Signal transducer and activator of transcription 3 (STAT3) is an attractive cancer therapeutic target. Unfortunately, targeting STAT3 with small molecules has proven to be very challenging, and for full activation of STAT3, the cooperative phosphorylation of both tyrosine 705 (Tyr705) and serine 727 (Ser727) is needed. Further, a selective inhibitor of STAT3 dual phosphorylation has not been developed. Here, we identified a low nanomolar potency and highly selective small-molecule STAT3 inhibitor that simultaneously inhibits both STAT3 Tyr705 and Ser727 phosphorylation. YY002 potently inhibited STAT3-dependent tumor cell growth in vitro and achieved potent suppression of tumor growth and metastasis in vivo. More importantly, YY002 exhibited favorable pharmacokinetics, an acceptable safety profile, and superior antitumor efficacy compared to BBI608 (STAT3 inhibitor that has advanced into phase III trials). For the mechanism, YY002 is selectively bound to the STAT3 Src Homology 2 (SH2) domain over other STAT members, which strongly suppressed STAT3 nuclear and mitochondrial functions in STAT3-dependent cells. Collectively, this study suggests the potential of small-molecule STAT3 inhibitors as possible anticancer therapeutic agents.
YY002 is the highly selective and potent small molecular inhibitor that simultaneously inhibited STAT3 Tyr705 and Ser727 phosphorylation, demonstrating promising antitumor activity.
{"title":"Discovery of the Highly Selective and Potent STAT3 Inhibitor for Pancreatic Cancer Treatment","authors":"Huang Chen, Aiwu Bian, Wenbo Zhou, Ying Miao, Jiangnan Ye, Jiahui Li, Peng He, Qiansen Zhang, Yue Sun, Zhenliang Sun, Chaowen Ti, Yihua Chen*, Zhengfang Yi* and Mingyao Liu*, ","doi":"10.1021/acscentsci.3c01440","DOIUrl":"10.1021/acscentsci.3c01440","url":null,"abstract":"<p >Signal transducer and activator of transcription 3 (STAT3) is an attractive cancer therapeutic target. Unfortunately, targeting STAT3 with small molecules has proven to be very challenging, and for full activation of STAT3, the cooperative phosphorylation of both tyrosine 705 (Tyr705) and serine 727 (Ser727) is needed. Further, a selective inhibitor of STAT3 dual phosphorylation has not been developed. Here, we identified a low nanomolar potency and highly selective small-molecule STAT3 inhibitor that simultaneously inhibits both STAT3 Tyr705 and Ser727 phosphorylation. YY002 potently inhibited STAT3-dependent tumor cell growth <i>in vitro</i> and achieved potent suppression of tumor growth and metastasis <i>in vivo</i>. More importantly, YY002 exhibited favorable pharmacokinetics, an acceptable safety profile, and superior antitumor efficacy compared to BBI608 (STAT3 inhibitor that has advanced into phase III trials). For the mechanism, YY002 is selectively bound to the STAT3 Src Homology 2 (SH2) domain over other STAT members, which strongly suppressed STAT3 nuclear and mitochondrial functions in STAT3-dependent cells. Collectively, this study suggests the potential of small-molecule STAT3 inhibitors as possible anticancer therapeutic agents.</p><p >YY002 is the highly selective and potent small molecular inhibitor that simultaneously inhibited STAT3 Tyr705 and Ser727 phosphorylation, demonstrating promising antitumor activity.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01440","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139766834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-08DOI: 10.1021/acscentsci.3c01372
Chao Duan, and , Rui Wang*,
Protein aggregation via liquid–liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.
This work uses a simple theory to capture the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect in the liquid−liquid phase separation of proteins.
