ACS Bio & Med Chem Au最新文献

{"title":"Application of Rational Design and Molecular Metadynamics for the Estimation of Changes in Trans-Splicing Efficiency during the Mutagenesis of Ssp DnaE Intein","authors":"Matvei O. Sabantsev,&nbsp;Andrew N. Brovin*,&nbsp;Maxim A. Gureev,&nbsp;Yuri B. Porozov,&nbsp;Sergey A. Chuvpilo and Alexander V. Karabelsky,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00091","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00091","url":null,"abstract":"<p >Currently, inteins are some of the most popular multifunctional tools in the fields of molecular biology and biotechnology. In this study, we used the surface analysis method to identify the sites of intermolecular interactions between the N and C-parts of the Ssp DnaE intein. The obtained results were used to determine the key amino acids that define the binding energy and type of contact between intein subunits. <i>In silico</i> substitution of five neutral amino acids in the C-part of Ssp DnaE with methionine was validated by using oligomutagenesis of a previously assembled plasmid, which was then used for <i>in vitro</i> tests with HEK293 cells. GFP reconstruction assays were used to estimate changes in trans-splicing efficiency using quantitative metrics such as the number of GFP+ cells and median fluorescence intensity as well as qualitative metrics such as microphotography and fluorescence curve analysis using live-cell microscopy. The results of the <i>in vitro</i> tests revealed significantly decreased splicing efficiency in four out of six mutant variants, with no significant differences in the other two cases. Additionally, we performed metadynamics modeling to explain how these mutations affect the molecular mechanisms of intein-intein interactions. Finally, we found a positive correlation between the structural and free energy changes in the local minima distribution and the decrease in splicing efficiency in the I151M and A162M+A165M cases. The resulting method was used with control mutations that had an experimentally confirmed positive (A168H) or negative (T198A) effect on the splicing reaction. In summary, we propose a method of free energy surface analysis in collective variables for quick and visual evaluation of mutation effects. This approach could be applied for the development of new biotechnological and gene therapy products to overcome AAV capacity limitations.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"738–752"},"PeriodicalIF":4.3,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00091","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Thermodynamic Coupling between Folding Correctors and the First of Dimerized Nucleotide Binding Domains in CFTR","authors":"Guangyu Wang*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00014","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00014","url":null,"abstract":"<p >The most common cystic fibrosis mutation is the F508del mutation in the human cystic fibrosis transmembrane conductance regulator (hCFTR), which causes misfolding of the first of two nucleotide binding domains (NBD1/2), preventing Mg/ATP-dependent NBD dimerization for normal function. Although folding correctors elexacaftor/VX-445 and lumacaftor/VX-809 have been combined to correct the NBD1 misfolding, the exact correction pathway is still unknown. In this study, the constrained tertiary noncovalent interaction networks or the thermoring structures of dimerized NBD1 in hCFTR/E1371Q with or without F508del were analyzed to identify the weakest noncovalent bridge as the final post-translational tertiary folding of dimerized NBD1 in response to folding correctors. These computational analyses suggested that hCFTR primarily used cooperative folding between α- and β-subdomains in dimerized NBD1 as the last step upon binding of the potentiator ivacaftor/VX-770. However, the binding of folding correctors allosterically protected the α-subdomain from misfolding until subsequent core formation. This thermodynamic protective mechanism, unlike the chaperone-based one in cotranslational NBD1 folding, may restore posttranslational NBD1 folding for tight Mg/ATP-mediated NBD dimerization in the F508del mutation and also potentially apply to treating other cystic fibrosis patients with rare mutations.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"593–601"},"PeriodicalIF":4.