1
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Fan C, Li J, Dong R, Xu Y, Liu L. Investigation of Enzyme Immobilization and Clogging Mechanisms in the Enzymatic Synthesis of Amoxicillin. Int J Mol Sci 2024; 25:8557. [PMID: 39201244 PMCID: PMC11354056 DOI: 10.3390/ijms25168557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
This study investigated the blocking mechanism of immobilized penicillin G acylase (PGA) during the enzymatic synthesis of amoxicillin. Laboratory observations revealed that the primary cause of clogging was the crystallization of the substrate and product on the enzyme surface. Adjusting key parameters can significantly reduce clogging and improve catalytic efficiency. Methanol can decrease enzyme activity, but isopropyl alcohol cleaners can effectively remove clogs and protect enzyme activity. These findings provide an experimental foundation for optimizing the PGA immobilization process, which is crucial for achieving high efficiency and sustainability in industrial production.
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Affiliation(s)
| | | | | | | | - Liqiang Liu
- College of Food and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China; (C.F.); (J.L.); (R.D.); (Y.X.)
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2
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Krivitskaya AV, Kuryshkina MS, Eremina MY, Smirnov IV, Khrenova MG. Molecular Basis of Influence of A501X Mutations in Penicillin-Binding Protein 2 of Neisseria gonorrhoeae Strain 35/02 on Ceftriaxone Resistance. Int J Mol Sci 2024; 25:8260. [PMID: 39125830 PMCID: PMC11312080 DOI: 10.3390/ijms25158260] [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: 06/14/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 08/12/2024] Open
Abstract
The increase in the resistance of mutant strains of Neisseria gonorrhoeae to the antibiotic ceftriaxone is pronounced in the decrease in the second-order acylation rate constant, k2/KS, by penicillin-binding protein 2 (PBP2). These changes can be caused by both the decrease in the acylation rate constant, k2, and the weakening of the binding affinity, i.e., an increase in the substrate constant, KS. A501X mutations in PBP2 affect second-order acylation rate constants. The PBP2A501V variant exhibits a higher k2/KS value, whereas for PBP2A501R and PBP2A501P variants, these values are lower. We performed molecular dynamic simulations with both classical and QM/MM potentials to model both acylation energy profiles and conformational dynamics of four PBP2 variants to explain the origin of k2/KS changes. The acylation reaction occurs in two elementary steps, specifically, a nucleophilic attack by the oxygen atom of the Ser310 residue and C-N bond cleavage in the β-lactam ring accompanied by the elimination of the leaving group of ceftriaxone. The energy barrier of the first step increases for PBP2 variants with a decrease in the observed k2/KS value. Submicrosecond classic molecular dynamic trajectories with subsequent cluster analysis reveal that the conformation of the β3-β4 loop switches from open to closed and its flexibility decreases for PBP2 variants with a lower k2/KS value. Thus, the experimentally observed decrease in the k2/KS in A501X variants of PBP2 occurs due to both the decrease in the acylation rate constant, k2, and the increase in KS.
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Affiliation(s)
- Alexandra V. Krivitskaya
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Maria S. Kuryshkina
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.S.K.); (I.V.S.)
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Maria Y. Eremina
- Biology Department, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Ivan V. Smirnov
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.S.K.); (I.V.S.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology”, Russian Academy of Sciences, 119071 Moscow, Russia;
- Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.S.K.); (I.V.S.)
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3
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Mato S, Mata S, Alonso ER, León I. Revealing the Structure of 6-Aminopenillanic Acid: The Active Nucleus of Penicillins. J Phys Chem Lett 2024; 15:1908-1913. [PMID: 38345549 PMCID: PMC10895660 DOI: 10.1021/acs.jpclett.3c03301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
6-Aminopenicillanic acid is a penicillanic acid compound and is the active nucleus common to all penicillins. Using laser ablation techniques, we transformed the solid into the gas phase and characterized its conformational panorama by combining supersonic expansions and Fourier transform microwave techniques. Five conformers were determined, adopting different spatial configurations. Among them, the axial and equatorial forms, which are biologically relevant, have been observed. The structural similarity to d-Ala-d-Ala and the detection of both axial and equatorial forms could explain its potential as a penicillin core and its capability as an antibiotic.
