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  1. Article ; Online: Seven-membered ring nucleobases as inhibitors of human cytidine deaminase and APOBEC3A.

    Kurup, Harikrishnan M / Kvach, Maksim V / Harjes, Stefan / Jameson, Geoffrey B / Harjes, Elena / Filichev, Vyacheslav V

    Organic & biomolecular chemistry

    2023  Volume 21, Issue 24, Page(s) 5117–5128

    Abstract: The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis ... ...

    Abstract The APOBEC3 (APOBEC3A-H) enzyme family as a part of the human innate immune system deaminates cytosine to uracil in single-stranded DNA (ssDNA) and thereby prevents the spread of pathogenic genetic information. However, APOBEC3-induced mutagenesis promotes viral and cancer evolution, thus enabling the progression of diseases and development of drug resistance. Therefore, APOBEC3 inhibition offers a possibility to complement existing antiviral and anticancer therapies and prevent the emergence of drug resistance, thus making such therapies effective for longer periods of time. Here, we synthesised nucleosides containing seven-membered nucleobases based on azepinone and compared their inhibitory potential against human cytidine deaminase (hCDA) and APOBEC3A with previously described 2'-deoxyzebularine (dZ) and 5-fluoro-2'-deoxyzebularine (FdZ). The nanomolar inhibitor of wild-type APOBEC3A was obtained by the incorporation of 1,3,4,7-tetrahydro-2
    MeSH term(s) Humans ; Proteins/metabolism ; Cytidine Deaminase ; Mutagenesis ; Neoplasms/genetics ; Minor Histocompatibility Antigens
    Chemical Substances APOBEC3A protein, human (EC 3.5.4.5) ; Proteins ; Cytidine Deaminase (EC 3.5.4.5) ; APOBEC3B protein, human (EC 3.5.4.5) ; Minor Histocompatibility Antigens
    Language English
    Publishing date 2023-06-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2097583-1
    ISSN 1477-0539 ; 1477-0520
    ISSN (online) 1477-0539
    ISSN 1477-0520
    DOI 10.1039/d3ob00392b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A.

    Kurup, Harikrishnan M / Kvach, Maksim V / Harjes, Stefan / Barzak, Fareeda M / Jameson, Geoffrey B / Harjes, Elena / Filichev, Vyacheslav V

    Biochemistry

    2022  Volume 61, Issue 22, Page(s) 2568–2578

    Abstract: Drug resistance is a major problem associated with anticancer chemo- and immunotherapies. Recent advances in the understanding of resistance mechanisms have revealed that enzymes of the APOBEC3 (A3) family contribute to the development of drug resistance ...

    Abstract Drug resistance is a major problem associated with anticancer chemo- and immunotherapies. Recent advances in the understanding of resistance mechanisms have revealed that enzymes of the APOBEC3 (A3) family contribute to the development of drug resistance in multiple cancers. A3 enzymes are polynucleotide cytidine deaminases that convert cytosine to uracil (C→U) in single-stranded DNA (ssDNA) and in this way protect humans against viruses and mobile retroelements. On the other hand, cancer cells use A3s, especially A3A and A3B, to mutate human DNA, and thus by increasing rates of evolution, cancer cells escape adaptive immune responses and resist drugs. However, as A3A and A3B are non-essential for primary metabolism, their inhibition opens up a strategy to augment existing anticancer therapies and suppress cancer evolution. To test our hypothesis that pre-shaped ssDNA mimicking the
    MeSH term(s) Humans ; Oligonucleotides ; Cytidine Deaminase/metabolism ; DNA, Single-Stranded ; Cytidine/chemistry ; Cytosine
    Chemical Substances APOBEC3A protein, human (EC 3.5.4.5) ; Oligonucleotides ; Cytidine Deaminase (EC 3.5.4.5) ; DNA, Single-Stranded ; Cytidine (5CSZ8459RP) ; Cytosine (8J337D1HZY)
    Language English
    Publishing date 2022-10-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.2c00449
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Cyclic peptides bearing the d-Phe-2-Abz turn motif: Structural characterization and antimicrobial potential.