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetic Characterization of F420-Dependent Sugar-6-Phosphate Dehydrogenase from Cryptosporangium arvum","authors":"Alaa Aziz,&nbsp;Desiree R. Czapski,&nbsp;Ravi Ramkissoon,&nbsp;Md Sabid Ahamed,&nbsp;Sarah Al-Noubani,&nbsp;Andrew J. Mier,&nbsp;Oreoluwa Adeleke,&nbsp;Sharel Cornelius,&nbsp;Saiful Chowdhury,&nbsp;Frank W. Foss Jr,&nbsp;Joseph A. Buonomo,&nbsp;Ghader Bashiri and Kayunta L. Johnson-Winters*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00085","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00085","url":null,"abstract":"<p ><i>F</i>₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the oxidation of glucose-6-phosphate (G6P) to 6-phosphogluconolactone (6PG). Recent phylogenetic analyses have identified a new subclass of these enzymes, <i>F</i>₄₂₀-dependent sugar-6-phosphate dehydrogenases (FSDs), which act on a broader range of 6-phosphate sugars, including fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P). One such enzyme from <i>Cryptosporangium arvum</i> (<i>Cryar</i>-FGD) was characterized by using binding assays and kinetic analyses, nuclear magnetic resonance (NMR), and mass spectrometry. Results showed strong binding affinities for all substrates. Steady-state kinetic analysis revealed that G6P has the highest catalytic efficiency, with a <i>k</i>_cat(app) of 6.4 ± 0.2 s^–1, compared to 1.4 ± 0.1 s^–1 for F6P and 0.32 ± 0.02 s^–1 for M6P. Pre steady-state spectral features for the G6P reaction resembled those of <i>Mycobacterium tuberculosis</i> FGD. While the F6P reaction displayed distinct spectral features, <i>F</i>₄₂₀ reduction was still observed. In contrast, the spectra for the M6P reaction were markedly different from those of G6P and F6P. Across all substrates, no catalytic intermediates were detected, and hydride transfer was not rate-limiting. As with G6P, the reaction with F6P also produced 6PG. Notably, NMR data showed that F6P was isomerized to G6P, suggesting isomerase activity. In contrast, M6P induced only spectral shifts with no evidence of isomerization or 6PG formation. However, mass spectrometry confirmed oxidized products for all three sugars, each with a mass of 299.0 ± 0.1. Collectively, these findings reveal that <i>Cryar</i>-FGD exhibits both dehydrogenase and isomerase activity, uncovering a newly identified dual enzymatic function and establishing its role as a multifunctional enzyme.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"726–737"},"PeriodicalIF":4.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00085","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toward a Beautiful Amalgam: The Necessity of Heterogeneity in RNA Science and Research Culture","authors":"Sudeshi M. Abedeera,&nbsp;Mary Donnelly,&nbsp;James Hagerty,&nbsp;Shaila Kolli,&nbsp;Srinivasa R. Penumutchu,&nbsp;Louis G. Smith and Blanton S. Tolbert*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00114","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00114","url":null,"abstract":"<p >RNA biology exemplifies functional heterogeneity─distinct RNA classes are expressed in tissue- and development-specific contexts, adopt dynamic conformational ensembles, and form intricate, context-dependent interactions with proteins and other molecules to regulate gene expression. These features make RNA a powerful metaphor for reimagining scientific culture. Just as RNA achieves biological complexity through versatility, feedback loops, and communication, research environments thrive when they support dynamic interactions, structural adaptability, and the intentional inclusion of divergent perspectives and experiences. However, unlike RNA, research culture is shaped by human behavior, institutional norms, and systemic barriers─forces that can suppress innovation and limit who contributes to scientific discovery. Scientific excellence demands the integration of wide-ranging perspectives to challenge paradigms and push boundaries. Yet entrenched structures often reward conformity and marginalize creativity born from difference. By embracing the principles inherent to RNA biology─contextual responsiveness, structural plasticity, and cooperativity─we can transform scientific culture into one that is more inclusive, welcoming, and adaptable. This perspective argues that the biological elegance of RNA offers more than molecular insight; it provides a conceptual framework for building research environments that harness the full spectrum of talent in our richly heterogeneous society, ultimately accelerating scientific progress and broadening its societal impact.