1
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García-García A, Cristobal-Cueto P, Hidalgo T, Vitórica-Yrezábal IJ, Rodríguez-Diéguez A, Horcajada P, Rojas S. Potential antiprostatic performance of novel lanthanide-complexes based on 5-nitropicolinic acid. J Biol Inorg Chem 2024; 29:331-338. [PMID: 38717473 PMCID: PMC11111526 DOI: 10.1007/s00775-024-02054-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/20/2024] [Indexed: 05/24/2024]
Abstract
Two new lanthanide-complexes based on the 5-nitropicolinate ligand (5-npic) were obtained and fully characterized. Single-crystal X-ray diffraction revealed that these compounds are isostructural to a Dy-complex, previously published by us, based on dinuclear monomers link together with an extended hydrogen bond network, providing a final chemical formula of [Ln2(5-npic)6(H2O)4]·(H2O)2, where Ln = Dy (1), Gd (2), and Tb (3). Preliminary photoluminescent studies exhibited a ligand-centered emission for all complexes. The potential antitumoral activity of these materials was assayed in a prostatic cancer cell line (PC-3; the 2nd most common male cancerous disease), showing a significant anticancer activity (50-60% at 500 μg·mL-1). In turn, a high biocompatibility by both, the complexes and their precursors in human immunological HL-60 cells, was evidenced. In view of the strongest toxic effect in the tumoral cell line provided by the free 5-npic ligand (~ 40-50%), the overall anticancer complex performance seems to be triggered by the presence of this molecule.
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Affiliation(s)
- Amalia García-García
- Department of Inorganic Chemistry, Faculty of Science, University of Granada, Av. Fuente Nueva S/N, 18071, Granada, Spain
| | - Pablo Cristobal-Cueto
- Advanced Porous Material Unit, IMDEA Energy Institute, Av. Ramón de La Sagra 3, 28935, Móstoles, Madrid, Spain
| | - Tania Hidalgo
- Advanced Porous Material Unit, IMDEA Energy Institute, Av. Ramón de La Sagra 3, 28935, Móstoles, Madrid, Spain
| | - Iñigo J Vitórica-Yrezábal
- Department of Inorganic Chemistry, Faculty of Science, University of Granada, Av. Fuente Nueva S/N, 18071, Granada, Spain
| | - Antonio Rodríguez-Diéguez
- Department of Inorganic Chemistry, Faculty of Science, University of Granada, Av. Fuente Nueva S/N, 18071, Granada, Spain
| | - Patricia Horcajada
- Advanced Porous Material Unit, IMDEA Energy Institute, Av. Ramón de La Sagra 3, 28935, Móstoles, Madrid, Spain.
| | - Sara Rojas
- Department of Inorganic Chemistry, Faculty of Science, University of Granada, Av. Fuente Nueva S/N, 18071, Granada, Spain.
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2
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Weng C, Tan YLK, Koh WG, Ang WH. Harnessing Transition Metal Scaffolds for Targeted Antibacterial Therapy. Angew Chem Int Ed Engl 2023; 62:e202310040. [PMID: 37621226 DOI: 10.1002/anie.202310040] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 08/26/2023]
Abstract
Antimicrobial resistance, caused by persistent adaptation and growing resistance of pathogenic bacteria to overprescribed antibiotics, poses one of the most serious and urgent threats to global public health. The limited pipeline of experimental antibiotics in development further exacerbates this looming crisis and new drugs with alternative modes of action are needed to tackle evolving pathogenic adaptation. Transition metal complexes can replenish this diminishing stockpile of drug candidates by providing compounds with unique properties that are not easily accessible using pure organic scaffolds. We spotlight four emerging strategies to harness these unique properties to develop new targeted antibacterial agents.
