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Schmiech M, Abdel-Kahaar E, Ulrich J, Pfeiffer M, Duweb A, Zolk O, Syrovets T, Simmet T. Single-dose comparative pharmacokinetic/pharmacodynamic study of a micellar formulation versus a native Boswellia serrata dry extract in healthy volunteers. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 132:155863. [PMID: 39033725 DOI: 10.1016/j.phymed.2024.155863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/18/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
BACKGROUND Extracts of oleogum resins of Boswellia trees possess anti-inflammatory activities. Micellar formulations have been developed to increase the oral bioavailability of bioactive boswellic and lupeolic acids. PURPOSE The current single-dose crossover clinical trial compares for the first time pharmacokinetics/pharmacodynamics of two Boswellia serrata nutraceuticals, native Biotikon® BS-85 and micellar Boswellia-Loges®. METHODS After oral administration of the study preparations (800 mg) to 20 healthy volunteers, plasma concentrations of 8 boswellic and lupeolic acids were measured by using HPLC-MS/MS for up to 48 h Blood samples collected 2 and 5 h after drug administration were stimulated for 24 h with endotoxic lipopolysaccharide. The release of proinflammatory cytokines analyzed by flow cytometry was used as readout of the pharmacodynamic properties of the preparations. REGISTRATION German Clinical Trials Register (DRKS) No. DRKS00027369. RESULTS Administration of the micellar extract significantly increased Cmax, AUC0-48, and shortened Tmax for all boswellic and lupeolic acids compared to native extract. Accordingly, their relative bioavailability increased to 1,720-4,291 % with the highest difference for acetyl-11-keto-β-boswellic acid (AKBA). Both preparations reduced the release of TNF-α and the native formulation diminished also IL-1β and IL-6. However, no significant differences were observed between the preparations, except for a higher decrease in IL-1β by the native formulation Biotikon® BS-85. In a lymphocytic gene reporter cell line, both nutraceuticals similarly inhibited the NF-κB transcription factor activity as well as the TNF-α release, yet the native formulation Biotikon®BS-85 was more efficient in inhibiting TNF-α. CONCLUSION Administration of the micellar Boswellia serrata nutraceutical increased the oral bioavailability of boswellic and lupeolic acids. Yet, the increase in plasma concentration did not enhance the anti-inflammatory efficacy of the micellar extract compared to the native extract in this ex vivo model.
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Affiliation(s)
- Michael Schmiech
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany
| | - Emaad Abdel-Kahaar
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany
| | - Judith Ulrich
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany
| | - Maximilian Pfeiffer
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany
| | - Amira Duweb
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany; Department of Pharmacology, Faculty of Medicine, University of Tripoli, Tripoli 13628, Libya
| | - Oliver Zolk
- Institute of Clinical Pharmacology, Brandenburg Medical School, Immanuel Hospital Rüdersdorf, Rüdersdorf 15562, Germany
| | - Tatiana Syrovets
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany
| | - Thomas Simmet
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University, Helmholtzstr. 20, Ulm 89081, Germany.
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Nieto-Fabregat F, Lenza MP, Marseglia A, Di Carluccio C, Molinaro A, Silipo A, Marchetti R. Computational toolbox for the analysis of protein-glycan interactions. Beilstein J Org Chem 2024; 20:2084-2107. [PMID: 39189002 PMCID: PMC11346309 DOI: 10.3762/bjoc.20.180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/01/2024] [Indexed: 08/28/2024] Open
Abstract
Protein-glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein-glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein-ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein-glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.
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Affiliation(s)
- Ferran Nieto-Fabregat
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Maria Pia Lenza
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Angela Marseglia
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Cristina Di Carluccio
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Via Cinthia 4, 80126, Italy
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Wang L, Lin H, Yang B, Jiang X, Chen J, Roy Chowdhury S, Cheng N, Nakata PA, Lonard DM, Wang MC, Wang J. Development of a Novel Amplifiable System to Quantify Hydrogen Peroxide in Living Cells. J Am Chem Soc 2024; 146:22396-22404. [PMID: 39079063 DOI: 10.1021/jacs.4c05366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Although many redox signaling molecules are present at low concentrations, typically ranging from micromolar to submicromolar levels, they often play essential roles in a wide range of biological pathways and disease mechanisms. However, accurately measuring low-abundant analytes has been a significant challenge due to the lack of sensitivity and quantitative capability of existing measurement methods. In this study, we introduced a novel chemically induced amplifiable system for quantifying low-abundance redox signaling molecules in living cells. We utilized H2O2 as a proof-of-concept analyte and developed a probe that quantifies cellular peroxide levels by combining the NanoBiT system with androgen receptor dimerization as a reporting mechanism. Our system demonstrated a highly sensitive response to cellular peroxide changes induced both endogenously and exogenously. Furthermore, the system can be adapted for the quantification of other signaling molecules if provided with suitable probing chemistry.
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Affiliation(s)
- Lingfei Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hanfeng Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Bin Yang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xiqian Jiang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jianwei Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Sandipan Roy Chowdhury
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ninghui Cheng
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Paul A Nakata
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David M Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Meng C Wang
- Department of Molecular and Human Genetics, Huffington Center on Aging, and Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
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Mitsuta Y, Asada T. Parameter Optimization Method in Multidimensional Umbrella Sampling. J Chem Theory Comput 2024. [PMID: 39101750 DOI: 10.1021/acs.jctc.4c00282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Umbrella sampling (US) is an effective method for calculating free-energy landscapes (FELs). However, the complexity of controlling the sampling positions complicates multidimensional FEL calculations. In this study, we proposed a method for controlling sampling by optimizing the US parameters. This method comprises the introduction of a target point and the optimization of the parameters to sample a window around this point. We approximated each window to normal distributions using an umbrella integration method and calculated the divergences between the window distributions and the state distributed at the target position by a variationally enhanced sampling method. Thus, the minimization of the divergence facilitated sampling around the target point, after which the parameters could be optimized on the fly while performing equilibration simulation. In practice, our method employs bias potentials with off-diagonal terms, ensuring a more efficient calculation of multidimensional FEL. Additionally, we developed an algorithm for determining the target point for automated FEL search; the algorithm samples in a specified direction while controlling the overlap of distributions. We performed three different FEL calculations as examples: (1) the calculation of the permeation of a water molecule through a lipid bilayer (one-dimensional FEL), (2) the calculation of the internal structural changes in alanine dipeptide in water (two-dimensional FEL), and (3) the calculation of the internal structural changes from a β-strand structure to an α-helix structure in alanine decapeptide (Ala10, 16-dimensional FEL). These results confirmed that our method could control the number of US windows and calculate the high-dimensional FELs that could not be evaluated by the conventional US method.
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Affiliation(s)
- Yuki Mitsuta
- Department of Chemistry, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- RIMED, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Toshio Asada
- Department of Chemistry, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
- RIMED, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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Hashemi P, Mardani P, Eghbali Raz Z, Saedi A, Fatahi E, Izapanah E, Ahmadi S. Alpha-Pinene Decreases the Elevated Levels of Astrogliosis, Pyroptosis, and Autophagy Markers in the Hippocampus Triggered by Kainate in a Rat Model of Temporal Lobe Epilepsy. Mol Neurobiol 2024:10.1007/s12035-024-04407-x. [PMID: 39096444 DOI: 10.1007/s12035-024-04407-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 07/28/2024] [Indexed: 08/05/2024]
Abstract
The development and progression of temporal lobe epilepsy (TLE) are heavily influenced by inflammation, excessive activation of glial cells, and neuronal cell death. This study aimed to investigate the effects of treatment with alpha-pinene (APN) on pro-and anti-inflammatory cytokine levels, astrogliosis, pyroptosis, and autophagy markers in the hippocampus in a rat model of TLE induced by kainic acid (KA). Male Wistar rats were employed, and TLE was induced by intracerebroventricular injection of KA. APN (50 mg/kg) was intraperitoneally administered for 19 days, including two weeks before and five days after the administration of KA. After full recovery from anesthesia and KA injection, the seizure-related behavioral expressions were evaluated. On day 19, the hippocampal levels of IL-1β, TNF-α, progranulin, IL-10, ERK1/2, phospho-ERK1/2, NF-κB, GFAP, S100-B, NLRP1, NLRP3, caspase-1, and becline-1 were examined. The results revealed that treatment with APN significantly diminished the heightened levels of IL-1β, TNF-α, progranulin, ERK1/2, and NF-κB and reversed the reduced levels of the anti-inflammatory cytokine, IL-10, in the hippocampus caused by KA. Furthermore, administration of APN significantly reduced the levels of astrogliosis, pyroptosis, and autophagy markers in the hippocampus that were elevated by KA. It can be concluded that treatment with APN for 19 days alleviated neuroinflammation by inhibiting ERK1/2 and NF-κB signaling pathways and prevented increases in astrogliosis, pyroptosis, and autophagy markers in the hippocampus in a rat model of TLE.
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Affiliation(s)
- Paria Hashemi
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | | | - Zabihollah Eghbali Raz
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Ali Saedi
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Ehsan Fatahi
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Esmael Izapanah
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Shamseddin Ahmadi
- Department of Biological Science, Faculty of Science, University of Kurdistan, P.O. Box 416, Sanandaj, Iran.
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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Jaiyesimi O, Kuppuswamy S, Zhang G, Batan S, Zhi W, Ganta VC. Glycolytic PFKFB3 and Glycogenic UGP2 Axis Regulates Perfusion Recovery in Experimental Hind Limb Ischemia. Arterioscler Thromb Vasc Biol 2024; 44:1764-1783. [PMID: 38934117 PMCID: PMC11323258 DOI: 10.1161/atvbaha.124.320665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Despite being in an oxygen-rich environment, endothelial cells (ECs) use anaerobic glycolysis (Warburg effect) as the primary metabolic pathway for cellular energy needs. PFKFB (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase)-3 regulates a critical enzymatic checkpoint in glycolysis and has been shown to induce angiogenesis. This study builds on our efforts to determine the metabolic regulation of ischemic angiogenesis and perfusion recovery in the ischemic muscle. METHODS Hypoxia serum starvation (HSS) was used as an in vitro peripheral artery disease (PAD) model, and hind limb ischemia by femoral artery ligation and resection was used as a preclinical PAD model. RESULTS Despite increasing PFKFB3-dependent glycolysis, HSS significantly decreased the angiogenic capacity of ischemic ECs. Interestingly, inhibiting PFKFB3 significantly induced the angiogenic capacity of HSS-ECs. Since ischemia induced a significant in PFKFB3 levels in hind limb ischemia muscle versus nonischemic, we wanted to determine whether glucose bioavailability (rather than PFKFB3 expression) in the ischemic muscle is a limiting factor behind impaired angiogenesis. However, treating the ischemic muscle with intramuscular delivery of D-glucose or L-glucose (osmolar control) showed no significant differences in the perfusion recovery, indicating that glucose bioavailability is not a limiting factor to induce ischemic angiogenesis in experimental PAD. Unexpectedly, we found that shRNA-mediated PFKFB3 inhibition in the ischemic muscle resulted in an increased perfusion recovery and higher vascular density compared with control shRNA (consistent with the increased angiogenic capacity of PFKFB3 silenced HSS-ECs). Based on these data, we hypothesized that inhibiting HSS-induced PFKFB3 expression/levels in ischemic ECs activates alternative metabolic pathways that revascularize the ischemic muscle in experimental PAD. A comprehensive glucose metabolic gene qPCR arrays in PFKFB3 silenced HSS-ECs, and PFKFB3-knock-down ischemic muscle versus respective controls identified UGP2 (uridine diphosphate-glucose pyrophosphorylase 2), a regulator of protein glycosylation and glycogen synthesis, is induced upon PFKFB3 inhibition in vitro and in vivo. Antibody-mediated inhibition of UGP2 in the ischemic muscle significantly impaired perfusion recovery versus IgG control. Mechanistically, supplementing uridine diphosphate-glucose, a metabolite of UGP2 activity, significantly induced HSS-EC angiogenic capacity in vitro and enhanced perfusion recovery in vivo by increasing protein glycosylation (but not glycogen synthesis). CONCLUSIONS Our data present that inhibition of maladaptive PFKFB3-driven glycolysis in HSS-ECs is necessary to promote the UGP2-uridine diphosphate-glucose axis that enhances ischemic angiogenesis and perfusion recovery in experimental PAD.
