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Article ; Online: Three-Dimensional-QSAR and Relative Binding Affinity Estimation of Focal Adhesion Kinase Inhibitors.

Ghosh, Suparna / Cho, Seung Joo

2023 Volume 28, Issue 3

Abstract: Precise binding affinity predictions are essential for structure-based drug discovery (SBDD). Focal adhesion kinase (FAK) is a member of the tyrosine kinase protein family and is overexpressed in a variety of human malignancies. Inhibition of FAK using ... ...

Abstract	Precise binding affinity predictions are essential for structure-based drug discovery (SBDD). Focal adhesion kinase (FAK) is a member of the tyrosine kinase protein family and is overexpressed in a variety of human malignancies. Inhibition of FAK using small molecules is a promising therapeutic option for several types of cancer. Here, we conducted computational modeling of FAK-targeting inhibitors using three-dimensional structure-activity relationship (3D-QSAR), molecular dynamics (MD), and hybrid topology-based free energy perturbation (FEP) methods. The structure-activity relationship (SAR) studies between the physicochemical descriptors and inhibitory activities of the chemical compounds were performed with reasonable statistical accuracy using CoMFA and CoMSIA. These are two well-known 3D-QSAR methods based on the principle of supervised machine learning (ML). Essential information regarding residue-specific binding interactions was determined using MD and MM-PB/GBSA methods. Finally, physics-based relative binding free energy (ΔΔGRBFEA→B) terms of analogous ligands were estimated using alchemical FEP simulation. An acceptable agreement was observed between the experimental and computed relative binding free energies. Overall, the results suggested that using ML and physics-based hybrid approaches could be useful in synergy for the rational optimization of accessible lead compounds with similar scaffolds targeting the FAK receptor.
MeSH term(s)	Humans ; Binding Sites ; Entropy ; Focal Adhesion Protein-Tyrosine Kinases/antagonists & inhibitors ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Quantitative Structure-Activity Relationship ; Tyrosine Kinase Inhibitors/chemistry ; Tyrosine Kinase Inhibitors/pharmacology
Chemical Substances	Focal Adhesion Protein-Tyrosine Kinases (EC 2.7.10.2) ; Ligands ; Tyrosine Kinase Inhibitors
Language	English
Publishing date	2023-02-02
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/molecules28031464
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Article: Structural Insights from Molecular Modeling of Isoindolin-1-One Derivatives as PI3Kγ Inhibitors against Gastric Carcinoma.

Ghosh, Suparna / Cho, Seung Joo

Biomedicines

2022 Volume 10, Issue 4

Abstract: The upregulation of phosphoinositol-3-kinase γ (PI3Kγ) is deemed to be positively correlated with tumor-associated-macrophage (TAM)-mediated gastric carcinoma (GC). PI3Kγ suppresses tumor necrosis factor-alpha (TNF-α) and interleukin-12 (IL-12) through ... ...

Abstract	The upregulation of phosphoinositol-3-kinase γ (PI3Kγ) is deemed to be positively correlated with tumor-associated-macrophage (TAM)-mediated gastric carcinoma (GC). PI3Kγ suppresses tumor necrosis factor-alpha (TNF-α) and interleukin-12 (IL-12) through activation of the AKT/mTOR pathway, which promotes the immunosuppressant phenotype of TAM. Unlike α and β isoforms, δ and γ isoforms are primarily distributed in leucocytes and macrophages. Dual inhibitors against PI3Kδ and PI3Kγ have been proven to have merits in targeting solid tumors. Furthermore, it has been found that PI3Kδ is activated by cytokines, while PI3Kγ is activated by G-protein-coupled receptors (GPCRs). This facilitates determining the functional difference between these two isoforms. For this goal, selective inhibitors would be immensely helpful. In the current manuscript, we conducted various molecular modeling studies with a series of isoindolin-1-one derivatives as potent PI3Kγ inhibitors by combining molecular docking, molecular dynamics (MD), molecular mechanics, Poisson-Boltzmann/generalized Born surface area (MM-PB/GBSA) binding free energy calculation, and three-dimensional structure-activity relationship (3D-QSAR) study. To evaluate the selectivity of γ isoform over δ, the molecular modeling studies of idelalisib analogs reported as PI3Kδ inhibitors were also investigated. The contour polyhedrons were generated from the comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) around the ligand-bound active site for both isoforms, which could emphasize plausible explanations for the physicochemical factors that affect selective ligand recognition. The binding modalities of the two isoforms using CoMFA and MD models were compared, which suggested some key differences in the molecular interactions with the ligands and could be summarized as three subsites (one affinity subsite near the C-helix and DFG and two hydrophobic subsites). In the context of the structure-activity relationship (SAR), several new compounds were designed using a fragment-substitution strategy with the aim of selectively targeting PI3Kγ. The pIC
Language	English
Publishing date	2022-03-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines10040813
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Article ; Online: Binding Studies and Lead Generation of Pteridin-7(8

