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  1. Article ; Online: Identification of the functional PD-L1 interface region responsible for PD-1 binding and initiation of PD-1 signaling.

    Carter, Rachel / Alanazi, Fatimah / Sharp, Amanda / Roman, Jessica / Luchini, Alessandra / Liotta, Lance / Paige, Mikell / Brown, Anne M / Haymond, Amanda

    The Journal of biological chemistry

    2023  Volume 299, Issue 12, Page(s) 105353

    Abstract: The PD-1/PD-L1 checkpoint pathway is important for regulating immune responses and can be targeted by immunomodulatory drugs to treat a variety of immune disorders. However, the precise protein-protein interactions required for the initiation of PD-1/PD- ... ...

    Abstract The PD-1/PD-L1 checkpoint pathway is important for regulating immune responses and can be targeted by immunomodulatory drugs to treat a variety of immune disorders. However, the precise protein-protein interactions required for the initiation of PD-1/PD-L1 signaling are currently unknown. Previously, we designed a series of first-generation PD-1 targeting peptides based on the native interface region of programmed death ligand 1 (PD-L1) that effectively reduced PD-1/PD-L1 binding. In this work, we further characterized the previously identified lead peptide, MN1.1, to identify key PD-1 binding residues and design an optimized peptide, MN1.4. We show MN1.4 is significantly more stable than MN1.1 in serum and retains the ability to block PD-1/PD-L1 complex formation. We further characterized the immunomodulatory effects of MN1.4 treatment by measuring markers of T cell activation in a co-culture model with ovarian cancer cells and peripheral blood mononuclear cells. We found MN1.4 treatment reduced cytokine secretion and suppressed T cell responses in a similar manner as recombinant PD-L1. Therefore, the PD-L1 interface region used to design MN1.4 appeared sufficient to initiate PD-1 signaling and likely represents the minimum necessary region of PD-L1 required for PD-1 recognition. We propose a peptide agonist for PD-1, such as MN1.4, could have several applications for treating autoimmune disorders caused by PD-1 deficiencies such as type 1 diabetes, inflammatory arthritis, or autoimmune side effects arising from monoclonal antibody-based cancer immunotherapies.
    MeSH term(s) Humans ; B7-H1 Antigen/chemistry ; B7-H1 Antigen/genetics ; B7-H1 Antigen/metabolism ; Immunotherapy ; Leukocytes, Mononuclear/metabolism ; Neoplasms/drug therapy ; Peptides/pharmacology ; Programmed Cell Death 1 Receptor/agonists ; Programmed Cell Death 1 Receptor/chemistry ; Programmed Cell Death 1 Receptor/metabolism ; Protein Binding ; Signal Transduction ; Mutation ; Models, Molecular ; Protein Structure, Quaternary ; Cell Line, Tumor ; Immunity/drug effects
    Chemical Substances B7-H1 Antigen ; Peptides ; Programmed Cell Death 1 Receptor
    Language English
    Publishing date 2023-10-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2023.105353
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Serological Testing for COVID-19 Disease: Moving the Field of Serological Surveillance Forward.

    Damluji, Abdulla A / Rajan, Devin / Haymond, Amanda / deFilippi, Christopher

    The journal of applied laboratory medicine

    2021  Volume 6, Issue 3, Page(s) 584–587

    MeSH term(s) Antibodies, Neutralizing ; COVID-19 ; COVID-19 Testing ; Humans ; Immunoglobulin G ; SARS-CoV-2
    Chemical Substances Antibodies, Neutralizing ; Immunoglobulin G
    Language English
    Publishing date 2021-03-11
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 2576-9456
    ISSN 2576-9456
    DOI 10.1093/jalm/jfab018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Proteomics for cancer drug design.

    Haymond, Amanda / Davis, Justin B / Espina, Virginia

    Expert review of proteomics

    2019  Volume 16, Issue 8, Page(s) 647–664

    Abstract: ... ...

    Abstract Introduction
    MeSH term(s) Animals ; Antineoplastic Agents/therapeutic use ; Drug Discovery ; Humans ; Mass Spectrometry ; Neoplasms/drug therapy ; Neoplasms/metabolism ; Proteomics/methods
    Chemical Substances Antineoplastic Agents
    Language English
    Publishing date 2019-08-04
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2299100-1
    ISSN 1744-8387 ; 1478-9450
    ISSN (online) 1744-8387
    ISSN 1478-9450
    DOI 10.1080/14789450.2019.1650025
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Next Generation Techniques for Determination of Protein-Protein Interactions: Beyond the Crystal Structure.