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Affiliation(s)
- Cheng Weng
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | | | - Wayne Gareth Koh
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
- NUS Graduate School of Integrative Sciences and Engineering, 28 Medical Drive, Singapore, 117456, Singapore
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3
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Zhu H, Wang J, Lu Y, Soloshonok VA, Lan L, Xu J, Liu H. Pd(II) Complexes of Chiral Proline-Derived Ligands: Application for Dynamic Thermodynamic Resolution of α-Amino Acids and Their Antibacterial Activities. J Org Chem 2023; 88:3808-3821. [PMID: 36867436 DOI: 10.1021/acs.joc.3c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Novel type of Pd(II) complexes have been synthesized under operationally simple and convenient conditions and applied in the dynamic thermodynamic resolution of racemic N,C-unprotected α-amino acids. After rapid hydrolysis, these Pd(II) complexes produced the corresponding α-amino acids in satisfactory yields and enantioselectivities, accompanied by the recyclable proline-derived ligand. In addition, the method can be readily applied for S/R interconversion to obtain unnatural (R)-α-amino acids from readily available (S)-α-amino acids. Furthermore, biological assays showed that Pd(II) complexes (S,S)-3i and (S,S)-3m exhibited significant antibacterial activities similar to vancomycin, which may represent promising lead structures for further development of antibacterial agents.
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Affiliation(s)
- Huajian Zhu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, P. R. China
| | - Jiang Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China.,Lingang Laboratory, Shanghai 200031, P. R. China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
| | - Yunfu Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China
| | - Vadim A Soloshonok
- Department of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country UPV/EHU, San Sebastian 20018, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Lefu Lan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
| | - Jinyi Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, P. R. China
| | - Hong Liu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing 210009, P. R. China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, P. R. China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, P. R. China
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4
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Mukherjee G, Braka A, Wu S. Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design. J Chem Inf Model 2023; 63:2073-2083. [PMID: 36881497 DOI: 10.1021/acs.jcim.3c00050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
A functional group in a molecule is a structural fragment consisting of a few atoms or a single atom that imparts reactivity to a molecule. Hence, defining functional groups is crucial in chemistry to predict the properties and reactivities of molecules. However, there is no established method in the literature for defining functional groups based on reactivity parameters. In this work, we addressed this issue by designing a set of predefined structural fragments along with reactivity parameters like electron conjugation and ring strain. This approach uses bond orders and atom connectivities to quantify the presence of these fragments within an organic molecule based on a given input molecular coordinate. To assess the effectiveness of this approach, we performed a case study to show the benefits of using these newly designed structural fragments instead of traditional fingerprint-based methods for grouping potential COX1/COX2 inhibitors by screening an approved drug library against aspirin molecule. The structural fragment-based model for ternary classification of rat oral LD50 of chemicals showed performance similar to the fingerprint-based models. In evaluating the regression model performance for aqueous solubility, log(S), predictions, our approach outperformed the fingerprint-based model.
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Affiliation(s)
- Goutam Mukherjee
- R&D Center, PharmCADD Co. Ltd., 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea
| | - Abdennour Braka
- R&D Center, PharmCADD Co. Ltd., 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea
| | - Sangwook Wu
- R&D Center, PharmCADD Co. Ltd., 12F, 331, Jungang-daero, Dong-gu, Busan 48792, Republic of Korea.,Department of Physics, Pukyong National University, Busan 48513, Republic of Korea
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5
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Frei A, Verderosa AD, Elliott AG, Zuegg J, Blaskovich MAT. Metals to combat antimicrobial resistance. Nat Rev Chem 2023; 7:202-224. [PMID: 37117903 PMCID: PMC9907218 DOI: 10.1038/s41570-023-00463-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2023] [Indexed: 02/10/2023]
Abstract
Bacteria, similar to most organisms, have a love-hate relationship with metals: a specific metal may be essential for survival yet toxic in certain forms and concentrations. Metal ions have a long history of antimicrobial activity and have received increasing attention in recent years owing to the rise of antimicrobial resistance. The search for antibacterial agents now encompasses metal ions, nanoparticles and metal complexes with antimicrobial activity ('metalloantibiotics'). Although yet to be advanced to the clinic, metalloantibiotics are a vast and underexplored group of compounds that could lead to a much-needed new class of antibiotics. This Review summarizes recent developments in this growing field, focusing on advances in the development of metalloantibiotics, in particular, those for which the mechanism of action has been investigated. We also provide an overview of alternative uses of metal complexes to combat bacterial infections, including antimicrobial photodynamic therapy and radionuclide diagnosis of bacterial infections.