Ghosh, Suparna / Cho, Seung Joo

International journal of molecular sciences

2022 Volume 23, Issue 14

Abstract: Ligand modification by substituting chemical groups within the binding pocket is a popular strategy for kinase drug development. In this study, a series of pteridin-7( ... ...

Abstract	Ligand modification by substituting chemical groups within the binding pocket is a popular strategy for kinase drug development. In this study, a series of pteridin-7(8
MeSH term(s)	Binding Sites ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Pteridines ; Quantitative Structure-Activity Relationship ; fms-Like Tyrosine Kinase 3/genetics
Chemical Substances	Ligands ; Pteridines ; fms-Like Tyrosine Kinase 3 (EC 2.7.10.1)
Language	English
Publishing date	2022-07-12
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/ijms23147696
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Article ; Online: Molecular Modeling Studies of

Ghosh, Suparna / Keretsu, Seketoulie / Cho, Seung Joo

International journal of molecular sciences

2021 Volume 22, Issue 22

Abstract: Overexpression and frequent mutations in FMS-like tyrosine kinase-3 (FLT3) are considered risk factors for severe acute myeloid leukemia (AML). Hyperactive FLT3 induces premature activation of multiple intracellular signaling pathways, resulting in cell ... ...

Abstract	Overexpression and frequent mutations in FMS-like tyrosine kinase-3 (FLT3) are considered risk factors for severe acute myeloid leukemia (AML). Hyperactive FLT3 induces premature activation of multiple intracellular signaling pathways, resulting in cell proliferation and anti-apoptosis. We conducted the computational modeling studies of 40 pyrimidine-4,6-diamine-based compounds by integrating docking, molecular dynamics, and three-dimensional structure-activity relationship (3D-QSAR). Molecular docking showed that K644, C694, F691, E692, N701, D829, and F830 are critical residues for the binding of ligands at the hydrophobic active site. Molecular dynamics (MD), together with Molecular Mechanics Poison-Boltzmann/Generalized Born Surface Area, i.e., MM-PB(GB)SA, and linear interaction energy (LIE) estimation, provided critical information on the stability and binding affinity of the selected docked compounds. The MD study suggested that the mutation in the gatekeeper residue F691 exhibited a lower binding affinity to the ligand. Although, the mutation in D835 in the activation loop did not exhibit any significant change in the binding energy to the most active compound. We developed the ligand-based comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models. CoMFA (
MeSH term(s)	Amines/chemistry ; Amines/therapeutic use ; Binding Sites/drug effects ; Catalytic Domain/drug effects ; Computer Simulation ; Humans ; Leukemia, Myeloid, Acute/drug therapy ; Leukemia, Myeloid, Acute/genetics ; Leukemia, Myeloid, Acute/pathology ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/therapeutic use ; Pyrimidines/chemistry ; Pyrimidines/therapeutic use ; Quantitative Structure-Activity Relationship ; Signal Transduction/drug effects ; Structure-Activity Relationship ; fms-Like Tyrosine Kinase 3/antagonists & inhibitors ; fms-Like Tyrosine Kinase 3/chemistry ; fms-Like Tyrosine Kinase 3/genetics
Chemical Substances	Amines ; Ligands ; Protein Kinase Inhibitors ; Pyrimidines ; fms-Like Tyrosine Kinase 3 (EC 2.7.10.1) ; pyrimidine (K8CXK5Q32L)
Language	English
Publishing date	2021-11-19
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/ijms222212511
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Article: Designing of the N-ethyl-4-(pyridin-4-yl)benzamide based potent ROCK1 inhibitors using docking, molecular dynamics, and 3D-QSAR.

