1
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Jacobs FJ, Helliwell JR, Brink A. Time-series analysis of rhenium(I) organometallic covalent binding to a model protein for drug development. IUCRJ 2024; 11:359-373. [PMID: 38639558 PMCID: PMC11067751 DOI: 10.1107/s2052252524002598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
Metal-based complexes with their unique chemical properties, including multiple oxidation states, radio-nuclear capabilities and various coordination geometries yield value as potential pharmaceuticals. Understanding the interactions between metals and biological systems will prove key for site-specific coordination of new metal-based lead compounds. This study merges the concepts of target coordination with fragment-based drug methodologies, supported by varying the anomalous scattering of rhenium along with infrared spectroscopy, and has identified rhenium metal sites bound covalently with two amino acid types within the model protein. A time-based series of lysozyme-rhenium-imidazole (HEWL-Re-Imi) crystals was analysed systematically over a span of 38 weeks. The main rhenium covalent coordination is observed at His15, Asp101 and Asp119. Weak (i.e. noncovalent) interactions are observed at other aspartic, asparagine, proline, tyrosine and tryptophan side chains. Detailed bond distance comparisons, including precision estimates, are reported, utilizing the diffraction precision index supplemented with small-molecule data from the Cambridge Structural Database. Key findings include changes in the protein structure induced at the rhenium metal binding site, not observed in similar metal-free structures. The binding sites are typically found along the solvent-channel-accessible protein surface. The three primary covalent metal binding sites are consistent throughout the time series, whereas binding to neighbouring amino acid residues changes through the time series. Co-crystallization was used, consistently yielding crystals four days after setup. After crystal formation, soaking of the compound into the crystal over 38 weeks is continued and explains these structural adjustments. It is the covalent bond stability at the three sites, their proximity to the solvent channel and the movement of residues to accommodate the metal that are important, and may prove useful for future radiopharmaceutical development including target modification.
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Affiliation(s)
- Francois J.F. Jacobs
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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2
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Qi Q, Wang Q, Li Y, Silva DZ, Ruiz MEL, Ouyang R, Liu B, Miao Y. Recent Development of Rhenium-Based Materials in the Application of Diagnosis and Tumor Therapy. Molecules 2023; 28:molecules28062733. [PMID: 36985704 PMCID: PMC10051626 DOI: 10.3390/molecules28062733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023] Open
Abstract
Rhenium (Re) is widely used in the diagnosis and treatment of cancer due to its unique physical and chemical properties. Re has more valence electrons in its outer shell, allowing it to exist in a variety of oxidation states and to form different geometric configurations with many different ligands. The luminescence properties, lipophilicity, and cytotoxicity of complexes can be adjusted by changing the ligand of Re. This article mainly reviews the development of radionuclide 188Re in radiotherapy and some innovative applications of Re as well as the different therapeutic approaches and imaging techniques used in cancer therapy. In addition, the current application and future challenges and opportunities of Re are also discussed.
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Affiliation(s)
- Qingwen Qi
- School of Materials and Chemistry, Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China; (Q.Q.); (Q.W.); (R.O.)
| | - Qian Wang
- School of Materials and Chemistry, Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China; (Q.Q.); (Q.W.); (R.O.)
| | - Yuhao Li
- School of Materials and Chemistry, Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China; (Q.Q.); (Q.W.); (R.O.)
- USST-UH International Joint Laboratory for Tumor Diagnosis and Energy Treatment, University of Shanghai for Science and Technology, Shanghai 200093, China; (M.E.L.R.); (B.L.)
- Correspondence: (Y.L.); (D.Z.S.); (Y.M.)
| | - Dionisio Zaldivar Silva
- USST-UH International Joint Laboratory for Tumor Diagnosis and Energy Treatment, University of Shanghai for Science and Technology, Shanghai 200093, China; (M.E.L.R.); (B.L.)
