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Plubell DL, Remes PM, Wu CC, Jacob CC, Merrihew GE, Hsu C, Shulman N, MacLean BX, Heil L, Poston K, Montine T, MacCoss MJ. Development of highly multiplex targeted proteomics assays in biofluids using the Stellar mass spectrometer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597431. [PMID: 38895256 PMCID: PMC11185584 DOI: 10.1101/2024.06.04.597431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale clinical studies. Targeted assays are currently unable to scale to hundreds or thousands of targets. We demonstrate the generation of large-scale assays using a novel hybrid nominal mass instrument. The scale of these assays is achievable with the Stellar™ mass spectrometer through the accommodation of shifting retention times by real-time alignment, while being sensitive and fast enough to handle many concurrent targets. Assays were constructed using precursor information from gas-phase fractionated (GPF) data-independent acquisition (DIA). We demonstrate the ability to schedule methods from an orbitrap and linear ion trap acquired GPF DIA library and compare the quantification of a matrix-matched calibration curve from orbitrap DIA and linear ion trap parallel reaction monitoring (PRM). Two applications of these proposed workflows are shown with a cerebrospinal fluid (CSF) neurodegenerative disease protein PRM assay and with a Mag-Net enriched plasma extracellular vesicle (EV) protein survey PRM assay.
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Affiliation(s)
- Deanna L Plubell
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | - Christine C Wu
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | | | - Chris Hsu
- Department of Genome Sciences, University of Washington, Seattle WA
| | - Nick Shulman
- Department of Genome Sciences, University of Washington, Seattle WA
| | | | | | - Kathleen Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | - Tom Montine
- Department of Pathology, Stanford University, Palo Alto CA, USA
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Naviaux RK. Mitochondrial and metabolic features of salugenesis and the healing cycle. Mitochondrion 2023; 70:131-163. [PMID: 37120082 DOI: 10.1016/j.mito.2023.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/24/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Pathogenesis and salugenesis are the first and second stages of the two-stage problem of disease production and health recovery. Salugenesis is the automatic, evolutionarily conserved, ontogenetic sequence of molecular, cellular, organ system, and behavioral changes that is used by living systems to heal. It is a whole-body process that begins with mitochondria and the cell. The stages of salugenesis define a circle that is energy- and resource-consuming, genetically programmed, and environmentally responsive. Energy and metabolic resources are provided by mitochondrial and metabolic transformations that drive the cell danger response (CDR) and create the three phases of the healing cycle: Phase 1-Inflammation, Phase 2-Proliferation, and Phase 3-Differentiation. Each phase requires a different mitochondrial phenotype. Without different mitochondria there can be no healing. The rise and fall of extracellular ATP (eATP) signaling is a key driver of the mitochondrial and metabolic reprogramming required to progress through the healing cycle. Sphingolipid and cholesterol-enriched membrane lipid rafts act as rheostats for tuning cellular sensitivity to purinergic signaling. Abnormal persistence of any phase of the CDR inhibits the healing cycle, creates dysfunctional cellular mosaics, causes the symptoms of chronic disease, and accelerates the process of aging. New research reframes the rising tide of chronic disease around the world as a systems problem caused by the combined action of pathogenic triggers and anthropogenic factors that interfere with the mitochondrial functions needed for healing. Once chronic pain, disability, or disease is established, salugenesis-based therapies will start where pathogenesis-based therapies end.
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Affiliation(s)
- Robert K Naviaux
- The Mitochondrial and Metabolic Disease Center, Departments of Medicine, and Pediatrics, University of California, San Diego School of Medicine, 214 Dickinson St., Bldg CTF, Rm C107, MC#8467, San Diego, CA 92103.
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Zuglianello C, Lemos-Senna E. The nanotechnological approach for nasal delivery of peptide drugs: a comprehensive review. J Microencapsul 2022; 39:156-175. [PMID: 35262455 DOI: 10.1080/02652048.2022.2051626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This review gathers recent studies, patents, and clinical trials involving the nasal administration of peptide drugs to supply a panorama of developing nanomedicine advances in this field. Peptide drugs have been featured in the pharmaceutical market, due to their high efficacy, biological activity, and low immunogenicity. Pharmaceutical industries need technology to circumvent issues relating to peptide stability and bioavailability. The oral route offers very harsh and unfavourable conditions for peptide administration, while the parenteral route is inconvenient and risky for patients. Nasal administration is an attractive alternative, mainly when associated with nanotechnological approaches. Nanomedicines may improve the nasal administration of peptide drugs by providing protection for the macromolecules from enzymes while also increasing their time of retention and permeability in the nasal mucosa. Nanomedicines for nasal administration containing peptide drugs have been acclaimed for both prevention, and treatment, of infections, including the pandemic COVID-19, cancers, metabolic and neurodegenerative diseases.
