1
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Guijarro MV, Kellish PC, Dib PE, Paciaroni NG, Nawab A, Andring J, Kulemina L, Borrero NV, Modenutti C, Feely M, Nasri E, Seifert RP, Luo X, Bennett RL, Shabashvili D, Licht JD, McKenna R, Roitberg A, Huigens RW, Kaye FJ, Zajac-Kaye M. First-in-class multifunctional TYMS nonclassical antifolate inhibitor with potent in vivo activity that prolongs survival. JCI Insight 2023; 8:e158798. [PMID: 37097751 PMCID: PMC10386886 DOI: 10.1172/jci.insight.158798] [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] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/18/2023] [Indexed: 04/26/2023] Open
Abstract
Although thymidylate synthase (TYMS) inhibitors have served as components of chemotherapy regimens, the currently available inhibitors induce TYMS overexpression or alter folate transport/metabolism feedback pathways that tumor cells exploit for drug resistance, limiting overall benefit. Here we report a small molecule TYMS inhibitor that i) exhibited enhanced antitumor activity as compared with current fluoropyrimidines and antifolates without inducing TYMS overexpression, ii) is structurally distinct from classical antifolates, iii) extended survival in both pancreatic xenograft tumor models and an hTS/Ink4a/Arf null genetically engineered mouse tumor model, and iv) is well tolerated with equal efficacy using either intraperitoneal or oral administration. Mechanistically, we verify the compound is a multifunctional nonclassical antifolate, and using a series of analogs, we identify structural features allowing direct TYMS inhibition while maintaining the ability to inhibit dihydrofolate reductase. Collectively, this work identifies nonclassical antifolate inhibitors that optimize inhibition of thymidylate biosynthesis with a favorable safety profile, highlighting the potential for enhanced cancer therapy.
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Affiliation(s)
| | | | | | | | | | - Jacob Andring
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | | | | | - Carlos Modenutti
- Department of Biological Chemistry, Faculty of Exact and Natural Sciences, University of Buenos Aires, and
- Institute of Biological Chemistry of the Faculty of Exact and Natural Sciences (IQUIBICEN) CONICET, University City, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Michael Feely
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Elham Nasri
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Robert P. Seifert
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | | | - Richard L. Bennett
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, Florida, USA
| | | | - Jonathan D. Licht
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, Florida, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | - Adrian Roitberg
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | | | - Frederic J. Kaye
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, Florida, USA
| | - Maria Zajac-Kaye
- Department of Anatomy and Cell Biology
- Department of Medicine, University of Florida Health Cancer Center, Gainesville, Florida, USA
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2
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Zhang H, Modenutti C, Nekkanti YPK, Denis M, Bermejo IA, Lefèbre J, Che K, Kim D, Kagelmacher M, Kurzbach D, Nazaré M, Rademacher C. Identification of the Allosteric Binding Site for Thiazolopyrimidine on the C-Type Lectin Langerin. ACS Chem Biol 2022; 17:2728-2733. [PMID: 36153965 PMCID: PMC9594047 DOI: 10.1021/acschembio.2c00626] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Langerin is a mammalian C-type lectin expressed on Langerhans cells in the skin. As an innate immune cell receptor, Langerin is involved in coordinating innate and adaptive immune responses against various incoming threats. We have previously reported a series of thiazolopyrimidines as murine Langerin ligands. Prompted by the observation that its human homologue exhibits different binding specificities for these small molecules, we report here our investigations to define their exact binding site. By using structural comparison and molecular dynamics simulations, we showed that the nonconserved short loops have a high degree of conformational flexibility between the human and murine homologues. Sequence analysis and mutational studies indicated that a pair of residues are essential for the recognition of the thiazolopyrimidines. Taking solvent paramagnetic relaxation enhancement NMR studies together with a series of peptides occupying the same site, we could define the cleft between the short and long loops as the allosteric binding site for these aromatic heterocycles.
