1
|
Rajapaksha N, Yao H, Cook A, Seibold S, Liu L, Battaile KP, Fontenot L, Donnarumma F, Lovell S, Rivera M. Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity. Front Mol Biosci 2024; 11:1390745. [PMID: 38841187 PMCID: PMC11150526 DOI: 10.3389/fmolb.2024.1390745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the P. aeruginosa PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of P. aeruginosa bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as P. aeruginosa Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe2+ utilizing O2 or H2O2 as oxidant, and the resultant Fe3+ is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of P. aeruginosa cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases.
Collapse
Affiliation(s)
- Nimesha Rajapaksha
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Huili Yao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Aisha Cook
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Steve Seibold
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | - Lijun Liu
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | | | - Leo Fontenot
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Scott Lovell
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| |
Collapse
|
2
|
Morais KLP, Ciccone L, Stura E, Alvarez-Flores MP, Mourier G, Driessche MV, Sciani JM, Iqbal A, Kalil SP, Pereira GJ, Marques-Porto R, Cunegundes P, Juliano L, Servent D, Chudzinski-Tavassi AM. Structural and functional properties of the Kunitz-type and C-terminal domains of Amblyomin-X supporting its antitumor activity. Front Mol Biosci 2023; 10:1072751. [PMID: 36845546 PMCID: PMC9948614 DOI: 10.3389/fmolb.2023.1072751] [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: 10/17/2022] [Accepted: 01/12/2023] [Indexed: 02/11/2023] Open
Abstract
Amblyomin-X is a Kunitz-type FXa inhibitor identified through the transcriptome analysis of the salivary gland from Amblyomma sculptum tick. This protein consists of two domains of equivalent size, triggers apoptosis in different tumor cell lines, and promotes regression of tumor growth, and reduction of metastasis. To study the structural properties and functional roles of the N-terminal (N-ter) and C-terminal (C-ter) domains of Amblyomin-X, we synthesized them by solid-phase peptide synthesis, solved the X-Ray crystallographic structure of the N-ter domain, confirming its Kunitz-type signature, and studied their biological properties. We show here that the C-ter domain is responsible for the uptake of Amblyomin-X by tumor cells and highlight the ability of this domain to deliver intracellular cargo by the strong enhancement of the intracellular detection of molecules with low cellular-uptake efficiency (p15) after their coupling with the C-ter domain. In contrast, the N-ter Kunitz domain of Amblyomin-X is not capable of crossing through the cell membrane but is associated with tumor cell cytotoxicity when it is microinjected into the cells or fused to TAT cell-penetrating peptide. Additionally, we identify the minimum length C-terminal domain named F2C able to enter in the SK-MEL-28 cells and induces dynein chains gene expression modulation, a molecular motor that plays a role in the uptake and intracellular trafficking of Amblyomin-X.
Collapse
Affiliation(s)
- K. L. P. Morais
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil,Laboratory of Development and Innovation, Butantan Institute, São Paulo, Brazil,Department of Biochemistry, Federal University of São Paulo, São Paulo, Brazil
| | - L. Ciccone
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA SIMoS, Gif-sur-Yvette, France,Department of Pharmacy, University of Pisa, Pisa, Italy
| | - E. Stura
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA SIMoS, Gif-sur-Yvette, France
| | - M. P. Alvarez-Flores
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil
| | - G. Mourier
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA SIMoS, Gif-sur-Yvette, France
| | - M. Vanden Driessche
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA SIMoS, Gif-sur-Yvette, France
| | - J. M. Sciani
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil
| | - A. Iqbal
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil,Laboratory of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - S. P. Kalil
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil
| | - G. J. Pereira
- Department of Pharmacology, Federal University of São Paulo, São Paulo, Brazil
