1
|
Asfa SS, Arshinchi Bonab R, Önder O, Uça Apaydın M, Döşeme H, Küçük C, Georgakilas AG, Stadler BM, Logotheti S, Kale S, Pavlopoulou A. Computer-Aided Identification and Design of Ligands for Multi-Targeting Inhibition of a Molecular Acute Myeloid Leukemia Network. Cancers (Basel) 2024; 16:3607. [PMID: 39518047 PMCID: PMC11544916 DOI: 10.3390/cancers16213607] [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: 08/29/2024] [Revised: 10/07/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND/OBJECTIVES Acute myeloid leukemia (AML) is characterized by therapeutic failure and long-term risk for disease relapses. As several therapeutic targets participate in networks, they can rewire to eventually evade single-target drugs. Hence, multi-targeting approaches are considered on the expectation that interference with many different components could synergistically hinder activation of alternative pathways and demolish the network one-off, leading to complete disease remission. METHODS Herein, we established a network-based, computer-aided approach for the rational design of drug combinations and de novo agents that interact with many AML network components simultaneously. RESULTS A reconstructed AML network guided the selection of suitable protein hubs and corresponding multi-targeting strategies. For proteins responsive to existing drugs, a greedy algorithm identified the minimum amount of compounds targeting the maximum number of hubs. We predicted permissible combinations of amiodarone, artenimol, fostamatinib, ponatinib, procaine, and vismodegib that interfere with 3-8 hubs, and we elucidated the pharmacological mode of action of procaine on DNMT3A. For proteins that do not respond to any approved drugs, namely cyclins A1, D2, and E1, we used structure-based de novo drug design to generate a novel triple-targeting compound of the chemical formula C15H15NO5, with favorable pharmacological and drug-like properties. CONCLUSIONS Overall, by integrating network and structural pharmacology with molecular modeling, we determined two complementary strategies with the potential to annihilate the AML network, one in the form of repurposable drug combinations and the other as a de novo synthesized triple-targeting agent. These target-drug interactions could be prioritized for preclinical and clinical testing toward precision medicine for AML.
Collapse
Affiliation(s)
- Seyedeh Sadaf Asfa
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balçova, İzmir, Türkiye
- Department of Pharmacology and Therapeutics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB R3E 0W2, Canada
| | - Reza Arshinchi Bonab
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balçova, İzmir, Türkiye
- Department of Pharmacology and Therapeutics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Division of Neurodegenerative Disorders, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB R3E 0W2, Canada
| | - Onur Önder
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balçova, İzmir, Türkiye
| | - Merve Uça Apaydın
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balçova, İzmir, Türkiye
| | - Hatice Döşeme
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balçova, İzmir, Türkiye
| | - Can Küçük
- Department of Medical Biology, Faculty of Medicine, Dokuz Eylül University, 35330 Balçova, İzmir, Türkiye;
| | - Alexandros G. Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou Campous, 15780 Athens, Greece;
| | - Bernhard M. Stadler
- Technische Hochschule Nürnberg, Faculty of Applied Chemistry, 90489 Nuremberg, Germany;
| | - Stella Logotheti
- Biomedical Physics in Radiation Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
| | - Seyit Kale
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Department of Biophysics, Faculty of Medicine, Izmir Katip Çelebi University, 35330 Çiğli, İzmir, Türkiye
| | - Athanasia Pavlopoulou
- Izmir Biomedicine and Genome Center, 35340 Balçova, İzmir, Türkiye; (S.S.A.); (R.A.B.); (O.Ö.); (M.U.A.); (H.D.); (S.K.)
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 Balçova, İzmir, Türkiye
| |
Collapse
|
2
|
Chen C, Lv M, Hu H, Huai L, Zhu B, Fan S, Wang Q, Zhang J. 5-Hydroxymethylfurfural and its Downstream Chemicals: A Review of Catalytic Routes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2311464. [PMID: 38808666 DOI: 10.1002/adma.202311464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Biomass assumes an increasingly vital role in the realm of renewable energy and sustainable development due to its abundant availability, renewability, and minimal environmental impact. Within this context, 5-hydroxymethylfurfural (HMF), derived from sugar dehydration, stands out as a critical bio-derived product. It serves as a pivotal multifunctional platform compound, integral in synthesizing various vital chemicals, including furan-based polymers, fine chemicals, and biofuels. The high reactivity of HMF, attributed to its highly active aldehyde, hydroxyl, and furan ring, underscores the challenge of selectively regulating its conversion to obtain the desired products. This review highlights the research progress on efficient catalytic systems for HMF synthesis, oxidation, reduction, and etherification. Additionally, it outlines the techno-economic analysis (TEA) and prospective research directions for the production of furan-based chemicals. Despite significant progress in catalysis research, and certain process routes demonstrating substantial economics, with key indicators surpassing petroleum-based products, a gap persists between fundamental research and large-scale industrialization. This is due to the lack of comprehensive engineering research on bio-based chemicals, making the commercialization process a distant goal. These findings provide valuable insights for further development of this field.