    Carter, Rachel / Luchini, Alessandra / Liotta, Lance / Haymond, Amanda

    Current pathobiology reports

    2019  Volume 7, Issue 3, Page(s) 61–71

    Abstract: Purpose of review: We discuss recent advancements in structural biology methods for investigating sites of protein-protein interactions. We will inform readers outside the field of structural biology about techniques beyond crystallography, and how ... ...

    Abstract Purpose of review: We discuss recent advancements in structural biology methods for investigating sites of protein-protein interactions. We will inform readers outside the field of structural biology about techniques beyond crystallography, and how these different technologies can be utilized for drug development.
    Recent findings: Advancements in cryo-electron microscopy (cryoEM) and micro-electron diffraction (microED) may change how we view atomic resolution structural biology, such that well-ordered macrocrystals of protein complexes are not required for interface identification. However, some drug discovery applications, such as lead peptide compound generation, may not require atomic resolution; mass spectrometry techniques can provide an expedited path to generation of lead compounds. New crosslinking compounds, more user-friendly data analysis, and novel protocols such as protein painting can advance drug discovery programs, even in the absence of atomic resolution structural data. Finally, artificial intelligence and machine learning methods, while never truly replacing experimental methods, may provide rational ways to stratify potential druggable regions identified with mass spectrometry into higher and lower priority candidates.
    Summary: Electron diffraction of nanocrystals combines the benefits of both x-ray diffraction and cryoEM, and may prove to be the next generation of atomic resolution protein-protein interface identification. However, in situations such as peptide drug discovery, mass spectrometry techniques supported by advancements in computational methods will likely prove sufficient to support drug discovery efforts. In addition, these methods can be significantly faster than any crystallographic or cryoEM methods for identification of interacting regions.
    Language English
    Publishing date 2019-07-01
    Publishing country United States
    Document type Journal Article
    ISSN 2167-485X
    ISSN 2167-485X
    DOI 10.1007/s40139-019-00198-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: MEPicides: α,β-unsaturated Fosmidomycin

    Wang, Xu / Edwards, Rachel L / Ball, Haley S / Heidel, Kenneth M / Brothers, Robert C / Johnson, Claire / Haymond, Amanda / Girma, Misgina / Dailey, Allyson / Roma, Jose Santinni / Boshoff, Helena I / Osbourn, Damon M / Meyers, Marvin J / Couch, Robin D / Odom John, Audrey R / Dowd, Cynthia S

    ACS infectious diseases

    2023  Volume 9, Issue 7, Page(s) 1387–1395

    Abstract: Malaria, a mosquito-borne disease caused by several parasites of ... ...

    Abstract Malaria, a mosquito-borne disease caused by several parasites of the
    MeSH term(s) Child ; Humans ; Animals ; Mice ; Plasmodium falciparum ; Fosfomycin/pharmacology ; Fosfomycin/chemistry ; Pentosephosphates/metabolism ; Antimalarials/pharmacology ; Antimalarials/chemistry
    Chemical Substances fosmidomycin (5829E3D9I9) ; xylulose-5-phosphate (60802-29-1) ; Fosfomycin (2N81MY12TE) ; Pentosephosphates ; Antimalarials
    Language English
    Publishing date 2023-06-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2373-8227
    ISSN (online) 2373-8227
    DOI 10.1021/acsinfecdis.3c00132
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Drug discovery efforts at George Mason University.

    Andalibi, Ali / Veneziano, Remi / Paige, Mikell / Buschmann, Michael / Haymond, Amanda / Espina, Virginia / Luchini, Alessandra / Liotta, Lance / Bishop, Barney / Van Hoek, Monique

    SLAS discovery : advancing life sciences R & D

    2023  Volume 28, Issue 6, Page(s) 270–274

    Abstract: With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the ... ...