| | - R. Marques-Porto
- Laboratory of Development and Innovation, Butantan Institute, São Paulo, Brazil
| | - P. Cunegundes
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil,Department of Biochemistry, Federal University of São Paulo, São Paulo, Brazil
| | - L. Juliano
- Department of Biophysics, Federal University of São Paulo, São Paulo, Brazil
| | - D. Servent
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA SIMoS, Gif-sur-Yvette, France,*Correspondence: D. Servent, ; A. M. Chudzinski-Tavassi,
| | - A. M. Chudzinski-Tavassi
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, São Paulo, Brazil,Laboratory of Development and Innovation, Butantan Institute, São Paulo, Brazil,*Correspondence: D. Servent, ; A. M. Chudzinski-Tavassi,
| |
Collapse
|
3
|
Fruchart Gaillard C, Ouadda ABD, Ciccone L, Girard E, Mikaeeli S, Evagelidis A, Le Dévéhat M, Susan-Resiga D, Lajeunesse EC, Nozach H, Ramos OHP, Thureau A, Legrand P, Prat A, Dive V, Seidah NG. Molecular interactions of PCSK9 with an inhibitory nanobody, CAP1 and HLA-C: Functional regulation of LDLR levels. Mol Metab 2022; 67:101662. [PMID: 36566984 PMCID: PMC9816786 DOI: 10.1016/j.molmet.2022.101662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE The liver-derived circulating PCSK9 enhances the degradation of the LDL receptor (LDLR) in endosomes/lysosomes. PCSK9 inhibition or silencing is presently used in clinics worldwide to reduce LDL-cholesterol, resulting in lower incidence of cardiovascular disease and possibly cancer/metastasis. The mechanism by which the PCSK9-LDLR complex is sorted to degradation compartments is not fully understood. We previously suggested that out of the three M1, M2 and M3 subdomains of the C-terminal Cys/His-rich-domain (CHRD) of PCSK9, only M2 is critical for the activity of extracellular of PCSK9 on cell surface LDLR. This likely implicates the binding of M2 to an unknown membrane-associated "protein X" that would escort the complex to endosomes/lysosomes for degradation. We reported that a nanobody P1.40 binds the M1 and M3 domains of the CHRD and inhibits the function of PCSK9. It was also reported that the cytosolic adenylyl cyclase-associated protein 1 (CAP1) could bind M1 and M3 subdomains and enhance the activity of PCSK9. In this study, we determined the 3-dimensional structure of the CHRD-P1.40 complex to understand the intricate interplay between P1.40, CAP1 and PCSK9 and how they regulate LDLR degradation. METHODS X-ray diffraction of the CHRD-P1.40 complex was analyzed with a 2.2 Å resolution. The affinity and interaction of PCSK9 or CHRD with P1.40 or CAP1 was analyzed by atomic modeling, site-directed mutagenesis, bio-layer interferometry, expression in hepatic cell lines and immunocytochemistry to monitor LDLR degradation. The CHRD-P1.40 interaction was further analyzed by deep mutational scanning and binding assays to validate the role of predicted critical residues. Conformational changes and atomic models were obtained by small angle X-ray scattering (SAXS). RESULTS We demonstrate that PCSK9 exists in a closed or open conformation and that P1.40 favors the latter by binding key residues in the M1 and M3 subdomains of the CHRD. Our data show that CAP1 is well secreted by hepatic cells and binds extracellular PCSK9 at distinct residues in the M1 and M3 modules and in the acidic prodomain. CAP1 stabilizes the closed conformation of PCSK9 and prevents P1.40 binding. However, CAP1 siRNA only partially inhibited PCSK9 activity on the LDLR. By modeling the previously reported interaction between M2 and an R-X-E motif in HLA-C, we identified Glu567 and Arg549 as critical M2 residues binding HLA-C. Amazingly, these two residues are also required for the PCSK9-induced LDLR degradation. CONCLUSIONS The present study reveals that CAP1 enhances the function of PCSK9, likely by twisting the protein into a closed configuration that exposes the M2 subdomain needed for targeting the PCSK9-LDLR complex to degradation compartments. We hypothesize that "protein X", which is expected to guide the LDLR-PCSK9-CAP1 complex to these compartments after endocytosis into clathrin-coated vesicles, is HLA-C or a similar MHC-I family member. This conclusion is supported by the PCSK9 natural loss-of-function Q554E and gain-of-function H553R M2 variants, whose consequences are anticipated by our modeling.
