1
|
Stachowiak K, Zabiszak M, Grajewski J, Teubert A, Bajek A, Jastrzab R. Thermodynamic Studies of Complexes in Cu(II)/Uridine-5'-Diphosphoglucuronic Acid System. Molecules 2024; 29:3695. [PMID: 39125099 PMCID: PMC11314288 DOI: 10.3390/molecules29153695] [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: 07/05/2024] [Revised: 07/28/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
A binary system of uridine-5'-diphosphoglucuronic acid with copper (II) ions was studied. Potentiometric studies in aqueous solutions using computer data analysis were carried out. The pH of dominance, the overall stability constants (logβ), and the equilibrium constants of the formation reaction (logKe) were determined for each complex compound formed in the studied system. Spectroscopic studies were carried out to determine the mode of coordination in the compounds studied. Cytotoxicity and metabolic activity tests of the compounds obtained showed an increase in the biological activity of the complexes tested against the free ligand. The current research may contribute to the knowledge of complex compounds of biomolecules found in the human body and may also contribute to the characterization of a group of complex compounds with potential anticancer properties.
Collapse
Affiliation(s)
- Klaudia Stachowiak
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| | - Michal Zabiszak
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| | - Jakub Grajewski
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| | - Anna Teubert
- Institute of Bioorganic Chemistry, Polish Academy of Science, Zygmunta Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Anna Bajek
- Faculty of Medicine, Department of Urology and Andrology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Jagiellonska 13, 85-067 Bydgoszcz, Poland;
| | - Renata Jastrzab
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| |
Collapse
|
2
|
Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024; 64:4485-4499. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [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: 05/22/2024]
Abstract
With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.
Collapse
Affiliation(s)
- Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch.Weg 15, 55128 Mainz, Germany
| | - Philippe Archambault
- Chemical Computing Group, 910-1010 Sherbrooke W., Montreal, Quebec, Canada H3A 2R7
| | - Luca P Köhler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
| |
Collapse
|
3
|
Cataldo PG, Iramain MA, Castillo MV, Manzur ME, Romano E, Brandán SA. Vibrational assignments of cyclic dimers and inter-monomers of adenine relating FT-IR, FT-Raman and UV spectra with SQMFF and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123540. [PMID: 37898058 DOI: 10.1016/j.saa.2023.123540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/30/2023]
Abstract
In this work, three different cyclic dimers and a tetramer of adenine taken from the experimental structure determined by X-ray diffraction have been studied by combination of experimental FT-IR, FT-Raman and UV-Visible spectra with hybrid B3LYP/6-311++G** and scaled quantum mechanical force field (SQMFF) calculations in order to perform the complete assignments of bands observed in the vibrational spectra. The characteristics of different N-H···N interactions of those three cyclic structures together with the group of IR bands observed between 2865 and 2599 cm-1 have been elucidated considering the tetrameric structure. The cyclic dimers and the tetramer of adenine confirm that the bands observed between 2865 and 2599 cm-1 are not due to N-H···N interactions but to bands of combination, as was previously suggested. The experimental available deuterated IR and terahertz spectra have allowed the complete assignments of regions of higher and lower wavenumbers. Good correlations were acquired comparing the theoretical IR, Raman and UV spectra of three species and the tetramer with the analogous experimental ones, suggesting the presence of all species in both phases. Vibronic bands are observed in the electronic spectra when adenine concentration is increased in aqueous solution evidencing the presence of monomer, tautomers and dimers, as reported by different studies. Similar characteristics of H bonds interactions are predicted for dimers 1 and 2 but different from the dimer 3, as revealed by using NBO and AIM calculations. Different scaled force constants values were found for the cyclic dimers 1 and 2, as compared to the corresponding to dimer 3.
Collapse
Affiliation(s)
- Pablo G Cataldo
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucumán, Tucumán, Argentina
| | - Maximiliano A Iramain
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucumán, Tucumán, Argentina
| | - María V Castillo
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucumán, Tucumán, Argentina
| | - María E Manzur
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucumán, Tucumán, Argentina
| | - Elida Romano
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucumán, Tucumán, Argentina
| | - Silvia Antonia Brandán
- Cátedra de Química General, Instituto de Química Inorgánica, Facultad de Bioquímica. Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, (4000) San Miguel de Tucumán, Tucumán, Argentina.
| |
Collapse
|
4
|
Perez FP, Morisaki J, Kanakri H, Rizkalla M. Electromagnetic Field Stimulation Therapy for Alzheimer's Disease. NEUROLOGY (CHICAGO, ILL.) 2024; 3:1020. [PMID: 38699565 PMCID: PMC11064876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative dementia worldwide. AD is a multifactorial disease that causes a progressive decline in memory and function precipitated by toxic beta-amyloid (Aβ) proteins, a key player in AD pathology. In 2022, 6.5 million Americans lived with AD, costing the nation $321billion. The standard of care for AD treatment includes acetylcholinesterase inhibitors (AchEIs), NMDA receptor antagonists, and monoclonal antibodies (mAbs). However, these methods are either: 1) ineffective in improving cognition, 2) unable to change disease progression, 3) limited in the number of therapeutic targets, 4) prone to cause severe side effects (brain swelling, microhemorrhages with mAb, and bradycardia and syncope with AchEIs), 5) unable to effectively cross the blood-brain barrier, and 6) lack of understanding of the aging process on the disease. mAbs are available to lower Aβ, but the difficulties of reducing the levels of the toxic Aβ proteins in the brain without triggering brain swelling or microhemorrhages associated with mAbs make the risk-benefit profile of mAbs unclear. A novel multitarget, effective, and safe non-invasive approach utilizing Repeated Electromagnetic Field Stimulation (REMFS) lowers Aβ levels in human neurons and memory areas, prevents neuronal death, stops disease progression, and improves memory without causing brain edema or bleeds in AD mice. This REMFS treatment has not been developed for humans because current EMF devices have poor penetration depth and inhomogeneous E-field distribution in the brain. Here, we discussed the biology of these effects in neurons and the design of optimal devices to treat AD.
Collapse
Affiliation(s)
- Felipe P Perez
- Department of Medicine, Indiana University School of Medicine, USA
| | - Jorge Morisaki
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Haitham Kanakri
- Department of Electrical and Computer Engineering, Indiana University-Purdue University, Indianapolis, IN, USA
| | - Maher Rizkalla
- Department of Electrical and Computer Engineering, Indiana University-Purdue University, Indianapolis, IN, USA
| |
Collapse
|
5
|
Samir S. Human DNA Mutations and their Impact on Genetic Disorders. Recent Pat Biotechnol 2024; 18:288-315. [PMID: 37936448 DOI: 10.2174/0118722083255081231020055309] [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: 04/08/2023] [Revised: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 11/09/2023]
Abstract
DNA is a remarkably precise medium for copying and storing biological information. It serves as a design for cellular machinery that permits cells, organs, and even whole organisms to work. The fidelity of DNA replication results from the action of hundreds of genes involved in proofreading and damage repair. All human cells can acquire genetic changes in their DNA all over life. Genetic mutations are changes to the DNA sequence that happen during cell division when the cells make copies of themselves. Mutations in the DNA can cause genetic illnesses such as cancer, or they could help humans better adapt to their environment over time. The endogenous reactive metabolites, therapeutic medicines, and an excess of environmental mutagens, such as UV rays all continuously damage DNA, compromising its integrity. One or more chromosomal alterations and point mutations at a single site (monogenic mutation) including deletions, duplications, and inversions illustrate such DNA mutations. Genetic conditions can occur when an altered gene is inherited from parents, which increases the risk of developing that particular condition, or some gene alterations can happen randomly. Moreover, symptoms of genetic conditions depend on which gene has a mutation. There are many different diseases and conditions caused by mutations. Some of the most common genetic conditions are Alzheimer's disease, some cancers, cystic fibrosis, Down syndrome, and sickle cell disease. Interestingly, scientists find that DNA mutations are more common than formerly thought. This review outlines the main DNA mutations that occur along the human genome and their influence on human health. The subject of patents pertaining to DNA mutations and genetic disorders has been brought up.
Collapse
Affiliation(s)
- Safia Samir
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Giza, Egypt
| |
Collapse
|
6
|
Sieg JP, Jolley EA, Huot MJ, Babitzke P, Bevilacqua P. In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells. Nucleic Acids Res 2023; 51:11298-11317. [PMID: 37855684 PMCID: PMC10639048 DOI: 10.1093/nar/gkad807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/11/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023] Open
Abstract
We conducted a thermodynamic analysis of RNA stability in Eco80 artificial cytoplasm, which mimics in vivo conditions, and compared it to transcriptome-wide probing of mRNA. Eco80 contains 80% of Escherichia coli metabolites, with biological concentrations of metal ions, including 2 mM free Mg2+ and 29 mM metabolite-chelated Mg2+. Fluorescence-detected binding isotherms (FDBI) were used to conduct a thermodynamic analysis of 24 RNA helices and found that these helices, which have an average stability of -12.3 kcal/mol, are less stable by ΔΔGo37 ∼1 kcal/mol. The FDBI data was used to determine a set of Watson-Crick free energy nearest neighbor parameters (NNPs), which revealed that Eco80 reduces the stability of three NNPs. This information was used to adjust the NN model using the RNAstructure package. The in vivo-like adjustments have minimal effects on the prediction of RNA secondary structures determined in vitro and in silico, but markedly improve prediction of fractional RNA base pairing in E. coli, as benchmarked with our in vivo DMS and EDC RNA chemical probing data. In summary, our thermodynamic and chemical probing analyses of RNA helices indicate that RNA secondary structures are less stable in cells than in artificially stable in vitro buffer conditions.
