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Škulj S, Kožić M, Barišić A, Vega A, Biarnés X, Piantanida I, Barisic I, Bertoša B. Comparison of two peroxidases with high potential for biotechnology applications - HRP vs. APEX2. Comput Struct Biotechnol J 2024; 23:742-751. [PMID: 38298178 PMCID: PMC10828542 DOI: 10.1016/j.csbj.2024.01.001] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/01/2024] [Accepted: 01/01/2024] [Indexed: 02/02/2024] Open
Abstract
Peroxidases are essential elements in many biotechnological applications. An especially interesting concept involves split enzymes, where the enzyme is separated into two smaller and inactive proteins that can dimerize into a fully active enzyme. Such split forms were developed for the horseradish peroxidase (HRP) and ascorbate peroxidase (APX) already. Both peroxidases have a high potential for biotechnology applications. In the present study, we performed biophysical comparisons of these two peroxidases and their split analogues. The active site availability is similar for all four structures. The split enzymes are comparable in stability with their native analogues, meaning that they can be used for further biotechnology applications. Also, the tertiary structures of the two peroxidases are similar. However, differences that might help in choosing one system over another for biotechnology applications were noticed. The main difference between the two systems is glycosylation which is not present in the case of APX/sAPEX2, while it has a high impact on the HRP/sHRP stability. Further differences are calcium ions and cysteine bridges that are present only in the case of HRP/sHRP. Finally, computational results identified sAPEX2 as the systems with the smallest structural variations during molecular dynamics simulations showing its dominant stability comparing to other simulated proteins. Taken all together, the sAPEX2 system has a high potential for biotechnological applications due to the lack of glycans and cysteines, as well as due to high stability.
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Affiliation(s)
- Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
- Institute of Physiology, Pathophysiology and Biophysics, Department of Biomedical Sciences, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
| | - Aitor Vega
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10 000 Zagreb, Croatia
| | - Ivan Barisic
- Molecular Diagnostics, Center for Health and Bioresources, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, Vienna 1210, Austria
- Eko Refugium, Crno Vrelo 2, Slunj 47240, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb HR-10000, Croatia
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2
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Jednačak T, Mikulandra I, Smokrović K, Hloušek-Kasun A, Kapustić M, Delaš K, Piantanida I, Jurković M, Bertoša B, Zangger K, Novak P. Antimicrobial macrozones interact with biological macromolecules via two-site binding mode of action: Fluorimetric, NMR and docking studies. Bioorg Chem 2024; 147:107338. [PMID: 38583253 DOI: 10.1016/j.bioorg.2024.107338] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/09/2024]
Abstract
Macrozones are novel conjugates of azithromycin and thiosemicarbazones, which exhibit very good in vitro antibacterial activities against susceptible and some resistant bacterial strains thus showing a potential for further development. A combination of spectrometric (fluorimetry, STD and WaterLOGSY NMR) and molecular docking studies provided insights into atomic details of interactions between selected macrozones and biological receptors such as E. coli ribosome and bovine serum albumin. Fluorimetric measurements revealed binding constants in the micro-molar range while NMR experiments provided data on binding epitopes. It has been demonstrated that both STD and WaterLOGSY gave comparable and consistent results unveiling atoms in intimate contacts with biological receptors. Docking studies pointed towards main interactions between macrozones and E. coli ribosome which included specific π - π stacking and hydrogen bonding interactions with thiosemicarbazone part extending down the ribosome exit tunnel. The results of the docking experiments were in fine correlation with those obtained by NMR and fluorimetry. Our investigation pointed towards a two-site binding mechanism of interactions between macrozones and E. coli ribosome which is the most probable reason for their activity against azithromycin-resistant strains. Much better activity of macrozone-nickel coordinated compound against E. coli ribosome compared to other macrozones has been attributed to the higher polarity which enabled better bacterial membrane penetration and binding of the two thiosemicarbazone units thus additionally contributing to the overall binding energy. The knowledge gained in this study should play an important role in anti-infective macrolide design in the future.
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Affiliation(s)
- Tomislav Jednačak
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Ivana Mikulandra
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Kristina Smokrović
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Andrea Hloušek-Kasun
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Monika Kapustić
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Kristina Delaš
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Ivo Piantanida
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička 54 HR-10000 Zagreb, Croatia.
| | - Marta Jurković
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička 54 HR-10000 Zagreb, Croatia
| | - Branimir Bertoša
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia
| | - Klaus Zangger
- University of Graz, Institute of Chemistry, Organic and Bioorganic Chemistry, Heinrichstraße 28 A-8010 Graz, Austria
| | - Predrag Novak
- University of Zagreb, Faculty of Science, Department of Chemistry, Horvatovac 102a HR-10000 Zagreb, Croatia.
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3
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Kožić M, Bertoša B. Trajectory maps: molecular dynamics visualization and analysis. NAR Genom Bioinform 2024; 6:lqad114. [PMID: 38226394 PMCID: PMC10789246 DOI: 10.1093/nargab/lqad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/01/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024] Open
Abstract
Molecular dynamics simulations generate trajectories that depict system's evolution in time and are analyzed visually and quantitatively. Commonly conducted analyses include RMSD, Rgyr, RMSF, and more. However, those methods are all limited by their strictly statistical nature. Here we present trajectory maps, a novel method to analyze and visualize protein simulation courses intuitively and conclusively. By plotting protein's backbone movements during the simulation as a heatmap, trajectory maps provide new tools to directly visualize protein behavior over time, compare multiple simulations, and complement established methods. A user-friendly Python application developed for this purpose is presented, alongside detailed documentation for easy usage and implementation. The method's validation is demonstrated on three case studies. Considering its benefits, trajectory maps are expected to adopt broad application in obtaining and communicating meaningful results of protein molecular dynamics simulations in many associated fields such as biochemistry, structural biology, pharmaceutical research etc.
