1
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Rodríguez-Hernández D, Fenwick MK, Zigweid R, Sankaran B, Myler PJ, Sunnerhagen P, Kaushansky A, Staker BL, Grøtli M. Exploring Subsite Selectivity within Plasmodium vivax N-Myristoyltransferase Using Pyrazole-Derived Inhibitors. J Med Chem 2024; 67:7312-7329. [PMID: 38680035 PMCID: PMC11089503 DOI: 10.1021/acs.jmedchem.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
N-myristoyltransferase (NMT) is a promising antimalarial drug target. Despite biochemical similarities between Plasmodium vivax and human NMTs, our recent research demonstrated that high selectivity is achievable. Herein, we report PvNMT-inhibiting compounds aimed at identifying novel mechanisms of selectivity. Various functional groups are appended to a pyrazole moiety in the inhibitor to target a pocket formed beneath the peptide binding cleft. The inhibitor core group polarity, lipophilicity, and size are also varied to probe the water structure near a channel. Selectivity index values range from 0.8 to 125.3. Cocrystal structures of two selective compounds, determined at 1.97 and 2.43 Å, show that extensions bind the targeted pocket but with different stabilities. A bulky naphthalene moiety introduced into the core binds next to instead of displacing protein-bound waters, causing a shift in the inhibitor position and expanding the binding site. Our structure-activity data provide a conceptual foundation for guiding future inhibitor optimizations.
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Affiliation(s)
- Diego Rodríguez-Hernández
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
- Department
of Structural and Functional Biology, Synthetic Biology Laboratory,
Institute of Biology, University of Campinas, Campinas, SP 13083-862, Brazil
| | - Michael K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Molecular
Biophysics and Integrated Bioimaging, Berkeley Center for Structural
Biology, Advanced Light Source, Berkeley
National Laboratory, Berkeley, California 94720, United States
| | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Per Sunnerhagen
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease, Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Morten Grøtli
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, S-405 30 Gothenburg, Sweden
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2
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Shome M, MacKenzie TMG, Subbareddy SR, Snyder MP. The Importance, Challenges, and Possible Solutions for Sharing Proteomics Data While Safeguarding Individuals' Privacy. Mol Cell Proteomics 2024; 23:100731. [PMID: 38331191 PMCID: PMC10915627 DOI: 10.1016/j.mcpro.2024.100731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/28/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024] Open
Abstract
Proteomics data sharing has profound benefits at the individual level as well as at the community level. While data sharing has increased over the years, mostly due to journal and funding agency requirements, the reluctance of researchers with regard to data sharing is evident as many shares only the bare minimum dataset required to publish an article. In many cases, proper metadata is missing, essentially making the dataset useless. This behavior can be explained by a lack of incentives, insufficient awareness, or a lack of clarity surrounding ethical issues. Through adequate training at research institutes, researchers can realize the benefits associated with data sharing and can accelerate the norm of data sharing for the field of proteomics, as has been the standard in genomics for decades. In this article, we have put together various repository options available for proteomics data. We have also added pros and cons of those repositories to facilitate researchers in selecting the repository most suitable for their data submission. It is also important to note that a few types of proteomics data have the potential to re-identify an individual in certain scenarios. In such cases, extra caution should be taken to remove any personal identifiers before sharing on public repositories. Data sets that will be useless without personal identifiers need to be shared in a controlled access repository so that only authorized researchers can access the data and personal identifiers are kept safe.
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Affiliation(s)
- Mahasish Shome
- Department of Genetics, Stanford University, Palo Alto, California, USA
| | - Tim M G MacKenzie
- Department of Genetics, Stanford University, Palo Alto, California, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University, Palo Alto, California, USA.