Collapse
Affiliation(s)
- Jacob P Sieg
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth A Jolley
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Melanie J Huot
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
7
|
Romero AH, Fuentes G, Suescun L, Piro O, Echeverría G, Gotopo L, Pezaroglo H, Álvarez G, Cabrera G, Cerecetto H, Couto M. Tautomerism and Rotamerism of Favipiravir and Halogenated Analogues in Solution and in the Solid State. J Org Chem 2023; 88:10735-10752. [PMID: 37452781 DOI: 10.1021/acs.joc.3c00777] [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: 07/18/2023]
Abstract
Favipiravir is an important selective antiviral against RNA-based viruses, and currently, it is being repurposed as a potential drug for the treatment of COVID-19. This type of chemical system presents different carboxamide-rotameric and hydroxyl-tautomeric states, which could be essential for interpreting its selective antiviral activity. Herein, the tautomeric 3-hydroxypyrazine/3-pyrazinone pair of favipiravir and its 6-substituted analogues, 6-Cl, 6-Br, 6-I, and 6-H, were fully investigated in solution and in the solid state through ultraviolet-visible, 1H nuclear magnetic resonance, infrared spectroscopy, and X-ray diffraction techniques. Also, a study of the gas phase was performed using density functional theory calculations. In general, the keto-enol balance in these 3-hydroxy-2-pyrazinecarboxamides is finely modulated by external and internal electrical variations via changes in solvent polarity or by replacement of substituents at position 6. The enol tautomer was prevalent in an apolar environment, whereas an increase in the level of the keto tautomer was favored by an increase in solvent polarity and, even moreso, with a strong hydrogen-donor solvent. Keto tautomerization was favored either in solution or in the solid state with a decrease in 6-substituent electronegativity as follows: H ≫ I ≈ Br > Cl ≥ F. Specific rotameric states based on carboxamide, "cisoide" and "transoide", were identified for the enol and keto tautomer, respectively; their rotamerism is dependent on the tautomerism and not the aggregation state.
Collapse
Affiliation(s)
- Angel H Romero
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Germán Fuentes
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| | - Leopoldo Suescun
- Cryssmat-Lab/DETEMA, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Oscar Piro
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, La Plata 1900, Argentina
| | - Gustavo Echeverría
- Departamento de Física, Facultad de Ciencias Exactas, Universidad Nacional de la Plata, La Plata 1900, Argentina
| | - Lourdes Gotopo
- Laboratorio de Síntesis Orgánica, Escuela de Química, Facultad de Ciencias, Universidad Central de Venezuela, Los Chaguaramos, 1040 Caracas, Venezuela
| | - Horacio Pezaroglo
- Laboratorio de Resonancia Magnética Nuclear, Facultad de Química, Universidad de la República, 11800 Montevideo, Uruguay
| | - Guzmán Álvarez
- Laboratorio de Moléculas Bioactivas, CENUR Litoral Norte, Universidad de la República, 60000 Paysandú, Uruguay
| | - Gustavo Cabrera
- Laboratorio de Síntesis Orgánica, Escuela de Química, Facultad de Ciencias, Universidad Central de Venezuela, Los Chaguaramos, 1040 Caracas, Venezuela
| | - Hugo Cerecetto
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
- Area de Radiofarmacia, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Marcos Couto
- Grupo de Química Orgánica Medicinal, Facultad de Ciencias, Universidad de la República, 11400 Montevideo, Uruguay
| |
Collapse
|
8
|
Henry B, Samokhvalov A. Characterization of tautomeric forms of anti-cancer drug gemcitabine and their interconversion upon mechano-chemical treatment, using ATR-FTIR spectroscopy and complementary methods. J Pharm Biomed Anal 2023; 226:115243. [PMID: 36657351 PMCID: PMC9977068 DOI: 10.1016/j.jpba.2023.115243] [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: 11/08/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Gemcitabine is a widely used anti-cancer drug of pyrimidine structure, which can exist as a free base molecular form in crystals. Tautomers are structural isomers of molecules, which interconvert via proton transfer. Mechano-chemistry studies reactions of solids under mechanical impact. We investigated gemcitabine free base for the presence of specific molecular tautomers, using ATR-FTIR spectroscopic analysis, powder XRD, optical microscopy and HPLC. The amino-keto tautomer has the characteristic infrared (IR) peak of the amino group at 3390 cm-1. For the first time, the imino-keto tautomer of gemcitabine free base was detected. The imino-keto tautomer has the characteristic IR peak of the =N-H group, and its peak due to the CO group in pyrimidine ring is shifted vs. that of the amino-keto tautomer. This serves as the unique spectroscopic "fingerprints" of these tautomers. The ATR-FTIR spectroscopic analysis shows that gemcitabine free base can be enriched with the amino-keto or the imino-keto tautomer. Further, we studied the transformation of gemcitabine free base in crystals between its tautomers under conditions of liquid-assisted grinding (LAG). The imino-keto tautomer undergoes tautomerization to the amino-keto tautomer, while the amino-keto tautomer remains stable. No destruction of molecules of gemcitabine free base, when present as either tautomer, occurs during LAG as was verified by the HPLC-UV analysis. LAG is a new, straightforward, facile and fast method to interconvert tautomers in crystals, and ATR-FTIR spectroscopy is a method of choice to study tautomerization reactions of pharmaceuticals. The presented approach is promising for analysis of crystals of drugs containing one or more than one tautomer, and the knowledge-driven design of composite materials, which contain specific tautomeric molecular forms of pyrimidines, purines and other biologically active heterocyclic compounds.
Collapse
Affiliation(s)
- Barrington Henry
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA
| | - Alexander Samokhvalov
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA.
| |
Collapse
|
9
|
Intramolecular Interactions in Derivatives of Uracil Tautomers. Molecules 2022; 27:molecules27217240. [PMID: 36364066 PMCID: PMC9656941 DOI: 10.3390/molecules27217240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/17/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022] Open
Abstract
The influence of solvents on intramolecular interactions in 5- or 6-substituted nitro and amino derivatives of six tautomeric forms of uracil was investigated. For this purpose, the density functional theory (B97-D3/aug-cc-pVDZ) calculations were performed in ten environments (1 > ε > 109) using the polarizable continuum model (PCM) of solvation. The substituents were characterized by electronic (charge of the substituent active region, cSAR) and geometric parameters. Intramolecular interactions between non-covalently bonded atoms were investigated using the theory of atoms in molecules (AIM) and the non-covalent interaction index (NCI) method, which allowed discussion of possible interactions between the substituents and N/NH endocyclic as well as =O/−OH exocyclic groups. The nitro group was more electron-withdrawing in the 5 than in the 6 position, while the opposite effect was observed in the case of electron donation of the amino group. These properties of both groups were enhanced in polar solvents; the enhancement depended on the ortho interactions. Substitution or solvation did not change tautomeric preferences of uracil significantly. However, the formation of a strong NO∙∙∙HO intramolecular hydrogen bond in the 5-NO2 derivative stabilized the dienol tautomer from +17.9 (unsubstituted) to +5.4 kcal/mol (substituted, energy relative to the most stable diketo tautomer).
Collapse
|
10
|
Göç YB, Poziemski J, Smolińska W, Suwała D, Wieczorek G, Niedzialek D. Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding. Int J Mol Sci 2022; 23:ijms231910990. [PMID: 36232294 PMCID: PMC9570295 DOI: 10.3390/ijms231910990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
The initial aim of this work was to elucidate the mutual influence of different single-stranded segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this end, we used a new NAB-GQ-builder software program, to construct dozens of two-tetrad G-quadruplex topologies, based on a designed library of sequences. Then, to probe the sequence–morphology–stability relationships of the designed topologies, we performed molecular dynamics simulations. Their results provide guidance for the design of G-quadruplexes with balanced structures, and in turn programmable physicochemical properties for applications as biomaterials. Moreover, by comparative examinations of the single-stranded segments of three oncogene promoter G-quadruplexes, we assess their druggability potential for future therapeutic strategies. Finally, on the basis of a thorough analysis at the quantum mechanical level of theory on a series of guanine assemblies, we demonstrate how a valence tautomerism, triggered by a coordination of cations, initiates the process of G-quadruplex folding, and we propose a sequential folding mechanism, otherwise dictated by the cancellation of the dipole moments on guanines.
Collapse
Affiliation(s)
- Yavuz Burak Göç
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Faculty of Chemistry, Biological & Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Jakub Poziemski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
| | - Weronika Smolińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Faculty of Chemical and Process Engineering, Warsaw University of Technology, Waryńskiego 1, 00-645 Warsaw, Poland
| | - Dominik Suwała
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Grzegorz Wieczorek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Molecure SA, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Dorota Niedzialek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland or
- Correspondence:
| |
Collapse
|
11
|
Kallert E, Fischer TR, Schneider S, Grimm M, Helm M, Kersten C. Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ 1-Riboswitch. J Chem Inf Model 2022; 62:4134-4148. [PMID: 35994617 DOI: 10.1021/acs.jcim.2c00751] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ1-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.
