Acta crystallographica. Section F, Structural biology communications最新文献

High-throughput protein crystallography to empower natural product-based drug discovery 高通量蛋白质晶体学使基于天然产物的药物发现成为可能

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-17 DOI: 10.1107/S2053230X25001542

Raphael Meneghello, Joane K. Rustiguel, Evandro Ares de Araújo, Rafael de Felício, Arthur Zanetti N. Fernandes, Everton L. F. Ferreira, Juliana R. Gubiani, Agnes A. S. Takeda, Amanda Araujo, Caio C. de Lima Silva, Ariane F. Bertonha, Raquel P. M. Urano, Daniel M. Trindade, Thiago M. Cunha, Alisson C. Cardoso, Roberto G. S. Berlinck, Andrey F. Ziem Nascimento, Daniela B. B. Trivella

{"title":"High-throughput protein crystallography to empower natural product-based drug discovery","authors":"Raphael Meneghello, Joane K. Rustiguel, Evandro Ares de Araújo, Rafael de Felício, Arthur Zanetti N. Fernandes, Everton L. F. Ferreira, Juliana R. Gubiani, Agnes A. S. Takeda, Amanda Araujo, Caio C. de Lima Silva, Ariane F. Bertonha, Raquel P. M. Urano, Daniel M. Trindade, Thiago M. Cunha, Alisson C. Cardoso, Roberto G. S. Berlinck, Andrey F. Ziem Nascimento, Daniela B. B. Trivella","doi":"10.1107/S2053230X25001542","DOIUrl":"https://doi.org/10.1107/S2053230X25001542","url":null,"abstract":"Nature is a rich and largely untapped reservoir of small molecules, the latter historically being the main source of new drugs. Three-dimensional structures of proteins in complex with small-molecule ligands represent key information to progress drug-discovery projects, in particular in the hit-to-lead phase. High-throughput crystallography has been of extensive use in recent years, especially to obtain crystallographic complexes of synthetic ligands and fragments. However, the process of discovering novel bioactive natural products has experienced limitations that have long prevented large drug-discovery programs using this outstanding source of molecules. Recent technologies have contributed to the re-emergence of natural products in modern drug discovery. We present the use of high-throughput protein crystallography to directly capture bioactive natural products from unpurified biota chemical samples using protein crystals. These routines, which are currently in use at the Brazilian Centre for Research in Energy and Materials (CNPEM), are introduced with a description of crystal preparation, automated data collection and processing at the MANACÁ beamline (Sirius, LNLS, CNPEM), along with case examples of bioactive natural product capture using protein crystals. The usefulness of this pipeline, which accelerates the discovery and structural elucidation of both known and previously unknown bioactive natural products, paves the way for the development of innovative therapeutic agents, thus contributing to the new era of natural product-based drug discovery.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 5","pages":"179-192"},"PeriodicalIF":1.1,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143879984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crystallization and initial X-ray crystallographic analysis of a de novo-designed protein with left-handed βαβ units 具有左旋βαβ单元的新设计蛋白的结晶和初始x射线晶体学分析

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-16 DOI: 10.1107/S2053230X25003097

Naoki Tomita, Riu Hirano, Hiroto Murata, Yasufumi Umena, Hiroki Onoda, George Chikenji, Leonard M. G. H. Chavas

