1
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Livesay B, Schmidt JG, Williams RF, Billow BS, Tondreau AM. Reactivity of [(PNP)Mn(CO) 2] with Organophosphates. ACS Org Inorg Au 2023; 3:199-208. [PMID: 37545657 PMCID: PMC10401673 DOI: 10.1021/acsorginorgau.3c00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 08/08/2023]
Abstract
Organophosphorus nerve agents (OPAs) are a toxic class of synthetic compounds that cause adverse effects with many biological systems. Development of methods for environmental remediation and passivation has been ongoing for years. However, little progress has been made in therapeutic development for exposure victims. Given the postexposure behavior of OPA materials in enzymes such as acetylcholinesterase (AChE), development of electrophilic compounds as therapeutics may be more beneficial than the currently employed nucleophilic countermeasures. In this report, we present our studies with an electrophilic, 16-electron manganese complex (iPrPNP)Mn(CO)2 (1) and the nucleophilic hydroxide derivative (iPrPNHP)Mn(CO)2(OH) (2). The reactivity of 1 with phosphorus acids and the reactivity of 2 with the P-F bond of diisopropylfluorophosphate (DIPF) were studied. The role of water in both nucleophilic and electrophilic reactivity was investigated with the use of 17O-labeled water. Promising results arising from reactions of both 1 and 2 with organophosphorus substrates are reported.
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2
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Sanders BC, Pokhrel S, Labbe AD, Mathews II, Cooper CJ, Davidson RB, Phillips G, Weiss KL, Zhang Q, O'Neill H, Kaur M, Schmidt JG, Reichard W, Surendranathan S, Parvathareddy J, Phillips L, Rainville C, Sterner DE, Kumaran D, Andi B, Babnigg G, Moriarty NW, Adams PD, Joachimiak A, Hurst BL, Kumar S, Butt TR, Jonsson CB, Ferrins L, Wakatsuki S, Galanie S, Head MS, Parks JM. Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2. Nat Commun 2023; 14:1733. [PMID: 36977673 PMCID: PMC10044120 DOI: 10.1038/s41467-023-37254-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with kinact/KI = 9,600 M-1 s-1, achieves sub-μM EC50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.
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Affiliation(s)
- Brian C Sanders
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Suman Pokhrel
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Audrey D Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Manat Kaur
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jurgen G Schmidt
- B-11 Bioenergy and Biome Sciences, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Surekha Surendranathan
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lexi Phillips
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Babak Andi
- Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Gyorgy Babnigg
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Brett L Hurst
- Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA
| | | | | | - Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Lori Ferrins
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Soichi Wakatsuki
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Computational and Data Sciences, Center for Research Acceleration by Digital Innovation, Amgen, Inc., Thosand Oaks, CA, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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3
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Kim HB, Bacik JP, Wu R, Jha RK, Hebron M, Triandafillou C, McCown JE, Baek NI, Kim JH, Kim YJ, Goulding CW, Strauss CEM, Schmidt JG, Shetye GS, Ryoo S, Jo EK, Jeon YH, Hung LW, Terwilliger TC, Kim CY. Label-free affinity screening, design and synthesis of inhibitors targeting the Mycobacterium tuberculosis L-alanine dehydrogenase. PLoS One 2022; 17:e0277670. [PMID: 36395154 PMCID: PMC9671377 DOI: 10.1371/journal.pone.0277670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
The ability of Mycobacterium tuberculosis (Mtb) to persist in its host may enable an evolutionary advantage for drug resistant variants to emerge. A potential strategy to prevent persistence and gain drug efficacy is to directly target the activity of enzymes that are crucial for persistence. We present a method for expedited discovery and structure-based design of lead compounds by targeting the hypoxia-associated enzyme L-alanine dehydrogenase (AlaDH). Biochemical and structural analyses of AlaDH confirmed binding of nucleoside derivatives and showed a site adjacent to the nucleoside binding pocket that can confer specificity to putative inhibitors. Using a combination of dye-ligand affinity chromatography, enzyme kinetics and protein crystallographic studies, we show the development and validation of drug prototypes. Crystal structures of AlaDH-inhibitor complexes with variations at the N6 position of the adenyl-moiety of the inhibitor provide insight into the molecular basis for the specificity of these compounds. We describe a drug-designing pipeline that aims to block Mtb to proliferate upon re-oxygenation by specifically blocking NAD accessibility to AlaDH. The collective approach to drug discovery was further evaluated through in silico analyses providing additional insight into an efficient drug development strategy that can be further assessed with the incorporation of in vivo studies.
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Affiliation(s)
- Heung-Bok Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - John-Paul Bacik
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Ruilian Wu
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ramesh K. Jha
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Michaeline Hebron
- Georgetown University Medical Center, Washington, D.C., United States of America
| | - Catherine Triandafillou
- Biophysical Sciences Graduate Program, University of Chicago, Chicago, Illinois, United States of America
| | - Joseph E. McCown
- Array BioPharma Inc., Boulder, Colorado, United States of America
| | - Nam-In Baek
- Graduate School of Biotechnology and Department of Oriental Medicine Biotechnology, Kyung-Hee University, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Jeong Han Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Jae Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, United States of America
| | - Charlie E. M. Strauss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Gauri S. Shetye
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois, Chicago, Illinois, United States of America
| | - Sungweon Ryoo
- Clinical Research Centre, Masan National Tuberculosis Hospital, Changwon-si, Gyeongsangnam-do, Republic of Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Department of Medical Science, Chungnam National University School of Medicine, Daejeon, Republic of Korea
- Infection Control Convergence Research Center, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong, Republic of Korea
| | - Li-Wei Hung
- Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - Chang-Yub Kim
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- * E-mail:
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4
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Schein CH, Rafael G, Baker WS, Anaya ES, Schmidt JG, Weaver SC, Negi S, Braun W. PCP consensus protein/peptide alphavirus antigens stimulate broad spectrum neutralizing antibodies. Peptides 2022; 157:170844. [PMID: 35878658 DOI: 10.1016/j.peptides.2022.170844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022]
Abstract
Vaccines based on proteins and peptides may be safer and if calculated based on many sequences, more broad-spectrum than those designed based on single strains. Physicochemical Property Consensus (PCPcon) alphavirus (AV) antigens from the B-domain of the E2 envelope protein were designed, synthesized recombinantly and shown to be immunogenic (i.e. sera after inoculation detected the antigen in dotspots and ELISA). Antibodies in sera after inoculation with B-region antigens based on individual AV species (eastern or Venezuelan equine encephalitis (EEEVcon, VEEVcon), or chikungunya (CHIKVcon) bound only their cognate protein, while those designed against multiple species (Mosaikcon and EVCcon) recognized all three serotype specific antigens. The VEEVcon and EEEVcon sera only showed antiviral activity against their related strains (in plaque reduction neutralization assays (PRNT50/80). Peptides designed to surface exposed areas of the E2-A-domain of CHIKVcon were added to CHIKVcon inocula to provide anti-CHIKV antibodies. EVCcon, based on three different alphavirus species, combined with E2-A-domain peptides from AllAVcon, a PCPcon of 24 diverse AV, generated broad spectrum, antiviral antibodies against VEEV, EEEV and CHIKV, AV with less than 35% amino acid identity to each other (>65% diversity). This is a promising start to a molecularly defined vaccine against all AV. Further study with these antigens can illuminate what areas are most important for a robust immune response, resistant to mutations in rapidly evolving viruses. The validated computational methods can also be used to design broad spectrum antigens against many other pathogen families.