Collapse
Affiliation(s)
- Carole Fruchart Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191 Gif-sur-Yvette, France
| | - Ali Ben Djoudi Ouadda
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Lidia Ciccone
- Synchrotron SOLEIL, HelioBio group, l'Orme des Merisiers, 91190 Saint-Aubin, France; Department of Pharmacy, University of Pisa, Via Bonanno, 6, 56126 Pisa, Italy
| | - Emmanuelle Girard
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Sepideh Mikaeeli
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Alexandra Evagelidis
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Maïlys Le Dévéhat
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Delia Susan-Resiga
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Evelyne Cassar Lajeunesse
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191 Gif-sur-Yvette, France
| | - Hervé Nozach
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191 Gif-sur-Yvette, France
| | - Oscar Henrique Pereira Ramos
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191 Gif-sur-Yvette, France
| | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio group, l'Orme des Merisiers, 91190 Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio group, l'Orme des Merisiers, 91190 Saint-Aubin, France
| | - Annik Prat
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada
| | - Vincent Dive
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SIMoS, 91191 Gif-sur-Yvette, France
| | - Nabil G Seidah
- Montreal Clinical Research Institute (IRCM), affiliated to the University of Montreal, Laboratory of Biochemical Neuroendocrinology, Montreal, Quebec H2W 1R7, Canada.
| |
Collapse
|
4
|
MT9, a natural peptide from black mamba venom antagonizes the muscarinic type 2 receptor and reverses the M2R-agonist-induced relaxation in rat and human arteries. Biomed Pharmacother 2022; 150:113094. [PMID: 35658242 DOI: 10.1016/j.biopha.2022.113094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/25/2022] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
All five muscarinic receptors have important physiological roles. The endothelial M2 and M3 subtypes regulate arterial tone through direct coupling to Gq or Gi/o proteins. Yet, we lack selective pharmacological drugs to assess the respective contribution of muscarinic receptors to a given function. We used mamba snake venoms to identify a selective M2R ligand to investigate its contribution to arterial contractions. Using a bio-guided screening binding assay, we isolated MT9 from the black mamba venom, a three-finger toxin active on the M2R subtype. After sequencing and chemical synthesis of MT9, we characterized its structure by X-ray diffraction and determined its pharmacological characteristics by binding assays, functional tests, and ex vivo experiments on rat and human arteries. Although MT9 belongs to the three-finger fold toxins family, it is phylogenetically apart from the previously discovered muscarinic toxins, suggesting that two groups of peptides evolved independently and in a convergent way to target muscarinic receptors. The affinity of MT9 for the M2R is 100 times stronger than that for the four other muscarinic receptors. It also antagonizes the M2R/Gi pathways in cell-based assays. MT9 acts as a non-competitive antagonist against acetylcholine or arecaine, with low nM potency, for the activation of isolated rat mesenteric arteries. These results were confirmed on human internal mammary arteries. In conclusion, MT9 is the first fully characterized M2R-specific natural toxin. It should provide a tool for further understanding of the effect of M2R in various arteries and may position itself as a new drug candidate in cardio-vascular diseases.
Collapse
|
5
|
Antioxidant Quercetin 3-O-Glycosylated Plant Flavonols Contribute to Transthyretin Stabilization. CRYSTALS 2022. [DOI: 10.3390/cryst12050638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Plants are rich in secondary metabolites, which are often useful as a relevant source of nutraceuticals. Quercetin (QUE) is a flavonol aglycone able to bind Transthyretin (TTR), a plasma protein that under pathological conditions can lose its native structure leading to fibrils formation and amyloid diseases onset. Here, the dual nature of five quercetin 3-O-glycosylated flavonol derivatives, isolated from different plant species, such as possible binders of TTR and antioxidants, was investigated. The crystal structure of 3-O-β-D-galactopyranoside in complex with TTR was solved, suggesting that not only quercetin but also its metabolites can contribute to stabilizing the TTR tetramer.