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Affiliation(s)
- Carine Zuglianello
- Pharmaceutical Nanotechnology Post-Graduation Program, University of Santa Catarina, Florianópolis, Brazil
| | - Elenara Lemos-Senna
- Pharmaceutical Nanotechnology Post-Graduation Program, University of Santa Catarina, Florianópolis, Brazil
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Markulin I, Matasin M, Turk VE, Salković-Petrisic M. Challenges of repurposing tetracyclines for the treatment of Alzheimer's and Parkinson's disease. J Neural Transm (Vienna) 2022; 129:773-804. [PMID: 34982206 DOI: 10.1007/s00702-021-02457-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/20/2021] [Indexed: 12/13/2022]
Abstract
The novel antibiotic-exploiting strategy in the treatment of Alzheimer's (AD) and Parkinson's (PD) disease has emerged as a potential breakthrough in the field. The research in animal AD/PD models provided evidence on the antiamyloidogenic, anti-inflammatory, antioxidant and antiapoptotic activity of tetracyclines, associated with cognitive improvement. The neuroprotective effects of minocycline and doxycycline in animals initiated investigation of their clinical efficacy in AD and PD patients which led to inconclusive results and additionally to insufficient safety data on a long-standing doxycycline and minocycline therapy in these patient populations. The safety issues should be considered in two levels; in AD/PD patients (particularly antibiotic-induced alteration of gut microbiota and its consequences), and as a world-wide threat of development of bacterial resistance to these antibiotics posed by a fact that AD and PD are widespread incurable diseases which require daily administered long-lasting antibiotic therapy. Recently proposed subantimicrobial doxycycline doses should be thoroughly explored for their effectiveness and long-term safety especially in AD/PD populations. Keeping in mind the antibacterial activity-related far-reaching undesirable effects both for the patients and globally, further work on repurposing these drugs for a long-standing therapy of AD/PD should consider the chemically modified tetracycline compounds tailored to lack antimicrobial but retain (or introduce) other activities effective against the AD/PD pathology. This strategy might reduce the risk of long-term therapy-related adverse effects (particularly gut-related ones) and development of bacterial resistance toward the tetracycline antibiotic agents but the therapeutic potential and desirable safety profile of such compounds in AD/PD patients need to be confirmed.
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Affiliation(s)
- Iva Markulin
- Community Health Centre Zagreb-Centre, Zagreb, Croatia
| | | | - Viktorija Erdeljic Turk
- Division of Clinical Pharmacology, Department of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Melita Salković-Petrisic
- Department of Pharmacology, Croatian Institute for Brain Research, University of Zagreb School of Medicine, Salata 11, 10 000, Zagreb, Croatia.
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Shahrabi Farahani M, Saraygord-Afshari N, M Farajollahi M. Optimizing the Preparation Procedure of Recombinant PSCA, as a Practical Biomarker in Prostate Cancer. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2631. [PMID: 34435055 PMCID: PMC8358172 DOI: 10.30498/ijb.2021.2631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: The unique expression pattern of prostate stem cell antigen (PSCA) in a number of prevalent neoplasms has made the antigen a great target for cancer researches,
and many clinical methods have been developed based on the application of this tumor marker. Hence, optimal PSCA laboratory production can be considered a hallmark for many researchers. Objective: An analytical study was designed to improve the quality and quantity of PSCA production. Materials and Methods: The effects of different compositions of lysis buffers and some ultrasound durations were assessed by calculation of the protein recovery followed by PSCA specific blotting experiments.
Then, based on the results of the web-based characterization, interference removal, followed by re-solubilization of the protein in various buffers, was designed, applied, and assessed. Results: Since the selection of an appropriate methodology depends merely on the research purposes, we tried to discuss the pros and cons of the investigated methods according
to the hydrophobic nature of PSCA as well as its dramatic tendency to aggregate in the form of inclusion bodies in the expression hosts. Conclusions: We introduced a newly designed method to fit the delicate immunological surveys and overcome some limiting factors in PSCA production.
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Affiliation(s)
- Mahboube Shahrabi Farahani
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Neda Saraygord-Afshari
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad M Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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Pandey G, Ramakrishnan V. Invasive and non-invasive therapies for Alzheimer's disease and other amyloidosis. Biophys Rev 2020; 12:1175-1186. [PMID: 32930962 PMCID: PMC7575678 DOI: 10.1007/s12551-020-00752-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Advancements in medical science have facilitated in extending human lives. The increased life expectancy, though, has come at a cost. The cases of an aging population suffering from degenerative diseases like Alzheimer's disease (AD) are presently at its all-time high. Amyloidosis disorders such as AD are triggered by an abnormal transition of soluble proteins into their highly ordered aggregated forms. The landscape of amyloidosis treatment remains unchanged, and there is no cure for such disorders. However, an increased understanding of the mechanism of amyloid self-assembly has given hope for a possible therapeutic solution. In this review, we will discuss the current state of molecular and non-molecular options for therapeutic intervention of amyloidosis. We highlight the efficacy of non-invasive physical therapies as possible alternatives to their molecular counterparts. Graphical abstract.