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Affiliation(s)
- Catherine H Schein
- Departments of Biochemistry and Molecular Biology, UTMB; Institute for Human Infections and Immunity (IHII), UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA.
| | - Grace Rafael
- Microbiology and Immunology, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Wendy S Baker
- Departments of Biochemistry and Molecular Biology, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | | | | | - Scott C Weaver
- Microbiology and Immunology, UTMB; Institute for Human Infections and Immunity (IHII), UTMB; World Reference Center for Emerging Viruses and Arboviruses, UTMB; Sealy Center for Structural Biology and Molecular Biophysics, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Surendra Negi
- Departments of Biochemistry and Molecular Biology, UTMB; Sealy Center for Structural Biology and Molecular Biophysics, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Werner Braun
- Departments of Biochemistry and Molecular Biology, UTMB; Sealy Center for Structural Biology and Molecular Biophysics, UTMB; University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
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5
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Andi B, Kumaran D, Kreitler DF, Soares AS, Keereetaweep J, Jakoncic J, Lazo EO, Shi W, Fuchs MR, Sweet RM, Shanklin J, Adams PD, Schmidt JG, Head MS, McSweeney S. Hepatitis C virus NS3/4A inhibitors and other drug-like compounds as covalent binders of SARS-CoV-2 main protease. Sci Rep 2022; 12:12197. [PMID: 35842458 PMCID: PMC9287821 DOI: 10.1038/s41598-022-15930-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 07/01/2022] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), threatens global public health. The world needs rapid development of new antivirals and vaccines to control the current pandemic and to control the spread of the variants. Among the proteins synthesized by the SARS-CoV-2 genome, main protease (Mpro also known as 3CLpro) is a primary drug target, due to its essential role in maturation of the viral polyproteins. In this study, we provide crystallographic evidence, along with some binding assay data, that three clinically approved anti hepatitis C virus drugs and two other drug-like compounds covalently bind to the Mpro Cys145 catalytic residue in the active site. Also, molecular docking studies can provide additional insight for the design of new antiviral inhibitors for SARS-CoV-2 using these drugs as lead compounds. One might consider derivatives of these lead compounds with higher affinity to the Mpro as potential COVID-19 therapeutics for further testing and possibly clinical trials.
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Affiliation(s)
- Babak Andi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
| | - Dale F Kreitler
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Alexei S Soares
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | | | - Jean Jakoncic
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Edwin O Lazo
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Wuxian Shi
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Martin R Fuchs
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Robert M Sweet
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Martha S Head
- Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA
| | - Sean McSweeney
- Center for BioMolecular Structure, NSLS-II, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA. .,National Virtual Biotechnology Laboratory (NVBL), US Department of Energy, Washington, DC, USA.
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6
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Clyde A, Galanie S, Kneller DW, Ma H, Babuji Y, Blaiszik B, Brace A, Brettin T, Chard K, Chard R, Coates L, Foster I, Hauner D, Kertesz V, Kumar N, Lee H, Li Z, Merzky A, Schmidt JG, Tan L, Titov M, Trifan A, Turilli M, Van Dam H, Chennubhotla SC, Jha S, Kovalevsky A, Ramanathan A, Head MS, Stevens R. High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. J Chem Inf Model 2022; 62:116-128. [PMID: 34793155 PMCID: PMC8610012 DOI: 10.1021/acs.jcim.1c00851] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/27/2022]
Abstract
Despite the recent availability of vaccines against the acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the search for inhibitory therapeutic agents has assumed importance especially in the context of emerging new viral variants. In this paper, we describe the discovery of a novel noncovalent small-molecule inhibitor, MCULE-5948770040, that binds to and inhibits the SARS-Cov-2 main protease (Mpro) by employing a scalable high-throughput virtual screening (HTVS) framework and a targeted compound library of over 6.5 million molecules that could be readily ordered and purchased. Our HTVS framework leverages the U.S. supercomputing infrastructure achieving nearly 91% resource utilization and nearly 126 million docking calculations per hour. Downstream biochemical assays validate this Mpro inhibitor with an inhibition constant (Ki) of 2.9 μM (95% CI 2.2, 4.0). Furthermore, using room-temperature X-ray crystallography, we show that MCULE-5948770040 binds to a cleft in the primary binding site of Mpro forming stable hydrogen bond and hydrophobic interactions. We then used multiple μs-time scale molecular dynamics (MD) simulations and machine learning (ML) techniques to elucidate how the bound ligand alters the conformational states accessed by Mpro, involving motions both proximal and distal to the binding site. Together, our results demonstrate how MCULE-5948770040 inhibits Mpro and offers a springboard for further therapeutic design.
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Affiliation(s)
- Austin Clyde
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Stephanie Galanie
- Biosciences Division, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Heng Ma
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Yadu Babuji
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ben Blaiszik
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Alexander Brace
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Thomas Brettin
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Kyle Chard
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ryan Chard
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Ian Foster
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Darin Hauner
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Vlimos Kertesz
- Neutron Scattering Division, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division,
Pacific Northwest National Laboratory, Richland, Washington
99352, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hyungro Lee
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Zhuozhao Li
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andre Merzky
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Jurgen G. Schmidt
- Bioscience Division, Los Alamos National
Laboratory, Los Alamos, New Mexico 87545, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Li Tan
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Mikhail Titov
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Anda Trifan
- University of Illinois at
Urbana-Champaign, Champaign, Illinois 61820, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Matteo Turilli
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Hubertus Van Dam
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Srinivas C. Chennubhotla
- Department of Computational and Systems
Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Shantenu Jha
- Department of Electrical and Computer Engineering,
Rutgers University, Piscataway, New Jersey 08854,
United States
- Computational Science Initiative,
Brookhaven National Laboratory, Upton, New York 11973,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Andrey Kovalevsky
- Second Target Station, Oak Ridge
National Laboratory, Oak Ridge, Tennessee 37831, United
States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Arvind Ramanathan
- Data Science and Learning Division,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Martha S. Head
- Joint Institute for Biological Sciences,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
| | - Rick Stevens
- Department of Computer Science,
University of Chicago, Chicago, Illinois 60615,
United States
- Computing Environment and Life Sciences Directorate,
Argonne National Laboratory, Lemont, Illinois 60439,
United States
- National Virtual Biotechnology
Laboratory, Washington, District of Columbia 20585, United
States
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7
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Rajale T, Miner JC, Michalczyk R, Phipps ML, Schmidt JG, Gilbertson RD, Williams RF, Strauss CEM, Martinez JS. Conformational control via sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling. Chem Commun (Camb) 2021; 57:9922-9925. [PMID: 34498621 DOI: 10.1039/d1cc01992a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis. Their sequence-structure propensity is confirmed by circular dichroism, and conformer subtypes are enumerated by NMR. Biasing the ψ-angle backbone to trans (180°) in Monte Carlo modelling favors i to i + 3 naphthyl-naphthyl stacking, and matches experimental ensemble distributions. Taken together, high-yield synthesis of heterooligomers and NMR with structure prediction enables rapid determination of sequences that induce secondary structural propensities for predictive design of hydrophilic peptidomimetic foldamers and their future libraries.