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Affiliation(s)
- Sergio Mato
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Santiago Mata
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Elena R Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011 Valladolid, Spain
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4
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Sri Varalakshmi G, Pawar C, Selvam R, Gem Pearl W, Manikantan V, Sumohan Pillai A, Alexander A, Rajendra Prasad N, Enoch IVMV, Dhanaraj P. Nickel sulfide and dysprosium-doped nickel sulfide nanoparticles: Dysprosium-induced variation in properties, in vitro chemo-photothermal behavior, and antibacterial activity. Int J Pharm 2023; 643:123282. [PMID: 37524253 DOI: 10.1016/j.ijpharm.2023.123282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
Newer materials for utilization in multi-directional therapeutic actions are investigated, considering delicate design principles involving size and shape control, surface modification, and controllable drug loading and release. Multi-faceted properties are imparted to the engineered nanoparticles, like magnetism, near-infrared absorption, photothermal efficiency, and suitable size and shape. This report presents nickel sulfide and dysprosium-doped nickel sulfide nanoparticles with poly-β-cyclodextrin polymer coating. The nanoparticles belong to the orthorhombic crystal systems, as indicated by X-ray diffraction studies. The size and shape of the nanoparticles are investigated using Transmission Electron Microscope (TEM) and a particle-size analyzer. The particles show soft ferromagnetic characteristics with definite and moderate saturation magnetization values. The nickel sulfide nanoparticles' in vitro anticancer and antibacterial activities are investigated in free and 5-fluorouracil/penicillin benzathine-loaded forms. The 5-fluorouracil-encapsulation efficiency of the nanoparticles is around 87%, whereas it is above 92% in the case of penicillin benzathine. Both drugs are released slowly in a controlled fashion. The dysprosium-doped nickel sulfide nanoparticles show better anticancer activity, and the efficacy is more significant than the free drug. The nanoparticles are irradiated with a low-power 808 nm laser. The dysprosium-doped nickel sulfide nanoparticles attain a higher temperature on irradiation, i.e., above 59 °C. The photothermal conversion efficiency of this material is determined, and the significance of dysprosium doping is discussed. Contrarily, the undoped nickel sulfide nanoparticles show more significant antibacterial activity. This study presents a novel designed nanoparticle system and the exciting variation of properties on dysprosium doping in nickel sulfide nanoparticles.
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Affiliation(s)
- Govindaraj Sri Varalakshmi
- Department of Applied Chemistry, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India
| | - Charansingh Pawar
- Department of Biochemistry and Biotechnology, Annamalai University, Chidambaram 608002, Tamil Nadu, India
| | - Rajakar Selvam
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India
| | - Wrenit Gem Pearl
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India
| | - Varnitha Manikantan
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India
| | - Archana Sumohan Pillai
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India
| | - Aleyamma Alexander
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India
| | - N Rajendra Prasad
- Department of Biochemistry and Biotechnology, Annamalai University, Chidambaram 608002, Tamil Nadu, India
| | - Israel V M V Enoch
- Centre for Nanoscience and Genomics, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India.
| | - Premnath Dhanaraj
- Department of Biotechnology, Karunya Institute of Technology and Sciences (Deemed University), Coimbatore 641114, Tamil Nadu, India.