{"title":"Crystallization and initial X-ray crystallographic analysis of a de novo-designed protein with left-handed βαβ units","authors":"Naoki Tomita, Riu Hirano, Hiroto Murata, Yasufumi Umena, Hiroki Onoda, George Chikenji, Leonard M. G. H. Chavas","doi":"10.1107/S2053230X25003097","DOIUrl":"https://doi.org/10.1107/S2053230X25003097","url":null,"abstract":"A newly designed protein featuring a rare left-handed βαβ motif has successfully been crystallized and characterized by preliminary X-ray diffraction. The computational design was conducted using a combination of Rosetta BluePrintBDR, ProteinMPNN and AlphaFold2, generating eight candidates based on predicted stability and folding accuracy. The final construct was expressed, purified and crystallized in space group P21. Complete X-ray diffraction data were collected on the BL2S1 beamline at the Aichi Synchrotron and processed to 1.95 Å resolution. Despite multiple attempts, molecular replacement using the AlphaFold2 model did not yield a conclusive solution, suggesting that alternative phasing methods or refined modeling approaches will be needed. This work highlights both the promise and the challenges of pushing protein biodesign into underexplored structural motifs and provides a foundation for future structural and functional investigations.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 5","pages":"216-220"},"PeriodicalIF":1.1,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-16

引用次数: 0

Molecular interactions between piperine and peroxisome proliferator-activated receptor gamma ligand-binding domain revealed using co-crystallization studies 胡椒碱与过氧化物酶体增殖体激活受体γ配体结合域之间的分子相互作用通过共结晶研究揭示。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-16 DOI: 10.1107/S2053230X25002377

Daichi Egawa, Hiroaki Ishida, Kazuaki Katakawa

{"title":"Molecular interactions between piperine and peroxisome proliferator-activated receptor gamma ligand-binding domain revealed using co-crystallization studies","authors":"Daichi Egawa, Hiroaki Ishida, Kazuaki Katakawa","doi":"10.1107/S2053230X25002377","DOIUrl":"10.1107/S2053230X25002377","url":null,"abstract":"Piperine has been investigated for a diverse array of biological effects, including a potential role in modulating peroxisome proliferator-activated receptor gamma (PPARγ), a nuclear receptor that plays a pivotal role in regulating lipid and glucose metabolism. This study conducted a comprehensive co-crystallographic analysis of the complex of piperine with the PPARγ ligand-binding domain (PPARγ-LBD), with the objective of elucidating the precise binding interactions of piperine. The co-crystal structure revealed that piperine binds within the ligand-binding pocket of PPARγ-LBD via hydrogen-bonding and hydrophobic interactions with residues of the ligand-binding site. Notably, in contrast to conventional full agonists, piperine does not directly stabilize helix H12. This could contribute to the comparatively weaker agonistic activity of piperine. The results of this study also suggest that piperine binding facilitates a role as a partial agonist or even an antagonist under certain physiological conditions. Collectively, these findings contribute to a greater understanding of the manner in which piperine modulates PPARγ function and its potential as a therapeutic candidate for the treatment of metabolic disorders. Given its natural origin and relatively minimal side-effect profile, piperine and its derivatives could be promising alternatives to synthetic PPARγ modulators such as thiazolidinediones, which have significant side effects.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 5","pages":"201-206"},"PeriodicalIF":1.1,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Purification, crystallization and preliminary crystallographic studies of a Kunitz-type proteinase inhibitor from tamarind (Tamarindus indica) seeds. Corrigendum 罗望子库尼茨型蛋白酶抑制剂的纯化、结晶及初步结晶学研究。应改正的错误。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-16 DOI: 10.1107/S2053230X25002845

Dipak N. Patil, Preeti, Anshul Chaudhary, Ashwani K. Sharma, Shailly Tomar, Pravindra Kumar

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-16

引用次数: 0

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-02

引用次数: 0

The structure of the Gemella haemolysans M26 IgA1 protease trypsin-like domain. Gemella haemolysans M26 IgA1 蛋白酶胰蛋白酶样结构域的结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-01 Epub Date: 2025-02-28 DOI: 10.1107/S2053230X25001219