Collapse
|
6
|
Ciccone L, Nencetti S, Camodeca C, Ortore G, Cuffaro D, Socci S, Orlandini E. Synthesis and Evaluation of Monoaryl Derivatives as Transthyretin Fibril Formation Inhibitors. Pharm Chem J 2022. [DOI: 10.1007/s11094-022-02600-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
7
|
Cuffaro D, Camodeca C, Tuccinardi T, Ciccone L, Bartsch JW, Kellermann T, Cook L, Nuti E, Rossello A. Discovery of Dimeric Arylsulfonamides as Potent ADAM8 Inhibitors. ACS Med Chem Lett 2021; 12:1787-1793. [PMID: 35111280 PMCID: PMC8805605 DOI: 10.1021/acsmedchemlett.1c00411] [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: 07/28/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
![]()
The metalloproteinase
ADAM8 is upregulated in several cancers but
has a dispensable function under physiological conditions. In tumor
cells, ADAM8 is involved in invasion, migration, and angiogenesis.
The use of bivalent inhibitors could impair migration and invasion
through the double binding to a homodimeric form of ADAM8 located
on the cell surface of tumor cells. Herein we report the rational
design and synthesis of the first dimeric ADAM8 inhibitors selective
over ADAM10 and matrix metalloproteinases. Bivalent derivatives have
been obtained by dimerizing the structure of a previously described
ADAM17 inhibitor, JG26. In particular, derivative 2 was
shown to inhibit ADAM8 proteolytic activity in vitro and in cell-based assays at nanomolar concentration. Moreover, it
was more effective than the parent monomeric compound in blocking
invasiveness in the breast cancer MDA-MB-231 cell line, thus supporting
our hypothesis about the importance of inhibiting the active homodimer
of ADAM8.
Collapse
Affiliation(s)
- Doretta Cuffaro
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Caterina Camodeca
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Lidia Ciccone
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Jörg W Bartsch
- Department of Neurosurgery, Marburg University, Baldingerstrasse, 35033 Marburg, Germany
| | - Tanja Kellermann
- Department of Neurosurgery, Marburg University, Baldingerstrasse, 35033 Marburg, Germany
| | - Lena Cook
- Department of Neurosurgery, Marburg University, Baldingerstrasse, 35033 Marburg, Germany
| | - Elisa Nuti
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Armando Rossello
- Department of Pharmacy, University of Pisa, via Bonanno 6, 56126 Pisa, Italy
| |
Collapse
|
8
|
Physiological Metals Can Induce Conformational Changes in Transthyretin Structure: Neuroprotection or Misfolding Induction? CRYSTALS 2021. [DOI: 10.3390/cryst11040354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Transthyretin (TTR) is a plasma homotetrameric protein that transports thyroxine and retinol. TTR itself, under pathological conditions, dissociates into partially unfolded monomers that aggregate and form fibrils. Metal ions such as Zn2+, Cu2+, Fe2+, Mn2+ and Ca2+ play a controversial role in the TTR amyloidogenic pathway. TTR is also present in cerebrospinal fluid (CSF), where it behaves as one of the major Aβ-binding-proteins. The interaction between TTR and Aβ is stronger in the presence of high concentrations of Cu2+. Crystals of TTR, soaked in solutions of physiological metals such as Cu2+ and Fe2+, but not Mn2+, Zn2+, Fe3+, Al3+, Ni2+, revealed an unusual conformational change. Here, we investigate the effects that physiological metals have on TTR, in order to understand if metals can induce a specific and active conformation of TTR that guides its Aβ-scavenging role. The capability of certain metals to induce and accelerate its amyloidogenic process is also discussed.
