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Arrigoni R, Ballini A, Santacroce L, Palese LL. The Dynamics of OXA-23 β-Lactamase from Acinetobacter baumannii. Int J Mol Sci 2023; 24:17527. [PMID: 38139363 PMCID: PMC10743560 DOI: 10.3390/ijms242417527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Antibiotic resistance is a pressing topic, which also affects β-lactam antibiotic molecules. Until a few years ago, it was considered no more than an interesting species from an academic point of view, Acinetobacter baumanii is today one of the most serious threats to public health, so much so that it has been declared one of the species for which the search for new antibiotics, or new ways to avoid its resistance, is an absolute priority according to WHO. Although there are several molecular mechanisms that are responsible for the extreme resistance of A. baumanii to antibiotics, a class D β-lactamase is the main cause for the clinical concern of this bacterial species. In this work, we analyzed the A. baumanii OXA-23 protein via molecular dynamics. The results obtained show that this protein is able to assume different conformations, especially in some regions around the active site. Part of the OXA-23 protein has considerable conformational motility, while the rest is less mobile. The importance of these observations for understanding the functioning mechanism of the enzyme as well as for designing new effective molecules for the treatment of A. baumanii is discussed.
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Affiliation(s)
- Roberto Arrigoni
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy;
| | - Andrea Ballini
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine (DIM), University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
| | - Luigi Leonardo Palese
- Department of Translational Biomedicine and Neurosciences—(DiBraiN), University of Bari ‘Aldo Moro’, 70124 Bari, Italy
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2
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Palmieri EM, Holewinski R, McGinity CL, Pierri CL, Maio N, Weiss JM, Tragni V, Miranda KM, Rouault TA, Andresson T, Wink DA, McVicar DW. Pyruvate dehydrogenase operates as an intramolecular nitroxyl generator during macrophage metabolic reprogramming. Nat Commun 2023; 14:5114. [PMID: 37607904 PMCID: PMC10444860 DOI: 10.1038/s41467-023-40738-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/04/2023] [Indexed: 08/24/2023] Open
Abstract
M1 macrophages enter a glycolytic state when endogenous nitric oxide (NO) reprograms mitochondrial metabolism by limiting aconitase 2 and pyruvate dehydrogenase (PDH) activity. Here, we provide evidence that NO targets the PDH complex by using lipoate to generate nitroxyl (HNO). PDH E2-associated lipoate is modified in NO-rich macrophages while the PDH E3 enzyme, also known as dihydrolipoamide dehydrogenase (DLD), is irreversibly inhibited. Mechanistically, we show that lipoate facilitates NO-mediated production of HNO, which interacts with thiols forming irreversible modifications including sulfinamide. In addition, we reveal a macrophage signature of proteins with reduction-resistant modifications, including in DLD, and identify potential HNO targets. Consistently, DLD enzyme is modified in an HNO-dependent manner at Cys477 and Cys484, and molecular modeling and mutagenesis show these modifications impair the formation of DLD homodimers. In conclusion, our work demonstrates that HNO is produced physiologically. Moreover, the production of HNO is dependent on the lipoate-rich PDH complex facilitating irreversible modifications that are critical to NO-dependent metabolic rewiring.
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Affiliation(s)
- Erika M Palmieri
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Ronald Holewinski
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | | | - Ciro L Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Jonathan M Weiss
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Vincenzo Tragni
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via E. Orabona, 4, Bari, 70125, Italy
| | - Katrina M Miranda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21702, USA
| | - David A Wink
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA
| | - Daniel W McVicar
- Cancer Innovation Laboratory, NCI-Frederick, Frederick, MD, 21702, USA.
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3
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Arrigoni R, Santacroce L, Ballini A, Palese LL. AI-Aided Search for New HIV-1 Protease Ligands. Biomolecules 2023; 13:biom13050858. [PMID: 37238727 DOI: 10.3390/biom13050858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The availability of drugs capable of blocking the replication of microorganisms has been one of the greatest triumphs in the history of medicine, but the emergence of an ever-increasing number of resistant strains poses a serious problem for the treatment of infectious diseases. The search for new potential ligands for proteins involved in the life cycle of pathogens is, therefore, an extremely important research field today. In this work, we have considered the HIV-1 protease, one of the main targets for AIDS therapy. Several drugs are used today in clinical practice whose mechanism of action is based on the inhibition of this enzyme, but after years of use, even these molecules are beginning to be interested by resistance phenomena. We used a simple artificial intelligence system for the initial screening of a data set of potential ligands. These results were validated by docking and molecular dynamics, leading to the identification of a potential new ligand of the enzyme which does not belong to any known class of HIV-1 protease inhibitors. The computational protocol used in this work is simple and does not require large computational power. Furthermore, the availability of a large number of structural information on viral proteins and the presence of numerous experimental data on their ligands, with which it is possible to compare the results obtained with computational methods, make this research field the ideal terrain for the application of these new computational techniques.
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Affiliation(s)
- Roberto Arrigoni
- Bioenergetics and Molecular Biotechnologies (IBIOM), CNR Institute of Biomembranes, 70125 Bari, Italy
| | - Luigi Santacroce
- Interdisciplinary Department of Medicine (DIM), University of Bari Aldo Moro, 70124 Bari, Italy
| | - Andrea Ballini
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy
| | - Luigi Leonardo Palese
- Department of Translational Biomedicine and Neurosciences-(DiBraiN), University of Bari Aldo Moro, 70124 Bari, Italy
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4
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Targeting mitochondrial impairment for the treatment of cardiovascular diseases: From hypertension to ischemia-reperfusion injury, searching for new pharmacological targets. Biochem Pharmacol 2023; 208:115405. [PMID: 36603686 DOI: 10.1016/j.bcp.2022.115405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
Mitochondria and mitochondrial proteins represent a group of promising pharmacological target candidates in the search of new molecular targets and drugs to counteract the onset of hypertension and more in general cardiovascular diseases (CVDs). Indeed, several mitochondrial pathways result impaired in CVDs, showing ATP depletion and ROS production as common traits of cardiac tissue degeneration. Thus, targeting mitochondrial dysfunction in cardiomyocytes can represent a successful strategy to prevent heart failure. In this context, the identification of new pharmacological targets among mitochondrial proteins paves the way for the design of new selective drugs. Thanks to the advances in omics approaches, to a greater availability of mitochondrial crystallized protein structures and to the development of new computational approaches for protein 3D-modelling and drug design, it is now possible to investigate in detail impaired mitochondrial pathways in CVDs. Furthermore, it is possible to design new powerful drugs able to hit the selected pharmacological targets in a highly selective way to rescue mitochondrial dysfunction and prevent cardiac tissue degeneration. The role of mitochondrial dysfunction in the onset of CVDs appears increasingly evident, as reflected by the impairment of proteins involved in lipid peroxidation, mitochondrial dynamics, respiratory chain complexes, and membrane polarization maintenance in CVD patients. Conversely, little is known about proteins responsible for the cross-talk between mitochondria and cytoplasm in cardiomyocytes. Mitochondrial transporters of the SLC25A family, in particular, are responsible for the translocation of nucleotides (e.g., ATP), amino acids (e.g., aspartate, glutamate, ornithine), organic acids (e.g. malate and 2-oxoglutarate), and other cofactors (e.g., inorganic phosphate, NAD+, FAD, carnitine, CoA derivatives) between the mitochondrial and cytosolic compartments. Thus, mitochondrial transporters play a key role in the mitochondria-cytosol cross-talk by leading metabolic pathways such as the malate/aspartate shuttle, the carnitine shuttle, the ATP export from mitochondria, and the regulation of permeability transition pore opening. Since all these pathways are crucial for maintaining healthy cardiomyocytes, mitochondrial carriers emerge as an interesting class of new possible pharmacological targets for CVD treatments.