Ghosh, Suparna / Keretsu, Seketoulie / Cho, Seung Joo

PeerJ

2021 Volume 9, Page(s) e11951

Abstract: Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth ... ...

Abstract	Rho-associated kinase-1 (ROCK1) has been recognized for its pivotal role in heart diseases, different types of malignancy, and many neurological disorders. Hyperactivity of ROCK phosphorylates the protein kinase-C (PKC), which ultimately induces smooth muscle cell contraction in the vascular system. Inhibition of ROCK1 has been shown to be a promising therapy for patients with cardiovascular disease. In this study, we have conducted molecular modeling techniques such as docking, molecular dynamics (MD), and 3-Dimensional structure-activity relationship (3D-QSAR) on a series of N-ethyl-4-(pyridin-4-yl)benzamide-based compounds. Docking and MD showed critical interactions and binding affinities between ROCK1 and its inhibitors. To establish the structure-activity relationship (SAR) of the compounds, 3D-QSAR techniques such as Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were used. The CoMFA (
Language	English
Publishing date	2021-08-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.11951
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Article ; Online: Computer aided designing of novel pyrrolopyridine derivatives as JAK1 inhibitors.

Keretsu, Seketoulie / Ghosh, Suparna / Cho, Seung Joo

Scientific reports

2021 Volume 11, Issue 1, Page(s) 23051

Abstract: Janus kinases (JAKs) are a family of non-receptor kinases that play a key role in cytokine signaling and their aberrant activities are associated with the pathogenesis of various immune diseases. The JAK1 isoform plays an essential role in the types 1 ... ...

Abstract	Janus kinases (JAKs) are a family of non-receptor kinases that play a key role in cytokine signaling and their aberrant activities are associated with the pathogenesis of various immune diseases. The JAK1 isoform plays an essential role in the types 1 and II interferon signaling and elicits signals from the interleukin-2, interleukin-4, gp130, and class 2 receptor families. It is ubiquitously expressed in humans and its overexpression has been linked with autoimmune diseases such as myeloproliferative neoplasm. Although JAK1 inhibitors such as Tofacitinib have been approved for medical use, the low potency and off-target effects of these inhibitors have limited their use and calls for the development of novel JAK1 inhibitors. In this study, we used computational methods on a series of pyrrolopyridine derivatives to design new JAK1 inhibitors. Molecular docking and molecular dynamics simulation methods were used to study the protein-inhibitor interactions. 3D-quantitative structure-activity relationship models were developed and were used to predict the activity of newly designed compounds. Free energy calculation methods were used to study the binding affinity of the inhibitors with JAK1. Of the designed compounds, seventeen of the compounds showed a higher binding energy value than the most active compound in the dataset and at least six of the compounds showed higher binding energy value than the pan JAK inhibitor Tofacitinib. The findings made in this study could be utilized for the further development of JAK1 inhibitors.
MeSH term(s)	Chemistry, Pharmaceutical/methods ; Computational Biology ; Computer Simulation ; Drug Design ; Gene Expression Regulation, Neoplastic ; Humans ; Hydrogen Bonding ; Inhibitory Concentration 50 ; Janus Kinase 1/chemistry ; Janus Kinase Inhibitors ; Janus Kinases/metabolism ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Piperidines/pharmacology ; Protein Isoforms ; Protein Kinase Inhibitors/pharmacology ; Pyridines/chemistry ; Pyrimidines/pharmacology ; Quantitative Structure-Activity Relationship ; Software ; Static Electricity
Chemical Substances	Janus Kinase Inhibitors ; Ligands ; Piperidines ; Protein Isoforms ; Protein Kinase Inhibitors ; Pyridines ; Pyrimidines ; tofacitinib (87LA6FU830) ; JAK1 protein, human (EC 2.7.10.2) ; Janus Kinase 1 (EC 2.7.10.2) ; Janus Kinases (EC 2.7.10.2)
Language	English
Publishing date	2021-11-29
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/s41598-021-02364-2
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Article ; Online: Molecular Modeling Study of c-KIT/PDGFRα Dual Inhibitors for the Treatment of Gastrointestinal Stromal Tumors.