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Affiliation(s)
- Trideep Rajale
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jacob C Miner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ryszard Michalczyk
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - M Lisa Phipps
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert D Gilbertson
- Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert F Williams
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Charlie E M Strauss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jennifer S Martinez
- Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, Arizona 86011, USA. .,Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, Arizona 86011, USA
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8
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Affiliation(s)
- Pavel A. Dub
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Rami J. Batrice
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - John C. Gordon
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Brian L. Scott
- Materials and Physics Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Yury Minko
- Biochemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jurgen G. Schmidt
- Biochemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Robert F. Williams
- Biochemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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9
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Wu R, Williams RF, Silks LAP, Schmidt JG. Synthesis of stable isotope-labeled chloroquine and amodiaquine and their metabolites. J Labelled Comp Radiopharm 2019; 62:230-248. [PMID: 30882940 DOI: 10.1002/jlcr.3721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/17/2019] [Accepted: 03/07/2019] [Indexed: 11/06/2022]
Abstract
Anti-malaria drugs chloroquine and amodiaquine and their metabolites were synthesized to incorporate 13 C and 15 N starting from U-13 C-labeled benzene to give M + 7 isotopomers. Chloroquine and its metabolites were prepared from 7-chloro-1,2,3,4-tetrahydroquinolin-4-one through an aryl substitution with the corresponding amines; and the amodiaquine and its metabolites were prepared from 4,7-dichloroquinoline in a similar fashion.
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Affiliation(s)
- Ruilian Wu
- Bioenergy and Biome Sciences, Group-B11, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Robert F Williams
- Bioenergy and Biome Sciences, Group-B11, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - L A Pete Silks
- Bioenergy and Biome Sciences, Group-B11, Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Jurgen G Schmidt
- Inorganic, Isotope, and Actinide Chemistry, Group-IIAC, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
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10
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Schmidt JG, Andersen EW, Ersbøll BK, Nielsen ME. Muscle wound healing in rainbow trout (Oncorhynchus mykiss). Fish Shellfish Immunol 2016; 48:273-284. [PMID: 26702558 DOI: 10.1016/j.fsi.2015.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/30/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
We followed the progression of healing of deep excisional biopsy punch wounds over the course of 365 days in rainbow trout (Oncorhynchus mykiss) by monitoring visual wound healing and gene expression in the healing muscle at regular intervals (1, 3, 7, 14, 38 and 100 days post-wounding). In addition, we performed muscle texture analysis one year after wound infliction. The selected genes have all previously been investigated in relation to vertebrate wound healing, but only few specifically in fish. The selected genes were interleukin (IL)-1β, IL-6, transforming growth factor (TGF)-β1 and -β3, matrix metalloproteinase (MMP) -9 and -13, inducible nitric oxide synthase (iNOS), fibronectin (FN), tenascin-C (TN-C), prolyl 4-hydroxylase α1-chain (P4Hα1), lysyl oxidase (LOX), collagen type I α1-chain (ColIα1), CD41 and CD163. Wound healing progressed slowly in the presented study, which is at least partially due to the low temperature of about 8.5 °C during the first 100 days. The inflammation phase lasted more than 14 days, and the genes relating to production and remodeling of new extracellular matrix (ECM) exhibited a delayed but prolonged upregulation starting 1-2 weeks post-wounding and lasting until at least 100 days post-wounding. The gene expression patterns and histology reveal limited capacity for muscle regeneration in rainbow trout, and muscle texture analyses one year after wound infliction confirm that wounds heal with fibrosis. At 100 dpw epidermis had fully regenerated, and dermis partially regenerated. Scales had not regenerated even after one year. CD163 is a marker of "wound healing"-type M2c macrophages in mammals. M2 macrophage markers are as yet poorly described in fish. The pattern of CD163 expression in the present study is consistent with the expected timing of presence of M2c macrophages in the wound. CD163 may thus potentially prove a valuable marker of M2 macrophages - or a subset hereof - in fish. We subjected a group of fish to bathing in an immunomodulatory β-glucan product during wound healing, but found this to have very limited effect on wound healing in contrast to a previously published study on common carp.
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Affiliation(s)
- J G Schmidt
- Laboratory of Aquatic Pathobiology, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 7, DK-1970 Frederiksberg, Denmark.
| | - E W Andersen
- Technical University of Denmark, Department of Applied Mathematics and Computer Science, Statistics and Data Analysis, Matematiktorvet, Building 324, DK-2800 Kgs. Lyngby, Denmark
| | - B K Ersbøll
- Technical University of Denmark, Department of Applied Mathematics and Computer Science, Statistics and Data Analysis, Matematiktorvet, Building 324, DK-2800 Kgs. Lyngby, Denmark
| | - M E Nielsen
- Leo Pharma A/S, Industriparken 55, DK-2750 Ballerup, Denmark
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11
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Przybylska-Diaz DA, Schmidt JG, Vera-Jiménez NI, Steinhagen D, Nielsen ME. β-glucan enriched bath directly stimulates the wound healing process in common carp (Cyprinus carpio L.). Fish Shellfish Immunol 2013; 35:998-1006. [PMID: 23770625 DOI: 10.1016/j.fsi.2013.05.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 05/09/2013] [Accepted: 05/20/2013] [Indexed: 06/02/2023]
Abstract
Wound healing is a complex and well-organized process in which physiological factors and immune mechanisms are involved. A number of different immune modulators have been found to enhance the non-specific defence system in vertebrates, among which β-glucans are the most powerful and extensively investigated. The aim of the present study was to investigate the biological impact of two different commercially available β glucan containing products on the wound healing process in carp. Throughout a two week experiment fish were kept either untreated (control), or in water supplemented with the two different types of β-glucans. The wound healing process was monitored using a multispectral visualisation system. The correlation between wound closure and immune response was investigated by measuring the gene expression patterns of IL-1β, IL-6 family member M17, IL-8 and Muc5b, and measurement of production of radical oxygen species. PAMPs/DAMPs stimulation caused by the wounding and or β-glucans resulted in an inflammatory response by activating IL-1β, IL-6 family member M17 and IL-8 and differences in the expression pattern were seen depending on stimuli. IL-1β, IL-6 family member M17 and IL-8 were activated in all wounds regardless of treatment. Expression of all three interleukins was highly up regulated in control wounded muscle already at day 1 post-wounding and decreased at subsequent time-points. The reverse was the case with control wounded skin, where expression increased from day 1 through day 14. The results for the β-glucan treated wounds were more complex. The images showed significantly faster wound contraction in both treated groups compared to the control. The obtained results clearly demonstrated that a β glucan enriched bath promotes the closure of wounds in common carp and induce a local change in cytokine expression.