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5
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Gomari MM, Tarighi P, Choupani E, Abkhiz S, Mohamadzadeh M, Rostami N, Sadroddiny E, Baammi S, Uversky VN, Dokholyan NV. Structural evolution of Delta lineage of SARS-CoV-2. Int J Biol Macromol 2023; 226:1116-1140. [PMID: 36435470 PMCID: PMC9683856 DOI: 10.1016/j.ijbiomac.2022.11.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022]
Abstract
One of the main obstacles in prevention and treatment of COVID-19 is the rapid evolution of the SARS-CoV-2 Spike protein. Given that Spike is the main target of common treatments of COVID-19, mutations occurring at this virulent factor can affect the effectiveness of treatments. The B.1.617.2 lineage of SARS-CoV-2, being characterized by many Spike mutations inside and outside of its receptor-binding domain (RBD), shows high infectivity and relative resistance to existing cures. Here, utilizing a wide range of computational biology approaches, such as immunoinformatics, molecular dynamics (MD), analysis of intrinsically disordered regions (IDRs), protein-protein interaction analyses, residue scanning, and free energy calculations, we examine the structural and biological attributes of the B.1.617.2 Spike protein. Furthermore, the antibody design protocol of Rosetta was implemented for evaluation the stability and affinity improvement of the Bamlanivimab (LY-CoV55) antibody, which is not capable of interactions with the B.1.617.2 Spike. We observed that the detected mutations in the Spike of the B1.617.2 variant of concern can cause extensive structural changes compatible with the described variation in immunogenicity, secondary and tertiary structure, oligomerization potency, Furin cleavability, and drug targetability. Compared to the Spike of Wuhan lineage, the B.1.617.2 Spike is more stable and binds to the Angiotensin-converting enzyme 2 (ACE2) with higher affinity.
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Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences, Tehran 1449614535, Iran,Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Parastoo Tarighi
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Shadi Abkhiz
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Masoud Mohamadzadeh
- Department of Chemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas 7916193145, Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak 3848177584, Iran
| | - Esmaeil Sadroddiny
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Soukayna Baammi
- African Genome Centre (AGC), Mohammed VI Polytechnic University, Benguerir 43150, Morocco
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA,Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia,Correspondence to: V.N. Uversky, Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33620, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 16802, USA,Corresponding author
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6
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Miniero DV, Gambacorta N, Spagnoletta A, Tragni V, Loizzo S, Nicolotti O, Pierri CL, De Palma A. New Insights Regarding Hemin Inhibition of the Purified Rat Brain 2-Oxoglutarate Carrier and Relationships with Mitochondrial Dysfunction. J Clin Med 2022; 11:7519. [PMID: 36556135 PMCID: PMC9785169 DOI: 10.3390/jcm11247519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
A kinetic analysis of the transport assays on the purified rat brain 2-oxoglutarate/malate carrier (OGC) was performed starting from our recent results reporting about a competitive inhibitory behavior of hemin, a physiological porphyrin derivative, on the OGC reconstituted in an active form into proteoliposomes. The newly provided transport data and the elaboration of the kinetic equations show evidence that hemin exerts a mechanism of partially competitive inhibition, coupled with the formation of a ternary complex hemin-carrier substrate, when hemin targets the OGC from the matrix face. A possible interpretation of the provided kinetic analysis, which is supported by computational studies, could indicate the existence of a binding region responsible for the inhibition of the OGC and supposedly involved in the regulation of OGC activity. The proposed regulatory binding site is located on OGC mitochondrial matrix loops, where hemin could establish specific interactions with residues involved in the substrate recognition and/or conformational changes responsible for the translocation of mitochondrial carrier substrates. The regulatory binding site would be placed about 6 Å below the substrate binding site of the OGC, facing the mitochondrial matrix, and would allow the simultaneous binding of hemin and 2-oxoglutarate or malate to different regions of the carrier. Overall, the presented experimental and computational analyses help to shed light on the possible existence of the hemin-carrier substrate ternary complex, confirming the ability of the OGC to bind porphyrin derivatives, and in particular hemin, with possible consequences for the mitochondrial redox state mediated by the malate/aspartate shuttle led by the mitochondrial carriers OGC and AGC.
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Affiliation(s)
- Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Environment, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Nicola Gambacorta
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Anna Spagnoletta
- ENEA Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Trisaia Research Centre, S.S. 106 Jonica, Km 419,500, 75026 Rotondella (MT), Italy
| | - Vincenzo Tragni
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Stefano Loizzo
- Department of Cardiovascular, Endocrine-Metabolic Diseases and Aging, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Roma, Italy
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Ciro Leonardo Pierri
- Department of Pharmacy-Pharmaceutical Sciences, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies and Environment, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70125 Bari, Italy
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7
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Giangregorio N, Pierri CL, Tonazzi A, Incampo G, Tragni V, De Grassi A, Indiveri C. Proline/Glycine residues of the PG-levels guide conformational changes along the transport cycle in the mitochondrial carnitine/acylcarnitine carrier (SLC25A20). Int J Biol Macromol 2022; 221:1453-1465. [PMID: 36122779 DOI: 10.1016/j.ijbiomac.2022.09.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
Mitochondrial carnitine/acylcarnitine carrier (CAC) is a member of the mitochondrial carrier (MC) family and imports acylcarnitine into the mitochondrial matrix in exchange for carnitine, playing a pivotal role in carnitine shuttle, crucial for fatty acid oxidation. The crystallized structure of CAC has not been solved yet, however, the availability of several in vitro/in silico studies, also based on the crystallized structures of the ADP/ATP carrier in the cytosolic-conformation and in the matrix-conformation, has made possible to confirm the hypothesis of the single-binding centered-gated pore mechanism for all the members of the MC family. In addition, our recent bioinformatics analyses allowed quantifying in silico the importance of protein residues of MC substrate binding region, of those involved in the formation of the matrix and cytosolic gates, and of those belonging to the Pro/Gly (PG) levels, proposed to be crucial for the tilting/kinking/bending of the six MC transmembrane helices, funneling the substrate translocation pathway. Here we present a combined in silico/in vitro analysis employed for investigating the role played by a group of 6 proline residues and 6 glycine residues, highly conserved in CAC, belonging to MC PG-levels. Residues of the PG-levels surround the similarly located MC common substrate binding region, and were proposed to lead conformational changes and substrate translocation, following substrate binding. For our analysis, we employed 3D molecular modeling approaches, alanine scanning site-directed mutagenesis and in vitro transport assays. Our analysis reveals that P130 (H3), G268 (H6) and G220 (H5), mutated in alanine, affect severely CAC transport activity (mutant catalytic efficiency lower than 5 % compared to the wild type CAC), most likely due to their major role in triggering CAC conformational changes, following carnitine binding. Notably, P30A (H1) and G121A (H3) CAC mutants, increase the carnitine uptake up to 217 % and 112 %, respectively, compared to the wild type CAC.
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Affiliation(s)
- Nicola Giangregorio
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy.