Collapse
|
9
|
Soldano A, Yao H, Punchi Hewage AND, Meraz K, Annor-Gyamfi JK, Bunce RA, Battaile KP, Lovell S, Rivera M. Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells. ACS Infect Dis 2021; 7:123-140. [PMID: 33269912 PMCID: PMC7802073 DOI: 10.1021/acsinfecdis.0c00669] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 01/05/2023]
Abstract
Bacteria depend on a well-regulated iron homeostasis to survive adverse environments. A key component of the iron homeostasis machinery is the compartmentalization of Fe3+ in bacterioferritin and its subsequent mobilization as Fe2+ to satisfy metabolic requirements. In Pseudomonas aeruginosa Fe3+ is compartmentalized in bacterioferritin (BfrB), and its mobilization to the cytosol requires binding of a ferredoxin (Bfd) to reduce the stored Fe3+ and release the soluble Fe2+. Blocking the BfrB-Bfd complex in P. aeruginosa by deletion of the bfd gene triggers an irreversible accumulation of Fe3+ in BfrB, concomitant cytosolic iron deficiency and significant impairment of biofilm development. Herein we report that small molecules developed to bind BfrB at the Bfd binding site block the BfrB-Bfd complex, inhibit the mobilization of iron from BfrB in P. aeruginosa cells, elicit a bacteriostatic effect on planktonic cells, and are bactericidal to cells embedded in mature biofilms.
Collapse
Affiliation(s)
- Anabel Soldano
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | - Huili Yao
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| | | | - Kevin Meraz
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Joel K. Annor-Gyamfi
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Richard A. Bunce
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Kevin P. Battaile
- NYX, New York Structural Biology Center, Upton, New York 11973, United States
| | - Scott Lovell
- Protein
Structure Laboratory, University of Kansas, 2034 Becker Drive, Lawrence, Kansas 66047, United States
| | - Mario Rivera
- Department
of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
10
|
Thompson AP, Wegener KL, Booker GW, Polyak SW, Bruning JB. Precipitant-ligand exchange technique reveals the ADP binding mode in Mycobacterium tuberculosis dethiobiotin synthetase. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:965-972. [PMID: 30289406 DOI: 10.1107/s2059798318010136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/13/2018] [Indexed: 11/10/2022]
Abstract
Dethiobiotin synthetase from Mycobacterium tuberculosis (MtDTBS) is a promising antituberculosis drug target. Small-molecule inhibitors that target MtDTBS provide a route towards new therapeutics for the treatment of antibiotic-resistant tuberculosis. Adenosine diphosphate (ADP) is an inhibitor of MtDTBS; however, structural studies into its mechanism of inhibition have been unsuccessful owing to competitive binding to the enzyme by crystallographic precipitants such as citrate and sulfate. Here, a crystallographic technique termed precipitant-ligand exchange has been developed to exchange protein-bound precipitants with ligands of interest. Proof of concept for the exchange method was demonstrated using cytidine triphosphate (CTP), which adopted the same binding mechanism as that obtained with traditional crystal-soaking techniques. Precipitant-ligand exchange also yielded the previously intractable structure of MtDTBS in complex with ADP solved to 2.4 Å resolution. This result demonstrates the utility of precipitant-ligand exchange, which may be widely applicable to protein crystallography.
Collapse
Affiliation(s)
- Andrew P Thompson
- Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Kate L Wegener
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Grant W Booker
- Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - Steven W Polyak
- Molecular and Biomedical Science, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| |
Collapse
|
11
|
Ciccone L, Fruchart-Gaillard C, Mourier G, Savko M, Nencetti S, Orlandini E, Servent D, Stura EA, Shepard W. Copper mediated amyloid-β binding to Transthyretin. Sci Rep 2018; 8:13744. [PMID: 30213975 PMCID: PMC6137083 DOI: 10.1038/s41598-018-31808-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/23/2018] [Indexed: 01/27/2023] Open
Abstract
Transthyretin (TTR), a homotetrameric protein that transports thyroxine and retinol both in plasma and in cerebrospinal (CSF) fluid provides a natural protective response against Alzheimer's disease (AD), modulates amyloid-β (Aβ) deposition by direct interaction and co-localizes with Aβ in plaques. TTR levels are lower in the CSF of AD patients. Zn2+, Mn2+ and Fe2+ transform TTR into a protease able to cleave Aβ. To explain these activities, monomer dissociation or conformational changes have been suggested. Here, we report that when TTR crystals are exposed to copper or iron salts, the tetramer undergoes a significant conformational change that alters the dimer-dimer interface and rearranges residues implicated in TTR's ability to neutralize Aβ. We also describe the conformational changes in TTR upon the binding of the various metal ions. Furthermore, using bio-layer interferometry (BLI) with immobilized Aβ(1-28), we observe the binding of TTR only in the presence of copper. Such Cu2+-dependent binding suggests a recognition mechanism whereby Cu2+ modulates both the TTR conformation, induces a complementary Aβ structure and may participate in the interaction. Cu2+-soaked TTR crystals show a conformation different from that induced by Fe2+, and intriguingly, TTR crystals grown in presence of Aβ(1-28) show different positions for the copper sites from those grown its absence.
