Pub Date : 2024-09-17DOI: 10.1038/s42004-024-01294-0
Wenju Zhou, Yuqing Yin, Dominique Laniel, Andrey Aslandukov, Elena Bykova, Anna Pakhomova, Michael Hanfland, Tomasz Poreba, Mohamed Mezouar, Leonid Dubrovinsky, Natalia Dubrovinskaia
Structural studies of pyrene have been limited to below 2 GPa. Here, we report on investigations of pyrene up to ~35 GPa using in situ single-crystal synchrotron X-ray diffraction in diamond anvil cells and ab initio calculations. They reveal the phase transitions from pyrene-I to pyrene-II (0.7 GPa), and to the previously unreported pyrene-IV (2.7 GPa), and pyrene-V (7.3 GPa). The structure and bonding analysis shows that gradual compression results in continuous compaction of molecular packing, eventually leading to curvature of molecules, which has never been observed before. Large organic molecules exhibit unexpectedly high conformational flexibility preserving pyrene-V up to 35 GPa. Ab initio calculations suggest that the phases we found are thermodynamically metastable compared to pyrene-III previously reported at 0.3 and 0.5 GPa. Our study contributes to the fundamental understanding of the polymorphism of polycyclic aromatic hydrocarbons and calls for further theoretical exploration of their structure–property relationships. Structural studies of pyrene, a polycyclic aromatic hydrocarbon, have so far been limited to below 2 GPa. Here, studying the crystal structure of pyrene up to ~35 GPa using in situ single-crystal synchrotron X-ray diffraction in diamond anvil cells, the authors discover two previously unobserved polymorphs, and find that gradual compression results in continuous compaction of molecular packing, eventually leading to a curvature of the molecules.
对芘的结构研究仅限于 2 GPa 以下。在此，我们报告了利用金刚石砧室中的原位单晶同步辐射 X 射线衍射和 ab initio 计算对高达 ~35 GPa 的芘进行的研究。研究揭示了芘-I 到芘-II（0.7 GPa）、芘-IV（2.7 GPa）和芘-V（7.3 GPa）的相变。结构和键合分析表明，逐渐压缩会导致分子堆积不断压缩，最终导致分子弯曲，这是以前从未观察到的。大有机分子表现出意想不到的高构象灵活性，保留了高达 35 GPa 的芘-V。Ab initio 计算表明，与之前报道的在 0.3 和 0.5 GPa 下的芘-III 相比，我们发现的物相在热力学上是稳定的。我们的研究有助于从根本上理解多环芳烃的多态性，并要求对其结构-性质关系进行进一步的理论探索。迄今为止，对多环芳烃芘的结构研究仅限于 2 GPa 以下。在此，作者利用金刚石砧室中的原位单晶同步辐射 X 射线衍射技术研究了高达约 35 GPa 的芘晶体结构，发现了两种以前从未观察到的多晶体，并发现逐渐压缩会导致分子堆积的持续压实，最终导致分子弯曲。
{"title":"Polymorphism of pyrene on compression to 35 GPa in a diamond anvil cell","authors":"Wenju Zhou, Yuqing Yin, Dominique Laniel, Andrey Aslandukov, Elena Bykova, Anna Pakhomova, Michael Hanfland, Tomasz Poreba, Mohamed Mezouar, Leonid Dubrovinsky, Natalia Dubrovinskaia","doi":"10.1038/s42004-024-01294-0","DOIUrl":"10.1038/s42004-024-01294-0","url":null,"abstract":"Structural studies of pyrene have been limited to below 2 GPa. Here, we report on investigations of pyrene up to ~35 GPa using in situ single-crystal synchrotron X-ray diffraction in diamond anvil cells and ab initio calculations. They reveal the phase transitions from pyrene-I to pyrene-II (0.7 GPa), and to the previously unreported pyrene-IV (2.7 GPa), and pyrene-V (7.3 GPa). The structure and bonding analysis shows that gradual compression results in continuous compaction of molecular packing, eventually leading to curvature of molecules, which has never been observed before. Large organic molecules exhibit unexpectedly high conformational flexibility preserving pyrene-V up to 35 GPa. Ab initio calculations suggest that the phases we found are thermodynamically metastable compared to pyrene-III previously reported at 0.3 and 0.5 GPa. Our study contributes to the fundamental understanding of the polymorphism of polycyclic aromatic hydrocarbons and calls for further theoretical exploration of their structure–property relationships. Structural studies of pyrene, a polycyclic aromatic hydrocarbon, have so far been limited to below 2 GPa. Here, studying the crystal structure of pyrene up to ~35 GPa using in situ single-crystal synchrotron X-ray diffraction in diamond anvil cells, the authors discover two previously unobserved polymorphs, and find that gradual compression results in continuous compaction of molecular packing, eventually leading to a curvature of the molecules.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01294-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-16DOI: 10.1038/s42004-024-01289-x
Elaine C. Petronilho, Guilherme C. de Andrade, Gileno dos S. de Sousa, Fernando P. Almeida, Michelle F. Mota, Ana Vitória dos S. Gomes, Carlos Henrique S. Pinheiro, Mylena C. da Silva, Hiam R. S. Arruda, Mayra A. Marques, Tuane C. R. G. Vieira, Guilherme A. P. de Oliveira, Jerson L. Silva