Collapse
Affiliation(s)
- Elisabeth Kallert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Simon Schneider
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Maike Grimm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, Mainz 55128, Germany
| |
Collapse
|
12
|
Datar A, Paithankar H, Deb P, Chugh J, Bagchi S, Mukherjee A, Hazra A. Water-Controlled Keto-Enol Tautomerization of a Prebiotic Nucleobase. J Phys Chem B 2022; 126:5735-5743. [PMID: 35895006 DOI: 10.1021/acs.jpcb.2c02507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Barbituric acid is believed to be a proto-RNA nucleobase that was used for biological information transfer on prebiotic earth before DNA and RNA in their present forms evolved. Nucleobases have various tautomeric forms and the relative stability of these forms is critical to their biological function. It has been shown that barbituric acid has a tri-keto form in the gas phase and an enol form in the solid state. However, its dominant tautomeric form in aqueous medium that is most relevant for biology has been investigated only to a limited extent and the findings are inconclusive. We have used multiple approaches, namely, molecular dynamics, quantum chemistry, NMR, and IR spectroscopy to determine the most stable tautomer of barbituric acid in solution. We find a delicate balance in the stability of the two tautomers, tri-keto and enol, which is tipped toward the enol as the extent of solvation by water increases.
Collapse
Affiliation(s)
- Avdhoot Datar
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | | | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | | |
Collapse
|
13
|
Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
14
|
Perez FP, Bandeira JP, Perez Chumbiauca CN, Lahiri DK, Morisaki J, Rizkalla M. Multidimensional insights into the repeated electromagnetic field stimulation and biosystems interaction in aging and age-related diseases. J Biomed Sci 2022; 29:39. [PMID: 35698225 PMCID: PMC9190166 DOI: 10.1186/s12929-022-00825-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
We provide a multidimensional sequence of events that describe the electromagnetic field (EMF) stimulation and biological system interaction. We describe this process from the quantum to the molecular, cellular, and organismal levels. We hypothesized that the sequence of events of these interactions starts with the oscillatory effect of the repeated electromagnetic stimulation (REMFS). These oscillations affect the interfacial water of an RNA causing changes at the quantum and molecular levels that release protons by quantum tunneling. Then protonation of RNA produces conformational changes that allow it to bind and activate Heat Shock Transcription Factor 1 (HSF1). Activated HSF1 binds to the DNA expressing chaperones that help regulate autophagy and degradation of abnormal proteins. This action helps to prevent and treat diseases such as Alzheimer’s and Parkinson’s disease (PD) by increasing clearance of pathologic proteins. This framework is based on multiple mathematical models, computer simulations, biophysical experiments, and cellular and animal studies. Results of the literature review and our research point towards the capacity of REMFS to manipulate various networks altered in aging (Reale et al. PloS one 9, e104973, 2014), including delay of cellular senescence (Perez et al. 2008, Exp Gerontol 43, 307-316) and reduction in levels of amyloid-β peptides (Aβ) (Perez et al. 2021, Sci Rep 11, 621). Results of these experiments using REMFS at low frequencies can be applied to the treatment of patients with age-related diseases. The use of EMF as a non-invasive therapeutic modality for Alzheimer’s disease, specifically, holds promise. It is also necessary to consider the complicated and interconnected genetic and epigenetic effects of the REMFS-biological system’s interaction while avoiding any possible adverse effects.
Collapse
Affiliation(s)
- Felipe P Perez
- Indiana University School of Medicine, Indianapolis, IN, USA. .,Division of General Internal Medicine and Geriatrics, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Joseph P Bandeira
- Indiana University School of Medicine, Indianapolis, IN, USA.,Division of General Internal Medicine and Geriatrics, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cristina N Perez Chumbiauca
- Indiana University School of Medicine, Indianapolis, IN, USA.,Division of Rheumatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Debomoy K Lahiri
- Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Psychiatry, Institute of Psychiatric Research, Neuroscience Research Center, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jorge Morisaki
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Maher Rizkalla
- Department of Electrical and Computer Engineering, Indiana University-Purdue University, Indianapolis, IN, USA
| |
Collapse
|
15
|
Investigation of interactions of doxorubicin with purine nucleobases by molecular modeling. J Mol Model 2022; 28:69. [PMID: 35218423 DOI: 10.1007/s00894-022-05031-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
Doxorubicin, an anthracycline antibiotic with anti-tumor activity, is produced by the bacterium Streptomyces peucetius. The interactions between doxorubicin and genetic material and the details of the intercalation with DNA have been controversial issues. Thus, the interactions of doxorubicin with purine nucleobases were studied by quantum mechanical methods. Initially, conformer analyses of doxorubicin were performed with Spartan 08 software and 319 different conformers from 422 initial structures for doxorubicin were obtained. Geometry optimizations and frequency analyses were performed for each structure using density functional theory (DFT) at B3LYP/6-31G** level using Gaussian 09 software. The most stable 20 conformers of doxorubicin and tautomers of purine nucleobases were optimized again with ɷB97XD/6-31G** level and their interactions were also analyzed at the same level. The Discovery Studio 3.5 Visualizer was used to draw the initial and optimized structures of investigated geometries. The noncovalent interactions (NCIs) were visualized by calculating reduced density gradient (RDG) with Multiwfn program. The color-filled isosurfaces and RDG scatter maps of most stable interaction geometries were plotted by Visual Molecular Dynamics (VMD) software and Gnuplot 5.3 software, respectively. This study showed that adenine, guanine, and hypoxanthine nucleobases interact with doxorubicin by forming strong hydrogen bonds and π-π interactions. Considering the normal cellular conditions, the effect of solvent (water) on the interaction geometries were also analyzed and when compared to gas phase it was determined that the movements of the molecules were restricted and there was a minimal change between initial and optimized structures in the aqueous phase.
Collapse
|
16
|
Zhang L, Farkhondeh H, Rahsepar FR, Chatterjee A, Leung KT. Surface-Induced Keto-Enol Tautomerization of DNA Base Molecules and Consequent [4 + 2]-like Cycloaddition on Si(111)7×7. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1266-1276. [PMID: 35020402 DOI: 10.1021/acs.langmuir.1c03173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Adsorption and film growth of deoxyribonucleic acid (DNA) base molecules (cytosine, guanine, thymine, and adenine) on Si(111)7×7 have been studied by combining X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). Multiple tautomeric forms and keto-enol tautomerization are revealed by the O 1s, N 1s, and C 1s XPS spectra of the O-containing DNA bases: cytosine, guanine, and thymine. While the carbonyl group-containing keto tautomer is more stable in a thick film and in powder, the hydroxyl group-containing enol tautomer is found at the interface. The keto-enol tautomerization, as induced by the reactive Si(111)7×7 surface, leads to the formation of a conjugated aromatic six-membered ring with a delocalized π electron system and to the consequent [4 + 2]-like cycloaddition between the enol tautomer and the 7×7 surface. The DFT calculation suggests that the enol tautomer exhibits a kinetic advantage over the keto one for the [4 + 2]-like cycloaddition. Among the several plausible pathways for the cycloaddition provided by the enol tautomer, the experimentally determined one involves a ring N and ring C atom (a polar pair), rather than two ring C atoms (a nonpolar pair), to better match the polar Si adatom-restatom pair of the 7×7 surface. Furthermore, the reacted ring C atom does not have any attached terminal functional group (e.g., -NH2 and -OH). Further deposition leads to continuous film growth in the keto tautomeric form for cytosine and guanine. For the only O-free DNA base molecule, adenine, dative bonding N → Si, rather than the [4 + 2]-like cycloaddition, is observed on the 7×7 surface. Of the four DNA base molecules, adenine is also the only one with its aromaticity maintained when adsorbed on the Si(111)7×7 surface. A reactive surface like the 7×7 surface could therefore provide a new control to trigger tautomerization that is often associated with genetic mutation.
Collapse
Affiliation(s)
- Lei Zhang
- WATLab, and Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Hanieh Farkhondeh
- WATLab, and Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Fatemeh Rahnemaye Rahsepar
- WATLab, and Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- School of Chemistry, College of Science, University of Tehran, Tehran 1417614411, Iran
| | - Avisek Chatterjee
- WATLab, and Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Kam Tong Leung
- WATLab, and Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
17
|
Fedeles BI, Li D, Singh V. Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs. Front Mol Biosci 2022; 8:823253. [PMID: 35145998 PMCID: PMC8822119 DOI: 10.3389/fmolb.2021.823253] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/30/2021] [Indexed: 11/20/2022] Open
Abstract
DNA (2'-deoxyribonucleic acid) and RNA (ribonucleic acid) play diverse functional roles in biology and disease. Despite being comprised primarily of only four cognate nucleobases, nucleic acids can adopt complex three-dimensional structures, and RNA in particular, can catalyze biochemical reactions to regulate a wide variety of biological processes. Such chemical versatility is due in part to the phenomenon of nucleobase tautomerism, whereby the bases can adopt multiple, yet distinct isomeric forms, known as tautomers. For nucleobases, tautomers refer to structural isomers that differ from one another by the position of protons. By altering the position of protons on nucleobases, many of which play critical roles for hydrogen bonding and base pairing interactions, tautomerism has profound effects on the biochemical processes involving nucleic acids. For example, the transient formation of minor tautomers during replication could generate spontaneous mutations. These mutations could arise from the stabilization of mismatches, in the active site of polymerases, in conformations involving minor tautomers that are indistinguishable from canonical base pairs. In this review, we discuss the evidence for tautomerism in DNA, and its consequences to the fidelity of DNA replication. Also reviewed are RNA systems, such as the riboswitches and self-cleaving ribozymes, in which tautomerism plays a functional role in ligand recognition and catalysis, respectively. We also discuss tautomeric nucleoside analogs that are efficacious as antiviral drug candidates such as molnupiravir for coronaviruses and KP1212 for HIV. The antiviral efficacy of these analogs is due, in part, to their ability to exist in multiple tautomeric forms and induce mutations in the replicating viral genomes. From a technical standpoint, minor tautomers of nucleobases are challenging to identify directly because they are rare and interconvert on a fast, millisecond to nanosecond, time scale. Nevertheless, many approaches including biochemical, structural, computational and spectroscopic methods have been developed to study tautomeric dynamics in RNA and DNA systems, and in antiviral nucleoside analogs. An overview of these methods and their applications is included here.