{"title":"A Unified Description of Salt Effects on the Liquid–Liquid Phase Separation of Proteins","authors":"Chao Duan, and , Rui Wang*, ","doi":"10.1021/acscentsci.3c01372","DOIUrl":"10.1021/acscentsci.3c01372","url":null,"abstract":"<p >Protein aggregation via liquid–liquid phase separation (LLPS) is ubiquitous in nature and is intimately connected to many human diseases. Although it is widely known that the addition of salt has crucial impacts on the LLPS of proteins, full understanding of the salt effects remains an outstanding challenge. Here, we develop a molecular theory that systematically incorporates the self-consistent field theory for charged macromolecules into the solution thermodynamics. The electrostatic interaction, hydrophobicity, ion solvation, and translational entropy are included in a unified framework. Our theory fully captures the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect. We find that proteins show salting-out at low salt concentrations due to ionic screening. The solubility follows the inverse Hofmeister series. In the high salt concentration regime, protein continues salting-out for small ions but turns to salting-in for larger ions, accompanied by the reversal of the Hofmeister series. We reveal that the solubility at high salt concentrations is determined by the competition between the solvation energy and translational entropy of the ion. Furthermore, we derive an analytical criterion for determining the boundary between the salting-in and salting-out regimes, which is in good agreement with experimental results for various proteins and salt ions.</p><p >This work uses a simple theory to capture the long-standing puzzles of the nonmonotonic salt concentration dependence and the specific ion effect in the liquid−liquid phase separation of proteins.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01372","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-08DOI: 10.1021/acscentsci.4c00159
Robin Donovan,
As climate change accelerates, small populations are influencing ecosystems more than they used to.
随着气候变化的加速,小种群对生态系统的影响比以往更大。
{"title":"Zoogeochemists Measure How Muddy Animals Change Their Environments’ Chemistry","authors":"Robin Donovan, ","doi":"10.1021/acscentsci.4c00159","DOIUrl":"10.1021/acscentsci.4c00159","url":null,"abstract":"<p >As climate change accelerates, small populations are influencing ecosystems more than they used to.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.4c00159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-07DOI: 10.1021/acscentsci.3c01598
Cristina Di Carluccio, Linda Cerofolini, Miguel Moreira, Frédéric Rosu, Luis Padilla-Cortés, Giulia Roxana Gheorghita, Zhuojia Xu, Abhishek Santra, Hai Yu, Shinji Yokoyama, Taylor E. Gray, Chris D. St. Laurent, Yoshiyuki Manabe, Xi Chen, Koichi Fukase, Matthew S. Macauley, Antonio Molinaro, Tiehai Li, Barbara A. Bensing, Roberta Marchetti*, Valérie Gabelica, Marco Fragai and Alba Silipo*,
Streptococcus gordonii is a Gram-positive bacterial species that typically colonizes the human oral cavity, but can also cause local or systemic diseases. Serine-rich repeat (SRR) glycoproteins exposed on the S. gordonii bacterial surface bind to sialylated glycans on human salivary, plasma, and platelet glycoproteins, which may contribute to oral colonization as well as endocardial infections. Despite a conserved overall domain organization of SRR adhesins, the Siglec-like binding regions (SLBRs) are highly variable, affecting the recognition of a wide range of sialoglycans. SLBR-N from the SRR glycoprotein of S. gordonii UB10712 possesses the remarkable ability to recognize complex core 2 O-glycans. We here employed a multidisciplinary approach, including flow cytometry, native mass spectrometry, isothermal titration calorimetry, NMR spectroscopy from both protein and ligand perspectives, and computational methods, to investigate the ligand specificity and binding preferences of SLBR-N when interacting with mono- and disialylated core 2 O-glycans. We determined the means by which SLBR-N preferentially binds branched α2,3-disialylated core 2 O-glycans: a selected conformation of the 3′SLn branch is accommodated into the main binding site, driving the sTa branch to further interact with the protein. At the same time, SLBR-N assumes an open conformation of the CD loop of the glycan-binding pocket, allowing one to accommodate the entire complex core 2 O-glycan. These findings establish the basis for the generation of novel tools for the detection of specific complex O-glycan structures and pave the way for the design and development of potential therapeutics against streptococcal infections.
A multidisciplinary approach combining NMR spectroscopy, native mass spectrometry, flow cytometry, ITC and MD simulation unveiled the binding details of core 2 O-glycans to the Siglec-like adhesin SLBR-N of S. gordonii.
