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Avilés-Moreno JR, Gámez F, Berden G, Oomens J, Martínez-Haya B. Inclusion complexes of the macrocycle nonactin with benchmark protonated amines: aniline and serine. Phys Chem Chem Phys 2022; 24:8422-8431. [PMID: 35343526 DOI: 10.1039/d2cp00264g] [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
The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. While the focus of most investigations on nonactin has been on the binding of metal cations and small molecular ions, this study pursues the characterization of its inclusion complexes with primary amines with bulky structured side groups of different polarity. To this end, the complexes of nonactin with aniline and with the amino acid L-serine, both in protonated form, are considered as case studies and their relevant coordination arrangements are assessed by means of infrared action spectroscopy, quantum chemical density functional theory and Born-Oppenheimer molecular dynamics. The study suggests that the oxygen atoms from the oxolane (tetrahydrofuran) groups of nonactin constitute the preferential docking sites of the ammonium moiety of the guest cation, although conformational constraints promote interactions with the ester carbonyl backbone groups. In the aniline complex, the benzyl side ring is oriented outwards from the cavity, whereas in the case of L-serine, the side carboxylic acid and alcohol groups participate actively in the coordination process. Interestingly, the accommodation of L-serine is favoured when nonactin adopts an enantiomeric-selective folding, that promotes the tripodal coordination of the protonated amine group with oxolane rings from three nonactinic acid blocks with enantiomeric sequence (+)-(-)-(+), which allows for a facile coordination of the serine side groups. This is recognized as a general feature associated with the alternation of chiral domains in globally achiral natural nonactin, yielding mirror-symmetric complexes with the enantiomers of chiral amines.
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Affiliation(s)
| | - Francisco Gámez
- Departamento de Química Física, Universidad Complutense, 28040 Madrid, Spain
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7, 6525ED Nijmegen, The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain.
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Matarrita-Carranza B, Murillo-Cruz C, Avendaño R, Ríos MI, Chavarría M, Gómez-Calvo ML, Tamayo-Castillo G, Araya JJ, Pinto-Tomás AA. Streptomyces sp. M54: an actinobacteria associated with a neotropical social wasp with high potential for antibiotic production. Antonie van Leeuwenhoek 2021; 114:379-398. [PMID: 33587228 DOI: 10.1007/s10482-021-01520-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/17/2021] [Indexed: 11/28/2022]
Abstract
Streptomyces symbionts in insects have shown to be a valuable source of new antibiotics. Here, we report the genome sequence and the potential for antibiotic production of "Streptomyces sp. M54", an Actinobacteria associated with the eusocial wasp, Polybia plebeja. The Streptomyces sp. M54 genome is composed of a chromosome (7.96 Mb), and a plasmid (1.91 Kb) and harbors 30 biosynthetic gene clusters for secondary metabolites, of which only one third has been previously characterized. Growth inhibition bioassays show that this bacterium produces antimicrobial compounds that are active against Hirsutella citriformis, a natural fungal enemy of its host, and the human pathogens Staphylococcus aureus and Candida albicans. Analyses through TLC-bioautography, LC-MS/MS and NMR allowed the identification of five macrocyclic ionophore antibiotics, with previously reported antibacterial, antitumor and antiviral properties. Phylogenetic analyses placed Streptomyces sp. M54 in a clade of other host-associated strains taxonomically related to Streptomyces griseus. Pangenomic and ANI analyses confirm the identity of one of its closest relatives as Streptomyces sp. LaPpAH-199, a strain isolated from an ant-plant symbiosis in Africa. In summary, our results suggest an insect-microbe association in distant geographic areas and showcase the potential of Streptomyces sp. M54 and related strains for the discovery of novel antibiotics.
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Affiliation(s)
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica
| | - María Isabel Ríos
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, 1174-1200, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - María Luisa Gómez-Calvo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Giselle Tamayo-Castillo
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Juan J Araya
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, 11501-2060, San José, Costa Rica
| | - Adrián A Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas (CIEMic), Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, 11501-2060, San José, Costa Rica. .,Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, 11501-2060, San José, Costa Rica.
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Avilés-Moreno JR, Gámez F, Berden G, Martens J, Oomens J, Martínez-Haya B. Multipodal coordination and mobility of molecular cations inside the macrocycle valinomycin. Phys Chem Chem Phys 2020; 22:19725-19734. [DOI: 10.1039/d0cp02996c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small cations (K+, NH4+) occupy the center of the valinomycin cavity. Bulkier cations like H4PO4+ stretch the valinomycin backbone, which adopts barrel-like and funnel-like configurations, depending on the dynamically varying position of the cation.
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Affiliation(s)
| | - Francisco Gámez
- Department of Applied Physical Chemistry
- Universidad Autónoma de Madrid
- Madrid
- Spain
| | - Giel Berden
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jonathan Martens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525ED Nijmegen
- The Netherlands
| | - Bruno Martínez-Haya
- Department of Physical
- Chemical and Natural Systems
- Universidad Pablo de Olavide
- 41013 Seville
- Spain
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Martínez-Haya B, Avilés-Moreno JR, Gámez F, Berden G, Oomens J. Preferential host-guest coordination of nonactin with ammonium and hydroxylammonium. J Chem Phys 2018; 149:225101. [PMID: 30553267 DOI: 10.1063/1.5049956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The biological activity of the macrocycle nonactin is intimately related to its ionophore properties and ability to act as a selective cation carrier. The competitive binding of small protonated amines constitutes a particularly key issue in the biochemistry of nonactin, which finds application in sensing and extraction technologies. In this study, isolated complexes of nonactin with ammonium and hydroxylammonium are investigated with infrared action spectroscopy and quantum chemical computations. The focus of the investigation is on the coordination achieved by the protonated guest with the oxygen atoms of either the oxolane groups or the carboxyl groups in the ester linkages of the macrocyle host and their relative contributions to the stability of the complexes. The experimental and computational data converge to a preferred coordination arrangement associated with a tight binding of the N-H δ+ bonds with the oxolane groups. In the N H 4 + complex, this results in a compact complex of S 4 symmetry. In contrast, symmetry is disrupted in the NH3OH+ complex, as it incorporates a bifurcated coordination of the -OH bond with a carbonyl group and an oxolane group of the host, involving also a more stretched arrangement of the nonactin backbone. These gas-phase conformations are in agreement with the structures postulated for these complexes in condensed phases, from previous Raman and crystallographic experiments.
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Affiliation(s)
- Bruno Martínez-Haya
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Juan Ramón Avilés-Moreno
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Francisco Gámez
- Department of Physical, Chemical and Natural Systems, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Giel Berden
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
| | - Jos Oomens
- Radboud University, Institute for Molecules and Materials, FELIX Laboratory, Toernooiveld 7c, 6525ED Nijmegen, The Netherlands
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