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Affiliation(s)
- Angelo Frei
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Anthony D Verderosa
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Alysha G Elliott
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Johannes Zuegg
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Mark A T Blaskovich
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
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6
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Bajorath J, Chávez-Hernández AL, Duran-Frigola M, Fernández-de Gortari E, Gasteiger J, López-López E, Maggiora GM, Medina-Franco JL, Méndez-Lucio O, Mestres J, Miranda-Quintana RA, Oprea TI, Plisson F, Prieto-Martínez FD, Rodríguez-Pérez R, Rondón-Villarreal P, Saldívar-Gonzalez FI, Sánchez-Cruz N, Valli M. Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. J Cheminform 2022; 14:82. [PMID: 36461094 PMCID: PMC9716667 DOI: 10.1186/s13321-022-00661-0] [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: 08/09/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City, June 15-17, 2022. Fifteen lectures were presented during a virtual public event with speakers from industry, academia, and non-for-profit organizations. Twelve hundred and ninety students and academics from more than 60 countries. During the meeting, applications, challenges, and opportunities in drug discovery, de novo drug design, ADME-Tox (absorption, distribution, metabolism, excretion and toxicity) property predictions, organic chemistry, peptides, and antibiotic resistance were discussed. The program along with the recordings of all sessions are freely available at https://www.difacquim.com/english/events/2022-colloquium/ .
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Affiliation(s)
- Jürgen Bajorath
- grid.10388.320000 0001 2240 3300Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Friedrich-Hirzebruch-Allee 5/6, 53113 Bonn, Germany
| | - Ana L. Chávez-Hernández
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Miquel Duran-Frigola
- Ersilia Open Source Initiative, Cambridge, UK ,grid.7722.00000 0001 1811 6966Joint IRB-BSC-CRG Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Catalonia Spain
| | - Eli Fernández-de Gortari
- grid.420330.60000 0004 0521 6935Nanosafety Laboratory, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Johann Gasteiger
- grid.5330.50000 0001 2107 3311Computer-Chemie-Centrum, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Edgar López-López
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico ,grid.512574.0Department of Pharmacology, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV), 07360 Mexico City, Mexico
| | - Gerald M. Maggiora
- grid.134563.60000 0001 2168 186XBIO5 Institute, University of Arizona, Tucson, AZ 85721 USA
| | - José L. Medina-Franco
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | | | - Jordi Mestres
- grid.5841.80000 0004 1937 0247Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia Spain ,grid.20522.370000 0004 1767 9005Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pompeu Fabra, Parc de Recerca Biomedica (PRBB), 08003 Barcelona, Catalonia Spain
| | | | - Tudor I. Oprea
- grid.266832.b0000 0001 2188 8502Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131 USA ,grid.8761.80000 0000 9919 9582Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy at Gothenburg University, 40530 Gothenburg, Sweden ,grid.5254.60000 0001 0674 042XNovo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark ,Present Address: Roivant Discovery Sciences, Inc., 451 D Street, Boston, MA 02210 USA
| | - Fabien Plisson
- grid.512574.0Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824 Irapuato, Gto Mexico
| | - Fernando D. Prieto-Martínez
- grid.9486.30000 0001 2159 0001Chemistry Institute, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Raquel Rodríguez-Pérez
- grid.419481.10000 0001 1515 9979Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Paola Rondón-Villarreal
- grid.442204.40000 0004 0486 1035Universidad de Santander, Facultad de Ciencias Médicas y de la Salud, Instituto de Investigación Masira, Calle 70 No. 55-210, 680003 Santander, Bucaramanga Colombia
| | - Fernanda I. Saldívar-Gonzalez
- grid.9486.30000 0001 2159 0001DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Norberto Sánchez-Cruz
- grid.5841.80000 0004 1937 0247Chemotargets SL, Baldiri Reixac 4, Parc Cientific de Barcelona (PCB), 08028 Barcelona, Catalonia Spain ,grid.9486.30000 0001 2159 0001Instituto de Química, Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Yucatán, 97357 Ucú, Mexico
| | - Marilia Valli
- grid.410543.70000 0001 2188 478XNuclei of Bioassays, Biosynthesis and Ecophysiology of Natural Products (NuBBE), Department of Organic Chemistry, Institute of Chemistry, São Paulo State University-UNESP, Araraquara, Brazil