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Affiliation(s)
- Matej Kožić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
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4
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Radman K, Jelić Matošević Z, Žilić D, Crnolatac I, Bregović N, Kveder M, Piantanida I, Fernandes PA, Ašler IL, Bertoša B. Structural and dynamical changes of the Streptococcus gordonii metalloregulatory ScaR protein induced by Mn 2+ ion binding. Int J Biol Macromol 2023; 253:127572. [PMID: 37866578 DOI: 10.1016/j.ijbiomac.2023.127572] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Divalent metal ions are essential micronutrients for many intercellular reactions. Maintaining their homeostasis is necessary for the survival of bacteria. In Streptococcus gordonii, one of the primary colonizers of the tooth surface, the cellular concentration of manganese ions (Mn2+) is regulated by the manganese-sensing transcriptional factor ScaR which controls the expression of proteins involved in manganese homeostasis. To resolve the molecular mechanism through which the binding of Mn2+ ions increases the binding affinity of ScaR to DNA, a variety of computational (QM and MD) and experimental (ITC, DSC, EMSA, EPR, and CD) methods were applied. The computational results showed that Mn2+ binding induces a conformational change in ScaR that primarily affects the position of the DNA binding domains and, consequently, the DNA binding affinity of the protein. In addition, experimental results revealed a 1:4 binding stoichiometry between ScaR dimer and Mn2+ ions, while the computational results showed that the binding of Mn2+ ions in the primary binding sites is sufficient to induce the observed conformational change of ScaR.
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Affiliation(s)
- Katarina Radman
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
| | - Zoe Jelić Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
| | - Dijana Žilić
- Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Nikola Bregović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
| | - Marina Kveder
- Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Science, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
| | - Ivana Leščić Ašler
- Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia.
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia.
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5
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Vujica L, Lončar J, Mišić L, Lučić B, Radman K, Mihaljević I, Bertoša B, Mesarić J, Horvat M, Smital T. Environmental contaminants modulate transport activity of zebrafish (Danio rerio) multidrug and toxin extrusion protein 3 (Mate3/Slc47a2.1). Sci Total Environ 2023; 901:165956. [PMID: 37541507 DOI: 10.1016/j.scitotenv.2023.165956] [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] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/06/2023]
Abstract
Zebrafish Mate3 is one of six co-orthologs of human multidrug and toxin extrusion proteins. It is highly expressed in the kidneys, intestine, testes, and brain of males. Initial interaction studies showed its interaction with xenobiotic compounds, suggesting a role in the efflux of toxic compounds. In this study, we aimed to test various environmental contaminants for their interaction with zebrafish Mate3. We developed a stable zebrafish Mate3 cell line and optimized a high-throughput screening assay using DAPI and ASP+ as fluorescent model substrates. To gain insight into the structure and function of the Mate3 protein and relate these to the results of the DAPI and ASP+ transport measurements, we predicted its 3D structure using the AlphaFold2 algorithm. A 3D structure with high per residue confidence scores with 13 transmembrane segments (TMs) was obtained, with topology and mutual positioning characteristic of the Mate protein family in a shape open to the extracellular part. Molecular docking methods were used to identify DAPI and ASP+ binding sites on the surface and in the center of the protein cavity. Because our kinetics experiments combined with molecular docking indicated that there may be additional active sites in zebrafish Mate3, additional cytotoxicity experiments were performed and highly potent Mate3 interactors were identified from a set of 55 different environmental contaminants. Our results suggest that some of the identified interactors may be of environmental concern, as their interaction with Mate3 could lead to an impairment of its normal efflux function, making fish more sensitive to harmful substances commonly released into the aquatic environment. Finally, the quality of zebrafish Mate3 structures predicted by the AlphaFold2 algorithm opens up the possibility of successfully using this tool for in silico research on transport preferences of other Mate proteins.
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Affiliation(s)
- Lana Vujica
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Jovica Lončar
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Lana Mišić
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Bono Lučić
- NMR Center, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Katarina Radman
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Ivan Mihaljević
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Josip Mesarić
- Centre for Informatics and Computing, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Marina Horvat
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Tvrtko Smital
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia.
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6
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Lever R, Simmons E, Gamble-Milner R, Buckley R, Harrison C, Parkes A, Mitchell L, Gausden J, Škulj S, Bertoša B, Bolt E, Allers T. Archaeal Hel308 suppresses recombination through a catalytic switch that controls DNA annealing. Nucleic Acids Res 2023; 51:8563-8574. [PMID: 37409572 PMCID: PMC10484726 DOI: 10.1093/nar/gkad572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/14/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023] Open
Abstract
Hel308 helicases promote genome stability in archaea and are conserved in metazoans, where they are known as HELQ. Their helicase mechanism is well characterised, but it is unclear how they specifically contribute to genome stability in archaea. We show here that a highly conserved motif of Hel308/HELQ helicases (motif IVa, F/YHHAGL) modulates both DNA unwinding and a newly identified strand annealing function of archaeal Hel308. A single amino acid substitution in motif IVa results in hyper-active DNA helicase and annealase activities of purified Hel308 in vitro. All-atom molecular dynamics simulations using Hel308 crystal structures provided a molecular basis for these differences between mutant and wild type Hel308. In archaeal cells, the same mutation results in 160000-fold increased recombination, exclusively as gene conversion (non-crossover) events. However, crossover recombination is unaffected by the motif IVa mutation, as is cell viability or DNA damage sensitivity. By contrast, cells lacking Hel308 show impaired growth, increased sensitivity to DNA cross-linking agents, and only moderately increased recombination. Our data reveal that archaeal Hel308 suppresses recombination and promotes DNA repair, and that motif IVa in the RecA2 domain acts as a catalytic switch to modulate the separable recombination and repair activities of Hel308.