戈登链球菌(Streptococcus gordonii)是一种革兰氏阳性细菌,通常在人的口腔中定植,但也可引起局部或全身性疾病。暴露在戈登链球菌表面的富丝氨酸重复(SRR)糖蛋白与人类唾液、血浆和血小板糖蛋白上的糖基化聚糖结合,这可能会导致口腔定植和心内膜感染。尽管 SRR 粘附蛋白的整体结构域是保守的,但 Siglec 样结合区(SLBR)的变化很大,影响了对多种聚糖的识别。来自 S. gordonii UB10712 的 SRR 糖蛋白的 SLBR-N 具有识别复杂的核心 2 O-聚糖的非凡能力。在此,我们采用了一种多学科方法,包括流式细胞术、原生质谱法、等温滴定量热法、从蛋白质和配体角度进行的核磁共振波谱分析以及计算方法,来研究 SLBR-N 与单酰化和二酰化核心 2 O-聚糖相互作用时的配体特异性和结合偏好。我们确定了 SLBR-N 优先结合支化的 α2,3-二氨酰化核心 2 O-聚糖的方式:3′SLn 支的选定构象被容纳到主结合位点,驱动 sTa 支进一步与蛋白质相互作用。与此同时,SLBR-N 在聚糖结合袋的 CD 环上呈现开放构象,从而可以容纳整个复合核心 2 O-聚糖。这些发现为开发新型工具检测特定的复合 O 型糖结构奠定了基础,并为设计和开发潜在的链球菌感染治疗药物铺平了道路。
{"title":"Molecular Insights into O-Linked Sialoglycans Recognition by the Siglec-Like SLBR-N (SLBRUB10712) of Streptococcus gordonii","authors":"Cristina Di Carluccio, Linda Cerofolini, Miguel Moreira, Frédéric Rosu, Luis Padilla-Cortés, Giulia Roxana Gheorghita, Zhuojia Xu, Abhishek Santra, Hai Yu, Shinji Yokoyama, Taylor E. Gray, Chris D. St. Laurent, Yoshiyuki Manabe, Xi Chen, Koichi Fukase, Matthew S. Macauley, Antonio Molinaro, Tiehai Li, Barbara A. Bensing, Roberta Marchetti*, Valérie Gabelica, Marco Fragai and Alba Silipo*, ","doi":"10.1021/acscentsci.3c01598","DOIUrl":"10.1021/acscentsci.3c01598","url":null,"abstract":"<p ><i>Streptococcus gordonii</i> is a Gram-positive bacterial species that typically colonizes the human oral cavity, but can also cause local or systemic diseases. Serine-rich repeat (SRR) glycoproteins exposed on the <i>S. gordonii</i> bacterial surface bind to sialylated glycans on human salivary, plasma, and platelet glycoproteins, which may contribute to oral colonization as well as endocardial infections. Despite a conserved overall domain organization of SRR adhesins, the Siglec-like binding regions (SLBRs) are highly variable, affecting the recognition of a wide range of sialoglycans. SLBR-N from the SRR glycoprotein of <i>S. gordonii</i> UB10712 possesses the remarkable ability to recognize complex core 2 <i>O</i>-glycans. We here employed a multidisciplinary approach, including flow cytometry, native mass spectrometry, isothermal titration calorimetry, NMR spectroscopy from both protein and ligand perspectives, and computational methods, to investigate the ligand specificity and binding preferences of SLBR-N when interacting with mono- and disialylated core 2 <i>O</i>-glycans. We determined the means by which SLBR-N preferentially binds branched α2,3-disialylated core 2 <i>O</i>-glycans: a selected conformation of the 3′SLn branch is accommodated into the main binding site, driving the sTa branch to further interact with the protein. At the same time, SLBR-N assumes an open conformation of the CD loop of the glycan-binding pocket, allowing one to accommodate the entire complex core 2 <i>O</i>-glycan. These findings establish the basis for the generation of novel tools for the detection of specific complex <i>O</i>-glycan structures and pave the way for the design and development of potential therapeutics against streptococcal infections.</p><p >A multidisciplinary approach combining NMR spectroscopy, native mass spectrometry, flow cytometry, ITC and MD simulation unveiled the binding details of core 2 <i>O</i>-glycans to the Siglec-like adhesin SLBR-N of <i>S. gordonii</i>.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01598","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-07DOI: 10.1021/acscentsci.3c01340
Angela Casini*, and , Alexander Pöthig,
The discovery of the medicinal properties of platinum complexes has fueled the design and synthesis of new anticancer metallodrugs endowed with unique modes of action (MoA). Among the various families of experimental antiproliferative agents, organometallics have emerged as ideal platforms to control the compounds’ reactivity and stability in a physiological environment. This is advantageous to efficiently deliver novel prodrug activation strategies, as well as to design metallodrugs acting only via noncovalent interactions with their pharmacological targets. Noteworthy, another justification for the advance of organometallic compounds for therapy stems from their ability to catalyze bioorthogonal reactions in cancer cells. When not yet ideal as drug leads, such compounds can be used as selective chemical tools that benefit from the advantages of catalytic amplification to either label the target of interest (e.g., proteins) or boost the output of biochemical signals. Examples of metallodrugs for the so-called “catalysis in cells” are considered in this Outlook together with other organometallic drug candidates. The selected case studies are discussed in the frame of more general challenges in the field of medicinal inorganic chemistry.