Collapse
Affiliation(s)
- Chunlin Chen
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingxin Lv
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hualei Hu
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Liyuan Huai
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Zhu
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Shilin Fan
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuge Wang
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhang
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, 1219 Zhongguan West Road, Ningbo, 315201, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
3
|
Liu C, Chen F, Zhao BH, Wu Y, Zhang B. Electrochemical hydrogenation and oxidation of organic species involving water. Nat Rev Chem 2024; 8:277-293. [PMID: 38528116 DOI: 10.1038/s41570-024-00589-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Fossil fuel-driven thermochemical hydrogenation and oxidation using high-pressure H2 and O2 are still popular but energy-intensive CO2-emitting processes. At present, developing renewable energy-powered electrochemical technologies, especially those using clean, safe and easy-to-handle reducing agents and oxidants for organic hydrogenation and oxidation reactions, is urgently needed. Water is an ideal carrier of hydrogen and oxygen. Electrochemistry provides a powerful route to drive water splitting under ambient conditions. Thus, electrochemical hydrogenation and oxidation transformations involving water as the hydrogen source and oxidant, respectively, have been developed to be mild and efficient tools to synthesize organic hydrogenated and oxidized products. In this Review, we highlight the advances in water-participating electrochemical hydrogenation and oxidation reactions of representative organic molecules. Typical electrode materials, performance metrics and key characterization techniques are firstly introduced. General electrocatalyst design principles and controlling the microenvironment for promoting hydrogenation and oxygenation reactions involving water are summarized. Furthermore, paired hydrogenation and oxidation reactions are briefly introduced before finally discussing the challenges and future opportunities of this research field.
Collapse
Affiliation(s)
- Cuibo Liu
- Institute of Molecular Plus, Department of Chemistry, School of Science, Tianjin University, Tianjin, China
| | - Fanpeng Chen
- Institute of Molecular Plus, Department of Chemistry, School of Science, Tianjin University, Tianjin, China
| | - Bo-Hang Zhao
- Institute of Molecular Plus, Department of Chemistry, School of Science, Tianjin University, Tianjin, China
| | - Yongmeng Wu
- Institute of Molecular Plus, Department of Chemistry, School of Science, Tianjin University, Tianjin, China
| | - Bin Zhang
- Institute of Molecular Plus, Department of Chemistry, School of Science, Tianjin University, Tianjin, China.
- Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Frontiers Science Center for Synthetic Biology, Tianjin University, Tianjin, China.
| |
Collapse
|
4
|
Shen D, Zhong F, Ren T, Li L, Li Z, Yin J, Gong P, Zhang F, Lv C, Chao M. Alkyne Oxidation by a Vitamin B2-Based Photocatalytic System with Both H 2O and O 2 as the Oxygen Source. J Org Chem 2023; 88:15270-15281. [PMID: 37852799 DOI: 10.1021/acs.joc.3c01760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
The employment of readily available photocatalysts and green oxygen atom sources is recognized as a promising strategy to develop sustainable catalysis for oxidation reactions. We herein reported a sacrificial reagent-free system consisting of riboflavin tetraacetate (RFT), an ester of natural vitamin B2 as the photocatalyst, and Sc(OTf)3 and NaCl as the cocatalysts for alkyne oxidation under blue light or even sunlight irradiation to produce 1,2-diketone in which the oxygen atoms were from both water and molecular oxygen, respectively. A major Cl-/Cl• cycle was proposed to be involved and achieved by the excited [RFT-2Sc3+]* complex via single electron transfer for the first time, distinguished from the OCl- active species by a two-electron process in previous flavin-halide photo-oxidation systems.