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Affiliation(s)
- Rebecca J Lever
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Emily Simmons
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | | | - Ryan J Buckley
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Catherine Harrison
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Ashley J Parkes
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Laura Mitchell
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Jacob A Gausden
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Edward L Bolt
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK
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7
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Ban Ž, Barišić A, Crnolatac I, Kazazić S, Škulj S, Savini F, Bertoša B, Barišić I, Piantanida I. Highly selective preparation of N-terminus Horseradish peroxidase-DNA conjugate with fully retained enzymatic activity: HRP-DNA structure - activity relation. Enzyme Microb Technol 2023; 168:110257. [PMID: 37209508 DOI: 10.1016/j.enzmictec.2023.110257] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
Within the last decade, the field of bio-nanoengineering has achieved significant advances allowing us to generate, e.g., nanoscaled molecular machineries with arbitrary shapes. To unleash the full potential of novel methods such as DNA origami technology, it is important to functionalise complex molecules and nanostructures precisely. Thus, considerable attention has been given to site-selective modifications of proteins allowing further incorporation of various functionalities. Here, we describe a method for the covalent attachment of oligonucleotides to the glycosylated horseradish peroxidase protein (HRP) with high N-terminus selectivity and significant yield while conserving the enzymatic activity. This two-step process includes a pH-controlled metal-free diazotransfer reaction using imidazole-1-sulfonyl azide hydrogen sulfate, which at pH 8.5 results in an N-terminal azide-functionalized protein, followed by the Cu-free click SPAAC reaction to dibenzocyclooctyne- (DBCO) modified oligonucleotides. The reaction conditions were optimised to achieve maximum yield and the best performance. The resulting protein-oligonucleotide conjugates (HRP-DNA) were characterised by electrophoresis and mass spectrometry (MS). Native-PAGE experiments demonstrated different migration patterns for HRP-DNA and the azido-modified protein allowing zymogram experiments. Structure-activity relationships of novel HRP-DNA conjugates were assessed using molecular dynamics simulations, characterising the molecular interactions that define the structural and dynamical properties of the obtained protein-oligonucleotide conjugates (POC).
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Saša Kazazić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Škulj
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia.
| | - Ivan Barišić
- AIT Austrian Institute of Technology,Vienna, Austria.
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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8
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Bubić A, Narczyk M, Petek A, Wojtyś MI, Maksymiuk W, Wielgus-Kutrowska B, Winiewska-Szajewska M, Pavkov-Keller T, Bertoša B, Štefanić Z, Luić M, Bzowska A, Leščić Ašler I. The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site. Int J Biol Macromol 2023; 226:37-50. [PMID: 36470440 DOI: 10.1016/j.ijbiomac.2022.12.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/11/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Purine nucleotide synthesis is realised only through the salvage pathway in pathogenic bacterium Helicobacter pylori. Therefore, the enzymes of this pathway, among them also the adenylosuccinate synthetase (AdSS), present potential new drug targets. This paper describes characterization of His6-tagged AdSS from H. pylori. Thorough analysis of 3D-structures of fully ligated AdSS (in a complex with guanosine diphosphate, 6-phosphoryl-inosine monophosphate, hadacidin and Mg2+) and AdSS in a complex with inosine monophosphate (IMP) only, enabled identification of active site interactions crucial for ligand binding and enzyme activity. Combination of experimental and molecular dynamics (MD) simulations data, particularly emphasized the importance of hydrogen bond Arg135-IMP for enzyme dimerization and active site formation. The synergistic effect of substrates (IMP and guanosine triphosphate) binding was suggested by MD simulations. Several flexible elements of the structure (loops) are stabilized by the presence of IMP alone, however loops comprising residues 287-293 and 40-44 occupy different positions in two solved H. pylori AdSS structures. MD simulations discovered the hydrogen bond network that stabilizes the closed conformation of the residues 40-50 loop, only in the presence of IMP. Presented findings provide a solid basis for the design of new AdSS inhibitors as potential drugs against H. pylori.
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Affiliation(s)
- Ante Bubić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Ana Petek
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Marta Ilona Wojtyś
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Weronika Maksymiuk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maria Winiewska-Szajewska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/III, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, Graz 8010, Austria; BioHealth Field of Excellence, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000 Zagreb, Croatia
| | - Zoran Štefanić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Marija Luić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Ivana Leščić Ašler
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
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9
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Dyzma A, Wielgus-Kutrowska B, Girstun A, Matošević ZJ, Staroń K, Bertoša B, Trylska J, Bzowska A. Trimeric Architecture Ensures the Stability and Biological Activity of the Calf Purine Nucleoside Phosphorylase: In Silico and In Vitro Studies of Monomeric and Trimeric Forms of the Enzyme. Int J Mol Sci 2023; 24:ijms24032157. [PMID: 36768477 PMCID: PMC9916683 DOI: 10.3390/ijms24032157] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
Mammalian purine nucleoside phosphorylase (PNP) is biologically active as a homotrimer, in which each monomer catalyzes a reaction independently of the others. To answer the question of why the native PNP forms a trimeric structure, we constructed, in silico and in vitro, the monomeric form of the enzyme. Molecular dynamics simulations showed different geometries of the active site in the non-mutated trimeric and monomeric PNP forms, which suggested that the active site in the isolated monomer could be non-functional. To confirm this hypothesis, six amino acids located at the interface of the subunits were selected and mutated to alanines to disrupt the trimer and obtain a monomer (6Ala PNP). The effects of these mutations on the enzyme structure, stability, conformational dynamics, and activity were examined. The solution experiments confirmed that the 6Ala PNP mutant occurs mainly as a monomer, with a secondary structure almost identical to the wild type, WT PNP, and importantly, it shows no enzymatic activity. Simulations confirmed that, although the secondary structure of the 6Ala monomer is similar to the WT PNP, the positions of the amino acids building the 6Ala PNP active site significantly differ. These data suggest that a trimeric structure is necessary to stabilize the geometry of the active site of this enzyme.
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Affiliation(s)
- Alicja Dyzma
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Correspondence: (B.W.-K.); (A.B.)
| | - Agnieszka Girstun
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Zoe Jelić Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Krzysztof Staroń
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
- Correspondence: (B.W.-K.); (A.B.)