The unique and exceptional features of metal-based compounds, markedly distinct from classical small-molecule organic drugs, are at the frontiers in the progress of cancer therapy and drug discovery.
{"title":"Metals in Cancer Research: Beyond Platinum Metallodrugs","authors":"Angela Casini*, and , Alexander Pöthig, ","doi":"10.1021/acscentsci.3c01340","DOIUrl":"10.1021/acscentsci.3c01340","url":null,"abstract":"<p >The discovery of the medicinal properties of platinum complexes has fueled the design and synthesis of new anticancer metallodrugs endowed with unique modes of action (MoA). Among the various families of experimental antiproliferative agents, organometallics have emerged as ideal platforms to control the compounds’ reactivity and stability in a physiological environment. This is advantageous to efficiently deliver novel prodrug activation strategies, as well as to design metallodrugs acting only via noncovalent interactions with their pharmacological targets. Noteworthy, another justification for the advance of organometallic compounds for therapy stems from their ability to catalyze bioorthogonal reactions in cancer cells. When not yet ideal as drug leads, such compounds can be used as selective chemical tools that benefit from the advantages of catalytic amplification to either label the target of interest (e.g., proteins) or boost the output of biochemical signals. Examples of metallodrugs for the so-called “catalysis in cells” are considered in this Outlook together with other organometallic drug candidates. The selected case studies are discussed in the frame of more general challenges in the field of medicinal inorganic chemistry.</p><p >The unique and exceptional features of metal-based compounds, markedly distinct from classical small-molecule organic drugs, are at the frontiers in the progress of cancer therapy and drug discovery.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01340","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-07DOI: 10.1021/acscentsci.3c01363
Le-Le Zhu, Qingyu Yang, De-Gao Wang, Luo Niu, Zhuo Pan, Shengying Li, Yue-Zhong Li*, Wei Zhang* and Changsheng Wu*,
Myxobacteria are a prolific source of secondary metabolites with sheer chemical complexity, intriguing biosynthetic enzymology, and diverse biological activities. In this study, we report the discovery, biosynthesis, biomimetic total synthesis, physiological function, structure–activity relationship, and self-resistance mechanism of the 5-methylated pyrazinone coralinone from a myxobacterium Corallococcus exiguus SDU70. A single NRPS/PKS gene corA was genetically and biochemically demonstrated to orchestrate coralinone, wherein the integral PKS part is responsible for installing the 5-methyl group. Intriguingly, coralinone exacerbated cellular aggregation of myxobacteria grown in liquid cultures by enhancing the secretion of extracellular matrix, and the 5-methylation is indispensable for the alleged activity. We provided an evolutionary landscape of the corA-associated biosynthetic gene clusters (BGCs) distributed in the myxobacterial realm, revealing the divergent evolution for the diversity-oriented biosynthesis of 5-alkyated pyrazinones. This phylogenetic contextualization provoked us to identify corB located in the proximity of corA as a self-resistance gene. CorB was experimentally verified to be a protease that hydrolyzes extracellular proteins to antagonize the agglutination-inducing effect of coralinone. Overall, we anticipate these findings will provide new insights into the chemical ecology of myxobacteria and lay foundations for the maximal excavation of these largely underexplored resources.
corA autonomously codes for 5-methylated pyrazinone that promotes secretion of extracellular matrix to induce agglutination of myxobacteria, and corB encoding a protease is the self-resistance gene.