Collapse
Affiliation(s)
- Bogdan I. Fedeles
- Departments of Chemistry and Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Deyu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Vipender Singh
- Department of Biochemistry and Biophysics, Novartis Institute of Biomedical Research, Cambridge, MA, United States
| |
Collapse
|
18
|
Focosi D, Maggi F, Franchini M, McConnell S, Casadevall A. Analysis of Immune Escape Variants from Antibody-Based Therapeutics against COVID-19: A Systematic Review. Int J Mol Sci 2021; 23:29. [PMID: 35008446 PMCID: PMC8744556 DOI: 10.3390/ijms23010029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 12/31/2022] Open
Abstract
The accelerated SARS-CoV-2 evolution under selective pressure by massive deployment of neutralizing antibody-based therapeutics is a concern with potentially severe implications for public health. We review here reports of documented immune escape after treatment with monoclonal antibodies and COVID-19-convalescent plasma (CCP). While the former is mainly associated with specific single amino acid mutations at residues within the receptor-binding domain (e.g., E484K/Q, Q493R, and S494P), a few cases of immune evasion after CCP were associated with recurrent deletions within the N-terminal domain of the spike protein (e.g., ΔHV69-70, ΔLGVY141-144 and ΔAL243-244). The continuous genomic monitoring of non-responders is needed to better understand immune escape frequencies and the fitness of emerging variants.
Collapse
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy;
- Laboratory of Microbiology, Azienda Socio Sanitaria Territoriale Sette Laghi, 21100 Varese, Italy
| | - Massimo Franchini
- Division of Transfusion Medicine, Carlo Poma Hospital, 46100 Mantua, Italy;
| | - Scott McConnell
- Department of Medicine, Johns Hopkins School of Public Health, Baltimore, MD 21218, USA; (S.M.); (A.C.)
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| | - Arturo Casadevall
- Department of Medicine, Johns Hopkins School of Public Health, Baltimore, MD 21218, USA; (S.M.); (A.C.)
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21218, USA
| |
Collapse
|
19
|
Heldmaier FV, Coughlan NJA, Haack A, Huard R, Guna M, Schneider BB, Le Blanc JCY, Campbell JL, Nooijen M, Hopkins WS. UVPD spectroscopy of differential mobility-selected prototropic isomers of protonated adenine. Phys Chem Chem Phys 2021; 23:19892-19900. [PMID: 34525152 DOI: 10.1039/d1cp02688g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two prototropic isomers of adenine are formed in an electrospray ion source and are resolved spatially in a differential mobility spectrometer before detection in a triple quadrupole mass spectrometer. Each isomer is gated in CV space before being trapped in the linear ion trap of the modified mass spectrometer, where they are irradiated by the tuneable output of an optical parametric oscillator and undergo photodissociation to form charged fragments with m/z 119, 109, and 94. The photon-normalised intensity of each fragmentation channel is measured and the action spectra for each DMS-gated tautomer are obtained. Our analysis of the action spectra, aided by calculated vibronic spectra and thermochemical data, allow us to assign the two signals in our measured ionograms to specific tautomers of protonated adenine.
Collapse
Affiliation(s)
- Fiorella Villanueva Heldmaier
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Neville J A Coughlan
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Alexander Haack
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Rebecca Huard
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Mircea Guna
- SCIEX, Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | | | | | - J Larry Campbell
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Bedrock Scientific Inc., Milton, Ontario, Canada
| | - Marcel Nooijen
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada. .,Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.,Centre for Eye and Vision Research, Hong Kong Science Park, New Territories, Hong Kong.,Watermine Innovation, Waterloo, Ontario, Canada
| |
Collapse
|
20
|
Colson P, Devaux CA, Lagier JC, Gautret P, Raoult D. A Possible Role of Remdesivir and Plasma Therapy in the Selective Sweep and Emergence of New SARS-CoV-2 Variants. J Clin Med 2021; 10:3276. [PMID: 34362060 PMCID: PMC8348317 DOI: 10.3390/jcm10153276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/24/2021] [Indexed: 01/18/2023] Open
Abstract
Since summer 2020, SARS-CoV-2 strains at the origin of the COVID-19 pandemic have suddenly been replaced by new SARS-CoV-2 variants, some of which are highly transmissible and spread at a high rate. These variants include the Marseille-4 lineage (Nextclade 20A.EU2) in Europe, the 20I/501Y.V1 variant first detected in the UK, the 20H/501Y.V2 variant first detected in South Africa, and the 20J/501Y.V3 variant first detected in Brazil. These variants are characterized by multiple mutations in the viral spike protein that is targeted by neutralizing antibodies elicited in response to infection or vaccine immunization. The usual coronavirus mutation rate through genetic drift alone cannot account for such rapid changes. Recent reports of the occurrence of such mutations in immunocompromised patients who received remdesivir and/or convalescent plasma or monoclonal antibodies to treat prolonged SARS-CoV-2 infections led us to hypothesize that experimental therapies that fail to cure the patients from COVID-19 could favor the emergence of immune escape SARS-CoV-2 variants. We review here the data that support this hypothesis and urge physicians and clinical trial promoters to systematically monitor viral mutations by whole-genome sequencing for patients who are administered these treatments.
Collapse
Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Christian A. Devaux
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- CNRS, 13009 Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
- Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| |
Collapse
|
21
|
Vazquez-Salazar LI, Boittier ED, Unke OT, Meuwly M. Impact of the Characteristics of Quantum Chemical Databases on Machine Learning Prediction of Tautomerization Energies. J Chem Theory Comput 2021; 17:4769-4785. [PMID: 34288675 DOI: 10.1021/acs.jctc.1c00363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
An essential aspect for adequate predictions of chemical properties by machine learning models is the database used for training them. However, studies that analyze how the content and structure of the databases used for training impact the prediction quality are scarce. In this work, we analyze and quantify the relationships learned by a machine learning model (Neural Network) trained on five different reference databases (QM9, PC9, ANI-1E, ANI-1, and ANI-1x) to predict tautomerization energies from molecules in Tautobase. For this, characteristics such as the number of heavy atoms in a molecule, number of atoms of a given element, bond composition, or initial geometry on the quality of the predictions are considered. The results indicate that training on a chemically diverse database is crucial for obtaining good results and also that conformational sampling can partly compensate for limited coverage of chemical diversity. The overall best-performing reference database (ANI-1x) performs on average by 1 kcal/mol better than PC9, which, however, contains about 2 orders of magnitude fewer reference structures. On the other hand, PC9 is chemically more diverse by a factor of ∼5 as quantified by the number of atom-in-molecule-based fragments (amons) it contains compared with the ANI family of databases. A quantitative measure for deficiencies is the Kullback-Leibler divergence between reference and target distributions. It is explicitly demonstrated that when certain types of bonds need to be covered in the target database (Tautobase) but are undersampled in the reference databases, the resulting predictions are poor. Examples of this include the poor performance of all databases analyzed to predict C(sp2)-C(sp2) double bonds close to heteroatoms and azoles containing N-N and N-O bonds. Analysis of the results with a Tree MAP algorithm provides deeper understanding of specific deficiencies in predicting tautomerization energies by the reference datasets due to inadequate coverage of chemical space. Capitalizing on this information can be used to either improve existing databases or generate new databases of sufficient diversity for a range of machine learning (ML) applications in chemistry.
Collapse
Affiliation(s)
| | - Eric D Boittier
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Oliver T Unke
- Machine Learning Group, Technische Universität Berlin, 10587 Berlin, Germany.,DFG Cluster of Excellence "Unifying Systems in Catalysis" (UniSysCat), Technische Universität Berlin, 10623 Berlin, Germany
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland.,Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| |
Collapse
|
22
|
Artemyeva-Isman OV, Porter ACG. U5 snRNA Interactions With Exons Ensure Splicing Precision. Front Genet 2021; 12:676971. [PMID: 34276781 PMCID: PMC8283771 DOI: 10.3389/fgene.2021.676971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with the precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron start. Association between these guanines cannot be explained solely by base-pairing with U1 snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon end. Current U5 snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: (1) optimal binding register for human exons and U5-the exon junction positioned at U5Loop1 C39|C38; (2) common mechanism for base-pairing of human U5 snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition-guided by base pair geometry; and (3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Statistical analyses showed increased U5 Watson-Crick pairs with the 5'exon in the absence of +5G at the intron start. In 5'exon positions -3 and -5, this effect is specific to U5 snRNA rather than U1 snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3'exon position +1 coincide with substitutions of the conserved -3C at the intron 3'end. Based on mutation and X-ray evidence, we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3'intron end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3'intron end ensure that the 3'exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6, and U2 snRNAs that stabilize the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA therapeutics and gene repair by reverse splicing.