- Faculty of Biology, University of Havana, Havana 10400, Cuba
- Correspondence: (Y.L.); (D.Z.S.); (Y.M.)
| | - Maria Eliana Lanio Ruiz
- USST-UH International Joint Laboratory for Tumor Diagnosis and Energy Treatment, University of Shanghai for Science and Technology, Shanghai 200093, China; (M.E.L.R.); (B.L.)
- Faculty of Biology, University of Havana, Havana 10400, Cuba
| | - Ruizhuo Ouyang
- School of Materials and Chemistry, Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China; (Q.Q.); (Q.W.); (R.O.)
- USST-UH International Joint Laboratory for Tumor Diagnosis and Energy Treatment, University of Shanghai for Science and Technology, Shanghai 200093, China; (M.E.L.R.); (B.L.)
| | - Baolin Liu
- USST-UH International Joint Laboratory for Tumor Diagnosis and Energy Treatment, University of Shanghai for Science and Technology, Shanghai 200093, China; (M.E.L.R.); (B.L.)
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yuqing Miao
- School of Materials and Chemistry, Institute of Bismuth and Rhenium, University of Shanghai for Science and Technology, Shanghai 200093, China; (Q.Q.); (Q.W.); (R.O.)
- USST-UH International Joint Laboratory for Tumor Diagnosis and Energy Treatment, University of Shanghai for Science and Technology, Shanghai 200093, China; (M.E.L.R.); (B.L.)
- Correspondence: (Y.L.); (D.Z.S.); (Y.M.)
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3
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Brink A, Jacobs FJF, Helliwell JR. Trends in coordination of rhenium organometallic complexes in the Protein Data Bank. IUCRJ 2022; 9:180-193. [PMID: 35371500 PMCID: PMC8895017 DOI: 10.1107/s2052252522000665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Radiopharmaceutical development has similar overall characteristics to any biomedical drug development requiring a compound's stability, aqueous solubility and selectivity to a specific disease site. However, organometallic complexes containing 188/186Re or 99mTc involve a d-block transition-metal radioactive isotope and therefore bring additional factors such as metal oxidation states, isotope purity and half life into play. This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. Technetium is used as a medical diagnostic agent and involves the 99mTc isotope which decays to release gamma radiation, thereby employed for its use in gamma imaging. Due to the periodic relationship among group 7 transition metals, the coordination chemistry of rhenium is similar (but not identical) to that of technetium. The types of reactions the potential model radiopharmaceutical would prefer to partake in, and by extension knowing which proteins and biomolecules the compound would react with in vivo, are needed. Crystallography studies, both small molecule and macromolecular, are a key aspect in understanding chemical coordination. Analyses of bonding modes, coordination to particular residues and crystallization conditions are presented. In our Forward look as a concluding summary of this topical review, the question we ask is: what is the best way for this field to progress?
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Affiliation(s)
- Alice Brink
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Francois J. F. Jacobs
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
| | - John R. Helliwell
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
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4
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Helliwell JR. Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography. Methods Mol Biol 2022; 2449:235-261. [PMID: 35507266 DOI: 10.1007/978-1-0716-2095-3_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Like an article narrative is deemed by an editor and referees to be worthy of being a version of record on acceptance as a publication, so must the underpinning data also be scrutinized before passing it as a version of record. Indeed without the underpinning data, a study and its conclusions cannot be reproduced at any stage of evaluation, pre- or post-publication. Likewise, an independent study without its own underpinning data also cannot be reproduced let alone be considered a replicate of the first study. The PDB is a modern marvel of achievement providing an organized open access to depositor and user of the data held there opening numerous applications. Methods for modeling protein structures and for determination of structures are still improving their precision, and artifacts of the method exist. So their accuracy is realized if they are reproduced by other methods. It is on such foundations that reproducible data mining is based. Data rates are expanding considerably be they at synchrotrons, the X-ray free electron lasers (XFELs), electron cryomicroscopes (cryoEM), or at the neutron facilities. The work of a person as a referee or user with a narrative and its underpinning data may well be complemented in future by artificial intelligence with machine learning, the former for specific refereeing and the latter for the more general validation, both ideally before publication. Examples are described involving rhenium theranostics, the anti-cancer platins and the SARS-CoV-2 main protease.
