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Article ; Online: New tamoxifen analogs for breast cancer therapy: synthesis, aromatase inhibition and

Al-Kelabi, Hasan / Al-Duhaidahawi, Dunya / Al-Khafaji, Khattab / Al-Masoudi, Najim A

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 22, Page(s) 12798–12807

Abstract: A new class of tamoxifen analogues, using McMurry reaction conditions, is described. The scheme involved the conversion of ketoprofen ( ...

Abstract	A new class of tamoxifen analogues, using McMurry reaction conditions, is described. The scheme involved the conversion of ketoprofen (
MeSH term(s)	Pregnancy ; Female ; Humans ; Tamoxifen/pharmacology ; Breast Neoplasms/drug therapy ; Breast Neoplasms/metabolism ; Aromatase Inhibitors/pharmacology ; Aromatase ; Receptors, Estrogen ; Placenta/metabolism ; Cell Proliferation
Chemical Substances	Tamoxifen (094ZI81Y45) ; Aromatase Inhibitors ; Aromatase (EC 1.14.14.1) ; Receptors, Estrogen
Language	English
Publishing date	2023-02-10
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2175375
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Article ; Online: Molecular dynamics simulation, free energy landscape and binding free energy computations in exploration the anti-invasive activity of amygdalin against metastasis.

Al-Khafaji, Khattab / Taskin Tok, Tugba

Computer methods and programs in biomedicine

2020 Volume 195, Page(s) 105660

Abstract: Background and objective: Historically, amygdalin has been used as alternative medicine or in vitro and in vivo studies, but no single study exists which discusses the structural mechanism of amygdalin at a molecular level. This paper inquiries into the ...

Abstract	Background and objective: Historically, amygdalin has been used as alternative medicine or in vitro and in vivo studies, but no single study exists which discusses the structural mechanism of amygdalin at a molecular level. This paper inquiries into the inhibitory actions of amygdalin on the selected targets: AKT1, FAK, and ILK, which are regulators for various mediated signaling pathways, and are associated with cell adhesion, migration, and differentiation. In order to get details at the molecular level of amygdalin's inhibitory activities against chosen proteins, molecular modeling and simulation techniques including double docking, molecular dynamics simulation, free energy landscape analysis, and binding free energy calculation were exerted. Methods: To get molecular level details of amygdalin inhibitory effects against the relevant proteins; here the utilized tools are the following: the double docking, molecular dynamics simulation, free energy landscape analysis, g_mmpbsa, and interaction entropy were used to evaluate the inhibitory activity against targeted proteins. Results: The computational calculations revealed that amygdalin inhibits the selected targets via block the ATP-binding pocket of AKT1, FAK, and ILK by forming stable hydrogen bonds. Moreover, free energy landscape, FEL exposed that amygdalin stabilized the global conformations of both FAK and ILK proteins to the minimum global energy besides it reduced the essential dynamics of FAK and ILK proteins. MMPBSA computations provided further evidence for amygdalin's stability inside the ATP-binding pocket of AKT1, FAK, and ILK with a binding free energy of 45.067, -13.033, 13.109 kJ/mol, respectively. The binding free energies are lastly consistent with the hydrogen bonding and pairs within 0.35 nm results. The decomposition of binding energy shows the pivotal amino acid residues responsible for the stability of amygdalin's interactions inside the ATP-binding sites by forming hydrogen bonds. Conclusions: Before this work, it was enigmatic to make predictions about how amygdalin inhibits metastasis of cancer. But the computational results contribute in several ways to our understanding of amygdalin activity and provide a basic insight into the activity of amygdalin as a multi-target drug in the metastasis and invasion of cancer.
MeSH term(s)	Amygdalin ; Binding Sites ; Entropy ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Neoplasms ; Protein Binding
Chemical Substances	Amygdalin (214UUQ9N0H)
Language	English
Publishing date	2020-07-14
Publishing country	Ireland
Document type	Journal Article
ZDB-ID	632564-6
ISSN	1872-7565 ; 0169-2607
ISSN (online)	1872-7565
ISSN	0169-2607
DOI	10.1016/j.cmpb.2020.105660
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Article ; Online: Amygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation.

