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Article: Exploring the anticancer potential of fluoro flavone analogues: insights from molecular docking and dynamics studies with Aurora Kinase B.

Singh, Ipsa A / Lokhande, Kiran Bharat / Swamy, K Venkateswara

2024 Volume 12, Issue 1, Page(s) 26

Language	English
Publishing date	2024-04-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2702993-1
ISSN	2193-9616
ISSN	2193-9616
DOI	10.1007/s40203-024-00200-9
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Article ; Online: Docking and simulation studies on cyclin D/CDK4 complex for targeting cell cycle arrest in cancer using flavanone and its congener.

Nagare, Sagar / Lokhande, Kiran Bharat / Swamy, K Venkateswara

Journal of molecular modeling

2023 Volume 29, Issue 4, Page(s) 90

Abstract: Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor ... ...

Abstract	Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor bioavailability, natural flavanones were not used as therapeutic targets so flavanone congeners were prepared by modifying at B-functional group using compound libraries such as PubChem Database. Cyclin-dependent kinase is primarily activating the cell cycle and potentiating the M phase, in order to control the cell cycle in cancer cyclin-dependent pathway was targeted and potential cyclin D/CDK4 receptor protein was retrieved from Protein Data Bank (PDBID:2W9Z). The binding site was determined using FlexX docking. Flavanone and its congeners were docked against the 2W9Z receptor protein with the docking software FlexX. For validation of docking results, molecular dynamics simulations of the best-fitting molecule were carried out using Desmond Package. Noncovalent interactions like hydrogen bonds, electrostatic interaction, and Van der walls potentials for stable conformations were calculated. Thus, upon docking and molecular dynamics studies, we discovered the potential flavanone derivatives such as Flavanone 20, Flavanone 25, and Flavanone 29, will become a potential drug target in controlling cell cycle arrest and may become a futuristic candidate in targeting cancer.
MeSH term(s)	Humans ; Cyclins ; Cell Cycle Checkpoints ; Flavanones/pharmacology ; Molecular Dynamics Simulation ; Neoplasms/drug therapy ; Cyclin D ; Cyclin-Dependent Kinase 4
Chemical Substances	Cyclins ; flavanone (WX22P730FB) ; Flavanones ; Cyclin D ; CDK4 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 4 (EC 2.7.11.22)
Language	English
Publishing date	2023-03-07
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05496-6
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Article ; Online: Docking and simulation studies on cyclin D/CDK4 complex for targeting cell cycle arrest in cancer using flavanone and its congener

Nagare, Sagar / Lokhande, Kiran Bharat / Swamy, K. Venkateswara

J Mol Model. 2023 Apr., v. 29, no. 4 p.90-90

2023

Abstract	Flavanone compounds are naturally occurring phytochemicals present in most of citrus fruits reported to be a potential anticancer moiety as it majorly participates in the inhibition of the cell cycle, apoptosis, and angiogenesis. Because of poor bioavailability, natural flavanones were not used as therapeutic targets so flavanone congeners were prepared by modifying at B-functional group using compound libraries such as PubChem Database. Cyclin-dependent kinase is primarily activating the cell cycle and potentiating the M phase, in order to control the cell cycle in cancer cyclin-dependent pathway was targeted and potential cyclin D/CDK4 receptor protein was retrieved from Protein Data Bank (PDBID:2W9Z). The binding site was determined using FlexX docking. Flavanone and its congeners were docked against the 2W9Z receptor protein with the docking software FlexX. For validation of docking results, molecular dynamics simulations of the best-fitting molecule were carried out using Desmond Package. Noncovalent interactions like hydrogen bonds, electrostatic interaction, and Van der walls potentials for stable conformations were calculated. Thus, upon docking and molecular dynamics studies, we discovered the potential flavanone derivatives such as Flavanone 20, Flavanone 25, and Flavanone 29, will become a potential drug target in controlling cell cycle arrest and may become a futuristic candidate in targeting cancer.
Keywords	Citrus ; angiogenesis ; apoptosis ; bioavailability ; cell cycle checkpoints ; computer software ; cyclin-dependent kinase ; cyclins ; databases ; drugs ; electrostatic interactions ; flavanones ; hydrogen ; models ; moieties ; molecular dynamics ; therapeutics
Language	English
Dates of publication	2023-04
Size	p. 90.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-023-05496-6
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Article ; Online: Identification and Screening of Novel Anti-Cancer Compounds for Aurora Kinase-A from Chemical Database.