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy.
| | - Annamaria Tonazzi
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy
| | - Giovanna Incampo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Vincenzo Tragni
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy; Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Italy, Via E. Orabona, 4, 70126 Bari, Italy
| | - Cesare Indiveri
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Amendola 122/O, 70126 Bari, Italy; Department DiBEST (Biologia, Ecologia, Scienze della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, Via Bucci 4C, 87036 Arcavacata di Rende, Italy
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8
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Porcelli L, Di Fonte R, Pierri CL, Fucci L, Saponaro C, Armenio A, Serratì S, Strippoli S, Fasano R, Volpicella M, Daprile R, Tommasi S, Ressa CM, Guida M, Azzariti A. BRAF V600E;K601Q metastatic melanoma patient-derived organoids and docking analysis to predict the response to targeted therapy. Pharmacol Res 2022; 182:106323. [PMID: 35752358 DOI: 10.1016/j.phrs.2022.106323] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/31/2022] [Accepted: 06/19/2022] [Indexed: 10/17/2022]
Abstract
The V600E mutation in BRAF is associated with increased phosphorylation of Erk1/2 and high sensitivity to BRAFi/MEKi combination in metastatic melanoma. In very few patients, a tandem mutation in BRAF, V600 and K601, causes a different response to BRAFi/MEKi combination. BRAFV600E;K601Q patient-derived organoids (PDOs) were generated to investigate targeted therapy efficacy and docking analysis was used to assess BRAFV600E;K601Q interactions with Vemurafenib. PDOs were not sensitive to Vemurafenib and Cobimetinib given alone and sensitive to their combination, although not as responsive as BRAFV600E PDOs. The docking analysis justified such a result showing that the tandem mutation in BRAF reduced the affinity for Vemurafenib. Tumor analysis showed that BRAFV600E;K601Q displayed both increased phosphorylation of Erk1/2 at cytoplasmic level and activation of Notch resistance signaling. This prompted us to inhibit Notch signaling with Nirogacestat, achieving a greater antitumor response and providing PDOs-based evaluation of treatment efficacy in such rare metastatic melanoma.
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Affiliation(s)
- Letizia Porcelli
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Roberta Di Fonte
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Livia Fucci
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Concetta Saponaro
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Andrea Armenio
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Simona Serratì
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Sabino Strippoli
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Rossella Fasano
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Rossana Daprile
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Stefania Tommasi
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Cosmo M Ressa
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Michele Guida
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy
| | - Amalia Azzariti
- IRCCS Istituto Tumori Giovanni Paolo II, V.le O. Flacco, 65, 70124 Bari, Italy.
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9
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Tragni V, Primiano G, Tummolo A, Cafferati Beltrame L, La Piana G, Sgobba MN, Cavalluzzi MM, Paterno G, Gorgoglione R, Volpicella M, Guerra L, Marzulli D, Servidei S, De Grassi A, Petrosillo G, Lentini G, Pierri CL. Personalized Medicine in Mitochondrial Health and Disease: Molecular Basis of Therapeutic Approaches Based on Nutritional Supplements and Their Analogs. Molecules 2022; 27:3494. [PMID: 35684429 PMCID: PMC9182050 DOI: 10.3390/molecules27113494] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/24/2022] [Accepted: 05/26/2022] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial diseases (MDs) may result from mutations affecting nuclear or mitochondrial genes, encoding mitochondrial proteins, or non-protein-coding mitochondrial RNA. Despite the great variability of affected genes, in the most severe cases, a neuromuscular and neurodegenerative phenotype is observed, and no specific therapy exists for a complete recovery from the disease. The most used treatments are symptomatic and based on the administration of antioxidant cocktails combined with antiepileptic/antipsychotic drugs and supportive therapy for multiorgan involvement. Nevertheless, the real utility of antioxidant cocktail treatments for patients affected by MDs still needs to be scientifically demonstrated. Unfortunately, clinical trials for antioxidant therapies using α-tocopherol, ascorbate, glutathione, riboflavin, niacin, acetyl-carnitine and coenzyme Q have met a limited success. Indeed, it would be expected that the employed antioxidants can only be effective if they are able to target the specific mechanism, i.e., involving the central and peripheral nervous system, responsible for the clinical manifestations of the disease. Noteworthily, very often the phenotypes characterizing MD patients are associated with mutations in proteins whose function does not depend on specific cofactors. Conversely, the administration of the antioxidant cocktails might determine the suppression of endogenous oxidants resulting in deleterious effects on cell viability and/or toxicity for patients. In order to avoid toxicity effects and before administering the antioxidant therapy, it might be useful to ascertain the blood serum levels of antioxidants and cofactors to be administered in MD patients. It would be also worthwhile to check the localization of mutations affecting proteins whose function should depend (less or more directly) on the cofactors to be administered, for estimating the real need and predicting the success of the proposed cofactor/antioxidant-based therapy.
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Affiliation(s)
- Vincenzo Tragni
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Guido Primiano
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Albina Tummolo
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Lucas Cafferati Beltrame
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Gianluigi La Piana
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Noemi Sgobba
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Maria Maddalena Cavalluzzi
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Giulia Paterno
- Department of Metabolic Diseases, Clinical Genetics and Diabetology, Giovanni XXIII Children Hospital, Azienda Ospedaliero-Universitaria Consorziale, Via Amendola 207, 70126 Bari, Italy; (A.T.); (G.P.)
| | - Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Lorenzo Guerra
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Domenico Marzulli
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Serenella Servidei
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (G.P.); (S.S.)
- Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
| | - Giuseppe Petrosillo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), 70126 Bari, Italy;
| | - Giovanni Lentini
- Department of Pharmacy—Pharmaceutical Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy;
| | - Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona, 4, 70125 Bari, Italy; (V.T.); (L.C.B.); (G.L.P.); (M.N.S.); (R.G.); (M.V.); (L.G.); (A.D.G.)
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Favia M, Gerbino A, Notario E, Tragni V, Sgobba MN, Dell’Aquila ME, Pierri CL, Guerra L, Ciani E. The Non-Gastric H+/K+ ATPase (ATP12A) Is Expressed in Mammalian Spermatozoa. Int J Mol Sci 2022; 23:ijms23031048. [PMID: 35162971 PMCID: PMC8835340 DOI: 10.3390/ijms23031048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/15/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
H+/K+ ATPase Type 2 is an heteromeric membrane protein involved in cation transmembrane transport and consists of two subunits: a specific α subunit (ATP12A) and a non-specific β subunit. The aim of this study was to demonstrate the presence and establish the localization of ATP12A in spermatozoa from Bubalus bubalis, Bos taurus and Ovis aries. Immunoblotting revealed, in all three species, a major band (100 kDa) corresponding to the expected molecular mass. The ATP12A immunolocalization pattern showed, consistently in the three species, a strong signal at the acrosome. These results, described here for the first time in spermatozoa, are consistent with those observed for the β1 subunit of Na+/K+ ATPase, suggesting that the latter may assemble with the α subunit to produce a functional ATP12A dimer in sperm cells. The above scenario appeared to be nicely supported by 3D comparative modeling and interaction energy calculations. The expression of ATP12A during different stages of bovine sperm maturation progressively increased, moving from epididymis to deferent ducts. Based on overall results, we hypothesize that ATP12A may play a role in acrosome reactions. Further studies will be required in order to address the functional role of this target protein in sperm physiology.