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Affiliation(s)
- Hengxi Zhang
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Biology, Chemistry, and Pharmacy, Freie
Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo), University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - Carlos Modenutti
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Departamento
de Química Biológica, Facultad
de Ciencias Exactas y Naturales, C1428EHA Buenos Aires, Argentina,Instituto
de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, C1428EHA Buenos
Aires, Argentina
| | - Yelha Phani Kumar Nekkanti
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany,Berlin
Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Maxime Denis
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Iris A. Bermejo
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jonathan Lefèbre
- Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,Vienna
Doctoral School of Pharmaceutical, Nutritional and Sport Sciences
(PhaNuSpo), University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - Kateryna Che
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria,Doctoral
School in Chemistry (DoSChem), University
of Vienna, Währingerstr. 42, 1090 Vienna, Austria
| | - Dongyoon Kim
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria
| | - Marten Kagelmacher
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Biology, Chemistry, and Pharmacy, Freie
Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Marc Nazaré
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Strasse 10, 13125 Berlin, Germany,Berlin
Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany
| | - Christoph Rademacher
- Biomolecular
Systems, Max Planck Institute of Colloids
and Interfaces, Am Mühlenberg
1 14424 Potsdam, Germany,Department
of Biology, Chemistry, and Pharmacy, Freie
Universität Berlin, Takustrasse 3, 14195 Berlin, Germany,Department
of Pharmaceutical Sciences, University of
Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria,Department
of Microbiology and Immunobiology, Max F. Perutz Laboratories, University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria,
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3
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Guijarro MV, Kellish PC, Dib PE, Paciaroni NG, Nawab A, Andring J, Kulemina L, Borrero NV, Modenutti C, Bennett RL, Shabashvili D, Licht JD, McKenna R, Roitberg A, Huigens RW, Kaye FJ, Zajac-Kaye M. Abstract 4055: First in class multifunctional non classical antifolates inhibits thymidylate synthase and extends survival in pancreatic cancer model. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-4055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Thymidylate synthase (TS) inhibitors are an integral component of chemotherapy regimens for difficult to treat cancer subtypes. Despite initial therapeutic benefit, current inhibitors induce TS overexpression or alter folate transport metabolism feedback pathways that tumor cells exploit for drug resistance. Here we report a small molecule TS inhibitor that exhibits i) enhanced antitumor activity as compared to current fluoropyrimidines and antifolates without inducing TS overexpression, ii) is structurally distinct from classical antifolates, iii) extends survival in a pancreatic tumor mouse model, iv) and is well tolerated with equal efficacy using either intraperitoneal or oral administration. Mechanistically, we confirm the compound is a multifunctional non classical antifolate and through a series of analogues identify structural features allowing direct TS inhibition while also maintaining the ability to inhibit dihydrofolate reductase (DHFR). Collectively, this work identifies new non classical antifolate inhibitors that optimize inhibition of thymidylate biosynthesis with a favorable safety profile highlighting potential for enhanced cancer therapy.
Citation Format: Maria V. Guijarro, Patrick C. Kellish, Peter E. Dib, Nicholas G. Paciaroni, Akbar Nawab, Jacob Andring, Lidia Kulemina, Nicholas V. Borrero, Carlos Modenutti, Richard L. Bennett, Daniil Shabashvili, Jonathan D. Licht, Robert McKenna, Adrian Roitberg, Robert W. Huigens, Frederic J. Kaye, Maria Zajac-Kaye. First in class multifunctional non classical antifolates inhibits thymidylate synthase and extends survival in pancreatic cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 4055.
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4
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Wawrzinek R, Wamhoff EC, Lefebre J, Rentzsch M, Bachem G, Domeniconi G, Schulze J, Fuchsberger FF, Zhang H, Modenutti C, Schnirch L, Marti MA, Schwardt O, Bräutigam M, Guberman M, Hauck D, Seeberger PH, Seitz O, Titz A, Ernst B, Rademacher C. A Remote Secondary Binding Pocket Promotes Heteromultivalent Targeting of DC-SIGN. J Am Chem Soc 2021; 143:18977-18988. [PMID: 34748320 PMCID: PMC8603350 DOI: 10.1021/jacs.1c07235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Indexed: 12/19/2022]
Abstract
![]()
Dendritic cells (DC)
are antigen-presenting cells coordinating
the interplay of the innate and the adaptive immune response. The
endocytic C-type lectin receptors DC-SIGN and Langerin display expression
profiles restricted to distinct DC subtypes and have emerged as prime
targets for next-generation immunotherapies and anti-infectives. Using
heteromultivalent liposomes copresenting mannosides bearing aromatic
aglycones with natural glycan ligands, we serendipitously discovered
striking cooperativity effects for DC-SIGN+ but not for
Langerin+ cell lines. Mechanistic investigations combining
NMR spectroscopy with molecular docking and molecular dynamics simulations
led to the identification of a secondary binding pocket for the glycomimetics.