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10
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Jelić Matošević Z, Radman K, Loubser J, Crnolatac I, Piantanida I, Cukrowski I, Ašler IL, Bertoša B. Structural Dynamics of the Bacillus subtilis MntR Transcription Factor Is Locked by Mn 2+ Binding. Int J Mol Sci 2023; 24:ijms24020957. [PMID: 36674477 PMCID: PMC9861239 DOI: 10.3390/ijms24020957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Manganese (II) ions are essential for a variety of bacterial cellular processes. The transcription factor MntR is a metallosensor that regulates Mn2+ ion homeostasis in the bacterium Bacillus subtilis. Its DNA-binding affinity is increased by Mn2+ ion binding, allowing it to act as a transcriptional repressor of manganese import systems. Although experimentally well-researched, the molecular mechanism that regulates this process is still a puzzle. Computational simulations supported by circular dichroism (CD), differential scanning calorimetry (DSC) and native gel electrophoresis (native-PAGE) experiments were employed to study MntR structural and dynamical properties in the presence and absence of Mn2+ ions. The results of molecular dynamics (MD) simulations revealed that Mn2+ ion binding reduces the structural dynamics of the MntR protein and shifts the dynamic equilibrium towards the conformations adequate for DNA binding. Results of CD and DSC measurements support the computational results showing the change in helical content and stability of the MntR protein upon Mn2+ ion binding. Further, MD simulations show that Mn2+ binding induces polarization of the protein electrostatic potential, increasing the positive electrostatic potential of the DNA-binding helices in particular. In order to provide a deeper understanding of the changes in protein structure and dynamics due to Mn2+ binding, a mutant in which Mn2+ binding is mimicked by a cysteine bridge was constructed and also studied computationally and experimentally.
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Affiliation(s)
- Zoe Jelić Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Katarina Radman
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Jolene Loubser
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Ivo Crnolatac
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Ignacy Cukrowski
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, Pretoria 0002, South Africa
| | - Ivana Leščić Ašler
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4606-132
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11
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Hloušek-Kasun A, Mikolčević P, Rack JGM, Tromans-Coia C, Schuller M, Jankevicius G, Matković M, Bertoša B, Ahel I, Mikoč A. Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA. Comput Struct Biotechnol J 2022; 20:4337-4350. [PMID: 36051881 PMCID: PMC9411070 DOI: 10.1016/j.csbj.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/01/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022] Open
Abstract
ADP-ribosylation is an ancient, highly conserved, and reversible covalent modification critical for a variety of endogenous processes in both prokaryotes and eukaryotes. ADP-ribosylation targets proteins, nucleic acids, and small molecules (including antibiotics). ADP-ribosylation signalling involves enzymes that add ADP-ribose to the target molecule, the (ADP-ribosyl)transferases; and those that remove it, the (ADP-ribosyl)hydrolases. Recently, the toxin/antitoxin pair DarT/DarG composed of a DNA ADP-ribosylating toxin, DarT, and (ADP-ribosyl)hydrolase antitoxin, DarG, was described. DarT modifies thymidine in single-stranded DNA in a sequence-specific manner while DarG reverses this modification, thereby rescuing cells from DarT toxicity. We studied the DarG homologue SCO6735 which is highly conserved in all Streptomyces species and known to be associated with antibiotic production in the bacterium S. coelicolor. SCO6735 shares a high structural similarity with the bacterial DarG and human TARG1. Like DarG and TARG1, SCO6735 can also readily reverse thymidine-linked ADP-ribosylation catalysed by DarT in vitro and in cells. SCO6735 active site analysis including molecular dynamic simulations of its complex with ADP-ribosylated thymidine suggests a novel catalytic mechanism of DNA-(ADP-ribose) hydrolysis. Moreover, a comparison of SCO6735 structure with ALC1-like homologues revealed an evolutionarily conserved feature characteristic for this subclass of macrodomain hydrolases.
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Affiliation(s)
| | - Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | | | - Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Gytis Jankevicius
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Marija Matković
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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12
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Kuťák D, Melo L, Schroeder F, Jelic-Matošević Z, Mutter N, Bertoša B, Barišić I. CATANA: an online modelling environment for proteins and nucleic acid nanostructures. Nucleic Acids Res 2022; 50:W152-W158. [PMID: 35544315 PMCID: PMC9252799 DOI: 10.1093/nar/gkac350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/19/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
In the last decade, significant advances have been made towards the rational design of proteins, DNA, and other organic nanostructures. The emerging possibility to precisely engineer molecular structures resulted in a wide range of new applications in fields such as biotechnology or medicine. The complexity and size of the artificial molecular systems as well as the number of interactions are greatly increasing and are manifesting the need for computational design support. In addition, a new generation of AI-based structure prediction tools provides researchers with completely new possibilities to generate recombinant proteins and functionalized DNA nanostructures. In this study, we present Catana, a web-based modelling environment suited for proteins and DNA nanostructures. User-friendly features were developed to create and modify recombinant fusion proteins, predict protein structures based on the amino acid sequence, and manipulate DNA origami structures. Moreover, Catana was jointly developed with the novel Unified Nanotechnology Format (UNF). Therefore, it employs a state-of-the-art coarse-grained data model, that is compatible with other established and upcoming applications. A particular focus was put on an effortless data export to allow even inexperienced users to perform in silico evaluations of their designs by means of molecular dynamics simulations. Catana is freely available at http://catana.ait.ac.at/.