Singh, Ipsa A / Lokhande, Kiran Bharat / Swamy, K Venkateswara

Drug research

2022

Abstract: Aurora kinase is a group of enzymes that belongs to a serine-threonine family and plays a critical role in cellular division. Aurora Kinase A is overexpressed and distributed beyond the nucleus and is involved in tumorigenesis. Flavones are a class of ... ...

Abstract	Aurora kinase is a group of enzymes that belongs to a serine-threonine family and plays a critical role in cellular division. Aurora Kinase A is overexpressed and distributed beyond the nucleus and is involved in tumorigenesis. Flavones are a class of flavonoids that are present in plants that show anticancer activity. Similar compounds of 2'Fluoroflavones are retrieved from the PubChem database. Then drug-like filters viz. REOS and PAINS were applied to remove toxic compounds using Canvas software, resulting in 3882 compounds being subjected to Glide docking with Aurora kinase A. The lead compounds were selected on the merit of hydrogen bonding, salt bridge, as well as pi-pi interactions, 4-(6-Fluoro-4-oxychromen-2yl) benzoic acid, has been found one of the best molecules from docking studies. The binding mode of the lead compound with AURKA reveals that the amino acid residues viz, Lys162, Ala213, and His280 are more important for binding with the binding affinity of -11.760 kcal/mol. The molecular dynamics simulations of 100 ns were done, which shows the mean RMSD value of 1.77 Å for all 3 complexes of the protein and Fluoroflavone and its analogs. This shows that Fluoroflavone and its 2 best analogs are tightly attached to the active sites and thus have conformational stability. Our finding suggests that 4-(6-fluoro-4-oxochromen-2-yl)benzoic acid and 4-(4-Oxochromen-2-yl)benzoate can be further used
Language	English
Publishing date	2022-09-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2703847-6
ISSN	2194-9387 ; 2194-9379
ISSN (online)	2194-9387
ISSN	2194-9379
DOI	10.1055/a-1877-4693
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Article ; Online: Molecular Docking and Simulation Studies of Flavanone and its Derived Compounds on PI3K-AKT Pathway Targeting against Cancer.

Nagare, Sagar / Lokhande, Kiran Bharat / Swamy, K Venkateswara

Current drug discovery technologies

2022 Volume 20, Issue 1, Page(s) e260522205302

Abstract: Background: Flavanone compounds and their related derivatives are reported in controlling cell cycle, angiogenesis, and metastasis. Phosphoinositide 3-kinases is a major drug target.: Methods: Crystalize structure of Phosphoinositide 3-kinases-Akt ... ...

Abstract	Background: Flavanone compounds and their related derivatives are reported in controlling cell cycle, angiogenesis, and metastasis. Phosphoinositide 3-kinases is a major drug target. Methods: Crystalize structure of Phosphoinositide 3-kinases-Akt complex obtained from Protein Data Bank (PDBID: 3CQW) was selected as receptor protein and the binding site has been identified with PDBSum Database. Flavanone and its derivatives were retrieved using freely available existing drug databases like Drug Bank, Zinc, and PubChem. New derivatives were modified by altering the flavanone at Beta ring position. This modification would help in maintaining stable structural conformation and retaining better anticancer activity. Retrieved Flavanone derivatives from the drug database were docked against 3CQW Protein with the advanced docking tool FlexX. MD simulations of the best molecule were performed with the Desmond package by calculating nonbonding interactions such as electrostatic interaction and hydrogen bond stable and favorable conformations were calculated. Results: These interaction studies would help identify new potential drug candidates with the help of computer-aided drug designing techniques. Conclusion: Natural chemicals have received a lot of attention because of their vast range of applications in human health and disease prevention without creating any negative side effects. Molecular docking is an essential approach for drug development since it allows for effective screening of potential therapeutics in a short time. We hypothesized in this paper that natural flavanone and its derivatives may be effective as Akt-1 inhibitors.
MeSH term(s)	Humans ; Molecular Docking Simulation ; Phosphatidylinositol 3-Kinases ; Proto-Oncogene Proteins c-akt ; Molecular Dynamics Simulation ; Neoplasms/drug therapy ; Protein Kinase Inhibitors/pharmacology ; Phosphatidylinositols
Chemical Substances	Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Protein Kinase Inhibitors ; Phosphatidylinositols
Language	English
Publishing date	2022-07-13
Publishing country	United Arab Emirates
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1875-6220
ISSN (online)	1875-6220
DOI	10.2174/1570163819666220526150152
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Article: [No title information]