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5
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Dumitru MV, Sandu T, Miron A, Zaharia A, Radu IC, Gavrilă AM, Sârbu A, Iovu H, Chiriac AL, Iordache TV. Hybrid Cryogels with Superabsorbent Properties as Promising Materials for Penicillin G Retention. Gels 2023; 9:443. [PMID: 37367113 DOI: 10.3390/gels9060443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
This present study describes the investigation of new promising hybrid cryogels able to retain high amounts of antibiotics, specifically penicillin G, using chitosan or chitosan-biocellulose blends along with a naturally occurring clay, i.e., kaolin. In order to evaluate and optimize the stability of cryogels, three types of chitosan were used in this study, as follows: (i) commercial chitosan; (ii) chitosan prepared in the laboratory from commercial chitin; and (iii) chitosan prepared in the laboratory from shrimp shells. Biocellulose and kaolin, previously functionalized with an organosilane, were also investigated in terms of their potential to improve the stability of cryogels during prolonged submergence under water. The organophilization and incorporation of the clay into the polymer matrix were confirmed by different characterization techniques (such as FTIR, TGA, SEM), while their stability in time underwater was investigated by swelling measurements. As final proof of their superabsorbent behavior, the cryogels were tested for antibiotic adsorption in batch experiments, in which case cryogels based on chitosan extracted from shrimp shells seem to exhibit excellent adsorption properties for penicillin G.
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Affiliation(s)
- Marinela Victoria Dumitru
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Teodor Sandu
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Andreea Miron
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Anamaria Zaharia
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Ionuț Cristian Radu
- Faculty of Chemical Engineering and Biotechnology, University POLITEHNICA of Bucharest, 1-7 Gheorghe Polizu Street, 011061 Bucharest, Romania
| | - Ana-Mihaela Gavrilă
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Andrei Sârbu
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Horia Iovu
- Faculty of Chemical Engineering and Biotechnology, University POLITEHNICA of Bucharest, 1-7 Gheorghe Polizu Street, 011061 Bucharest, Romania
| | - Anita-Laura Chiriac
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
| | - Tanța Verona Iordache
- National Institute for Research & Development in Chemistry and Petrochemistry-ICECHIM, 202 Splaiul Independenței, 060021 Bucharest, Romania
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6
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Synthesis of novel β-lactams: Antioxidant activity, acetylcholinesterase inhibition and computational studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130092] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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7
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Alves NG, Bártolo I, Alves AJS, Fontinha D, Francisco D, Lopes SMM, Soares MIL, Simões CJV, Prudêncio M, Taveira N, Pinho E Melo TMVD. Synthesis and structure-activity relationships of new chiral spiro-β-lactams highly active against HIV-1 and Plasmodium. Eur J Med Chem 2021; 219:113439. [PMID: 33887681 DOI: 10.1016/j.ejmech.2021.113439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 12/20/2022]
Abstract
The synthesis and antimicrobial activity of new spiro-β-lactams is reported. The design of the new molecules was based on the structural modulation of two previously identified lead spiro-penicillanates with dual activity against HIV and Plasmodium. The spiro-β-lactams synthesized were assayed for their in vitro activity against HIV-1, providing relevant structure-activity relationship information. Among the tested compounds, two spirocyclopentenyl-β-lactams were identified as having remarkable nanomolar activity against HIV-1. Additionally, the same molecules showed promising antiplasmodial activity, inhibiting both the hepatic and blood stages of Plasmodium infection.
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Affiliation(s)
- Nuno Guerreiro Alves
- University of Coimbra, Coimbra Chemistry Centre and Department of Chemistry, 3004-535, Coimbra, Portugal
| | - Inês Bártolo
- Instituto de Investigação Do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Américo J S Alves
- University of Coimbra, Coimbra Chemistry Centre and Department of Chemistry, 3004-535, Coimbra, Portugal
| | - Diana Fontinha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Denise Francisco
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Susana M M Lopes
- University of Coimbra, Coimbra Chemistry Centre and Department of Chemistry, 3004-535, Coimbra, Portugal
| | - Maria I L Soares
- University of Coimbra, Coimbra Chemistry Centre and Department of Chemistry, 3004-535, Coimbra, Portugal
| | - Carlos J V Simões
- University of Coimbra, Coimbra Chemistry Centre and Department of Chemistry, 3004-535, Coimbra, Portugal; BSIM Therapeutics, Instituto Pedro Nunes, Coimbra, Portugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Nuno Taveira
- Instituto de Investigação Do Medicamento (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Universitário Egas Moniz (IUEM), Caparica, Portugal
| | - Teresa M V D Pinho E Melo
- University of Coimbra, Coimbra Chemistry Centre and Department of Chemistry, 3004-535, Coimbra, Portugal.