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Affiliation(s)
- John R Helliwell
- Department of Chemistry, University of Manchester, Manchester, UK.
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5
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Komane WK, Mokolokolo P, Vatsha B, Manicum ALE. The crystal structure of fac-tricarbonyl ( N′-benzoyl- N, N-diphenylcarbamimidothioato-κ 2
S,O)-(pyrazole-κ N)rhenium(I) — methanol (1/1) C 26H 23O 4N 4SRe. Z KRIST-NEW CRYST ST 2021. [DOI: 10.1515/ncrs-2021-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C26H23O4N4SRe, triclinic, P
1
‾
$\bar{1}$
(no. 2), a = 9.919(2) Å, b = 11.752(3) Å, c = 12.717(3) Å, α = 111.098(7)°, β = 94.467(7)°, γ = 98.295(7)°, V = 1354.9(5) Å3, Z = 2, Rgt
(F) = 0.0342, wRref
(F
2) = 0.0843, T = 102.0(2) K.
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Affiliation(s)
- Wesley K. Komane
- Department of Chemistry , Tshwane University of Technology , Pretoria , 0001 , South Africa
| | - Pennie Mokolokolo
- Department of Chemistry , University of the Free State , Bloemfontein , 9301 , South Africa
| | - Banele Vatsha
- Department of Chemistry , University of Johannesburg , Auckland Park , 2006 , South Africa
| | - Amanda-Lee E. Manicum
- Department of Chemistry , Tshwane University of Technology , Pretoria , 0001 , South Africa
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6
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The kinetic substitution reactions and structural analysis of manganese(I) acetylacetonato complexes. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Abstract
Recent advances in structural studies unveiling the basis of the metal compounds/protein recognition process are discussed.
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Affiliation(s)
- Antonello Merlino
- Department of Chemical Sciences
- University of Naples Federico II
- Complesso Universitario di Monte Sant’Angelo
- Napoli
- Italy
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8
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Kama DV, Frei A, Schutte-Smith M, Brink A, Swart C, Braband H, Alberto R, Roodt A. Exploring preliminary structural relationships and mitochondrial targeting of fac-[MI(CO)3]-bis(diarylphosphino)alkylamine complexes (M = 99Tc, Re). NEW J CHEM 2021. [DOI: 10.1039/d1nj04273d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Preliminary structural relationships in fac-[MI(CO)3]-bis(diarylphosphino)alkylamine complexes (M = 99Tc, Re), antimicrobial and mitochondrial targeting are reported.
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Affiliation(s)
- Dumisani V. Kama
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - Angelo Frei
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Marietjie Schutte-Smith
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - Alice Brink
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - Chantel Swart
- Department of Biochemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
| | - Henrik Braband
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Roger Alberto
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Andreas Roodt
- Department of Chemistry, University of the Free State, PO Box 339, Bloemfontein 9300, South Africa
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9
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Aimene Y, Eychenne R, Mallet-Ladeira S, Saffon N, Winum JY, Nocentini A, Supuran CT, Benoist E, Seridi A. Novel Re(I) tricarbonyl coordination compounds based on 2-pyridyl-1,2,3-triazole derivatives bearing a 4-amino-substituted benzenesulfonamide arm: synthesis, crystal structure, computational studies and inhibitory activity against carbonic anhydrase I, II, and IX isoforms†. J Enzyme Inhib Med Chem 2019; 34:773-782. [PMID: 30843736 PMCID: PMC6407592 DOI: 10.1080/14756366.2019.1585835] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 12/27/2022] Open
Abstract
In this work, two bidentate 2-pyridyl-1,2,3-triazole ligands (3a and 3b) containing a 4-substituted benzenesulfonamide pharmacophore prepared by classical click chemistry procedures, as well as their corresponding rhenium complexes, 4a and 4b of general formula [ReCl(CO)3(L)] (L = 3a or 3b) were prepared and fully characterised by spectroscopic methods (IR, NMR, MS, UV-Vis), elemental analysis, X-ray diffraction, and theoretical studies using DFT and TD-DFT methods. In particular, we showed that, in the solid state, the pyridine and the triazole rings of 3b adopted an uncommon cis configuration which stems from intermolecular hydrogen bonds. Preliminary assays demonstrated a promising nanomolar inhibitory activity against carbonic anhydrase isoform IX for both ligands and complexes with a strong affinity Ki of 2.8 nM for ligand 3a. More interestingly, complex 4b exhibited a pronounced selectivity against hCA IX over the off-targets hCA I and hCA II which makes this compound a promising potential anticancer drug candidate.
