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1.
Sci Rep ; 14(1): 10787, 2024 05 11.
Article En | MEDLINE | ID: mdl-38734765

Radioligand therapy with [177Lu]Lu-PSMA-617 can be used to prolong life and reduce tumor burden in terminally ill castration resistant prostate cancer patients. Still, accumulation in healthy tissue limits the activity that can be administered. Therefore, fractionated therapy is used to lower toxicity. However, there might be a need to reduce toxicity even further with e.g. radioprotectors. The aim of this study was to (i). establish a preclinical mouse model with fractionated high activity therapy of three consecutive doses of 200 MBq [177Lu]Lu-PSMA-617 in which we aimed to (ii). achieve measurable hematotoxicity and nephrotoxicity and to (iii). analyze the potential protective effect of co-injecting recombinant α1-microglobulin (rA1M), a human antioxidant previously shown to have radioprotective effects. In both groups, three cycles resulted in increased albuminuria for each cycle, with large individual variation. Another marker of kidney injury, serum blood urea nitrogen (BUN), was only significantly increased compared to control animals after the third cycle. The number of white and red blood cells decreased significantly and did not reach the levels of control animals during the experiment. rA1M did reduce absorbed dose to kidney but did not show significant protection here, but future studies are warranted due to the recent clinical studies showing a significant renoprotective effect in patients.


Alpha-Globulins , Dipeptides , Heterocyclic Compounds, 1-Ring , Lutetium , Animals , Alpha-Globulins/metabolism , Mice , Male , Humans , Dipeptides/pharmacology , Kidney/pathology , Kidney/radiation effects , Kidney/drug effects , Kidney/metabolism , Radiopharmaceuticals , Prostatic Neoplasms, Castration-Resistant/radiotherapy , Prostatic Neoplasms, Castration-Resistant/pathology , Blood Urea Nitrogen , Prostate-Specific Antigen
2.
J Chem Phys ; 160(17)2024 May 07.
Article En | MEDLINE | ID: mdl-38748013

Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a number of limitations. In this paper, we address these challenges by introducing a new path-like collective variable called the "deep-locally non-linear-embedding," which is inspired by principles of the locally linear embedding technique and is trained on a reactive trajectory. The variable mimics the ideal reaction coordinate by automatically generating a non-linear combination of features through a differentiable generalized autoencoder that combines a neural network with a continuous k-nearest neighbor selection. Among the key advantages of this method is its capability to automatically choose the metric for searching neighbors and to learn the path from state A to state B without the need to handpick landmarks a priori. We demonstrate the effectiveness of DeepLNE by showing that the progression along the path variable closely approximates the ideal reaction coordinate in toy models, such as the Müller-Brown potential and alanine dipeptide. Then, we use it in the molecular dynamics simulations of an RNA tetraloop, where we highlight its capability to accelerate transitions and estimate the free energy of folding.


Deep Learning , Molecular Dynamics Simulation , RNA/chemistry , Thermodynamics , Dipeptides/chemistry
3.
Cancer Imaging ; 24(1): 57, 2024 May 06.
Article En | MEDLINE | ID: mdl-38711135

BACKGROUND: PSMA PET/CT is a predictive and prognostic biomarker for determining response to [177Lu]Lu-PSMA-617 in patients with metastatic castration resistant prostate cancer (mCRPC). Thresholds defined to date may not be generalizable to newer image reconstruction algorithms. Bayesian penalized likelihood (BPL) reconstruction algorithm is a novel reconstruction algorithm that may improve contrast whilst preventing introduction of image noise. The aim of this study is to compare the quantitative parameters obtained using BPL and the Ordered Subset Expectation Maximization (OSEM) reconstruction algorithms. METHODS: Fifty consecutive patients with mCRPC who underwent [68Ga]Ga-PSMA-11 PET/CT using OSEM reconstruction to assess suitability for [177Lu]Lu-PSMA-617 therapy were selected. BPL algorithm was then used retrospectively to reconstruct the same PET raw data. Quantitative and volumetric measurements such as tumour standardised uptake value (SUV)max, SUVmean and Molecular Tumour Volume (MTV-PSMA) were calculated on both reconstruction methods. Results were compared (Bland-Altman, Pearson correlation coefficient) including subgroups with low and high-volume disease burdens (MTV-PSMA cut-off 40 mL). RESULTS: The SUVmax and SUVmean were higher, and MTV-PSMA was lower in the BPL reconstructed images compared to the OSEM group, with a mean difference of 8.4 (17.5%), 0.7 (8.2%) and - 21.5 mL (-3.4%), respectively. There was a strong correlation between the calculated SUVmax, SUVmean, and MTV-PSMA values in the OSEM and BPL reconstructed images (Pearson r values of 0.98, 0.99, and 1.0, respectively). No patients were reclassified from low to high volume disease or vice versa when switching from OSEM to BPL reconstruction. CONCLUSIONS: [68Ga]Ga-PSMA-11 PET/CT quantitative and volumetric parameters produced by BPL and OSEM reconstruction methods are strongly correlated. Differences are proportional and small for SUVmean, which is used as a predictive biomarker. Our study suggests that both reconstruction methods are acceptable without clinical impact on quantitative or volumetric findings. For longitudinal comparison, committing to the same reconstruction method would be preferred to ensure consistency.