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8
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Bianco G, Goodsell DS, Forli S. Selective and Effective: Current Progress in Computational Structure-Based Drug Discovery of Targeted Covalent Inhibitors. Trends Pharmacol Sci 2020; 41:1038-1049. [PMID: 33153778 PMCID: PMC7669701 DOI: 10.1016/j.tips.2020.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022]
Abstract
Targeted covalent inhibitors are currently showing great promise for systems that are normally difficult to target with small molecule therapies. This renewed interest has spurred the refinement of existing computational methods as well as the designof new ones, expanding the toolbox for discovery and optimization of selectiveand effective covalent inhibitors. Commonly applied approaches are covalentdocking methods that predict the conformation of the covalent complex with known residues. More recently, a new predictive method, reactive docking, was developed, building on the growing corpus of data generated by large proteomics experiments. This method was successfully used in several 'inverse drug discovery' programs that use high-throughput techniques to isolate effective compounds based on screening of entire compound libraries based on desired phenotypes.
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Affiliation(s)
- Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Research Collaboratory for Structure Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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9
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Biosensors for penicillin quantification: a comprehensive review. Biotechnol Lett 2020; 42:1829-1846. [DOI: 10.1007/s10529-020-02970-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022]
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10
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Theoretical Insights into the Structure of the Aminotris(Methylenephosphonic Acid) (ATMP) Anion: A Possible Partner for Conducting Ionic Media. Symmetry (Basel) 2020. [DOI: 10.3390/sym12060920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We present a computational characterisation of Aminotris(methylenephosphonic acid) (ATMP) and its potential use as an anionic partner for conductive ionic liquids (ILs). We argue that for an IL to be a good candidate for a conducting medium, two conditions must be fulfilled: (i) the charge must be transported by light carriers; and (ii) the system must maintain a high degree of ionisation. The result trends presented herein show that there are molecular ion combinations that do comply with these two criteria, regardless of the specific system used. ATMP is a symmetric molecule with a total of six protons. In the bulk phase, breaking the symmetry of the fully protonated state and creating singly and doubly charged anions induces proton transfer mechanisms. To demonstrate this, we used molecular dynamics (MD) simulations employing a variable topology approach based on the reasonably reliable semiempirical density functional tight binding (DFTB) evaluation of the atomic forces. We show that, by choosing common and economical starting compounds, we can devise a viable prototype for a highly conductive medium where charge transfer is achieved by proton motion.
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11
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Mucsi Z, Chass GA, Csizmadia IG. Reply to the 'Comment on "Penicillin's catalytic mechanism revealed by inelastic neutrons and quantum chemical theory"' by S. A. Glover, Phys. Chem. Chem. Phys., 2019, 21, 18012. Phys Chem Chem Phys 2019; 21:25513-25517. [PMID: 31712790 DOI: 10.1039/c9cp00152b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we comparatively comment on the molecular metric 'amidicity', a descriptor of amide reactivity, and differing methods to determining it; with focus on lactam-rings. Specifically, our established amidicity percentage (AM%) approach is quantitatively contrasted with the transamidation (TA) method. This comment is organised into two sections, firstly addressing the differing methods in context of the computational bases of amidicity. This is followed by the quantitative demonstration that although both the AM% and HRS methods provide estimates of resonance enthalpy (ΔHRE), the former is more reliable across a wider set of systems. The robustness of the AM% approach is affirmed by quantitative matching of experimental NMR and kinetics measurements tracking changes in amide reactivities, including in Penicillin arising from modulation of its amide group and environmental effects.
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Affiliation(s)
- Zoltan Mucsi
- Department of Chemistry, Femtonics Ltd., Budapest H-1094, Hungary.
| | - Gregory A Chass
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK. and Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China and Department of Chemistry, McMaster University, Hamilton, L8S 4M1, Canada
| | - Imre G Csizmadia
- Department of Chemistry, University of Toronto, Toronto, M5S 3H6, Canada.