    Varnava, Kyriakos G / Edwards, Patrick J B / Cameron, Alan J / Harjes, Elena / Sarojini, Vijayalekshmi

    Journal of peptide science : an official publication of the European Peptide Society

    2020  Volume 27, Issue 2, Page(s) e3291

    Abstract: The effect on secondary structure and antimicrobial activity of introducing different cyclic constraints in linear β-hairpin antimicrobial peptides has been investigated with the intention of generating cyclic β sheets as promising antimicrobials with ... ...

    Abstract The effect on secondary structure and antimicrobial activity of introducing different cyclic constraints in linear β-hairpin antimicrobial peptides has been investigated with the intention of generating cyclic β sheets as promising antimicrobials with improved therapeutic potential. The linear peptides were cyclized head to tail either directly or after the addition of either a second turn motif or a disulfide bridge. The propensity of these peptides to adopt a cyclic β-sheet structure has been correlated to their antibacterial activity. All cyclic peptides showed enhanced activity, compared with their linear counterparts against methicillin-resistant Staphylococcus aureus. Scanning electron microscopy and transmission electron microscopy studies showed that this family kills bacteria through membrane lysis. The peptide that showed the best efficacy against all strains (exhibiting nanomolar activity), while retaining low haemolysis, bears two symmetrical, homochiral d-phe-2-Abz-d-ala turns and adopted a flexible structure. Its twin peptide that bears heterochiral turns (one with d-ala and one with L-Ala) showed reduced antibacterial activity and higher percentage of haemolysis. Circular dichroism and nuclear magnetic resonance spectroscopy indicate that heterochirality in the two turns leads to oligomerization of the peptide at higher concentrations, stabilizing the β-sheet secondary structure. More rigid secondary structure is associated with lower activity against bacteria and loss of selectivity.
    Language English
    Publishing date 2020-12-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 1234416-3
    ISSN 1099-1387 ; 1075-2617
    ISSN (online) 1099-1387
    ISSN 1075-2617
    DOI 10.1002/psc.3291
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.

    Harjes, Stefan / Kurup, Harikrishnan M / Rieffer, Amanda E / Bayarjargal, Maitsetseg / Filitcheva, Jana / Su, Yongdong / Hale, Tracy K / Filichev, Vyacheslav V / Harjes, Elena / Harris, Reuben S / Jameson, Geoffrey B

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6382

    Abstract: The normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA ... ...

    Abstract The normally antiviral enzyme APOBEC3A is an endogenous mutagen in human cancer. Its single-stranded DNA C-to-U editing activity results in multiple mutagenic outcomes including signature single-base substitution mutations (isolated and clustered), DNA breakage, and larger-scale chromosomal aberrations. APOBEC3A inhibitors may therefore comprise a unique class of anti-cancer agents that work by blocking mutagenesis, slowing tumor evolvability, and preventing detrimental outcomes such as drug resistance and metastasis. Here we reveal the structural basis of competitive inhibition of wildtype APOBEC3A by hairpin DNA bearing 2'-deoxy-5-fluorozebularine in place of the cytidine in the TC substrate motif that is part of a 3-nucleotide loop. In addition, the structural basis of APOBEC3A's preference for YTCD motifs (Y = T, C; D = A, G, T) is explained. The nuclease-resistant phosphorothioated derivatives of these inhibitors have nanomolar potency in vitro and block APOBEC3A activity in human cells. These inhibitors may be useful probes for studying APOBEC3A activity in cellular systems and leading toward, potentially as conjuvants, next-generation, combinatorial anti-mutator and anti-cancer therapies.
    MeSH term(s) Humans ; Proteins/chemistry ; Mutagenesis ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/pathology ; DNA ; Cytidine Deaminase/genetics ; Cytidine Deaminase/chemistry
    Chemical Substances APOBEC3A protein, human (EC 3.5.4.5) ; Proteins ; DNA (9007-49-2) ; Cytidine Deaminase (EC 3.5.4.5)
    Language English
    Publishing date 2023-10-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42174-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Structure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A.