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"519–530"},"PeriodicalIF":4.3,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00114","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introducing the Tutorial Manuscript Type at the ACS Au Community Journals","authors":"Squire J. Booker,&nbsp;Stephanie L. Brock,&nbsp;Xiangdong Li,&nbsp;Géraldine Masson,&nbsp;Sébastien Perrier,&nbsp;Vivek V. Ranade,&nbsp;Raymond E. Schaak,&nbsp;Gemma C. Solomon and Shelley D. Minteer*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00143","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00143","url":null,"abstract":"","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"484–485"},"PeriodicalIF":4.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144862844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Poly-Arginine Tails and Helical Segments of Natural Antimicrobial Peptides Display Concerted Action at Membranes for Enhanced Antimicrobial Effects","authors":"Navleen Kaur,&nbsp;Kinjal Mondal,&nbsp;Megan E. Mitchell,&nbsp;Sarala Padi,&nbsp;Jeffery B. Klauda,&nbsp;Antonio Cardone,&nbsp;Frank Heinrich,&nbsp;Christina R. Harris,&nbsp;David K. Giles,&nbsp;Mary T. Rooney,&nbsp;Erik B. Watkins,&nbsp;Myriam L. Cotten,&nbsp;David P. Hoogerheide and Mihaela Mihailescu*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00084","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00084","url":null,"abstract":"<p >Sequence motifs or patterns found in natural antimicrobial peptides (AMPs) have a great impact on their microbicidal activities. Here, through database inquiries and biological assays, we explore the enhanced antibacterial function associated with poly arginine (poly-R) motifs that typically occur as 3–5 concatenated R residues in many natural AMPs. Using a suite of biophysical techniques, we explore the structural consequences of a C-terminal poly-R motif at membranes and correlate our findings with the functional assays. We use natural peptides, such as Tilapia piscidin 4 (TP4), as an example of how various segments in an AMP play separate and synergistic roles to achieve unmatched bactericidal effects. The function of the poly-R segment is highly consequential since the simple addition of a five-arginine (R5) tail to an otherwise inert and weakly binding helical peptide creates a potent AMP. We investigate interactions of AMPs with lipid bilayers mimicking bacterial membrane compositions, including lipopolysaccharides, to show that the poly-R tail has a key role in initiating membrane destabilization through lipid segregation and water sequestration effects, all of which facilitate insertion and translocation of the amphipathic, α-helical N-terminal segment through the membrane. We compiled a large set of natural AMP sequences and MIC values to show that, statistically, the poly-R sequence motifs have, in average, a greater impact on the overall antimicrobial efficacy than equivalent sequences with poly-K motifs and similar charge densities. We discuss our observations in light of the unique structural and hydration properties of arginine residues.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"706–725"},"PeriodicalIF":4.3,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00084","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bridging Health Disparity Gaps in Alzheimer’s Disease among Marginalized Populations: Clinical Proteomics as a Case Study","authors":"Henry A. Adeola,&nbsp; and ,&nbsp;Renã A. S. Robinson*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00074","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00074","url":null,"abstract":"<p >Alzheimer’s disease (AD) and AD-related dementias (ADRD) represent a significant health challenge, with a growing impact on marginalized populations who often experience inequities in overall healthcare access and outcomes. Many factors contribute to these inequalities and can impact the benefits of broad appreciation of new technologies in AD/ADRD to these populations. For example, clinical proteomics offers a promising avenue for early and timely detection of disease and elucidation of the mechanisms of AD/ADRD. Unfortunately, gaps exist in the access and application of proteomic innovations for the health of marginalized communities. This editorial (1) highlights systemic barriers and explores the underlying factors that contribute to these inequities, (2) examines health disparities in the implementation of clinical proteomics tools for the management of AD/ADRD among marginalized populations, and (3) offers opportunities for advancing clinical proteomics in AD/ADRD. Implementation by basic and clinical researchers will lead to a more effective and inclusive approach to combatting AD/ADRD disparities.