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Functional Proteomics for Biomarker and Drug Discovery

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Chemical Biology".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 3440

Special Issue Editors

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Guest Editor
CSIC-USAL, Instituto de Biologia Molecular y Celular del Cancer de Salamanca (IBMCC), Salamanca, Spain
Interests: immuno-oncology; immunoproteomics; drug discovery; cell immunogenic death; cell signaling pathways; multi-omics analysis; functional proteomics; translational proteomics; nanomedicine; drug–polymer conjugates; nanomaterials

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Guest Editor
Department of Pharmaceutical Sciences: Pharmaceutical Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, 37007 Salamanca, Spain
Interests: medicinal chemistry; organic synthesis; drug development; natural products; hybridization; antitumoral; immunotherapy
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Special Issue Information

Dear Colleagues,

Once the human genome has largely been sequenced, one of the most important pursuits is to understand the function of the proteins it encodes. Despite the immense progress in molecular biology and genetic, only a small fraction of the proteome is understood at the biochemical level. Systems biology and proteomics strive to create detailed predictive models for molecular pathways based upon the quantitative behavior of proteins. Understanding these dynamics networks provides clues into the consequences of aberrant interactions and why they lead to diseases such as cancer, and it could be source of biomarkers or targeted proteins for novel drug design and development.

However, collecting quantitative biochemical data on protein behavior at a high scale has been dauting. Thus, methods capable of collecting quantitative data at hight-throughput level are requiered to determine differential protein profiles which could represent novel targets for new drugs or development of novel therapies.

Furthermore, the intracellular signaling pathways triggered when drugs interact with their therapeutic targets are one of the most accurate strategies to find the mechanism of action of any pharmaceutical entity. Thanks to the enormous amount of information provided by functional proteomics, the entire pharmacological profile can be established and the structure–activity relationship (SAR) of the drugs could be more precisely determined.

Hence, functional proteomics is one of the approaches which could determine targeted proteins as potential candidates for biomarkers and novel drug design.

The aim of this Special Issue is to attract contributions on all aspects of functional proteomics and pharmaceutical synthesis, with a special emphasis on recent/novel technologies and multipronged strategies that make them able to address biological problems that have not yet been faced.

Dr. Manuel Fuentes
Dr. Angela-Patricia Hernández
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • proteomics
  • drug discovery
  • biomarkers
  • drug design
  • cell signaling pathway

Published Papers (1 paper)

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17 pages, 1276 KiB  
Functional Analysis of Autoantibody Signatures in Rheumatoid Arthritis
by Lisa Milchram, Anita Fischer, Jasmin Huber, Regina Soldo, Daniela Sieghart, Klemens Vierlinger, Stephan Blüml, Günter Steiner and Andreas Weinhäusel
Molecules 2022, 27(4), 1452; - 21 Feb 2022
Cited by 3 | Viewed by 2460
For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced [...] Read more.
For the identification of antigenic protein biomarkers for rheumatoid arthritis (RA), we conducted IgG profiling on high density protein microarrays. Plasma IgG of 96 human samples (healthy controls, osteoarthritis, seropositive and seronegative RA, n = 24 each) and time-series plasma of a pristane-induced arthritis (PIA) rat model (n = 24 total) were probed on AIT’s 16k protein microarray. To investigate the analogy of underlying disease pathways, differential reactivity analysis was conducted. A total of n = 602 differentially reactive antigens (DIRAGs) at a significance cutoff of p < 0.05 were identified between seropositive and seronegative RA for the human samples. Correlation with the clinical disease activity index revealed an inverse correlation of antibodies against self-proteins found in pathways relevant for antigen presentation and immune regulation. The PIA model showed n = 1291 significant DIRAGs within acute disease. Significant DIRAGs for (I) seropositive, (II) seronegative and (III) PIA were subjected to the Reactome pathway browser which also revealed pathways relevant for antigen presentation and immune regulation; of these, seven overlapping pathways had high significance. We therefore conclude that the PIA model reflects the biological similarities of the disease pathogenesis. Our data show that protein array analysis can elucidate biological differences and pathways relevant in disease as well be a useful additional layer of omics information. Full article
(This article belongs to the Special Issue Functional Proteomics for Biomarker and Drug Discovery)
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