Singh, Ipsa A. / Lokhande, Kiran Bharat / Swamy, K. Venkateswara

Drug Research

2022 Volume 73, Issue 01, Page(s) 30–39

Abstract	Aurora kinase is a group of enzymes that belongs to a serine-threonine family and plays a critical role in cellular division. Aurora Kinase A is overexpressed and distributed beyond the nucleus and is involved in tumorigenesis. Flavones are a class of flavonoids that are present in plants that show anticancer activity. Similar compounds of 2’Fluoroflavones are retrieved from the PubChem database. Then drug-like filters viz. REOS and PAINS were applied to remove toxic compounds using Canvas software, resulting in 3882 compounds being subjected to Glide docking with Aurora kinase A. The lead compounds were selected on the merit of hydrogen bonding, salt bridge, as well as pi-pi interactions, 4-(6-Fluoro-4-oxychromen-2yl) benzoic acid, has been found one of the best molecules from docking studies. The binding mode of the lead compound with AURKA reveals that the amino acid residues viz, Lys162, Ala213, and His280 are more important for binding with the binding affinity of -11.760 kcal/mol. The molecular dynamics simulations of 100 ns were done, which shows the mean RMSD value of 1.77 Å for all 3 complexes of the protein and Fluoroflavone and its analogs. This shows that Fluoroflavone and its 2 best analogs are tightly attached to the active sites and thus have conformational stability. Our finding suggests that 4-(6-fluoro-4-oxochromen-2-yl)benzoic acid and 4-(4-Oxochromen-2-yl)benzoate can be further used in vitro and in vivo experiments and can probably serve as a novel drug for cancer treatment.
Keywords	Aurora kinase A ; Fluoroflavones ; chemoinformatics ; Glide docking ; MD simulation ; Enrichment calculations
Language	English
Publishing date	2022-09-22
Publisher	Georg Thieme Verlag
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	2703847-6
ISSN	2194-9387 ; 2194-9379
ISSN (online)	2194-9387
ISSN	2194-9379
DOI	10.1055/a-1877-4693
Database	Thieme publisher's database

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Article ; Online: GC-MS profiling of Bauhinia variegata major phytoconstituents with computational identification of potential lead inhibitors of SARS-CoV-2 M

More-Adate, Pallavi / Lokhande, Kiran Bharat / Swamy, K Venkateswara / Nagar, Shuchi / Baheti, Akshay

Computers in biology and medicine

2022 Volume 147, Page(s) 105679

Abstract: Severe acute respiratory syndrome coronavirus 2 was originally identified in Wuhan city of China in December 2019 and it spread rapidly throughout the globe, causing a threat to human life. Since targeted therapies are deficient, scientists all over the ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 was originally identified in Wuhan city of China in December 2019 and it spread rapidly throughout the globe, causing a threat to human life. Since targeted therapies are deficient, scientists all over the world have an opportunity to develop novel drug therapies to combat COVID-19. After the declaration of a global medical emergency, it was established that the Food and Drug Administration (FDA) could permit the use of emergency testing, treatments, and vaccines to decrease suffering, and loss of life, and restore the nation's health and security. The FDA has approved the use of remdesivir and its analogs as an antiviral medication, to treat COVID-19. The primary protease of SARS-CoV-2, which has the potential to regulate coronavirus proliferation, has been a viable target for the discovery of medicines against SARS-CoV-2. The present research deals with the in silico technique to screen phytocompounds from a traditional medicinal plant, Bauhinia variegata for potential inhibitors of the SARS-CoV-2 main protease. Dried leaves of the plant B. variegata were used to prepare aqueous and methanol extract and the constituents were analyzed using the GC-MS technique. A total of 57 compounds were retrieved from the aqueous and methanol extract analysis. Among these, three lead compounds (2,5 dimethyl 1-H Pyrrole, 2,3 diphenyl cyclopropyl methyl phenyl sulphoxide, and Benzonitrile m phenethyl) were shown to have the highest binding affinity (-5.719 to -5.580 kcal/mol) towards SARS-CoV-2 M
MeSH term(s)	Bauhinia/metabolism ; COVID-19/drug therapy ; Gas Chromatography-Mass Spectrometry ; Humans ; Methanol ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Protease Inhibitors ; Viral Nonstructural Proteins ; Methanol (Y4S76JWI15)
Language	English
Publishing date	2022-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105679
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Article: Free Fatty Acids from Cow Urine DMSO Fraction Induce Cell Death in Breast Cancer Cells without Affecting Normal GMSCs.