Algorithms , Bayes Theorem , Gallium Isotopes , Gallium Radioisotopes , Positron Emission Tomography Computed Tomography , Prostatic Neoplasms, Castration-Resistant , Humans , Male , Positron Emission Tomography Computed Tomography/methods , Prostatic Neoplasms, Castration-Resistant/diagnostic imaging , Prostatic Neoplasms, Castration-Resistant/pathology , Aged , Middle Aged , Retrospective Studies , Oligopeptides , Edetic Acid/analogs & derivatives , Whole Body Imaging/methods , Radiopharmaceuticals , Aged, 80 and over , Neoplasm Metastasis , Image Processing, Computer-Assisted/methods , Dipeptides/therapeutic use
4.
Appl Microbiol Biotechnol ; 108(1): 326, 2024 May 08.
Article En | MEDLINE | ID: mdl-38717487

Aspartyl dipeptidase (dipeptidase E) can hydrolyze Asp-X dipeptides (where X is any amino acid), and the enzyme plays a key role in the degradation of peptides as nutrient sources. Dipeptidase E remains uncharacterized in Streptomyces. Orf2 from Streptomyces sp. 139 is located in the exopolysaccharide biosynthesis gene cluster, which may be a novel dipeptidase E with "S134-H170-D198" catalytic triad by sequence and structure comparison. Herein, recombinant Orf2 was expressed in E. coli and characterized dipeptidase E activity using the Asp-ρNA substrate. The optimal pH and temperature for Orf2 are 7.5 and 40 ℃; Vmax and Km of Orf2 are 0.0787 mM·min-1 and 1.709 mM, respectively. Orf2 exhibits significant degradation activities to Asp-Gly-Gly, Asp-Leu, Asp-His, and isoAsp-Leu and minimal activities to Asp-Pro and Asp-Ala. Orf2 contains a Ser-His-Asp catalytic triad characterized by point mutation. In addition, the Asp147 residue of Orf2 is also proven to be critical for the enzyme's activity through molecular docking and point mutation. Transcriptome analysis reveals the upregulation of genes associated with ribosomes, amino acid biosynthesis, and aminoacyl-tRNA biosynthesis in the orf2 mutant strain. Compared with the orf2 mutant strain and WT, the yield of crude polysaccharide does not change significantly. However, crude polysaccharides from the orf2 mutant strain exhibit a wider range of molecular weight distribution. The results indicate that the Orf2 links nutrient stress to secondary metabolism as a novel dipeptidase E. KEY POINTS: • A novel dipeptidase E with a Ser-His-Asp catalytic triad was characterized from Streptomyces sp. 139. • Orf2 was involved in peptide metabolism both in vitro and in vivo. • Orf2 linked nutrient stress to mycelia formation and secondary metabolism in Streptomyces.


Escherichia coli , Streptomyces , Streptomyces/genetics , Streptomyces/enzymology , Escherichia coli/genetics , Escherichia coli/metabolism , Substrate Specificity , Dipeptidases/metabolism , Dipeptidases/genetics , Dipeptidases/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Recombinant Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Molecular Docking Simulation , Multigene Family , Hydrogen-Ion Concentration , Dipeptides/metabolism , Temperature , Kinetics
5.
Nat Commun ; 15(1): 4386, 2024 May 23.
Article En | MEDLINE | ID: mdl-38782953

Sialin, a member of the solute carrier 17 (SLC17) transporter family, is unique in its ability to transport not only sialic acid using a pH-driven mechanism, but also transport mono and diacidic neurotransmitters, such as glutamate and N-acetylaspartylglutamate (NAAG), into synaptic vesicles via a membrane potential-driven mechanism. While most transporters utilize one of these mechanisms, the structural basis of how Sialin transports substrates using both remains unclear. Here, we present the cryogenic electron-microscopy structures of human Sialin: apo cytosol-open, apo lumen-open, NAAG-bound, and inhibitor-bound. Our structures show that a positively charged cytosol-open vestibule accommodates either NAAG or the Sialin inhibitor Fmoc-Leu-OH, while its luminal cavity potentially binds sialic acid. Moreover, functional analyses along with molecular dynamics simulations identify key residues in binding sialic acid and NAAG. Thus, our findings uncover the essential conformational states in NAAG and sialic acid transport, demonstrating a working model of SLC17 transporters.