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7
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Frei A, Elliott AG, Kan A, Dinh H, Bräse S, Bruce AE, Bruce MR, Chen F, Humaidy D, Jung N, King AP, Lye PG, Maliszewska HK, Mansour AM, Matiadis D, Muñoz MP, Pai TY, Pokhrel S, Sadler PJ, Sagnou M, Taylor M, Wilson JJ, Woods D, Zuegg J, Meyer W, Cain AK, Cooper MA, Blaskovich MAT. Metal Complexes as Antifungals? From a Crowd-Sourced Compound Library to the First In Vivo Experiments. JACS AU 2022; 2:2277-2294. [PMID: 36311838 PMCID: PMC9597602 DOI: 10.1021/jacsau.2c00308] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/01/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
There are currently fewer than 10 antifungal drugs in clinical development, but new fungal strains that are resistant to most current antifungals are spreading rapidly across the world. To prevent a second resistance crisis, new classes of antifungal drugs are urgently needed. Metal complexes have proven to be promising candidates for novel antibiotics, but so far, few compounds have been explored for their potential application as antifungal agents. In this work, we report the evaluation of 1039 metal-containing compounds that were screened by the Community for Open Antimicrobial Drug Discovery (CO-ADD). We show that 20.9% of all metal compounds tested have antimicrobial activity against two representative Candida and Cryptococcus strains compared with only 1.1% of the >300,000 purely organic molecules tested through CO-ADD. We identified 90 metal compounds (8.7%) that show antifungal activity while not displaying any cytotoxicity against mammalian cell lines or hemolytic properties at similar concentrations. The structures of 21 metal complexes that display high antifungal activity (MIC ≤1.25 μM) are discussed and evaluated further against a broad panel of yeasts. Most of these have not been previously tested for antifungal activity. Eleven of these metal complexes were tested for toxicity in the Galleria mellonella moth larva model, revealing that only one compound showed signs of toxicity at the highest injected concentration. Lastly, we demonstrated that the organo-Pt(II) cyclooctadiene complex Pt1 significantly reduces fungal load in an in vivo G. mellonella infection model. These findings showcase that the structural and chemical diversity of metal-based compounds can be an invaluable tool in the development of new drugs against infectious diseases.
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Affiliation(s)
- Angelo Frei
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
- Department
of Chemistry, Biochemistry & Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012Bern, Switzerland
| | - Alysha G. Elliott
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
| | - Alex Kan
- Molecular
Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology,
Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical
School, Sydney Institute for Infectious Diseases, Westmead Hospital-Research
and Education Network, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW2145, Australia
| | - Hue Dinh
- School
of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW2109, Australia
| | - Stefan Bräse
- Institute
of Organic Chemistry, Karlsruhe Institute
of Technology, Fritz-Haber-Weg 6, 76131Karlsruhe, Germany
- Institute
of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, 76344Eggenstein-Leopoldshafen, Germany
| | - Alice E. Bruce
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Mitchell R. Bruce
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Feng Chen
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CoventryCV4 7AL, U.K.
| | - Dhirgam Humaidy
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Nicole Jung
- Karlsruhe
Nano Micro Facility (KNMF), Karlsruhe Institute
of Technology, Hermann-von-Helmholtz-Platz 1, 76344Eggenstein-Leopoldshafen, Germany
- Institute
of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, 76344Eggenstein-Leopoldshafen, Germany
| | - A. Paden King
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14853, United States
| | - Peter G. Lye
- School
of Science and Technology, University of
New England, Armidale, NSW2351, Australia
| | - Hanna K. Maliszewska
- School
of Chemistry, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, U.K.
| | - Ahmed M. Mansour
- Chemistry
Department, Faculty of Science, Cairo University, Giza12613, Egypt
| | - Dimitris Matiadis
- Institute
of Biosciences & Applications, National
Centre for Scientific Research “Demokritos”, 15310Athens, Greece
| | - María Paz Muñoz
- School
of Chemistry, University of East Anglia, Norwich Research Park, NorwichNR4 7TJ, U.K.
