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Article ; Online: Copper(II) Driven Fluorescence switch-on Detection of Ovalbumin and GSH Using a Pyridoxal 5'-phosphate Derived Tetradentate Schiff Base and its Applications.

Dhanshri, Sonkeshriya / Vardhan, Seshu / Sahoo, Suban K

2024

Abstract: The facile detection of glutathione (GSH) and ovalbumin (OVA) is of great importance in biological research. Herein, a tetradentate Schiff base N, N'-bis(pyridoxal-5-phosphate)-o-phenylenediamine (L) obtained by condensing two moles of pyridoxal 5'- ... ...

Abstract	The facile detection of glutathione (GSH) and ovalbumin (OVA) is of great importance in biological research. Herein, a tetradentate Schiff base N, N'-bis(pyridoxal-5-phosphate)-o-phenylenediamine (L) obtained by condensing two moles of pyridoxal 5'-phosphate (PLP) with one mole of 1,2-phenylenediamine was employed for the fluorescence switch-on detection of GSH and OVA. When excited at 389 nm, receptor L showed a weak emission at 454 nm in an aqueous medium. The addition of GSH to the solution of L caused a significant fluorescence enhancement at 454 nm. Amino acids (leucine, glycine, serine, tryptophan, homocysteine, alanine, methionine, arginine and proline) and albumins (bovine serum albumin and OVA) failed to alter the fluorescence profile of L. Receptor L can be applied to detect GSH down to 1.16 µM. However, the fluorescence emission of L was quenched upon the formation of the L-Cu
Language	English
Publishing date	2024-04-25
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2016892-5
ISSN	1573-4994 ; 1053-0509
ISSN (online)	1573-4994
ISSN	1053-0509
DOI	10.1007/s10895-024-03735-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Computational studies on searching potential phytochemicals against DNA polymerase activity of the monkeypox virus.

Vardhan, Seshu / Sahoo, Suban K

Journal of traditional and complementary medicine

2023

Abstract: Objectives: The outbreak of monkeypox virus (MPXV) is an emerging epidemic of medical concern with 65353 confirmed cases of infection and a fatality of 115 worldwide. Since May 2022, MPXV has been rapidly disseminating across the globe through various ... ...

Abstract	Objectives: The outbreak of monkeypox virus (MPXV) is an emerging epidemic of medical concern with 65353 confirmed cases of infection and a fatality of 115 worldwide. Since May 2022, MPXV has been rapidly disseminating across the globe through various modes of transmission, including direct contact, respiratory droplets, and consensual sex. Because of the limited medical countermeasures available to treat MPXV, the present study aimed to identify potential phytochemicals (limonoids, triterpenoids, and polyphenols) as antagonists to target the DNA polymerase protein of MPXV with the ultimate goal to inhibit the viral DNA replication mechanism and immune-mediated responses. Methods: The protein-DNA and protein-ligand molecular docking were performed with the help of computational programs AutoDock Vina, iGEMDOCK and HDOCK server. The BIOVIA Discovery studio and ChimeraX were used to evaluate the protein-ligand interactions. The GROMACS 2021 was used for the molecular dynamics simulations. The ADME and toxicity properties were computed by using online servers SwissADME and pKCSM. Results: Molecular docking of 609 phytochemicals and molecular dynamics simulations of lead phytochemicals glycyrrhizinic acid and apigenin-7-O-glucuronide generated useful data that supported the ability of phytochemicals to obstruct the DNA polymerase activity of the monkeypox virus. Conclusions: The computational results supported that appropriate phytochemicals can be used to formulate an adjuvant therapy for the monkeypox virus.
Language	English
Publishing date	2023-05-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2709698-1
ISSN	2225-4110
ISSN	2225-4110
DOI	10.1016/j.jtcme.2023.04.002
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Article ; Online: Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols.

Vardhan, Seshu / Sahoo, Suban K

Phytochemical analysis : PCA

2023 Volume 34, Issue 7, Page(s) 800–815

Abstract: Introduction: The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes ... ...

Abstract	Introduction: The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3. Objective: In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3. Methods: Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021. Results: Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule. Conclusion: Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2.
MeSH term(s)	Humans ; Angiotensin-Converting Enzyme 2/chemistry ; COVID-19 ; Ligands ; Molecular Docking Simulation ; SARS-CoV-2/genetics ; Polyphenols/chemistry
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Ligands ; ACE2 protein, human (EC 3.4.17.23) ; Polyphenols
Language	English
Publishing date	2023-01-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1073576-8
ISSN	1099-1565 ; 0958-0344
ISSN (online)	1099-1565
ISSN	0958-0344
DOI	10.1002/pca.3204
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Article ; Online: Computational studies on the interaction of SARS-CoV-2 Omicron SGp RBD with human receptor ACE2, limonin and glycyrrhizic acid.