Cryoelectron Microscopy , Molecular Dynamics Simulation , Humans , N-Acetylneuraminic Acid/metabolism , N-Acetylneuraminic Acid/chemistry , Lysosomes/metabolism , HEK293 Cells , Protein Conformation , Organic Anion Transporters/metabolism , Organic Anion Transporters/chemistry , Organic Anion Transporters/antagonists & inhibitors , Dipeptides/chemistry , Dipeptides/metabolism , Dipeptides/pharmacology , Symporters
6.
J Med Chem ; 67(10): 8247-8260, 2024 May 23.
Article En | MEDLINE | ID: mdl-38716576

Prostate-specific membrane antigen (PSMA)-targeted radio ligand therapeutics (RLTs), such as [177Lu]Lu-PSMA-617 (Pluvicto), have been shown to accumulate in salivary glands and kidneys, potentially leading to undesired side effects. As unwanted accumulation in normal organs may derive from the cross-reactivity of PSMA ligands to glutamate carboxypeptidase III (GCPIII), it may be convenient to block this interaction with GCPIII-selective ligands. Parallel screening of a DNA-encoded chemical library (DEL) against GCPIII and PSMA allowed the identification of GCPIII binders. Structure-activity relationship (SAR) studies resulted in the identification of nanomolar GCPIII ligands with up to 1000-fold selectivity over PSMA. We studied the ability of GCPIII ligands to counteract the binding of [177Lu]Lu-PSMA-617 to human salivary glands by autoradiography and could demonstrate a partial radioprotection.


Dipeptides , Heterocyclic Compounds, 1-Ring , Lutetium , Humans , Antigens, Surface , Autoradiography , Dipeptides/chemistry , Dipeptides/metabolism , Glutamate Carboxypeptidase II , Heterocyclic Compounds, 1-Ring/chemistry , Heterocyclic Compounds, 1-Ring/metabolism , Ligands , Lutetium/chemistry , Lutetium/metabolism , Prostate-Specific Antigen , Radioisotopes/chemistry , Radioisotopes/metabolism , Radiopharmaceuticals/chemistry , Radiopharmaceuticals/metabolism , Radiopharmaceuticals/pharmacokinetics , Salivary Glands/metabolism , Structure-Activity Relationship , Tissue Distribution
7.
Exp Cell Res ; 438(2): 114061, 2024 May 15.
Article En | MEDLINE | ID: mdl-38692345

Acute myocardial infarction (AMI) is a prevalent cardiovascular disease with high morbidity and mortality rates worldwide. Pyroptosis is an inflammatory form of programmed cell death that has been linked to various pathological conditions. However, its exact contribution to the onset and progression of heart injury in AMI has not yet fully elucidated. Herein, we established mouse AMI model by ligating the left anterior descending artery and performed transcriptome analysis during the early phase of AMI. Mouse HL-1 and human AC-16 cardiomyocytes were subjected to hypoxia to simulate ischemic injury in vitro. Our results revealed a significant activation of the inflammatory response at 3 h post-ligation, as confirmed by RNA sequencing. We identified the occurrence of NLRP3 inflammasome-mediated pyroptosis in the cardiac tissues of human cases with AMI, as well as in mouse models of AMI and hypoxia-induced cardiomyocytes, using immunohistochemistry staining and Western blotting assays. Concurrently, pharmacological inhibition of NLRP3 inflammasome-mediated pyroptosis with MCC950 and VX-765 effectively decreased hypoxia-induced cardiomyocytes injury, while mitigating myocardial oxidative stress, apoptosis and inflammation caused by hypoxia. Moreover, the circulating levels of gasdermin D (GSDMD), the pyroptosis executor, were remarkably elevated in the plasma of mice with early AMI and in the supernatant of hypoxia-exposed cardiomyocytes in a time-dependent manner using ELISA and Western blotting. Furthermore, the change in circulating GSDMD positively correlated with Creatine Kinase-MB (CK-MB) in the plasma of early-stage AMI mouse. In summary, these findings indicated a critical role for NLRP3 inflammasome-mediated pyroptosis in the progression of AMI, the administration of MCC950 and VX-765 may be attractive candidate therapeutic approaches for cardiac injury caused by acute hypoxia or even AMI. Additionally, the circulating GSDMD exhibits potential as a newly diagnostic biomarker for AMI.