P53 Phase separation is crucial towards amyloid aggregation and p63 and p73 have enhanced expression in tumors. This study examines the phase behaviors of p53, p63, and p73. Here we show that unlike the DNA-binding domain of p53 (p53C), the p63C and p73C undergo phase separation, but do not form amyloids under physiological temperatures. Wild-type and mutant p53C form droplets at 4°C and aggregates at 37 °C with amyloid properties. Mutant p53C promotes amyloid-like states in p63C and p73C, recruiting them into membraneless organelles. Amyloid conversion is supported by thioflavin T and Congo red binding, increased light scattering, and circular dichroism. Full-length mutant p53 and p63C (or p73C) co-transfection shows reduced fluorescence recovery after photobleaching. Heparin inhibits the prion-like aggregation of p63C and p73C induced by p53C. These findings highlight the role of p53 in initiating amyloid aggregation in p63 and p73, opening avenues for targeting prion-like conversion in cancer therapy. Phase separation of p53 is crucial in its progression towards amyloid aggregation, while its paralogous forms p63 and p73 have enhanced expression in tumors but reduced aggregation propensity. Here, the authors report the prion-like aggregation of p63 and p73 mediated by p53 and outline that this process can be inhibited by heparin.
{"title":"Oncogenic p53 triggers amyloid aggregation of p63 and p73 liquid droplets","authors":"Elaine C. Petronilho, Guilherme C. de Andrade, Gileno dos S. de Sousa, Fernando P. Almeida, Michelle F. Mota, Ana Vitória dos S. Gomes, Carlos Henrique S. Pinheiro, Mylena C. da Silva, Hiam R. S. Arruda, Mayra A. Marques, Tuane C. R. G. Vieira, Guilherme A. P. de Oliveira, Jerson L. Silva","doi":"10.1038/s42004-024-01289-x","DOIUrl":"10.1038/s42004-024-01289-x","url":null,"abstract":"P53 Phase separation is crucial towards amyloid aggregation and p63 and p73 have enhanced expression in tumors. This study examines the phase behaviors of p53, p63, and p73. Here we show that unlike the DNA-binding domain of p53 (p53C), the p63C and p73C undergo phase separation, but do not form amyloids under physiological temperatures. Wild-type and mutant p53C form droplets at 4°C and aggregates at 37 °C with amyloid properties. Mutant p53C promotes amyloid-like states in p63C and p73C, recruiting them into membraneless organelles. Amyloid conversion is supported by thioflavin T and Congo red binding, increased light scattering, and circular dichroism. Full-length mutant p53 and p63C (or p73C) co-transfection shows reduced fluorescence recovery after photobleaching. Heparin inhibits the prion-like aggregation of p63C and p73C induced by p53C. These findings highlight the role of p53 in initiating amyloid aggregation in p63 and p73, opening avenues for targeting prion-like conversion in cancer therapy. Phase separation of p53 is crucial in its progression towards amyloid aggregation, while its paralogous forms p63 and p73 have enhanced expression in tumors but reduced aggregation propensity. Here, the authors report the prion-like aggregation of p63 and p73 mediated by p53 and outline that this process can be inhibited by heparin.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01289-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-16DOI: 10.1038/s42004-024-01298-w
Xue Zhi Zhao, Idris A. Barakat, George T. Lountos, Wenjie Wang, Keli Agama, Md Rasel Al Mahmud, Kiall F. Suazo, Thorkell Andresson, Yves Pommier, Terrence R. Burke Jr.
Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) has been challenging because of the enzyme shallow catalytic pocket and non-specific substrate binding interactions. Recently, we discovered a quinolone-binding hot spot in TDP1’s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1 ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting and adds to the chemical biology resource toolbox for studying TDP1. Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) is challenging because of the enzyme’s shallow catalytic pocket and non-specific substrate binding interactions. Here, the authors use Sulfur (VI) fluoride exchange chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with the Y204 residue that position DNA.