    Abstract With over 39,000 students, and research expenditures in excess of $200 million, George Mason University (GMU) is the largest R1 (Carnegie Classification of very high research activity) university in Virginia. Mason scientists have been involved in the discovery and development of novel diagnostics and therapeutics in areas as diverse as infectious diseases and cancer. Below are highlights of the efforts being led by Mason researchers in the drug discovery arena. To enable targeted cellular delivery, and non-biomedical applications, Veneziano and colleagues have developed a synthesis strategy that enables the design of self-assembling DNA nanoparticles (DNA origami) with prescribed shape and size in the 10 to 100 nm range. The nanoparticles can be loaded with molecules of interest such as drugs, proteins and peptides, and are a promising new addition to the drug delivery platforms currently in use. The investigators also recently used the DNA origami nanoparticles to fine tune the spatial presentation of immunogens to study the impact on B cell activation. These studies are an important step towards the rational design of vaccines for a variety of infectious agents. To elucidate the parameters for optimizing the delivery efficiency of lipid nanoparticles (LNPs), Buschmann, Paige and colleagues have devised methods for predicting and experimentally validating the pKa of LNPs based on the structure of the ionizable lipids used to formulate the LNPs. These studies may pave the way for the development of new LNP delivery vehicles that have reduced systemic distribution and improved endosomal release of their cargo post administration. To better understand protein-protein interactions and identify potential drug targets that disrupt such interactions, Luchini and colleagues have developed a methodology that identifies contact points between proteins using small molecule dyes. The dye molecules noncovalently bind to the accessible surfaces of a protein complex with very high affinity, but are excluded from contact regions. When the complex is denatured and digested with trypsin, the exposed regions covered by the dye do not get cleaved by the enzyme, whereas the contact points are digested. The resulting fragments can then be identified using mass spectrometry. The data generated can serve as the basis for designing small molecules and peptides that can disrupt the formation of protein complexes involved in disease processes. For example, using peptides based on the interleukin 1 receptor accessory protein (IL-1RAcP), Luchini, Liotta, Paige and colleagues disrupted the formation of IL-1/IL-R/IL-1RAcP complex and demonstrated that the inhibition of complex formation reduced the inflammatory response to IL-1B. Working on the discovery of novel antimicrobial agents, Bishop, van Hoek and colleagues have discovered a number of antimicrobial peptides from reptiles and other species. DRGN-1, is a synthetic peptide based on a histone H1-derived peptide that they had identified from Komodo Dragon plasma. DRGN-1 was shown to disrupt bacterial biofilms and promote wound healing in an animal model. The peptide, along with others, is being developed and tested in preclinical studies. Other research by van Hoek and colleagues focuses on in silico antimicrobial peptide discovery, screening of small molecules for antibacterial properties, as well as assessment of diffusible signal factors (DFS) as future therapeutics. The above examples provide insight into the cutting-edge studies undertaken by GMU scientists to develop novel methodologies and platform technologies important to drug discovery.
    MeSH term(s) Animals ; Interleukin-1 Receptor Accessory Protein ; Universities ; Drug Delivery Systems ; DNA ; Drug Discovery
    Chemical Substances Interleukin-1 Receptor Accessory Protein ; DNA (9007-49-2)
    Language English
    Publishing date 2023-03-14
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2885123-7
    ISSN 2472-5560 ; 2472-5552
    ISSN (online) 2472-5560
    ISSN 2472-5552
    DOI 10.1016/j.slasd.2023.03.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Laser Capture Proteomics: spatial tissue molecular profiling from the bench to personalized medicine.

    Liotta, Lance A / Pappalardo, Philip A / Carpino, Alan / Haymond, Amanda / Howard, Marissa / Espina, Virginia / Wulfkuhle, Julie / Petricoin, Emanuel

    Expert review of proteomics

    2021  Volume 18, Issue 10, Page(s) 845–861

    Abstract: Introduction: Laser Capture Microdissection (LCM) uses a laser to isolate, or capture, specific cells of interest in a complex heterogeneous tissue section, under direct microscopic visualization. Recently, there has been a surge of publications using ... ...