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Affiliation(s)
- Olukemi Jaiyesimi
- Vascular Biology Center and Department of Medicine (J.O., S.K., G.Z., S.B., V.C.G.), Augusta University, GA
| | - Sivaraman Kuppuswamy
- Vascular Biology Center and Department of Medicine (J.O., S.K., G.Z., S.B., V.C.G.), Augusta University, GA
| | - Guangwei Zhang
- Vascular Biology Center and Department of Medicine (J.O., S.K., G.Z., S.B., V.C.G.), Augusta University, GA
| | - Sonia Batan
- Vascular Biology Center and Department of Medicine (J.O., S.K., G.Z., S.B., V.C.G.), Augusta University, GA
| | - Wenbo Zhi
- Department of Obstetrics and Gynecology, Center for Biotechnology and Genomic Medicine (W.Z.), Augusta University, GA
| | - Vijay C Ganta
- Vascular Biology Center and Department of Medicine (J.O., S.K., G.Z., S.B., V.C.G.), Augusta University, GA
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Junior DBC, Lacerda PS, de Pilla Varotti F, Leite FHA. Towards development of new antimalarial compounds through in silico and in vitro assays. Comput Biol Chem 2024; 111:108093. [PMID: 38772047 DOI: 10.1016/j.compbiolchem.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/17/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Malaria is one of most widespread infectious disease in world. The antimalarial therapy presents a series of limitations, such as toxicity and the emergence of resistance, which makes the search for new drugs urgent. Thus, it becomes necessary to explore essential and exclusive therapeutic targets of the parasite to achieve selective inhibition. Enoyl-ACP reductase is an enzyme of the type II fatty acid biosynthetic pathway and is responsible for the rate-limiting step in the fatty acid elongation cycle. In this work, we use hierarchical virtual screening and drug repositioning strategies to prioritize compounds for phenotypic assays and molecular dynamics studies. The molecules were tested against chloroquine-resistant W2 strain of Plasmodium falciparum (EC50 between 330.05 and 13.92 µM). Nitrofurantoin was the best antimalarial activity at low micromolar range (EC50 = 13.92 µM). However, a hit compound against malaria must have a biological activity value below 1 µM. A large number of molecules present problems with permeability in biological membranes and reaching an effective concentration in their target's microenvironment. Nitrofurantoin derivatives with inclusions of groups which confer increased lipid solubility (methyl groups, halogens and substituted and unsubstituted aromatic rings) have been proposed. These derivatives were pulled through the lipid bilayer in molecular dynamics simulations. Molecules 14, 18 and 21 presented lower free energy values than nitrofurantoin when crossing the lipid bilayer.
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Affiliation(s)
| | - Pedro Sousa Lacerda
- Laboratório de Bioinformática e Modelagem Molecular, Universidade Federal da Bahia, Brazil
| | | | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Brazil; Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Brazil.
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9
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Wang J, Liu J, Sümbelli Y, Shao J, Shi X, van Hest JCM. Nanogel-based nitric oxide-driven nanomotor for deep tissue penetration and enhanced tumor therapy. J Control Release 2024; 372:59-68. [PMID: 38866242 DOI: 10.1016/j.jconrel.2024.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Antitumor agents often lack effective penetration and accumulation to achieve high therapeutic efficacy in treating solid tumors. Nanomotor-based nanomaterials offer a potential solution to address this obstacle. Among them, nitric oxide (NO) based nanomotors have garnered attention for their potential applications in nanomedicine. However, there widespread clinical adoption has been hindered by their complex preparation processes. To address this limitation, we have developed a NO-driven nanomotor utilizing a convenient and scalable nanogel preparation procedure. These nanomotors, loaded with the fluorescent probe / sonosensitizer chlorin e6 (Ce6), were specifically engineered for sonodynamic therapy. Through comprehensive in vitro investigations using both 2D and 3D cell models, as well as in vivo analysis of Ce6 fluorescent signal distribution in solid tumor models, we observed that the self-propulsion of these nanomotors significantly enhances cellular uptake and tumor penetration, particularly in solid tumors. This phenomenon enables efficient access to challenging tumor regions and, in some cases, results in complete tumor coverage. Notably, our nanomotors have demonstrated long-term in vivo biosafety. This study presents an effective approach to enhancing drug penetration and improving therapeutic efficacy in tumor treatment, with potential clinical relevance for future applications.
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Affiliation(s)
- Jianhong Wang
- Bio-Organic Chemistry, Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, the Netherlands
| | - Junjie Liu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering Donghua University, 201620 Shanghai, PR China
| | - Yiǧitcan Sümbelli
- Bio-Organic Chemistry, Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, the Netherlands
| | - Jingxin Shao
- Bio-Organic Chemistry, Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, the Netherlands.
| | - Xiangyang Shi
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, Shanghai Engineering Research Center of Nano-Biomaterials and Regenerative Medicine, College of Biological Science and Medical Engineering Donghua University, 201620 Shanghai, PR China.
| | - Jan C M van Hest
- Bio-Organic Chemistry, Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, the Netherlands.
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Birk D, Siepmann E, Simon S, Sommerhoff CP. Human Neutrophil Elastase: Characterization of Intra- vs. Extracellular Inhibition. Int J Mol Sci 2024; 25:7917. [PMID: 39063160 PMCID: PMC11276905 DOI: 10.3390/ijms25147917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Neutrophil elastase (HNE), like other members of the so-called GASPIDs (Granule-Associated Serine Peptidases of Immune Defense), is activated during protein biosynthesis in myeloid precursors and stored enzymatically active in cytoplasmic granules of resting neutrophils until secreted at sites of host defense and inflammation. Inhibitors thus could bind to the fully formed active site of the protease intracellularly in immature progenitors, in circulating neutrophils, or to HNE secreted into the extracellular space. Here, we have compared the ability of a panel of diverse inhibitors to inhibit HNE in the U937 progenitor cell line, in human blood-derived neutrophils, and in solution. Most synthetic inhibitors and, surprisingly, even a small naturally occurring proteinaceous inhibitor inhibit HNE intracellularly, but the extent and dynamics differ markedly from classical enzyme kinetics describing extracellular inhibition. Intracellular inhibition of HNE potentially affects neutrophil functions and has side effects, but it avoids competition of inhibitors with extracellular substrates that limit its efficacy. As both intra- and extracellular inhibition have advantages and disadvantages, the quantification of intracellular inhibition, in addition to classical enzyme kinetics, will aid the design of novel, clinically applicable HNE inhibitors with targeted sites of action.
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Affiliation(s)
- Denise Birk
- Institute of Laboratory Medicine, University Hospital, LMU Munich, 80336 Munich, Germany
- Department of Neurology, LMU University Hospital, LMU Munich, 81377 Munich, Germany
| | - Erika Siepmann
- Institute of Laboratory Medicine, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Stefan Simon
- Institute of Laboratory Medicine, University Hospital, LMU Munich, 80336 Munich, Germany
| | - Christian P. Sommerhoff
- Institute of Laboratory Medicine, University Hospital, LMU Munich, 80336 Munich, Germany
- Institute of Medical Education, University Hospital, LMU Munich, 80336 Munich, Germany
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11
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Mun SJ, Cho E, Kim HK, Gil WJ, Yang CS. Enhancing acute inflammatory and sepsis treatment: superiority of membrane receptor blockade. Front Immunol 2024; 15:1424768. [PMID: 39081318 PMCID: PMC11286478 DOI: 10.3389/fimmu.2024.1424768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024] Open
Abstract
Conditions such as acute pancreatitis, ulcerative colitis, delayed graft function and infections caused by a variety of microorganisms, including gram-positive and gram-negative organisms, increase the risk of sepsis and therefore mortality. Immune dysfunction is a characterization of sepsis, so timely and effective treatment strategies are needed. The conventional approaches, such as antibiotic-based treatments, face challenges such as antibiotic resistance, and cytokine-based treatments have shown limited efficacy. To address these limitations, a novel approach focusing on membrane receptors, the initiators of the inflammatory cascade, is proposed. Membrane receptors such as Toll-like receptors, interleukin-1 receptor, endothelial protein C receptor, μ-opioid receptor, triggering receptor expressed on myeloid cells 1, and G-protein coupled receptors play pivotal roles in the inflammatory response, offering opportunities for rapid regulation. Various membrane receptor blockade strategies have demonstrated efficacy in both preclinical and clinical studies. These membrane receptor blockades act as early stage inflammation modulators, providing faster responses compared to conventional therapies. Importantly, these blockers exhibit immunomodulatory capabilities without inducing complete immunosuppression. Finally, this review underscores the critical need for early intervention in acute inflammatory and infectious diseases, particularly those posing a risk of progressing to sepsis. And, exploring membrane receptor blockade as an adjunctive treatment for acute inflammatory and infectious diseases presents a promising avenue. These novel approaches, when combined with antibiotics, have the potential to enhance patient outcomes, particularly in conditions prone to sepsis, while minimizing risks associated with antibiotic resistance and immune suppression.
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Affiliation(s)
- Seok-Jun Mun
- Department of Bionano Engineering, Hanyang University, Seoul, Republic of Korea
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
| | - Euni Cho
- Department of Bionano Engineering, Hanyang University, Seoul, Republic of Korea
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
| | - Hyo Keun Kim
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Woo Jin Gil
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
| | - Chul-Su Yang
- Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, Republic of Korea
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
- Department of Medicinal and Life Science, Hanyang University, Ansan, Republic of Korea
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12
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Mondal J, Maji D, Mitra S, Biswas R. Temperature-Dependent Dielectric Relaxation Measurements of (Betaine + Urea + Water) Deep Eutectic Solvent in Hz-GHz Frequency Window: Microscopic Insights into Constituent Contributions and Relaxation Mechanisms. J Phys Chem B 2024; 128:6567-6580. [PMID: 38949428 DOI: 10.1021/acs.jpcb.4c02784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
A combined experimental and simulation study of dielectric relaxation (DR) of a deep eutectic solvent (DES) composed of betaine, urea, and water with the composition [Betaine:Urea:Water = 11.7:12:1 (weight ratio) and 9:18:5 (molar ratio)] was performed to explore and understand the interaction and dynamics of this system. Temperature-dependent (303 ≤ T/K ≤ 343) measurements were performed over 9 decades of frequency, combining three different measurement setups. Measured DR, comprising four distinct steps with relaxation times spreading over a few picoseconds to several nanoseconds, was found to agree well with simulations. The simulated total DR spectra, upon dissection into three self (intraspecies) and three cross (interspecies) interaction contributions, revealed that the betaine-betaine self-term dominated (∼65%) the relaxation, while the urea-urea and water-water interactions contributed only ∼7% and ∼1%, respectively. The cross-terms (betaine-urea, betaine-water, and urea-water) together accounted for <30% of the total DR. The slowest DR component with a time constant of ∼1-10 ns derived dominant contribution from betaine-betaine interactions, where betaine-water and urea-water interactions also contributed. The subnanosecond (0.1-0.6 ns) time scale originated from all interactions except betaine-water interaction. An extensive interaction of water with betaine and urea severely reduced the average number of water-water H-bonds (∼0.7) and heavily decreased the static dielectric constant of water in this DES (εs ∼ 2). Furthermore, simulated first rank collective single particle reorientational relaxations (C1(t)) and the structural H-bond fluctuation dynamics (CHB (t)) exhibited multiexponential kinetics with time scales that corresponded well with those found both in the simulated and measured DR.