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Affiliation(s)
- David Kuťák
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia.,Visitlab, Faculty of Informatics, Masaryk University, Brno 602 00, Czech Republic
| | - Lucas Melo
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Fabian Schroeder
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
| | - Zoe Jelic-Matošević
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Natalie Mutter
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, AIT Austrian Institute of Technology, 1210 Vienna, Austria.,Eko Refugium, 47240 Slunj, Croatia
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13
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Beč A, Mioč M, Bertoša B, Kos M, Debogović P, Kralj M, Starčević K, Hranjec M. Design, synthesis, biological evaluation and QSAR analysis of novel N-substituted benzimidazole derived carboxamides. J Enzyme Inhib Med Chem 2022; 37:1327-1339. [PMID: 35514167 PMCID: PMC9090388 DOI: 10.1080/14756366.2022.2070910] [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] [Indexed: 10/31/2022] Open
Abstract
As a result of our previous research focussed on benzimidazoles, herein we present design, synthesis, QSAR analysis and biological activity of novel N-substituted benzimidazole derived carboxamides. Carboxamides were designed to study the influence of the number of methoxy groups, the type of the substituent placed at the benzimidazole core on biological activity. Pronounced antioxidative activity displayed unsubstituted 28 (IC50 ≈ 3.78 mM, 538.81 mmolFe2+/mmolC) and dimethoxy substituted derivative 34 (IC50 ≈ 5.68 mM, 618.10 mmolFe2+/mmolC). Trimethoxy substituted 43 and unsubstituted compound 40 with isobutyl side chain at N atom showed strong activity against HCT116 (IC50 ≈ 0.6 µM, both) and H 460 cells (IC50 ≈ 2.5 µM; 0.4 µM), being less cytotoxic towards non-tumour cell. Antioxidative activity in cell generally confirmed relatively modest antioxidant capacity obtained in DPPH/FRAP assays of derivatives 34 and 40. The 3D-QSAR models were generated to explore molecular properties that have the highest influence on antioxidative activity.
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Affiliation(s)
- Anja Beč
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
| | - Marija Mioč
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marija Kos
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
| | - Patricia Debogović
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
| | - Marijeta Kralj
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Kristina Starčević
- Department of Chemistry and Biochemistry, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Zagreb, Croatia
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14
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Škulj S, Barišić A, Mutter N, Spadiut O, Barišić I, Bertoša B. Effect of N-glycosylation on horseradish peroxidase structural and dynamical properties. Comput Struct Biotechnol J 2022; 20:3096-3105. [PMID: 35782731 PMCID: PMC9233188 DOI: 10.1016/j.csbj.2022.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 11/03/2022] Open
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15
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Špehar TK, Pocrnić M, Klarić D, Bertoša B, Čikoš A, Jug M, Padovan J, Dragojević S, Galić N. Investigation of Praziquantel/Cyclodextrin Inclusion Complexation by NMR and LC-HRMS/MS: Mechanism, Solubility, Chemical Stability, and Degradation Products. Mol Pharm 2021; 18:4210-4223. [PMID: 34670371 PMCID: PMC8564759 DOI: 10.1021/acs.molpharmaceut.1c00716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Indexed: 01/04/2023]
Abstract
Praziquantel (PZQ) is a biopharmaceutical classification system (BCS) class II anthelmintic drug characterized by poor solubility and a bitter taste, both of which can be addressed by inclusion complexation with cyclodextrins (CD). In this work, a comprehensive investigation of praziquantel/cyclodextrin (PZQ/CD) complexes was conducted by means of UV-vis spectroscopy, spectrofluorimetry, NMR spectroscopy, liquid chromatography-high-resolution mass spectrometry (LC-HRMS/MS), and molecular modeling. Phase solubility studies revealed that among four CDs tested, the randomly methylated β-CD (RMβCD) and the sulfobutylether sodium salt β-CD (SBEβCD) resulted in the highest increase in PZQ solubility (approximately 16-fold). The formation of 1:1 inclusion complexes was confirmed by HRMS, NMR, and molecular modeling. Both cyclohexane and the central pyrazino ring, as well as an aromatic part of PZQ are included in the CD central cavity through several different binding modes, which exist simultaneously. Furthermore, the influence of CDs on PZQ stability was investigated in solution (HCl, NaOH, H2O2) and in the solid state (accelerated degradation, photostability) by ultra-high-performance liquid chromatography-diode array detection-tandem mass spectrometry (UPLC-DAD/MS). CD complexation promoted new degradation pathways of the drug. In addition to three already known PZQ degradants, seven new degradation products were identified (m/z 148, 215, 217, 301, 327, 343, and 378) and their structures were proposed based on HRMS/MS data. Solid complexes were prepared by mechanochemical activation, a solvent-free and ecologically acceptable method.
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Affiliation(s)
| | - Marijana Pocrnić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - David Klarić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Ana Čikoš
- Institute Ruđer Bošković, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Mario Jug
- Department of Pharmaceutical Technology, Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10 000 Zagreb, Croatia
| | - Jasna Padovan
- Fidelta Ltd., Prilaz baruna Filipovića 29, 10 000 Zagreb, Croatia
| | | | - Nives Galić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
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16
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Dražić T, Kopf S, Corridan J, Leuthold MM, Bertoša B, Klein CD. Correction to Peptide-β-lactam Inhibitors of Dengue and West Nile Virus NS2B-NS3 Protease Display Two Distinct Binding Modes. J Med Chem 2020; 63:10530. [DOI: 10.1021/acs.jmedchem.0c01358] [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]
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17
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Kekic T, Fulgosi H, Vojta L, Bertoša B. Molecular basis of ferredoxin:NADP(+) reductase interactions with FNR binding domains from TROL and Tic62 proteins. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Grgičević I, Mikulandra I, Bukvić M, Banjanac M, Radovanović V, Habinovec I, Bertoša B, Novak P. Discovery of macrozones, new antimicrobial thiosemicarbazone-based azithromycin conjugates: design, synthesis and in vitro biological evaluation. Int J Antimicrob Agents 2020; 56:106147. [PMID: 32853671 DOI: 10.1016/j.ijantimicag.2020.106147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/09/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Increasing bacterial resistance to existing antibiotics presents a serious threat to human health, and new antibacterial agents are desperately needed. Unfortunately, the number of newly marketed antibiotics has decreased dramatically in recent years. Withdrawal of the macrolide antibiotic telithromycin and the inability of solithromycin to gain marketing approval have prompted our efforts to search for new anti-infective macrolide compounds. Here we present the design, synthesis and biological evaluation of a novel hybrid class of azithromycin conjugates, the macrozones. Evaluation of prepared compounds against a panel of pathogenic bacteria revealed that these molecules showed excellent activities against susceptible Streptococcus pneumoniae, Streptococcus pyogenes and Enterococcus faecalis strains comparable with or better than azithromycin. Furthermore, prepared macrozones exhibited excellent activity against efflux resistant S. pneumoniae, which was 32 times better than that of azithromycin, and very good activity against an efflux resistant Staphylococcus aureus strain against which azithromycin is inactive. The results described here can serve as a good basis to guide further activities directed toward the discovery of more potent macrolide anti-infectives.
