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Article: An Intriguing Purview on the Design of Macrocyclic Inhibitors for Unexplored Protein Kinases through Their Binding Site Comparison.

Bhujbal, Swapnil P / Hah, Jung-Mi

2023 Volume 16, Issue 7

Abstract: Kinases play an important role in regulating various intracellular signaling pathways that control cell proliferation, differentiation, survival, and other cellular processes, and their deregulation causes more than 400 diseases. Consequently, ... ...

Abstract	Kinases play an important role in regulating various intracellular signaling pathways that control cell proliferation, differentiation, survival, and other cellular processes, and their deregulation causes more than 400 diseases. Consequently, macrocyclization can be considered a noteworthy approach to developing new therapeutic agents for human diseases. Macrocyclization has emerged as an effective drug discovery strategy over the past decade to improve target selectivity and potency of small molecules. Small compounds with linear structures upon macrocyclization can lead to changes in their physicochemical and biological properties by firmly reducing conformational flexibility. A number of distinct protein kinases exhibit similar binding sites. Comparison of protein binding sites provides crucial insights for drug discovery and development. Binding site similarities are helpful in understanding polypharmacology, identifying potential off-targets, and repurposing known drugs. In this review, we focused on comparing the binding sites of those kinases for which macrocyclic inhibitors are available/studied so far. Furthermore, we calculated the volume of the binding site pocket for each targeted kinase and then compared it with the binding site pocket of the kinase for which only acyclic inhibitors were designed to date. Our review and analysis of several explored kinases might be useful in targeting new protein kinases for macrocyclic drug discovery.
Language	English
Publishing date	2023-07-17
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph16071009
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Article: An Innovative Approach to Address Neurodegenerative Diseases through Kinase-Targeted Therapies: Potential for Designing Covalent Inhibitors.

Bhujbal, Swapnil P / Hah, Jung-Mi

Pharmaceuticals (Basel, Switzerland)

2023 Volume 16, Issue 9

Abstract: Owing to the dysregulation of protein kinase activity in various diseases such as cancer and autoimmune, cardiovascular, neurodegenerative, and inflammatory conditions, the protein kinase family has emerged as a crucial drug target in the 21st century. ... ...

Abstract	Owing to the dysregulation of protein kinase activity in various diseases such as cancer and autoimmune, cardiovascular, neurodegenerative, and inflammatory conditions, the protein kinase family has emerged as a crucial drug target in the 21st century. Notably, many kinases have been targeted to address cancer and neurodegenerative diseases using conventional ATP-mimicking kinase inhibitors. Likewise, irreversible covalent inhibitors have also been developed for different types of cancer. The application of covalent modification to target proteins has led to significant advancements in the treatment of cancer. However, while covalent drugs have significantly impacted medical treatment, their potential for neurodegenerative diseases remains largely unexplored. Neurodegenerative diseases present significant risks to brain function, leading to progressive deterioration in sensory, motor, and cognitive abilities. Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), and multiple sclerosis (MS) are among the various examples of such disorders. Numerous research groups have already reported insights through reviews and research articles on FDA-approved covalent inhibitors, revealing their mechanisms and the specific covalent warheads that preferentially interact with particular amino acid residues in intricate detail. Hence, in this review, we aim to provide a concise summary of these critical topics. This summary endeavors to guide medicinal chemists in their quest to design covalent inhibitors for protein kinases, specifically targeting neurodegenerative diseases.
Language	English
Publishing date	2023-09-13
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph16091295
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Article ; Online: Generation of Non-Nucleotide CD73 Inhibitors Using a Molecular Docking and 3D-QSAR Approach.

Bhujbal, Swapnil P / Hah, Jung-Mi

International journal of molecular sciences

2021 Volume 22, Issue 23

Abstract: Radiotherapy and chemotherapy are conventional cancer treatments. Around 60% of all patients who are diagnosed with cancer receive radio- or chemotherapy in combination with surgery during their disease. Only a few patients respond to the blockage of ... ...

