{"entity": "journal", "iuid": "a5c0f0705a5541a693edf46c4f8225df", "timestamp": "2026-08-20T20:45:18.027Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/journal/Commun%20Chem.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/journal/Commun%20Chem"}}, "title": "Commun Chem", "issn": "2399-3669", "issn-l": null, "publications_count": 6, "publications": [{"entity": "publication", "iuid": "c2d83a423ae742cfb6fac787734d6525", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c2d83a423ae742cfb6fac787734d6525.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c2d83a423ae742cfb6fac787734d6525"}}, "title": "Progress and future outlook towards a safe and sustainable production and use of chemicals.", "authors": [{"family": "Munthe", "given": "John", "initials": "J", "orcid": "0000-0001-6118-5561", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f2e53786d4946a190cab75f4f8d48ac.json"}}, {"family": "Bergstr\u00f6m", "given": "Lennart", "initials": "L"}, {"family": "Bolinius", "given": "D\u00e4mien", "initials": "D"}, {"family": "Cotgreave", "given": "Ian", "initials": "I"}, {"family": "Hellstr\u00f6m", "given": "Anna-Karin", "initials": "AK"}, {"family": "Holmquist", "given": "Hanna", "initials": "H"}, {"family": "Johansson", "given": "Magnus J", "initials": "MJ", "orcid": "0000-0002-0904-2835", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ee8ab1a1e3b4480b2d1db9d62e0ded0.json"}}, {"family": "Julander", "given": "Anneli", "initials": "A", "orcid": "0000-0003-2131-4896", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5e53578912d48ed8005581325c4ce46.json"}}, {"family": "Lihammar", "given": "Richard", "initials": "R"}, {"family": "Martin", "given": "Jonathan", "initials": "J"}, {"family": "Mart\u00edn-Matute", "given": "Bel\u00e9n", "initials": "B", "orcid": "0000-0002-7898-317X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6cfa83f2d4934ca5ab35c1276207d874.json"}}, {"family": "Mathew", "given": "Aji P", "initials": "AP"}, {"family": "Rydberg", "given": "Tomas", "initials": "T"}, {"family": "Skedung", "given": "Lisa", "initials": "L", "orcid": "0000-0001-6657-1592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/12997dc67f144cda8a200b01095ba2c2.json"}}, {"family": "Witala", "given": "Monika", "initials": "M", "orcid": "0009-0008-4174-2082", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db5a442579284d46ba0a2d9a756b74e8.json"}}, {"family": "Syr\u00e9n", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0002-4066-2776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b035f26bd71e42f9942f9a4943ed0d1a.json"}}], "type": "journal article", "published": "2025-11-14", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "8", "issue": "1", "pages": "350", "issn-l": null}, "abstract": "The demands on chemical industry to transform towards safety and sustainability will require multi-disciplinary research and development where experts on chemistry and chemical engineering, toxicology, ecotoxicology, and life cycle assessment collaborate to develop novel production methods, chemicals and materials. Here we summarise the results of the Mistra SafeChem programme which has yielded considerable output in the areas of catalysis/bio-catalysis, hazard screening for humans and ecosystems and life cycle assessment with chemical footprints, both as individual scientific achievements and as part of an integrated approach to assess safety and sustainability of novel chemicals and chemical synthesis processes, in chemical value chains and across collaborations between industry- academia/ industry-industry. The outcomes from the programme are summarised and discussed and experiences from dialogues on the future of safe and sustainable chemistry are presented.", "doi": "10.1038/s42004-025-01785-8", "pmid": "41238739", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12618680"}, {"db": "pii", "key": "10.1038/s42004-025-01785-8"}], "notes": [], "created": "2026-08-20T09:25:46.841Z", "modified": "2026-08-20T09:25:47.173Z"}, {"entity": "publication", "iuid": "09bbba2a100d4e638b92dd9795730f18", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/09bbba2a100d4e638b92dd9795730f18.