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Affiliation(s)
- D A Przybylska-Diaz
- DTU Food, National Food Institute, Biological Quality Research Group, Mørkhøj Bygade 19, DK 2860 Søborg, Denmark
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12
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Wu R, Lodwig SN, Schmidt JG, Williams RF, Silks LA"P. Synthesis of 13C labeled sulfur and nitrogen mustard metabolites as mass spectrometry standards for monitoring and detecting chemical warfare agents. J Labelled Comp Radiopharm 2012. [DOI: 10.1002/jlcr.2929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Ruilian Wu
- Bioscience Division, Bioenergy and Environmental Science, the National Stable Isotope Resource, Group B8, MS E529; Los Alamos National Laboratory; Los Alamos; NM; 87545; USA
| | - Siegfried N. Lodwig
- Bioscience Division, Bioenergy and Environmental Science, the National Stable Isotope Resource, Group B8, MS E529; Los Alamos National Laboratory; Los Alamos; NM; 87545; USA
| | - Jurgen G. Schmidt
- Chemistry Division; Los Alamos National Laboratory; Los Alamos; NM; 87545; USA
| | - Robert F. Williams
- Bioscience Division, Biosecurity and Public Health Group; Los Alamos National Laboratory; Los Alamos; NM; 87545; USA
| | - Louis A. " Pete" Silks
- Bioscience Division, Bioenergy and Environmental Science, the National Stable Isotope Resource, Group B8, MS E529; Los Alamos National Laboratory; Los Alamos; NM; 87545; USA
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13
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Wolfenden ML, Sakamuri RM, Anderson AS, Prasad L, Schmidt JG, Mukundan H. Determination of bacterial viability by selective capture using surface-bound siderophores. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/abc.2012.24049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Villa-Uriol MC, Berti G, Hose DR, Marzo A, Chiarini A, Penrose J, Pozo J, Schmidt JG, Singh P, Lycett R, Larrabide I, Frangi AF. @neurIST complex information processing toolchain for the integrated management of cerebral aneurysms. Interface Focus 2011; 1:308-19. [PMID: 22670202 DOI: 10.1098/rsfs.2010.0033] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Accepted: 02/08/2011] [Indexed: 11/12/2022] Open
Abstract
Cerebral aneurysms are a multi-factorial disease with severe consequences. A core part of the European project @neurIST was the physical characterization of aneurysms to find candidate risk factors associated with aneurysm rupture. The project investigated measures based on morphological, haemodynamic and aneurysm wall structure analyses for more than 300 cases of ruptured and unruptured aneurysms, extracting descriptors suitable for statistical studies. This paper deals with the unique challenges associated with this task, and the implemented solutions. The consistency of results required by the subsequent statistical analyses, given the heterogeneous image data sources and multiple human operators, was met by a highly automated toolchain combined with training. A testimonial of the successful automation is the positive evaluation of the toolchain by over 260 clinicians during various hands-on workshops. The specification of the analyses required thorough investigations of modelling and processing choices, discussed in a detailed analysis protocol. Finally, an abstract data model governing the management of the simulation-related data provides a framework for data provenance and supports future use of data and toolchain. This is achieved by enabling the easy modification of the modelling approaches and solution details through abstract problem descriptions, removing the need of repetition of manual processing work.
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Affiliation(s)
- M C Villa-Uriol
- Centre for Computational Imaging and Simulation Technologies in Biomedicine (CISTIB), Information and Communication Technologies Department, Universitat Pompeu Fabra, c/ Tanger 122-140, E08018 Barcelona, Spain
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15
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Sporty JLS, Lemire SW, Jakubowski EM, Renner JA, Evans RA, Williams RF, Schmidt JG, van der Schans MJ, Noort D, Johnson RC. Immunomagnetic separation and quantification of butyrylcholinesterase nerve agent adducts in human serum. Anal Chem 2010; 82:6593-600. [PMID: 20617824 DOI: 10.1021/ac101024z] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel method for extracting butyrylcholinesterase (BuChE) from serum as a means of identifying and measuring nerve agent adducts to human BuChE is presented here. Antibutyrylcholinesterase monoclonal antibodies were conjugated to protein-G ferromagnetic particles and mixed with 500 microL serum samples. The particle-antibody-BuChE product was rinsed and directly digested with pepsin. Native and isotopically enriched nonapeptides corresponding to the pepsin digest products for uninhibited BuChE, and sarin, cyclohexylsarin, VX, and Russian VX nerve agent-inhibited BuChE were synthesized for use as calibrators and internal standards, respectively. Internal standards were added to the filtered digest sample, and the samples were quantified via high performance liquid chromatography-isotope dilution-tandem mass spectrometry. The ratio of adducted to total BuChE nonapeptides was calculated for each nerve agent-exposed serum sample using data collected in a single chromatogram. Nerve agent-inhibited quality control serum pools were characterized as part of method validation; the method was observed to have extremely low background noise. The measurement of both uninhibited and inhibited BuChE peptides compensated for any variations in the pepsin digestion before the internal standard peptide was added to the sample and may prove useful in individualizing patient results following a nerve agent exposure.