Collapse
Affiliation(s)
- Lidia Ciccone
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France.,Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Carole Fruchart-Gaillard
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Gilles Mourier
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Martin Savko
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France
| | - Susanna Nencetti
- Dipartimento di Farmacia, Universitá di Pisa, Via Bonanno 6, 56126, Pisa, Italy
| | - Elisabetta Orlandini
- Dipartimento di Scienze della Terra, Universitá di Pisa, Via Santa Maria 53-55, 56100, Pisa, Italy
| | - Denis Servent
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Enrico A Stura
- CEA Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingènierie Moléculaire des Protéines (SIMOPRO), Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - William Shepard
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, BP 48, 91192, Gif-sur-Yvette, France.
| |
Collapse
|
12
|
Crystallization of Liganded Phosphatases in the HAD Superfamily. Methods Enzymol 2018; 607:157-184. [PMID: 30149857 DOI: 10.1016/bs.mie.2018.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Phosphotransferases catalyze reactions on chemically diverse molecules in organisms from all domains of life. The haloalkanoate dehalogenase superfamily (HADSF) is a model system for phosphoryl transfer enzymes as members catalyze phosphoester hydrolase, phosphonate hydrolase, and phosphomutase reactions on sugars, lipids, nucleotides, and peptides. Because these reactions are fundamental to essential metabolic transformations, understanding the mechanism and determinants of substrate specificity in the HADSF is critical. Structure/function relationships in the superfamily have also been leveraged in the development of methodologies for the assignment of enzyme function. Enzyme complexes with substrate, product, and analogs of the ground state or intermediate/transition state can be studied via high-resolution macromolecular crystallography to provide insight to the relative location of residues and ligands, as well as associated enzyme conformational states. This knowledge can aid in inhibitor design for phosphohydrolase reactions and target-specific therapeutics. Here we describe experimental approaches to capture liganded X-ray crystallographic structures of HADSF members. A number of these methods can be employed generally, including other families of phosphohydrolases and enzymes catalyzing phosphoryl transfer.
Collapse
|
13
|
Ciccone L, Policar C, Stura EA, Shepard W. Human TTR conformation altered by rhenium tris-carbonyl derivatives. J Struct Biol 2016; 195:353-364. [PMID: 27402536 DOI: 10.1016/j.jsb.2016.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/13/2023]
Abstract
Transthyretin (TTR) is a 54 kDa homotetrameric serum protein that transports thyroxine (T4) and retinol. TTR is potentially amyloidogenic due to homotetramer dissociation into monomeric intermediates that self-assemble as amyloid deposits and insoluble fibrils. Most crystallographic structures, including those of amyloidogenic variants show the same tetramer without major variations in the monomer-monomer interface nor in the volume of the interdimeric cavity. Soaking TTR crystals in a solution containing rhenium tris-carbonyl derivatives yields a TTR conformer never observed before. Only one of the two monomers of the crystallographic dimer is significantly altered, and the inner part of the T4 binding cavity is expanded at one end and shrunk at the other. The result redefines the mechanism of allosteric communication between the two sites, suggesting that negative cooperativity is a function of dimer asymmetry, which can be induced through internal or external binding. An aspect that remains unexplained is why the conformational changes are ubiquitous throughout the crystal although the heavy metal content of the derivatized crystals is relatively low. The conformational changes observed, which include Leu(82), may represent a form of TTR better at scavenging β-Amyloid. At a resolution of 1.69Å, with excellent refinement statistics and well defined electron density for all parts of the structure, it is possible to envisage answering important questions that range from protein cooperative behavior to heavy atom induced protein conformational modifications that can result in crystallographic non-isomorphism.