Vardhan, Seshu / Sahoo, Suban K

Computers in biology and medicine

2022 Volume 144, Page(s) 105367

Abstract: On November 24, 2021, the SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in South Africa. The World Health Organization (WHO) declared the Omicron as a variant of concern (VoC) because of the unexpected and large numbers of mutations ... ...

Abstract	On November 24, 2021, the SARS-CoV-2 Omicron variant (B.1.1.529) was first identified in South Africa. The World Health Organization (WHO) declared the Omicron as a variant of concern (VoC) because of the unexpected and large numbers of mutations occurred in the genome, higher viral transmission and immune evasions. The present study was performed to explore the interactions of SARS-CoV-2 spike glycoprotein receptor-binding domain (SGp RBD) of the three variants (Omicron, Delta, and WT) with the receptor hACE2. The structural changes occurred in Omicron due to the mutations at key positions improved the ability to mediate SARS-CoV-2 viral infection compared to other VoCs. The phytochemicals limonin and glycyrrhizic acid were docked with the SGp RBD of the variants WT, Delta and Omicron. The computed dock score revealed that limonin and glycyrrhizic acid binds effectively at the SGp RBD of all three variants, and showed almost similar binding affinity at the binding interface of ACE2. Therefore, despite the multiple mutations occurred in Omicron and its viral transmission is comparatively high, the computed binding affinity of the phytochemicals limonin and glycyrrhizic acid supported that the traditional medicines can be useful in formulating adjuvant therapies to fight against the SARS-CoV-2 Omicron.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19/drug therapy ; Glycyrrhizic Acid/pharmacology ; Humans ; Limonins ; Mutation ; SARS-CoV-2
Chemical Substances	Limonins ; Glycyrrhizic Acid (6FO62043WK) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; limonin (L0F260866S)
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105367
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Zs.A 653: Show issues

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Article ; Online: Virtual screening by targeting proteolytic sites of furin and TMPRSS2 to propose potential compounds obstructing the entry of SARS-CoV-2 virus into human host cells

Seshu Vardhan / Suban K. Sahoo

Journal of Traditional and Complementary Medicine, Vol 12, Iss 1, Pp 6-

2022 Volume 15

Abstract: Background and aim: The year 2020 begins with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that cause the disease COVID-19, and continue till today. As of March 23, 2021, the outbreak has infected 124,313,054 worldwide ... ...

Abstract	Background and aim: The year 2020 begins with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that cause the disease COVID-19, and continue till today. As of March 23, 2021, the outbreak has infected 124,313,054 worldwide with a total death of 2,735,707. The use of traditional medicines as an adjuvant therapy with western drugs can lower the fatality rate due to the COVID-19. Therefore, in silico molecular docking study was performed to search potential phytochemicals and drugs that can block the entry of SARS-CoV-2 into host cells by inhibiting the proteolytic cleavage activity of furin and TMPRSS2. Experimental procedure: The protein-protein docking of the host proteases furin and TMPRSS2 was carried out with the virus spike (S) protein to examine the conformational details and residues involved in the complex formation. Subsequently, a library of 163 ligands containing phytochemicals and drugs was virtually screened to propose potential hits that can inhibit the proteolytic cleavage activity of furin and TMPRSS2. Results and conclusion: The phytochemicals like limonin, gedunin, eribulin, pedunculagin, limonin glycoside and betunilic acid bind at the active site of both furin and TMPRSS2. Limonin and gedunin found mainly in the citrus fruits and neem showed the highest binding energy at the active site of furin and TMPRSS2, respectively. The polyphenols found in green tea can also be useful in suppressing the furin activity. Among the drugs, the drug nafamostat may be more beneficial than the camostat in suppressing the activity of TMPRSS2.
Keywords	COVID-19 ; SARS-CoV-2 ; Protein-protein docking ; Molecular docking ; Phytochemicals ; Drugs ; Medicine ; R
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Exploring the therapeutic nature of limonoids and triterpenoids against SARS-CoV-2 by targeting nsp13, nsp14, and nsp15 through molecular docking and dynamics simulations

Seshu Vardhan / Suban K. Sahoo

Journal of Traditional and Complementary Medicine, Vol 12, Iss 1, Pp 44-

2022 Volume 54

Abstract: Background and aim: The ongoing global pandemic due to SARS-CoV-2 caused a medical emergency. Since December 2019, the COVID-19 disease is spread across the globe through physical contact and respiratory droplets. Coronavirus caused a severe effect on ... ...