Collapse
Affiliation(s)
- Duyi Shen
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, CAS, Lanzhou 730000, P. R. China
| | - Fubi Zhong
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Ting Ren
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Linghui Li
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Zihan Li
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Junzhong Yin
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Peiwei Gong
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Fanjun Zhang
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| | - Chengwei Lv
- College of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, P. R. China
| | - Mianran Chao
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P. R. China
| |
Collapse
|
5
|
Roby O, Moutaouakil M, Tighadouini S, Loukhmi Z, Aboulmouhajir A, Saddik R. Highly Active Catecholase-Like Catalyst Based on the In-Situ Combination of Benzodiazepine Derivatives and Copper (II) Salts. CHEMISTRY AFRICA 2023. [DOI: 10.1007/s42250-023-00638-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
|
6
|
Li H, Li Y, Jiao J, Lin C. Recent research progress on crystallization strategies for difficult-to-crystallize organic molecules. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
|
7
|
Sustainable amidation through acceptorless dehydrogenative coupling by pincer-type catalysts: recent advances. PURE APPL CHEM 2023. [DOI: 10.1515/pac-2022-1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Abstract
The amide functional group is ubiquitous in living organisms, and is of particular importance in bioactive compounds and pharmaceuticals. Because of the prevalence and significance of the amide bond, considerable efforts have been invested throughout the years in developing new synthetic methodologies for its formation. Nevertheless, amide synthesis still largely relies on variants of the traditional condensation of carboxylic acids and amines, mediated by stoichiometric coupling reagents. This poses a sustainability challenge, since such reactions suffer from unfavorable atom and step economies, involve harmful chemicals and produce chemical waste. Hence, establishing sustainable approaches to amide synthesis is of great importance. Over the last two decades, we have developed homogeneous catalytic reactions for sustainable synthetic transformations, primarily based on transition metal complexes of pincer ligands. A considerable portion of these efforts has been devoted to acceptorless dehydrogenative coupling, including that of alcohols and amines through ruthenium-catalyzed reactions. These latter processes generate amides without resorting to coupling reagents and typically produce no waste, with their only byproduct being H2 gas, which is itself a valuable resource. In the present review, we chronicle our progress in this area of research since 2014. This includes the use of water and ammonia as amidation reagents, expanding the scope of amidation substrates and target amides, achieving milder reaction conditions, development of amidation-based liquid organic hydrogen carrier systems, and introduction of manganese-based catalysts.
Collapse
|
8
|
Antico E, Leutzsch M, Wessel N, Weyhermüller T, Werlé C, Leitner W. Selective oxidation of silanes into silanols with water using [MnBr(CO) 5] as a precatalyst. Chem Sci 2022; 14:54-60. [PMID: 36605749 PMCID: PMC9769106 DOI: 10.1039/d2sc05959b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022] Open
Abstract
The development of earth-abundant catalysts for the selective conversion of silanes to silanols with water as an oxidant generating valuable hydrogen as the only by-product continues to be a challenge. Here, we demonstrate that [MnBr(CO)5] is a highly active precatalyst for this reaction, operating under neutral conditions and avoiding the undesired formation of siloxanes. As a result, a broad substrate scope, including primary and secondary silanes, could be converted to the desired products. The turnover performances of the catalyst were also examined, yielding a maximum TOF of 4088 h-1. New light was shed on the debated mechanism of the interaction between [MnBr(CO)5] and Si-H bonds based on the reaction kinetics (including KIEs of PhMe2SiD and D2O) and spectroscopic techniques (FT-IR, GC-TCD, 1H-, 29Si-, and 13C-NMR). The initial activation of [MnBr(CO)5] was found to result from the formation of a manganese(i) hydride species and R3SiBr, and the experimental data are most consistent with a catalytic cycle comprising a cationic tricarbonyl Mn(i) unit as the active framework.
Collapse
Affiliation(s)
- Emanuele Antico
- Max Planck Institute for Chemical Energy ConversionStiftstr. 34–3645470 Mülheim an der RuhrGermany,Institut für Technische und Makromolekulare Chemie (ITMC), RWTH Aachen UniversityWorringer Weg 252074 AachenGermany
| | - Markus Leutzsch
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470 Mülheim an der RuhrGermany
| | - Niklas Wessel
- Max Planck Institute for Chemical Energy ConversionStiftstr. 34–3645470 Mülheim an der RuhrGermany,Institut für Technische und Makromolekulare Chemie (ITMC), RWTH Aachen UniversityWorringer Weg 252074 AachenGermany
| | - Thomas Weyhermüller
- Max Planck Institute for Chemical Energy ConversionStiftstr. 34–3645470 Mülheim an der RuhrGermany
| | - Christophe Werlé
- Max Planck Institute for Chemical Energy ConversionStiftstr. 34–3645470 Mülheim an der RuhrGermany,Ruhr University BochumUniversitätsstr. 15044801 BochumGermany
| | - Walter Leitner
- Max Planck Institute for Chemical Energy ConversionStiftstr. 34–3645470 Mülheim an der RuhrGermany,Institut für Technische und Makromolekulare Chemie (ITMC), RWTH Aachen UniversityWorringer Weg 252074 AachenGermany
| |
Collapse
|