Apoptosis , Furans , Inflammation , Mice, Inbred C57BL , Myocardial Infarction , Myocytes, Cardiac , Oxidative Stress , Pyroptosis , Sulfonamides , Pyroptosis/drug effects , Animals , Mice , Apoptosis/drug effects , Oxidative Stress/drug effects , Sulfonamides/pharmacology , Humans , Inflammation/metabolism , Inflammation/pathology , Inflammation/drug therapy , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/drug effects , Myocytes, Cardiac/pathology , Male , Furans/pharmacology , Myocardial Infarction/metabolism , Myocardial Infarction/pathology , Myocardial Infarction/drug therapy , Indenes/pharmacology , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , para-Aminobenzoates/pharmacology , Inflammasomes/metabolism , Inflammasomes/drug effects , Disease Models, Animal , Myocardium/metabolism , Myocardium/pathology , Hypoxia/metabolism , Hypoxia/complications , Dipeptides
8.
BMJ Open Diabetes Res Care ; 12(3)2024 May 06.
Article En | MEDLINE | ID: mdl-38719505

INTRODUCTION: There has been increasing evidence that the gut microbiota is closely related to type 2 diabetes (T2D). Metformin (Met) is often used in combination with saxagliptin (Sax) and repaglinide (Rep) for the treatment of T2D. However, little is known about the effects of these combination agents on gut microbiota in T2D. RESEARCH DESIGN AND METHODS: A T2D mouse model induced by a high-fat diet (HFD) and streptozotocin (STZ) was employed. The T2D mice were randomly divided into six groups, including sham, Met, Sax, Rep, Met+Sax and Met+Rep, for 4 weeks. Fasting blood glucose level, serum biochemical index, H&E staining of liver, Oil red O staining of liver and microbiota analysis by 16s sequencing were used to access the microbiota in the fecal samples. RESULTS: These antidiabetics effectively prevented the development of HFD/STZ-induced high blood glucose, and the combination treatment had a better effect in inhibiting lipid accumulation. All these dosing regimens restored the decreasing ratio of the phylum Bacteroidetes: Firmicutes, and increasing abundance of phylum Desulfobacterota, expect for Met. At the genus level, the antidiabetics restored the decreasing abundance of Muribaculaceae in T2D mice, but when Met was combined with Rep or Sax, the abundance of Muribaculaceae was decreased. The combined treatment could restore the reduced abundance of Prevotellaceae_UCG-001, while Met monotherapy had no such effect. In addition, the reduced Lachnospiraceae_NK4A136_group was well restored in the combination treatment groups, and the effect was much greater than that in the corresponding monotherapy group. Therefore, these dosing regimens exerted different effects on the composition of gut microbiota, which might be associated with the effect on T2D. CONCLUSIONS: Supplementation with specific probiotics may further improve the hypoglycemic effects of antidiabetics and be helpful for the development of new therapeutic drugs for T2D.


Adamantane , Blood Glucose , Carbamates , Diabetes Mellitus, Experimental , Diabetes Mellitus, Type 2 , Diet, High-Fat , Dipeptides , Gastrointestinal Microbiome , Hypoglycemic Agents , Metformin , Piperidines , Animals , Gastrointestinal Microbiome/drug effects , Metformin/pharmacology , Metformin/therapeutic use , Mice , Diet, High-Fat/adverse effects , Diabetes Mellitus, Type 2/drug therapy , Diabetes Mellitus, Type 2/microbiology , Hypoglycemic Agents/pharmacology , Hypoglycemic Agents/therapeutic use , Diabetes Mellitus, Experimental/drug therapy , Carbamates/pharmacology , Dipeptides/pharmacology , Male , Adamantane/analogs & derivatives , Adamantane/pharmacology , Adamantane/therapeutic use , Piperidines/pharmacology , Piperidines/therapeutic use , Blood Glucose/analysis , Blood Glucose/drug effects , Mice, Inbred C57BL , Drug Therapy, Combination , Streptozocin
9.
J Chromatogr A ; 1726: 464966, 2024 Jul 05.
Article En | MEDLINE | ID: mdl-38735116