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Affiliation(s)
- Gaurav Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
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Rawat P, Prabakaran R, Sakthivel R, Mary Thangakani A, Kumar S, Gromiha MM. CPAD 2.0: a repository of curated experimental data on aggregating proteins and peptides. Amyloid 2020; 27:128-133. [PMID: 31979981 DOI: 10.1080/13506129.2020.1715363] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Curated Protein Aggregation Database (CPAD) is a manually curated and open-access database dedicated to providing comprehensive information related to mechanistic, kinetic and structural aspects of protein and peptide aggregation. The database has been updated to CPAD 2.0 by significantly expanding datasets and improving the user-interface. Key features of CPAD 2.0 are (i) 83,098 data points on aggregation kinetics experiments, (ii) 565 structures related to aggregation, which are classified into proteins, fibrils, and protein-ligand complexes, (iii) 2031 aggregating/non-aggregating peptides with pre-calculated aggregation properties, and (iv) 912 aggregation-prone regions in amyloidogenic proteins. This database will help the scientific community (a) by facilitating research leading to improved understanding of protein aggregation, (b) by helping develop, validate and benchmark mechanistic and kinetic models of protein aggregation, and (c) by assisting experimentalists with design of their investigations and dissemination of data generated by their studies. CPAD 2.0 can be accessed at https://web.iitm.ac.in/bioinfo2/cpad2/index.html.
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Affiliation(s)
- Puneet Rawat
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - R Prabakaran
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - R Sakthivel
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - A Mary Thangakani
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sandeep Kumar
- Biotherapeutics Discovery, Boehringer-Ingelheim Inc, Ridgefield, CT, USA
| | - M Michael Gromiha
- Protein Bioinformatics Lab, Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.,Advanced Computational Drug Discovery Unit (ACDD), Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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Dułak D, Gadzała M, Banach M, Konieczny L, Roterman I. Alternative Structures of α-Synuclein. Molecules 2020; 25:molecules25030600. [PMID: 32019169 PMCID: PMC7038196 DOI: 10.3390/molecules25030600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
The object of our analysis is the structure of alpha-synuclein (ASyn), which, under in vivo conditions, associates with presynaptic vesicles. Misfolding of ASyn is known to be implicated in Parkinson's disease. The availability of structural information for both the micelle-bound and amyloid form of ASyn enables us to speculate on the specific mechanism of amyloid transformation. This analysis is all the more interesting given the fact that-Unlike in Aβ(1-42) amyloids-only the central fragment (30-100) of ASyn has a fibrillar structure, whereas, its N- and C-terminal fragments (1-30 and 100-140, respectively) are described as random coils. Our work addresses the following question: Can the ASyn chain-as well as the aforementioned individual fragments-adopt globular conformations? In order to provide an answer, we subjected the corresponding sequences to simulations carried out using Robetta and I-Tasser, both of which are regarded as accurate protein structure predictors. In addition, we also applied the fuzzy oil drop (FOD) model, which, in addition to optimizing the protein's internal free energy, acknowledges the presence of an external force field contributed by the aqueous solvent. This field directs hydrophobic residues to congregate near the center of the protein body while exposing hydrophilic residues on its surface. Comparative analysis of the obtained models suggests that fragments which do not participate in forming the amyloid fibril (i.e., 1-30 and 100-140) can indeed attain globular conformations. We also explain the influence of mutations observed in vivo upon the susceptibility of ASyn to undergo amyloid transformation. In particular, the 30-100 fragment (which adopts a fibrillar structure in PDB) is not predicted to produce a centralized hydrophobic core by any of the applied toolkits (Robetta, I-Tasser, and FOD). This means that in order to minimize the entropically disadvantageous contact between hydrophobic residues and the polar solvent, ASyn adopts the form of a ribbonlike micelle (rather than a spherical one). In other words, the ribbonlike micelle represents a synergy between the conformational preferences of the protein chain and the influence of its environment.
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Affiliation(s)
- Dawid Dułak
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland;
| | | | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Łazarza 16, 31-530 Krakow, Poland;
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University–Medical College, Kopernika 7, 31-034 Kraków, Poland;
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Łazarza 16, 31-530 Krakow, Poland;
- Correspondence:
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Donnarumma F, Leone S, Delfi M, Emendato A, Ami D, Laurents DV, Natalello A, Spadaccini R, Picone D. Probing structural changes during amyloid aggregation of the sweet protein MNEI. FEBS J 2019; 287:2808-2822. [DOI: 10.1111/febs.15168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Federica Donnarumma
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Serena Leone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Masoud Delfi
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Alessandro Emendato
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Douglas V. Laurents
- Institute of Physical Chemistry ‘Rocasolano’ Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Antonino Natalello
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Roberta Spadaccini
- Department of Science and Technology Università degli Studi del Sannio Benevento Italy
| | - Delia Picone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
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Al-Halifa S, Babych M, Zottig X, Archambault D, Bourgault S. Amyloid self-assembling peptides: Potential applications in nanovaccine engineering and biosensing. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24095] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Soultan Al-Halifa
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Margaryta Babych
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Ximena Zottig
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Denis Archambault
- Department of Biological Sciences; Université du Québec à Montréal; Montreal, QC Canada
- Swine and Poultry Infectious Diseases Research Centre, CRIPA; QC Canada
| | - Steve Bourgault
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
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