    Harjes, Stefan / Kurup, Harikrishnan M / Rieffer, Amanda E / Bayaijargal, Maitsetseg / Filitcheva, Jana / Su, Yongdong / Hale, Tracy K / Filichev, Vyacheslav V / Harjes, Elena / Harris, Reuben S / Jameson, Geoffrey B

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The normally antiviral enzyme ... ...

    Abstract The normally antiviral enzyme APOBEC3A
    Language English
    Publishing date 2023-02-17
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.17.528918
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: NMR Shows Why a Small Chemical Change Almost Abolishes the Antimicrobial Activity of Glycocin F.

    Harjes, Elena / Edwards, Patrick J B / Bisset, Sean W / Patchett, Mark L / Jameson, Geoffrey B / Yang, Sung-Hyun / Navo, Claudio D / Harris, Paul W R / Brimble, Margaret A / Norris, Gillian E

    Biochemistry

    2023  Volume 62, Issue 17, Page(s) 2669–2676

    Abstract: Glycocin F (GccF), a ribosomally synthesized, post-translationally modified peptide secreted ... ...

    Abstract Glycocin F (GccF), a ribosomally synthesized, post-translationally modified peptide secreted by
    MeSH term(s) Peptides/chemistry ; Magnetic Resonance Spectroscopy ; Magnetic Resonance Imaging ; Protein Structure, Secondary ; Anti-Infective Agents/pharmacology
    Chemical Substances Peptides ; Anti-Infective Agents
    Language English
    Publishing date 2023-08-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00197
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.

    Cameron, Alan J / Edwards, Patrick J B / Harjes, Elena / Sarojini, Vijayalekshmi

    Journal of medicinal chemistry

    2017  Volume 60, Issue 23, Page(s) 9565–9574

    Abstract: The d-Phe-Pro β-turn of the cyclic β-hairpin antimicrobial decapeptide tyrocidine A, (Tyrc A) was substituted with the d-Phe-2-aminobenzoic acid (2-Abz) motif in a synthetic analogue (1). The NMR structure of 1 demonstrated that compound 1 retained the β- ...

    Abstract The d-Phe-Pro β-turn of the cyclic β-hairpin antimicrobial decapeptide tyrocidine A, (Tyrc A) was substituted with the d-Phe-2-aminobenzoic acid (2-Abz) motif in a synthetic analogue (1). The NMR structure of 1 demonstrated that compound 1 retained the β-hairpin structure of Tyrc A with additional planarity, resulting in approximately 30-fold reduced hemolysis than Tyrc A. Although antibacterial activity was partially compromised, a single Gln to Lys substitution (2) restored activity equivalent to Tyrc A against S. aureus, enhanced activity against two Gram negative strains and maintained the reduced hemeloysis of 1. Analysis by transmission electron microscopy (TEM) suggested a membrane lytic mechanism of action for these peptides. Compound 2 also exhibits nanomolar antifungal activity in synergy with amphotericin B. The d-Phe-2-Abz turn may serve as a tool for the synthesis of structurally predictable β-hairpin libraries. Unlike traditional β-turn motifs such as d-Pro-Gly, both the 2-Abz and d-Phe rings may be further functionalized.
    MeSH term(s) Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/chemistry ; Anti-Infective Agents/pharmacology ; Antifungal Agents/chemistry ; Antifungal Agents/pharmacology ; Bacteria/drug effects ; Bacterial Infections/drug therapy ; Candida albicans/drug effects ; Candidiasis/drug therapy ; Escherichia coli/drug effects ; Hemolysis/drug effects ; Humans ; Models, Molecular ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus/drug effects ; Tyrocidine/analogs & derivatives ; Tyrocidine/pharmacology
    Chemical Substances Anti-Bacterial Agents ; Anti-Infective Agents ; Antifungal Agents ; Tyrocidine
    Language English
    Publishing date 2017-11-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218133-2
    ISSN 1520-4804 ; 0022-2623
    ISSN (online) 1520-4804
    ISSN 0022-2623
    DOI 10.1021/acs.jmedchem.7b00953
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity.