Chromatographic behavior of novel chiral stationary phases with bonded selectors based on Cinchona alkaloids modified with dipeptides was studied using dipeptides as probe molecules. Buffer-free and salt containing hydro-organic solutions were used as the mobile phases. The selectors exhibit pseudoenantiomeric behavior with respect to the L/D or LL/DD enantiomers and do not behave so with respect to the LD/DL enantiomers. The alkaloid part of the selectors is the driver of enantioselectivity, while the dipeptide substituent plays a modulating role. The quinidine-based selectors demonstrate stronger adsorption affinity and higher enantioselectivity as compared to the quinine-based selectors. The dipeptide analytes containing a glycyl fragment are weaker retained and their enantiomers are worse separated comparing to dipeptides with both units being larger amino acids. Moreover, a phenyl group in the structure of a dipeptide analyte facilitates enantioseparation. The effect of the mobile phase composition on retention depends on the hydrophobicity of an analyte. Hydrophobic dipeptides are better eluted by methanol-rich solvents, hydrophilic dipeptides are better eluted with water-rich solvents, and dipeptides with an intermediate hydrophobicity demonstrate a U-shaped or more complicated dependence of the retention factor on the percentage of methanol. Even a small buffer addition to the mobile phase decreases retention, but the ion-exchange mechanism was not confirmed. The effect of an electrolyte is rather due to the shielding of the charged groups of the selector reducing thereby electrostatic interaction between the selector and analyte. Efficiency of the novel columns is comparable to that of other brush-type chiral columns, the highest achieved number of the theoretical plates per 1 m varying between 30,000 and 40,000.


Chromatography, Reverse-Phase , Cinchona Alkaloids , Dipeptides , Hydrophobic and Hydrophilic Interactions , Cinchona Alkaloids/chemistry , Dipeptides/chemistry , Dipeptides/isolation & purification , Stereoisomerism , Chromatography, Reverse-Phase/methods , Chromatography, High Pressure Liquid/methods , Quinine/chemistry , Quinine/isolation & purification
10.
Cancer Treat Rev ; 127: 102748, 2024 Jun.
Article En | MEDLINE | ID: mdl-38703593

Clinical trials of prostate-specific membrane antigen (PSMA) targeted radiopharmaceuticals have shown encouraging results. Some agents, like lutetium-177 [177Lu]Lu-PSMA-617 ([177Lu]Lu-PSMA-617), are already approved for late line treatment of metastatic castration-resistant prostate cancer (mCRPC). Projections are for continued growth of this treatment modality; [177Lu]Lu-PSMA-617 is being studied both in earlier stages of disease and in combination with other anti-cancer therapies. Further, the drug development pipeline is deep with variations of PSMA-targeting radionuclides, including higher energy alpha particles conjugated to PSMA-honing vectors. It is safe to assume that an increasing number of patients will be exposed to PSMA-targeted radiopharmaceuticals during the course of their cancer treatment. In this setting, it is important to better understand and mitigate the most commonly encountered toxicities. One particularly vexing side effect is xerostomia. In this review, we discuss the scope of the problem, inventories to better characterize and monitor this troublesome side effect, and approaches to preserve salivary function and effectively palliate symptoms. This article aims to serve as a useful reference for prescribers of PSMA-targeted radiopharmaceuticals, while also commenting on areas of missing data and opportunities for future research.


Antigens, Surface , Glutamate Carboxypeptidase II , Radiopharmaceuticals , Humans , Radiopharmaceuticals/therapeutic use , Male , Glutamate Carboxypeptidase II/antagonists & inhibitors , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/radiotherapy , Lutetium/therapeutic use , Radioisotopes/adverse effects , Radioisotopes/administration & dosage , Salivary Glands/radiation effects , Salivary Glands/drug effects , Dipeptides/therapeutic use , Heterocyclic Compounds, 1-Ring/therapeutic use
11.
AAPS PharmSciTech ; 25(5): 116, 2024 May 20.
Article En | MEDLINE | ID: mdl-38769223

Oral dispersible films have received broad interest due to fast drug absorption and no first-path metabolism, leading to high bioavailability and better patient compliance. Saxagliptin (SXG) is an antidiabetic drug that undergoes first-path metabolism, resulting in a less active metabolite, so the development of SXG oral dispersible films (SXG-ODFs) improves SXG bioavailability. The formula optimisation included a response surface experimental design and the impact of three formulation factors, the type and concentration of polymer and plasticiser concentration on in-vitro disintegration time and folding endurance. Two optimised SXG-ODFs prepared using either polyvinyl alcohol (PVA) or hydroxypropyl methylcellulose were investigated. SXG-ODFs prepared with PVA demonstrated a superior rapid disintegration time, ranging from 17 to 890 s, with the fastest disintegration time recorded at 17 s. These short durations can be attributed to the hydrophilic nature of PVA, facilitating rapid hydration and disintegration upon contact with saliva. Additionally, PVA-based films displayed remarkable folding endurance, surpassing 200 folds without rupture, indicating flexibility and stability. The high tensile strength of PVA-based films further underscores their robust mechanical properties, with tensile strength values reaching up to 4.53 MPa. SXG exhibits a UV absorption wavelength of around 212 nm, posing challenges for traditional quantitative spectrophotometric analysis, so a polyaniline nanoparticles-based solid-contact screen-printed ion-selective electrode (SP-ISE) was employed for the determination of SXG release profile effectively in comparison to HPLC. SP-ISE showed a better real-time release profile of SXG-ODFs, and the optimised formula showed lower blood glucose levels than commercial tablets.