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12
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Glover SA. Comment on "Penicillin's catalytic mechanism revealed by inelastic neutrons and quantum chemical theory" by Z. Mucsi, G. A. Chass, P. Ábrányi-Balogh, B. Jójárt, D.-C. Fang, A. J. Ramirez-Cuesta, B. Viskolczc and I. G. Csizmadia, Phys. Chem. Chem. Phys., 2013, 15, 20447. Phys Chem Chem Phys 2019; 21:18012-18025. [PMID: 31363727 DOI: 10.1039/c8cp02413h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of amide resonance in the β-lactam ring of β-propiolactams and penicillin type structures has been evaluated by the Mucsi hydrogenation method on the one hand, and isodesmic trans-amidation (TA) and the carbonyl substitution nitrogen atom replacement (COSNAR) methods on the other hand. The discrepancy between the two approaches points to two errors, one arithmetic and the other conceptual, in the manner in which the hydrogenation method is applied to β-lactams and which leads to much lower resonance stabilisation and amidicities than found by the TA and COSNAR methodologies. Correction of these errors yields amidicities in line with the TA and COSNAR results demonstrating that amide bonds in simple β-propiolactams are not weakened by strain relative to normal amides such as N,N-dimethylacetamide. Mucsi's results for penicillin are similarly in error, critically so in light of their use of the drastically reduced resonance in rationalising their proposed mechanism of reaction of the antibiotic with transpeptidase. Correction of the errors in application to penicillin-models points to other difficulties in applying the methodology to complex molecules. A detailed analysis of penicillin-type structures has been carried out using the reliable TA and COSNAR methods, which both point to relatively modest reductions in amidicity or resonance stabilisation in accordance with the known stability of the penam-type structures. At the very least, penicillin retains about 60% the resonance of N,N-dimethylacetamide in stark contrast to the erroneous -36% reported from the hydrogenation method.
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Affiliation(s)
- Stephen A Glover
- Department of Chemistry, School of Science and Technology, University of New England, Armidale, New South Wales 2350, Australia.
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13
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Vu HT, Song FV, Tian KV, Su H, Chass GA. Systematic characterisation of the structure and radical scavenging potency of Pu'Er tea () polyphenol theaflavin. Org Biomol Chem 2019; 17:9942-9950. [DOI: 10.1039/c9ob02007a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resolving the functional 3D structural poses of Pu'Er tea antioxidant theaflavin.
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Affiliation(s)
- Huyen Trang Vu
- Materials Science and Engineering
- Nanyang Technological University
- Singapore
| | - Fu V. Song
- School of Biological and Chemical Sciences
- Queen Mary University of London
- UK
| | - Kun V. Tian
- Department of Physics
- Tor Vergata University of Rome II
- Rome
- Italy
| | - Haibin Su
- Department of Chemistry
- Hong Kong University of Science and Technology
- China
| | - Gregory A. Chass
- School of Biological and Chemical Sciences
- Queen Mary University of London
- UK
- Department of Chemistry
- The University of Hong Kong
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14
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Amide Activation in Ground and Excited States. Molecules 2018; 23:molecules23112859. [PMID: 30400217 PMCID: PMC6278462 DOI: 10.3390/molecules23112859] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 10/26/2018] [Accepted: 10/31/2018] [Indexed: 11/22/2022] Open
Abstract
Not all amide bonds are created equally. The purpose of the present paper is the reinterpretation of the amide group by means of two concepts: amidicity and carbonylicity. These concepts are meant to provide a new viewpoint in defining the stability and reactivity of amides. With the help of simple quantum-chemical calculations, practicing chemists can easily predict the outcome of a desired process. The main benefit of the concepts is their simplicity. They provide intuitive, but quasi-thermodynamic data, making them a practical rule of thumb for routine use. In the current paper we demonstrate the performance of our methods to describe the chemical character of an amide bond strength and the way of its activation methods. Examples include transamidation, acyl transfer and amide reductions. Also, the method is highly capable for simple interpretation of mechanisms for biological processes, such as protein splicing and drug mechanisms. Finally, we demonstrate how these methods can provide information about photo-activation of amides, through the examples of two caged neurotransmitter derivatives.