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Affiliation(s)
- Jayanta Mondal
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700106, India
| | - Dhrubajyoti Maji
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700106, India
| | - Sudipta Mitra
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700106, India
| | - Ranjit Biswas
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, JD Block, Sector III, Salt Lake, Kolkata 700106, India
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13
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Merlino F, Marzano S, Zizza P, D’Aria F, Grasso N, Carachino A, Iachettini S, Biroccio A, Fonzo SD, Grieco P, Randazzo A, Amato J, Pagano B. Unlocking the potential of protein-derived peptides to target G-quadruplex DNA: from recognition to anticancer activity. Nucleic Acids Res 2024; 52:6748-6762. [PMID: 38828773 PMCID: PMC11229374 DOI: 10.1093/nar/gkae471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/11/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Noncanonical nucleic acid structures, particularly G-quadruplexes, have garnered significant attention as potential therapeutic targets in cancer treatment. Here, the recognition of G-quadruplex DNA by peptides derived from the Rap1 protein is explored, with the aim of developing novel peptide-based G-quadruplex ligands with enhanced selectivity and anticancer activity. Biophysical techniques were employed to assess the interaction of a peptide derived from the G-quadruplex-binding domain of the protein with various biologically relevant G-quadruplex structures. Through alanine scanning mutagenesis, key amino acids crucial for G-quadruplex recognition were identified, leading to the discovery of two peptides with improved G-quadruplex-binding properties. However, despite their in vitro efficacy, these peptides showed limited cell penetration and anticancer activity. To overcome this challenge, cell-penetrating peptide (CPP)-conjugated derivatives were designed, some of which exhibited significant cytotoxic effects on cancer cells. Interestingly, selected CPP-conjugated peptides exerted potent anticancer activity across various tumour types via a G-quadruplex-dependent mechanism. These findings underscore the potential of peptide-based G-quadruplex ligands in cancer therapy and pave the way for the development of novel therapeutic strategies targeting these DNA structures.
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Affiliation(s)
- Francesco Merlino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Federica D’Aria
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Alice Carachino
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Sara Iachettini
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Translational Oncology Research Unit, IRCCS-Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste 34149, Italy
| | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
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14
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Liang B, Deng Y, Zhong Y, Chen X, Huang Y, Li Z, Huang X, Yang X, Du J, Ye R, Xian H, Feng Y, Bai R, Fan B, Yang X, Huang Z. Gastrointestinal Incomplete Degradation Exacerbates Neurotoxic Effects of PLA Microplastics via Oligomer Nanoplastics Formation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401009. [PMID: 38751156 PMCID: PMC11267364 DOI: 10.1002/advs.202401009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/06/2024] [Indexed: 07/25/2024]
Abstract
Biodegradable plastics, hailed for their environmental friendliness, may pose unforeseen risks as they undergo gastrointestinal degradation, forming oligomer nanoplastics. Despite this, the influence of gastrointestinal degradation on the potential human toxicity of biodegradable plastics remains poorly understood. To this end, the impact of the murine in vivo digestive system is investigated on the biotransformation, biodistribution, and toxicity of PLA polymer and PLA oligomer MPs. Through a 28-day repeated oral gavage study in mice, it is revealed that PLA polymer and oligomer microplastics undergo incomplete and complete degradation, respectively, in the gastrointestinal tract. Incompletely degraded PLA polymer microplastics transform into oligomer nanoplastics, heightening bioavailability and toxicity, thereby exacerbating overall toxic effects. Conversely, complete degradation of PLA oligomer microplastics reduces bioavailability and mitigates toxicity, offering a potential avenue for toxicity reduction. Additionally, the study illuminates shared targets and toxicity mechanisms in Parkinson's disease-like neurotoxicity induced by both PLA polymer and PLA oligomer microplastics. This involves the upregulation of MICU3 in midbrains, leading to neuronal mitochondrial calcium overload. Notably, neurotoxicity is mitigated by inhibiting mitochondrial calcium influx with MCU-i4 or facilitating mitochondrial calcium efflux with DBcAMP in mice. These findings enhance the understanding of the toxicological implications of biodegradable microplastics on human health.
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Affiliation(s)
- Boxuan Liang
- The Tenth Affiliated Hospital, Southern Medical University (Dongguan People's Hospital)Southern Medical UniversityDongguan523059China
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yanhong Deng
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yizhou Zhong
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xiaoqing Chen
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yuji Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhiming Li
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xiyun Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xiaohong Yang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Jiaxin Du
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Rongyi Ye
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Hongyi Xian
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Yu Feng
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Ruobing Bai
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Bingchi Fan
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Xingfen Yang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchResearch Center for Food safety and HealthSchool of Public HealthSouthern Medical UniversityGuangzhou510515China
| | - Zhenlie Huang
- NMPA Key Laboratory for Safety Evaluation of CosmeticsGuangdong Provincial Key Laboratory of Tropical Disease ResearchDepartment of Toxicology, School of Public HealthSouthern Medical UniversityGuangzhou510515China
- Department of Cardiovascular SurgeryZhujiang Hospital, Southern Medical UniversityGuangzhou510280China
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15
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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 PMCID: PMC11332354 DOI: 10.1128/mmbr.00181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J. Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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16
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Ben Trad F, Delacotte J, Lemaître F, Guille-Collignon M, Arbault S, Sojic N, Labbé E, Buriez O. Shadow electrochemiluminescence imaging of giant liposomes opening at polarized electrodes. Analyst 2024; 149:3317-3324. [PMID: 38742381 DOI: 10.1039/d4an00470a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
In this work, the release of giant liposome (∼100 μm in diameter) content was imaged by shadow electrochemiluminescence (ECL) microscopy. Giant unilamellar liposomes were pre-loaded with a sucrose solution and allowed to sediment at an ITO electrode surface immersed in a solution containing a luminophore ([Ru(bpy)3]2+) and a sacrificial co-reactant (tri-n-propylamine). Upon polarization, the electrode exhibited illumination over its entire surface thanks to the oxidation of ECL reagents. However, as soon as liposomes reached the electrode surface, dark spots appeared and then spread over time on the surface. This observation reflected a blockage of the electrode surface at the contact point between the liposome and the electrode surface, followed by the dilution of ECL reagents after the rupture of the liposome membrane and release of its internal ECL-inactive solution. Interestingly, ECL reappeared in areas where it initially faded, indicating back-diffusion of ECL reagents towards the previously diluted area and thus confirming liposome permeabilization. The whole process was analyzed qualitatively and quantitatively within the defined region of interest. Two mass transport regimes were identified: a gravity-driven spreading process when the liposome releases its content leading to ECL vanishing and a diffusive regime when ECL recovers. The reported shadow ECL microscopy should find promising applications for the imaging of transient events such as molecular species released by artificial or biological vesicles.
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Affiliation(s)
- Fatma Ben Trad
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Jérôme Delacotte
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Frédéric Lemaître
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Manon Guille-Collignon
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Stéphane Arbault
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
| | - Neso Sojic
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 CNRS, 33400 Talence, France.
| | - Eric Labbé
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Olivier Buriez
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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17
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Dai Y, Kretz CA, Kim PY, Gross PL. A specific fluorescence resonance energy quenching-based biosensor for measuring thrombin activity in whole blood. J Thromb Haemost 2024; 22:1627-1639. [PMID: 38382740 DOI: 10.1016/j.jtha.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND At sites of vessel injury, thrombin acts as the central mediator of coagulation by catalyzing fibrin clot formation and platelet activation. Thrombin generation is most frequently measured in plasma samples using small-molecule substrates; however, these have low specificity for thrombin and limited utility in whole blood. Plasma assays are limited because they ignore the hemostatic contributions of blood cells and require anticoagulation and the addition of supraphysiological concentrations of calcium. OBJECTIVES To overcome these limitations, we designed and characterized a fluorescence resonance energy quenching-based thrombin sensor (FTS) protein. METHODS The fluorescence resonance energy quenching pair of mAmetrine and tTomato, separated by a thrombin recognition sequence, was developed. The protein was expressed using Escherichia coli, and purity was assessed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The cleavage of FTS was monitored by fluorescence using excitation at 406 nm and emission at 526 nm and 581 nm. RESULTS Compared with small-molecule substrates, the FTS demonstrated high specificity for thrombin; it is not cleaved by thrombin or inhibited by α2-macroglobulin and interacts with thrombin's anion-binding exosite I. The FTS can effectively measure thrombin generation in plasma and in finger-prick whole blood, which allows it to be developed into a point-of-care test of thrombin generation. The FTS does not inhibit standard thrombin-generation assays. Lastly, FTS-based thrombin generation in nonanticoagulated finger-prick blood was delayed but enhanced compared with that in citrated plasma. CONCLUSION The FTS will broaden our understanding of thrombin generation in ways that are not attainable with current methods.
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Affiliation(s)
- Ying Dai
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Colin A Kretz
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Y Kim
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Peter L Gross
- Hamilton Health Sciences and Departments of Medicine and Medical Sciences, Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, Ontario, Canada.
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18
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Delibegović M, Dall'Angelo S, Dekeryte R. Protein tyrosine phosphatase 1B in metabolic diseases and drug development. Nat Rev Endocrinol 2024; 20:366-378. [PMID: 38519567 DOI: 10.1038/s41574-024-00965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/25/2024]
Abstract
Protein tyrosine phosphatase 1B (PTP1B), a non-transmembrane phosphatase, has a major role in a variety of signalling pathways, including direct negative regulation of classic insulin and leptin signalling pathways, and is implicated in the pathogenesis of several cardiometabolic diseases and cancers. As such, PTP1B has been a therapeutic target for over two decades, with PTP1B inhibitors identified either from natural sources or developed throughout the years. Some of these inhibitors have reached phase I and/or II clinical trials in humans for the treatment of type 2 diabetes mellitus, obesity and/or metastatic breast cancer. In this Review, we summarize the cellular processes and regulation of PTP1B, discuss evidence from in vivo preclinical and human studies of the association between PTP1B and different disorders, and discuss outcomes of clinical trials. We outline challenges associated with the targeting of this phosphatase (which was, until the past few years, viewed as difficult to target), the current state of the field of PTP1B inhibitors (and dual phosphatase inhibitors) and future directions for manipulating the activity of this key metabolic enzyme.
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Affiliation(s)
- Mirela Delibegović
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK.
| | - Sergio Dall'Angelo
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
| | - Ruta Dekeryte
- Aberdeen Cardiovascular and Diabetes Centre, University of Aberdeen, Institute of Medical Sciences, Aberdeen, UK
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19
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Chau CC, Maffeo CM, Aksimentiev A, Radford SE, Hewitt EW, Actis P. Single molecule delivery into living cells. Nat Commun 2024; 15:4403. [PMID: 38782907 PMCID: PMC11116494 DOI: 10.1038/s41467-024-48608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Controlled manipulation of cultured cells by delivery of exogenous macromolecules is a cornerstone of experimental biology. Here we describe a platform that uses nanopipettes to deliver defined numbers of macromolecules into cultured cell lines and primary cells at single molecule resolution. In the nanoinjection platform, the nanopipette is used as both a scanning ion conductance microscope (SICM) probe and an injection probe. The SICM is used to position the nanopipette above the cell surface before the nanopipette is inserted into the cell into a defined location and to a predefined depth. We demonstrate that the nanoinjection platform enables the quantitative delivery of DNA, globular proteins, and protein fibrils into cells with single molecule resolution and that delivery results in a phenotypic change in the cell that depends on the identity of the molecules introduced. Using experiments and computational modeling, we also show that macromolecular crowding in the cell increases the signal-to-noise ratio for the detection of translocation events, thus the cell itself enhances the detection of the molecules delivered.
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Affiliation(s)
- Chalmers C Chau
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
| | - Christopher M Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sheena E Radford
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Eric W Hewitt
- School of Molecular and Cellular Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, LS2 9JT, UK.
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK.