Norman Tran, Jasmina S Redzic, Elan Z Eisenmesser, Todd Holyoak

{"title":"The structure of the Gemella haemolysans M26 IgA1 protease trypsin-like domain.","authors":"Norman Tran, Jasmina S Redzic, Elan Z Eisenmesser, Todd Holyoak","doi":"10.1107/S2053230X25001219","DOIUrl":"10.1107/S2053230X25001219","url":null,"abstract":"Immunoglobulin A (IgA) proteases are a group of bacterial-derived enzymes that selectivity hydrolyze human IgA in the hinge region that is unique to this immunoglobulin. Several IgA protease (IgAP) families have evolved this ability using both metalloprotease and serine protease chemical mechanisms. One family of metal-dependent IgAPs is the M26 family. This family can be grouped into two subfamilies based upon the presence or absence of a trypsin-like domain found N-terminal to the IgAP domain. The role of this domain in IgAP structure and function is poorly understood. Here, we present the first structural characterization of an M26 IgAP trypsin-like domain from Gemella haemolysans (GhTrp). These structural data demonstrate that the GhTrp domain possesses a trypsin-like fold but contains significant deviations in the surface-loop structure that is known to be coupled to protease selectivity. The lack of observable catalytic function coupled with the structural data suggest that this domain may exist in a pro-enzyme-like state that can potentially be activated when the domain is N-terminally proteolytically excised from the larger M26 IgAP structure.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":" ","pages":"124-129"},"PeriodicalIF":1.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11970125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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The first report of structural analysis of a nucleic acid using crystals grown in space. Corrigendum. 利用在太空中生长的晶体对核酸进行结构分析的第一份报告。应改正的错误。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-04-01 DOI: 10.1107/S2053230X25002766

Shin Ando, Moena Takahashi, Jiro Kondo

引用次数: 0

Structures of Legionella pneumophila serogroup 1 peptide deformylase bound to nickel(II) and actinonin 嗜肺军团菌血清1组肽脱甲酰基酶与镍和肌动蛋白结合的结构。

IF 1.1 4区生物学

Acta crystallographica. Section F, Structural biology communications Pub Date : 2025-03-17 DOI: 10.1107/S2053230X25001876

Chi L. Nguyen, William Fan, Sean Fisher, Krystal Matthews, Jordan O. Norman, Jan Abendroth, Kayleigh F. Barrett, Justin K. Craig, Thomas E. Edwards, Donald D. Lorimer, Krystle J. McLaughlin

{"title":"Structures of Legionella pneumophila serogroup 1 peptide deformylase bound to nickel(II) and actinonin","authors":"Chi L. Nguyen, William Fan, Sean Fisher, Krystal Matthews, Jordan O. Norman, Jan Abendroth, Kayleigh F. Barrett, Justin K. Craig, Thomas E. Edwards, Donald D. Lorimer, Krystle J. McLaughlin","doi":"10.1107/S2053230X25001876","DOIUrl":"10.1107/S2053230X25001876","url":null,"abstract":"Legionella pneumophila serogroup 1 is the primary causative agent of Legionnaires' disease, a rare but severe respiratory infection. While the fatality rate of Legionnaires' disease is low in the general population, it is more pronounced in vulnerable communities such as the immunocompromised. Thus, the development of new antimicrobials is of interest for use when existing antibiotics may not be applicable. Peptide deformylases (PDFs) have been under continued investigation as targets for novel antimicrobial compounds. PDF plays an essential role in protein synthesis, removing the N-terminal formyl group from new polypeptides, and is required for growth in most bacteria. Here, we report two crystal structures of L. pneumophila serogroup 1 PDF (LpPDF) bound to either Ni2+, an active state, or inhibited by actinonin and Zn2+; the structures were determined to 1.5 and 1.65 Å resolution, respectively, and were solved by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is charged with determining structures of biologically important proteins and molecules from human pathogens. As actinonin is an antimicrobial natural product that has been used as a reference compound in drug development, these structures will help support the ongoing drug-development process.","PeriodicalId":7029,"journal":{"name":"Acta crystallographica. Section F, Structural biology communications","volume":"81 4","pages":"163-170"},"PeriodicalIF":1.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143646730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0