由于 DNA 修复酶酪氨酰-DNA 磷酸二酯酶 1（TDP1）的催化袋较浅，且存在非特异性底物结合相互作用，因此开发有效的抑制剂一直是一项挑战。最近，我们在 TDP1 的活性位点中发现了一个喹诺酮结合热点，它位于进化保守的 Y204 和 F259 残基附近，而这两个残基是 DNA 的定位残基。硫（VI）氟化物交换（SuFEx）是一种生物兼容的点击化学反应，能使包括酪氨酸在内的蛋白质残基酰化。对蛋白质进行选择性修饰可以深入了解蛋白质的生物学作用，并为配体设计提供信息。正如我们在本文中所报告的，我们利用 SuFEx 化学反应制备了与 TDP1 结合的共价结合剂，该结合剂显示了与 Y204 的位点特异性共价键。我们的研究首次将 SuFEx 化学方法应用于 TDP1 配体。它验证了通过设计靶向共价修饰特定 TDP1 残基的能力，并增加了研究 TDP1 的化学生物学资源工具箱。由于 DNA 修复酶酪氨酰-DNA 磷酸二酯酶 1（TDP1）的催化袋较浅，且存在非特异性底物结合相互作用，因此开发有效的抑制剂具有挑战性。在本文中，作者使用氟化硫（VI）交换化学方法制备了与 TDP1 结合的共价结合剂，这些结合剂显示了与定位 DNA 的 Y204 残基的位点特异性共价键。
{"title":"Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1","authors":"Xue Zhi Zhao, Idris A. Barakat, George T. Lountos, Wenjie Wang, Keli Agama, Md Rasel Al Mahmud, Kiall F. Suazo, Thorkell Andresson, Yves Pommier, Terrence R. Burke Jr.","doi":"10.1038/s42004-024-01298-w","DOIUrl":"10.1038/s42004-024-01298-w","url":null,"abstract":"Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) has been challenging because of the enzyme shallow catalytic pocket and non-specific substrate binding interactions. Recently, we discovered a quinolone-binding hot spot in TDP1’s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1 ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting and adds to the chemical biology resource toolbox for studying TDP1. Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) is challenging because of the enzyme’s shallow catalytic pocket and non-specific substrate binding interactions. Here, the authors use Sulfur (VI) fluoride exchange chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with the Y204 residue that position DNA.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01298-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1038/s42004-024-01280-6
Jackson Penfield, Liqun Zhang
Chemokine receptor CXCR4 is involved in diverse diseases. A comparative study was conducted on CXCR4 embedded in a POPC lipid bilayer binding with CXCL12 in full and truncated forms, hBD-3 in wildtype, analog, and mutant forms based on in total 63 µs all-atom MD simulations. The initial binding structures of CXCR4 with ligands were predicted using HADDOCK docking or random-seed method, then μs-long simulations were performed to refine the structures. CXCR4&ligand binding structures predicted agree with available literature data. Both kinds of ligands bind stably to the N-terminus, extracellular loop 2 (ECL2), and ECL3 regions of CXCR4; the C2-C3 (K32-R38) region and occasionally the head of hBD-3 bind stably with CXCR4. hBD-3 analogs with Cys11-Cys40 disulfide bond can activate CXCR4 based on the Helix3-Helix6 distance calculation, but not other analogs or mutant. The results provide insight into understanding the dynamics and activation mechanism of CXCR4 receptor binding with different ligands. The chemokine receptor CXCR4 is involved in cancers and diverse diseases, however, molecular details surrounding the binding of different ligands to this receptor remain incomplete. Here, the authors study the binding and interaction between CXCR4 with CXCL12 and hBD-3 in different forms, and find that both ligands can bind with CXCR4 at the same site, and analogs of hBD-3 with a Cys11-Cys40 disulfide bond can activate CXCR4.