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3
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Fenwick M, Reers AR, Liu Y, Zigweid R, Sankaran B, Shin J, Hulverson MA, Hammerson B, Fernández Álvaro E, Myler PJ, Kaushansky A, Van Voorhis WC, Fan E, Staker BL. Identification of and Structural Insights into Hit Compounds Targeting N-Myristoyltransferase for Cryptosporidium Drug Development. ACS Infect Dis 2023; 9:1821-1833. [PMID: 37722671 PMCID: PMC10580320 DOI: 10.1021/acsinfecdis.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 09/20/2023]
Abstract
Each year, approximately 50,000 children under 5 die as a result of diarrhea caused by Cryptosporidium parvum, a protozoan parasite. There are currently no effective drugs or vaccines available to cure or prevent Cryptosporidium infection, and there are limited tools for identifying and validating targets for drug or vaccine development. We previously reported a high throughput screening (HTS) of a large compound library against Plasmodium N-myristoyltransferase (NMT), a validated drug target in multiple protozoan parasite species. To identify molecules that could be effective against Cryptosporidium, we counter-screened hits from the Plasmodium NMT HTS against Cryptosporidium NMT. We identified two potential hit compounds and validated them against CpNMT to determine if NMT might be an attractive drug target also for Cryptosporidium. We tested the compounds against Cryptosporidium using both cell-based and NMT enzymatic assays. We then determined the crystal structure of CpNMT bound to Myristoyl-Coenzyme A (MyrCoA) and structures of ternary complexes with MyrCoA and the hit compounds to identify the ligand binding modes. The binding site architectures display different conformational states in the presence of the two inhibitors and provide a basis for rational design of selective inhibitors.
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Affiliation(s)
- Michael
K. Fenwick
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Alexandra R. Reers
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Yi Liu
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Rachael Zigweid
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Advanced Light Source, Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Janis Shin
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Bradley Hammerson
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
| | | | - Peter J. Myler
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
- Department
of Pediatrics, University of Washington, Seattle, Washington 98195, United States
| | - Alexis Kaushansky
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
- Department
of Global Health, University of Washington, Seattle, Washington 98195, United States
| | - Wesley C. Van Voorhis
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Emerging and Re-emerging Infectious Diseases, Division of Allergy
and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bart L. Staker
- Seattle
Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
- Center
for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington 98109, United States
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4
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Rodríguez-Hernández D, Vijayan K, Zigweid R, Fenwick MK, Sankaran B, Roobsoong W, Sattabongkot J, Glennon EKK, Myler PJ, Sunnerhagen P, Staker BL, Kaushansky A, Grøtli M. Identification of potent and selective N-myristoyltransferase inhibitors of Plasmodium vivax liver stage hypnozoites and schizonts. Nat Commun 2023; 14:5408. [PMID: 37669940 PMCID: PMC10480161 DOI: 10.1038/s41467-023-41119-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/22/2023] [Indexed: 09/07/2023] Open
Abstract
Drugs targeting multiple stages of the Plasmodium vivax life cycle are needed to reduce the health and economic burdens caused by malaria worldwide. N-myristoyltransferase (NMT) is an essential eukaryotic enzyme and a validated drug target for combating malaria. However, previous PvNMT inhibitors have failed due to their low selectivity over human NMTs. Herein, we apply a structure-guided hybridization approach combining chemical moieties of previously reported NMT inhibitors to develop the next generation of PvNMT inhibitors. A high-resolution crystal structure of PvNMT bound to a representative selective hybrid compound reveals a unique binding site architecture that includes a selective conformation of a key tyrosine residue. The hybridized compounds significantly decrease P. falciparum blood-stage parasite load and consistently exhibit dose-dependent inhibition of P. vivax liver stage schizonts and hypnozoites. Our data demonstrate that hybridized NMT inhibitors can be multistage antimalarials, targeting dormant and developing forms of liver and blood stage.
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Affiliation(s)
- Diego Rodríguez-Hernández
- Department of Chemistry and Molecular Biology, University of Gothenburg; S-405 30, Gothenburg, Sweden
- Department of Chemistry, University of Bergen, Allegaten 41, NO-5007, Bergen, Norway
| | - Kamalakannan Vijayan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Rachael Zigweid
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
| | - Michael K Fenwick
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Advanced Light Source; Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wanlapa Roobsoong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Elizabeth K K Glennon
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
| | - Peter J Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg; S-405 30, Gothenburg, Sweden
| | - Bart L Staker
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA
- Seattle Structural Genomics Center for Infectious Disease, Seattle, WA, 98109, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, 98109, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg; S-405 30, Gothenburg, Sweden.