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20
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Li D, Cheng J, Yuan Z, Deng K. Evolution and impact of molecular glue research: a bibliometric analysis from 2000 to 2023. Front Oncol 2024; 14:1401257. [PMID: 38817889 PMCID: PMC11138103 DOI: 10.3389/fonc.2024.1401257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024] Open
Abstract
Background Molecular glues, which reshape E3 ligase receptors to promote targeted protein degradation, are emerging as a promising therapeutic strategy, particularly in oncology, driven by rapidly advancing insights into their mechanisms and structural properties. Objective This study aims to offer an insightful depiction and visualization of the knowledge structure, prevalent themes, and emerging trends within the domain since the year 2000, employing bibliometric analysis to achieve this goal. Methods To conduct this research, a comprehensive collection of literature on molecular glues was sourced from the Web of Science database. Subsequently, the data underwent analysis utilizing CiteSpace and VOSviewer tools, enabling the identification of pivotal countries, institutions, authors, and journals, as well as the delineation of subject hotspots, trends, and the forefront of research in this evolving field. Result Since 2000, 388 papers on molecular glues have been published, with a notable increase to an annual average of 43 articles post-2018. This research, contributed by 506 authors across 329 institutions, highlights the United States and China as leading nations in output, with 122 and 104 articles respectively. Takuzo Aida, Luc Brunsveld, and Christian Ottmann are identified as key authors. Nature emerges as the foremost publication venue, while the Chinese Academy of Sciences is the top contributing institution, underscoring the global engagement and interdisciplinary nature of molecular glue research. This study identified 19 distinct research clusters within the molecular glues domain. Conclusion We reveal the current status, hotspots, and trends of molecular glue research since 2000, offering insights and novel scholarly perspectives on the field's prevailing limitations.
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Affiliation(s)
- Dian Li
- Department of Orthopaedics, Brain Hospital of Hunan Province (The Second People's Hospital of Hunan Province), Changsha, Hunan, China
- Department of Epidemiology, University of California, Los Angeles Fielding School of Public Health, Los Angeles, CA, United States
| | - Jingyi Cheng
- Xiangya Stomatological Hospital and Xiangya School of Stomatology, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Oral Health Research and Hunan Clinical Research Center of Oral Major Diseases and Oral Health and Academician Workstation for Oral-Maxilofacial and Regenerative Medicine, Central South University, Changsha, Hunan, China
| | - Zhigen Yuan
- Department of Orthopaedics, Brain Hospital of Hunan Province (The Second People's Hospital of Hunan Province), Changsha, Hunan, China
| | - Kexin Deng
- Department of Plastic and Reconstruction, The Third Xiangya Hospital of Central South University, Changsha, Hunan, China
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21
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Lv L, Li Q, Wang K, Zhao J, Deng K, Zhang R, Chen Z, Khan IA, Gui C, Feng S, Yang S, Liu Y, Xu Q. Discovery of a New Anti-Inflammatory Agent from Anemoside B4 Derivatives and Its Therapeutic Effect on Colitis by Targeting Pyruvate Carboxylase. J Med Chem 2024; 67:7385-7405. [PMID: 38687956 DOI: 10.1021/acs.jmedchem.4c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Anemoside B4 (AB4), a triterpenoidal saponin from Pulsatilla chinensis, shows significant anti-inflammatory activity, and may be used for treating inflammatory bowel disease (IBD). Nevertheless, its application is limited due to its high molecular weight and pronounced water solubility. To discover new effective agents for treating IBD, we synthesized 28 AB4 derivatives and evaluated their cytotoxic and anti-inflammatory activities in vitro. Among them, A3-6 exhibited significantly superior anti-inflammatory activity compared to AB4. It showed a significant improvement in the symptoms of DSS-induced colitis in mice, with a notably lower oral effective dose compared to AB4. Furthermore, we discovered that A3-6 bound with pyruvate carboxylase (PC), then inhibited PC activity, reprogramming macrophage function, and alleviated colitis. These findings indicate that A3-6 is a promising therapeutic candidate for colitis, and PC may be a potential new target for treating colitis.
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Affiliation(s)
- Lijuan Lv
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qiurong Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Kexin Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Jianping Zhao
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Kejun Deng
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China
| | - Ran Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhong Chen
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Ikhlas A Khan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Chunshan Gui
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Suxiang Feng
- Academy of Chinese Medicine Sciences, Henan University of Chinese Medicine, Zhengzhou, Henan 450018, China
| | - Shilin Yang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yanli Liu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Qiongming Xu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
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22
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Agarwal P, Vibhandik R, Agrahari R, Daverey A, Rani R. Role of Root Exudates on the Soil Microbial Diversity and Biogeochemistry of Heavy Metals. Appl Biochem Biotechnol 2024; 196:2673-2693. [PMID: 37191824 DOI: 10.1007/s12010-023-04465-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2023] [Indexed: 05/17/2023]
Abstract
Due to extensive industrialization and escalation in pollution, the world is facing problems related to soil heavy metal pollution. The traditional ways of soil remediation are neither feasible nor cost-effective in most of the real-world scenarios, where metal concentration is relatively low in soil. Therefore, phytoremediation using plants and plant secretions to remediate heavy metal-contaminated soil is recently getting more attention. The plant root exudates act as an ecological driver in the rhizospheric region where they influence and guide the microbial community to function in such a way that can be advantageous for plant growth. They also promote phytoremediation process by altering the bioavailability of pollutants in soil. Root exudates affect the biogeochemical properties of heavy metals as well. In this review, existing literature on the role of root exudates (natural as well as artificial) on the phytoremediation of heavy metal-contaminated (particularly lead) soil is reviewed. The effect of root exudates on the biogeochemistry of lead in soil is also discussed.
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Affiliation(s)
- Priyanka Agarwal
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Teliyarganj, Uttar Pradesh, 211004, India
| | - Rutuja Vibhandik
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Teliyarganj, Uttar Pradesh, 211004, India
| | - Roma Agrahari
- Department of Biochemical Engineering, Harcourt Butler Technical University, Kanpur, Uttar Pradesh, 208002, India
| | - Achlesh Daverey
- School of Environment and Natural Resources, Doon University, Dehradun, Uttarakhand, 248001, India
| | - Radha Rani
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, Teliyarganj, Uttar Pradesh, 211004, India.
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23
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Mauker P, Beckmann D, Kitowski A, Heise C, Wientjens C, Davidson AJ, Wanderoy S, Fabre G, Harbauer AB, Wood W, Wilhelm C, Thorn-Seshold J, Misgeld T, Kerschensteiner M, Thorn-Seshold O. Fluorogenic Chemical Probes for Wash-free Imaging of Cell Membrane Damage in Ferroptosis, Necrosis, and Axon Injury. J Am Chem Soc 2024. [PMID: 38592946 DOI: 10.1021/jacs.3c07662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Selectively labeling cells with damaged membranes is needed not only for identifying dead cells in culture, but also for imaging membrane barrier dysfunction in pathologies in vivo. Most membrane permeability stains are permanently colored or fluorescent dyes that need washing to remove their non-uptaken extracellular background and reach good image contrast. Others are DNA-binding environment-dependent fluorophores, which lack design modularity, have potential toxicity, and can only detect permeabilization of cell volumes containing a nucleus (i.e., cannot delineate damaged volumes in vivo nor image non-nucleated cell types or compartments). Here, we develop modular fluorogenic probes that reveal the whole cytosolic volume of damaged cells, with near-zero background fluorescence so that no washing is needed. We identify a specific disulfonated fluorogenic probe type that only enters cells with damaged membranes, then is enzymatically activated and marks them. The esterase probe MDG1 is a reliable tool to reveal live cells that have been permeabilized by biological, biochemical, or physical membrane damage, and it can be used in multicolor microscopy. We confirm the modularity of this approach by also adapting it for improved hydrolytic stability, as the redox probe MDG2. We conclude by showing the unique performance of MDG probes in revealing axonal membrane damage (which DNA fluorogens cannot achieve) and in discriminating damage on a cell-by-cell basis in embryos in vivo. The MDG design thus provides powerful modular tools for wash-free in vivo imaging of membrane damage, and indicates how designs may be adapted for selective delivery of drug cargoes to these damaged cells: offering an outlook from selective diagnosis toward therapy of membrane-compromised cells in disease.
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Affiliation(s)
- Philipp Mauker
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, 81377 Munich, Germany
| | - Daniela Beckmann
- Institute of Clinical Neuroimmunology, LMU University Hospital, Ludwig-Maximilians University of Munich, Marchioninistr. 15, 81377 Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians University of Munich, Grosshaderner Strasse 9, 82152 Martinsried, Germany
| | - Annabel Kitowski
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, 81377 Munich, Germany
| | - Constanze Heise
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, 81377 Munich, Germany
| | - Chantal Wientjens
- Immunopathology Unit, Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Andrew J Davidson
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, U.K
| | - Simone Wanderoy
- University Hospital, Technical University of Munich, Ismaninger Straße 22, 81675 Munich, Germany
- Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Gabin Fabre
- Pharmacology & Transplantation, UMR 1248 INSERM, University of Limoges, 87000 Limoges, France
| | - Angelika B Harbauer
- Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Biedersteiner Straße 29, 80802 Munich, Germany
| | - Will Wood
- Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, U.K
| | - Christoph Wilhelm
- Immunopathology Unit, Institute of Clinical Chemistry and Clinical Pharmacology, Medical Faculty, University Hospital Bonn, University of Bonn, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Julia Thorn-Seshold
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, 81377 Munich, Germany
| | - Thomas Misgeld
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
- Institute of Neuronal Cell Biology, Technical University of Munich, Biedersteiner Straße 29, 80802 Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
| | - Martin Kerschensteiner
- Institute of Clinical Neuroimmunology, LMU University Hospital, Ludwig-Maximilians University of Munich, Marchioninistr. 15, 81377 Munich, Germany
- Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians University of Munich, Grosshaderner Strasse 9, 82152 Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Strasse 17, 81377 Munich, Germany
| | - Oliver Thorn-Seshold
- Department of Pharmacy, Ludwig-Maximilians University of Munich, Butenandtstr. 7, 81377 Munich, Germany
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24
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Hołyst R, Bubak G, Kalwarczyk T, Kwapiszewska K, Michalski J, Pilz M. Living Cell as a Self-Synchronized Chemical Reactor. J Phys Chem Lett 2024; 15:3559-3570. [PMID: 38526849 PMCID: PMC11000238 DOI: 10.1021/acs.jpclett.4c00190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024]
Abstract
Thermal fluctuations power all processes inside living cells. Therefore, these processes are inherently random. However, myriad multistep chemical reactions act in concerto inside a cell, finally leading to this chemical reactor's self-replication. We speculate that an underlying mechanism in nature must exist that allows all of these reactions to synchronize at multiple time and length scales, overcoming in this way the random nature of any single process in a cell. This Perspective discusses what type of research is needed to understand this undiscovered synchronization law.
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Affiliation(s)
- Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Grzegorz Bubak
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Tomasz Kalwarczyk
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Karina Kwapiszewska
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jarosław Michalski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marta Pilz
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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25
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Jiang G, Liu H, Liu H, Ke G, Ren TB, Xiong B, Zhang XB, Yuan L. Chemical Approaches to Optimize the Properties of Organic Fluorophores for Imaging and Sensing. Angew Chem Int Ed Engl 2024; 63:e202315217. [PMID: 38081782 DOI: 10.1002/anie.202315217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 12/30/2023]
Abstract
Organic fluorophores are indispensable tools in cells, tissue and in vivo imaging, and have enabled much progress in the wide range of biological and biomedical fields. However, many available dyes suffer from insufficient performances, such as short absorption and emission wavelength, low brightness, poor stability, small Stokes shift, and unsuitable permeability, restricting their application in advanced imaging technology and complex imaging. Over the past two decades, many efforts have been made to improve these performances of fluorophores. Starting with the luminescence principle of fluorophores, this review clarifies the mechanisms of the insufficient performance for traditional fluorophores to a certain extent, systematically summarizes the modified approaches of optimizing properties, highlights the typical applications of the improved fluorophores in imaging and sensing, and indicates existing problems and challenges in this area. This progress not only proves the significance of improving fluorophores properties, but also provide a theoretical guidance for the development of high-performance fluorophores.