{"title":"Interaction and dynamics of chemokine receptor CXCR4 binding with CXCL12 and hBD-3","authors":"Jackson Penfield, Liqun Zhang","doi":"10.1038/s42004-024-01280-6","DOIUrl":"10.1038/s42004-024-01280-6","url":null,"abstract":"Chemokine receptor CXCR4 is involved in diverse diseases. A comparative study was conducted on CXCR4 embedded in a POPC lipid bilayer binding with CXCL12 in full and truncated forms, hBD-3 in wildtype, analog, and mutant forms based on in total 63 µs all-atom MD simulations. The initial binding structures of CXCR4 with ligands were predicted using HADDOCK docking or random-seed method, then μs-long simulations were performed to refine the structures. CXCR4&ligand binding structures predicted agree with available literature data. Both kinds of ligands bind stably to the N-terminus, extracellular loop 2 (ECL2), and ECL3 regions of CXCR4; the C2-C3 (K32-R38) region and occasionally the head of hBD-3 bind stably with CXCR4. hBD-3 analogs with Cys11-Cys40 disulfide bond can activate CXCR4 based on the Helix3-Helix6 distance calculation, but not other analogs or mutant. The results provide insight into understanding the dynamics and activation mechanism of CXCR4 receptor binding with different ligands. The chemokine receptor CXCR4 is involved in cancers and diverse diseases, however, molecular details surrounding the binding of different ligands to this receptor remain incomplete. Here, the authors study the binding and interaction between CXCR4 with CXCL12 and hBD-3 in different forms, and find that both ligands can bind with CXCR4 at the same site, and analogs of hBD-3 with a Cys11-Cys40 disulfide bond can activate CXCR4.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01280-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-13DOI: 10.1038/s42004-024-01299-9
Kangning Liu, Qi Ding, Doudou Cao, Enpeng Xi, Yun Zhao, Nan Gao, Yajie Yang, Ye Yuan
Although the pathogenesis of Alzheimer’s disease (AD) is still unknown, the molecular pathological phenomena is clear, mainly due to mitochondrial dysfunction and central nervous system inflammation caused by imbalanced antioxidant capacity and synaptic dysfunction, so antioxidant therapy is still the preferred treatment for AD. However, although antioxidant enzymes have high catalytic efficiency, the substrate spectrum is narrow; Antioxidants have wider range of effects, but their efficiency is low. Since the antioxidant defense system in high-grade organisms is composed of both enzymatic and non-enzymatic systems, therefore we synthesized a metal-organic framework (MOF) with superoxide dismutase activity, and depending on the interface potential effect, curcumin was loaded to construct a synergistic antioxidant treatment system. More importantly, due to the complementary surface electrostatic potential between MOF and curcumin, the system exhibited both good antioxidant activity and efficient β-amyloid plaque scavenging ability, which slowed down the cognitive dysfunction in the brain of AD mice. Although the pathogenesis of Alzheimer’s disease (AD) is still unknown, imbalanced antioxidant capacity in nerve cells is a successfully targeted pathological phenomenon in clinical practice. Here, the authors show that the complementary surface electrostatic potential between a metal-organic framework and curcumin results in a complex with good antioxidant activity and efficient β-amyloid plaque scavenging ability, which slows down the cognitive dysfunction in the brain of AD mice.
{"title":"Interface potential-induced natural antioxidant mimic system for the treatment of Alzheimer’s disease","authors":"Kangning Liu, Qi Ding, Doudou Cao, Enpeng Xi, Yun Zhao, Nan Gao, Yajie Yang, Ye Yuan","doi":"10.1038/s42004-024-01299-9","DOIUrl":"10.1038/s42004-024-01299-9","url":null,"abstract":"Although the pathogenesis of Alzheimer’s disease (AD) is still unknown, the molecular pathological phenomena is clear, mainly due to mitochondrial dysfunction and central nervous system inflammation caused by imbalanced antioxidant capacity and synaptic dysfunction, so antioxidant therapy is still the preferred treatment for AD. However, although antioxidant enzymes have high catalytic efficiency, the substrate spectrum is narrow; Antioxidants have wider range of effects, but their efficiency is low. Since the antioxidant defense system in high-grade organisms is composed of both enzymatic and non-enzymatic systems, therefore we synthesized a metal-organic framework (MOF) with superoxide dismutase activity, and depending on the interface potential effect, curcumin was loaded to construct a synergistic antioxidant treatment system. More importantly, due to the complementary surface electrostatic potential between MOF and curcumin, the system exhibited both good antioxidant activity and efficient β-amyloid plaque scavenging ability, which slowed down the cognitive dysfunction in the brain of AD mice. Although the pathogenesis of Alzheimer’s disease (AD) is still unknown, imbalanced antioxidant capacity in nerve cells is a successfully targeted pathological phenomenon in clinical practice. Here, the authors show that the complementary surface electrostatic potential between a metal-organic framework and curcumin results in a complex with good antioxidant activity and efficient β-amyloid plaque scavenging ability, which slows down the cognitive dysfunction in the brain of AD mice.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01299-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1038/s42004-024-01296-y
Krishna Puri, Suvarn S. Kulkarni
Zwitterionic polysaccharides (ZPSs) present on the surface of a common gut commensal Bacteroides fragilis are endowed with unique immunological properties as they can directly bind to T-cells in the absence of protein conjugation. ZPSs are therefore considered to be potential antigens for the development of totally carbohydrate-based vaccines. Herein, we disclose the first total synthesis of a highly branched phosphorylated zwitterionic capsular polysaccharide repeating unit of Bacteroides fragilis. The hexasaccharide repeating unit bearing six different monosaccharides comprises three 1,2-cis-glycosidic linkages, a challenging 1,2-trans linkage in D-QuipNAc-β-(1→4)-D-Gal motif, and a 2-aminoethyl phosphonate appendage. The synthesis of target ZPS was accomplished utilizing an expeditious, highly stereoselective and convergent (1 + 2 + 2 + 1) one-pot glycosylation strategy. The striking features include efficient synthesis of rare deoxy amino sugars D- and L-quinovosamine, stereoselective installation of three 1,2-cis glycosidic linkages, glycosylation of D-quinovosamine donor with a sterically crowded, poorly reactive 4-OH galactose moiety, as well as late stage phosphorylation. Zwitterionic polysaccharides present on the surface of a common gut commensal Bacteroides fragilis are considered to be potential antigens for the development of totally carbohydrate-based vaccines. Here, the authors report the total synthesis of a highly branched phosphorylated zwitterionic capsular hexasaccharide repeating unit of Bacteroides fragilis via a one-pot glycosylation strategy.