Abstract	Radiotherapy and chemotherapy are conventional cancer treatments. Around 60% of all patients who are diagnosed with cancer receive radio- or chemotherapy in combination with surgery during their disease. Only a few patients respond to the blockage of immune checkpoints alone, or in combination therapy, because their tumours might not be immunogenic. Under these circumstances, an increasing level of extracellular adenosine via the activation of ecto-5'-nucleotidase (CD73) and consequent adenosine receptor signalling is a typical mechanism that tumours use to evade immune surveillance. CD73 is responsible for the conversion of adenosine monophosphate to adenosine. CD73 is overexpressed in various tumour types. Hence, targetting CD73's signalling is important for the reversal of adenosine-facilitated immune suppression. In this study, we selected a potent series of the non-nucleotide small molecule inhibitors of CD73. Molecular docking studies were performed in order to examine the binding mode of the inhibitors inside the active site of CD73 and 3D-QSAR was used to study the structure-activity relationship. The obtained CoMFA (
MeSH term(s)	5'-Nucleotidase/antagonists & inhibitors ; Binding Sites ; Catalytic Domain ; Computer Simulation ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacokinetics ; GPI-Linked Proteins/antagonists & inhibitors ; Humans ; Models, Molecular ; Molecular Docking Simulation ; Molecular Structure ; Protein Binding ; Quantitative Structure-Activity Relationship
Chemical Substances	Enzyme Inhibitors ; GPI-Linked Proteins ; 5'-Nucleotidase (EC 3.1.3.5) ; NT5E protein, human (EC 3.1.3.5)
Language	English
Publishing date	2021-11-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms222312745
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Article ; Online: Analysis of the effect of skin in-situ regeneration and restoration technique in the treatment of burn system.

He, Weijie / Bhujbal, Swapnil P

Minerva medica

2021 Volume 113, Issue 6, Page(s) 1043–1045

MeSH term(s)	Humans ; Skin ; Wound Healing ; Burns/therapy
Language	English
Publishing date	2021-10-21
Publishing country	Italy
Document type	Journal Article
ZDB-ID	123586-2
ISSN	1827-1669 ; 0026-4806
ISSN (online)	1827-1669
ISSN	0026-4806
DOI	10.23736/S0026-4806.21.07828-9
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Article ; Online: Design of Novel IRAK4 Inhibitors Using Molecular Docking, Dynamics Simulation and 3D-QSAR Studies.

Bhujbal, Swapnil P / He, Weijie / Hah, Jung-Mi

Molecules (Basel, Switzerland)

2022 Volume 27, Issue 19

Abstract: Treatment of several autoimmune diseases and types of cancer has been an intense area of research over the past two decades. Many signaling pathways that regulate innate and/or adaptive immunity, as well as those that induce overexpression or mutation of ...

Abstract	Treatment of several autoimmune diseases and types of cancer has been an intense area of research over the past two decades. Many signaling pathways that regulate innate and/or adaptive immunity, as well as those that induce overexpression or mutation of protein kinases, have been targeted for drug discovery. One of the serine/threonine kinases, Interleukin-1 Receptor Associated Kinase 4 (IRAK4) regulates signaling through various Toll-like receptors (TLRs) and interleukin-1 receptor (IL1R). It controls diverse cellular processes including inflammation, apoptosis, and cellular differentiation. MyD88 gain-of-function mutations or overexpression of IRAK4 has been implicated in various types of malignancies such as Waldenström macroglobulinemia, B cell lymphoma, colorectal cancer, pancreatic ductal adenocarcinoma, breast cancer, etc. Moreover, over activation of IRAK4 is also associated with several autoimmune diseases. The significant role of IRAK4 makes it an interesting target for the discovery and development of potent small molecule inhibitors. A few potent IRAK4 inhibitors such as PF-06650833, RA9 and BAY1834845 have recently entered phase I/II clinical trial studies. Nevertheless, there is still a need of selective inhibitors for the treatment of cancer and various autoimmune diseases. A great need for the same intrigued us to perform molecular modeling studies on 4,6-diaminonicotinamide derivatives as IRAK4 inhibitors. We performed molecular docking and dynamics simulation of 50 ns for one of the most active compounds of the dataset. We also carried out MM-PBSA binding free energy calculation to identify the active site residues, interactions of which are contributing to the total binding energy. The final 50 ns conformation of the most active compound was selected to perform dataset alignment in a 3D-QSAR study. Generated RF-CoMFA (
MeSH term(s)	Humans ; Autoimmune Diseases/drug therapy ; Interleukin-1 Receptor-Associated Kinases ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Myeloid Differentiation Factor 88/metabolism ; Protein Kinase Inhibitors/chemistry ; Quantitative Structure-Activity Relationship ; Receptors, Interleukin-1 ; Serine ; Threonine
Chemical Substances	Interleukin-1 Receptor-Associated Kinases (EC 2.7.11.1) ; IRAK4 protein, human (EC 2.7.11.1) ; Ligands ; Myeloid Differentiation Factor 88 ; Protein Kinase Inhibitors ; Receptors, Interleukin-1 ; Serine (452VLY9402) ; Threonine (2ZD004190S)
Language	English
Publishing date	2022-09-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules27196307
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Article: Design and Synthesis of Aminopyrimidinyl Pyrazole Analogs as PLK1 Inhibitors Using Hybrid 3D-QSAR and Molecular Docking.