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Affiliation(s)
- Jennifer L S Sporty
- Emergency Response and Air Toxicants Branch, Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, MS F44, Chamblee, Georgia 30341, USA
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16
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Kale RR, Mukundan H, Price DN, Harris JF, Lewallen DM, Swanson BI, Schmidt JG, Iyer SS. Detection of Intact Influenza Viruses using Biotinylated Biantennary S-Sialosides. J Am Chem Soc 2008; 130:8169-71. [DOI: 10.1021/ja800842v] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ramesh R. Kale
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - Harshini Mukundan
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - Dominique N. Price
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - J. Foster Harris
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - Daniel M. Lewallen
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - Basil I. Swanson
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - Jurgen G. Schmidt
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
| | - Suri S. Iyer
- Chemical and Biosensors group, 805 Crosley, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, Physical Chemistry and Applied Spectroscopy (C-PCS), Los Alamos National Laboratory, P.O. Box 1663, MS J567, Los Alamos, New Mexico 87545, and Bioscience Division (B-7 and B-9), Los Alamos National Laboratory, PO Box 1663, MS E 529, Los Alamos, New Mexico 87545
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17
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Anderson AS, Dattelbaum AM, Montaño GA, Price DN, Schmidt JG, Martinez JS, Grace WK, Grace KM, Swanson BI. Functional PEG-modified thin films for biological detection. Langmuir 2008; 24:2240-2247. [PMID: 18229965 DOI: 10.1021/la7033438] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We report a general procedure to prepare functional organic thin films for biological assays on oxide surfaces. Silica surfaces were functionalized by self-assembly of an amine-terminated silane film using both vapor- and solution-phase deposition of 3'-aminopropylmethyldiethoxysilane (APMDES). We found that vapor-phase deposition of APMDES under reduced pressure produced the highest quality monolayer films with uniform surface coverage, as determined by atomic force microscopy (AFM), ellipsometry, and contact angle measurements. The amine-terminated films were chemically modified with a mixture of carboxylic acid-terminated poly(ethylene glycol) (PEG) chains of varying functionality. A fraction of the PEG chains (0.1-10 mol %) terminated in biotin, which produced a surface with an affinity toward streptavidin. When used in pseudo-sandwich assays on waveguide platforms for the detection of Bacillus anthracis protective antigen (PA), these functional PEG surfaces significantly reduced nonspecific binding to the waveguide surface while allowing for highly specific binding. Detection of PA was used to validate these films for sensing applications in both buffer and complex media. Ultimately, these results represent a step toward the realization of a robust, reusable, and autonomous biosensor.
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Affiliation(s)
- Aaron S Anderson
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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18
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Boyer AE, Moura H, Woolfitt AR, Kalb SR, McWilliams LG, Pavlopoulos A, Schmidt JG, Ashley DL, Barr JR. From the mouse to the mass spectrometer: detection and differentiation of the endoproteinase activities of botulinum neurotoxins A-G by mass spectrometry. Anal Chem 2007; 77:3916-24. [PMID: 15987092 DOI: 10.1021/ac050485f] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed an assay (Endopep-MS) that detects the specific endoproteinase activities of all seven BoNT types by mass spectrometry (MS). Each BoNT type cleaves a unique site on proteins involved in neuronal transmission. Target peptide substrates based on these proteins identify a BoNT type by its enzymatic action on the substrate and the production of two peptide products, which are then detected by matrix-assisted laser desorption/ionization time-of-flight MS or liquid chromatography electrospray ionization MS/MS. We showed the ability to detect all seven toxin types in a multiplexed assay format. The detection limits achieved range from 0.039 to 0.625 mouse LD(50)/mL for toxin types A, B, E, and F in a buffer system. The Endopep-MS assay is the first to differentiate all seven BoNT types, is sensitive, specific, and has the potential to quantify toxin activity.
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Affiliation(s)
- Anne E Boyer
- National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Highway, NE, Atlanta, Georgia 30341-3724, USA.
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19
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Barr JR, Moura H, Boyer AE, Woolfitt AR, Kalb SR, Pavlopoulos A, McWilliams LG, Schmidt JG, Martinez RA, Ashley DL. Botulinum neurotoxin detection and differentiation by mass spectrometry. Emerg Infect Dis 2006; 11:1578-83. [PMID: 16318699 PMCID: PMC3366733 DOI: 10.3201/eid1110.041279] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A new rapid, mass spectrometry-based method to detect and differentiate botulinal neurotoxins is described. Botulinum neurotoxins (BoNTs) are proteases that cleave specific cellular proteins essential for neurotransmitter release. Seven BoNT serotypes (A–G) exist; 4 usually cause human botulism (A, B, E, and F). We developed a rapid, mass spectrometry–based method (Endopep-MS) to detect and differentiate active BoNTs A, B, E, and F. This method uses the highly specific protease activity of the toxins with target peptides specific for each toxin serotype. The product peptides derived from the endopeptidase activities of BoNTs are detected by matrix-assisted laser-desorption ionization time-of-flight mass spectrometry. In buffer, this method can detect toxin equivalents of as little as 0.01 mouse lethal dose (MLD)50 and concentrations as low as 0.62 MLD50/mL. A high-performance liquid chromatography–tandem mass spectrometry method for quantifying active toxin, where the amount of toxin can be correlated to the amount of product peptides, is also described.
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Affiliation(s)
- John R Barr
- Centers for Disease Control and Prevention, Atlanta, Georgia 30341, USA.
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20
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Abstract
Objective: To describe the clinical effects of amantadine and propranolol in an agitated pediatric patient with cognitive deficits, hyperactivity, and hypersexualism secondary to “shaken-baby syndrome.” Background: Patients with shaken-baby syndrome can present with cognitive and behavioral impairments. Case: A 9-year-old girl presented with cognitive impairments secondary to shaken-baby syndrome at 3 weeks of age. She was receiving many medications, including dextroamphetamine, methylphenidate, and clonidine, that were not effective in improving her cognitive status or decreasing her hypersexuality. She was weaned from stimulants and clonidine and prescribed amantadine 100 mg bid with improvement of attention, concentration, and cognition, although hypersexuality remained. She was then started on propranolol 10 mg tid and a gradual increase to 40 mg tid with amelioration of hypersexuality and hyperactivity and no unwanted effects noted. Self-weaning of propranolol was associated with the return of hypersexuality. The combination of amantadine and propranolol led to improvement of cognition and behavior, especially intellectual functioning and appropriate socialization with peers, respectively. Conclusion: Cognitive deficits and hypersexuality with hyperactive features due to shaken-baby syndrome may respond to the drug regimen of amantadine and propranolol.
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Affiliation(s)
- J G Schmidt
- Department of Rehabilitation and Neurology, St. Mary's Hospital, Unity Health Systems, Rochester, NY 14611, USA
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21
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Schmidt JG. [Evidence-based medicine: modern scientific methods for determining usefulness]. Swiss Surg 1999; 5:177-82. [PMID: 10467873 DOI: 10.1024/1023-9332.5.4.177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
For quite some time, clinical epidemiology has introduced the art of critical appraisal of evidence as well as the methods of how to design sound clinical studies and trials. Almost unnoticed by most medical institutions a new hierarchy of evidence has emerged which puts well thought out trials, able to document unbiased treatment benefit in terms of patient suffering, above pathophysiological theory. Many controlled trials have shown, in the meantime, that the control of laboratory or other kind of pathologies and the correction of anatomical abnormalities do not necessarily mean a benefit for the patient. Concepts relating to this dissection of evidence include: Surrogate fallacy ("cosmetics" of laboratory results or ligament or cartilage "cosmetics" in surgery), confounding (spurious causal relationships), selection bias (comparison with selected groups) as well as lead-time bias (mistaking earlier diagnosis as increase of survival), length bias (overlooking differences in the aggressiveness of diseases as determinants of disease stage distributions) and overdiagnosis bias (mistaking the increasing detection of clinically silent pathologies as improvement of prognosis). Moreover, absolute instead of relative risk reduction needs to be used to measure patient benefit. The incorporation of decision-analysis and of the concepts or clinical epidemiology will improve the efficiency and quality of medicine much more effectively than the sole focus on technical medical performance. Evidence based medicine is the systematic and critical appraisal of medical interventions, based on the understanding how to avoid the fallacies and biases mentioned.