| | - Tsung-Yu Pai
- Molecular
Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology,
Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical
School, Sydney Institute for Infectious Diseases, Westmead Hospital-Research
and Education Network, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW2145, Australia
| | - Shyam Pokhrel
- Department
of Chemistry, University of Maine, Orono, Maine04469, United States
| | - Peter J. Sadler
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, CoventryCV4 7AL, U.K.
| | - Marina Sagnou
- Institute
of Biosciences & Applications, National
Centre for Scientific Research “Demokritos”, 15310Athens, Greece
| | - Michelle Taylor
- School
of Science and Technology, University of
New England, Armidale, NSW2351, Australia
| | - Justin J. Wilson
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York14853, United States
| | - Dean Woods
- School
of Science and Technology, University of
New England, Armidale, NSW2351, Australia
| | - Johannes Zuegg
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
| | - Wieland Meyer
- Molecular
Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology,
Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical
School, Sydney Institute for Infectious Diseases, Westmead Hospital-Research
and Education Network, Westmead Institute for Medical Research, University of Sydney, Sydney, NSW2145, Australia
| | - Amy K. Cain
- School
of Natural Sciences, ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW2109, Australia
| | - Matthew A. Cooper
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
| | - Mark A. T. Blaskovich
- Centre
for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland4072, Australia
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8
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Prediction of the Ibuprofen Loading Capacity of MOFs by Machine Learning. BIOENGINEERING (BASEL, SWITZERLAND) 2022; 9:bioengineering9100517. [PMID: 36290485 PMCID: PMC9598200 DOI: 10.3390/bioengineering9100517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
Abstract
Metal-organic frameworks (MOFs) have been widely researched as drug delivery systems due to their intrinsic porous structures. Herein, machine learning (ML) technologies were applied for the screening of MOFs with high drug loading capacity. To achieve this, first, a comprehensive dataset was gathered, including 40 data points from more than 100 different publications. The organic linkers, metal ions, and the functional groups, as well as the surface area and the pore volume of the investigated MOFs, were chosen as the model’s inputs, and the output was the ibuprofen (IBU) loading capacity. Thereafter, various advanced and powerful machine learning algorithms, such as support vector regression (SVR), random forest (RF), adaptive boosting (AdaBoost), and categorical boosting (CatBoost), were employed to predict the ibuprofen loading capacity of MOFs. The coefficient of determination (R2) of 0.70, 0.72, 0.66, and 0.76 were obtained for the SVR, RF, AdaBoost, and CatBoost approaches, respectively. Among all the algorithms, CatBoost was the most reliable, exhibiting superior performance regarding the sparse matrices and categorical features. Shapley additive explanations (SHAP) analysis was employed to explore the impact of the eigenvalues of the model’s outputs. Our initial results indicate that this methodology is a well generalized, straightforward, and cost-effective method that can be applied not only for the prediction of IBU loading capacity, but also in many other biomaterials projects.
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9
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Andreini C, Rosato A. Structural Bioinformatics and Deep Learning of Metalloproteins: Recent Advances and Applications. Int J Mol Sci 2022; 23:ijms23147684. [PMID: 35887033 PMCID: PMC9323969 DOI: 10.3390/ijms23147684] [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: 06/16/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 02/04/2023] Open
Abstract
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids). The proteins that require binding to one or more metal ions in order to be able to carry out their physiological function are called metalloproteins. About one third of all protein structures in the Protein Data Bank involve metalloproteins. Over the past few years there has been tremendous progress in the number of computational tools and techniques making use of 3D structural information to support the investigation of metalloproteins. This trend has been boosted by the successful applications of neural networks and machine/deep learning approaches in molecular and structural biology at large. In this review, we discuss recent advances in the development and availability of resources dealing with metalloproteins from a structure-based perspective. We start by addressing tools for the prediction of metal-binding sites (MBSs) using structural information on apo-proteins. Then, we provide an overview of the methods for and lessons learned from the structural comparison of MBSs in a fold-independent manner. We then move to describing databases of metalloprotein/MBS structures. Finally, we summarizing recent ML/DL applications enhancing the functional interpretation of metalloprotein structures.
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Affiliation(s)
- Claudia Andreini
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Consorzio Interuniversitario di Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy;
- Magnetic Resonance Center (CERM), Department of Chemistry, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Correspondence:
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