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15
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Fuentes-Paniagua E, Hernández-Ros JM, Soliveri J, Copa-Patiño JL, Gómez R, Sánchez-Nieves J, de la Mata FJ. Strategies for penicillin V dendronization with cationic carbosilane dendrons and study of antibacterial properties. CAN J CHEM 2017. [DOI: 10.1139/cjc-2017-0059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Strategies to synthesize a cationic carbosilane dendron containing the antibiotic penicillin V potassium salt (PenVK) at the focal point are discussed. The preparation of such a compound requires the use of systems with no donor atoms such as N or S in their framework, because their presence favours the rupture of the penicillin β-lactam ring. The antibacterial activity of the new dendron containing ammonium groups, at the periphery, and the PenV moiety, at the focal point, against gram-positive Staphylococcus aureus strains was evaluated. These results were compared with those obtained for free PenVK, a related cationic dendron without a penicillin moiety at the focal point, and also compared with an equimolar mixture of this last dendron with free PenV. The data obtained indicate that, on one hand, the conjugation or interaction of PenV with cationic dendrons reduces its activity in comparison with free PenVK. On the other hand, the penicillin dendron is able to release the antibiotic in the presence of esterease, due to the breaking of the ester bond in this derivative.
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Affiliation(s)
- Elena Fuentes-Paniagua
- Departamento de Química Orgánica y Química Inorgánica, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - José M. Hernández-Ros
- Departamento de Biomedicina y Biotecnología, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Juan Soliveri
- Departamento de Biomedicina y Biotecnología, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
| | - José L. Copa-Patiño
- Departamento de Biomedicina y Biotecnología, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
| | - Rafael Gómez
- Departamento de Química Orgánica y Química Inorgánica, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - Javier Sánchez-Nieves
- Departamento de Química Orgánica y Química Inorgánica, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - F. Javier de la Mata
- Departamento de Química Orgánica y Química Inorgánica, Campus Universitario, Universidad de Alcalá, Alcalá de Henares, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
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16
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Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Sci Rep 2017; 7:7533. [PMID: 28790348 PMCID: PMC5548911 DOI: 10.1038/s41598-017-07757-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/29/2017] [Indexed: 01/29/2023] Open
Abstract
Standard cell culture guidelines often use media supplemented with antibiotics to prevent cell contamination. However, relatively little is known about the effect of antibiotic use in cell culture on gene expression and the extent to which this treatment could confound results. To comprehensively characterize the effect of antibiotic treatment on gene expression, we performed RNA-seq and ChIP-seq for H3K27ac on HepG2 cells, a human liver cell line commonly used for pharmacokinetic, metabolism and genomic studies, cultured in media supplemented with penicillin-streptomycin (PenStrep) or vehicle control. We identified 209 PenStrep-responsive genes, including transcription factors such as ATF3 that are likely to alter the regulation of other genes. Pathway analyses found a significant enrichment for "xenobiotic metabolism signaling" and "PXR/RXR activation" pathways. Our H3K27ac ChIP-seq identified 9,514 peaks that are PenStrep responsive. These peaks were enriched near genes that function in cell differentiation, tRNA modification, nuclease activity and protein dephosphorylation. Our results suggest that PenStrep treatment can significantly alter gene expression and regulation in a common liver cell type such as HepG2, advocating that antibiotic treatment should be taken into account when carrying out genetic, genomic or other biological assays in cultured cells.