Raj, Ajay Kumar / Upadhyay, Vidhi / Lokhande, Kiran Bharat / Swamy, K Venkateswara / Bhonde, Ramesh Ramchandra / Sarode, Sachin C / Sharma, Nilesh Kumar

Biomedicines

2023 Volume 11, Issue 3

Abstract: Objective: The objective of this study was to explore the biological relevance of free fatty acids derived from cow urine DMSO fraction (CUDF) by employing in vitro and in silico approaches.: Background: Metabolic heterogeneity at the intra- and ... ...

Abstract	Objective: The objective of this study was to explore the biological relevance of free fatty acids derived from cow urine DMSO fraction (CUDF) by employing in vitro and in silico approaches. Background: Metabolic heterogeneity at the intra- and intercellular levels contributes to the metabolic plasticity of cancer cells during drug-induced response. Free fatty acid (FFA) availability at intra- and intercellular levels is related to tumor heterogeneity at interpatient and xeno-heterogeneity levels. Methods: We collected fresh urine from healthy cows and subjected it to fractionation in DMSO using drying, vortexing, and centrifugation. Finally, the sterile filtrate of cow urine DMSO fraction (CUDF) was evaluated for antiproliferative and proapoptotic effects in MCF-7 and ZR-75-1 breast cancer cells using routine cell-based assays. Intracellular metabolites were studied with the help of a novel in-house vertical tube gel electrophoresis (VTGE) method to reveal the nature of CUDF components in MCF-7 cells. Identified intracellular FFAs were studied for their molecular interactions with targeted receptor histone deacetylase (HDAC) using molecular docking and molecular dynamics (MD) simulations. Results: CUDF showed a significant reduction in cell viability and cell death in MCF-7 and ZR-75-1 breast cancer cells. Interestingly, FFAs tetracosanedioic acid, 13Z-docosenoic acid (erucic acid), nervonic acid, 3-hydroxy-tetradecanoic acid, and 3-hydroxcapric acid were found inside the treated MCF-7 cancer cells. These FFAs, including tetracosanedioic acid, indicated a specific affinity to HDAC at their inhibitory sites, similar to trichostatin A, a known inhibitor. Conclusions: This study reports on FFAs derived from CUDF as potential antiproliferative and pro-cell death agents against breast cancer cells. MD simulations hinted at tetracosanedioic acid and other FFAs as inhibitors of HDAC that could explain the observed effects of FFAs in cancer cells.
Language	English
Publishing date	2023-03-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines11030889
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Article ; Online: Design, Synthesis, and Biological Evaluation of Novel Quercetin Derivatives as PPAR-γ Partial Agonists by Modulating Epithelial-Mesenchymal Transition in Lung Cancer Metastasis.

Ballav, Sangeeta / Bhosale, Mrinalini / Lokhande, Kiran Bharat / Paul, Manash K / Padhye, Subhash / Swamy, K Venkateswara / Ranjan, Amit / Basu, Soumya

Advanced biology

2023 Volume 7, Issue 10, Page(s) e2300036

Abstract: Epithelial-to-mesenchymal transition (EMT) is responsible for driving metastasis of multiple cancer types including lung cancer. Peroxisome proliferator-activated receptor (PPAR)-γ, a ligand-activated transcription factor, controls expression of variety ... ...