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Affiliation(s)
- Gangwei Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Han Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Hong Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Guoliang Ke
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Tian-Bing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Bin Xiong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, 410082, Changsha, P. R. China
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26
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Park SG, Lee HB, Kang S. Development of plug-and-deliverable intracellular protein delivery platforms based on botulinum neurotoxin. Int J Biol Macromol 2024; 261:129622. [PMID: 38266854 DOI: 10.1016/j.ijbiomac.2024.129622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/04/2024] [Accepted: 01/18/2024] [Indexed: 01/26/2024]
Abstract
Intracellular protein delivery systems have great potential in the fields of therapeutics development and biomedical research. However, targeted delivery, passing through the cell membrane without damaging the cells, and escaping from endosomal entrapment of endocytosed molecular cargos are major challenges of the system. Here, we present a novel intracellular protein delivery system based on modularly engineered botulinum neurotoxin type A (BoNT/A). LHNA domain, consisting of light chain and endosomal escape machinery of BoNT/A, was genetically fused with SpyCatcher (SC) and EGFR targeting affibody (EGFRAfb) to create SC-LHNA-EGFRAfb, a target-specific and protein cargo-switchable BoNT/A-based intracellular protein delivery platform. SC-LHNA-EGFRAfb was purely purified in large quantities, efficiently ligated with multiple ST-fused protein cargos individually, generating a variety of protein cargo-containing intracellular delivery complexes, and successfully delivered ligated protein cargos into the cytosol of target cells via receptor-mediated endocytosis, followed by endosomal escape and subsequent cytosolic delivery. SC-LHNA-EGFRAfb enhanced intracellular delivery efficiency of protein toxin, gelonin, by approximately 100-fold, highlighting the crucial roles of EGFRAfb and LHNA domain as a targeting ligand and an endosomal escape machinery, respectively, in the delivery process. The BoNT-based plug-and-deliverable intracellular protein delivery system has the potential to expand its applications in protein therapeutics and manipulating cellular processes.
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Affiliation(s)
- Seong Guk Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyun Bin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sebyung Kang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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27
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Chen Y, Jiang Y, Xue T, Cheng J. Strategies for the eradication of intracellular bacterial pathogens. Biomater Sci 2024; 12:1115-1130. [PMID: 38284808 DOI: 10.1039/d3bm01498c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Intracellular pathogens affect a significant portion of world population and cause millions of deaths each year. They can invade host cells and survive inside them and are extremely resistant to immune systems and antibiotics. Current treatments have limitations, and therefore, new effective therapies are needed to combat this ongoing health challenge. Active research efforts have been made to develop many new strategies to eradicate these intracellular pathogens. In this review, we focus on the intracellular bacterial pathogens and first introduce several representative intracellular bacteria and the diseases they cause. We then discuss the challenges in eradicating these bacteria and summarize the current therapeutics for intracellular bacteria. Finally, recent advances in intracellular bacteria eradication are highlighted.
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Affiliation(s)
- Yingying Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Yunjiang Jiang
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- BayRay Innovation Center, Shenzhen Bay Laboratory, Shenzhen, 518071, China
| | - Tianrui Xue
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jianjun Cheng
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Biomaterials and Drug Delivery Laboratory, School of Engineering, Westlake University, Hangzhou 310024, China
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28
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Sugiyama S, Suda K, Kono K. Cytoplasmic zoning by protein phase transition after membrane permeabilization. J Biochem 2024; 175:147-153. [PMID: 37972304 PMCID: PMC10873517 DOI: 10.1093/jb/mvad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Biological membranes, including plasma membrane (PM) and organelle membranes, restrict the flux of ions, molecules and organelles. However, the barrier function of biological membranes is frequently compromised by various perturbations, including physical membrane damage and protein- or chemical-induced pore formation. Recent evidence suggests that, upon PM damage, protein gelation and solid condensation are utilized to restrict ion/molecule/organelle flux across the damaged membranes by zoning the cytoplasm. In addition, membrane permeabilization dramatically alters intramembrane and extramembrane ion/molecule concentrations via the flux across the permeabilized membrane. The changes in ion/molecule concentration and their downstream pathways induce protein phase transition to form zones for biological processes or protein sequestration. Here, we review the mechanisms and functions of protein phase transition after biological membrane permeabilization.
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Affiliation(s)
- Shinju Sugiyama
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Kojiro Suda
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Keiko Kono
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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29
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Shobhna, Dutta A, Kumari P, Kashyap HK. Stability of Cytoplasmic Membrane of Escherichia coli Bacteria in Aqueous and Ethanolic Environment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:2893-2906. [PMID: 38311936 DOI: 10.1021/acs.langmuir.3c02780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The mechanism of action of any antibacterial agent or disinfectant depends largely on their interaction with the bacterial membrane. Herein, we use the SPICA (surface property fitting coarse graining) force-field and develop a coarse-grained (CG) model for the structure of the cytoplasmic membrane of Escherichia coli (E. coli) and its interaction with water and ethanol. We elucidate the impact of different concentrations of ethanol on the cytoplasmic membrane bilayers and vesicles of E. coli using the CG molecular dynamics (CG MD) simulations. Our modeling approach first focuses on the parametrization of the required force-field for POPG lipid and its interaction with water, ethanol, and POPE lipid. Subsequently, the structural stability of the E. coli bacterial membrane in the presence of high and low concentrations of ethanol is delineated. Both flat bilayers as well as vesicles of E. coli membrane were considered for the CG MD. Our results reveal that, at low ethanol concentrations (<30 mol %), the size of the E. coli vesicles increases with discernible deformations in their shapes. Because of ethanol-induced interdigitation, thinning of the E. coli vesicular membrane is also observed. However, at higher ethanol concentrations (>30 mol %), the integrity of the vesicles is lost because of deteriorating invasion of ethanol molecules into the vesicle bilayer and significant weakening of lipid-lipid interactions. At higher ethanol concentrations (40 and 70 mol %), both the multivesicle and single-vesicle bacterial membranes exhibit a similar rupturing pattern wherein the extraction of lipids from the membrane and formation of aggregates of the component lipids are observed. These aggregates consist of polar head groups of 3-5 POPE/POPG lipids with intertwined nonpolar tails.
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Affiliation(s)
- Shobhna
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ayishwarya Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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30
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Pawlędzio S, Ziemniak M, Trzybiński D, Arhangelskis M, Makal A, Woźniak K. Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography. RSC Adv 2024; 14:5340-5350. [PMID: 38348299 PMCID: PMC10859733 DOI: 10.1039/d3ra08081a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine. The application of quantum crystallography, including aspherical atom refinement, has enriched the depiction of electron density in the studied systems and non-covalent interactions, providing more details than previous studies. Our experimental results, combined with a topological analysis of the electron density and its Laplacian, provided detailed descriptions of how protonation changes the electron density distribution around the amine group and water molecule, concurrently decreasing the electron density at bond critical points of N/O-H bonds. Protonation also alters the molecular architecture of the systems under investigation. This is reflected in different proportions of the N⋯H and O⋯H intermolecular contacts for the neutral and protonated forms. Periodic DFT calculations of the cohesive energies of the crystal lattice, as well as computed interaction energies between molecules in the crystal, confirm that protonation stabilises the crystal structure due to a positive synergy between strong halogen and hydrogen bonds. Our findings highlight the potential of quantum crystallography in predicting crystal structure properties and point to its possible applications in developing new formulations for poorly soluble drugs.
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Affiliation(s)
- Sylwia Pawlędzio
- Neutron Scattering Division, Oak Ridge National Laboratory Oak Ridge TN 37831 USA
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Marcin Ziemniak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Damian Trzybiński
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Mihails Arhangelskis
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Anna Makal
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
| | - Krzysztof Woźniak
- Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw Żwirki i Wigury 101 02-093 Warszawa Poland
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31
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Vugmeyster L, Au DF, Frazier B, Qiang W, Ostrovsky D. Rigidifying of the internal dynamics of amyloid-beta fibrils generated in the presence of synaptic plasma vesicles. Phys Chem Chem Phys 2024; 26:5466-5478. [PMID: 38277177 PMCID: PMC10956644 DOI: 10.1039/d3cp04824a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
We investigated the changes in internal flexibility of amyloid-β1-40 (Aβ) fibrils grown in the presence of rat synaptic plasma vesicles. The fibrils are produced using a modified seeded growth protocol, in which the Aβ concentration is progressively increased at the expense of the decreased lipid to protein ratio. The morphologies of each generation are carefully assessed at several fibrils' growth time points using transmission electron microscopy. The side-chain dynamics in the fibrils is investigated using deuterium solid-state NMR measurements, with techniques spanning line shapes analysis and several NMR relaxation rates measurements. The dynamics is probed in the site-specific fashion in the hydrophobic C-terminal domain and the disordered N-terminal domain. An overall strong rigidifying effect is observed in comparison with the wild-type fibrils generated in the absence of the membranes. In particular, the overall large-scale fluctuations of the N-terminal domain are significantly reduced, and the activation energies of rotameric inter-conversion in methyl-bearing side-chains of the core (L17, L34, M35, V36), as well as the ring-flipping motions of F19 are increased, indicating a restricted core environment. Membrane-induced flexibility changes in Aβ aggregates can be important for the re-alignment of protein aggregates within the membrane, which in turn would act as a disruption pathway of the bilayers' integrity.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Dan Fai Au
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Bailey Frazier
- Department of Chemistry, University of Colorado Denver, Denver, CO, USA, 80204.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York, USA, 13902
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, CO, USA, 80204
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Townsend JA, Fapohunda O, Wang Z, Pham H, Taylor MT, Kloss B, Ho Park S, Opella S, Aspinwall CA, Marty MT. Differences in Oligomerization of the SARS-CoV-2 Envelope Protein, Poliovirus VP4, and HIV Vpu. Biochemistry 2024; 63:241-250. [PMID: 38216552 PMCID: PMC10872257 DOI: 10.1021/acs.biochem.3c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Viroporins constitute a class of viral membrane proteins with diverse roles in the viral life cycle. They can self-assemble and form pores within the bilayer that transport substrates, such as ions and genetic material, that are critical to the viral infection cycle. However, there is little known about the oligomeric state of most viroporins. Here, we use native mass spectrometry in detergent micelles to uncover the patterns of oligomerization of the full-length SARS-CoV-2 envelope (E) protein, poliovirus VP4, and HIV Vpu. Our data suggest that the E protein is a specific dimer, VP4 is exclusively monomeric, and Vpu assembles into a polydisperse mixture of oligomers under these conditions. Overall, these results revealed the diversity in the oligomerization of viroporins, which has implications for the mechanisms of their biological functions as well as their potential as therapeutic targets.
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Affiliation(s)
- Julia A. Townsend
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Oluwaseun Fapohunda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Zhihan Wang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Hieu Pham
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Taylor
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Brian Kloss
- New York Consortium on Membrane Protein Structure, New York Structural Biology Center, New York, NY 10027, USA
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stanley Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Craig A. Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
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Dang M, Shoichet MS. Long-Acting Ocular Injectables: Are We Looking In The Right Direction? ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306463. [PMID: 38018313 PMCID: PMC10885661 DOI: 10.1002/advs.202306463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/24/2023] [Indexed: 11/30/2023]
Abstract
The complex anatomy and physiological barriers of the eye make delivering ocular therapeutics challenging. Generally, effective drug delivery to the eye is hindered by rapid clearance and limited drug bioavailability. Biomaterial-based approaches have emerged to enhance drug delivery to ocular tissues and overcome existing limitations. In this review, some of the most promising long-acting injectables (LAIs) in ocular drug delivery are explored, focusing on novel design strategies to improve therapeutic outcomes. LAIs are designed to enable sustained therapeutic effects, thereby extending local drug residence time and facilitating controlled and targeted drug delivery. Moreover, LAIs can be engineered to enhance drug targeting and penetration across ocular physiological barriers.