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Affiliation(s)
- Ivan Grgičević
- Fidelta, Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Ivana Mikulandra
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Mirjana Bukvić
- Fidelta, Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Mihailo Banjanac
- Fidelta, Ltd., Prilaz baruna Filipovića 29, 10000 Zagreb, Croatia
| | | | - Iva Habinovec
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia.
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19
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Mrnjavac N, Vazdar M, Bertoša B. Molecular dynamics study of functionally relevant interdomain and active site interactions in the autotransporter esterase EstA from Pseudomonas aeruginosa. Molecular Simulation 2020. [DOI: 10.1080/08927022.2020.1770750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Natalia Mrnjavac
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
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20
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Dražić T, Kopf S, Corridan J, Leuthold MM, Bertoša B, Klein CD. Peptide-β-lactam Inhibitors of Dengue and West Nile Virus NS2B-NS3 Protease Display Two Distinct Binding Modes. J Med Chem 2019; 63:140-156. [DOI: 10.1021/acs.jmedchem.9b00759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Sara Kopf
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - James Corridan
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Mila M. Leuthold
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia
| | - Christian D. Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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21
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Sović I, Cindrić M, Perin N, Boček I, Novaković I, Damjanović A, Stanojković T, Zlatović M, Hranjec M, Bertoša B. Biological Potential of Novel Methoxy and Hydroxy Substituted Heteroaromatic Amides Designed as Promising Antioxidative Agents: Synthesis, 3D-QSAR Analysis, and Biological Activity. Chem Res Toxicol 2019; 32:1880-1892. [PMID: 31381319 DOI: 10.1021/acs.chemrestox.9b00256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper discusses antioxidative and biological activities of 25 novel amidino substituted benzamides with a variety of heteroaromatic nuclei attached to the benzamide moiety and with a variable number of methoxy or hydroxy substituents. Targeted compounds, bearing either amidino or 2-imidazolinyl substituent, were obtained in the Pinner reaction from cyano precursors. 3D-QSAR models were generated to predict antioxidative activity of the 25 novel aromatic and heteroaromatic benzamide derivatives. The compounds were tested for antioxidative activity using in vitro spectrophotometric assays. Direct validation of 3D-QSAR approach for predicting activities of novel benzamide derivatives was carried out by comparing experimental and computationally predicted antioxidative activity. Experimentally determined activities for all novel compounds were found to be within a standard deviation of error of the models. Following this, structure-activity relationships among the synthesized compounds are discussed. Furthermore, antiproliferative activity in vitro against HeLa cells as well as antibacterial and antifungal activity was tested to confirm the other biological activities of the prepared compounds.
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Affiliation(s)
- Irena Sović
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Marulićev trg 20, P.O. Box 177 , HR-10000 Zagreb , Croatia
| | - Maja Cindrić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Marulićev trg 20, P.O. Box 177 , HR-10000 Zagreb , Croatia
| | - Nataša Perin
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Marulićev trg 20, P.O. Box 177 , HR-10000 Zagreb , Croatia
| | - Ida Boček
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Marulićev trg 20, P.O. Box 177 , HR-10000 Zagreb , Croatia
| | - Irena Novaković
- Institute of Chemistry, Technology and Metallurgy , University of Belgrade , Njegoševa 12, PO Box 815 , 11000 Belgrade , Serbia
| | - Ana Damjanović
- Institute of Oncology and Radiology , Pasterova 14 , 11000 Belgrade , Serbia
| | - Tatjana Stanojković
- Institute of Oncology and Radiology , Pasterova 14 , 11000 Belgrade , Serbia
| | - Mario Zlatović
- Faculty of Chemistry , University of Belgrade , Studentski trg 12-16 , 11000 Belgrade , Serbia
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology , University of Zagreb , Marulićev trg 20, P.O. Box 177 , HR-10000 Zagreb , Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science , University of Zagreb , Horvatovac 102a , HR 10000 Zagreb , Croatia
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22
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Sviben D, Bertoša B, Hloušek-Kasun A, Forcic D, Halassy B, Brgles M. Investigation of the thermal shift assay and its power to predict protein and virus stabilizing conditions. J Pharm Biomed Anal 2018; 161:73-82. [DOI: 10.1016/j.jpba.2018.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 07/30/2018] [Accepted: 08/07/2018] [Indexed: 12/21/2022]
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Narczyk M, Bertoša B, Papa L, Vuković V, Leščić Ašler I, Wielgus-Kutrowska B, Bzowska A, Luić M, Štefanić Z. Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features. FEBS J 2018; 285:1305-1325. [PMID: 29430816 DOI: 10.1111/febs.14403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/24/2018] [Accepted: 02/06/2018] [Indexed: 01/06/2023]
Abstract
Even with decades of research, purine nucleoside phosphorylases (PNPs) are enzymes whose mechanism is yet to be fully understood. This is especially true in the case of hexameric PNPs, and is probably, in part, due to their complex oligomeric nature and a whole spectrum of active site conformations related to interactions with different ligands. Here we report an extensive structural characterization of the apo forms of hexameric PNP from Helicobacter pylori (HpPNP), as well as its complexes with phosphate (Pi ) and an inhibitor, formycin A (FA), together with kinetic, binding, docking and molecular dynamics studies. X-ray structures show previously unseen distributions of open and closed active sites. Microscale thermophoresis results indicate that a two-site model describes Pi binding, while a three-site model is needed to characterize FA binding, irrespective of Pi presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with Pi and FA shows, however, that Pi binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that Pi moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. Altogether, these findings show some unique features of HpPNP and provide new insights into the functioning of the active sites, with implications for understanding the complex mechanism of catalysis of this enzyme. DATABASES The atomic coordinates and structure factors have been deposited in the Protein Data Bank: with accession codes 6F52 (HpPNPapo_1), 6F5A (HpPNPapo_2), 6F5I (HpPNPapo_3), 5LU0 (HpPNP_PO4), 6F4W (HpPNP_FA) and 6F4X (HpPNP_PO4_FA). ENZYMES Purine nucleoside orthophosphate ribosyl transferase, EC2.4.2.1, UniProtID: P56463.