Collapse
Affiliation(s)
- Olga V Artemyeva-Isman
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
23
|
Aschi M, Toto Brocchi G, Portalone G. A Combined Experimental and Computational Study of Halogen and Hydrogen Bonding in Molecular Salts of 5-Bromocytosine. Molecules 2021; 26:molecules26113111. [PMID: 34070959 PMCID: PMC8196974 DOI: 10.3390/molecules26113111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 11/16/2022] Open
Abstract
Although natural or artificial modified pyrimidine nucleobases represent important molecules with valuable properties as constituents of DNA and RNA, no systematic analyses of the structural aspects of bromo derivatives of cytosine have appeared so far in the literature. In view of the biochemical and pharmaceutical relevance of these compounds, six different crystals containing proton-transfer derivatives of 5-bromocytosine are prepared and analyzed in the solid-state by single crystal X-ray diffraction. All six compounds are organic salts, with proton transfer occurring to the Nimino atom of the pyridine ring. Experimental results are then complemented with Hirshfeld surface analysis to quantitively evaluate the contribution of different intermolecular interactions in the crystal packing. Furthermore, theoretical calculations, based on different arrangements of molecules extracted from the crystal structure determinations, are carried out to analyze the formation mechanism of halogen bonds (XBs) in these compounds and provide insights into the nature and strength of the observed interactions. The results show that the supramolecular architectures of the six molecular salts involve extensive classical intermolecular hydrogen bonds. However, in all but one proton-transfer adducts, weak to moderate XBs are revealed by C-Br…O short contacts between the bromine atom in the fifth position, which acts as XB donor (electron acceptor). Moreover, the lone pair electrons of the oxygen atom of adjacent pyrimidine nucleobases and/or counterions or water molecules, which acts as XB acceptor (electron donor).
Collapse
Affiliation(s)
- Massimiliano Aschi
- Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi di L’Aquila, Via Vetoio 10, 67100 Coppito, Italy;
| | - Giorgia Toto Brocchi
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Roma, Italy;
| | - Gustavo Portalone
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, 00185 Roma, Italy;
- Correspondence:
| |
Collapse
|
24
|
Multiscale Modeling of Wobble to Watson-Crick-Like Guanine-Uracil Tautomerization Pathways in RNA. Int J Mol Sci 2021; 22:ijms22115411. [PMID: 34063755 PMCID: PMC8196565 DOI: 10.3390/ijms22115411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/09/2021] [Indexed: 01/02/2023] Open
Abstract
Energetically unfavorable Watson–Crick (WC)-like tautomeric forms of nucleobases are known to introduce spontaneous mutations, and contribute to replication, transcription, and translation errors. Recent NMR relaxation dispersion techniques were able to show that wobble (w) G•U mispair exists in equilibrium with the short-lived, low-population WC-like enolic tautomers. Presently, we have investigated the wG•U → WC-like enolic reaction pathway using various theoretical methods: quantum mechanics (QM), molecular dynamics (MD), and combined quantum mechanics/molecular mechanics (QM/MM). The previous studies on QM gas phase calculations were inconsistent with experimental data. We have also explored the environmental effects on the reaction energies by adding explicit water. While the QM-profile clearly becomes endoergic in the presence of water, the QM/MM-profile remains consistently endoergic in the presence and absence of water. Hence, by including microsolvation and QM/MM calculations, the experimental data can be explained. For the G•Uenol→ Genol•U pathway, the latter appears to be energetically more favorable throughout all computational models. This study can be considered as a benchmark of various computational models of wG•U to WC-like tautomerization pathways with and without the environmental effects, and may contribute on further studies of other mispairs as well.
Collapse
|
25
|
Parshotam S, Joy M, Rossano-Tapia M, Mora-Gomez VA, Brown A. The thermochemical, structural, and spectroscopic analyses of the tautomers of sulfur and selenium modified emissive nucleobases. CAN J CHEM 2021. [DOI: 10.1139/cjc-2020-0294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, density functional theory (DFT) and time dependent density functional theory (TD-DFT) are used to investigate the stabilities and spectral properties [IR, UV–vis, and two-photon absorption (2PA)] of two sets of modified RNA nucleobase tautomers. The modifications introduce either a sulfur or selenium atom to form an isothiazolo[4,3-d]pyrimidine or isoselenazolo[4,3-d]pyrimidine heterocyclic core, respectively. The relative stabilities of both sets of modified tautomers determined with B3LYP/6-31++G(d,p) reveal that in water (with a polarizable continuum model), the 6-keto-2-amino tautomer of guanine and the rare 4-imino-2-keto tautomer of cytosine may be present at significant populations, whereas the 6-enol-2-amino tautomer of guanine is more common in the gas phase. The identification of these modified tautomers is possible due to the natural differences in their vibrational modes and hence IR spectra. Furthermore, the photophysical properties of both these sets of modified tautomers indicate that excitation and emission energies are shifted relative to their more abundant form in both one photon absorption and emission and 2PA spectra, as determined at the B3LYP/6-31++G(d,p) and CAM-B3LYP/aug-cc-pVDZ levels of theory, respectively. Even though the 2PA cross sections in water for all of the species are small (0.3–2.3 GM), the modified cytosine tautomer shows promise, as its cross section is larger than the more dominant form. The spectral separation between the dominant form and the tautomers of isoselenazole and isothiazole modified cytosine and guanine are relatively similar, suggesting both modifications could be useful in elucidating the tautomers from their more abundant counterparts.
Collapse
Affiliation(s)
- Shyam Parshotam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Megan Joy
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - V. A. Mora-Gomez
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2
| |
Collapse
|
26
|
Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
Collapse
Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
27
|
Büchner R, Fondell M, Mascarenhas EJ, Pietzsch A, Vaz da Cruz V, Föhlisch A. How Hydrogen Bonding Amplifies Isomeric Differences in Pyridones toward Strong Changes in Acidity and Tautomerism. J Phys Chem B 2021; 125:2372-2379. [PMID: 33562959 PMCID: PMC7957858 DOI: 10.1021/acs.jpcb.0c10873] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Steric hindrance
of hydration and hydrogen bond enhancement by
localized charges have been identified as key factors for the massive
chemical differences between the hydroxypyridine/pyridone isomers
in aqueous solution. While all isomers occur mainly in the hydroxypyridine
form in the gas phase, they differ by more than 3 orders of magnitude
both in their acidity and tautomeric equilibrium constants upon hydration.
By monitoring the electronic and solvation structures as a function
of the protonation state and the O– substitution
position on the pyridine ring, the amplification of the isomeric differences
in aqueous solution has been investigated. Near-edge X-ray absorption
fine structure (NEXAFS) measurements at the N K-edge served as the
probe of the chemical state. The combination of molecular dynamics
simulations, complete active space self-consistent field (CASSCF),
and time-dependent density functional theory (TD-DFT) spectral calculations
contributes to unraveling the principles of tautomerism and acidity
in multiple biochemical systems based on tautomerism.
Collapse
Affiliation(s)
- Robby Büchner
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Mattis Fondell
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Eric J Mascarenhas
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.,Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Annette Pietzsch
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Vinícius Vaz da Cruz
- Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| | - Alexander Föhlisch
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.,Institute for Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz-Zentrum Berlin für Materialien und Energie, Albert-Einstein-Str. 15, 12489 Berlin, Germany
| |
Collapse
|
28
|
Phototransformations of acrylamide derivatives of piperazine-substituted polyfluorinated chalcones. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.112973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
29
|
Miao S, Liang Y, Rundell S, Bhunia D, Devari S, Munyaradzi O, Bong D. Unnatural bases for recognition of noncoding nucleic acid interfaces. Biopolymers 2021; 112:e23399. [PMID: 32969496 PMCID: PMC7855516 DOI: 10.1002/bip.23399] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/25/2020] [Indexed: 12/20/2022]
Abstract
The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co-opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
Collapse
Affiliation(s)
- Shiqin Miao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Yufeng Liang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Sarah Rundell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Debmalya Bhunia
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Shekar Devari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Oliver Munyaradzi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Dennis Bong
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
30
|
Mohammed SJ, Salih AK, Rashid MAM, Omer KM, Abdalkarim KA. Synthesis, Spectroscopic Studies and Keto-Enol Tautomerism of Novel 1,3,4-Thiadiazole Derivative Containing 3-Mercaptobutan-2-one and Quinazolin-4-one Moieties. Molecules 2020; 25:molecules25225441. [PMID: 33233669 PMCID: PMC7699804 DOI: 10.3390/molecules25225441] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 11/16/2022] Open
Abstract
In this study, a novel 1,3,4-thiadiazole derivative containing 3-mercaptobutan-2-one and quinazolin-4-one moieties (Compound 3) is synthesized by the coupling of 2-amino-1,3,4-thiadiazole-5-(3-mercaptobutan-2-one) (Compound 1) with 2-Phenyl-4H-3,1-benzoxazin-4-one (Compound 2) in one molecule moiety. Compound 3 is found to exist as two types of intra-molecular hydrogen bonding with keto-enol tautomerism characters, which is further confirmed using FTIR, 1H-NMR, 13C-NMR, mass spectrometer, and UV-Visible spectra. The 1H-NMR and UV-Visible spectra of Compound 3 are investigated in different solvents such as methanol, chloroform, and DMSO. Compound 3 exhibits keto-enol tautomeric forms in solvents with different percentage ratios depending on the solvent polarity. The 1H-NMR and UV-Visible spectral results show that Compound 3 favors the keto over the enol form in polar aprotic solvents such as DMSO and the enol over the keto form in non-polar solvents such as chloroform. The 13C-NMR spectrum gives two singles at δ 204.5 ppm, due to ketonic carbon, and δ 155.5 ppm, due to enolic carbon, confirming the keto-enol tautomerism of Compound 3. Furthermore, the molecular ion at m/z 43 and m/z 407 in the mass spectrum of Compound 3 and fragmentation mechanisms proposed reveal the existence of the keto and enol forms, respectively.