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5
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DeBouver ND, Bolejack MJ, Esan TE, Krysan DJ, Hagen TJ, Abendroth J. Bacterial structural genomics target enabled by a recently discovered potent fungal acetyl-CoA synthetase inhibitor. Acta Crystallogr F Struct Biol Commun 2023; 79:137-143. [PMID: 37223974 PMCID: PMC10231259 DOI: 10.1107/s2053230x23003801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023] Open
Abstract
The compound ethyl-adenosyl monophosphate ester (ethyl-AMP) has been shown to effectively inhibit acetyl-CoA synthetase (ACS) enzymes and to facilitate the crystallization of fungal ACS enzymes in various contexts. In this study, the addition of ethyl-AMP to a bacterial ACS from Legionella pneumophila resulted in the determination of a co-crystal structure of this previously elusive structural genomics target. The dual functionality of ethyl-AMP in both inhibiting ACS enzymes and promoting crystallization establishes its significance as a valuable resource for advancing structural investigations of this class of proteins.
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Affiliation(s)
- Nicholas D. DeBouver
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98102, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Madison J. Bolejack
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98102, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
| | - Taiwo E. Esan
- Department of Chemistry and Biochemistry, Northern Illinois University, 1426 Lincoln Highway, DeKalb, IL 60115, USA
| | - Damian J. Krysan
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Timothy J. Hagen
- Department of Chemistry and Biochemistry, Northern Illinois University, 1426 Lincoln Highway, DeKalb, IL 60115, USA
| | - Jan Abendroth
- UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98102, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA
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6
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Lenkiewicz J, Bijak V, Poonuganti S, Szczygiel M, Gucwa M, Murzyn K, Minor W. Structural biology and public health response to biomedical threats. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:034701. [PMID: 37350851 PMCID: PMC10284607 DOI: 10.1063/4.0000186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/27/2023] [Indexed: 06/24/2023]
Abstract
Over the course of the pandemic caused by SARS-CoV-2, structural biologists have worked hand in hand with groups developing vaccines and treatments. However, relying solely on in vitro and clinical studies may be insufficient to guide vaccination and treatment developments, and other healthcare policies during virus mutations or peaks in infections and fatalities. Therefore, it is crucial to track statistical data related to the number of infections, deaths, and vaccinations in specific regions and present it in an easy-to-understand way.
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Affiliation(s)
- Joanna Lenkiewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA
| | - Vanessa Bijak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA
| | - Shrisha Poonuganti
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA
| | | | | | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Jagiellonian University, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA
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7
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Roquet-Banères F, Alcaraz M, Hamela C, Abendroth J, Edwards TE, Kremer L. In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum. Antimicrob Agents Chemother 2023; 67:e0160722. [PMID: 36920188 PMCID: PMC10112203 DOI: 10.1128/aac.01607-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
Mycobacterium fortuitum represents one of the most clinically relevant rapid-growing mycobacterial species. Treatments are complex due to antibiotic resistance and to severe side effects of effective drugs, prolonged time of treatment, and co-infection with other pathogens. Herein, we explored the activity of NITD-916, a direct inhibitor of the enoyl-ACP reductase InhA of the type II fatty acid synthase in Mycobacterium tuberculosis. We found that this compound displayed very low MIC values against a panel of M. fortuitum clinical strains and exerted potent antimicrobial activity against M. fortuitum in macrophages. Remarkably, the compound was also highly efficacious in a zebrafish model of infection. Short duration treatments were sufficient to significantly protect the infected larvae from M. fortuitum-induced killing, which correlated with reduced bacterial burdens and abscesses. Biochemical analyses demonstrated an inhibition of de novo synthesis of mycolic acids. Resolving the crystal structure of the InhAMFO in complex with NAD and NITD-916 confirmed that NITD-916 is a direct inhibitor of InhAMFO. Importantly, single nucleotide polymorphism leading to a G96S substitution in InhAMFO conferred high resistance levels to NITD-916, thus resolving its target in M. fortuitum. Overall, these findings indicate that NITD-916 is highly active against M. fortuitum both in vitro and in vivo and should be considered in future preclinical evaluations for the treatment of M. fortuitum pulmonary diseases.