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Affiliation(s)
- Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Lucija Papa
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vedran Vuković
- Department of Chemistry, Faculty of Science, University of Zagreb, Croatia
| | - Ivana Leščić Ašler
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland
| | - Marija Luić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Zoran Štefanić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
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Bregović N, Cindro N, Bertoša B, Barišić D, Frkanec L, Užarević K, Tomišić V. Dehydroacetic Acid Derivatives Bearing Amide or Urea Moieties as Effective Anion Receptors. Chemistry 2017; 23:10396-10406. [PMID: 28493492 DOI: 10.1002/chem.201701677] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 01/07/2023]
Abstract
Derivatives of dehydroacetic acid comprising amide or urea subunits have been synthesized and their anion-binding properties investigated. Among a series of halides and oxyanions, the studied compounds selectively bind acetate and dihydrogen phosphate in acetonitrile and dimethyl sulfoxide. The corresponding complexation processes were characterized by means of 1 H NMR titrations, which revealed a 1:1 complex stoichiometry in most cases, with the exception of dihydrogen phosphate, which formed 2:1 (anion/ligand) complexes in acetonitrile. The complex stability constants were determined and are discussed with respect to the structural properties of the receptors, the hydrogen-bond-forming potential of the anions, and the characteristics of the solvents used. Based on the spectroscopic data and results of Monte Carlo simulations, the amide or urea groups were affirmed as the primary binding sites in all cases. The results of the computational methods indicate that an array of both inter- and intramolecular hydrogen bonds can form in the studied systems, and these were shown to play an important role in defining the overall stability of the complexes. Solubility measurements were carried out in both solvents and the thermodynamics of transfer from acetonitrile to dimethyl sulfoxide were characterized on a quantitative level. This has afforded a detailed insight into the impact of the medium on the complexation reactions.
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Affiliation(s)
- Nikola Bregović
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Nikola Cindro
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Dajana Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
| | - Leo Frkanec
- Laboratory for Supramolecular Chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Krunoslav Užarević
- Laboratory for Green Synthesis, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Vladislav Tomišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, Zagreb, Croatia
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Vušak D, Perin N, Martin-Kleiner I, Kralj M, Karminski-Zamola G, Hranjec M, Bertoša B. Synthesis and antiproliferative activity of amino-substituted benzimidazo[1,2-
$${\varvec{a}}$$
a
]quinolines as mesylate salts designed by 3D-QSAR analysis. Mol Divers 2017; 21:621-636. [DOI: 10.1007/s11030-017-9753-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/27/2017] [Indexed: 12/31/2022]
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Perin N, Nhili R, Cindrić M, Bertoša B, Vušak D, Martin-Kleiner I, Laine W, Karminski-Zamola G, Kralj M, David-Cordonnier MH, Hranjec M. Amino substituted benzimidazo[1,2- a ]quinolines: Antiproliferative potency, 3D QSAR study and DNA binding properties. Eur J Med Chem 2016; 122:530-545. [DOI: 10.1016/j.ejmech.2016.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 06/27/2016] [Accepted: 07/05/2016] [Indexed: 11/26/2022]
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Kazazić S, Bertoša B, Luić M, Mikleušević G, Tarnowski K, Dadlez M, Narczyk M, Bzowska A. New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations. J Am Soc Mass Spectrom 2016; 27:73-82. [PMID: 26337516 DOI: 10.1007/s13361-015-1239-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 07/24/2015] [Accepted: 07/26/2015] [Indexed: 06/05/2023]
Abstract
The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.
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Affiliation(s)
- Saša Kazazić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Branimir Bertoša
- Division of Physical Chemistry, Faculty of Science at University of Zagreb, Zagreb, Croatia.
| | - Marija Luić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Goran Mikleušević
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krzysztof Tarnowski
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics Department, Polish Academy of Science, Warsaw, Poland
| | - Marta Narczyk
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Warsaw, Poland
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Sović I, Viskić M, Bertoša B, Ester K, Kralj M, Hranjec M, Karminski-Zamola G. Exploring antiproliferative activity of heteroaromatic amides and their fused derivatives using 3D-QSAR, synthesis, and biological tests. Monatsh Chem 2015. [DOI: 10.1007/s00706-015-1478-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Bertoša B, Mikleušević G, Wielgus-Kutrowska B, Narczyk M, Hajnić M, Leščić Ašler I, Tomić S, Luić M, Bzowska A. Homooligomerization is needed for stability: a molecular modelling and solution study of Escherichia coli purine nucleoside phosphorylase. FEBS J 2014; 281:1860-71. [PMID: 24785777 DOI: 10.1111/febs.12746] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
UNLABELLED Although many enzymes are homooligomers composed of tightly bound subunits, it is often the case that smaller assemblies of such subunits, or even individual monomers, seem to have all the structural features necessary to independently conduct catalysis. In this study, we investigated the reasons justifying the necessity for the hexameric form of Escherichia coli purine nucleoside phosphorylase - a homohexamer composed of three linked dimers - since it appears that the dimer is the smallest unit capable of catalyzing the reaction, according to the currently accepted mechanism. Molecular modelling was employed to probe mutations at the dimer-dimer interface that would result in a dimeric enzyme form. In this way, both in silico and in vitro, the hexamer was successfully transformed into dimers. However, modelling and solution studies show that, when isolated, dimers cannot maintain the appropriate three-dimensional structure, including the geometry of the active site and the position of the catalytically important amino acids. Analytical ultracentrifugation proves that E. coli purine nucleoside phosphorylase dimeric mutants tend to dissociate into monomers with dissociation constants of 20-80 μm. Consistently, the catalytic activity of these mutants is negligible, at least 6 orders of magnitude smaller than for the wild-type enzyme. We conclude that the hexameric architecture of E. coli purine nucleoside phosphorylase is necessary to provide stabilization of the proper three-dimensional structure of the dimeric assembly, and therefore this enzyme is the obligate (obligatory) hexamer. STRUCTURED DIGITAL ABSTRACT ●PNP and PNP bind by molecular sieving (1, 2, 3, 4).