Bhujbal, Swapnil P / Kim, Hyejin / Bae, Hyunah / Hah, Jung-Mi

Pharmaceuticals (Basel, Switzerland)

2022 Volume 15, Issue 10

Abstract: Cancer continues to be one of the world's most severe public health issues. Polo-like kinase 1 (PLK1) is one of the most studied members of the polo-like kinase subfamily of serine/threonine protein kinases. PLK1 is a key mitotic regulator responsible ... ...

Abstract	Cancer continues to be one of the world's most severe public health issues. Polo-like kinase 1 (PLK1) is one of the most studied members of the polo-like kinase subfamily of serine/threonine protein kinases. PLK1 is a key mitotic regulator responsible for cell cycle processes, such as mitosis initiation, bipolar mitotic spindle formation, centrosome maturation, the metaphase to anaphase transition, and mitotic exit, whose overexpression is often associated with oncogenesis. Moreover, it is also involved in DNA damage response, autophagy, cytokine signaling, and apoptosis. Due to its fundamental role in cell cycle regulation, PLK1 has been linked to various types of cancer onset and progression, such as lung, colon, prostate, ovary, breast cancer, melanoma, and AML. Hence, PLK1 is recognized as a critical therapeutic target in the treatment of various proliferative diseases. PLK1 inhibitors developed in recent years have been researched and studied through clinical trials; however, most of them have failed because of their toxicity and poor therapeutic response. To design more potent and selective PLK1 inhibitors, we performed a receptor-based hybrid 3D-QSAR study of two datasets, possessing similar common scaffolds. The developed hybrid CoMFA (
Language	English
Publishing date	2022-09-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph15101170
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Article ; Online: Molecular Modelling Studies on Pyrazole Derivatives for the Design of Potent Rearranged during Transfection Kinase Inhibitors.

Bhujbal, Swapnil P / Keretsu, Seketoulie / Cho, Seung Joo

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 3

Abstract: RET (rearranged during transfection) kinase, one of the receptor tyrosine kinases, plays a crucial role in the development of the human nervous system. It is also involved in various cell signaling networks responsible for the normal cell division, ... ...

Abstract	RET (rearranged during transfection) kinase, one of the receptor tyrosine kinases, plays a crucial role in the development of the human nervous system. It is also involved in various cell signaling networks responsible for the normal cell division, growth, migration, and survival. Previously reported clinical studies revealed that deregulation or aberrant activation of RET signaling can cause several types of human cancer. For example, medullary thyroid carcinoma (MTC) and multiple endocrine neoplasia (MEN2A, MEN2B) occur due to sporadic mutation or germline RET mutation. A number of RET kinase inhibitors have been approved by the FDA for the treatment of cancer, such as cabozantinib, vandetanib, lenvatinib, and sorafenib. However, each of these drugs is a multikinase inhibitor. Hence, RET is an important therapeutic target for cancer drug design. In this work, we have performed various molecular modelling studies, such as molecular docking and dynamics simulation for the most active compound of the pyrazole series as RET kinase inhibitors. Furthermore, molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) free energy calculation and 3-dimensional quantitative structure-activity relationship (3D-QSAR) were performed using g_mmpbsa and SYBYL-X 2.1 package. The results of this study revealed the crucial binding site residues at the active site of RET kinase and contour map analysis showed important structural characteristics for the design of new highly active inhibitors. Therefore, we have designed ten RET kinase inhibitors, which showed higher inhibitory activity than the most active compound of the series. The results of our study provide insights to design more potent and selective RET kinase inhibitors.
MeSH term(s)	Antineoplastic Agents/pharmacology ; Carcinoma, Neuroendocrine/drug therapy ; Carcinoma, Neuroendocrine/metabolism ; Cell Line, Tumor ; Humans ; Molecular Docking Simulation/methods ; Protein Kinase Inhibitors/pharmacology ; Pyrazoles/pharmacology ; Quantitative Structure-Activity Relationship ; Receptor Protein-Tyrosine Kinases/metabolism ; Signal Transduction/drug effects ; Thyroid Neoplasms/drug therapy ; Thyroid Neoplasms/metabolism ; Transfection/methods
Chemical Substances	Antineoplastic Agents ; Protein Kinase Inhibitors ; Pyrazoles ; Receptor Protein-Tyrosine Kinases (EC 2.7.10.1)
Language	English
Publishing date	2021-01-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26030691
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Article ; Online: Molecular modeling studies of pyrrolo[2,3-d]pyrimidin-4-amine derivatives as JAK1 inhibitors based on 3D-QSAR, molecular docking, molecular dynamics (MD) and MM-PBSA calculations.