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11
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Modeling SARS-CoV-2 spike/ACE2 protein-protein interactions for predicting the binding affinity of new spike variants for ACE2, and novel ACE2 structurally related human protein targets, for COVID-19 handling in the 3PM context. EPMA J 2022; 13:149-175. [PMID: 35013687 PMCID: PMC8732965 DOI: 10.1007/s13167-021-00267-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/04/2021] [Indexed: 12/12/2022]
Abstract
Aims The rapid spread of new SARS-CoV-2 variants has highlighted the crucial role played in the infection by mutations occurring at the SARS-CoV-2 spike receptor binding domain (RBD) in the interactions with the human ACE2 receptor. In this context, it urgently needs to develop new rapid tools for quickly predicting the affinity of ACE2 for the SARS-CoV-2 spike RBD protein variants to be used with the ongoing SARS-CoV-2 genomic sequencing activities in the clinics, aiming to gain clues about the transmissibility and virulence of new variants, to prevent new outbreaks and to quickly estimate the severity of the disease in the context of the 3PM. Methods In our study, we used a computational pipeline for calculating the interaction energies at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface for a selected group of characterized infectious variants of concern/interest (VoC/VoI). By using our pipeline, we built 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for the VoC B.1.1.7-United Kingdom (carrying the mutations of concern/interest N501Y, S494P, E484K at the RBD), P.1-Japan/Brazil (RBD mutations: K417T, E484K, N501Y), B.1.351-South Africa (RBD mutations: K417N, E484K, N501Y), B.1.427/B.1.429-California (RBD mutations: L452R), the B.1.141 (RBD mutations: N439K), and the recent B.1.617.1-India (RBD mutations: L452R; E484Q) and the B.1.620 (RBD mutations: S477N; E484K). Then, we used the obtained 3D comparative models of the SARS-CoV-2 spike RBD/ACE2 protein complexes for predicting the interaction energies at the protein–protein interface. Results Along SARS-CoV-2 mutation database screening and mutation localization analysis, it was ascertained that the most dangerous mutations at VoC/VoI spike proteins are located mainly at three regions of the SARS-CoV-2 spike “boat-shaped” receptor binding motif, on the RBD domain. Notably, the P.1 Japan/Brazil variant present three mutations, K417T, E484K, N501Y, located along the entire receptor binding motif, which apparently determines the highest interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, among those calculated. Conversely, it was also observed that the replacement of a single acidic/hydrophilic residue with a basic residue (E484K or N439K) at the “stern” or “bow” regions, of the boat-shaped receptor binding motif on the RBD, appears to determine an interaction energy with ACE2 receptor higher than that observed with single mutations occurring at the “hull” region or with other multiple mutants. In addition, our pipeline allowed searching for ACE2 structurally related proteins, i.e., THOP1 and NLN, which deserve to be investigated for their possible involvement in interactions with the SARS-CoV-2 spike protein, in those tissues showing a low expression of ACE2, or as a novel receptor for future spike variants. A freely available web-tool for the in silico calculation of the interaction energy at the SARS-CoV-2 spike RBD/ACE2 protein–protein interface, starting from the sequences of the investigated spike and/or ACE2 variants, was made available for the scientific community at: https://www.mitoairm.it/covid19affinities. Conclusion In the context of the PPPM/3PM, the employment of the described pipeline through the provided webservice, together with the ongoing SARS-CoV-2 genomic sequencing, would help to predict the transmissibility of new variants sequenced from future patients, depending on SARS-CoV-2 genomic sequencing activities and on the specific amino acid replacement and/or on its location on the SARS-CoV-2 spike RBD, to put in play all the possible counteractions for preventing the most deleterious scenarios of new outbreaks, taking into consideration that a greater transmissibility has not to be necessarily related to a more severe manifestation of the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00267-w.
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12
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Menga A, Favia M, Spera I, Vegliante MC, Gissi R, De Grassi A, Laera L, Campanella A, Gerbino A, Carrà G, Canton M, Loizzi V, Pierri CL, Cormio G, Mazzone M, Castegna A. N-acetylaspartate release by glutaminolytic ovarian cancer cells sustains protumoral macrophages. EMBO Rep 2021; 22:e51981. [PMID: 34260142 PMCID: PMC8419692 DOI: 10.15252/embr.202051981] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Glutaminolysis is known to correlate with ovarian cancer aggressiveness and invasion. However, how this affects the tumor microenvironment is elusive. Here, we show that ovarian cancer cells become addicted to extracellular glutamine when silenced for glutamine synthetase (GS), similar to naturally occurring GS-low, glutaminolysis-high ovarian cancer cells. Glutamine addiction elicits a crosstalk mechanism whereby cancer cells release N-acetylaspartate (NAA) which, through the inhibition of the NMDA receptor, and synergistically with IL-10, enforces GS expression in macrophages. In turn, GS-high macrophages acquire M2-like, tumorigenic features. Supporting this in␣vitro model, in silico data and the analysis of ascitic fluid isolated from ovarian cancer patients prove that an M2-like macrophage phenotype, IL-10 release, and NAA levels positively correlate with disease stage. Our study uncovers the unprecedented role of glutamine metabolism in modulating macrophage polarization in highly invasive ovarian cancer and highlights the anti-inflammatory, protumoral function of NAA.
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Affiliation(s)
- Alessio Menga
- Department of Molecular Biotechnologies and Health SciencesUniversity of TurinTurinItaly
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Molecular Biotechnology CenterTurinItaly
| | - Maria Favia
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Iolanda Spera
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Maria C Vegliante
- Haematology and Cell Therapy UnitIRCCS‐Istituto Tumori ‘Giovanni Paolo II'BariItaly
| | - Rosanna Gissi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Luna Laera
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Annalisa Campanella
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Andrea Gerbino
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Giovanna Carrà
- Molecular Biotechnology CenterTurinItaly
- Department of Clinical and Biological SciencesUniversity of TurinOrbassanoItaly
| | - Marcella Canton
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza ‐ IRPPadovaItaly
| | - Vera Loizzi
- Policlinico University of Bari “Aldo Moro”BariItaly
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Gennaro Cormio
- Policlinico University of Bari “Aldo Moro”BariItaly
- Gynecologic Oncology UnitIRCCSIstituto Tumori Giovanni Paolo IIBariItaly
| | - Massimiliano Mazzone
- Department of Molecular Biotechnologies and Health SciencesUniversity of TurinTurinItaly
- Molecular Biotechnology CenterTurinItaly
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer BiologyDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza ‐ IRPPadovaItaly
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13
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Maqoud F, Scala R, Tragni V, Pierri CL, Perrone MG, Scilimati A, Tricarico D. Zoledronic Acid as a Novel Dual Blocker of KIR6.1/2-SUR2 Subunits of ATP-Sensitive K + Channels: Role in the Adverse Drug Reactions. Pharmaceutics 2021; 13:pharmaceutics13091350. [PMID: 34575427 PMCID: PMC8465290 DOI: 10.3390/pharmaceutics13091350] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 12/17/2022] Open
Abstract
Zoledronic acid (ZOL) is used as a bone-specific antiresorptive drug with antimyeloma effects. Adverse drug reactions (A.D.R.) are associated with ZOL-therapy, whose mechanics are unknown. ZOL is a nitrogen-containing molecule whose structure shows similarities with nucleotides, ligands of ATP-sensitive K+ (KATP) channels. We investigated the action of ZOL by performing in vitro patch-clamp experiments on native KATP channels in murine skeletal muscle fibers, bone cells, and recombinant subunits in cell lines, and by in silico docking the nucleotide site on KIR and SUR, as well as the glibenclamide site. ZOL fully inhibited the KATP currents recorded in excised macro-patches from Extensor digitorum longus (EDL) and Soleus (SOL) muscle fibers with an IC50 of 1.2 ± 1.4 × 10−6 and 2.1 ± 3.7 × 10−10 M, respectively, and the KATP currents recorded in cell-attached patches from primary long bone cells with an IC50 of 1.6 ± 2.8 × 10−10 M. ZOL fully inhibited a whole-cell KATP channel current of recombinant KIR6.1-SUR2B and KIR6.2-SUR2A subunits expressed in HEK293 cells with an IC50 of 3.9 ± 2.7 × 10−10 M and 7.1 ± 3.1 × 10−6 M, respectively. The rank order of potency in inhibiting the KATP currents was: KIR6.1-SUR2B/SOL-KATP/osteoblast-KATP > KIR6.2-SUR2A/EDL-KATP >>> KIR6.2-SUR1 and KIR6.1-SUR1. Docking investigation revealed that the drug binds to the ADP/ATP sites on KIR6.1/2 and SUR2A/B and on the sulfonylureas site showing low binding energy <6 Kcal/mol for the KIR6.1/2-SUR2 subunits vs. the <4 Kcal/mol for the KIR6.2-SUR1. The IC50 of ZOL to inhibit the KIR6.1/2-SUR2A/B channels were correlated with its musculoskeletal and cardiovascular risks. We first showed that ZOL blocks at subnanomolar concentration musculoskeletal KATP channels and cardiac and vascular KIR6.2/1-SUR2 channels.