Adamantane , Aniline Compounds , Dipeptides , Drug Liberation , Nanoparticles , Polyvinyl Alcohol , Adamantane/chemistry , Adamantane/analogs & derivatives , Dipeptides/chemistry , Dipeptides/pharmacokinetics , Dipeptides/administration & dosage , Aniline Compounds/chemistry , Nanoparticles/chemistry , Administration, Oral , Polyvinyl Alcohol/chemistry , Hypoglycemic Agents/chemistry , Hypoglycemic Agents/administration & dosage , Hypoglycemic Agents/pharmacokinetics , Humans , Hypromellose Derivatives/chemistry , Tensile Strength , Chemistry, Pharmaceutical/methods , Biological Availability , Solubility , Electrodes
12.
Biomacromolecules ; 25(5): 3169-3177, 2024 May 13.
Article En | MEDLINE | ID: mdl-38684138

Achieving precise control over gelator alignment and morphology is crucial for crafting tailored materials and supramolecular structures with distinct properties. We successfully aligned the self-assembled micelles formed by a functionalized dipeptide 2NapFF into long 1-D "gel noodles" by cross-linking with divalent metal chlorides. We identify the most effective cross-linker for alignment, enhancing mechanical stability, and imparting functional properties. Our study shows that Group 2 metal ions are particularly suited for creating mechanically robust yet flexible gel noodles because of their ionic and nondirectional bonding with carboxylate groups. In contrast, the covalent nature and high directional bonds of d-block metal ions with carboxylates tend to disrupt the self-assembly of 2NapFF. Furthermore, the 2NapFF-Cu noodles demonstrated selective antibacterial activity, indicating that the potent antibacterial property of the copper(II) ion is preserved within the cross-linked system. By merging insights into molecular alignment, gel extrusion processing, and integrating specific functionalities, we illustrate how the versatility of dipeptide-based gels can be utilized in creating next-generation soft materials.


Anti-Bacterial Agents , Copper , Gels , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Copper/chemistry , Copper/pharmacology , Gels/chemistry , Cross-Linking Reagents/chemistry , Dipeptides/chemistry , Dipeptides/pharmacology , Micelles , Microbial Sensitivity Tests , Staphylococcus aureus/drug effects , Escherichia coli/drug effects
14.
Proc Natl Acad Sci U S A ; 121(17): e2307814121, 2024 Apr 23.
Article En | MEDLINE | ID: mdl-38621131

Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived induced pluripotent stem cell (iPSC) line and a non-diseased wild-type (WT) line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 frontotemporal dementia/amyotrophic lateral sclerosis in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding single nucleotide polymorphism in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using digital droplet PCR (ddPCR), we determined that transcription from the mutant allele is upregulated at least 10-fold, and that sense transcription is independently regulated from each allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat poly-GP expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production, and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all dipeptide repeat proteins, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including antisense oligonucleotides (ASOs) and CRISPR gene editing.


Amyotrophic Lateral Sclerosis , Frontotemporal Dementia , Humans , C9orf72 Protein/genetics , C9orf72 Protein/metabolism , Alleles , Amyotrophic Lateral Sclerosis/metabolism , Frontotemporal Dementia/metabolism , Motor Neurons/metabolism , Mutation , DNA Repeat Expansion/genetics , Dipeptides/metabolism
15.
Nat Commun ; 15(1): 3574, 2024 Apr 27.
Article En | MEDLINE | ID: mdl-38678027

Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,ß-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.