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Affiliation(s)
- J G Schmidt
- Institut für Klinische Epidemiologie, Einsiedeln
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Schmidt JG. Empirie und Dogma in den <<Jahreszeiten>> medizinischer Wissenschaft. Forsch Komplementarmed 1999; 5 Suppl S1:60-63. [PMID: 9892832 DOI: 10.1159/000057110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Empiric and Dogmatic 'Seasons' in the Progress of Medical ScienceThe current 'postmodern' times are not simply permissive towards any theory whatever. In medicine, the 'external validity' of theories and the exact place of various healing schools has become an important subject. 'Critical appraisal' of the empiric evidence for treatment benefit in all areas of medicine, conventional or unconventional, will separate the wheat from the chaff. Pluralistic evidence-based medicine constitutes the flail for achieving this task. This happens in late summer. Later in winter, the chaff of useless medicine will decay; a new therapeutic spring will only be possible when the current task of identifying effective and beneficial treatments in all areas and of abandoning useless therapies will be fulfilled. The current primacy of the empiric study of medicine, rather than the dogmatic, should not be misunderstood as a pure empirism. Rather, we are in the empiric 'season'. Questions about mechanisms of action will remain, but will retreat to the back of the mind for some time.
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Schmidt JG. Die Vision einer pragmatischen klinischen Forschung oder das Ende der Diskussion über <<Placebo>> und <<spezifische Wirkungen>>. Forsch Komplementarmed 1999; 5 Suppl S1:102-111. [PMID: 9892839 DOI: 10.1159/000021086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Concept of Pragmatic Clinical Research or the End of Discussion about 'Placebo' and 'Specific Effects&rsquoThe reorientation of clinical research towards the questions of treatment benefit (beyond the question of treatment efficacy) and of how much clinical trials represent actual practice (external validity) is the timely path to clinical research questions of real interest and importance. Postmodern 'anything goes' makes it possible to also consider thus far looked down on placebo effects as valuable, however, it requires the precise documentation of the external validity of such effects. Not disease as such, but the disease context, not therapy as such, but the therapy context, not the patient as such, but the patient context, not a test as such, but the test situation have become the important focuses of clinical research. In respect to test results current medicine has to recognize its illiterate mystification of allegedly 'objective' and 'hard' data. The patient context can determine whether an 'efficacious' therapy is beneficial or harmful, and thus, it is the proper definition of the patient context which makes medicine scientific, no matter how 'objective' or 'subjective' the effect of therapy is. The consideration of the therapy context leads to the important distinction between efficacy and effectiveness (or benefit), and it becomes intelligible that the randomised controlled trial in its traditional design as the placebo-controlled double-blind trial is limited to the evaluation of an agent theory. The evaluation of treatment effectiveness requires more pragmatic trials which study treatment operations and not isolated components and which may even compare entire treatment strategies. Pragmatic clinical trials, in future, will not only allow the study of 'pathogenesis blockers'., but also the study of 'salutogenetic' interventions working with the formation of the host. The focus of attention and research in the new school of evidencebased medicine with clinical epidemiology as its basic science (if not superficially understood as mere literature medicine) has long ago been identified as illness as the product of host, disease and environment. The dispute about 'placebo' and 'specific effects', in the meantime, has become obsolete.
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Fonseca SN, Melon Kunzle SR, Barbosa Silva SA, Schmidt JG, Mele RR. Cost reduction with successful implementation of an antibiotic prophylaxis program in a private hospital in Ribeirão Preto, Brazil. Infect Control Hosp Epidemiol 1999; 20:77-9. [PMID: 9927275 DOI: 10.1086/501543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To describe the implementation and results of a perioperative antibiotic prophylaxis (PAP) program. DESIGN A protocol for correct use of PAP was implemented in December 1994. For selected months we measured the PAP protocol compliance of a random sample of clean and clean-contaminated procedures and calculated the cost of incorrect use of PAP. SELLING: A 180-bed general hospital in Ribeirão Preto, Brazil. RESULTS The cost of unnecessary PAP in the obstetric and gynecologic, cardiothoracic, and orthopedic services dropped from $4,224.54 ($23.47/procedure) in November 1994 to $1,147.24 ($6.17/procedure, January 1995), $544.42 ($3.58/procedure, May 1995), $99.06 ($0.50/procedure, August 1995), and $30 ($0.12/procedure, March 1996). In November 1994, only 13.6% of all surgical procedures were done with correct use of PAP, compared to 59% in January 1995, 73% in August 1995, 78% in March 1996, 92% in November 1996, and 98% in May 1997. CONCLUSIONS Incorrect PAP use wastes resources, which is a particular problem in developing countries. Our program is simple and can be implemented without the use of computers and now is being adopted in other hospitals in our region. We credit the success of our program to the commitment of all participants and to the strong support of the hospital directors.
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Affiliation(s)
- S N Fonseca
- Hospital Infection Control Department of Hospital São Francisco, Ribeirão Preto, Brazil
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Bucher HC, Schmidt JG, Steurer J. [Critical evaluation of a publication on a diagnostic test ]. Praxis (Bern 1994) 1998; 87:1096-1102. [PMID: 9782748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- H C Bucher
- Medizinische Universitäts-Poliklinik, Kantonsspital Basel
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Schmidt JG. [Comment on: Speich R. The diagnostic process in internal medicine]. Schweiz Med Wochenschr 1998; 128:599-601. [PMID: 9679003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Abstract
Peptide nucleic acids (PNAs) are uncharged analogs of DNA and RNA in which the ribose-phosphate backbone is substituted by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. A PNA C10 oligomer has been shown to act as template for efficient formation of oligoguanylates from activated guanosine ribonucleotides. In a previous paper we used heterosequences of DNA as templates in sequence-dependent polymerization of PNA dimers. In this paper we show that information can be transferred from PNA to RNA. We describe the reactions of activated mononucleotides on heterosequences of PNA. Adenylic, cytidylic and guanylic acids were incorporated into the products opposite their complement on PNA, although less efficiently than on DNA templates.