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Affiliation(s)
- Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Claire Hamela
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Thomas E. Edwards
- UCB BioSciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, Montpellier, France
- INSERM, IRIM, Montpellier, France
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8
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Alcaraz M, Roquet-Banères F, Leon-Icaza SA, Abendroth J, Boudehen YM, Cougoule C, Edwards TE, Kremer L. Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA. ACS Infect Dis 2022; 8:2171-2186. [PMID: 36107992 DOI: 10.1021/acsinfecdis.2c00314] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
There is an unmet medical need for effective treatments against Mycobacterium abscessus pulmonary infections, to which cystic fibrosis (CF) patients are particularly vulnerable. Recent studies showed that the antitubercular drug isoniazid is inactive against M. abscessus due to the incapacity of the catalase-peroxidase to convert the pro-drug into a reactive metabolite that inhibits the enoyl-ACP reductase InhA. To validate InhAMAB as a druggable target in M. abscessus, we assayed the activity of NITD-916, a 4-hydroxy-2-pyridone lead candidate initially described as a direct inhibitor of InhA that bypasses KatG bioactivation in Mycobacterium tuberculosis. The compound displayed low MIC values against rough and smooth clinical isolates in vitro and significantly reduced the bacterial burden inside human macrophages. Moreover, treatment with NITD-916 reduced the number and size of intracellular mycobacterial cords, regarded as markers of the severity of the infection. Importantly, NITD-916 significantly lowered the M. abscessus burden in CF-derived lung airway organoids. From a mechanistic perspective, NITD-916 abrogated de novo synthesis of mycolic acids and NITD-916-resistant spontaneous mutants harbored point mutations in InhAMAB at residue 96. That NITD-916 targets InhAMAB directly without activation requirements was confirmed genetically and by resolving the crystal structure of the protein in complex with NADH and NITD-916. These findings collectively indicate that InhAMAB is an attractive target to be exploited for future chemotherapeutic developments against this difficult-to-treat mycobacterium and highlight the potential of NITD-916 derivatives for further evaluation in preclinical settings.
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Affiliation(s)
- Matthéo Alcaraz
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Françoise Roquet-Banères
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Stephen Adonai Leon-Icaza
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Jan Abendroth
- UCB BioSciences, Bainbridge Island, Washington 98109, United States.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Yves-Marie Boudehen
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
| | - Céline Cougoule
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Thomas E Edwards
- UCB BioSciences, Bainbridge Island, Washington 98109, United States.,Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington 98109, United States
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France.,INSERM, IRIM, 34293 Montpellier, France
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9
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Barends TR, Stauch B, Cherezov V, Schlichting I. Serial femtosecond crystallography. NATURE REVIEWS. METHODS PRIMERS 2022; 2:59. [PMID: 36643971 PMCID: PMC9833121 DOI: 10.1038/s43586-022-00141-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
With the advent of X-ray Free Electron Lasers (XFELs), new, high-throughput serial crystallography techniques for macromolecular structure determination have emerged. Serial femtosecond crystallography (SFX) and related methods provide possibilities beyond canonical, single-crystal rotation crystallography by mitigating radiation damage and allowing time-resolved studies with unprecedented temporal resolution. This primer aims to assist structural biology groups with little or no experience in serial crystallography planning and carrying out a successful SFX experiment. It discusses the background of serial crystallography and its possibilities. Microcrystal growth and characterization methods are discussed, alongside techniques for sample delivery and data processing. Moreover, it gives practical tips for preparing an experiment, what to consider and do during a beamtime and how to conduct the final data analysis. Finally, the Primer looks at various applications of SFX, including structure determination of membrane proteins, investigation of radiation damage-prone systems and time-resolved studies.
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Affiliation(s)
- Thomas R.M. Barends
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Benjamin Stauch
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, The Bridge Institute, University of Southern California, Los Angeles, CA, USA
| | - Ilme Schlichting
- Department for Biological Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,
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10
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Hoy MJ, Park E, Lee H, Lim WY, Cole DC, DeBouver ND, Bobay BG, Pierce PG, Fox D, Ciofani M, Juvvadi PR, Steinbach W, Hong J, Heitman J. Structure-Guided Synthesis of FK506 and FK520 Analogs with Increased Selectivity Exhibit In Vivo Therapeutic Efficacy against Cryptococcus. mBio 2022; 13:e0104922. [PMID: 35604094 PMCID: PMC9239059 DOI: 10.1128/mbio.01049-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 01/04/2023] Open
Abstract