Streptomyces , Streptomyces/enzymology , Streptomyces/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Dipeptides/chemistry , Dipeptides/metabolism , Oxidoreductases/metabolism , Oxidoreductases/chemistry , Flavin Mononucleotide/metabolism , Flavin Mononucleotide/chemistry , Peptides, Cyclic/chemistry , Peptides, Cyclic/metabolism , Crystallography, X-Ray , Models, Molecular , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/metabolism , Anti-Bacterial Agents/biosynthesis
16.
J Chem Theory Comput ; 20(9): 3492-3502, 2024 May 14.
Article En | MEDLINE | ID: mdl-38662196

Quantifying the conformational ensembles of biomolecules is fundamental to describing mechanisms of processes such as protein folding, interconversion between folded states, ligand binding, and allosteric regulation. Accurate quantification of these ensembles remains a challenge for conventional molecular simulations of all but the simplest molecules due to insufficient sampling. Enhanced sampling approaches, such as metadynamics, were designed to overcome this challenge; however, the nonuniform frame weights that result from many of these approaches present an additional challenge to ensemble quantification techniques such as Markov State Modeling or structural clustering. Here, we present rigorous inclusion of nonuniform frame weights into a structural clustering method entitled shapeGMM. The result of frame-weighted shapeGMM is a high dimensional probability density and generative model for the unbiased system from which we can compute important thermodynamic properties such as relative free energies and configurational entropy. The accuracy of this approach is demonstrated by the quantitative agreement between GMMs computed by Hamiltonian reweighting and direct simulation of a coarse-grained helix model system. Furthermore, the relative free energy computed from a shapeGMM probability density of alanine dipeptide reweighted from a metadynamics simulation quantitatively reproduces the underlying free energy in the basins. Finally, the method identifies hidden structures along the actin globular to filamentous-like structural transition from a metadynamics simulation on a linear discriminant analysis coordinate trained on GMM states, illustrating how structural clustering of biased data can lead to biophysical insight. Combined, these results demonstrate that frame-weighted shapeGMM is a powerful approach to quantifying biomolecular ensembles from biased simulations.


Molecular Dynamics Simulation , Thermodynamics , Dipeptides/chemistry , Protein Conformation , Protein Folding
17.
JCO Precis Oncol ; 8: e2300634, 2024 Apr.
Article En | MEDLINE | ID: mdl-38662984

PURPOSE: While 177Lu-PSMA-617 (LuPSMA) is an effective therapy for many patients with metastatic castration-resistant prostate cancer (mCRPC), biomarkers associated with outcomes are not well defined. We hypothesized that prostate cancer mutational profile may associate with clinical activity of LuPSMA. We devised a study to evaluate associations between mCRPC mutational profile with LuPSMA clinical outcomes. METHODS: This was a multicenter retrospective analysis of patients with mCRPC with next-generation sequencing (NGS) who received LuPSMA. PSA50 response (ie, ≥50% decline in prostate-specific antigen [PSA]) rate, PSA progression free survival (PSA PFS), and overall survival (OS) were compared between genetically defined subgroups. RESULTS: One hundred twenty-six patients with NGS results who received at least one cycle of LuPSMA were identified. The median age was 73 (IQR, 68-78) years, 124 (98.4%) received ≥1 prior androgen receptor-signaling inhibitor, and 121 (96%) received ≥1 taxane-based chemotherapy regimen. Fifty-eight (46%) patients with a DNA damage repair gene mutation (DNA damage response group) and 59 (46.8%) with a mutation in TP53, RB1, or PTEN tumor suppressor genes (TSG group) were identified. After adjusting for relevant confounders, the presence of ≥1 TSG mutation was associated with shorter PSA PFS (hazard ratio [HR], 1.93 [95% CI, 1.05 to 3.54]; P = .034) and OS (HR, 2.65 [95% CI, 1.15 to 6.11]; P = .023). There was improved OS favoring the DNA damage response group (HR, 0.37 [95% CI, 0.14 to 0.97]; P = .044) on multivariable analysis. Univariate analysis of patients with ATM mutations had significantly higher rates of PSA50 response, PSA PFS, and OS. CONCLUSION: Outcomes on LuPSMA varied on the basis of mutational profile. Prospective studies to define the clinical activity of LuPSMA in predefined genomic subgroups are justified.


Dipeptides , Lutetium , Prostatic Neoplasms, Castration-Resistant , Humans , Male , Retrospective Studies , Aged , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology , Prostatic Neoplasms, Castration-Resistant/blood , Prostatic Neoplasms, Castration-Resistant/drug therapy , Lutetium/therapeutic use , Dipeptides/therapeutic use , Heterocyclic Compounds, 1-Ring/therapeutic use , Prostate-Specific Antigen/blood , Antigens, Surface/genetics , Cohort Studies , Glutamate Carboxypeptidase II/genetics
18.
Clin Nucl Med ; 49(6): 587-588, 2024 Jun 01.
Article En | MEDLINE | ID: mdl-38557426

ABSTRACT: Prostate carcinoma (PC) is the second most common malignant tumor in males globally. The metastatic spread of PC usually involves the pelvic and abdominal lymph nodes and the skeletal system. Cutaneous metastases are exceedingly uncommon and typically manifest themselves late in the disease course, considered as ominous sign with limited treatment options and a poor prognosis. We describe a patient wherein 68 Ga-PSMA-11 PET/CT detected multiple uncommon metastatic sites in the cutaneous region of the scrotum, penis, and thigh, as well as in the subcutaneous region of anterior abdominal wall, and in bilateral adrenal glands. These findings served as a theranostic tool for selecting 177 Lu-PSMA-617 treatment for these extremely rare metastatic sites.