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Affiliation(s)
- J G Schmidt
- The Salk Institute for Biological Studies, PO Box 85800, San Diego, CA 92186, USA
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Abstract
Peptide nucleic acids (PNAs) are analogs of nucleic acids in which the ribose-phosphate backbone is replaced by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. Oligocytidylates have been shown to act as templates for formation of longer oligomers of G from PNA G2 dimers. In this paper we show that information can be transferred from DNA to PNA. DNA C4T2C4 is an efficient template for synthesis of PNA G4A2G4 using G2 and A2 units as substrates. The corresponding synthesis of PNA G4C2G4 on DNA C4G2C4 is less efficient. Incorporation of PNA T2 into PNA products on DNA C4A2C4 is the least efficient of the three reactions. These results, obtained using PNA dimers as substrates, parallel those obtained using monomeric activated nucleotides.
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Affiliation(s)
- J G Schmidt
- The Salk Institute for Biological Studies, PO Box 85800, San Diego, CA 92186, USA
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Schmidt JG. Delays in diagnosing oesophagogastric cancer. Attempts to reduce delays in diagnosis should be done in controlled trial. BMJ 1997; 315:426-7. [PMID: 9277613 PMCID: PMC2127281 DOI: 10.1136/bmj.315.7105.426b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Bucher HC, Egger M, Schmidt JG, Antes G, Lengeler C. [Evidence-based medicine: approach to a more rational medicine. Arbeitsgemeinschaft Cochrane Collaboration Schweiz]. Praxis (Bern 1994) 1997; 86:606-612. [PMID: 9213911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- H C Bucher
- Medizinische Universitäts-Poliklinik, Kantonsspital Basel
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Affiliation(s)
- J G Schmidt
- The Salk Institute for Biological Studies, San Diego, California 92186, USA
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Affiliation(s)
- J G Schmidt
- The Salk Institute for Biological Studies, San Diego, California 92186-5800, USA
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Schmidt JG. [What is the benefit of screening for breast cancer? Contra]. Arch Gynecol Obstet 1996; 259 Suppl 1:S178-98. [PMID: 9133272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J G Schmidt
- Institut für Klinische Epidemiologie, Einsiedeln, Switzerland
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Schmidt JG. [The effect of lowering cholesterol on mortality]. Schweiz Med Wochenschr 1993; 123:2150-5. [PMID: 8266036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
There is little doubt about the validity of the lipid hypothesis as a pathogenetic theory for atherosclerosis. However, this theory does not allow the conclusion that cholesterol-lowering treatment is necessarily beneficial in practice. As a consequence of the probabilistic nature of risk factors, the classification of plasma cholesterol levels into "normal" and "pathological" can be misleading in clinical practice. The potential benefit of cholesterol-lowering treatment is a direct function of the overall coronary risk, more or less independently of plasma cholesterol. Therefore, plasma cholesterol is of clinical significance only in patients with established CHD and a high overall risk of infarction. Total mortality has been prospectively included as one end-point in addition to infarct mortality in the many intervention studies on cholesterol-lowering. Meta-analyses of these studies show a non-significant decrease in infarct mortality through cholesterol-lowering drug treatment, with a concomitant, highly significant increase in non-infarct mortality. Lowering cholesterol in asymptomatic persons and in coronary patients with a relatively low risk of infarction results in a significant increase in total mortality. Only in a very small group of coronary patients with a very high risk of myocardial infarction, due to the presence of several additional risk factors, may cholesterol-lowering treatment be beneficial.
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Abstract
OBJECTIVE To evaluate the effectiveness of routine ultrasound scanning in pregnancy by a meta-analysis of various outcome measures. DESIGN Meta-analysis of randomised controlled trials evaluating the effect of routine ultrasound scanning on perinatal mortality and morbidity. Live birth rate (that is, live births per pregnancy) is included as a measure of pregnancy outcome in addition to the conventional perinatal mortality. SUBJECTS 15,935 pregnancies (7992 in which routine ultrasound scanning was used and 7943 controls with selective scanning) from four randomised controlled trials. MAIN OUTCOME MEASURES Perinatal mortality, live birth rate, rate of miscarriage, Apgar score < 7 at 1 minute, and number of induced labours. RESULTS The live birth rate was identical in both screening and control groups (odds ratio = 0.99; 95% confidence interval 0.88 to 1.12) although the perinatal mortality was significantly lower in the group who had routine ultrasonography (0.64, 0.43 to 0.97). Differences in perinatal morbidity between the two groups as measured by the proportion of newborn babies with Apgar score < 7 at 1 minute were not significant (1.05; 0.93 to 1.19). CONCLUSION Routine ultrasound scanning does not improve the outcome of pregnancy in terms of an increased number of live births or of reduced perinatal morbidity. Routine ultrasound scanning may be effective and useful as a screening for malformation. Its use for this purpose, however, should be made explicit and take into account the risk of false positive diagnosis in addition to ethical issues.
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Affiliation(s)
- H C Bucher
- Department of Internal Medicine, University Polyclinic, Kantonsspital Basel, Switzerland
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Schmidt JG. Natural history of breast cancer. Lancet 1992; 339:810. [PMID: 1347831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
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Abstract
The present paper analyses the epidemiologic effects of mass breast cancer screening. Mass mammography may possibly achieve a breast cancer mortality reduction in relative risk terms. However, this does not necessarily represent a net benefit. It is argued that the benefits and adverse effects of a screening programme must be measured in terms of absolute risks. According to this measure, the mortality reduction achieved by a mass breast screening programme is only one death per approx. 15,000 women-years. Many thousands of mammograms are needed to prevent one cancer death, and for each woman who can derive a direct benefit in terms of a prevented breast cancer death, hundreds of women have to suffer the anxiety of a positive screening mammography. Moreover, it is possible that adverse effects of breast cancer screening may contribute to mortality from other causes. Even with the assumption that screening can save lives, the net health effect of mass breast cancer screening is questionable and appears to be rather detrimental. It may be an error to recommend mass breast screening.
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Affiliation(s)
- J G Schmidt
- Centre for Clinical Epidemiology, University of Newcastle, NSW, Australia
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Abstract
This is a report on the effects of various equally sized copper alloys implanted in the vitreous body of 52 Wistar rats. The main results are as follows: (1) The alloy of 99.9% copper with 0.1% silver (A) destroyed the electroretinogram (ERG) faster than specially purified copper (B). In contrast, copper-zinc alloys (C and D) affected the ERG more slowly than B. This effect is more obvious in alloys containing a large amount of zinc (D). (2) The degree of complication in the anterior segment (iridocyclitis, corneal opacity, hypopyon) and in the vitreous body (intensity and rate of opacity) depend essentially on the type of alloy. The frequency and extent of inflammatory responses decreased in the following order: alloy A, B, C and D.