    Barzak, Fareeda M / Ryan, Timothy M / Mohammadzadeh, Nazanin / Harjes, Stefan / Kvach, Maksim V / Kurup, Harikrishnan M / Krause, Kurt L / Chelico, Linda / Filichev, Vyacheslav V / Harjes, Elena / Jameson, Geoffrey B

    Viruses

    2022  Volume 14, Issue 9

    Abstract: APOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although ... ...

    Abstract APOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although X-ray single-crystal structures of individual catalytic domains of APOBEC3G with ssDNA as well as full-length APOBEC3G have been solved recently, there is little structural information available about ssDNA interaction with the full-length APOBEC3G or any other two-domain APOBEC3. Here, we investigated the solution-state structures of full-length APOBEC3G with and without a 40-mer modified ssDNA by small-angle X-ray scattering (SAXS), using size-exclusion chromatography (SEC) immediately prior to irradiation to effect partial separation of multi-component mixtures. To prevent cytosine deamination, the target 2'-deoxycytidine embedded in 40-mer ssDNA was replaced by 2'-deoxyzebularine, which is known to inhibit APOBEC3A, APOBEC3B and APOBEC3G when incorporated into short ssDNA oligomers. Full-length APOBEC3G without ssDNA comprised multiple multimeric species, of which tetramer was the most scattering species. The structure of the tetramer was elucidated. Dimeric interfaces significantly occlude the DNA-binding interface, whereas the tetrameric interface does not. This explains why dimers completely disappeared, and monomeric protein species became dominant, when ssDNA was added. Data analysis of the monomeric species revealed a full-length APOBEC3G-ssDNA complex that gives insight into the observed "jumping" behavior revealed in studies of enzyme processivity. This solution-state SAXS study provides the first structural model of ssDNA binding both domains of APOBEC3G and provides data to guide further structural and enzymatic work on APOBEC3-ssDNA complexes.
    MeSH term(s) APOBEC-3G Deaminase/metabolism ; Cytidine Deaminase ; Cytosine ; DNA, Single-Stranded ; Deoxycytidine ; Polynucleotides ; Protein Binding ; Proteins ; RNA/metabolism ; Retroelements ; Scattering, Small Angle ; Uracil ; X-Ray Diffraction ; X-Rays
    Chemical Substances DNA, Single-Stranded ; Polynucleotides ; Proteins ; Retroelements ; Deoxycytidine (0W860991D6) ; Uracil (56HH86ZVCT) ; RNA (63231-63-0) ; Cytosine (8J337D1HZY) ; APOBEC-3G Deaminase (EC 3.5.4.5) ; APOBEC3A protein, human (EC 3.5.4.5) ; Cytidine Deaminase (EC 3.5.4.5)
    Language English
    Publishing date 2022-09-06
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14091974
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Small-Angle X-ray Scattering (SAXS) Measurements of APOBEC3G Provide Structural Basis for Binding of Single-Stranded DNA and Processivity

    Barzak, Fareeda M. / Ryan, Timothy M. / Mohammadzadeh, Nazanin / Harjes, Stefan / Kvach, Maksim V. / Kurup, Harikrishnan M. / Krause, Kurt L. / Chelico, Linda / Filichev, Vyacheslav V. / Harjes, Elena / Jameson, Geoffrey B.

    Viruses. 2022 Sept. 06, v. 14, no. 9

    2022  

    Abstract: APOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although ... ...