Collapse
Affiliation(s)
- Lidia Ciccone
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France
| | - Clotilde Policar
- Ecole Normale Supérieure, Département de chimie, 24, rue Lhomond, 75005 Paris, France; Université Pierre et Marie Curie Paris 6, 4, Place Jussieu, 75005 Paris, France; CNRS, UMR7203, 75005 Paris, France
| | - Enrico A Stura
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France.
| | - William Shepard
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| |
Collapse
|
14
|
Ciccone L, Nencetti S, Rossello A, Stura EA, Orlandini E. Synthesis and structural analysis of halogen substituted fibril formation inhibitors of Human Transthyretin (TTR). J Enzyme Inhib Med Chem 2016; 31:40-51. [PMID: 27067161 DOI: 10.3109/14756366.2016.1167048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transthyretin (TTR), a β-sheet-rich tetrameric protein, in equilibrium with an unstable amyloidogenic monomeric form is responsible for extracellular deposition of amyloid fibrils, is associated with the onset of neurodegenerative diseases, such as senile systemic amyloidosis, familial amyloid polyneuropathy and familial amyloid cardiomyopathy. One of the therapeutic strategies is to use small molecules to stabilize the TTR tetramer and thus curb amyloid fibril formation. Here, we report the synthesis, the in vitro evaluation of several halogen substituted 9-fluorenyl- and di-benzophenon-based ligands and their three-dimensional crystallographic analysis in complex with TTR. The synthesized compounds bind TTR and stabilize the tetramer with different potency. Of these compounds, 2c is the best inhibitor. The dual binding mode prevalent in the absence of substitutions on the fluorenyl ring, is disfavored by (2,7-dichloro-fluoren-9-ylideneaminooxy)-acetic acid (1b), (2,7-dibromo-fluoren-9-ylideneaminooxy)-acetic acid (1c) and (E/Z)-((3,4-dichloro-phenyl)-methyleneaminooxy)-acetic acid (2c), all with halogen substitutions.
Collapse
Affiliation(s)
- Lidia Ciccone
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy and.,b CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France
| | - Susanna Nencetti
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy and
| | - Armando Rossello
- a Dipartimento di Farmacia , Università di Pisa , Pisa , Italy and
| | - Enrico Adriano Stura
- b CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France
| | | |
Collapse
|
15
|
Camodeca C, Nuti E, Tepshi L, Boero S, Tuccinardi T, Stura EA, Poggi A, Zocchi MR, Rossello A. Discovery of a new selective inhibitor of A Disintegrin And Metalloprotease 10 (ADAM-10) able to reduce the shedding of NKG2D ligands in Hodgkin's lymphoma cell models. Eur J Med Chem 2016; 111:193-201. [PMID: 26871660 DOI: 10.1016/j.ejmech.2016.01.053] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 11/29/2022]
Abstract
Hodgkin's lymphoma (HL) is the most common malignant lymphoma in young adults in the western world. This disease is characterized by an overexpression of ADAM-10 with increased release of NKG2D ligands, involved in an impaired immune response against tumor cells. We designed and synthesized two new ADAM-10 selective inhibitors, 2 and 3 based on previously published ADAM-17 selective inhibitor 1. The most promising compound was the thiazolidine derivative 3, with nanomolar activity for ADAM-10, high selectivity over ADAM-17 and MMPs and good efficacy in reducing the shedding of NKG2D ligands (MIC-B and ULBP3) in three different HL cell lines at non-toxic doses. Molecular modeling studies were used to drive the design and X-ray crystallography studies were carried out to explain the selectivity of 3 for ADAM-10 over MMPs.