    Abstract Introduction: Laser Capture Microdissection (LCM) uses a laser to isolate, or capture, specific cells of interest in a complex heterogeneous tissue section, under direct microscopic visualization. Recently, there has been a surge of publications using LCM for tissue spatial molecular profiling relevant to a wide range of research topics.
    Areas covered: We summarize the many advances in tissue Laser Capture Proteomics (LCP) using mass spectrometry for discovery, and protein arrays for signal pathway network mapping. This review emphasizes: a) transition of LCM phosphoproteomics from the lab to the clinic for individualized cancer therapy, and b) the emerging frontier of LCM single cell molecular analysis combining proteomics with genomic, and transcriptomic analysis. The search strategy was based on the combination of MeSH terms with expert refinement.
    Expert opinion: LCM is complemented by a rich set of instruments, methodology protocols, and analytical A.I. (artificial intelligence) software for basic and translational research. Resolution is advancing to the tissue single cell level. A vision for the future evolution of LCM is presented. Emerging LCM technology is combining digital and AI guided remote imaging with automation, and telepathology, to a achieve multi-omic profiling that was not previously possible.
    MeSH term(s) Artificial Intelligence ; Laser Capture Microdissection ; Lasers ; Precision Medicine ; Proteomics
    Language English
    Publishing date 2021-12-14
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2299100-1
    ISSN 1744-8387 ; 1478-9450
    ISSN (online) 1744-8387
    ISSN 1478-9450
    DOI 10.1080/14789450.2021.1984886
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A New Structural Model of Apolipoprotein B100 Based on Computational Modeling and Cross Linking.

    Jeiran, Kianoush / Gordon, Scott M / Sviridov, Denis O / Aponte, Angel M / Haymond, Amanda / Piszczek, Grzegorz / Lucero, Diego / Neufeld, Edward B / Vaisman, Iosif I / Liotta, Lance / Baranova, Ancha / Remaley, Alan T

    International journal of molecular sciences

    2022  Volume 23, Issue 19

    Abstract: ApoB-100 is a member of a large lipid transfer protein superfamily and is one of the main apolipoproteins found on low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) particles. Despite its clinical significance for the development of ... ...

    Abstract ApoB-100 is a member of a large lipid transfer protein superfamily and is one of the main apolipoproteins found on low-density lipoprotein (LDL) and very low-density lipoprotein (VLDL) particles. Despite its clinical significance for the development of cardiovascular disease, there is limited information on apoB-100 structure. We have developed a novel method based on the "divide and conquer" algorithm, using PSIPRED software, by dividing apoB-100 into five subunits and 11 domains. Models of each domain were prepared using I-TASSER, DEMO, RoseTTAFold, Phyre2, and MODELLER. Subsequently, we used disuccinimidyl sulfoxide (DSSO), a new mass spectrometry cleavable cross-linker, and the known position of disulfide bonds to experimentally validate each model. We obtained 65 unique DSSO cross-links, of which 87.5% were within a 26 Å threshold in the final model. We also evaluated the positions of cysteine residues involved in the eight known disulfide bonds in apoB-100, and each pair was measured within the expected 5.6 Å constraint. Finally, multiple domains were combined by applying constraints based on detected long-range DSSO cross-links to generate five subunits, which were subsequently merged to achieve an uninterrupted architecture for apoB-100 around a lipoprotein particle. Moreover, the dynamics of apoB-100 during particle size transitions was examined by comparing VLDL and LDL computational models and using experimental cross-linking data. In addition, the proposed model of receptor ligand binding of apoB-100 provides new insights into some of its functions.
    MeSH term(s) Apolipoprotein B-100 ; Apolipoproteins B/metabolism ; Computer Simulation ; Cysteine ; Disulfides ; Ligands ; Lipoproteins, LDL/chemistry ; Lipoproteins, VLDL ; Models, Structural ; Sulfoxides
    Chemical Substances Apolipoprotein B-100 ; Apolipoproteins B ; Disulfides ; Ligands ; Lipoproteins, LDL ; Lipoproteins, VLDL ; Sulfoxides ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2022-09-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231911480
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  9. Article ; Online: VOC fingerprints: metabolomic signatures of biothreat agents with and without antibiotic resistance.

    Dailey, Allyson / Saha, Jessica / Zaidi, Fatima / Abdirahman, Hafsa / Haymond, Amanda / Alem, Farhang / Hakami, Ramin / Couch, Robin

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 11746

    Abstract: Category A and B biothreat agents are deemed to be of great concern by the US Centers for Disease Control and Prevention (CDC) and include the bacteria Francisella tularensis, Yersinia pestis, Burkholderia mallei, and Brucella species. Underscored by the ...