Abstract	Background and aim: The ongoing global pandemic due to SARS-CoV-2 caused a medical emergency. Since December 2019, the COVID-19 disease is spread across the globe through physical contact and respiratory droplets. Coronavirus caused a severe effect on the human immune system where some of the non-structural proteins (nsp) are involved in virus-mediated immune response and pathogenesis. To suppress the viral RNA replication mechanism and immune-mediated responses, we aimed to identify limonoids and triterpenoids as antagonists by targeting helicases (nsp13), exonuclease (nsp14), and endoribonuclease (nsp15) of SARS-CoV-2 as therapeutic proteins. Experimental procedure: In silico molecular docking and drug-likeness of a library of 369 phytochemicals from limonoids and triterpenoids were performed to screen the potential hits that binds effectively at the active site of the proteins target. In addition, the molecular dynamics simulations of the proteins and their complexes with the potential hits were performed for 100 ns by using GROMACS. Results and conclusion: The potential compounds 26-deoxyactein and 25-O-anhydrocimigenol 3-O-beta-d-xylopyranoside posing strong interactions with a minimum binding energy of −10.1 and −9.5 kcal/mol, respectively and sustained close contact with nsp13 for 100 ns. The nsp14 replication fork activity was hindered by the tomentosolic acid, timosaponin A-I, and shizukaol A with the binding affinity score of −9.2, −9.2, and −9.0 kcal/mol, respectively. The nsp15 endoribonuclease catalytic residues were inhibited potentially by limonin, 25-O-anhydrocimigenol 3-O-alpha-l-arabinopyranoside, and asperagenin posing strong binding affinity scores of −9.0, −8.8, and −8.7 kcal/mol, respectively. Computationally predicted potential phytochemicals for SARS-CoV-2 are known to possess various medicinal properties.
Keywords	COVID-19 ; Limonoids ; Triterpenoids ; Molecular docking ; Dynamics simulation ; Medicine ; R
Subject code	540
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Chronic Kidney Disease Interplay with Comorbidities and Carbohydrate Metabolism: A Review.

Kushwaha, Radha / Vardhan, Pothabathula Seshu / Kushwaha, Prem Prakash

Life (Basel, Switzerland)

2023 Volume 14, Issue 1

Abstract: Chronic kidney disease (CKD) poses a global health challenge, engendering various physiological and metabolic shifts that significantly impact health and escalate the susceptibility to severe illnesses. This comprehensive review delves into the intricate ...

Abstract	Chronic kidney disease (CKD) poses a global health challenge, engendering various physiological and metabolic shifts that significantly impact health and escalate the susceptibility to severe illnesses. This comprehensive review delves into the intricate complexities of CKD, scrutinizing its influence on cellular growth homeostasis, hormonal equilibrium, wasting, malnutrition, and its interconnectedness with inflammation, oxidative stress, and cardiovascular diseases. Exploring the genetic, birth-related, and comorbidity factors associated with CKD, alongside considerations of metabolic disturbances, anemia, and malnutrition, the review elucidates how CKD orchestrates cellular growth control. A pivotal focus lies on the nexus between CKD and insulin resistance, where debates persist regarding its chronological relationship with impaired kidney function. The prevalence of insulin abnormalities in CKD is emphasized, contributing to glucose intolerance and raising questions about its role as a precursor or consequence. Moreover, the review sheds light on disruptions in the growth hormone and insulin-like growth factor axis in CKD, underscoring the heightened vulnerability to illness and mortality in cases of severe growth retardation. Wasting, a prevalent concern affecting up to 75% of end-stage renal disease (ESRD) patients, is analyzed, elucidating the manifestations of cachexia and its impact on appetite, energy expenditure, and protein reserves. Taste disturbances in CKD, affecting sour, umami, and salty tastes, are explored for their implications on food palatability and nutritional status. Independent of age and gender, these taste alterations have the potential to sway dietary choices, further complicating the management of CKD. The intricate interplay between CKD, inflammation, oxidative stress, and cardiovascular diseases is unraveled, emphasizing the profound repercussions on overall health. Additionally, the review extends its analysis to CKD's broader impact on cognitive function, emotional well-being, taste perception, and endothelial dysfunction. Concluding with an emphasis on dietary interventions as crucial components in CKD management, this comprehensive review navigates the multifaceted dimensions of CKD, providing a nuanced understanding essential for developing targeted therapeutic strategies.
Language	English
Publishing date	2023-12-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662250-6
ISSN	2075-1729
ISSN	2075-1729
DOI	10.3390/life14010013
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Article: Exploring the therapeutic nature of limonoids and triterpenoids against SARS-CoV-2 by targeting nsp13, nsp14, and nsp15 through molecular docking and dynamics simulations.