Collapse
Affiliation(s)
- Caterina Camodeca
- Division of Immunology, Transplants and Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Elisa Nuti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Livia Tepshi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy; CEA, iBiTec-S, Service d'Ingenierie Moleculaire des Proteines, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Silvia Boero
- Unit of Molecular Oncology and Angiogenesis, IRCCS AOU San Martino-IST, 16132 Genoa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Enrico A Stura
- CEA, iBiTec-S, Service d'Ingenierie Moleculaire des Proteines, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Alessandro Poggi
- Unit of Molecular Oncology and Angiogenesis, IRCCS AOU San Martino-IST, 16132 Genoa, Italy
| | - Maria Raffaella Zocchi
- Division of Immunology, Transplants and Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Armando Rossello
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy.
| |
Collapse
|
16
|
Polsinelli I, Nencetti S, Shepard W, Ciccone L, Orlandini E, Stura EA. A new crystal form of human transthyretin obtained with a curcumin derived ligand. J Struct Biol 2016; 194:8-17. [PMID: 26796656 DOI: 10.1016/j.jsb.2016.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 12/18/2022]
Abstract
Transthyretin (TTR), a 54kDa homotetrameric protein that transports thyroxine (T4), has been associated with clinical cases of TTR amyloidosis for its tendency to aggregate to form fibrils. Many ligands with a potential to inhibit fibril formation have been studied by X-ray crystallography in complex with TTR. Unfortunately, the ligand is often found in ambiguous electron density that is difficult to interpret. The ligand validation statistics suggest over-interpretation, even for the most active compounds like diflunisal. The primary technical reason is its position on a crystallographic 2-fold axis in the most common crystal form. Further investigations with the use of polyethylene glycol (PEG) to crystallize TTR complexes have resulted in a new trigonal polymorph with two tetramers in the asymmetric unit. The ligand used to obtain this new polymorph, 4-hydroxychalcone, is related to curcumin. Here we evaluate this crystal form to understand the contribution it may bring to the study of TTR ligands complexes, which are often asymmetric.
Collapse
Affiliation(s)
- Ivan Polsinelli
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Susanna Nencetti
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - William Shepard
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Dipartimento di Farmacia, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Enrico A Stura
- Synchrotron SOLEIL, l'Orme des Merisiers, Saint Aubin, BP 48, 91192 Gif-sur-Yvette, France; CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Gif-sur-Yvette F-91191, France.
| |
Collapse
|
17
|
Ciccone L, Nencetti S, Rossello A, Tepshi L, Stura EA, Orlandini E. X-ray crystal structure and activity of fluorenyl-based compounds as transthyretin fibrillogenesis inhibitors. J Enzyme Inhib Med Chem 2015; 31:824-33. [PMID: 26235916 DOI: 10.3109/14756366.2015.1070265] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Transthyretin (TTR) is a 54 kDa homotetrameric protein that transports thyroxine (T4) and retinol (vitamin A), through its association with retinol binding protein (RBP). Under unknown conditions, it aggregates to form fibrils associated with TTR amyloidosis. Ligands able to inhibit fibril formation have been studied by X-ray crystallography. The use of polyethylene glycol (PEG) instead of ammonium sulphate or citrate has been evaluated as an alternative to obtain new TTR complexes with (R)-3-(9-fluoren-9-ylideneaminooxy)-2-methyl-N-(methylsulfonyl) propionamide (48R(1)) and 2-(9H-fluoren-9-ylideneaminooxy) acetic acid (ES8(2)). The previously described fluorenyl based inhibitors (S)-3-((9H-fluoren-9-ylideneamino)oxy)-2-methylpropanoic acid (6BD) and 3-((9H-fluoren-9-ylideneamino)oxy)propanoic acid (7BD) have been re-evaluated with the changed crystallization method. The new TTR complexes with compounds of the same family show that the 9-fluorenyl motif can occupy alternative hydrophobic binding sites. This augments the potential use of this scaffold to yield a large variety of differently substituted mono-aryl compounds able to inhibit TTR fibril formation.
Collapse
Affiliation(s)
- Lidia Ciccone
- a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and.,b Dipartimento di Farmacia , Università di Pisa , Pisa , Italy
| | | | | | - Livia Tepshi
- a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and.,b Dipartimento di Farmacia , Università di Pisa , Pisa , Italy
| | - Enrico A Stura
- a CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Gif-sur-Yvette , France and
| | | |
Collapse
|