Keretsu, Seketoulie / Bhujbal, Swapnil P / Cho, Seung Joo

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 3, Page(s) 753–765

Abstract: Rheumatoid Arthritis (RA) is an autoimmune disease caused by overproduction of pro-inflammatory cytokines. Janus Kinases (JAKs) mediate cytokines signaling through the Janus Kinase (JAK)/signal transducer and activator of transcription (STAT) signaling ... ...

Abstract	Rheumatoid Arthritis (RA) is an autoimmune disease caused by overproduction of pro-inflammatory cytokines. Janus Kinases (JAKs) mediate cytokines signaling through the Janus Kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathways. Clinical studies have shown that Janus kinase 1 (JAK1) mediated signaling plays a key role in synovial response in rheumatoid arthritis. Hence, the inhibition JAK1 is considered as an important therapeutic route for treatment of rheumatoid arthritis. In this study, we have performed three-dimensional quantitative structure-activity relationship (3 D-QSAR), molecular docking, molecular dynamics (MD) and free energy calculations on a series of pyrrolo[
MeSH term(s)	Amines ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Quantitative Structure-Activity Relationship
Chemical Substances	Amines
Language	English
Publishing date	2020-01-21
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1714483
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Article ; Online: Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation.

Keretsu, Seketoulie / Bhujbal, Swapnil P / Cho, Seung Joo

Scientific reports

2020 Volume 10, Issue 1, Page(s) 17716

Abstract: In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. ... ...

Abstract	In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. The 3C-Like proteinase (3CL
MeSH term(s)	Aclarubicin/chemistry ; Aclarubicin/metabolism ; Aminoisobutyric Acids ; Betacoronavirus/enzymology ; Betacoronavirus/isolation & purification ; Binding Sites ; COVID-19 ; Coronavirus 3C Proteases ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Cysteine Endopeptidases/metabolism ; Databases, Factual ; Humans ; Hydrogen Bonding ; Leucine/analogs & derivatives ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Oligopeptides/chemistry ; Oligopeptides/metabolism ; Pandemics ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Proline/analogs & derivatives ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Quinolines ; SARS-CoV-2 ; Thermodynamics ; Thiazoles/chemistry ; Thiazoles/metabolism ; Viral Nonstructural Proteins/antagonists & inhibitors ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Aminoisobutyric Acids ; Oligopeptides ; Protease Inhibitors ; Quinolines ; Thiazoles ; Viral Nonstructural Proteins ; Aclarubicin (74KXF8I502) ; faldaprevir (958X4J301A) ; Proline (9DLQ4CIU6V) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Leucine (GMW67QNF9C)
Keywords	covid19
Language	English
Publishing date	2020-10-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-74468-0
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Article ; Online: Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1.

Keretsu, Seketoulie / Bhujbal, Swapnil P / Joo Cho, Seung

Scientific reports

2019 Volume 9, Issue 1, Page(s) 13053

Abstract: The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for ... ...

Abstract	The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for the treatment of heart failure. Due to the high sequence similarity of GRK2 with the A, G, and C family (AGC family) of kinases, the inhibition of GRK2 also leads to the inhibition of AGC kinases such as Rho-associated coiled-coil kinase 1 (ROCK1). Therefore, unraveling the mechanisms to selectively inhibit GRK2 poses an important challenge. We have performed molecular docking, three dimensional quantitative structure activity relationship (3D-QSAR), molecular dynamics (MD) simulation, and free energy calculations techniques on a series of 53 paroxetine-like compounds to understand the structural properties desirable for enhancing the inhibitory activity for GRK2 with selectivity over ROCK1. The formation of stable hydrogen bond interactions with the residues Phe202 and Lys220 of GRK2 seems to be important for selective inhibition of GRK2. Electropositive substituents at the piperidine ring and electronegative substituents near the amide linker between the benzene ring and pyrazole ring showed a higher inhibitory preference for GRK2 over ROCK1. This study may be used in designing more potent and selective GRK2 inhibitors for therapeutic intervention of heart failure.
MeSH term(s)	Algorithms ; Binding Sites ; Catalytic Domain ; Drug Design ; Enzyme Activation/drug effects ; G-Protein-Coupled Receptor Kinase 2/antagonists & inhibitors ; G-Protein-Coupled Receptor Kinase 2/chemistry ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Paroxetine/chemistry ; Paroxetine/pharmacology ; Protein Binding ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology ; Quantitative Structure-Activity Relationship ; rho-Associated Kinases/antagonists & inhibitors ; rho-Associated Kinases/chemistry
Chemical Substances	Protein Kinase Inhibitors ; Paroxetine (41VRH5220H) ; ROCK1 protein, human (EC 2.7.11.1) ; rho-Associated Kinases (EC 2.7.11.1) ; G-Protein-Coupled Receptor Kinase 2 (EC 2.7.11.16)
Language	English
Publishing date	2019-09-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-48949-w
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