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"505–518"},"PeriodicalIF":4.3,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00074","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overcoming Global Antifungal Challenges: Medical and Agricultural Aspects","authors":"László Galgóczy*,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00103","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00103","url":null,"abstract":"<p >The prevalence of fungal infections and contamination has increased alarmingly over the past decade, posing a significant threat to human health and the food supply and negatively affecting welfare. This escalating concern is primarily attributed to the lack of safe, effective, and widely available antifungal agents; the increasing spread of (multi)drug resistance to conventional antifungal treatments; and substantial epidemiological shifts in fungal pathogens. Decision-making bodies have recognized the urgency of this situation and prioritized efforts to address and mitigate the spread of drug-resistant fungal infections by developing and implementing innovative antifungal strategies, including using drug combinations, designing fundamentally new antifungal compounds with fungus-specific mechanisms of action and a minimal risk of resistance development, drug repurposing, and exploring alternative approaches, such as biomolecules, nanotechnology, and biological control. This review aims to provide a comprehensive overview of the current challenges associated with fungal infections in medicine and agriculture as well as the latest advancements and potential solutions.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"531–552"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863059","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Potent Inhibitor of Caspase-8 Based on the IL-18 Tetrapeptide Sequence Reveals Shared Specificities between Inflammatory and Apoptotic Initiator Caspases","authors":"Christopher M. Bourne,&nbsp;Nicole R. Raniszewski,&nbsp;Ashutosh B. Mahale,&nbsp;Madhura Kulkarni,&nbsp;Patrick M. Exconde,&nbsp;Sherry Liu,&nbsp;Winslow Yost,&nbsp;Tristan J. Wrong,&nbsp;Robert C. Patio,&nbsp;Matilda Kardhashi,&nbsp;Teni Shosanya,&nbsp;Mirai Kambayashi,&nbsp;Bohdana M. Discher,&nbsp;Igor E. Brodsky,&nbsp;George M. Burslem* and Cornelius Y. Taabazuing*,&nbsp;","doi":"10.1021/acsbiomedchemau.4c00146","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.4c00146","url":null,"abstract":"<p >Caspases are a family of cysteine proteases that act as molecular scissors to cleave substrates and regulate biological processes, such as programmed cell death and inflammation. Extensive efforts have been made to identify caspase substrates and to determine the factors that dictate specificity. We recently discovered that human inflammatory caspases (caspases-1, -4, and -5) cleave the cytokines IL-1β and IL-18 in a sequence-dependent manner. Here, we report the development of a new peptide-based probe and inhibitor derived from the tetrapeptide sequence of IL-18 (LESD). The LESD-based inhibitor showed a strong preference for caspase-8 with an IC₅₀ of 50 nM, and was more potent <i>in vitro</i> than the commonly used zIETD-FMK inhibitor, which is considered the most selective and potent caspase-8 inhibitor. We further demonstrated that the LESD-based inhibitor prevents caspase-8 activation during <i>Yersinia pseudotuberculosis</i> infection in primary bone marrow-derived macrophages. In addition, we systematically characterized the selectivity and potency of known substrates and inhibitors of the apoptotic and inflammatory caspases using standardized activity units of each caspase. Our findings reveal that VX-765, a known inhibitor of caspases-1 and -4, also inhibits caspase-8 (IC₅₀ = 1 μM). Even when specificities are shared, the caspases exhibit different efficiencies and potencies for shared substrates and inhibitors. Altogether, we report the development of new tools that will facilitate the study of caspases and their roles in biology.</p>","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"565–581"},"PeriodicalIF":4.3,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.4c00146","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ACS Bio & Med Chem Au Recognizes Juneteenth 2025","authors":"Squire J. Booker,&nbsp; and ,&nbsp;Tamra C. Blue-Lahom,&nbsp;","doi":"10.1021/acsbiomedchemau.5c00159","DOIUrl":"https://doi.org/10.1021/acsbiomedchemau.5c00159","url":null,"abstract":"","PeriodicalId":29802,"journal":{"name":"ACS Bio & Med Chem Au","volume":"5 4","pages":"475–483"},"PeriodicalIF":4.3,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acsbiomedchemau.5c00159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}