This pocket, located remotely of DC-SIGN’s carbohydrate bindings
site, can be leveraged by heteromultivalent avidity enhancement. We
further present preliminary evidence that the aglycone allosterically
activates glycan recognition and thereby contributes to DC-SIGN-specific
cell targeting. Our findings have important implications for both
translational and basic glycoscience, showcasing heteromultivalent
targeting of DCs to improve specificity and supporting potential allosteric
regulation of DC-SIGN and CLRs in general.
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Affiliation(s)
- Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Eike-Christian Wamhoff
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Jonathan Lefebre
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Mareike Rentzsch
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Gunnar Bachem
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Gary Domeniconi
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Jessica Schulze
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Felix F Fuchsberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Hengxi Zhang
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Carlos Modenutti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Lennart Schnirch
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Marcelo A Marti
- Departamento de Química Biológica e IQUIBICEN-CONICET, Universidad de Buenos Aires, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Oliver Schwardt
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Maria Bräutigam
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Mónica Guberman
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Dirk Hauck
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.,German Centre for Infection Research, Campus Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University of Berlin, 12489 Berlin, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research, 66123 Saarbrücken, Germany.,German Centre for Infection Research, Campus Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Beat Ernst
- Department of Pharmaceutical Sciences, University of Basel, 4056 Basel, Switzerland
| | - Christoph Rademacher
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.,Department of Chemistry and Biochemistry, Freie University of Berlin, 14195 Berlin, Germany.,University of Vienna, Department of Pharmaceutical Sciences, Althanstrasse 14, 1090 Vienna, Austria.,University of Vienna, Department of Microbiology, Immunology and Genetics, Max F. Perutz Laboratories, Biocenter 5, 1030 Vienna, Austria
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5
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Serral F, Castello FA, Sosa EJ, Pardo AM, Palumbo MC, Modenutti C, Palomino MM, Lazarowski A, Auzmendi J, Ramos PIP, Nicolás MF, Turjanski AG, Martí MA, Fernández Do Porto D. From Genome to Drugs: New Approaches in Antimicrobial Discovery. Front Pharmacol 2021; 12:647060. [PMID: 34177572 PMCID: PMC8219968 DOI: 10.3389/fphar.2021.647060] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/17/2021] [Indexed: 01/31/2023] Open
Abstract
Decades of successful use of antibiotics is currently challenged by the emergence of increasingly resistant bacterial strains. Novel drugs are urgently required but, in a scenario where private investment in the development of new antimicrobials is declining, efforts to combat drug-resistant infections become a worldwide public health problem. Reasons behind unsuccessful new antimicrobial development projects range from inadequate selection of the molecular targets to a lack of innovation. In this context, increasingly available omics data for multiple pathogens has created new drug discovery and development opportunities to fight infectious diseases. Identification of an appropriate molecular target is currently accepted as a critical step of the drug discovery process. Here, we review how diverse layers of multi-omics data in conjunction with structural/functional analysis and systems biology can be used to prioritize the best candidate proteins. Once the target is selected, virtual screening can be used as a robust methodology to explore molecular scaffolds that could act as inhibitors, guiding the development of new drug lead compounds. This review focuses on how the advent of omics and the development and application of bioinformatics strategies conduct a "big-data era" that improves target selection and lead compound identification in a cost-effective and shortened timeline.
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Affiliation(s)
- Federico Serral
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Florencia A Castello
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ezequiel J Sosa
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Agustín M Pardo
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Miranda Clara Palumbo
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Carlos Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - María Mercedes Palomino
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Alberto Lazarowski
- Departamento de Bioquímica Clínica, Instituto de Investigaciones en Fisiopatología y Bioquímica Clínica (INFIBIOC), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jerónimo Auzmendi
- Departamento de Bioquímica Clínica, Instituto de Investigaciones en Fisiopatología y Bioquímica Clínica (INFIBIOC), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Ivan P Ramos
- Centro de Integração de Dados e Conhecimentos para Saúde (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador, Brazil
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Buenos Aires, Argentina
| | - Darío Fernández Do Porto
- Instituto de Cálculo, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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6
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Cevallos C, Culasso ACA, Modenutti C, Gun A, Sued O, Avila MM, Flichman D, Delpino MV, Quarleri J. Longitudinal characterization of HIV-1 pol-gene in treatment-naïve men-who-have-sex-with-men from acute to chronic infection stages. Heliyon 2020; 6:e05679. [PMID: 33319116 PMCID: PMC7723807 DOI: 10.1016/j.heliyon.2020.e05679] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/09/2020] [Accepted: 12/03/2020] [Indexed: 01/18/2023] Open
Abstract
HIV-1 is characterized by its ability to mutate and recombine even at polymerase (pol) gene. However, pol-gene diversity is limited due to functional constraints. The aim of this study was to characterize longitudinally, by next-generation sequencing (NGS), HIV-1 variants based on pol-gene sequences, at intra- and inter-host level, from acute/early to chronic stages of infection, in the absence of antiretroviral therapy. Ten men who have sex with men (MSM) were recruited during primary infection and yearly followed for five years. Even after a maximum of a five-year follow-up period, the phylogenetic analysis of HIV-1 pol-gene sequences showed a host-defined structured pattern, with a predominance of purifying selection forces during the follow-up. MSM had been acutely infected by different HIV-1 variants mainly ascribed to pure subtype B, or BF recombinant variants and showed different genetic mosaicism patterns that last until the chronic stage, representing a major challenge for prevention strategies.