Collapse
Affiliation(s)
- Sewara J. Mohammed
- Department of Chemistry, College of Science, University of Sulaimani, Qlyasan Street, Kurdistan Regional Government, Sulaimani 46002, Iraq; (A.K.S.); (M.A.M.R.); (K.A.A.)
- Correspondence: (S.J.M.); (K.M.O.); Tel.: +964-770-193-2570 (S.J.M.); +964-770-505-6061 (K.M.O.)
| | - Akam K. Salih
- Department of Chemistry, College of Science, University of Sulaimani, Qlyasan Street, Kurdistan Regional Government, Sulaimani 46002, Iraq; (A.K.S.); (M.A.M.R.); (K.A.A.)
| | - Mohammad Amin M. Rashid
- Department of Chemistry, College of Science, University of Sulaimani, Qlyasan Street, Kurdistan Regional Government, Sulaimani 46002, Iraq; (A.K.S.); (M.A.M.R.); (K.A.A.)
| | - Khalid M. Omer
- Department of Chemistry, College of Science, University of Sulaimani, Qlyasan Street, Kurdistan Regional Government, Sulaimani 46002, Iraq; (A.K.S.); (M.A.M.R.); (K.A.A.)
- Komar Research Center (KRC), Komar University of Science and Technology, Kurdistan Regional Government, Sulaimani 46002, Iraq
- Correspondence: (S.J.M.); (K.M.O.); Tel.: +964-770-193-2570 (S.J.M.); +964-770-505-6061 (K.M.O.)
| | - Karzan A. Abdalkarim
- Department of Chemistry, College of Science, University of Sulaimani, Qlyasan Street, Kurdistan Regional Government, Sulaimani 46002, Iraq; (A.K.S.); (M.A.M.R.); (K.A.A.)
| |
Collapse
|
31
|
Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
Collapse
Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
| | | |
Collapse
|
32
|
Rzepiela K, Buczek A, Kupka T, Broda MA. Factors Governing the Chemical Stability and NMR Parameters of Uracil Tautomers and Its 5-Halogen Derivatives. Molecules 2020; 25:E3931. [PMID: 32872098 PMCID: PMC7504704 DOI: 10.3390/molecules25173931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/10/2023] Open
Abstract
We report on the density functional theory (DFT) modelling of structural, energetic and NMR parameters of uracil and its derivatives (5-halogenouracil (5XU), X = F, Cl, Br and I) in vacuum and in water using the polarizable continuum model (PCM) and the solvent model density (SMD) approach. On the basis of the obtained results, we conclude that the intramolecular electrostatic interactions are the main factors governing the stability of the six tautomeric forms of uracil and 5XU. Two indices of aromaticity, the harmonic oscillator model of aromaticity (HOMA), satisfying the geometric criterion, and the nuclear independent chemical shift (NICS), were applied to evaluate the aromaticity of uracil and its derivatives in the gas phase and water. The values of these parameters showed that the most stable tautomer is the least aromatic. A good performance of newly designed xOPBE density functional in combination with both large aug-cc-pVQZ and small STO(1M)-3G basis sets for predicting chemical shifts of uracil and 5-fluorouracil in vacuum and water was observed. As a practical alternative for calculating the chemical shifts of challenging heterocyclic compounds, we also propose B3LYP calculations with small STO(1M)-3G basis set. The indirect spin-spin coupling constants predicted by B3LYP/aug-cc-pVQZ(mixed) method reproduce the experimental data for uracil and 5-fluorouracil well.
Collapse
Affiliation(s)
| | | | - Teobald Kupka
- Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, Poland; (K.R.); (A.B.)
| | - Małgorzata A. Broda
- Department of Physical Chemistry and Molecular Modeling, Faculty of Chemistry, University of Opole, 48 Oleska Street, 45−052 Opole, Poland; (K.R.); (A.B.)
| |
Collapse
|
33
|
Melandri S, Evangelisti L, Canola S, Sa'adeh H, Calabrese C, Coreno M, Grazioli C, Prince KC, Negri F, Maris A. Chlorination and tautomerism: a computational and UPS/XPS study of 2-hydroxypyridine ⇌ 2-pyridone equilibrium. Phys Chem Chem Phys 2020; 22:13440-13455. [PMID: 32519689 DOI: 10.1039/d0cp02304c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The prototropic tautomeric equilibrium in 2-hydroxypyridine serves as a prototype model for the study of nucleobases' behaviour. The position of such an equilibrium in parent and chlorine monosubstituted 2-hydroxypyridine compounds in the gas phase was determined using synchrotron based techniques. The lactim tautomer is dominant for the 5- and 6-substituted compounds, whereas the parent, 3- and 4-substituted isomers have comparable populations for both tautomers. Information was obtained by measuring valence band and core level photoemission spectra at the chlorine L-edge and carbon, nitrogen, and oxygen K-edges. The effect of chlorine on the core ionization potentials of the atoms in the heterocycle was evaluated and reasonable agreement with a simple model was obtained. Basic considerations of resonance structures correctly predicts the tautomeric equilibrium for the 5- and 6-substituted compounds. The vibrationally resolved structure of the low energy portion of the valence band photoionization spectra is assigned based on quantum-chemical calculations of the neutral and charged species followed by simulation of the vibronic structure. It is shown that the first ionization occurs from a π orbital of similar shape for both tautomers. In addition, the highly distinctive vibronic structure observed just above the first ionization of the lactim, for three of the five species investigated, is assigned to the second ionization of the lactam.
Collapse
Affiliation(s)
- Sonia Melandri
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Luca Evangelisti
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Sofia Canola
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Hanan Sa'adeh
- Department of Physics, The University of Jordan, Amman, JO-11942, Jordan
| | - Camilla Calabrese
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Apartado 644, E-48080 Bilbao, Spain and Basque Centre for Biophysics (CSIC, UPV/EHU), Barrio Sarriena, E-48940 Leioa, Spain
| | - Marcello Coreno
- CNR-ISM, Trieste LD2 Unit, Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Cesare Grazioli
- CNR-ISM, Trieste LD2 Unit, Elettra-Sincrotrone Trieste, I-34149 Basovizza, Trieste, Italy
| | - Kevin C Prince
- Elettra Sincrotrone Trieste, Area Science Park, I-34149 Basovizza, Trieste, Italy. and Centre for Translational Atomaterials, Swinburne University of Technology, Melbourne, Australia
| | - Fabrizia Negri
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| | - Assimo Maris
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via Selmi 2, I-40126 Bologna, Italy.
| |
Collapse
|
34
|
Li P, Rangadurai A, Al-Hashimi HM, Hammes-Schiffer S. Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. J Am Chem Soc 2020; 142:11183-11191. [PMID: 32459476 PMCID: PMC7354846 DOI: 10.1021/jacs.0c03774] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
DNA bases can adopt energetically unfavorable tautomeric forms that enable the formation of Watson-Crick-like (WC-like) mispairs, which have been proposed to give rise to spontaneous mutations in DNA and misincorporation errors in DNA replication and translation. Previous NMR and computational studies have indicated that the population of WC-like guanine-thymine (G-T) mispairs depends on the environment, such as the local nucleic acid sequence and solvation. To investigate these environmental effects, herein G-T mispair tautomerization processes are studied computationally in aqueous solution, in A-form and B-form DNA duplexes, and within the active site of a DNA polymerase λ variant. The wobble G-T (wG-T), WC-like G-T*, and WC-like G*-T forms are considered, where * indicates the enol tautomer of the base. The minimum free energy paths for the tautomerization from the wG-T to the WC-like G-T* and from the WC-like G-T* to the WC-like G*-T are computed with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The reaction free energies and free energy barriers are found to be significantly influenced by the environment. The wG-T→G-T* tautomerization is predicted to be endoergic in aqueous solution and the DNA duplexes but slightly exoergic in the polymerase, with Arg517 and Asn513 providing electrostatic stabilization of G-T*. The G-T*→G*-T tautomerization is also predicted to be slightly more thermodynamically favorable in the polymerase relative to these DNA duplexes. These simulations are consistent with an experimentally driven kinetic misincorporation model suggesting that G-T mispair tautomerization occurs in the ajar polymerase conformation or concertedly with the transition from the ajar to the closed polymerase conformation. Furthermore, the order of the associated two proton transfer reactions is predicted to be different in the polymerase than in aqueous solution and the DNA duplexes. These studies highlight the impact of the environment on the thermodynamics, kinetics, and fundamental mechanisms of G-T mispair tautomerization, which plays a role in a wide range of biochemically important processes.