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Affiliation(s)
- Yassine Aimene
- Laboratoire de Chimie, physique Université du 8 Mai 1945, Guelma, Algérie
- CNRS, Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, SPCMIB, Toulouse, France
- Université de Toulouse, UPS, Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, SPCMIB, Toulouse, France
| | - Romain Eychenne
- CNRS, Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, SPCMIB, Toulouse, France
- Université de Toulouse, UPS, Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, SPCMIB, Toulouse, France
| | | | | | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron, ENSCM, Université de Montpellier, Montpellier, France
| | - Alessio Nocentini
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Florence, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Florence, Italy
| | - Eric Benoist
- CNRS, Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, SPCMIB, Toulouse, France
- Université de Toulouse, UPS, Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, SPCMIB, Toulouse, France
| | - Achour Seridi
- Laboratoire de Chimie, physique Université du 8 Mai 1945, Guelma, Algérie
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10
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Collery P, Desmaele D, Vijaykumar V. Design of Rhenium Compounds in Targeted Anticancer Therapeutics. Curr Pharm Des 2019; 25:3306-3322. [DOI: 10.2174/1381612825666190902161400] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 08/30/2019] [Indexed: 12/25/2022]
Abstract
Background:
Many rhenium (Re) complexes with potential anticancer properties have been synthesized
in the recent years with the aim to overcome the clinical limitations of platinum agents. Re(I) tricarbonyl
complexes are the most common but Re compounds with higher oxidation states have also been investigated, as
well as hetero-metallic complexes and Re-loaded self-assembling devices. Many of these compounds display
promising cytotoxic and phototoxic properties against malignant cells but all Re compounds are still at the stage
of preclinical studies.
Methods:
The present review focused on the rhenium based cancer drugs that were in preclinical and clinical
trials were examined critically. The detailed targeted interactions and experimental evidences of Re compounds
reported by the patentable and non-patentable research findings used to write this review.
Results:
In the present review, we described the most recent and promising rhenium compounds focusing on their
potential mechanism of action including, phototoxicity, DNA binding, mitochondrial effects, oxidative stress
regulation or enzyme inhibition. Many ligands have been described that modulating the lipophilicity, the luminescent
properties, the cellular uptake, the biodistribution, and the cytotoxicity, the pharmacological and toxicological
profile.
Conclusion:
Re-based anticancer drugs can also be used in targeted therapies by coupling to a variety of biologically
relevant targeting molecules. On the other hand, combination with conventional cytotoxic molecules, such
as doxorubicin, allowed to take into profit the targeting properties of Re for example toward mitochondria.
Through the example of the diseleno-Re complex, we showed that the main target could be the oxidative status,
with a down-stream regulation of signaling pathways, and further on selective cell death of cancer cells versus
normal cells.