{"title":"Total synthesis of a structurally complex zwitterionic hexasaccharide repeating unit of polysaccharide B from Bacteroides fragilis via one-pot glycosylation","authors":"Krishna Puri, Suvarn S. Kulkarni","doi":"10.1038/s42004-024-01296-y","DOIUrl":"10.1038/s42004-024-01296-y","url":null,"abstract":"Zwitterionic polysaccharides (ZPSs) present on the surface of a common gut commensal Bacteroides fragilis are endowed with unique immunological properties as they can directly bind to T-cells in the absence of protein conjugation. ZPSs are therefore considered to be potential antigens for the development of totally carbohydrate-based vaccines. Herein, we disclose the first total synthesis of a highly branched phosphorylated zwitterionic capsular polysaccharide repeating unit of Bacteroides fragilis. The hexasaccharide repeating unit bearing six different monosaccharides comprises three 1,2-cis-glycosidic linkages, a challenging 1,2-trans linkage in D-QuipNAc-β-(1→4)-D-Gal motif, and a 2-aminoethyl phosphonate appendage. The synthesis of target ZPS was accomplished utilizing an expeditious, highly stereoselective and convergent (1 + 2 + 2 + 1) one-pot glycosylation strategy. The striking features include efficient synthesis of rare deoxy amino sugars D- and L-quinovosamine, stereoselective installation of three 1,2-cis glycosidic linkages, glycosylation of D-quinovosamine donor with a sterically crowded, poorly reactive 4-OH galactose moiety, as well as late stage phosphorylation. Zwitterionic polysaccharides present on the surface of a common gut commensal Bacteroides fragilis are considered to be potential antigens for the development of totally carbohydrate-based vaccines. Here, the authors report the total synthesis of a highly branched phosphorylated zwitterionic capsular hexasaccharide repeating unit of Bacteroides fragilis via a one-pot glycosylation strategy.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01296-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142236064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-12DOI: 10.1038/s42004-024-01297-x
Isabella Senini, Sara Tengattini, Francesca Rinaldi, Gabriella Massolini, Christoph Gstöttner, Dietmar Reusch, Marcello Donini, Carla Marusic, Peter A. van Veelen, Elena Domínguez-Vega, Manfred Wuhrer, Caterina Temporini, Simone Nicolardi
Monoclonal antibody (mAb) glycoengineering has the potential to improve the efficacy of biopharmaceuticals by fine-tuning specific biological properties. Glycosylation analysis is key to monitoring the glycoengineering process. Various mass spectrometry (MS)-based methods are available to characterize mAb glycosylation at different structural levels, but comprehensive analysis is typically time-consuming and costly. Here, we present an approach that combines conventional intact mass measurement of glycoforms by direct infusion ESI-MS with an advanced MALDI-in-source decay FT-ICR MS method for direct analysis of glycans in intact mAbs, without the need for enzymatic release and separation. Using a sodium-doped MALDI matrix, glycans were directly released as ISD fragment ions from the intact mAbs during the ionization process. Measurement of 0,2A fragment signals yielded reproducible glycan profiles that were consistent with conventional methods, yet was achieved with unprecedented speed, providing complementary information to that obtained through intact mass measurement. The methods were applied to standard and glycoengineered trastuzumab and rituximab, allowing rapid glycosylation profiling and structural analysis of glycans by tandem MS of selected ISD fragment ions. This fast approach can facilitate the early-phase development of glycoengineering processes by constraining further in-depth analyses. We envision a broader applicability in studies focused on glycosylation changes in mAbs. Glycoengineering of monoclonal antibodies (mAbs) has the potential to improve the efficacy of biopharmaceuticals, however, monitoring the glycoengineering process by glycosylation analysis often requires a multi-method approach. Here, the authors present a direct glycosylation analysis of intact mAbs by combining conventional ESI-MS of intact glycoforms and MALDI-in-source decay FT-ICR MS of glycan fragments.