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/09bbba2a100d4e638b92dd9795730f18"}}, "title": "Modeling cryo-EM structures in alternative states with AlphaFold2-based models and density-guided simulations.", "authors": [{"family": "Shugaeva", "given": "Tatiana", "initials": "T", "orcid": "0009-0001-8147-0762", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/63de5c5dca5a41709e0d811bebd87084.json"}}, {"family": "Howard", "given": "Rebecca J", "initials": "RJ", "orcid": "0000-0003-2049-3378", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ce04593b5b24aaa8978fda1447dd0bf.json"}}, {"family": "Haloi", "given": "Nandan", "initials": "N", "orcid": "0000-0003-3542-333X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a499486a86ba4df7a27d26dad6222b47.json"}}, {"family": "Lindahl", "given": "Erik", "initials": "E", "orcid": "0000-0002-2734-2794", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9eb30fa60f9b4b95842ac9d9f3a0eaa9.json"}}], "type": "journal article", "published": "2025-10-30", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "8", "issue": "1", "pages": "317", "issn-l": null}, "abstract": "Modeling atomic coordinates into a target cryo-electron microscopy map is a crucial step in structure determination. Despite recent advances, proteins with multiple functional states remain a challenge - particularly when suitable molecular templates are unavailable for certain states, and the map resolution is not high enough to build de novo models. This is a common scenario, for example, among pharmacologically relevant membrane-bound receptors and transporters. Here, we introduce a refinement approach in which (i) several initial models are generated by stochastic subsampling of the multiple sequence alignment (MSA) space in AlphaFold2, (ii) the resulting models are subjected to structure-based k-means clustering, iii) density-guided molecular dynamics simulations are performed from the cluster representatives, and (iv) a final model is selected on the basis of both map fit and model quality. This results in improved fitting accuracy compared to single starting point scenarios for three membrane proteins (the calcitonin receptor-like receptor, L-type amino acid transporter and alanine-serine-cysteine transporter) which undergo substantial conformational transitions between functional states. Our results indicate that ensemble construction using generative AI combined with simulation-based refinement facilitates building of alternative states in several families of membrane proteins.", "doi": "10.1038/s42004-025-01751-4", "pmid": "41168475", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12575730"}, {"db": "pii", "key": "10.1038/s42004-025-01751-4"}], "notes": [], "created": "2026-08-20T09:25:44.871Z", "modified": "2026-08-20T09:25:44.935Z"}, {"entity": "publication", "iuid": "b67ef61687144616a1fef1364c7daf2c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b67ef61687144616a1fef1364c7daf2c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b67ef61687144616a1fef1364c7daf2c"}}, "title": "Chemoenzymatic cascade depolymerization of plastics.", "authors": [{"family": "Sun", "given": "Shengwei", "initials": "S"}, {"family": "Syr\u00e9n", "given": "Per-Olof", "initials": "PO", "orcid": "0000-0002-4066-2776", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b035f26bd71e42f9942f9a4943ed0d1a.json"}}], "type": "journal article", "published": "2025-09-09", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "8", "issue": "1", "pages": "272", "issn-l": null}, "abstract": "Plastic waste management is challenged by the inefficiencies and environmental impact of traditional chemical recycling methods. Here, the authors explore the chemoenzymatic cascade depolymerization approach, which offers a promising and sustainable solution for transforming plastic waste into valuable products.", "doi": "10.1038/s42004-025-01679-9", "pmid": "40926055", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12420817"}, {"db": "pii", "key": "10.1038/s42004-025-01679-9"}], "notes": [], "created": "2026-08-20T09:25:43.144Z", "modified": "2026-08-20T09:25:43.206Z"}, {"entity": "publication", "iuid": "4ec73e602d0d425fb81dd9b99f1dd724", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4ec73e602d0d425fb81dd9b99f1dd724.