Calcineurin is an essential virulence factor that is conserved across human fungal pathogens, including Cryptococcus neoformans, Aspergillus fumigatus, and Candida albicans. Although an excellent target for antifungal drug development, the serine-threonine phosphatase activity of calcineurin is conserved in mammals, and inhibition of this activity results in immunosuppression. FK506 (tacrolimus) is a naturally produced macrocyclic compound that inhibits calcineurin by binding to the immunophilin FKBP12. Previously, our fungal calcineurin-FK506-FKBP12 structure-based approaches identified a nonconserved region of FKBP12 that can be exploited for fungus-specific targeting. These studies led to the design of an FK506 analog, APX879, modified at the C-22 position, which was less immunosuppressive yet maintained antifungal activity. We now report high-resolution protein crystal structures of fungal FKBP12 and a human truncated calcineurin-FKBP12 bound to a natural FK506 analog, FK520 (ascomycin). Based on information from these structures and the success of APX879, we synthesized and screened a novel panel of C-22-modified compounds derived from both FK506 and FK520. One compound, JH-FK-05, demonstrates broad-spectrum antifungal activity in vitro and is nonimmunosuppressive in vivo. In murine models of pulmonary and disseminated C. neoformans infection, JH-FK-05 treatment significantly reduced fungal burden and extended animal survival alone and in combination with fluconazole. Furthermore, molecular dynamic simulations performed with JH-FK-05 binding to fungal and human FKBP12 identified additional residues outside the C-22 and C-21 positions that could be modified to generate novel FK506 analogs with improved antifungal activity. IMPORTANCE Due to rising rates of antifungal drug resistance and a limited armamentarium of antifungal treatments, there is a paramount need for novel antifungal drugs to treat systemic fungal infections. Calcineurin has been established as an essential and conserved virulence factor in several fungi, making it an attractive antifungal target. However, due to the immunosuppressive action of calcineurin inhibitors, they have not been successfully utilized clinically for antifungal treatment in humans. Recent availability of crystal structures of fungal calcineurin-bound inhibitor complexes has enabled the structure-guided design of FK506 analogs and led to a breakthrough in the development of a compound with increased fungal specificity. The development of a calcineurin inhibitor with reduced immunosuppressive activity and maintained therapeutic antifungal activity would add a significant tool to the treatment options for these invasive fungal infections with exceedingly high rates of mortality.
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Affiliation(s)
- Michael J. Hoy
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Eunchong Park
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Hyunji Lee
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Won Young Lim
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - D. Christopher Cole
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas D. DeBouver
- UCB Biosciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | | | - Phillip G. Pierce
- UCB Biosciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - David Fox
- UCB Biosciences, Bainbridge Island, Washington, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Maria Ciofani
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, USA
| | - Praveen R. Juvvadi
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - William Steinbach
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jiyong Hong
- Department of Chemistry, Duke University, Durham, North Carolina, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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11
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Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D. Design of protein-binding proteins from the target structure alone. Nature 2022; 605:551-560. [PMID: 35332283 PMCID: PMC9117152 DOI: 10.1038/s41586-022-04654-9] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/15/2022] [Indexed: 12/03/2022]
Abstract
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1-5. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
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Affiliation(s)
- Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Buwei Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joon Sung Park
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Iva Marković
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Rameshwar U Kadam
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Koen H G Verschueren
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kenneth Verstraete
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Scott Thomas Russell Walsh
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- J.A.M.E.S. Farm, Clarksville, MD, USA
| | - Nathaniel Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Ashish Phal
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Aerin Yang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lora Picton
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren Miller
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Eva-Maria Strauch
- Deptartment of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Nicholas D DeBouver
- UCB Pharma, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Allison Pires
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
- Seattle Children's Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samer Halabiya
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Bradley Hammerson
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Steffen Bernard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Savvas N Savvides
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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12
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Minor W, Cymborowski M, Borek D, Cooper DR, Chruszcz M, Otwinowski Z. Optimal structure determination from sub-optimal diffraction data. Protein Sci 2022; 31:259-268. [PMID: 34783106 PMCID: PMC8740829 DOI: 10.1002/pro.4235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/06/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Herein we present the newest version of the HKL-3000 system that integrates data collection, data reduction, phasing, model building, refinement, and validation. The system significantly accelerates the process of structure determination and has proven its high value for the determination of very high-quality structures. The heuristic for choosing the best approach for every step of structure determination for various quality samples and diffraction data has been optimized. The latest modifications increase the likelihood of a successful structure determination with challenging data. The HKL-3000 is a successor of HKL and HKL-2000 programs. The use of the HKL family of programs has been reported for over 73,000 PDB deposits, that is, almost 50% of macromolecular structures determined with X-ray diffraction.