单克隆抗体（mAb）糖工程有可能通过微调特定的生物特性来提高生物制药的疗效。糖基化分析是监测糖工程过程的关键。目前有多种基于质谱（MS）的方法来表征不同结构水平的 mAb 糖基化，但全面的分析通常耗时且成本高昂。在这里，我们提出了一种方法，它将传统的直接注入 ESI-MS 测量糖型的完整质量测量方法与先进的 MALDI-in-source decay FT-ICR MS 方法相结合，直接分析完整 mAb 中的聚糖，而无需酶解和分离。使用掺钠 MALDI 基质，在离子化过程中，聚糖作为 ISD 片段离子从完整的 mAbs 中直接释放出来。对 0,2A 片段信号的测量得到了与传统方法一致的可重现的聚糖图谱，而且以前所未有的速度完成，提供了与通过完整质量测量获得的信息互补的信息。这些方法被应用于标准曲妥珠单抗和利妥昔单抗以及经过糖工程化的曲妥珠单抗和利妥昔单抗，从而可以通过对选定的 ISD 片段离子进行串联质谱分析来快速绘制糖基化图谱和分析聚糖的结构。这种快速方法可以限制进一步的深入分析，从而促进糖工程过程的早期开发。我们设想这种方法将更广泛地应用于以 mAbs 糖基化变化为重点的研究中。
{"title":"Direct glycosylation analysis of intact monoclonal antibodies combining ESI MS of glycoforms and MALDI-in source decay MS of glycan fragments","authors":"Isabella Senini, Sara Tengattini, Francesca Rinaldi, Gabriella Massolini, Christoph Gstöttner, Dietmar Reusch, Marcello Donini, Carla Marusic, Peter A. van Veelen, Elena Domínguez-Vega, Manfred Wuhrer, Caterina Temporini, Simone Nicolardi","doi":"10.1038/s42004-024-01297-x","DOIUrl":"10.1038/s42004-024-01297-x","url":null,"abstract":"Monoclonal antibody (mAb) glycoengineering has the potential to improve the efficacy of biopharmaceuticals by fine-tuning specific biological properties. Glycosylation analysis is key to monitoring the glycoengineering process. Various mass spectrometry (MS)-based methods are available to characterize mAb glycosylation at different structural levels, but comprehensive analysis is typically time-consuming and costly. Here, we present an approach that combines conventional intact mass measurement of glycoforms by direct infusion ESI-MS with an advanced MALDI-in-source decay FT-ICR MS method for direct analysis of glycans in intact mAbs, without the need for enzymatic release and separation. Using a sodium-doped MALDI matrix, glycans were directly released as ISD fragment ions from the intact mAbs during the ionization process. Measurement of 0,2A fragment signals yielded reproducible glycan profiles that were consistent with conventional methods, yet was achieved with unprecedented speed, providing complementary information to that obtained through intact mass measurement. The methods were applied to standard and glycoengineered trastuzumab and rituximab, allowing rapid glycosylation profiling and structural analysis of glycans by tandem MS of selected ISD fragment ions. This fast approach can facilitate the early-phase development of glycoengineering processes by constraining further in-depth analyses. We envision a broader applicability in studies focused on glycosylation changes in mAbs. Glycoengineering of monoclonal antibodies (mAbs) has the potential to improve the efficacy of biopharmaceuticals, however, monitoring the glycoengineering process by glycosylation analysis often requires a multi-method approach. Here, the authors present a direct glycosylation analysis of intact mAbs by combining conventional ESI-MS of intact glycoforms and MALDI-in-source decay FT-ICR MS of glycan fragments.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01297-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142210250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1038/s42004-024-01279-z
Sanfeng Dong, Hui Huang, Jintian Li, Xiaomei Li, Samuel Jacob Bunu, Yun Yang, Yong Zhang, Qi Jia, Zhijian Xu, Yingxia Li, Hu Zhou, Bo Li, Weiliang Zhu
Multi-functional cysteine-targeting covalent warheads possess significant therapeutic potential in medicinal chemistry and chemical biology. Herein, we present novel unsaturated and asymmetric ketone (oxazolinosene) scaffolds that selectively conjugate cysteine residues of peptides and bovine serum albumin under normal physiological conditions. This unsaturated saccharide depletes GSH in NCI-H1299 cells, leading to anti-tumor effects in vitro. The acetyl group of the ketal moiety on the saccharide ring can be converted to other carboxylic acids in a one-pot synthesis. In this way, the loaded acid can be click-released during cysteine conjugation, making the oxazolinosene a potential multifunctional therapeutic agent. The reaction kinetic model for oxazolinosene conjugation to GSH is well established and was used to evaluate oxazolinosene reactivity. The aforementioned oxazolinosenes were stereoselectively synthesized via a one-step reaction of nitriles with saccharides and conveniently converted into a series of α, β-unsaturated ketone N-glycosides as prevalent synthetic building blocks. The reaction mechanisms of oxazolinosene synthesis were investigated through calculations and validated with control experiments. Overall, these oxazolinosenes can be easily synthesized and developed as cysteine-targeted covalent warheads carrying useful click-releasing groups. Multifunctional cysteine targeting covalent warheads possess significant therapeutic potential in medicinal chemistry and chemical biology. Here, the authors develop an oxazolinosene scaffold from nitrile groups and saccharides that can selectively conjugate cysteine residues within peptides and proteins under physiological conditions, as well as deplete glutathione in cancer cells.