    Abstract APOBEC3 enzymes are polynucleotide deaminases, converting cytosine to uracil on single-stranded DNA (ssDNA) and RNA as part of the innate immune response against viruses and retrotransposons. APOBEC3G is a two-domain protein that restricts HIV. Although X-ray single-crystal structures of individual catalytic domains of APOBEC3G with ssDNA as well as full-length APOBEC3G have been solved recently, there is little structural information available about ssDNA interaction with the full-length APOBEC3G or any other two-domain APOBEC3. Here, we investigated the solution-state structures of full-length APOBEC3G with and without a 40-mer modified ssDNA by small-angle X-ray scattering (SAXS), using size-exclusion chromatography (SEC) immediately prior to irradiation to effect partial separation of multi-component mixtures. To prevent cytosine deamination, the target 2′-deoxycytidine embedded in 40-mer ssDNA was replaced by 2′-deoxyzebularine, which is known to inhibit APOBEC3A, APOBEC3B and APOBEC3G when incorporated into short ssDNA oligomers. Full-length APOBEC3G without ssDNA comprised multiple multimeric species, of which tetramer was the most scattering species. The structure of the tetramer was elucidated. Dimeric interfaces significantly occlude the DNA-binding interface, whereas the tetrameric interface does not. This explains why dimers completely disappeared, and monomeric protein species became dominant, when ssDNA was added. Data analysis of the monomeric species revealed a full-length APOBEC3G–ssDNA complex that gives insight into the observed “jumping” behavior revealed in studies of enzyme processivity. This solution-state SAXS study provides the first structural model of ssDNA binding both domains of APOBEC3G and provides data to guide further structural and enzymatic work on APOBEC3–ssDNA complexes.
    Keywords RNA ; X-radiation ; cytosine ; deamination ; enzymes ; gel chromatography ; innate immunity ; irradiation ; models ; retrotransposons ; single-stranded DNA ; small-angle X-ray scattering ; uracil
    Language English
    Dates of publication 2022-0906
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v14091974
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Acyclic peptides incorporating the d-Phe-2-Abz turn motif: Investigations on antimicrobial activity and propensity to adopt β-hairpin conformations.

    Cameron, Alan J / Varnava, Kyriakos G / Edwards, Patrick J B / Harjes, Elena / Sarojini, Vijayalekshmi

    Journal of peptide science : an official publication of the European Peptide Society

    2018  Volume 24, Issue 8-9, Page(s) e3094

    Abstract: Three linear peptides incorporating d-Phe-2-Abz as the turn motif are reported. Peptide 1, a hydrophobic β-hairpin, served as a proof of principle for the design strategy with both NMR and CD spectra strongly suggesting a β-hairpin conformation. Peptides ...

    Abstract Three linear peptides incorporating d-Phe-2-Abz as the turn motif are reported. Peptide 1, a hydrophobic β-hairpin, served as a proof of principle for the design strategy with both NMR and CD spectra strongly suggesting a β-hairpin conformation. Peptides 2 and 3, designed as amphipathic antimicrobials, exhibited broad spectrum antimicrobial activity, with potency in the nanomolar range against Staphylococcus aureus. Both compounds possess a high degree of selectivity, proving non-haemolytic at concentrations 500 to 800 times higher than their respective minimal inhibitory concentrations (MICs) against S. aureus. Peptide 2 induced cell membrane and cell wall disintegration in both S. aureus and Pseudomonas aeruginosa as observed by transmission electron microscopy. Peptide 2 also demonstrated moderate antifungal activity against Candida albicans with an MIC of 50 μM. Synergism was observed with sub-MIC levels of amphotericin B (AmB), leading to nanomolar MICs against C. albicans for peptide 2. Based on circular dichroism spectra, both peptides 2 and 3 appear to exist as a mixture of conformers with the β-hairpin as a minor conformer in aqueous solution, and a slight increase in hairpin population in 50% trifluoroethanol, which was more pronounced for peptide 3. NMR spectra of peptide 2 in a 1:1 CD
    MeSH term(s) Aminobenzoates/chemical synthesis ; Aminobenzoates/chemistry ; Aminobenzoates/pharmacology ; Anti-Bacterial Agents/chemical synthesis ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Antifungal Agents/chemical synthesis ; Antifungal Agents/chemistry ; Antifungal Agents/pharmacology ; Candida albicans/drug effects ; Microbial Sensitivity Tests ; Oligopeptides/chemistry ; Oligopeptides/isolation & purification ; Oligopeptides/pharmacology ; Protein Conformation ; Staphylococcus aureus/drug effects
    Chemical Substances Aminobenzoates ; Anti-Bacterial Agents ; Antifungal Agents ; Oligopeptides
    Language English
    Publishing date 2018-06-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 1234416-3
    ISSN 1099-1387 ; 1075-2617
    ISSN (online) 1099-1387
    ISSN 1075-2617
    DOI 10.1002/psc.3094
    Database MEDical Literature Analysis and Retrieval System OnLINE

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