Abstract	Epithelial-to-mesenchymal transition (EMT) is responsible for driving metastasis of multiple cancer types including lung cancer. Peroxisome proliferator-activated receptor (PPAR)-γ, a ligand-activated transcription factor, controls expression of variety of genes involved in EMT. Although several synthetic compounds act as potent full agonists for PPAR-γ, their long term application is restricted due to serious adverse effects. Therefore, partial agonists involving reduced and balanced PPAR-γ activity are more effective and valued. A previous study discerned the efficacy of quercetin and its derivatives to attain favorable stabilization with PPAR-γ. Here this work is extended by synthesizing five novel quercetin derivatives (QDs) namely thiosemicarbazone (QUETSC)) and hydrazones (quercetin isonicotinic acid hydrazone (QUEINH), quercetin nicotinic acid hydrazone (QUENH), quercetin 2-furoic hydrazone (QUE2FH), and quercetin salicyl hydrazone (QUESH)) and their effects are analyzed in modulating EMT in lung cancer cell lines via PPAR-γ partial activation. QDs-treated A549 cells diminish cell proliferation strongly at nanomolar concentration compared to NCI-H460 cells. Of the five screened derivatives, QUETSC, QUE2FH, and QUESH exhibit the property of partial activation as compared to the overexpressive level of rosiglitazone. Consistently, these QDs also suppress EMT process by markedly downregulating the levels of mesenchymal markers (Snail, Slug, and zinc finger E-box binding homeobox 1) and concomitant upregulation of epithelial marker (E-cadherin).
Language	English
Publishing date	2023-04-05
Publishing country	Germany
Document type	Journal Article
ISSN	2701-0198
ISSN (online)	2701-0198
DOI	10.1002/adbi.202300036
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Article ; Online: Terpenoid phytocompounds from mangrove plant Xylocarpus moluccensis as possible inhibitors against SARS-CoV-2: In silico strategy.

Lokhande, Kiran Bharat / Kale, Arti / Shahakar, Bhagyashree / Shrivastava, Ashish / Nawani, Neelu / Swamy, K Venkateswara / Singh, Ashutosh / Pawar, Sarika Vishnu

Computational biology and chemistry

2023 Volume 106, Page(s) 107912

Abstract: COVID-19 shook the world during the pandemic, where the climax it reached was vaccine manufacturing at an unfathomable pace. Alternative promising solutions to prevent infection from SARS-CoV-2 and its variants will remain crucial in the years to come. ... ...

Abstract	COVID-19 shook the world during the pandemic, where the climax it reached was vaccine manufacturing at an unfathomable pace. Alternative promising solutions to prevent infection from SARS-CoV-2 and its variants will remain crucial in the years to come. Due to its key role in viral replication, the major protease (Mpro) enzyme of SARS-CoV-2 can be an attractive therapeutic target. In the present work, natural terpenoids from mangrove medicinal plant Xylocarpus moluccensis (Lam.) M. Roem. were screened using computational methods for inhibition of Mpro protein. Out of sixty-seven terpenoids, Angolensic acid methyl ester, Moluccensin V, Thaixylomolin F, Godavarin J, and Xylomexicanolide A were shortlisted based on their docking scores and interaction affinities (- 13.502 to - 15.52 kcal/mol). The efficacy was validated by the 100 ns molecular dynamics study. Lead terpenoids were within the acceptable range of RMSD and RMSF with a mean value of 2.5 Å and 1.5 Å, respectively indicating that they bound tightly within Mpro and there was minimal fluctuation and stability of Mpro upon binding of these terpenoids. The utmost favorable binding strengths as calculated by MM-GBSA, were of Angolensic acid methyl ester and Moluccensin V with binding free energies (ΔG
MeSH term(s)	Computer Simulation ; Magnoliopsida/chemistry ; Terpenes/chemistry ; SARS-CoV-2 ; Coronavirus 3C Proteases/antagonists & inhibitors ; Molecular Docking Simulation ; COVID-19 Drug Treatment ; Antiviral Agents/chemistry ; Thermodynamics
Chemical Substances	Terpenes ; Coronavirus 3C Proteases (EC 3.4.22.28) ; Antiviral Agents
Language	English
Publishing date	2023-07-06
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2023.107912
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