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Affiliation(s)
- Mickael Dang
- Department of Chemical Engineering and Applied ChemistryUniversity of Toronto200 College StreetTorontoONM5S 3E5Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto160 College StreetTorontoONM5S 3E1Canada
| | - Molly S. Shoichet
- Department of Chemical Engineering and Applied ChemistryUniversity of Toronto200 College StreetTorontoONM5S 3E5Canada
- Donnelly Centre for Cellular and Biomolecular ResearchUniversity of Toronto160 College StreetTorontoONM5S 3E1Canada
- Institute of Biomedical Engineering164 College StreetTorontoONM5S 3G9Canada
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Lone JB, Long JZ, Svensson KJ. Size matters: the biochemical logic of ligand type in endocrine crosstalk. LIFE METABOLISM 2024; 3:load048. [PMID: 38425548 PMCID: PMC10904031 DOI: 10.1093/lifemeta/load048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The endocrine system is a fundamental type of long-range cell-cell communication that is important for maintaining metabolism, physiology, and other aspects of organismal homeostasis. Endocrine signaling is mediated by diverse blood-borne ligands, also called hormones, including metabolites, lipids, steroids, peptides, and proteins. The size and structure of these hormones are fine-tuned to make them bioactive, responsive, and adaptable to meet the demands of changing environments. Why has nature selected such diverse ligand types to mediate communication in the endocrine system? What is the chemical, signaling, or physiologic logic of these ligands? What fundamental principles from our knowledge of endocrine communication can be applied as we continue as a field to uncover additional new circulating molecules that are claimed to mediate long-range cell and tissue crosstalk? This review provides a framework based on the biochemical logic behind this crosstalk with respect to their chemistry, temporal regulation in physiology, specificity, signaling actions, and evolutionary development.
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Affiliation(s)
- Jameel Barkat Lone
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan Z. Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA 94305, USA
| | - Katrin J. Svensson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Wu Tsai Human Performance Alliance, Stanford University, Stanford, CA 94305, USA
- Stanford Cardiovascular Institute, Stanford University School of Medicine, CA 94305, USA
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Ouyang X, Liu Y, Zheng K, Pang Z, Peng S. Recent advances in zwitterionic nanoscale drug delivery systems to overcome biological barriers. Asian J Pharm Sci 2024; 19:100883. [PMID: 38357524 PMCID: PMC10861844 DOI: 10.1016/j.ajps.2023.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/28/2023] [Accepted: 12/22/2023] [Indexed: 02/16/2024] Open
Abstract
Nanoscale drug delivery systems (nDDS) have been employed widely in enhancing the therapeutic efficacy of drugs against diseases with reduced side effects. Although several nDDS have been successfully approved for clinical use up to now, biological barriers between the administration site and the target site hinder the wider clinical adoption of nDDS in disease treatment. Polyethylene glycol (PEG)-modification (or PEGylation) has been regarded as the gold standard for stabilising nDDS in complex biological environment. However, the accelerated blood clearance (ABC) of PEGylated nDDS after repeated injections becomes great challenges for their clinical applications. Zwitterionic polymer, a novel family of anti-fouling materials, have evolved as an alternative to PEG due to their super-hydrophilicity and biocompatibility. Zwitterionic nDDS could avoid the generation of ABC phenomenon and exhibit longer blood circulation time than the PEGylated analogues. More impressively, zwitterionic nDDS have recently been shown to overcome multiple biological barriers such as nonspecific organ distribution, pressure gradients, impermeable cell membranes and lysosomal degradation without the need of any complex chemical modifications. The realization of overcoming multiple biological barriers by zwitterionic nDDS may simplify the current overly complex design of nDDS, which could facilitate their better clinical translation. Herein, we summarise the recent progress of zwitterionic nDDS at overcoming various biological barriers and analyse their underlying mechanisms. Finally, prospects and challenges are introduced to guide the rational design of zwitterionic nDDS for disease treatment.
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Affiliation(s)
- Xumei Ouyang
- Zhuhai Institute of Translational Medicine, Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai 519000, China
| | - Yu Liu
- Zhuhai Institute of Translational Medicine, Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai 519000, China
| | - Ke Zheng
- School of Materials Science and Engineering, Dongguan University of Technology, Dongguan 523808, China
| | - Zhiqing Pang
- Key Laboratory of Smart Drug Delivery, Ministry of Education, Department of Pharmaceutics, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Shaojun Peng
- Zhuhai Institute of Translational Medicine, Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated with Jinan University), Zhuhai 519000, China
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Beaven E, Kumar R, An JM, Mendoza H, Sutradhar SC, Choi W, Narayan M, Lee YK, Nurunnabi M. Potentials of ionic liquids to overcome physical and biological barriers. Adv Drug Deliv Rev 2024; 204:115157. [PMID: 38104896 PMCID: PMC10787599 DOI: 10.1016/j.addr.2023.115157] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Over the last decades, ionic liquids (IL) have shown great potential in non-invasive delivery starting from synthetic small molecules to biological large molecules. ILs are emerging as a particular class of drug delivery systems due to their unique physiochemical properties, simple surface modification, and functionalization. These features of IL help achieve specific design principles that are essential for a non-invasive drug delivery system. In this review, we have discussed IL and their applications in non-invasive drug delivery systems. We evaluated state-of-the-art development and advances of IL aiming to mitigate the biological and physical barriers to improve transdermal and oral delivery, summarized in this review. We also provided an overview of the various factors determining the systemic transportation of IL-based formulation. Additionally, we have emphasized how the ILs facilitate the transportation of therapeutic molecules by overcoming biological barriers.
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Affiliation(s)
- Elfa Beaven
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79902, United States; Biomedical Engineering Program, College of Engineering, University of Texas at El Paso, El Paso, TX 79968, United States
| | - Raj Kumar
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79902, United States; Biomedical Engineering Program, College of Engineering, University of Texas at El Paso, El Paso, TX 79968, United States
| | - Jeong Man An
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Republic of Korea
| | - Hannia Mendoza
- Department of Chemistry and Biochemistry, College of Science, University of Texas at El Paso, El Paso, TX 79968, United States
| | - Sabuj Chandra Sutradhar
- 4D Convergence Technology Institute, Korea National University of Transportation, Jungpyeong 27909, Republic of Korea
| | - Wonho Choi
- 4D Convergence Technology Institute, Korea National University of Transportation, Jungpyeong 27909, Republic of Korea
| | - Mahesh Narayan
- Department of Chemistry and Biochemistry, College of Science, University of Texas at El Paso, El Paso, TX 79968, United States
| | - Yong-Kyu Lee
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 04763, Republic of Korea; Department of Chemical and Biological Engineering, College of Engineering, Korea National University of Transportation, Chungju 380-702, Republic of Korea; 4D Convergence Technology Institute, Korea National University of Transportation, Jungpyeong 27909, Republic of Korea.
| | - Md Nurunnabi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79902, United States; Biomedical Engineering Program, College of Engineering, University of Texas at El Paso, El Paso, TX 79968, United States; Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, United States.
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Yu IS, Choi YR, Choi J, Kim MK, Jung CH, Um MY, Kim MJ. Discovery of Novel Stimulators of Pax7 and/or MyoD: Enhancing the Efficacy of Cultured Meat Production through Culture Media Enrichment. BIOSENSORS 2023; 14:24. [PMID: 38248401 PMCID: PMC10813534 DOI: 10.3390/bios14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/26/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024]
Abstract
The principles of myogenesis play crucial roles in the production of cultured meat, and identifying protein stimulators associated with myogenesis holds great potential to enhance the efficiency of this process. In this study, we used surface plasmon resonance (SPR)-based screening of a natural product library to discover ligands for Pax7 and MyoD, key regulators of satellite cells (SCs), and performed cell-based assays on Hanwoo SCs (HWSCs) to identify substances that promote cell proliferation and/or differentiation. Through an SPR analysis, we found that six chemicals, including one Pax7+/MyoD- chemical, four Pax7+/MyoD+ chemicals, and one Pax7-/MyoD+ chemical, bound to Pax7 and/or MyoD proteins. Among four Pax7+/MyoD+ chemicals, parthenolide (0.5 and 1 µM) and rutin (100 and 200 µM) stimulated cell proliferation in the medium with 10% FBS similar to the medium with 20% FBS, without affecting differentiation. Adenosine, a Pax7-/MyoD+ chemical, accelerated differentiation. These chemicals could be potential additives to reduce the reliance of FBS required for HWSC proliferation and differentiation in cultured meat production.
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Affiliation(s)
- In-Sun Yu
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (I.-S.Y.); (Y.R.C.); (C.H.J.); (M.Y.U.)
- Department of Food Science and Human Nutrition and K-Food Research Center, Jeonbuk National University, Jeonju-si 54896, Republic of Korea;
| | - Yae Rim Choi
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (I.-S.Y.); (Y.R.C.); (C.H.J.); (M.Y.U.)
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jungseok Choi
- Department of Animal Science, Chungbuk National University, Cheongju-si 28644, Republic of Korea;
| | - Mina K. Kim
- Department of Food Science and Human Nutrition and K-Food Research Center, Jeonbuk National University, Jeonju-si 54896, Republic of Korea;
| | - Chang Hwa Jung
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (I.-S.Y.); (Y.R.C.); (C.H.J.); (M.Y.U.)
| | - Min Young Um
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (I.-S.Y.); (Y.R.C.); (C.H.J.); (M.Y.U.)
| | - Min Jung Kim
- Division of Food Functionality Research, Korea Food Research Institute, Wanju-gun 55365, Republic of Korea; (I.-S.Y.); (Y.R.C.); (C.H.J.); (M.Y.U.)
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Krok E, Franquelim HG, Chattopadhyay M, Orlikowska-Rzeznik H, Schwille P, Piatkowski L. Nanoscale structural response of biomimetic cell membranes to controlled dehydration. NANOSCALE 2023; 16:72-84. [PMID: 38062887 DOI: 10.1039/d3nr03078d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Although cell membranes exist in excess of water under physiological conditions, there are a number of biochemical processes, such as adsorption of biomacromolecules or membrane fusion events, that require partial or even complete transient dehydration of lipid membranes. Even though the dehydration process is crucial for understanding all fusion events, still little is known about the structural adaptation of lipid membranes when their interfacial hydration layer is perturbed. Here, we present the study of the nanoscale structural reorganization of phase-separated, supported lipid bilayers (SLBs) under a wide range of hydration conditions. Model lipid membranes were characterised using a combination of fluorescence microscopy and atomic force microscopy and, crucially, without applying any chemical or physical modifications that have previously been considered essential for maintaining the membrane integrity upon dehydration. We revealed that decreasing the hydration state of the membrane leads to an enhanced mixing of lipids characteristic of the liquid-disordered (Ld) phase with those forming the liquid-ordered (Lo) phase. This is associated with a 2-fold decrease in the hydrophobic mismatch between the Ld and Lo lipid phases and a 3-fold decrease in the line tension for the fully desiccated membrane. Importantly, the observed changes in the hydrophobic mismatch, line tension, and lipid miscibility are fully reversible upon subsequent rehydration of the membrane. These findings provide a deeper insight into the fundamental processes, such as cell-cell fusion, that require partial dehydration at the interface of two membranes.
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Affiliation(s)
- Emilia Krok
- Poznan University of Technology, Faculty of Materials Engineering and Technical Physics, Institute of Physics, Piotrowo 3, 60-965 Poznan, Poland.
| | - Henri G Franquelim
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Leipzig University, Research and Transfer Center for Bioactive Matter, Deutscher Platz 5, 04103 Leipzig, Germany
| | - Madhurima Chattopadhyay
- Poznan University of Technology, Faculty of Materials Engineering and Technical Physics, Institute of Physics, Piotrowo 3, 60-965 Poznan, Poland.
| | - Hanna Orlikowska-Rzeznik
- Poznan University of Technology, Faculty of Materials Engineering and Technical Physics, Institute of Physics, Piotrowo 3, 60-965 Poznan, Poland.
