpoint inhibition in cancer immunotherapy and is currently undergoing clinical evaluation.
MeSH term(s)	Animals ; Antibodies, Monoclonal/therapeutic use ; Cell Count ; Epitopes ; Humans ; Immunotherapy ; Macaca mulatta ; Mice ; Neoplasms/drug therapy ; Programmed Cell Death 1 Receptor ; Tumor Necrosis Factor Receptor Superfamily, Member 7
Chemical Substances	Antibodies, Monoclonal ; Epitopes ; Programmed Cell Death 1 Receptor ; Tumor Necrosis Factor Receptor Superfamily, Member 7
Language	English
Publishing date	2022-09-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2022-005049
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Article ; Online: Potent, non-covalent reversible BTK inhibitors with 8-amino-imidazo[1,5-a]pyrazine core featuring 3-position bicyclic ring substitutes.

Liu, Jian / Guiadeen, Deodial / Krikorian, Arto / Gao, Xiaolei / Wang, James / Babu Boga, Sobhana / Alhassan, Abdul-Basit / Yu, Wensheng / Selyutin, Oleg / Yu, Younong / Anand, Rajan / Xu, Jiayi / Kelly, Joseph / Duffy, Joseph L / Liu, Shilan / Yang, Chundao / Wu, Hao / Cai, Jiaqiang / Bennett, Chad /

Maloney, Kevin M / Tyagarajan, Sriram / Gao, Ying-Duo / Fischmann, Thierry O / Presland, Jeremy / Mansueto, My / Xu, Zangwei / Leccese, Erica / Zhang-Hoover, Jie / Knemeyer, Ian / Garlisi, Charles G / Stivers, Peter / Brandish, Philip E / Hicks, Alexandra / Kim, Ronald / Kozlowski, Joseph A

Bioorganic & medicinal chemistry letters

2020 Volume 30, Issue 17, Page(s) 127390

Abstract: Bruton's tyrosine kinase (BTK) is a Tec family kinase with a well-defined role in the B cell receptor (BCR) pathway. It has become an attractive kinase target for selective B cell inhibition, and for the treatment of B cell related diseases. Many BTK ... ...

Abstract	Bruton's tyrosine kinase (BTK) is a Tec family kinase with a well-defined role in the B cell receptor (BCR) pathway. It has become an attractive kinase target for selective B cell inhibition, and for the treatment of B cell related diseases. Many BTK inhibitors have been discovered for the treatment of cancer and rheumatoid arthritis, including a series of BTK inhibitors based on 8-amino-imidazo[1,5-a]pyrazine we recently reported. The X-ray crystal structures of BTK with inhibitors were also published, which provided great help for the SAR design. Here we report our SAR work introducing ring constraints for the 3-position piperidine amides on the BTK inhibitors based on 8-amino-imidazo[1,5-a]pyrazine. This modification improved the potency in BTK inhibitions, as well as the PK profile and the off-target selectivity. The dose-dependent efficacy of two BTK inhibitors was observed in the rat collagen induced arthritis (CIA) model.
MeSH term(s)	Agammaglobulinaemia Tyrosine Kinase/antagonists & inhibitors ; Agammaglobulinaemia Tyrosine Kinase/metabolism ; Animals ; Arthritis, Experimental/drug therapy ; Binding Sites ; Bridged Bicyclo Compounds/chemistry ; Crystallography, X-Ray ; Disease Models, Animal ; Dogs ; Dose-Response Relationship, Drug ; Half-Life ; Humans ; Imidazoles/chemistry ; Imidazoles/metabolism ; Imidazoles/therapeutic use ; Molecular Dynamics Simulation ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/metabolism ; Protein Kinase Inhibitors/therapeutic use ; Pyrazines/chemistry ; Pyrazines/metabolism ; Pyrazines/therapeutic use ; Rats ; Rats, Wistar ; Structure-Activity Relationship ; src-Family Kinases/antagonists & inhibitors ; src-Family Kinases/metabolism
Chemical Substances	Bridged Bicyclo Compounds ; Imidazoles ; Protein Kinase Inhibitors ; Pyrazines ; imidazo(1,5-a)pyrazine ; Agammaglobulinaemia Tyrosine Kinase (EC 2.7.10.2) ; src-Family Kinases (EC 2.7.10.2)
Language	English
Publishing date	2020-07-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1063195-1
ISSN	1464-3405 ; 0960-894X
ISSN (online)	1464-3405
ISSN	0960-894X
DOI	10.1016/j.bmcl.2020.127390
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Article: Discovery of a Novel Series of CHK1 Kinase Inhibitors with a Distinctive Hinge Binding Mode.

