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Article: Integrative Approach for Designing Novel Triazole Derivatives as α-Glucosidase Inhibitors: QSAR, Molecular Docking, ADMET, and Molecular Dynamics Investigations.

Abchir, Oussama / Khedraoui, Meriem / Nour, Hassan / Yamari, Imane / Errougui, Abdelkbir / Samadi, Abdelouahid / Chtita, Samir

Pharmaceuticals (Basel, Switzerland)

2024 Volume 17, Issue 2

Abstract: In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit ... ...

Abstract	In response to the increasing prevalence of diabetes mellitus and the limitations associated with the current treatments, there is a growing need to develop novel medications for this disease. This study is focused on creating new compounds that exhibit a strong inhibition of alpha-glucosidase, which is a pivotal enzyme in diabetes control. A set of 33 triazole derivatives underwent an extensive QSAR analysis, aiming to identify the key factors influencing their inhibitory activity against α-glucosidase. Using the multiple linear regression (MLR) model, seven promising compounds were designed as potential drugs. Molecular docking and dynamics simulations were employed to shed light on the mode of interaction between the ligands and the target, and the stability of the obtained complexes. Furthermore, the pharmacokinetic properties of the designed compounds were assessed to predict their behavior in the human body. The binding free energy was also calculated using MMGBSA method and revealed favorable thermodynamic properties. The results highlighted three novel compounds with high biological activity, strong binding affinity to the target enzyme, and suitability for oral administration. These results offer interesting prospects for the development of effective and well-tolerated medications against diabetes mellitus.
Language	English
Publishing date	2024-02-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2193542-7
ISSN	1424-8247
ISSN	1424-8247
DOI	10.3390/ph17020261
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Article ; Online: A comprehensive computational study to explore promising natural bioactive compounds targeting glycosyltransferase MurG in Escherichia coli for potential drug development.

Shtaiwi, Amneh / Khan, Shafi Ullah / Khedraoui, Meriem / Alaraj, Mohd / Samadi, Abdelouahid / Chtita, Samir

Scientific reports

2024 Volume 14, Issue 1, Page(s) 7098

Abstract: Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is ... ...

Abstract	Peptidoglycan is a carbohydrate with a cross-linked structure that protects the cytoplasmic membrane of bacterial cells from damage. The mechanism of peptidoglycan biosynthesis involves the main synthesizing enzyme glycosyltransferase MurG, which is known as a potential target for antibiotic therapy. Many MurG inhibitors have been recognized as MurG targets, but high toxicity and drug-resistant Escherichia coli strains remain the most important problems for further development. In addition, the discovery of selective MurG inhibitors has been limited to the synthesis of peptidoglycan-mimicking compounds. The present study employed drug discovery, such as virtual screening using molecular docking, drug likeness ADMET proprieties predictions, and molecular dynamics (MD) simulation, to identify potential natural products (NPs) for Escherichia coli. We conducted a screening of 30,926 NPs from the NPASS database. Subsequently, 20 of these compounds successfully passed the potency, pharmacokinetic, ADMET screening assays, and their validation was further confirmed through molecular docking. The best three hits and the standard were chosen for further MD simulations up to 400 ns and energy calculations to investigate the stability of the NPs-MurG complexes. The analyses of MD simulations and total binding energies suggested the higher stability of NPC272174. The potential compounds can be further explored in vivo and in vitro for promising novel antibacterial drug discovery.
MeSH term(s)	Glycosyltransferases/metabolism ; Escherichia coli/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Molecular Docking Simulation ; Peptidoglycan ; Anti-Bacterial Agents/pharmacology ; Molecular Dynamics Simulation ; Drug Development
Chemical Substances	Glycosyltransferases (EC 2.4.-) ; Bacterial Outer Membrane Proteins ; Peptidoglycan ; Anti-Bacterial Agents
Language	English
Publishing date	2024-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-024-57702-x
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Article ; Online: Ligand-Based Design of Novel Quinoline Derivatives as Potential Anticancer Agents: An In-Silico Virtual Screening Approach.