Collapse
Affiliation(s)
- Pengfei Li
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520
| | - Atul Rangadurai
- Department of Biochemistry, Duke University, Durham, NC, 27710
| | | | | |
Collapse
|
35
|
Gop S, Sutradhar R, Chakraborty S, Sinha TP. Tautomeric effect of guanine on stability, spectroscopic and absorbance properties in cytosine–guanine base pairs: a DFT and TD-DFT perspective. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2551-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
36
|
Tautomerism of Guanine Analogues. Biomolecules 2020; 10:biom10020170. [PMID: 31979043 PMCID: PMC7072560 DOI: 10.3390/biom10020170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/17/2020] [Accepted: 01/19/2020] [Indexed: 01/18/2023] Open
Abstract
Tautomerism of nucleic acid (NA) bases is a crucial factor for the maintenance and translation of genetic information in organisms. Only canonical tautomers of NA bases can form hydrogen-bonded complexes with their natural counterparts. On the other hand, rare tautomers of nucleobases have been proposed to be involved in processes catalysed by NA enzymes. Isocytosine, which can be considered as a structural fragment of guanine, is known to have two stable tautomers both in solution and solid states. The tautomer equilibrium of isocytosine contrasts with the remarkable stability of the canonical tautomer of guanine. This paper investigates the factors contributing to the stability of the canonical tautomer of guanine by a combination of NMR experiments and theoretical calculations. The electronic effects of substituents on the stability of the rare tautomers of isocytosine and guanine derivatives are studied by density functional theory (DFT) calculations. Selected derivatives are studied by variable-temperature NMR spectroscopy. Rare tautomers can be stabilised in solution by intermolecular hydrogen-bonding interactions with suitable partners. These intermolecular interactions give rise to characteristic signals in proton NMR spectra, which make it possible to undoubtedly confirm the presence of a rare tautomer.
Collapse
|
37
|
Seligmann H, Demongeot J. Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions. Int J Mol Sci 2020; 21:E347. [PMID: 31948054 PMCID: PMC6981979 DOI: 10.3390/ijms21010347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 01/23/2023] Open
Abstract
Background: Codon directional asymmetry (CDA) classifies the 64 codons into palindromes (XYX, CDA = 0), and 5'- and 3'-dominant (YXX and XXY, CDA < 0 and CDA > 0, respectively). Previously, CDA was defined by the purine/pyrimidine divide (A,G/C,T), where X is either a purine or a pyrimidine. For the remaining codons with undefined CDA, CDA was defined by the 5' or 3' nucleotide complementary to Y. This CDA correlates with cognate amino acid tRNA synthetase classes, antiparallel beta sheet conformation index and the evolutionary order defined by the self-referential genetic code evolution model (CDA < 0: class I, high beta sheet index, late genetic code inclusion). Methods: We explore associations of CDAs defined by nucleotide classifications according to complementarity strengths (A:T, weak; C:G, strong) and keto-enol/amino-imino groupings (G,T/A,C), also after swapping 1st and 2nd codon positions with amino acid physicochemical and structural properties. Results: Here, analyses show that for the eight codons whose purine/pyrimidine-based CDA requires using the rule of complementarity with the midposition, using weak interactions to define CDA instead of complementarity increases associations with tRNA synthetase classes, antiparallel beta sheet index and genetic code evolutionary order. CDA defined by keto-enol/amino-imino groups, 1st and 2nd codon positions swapped, correlates with amino acid parallel beta sheet formation indices and Doolittle's hydropathicities. Conclusions: Results suggest (a) prebiotic swaps from N2N1N3 to N1N2N3 codon structures, (b) that tRNA-mediated translation replaced direct codon-amino acid interactions, and (c) links between codon structures and cognate amino acid properties.
Collapse
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
- Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France;
| | - Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France;
| |
Collapse
|
38
|
Jena NR. Role of different tautomers in the base-pairing abilities of some of the vital antiviral drugs used against COVID-19. Phys Chem Chem Phys 2020; 22:28115-28122. [DOI: 10.1039/d0cp05297c] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Base-pair mutations induced by different tautomers of anti-viral drugs are the main reasons for their anti-viral activities.
Collapse
Affiliation(s)
- N. R. Jena
- Discipline of Natural Sciences
- Indian Institute of Information Technology
- Design, and Manufacturing
- Khamaria
- India
| |
Collapse
|
39
|
Brovarets’ OO, Hovorun DM. A new era of the prototropic tautomerism of the quercetin molecule: A QM/QTAIM computational advances. J Biomol Struct Dyn 2019; 38:4774-4800. [PMID: 31711364 DOI: 10.1080/07391102.2019.1691660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| |
Collapse
|
40
|
Pavlov MY, Ehrenberg M. Substrate-Induced Formation of Ribosomal Decoding Center for Accurate and Rapid Genetic Code Translation. Annu Rev Biophys 2019; 47:525-548. [PMID: 29792818 DOI: 10.1146/annurev-biophys-060414-034148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate translation of genetic information is crucial for synthesis of functional proteins in all organisms. We use recent experimental data to discuss how induced fit affects accuracy of initial codon selection on the ribosome by aminoacyl transfer RNA in ternary complex ( T3) with elongation factor Tu (EF-Tu) and guanosine-5'-triphosphate (GTP). We define actual accuracy ([Formula: see text]) of a particular protein synthesis system as its current accuracy and the effective selectivity ([Formula: see text]) as [Formula: see text] in the limit of zero ribosomal binding affinity for T3. Intrinsic selectivity ([Formula: see text]), defined as the upper thermodynamic limit of [Formula: see text], is determined by the free energy difference between near-cognate and cognate T3 in the pre-GTP hydrolysis state on the ribosome. [Formula: see text] is much larger than [Formula: see text], suggesting the possibility of a considerable increase in [Formula: see text] and [Formula: see text] at negligible kinetic cost. Induced fit increases [Formula: see text] and [Formula: see text] without affecting [Formula: see text], and aminoglycoside antibiotics reduce [Formula: see text] and [Formula: see text] at unaltered [Formula: see text].
Collapse
Affiliation(s)
- Michael Y Pavlov
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden;
| | - Måns Ehrenberg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden;
| |
Collapse
|
41
|
Exploration of tautomerizations of succinimide and maleimide assisted by ammonia and methanol: a theoretical perspective. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2446-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
42
|
Koag MC, Jung H, Lee S. Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-oxoadenine by Human DNA Polymerases. J Am Chem Soc 2019; 141:4584-4596. [PMID: 30817143 DOI: 10.1021/jacs.8b08551] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Reactive oxygen species attack DNA to produce 7,8-dihyro-8-oxoguanine (oxoG) and 7,8-dihydro-8-oxoadenine (oxoA) as major lesions. The structural basis for the mutagenicity of oxoG, which induces G to T mutations, is well understood. However, the structural basis for the mutagenic potential of oxoA, which induces A to C mutations, remains poorly understood. To gain insight into oxoA-induced mutagenesis, we conducted kinetic studies of human DNA polymerases β and η replicating across oxoA and structural studies of polβ incorporating dTTP/dGTP opposite oxoA. While polη readily bypassed oxoA, it incorporated dGTP opposite oxoA with a catalytic specificity comparable to that of correct insertion, underscoring the promutagenic nature of the major oxidative adenine lesion. Polη and polβ incorporated dGTP opposite oxoA ∼170-fold and ∼100-fold more efficiently than that opposite dA, respectively, indicating that the 8-oxo moiety greatly facilitated error-prone replication. Crystal structures of polβ showed that, when paired with an incoming dTTP, the templating oxoA adopted an anti conformation and formed Watson-Crick base pair. When paired with dGTP, oxoA adopted a syn conformation and formed a Hoogsteen base pair with Watson-Crick-like geometry, highlighting the dual-coding potential of oxoA. The templating oxoA was stabilized by Lys280-mediated stacking and hydrogen bonds. Overall, these results provide insight into the mutagenic potential and dual-coding nature of the major oxidative adenine lesion.
Collapse
Affiliation(s)
- Myong-Chul Koag
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Hunmin Jung
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Seongmin Lee
- The Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy , The University of Texas at Austin , Austin , Texas 78712 , United States
| |
Collapse
|
43
|
Ong AAL, Toh DFK, Patil KM, Meng Z, Yuan Z, Krishna MS, Devi G, Haruehanroengra P, Lu Y, Xia K, Okamura K, Sheng J, Chen G. General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase. Biochemistry 2019; 58:1319-1331. [PMID: 30775913 DOI: 10.1021/acs.biochem.8b01313] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA·RNA-RNA triplex formation. Triplex formation is favored for RNA duplexes with a purine tract within one of the RNA duplex strands, and is severely destabilized if the purine tract is interrupted by pyrimidine residues. Here, we report the synthesis of a PNA monomer incorporated with an artificial nucleobase S, followed by the binding studies of a series of S-modified PNAs. Our data suggest that an S residue incorporated into short 8-mer dsRNA-binding PNAs (dbPNAs) can recognize internal Watson-Crick C-G and U-A, and wobble U-G base pairs (but not G-C, A-U, and G-U pairs) in RNA duplexes. The short S-modified PNAs show no appreciable binding to DNA duplexes or single-stranded RNAs. Interestingly, replacement of the C residue in an S·C-G triple with a 5-methyl C results in the disruption of the triplex, probably due to a steric clash between S and 5-methyl C. Previously reported PNA E base shows recognition of U-A and A-U pairs, but not a U-G pair. Thus, S-modified dbPNAs may be uniquely useful for the general recognition of RNA U-G, U-A, and C-G pairs. Shortening the succinyl linker of our PNA S monomer by one carbon atom to have a malonyl linker causes a severe destabilization of triplex formation. Our experimental and modeling data indicate that part of the succinyl moiety in a PNA S monomer may serve to expand the S base forming stacking interactions with adjacent PNA bases.