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Affiliation(s)
- Wladek Minor
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Dominika Borek
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
| | - David R. Cooper
- Department of Molecular Physiology and Biological PhysicsUniversity of VirginiaCharlottesvilleVirginia
| | - Maksymilian Chruszcz
- Department of Chemistry and BiochemistryUniversity of South CarolinaColumbiaSouth Carolina
| | - Zbyszek Otwinowski
- Department of BiophysicsThe University of Texas Southwestern Medical CenterDallasTexas,Department of BiochemistryThe University of Texas Southwestern Medical CenterDallasTexas
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13
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Wilson SL, Way GP, Bittremieux W, Armache JP, Haendel MA, Hoffman MM. Sharing biological data: why, when, and how. FEBS Lett 2021; 595:847-863. [PMID: 33843054 PMCID: PMC10390076 DOI: 10.1002/1873-3468.14067] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Samantha L Wilson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Gregory P Way
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wout Bittremieux
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Computer Science, University of Antwerp, Antwerpen, Belgium
| | - Jean-Paul Armache
- Department of Biochemistry & Molecular Biology, The Huck Institutes of Life Sciences, Pennsylvania State University, University Park, PA, USA
| | | | - Michael M Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, Department of Computer Science, University of Toronto, Toronto, ON, Canada.,Vector Institute, Toronto, ON, Canada
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14
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Czyzewski A, Krawiec F, Brzezinski D, Porebski PJ, Minor W. Detecting anomalies in X-ray diffraction images using convolutional neural networks. EXPERT SYSTEMS WITH APPLICATIONS 2021; 174:114740. [PMID: 34366575 PMCID: PMC8341115 DOI: 10.1016/j.eswa.2021.114740] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Our understanding of life is based upon the interpretation of macromolecular structures and their dynamics. Almost 90% of currently known macromolecular models originated from electron density maps constructed using X-ray diffraction images. Even though diffraction images are critical for structure determination, due to their vast amounts and noisy, non-intuitive nature, their quality is rarely inspected. In this paper, we use recent advances in machine learning to automatically detect seven types of anomalies in X-ray diffraction images. For this purpose, we utilize a novel X-ray beam center detection algorithm, propose three different image representations, and compare the predictive performance of general-purpose classifiers and deep convolutional neural networks (CNNs). In benchmark tests on a set of 6,311 X-ray diffraction images, the proposed CNN achieved between 87% and 99% accuracy depending on the type of anomaly. Experimental results show that the proposed anomaly detection system can be considered suitable for early detection of sub-optimal data collection conditions and malfunctions at X-ray experimental stations.
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Affiliation(s)
- Adam Czyzewski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Faustyna Krawiec
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
| | - Dariusz Brzezinski
- Institute of Computing Science, Poznan University of
Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Center for Biocrystallographic Research, Institute of
Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-714, Poland
- Center for Artificial Intelligence and Machine Learning,
Poznan University of Technology, ul. Piotrowo 2, 60-965 Poznan, Poland
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Przemyslaw Jerzy Porebski
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics,
University of Virginia, Charlottesville, VA 22901, USA
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15
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Structural genomics and the Protein Data Bank. J Biol Chem 2021; 296:100747. [PMID: 33957120 PMCID: PMC8166929 DOI: 10.1016/j.jbc.2021.100747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
The field of Structural Genomics arose over the last 3 decades to address a large and rapidly growing divergence between microbial genomic, functional, and structural data. Several international programs took advantage of the vast genomic sequence information and evaluated the feasibility of structure determination for expanded and newly discovered protein families. As a consequence, structural genomics has developed structure-determination pipelines and applied them to a wide range of novel, uncharacterized proteins, often from “microbial dark matter,” and later to proteins from human pathogens. Advances were especially needed in protein production and rapid de novo structure solution. The experimental three-dimensional models were promptly made public, facilitating structure determination of other members of the family and helping to understand their molecular and biochemical functions. Improvements in experimental methods and databases resulted in fast progress in molecular and structural biology. The Protein Data Bank structure repository played a central role in the coordination of structural genomics efforts and the structural biology community as a whole. It facilitated development of standards and validation tools essential for maintaining high quality of deposited structural data.