    Abstract Category A and B biothreat agents are deemed to be of great concern by the US Centers for Disease Control and Prevention (CDC) and include the bacteria Francisella tularensis, Yersinia pestis, Burkholderia mallei, and Brucella species. Underscored by the impact of the 2020 SARS-CoV-2 outbreak, 2016 Zika pandemic, 2014 Ebola outbreak, 2001 anthrax letter attacks, and 1984 Rajneeshee Salmonella attacks, the threat of future epidemics/pandemics and/or terrorist/criminal use of pathogenic organisms warrants continued exploration and development of both classic and alternative methods of detecting biothreat agents. Volatile organic compounds (VOCs) comprise a large and highly diverse group of carbon-based molecules, generally related by their volatility at ambient temperature. Recently, the diagnostic potential of VOCs has been realized, as correlations between the microbial VOC metabolome and specific bacterial pathogens have been identified. Herein, we describe the use of microbial VOC profiles as fingerprints for the identification of biothreat-relevant microbes, and for differentiating between a kanamycin susceptible and resistant strain. Additionally, we demonstrate microbial VOC profiling using a rapid-throughput VOC metabolomics method we refer to as 'simultaneous multifiber headspace solid-phase microextraction' (simulti-hSPME). Finally, through VOC analysis, we illustrate a rapid non-invasive approach to the diagnosis of BALB/c mice infected with either F. tularensis SCHU S4 or Y. pestis CO92.
    MeSH term(s) Animals ; Betacoronavirus/isolation & purification ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/metabolism ; Coronavirus Infections/virology ; Disease Outbreaks ; Drug Resistance, Microbial/drug effects ; Drug Resistance, Microbial/genetics ; Female ; Francisella tularensis/drug effects ; Francisella tularensis/isolation & purification ; Francisella tularensis/metabolism ; Kanamycin/pharmacology ; Metabolomics/methods ; Mice ; Mice, Inbred BALB C ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/metabolism ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Solid Phase Microextraction ; Tularemia/metabolism ; Tularemia/microbiology ; Tularemia/pathology ; Tularemia/veterinary ; Volatile Organic Compounds/analysis ; Volatile Organic Compounds/isolation & purification ; Volatile Organic Compounds/metabolism ; Yersinia pestis/drug effects ; Yersinia pestis/isolation & purification ; Yersinia pestis/metabolism
    Chemical Substances Volatile Organic Compounds ; Kanamycin (59-01-8)
    Keywords covid19
    Language English
    Publishing date 2020-07-16
    Publishing country England
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-68622-x
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  10. Article ; Online: Durability of Viral Neutralization in Asymptomatic Coronavirus Disease 2019 for at Least 60 Days.

    Haymond, Amanda / Damluji, Abdulla A / Narayanan, Aarthi / Mueller, Claudius / Reeder, Alex / Alem, Farhang / Maxwell, G Larry / Petricoin, Emanuel F / Liotta, Lance / deFilippi, Christopher R

    The Journal of infectious diseases

    2021  Volume 223, Issue 10, Page(s) 1677–1680

    Abstract: A cohort consisting of asymptomatic healthcare workers donated temporal serum samples after infection with severe acute respiratory syndrome coronavirus 2. Analysis shows that all asymptomatic healthcare workers had neutralizing antibodies, that these ... ...

    Abstract A cohort consisting of asymptomatic healthcare workers donated temporal serum samples after infection with severe acute respiratory syndrome coronavirus 2. Analysis shows that all asymptomatic healthcare workers had neutralizing antibodies, that these antibodies persist for ≥60 days, and that anti-spike receptor-binding domain immunoglobulin G levels were correspondingly durable over the same time period.
    MeSH term(s) Antibodies, Neutralizing/blood ; Antibodies, Viral/blood ; Asymptomatic Diseases ; COVID-19/epidemiology ; COVID-19/immunology ; COVID-19 Nucleic Acid Testing ; Cohort Studies ; Enzyme-Linked Immunosorbent Assay ; Female ; Health Personnel ; Humans ; Male ; Neutralization Tests ; SARS-CoV-2/immunology ; Surveys and Questionnaires ; Time Factors ; Virginia/epidemiology
    Chemical Substances Antibodies, Neutralizing ; Antibodies, Viral
    Language English
    Publishing date 2021-02-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3019-3
    ISSN 1537-6613 ; 0022-1899
    ISSN (online) 1537-6613
    ISSN 0022-1899
    DOI 10.1093/infdis/jiab140
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