{"title":"Development of ketalized unsaturated saccharides as multifunctional cysteine-targeting covalent warheads","authors":"Sanfeng Dong, Hui Huang, Jintian Li, Xiaomei Li, Samuel Jacob Bunu, Yun Yang, Yong Zhang, Qi Jia, Zhijian Xu, Yingxia Li, Hu Zhou, Bo Li, Weiliang Zhu","doi":"10.1038/s42004-024-01279-z","DOIUrl":"10.1038/s42004-024-01279-z","url":null,"abstract":"Multi-functional cysteine-targeting covalent warheads possess significant therapeutic potential in medicinal chemistry and chemical biology. Herein, we present novel unsaturated and asymmetric ketone (oxazolinosene) scaffolds that selectively conjugate cysteine residues of peptides and bovine serum albumin under normal physiological conditions. This unsaturated saccharide depletes GSH in NCI-H1299 cells, leading to anti-tumor effects in vitro. The acetyl group of the ketal moiety on the saccharide ring can be converted to other carboxylic acids in a one-pot synthesis. In this way, the loaded acid can be click-released during cysteine conjugation, making the oxazolinosene a potential multifunctional therapeutic agent. The reaction kinetic model for oxazolinosene conjugation to GSH is well established and was used to evaluate oxazolinosene reactivity. The aforementioned oxazolinosenes were stereoselectively synthesized via a one-step reaction of nitriles with saccharides and conveniently converted into a series of α, β-unsaturated ketone N-glycosides as prevalent synthetic building blocks. The reaction mechanisms of oxazolinosene synthesis were investigated through calculations and validated with control experiments. Overall, these oxazolinosenes can be easily synthesized and developed as cysteine-targeted covalent warheads carrying useful click-releasing groups. Multifunctional cysteine targeting covalent warheads possess significant therapeutic potential in medicinal chemistry and chemical biology. Here, the authors develop an oxazolinosene scaffold from nitrile groups and saccharides that can selectively conjugate cysteine residues within peptides and proteins under physiological conditions, as well as deplete glutathione in cancer cells.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01279-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Although luminescent aluminum compounds have been utilized for emitting and electron transporting layers in organic light-emitting diodes, most of them often exhibit not phosphorescence but fluorescence with lower photoluminescent quantum yields in the aggregated state than those in the amorphous state due to concentration quenching. Here we show the synthesis and optical properties of β-diketiminate aluminum complexes, such as crystallization-induced emission (CIE) and room-temperature phosphorescence (RTP), and the substituent effects of the central element. The dihaloaluminum complexes were found to exhibit the CIE property, especially RTP from the diiodo complex, while the dialkyl ones showed almost no emission in both solution and solid states. Theoretical calculations suggested that undesired structural relaxation in the singlet excited state of dialkyl complexes should be suppressed by introducing electronegative halogens instead of alkyl groups. Our findings could provide a molecular design not only for obtaining luminescent complexes but also for achieving triplet-harvesting materials. Luminescent aluminum compounds have been utilized for emitting and electron transporting layers in organic light-emitting diodes, but most exhibit fluorescence as opposed to phosphorescence. Here, the photophysical properties of β-diketiminate aluminum complexes are shown to depend on the nature of the metal substituents, with a diiodoaluminum complex displaying room temperature phosphorescence.