Mkhayar, Khaoula / Daoui, Ossama / Haloui, Rachid / Elkhattabi, Kaouakeb / Elabbouchi, Abdelmoula / Chtita, Samir / Samadi, Abdelouahid / Elkhattabi, Souad

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 2

Abstract: In this study, using the Comparative Molecular Field Analysis (CoMFA) approach, the structure-activity relationship of 33 small quinoline-based compounds with biological anti-gastric cancer activity in vitro was analyzed in 3D space. Once the 3D ... ...

Abstract	In this study, using the Comparative Molecular Field Analysis (CoMFA) approach, the structure-activity relationship of 33 small quinoline-based compounds with biological anti-gastric cancer activity in vitro was analyzed in 3D space. Once the 3D geometric and energy structure of the target chemical library has been optimized and their steric and electrostatic molecular field descriptions computed, the ideal 3D-QSAR model is generated and matched using the Partial Least Squares regression (PLS) algorithm. The accuracy, statistical precision, and predictive power of the developed 3D-QSAR model were confirmed by a range of internal and external validations, which were interpreted by robust correlation coefficients (RTrain2=0.931; Qcv2=0.625; RTest2=0.875). After carefully analyzing the contour maps produced by the trained 3D-QSAR model, it was discovered that certain structural characteristics are beneficial for enhancing the anti-gastric cancer properties of Quinoline derivatives. Based on this information, a total of five new quinoline compounds were developed, with their biological activity improved and their drug-like bioavailability measured using POM calculations. To further explore the potential of these compounds, molecular docking and molecular dynamics simulations were performed in an aqueous environment for 100 nanoseconds, specifically targeting serine/threonine protein kinase. Overall, the new findings of this study can serve as a starting point for further experiments with a view to the identification and design of a potential next-generation drug for target therapy against cancer.
MeSH term(s)	Humans ; Ligands ; Molecular Docking Simulation ; Antineoplastic Agents/pharmacology ; Quinolines/pharmacology ; Quantitative Structure-Activity Relationship ; Stomach Neoplasms/drug therapy
Chemical Substances	Ligands ; Antineoplastic Agents ; Quinolines
Language	English
Publishing date	2024-01-15
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/molecules29020426
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Article ; Online: Computer-Aided Strategy on 5-(Substituted benzylidene) Thiazolidine-2,4-Diones to Develop New and Potent PTP1B Inhibitors: QSAR Modeling, Molecular Docking, Molecular Dynamics, PASS Predictions, and DFT Investigations.

Derki, Nour-El Houda / Kerassa, Aicha / Belaidi, Salah / Derki, Maroua / Yamari, Imane / Samadi, Abdelouahid / Chtita, Samir

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 4

Abstract: A set of 5-(substituted benzylidene) thiazolidine-2,4-dione derivatives was explored to study the main structural requirement for the design of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Utilizing multiple linear regression (MLR) analysis, we ... ...

Abstract	A set of 5-(substituted benzylidene) thiazolidine-2,4-dione derivatives was explored to study the main structural requirement for the design of protein tyrosine phosphatase 1B (PTP1B) inhibitors. Utilizing multiple linear regression (MLR) analysis, we constructed a robust quantitative structure-activity relationship (QSAR) model to predict inhibitory activity, resulting in a noteworthy correlation coefficient (R
MeSH term(s)	Humans ; Molecular Docking Simulation ; Quantitative Structure-Activity Relationship ; Thiazolidines/pharmacology ; Thiazolidines/chemistry ; Reproducibility of Results ; Molecular Dynamics Simulation ; Enzyme Inhibitors/chemistry ; Diabetes Mellitus/drug therapy
Chemical Substances	Thiazolidines ; Enzyme Inhibitors
Language	English
Publishing date	2024-02-10
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/molecules29040822
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Article ; Online: Identification of Potent Acetylcholinesterase Inhibitors as New Candidates for Alzheimer Disease via Virtual Screening, Molecular Docking, Dynamic Simulation, and Molecular Mechanics-Poisson-Boltzmann Surface Area Calculations.

Chennai, Hind Yassmine / Belaidi, Salah / Bourougaa, Lotfi / Ouassaf, Mebarka / Sinha, Leena / Samadi, Abdelouahid / Chtita, Samir

Molecules (Basel, Switzerland)

2024 Volume 29, Issue 6

Abstract: Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing ... ...