Keretsu, Seketoulie / Ghosh, Suparna / Cho, Seung Joo

International journal of molecular sciences

2020 Volume 21, Issue 21

Abstract: Gastrointestinal stromal tumors (GISTs) are the most common Mesenchymal Neoplasm of the gastrointestinal tract. The tumorigenesis of GISTs has been associated with the gain-of-function mutation and abnormal activation of the stem cell factor receptor (c- ... ...

Abstract	Gastrointestinal stromal tumors (GISTs) are the most common Mesenchymal Neoplasm of the gastrointestinal tract. The tumorigenesis of GISTs has been associated with the gain-of-function mutation and abnormal activation of the stem cell factor receptor (c-KIT) and platelet-derived growth factor receptor alpha (PDGFRα) kinases. Hence, inhibitors that target c-KIT and PDGFRα could be a therapeutic option for the treatment of GISTs. The available approved c-KIT/PDGFRα inhibitors possessed low efficacy with off-target effects, which necessitated the development of potent inhibitors. We performed computational studies of 48 pyrazolopyridine derivatives that showed inhibitory activity against c-KIT and PDGFRα to study the structural properties important for inhibition of both the kinases. The derivative of phenylurea, which has high activities for both c-KIT (pIC
MeSH term(s)	Amino Acid Substitution ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/isolation & purification ; Antineoplastic Agents/pharmacokinetics ; Antineoplastic Agents/therapeutic use ; Binding Sites ; Drug Screening Assays, Antitumor/methods ; Gastrointestinal Neoplasms/drug therapy ; Gastrointestinal Stromal Tumors/drug therapy ; Humans ; Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Mutant Proteins/chemistry ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/isolation & purification ; Protein Kinase Inhibitors/pharmacokinetics ; Protein Kinase Inhibitors/therapeutic use ; Proto-Oncogene Proteins c-kit/antagonists & inhibitors ; Proto-Oncogene Proteins c-kit/chemistry ; Proto-Oncogene Proteins c-kit/genetics ; Proto-Oncogene Proteins c-kit/metabolism ; Pyrazoles/chemistry ; Pyridines/chemistry ; Quantitative Structure-Activity Relationship ; Receptor, Platelet-Derived Growth Factor alpha/antagonists & inhibitors ; Receptor, Platelet-Derived Growth Factor alpha/chemistry ; Receptor, Platelet-Derived Growth Factor alpha/genetics ; Receptor, Platelet-Derived Growth Factor alpha/metabolism
Chemical Substances	Antineoplastic Agents ; Mutant Proteins ; Protein Kinase Inhibitors ; Pyrazoles ; Pyridines ; pyrazolopyridine ; Proto-Oncogene Proteins c-kit (EC 2.7.10.1) ; Receptor, Platelet-Derived Growth Factor alpha (EC 2.7.10.1)
Language	English
Publishing date	2020-11-03
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/ijms21218232
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Article: Ageratina adenophora

Chanu, Khaidem Devika / Sharma, Nanaocha / Kshetrimayum, Vimi / Chaudhary, Sushil Kumar / Ghosh, Suparna / Haldar, Pallab Kanti / Mukherjee, Pulok K

Frontiers in pharmacology

2023 Volume 14, Page(s) 1178904

Abstract: Type 2 diabetes has become one of the major health concerns of the 21st century, marked by hyperglycemia or glycosuria, and is associated with the development of several secondary health complications. Due to the fact that chemically synthesized drugs ... ...

Abstract	Type 2 diabetes has become one of the major health concerns of the 21st century, marked by hyperglycemia or glycosuria, and is associated with the development of several secondary health complications. Due to the fact that chemically synthesized drugs lead to several inevitable side effects, new antidiabetic medications from plants have gained substantial attention. Thus, the current study aims to evaluate the antidiabetic capacity of the
Language	English
Publishing date	2023-04-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2023.1178904
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Article ; Online: Membrane-encapsulated camouflaged nanomedicines in drug delivery.

Ghosh, Suparna / Girigoswami, Koyeli / Girigoswami, Agnishwar

Nanomedicine (London, England)

2019 Volume 14, Issue 15, Page(s) 2067–2082

Abstract: Owing to the limitations of conventional therapies, there has been an increasing need for nanomedicines for real-time diagnosis and effective treatment of life-threatening diseases. Despite the conceptual and technological success achieved by researchers ...