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4ec73e602d0d425fb81dd9b99f1dd724"}}, "title": "Design of linear and cyclic peptide binders from protein sequence information.", "authors": [{"family": "Li", "given": "Qiuzhen", "initials": "Q"}, {"family": "Vlachos", "given": "Efstathios Nikolaos", "initials": "EN"}, {"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}], "type": "journal article", "published": "2025-07-22", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "8", "issue": "1", "pages": "211", "issn-l": null}, "abstract": "Structure prediction technology has transformed protein design, yet key challenges remain, particularly in designing novel functions. Many proteins function through interactions with other proteins, making the rational design of these interactions a central problem. While most efforts focus on large, stable proteins, shorter peptides offer advantages such as lower manufacturing costs, reduced steric hindrance, and improved cell permeability when cyclised. However, their flexibility and limited structural data make them difficult to design. Here, we introduce EvoBind2, a method for designing novel linear and cyclic peptide binders of varying lengths using only the sequence of a target protein. Unlike existing approaches, EvoBind2 does not require prior knowledge of binding sites or predefined binder lengths, making it a fully blind design process. For one target protein, we demonstrate that linear and cyclic peptide binders of different lengths can be designed in a single shot, and adversarial designs can be avoided through orthogonal in silico evaluation.", "doi": "10.1038/s42004-025-01601-3", "pmid": "40691301", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12280060"}, {"db": "pii", "key": "10.1038/s42004-025-01601-3"}], "notes": [], "created": "2026-08-20T09:25:40.568Z", "modified": "2026-08-20T09:25:40.645Z"}, {"entity": "publication", "iuid": "c5a0289f354249e6bef64467dd3d572e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c5a0289f354249e6bef64467dd3d572e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c5a0289f354249e6bef64467dd3d572e"}}, "title": "Dynamically chiral phosphonic acid-type metallo-\u03b2-lactamase inhibitors.", "authors": [{"family": "Guly\u00e1s", "given": "Kinga Vir\u00e1g", "initials": "KV"}, {"family": "Zhou", "given": "Liping", "initials": "L"}, {"family": "Salamonsen", "given": "Daniel", "initials": "D"}, {"family": "Prester", "given": "Andreas", "initials": "A", "orcid": "0000-0003-2738-7682", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2c442f90408b4da78e8e57db6a5a5439.json"}}, {"family": "Bartels", "given": "Kim", "initials": "K"}, {"family": "Bosman", "given": "Robert", "initials": "R"}, {"family": "Haffke", "given": "Paul", "initials": "P"}, {"family": "Li", "given": "Jintian", "initials": "J"}, {"family": "Tam\u00e1si", "given": "Viola", "initials": "V"}, {"family": "Deufel", "given": "Fritz", "initials": "F", "orcid": "0000-0003-4910-3388", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42d0d8db764e44f594b21afccbac4e88.json"}}, {"family": "Thoma", "given": "Johannes", "initials": "J", "orcid": "0000-0003-3584-8274", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/797e143cdbef4336b6e16033bef5350b.json"}}, {"family": "Andersson Rasmussen", "given": "Anna", "initials": "A"}, {"family": "Csala", "given": "Mikl\u00f3s", "initials": "M", "orcid": "0000-0002-3829-4361", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bdfdd49618a1404ea56bd91cadfe6878.json"}}, {"family": "Schroder Leiros", "given": "Hanna-Kirsti", "initials": "HK", "orcid": "0000-0002-2726-6322", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/001e1fa1af7249d5a5ab0b5fd321f750.json"}}, {"family": "Xu", "given": "Zhijian", "initials": "Z", "orcid": "0000-0002-3063-8473", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f196d16a71a42d88bfda54f494333b7.json"}}, {"family": "Widersten", "given": "Mikael", "initials": "M", "orcid": "0000-0002-3203-3793", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e6504282ed7b439b804cdc51f8b4d43b.json"}}, {"family": "Rohde", "given": "Holger", "initials": "H", "orcid": "0000-0001-8587-4433", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fb2556337b3e483bac077fc710db4bd6.json"}}, {"family": "Schulz", "given": "Eike C", "initials": "EC", "orcid": "0000-0002-1685-8605", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/911f2e3f43ff48aa848b8a7c77756d0e.json"}}, {"family": "Zhu", "given": "Weiliang", "initials": "W", "orcid": "0000-0001-6699-5299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f45a8519ecb24a92a52cd584a6f82638.json"}}, {"family": "Erd\u00e9lyi", "given": "M\u00e1t\u00e9", "initials": "M", "orcid": "0000-0003-0359-5970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/541eea95344a4e918d30bc1a0f0429c9.json"}}], "type": "journal