{"entity": "researcher", "timestamp": "2026-09-23T16:43:19.343Z", "family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "affiliations": ["Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden.", "Pelago Bioscience AB, 171 48, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d"}}, "publications": [{"entity": "publication", "iuid": "5ba5804c476b43ef902981a147b9c4d2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5ba5804c476b43ef902981a147b9c4d2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5ba5804c476b43ef902981a147b9c4d2"}}, "title": "Role of Structural Modifications in Peptidomimetic Compounds as Potential Antimicrobial Agents against Staphylococcus aureus and Streptococcus pyogenes: Balancing Bioavailability, Safety, and Antimicrobial Activity.", "authors": [{"family": "Dzier\u017cy\u0144ska", "given": "Maria", "initials": "M", "orcid": "0000-0003-0861-2514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92354a2362e643c7ba76b1fc32285e00.json"}}, {"family": "Sawicka", "given": "Justyna", "initials": "J", "orcid": "0000-0002-1506-3202", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0eb17051ec614239a03f41da2d57baa6.json"}}, {"family": "\u0141ada", "given": "Katarzyna", "initials": "K"}, {"family": "Gajewicz-Skretna", "given": "Agnieszka", "initials": "A", "orcid": "0000-0001-7702-210X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6ec9be6c660496bb86ef4946ffa1e83.json"}}, {"family": "Deptu\u0142a", "given": "Milena", "initials": "M"}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.json"}}, {"family": "Pogorzelska", "given": "Aneta", "initials": "A"}, {"family": "Grubb", "given": "Anders", "initials": "A", "orcid": "0000-0002-0125-3662", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/49f08a18d2164b66b45a00a599ff637c.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3f9910c1ff434c8056bdecf537e9ef.json"}}, {"family": "Piku\u0142a", "given": "Micha\u0142", "initials": "M", "orcid": "0000-0001-7751-9781", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/35018507ff4e4208beaaccc9099713bf.json"}}, {"family": "Kasprzykowski", "given": "Franciszek", "initials": "F"}, {"family": "Rodziewicz-Motowid\u0142o", "given": "Sylwia", "initials": "S", "orcid": "0000-0002-4471-5951", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9153d8117d734517a04603c90d855715.json"}}], "type": "journal article", "published": "2025-08-05", "journal": {"title": "ACS Omega", "issn": "2470-1343", "volume": "10", "issue": "30", "pages": "33435-33460", "issn-l": "2470-1343"}, "abstract": "The emergence of drug-resistant Gram-positive pathogens, particularlyStaphylococcus aureusandStreptococcus pyogenes, has driven the need for novel antimicrobial agents. This study explores 21 newly synthesized peptidomimetic analogues of cystatin C N-terminal fragment, designed to enhance bioactivity, solubility, and safety. These compounds were evaluated for antimicrobial potency, cytotoxicity, pro-proliferative effects, and pharmacokinetic properties. Key findings indicate that analogues A-192 and A-164 exhibited the strongest antimicrobial effects against S. aureus and S. pyogenes. Most compounds were inactive against Gram-negative bacteria. Cytotoxicity profiling identified several derivatives with low to moderate toxicity and favorable pro-proliferative effects at specific concentrations. Stability tests confirmed the robustness in aqueous and plasma environments. Computational absorption, distribution, metabolism, excretion, and toxicity (ADMET) modeling revealed low gastrointestinal absorption, but favorable parameters for topical applications. Exploratory analyses (principal component analysis (PCA) and two-way hierarchical cluster analysis (2D-HCA)) linked structural features\ue5f8such as branching, molecular weight, and solubility, with biological activity. These results support the potential of structurally optimized peptidomimetics as targeted, topical therapeutics for Gram-positive infections and provide a rationale for further preclinical development.", "doi": "10.1021/acsomega.5c03775", "pmid": "40787370", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12332667"}], "notes": [], "created": "2026-09-23T15:49:20.729Z", "modified": "2026-09-23T15:49:20.996Z"}, {"entity": "publication", "iuid": "3ea25ac45a834483bdc7665a73b27f41", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3ea25ac45a834483bdc7665a73b27f41.