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Affiliation(s)
- Fatima Maqoud
- Section of Pharmacology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy; (F.M.); (R.S.)
| | - Rosa Scala
- Section of Pharmacology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy; (F.M.); (R.S.)
| | - Vincenzo Tragni
- Laboratory of Biochemistry, Structural and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy; (V.T.); (C.L.P.)
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Structural and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy; (V.T.); (C.L.P.)
- BROWSer S.r.l., University of Bari “Aldo Moro”, Via E. Orabona, 4, 70126 Bari, Italy
| | - Maria Grazia Perrone
- Medicinal Chemistry Section, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy; (M.G.P.); (A.S.)
| | - Antonio Scilimati
- Medicinal Chemistry Section, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy; (M.G.P.); (A.S.)
| | - Domenico Tricarico
- Section of Pharmacology, Department of Pharmacy-Pharmaceutical Sciences, University of Bari, Via Orabona 4, 70125 Bari, Italy; (F.M.); (R.S.)
- Correspondence:
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14
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Sachla AJ, Luo Y, Helmann JD. Manganese impairs the QoxABCD terminal oxidase leading to respiration-associated toxicity. Mol Microbiol 2021; 116:729-742. [PMID: 34097790 DOI: 10.1111/mmi.14767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/29/2022]
Abstract
Cell physiology relies on metalloenzymes and can be easily disrupted by imbalances in metal ion pools. Bacillus subtilis requires manganese for growth and has highly regulated mechanisms for import and efflux that help maintain homeostasis. Cells defective for manganese (Mn) efflux are highly sensitive to intoxication, but the processes impaired by Mn excess are often unknown. Here, we employed a forward genetics approach to identify pathways affected by manganese intoxication. Our results highlight a central role for the membrane-localized electron transport chain in metal intoxication during aerobic growth. In the presence of elevated manganese, there is an increased generation of reactive radical species associated with dysfunction of the major terminal oxidase, the cytochrome aa3 heme-copper menaquinol oxidase (QoxABCD). Intoxication is suppressed by diversion of menaquinol to alternative oxidases or by a mutation affecting heme A synthesis that is known to convert QoxABCD from an aa3 to a bo3 -type oxidase. Manganese sensitivity is also reduced by derepression of the MhqR regulon, which protects cells against reactive quinones. These results suggest that dysfunction of the cytochrome aa3 -type quinol oxidase contributes to metal-induced intoxication.
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Affiliation(s)
- Ankita J Sachla
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Yuanchan Luo
- Department of Microbiology, Cornell University, Ithaca, NY, USA.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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Sardanelli AM, Isgrò C, Palese LL. SARS-CoV-2 Main Protease Active Site Ligands in the Human Metabolome. Molecules 2021; 26:1409. [PMID: 33807773 PMCID: PMC7961382 DOI: 10.3390/molecules26051409] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
In late 2019, a global pandemic occurred. The causative agent was identified as a member of the Coronaviridae family, called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, we present an analysis on the substances identified in the human metabolome capable of binding the active site of the SARS-CoV-2 main protease (Mpro). The substances present in the human metabolome have both endogenous and exogenous origins. The aim of this research was to find molecules whose biochemical and toxicological profile was known that could be the starting point for the development of antiviral therapies. Our analysis revealed numerous metabolites-including xenobiotics-that bind this protease, which are essential to the lifecycle of the virus. Among these substances, silybin, a flavolignan compound and the main active component of silymarin, is particularly noteworthy. Silymarin is a standardized extract of milk thistle, Silybum marianum, and has been shown to exhibit antioxidant, hepatoprotective, antineoplastic, and antiviral activities. Our results-obtained in silico and in vitro-prove that silybin and silymarin, respectively, are able to inhibit Mpro, representing a possible food-derived natural compound that is useful as a therapeutic strategy against COVID-19.
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Affiliation(s)
- Anna Maria Sardanelli
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
- Department of Medicine, University Campus Bio-Medico of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Camilla Isgrò
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
- Department of Medicine, University Campus Bio-Medico of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy
| | - Luigi Leonardo Palese
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
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Tragni V, Cotugno P, De Grassi A, Massari F, Di Ronzo F, Aresta AM, Zambonin C, Sanzani SM, Ippolito A, Pierri CL. Targeting mitochondrial metabolite transporters in Penicillium expansum for reducing patulin production. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:158-181. [PMID: 33250320 DOI: 10.1016/j.plaphy.2020.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/30/2020] [Accepted: 07/13/2020] [Indexed: 06/12/2023]
Abstract
There is an increasing need of alternative treatments to control fungal infection and consequent mycotoxin accumulation in harvested fruits and vegetables. Indeed, only few biological targets of antifungal agents have been characterized and can be used for limiting fungal spread from decayed fruits/vegetables to surrounding healthy ones during storage. On this concern, a promising target of new antifungal treatments may be represented by mitochondrial proteins due to some species-specific functions played by mitochondria in fungal morphogenesis, drug resistance and virulence. One of the most studied mycotoxins is patulin produced by several species of Penicillium and Aspergillus genera. Patulin is toxic to many biological systems including bacteria, higher plants and animalia. Although precise biochemical mechanisms of patulin toxicity in humans are not completely clarified, its high presence in fresh and processed apple fruits and other apple-based products makes necessary developing a strategy for limiting its presence/accumulation. Patulin biosynthetic pathway consists of an enzymatic cascade, whose first step is represented by the synthesis of 6-methylsalicylic acid, obtained from the condensation of one acetyl-CoA molecule with three malonyl-CoA molecules. The most abundant acetyl-CoA precursor is represented by citrate produced by mitochondria. In the present investigation we report about the possibility to control patulin production through the inhibition of mitochondrial/peroxisome transporters involved in the export of acetyl-CoA precursors from mitochondria and/or peroxisomes, with specific reference to the predicted P. expansum mitochondrial Ctp1p, DTC, Sfc1p, Oac1p and peroxisomal PXN carriers.