article", "published": "2025-04-19", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "8", "issue": "1", "pages": "119", "issn-l": null}, "abstract": "Antibiotic resistance is a growing global health threat that risks the lives of millions. Among the resistance mechanisms, that mediated by metallo-\u03b2-lactamases is of particular concern as these bacterial enzymes dismantle most \u03b2-lactam antibiotics, which are our widest applied and cheapest to produce antibiotic agents. So far, no clinically applicable metallo-\u03b2-lactamase inhibitors are available. Aiming to adapt to structural variations, we introduce the inhibitor concept: dynamically chiral phosphonic acids. We demonstrate that they are straightforward to synthesize, penetrate bacterial membranes, inhibit the metallo-\u03b2-lactamase enzymes NDM-1, VIM-2 and GIM-1, and are non-toxic to human cells. Mimicking the transition state of \u03b2-lactam hydrolysis, they target the Zn ions of the metallo-\u03b2-lactamase active site. As a unique feature, both of their stereoisomers bind metallo-\u03b2-lactamases, which provides them unparalleled adaptability to the structural diversity of these enzymes, and may allow them to hamper bacteria's ability for resistance development.", "doi": "10.1038/s42004-025-01510-5", "pmid": "40253435", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12009420"}, {"db": "pii", "key": "10.1038/s42004-025-01510-5"}], "notes": [], "created": "2026-08-20T09:25:38.528Z", "modified": "2026-08-20T09:25:38.883Z"}, {"entity": "publication", "iuid": "85647eabbe644ebf93336f6e2534b98b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/85647eabbe644ebf93336f6e2534b98b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/85647eabbe644ebf93336f6e2534b98b"}}, "title": "Peptide binder design with inverse folding and protein structure prediction.", "authors": [{"family": "Bryant", "given": "Patrick", "initials": "P", "orcid": "0000-0003-3439-1866", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6a683bcf98234ff09b2398976583b66f.json"}}, {"family": "Elofsson", "given": "Arne", "initials": "A", "orcid": "0000-0002-7115-9751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/248e70e81bd64f31a5f83e6e329bba95.json"}}], "type": "journal article", "published": "2023-10-25", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "6", "issue": "1", "pages": "229", "issn-l": null}, "abstract": "The computational design of peptide binders towards a specific protein interface can aid diagnostic and therapeutic efforts. Here, we design peptide binders by combining the known structural space searched with Foldseek, the protein design method ESM-IF1, and AlphaFold2 (AF) in a joint framework. Foldseek generates backbone seeds for a modified version of ESM-IF1 adapted to protein complexes. The resulting sequences are evaluated with AF using an MSA representation for the receptor structure and a single sequence for the binder. We show that AF can accurately evaluate protein binders and that our bind score can select these (ROC AUC = 0.96 for the heterodimeric case). We find that designs created from seeds with more contacts per residue are more successful and tend to be short. There is a relationship between the sequence recovery in interface positions and the plDDT of the designs, where designs with \u226580% recovery have an average plDDT of 84 compared to 55 at 0%. Designed sequences have 60% higher median plDDT values towards intended receptors than non-intended ones. Successful binders (predicted interface RMSD \u2264 2 \u00c5) are designed towards 185 (6.5%) heteromeric and 42 (3.6%) homomeric protein interfaces with ESM-IF1 compared with 18 (1.5%) using ProteinMPNN from 100 samples.", "doi": "10.1038/s42004-023-01029-7", "pmid": "37880344", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10600234"}, {"db": "pii", "key": "10.1038/s42004-023-01029-7"}], "notes": [], "created": "2026-08-20T09:25:36.744Z", "modified": "2026-08-20T09:25:36.805Z"}], "created": "2026-08-20T09:25:36.774Z", "modified": "2026-08-20T09:25:36.774Z"}