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lukasz Piatkowski
- Poznan University of Technology, Faculty of Materials Engineering and Technical Physics, Institute of Physics, Piotrowo 3, 60-965 Poznan, Poland.
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Hoes L, Voordeckers K, Dok R, Boeckx B, Steemans B, Gopaul D, Pasero P, Govers SK, Lambrechts D, Nuyts S, Verstrepen KJ. Ethanol induces replication fork stalling and membrane stress in immortalized laryngeal cells. iScience 2023; 26:108564. [PMID: 38213791 PMCID: PMC10783606 DOI: 10.1016/j.isci.2023.108564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/11/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
Although ethanol is a class I carcinogen and is linked to more than 700,000 cancer incidences, a clear understanding of the molecular mechanisms underlying ethanol-related carcinogenesis is still lacking. Further understanding of ethanol-related cell damage can contribute to reducing or treating alcohol-related cancers. Here, we investigated the effects of both short- and long-term exposure of human laryngeal epithelial cells to different ethanol concentrations. RNA sequencing shows that ethanol altered gene expression patterns in a time- and concentration-dependent way, affecting genes involved in ribosome biogenesis, cytoskeleton remodeling, Wnt signaling, and transmembrane ion transport. Additionally, ethanol induced a slower cell proliferation, a delayed cell cycle progression, and replication fork stalling. In addition, ethanol exposure resulted in morphological changes, which could be associated with membrane stress. Taken together, our data yields a comprehensive view of molecular changes associated with ethanol stress in epithelial cells of the upper aerodigestive tract.
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Affiliation(s)
- Lore Hoes
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Karin Voordeckers
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Rüveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Bart Steemans
- Laboratory of Microbial Systems Cell Biology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Diyavarshini Gopaul
- Institute of Human Genetics, CNRS, University of Montpellier, 34396 Montpellier, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS, University of Montpellier, 34396 Montpellier, France
| | - Sander K. Govers
- Laboratory of Microbial Systems Cell Biology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, VIB-KU Leuven Center for Cancer Biology, 3000 Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
- Department of Radiation Oncology, Leuven Cancer Institute, University Hospital Leuven, 3000 Leuven, Belgium
| | - Kevin J. Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, 3000 Leuven
- Laboratory of Genetics and Genomics, Centre for Microbial and Plant Genetics, KU Leuven, 3000 Leuven, Belgium
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López de Sá A, Díaz-Tejeiro C, Poyatos-Racionero E, Nieto-Jiménez C, Paniagua-Herranz L, Sanvicente A, Calvo E, Pérez-Segura P, Moreno V, Moris F, Ocana A. Considerations for the design of antibody drug conjugates (ADCs) for clinical development: lessons learned. J Hematol Oncol 2023; 16:118. [PMID: 38087293 PMCID: PMC10717055 DOI: 10.1186/s13045-023-01519-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Antibody-drug conjugates (ADCs) have emerged as a novel therapeutic strategy that has successfully reached patient treatment in different clinical scenarios. ADCs are formed by an antibody against a specific tumor-associated antigen (TAA), a cytotoxic payload, and a chemical linker that binds both. To this regard, most efforts have been focused on target identification, antibody design and linker optimization, but other relevant aspects for clinical development have not received the necessary attention. In this article using data from approved ADCs, we evaluated all characteristics of these agents, including payload physicochemical properties, in vitro potency, drug antibody ratio (DAR), exposure-response relationships, and clinical development strategies. We suggest that compounds with best options for clinical development include those with optimal payload physicochemical properties and cleavable linkers that would lead to a bystander effect. These modalities can facilitate the development of ADCs in indications with low expression of the TAA. Early clinical development strategies including changes in the schedule of administration with more frequent doses are also discussed in the context of an efficient strategy. In conclusion, we highlight relevant aspects that are needed for the optimal development of ADCs in cancer, proposing options for improvement.
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Affiliation(s)
- Alfonso López de Sá
- Medical Oncology Department, Hospital Clínico Universitario San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), and CIBERONC, Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | | | - Cristina Nieto-Jiménez
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Lucía Paniagua-Herranz
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Adrián Sanvicente
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Emiliano Calvo
- START Madrid-HM Centro Integral Oncológico Clara Campal (CIOCC), Early Phase Program, HM Sanchinarro University Hospital, Madrid, Spain
| | - Pedro Pérez-Segura
- Medical Oncology Department, Hospital Clínico Universitario San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), and CIBERONC, Madrid, Spain
| | - Víctor Moreno
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, Madrid, Spain
| | | | - Alberto Ocana
- Medical Oncology Department, Hospital Clínico Universitario San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), and CIBERONC, Madrid, Spain.
- Experimental Therapeutics in Cancer Unit, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain.
- START Madrid-Fundación Jiménez Díaz (FJD) Early Phase Program, Fundación Jiménez Díaz Hospital, Madrid, Spain.
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Rocca R, Grillone K, Citriniti EL, Gualtieri G, Artese A, Tagliaferri P, Tassone P, Alcaro S. Targeting non-coding RNAs: Perspectives and challenges of in-silico approaches. Eur J Med Chem 2023; 261:115850. [PMID: 37839343 DOI: 10.1016/j.ejmech.2023.115850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
The growing information currently available on the central role of non-coding RNAs (ncRNAs) including microRNAs (miRNAS) and long non-coding RNAs (lncRNAs) for chronic and degenerative human diseases makes them attractive therapeutic targets. RNAs carry out different functional roles in human biology and are deeply deregulated in several diseases. So far, different attempts to therapeutically target the 3D RNA structures with small molecules have been reported. In this scenario, the development of computational tools suitable for describing RNA structures and their potential interactions with small molecules is gaining more and more interest. Here, we describe the most suitable strategies to study ncRNAs through computational tools. We focus on methods capable of predicting 2D and 3D ncRNA structures. Furthermore, we describe computational tools to identify, design and optimize small molecule ncRNA binders. This review aims to outline the state of the art and perspectives of computational methods for ncRNAs over the past decade.
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Affiliation(s)
- Roberta Rocca
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
| | - Katia Grillone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | | | | | - Anna Artese
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy.
| | | | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, Magna Græcia University, Catanzaro, Italy
| | - Stefano Alcaro
- Department of Health Science, Magna Graecia University, Catanzaro, Italy; Net4Science srl, Academic Spinoff, Magna Græcia University, Catanzaro, Italy
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42
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Lemière J, Chang F. Quantifying turgor pressure in budding and fission yeasts based upon osmotic properties. Mol Biol Cell 2023; 34:ar133. [PMID: 37903220 PMCID: PMC10848946 DOI: 10.1091/mbc.e23-06-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Abstract
Walled cells, such as plants, fungi, and bacteria cells, possess a high internal hydrostatic pressure, termed turgor pressure, that drives volume growth and contributes to cell shape determination. Rigorous measurement of turgor pressure, however, remains challenging, and reliable quantitative measurements, even in budding yeast are still lacking. Here, we present a simple and robust experimental approach to access turgor pressure in yeasts based upon the determination of isotonic concentration using protoplasts as osmometers. We propose three methods to identify the isotonic condition - three-dimensional cell volume, cytoplasmic fluorophore intensity, and mobility of a cytGEMs nano-rheology probe - that all yield consistent values. Our results provide turgor pressure estimates of 1.0 ± 0.1 MPa for Schizosaccharomyces pombe, 0.49 ± 0.01 MPa for Schizosaccharomyces japonicus, 0.5 ± 0.1 MPa for Saccharomyces cerevisiae W303a and 0.31 ± 0.03 MPa for Saccharomyces cerevisiae BY4741. Large differences in turgor pressure and nano-rheology measurements between the Saccharomyces cerevisiae strains demonstrate how fundamental biophysical parameters can vary even among wild-type strains of the same species. These side-by-side measurements of turgor pressure in multiple yeast species provide critical values for quantitative studies on cellular mechanics and comparative evolution.
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Affiliation(s)
- Joël Lemière
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, CA 94143
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43
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Wu WW, Choe M, Johannesen L, Vicente J, Bende G, Stockbridge NL, Strauss DG, Garnett C. ICH S7B In Vitro Assays Do Not Address Mechanisms of QT C Prolongation for Peptides and Proteins - Data in Support of Not Needing Dedicated QT C Studies. Clin Pharmacol Ther 2023; 114:1332-1341. [PMID: 37702218 DOI: 10.1002/cpt.3047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Current cardiac safety testing focuses on detecting drug-induced QTC prolongation as a surrogate for risk of Torsade de Pointes. The nonclinical strategy, described in International Conference on Harmonization (ICH) S7B, includes in vitro assessment of hERG block or ventricular repolarization delay and in vivo QT prolongation. Several studies have reported predictive values of ICH S7B results for clinical QTC outcomes for small molecules; none has examined peptides and proteins other than monoclonal antibodies. To address this knowledge gap, information for peptides and proteins submitted to the US Food and Drug Administration (FDA) was collected. Results of hERG assays, ventricular repolarization assays, and in vivo QT assessment were compared with clinical QTC study outcomes. The results show that 14% clinical QTC studies for approved and investigational products failed to exclude 10-ms QTC prolongation. Clinical QTC prolongation for these molecules lacked concentration-dependence which is expected for hERG block-mediated mechanism or QTC prolongation could not be excluded due to characterization in the clinical study. The hERG and ventricular repolarization assays do not identify clinical QTC prolongation potential for peptides and proteins. Lack of alignment between hERG and ventricular repolarization assay results and clinical QTC outcomes suggests that the mechanisms of QTC prolongation by some peptides and proteins are unrelated to direct cardiac ion channel block. Similar to large targeted proteins and monoclonal antibodies, peptides and proteins regardless of size have a low likelihood of direct cardiac ion channel interactions. This characteristic supports waiving the requirement for thorough QT assessment for products comprised of naturally occurring amino acids unless proarrhythmia potential is suggested by nonclinical or clinical data.
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Affiliation(s)
- Wendy W Wu
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Moran Choe
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
- Division of Hematology, Oncology, Toxicology, Office of Oncologic Diseases, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Lars Johannesen
- Division of Cardiology and Nephrology, Office of Cardiology, Hematology, Endocrinology and Nephrology, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jose Vicente
- Division of Cardiology and Nephrology, Office of Cardiology, Hematology, Endocrinology and Nephrology, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Girish Bende
- Division of Cardiometabolic and Endocrine Pharmacology, Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
- Takeda Pharmaceutical Company Limited, Cambridge, Massachusetts, USA
| | - Norman L Stockbridge
- Division of Cardiology and Nephrology, Office of Cardiology, Hematology, Endocrinology and Nephrology, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - David G Strauss
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translational Science, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Christine Garnett
- Division of Cardiology and Nephrology, Office of Cardiology, Hematology, Endocrinology and Nephrology, Office of New Drugs, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
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Salehi T, Raeisi Estabragh MA, Salarpour S, Ohadi M, Dehghannoudeh G. Absorption enhancer approach for protein delivery by various routes of administration: a rapid review. J Drug Target 2023; 31:950-961. [PMID: 37842966 DOI: 10.1080/1061186x.2023.2271680] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
As bioactive molecules, peptides and proteins are essential in living organisms, including animals and humans. Defects in their function lead to various diseases in humans. Therefore, the use of proteins in treating multiple diseases, such as cancers and hepatitis, is increasing. There are different routes to administer proteins, which have limitations due to their large and hydrophilic structure. Another limitation is the presence of biological and lipophilic membranes that do not allow proteins to pass quickly. There are different strategies to increase the absorption of proteins from these biological membranes. One of these strategies is to use compounds as absorption enhancers. Absorption enhancers are compounds such as surfactants, phospholipids and cyclodextrins that increase protein passage through the biological membrane and their absorption by different mechanisms. This review focuses on using other absorption enhancers and their mechanism in protein administration routes.