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Affiliation(s)
- Philippe Collery
- Society for the Coordination of Therapeutic Researches, 20220 Algajola, France
| | - Didier Desmaele
- Institut Galien, Universite Paris-Saclay, 92296 Chatenay-Malabry, France
| | - Veena Vijaykumar
- Biotechnology Department, REVA University, Bangalore, 560064, India
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11
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Brink A, Helliwell JR. Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? IUCRJ 2019; 6:788-793. [PMID: 31576212 PMCID: PMC6760442 DOI: 10.1107/s2052252519010972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, Free State 9301, South Africa
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
- Correspondence e-mail:
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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12
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Urzhumtsev AG, Lunin VY. Introduction to crystallographic refinement of macromolecular atomic models. CRYSTALLOGR REV 2019. [DOI: 10.1080/0889311x.2019.1631817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexandre G. Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Vladimir Y. Lunin
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
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13
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Brink A, Helliwell JR. Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging. IUCRJ 2019; 6:695-702. [PMID: 31316813 PMCID: PMC6608631 DOI: 10.1107/s2052252519006651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/09/2019] [Indexed: 05/22/2023]
Abstract
The fact that a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron-dense tetranuclear rhenium cluster compound from a rhenium tri-carbonyl tri-bromo starting compound adds to the fascination. Such a cluster has been synthesized previously in vitro, where it formed under basic conditions. Therefore, its synthesis in a protein crystal grown at pH 4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg-white lysozyme incubated with a rhenium tri-carbonyl tri-bromo compound for periods of one and two years. These reveal a completed, very well resolved, tetra-rhenium cluster after two years and an intermediate state, where the carbonyl ligands to the rhenium cluster are not yet clearly resolved, after one year. A dense tetranuclear rhenium cluster, and its technetium form, offer enhanced contrast in medical imaging. Stimulated by these crystallography results, the unusual formation of such a species directly in an in vivo situation has been considered. It offers a new option for medical imaging compounds, particularly when considering the application of the pre-formed tetranuclear cluster, suggesting that it may be suitable for medical diagnosis because of its stability, preference of formation and biological compatibility.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
- Correspondence e-mail:
| | - John R. Helliwell
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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14
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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15
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Russo Krauss I, Ferraro G, Pica A, Márquez JA, Helliwell JR, Merlino A. Principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign metal ligands. Metallomics 2018; 9:1534-1547. [PMID: 28967006 DOI: 10.1039/c7mt00219j] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The characterization of the interactions between biological macromolecules (proteins and nucleic acids) and metal-based drugs is a fundamental prerequisite for understanding their mechanisms of action. X-ray crystallography enables the structural analysis of such complexes with atomic level detail. However, this approach requires the preparation of highly diffracting single crystals, the measurement of diffraction patterns and the structural analysis and interpretation of macromolecule-metal interactions from electron density maps. In this review, we describe principles and methods used to grow and optimize crystals of protein-metallodrug adducts, to determine metal binding sites and to assign and validate metal ligands. Examples from the literature and experience in our own laboratory are provided and key challenges are described, notably crystallization and molecular model refinement against the X-ray diffraction data.
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Affiliation(s)
- Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy.
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Khurshid S, Govada L, Wills G, McClure MO, Helliwell JR, Chayen NE. Chlamydia protein Pgp3 studied at high resolution in a new crystal form. IUCRJ 2018; 5:439-448. [PMID: 30002845 PMCID: PMC6038952 DOI: 10.1107/s2052252518007637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
The protein Pgp3 is implicated in the sexually transmitted disease chlamydia and comprises an extended complex arrangement of a C-terminal domain (CTD) and an N-terminal domain (NTD) linked by a triple-helix coiled coil (THCC). Here, the X-ray crystal structure of Pgp3 from an LGV1 strain is reported at the highest X-ray diffraction resolution obtained to date for the full protein. The protein was crystallized using a high concentration of potassium bromide, which resulted in a new crystal form with relatively low solvent content that diffracted to a resolution of 1.98 Å. The three-dimensional structure of this new crystal form is described and compared with those of other crystal forms, and the potassium bromide binding sites and the relevance to chlamydia isolates from around the globe are described. The crystal packing is apparently driven by the CTDs. Since the threefold axes of the THCC and NTD are not collinear with the threefold axis of a CTD, this naturally leads to disorder in the THCC and the portion of the NTD that does not directly interact with the CTD via crystal packing. The key avenue to resolving these oddities in the crystal structure analysis was a complete new analysis in space group P1 and determining the space group as P212121. This space-group assignment was that originally determined from the diffraction pattern but was perhaps complicated by translational noncrystallographic symmetry. This crystal structure of a three-domain multi-macromolecular complex with two misaligned threefold axes was a unique challenge and has not been encountered before. It is suggested that a specific intermolecular interaction, possibly of functional significance in receptor binding in chlamydia, might allow the design of a new chemotherapeutic agent against chlamydia.