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Affiliation(s)
- Vincenzo Tragni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Pietro Cotugno
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy
| | - Federica Massari
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Francesco Di Ronzo
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy
| | - Antonella Maria Aresta
- Chemistry Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | - Carlo Zambonin
- Chemistry Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
| | | | - Antonio Ippolito
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy.
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125, Bari, Italy; BROWSer S.r.l. (https://browser-bioinf.com/) c/o, Department of Biosciences, Biotechnologies, Biopharmaceutics, University "Aldo Moro" of Bari, Via E. Orabona, 4, 70126, Bari, Italy.
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17
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Tragni V, Cotugno P, De Grassi A, Cavalluzzi MM, Mincuzzi A, Lentini G, Sanzani SM, Ippolito A, Pierri CL. Targeting Penicillium expansum GMC Oxidoreductase with High Affinity Small Molecules for Reducing Patulin Production. BIOLOGY 2020; 10:biology10010021. [PMID: 33396459 PMCID: PMC7824139 DOI: 10.3390/biology10010021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 12/21/2022]
Abstract
Simple Summary With the urgent necessity of potential treatments for limiting mycotoxin production and postharvest fungal rots, we propose a combined in silico/in vitro/in vivo strategy for the rapid and effective identification of bioactive small molecules, chosen among a chemical library hosting approved drugs and phytochemicals, to be used after harvest. The molecular target of our analysis was the GMC oxidoreductase from Penicillium expansum involved in the biosynthesis of patulin, a mycotoxin that can contaminate many foods, especially fruits and fruit-based products. The employed in silico/in vitro/in vivo assays described in our study proved the effectiveness of our strategy and in particular of two small molecules, 6-hydroxycoumarin (structurally related to umbelliferon, an already characterized patulin synthase inhibitor) and meticrane (an already approved drug) in reducing patulin accumulation. Our findings highly recommend the mentioned ligands to be subjected to further analysis for being used in the next future in place of other more toxic compounds, in postharvest treatments based on dipping or drenching methods. Abstract Flavine adenine dinucleotide (FAD) dependent glucose methanol choline oxidoreductase (GMC oxidoreductase) is the terminal key enzyme of the patulin biosynthetic pathway. GMC oxidoreductase catalyzes the oxidative ring closure of (E)-ascladiol to patulin. Currently, no protein involved in the patulin biosynthesis in Penicillium expansum has been experimentally characterized or solved by X-ray diffraction. Consequently, nothing is known about P. expansum GMC oxidoreductase substrate-binding site and mode of action. In the present investigation, a 3D comparative model for P. expansum GMC oxidoreductase has been described. Furthermore, a multistep computational approach was used to identify P. expansum GMC oxidoreductase residues involved in the FAD binding and in substrate recognition. Notably, the obtained 3D comparative model of P. expansum GMC oxidoreductase was used for performing a virtual screening of a chemical/drug library, which allowed to predict new GMC oxidoreductase high affinity ligands to be tested in in vitro/in vivo assays. In vitro assays performed in presence of 6-hydroxycoumarin and meticrane, among the highly affinity predicted binders, confirmed a dose-dependent inhibition (17–81%) of patulin production by 6-hydroxycoumarin (10 µM–1 mM concentration range), whereas the approved drug meticrane inhibited patulin production by 43% already at 10 µM. Furthermore, 6-hydroxycoumarin and meticrane caused a 60 and 41% reduction of patulin production, respectively, in vivo on apples at 100 µg/wound.
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Affiliation(s)
- Vincenzo Tragni
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
| | - Pietro Cotugno
- Biology Department, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy;
| | - Anna De Grassi
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy;
- BROWSer S.r.l., c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
| | - Maria Maddalena Cavalluzzi
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy; (M.M.C.); (G.L.)
| | - Annamaria Mincuzzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
| | - Giovanni Lentini
- Dipartimento di Farmacia—Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, via Orabona 4, 70125 Bari, Italy; (M.M.C.); (G.L.)
| | - Simona Marianna Sanzani
- CIHEAM Bari, Via Ceglie 9, 70010 Valenzano (BA), Italy
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
| | - Antonio Ippolito
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy; (V.T.); (A.M.)
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
| | - Ciro Leonardo Pierri
- Laboratory of Biochemistry, Molecular and Structural Biology, Department of Biosciences, Biotechnologies, Biopharmaceutics, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy;
- BROWSer S.r.l., c/o Department of Biosciences, Biotechnologies, Biopharmaceutics, University “Aldo Moro” of Bari, Via E. Orabona, 4, 70126 Bari, Italy
- Correspondence: (S.M.S.); (A.I.); ; (C.L.P.); Tel.: +39-0805443614 (C.L.P.); Fax: +39-0805442770 (C.L.P.)
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18
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Menga A, Serra M, Todisco S, Riera‐Domingo C, Ammarah U, Ehling M, Palmieri EM, Di Noia MA, Gissi R, Favia M, Pierri CL, Porporato PE, Castegna A, Mazzone M. Glufosinate constrains synchronous and metachronous metastasis by promoting anti-tumor macrophages. EMBO Mol Med 2020; 12:e11210. [PMID: 32885605 PMCID: PMC7539200 DOI: 10.15252/emmm.201911210] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 01/19/2023] Open
Abstract
Glutamine synthetase (GS) generates glutamine from glutamate and controls the release of inflammatory mediators. In macrophages, GS activity, driven by IL10, associates to the acquisition of M2-like functions. Conditional deletion of GS in macrophages inhibits metastasis by boosting the formation of anti-tumor, M1-like, tumor-associated macrophages (TAMs). From this basis, we evaluated the pharmacological potential of GS inhibitors in targeting metastasis, identifying glufosinate as a specific human GS inhibitor. Glufosinate was tested in both cultured macrophages and on mice bearing metastatic lung, skin and breast cancer. We found that glufosinate rewires macrophages toward an M1-like phenotype both at the primary tumor and metastatic site, countering immunosuppression and promoting vessel sprouting. This was also accompanied to a reduction in cancer cell intravasation and extravasation, leading to synchronous and metachronous metastasis growth inhibition, but no effects on primary tumor growth. Glufosinate treatment was well-tolerated, without liver and brain toxicity, nor hematopoietic defects. These results identify GS as a druggable enzyme to rewire macrophage functions and highlight the potential of targeting metabolic checkpoints in macrophages to treat cancer metastasis.
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Affiliation(s)
- Alessio Menga
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Marina Serra
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Simona Todisco
- Department of SciencesUniversity of BasilicataPotenzaItaly
| | - Carla Riera‐Domingo
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Ummi Ammarah
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| | - Manuel Ehling
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Erika M Palmieri
- Cancer & Inflammation ProgramNational Cancer InstituteFrederickMDUSA
| | | | - Rosanna Gissi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Maria Favia
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Paolo E Porporato
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- IBIOM‐CNRInstitute of Biomembranes, Bioenergetics and Molecular BiotechnologiesNational Research CouncilBariItaly
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
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19
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Palese LL. Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters. Biochim Biophys Acta Gen Subj 2020; 1864:129480. [DOI: 10.1016/j.bbagen.2019.129480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 10/27/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022]
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20
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Palese LL. The oxygen-oxygen distance of water in crystallographic data sets. Data Brief 2020; 28:105076. [PMID: 31970272 PMCID: PMC6965711 DOI: 10.1016/j.dib.2019.105076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 11/02/2022] Open
Abstract
Water is a key component of cellular biochemistry and numerous water molecules are visible in crystallographic structures. Here we report a series of data sets of crystallographic water: a high resolution data set, a cytochrome c oxidase (subunit I) data set and a carbonic anhydrase data set. These data support the evidence that short distance water molecule pairs are present both at the surface and inside the cavities of proteins. These data are related to article entitled “Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters” (Palese, 2020) [1].