Abstract	Owing to the limitations of conventional therapies, there has been an increasing need for nanomedicines for real-time diagnosis and effective treatment of life-threatening diseases. Despite the conceptual and technological success achieved by researchers worldwide, the complexities of biological systems, efficient engineering and formulation of monodispersed nanomedicines, inadequate information on bio-nano interactions, issues on health hazards, clinical trials and commercialization have set new challenges in biomedical research. This review highlights how the biological membrane improves the performance of nanomedicines in drug delivery. With the list of nanomedicines getting longer gradually to overcome the drawbacks of conventional therapeutics, it is important to concentrate on the interactions between nanostructures and living systems in order to improve the biocompatibility and therapeutic efficacy of functional nanomedicines.
MeSH term(s)	Animals ; Cell Membrane/chemistry ; Drug Carriers/chemistry ; Drug Carriers/therapeutic use ; Drug Delivery Systems/methods ; Humans ; Nanostructures/chemistry ; Nanostructures/therapeutic use ; Theranostic Nanomedicine/methods
Chemical Substances	Drug Carriers
Language	English
Publishing date	2019-07-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2277839-1
ISSN	1748-6963 ; 1743-5889
ISSN (online)	1748-6963
ISSN	1743-5889
DOI	10.2217/nnm-2019-0155
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Article ; Online: 6‐Gingerol contents of several ginger varieties of Northeast India and correlation of their antioxidant activity in respect to phenolics and flavonoids contents

Ghosh, Suparna / Das, Bhaskar / Haldar, Pallab Kanti / Kar, Amit / Chaudhary, Sushil K. / Singh, Keithellakpam Ojit / Bhardwaj, Pardeep K. / Sharma, Nanaocha / Mukherjee, Pulok K.

Phytochemical Analysis. 2023 Apr., v. 34, no. 3 p.259-268

2023

Abstract: INTRODUCTION: Ginger constitutes the rhizome part of the plant Zingiber officinale from the Zingiberaceae family. A large number of ginger varieties with high sensorial and functional quality are found in Northeast India. Hence, phytopharmacological ... ...

Abstract	INTRODUCTION: Ginger constitutes the rhizome part of the plant Zingiber officinale from the Zingiberaceae family. A large number of ginger varieties with high sensorial and functional quality are found in Northeast India. Hence, phytopharmacological screening of different ginger varieties is essential that will serve as a guideline in applied research to develop high‐end products and improve economical margins. OBJECTIVE: To determine the variation in total phenolics content (TPC), total flavonoids content (TFC), and antioxidant activities and correlate that with 6‐gingerol contents of different ginger varieties collected from Northeast India using Pearson's correlation analysis. MATERIALS AND METHODS: The TPC and TFC values were determined using standard methods. Antioxidant activities were measured using the 2,2‐diphenyl‐1‐picrylhydrazyl (DPPH) and hydroxyl radical scavenging assays, while reversed‐phase high‐performance liquid chromatography (RP‐HPLC) analysis was utilised for quantitative determination of 6‐gingerol content. RESULTS: The result revealed that ginger variety 6 (GV6) contains the highest 6‐gingerol content and TPC value showing maximum antioxidant activity, followed by GV5, GV4, GV9, GV3, GV2, GV8, GV1, and GV7. The findings also suggested that the antioxidant activity has much better correlations with TPC as compared with TFC values. Pearson's correlation analysis showed a significant correlation between 6‐gingerol contents and TPC values. CONCLUSION: This work underlines the importance of ginger varieties from Northeast India as a source of natural antioxidants with health benefits.
Keywords	2,2-diphenyl-1-picrylhydrazyl ; Zingiber officinale ; antioxidant activity ; applied research ; flavonoids ; ginger ; guidelines ; hydroxyl radicals ; quantitative analysis ; reversed-phase high performance liquid chromatography ; rhizomes ; India
Language	English
Dates of publication	2023-04
Size	p. 259-268.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	1073576-8
ISSN	1099-1565 ; 0958-0344
ISSN (online)	1099-1565
ISSN	0958-0344
DOI	10.1002/pca.3201
Database	NAL-Catalogue (AGRICOLA)

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