{"title":"Deciphering the Biosynthesis and Physiological Function of 5-Methylated Pyrazinones Produced by Myxobacteria","authors":"Le-Le Zhu, Qingyu Yang, De-Gao Wang, Luo Niu, Zhuo Pan, Shengying Li, Yue-Zhong Li*, Wei Zhang* and Changsheng Wu*, ","doi":"10.1021/acscentsci.3c01363","DOIUrl":"10.1021/acscentsci.3c01363","url":null,"abstract":"<p >Myxobacteria are a prolific source of secondary metabolites with sheer chemical complexity, intriguing biosynthetic enzymology, and diverse biological activities. In this study, we report the discovery, biosynthesis, biomimetic total synthesis, physiological function, structure–activity relationship, and self-resistance mechanism of the 5-methylated pyrazinone coralinone from a myxobacterium <i>Corallococcus exiguus</i> SDU70. A single NRPS/PKS gene <i>corA</i> was genetically and biochemically demonstrated to orchestrate coralinone, wherein the integral PKS part is responsible for installing the 5-methyl group. Intriguingly, coralinone exacerbated cellular aggregation of myxobacteria grown in liquid cultures by enhancing the secretion of extracellular matrix, and the 5-methylation is indispensable for the alleged activity. We provided an evolutionary landscape of the <i>corA</i>-associated biosynthetic gene clusters (BGCs) distributed in the myxobacterial realm, revealing the divergent evolution for the diversity-oriented biosynthesis of 5-alkyated pyrazinones. This phylogenetic contextualization provoked us to identify <i>corB</i> located in the proximity of <i>corA</i> as a self-resistance gene. CorB was experimentally verified to be a protease that hydrolyzes extracellular proteins to antagonize the agglutination-inducing effect of coralinone. Overall, we anticipate these findings will provide new insights into the chemical ecology of myxobacteria and lay foundations for the maximal excavation of these largely underexplored resources.</p><p ><i>corA</i> autonomously codes for 5-methylated pyrazinone that promotes secretion of extracellular matrix to induce agglutination of myxobacteria, and <i>corB</i> encoding a protease is the self-resistance gene.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01363","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139766845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-07DOI: 10.1021/acscentsci.3c01507
Xuemei Yang, Ruohan Wei, Han Liu, Tongyao Wei, Ping Zeng, Yan Chu Cheung, Heng Heng, Edward Waichi Chan, Xuechen Li* and Sheng Chen*,
The therapeutic effects of antibodies include neutralization of pathogens, activation of the host complement system, and facilitation of phagocytosis of pathogens. However, antibody alone has never been shown to exhibit bactericidal activity. In this study, we developed a monoclonal antibody that targets the bacterial cell surface component Pseudaminic acid (Pse). This monoclonal antibody, Pse-MAB1, exhibited direct bactericidal activity on Acinetobacter baumannii strains, even in the absence of the host complements or other immune factors, and was able to confer a protective effect against A. baumannii infections in mice. This study provides new insight into the potential of developing monoclonal antibody-based antimicrobial therapy of multidrug resistant bacterial infections, especially those which occurred among immunocompromised patients.
Monoclonal antibody targeting Pse was generated by immunization of mice with synthesized Pse-KLH conjugates. Pse-MAB1 could mediate direct bacterial cell death and promote in vivo protection against A. baumannii infection in mice.