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Abstract
UNLABELLED The electroretinogram (ERG) was recorded 20 times over a period of 360 days in 26 albino-rats with implanted intravitreal iron wires ranging in size between 0.15 and 1.2 mm2. RESULTS (i) The a- and b-wave amplitudes decreased rapidly within one day after iron wire implantation. During the following week the amplitudes recovered to some extent. In the course of the next few months the a- and b-wave amplitudes of the eyes implanted with the largest iron wires (1.2 mm2) decreased steadily to about 20% by the end of the observation time, whereas in the groups containing smaller iron wires the electroretinographic changes were limited. (ii) Implantation of equally-sized glass splinters reduced the a- and b-wave amplitudes to 65-75% in comparison to the intact fellow eye. Fast recovery of both potentials to 83-93% followed within two weeks. The mean values of the a-wave amplitudes reached nearly 100%, those of the b-wave 90-95% in the next month.
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Abstract
The influence of intravitreal zinc particles (1.3 mm2) in the eyes of rats caused the amplitudes of the electroretinogram to decrease to about 50% of the initial values within 24 hours, whereas the prolongation of the peak times began only on the third day after particle implantation. The removal of the zinc particles after 30 days led to only partial recovery of the amplitudes, whereas the peak times reached normal values. Dissociated behaviour of the amplitudes and peak times as described here was not found in earlier experiments with intravitreal iron, copper or lead particles of the same size. The extraction of intravitreal zinc particles (1.3 mm2) one day after implantation resulted in a recovery of the amplitudes up to 85%.
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Abstract
This report details the influence of the time lapse and surface area size of intravitreal copper foreign bodies on the electroretinogram (ERG) and the recovery of the potentials after removal of the particles. Pure copper wires were implanted temporarily into the vitreous body of rat eyes in the area of the ora serrata and the values of the ERG were compared with those of the intact fellow eyes. In three different procedures with groups of 12 animals each the following results were obtained: (1) The metal toxicity of small copper particles (0.3 mm2) remaining one day in the vitreous body reduced the amplitudes of the a1-, a2-, and b-wave only 10% by the end of the observation time of 260 days, (2) The loss of ERG amplitudes increased to about 25% under the influence of larger copper particles (1.3 mm2; time lapse one day); and (3) Copper particles with an active surface of 1.3 mm2 remaining two days in the vitreous body caused a permanent loss of about 50%.
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Schmidt JG, Mansfeld-Nies R, Nies C. [Regeneration capacity in retina and vitreous body changes following extraction of intravitreal copper particles]. Klin Monbl Augenheilkd 1986; 189:39-43. [PMID: 3531694 DOI: 10.1055/s-2008-1050746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
On the basis of experiments with 42 rats, quantitative statements are made regarding the influence of surface area and dwelling time of intravitreal copper particles on the electroretinogram. The influence of these factors on the extent of recovery of function after extraction of the foreign body is demonstrated. The rate of mental intoxication (metallosis retinae) is indicated separately from the mechanical damage. Ophthalmoscopic findings are also described. The practical relevance of these results to the clinical situation is discussed in detail in connection with earlier reports.
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Schmidt JG, Hummelsheim S. [Effect of decadron phosphate on ophthalmoscopic changes in the rat eye with intravitreal brass wires]. Klin Monbl Augenheilkd 1986; 188:234-8. [PMID: 3520128 DOI: 10.1055/s-2008-1050619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This paper reports on ophthalmoscopic findings after implantation of 0.3 mm2 copper-zinc wires (85:15) into the vitreous body of rat eyes (2 groups of 11 animals each) and the influence of daily administration of Decadron-Phosphate, equivalent to 0.05 mg dexamethasone. This drug, injected subconjunctivally over a period of 10 days, reduces the vitreal opacities and both retinal as well as vitreal vascularization, but increases the tendency of the foreign bodies to migrate. The dose-dependent decline in bodyweight gain is an indicator of the drug's systemic effect. In order to distinguish mechanical damage from the metal intoxication, glass splinters of the same size and shape were implanted in a further series of experiments, for the purpose of comparison.
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Abstract
Lead particles (1.4 mm2) were implanted into the vitreous body of rats (16 animals) for 10 days and the recovery rate of the ERG was measured over an observation time of 190 days. After extraction of the lead particles the a- and b-wave amplitudes show a recovery from about 60% to 87% in comparison to those of the intact fellow eyes between the 60th and 90th day of observation. In earlier experiments the mechanical damage was measured using glass splinters. The differences between these values and the above mentioned recovery rate after lead extraction correspond to the irreversible component of the metal intoxication. In another group of rats (16 animals) the lead particle was not removed before the end of the observation time of 190 days. Subtracting these ERG values from those of the first group of rats after lead extraction one gets small differences which correspond to the reversible component of the metal intoxication. The irreversible lead intoxication is much less than that of intravitreal iron particles as we found under the same conditions. The lead particles we used, are larger than those we have to handle in clinical cases taking the relation of surface area size of the particle to the total bulbus weight. The ophthalmoscopical findings are described.
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Abstract
The electroretinograms of 20 anesthetised but spontaneously breathing rats (Wistar) were recorded over a period of 60 minutes. Two anesthetical procedures were applied to each of these rats respectively: (I) halothane/nitrous oxide/oxygen (2% halothane in 0.81 N2O: 0.41 O2/min) and (II) halothane/nitrogen/oxygen (2% halothane in 0.81 N2: 0.41 O2/min). From the 10th up to the 60th min of anesthesia the ERG amplitudes decreased gradually (I: a-wave 17% and b-wave 14%; II: a-wave 15% and b-wave 12%). Body temperature was experimentally maintained at nearly 37.0 degrees C. Under considerable diminution in both procedures the frequency of respiration was significantly higher under procedure I in the first 20 minutes only. Under procedure I the b-wave amplitudes were significantly higher in contrast to procedure II. This occurred at all applied stimulus intensities (6; 24; 100; 400 and 1600 Lux at the cornea). The a-wave amplitudes and the peak times of the a- and b-waves did not show any significant differences between the two experimental conditions. These ERG responses to nitrous oxide in addition to halothane are discussed on the basis of the respiratory, circulatory and cerebral effects of these anesthetics.
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Abstract
A 46-year-old patient is described who presented with a pea-sized painless tumor in the upper eyelid. Surgical excision and histologic diagnosis revealed a proliferating spindle cell tumor with an inflammatory reaction, which was identified as nodular fasciitis. Differential diagnosis, incidence of such tumors in the orbit and treatment are discussed.
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Walzer P, Engelen S, Stellinger L, Schmidt JG, Heimann K. [Retinal changes in Wistar rats caused by light. Quantitative histological and electroretinographical examinations (author's transl)]. Klin Monbl Augenheilkd 1974; 164:233-42. [PMID: 4601771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Schmidt JG, Hartmann O. [Medicamentous and surgical treatment of acute glaucoma]. Klin Monbl Augenheilkd 1972; 161:16-24. [PMID: 4636856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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