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21
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Trisolini L, Gambacorta N, Gorgoglione R, Montaruli M, Laera L, Colella F, Volpicella M, De Grassi A, Pierri CL. FAD/NADH Dependent Oxidoreductases: From Different Amino Acid Sequences to Similar Protein Shapes for Playing an Ancient Function. J Clin Med 2019; 8:jcm8122117. [PMID: 31810296 PMCID: PMC6947548 DOI: 10.3390/jcm8122117] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Flavoprotein oxidoreductases are members of a large protein family of specialized dehydrogenases, which include type II NADH dehydrogenase, pyridine nucleotide-disulphide oxidoreductases, ferredoxin-NAD+ reductases, NADH oxidases, and NADH peroxidases, playing a crucial role in the metabolism of several prokaryotes and eukaryotes. Although several studies have been performed on single members or protein subgroups of flavoprotein oxidoreductases, a comprehensive analysis on structure-function relationships among the different members and subgroups of this great dehydrogenase family is still missing. Here, we present a structural comparative analysis showing that the investigated flavoprotein oxidoreductases have a highly similar overall structure, although the investigated dehydrogenases are quite different in functional annotations and global amino acid composition. The different functional annotation is ascribed to their participation in species-specific metabolic pathways based on the same biochemical reaction, i.e., the oxidation of specific cofactors, like NADH and FADH2. Notably, the performed comparative analysis sheds light on conserved sequence features that reflect very similar oxidation mechanisms, conserved among flavoprotein oxidoreductases belonging to phylogenetically distant species, as the bacterial type II NADH dehydrogenases and the mammalian apoptosis-inducing factor protein, until now retained as unique protein entities in Bacteria/Fungi or Animals, respectively. Furthermore, the presented computational analyses will allow consideration of FAD/NADH oxidoreductases as a possible target of new small molecules to be used as modulators of mitochondrial respiration for patients affected by rare diseases or cancer showing mitochondrial dysfunction, or antibiotics for treating bacterial/fungal/protista infections.
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Affiliation(s)
| | | | | | | | | | | | | | - Anna De Grassi
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
| | - Ciro Leonardo Pierri
- Correspondence: (A.D.G.); or (C.L.P.); Tel.: +39-080-544-3614 (A.D.G. & C.L.P.); Fax: +39-080-544-2770 (A.D.G. & C.L.P.)
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22
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Palese LL. Explaining leak states in the proton pump of heme-copper oxidases observed in single-molecule experiments. Biophys Chem 2019; 256:106276. [PMID: 31731070 DOI: 10.1016/j.bpc.2019.106276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 11/28/2022]
Abstract
Heme-copper oxidases couple the exergonic oxygen reduction with the endergonic proton translocation. Redox-linked structural changes have been localized in deeply buried regions of the protein, near the low-potential heme. How these movements can modulate distant gating events along the intramolecular proton path, where the entry (exit) of pumped proton occurs, is a major concern for the proton pump models. Generally, these models associate, more or less directly, all translocation events with redox transitions. Although they can account for many phenomenological aspects of the pump, evidences from single-molecules experiments about leak states of the pump represent a formidable challenge. Disconnecting the redox-linked pKa shifts of the proton loading site from the external barriers, we obtain a simple stochastic mechanism which behaves similarly to the real enzyme, able to reverse the flow of the proton transfer.
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23
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Ding Z, Sun C, Yi SM, Gennis RB, Dikanov SA. The Ubiquinol Binding Site of Cytochrome bo3 from Escherichia coli Accommodates Menaquinone and Stabilizes a Functional Menasemiquinone. Biochemistry 2019; 58:4559-4569. [PMID: 31644263 DOI: 10.1021/acs.biochem.9b00750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytochrome bo3, one of three terminal oxygen reductases in the aerobic respiratory chain of Escherichia coli, has been well characterized as a ubiquinol oxidase. The ability of cytochrome bo3 to catalyze the two-electron oxidation of ubiquinol-8 requires the enzyme to stabilize the one-electron oxidized ubisemiquinone species that is a transient intermediate in the reaction. Cytochrome bo3 has been shown recently to also utilize demethylmenaquinol-8 as a substrate that, along with menaquinol-8, replaces ubiquinol-8 when E. coli is grown under microaerobic or anaerobic conditions. In this work, we show that its steady-state turnover with 2,3-dimethyl-1,4-naphthoquinol, a water-soluble menaquinol analogue, is just as efficient as with ubiquinol-1. Using pulsed electron paramagnetic resonance spectroscopy, we demonstrate that the same residues in cytochrome bo3 that stabilize the semiquinone state of ubiquinone also stabilize the semiquinone state of menaquinone, with the hydrogen bond strengths and the distribution of unpaired spin density accommodated for the different substrate. Catalytic function with menaquinol is more tolerant of mutations at the active site than with ubiquinol. A mutation of one of the stabilizing residues (R71H in subunit I) that eliminates the ubiquinol oxidase activity of cytochrome bo3 does not abolish activity with soluble menaquinol analogues.
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Affiliation(s)
- Ziqiao Ding
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Chang Sun
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sophia M Yi
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Robert B Gennis
- Department of Biochemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Center for Biophysics and Computational Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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24
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Palese LL. Cytochrome c oxidase structures suggest a four-state stochastic pump mechanism. Phys Chem Chem Phys 2019; 21:4822-4830. [DOI: 10.1039/c8cp07365a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A simple stochastic model for a cytochrome c oxidase proton pump.
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Affiliation(s)
- Luigi Leonardo Palese
- University of Bari “Aldo Moro”
- Department of Basic Medical Sciences
- Neurosciences and Sense Organs (SMBNOS)
- Bari
- Italy
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25
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Melin F, Sabuncu S, Choi SK, Leprince A, Gennis RB, Hellwig P. Role of the tightly bound quinone for the oxygen reaction of cytochrome
bo
3
oxidase from
Escherichia coli. FEBS Lett 2018; 592:3380-3387. [DOI: 10.1002/1873-3468.13263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Frédéric Melin
- Chimie de la Matière Complexe UMR 7140 Laboratoire de Bioélectrochimie et Spectroscopie CNRS‐Université de Strasbourg France
| | - Sinan Sabuncu
- Chimie de la Matière Complexe UMR 7140 Laboratoire de Bioélectrochimie et Spectroscopie CNRS‐Université de Strasbourg France
| | - Sylvia K. Choi
- Center for Biophysics and Computational Biology University of Illinois Urbana IL USA
- Department of Biochemistry University of Illinois Urbana IL USA
| | - Agathe Leprince
- Chimie de la Matière Complexe UMR 7140 Laboratoire de Bioélectrochimie et Spectroscopie CNRS‐Université de Strasbourg France
| | | | - Petra Hellwig
- Chimie de la Matière Complexe UMR 7140 Laboratoire de Bioélectrochimie et Spectroscopie CNRS‐Université de Strasbourg France
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26
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Palese LL. Conformations of the HIV-1 protease: A crystal structure data set analysis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1416-1422. [PMID: 28846854 DOI: 10.1016/j.bbapap.2017.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 07/22/2017] [Accepted: 08/10/2017] [Indexed: 12/25/2022]
Abstract
The HIV protease is an important drug target for HIV/AIDS therapy, and its structure and function have been extensively investigated. This enzyme performs an essential role in viral maturation by processing specific cleavage sites in the Gag and Gag-Pol precursor polyproteins so as to release their mature forms. This 99 amino acid aspartic protease works as a homodimer, with the active site localized in a central cavity capped by two flexible flap regions. The dimer presents closed or open conformations, which are involved in the substrate binding and release. Here the results of the analysis of a HIV-1 protease data set containing 552 dimer structures are reported. Different dimensionality reduction methods have been used in order to get information from this multidimensional database. Most of the structures in the data set belong to two conformational clusters. An interesting observation that comes from the analysis of these data is that some protease sequences are localized preferentially in specific areas of the conformational landscape of this protein.