Abstract	Huperzine A (HUP) plays a crucial role in Alzheimer's therapy by enhancing cognitive function through increased cholinergic activity as a reversible acetylcholinesterase (AChE) inhibitor. Despite some limitations being seen in AChE inhibitors, ongoing research remains dedicated to finding innovative and more effective treatments for Alzheimer's disease. To achieve the goal of the discovery of potential HUP analogues with improved physicochemical properties, less toxic properties, and high biological activity, many in silico methods were applied. Based on the acetylcholinesterase-ligand complex, an e-pharmacophore model was developed. Subsequently, a virtual screening involving a collection of 1762 natural compounds, sourced from the PubChem database, was performed. This screening yielded 131 compounds that exhibited compatibility with the established pharmacophoric hypothesis. These selected ligands were then subjected to molecular docking within the active site of the 4EY5 receptor. As a result, we identified four compounds that displayed remarkable docking scores and exhibited low free binding energy to the target. These top four compounds, CID_162895946, CID_44461278, CID_44285285, and CID_81108419, were submitted to ADMET prediction and molecular dynamic simulations, yielding encouraging findings in terms of their pharmacokinetic characteristics and stability. Finally, the molecular dynamic simulation, cross-dynamic correlation matrix, free energy landscape, and MM-PBSA calculations demonstrated that two ligands from the selected ligands formed very resilient complexes with the enzyme acetylcholinesterase, with significant binding affinity. Therefore, these two compounds are recommended for further experimental research as possible (AChE) inhibitors.
MeSH term(s)	Humans ; Cholinesterase Inhibitors/chemistry ; Alzheimer Disease/drug therapy ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; Acetylcholinesterase/metabolism ; Ligands ; Alkaloids ; Sesquiterpenes
Chemical Substances	Cholinesterase Inhibitors ; Acetylcholinesterase (EC 3.1.1.7) ; huperzine A (0111871I23) ; Ligands ; Alkaloids ; Sesquiterpenes
Language	English
Publishing date	2024-03-10
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/molecules29061232
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Article ; Online: Novel Grafted Hydrogel for Iron and Ammonia Removal from Groundwater: A Synthesis and Computational Chemistry Study.

Abd El-Salam, H M / El Shafey, Ali M / Samadi, Abdelouahid / Abdel-Latif, Mahmoud K

Gels (Basel, Switzerland)

2023 Volume 9, Issue 10

Abstract: Current research is moving towards iron and ammonia elimination from groundwater. Here, we are using a poly acrylic-poly acrylamide hydrogel that is grafted with 3-chloroaniline. This copolymer was synthesized by addition polymerization technique. The ... ...

Abstract	Current research is moving towards iron and ammonia elimination from groundwater. Here, we are using a poly acrylic-poly acrylamide hydrogel that is grafted with 3-chloroaniline. This copolymer was synthesized by addition polymerization technique. The effects of agitation time, dosage and adsorbent temperature on the removal process sensitivity were investigated. The copolymer was described experientially and theoretically. Isothermal kinetic adsorption models are discussed. This hydrogel could be regenerated efficiently (98.3% removal of iron and 100% removal of ammonia). The density functional theory (DFT) method, using B3LYP/6-311G(d,p), and the LANL2DZ level of the theory were managed to investigate the stationary states of the grafted copolymer and the complexation energy of the hydrogel with the studied cations. DFT has been used to investigate the Natural Bond Orbital (NBO) properties to locate the most negative centers on the hydrogel. The calculated complexation energy showed hydrogel selectivity with regard to the studied cations.
Language	English
Publishing date	2023-09-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813982-3
ISSN	2310-2861 ; 2310-2861
ISSN (online)	2310-2861
ISSN	2310-2861
DOI	10.3390/gels9100781
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Article ; Online: Synthesis of novel thiourea-/urea-benzimidazole derivatives as anticancer agents

Siddig Lamia A. / Khasawneh Mohammad A. / Samadi Abdelouahid / Saadeh Haythem / Abutaha Nael / Wadaan Mohammad Ahmed

Open Chemistry, Vol 19, Iss 1, Pp 1062-

2021 Volume 1073

Abstract: A new series of urea and thiourea derivatives containing benzimidazole group as potential anticancer agents have been designed and synthesized. The structures of the synthesized compounds were characterized and confirmed by spectroscopic techniques such ... ...