{"title":"Discovery of a Monoclonal Antibody That Targets Cell-Surface Pseudaminic Acid of Acinetobacter baumannii with Direct Bactericidal Effect","authors":"Xuemei Yang, Ruohan Wei, Han Liu, Tongyao Wei, Ping Zeng, Yan Chu Cheung, Heng Heng, Edward Waichi Chan, Xuechen Li* and Sheng Chen*, ","doi":"10.1021/acscentsci.3c01507","DOIUrl":"10.1021/acscentsci.3c01507","url":null,"abstract":"<p >The therapeutic effects of antibodies include neutralization of pathogens, activation of the host complement system, and facilitation of phagocytosis of pathogens. However, antibody alone has never been shown to exhibit bactericidal activity. In this study, we developed a monoclonal antibody that targets the bacterial cell surface component Pseudaminic acid (Pse). This monoclonal antibody, Pse-MAB1, exhibited direct bactericidal activity on <i>Acinetobacter baumannii</i> strains, even in the absence of the host complements or other immune factors, and was able to confer a protective effect against <i>A. baumannii</i> infections in mice. This study provides new insight into the potential of developing monoclonal antibody-based antimicrobial therapy of multidrug resistant bacterial infections, especially those which occurred among immunocompromised patients.</p><p >Monoclonal antibody targeting Pse was generated by immunization of mice with synthesized Pse-KLH conjugates. Pse-MAB1 could mediate direct bacterial cell death and promote <i>in vivo</i> protection against <i>A. baumannii</i> infection in mice.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01507","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1021/acscentsci.3c01275
Jason Yang, Francesca-Zhoufan Li and Frances H. Arnold*,
Enzymes can be engineered at the level of their amino acid sequences to optimize key properties such as expression, stability, substrate range, and catalytic efficiency─or even to unlock new catalytic activities not found in nature. Because the search space of possible proteins is vast, enzyme engineering usually involves discovering an enzyme starting point that has some level of the desired activity followed by directed evolution to improve its “fitness” for a desired application. Recently, machine learning (ML) has emerged as a powerful tool to complement this empirical process. ML models can contribute to (1) starting point discovery by functional annotation of known protein sequences or generating novel protein sequences with desired functions and (2) navigating protein fitness landscapes for fitness optimization by learning mappings between protein sequences and their associated fitness values. In this Outlook, we explain how ML complements enzyme engineering and discuss its future potential to unlock improved engineering outcomes.
Machine learning can complement enzyme engineering by helping to discover enzymes with desired function and to accelerate the optimization of enzyme fitness.
可以在氨基酸序列的水平上对酶进行工程改造,以优化酶的关键特性,如表达、稳定性、底物范围和催化效率,甚至释放出在自然界中找不到的新催化活性。由于可能的蛋白质的搜索空间是巨大的,酶工程通常涉及发现一种具有某种程度所需活性的酶的起点,然后进行定向进化,以提高其在所需应用中的 "适应性"。最近,机器学习(ML)作为一种强大的工具出现,成为这一经验过程的补充。ML 模型可以:(1) 通过对已知蛋白质序列进行功能注释或生成具有所需功能的新型蛋白质序列来发现起点;(2) 通过学习蛋白质序列及其相关适应度值之间的映射关系来导航蛋白质适应度景观,从而优化适应度。在本《展望》中,我们将解释 ML 如何与酶工程相辅相成,并讨论其未来在改善工程成果方面的潜力。
{"title":"Opportunities and Challenges for Machine Learning-Assisted Enzyme Engineering","authors":"Jason Yang, Francesca-Zhoufan Li and Frances H. Arnold*, ","doi":"10.1021/acscentsci.3c01275","DOIUrl":"10.1021/acscentsci.3c01275","url":null,"abstract":"<p >Enzymes can be engineered at the level of their amino acid sequences to optimize key properties such as expression, stability, substrate range, and catalytic efficiency─or even to unlock new catalytic activities not found in nature. Because the search space of possible proteins is vast, enzyme engineering usually involves discovering an enzyme starting point that has some level of the desired activity followed by directed evolution to improve its “fitness” for a desired application. Recently, machine learning (ML) has emerged as a powerful tool to complement this empirical process. ML models can contribute to (1) starting point discovery by functional annotation of known protein sequences or generating novel protein sequences with desired functions and (2) navigating protein fitness landscapes for fitness optimization by learning mappings between protein sequences and their associated fitness values. In this Outlook, we explain how ML complements enzyme engineering and discuss its future potential to unlock improved engineering outcomes.</p><p >Machine learning can complement enzyme engineering by helping to discover enzymes with desired function and to accelerate the optimization of enzyme fitness.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-05DOI: 10.1021/acscentsci.3c01284