{"title":"Regulating the photoluminescence of aluminium complexes from non-luminescence to room-temperature phosphorescence by tuning the metal substituents","authors":"Shunichiro Ito, Takuya Hosokai, Kazuo Tanaka, Yoshiki Chujo","doi":"10.1038/s42004-024-01295-z","DOIUrl":"10.1038/s42004-024-01295-z","url":null,"abstract":"Although luminescent aluminum compounds have been utilized for emitting and electron transporting layers in organic light-emitting diodes, most of them often exhibit not phosphorescence but fluorescence with lower photoluminescent quantum yields in the aggregated state than those in the amorphous state due to concentration quenching. Here we show the synthesis and optical properties of β-diketiminate aluminum complexes, such as crystallization-induced emission (CIE) and room-temperature phosphorescence (RTP), and the substituent effects of the central element. The dihaloaluminum complexes were found to exhibit the CIE property, especially RTP from the diiodo complex, while the dialkyl ones showed almost no emission in both solution and solid states. Theoretical calculations suggested that undesired structural relaxation in the singlet excited state of dialkyl complexes should be suppressed by introducing electronegative halogens instead of alkyl groups. Our findings could provide a molecular design not only for obtaining luminescent complexes but also for achieving triplet-harvesting materials. Luminescent aluminum compounds have been utilized for emitting and electron transporting layers in organic light-emitting diodes, but most exhibit fluorescence as opposed to phosphorescence. Here, the photophysical properties of β-diketiminate aluminum complexes are shown to depend on the nature of the metal substituents, with a diiodoaluminum complex displaying room temperature phosphorescence.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01295-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-07DOI: 10.1038/s42004-024-01288-y
Guiyeoul Lim, Donato Calabrese, Allison Wolder, Paul R. F. Cordero, Dörte Rother, Florian F. Mulks, Caroline E. Paul, Lars Lauterbach
Despite the increasing demand for efficient and sustainable chemical processes, the development of scalable systems using biocatalysis for fine chemical production remains a significant challenge. We have developed a scalable flow system using immobilized enzymes to facilitate flavin-dependent biocatalysis, targeting as a proof-of-concept asymmetric alkene reduction. The system integrates a flavin-dependent Old Yellow Enzyme (OYE) and a soluble hydrogenase to enable H2-driven regeneration of the OYE cofactor FMNH2. Molecular hydrogen was produced by water electrolysis using a proton exchange membrane (PEM) electrolyzer and introduced into the flow system via a designed gas membrane addition module at a high diffusion rate. The flow system shows remarkable stability and reusability, consistently achieving >99% conversion of ketoisophorone to levodione. It also demonstrates versatility and selectivity in reducing various cyclic enones and can be extended to further flavin-based biocatalytic approaches and gas-dependent reactions. This electro-driven continuous flow system, therefore, has significant potential for advancing sustainable processes in fine chemical synthesis. Flavin-based biocatalysis using flavin mononucleotide (FMN) cofactor attracts significant attention for its application in asymmetric alkene reduction and various other reactions, however, the scale-up of flavin-based biocatalysis in flow remains unexplored. Here, the authors develop a closed-loop flow platform for H2-driven regeneration of cofactor FMNH2 and ene-reduction using immobilized Old Yellow Enzyme, achieving >99% conversion of ketoisophorone to levodione.
{"title":"H2-driven biocatalysis for flavin-dependent ene-reduction in a continuous closed-loop flow system utilizing H2 from water electrolysis","authors":"Guiyeoul Lim, Donato Calabrese, Allison Wolder, Paul R. F. Cordero, Dörte Rother, Florian F. Mulks, Caroline E. Paul, Lars Lauterbach","doi":"10.1038/s42004-024-01288-y","DOIUrl":"10.1038/s42004-024-01288-y","url":null,"abstract":"Despite the increasing demand for efficient and sustainable chemical processes, the development of scalable systems using biocatalysis for fine chemical production remains a significant challenge. We have developed a scalable flow system using immobilized enzymes to facilitate flavin-dependent biocatalysis, targeting as a proof-of-concept asymmetric alkene reduction. The system integrates a flavin-dependent Old Yellow Enzyme (OYE) and a soluble hydrogenase to enable H2-driven regeneration of the OYE cofactor FMNH2. Molecular hydrogen was produced by water electrolysis using a proton exchange membrane (PEM) electrolyzer and introduced into the flow system via a designed gas membrane addition module at a high diffusion rate. The flow system shows remarkable stability and reusability, consistently achieving >99% conversion of ketoisophorone to levodione. It also demonstrates versatility and selectivity in reducing various cyclic enones and can be extended to further flavin-based biocatalytic approaches and gas-dependent reactions. This electro-driven continuous flow system, therefore, has significant potential for advancing sustainable processes in fine chemical synthesis. Flavin-based biocatalysis using flavin mononucleotide (FMN) cofactor attracts significant attention for its application in asymmetric alkene reduction and various other reactions, however, the scale-up of flavin-based biocatalysis in flow remains unexplored. Here, the authors develop a closed-loop flow platform for H2-driven regeneration of cofactor FMNH2 and ene-reduction using immobilized Old Yellow Enzyme, achieving >99% conversion of ketoisophorone to levodione.","PeriodicalId":10529,"journal":{"name":"Communications Chemistry","volume":null,"pages":null},"PeriodicalIF":5.9,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s42004-024-01288-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142145335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：