Abstract	A new series of urea and thiourea derivatives containing benzimidazole group as potential anticancer agents have been designed and synthesized. The structures of the synthesized compounds were characterized and confirmed by spectroscopic techniques such as 1H NMR, 13C NMR, and mass spectrometry. In vitro anticancer assay against two breast cancer (BC) cell lines, MDA-MB-231ER(−)/PR(−) and MCF-7ER(+)/PR(+), revealed that the cytotoxicity of 1-(2-(1H-benzo[d]imidazol-2-ylamino)ethyl)-3-p-tolylthiourea (7b) and 4-(1H-benzo[d]imidazol-2-yl)-N-(3-chlorophenyl)piperazine-1-carboxamide (5d) were higher in MCF-7 with IC50 values of 25.8 and 48.3 µM, respectively, as compared with MDA-MB-231 cells. Furthermore, 7b and 5d were assessed for their apoptotic potential using 4′,6-diamidino-2-phenylindole, acridine orange/ethidium bromide staining, and Caspase-3/7. After incubation with MCF-7, the compounds 7b and 5d induced apoptosis through caspase-3/7 activation. In conclusion, the compounds 7b and 5d are potential candidates for inducing apoptosis in different genotypic BC cell lines.
Keywords	benzimidazole ; urea ; thiourea ; piperazine ; anticancer activity ; apoptosis ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	De Gruyter
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: First Exclusive Stereo- and Regioselective Preparation of 5-Arylimino-1,3,4-Selenadiazole Derivatives: Synthesis, NMR analysis, and Computational Studies.

Moussa, Ziad / Perez Paz, Alejandro / Khalaf, Mohamed A / Judeh, Zaher M A / Alzamly, Ahmed / Samadi, Abdelouahid / Al-Fahemi, Jabir H / Tatina, Madhu Babu / Al-Masri, Harbi Tomah / Jassas, Rabab S / Ahmed, Saleh A

Chemistry, an Asian journal

2023 Volume 18, Issue 17, Page(s) e202300475

Abstract: Isoselenocyanates are valuable coupling partners required for preparing key chemical intermediates and biologically active molecules in an accelerated and effective way. Likewise, (Z)-2-oxo-N-phenylpropanehydrazonoyl chlorides have been employed in ... ...

Abstract	Isoselenocyanates are valuable coupling partners required for preparing key chemical intermediates and biologically active molecules in an accelerated and effective way. Likewise, (Z)-2-oxo-N-phenylpropanehydrazonoyl chlorides have been employed in numerous one-step heteroannulation reactions to assemble the structural core of several various kinds of heterocyclic compounds. Here, we describe the inverse electron demand 1,3-dipolar cycloaddition reaction of isoselenocyanates with a variety of substituted (Z)-2-oxo-N-phenylpropanehydrazonoyl chlorides to generate, regioselectively and stereoselectively, a series of 5-arylimino-1,3,4-selenadiazole derivatives comprising a multitude of functional groups on both aryl rings. The synthetic method features gentle room-temperature conditions, wide substrate scope, and good to high reaction yields. The selenadiazoles were separated by gravity filtration in all instances and chemical structures were validated by multinuclear NMR spectroscopy and high accuracy mass spectral measurements. First conclusive molecular structure elucidation of the observed 5-arylimino-selenadiazole regioisomer was verified by single-crystal X-ray diffraction analysis. Crystal-structure measurement was successfully carried out on (Z)-1-(4-(4-iodophenyl)-5-(p-tolylimino)-4,5-dihydro-1,3,4-selenadiazol-2-yl)ethan-1-one and (Z)-1-(5-((4-methoxyphenyl)imino)-4-(4-(methylthio)phenyl)-4,5-dihydro-1,3,4-selenadiazol-2-yl)ethan-1-one. Likewise, the (Z)-geometry of the hydrazonoyl chloride reactant was proven by X-ray diffraction studies. As representative examples, crystal-structure determination was carried out on (Z)-2-oxo-N-phenylpropanehydrazonoyl chloride and (Z)-N-(3,5-bis(trifluoromethyl)phenyl)-2-oxopropanehydrazonoyl chloride. Density functional theory calculations at the B3LYP-D4/def2-TZVP level were conducted to support the noted experimental findings and suggested mechanism.
Language	English
Publishing date	2023-08-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2233006-9
ISSN	1861-471X ; 1861-4728
ISSN (online)	1861-471X
ISSN	1861-4728
DOI	10.1002/asia.202300475
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Article: The Reaction of Thiyl Radical with Methyl Linoleate: Completing the Picture