Al-Khafaji, Khattab / Taskin Tok, Tugba

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 6, Page(s) 1965–1974

Abstract: Cell-division protein kinases (CDKs) are gorgeous examples of targets for the helpful treatment of cancer by using multi-target inhibitors. Specifically, targeting cell-division protein kinase1/cyclin B (CDK1/Cyclin B), cell-division protein kinase 2/ ... ...

Abstract	Cell-division protein kinases (CDKs) are gorgeous examples of targets for the helpful treatment of cancer by using multi-target inhibitors. Specifically, targeting cell-division protein kinase1/cyclin B (CDK1/Cyclin B), cell-division protein kinase 2/cyclin A (CDK2/Cyclin A) and cell-division protein kinase 4/cyclin D1 (CDK4/Cyclin D1) are considered a safe strategy to over the toxicity complications which are emerging from low specificity. In this work, we conducted the double docking and molecular dynamics to explicate the effect of amygdalin upon conformational modifications of selected targets. Moreover, the principal component analysis (PCA) was employed to inspect the effect of amygdalin on the fundamental motions of the each protein as target. Docking results illustrated that the binding free energies of amygdalin (AMY) to CDK1/Cyclin B, CDK 2/Cyclin A and CDK 4/Cyclin D1 were to be -9.41, -9.02 and -10.6 kcal/mol, respectively. The PCA results disclosed that binding of the AMY minimized the fundamental dynamics of CDK1/Cyclin B and CDK2/Cyclin A. The obtained results can give an insight into inhibitory activity of amygdalin that could help in designing of potential inhibitors. In the other word, it can be used AMY to inhibit other mechanisms and/or hallmarks of cancer.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Amygdalin/pharmacology ; Antineoplastic Agents/pharmacology ; Cell Cycle ; Cyclin-Dependent Kinases/metabolism ; Cyclin-Dependent Kinases/pharmacology ; Humans ; Molecular Dynamics Simulation
Chemical Substances	Antineoplastic Agents ; Amygdalin (214UUQ9N0H) ; Cyclin-Dependent Kinases (EC 2.7.11.22)
Language	English
Publishing date	2020-03-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1742792
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Article ; Online: Understanding the mechanism of amygdalin's multifunctional anti-cancer action using computational approach.

Al-Khafaji, Khattab / Taskin Tok, Tugba

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 5, Page(s) 1600–1610

Abstract: Amygdalin possesses anticancer properties and induces apoptosis. Based on experimental studies the presence of amygdalin with cancer cells led to activate the caspase-3 and BAX and inhibits Bcl-2 and Poly (ADP-ribose) polymerase-1 (PARP-1) but without ... ...

Abstract	Amygdalin possesses anticancer properties and induces apoptosis. Based on experimental studies the presence of amygdalin with cancer cells led to activate the caspase-3 and BAX and inhibits Bcl-2 and Poly (ADP-ribose) polymerase-1 (PARP-1) but without deep information on action mode of these activities. Herein, we leaped forward to examine the molecular dynamics of the bound amygdalin and free ligand proteins, to identify precise action (conformation changes in targeted proteins) of amygdalin through using double docking and molecular dynamics (MD) simulations for 50 ns time scale. The MD simulations revealed that the binding of amygdalin led to disrupting the interaction between the Bcl-2/BAX complex. We furthermore conducted MD simulation for Bcl-2/amygdalin to investigate the stability of the complex which is responsible for inhibition of Bcl-2. It has been obtained a stable Bcl-2/amygdalin complex during the 50 ns. The results give a detail explanation of how amygdalin activates BAX and inhibits Bcl-2. For caspase-3, the matter is different, we found that amygdalin led to disrupting the interaction of caspase-3's two chains for intervals during 50 ns and then bind together repeatedly. The mechanism of caspase-3's activation through switching by disrupt the interacts for periodic intervals manner. For PARP-1, the dynamics simulations results indicated amygdalin interacts with PARP-1's binding site and forms stable interaction during simulation to render it inactive. Hence, amygdalin revealed a supernatural behavior through the MD simulations: it revealed a further clarification of the mystery amygdalin's experimental action which can act as a multifunctional drug in the cancer therapeutics.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Amygdalin ; Apoptosis ; Binding Sites ; Humans ; Molecular Dynamics Simulation ; Neoplasms ; Proto-Oncogene Proteins c-bcl-2/metabolism
Chemical Substances	Proto-Oncogene Proteins c-bcl-2 ; Amygdalin (214UUQ9N0H)
Language	English
Publishing date	2020-03-09
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1736159
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Article ; Online: Phytochemical constituents of