Tobias Schnitzer, Martin Schnurr, Andrew F. Zahrt, Nader Sakhaee, Scott E. Denmark* and Helma Wennemers*,
Peptides have been established as modular catalysts for various transformations. Still, the vast number of potential amino acid building blocks renders the identification of peptides with desired catalytic activity challenging. Here, we develop a machine-learning workflow for the optimization of peptide catalysts. First─in a hypothetical competition─we challenged our workflow to identify peptide catalysts for the conjugate addition reaction of aldehydes to nitroolefins and compared the performance of the predicted structures with those optimized in our laboratory. On the basis of the positive results, we established a universal training set (UTS) containing 161 catalysts to sample an in silico library of ∼30,000 tripeptide members. Finally, we challenged our machine learning strategy to identify a member of the library as a stereoselective catalyst for an annulation reaction that has not been catalyzed by a peptide thus far. We conclude with a comparison of data-driven versus expert-knowledge-guided peptide catalyst optimization.
Statistical learning methods were challenged to identify enantioselective peptide catalysts from a 30,000-member in silico library and compared with expert-knowledge-guided methods.
{"title":"Machine Learning to Develop Peptide Catalysts─Successes, Limitations, and Opportunities","authors":"Tobias Schnitzer, Martin Schnurr, Andrew F. Zahrt, Nader Sakhaee, Scott E. Denmark* and Helma Wennemers*, ","doi":"10.1021/acscentsci.3c01284","DOIUrl":"10.1021/acscentsci.3c01284","url":null,"abstract":"<p >Peptides have been established as modular catalysts for various transformations. Still, the vast number of potential amino acid building blocks renders the identification of peptides with desired catalytic activity challenging. Here, we develop a machine-learning workflow for the optimization of peptide catalysts. First─in a hypothetical competition─we challenged our workflow to identify peptide catalysts for the conjugate addition reaction of aldehydes to nitroolefins and compared the performance of the predicted structures with those optimized in our laboratory. On the basis of the positive results, we established a universal training set (UTS) containing 161 catalysts to sample an <i>in silico</i> library of ∼30,000 tripeptide members. Finally, we challenged our machine learning strategy to identify a member of the library as a stereoselective catalyst for an annulation reaction that has not been catalyzed by a peptide thus far. We conclude with a comparison of data-driven versus expert-knowledge-guided peptide catalyst optimization.</p><p >Statistical learning methods were challenged to identify enantioselective peptide catalysts from a 30,000-member <i>in silico</i> library and compared with expert-knowledge-guided methods.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c01284","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139767081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-01DOI: 10.1021/acscentsci.3c00777
Meranda M. Masse, Rachel B. Hutchinson, Christopher E. Morgan, Heather J. Allaman, Hongqing Guan, Edward W. Yu and Silvia Cavagnero*,
Interactions between ribosome-bound nascent chains (RNCs) and ribosomal components are critical to elucidate the mechanism of cotranslational protein folding. Nascent protein–ribosome contacts within the ribosomal exit tunnel were previously assessed mostly in the presence of C-terminal stalling sequences, yet little is known about contacts taking place in the absence of these strongly interacting motifs. Further, there is nearly no information about ribosomal proteins (r-proteins) interacting with nascent chains within the outer surface of the ribosome. Here, we combine chemical cross-linking, single-particle cryo-EM, and fluorescence anisotropy decays to determine the structural features of ribosome-bound apomyoglobin (apoMb). Within the ribosomal exit tunnel core, interactions are similar to those identified in previous reports. However, once the RNC enters the tunnel vestibule, it becomes more dynamic and interacts with ribosomal RNA (rRNA) and the L23 r-protein. Remarkably, on the outer surface of the ribosome, RNCs interact mainly with a highly conserved nonpolar patch of the L23 r-protein. RNCs also comprise a compact and dynamic N-terminal region lacking contact with the ribosome. In all, apoMb traverses the ribosome and interacts with it via its C-terminal region, while N-terminal residues sample conformational space and form a compact subdomain before the entire nascent protein sequence departs from the ribosome.