Chatgilialoglu, Chryssostomos / Bowry Vincent W / Ferreri Carla / Guerra Maurizio / Samadi Abdelouahid

Journal of the American Chemical Society. 2017 Apr. 05, v. 139, no. 13

2017

Abstract: Cis lipids can be converted by thiols and free radicals into trans lipids, which are therefore a valuable tell-tale for free radical activity in the cellâs lipidome. Our previous studies have shown that polyunsaturated lipids are isomerized by ... ...

Abstract	Cis lipids can be converted by thiols and free radicals into trans lipids, which are therefore a valuable tell-tale for free radical activity in the cellâs lipidome. Our previous studies have shown that polyunsaturated lipids are isomerized by alkanethiyl radicals (Sâ¢) in a cycle propagated by reversible double-bond addition and terminated by radical H-abstraction from the lipid. A critical flaw in this picture has long been that the reported lipid abstraction rate from radiolysis studies is faster than additionâisomerization, implying that the âcycleâ must be terminating faster than it is propagating! Herein, we resolved this longstanding puzzle by combining a detailed product analysis, with reinvestigation of the time-resolved kinetics, DFT calculations of the indicated pathways, and reformulation of the radical-stasis equations. We have determined thiol-coupled products in dilute solutions arise mainly from addition to the inside position of the bisallylic group, followed by rapid intramolecular Hâ¢ transfer, yielding allylic radicals (LZZ + Sâ¢ â SLâ¢ â SLâ²â¢) that are slowly reduced by thiol (SLâ²â¢ + SH â SLâ²H + Sâ¢). The first-order grow-in rate of the LâHâ¢ signal (kâââÂ²â¸â°â¿áµ) may therefore be dominated by the addition-H-translocation rather than slower direct Hâ¢-abstraction. Steady-state kinetic analysis of the new mechanism is consistent with products and the rates and trends for polyunsaturated fatty acids (PUFAs), monounsaturated fatty acids (MUFAs), and mixtures, with and without physiological [Oâ]. Implications of this new paradigm for the thiol-ene reactivity fall in an interdisciplinary research area spanning from synthetic applications to metabolomics.
Keywords	equations ; interdisciplinary research ; isomerization ; kinetics ; metabolomics ; monounsaturated fatty acids ; oxygen ; polyunsaturated fatty acids ; superoxide anion ; thiols
Language	English
Dates of publication	2017-0405
Size	p. 4704-4714.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021%2Fjacs.6b11320
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Reaction of Thiyl Radical with Methyl Linoleate: Completing the Picture.

Chatgilialoglu, Chryssostomos / Ferreri, Carla / Guerra, Maurizio / Samadi, Abdelouahid / Bowry, Vincent W

Journal of the American Chemical Society

2017 Volume 139, Issue 13, Page(s) 4704–4714

Abstract: Cis lipids can be converted by thiols and free radicals into trans lipids, which are therefore a valuable tell-tale for free radical activity in the cell's lipidome. Our previous studies have shown that polyunsaturated lipids are isomerized by ... ...

Abstract	Cis lipids can be converted by thiols and free radicals into trans lipids, which are therefore a valuable tell-tale for free radical activity in the cell's lipidome. Our previous studies have shown that polyunsaturated lipids are isomerized by alkanethiyl radicals (S
Language	English
Publishing date	2017-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.6b11320
Database	MEDical Literature Analysis and Retrieval System OnLINE

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