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Affiliation(s)
- Cintia Cevallos
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Andrés C A Culasso
- Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carlos Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Buenos Aires, Argentina
| | - Ana Gun
- Fundación Huésped, Pasaje Angel Peluffo 3932, C1202ABB, Ciudad Autónoma de Buenos Aires, Argentina
| | - Omar Sued
- Fundación Huésped, Pasaje Angel Peluffo 3932, C1202ABB, Ciudad Autónoma de Buenos Aires, Argentina
| | - María M Avila
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Flichman
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Victoria Delpino
- Instituto de Inmunología, Genética y Metabolismo (INIGEM), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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7
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González-Lebrero RM, Defelipe L, Modenutti C, Roitberg AE, Batastini NA, Noguera ME, Santos J, Roman EA. Folding and Dynamics Are Strongly pH-Dependent in a Psychrophile Frataxin. J Phys Chem B 2019; 123:7676-7686. [PMID: 31407901 DOI: 10.1021/acs.jpcb.9b05960] [Citation(s) in RCA: 1] [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: 11/29/2022]
Abstract
Protein dynamics, folding, and thermodynamics represent a central aspect of biophysical chemistry. pH, temperature, and denaturant perturbations inform our understanding of diverse contributors to stability and rates. In this work, we performed a thermodynamic analysis using a combined experimental and computational approach to gain insights into the role of electrostatics in the folding reaction of a psychrophile frataxin variant from Psychromonas ingrahamii. This folding reaction is strongly modulated by pH with a single, narrow, and well-defined transition state with ∼80% compactness, ∼70% electrostatic interactions, and ∼60% hydration shell compared to the native state (αD = 0.82, αH = 0.67, and αΔCp = 0.59). Our results are best explained by a two-proton/two-state model with very different pKa values of the native and denatured states (∼5.5 and ∼8.0, respectively). As a consequence, the stability strongly increases from pH 8.0 to 6.0 (|ΔΔG°| = 5.2 kcal mol-1), mainly because of a decrease in the TΔS°. Variation of ΔH° and ΔS° at pH below 7.0 is dominated by a change in ΔHf⧧ and ΔSf⧧, while at pH above 7.0, it is governed by ΔHu⧧ and ΔSu⧧. Molecular dynamics simulations showed that these pH modulations could be explained by the fluctuations of two regions, rich in electrostatic contacts, whose dynamics are pH-dependent and motions are strongly correlated. Results presented herein contribute to the understanding of the stability and dynamics of this frataxin variant, pointing to an intrinsic feature of the family topology to support different folding mechanisms.