Single-particle cryogenic EM and fluorescence anisotropy decays show that a nascent globin interacts with the L23 ribosomal protein. The interaction site is highly nonpolar, suggesting a chaperone behavior.
核糖体结合新生链(RNC)与核糖体成分之间的相互作用对于阐明共翻译蛋白质折叠机制至关重要。以前对核糖体出口隧道内新生蛋白与核糖体接触情况的评估大多是在存在 C 端停滞序列的情况下进行的,但对于在没有这些强相互作用基团的情况下发生的接触却知之甚少。此外,关于核糖体蛋白(r 蛋白)与核糖体外表面新生链相互作用的信息几乎为零。在这里,我们结合化学交联、单颗粒低温电子显微镜和荧光各向异性衰减来确定核糖体结合的肌红蛋白(apomyoglobin,apoMb)的结构特征。在核糖体出口隧道核心内,相互作用与以前报告中确定的相互作用相似。然而,一旦 RNC 进入隧道前庭,它就会变得更加活跃,并与核糖体 RNA(rRNA)和 L23 r 蛋白相互作用。值得注意的是,在核糖体的外表面,RNC 主要与 L23 r 蛋白的一个高度保守的非极性斑块相互作用。RNC 还包括一个紧凑而动态的 N 端区域,该区域缺乏与核糖体的接触。总之,apoMb穿过核糖体并通过其C端区域与核糖体相互作用,而N端残基则在整个新生蛋白质序列离开核糖体之前对构象空间进行采样并形成一个紧凑的亚域。该相互作用位点高度非极性,表明其具有伴侣行为。
{"title":"Mapping Protein–Protein Interactions at Birth: Single-Particle Cryo-EM Analysis of a Ribosome–Nascent Globin Complex","authors":"Meranda M. Masse, Rachel B. Hutchinson, Christopher E. Morgan, Heather J. Allaman, Hongqing Guan, Edward W. Yu and Silvia Cavagnero*, ","doi":"10.1021/acscentsci.3c00777","DOIUrl":"10.1021/acscentsci.3c00777","url":null,"abstract":"<p >Interactions between ribosome-bound nascent chains (RNCs) and ribosomal components are critical to elucidate the mechanism of cotranslational protein folding. Nascent protein–ribosome contacts within the ribosomal exit tunnel were previously assessed mostly in the presence of C-terminal stalling sequences, yet little is known about contacts taking place in the absence of these strongly interacting motifs. Further, there is nearly no information about ribosomal proteins (r-proteins) interacting with nascent chains within the outer surface of the ribosome. Here, we combine chemical cross-linking, single-particle cryo-EM, and fluorescence anisotropy decays to determine the structural features of ribosome-bound apomyoglobin (apoMb). Within the ribosomal exit tunnel core, interactions are similar to those identified in previous reports. However, once the RNC enters the tunnel vestibule, it becomes more dynamic and interacts with ribosomal RNA (rRNA) and the L23 r-protein. Remarkably, on the outer surface of the ribosome, RNCs interact mainly with a highly conserved nonpolar patch of the L23 r-protein. RNCs also comprise a compact and dynamic N-terminal region lacking contact with the ribosome. In all, apoMb traverses the ribosome and interacts with it via its C-terminal region, while N-terminal residues sample conformational space and form a compact subdomain before the entire nascent protein sequence departs from the ribosome.</p><p >Single-particle cryogenic EM and fluorescence anisotropy decays show that a nascent globin interacts with the L23 ribosomal protein. The interaction site is highly nonpolar, suggesting a chaperone behavior.</p>","PeriodicalId":10,"journal":{"name":"ACS Central Science","volume":null,"pages":null},"PeriodicalIF":18.2,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acscentsci.3c00777","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139685755","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}