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Affiliation(s)
- Luigi Leonardo Palese
- University of Bari "Aldo Moro", Department of Basic Medical Sciences, Neurosciences and Sense Organs (SMBNOS), Bari 70124, Italy.
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27
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Choi SK, Schurig-Briccio L, Ding Z, Hong S, Sun C, Gennis RB. Location of the Substrate Binding Site of the Cytochrome bo 3 Ubiquinol Oxidase from Escherichia coli. J Am Chem Soc 2017; 139:8346-8354. [PMID: 28538096 DOI: 10.1021/jacs.7b03883] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cytochrome bo3 is a respiratory proton-pumping oxygen reductase that is a member of the heme-copper superfamily that utilizes ubiquinol-8 (Q8H2) as a substrate. The current consensus model has Q8H2 oxidized at a low affinity site (QL), passing electrons to a tightly bound quinone cofactor at a high affinity site (QH site) that stabilizes the one-electron reduced ubisemiquinone, facilitating the transfer of electrons to the redox active metal centers where O2 is reduced to water. The current work shows that the Q8 bound to the QH site is more dynamic than previously thought. In addition, mutations of residues at the QH site that do not abolish activity have been re-examined and shown to have properties expected of mutations at the substrate binding site (QL): an increase in the KM of the substrate ubiquinol-1 (up to 4-fold) and an increase in the apparent Ki of the inhibitor HQNO (up to 8-fold). The data suggest that there is only one binding site for ubiquinol in cyt bo3 and that site corresponds to the QH site.
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Affiliation(s)
- Sylvia K Choi
- Center for Biophysics and Quantitative Biology, University of Illinois , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Lici Schurig-Briccio
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Ziqiao Ding
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Sangjin Hong
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Chang Sun
- Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
| | - Robert B Gennis
- Center for Biophysics and Quantitative Biology, University of Illinois , Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois , Urbana, Illinois 61801, United States
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28
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Choi SK, Lin MT, Ouyang H, Gennis RB. Searching for the low affinity ubiquinone binding site in cytochrome bo 3 from Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:366-370. [PMID: 28235459 DOI: 10.1016/j.bbabio.2017.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/11/2017] [Accepted: 02/14/2017] [Indexed: 11/25/2022]
Abstract
The cytochrome bo3 ubiquinol oxidase is one of three respiratory oxygen reductases in the aerobic respiratory chain of Escherichia coli. The generally accepted model of catalysis assumes that cyt bo3 contains two distinct ubiquinol binding sites: (i) a low affinity (QL) site which is the traditional substrate binding site; and (ii) a high affinity (QH) site where a "permanently" bound quinone acts as a cofactor, taking two electrons from the substrate quinol and passing them one-by-one to the heme b component of the enzyme which, in turn, transfers them to the heme o3/CuB active site. Whereas the residues at the QH site are well defined, the location of the QL site remains unknown. The published X-ray structure does not contain quinone, and substantial amounts of the protein are missing as well. A recent bioinformatics study by Bossis et al. [Biochem J. (2014) 461, 305-314] identified a sequence motif G163EFX3GWX2Y173 as the likely QL site in the family of related quinol oxidases. In the current work, this was tested by site-directed mutagenesis. The results show that these residues are not important for catalytic function and do not define the QL substrate binding site.
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Affiliation(s)
- Sylvia K Choi
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA
| | - Myat T Lin
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA
| | - Hanlin Ouyang
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Robert B Gennis
- Center for Biophysics and Quantitative Biology, University of Illinois, Urbana, IL 61801, USA; Department of Chemistry, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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29
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Abstract
Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate-specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophosphate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and dimethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O₂ is served by two major oxidoreductases (oxidases), cytochrome bo₃ encoded by cyoABCDE and cytochrome bd encoded by cydABX. Terminal oxidases of aerobic respiratory chains of bacteria, which use O₂ as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo₃ and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo₃ and cytochrome bd. The E. coli membrane contains three types of quinones that all have an octaprenyl side chain (C₄₀). It has been proposed that the bo₃ oxidase can have two ubiquinone-binding sites with different affinities. "WHAT'S NEW" IN THE REVISED ARTICLE: The revised article comprises additional information about subunit composition of cytochrome bd and its role in bacterial resistance to nitrosative and oxidative stresses. Also, we present the novel data on the electrogenic function of appBCX-encoded cytochrome bd-II, a second bd-type oxidase that had been thought not to contribute to generation of a proton motive force in E. coli, although its spectral properties closely resemble those of cydABX-encoded cytochrome bd.
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30
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Pierri CL, Bossis F, Punzi G, De Grassi A, Cetrone M, Parisi G, Tricarico D. Molecular modeling of antibodies for the treatment of TNFα-related immunological diseases. Pharmacol Res Perspect 2016; 4:e00197. [PMID: 26977294 PMCID: PMC4777268 DOI: 10.1002/prp2.197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 10/20/2015] [Accepted: 10/24/2015] [Indexed: 12/13/2022] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) have high efficacy in treating TNF α-related immunological diseases. Other than neutralizing TNF α, these IgG1 antibodies exert Fc receptor-mediated effector functions such as the complement-dependent cytotoxicity (CDC) and antibody-dependent cell cytotoxicity (ADCC). The crystallizable fragment (Fc) of these IgG1 contains a single glycosylation site at Asn 297/300 that is essential for the CDC and ADCC. Glycosylated antibodies lacking core fucosylation showed an improved ADCC. However, no structural data are available concerning the ligand-binding interaction of these mAbs used in TNF α-related diseases and the role of the fucosylation. We therefore used comparative modeling for generating complete 3D mAb models that include the antigen-binding fragment (Fab) portions of infliximab, complexed with TNF α (4G3Y.pdb), the Fc region of the human IGHG1 fucosylated (3SGJ) and afucosylated (3SGK) complexed with the Fc receptor subtype Fcγ RIIIA, and the Fc region of a murine immunoglobulin (1IGT). After few thousand steps of energy minimization on the resulting 3D mAb models, minimized final models were used to quantify interactions occurring between Fcγ RIIIA and the fucosylated/afucosylated Fc fragments. While fucosylation does not affect Fab-TNF α interactions, we found that in the absence of fucosylation the Fc-mAb domain and Fcγ RIIIA are closer and new strong interactions are established between G129 of the receptor and S301 of the Chimera 2 Fc mAb; new polar interactions are also established between the Chimera 2 Fc residues Y299, N300, and S301 and the Fcγ RIIIA residues K128, G129, R130, and R155. These data help to explain the reduced ADCC observed in the fucosylated mAbs suggesting the specific AA residues involved in binding interactions.
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Affiliation(s)
- Ciro Leonardo Pierri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Fabrizio Bossis
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Giuseppe Punzi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | | | - Giovanni Parisi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
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