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3ea25ac45a834483bdc7665a73b27f41"}}, "title": "Proteomics-Compatible Fourier Transform Isotopic Ratio Mass Spectrometry of Polypeptides.", "authors": [{"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Chernobrovkin", "given": "Alexey L", "initials": "AL", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.json"}}, {"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Zhang", "given": "Xuepei", "initials": "X"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.json"}}, {"family": "Makarov", "given": "Alexander A", "initials": "AA", "orcid": "0000-0002-7046-6709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/73e01f8c0f8641d894824a878ffcb8ff.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3f9910c1ff434c8056bdecf537e9ef.json"}}], "type": "journal article", "published": "2022-11-01", "journal": {"title": "Anal. Chem.", "issn": "1520-6882", "volume": "94", "issue": "43", "pages": "15048-15056", "issn-l": "0003-2700"}, "abstract": "Measuring the relative abundances of heavy stable isotopes of the elements C, H, N, and O in proteins is of interest in environmental science, archeology, zoology, medicine, and other fields. The isotopic abundance measurements of the fine structure of immonium ions with ultrahigh resolution mass spectrometry obtained in gas-phase fragmentation of polypeptides have previously uncovered anomalous deuterium enrichment in (hydroxy)proline of bone collagen in marine mammals. Here, we provide a detailed description and validation of this approach and demonstrate per mil-range precision of isotopic ratio measurements in aliphatic residues from proteins and cell lysates. The analysis consists of proteomics-type experiment demanding sub-microgram amounts of a protein sample and providing concomitantly protein sequence data allowing one to verify sample purity and establish its identity. A novel software tool protein amino acid-resolved isotopic ratio mass spectrometry (PAIR-MS) is presented for extracting isotopic ratio data from the raw data files acquired on an Orbitrap mass spectrometer.", "doi": "10.1021/acs.analchem.2c03119", "pmid": "36251694", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9631351"}], "notes": [], "created": "2026-09-23T11:15:36.689Z", "modified": "2026-09-23T11:15:36.865Z"}, {"entity": "publication", "iuid": "c28fb876d1334187af97136f2fff26d0", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c28fb876d1334187af97136f2fff26d0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c28fb876d1334187af97136f2fff26d0"}}, "title": "System-wide identification and prioritization of enzyme substrates by thermal analysis.", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Beusch", "given": "Christian M", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbb4771768354080ab5292c96fee0812.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4cf83f2cf534d7eb308dab89d6460e2.json"}}, {"family": "Wells", "given": "Juan Astorga", "initials": "JA", "orcid": "0000-0003-1017-8841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/855ef6e5db6f4791a52eeae9ffb95a30.json"}}, {"family": "Gharibi", "given": "Hassan", "initials": "H", "orcid": "0000-0002-3072-4929", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5825ec93851a42618425b67a5bbfbf3f.json"}}, {"family": "Meng", "given": "Zhaowei", "initials": "Z"}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.json"}}, {"family": "Rodin", "given": "Sergey", "initials": "S"}, {"family": "N\u00e4reoja", "given": "Katja", "initials": "K"}, {"family": "Thorsell", "given": "Ann-Gerd", "initials": "AG"}, {"family": "Karlberg", "given": "Tobias", "initials": "T"}, {"family": "Cheng", "given": "Qing", "initials": "Q"}, {"family": "Lundstr\u00f6m", "given": "Susanna L", "initials": "SL"}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Arn\u00e9r", "given": "Elias S J", "initials": "ESJ", "orcid": "0000-0002-4807-6114", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3502128dcae54dfcb6808356694bf4dc.json"}}, {"family": "Sch\u00fcler", "given": "Herwig", "initials": "H", "orcid": "0000-0003-4059-3501", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a66d04210ea41c2bbb0a5ee187c7b76.