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Affiliation(s)
- Toktam Salehi
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Amin Raeisi Estabragh
- Student Research Committee, Kerman University of Medical Sciences, Kerman, Iran
- Department of Pharmaceutics, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Soodeh Salarpour
- Department of Pharmaceutics, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mandana Ohadi
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamreza Dehghannoudeh
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
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45
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Wen A, Qin ARR, Tarnowski T, Ling KHJ, Zhang H, Humeniuk R, Regan S, Saquing J, Liu W, Venkatarangan L, Xiao D. Plasma Protein Binding Determination for Unstable Ester Prodrugs: Remdesivir and Tenofovir Alafenamide. J Pharm Sci 2023; 112:3224-3232. [PMID: 37722451 DOI: 10.1016/j.xphs.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
Remdesivir (RDV) and tenofovir alafenamide (TAF) are prodrugs designed to be converted to their respective active metabolites. Plasma protein binding (PPB) determination of these prodrugs is important for patients with possible alteration of free fraction of the drugs due to plasma protein changes in renal impairment, hepatic impairment, or pregnancy. However, the prodrugs' instability in human plasma presents a challenge for accurate PPB determination. In this research work, two approaches were used in the method development and qualification for PPB assessment of RDV and TAF. For RDV, dichlorvos was used to inhibit esterase activity to stabilize the prodrug in plasma during equilibrium dialysis (ED). The impact of dichlorvos on protein binding was evaluated and determined to be insignificant by comparing the unbound fraction (fu) determined by the ED method with dichlorvos present and the fu determined by an ultrafiltration method without dichlorvos. In contrast to RDV, TAF degradation in plasma is ∼3-fold slower, and TAF stability cannot be improved by dichlorvos. Fit-for-purpose acceptance criteria for the TAF PPB method were chosen, and an ED method was developed based on these criteria. These two methods were then qualified and applied for PPB determinations in clinical studies.
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Affiliation(s)
- Anita Wen
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA; Department of Nutrition, University of California, Davis, CA, USA
| | - Ann Ran-Ran Qin
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA
| | - Thomas Tarnowski
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA
| | | | - Haeyoung Zhang
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA
| | - Rita Humeniuk
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA
| | - Sean Regan
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA
| | | | | | | | - Deqing Xiao
- Department of Clinical Pharmacology, Gilead Sciences, Foster City, CA, USA.
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46
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Ishizaki Y, Umekita M, Arisaka R, Hatano M, Kimura T, Kubota Y, Shibuya Y, Hayashi C, Sawa R, Igarashi M. Cycloimidamicins, Novel natural lead compounds for translation inhibition in Pseudomonas aeruginosa. J Antibiot (Tokyo) 2023; 76:691-698. [PMID: 37758819 DOI: 10.1038/s41429-023-00656-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023]
Abstract
Pseudomonas aeruginosa is one of the most concerning pathogenic bacteria. We screened antibiotics using a highly drug-sensitive P. aeruginosa strain and an oligotrophic medium, and successfully isolated novel antibiotics, namely cycloimidamicins (CIMs), from a rare actinomycete strain, Lentzea sp. MM249-143F7. X-ray and nuclear magnetic resonance analyses revealed that CIMs possess a distinctive and unprecedented molecular structure, containing tetramic acid and an imidazole ring bound directly to indolone. The CIMs exhibited potent antibacterial activity against Gram-negative bacteria, as well as translation inhibition in Escherichia coli in both intact cells and in vitro. Additionally, E. coli strains resistant to known translation inhibitors did not exhibit cross-resistance to CIMs, suggesting that CIMs inhibit bacterial growth by blocking translation through a novel mechanism.
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Affiliation(s)
- Yoshimasa Ishizaki
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Maya Umekita
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Rie Arisaka
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Masaki Hatano
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Tomoyuki Kimura
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Yumiko Kubota
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Yuko Shibuya
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Chigusa Hayashi
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Ryuichi Sawa
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan
| | - Masayuki Igarashi
- Institute of Microbial Chemistry (BIKAKEN), 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo, 141-0021, Japan.
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47
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Stanchev LD, Møller-Hansen I, Lojko P, Rocha C, Borodina I. Screening of Saccharomyces cerevisiae metabolite transporters by 13C isotope substrate labeling. Front Microbiol 2023; 14:1286597. [PMID: 38116525 PMCID: PMC10729909 DOI: 10.3389/fmicb.2023.1286597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
The transportome of Saccharomyces cerevisiae comprises approximately 340 membrane-bound proteins, of which very few are well-characterized. Elucidating transporter proteins' function is essential not only for understanding central cellular processes in metabolite exchange with the external milieu but also for optimizing the production of value-added compounds in microbial cell factories. Here, we describe the application of 13C-labeled stable isotopes and detection by targeted LC-MS/MS as a screening tool for identifying Saccharomyces cerevisiae metabolite transporters. We compare the transport assay's sensitivity, reproducibility, and accuracy in yeast transporter mutant cell lines and Xenopus oocytes. As proof of principle, we analyzed the transport profiles of five yeast amino acid transporters. We first cultured yeast transporter deletion or overexpression mutants on uniformly labeled 13C-glucose and then screened their ability to facilitate the uptake or export of an unlabeled pool of amino acids. Individual transporters were further studied by heterologous expression in Xenopus oocytes, followed by an uptake assay with 13C labeled yeast extract. Uptake assays in Xenopus oocytes showed higher reproducibility and accuracy. Although having lower accuracy, the results from S. cerevisiae indicated the system's potential for initial high-throughput screening for native metabolite transporters. We partially confirmed previously reported substrates for all five amino acid transporters. In addition, we propose broader substrate specificity for two of the transporter proteins. The method presented here demonstrates the application of a comprehensive screening platform for the knowledge expansion of the transporter-substrate relationship for native metabolites in S. cerevisiae.
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Affiliation(s)
| | | | | | | | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
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48
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Chen Q, Sun M, Han X, Xu H, Liu Y. Structural determinants specific for retromer protein sorting nexin 5 in regulating subcellular retrograde membrane trafficking. J Biomed Res 2023; 37:492-506. [PMID: 37964759 PMCID: PMC10687533 DOI: 10.7555/jbr.37.20230112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 11/16/2023] Open
Abstract
The endosomal trafficking of signaling membrane proteins, such as receptors, transporters and channels, is mediated by the retromer-mediated sorting machinery, composed of a cargo-selective vacuolar protein sorting trimer and a membrane-deforming subunit of sorting nexin proteins. Recent studies have shown that the isoforms, sorting nexin 5 (SNX5) and SNX6, have played distinctive regulatory roles in retrograde membrane trafficking. However, the molecular insight determined functional differences within the proteins remains unclear. We reported that SNX5 and SNX6 had distinct binding affinity to the cargo protein vesicular monoamine transporter 2 (VMAT2). SNX5, but not SNX6, specifically interacted with VMAT2 through the Phox domain, which contains an alpha-helix binding motif. Using chimeric mutagenesis, we identified that several key residues within this domain were unique in SNX5, but not SNX6, and played an auxiliary role in its binding to VMAT2. Importantly, we generated a set of mutant SNX6, in which the corresponding key residues were mutated to those in SNX5. In addition to the gain in binding affinity to VMAT2, their overexpression functionally rescued the altered retrograde trafficking of VMAT2 induced by siRNA-mediated depletion of SNX5. These data strongly suggest that SNX5 and SNX6 have different functions in retrograde membrane trafficking, which is determined by the different structural elements within the Phox domain of two proteins. Our work provides a new information on the role of SNX5 and SNX6 in the molecular regulation of retrograde membrane trafficking and vesicular membrane targeting in monoamine neurotransmission and neurological diseases.
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Affiliation(s)
- Qing Chen
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Meiheng Sun
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xu Han
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Hongfei Xu
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yongjian Liu
- Jiangsu Key Laboratory of Xenotransplantation, and Department of Medical Genetics, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Department of Neuroscience, University of Pittsburgh Kenneth P. Dietrich School of Arts and Sciences, Pittsburgh, PA 15260, USA
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49
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Cai Y, Ren J, Jin J, Shao H, Wang P, Cheng K, Jiang P, Jiang P, Zhu S, Zhu G, Zhang L. Novel affibody molecules as potential agents in molecular imaging for MAGE-A3-positive tumor diagnosis. ENVIRONMENTAL RESEARCH 2023; 237:116895. [PMID: 37586454 DOI: 10.1016/j.envres.2023.116895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/07/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND The cancer-testis protein melanoma antigen A3 (MAGE-A3) is highly expressed in a broad range of malignant tumor forms. It has been confirmed that affibody molecules, a novel family of small (∼6.5 kDa) targeting proteins, are useful agents for molecular imaging and targeted tumor treatment. As a novel agent for in vivo molecular imaging detection of MAGE-A3-positive tumors, the efficacy of affibody molecules was assessed in this research. METHODS In this study, three cycles of phage display library screening resulted in the isolation of two new affibody molecules (ZMAGE-A3:172 and ZMAGE-A3:770) that attach to MAGE-A3. These molecules were then expressed in bacteria and purified. The affibody molecules with high affinity and specificity were evaluated using western blotting, immunohistochemistry, indirect immunofluorescence, surface plasmon resonance, and near-infrared optical imaging of tumor-bearing nude mice. RESULTS The selected ZMAGE-A3 affibodies can precisely bind to the MAGE-A3 protein in living cells and display high-affinity binding to the MAGE-A3 protein at the molecular level. Furthermore, the accumulation of DyLight755-labeled ZMAGE-A3:172 or ZMAGE-A3:770 in MAGE-A3-positive tumors was achieved as early as 30 min and disappeared at 48 h post-injection. CONCLUSION Our findings support the potential of the two MAGE-A3 protein-binding affibody molecules for their use as molecular imaging agents.
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Affiliation(s)
- Yiqi Cai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Jiahuan Ren
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Jinji Jin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Huanyi Shao
- Department of Pediatric Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Pengfei Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Kai Cheng
- Department of Dermatology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Peipei Jiang
- Department of Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Pengfei Jiang
- Institute of Molecular Virology and Immunology, Department of Medical Microbiology and Immunology, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Shanli Zhu
- Institute of Molecular Virology and Immunology, Department of Medical Microbiology and Immunology, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China
| | - Guanbao Zhu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China.
| | - Lifang Zhang
- Institute of Molecular Virology and Immunology, Department of Medical Microbiology and Immunology, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, PR China.
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50
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Fonseca Lopez F, Miao J, Damjanovic J, Bischof L, Braun MB, Ling Y, Hartmann MD, Lin YS, Kritzer JA. Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. J Chem Inf Model 2023; 63:6925-6937. [PMID: 37917529 PMCID: PMC10807374 DOI: 10.1021/acs.jcim.3c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The Nrf2 transcription factor is a master regulator of the cellular response to oxidative stress, and Keap1 is its primary negative regulator. Activating Nrf2 by inhibiting the Nrf2-Keap1 protein-protein interaction has shown promise for treating cancer and inflammatory diseases. A loop derived from Nrf2 has been shown to inhibit Keap1 selectively, especially when cyclized, but there are no reliable design methods for predicting an optimal macrocyclization strategy. In this work, we employed all-atom, explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the relative degree of preorganization for a series of peptides cyclized with a set of bis-thioether "staples". We then correlated these predictions to experimentally measured binding affinities for Keap1 and crystal structures of the cyclic peptides bound to Keap1. This work showcases a computational method for designing cyclic peptides by simulating and comparing their entire solution-phase ensembles, providing key insights into designing cyclic peptides as selective inhibitors of protein-protein interactions.
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Affiliation(s)
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Jovan Damjanovic
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Luca Bischof
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076 Tübingen, Germany
| | - Michael B Braun
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076 Tübingen, Germany
| | - Yingjie Ling
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, 72076 Tübingen, Germany
- Interfaculty Institute of Biochemistry, Tübingen University, 72076 Tübingen, Germany
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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