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Affiliation(s)
- Branimir Bertoša
- Division of Physical Chemistry, Faculty of Science at University of Zagreb, Croatia
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Šumanovac Ramljak T, Despotović I, Bertoša B, Mlinarić-Majerski K. Synthesis and alkali metal complexation studies of novel cage-functionalized cryptands. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.10.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Aleksić M, Bertoša B, Nhili R, Uzelac L, Jarak I, Depauw S, David-Cordonnier MH, Kralj M, Tomić S, Karminski-Zamola G. Novel Substituted Benzothiophene and Thienothiophene Carboxanilides and Quinolones: Synthesis, Photochemical Synthesis, DNA-Binding Properties, Antitumor Evaluation and 3D-Derived QSAR Analysis. J Med Chem 2012; 55:5044-60. [DOI: 10.1021/jm300505h] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Maja Aleksić
- Department of Organic Chemistry,
Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, P.O. Box 177, HR-10000
Zagreb, Croatia
| | | | - Raja Nhili
- INSERM U837-JPARC (Jean-Pierre
Aubert Research Center), Team “Molecular and Cellular Targeting
for Cancer Treatment”, Université Lille Nord de France, IFR-114, Institut pour la Recherche
sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | | | - Ivana Jarak
- Department of Organic Chemistry,
Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, P.O. Box 177, HR-10000
Zagreb, Croatia
| | - Sabine Depauw
- INSERM U837-JPARC (Jean-Pierre
Aubert Research Center), Team “Molecular and Cellular Targeting
for Cancer Treatment”, Université Lille Nord de France, IFR-114, Institut pour la Recherche
sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Marie-Hélène David-Cordonnier
- INSERM U837-JPARC (Jean-Pierre
Aubert Research Center), Team “Molecular and Cellular Targeting
for Cancer Treatment”, Université Lille Nord de France, IFR-114, Institut pour la Recherche
sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | | | | | - Grace Karminski-Zamola
- Department of Organic Chemistry,
Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, P.O. Box 177, HR-10000
Zagreb, Croatia
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Šumanovac Ramljak T, Mlinarić-Majerski K, Bertoša B. Alkali Metal Ion Complexation of Adamantane Functionalized Diaza-bibracchial Lariat Ethers. CROAT CHEM ACTA 2012. [DOI: 10.5562/cca2100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Musiani F, Bertoša B, Magistrato A, Zambelli B, Turano P, Losasso V, Micheletti C, Ciurli S, Carloni P. Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+ 2 Francesco Musiani and Branimir Bertoša contributed equally to the simulations presented here. J Chem Theory Comput 2010; 6:3503-15. [DOI: 10.1021/ct900635z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Branimir Bertoša
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Alessandra Magistrato
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Paola Turano
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Valeria Losasso
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Cristian Micheletti
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
| | - Paolo Carloni
- Laboratory of Bioinorganic Chemistry, University of Bologna, Viale G. Fanin 40, 40127 Bologna, Italy, International School for Advanced Studies (SISSA) and CNR-IOM-DEMOCRITOS National Simulation Center, via Bonomea 265, 34136 Trieste, Italy, Ruder Bošković Institute, Bijeniěka 54, 10000 Zagreb, Croatia, German Research School for Simulation Science, FZ-Jülichand RWTH, Wilhelm-Johnen-Strasse, 52428 Jülich, Germany, Center for Magnetic Resonance (CERM), University of Florence, Via Luigi Sacconi 6, 50019
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Rožman M, Bertoša B, Klasinc L, Srzić D. Gas phase H/D exchange of sodiated amino acids: why do we see zwitterions? J Am Soc Mass Spectrom 2006; 17:29-36. [PMID: 16352438 DOI: 10.1016/j.jasms.2005.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2005] [Revised: 08/26/2005] [Accepted: 08/26/2005] [Indexed: 05/05/2023]
Abstract
The gas-phase interaction of sodiated amino acids and sodiated amino acid methyl esters with various deuterium donors is investigated by combining results of H/D exchange reactions with those from density functional theory and molecular dynamics calculations. Discrepancy between experimentally and theoretically obtained structures for sodium cationized amino acids is explained by deuterium donor caused perturbation of the most stable amino acid conformation. Detailed study of H/D exchange mechanism on sodiated amino acids shows that the H/D exchange reaction is preceded by a multistep quasi-isoenergetic transition (perturbation) from a charge solvated to zwitterionic structure in the amino acid. Although the computation refers to the system AlaNa(+) and D(2)O, these mechanisms apply to all amino acids, except those where a functional side-chain group takes part in the perturbation process. The suggested perturbation mechanism applies also for other deuterium donors such as CD(3)OD or even ND(3) and indicates that a single water molecule suffices to convert the sodiated amino acid from charge solvated to zwitterionic form.
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Affiliation(s)
- Marko Rožman
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Croatia
| | - Branimir Bertoša
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
- Laboratory of Chemical and Biological Crystallography, Croatia
| | - Leo Klasinc
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Croatia
| | - Dunja Srzić
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Ruđer Bošković Institute, Bijenička 54, HR-10002, Zagreb, Croatia.
- Laboratory for Chemical Kinetics and Atmospheric Chemistry, Croatia.
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Tomić S, Bertoša B, Kojić-Prodić B, Kolosvary I. Stereoselectivity of Burkholderia cepacia lipase towards secondary alcohols: molecular modelling and 3D QSAR approach. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.02.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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