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17
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Ahmed KBA, Raman T, Veerappan A. Future prospects of antibacterial metal nanoparticles as enzyme inhibitor. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2016; 68:939-947. [PMID: 27524096 DOI: 10.1016/j.msec.2016.06.034] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/23/2016] [Accepted: 06/09/2016] [Indexed: 12/15/2022]
Abstract
Nanoparticles are being widely used as antibacterial agents with metal nanoparticles emerging as the most efficient antibacterial agents. There have been many studies which have reported the mechanism of antibacterial activity of nanoparticles on bacteria. In this review we aim to emphasize on all the possible mechanisms which are involved in the antibacterial activity of nanoparticles and also to understand their mode of action and role as bacterial enzyme inhibitor by comparing their antibacterial mechanism to that of antibiotics with enzyme inhibition as a major mechanism. With the emergence of widespread antibiotic resistance, nanoparticles offer a better alternative to our conventional arsenal of antibiotics. Once the biological safety of these nanoparticles is addressed, these nanoparticles can be of great medical importance in our fight against bacterial infections.
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Affiliation(s)
- Khan Behlol Ayaz Ahmed
- School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, Tamil Nadu, India
| | - Thiagarajan Raman
- School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, Tamil Nadu, India.
| | - Anbazhagan Veerappan
- School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, Tamil Nadu, India.
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18
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Beck TN, Lloyd D, Kuskovsky R, Minah J, Arora K, Plotkin BJ, Green JM, Boshoff HI, Barry C, Deschamps J, Konaklieva MI. Non-transpeptidase binding arylthioether β-lactams active against Mycobacterium tuberculosis and Moraxella catarrhalis. Bioorg Med Chem 2015; 23:632-47. [PMID: 25549898 PMCID: PMC6415315 DOI: 10.1016/j.bmc.2014.11.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/08/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
The prevalence of drug resistance in both clinical and community settings as a consequence of alterations of biosynthetic pathways, enzymes or cell wall architecture is a persistent threat to human health. We have designed, synthesized, and tested a novel class of non-transpeptidase, β-lactamase resistant monocyclic β-lactams that carry an arylthio group at C4. These thioethers exhibit inhibitory and cidal activity against serine β-lactamase producing Mycobacterium tuberculosis wild type strain (Mtb) and multiple (n=8) β-lactamase producing Moraxella catarrhalis clinical isolates.
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Affiliation(s)
- Tim N Beck
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Dina Lloyd
- Department of Chemistry, American University, Washington, DC 20016, USA
| | | | - Jeanette Minah
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Kriti Arora
- Tuberculosis Research Section, LCID, NIAID, NIH 33 North Drive, Bldg 33, Rm 2W20C, Bethesda, MD 20892, USA
| | - Balbina J Plotkin
- Department of Microbiology and Immunology, Midwestern University, Chicago, IL 60515, USA
| | - Jacalyn M Green
- Department of Microbiology and Immunology, Midwestern University, Chicago, IL 60515, USA
| | - Helena I Boshoff
- Tuberculosis Research Section, LCID, NIAID, NIH 33 North Drive, Bldg 33, Rm 2W20C, Bethesda, MD 20892, USA
| | - Clifton Barry
- Tuberculosis Research Section, LCID, NIAID, NIH 33 North Drive, Bldg 33, Rm 2W20C, Bethesda, MD 20892, USA
| | - Jeffrey Deschamps
- Naval Research Laboratory, Code 6930 4555 Overlook Ave., Washington, DC 20375, USA
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19
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Molecular Targets of β-Lactam-Based Antimicrobials: Beyond the Usual Suspects. Antibiotics (Basel) 2014; 3:128-42. [PMID: 27025739 PMCID: PMC4790389 DOI: 10.3390/antibiotics3020128] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
The common practice in antibacterial drug development has been to rapidly make an attempt to find ever-more stable and broad-spectrum variants for a particular antibiotic, once a drug resistance for that antibiotic is detected. We are now facing bacterial resistance toward our clinically relevant antibiotics of such a magnitude that the conversation for antimicrobial drug development ought to include effective new antibiotics with alternative mechanisms of action. The electrophilic β-lactam ring is amenable for the inhibition of different enzyme classes by a suitable decoration of the core scaffold. Monocyclic β-lactams lacking an ionizable group at the lactam nitrogen exhibit target preferences toward bacterial enzymes important for resistance and virulence. The present review intends to draw attention to the versatility of the β-lactams as antimicrobials with "unusual" molecular targets.
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