Jose, Sandra / Devi, Sreevidya S / P, Shakthi / Al-Khafaji, Khattab

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 22, Page(s) 11932–11947

Abstract: ... Shigella ... ...

Abstract	Shigella dysenteriae
MeSH term(s)	Dysentery, Bacillary ; Inula/metabolism ; Tetrahydrofolate Dehydrogenase/metabolism ; Molecular Dynamics Simulation ; Binding Sites ; Molecular Docking Simulation
Chemical Substances	Tetrahydrofolate Dehydrogenase (EC 1.5.1.3)
Language	English
Publishing date	2021-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1966508
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Article: A subunit vaccine against pneumonia: targeting S

Rafi, Md Oliullah / Al-Khafaji, Khattab / Mandal, Santi M / Meghla, Nigar Sultana / Biswas, Polash Kumar / Rahman, Md Shahedur

Network modeling and analysis in health informatics and bioinformatics

2023 Volume 12, Issue 1, Page(s) 21

Abstract: Community-acquired pneumonia is primarily caused by : Supplementary information: The online version contains supplementary material available at 10.1007/s13721-023-00416-3. ...

Abstract	Community-acquired pneumonia is primarily caused by Supplementary information: The online version contains supplementary material available at 10.1007/s13721-023-00416-3.
Language	English
Publishing date	2023-04-19
Publishing country	Austria
Document type	Journal Article
ZDB-ID	2649488-7
ISSN	2192-6670 ; 2192-6662
ISSN (online)	2192-6670
ISSN	2192-6662
DOI	10.1007/s13721-023-00416-3
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Article: Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods

Rafi, Md. Oliullah / Al-Khafaji, Khattab / Sarker, Md. Takim / Taskin-Tok, Tugba / Rana, Abdus Samad / Rahman, Md. Shahedur

RSC advances. 2022 Feb. 02, v. 12, no. 7

2022

Abstract: A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, ... ...

Abstract	A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.
Keywords	COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; T-lymphocytes ; adjuvants ; allergenicity ; cytotoxicity ; death ; epitopes ; glycoproteins ; immune response ; immunogenicity ; immunoinformatics ; interferon-gamma ; interleukin-2 ; membrane fusion ; pathogens ; respiratory tract diseases ; subunit vaccines
Language	English
Dates of publication	2022-0202
Size	p. 4288-4310.
Publishing place	The Royal Society of Chemistry
Document type	Article
ISSN	2046-2069
DOI	10.1039/d1ra06532g
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2.

Al-Khafaji, Khattab / Al-Duhaidahawi, Dunya / Taskin Tok, Tugba

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 9, Page(s) 3387–3395

Abstract: SARS-CoV-2 is a new generation of coronavirus, which was first determined in Wuhan, China, in December 2019. So far, however, there no effective treatment has been found to stop this new generation of coronavirus but discovering of the crystal structure ... ...