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16
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Grabowski M, Macnar JM, Cymborowski M, Cooper DR, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Dauter Z, Rupp B, Wlodawer A, Jaskolski M, Minor W. Rapid response to emerging biomedical challenges and threats. IUCRJ 2021; 8:395-407. [PMID: 33953926 PMCID: PMC8086160 DOI: 10.1107/s2052252521003018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/22/2021] [Indexed: 05/13/2023]
Abstract
As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Joanna M. Macnar
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA
| | - Bernhard Rupp
- k.-k Hofkristallamt, San Diego, California, USA
- Institute of Genetic Epidemiology, Medical University Innsbruck, Innsbruck, Austria
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, Maryland, USA
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
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17
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Grabowski M, Cooper DR, Brzezinski D, Macnar JM, Shabalin IG, Cymborowski M, Otwinowski Z, Minor W. Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective. NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH. SECTION B, BEAM INTERACTIONS WITH MATERIALS AND ATOMS 2021; 489:30-40. [PMID: 33603257 PMCID: PMC7886262 DOI: 10.1016/j.nimb.2020.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intense X-rays available at powerful synchrotron beamlines provide macromolecular crystallographers with an incomparable tool for investigating biological phenomena on an atomic scale. The resulting insights into the mechanism's underlying biological processes have played an essential role and shaped biomedical sciences during the last 30 years, considered the "golden age" of structural biology. In this review, we analyze selected aspects of the impact of synchrotron radiation on structural biology. Synchrotron beamlines have been used to determine over 70% of all macromolecular structures deposited into the Protein Data Bank (PDB). These structures were deposited by over 13,000 different research groups. Interestingly, despite the impressive advances in synchrotron technologies, the median resolution of macromolecular structures determined using synchrotrons has remained constant throughout the last 30 years, at about 2 Å. Similarly, the median times from the data collection to the deposition and release have not changed significantly. We describe challenges to reproducibility related to recording all relevant data and metadata during the synchrotron experiments, including diffraction images. Finally, we discuss some of the recent opinions suggesting a diminishing importance of X-ray crystallography due to impressive advances in Cryo-EM and theoretical modeling. We believe that synchrotrons of the future will increasingly evolve towards a life science center model, where X-ray crystallography, Cryo-EM, and other experimental and computational resources and knowledge are encompassed within a versatile research facility. The recent response of crystallographers to the COVID-19 pandemic suggests that X-ray crystallography conducted at synchrotron beamlines will continue to play an essential role in structural biology and drug discovery for years to come.
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Affiliation(s)
- Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA22903, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA22903, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA22903, USA
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Joanna M. Macnar
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA22903, USA
| | - Marcin Cymborowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA22903, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA22903, USA
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18
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Shabalin IG, Czub MP, Majorek KA, Brzezinski D, Grabowski M, Cooper DR, Panasiuk M, Chruszcz M, Minor W. Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy. IUCRJ 2020; 7:S2052252520012944. [PMID: 33063792 PMCID: PMC7553145 DOI: 10.1107/s2052252520012944] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/22/2020] [Indexed: 05/06/2023]
Abstract
Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Here, the first structure of serum albumin in complex with dexamethasone is reported. Dexamethasone binds to drug site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with an analysis of publicly available clinical data from Wuhan and suggests that an adjustment of the dexamethasone regimen should be further investigated as a strategy for patients affected by two major COVID-19 risk factors: low albumin levels and diabetes.
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Affiliation(s)
- Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz P. Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz Panasiuk
- Department of Clinical Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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19
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Mrugała B, Miłaczewska A, Porebski PJ, Niedzialkowska E, Guzik M, Minor W, Borowski T. A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates. FEBS J 2020; 288:1366-1386. [PMID: 32592631 DOI: 10.1111/febs.15462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/09/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Kanamycin A is an aminoglycoside antibiotic isolated from Streptomyces kanamyceticus and used against a wide spectrum of bacteria, including Mycobacterium tuberculosis. Biosynthesis of kanamycin involves an oxidative deamination step catalyzed by kanamycin B dioxygenase (KanJ), thereby the C2' position of kanamycin B is transformed into a keto group upon release of ammonia. Here, we present for the first time, structural models of KanJ with several ligands, which along with the results of ITC binding assays and HPLC activity tests explain substrate specificity of the enzyme. The large size of the binding pocket suggests that KanJ can accept a broad range of substrates, which was confirmed by activity tests. Specificity of the enzyme with respect to its substrate is determined by the hydrogen bond interactions between the methylamino group of the antibiotic and highly conserved Asp134 and Cys150 as well as between hydroxyl groups of the substrate and Asn120 and Gln80. Upon antibiotic binding, the C terminus loop is significantly rearranged and Gln80 and Asn120, which are directly involved in substrate recognition, change their conformations. Based on reaction energy profiles obtained by density functional theory (DFT) simulations, we propose a mechanism of ketone formation involving the reactive FeIV = O and proceeding either via OH rebound, which yields a hemiaminal intermediate or by abstraction of two hydrogen atoms, which leads to an imine species. At acidic pH, the latter involves a lower barrier than the OH rebound, whereas at basic pH, the barrier leading to an imine vanishes completely. DATABASES: Structural data are available in PDB database under the accession numbers: 6S0R, 6S0T, 6S0U, 6S0W, 6S0V, 6S0S. Diffraction images are available at the Integrated Resource for Reproducibility in Macromolecular Crystallography at http://proteindiffraction.org under DOIs: 10.18430/m36s0t, 10.18430/m36s0u, 10.18430/m36s0r, 10.18430/m36s0s, 10.18430/m36s0v, 10.18430/m36s0w. A data set collection of computational results is available in the Mendeley Data database under DOI: 10.17632/sbyzssjmp3.1 and in the ioChem-BD database under DOI: 10.19061/iochem-bd-4-18.