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Affiliation(s)
- Rodolfo M González-Lebrero
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica , Universidad de Buenos Aires , Buenos Aires C1113AAD , Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas , Instituto de Química y Fisicoquímica Biológicas , Buenos Aires C1113AAD , Argentina
| | | | | | - Adrian E Roitberg
- Department of Chemistry , University of Florida , Gainesville , Florida 32611 , United States
| | - Nicolas A Batastini
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica , Universidad de Buenos Aires , Buenos Aires C1113AAD , Argentina
| | - Martín E Noguera
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica , Universidad de Buenos Aires , Buenos Aires C1113AAD , Argentina
| | | | - Ernesto A Roman
- Consejo Nacional de Investigaciones Científicas y Técnicas , Instituto de Química y Fisicoquímica Biológicas , Buenos Aires C1113AAD , Argentina
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Radusky L, Modenutti C, Delgado J, Bustamante JP, Vishnopolska S, Kiel C, Serrano L, Marti M, Turjanski A. VarQ: A Tool for the Structural and Functional Analysis of Human Protein Variants. Front Genet 2018; 9:620. [PMID: 30574164 PMCID: PMC6291447 DOI: 10.3389/fgene.2018.00620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/23/2018] [Indexed: 12/17/2022] Open
Abstract
Understanding the functional effect of Single Amino acid Substitutions (SAS), derived from the occurrence of single nucleotide variants (SNVs), and their relation to disease development is a major issue in clinical genomics. Despite the existence of several bioinformatic algorithms and servers that predict if a SAS is pathogenic or not, they give little or no information at all on the reasons for pathogenicity prediction and on the actual predicted effect of the SAS on the protein function. Moreover, few actual methods take into account structural information when available for automated analysis. Moreover, many of these algorithms are able to predict an effect that no necessarily translates directly into pathogenicity. VarQ is a bioinformatic pipeline that incorporates structural information for the detailed analysis and prediction of SAS effect on protein function. It is an online tool which uses UniProt id and automatically analyzes known and user provided SAS for their effect on protein activity, folding, aggregation and protein interactions, among others. We show that structural information, when available, can improve the SAS pathogenicity diagnosis and more important explain its causes. We show that VarQ is able to correctly reproduce previous analysis of RASopathies related mutations, saving extensive and time consuming manual curation. VarQ assessment was performed over a set of previously manually curated RASopathies (diseases that affects the RAS/MAPK signaling pathway) related variants, showing its ability to correctly predict the phenotypic outcome and its underlying cause. This resource is available online at http://varq.qb.fcen.uba.ar/. Supporting Information & Tutorials may be found in the webpage of the tool.
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Affiliation(s)
- Leandro Radusky
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
| | - Carlos Modenutti
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
| | - Javier Delgado
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Juan P. Bustamante
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Facultad de Ingeniería de la Universidad Nacional de Entre Ríos, Oro Verde, Argentina
| | - Sebastian Vishnopolska
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
| | - Christina Kiel
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Marcelo Marti
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
| | - Adrián Turjanski
- Departamento de Química Biológica Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
- Instituto de Química Biológica Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Pabellón II de Ciudad Universitaria, Buenos Aires, Argentina
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Defelipe L, Radusky L, Modenutti C, Sosa E, Porto DFD, Marti M, Turjanski A. Open source Bioinformatics tools for the development of new TB drugs. Int J Infect Dis 2018. [DOI: 10.1016/j.ijid.2018.04.4188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Radusky L, Ruiz-Carmona S, Modenutti C, Barril X, Turjanski AG, Martí MA. LigQ: A Webserver to Select and Prepare Ligands for Virtual Screening. J Chem Inf Model 2017; 57:1741-1746. [PMID: 28700230 DOI: 10.1021/acs.jcim.7b00241] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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
Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousands of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The number of tested compounds is directly proportional to the cost, and thus, the best possible set of ligands is the one with the highest number of true binders, for the smallest possible compound set size. Therefore, methods that are able to trim down large universal data sets enriching them in potential binders are highly appreciated. Here we present LigQ, a free webserver that is able to (i) determine best structure and ligand binding pocket for a desired protein, (ii) find known binders, as well as potential ligands known to bind to similar protein domains, (iii) most importantly, select a small set of commercial compounds enriched in potential binders, and (iv) prepare them for virtual screening. LigQ was tested with several proteins, showing an impressive capacity to retrieve true ligands from large data sets, achieving enrichment factors of over 10%. LigQ is available at http://ligq.qb.fcen.uba.ar/ .
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Affiliation(s)
- Leandro Radusky
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
| | - Sergio Ruiz-Carmona
- Department of Physical Chemistry, Faculty of Pharmacy and Institute of Biomedicine (IBUB), University of Barcelona , Avgda. Diagonal 643, Barcelona 08028, Spain
| | - Carlos Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
| | - Xavier Barril
- Department of Physical Chemistry, Faculty of Pharmacy and Institute of Biomedicine (IBUB), University of Barcelona , Avgda. Diagonal 643, Barcelona 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys 23, Barcelona 08010, Spain
| | - Adrian G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
| | - Marcelo A Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires , 1053 Buenos Aires, Argentina.,Insituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN-CONICET) , Pabellón II, Buenos Aires C1428EHA, Argentina
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Modenutti C, Gauto D, Radusky L, Blanco J, Turjanski A, Hajos S, Marti M. Using crystallographic water properties for the analysis and prediction of lectin-carbohydrate complex structures. Glycobiology 2014; 25:181-96. [DOI: 10.1093/glycob/cwu102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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