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA", "orcid": "0000-0001-9839-2089", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5e3f9910c1ff434c8056bdecf537e9ef.json"}}], "type": "journal article", "published": "2021-02-26", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "1296", "issn-l": "2041-1723"}, "abstract": "Despite the immense importance of enzyme-substrate reactions, there is a lack of general and unbiased tools for identifying and prioritizing substrate proteins that are modified by the enzyme on the structural level. Here we describe a high-throughput unbiased proteomics method called System-wide Identification and prioritization of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that the enzymatic post-translational modification of substrate proteins is likely to change their thermal stability. In our proof-of-concept studies, SIESTA successfully identifies several known and novel substrate candidates for selenoprotein thioredoxin reductase 1, protein kinase B (AKT1) and poly-(ADP-ribose) polymerase-10 systems. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, opening opportunities to investigate the effect of post-translational modifications on signal transduction and facilitate drug discovery.", "doi": "10.1038/s41467-021-21540-6", "pmid": "33637753", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7910609"}, {"db": "pii", "key": "10.1038/s41467-021-21540-6"}], "notes": [], "created": "2026-09-23T08:34:01.574Z", "modified": "2026-09-23T08:34:01.919Z"}, {"entity": "publication", "iuid": "3296f3147d3b4070a92e1424a7f1b82d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3296f3147d3b4070a92e1424a7f1b82d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3296f3147d3b4070a92e1424a7f1b82d"}}, "title": "ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery.", "authors": [{"family": "Saei", "given": "Amir Ata", "initials": "AA", "orcid": "0000-0002-2639-6328", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebf703f0f2d44b14846ea1d9811b6e0d.json"}}, {"family": "Beusch", "given": "Christian Michel", "initials": "CM", "orcid": "0000-0001-9100-8283", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbb4771768354080ab5292c96fee0812.json"}}, {"family": "Chernobrovkin", "given": "Alexey", "initials": "A", "orcid": "0000-0001-7709-0161", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/011675da8d7a4fd68fbe5ce03227978d.json"}}, {"family": "Sabatier", "given": "Pierre", "initials": "P", "orcid": "0000-0002-2734-1791", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4cf83f2cf534d7eb308dab89d6460e2.json"}}, {"family": "Zhang", "given": "Bo", "initials": "B", "orcid": "0000-0001-8890-8416", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fab1ab9de65a430b97f0a84901798d6e.json"}}, {"family": "Tokat", "given": "\u00dclk\u00fc G\u00fcler", "initials": "\u00dcG"}, {"family": "Stergiou", "given": "Eleni", "initials": "E", "orcid": "0000-0001-9115-4985", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2912f51ad92a49069667f3947a32562e.json"}}, {"family": "Gaetani", "given": "Massimiliano", "initials": "M", "orcid": "0000-0001-5610-0797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a402c63fbe4f478daa286177f031b923.json"}}, {"family": "V\u00e9gv\u00e1ri", "given": "\u00c1kos", "initials": "\u00c1", "orcid": "0000-0002-1287-0906", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/724d65ef088147c4988093b2b6b5f318.json"}}, {"family": "Zubarev", "given": "Roman A", "initials": "RA"}], "type": "journal article", "published": "2019-12-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "10", "issue": "1", "pages": "5715", "issn-l": "2041-1723"}, "abstract": "Deconvolution of targets and action mechanisms of anticancer compounds is fundamental in drug development. Here, we report on ProTargetMiner as a publicly available expandable proteome signature library of anticancer molecules in cancer cell lines. Based on 287 A549 adenocarcinoma proteomes affected by 56 compounds, the main dataset contains 7,328 proteins and 1,307,859 refined protein-drug pairs. These proteomic signatures cluster by compound targets and action mechanisms. The targets and mechanistic proteins are deconvoluted by partial least square modeling, provided through the website http://protargetminer.genexplain.com. For 9 molecules representing the most diverse mechanisms and the common cancer cell lines MCF-7, RKO and A549, deep proteome datasets are obtained. Combining data from the three cell lines highlights common drug targets and cell-specific differences. The database can be easily extended and merged with new compound signatures. ProTargetMiner serves as a chemical proteomics resource for the cancer research community, and can become a valuable tool in drug discovery.", "doi": "10.1038/s41467-019-13582-8", "pmid": "31844049", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6915695"}, {"db": "pii", "key": "10.1038/s41467-019-13582-8"}], "notes": [], "created": "2026-09-23T07:49:29.913Z", "modified": "2026-09-23T07:49:30.074Z"}]}