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Affiliation(s)
- Beata Mrugała
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Przemyslaw Jerzy Porebski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Ewa Niedzialkowska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Maciej Guzik
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
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20
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Shabalin IG, Czub MP, Majorek KA, Brzezinski D, Grabowski M, Cooper DR, Panasiuk M, Chruszcz M, Minor W. Molecular determinants of vascular transport of dexamethasone in COVID-19 therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.07.21.212704. [PMID: 32743572 PMCID: PMC7386489 DOI: 10.1101/2020.07.21.212704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Dexamethasone, a widely used corticosteroid, has recently been reported as the first drug to increase the survival chances of patients with severe COVID-19. Therapeutic agents, including dexamethasone, are mostly transported through the body by binding to serum albumin. Herein, we report the first structure of serum albumin in complex with dexamethasone. We show that it binds to Drug Site 7, which is also the binding site for commonly used nonsteroidal anti-inflammatory drugs and testosterone, suggesting potentially problematic binding competition. This study bridges structural findings with our analysis of publicly available clinical data from Wuhan and suggests that an adjustment of dexamethasone regimen should be considered for patients affected by two major COVID-19 risk-factors: low albumin levels and diabetes.
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Affiliation(s)
- Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz P. Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Karolina A. Majorek
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Dariusz Brzezinski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
| | - Mateusz Panasiuk
- Medical University of Bialystok, Department of Clinical Medicine, 15-089 Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, 29208, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA
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21
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Czub MP, Handing KB, Venkataramany BS, Cooper DR, Shabalin IG, Minor W. Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma. J Med Chem 2020; 63:6847-6862. [PMID: 32469516 DOI: 10.1021/acs.jmedchem.0c00225] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Every day, hundreds of millions of people worldwide take nonsteroidal anti-inflammatory drugs (NSAIDs), often in conjunction with multiple other medications. In the bloodstream, NSAIDs are mostly bound to serum albumin (SA). We report the crystal structures of equine serum albumin complexed with four NSAIDs (ibuprofen, ketoprofen, etodolac, and nabumetone) and the active metabolite of nabumetone (6-methoxy-2-naphthylacetic acid, 6-MNA). These compounds bind to seven drug-binding sites on SA. These sites are generally well-conserved between equine and human SAs, but ibuprofen binds to both SAs in two drug-binding sites, only one of which is common. We also compare the binding of ketoprofen by equine SA to binding of it by bovine and leporine SAs. Our comparative analysis of known SA complexes with FDA-approved drugs clearly shows that multiple medications compete for the same binding sites, indicating possibilities for undesirable physiological effects caused by drug-drug displacement or competition with common metabolites. We discuss the consequences of NSAID binding to SA in a broader scientific and medical context, particularly regarding achieving desired therapeutic effects based on an individual's drug regimen.
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Affiliation(s)
- Mateusz P Czub
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Barat S Venkataramany
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - David R Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.,Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
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22
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Sauter NK, Rose JP, Bhat TN. Transactions from the 69th Annual Meeting of the American Crystallographic Association: Data best practices-current state and future needs. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:021301. [PMID: 32232073 PMCID: PMC7093206 DOI: 10.1063/4.0000011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 06/10/2023]
Affiliation(s)
- Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - John P. Rose
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Talapady N. Bhat
- Cell Systems Science Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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