Abstract	SARS-CoV-2 is a new generation of coronavirus, which was first determined in Wuhan, China, in December 2019. So far, however, there no effective treatment has been found to stop this new generation of coronavirus but discovering of the crystal structure of SARS-CoV-2 main protease (SARS-CoV-2 Mpro) may facilitate searching for new therapies for SARS-COV-2. The aim was to assess the effectiveness of available FDA approved drugs which can construct a covalent bond with Cys145 inside binding site SARS-CoV-2 main protease by using covalent docking screening. We conducted the covdock module MMGBSA module in the Schrodinger suite 2020-1, to examine the covalent bonding utilizing. Besides, we submitted the top three drugs to molecular dynamics simulations via Gromacs 2018.1. The covalent docking showed that saquinavir, ritonavir, remdesivir, delavirdine, cefuroxime axetil, oseltamivir and prevacid have the highest binding energies MMGBSA of -72.17, -72.02, -65.19, -57.65, -54.25, -51.8, and -51.14 kcal/mol, respectively. The 50 ns molecular dynamics simulation was conducted for saquinavir, ritonavir and remdesivir to evaluate the stability of these drugs inside the binding pocket of SARS-CoV-2 main protease. The current study provides a powerful in silico results, means for rapid screening of drugs as anti-protease medications and recommend that the above-mentioned drugs can be used in the treatment of SARS-CoV-2 in combined or sole therapy.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	COVID-19 ; Humans ; Molecular Docking Simulation ; Protease Inhibitors ; SARS-CoV-2 ; Viral Nonstructural Proteins
Chemical Substances	Protease Inhibitors ; Viral Nonstructural Proteins
Keywords	covid19
Language	English
Publishing date	2020-05-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1764392
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Article ; Online: A detailed understanding of the COL10A1 and SOX9 genes interaction based on potentially damaging mutations in gastric cancer using computational techniques.

Aktas, Sedef Hande / Taskin-Tok, Tugba / Al-Khafaji, Khattab / Akın-Balı, Dilara Fatma

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 22, Page(s) 11533–11544

Abstract: Gastric cancer (GC) has limited effective treatment options and is followed up with biomarkers that have insufficient sensitivity and specificity. Recent studies on Collagen Type X Alpha 1 Chain (COL10A1) show that the COL10A1 gene may be a diagnostic ... ...

Abstract	Gastric cancer (GC) has limited effective treatment options and is followed up with biomarkers that have insufficient sensitivity and specificity. Recent studies on Collagen Type X Alpha 1 Chain (COL10A1) show that the COL10A1 gene may be a diagnostic and/or prognostic biomarker for different cancer types. Moreover, its relationship with the Sex determining Region Y (SRY)-related High-Mobility Group (HMG) box (SOX9) gene which is also a transcription factor, was discovered recently, and co-expression of these two genes are associated with the development of GC. However, to the best of our knowledge, there is no study in the literature on how potential damaging mutations in the SOX9 and COL10A1 genes can affect their interactions. The aim of this study is to investigate the interactions of wild-type and potentially damaging mutated structures of COL10A1 and SOX9 genes. Thus, outputs for drug development and therapeutic strategies for GC can be obtained. For this purpose, structure validation and energy minimization analyses as well as docking and binding affinity calculations were performed. As a result, it was found that all investigated mutations (P563S, I588L, T624A, H165R and N110T) increased the binding affinity between the COL10A1-SOX9 complex, especially the N110T and H165R mutants in SOX9. As a conclusion, the N110T and H165R mutants in SOX9 may contribute to tumor progression. Therefore, it is important to consider these mutations for future therapeutic strategies.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Stomach Neoplasms/genetics ; Transcription Factors/genetics ; Gene Expression Regulation ; Mutation ; SOX9 Transcription Factor/genetics ; SOX9 Transcription Factor/metabolism
Chemical Substances	Transcription Factors ; SOX9 protein, human ; SOX9 Transcription Factor
Language	English
Publishing date	2021-08-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1960194
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Article ; Online: Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods.

Rafi, Md Oliullah / Al-Khafaji, Khattab / Sarker, Md Takim / Taskin-Tok, Tugba / Rana, Abdus Samad / Rahman, Md Shahedur

RSC advances

2022 Volume 12, Issue 7, Page(s) 4288–4310

Abstract	A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant
Language	English
Publishing date	2022-02-02
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d1ra06532g
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