Vardhan, Seshu / Sahoo, Suban K

Journal of traditional and complementary medicine

2021 Volume 12, Issue 1, Page(s) 44–54

Abstract	Background and aim: The ongoing global pandemic due to SARS-CoV-2 caused a medical emergency. Since December 2019, the COVID-19 disease is spread across the globe through physical contact and respiratory droplets. Coronavirus caused a severe effect on the human immune system where some of the non-structural proteins (nsp) are involved in virus-mediated immune response and pathogenesis. To suppress the viral RNA replication mechanism and immune-mediated responses, we aimed to identify limonoids and triterpenoids as antagonists by targeting helicases (nsp13), exonuclease (nsp14), and endoribonuclease (nsp15) of SARS-CoV-2 as therapeutic proteins. Experimental procedure: In silico Results and conclusion: The potential compounds 26-deoxyactein and 25-O-anhydrocimigenol 3-O-beta-d-xylopyranoside posing strong interactions with a minimum binding energy of -10.1 and -9.5 kcal/mol, respectively and sustained close contact with nsp13 for 100 ns. The nsp14 replication fork activity was hindered by the tomentosolic acid, timosaponin A-I, and shizukaol A with the binding affinity score of -9.2, -9.2, and -9.0 kcal/mol, respectively. The nsp15 endoribonuclease catalytic residues were inhibited potentially by limonin, 25-O-anhydrocimigenol 3-O-alpha-l-arabinopyranoside, and asperagenin posing strong binding affinity scores of -9.0, -8.8, and -8.7 kcal/mol, respectively. Computationally predicted potential phytochemicals for SARS-CoV-2 are known to possess various medicinal properties.
Language	English
Publishing date	2021-12-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2709698-1
ISSN	2225-4110
ISSN	2225-4110
DOI	10.1016/j.jtcme.2021.12.002
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Article: Virtual screening by targeting proteolytic sites of furin and TMPRSS2 to propose potential compounds obstructing the entry of SARS-CoV-2 virus into human host cells.

Vardhan, Seshu / Sahoo, Suban K

Journal of traditional and complementary medicine

2021 Volume 12, Issue 1, Page(s) 6–15

Abstract	Background and aim: The year 2020 begins with the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that cause the disease COVID-19, and continue till today. As of March 23, 2021, the outbreak has infected 124,313,054 worldwide with a total death of 2,735,707. The use of traditional medicines as an adjuvant therapy with western drugs can lower the fatality rate due to the COVID-19. Therefore, Experimental procedure: The protein-protein docking of the host proteases furin and TMPRSS2 was carried out with the virus spike (S) protein to examine the conformational details and residues involved in the complex formation. Subsequently, a library of 163 ligands containing phytochemicals and drugs was virtually screened to propose potential hits that can inhibit the proteolytic cleavage activity of furin and TMPRSS2. Results and conclusion: The phytochemicals like limonin, gedunin, eribulin, pedunculagin, limonin glycoside and betunilic acid bind at the active site of both furin and TMPRSS2. Limonin and gedunin found mainly in the citrus fruits and neem showed the highest binding energy at the active site of furin and TMPRSS2, respectively. The polyphenols found in green tea can also be useful in suppressing the furin activity. Among the drugs, the drug nafamostat may be more beneficial than the camostat in suppressing the activity of TMPRSS2.
Language	English
Publishing date	2021-04-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2709698-1
ISSN	2225-4110
ISSN	2225-4110
DOI	10.1016/j.jtcme.2021.04.001
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Article ; Online: Fluorescent turn-on sensing of albumin proteins (BSA and ovalbumin) using vitamin B

Dhanshri, Sonkeshriya / Vardhan, Seshu / Sahoo, Suban K

Methods (San Diego, Calif.)

2022 Volume 206, Page(s) 69–76

Abstract: The detection of albumin proteins with high accuracy by facile analytical approaches is important for the diagnosis of various diseases. This manuscript introduced an easy-to-prepare Schiff base L by condensing vitamin ... ...

Abstract	The detection of albumin proteins with high accuracy by facile analytical approaches is important for the diagnosis of various diseases. This manuscript introduced an easy-to-prepare Schiff base L by condensing vitamin B
MeSH term(s)	Ligands ; Molecular Docking Simulation ; Ovalbumin ; Phosphates ; Pyridoxal Phosphate/chemistry ; Pyridoxal Phosphate/metabolism ; Schiff Bases/chemistry ; Serum Albumin, Bovine/chemistry ; Spectrometry, Fluorescence ; Vitamin B 6/chemistry ; Vitamins
Chemical Substances	Ligands ; Phosphates ; Schiff Bases ; Vitamins ; Serum Albumin, Bovine (27432CM55Q) ; Pyridoxal Phosphate (5V5IOJ8338) ; Vitamin B 6 (8059-24-3) ; Ovalbumin (9006-59-1)
Language	English
Publishing date	2022-08-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2022.08.014
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