Huang, Xiaohua / Cheng, Cliff C / Fischmann, Thierry O / Duca, José S / Yang, Xianshu / Richards, Matthew / Shipps, Gerald W

ACS medicinal chemistry letters

2012 Volume 3, Issue 2, Page(s) 123–128

Abstract: A novel series of CHK1 inhibitors with a distinctive hinge binding mode, exemplified by 2-aryl-N-(2-(piperazin-1-yl)phenyl)thiazole-4-carboxamide, was discovered through high-throughput screening using the affinity selection-mass spectrometry (AS-MS)- ... ...

Abstract	A novel series of CHK1 inhibitors with a distinctive hinge binding mode, exemplified by 2-aryl-N-(2-(piperazin-1-yl)phenyl)thiazole-4-carboxamide, was discovered through high-throughput screening using the affinity selection-mass spectrometry (AS-MS)-based Automated Ligand Identification System (ALIS) platform. Structure-based ligand design and optimization led to significant improvements in potency to the single digit nanomolar range and hundred-fold selectivity against CDK2.
Language	English
Publishing date	2012-01-20
Publishing country	United States
Document type	Journal Article
ISSN	1948-5875
ISSN	1948-5875
DOI	10.1021/ml200249h
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Discovery and Structure Enabled Synthesis of 2,6-Diaminopyrimidin-4-one IRAK4 Inhibitors.

Seganish, W Michael / Fischmann, Thierry O / Sherborne, Brad / Matasi, Julius / Lavey, Brian / McElroy, William T / Tulshian, Deen / Tata, James / Sondey, Christopher / Garlisi, Charles G / Devito, Kristine / Fossetta, James / Lundell, Daniel / Niu, Xiaoda

ACS medicinal chemistry letters

2015 Volume 6, Issue 8, Page(s) 942–947

Abstract: We report the identification and synthesis of a series of aminopyrimidin-4-one IRAK4 inhibitors. Through high throughput screening, an aminopyrimidine hit was identified and modified via structure enabled design to generate a new, potent, and kinase ... ...

Abstract	We report the identification and synthesis of a series of aminopyrimidin-4-one IRAK4 inhibitors. Through high throughput screening, an aminopyrimidine hit was identified and modified via structure enabled design to generate a new, potent, and kinase selective pyrimidin-4-one chemotype. This chemotype is exemplified by compound 16, which has potent IRAK4 inhibition activity (IC50 = 27 nM) and excellent kinase selectivity (>100-fold against 99% of 111 tested kinases), and compound 31, which displays potent IRAK4 activity (IC50 = 93 nM) and good rat bioavailability (F = 42%).
Language	English
Publishing date	2015-07-12
Publishing country	United States
Document type	Journal Article
ISSN	1948-5875
ISSN	1948-5875
DOI	10.1021/acsmedchemlett.5b00279
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Atomic resolution mechanistic studies of ribocil: A highly selective unnatural ligand mimic of the E. coli FMN riboswitch

Howe, John A / Xiao, Li / Fischmann, Thierry O / Wang, Hao / Tang, Haifeng / Villafania, Artjohn / Zhang, Rumin / Barbieri, Christopher M / Roemer, Terry

RNA biology. 2016 Oct. 2, v. 13, no. 10

2016

Abstract	Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway. Although ribocil is structurally distinct from FMN, ribocil functions as a potent and highly selective synthetic mimic of the natural ligand to repress riboswitch-mediated ribB gene expression and inhibit bacterial growth both in vitro and in vivo. Herein, we expand our analysis of ribocil; including mode of binding in the FMN binding pocket of the riboswitch, mechanisms of resistance and structure-activity relationship guided efforts to generate more potent analogs.
Keywords	Escherichia coli ; Gram-negative bacteria ; antibiotics ; bacterial growth ; biochemical pathways ; biosynthesis ; gene expression ; ligands ; multiple drug resistance ; non-coding RNA ; phenotype ; riboflavin ; structure-activity relationships
Language	English
Dates of publication	2016-1002
Size	p. 946-954.
Publishing place	Taylor & Francis
Document type	Article
ISSN	1555-8584
DOI	10.1080/15476286.2016.1216304
Database	NAL-Catalogue (AGRICOLA)

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