Adrenal Gland Neoplasms , Gallium Isotopes , Gallium Radioisotopes , Lutetium , Positron Emission Tomography Computed Tomography , Prostatic Neoplasms , Skin Neoplasms , Humans , Male , Prostatic Neoplasms/diagnostic imaging , Prostatic Neoplasms/pathology , Adrenal Gland Neoplasms/diagnostic imaging , Adrenal Gland Neoplasms/secondary , Skin Neoplasms/diagnostic imaging , Skin Neoplasms/pathology , Heterocyclic Compounds, 1-Ring/therapeutic use , Edetic Acid/analogs & derivatives , Disease Progression , Radioisotopes/therapeutic use , Dipeptides/therapeutic use , Aged , Oligopeptides , Subcutaneous Tissue/diagnostic imaging , Subcutaneous Tissue/pathology , Precision Medicine
19.
Clin Nucl Med ; 49(6): 584-586, 2024 Jun 01.
Article En | MEDLINE | ID: mdl-38630998

ABSTRACT: A 69-year-old man diagnosed with progressive bone metastatic castration-resistant prostate adenocarcinoma and concurrent alcoholic cirrhosis with multiple hepatocellular carcinoma (HCC) nodules was referred to our nuclear medicine service for 177 Lu-PSMA-617 therapy. The patient's pretreatment screening using 68 Ga-PSMA-11 PET/CT revealed high prostate-specific membrane antigen expression in both prostatic and HCC lesions. The patient underwent 2 doses of 177 Lu-PSMA-617. Subsequent imaging assessments with 68 Ga-PSMA-11 PET/CT and hepatic MRI indicated progressive HCC nodules, while showing a partial response in prostatic bone metastases. Positive clinical and biological responses were observed only in prostatic disease, but not in HCC nodules.


Carcinoma, Hepatocellular , Liver Neoplasms , Lutetium , Humans , Male , Carcinoma, Hepatocellular/radiotherapy , Carcinoma, Hepatocellular/diagnostic imaging , Aged , Liver Neoplasms/radiotherapy , Liver Neoplasms/diagnostic imaging , Radioisotopes/therapeutic use , Positron Emission Tomography Computed Tomography , Dipeptides/therapeutic use , Heterocyclic Compounds, 1-Ring/therapeutic use
20.
Langmuir ; 40(17): 8971-8980, 2024 Apr 30.
Article En | MEDLINE | ID: mdl-38629792

Cells require oligonucleotides and polypeptides with specific, homochiral sequences to perform essential functions, but it is unclear how such oligomers were selected from random sequences at the origin of life. Cells were probably preceded by simple compartments such as fatty acid vesicles, and oligomers that increased the stability, growth, or division of vesicles could have thereby increased in frequency. We therefore tested whether prebiotic peptides alter the stability or growth of vesicles composed of a prebiotic fatty acid. We find that three of 15 dipeptides tested reduce salt-induced flocculation of vesicles. All three contain leucine, and increasing their length increases the efficacy. Also, leucine-leucine but not alanine-alanine increases the size of vesicles grown by multiple additions of micelles. In a molecular simulation, leucine-leucine docks to the membrane, with the side chains inserted into the hydrophobic core of the bilayer, while alanine-alanine fails to dock. Finally, the heterochiral forms of leucine-leucine, at a high concentration, rapidly shrink the vesicles and make them leakier and less stable to high pH than the homochiral forms do. Thus, prebiotic peptide-membrane interactions influence the flocculation, growth, size, leakiness, and pH stability of prebiotic vesicles, with differential effects due to sequence, length, and chirality. These differences could lead to a population of vesicles enriched for peptides with beneficial sequence and chirality, beginning selection for the functional oligomers that underpin life.


Peptides , Peptides/chemistry , Alanine/chemistry , Stereoisomerism , Artificial Cells/chemistry , Leucine/chemistry , Origin of Life , Dipeptides/chemistry
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