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Affiliation(s)
- Sahir Khurshid
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, England
| | - Lata Govada
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, England
| | - Gillian Wills
- Department of Medicine, Imperial College London, St Mary’s Campus, London W2 1PG, England
| | - Myra O. McClure
- Department of Medicine, Imperial College London, St Mary’s Campus, London W2 1PG, England
| | - John R. Helliwell
- School of Chemistry, The University of Manchester, Manchester M13 9PL, England
| | - Naomi E. Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, England
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Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W. Characterizing metal-binding sites in proteins with X-ray crystallography. Nat Protoc 2018; 13:1062-1090. [PMID: 29674755 PMCID: PMC6235626 DOI: 10.1038/nprot.2018.018] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Metals have crucial roles in many physiological, pathological, toxicological, pharmaceutical, and diagnostic processes. Proper handling of metal-containing macromolecule samples for structural studies is not trivial, and failure to handle them properly is often a source of irreproducibility caused by issues such as pH changes, incorporation of unexpected metals, or oxidization/reduction of the metal. This protocol outlines the guidelines and best practices for characterizing metal-binding sites in protein structures and alerts experimenters to potential pitfalls during the preparation and handling of metal-containing protein samples for X-ray crystallography studies. The protocol features strategies for controlling the sample pH and the metal oxidation state, recording X-ray fluorescence (XRF) spectra, and collecting diffraction data sets above and below the corresponding metal absorption edges. This protocol should allow experimenters to gather sufficient evidence to unambiguously determine the identity and location of the metal of interest, as well as to accurately characterize the coordinating ligands in the metal binding environment within the protein. Meticulous handling of metal-containing macromolecule samples as described in this protocol should enhance experimental reproducibility in biomedical sciences, especially in X-ray macromolecular crystallography. For most samples, the protocol can be completed within a period of 7-190 d, most of which (2-180 d) is devoted to growing the crystal. The protocol should be readily understandable to structural biologists, particularly protein crystallographers with an intermediate level of experience.
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Affiliation(s)
- Katarzyna B Handing
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Ewa Niedzialkowska
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Ivan G Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Misty L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, Charlottesville, Virginia, USA
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Brink A, Kroon RE, Visser HG, van Rensburg CEJ, Roodt A. Designing model imino bifunctional chelators for radiopharmaceuticals – in vitro antitumor activity, photoluminescence and structural analysis. NEW J CHEM 2018. [DOI: 10.1039/c7nj04208f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Designed bifunctional chelators for the radionuclides of 188/186Re or 99mTc. Structure, DFT calculations, antitumor and imaging properties are described.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State
- Bloemfontein 9300
- South Africa
| | - Robin E. Kroon
- Department of Physics, University of the Free State
- Bloemfontein 9300
- South Africa
| | - Hendrik G. Visser
- Department of Chemistry, University of the Free State
- Bloemfontein 9300
- South Africa
| | | | - Andreas Roodt
- Department of Chemistry, University of the Free State
- Bloemfontein 9300
- South Africa
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Konkankit CC, Marker SC, Knopf KM, Wilson JJ. Anticancer activity of complexes of the third row transition metals, rhenium, osmium, and iridium. Dalton Trans 2018; 47:9934-9974. [DOI: 10.1039/c8dt01858h] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A summary of recent developments on the anticancer activity of complexes of rhenium, osmium, and iridium is described.
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Affiliation(s)
| | - Sierra C. Marker
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Kevin M. Knopf
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
| | - Justin J. Wilson
- Department of Chemistry and Chemical Biology
- Cornell University
- Ithaca
- USA
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20
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Helliwell JR. New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences. Biosci Rep 2017; 37:BSR20170204. [PMID: 28572170 PMCID: PMC6434086 DOI: 10.1042/bsr20170204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.
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