Collapse
Affiliation(s)
- Alan Ann Lerk Ong
- NTU Institute for Health Technologies (HeathTech NTU), Interdisciplinary Graduate School , Nanyang Technological University , 50 Nanyang Drive , Singapore 637553.,Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kiran M Patil
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhenyu Meng
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhen Yuan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Katsutomo Okamura
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore , Singapore , 117604.,School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore , 639798
| | - Jia Sheng
- Department of Chemistry and The RNA Institute , University at Albany, State University of New York , 1400 Washington Avenue , Albany , New York 12222 , United States
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| |
Collapse
|
44
|
Ponce-Salvatierra A, Astha, Merdas K, Nithin C, Ghosh P, Mukherjee S, Bujnicki JM. Computational modeling of RNA 3D structure based on experimental data. Biosci Rep 2019; 39:BSR20180430. [PMID: 30670629 PMCID: PMC6367127 DOI: 10.1042/bsr20180430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/02/2023] Open
Abstract
RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case of proteins, RNA function is dictated by its structure and by its ability to adopt different conformations, which in turn is encoded in the sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, predictive computational methods were developed based on the accumulated knowledge of RNA structures determined so far, the physical basis of the RNA folding, and taking into account evolutionary considerations, such as conservation of functionally important motifs. However, all theoretical methods suffer from various limitations, and they are generally unable to accurately predict structures for RNA sequences longer than 100-nt residues unless aided by additional experimental data. In this article, we review experimental methods that can generate data usable by computational methods, as well as computational approaches for RNA structure prediction that can utilize data from experimental analyses. We outline methods and data types that can be potentially useful for RNA 3D structure modeling but are not commonly used by the existing software, suggesting directions for future development.
Collapse
Affiliation(s)
- Almudena Ponce-Salvatierra
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Astha
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Katarzyna Merdas
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Chandran Nithin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Pritha Ghosh
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, Warsaw PL-02-109, Poland
- Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, Poznan PL-61-614, Poland
| |
Collapse
|
45
|
Halder A, Vemuri S, Roy R, Katuri J, Bhattacharyya D, Mitra A. Evidence for Hidden Involvement of N3-Protonated Guanine in RNA Structure and Function. ACS OMEGA 2019; 4:699-709. [PMID: 30775644 PMCID: PMC6372247 DOI: 10.1021/acsomega.8b02908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/25/2018] [Indexed: 05/05/2023]
Abstract
Charged nucleobases have been found to occur in several known RNA molecules and are considered essential for their structure and function. The mechanism of their involvement is however not yet fully understood. Revelation of the role of N7-protonated guanine, in modulating the geometry and stability of noncanonical base pairs formed through its unprotonated edges [Watson-Crick (WC) and sugar], has triggered the need to evaluate the feasibility of similar roles of other protonated nucleobases [Halder et al., Phys Chem Chem Phys, 2015, 17, 26249]. In this context, N3 protonation of guanine makes an interesting case as its influence on the charge distribution of the WC edge is similar to that of N7 protonation, though its thermodynamic cost of protonation is significantly higher. In this work, we have carried out structural bioinformatics analyses and quantum mechanics-based calculations to show that N3 protonation of guanine may take place in a cellular environment, at least in the G:C W:W Trans and G:G W:H Cis base pairs. Our results provide a reasonable starting point for future investigations in order to address the larger mechanistic question.
Collapse
Affiliation(s)
- Antarip Halder
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Saurabh Vemuri
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Rohit Roy
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Jayanth Katuri
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| | - Dhananjay Bhattacharyya
- Computational
Science Division, Saha Institute of Nuclear
Physics (SINP), 1/AF,
Bidhannagar, Kolkata 700064, India
| | - Abhijit Mitra
- Center
for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology,
Hyderabad (IIIT-H), Gachibowli, Hyderabad 500032, Telangana, India
| |
Collapse
|
46
|
Affiliation(s)
- Nadezhda Markova
- Institute of Organic Chemistry with Center of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Venelin Enchev
- Institute of Organic Chemistry with Center of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| |
Collapse
|
47
|
Lee S, Johnson SN, Ellington TL, Mirsaleh-Kohan N, Tschumper GS. Energetics and Vibrational Signatures of Nucleobase Argyrophilic Interactions. ACS OMEGA 2018; 3:12936-12943. [PMID: 31458017 PMCID: PMC6645001 DOI: 10.1021/acsomega.8b01895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/27/2018] [Indexed: 06/10/2023]
Abstract
This study investigates the interactions of both purine (adenine and guanine) and pyrimidine (cytosine, thymine, and uracil) nucleobases with a pair of silver atoms (Ag2). Full geometry optimizations were performed on several structures of each nucleobase/Ag2 complex and the corresponding isolated monomers using the M06-2X density functional with a correlation consistent triple-ζ basis set augmented with diffuse functions on all atoms and a relativistic pseudopotential on Ag (aug-cc-pVTZ for H, C, N, and O and aug-cc-pVTZ-PP for Ag; denoted aVTZ). Harmonic vibrational frequency computations indicate that each optimized structure corresponds to a minimum on the M06-2X/aVTZ potential energy surface. Relative electronic energies for interactions between Ag2 and each nucleobase were compared to elucidate energetic differences between isomers. Further analysis of the changes in vibrational frequencies, infrared intensities, and Raman scattering activities reveals how different Ag2 binding sites might be differentiated spectroscopically. These results provide molecular-level insight into the interactions between nucleobases and silver, which may lead to better understanding and interpretation of surface-enhanced Raman spectroscopy experiments on nucleobases and related systems.
Collapse
Affiliation(s)
- Suhwan
Paul Lee
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Sarah N. Johnson
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Thomas L. Ellington
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| | - Nasrin Mirsaleh-Kohan
- Department
of Chemistry and Biochemistry, Texas Woman’s
University, Denton, Texas 76204, United States
| | - Gregory S. Tschumper
- Department
of Chemistry and Biochemistry, University
of Mississippi, University, Mississippi 38677-1848, United States
| |
Collapse
|
48
|
Abstract
Oligonucleotides (ONs) can interfere with biomolecules representing the entire extended central dogma. Antisense gapmer, steric block, splice-switching ONs, and short interfering RNA drugs have been successfully developed. Moreover, antagomirs (antimicroRNAs), microRNA mimics, aptamers, DNA decoys, DNAzymes, synthetic guide strands for CRISPR/Cas, and innate immunity-stimulating ONs are all in clinical trials. DNA-targeting, triplex-forming ONs and strand-invading ONs have made their mark on drug development research, but not yet as medicines. Both design and synthetic nucleic acid chemistry are crucial for achieving biologically active ONs. The dominating modifications are phosphorothioate linkages, base methylation, and numerous 2'-substitutions in the furanose ring, such as 2'-fluoro, O-methyl, or methoxyethyl. Locked nucleic acid and constrained ethyl, a related variant, are bridged forms where the 2'-oxygen connects to the 4'-carbon in the sugar. Phosphorodiamidate morpholino oligomers, carrying a modified heterocyclic backbone ring, have also been commercialized. Delivery remains a major obstacle, but systemic administration and intrathecal infusion are used for treatment of the liver and brain, respectively.
Collapse
Affiliation(s)
- C I Edvard Smith
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden; .,Stellenbosch Institute for Advanced Study, Wallenberg Research Centre, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Rula Zain
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86 Stockholm, Sweden; .,Department of Clinical Genetics, Centre for Rare Diseases, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| |
Collapse
|
49
|
Pusuluk O, Farrow T, Deliduman C, Burnett K, Vedral V. Proton tunnelling in hydrogen bonds and its implications in an induced-fit model of enzyme catalysis. Proc Math Phys Eng Sci 2018. [DOI: 10.1098/rspa.2018.0037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The role of proton tunnelling in biological catalysis is investigated here within the frameworks of quantum information theory and thermodynamics. We consider the quantum correlations generated through two hydrogen bonds between a substrate and a prototypical enzyme that first catalyses the tautomerization of the substrate to move on to a subsequent catalysis, and discuss how the enzyme can derive its catalytic potency from these correlations. In particular, we show that classical changes induced in the binding site of the enzyme spreads the quantum correlations among all of the four hydrogen-bonded atoms thanks to the directionality of hydrogen bonds. If the enzyme rapidly returns to its initial state after the binding stage, the substrate ends in a new transition state corresponding to a quantum superposition. Open quantum system dynamics can then naturally drive the reaction in the forward direction from the major tautomeric form to the minor tautomeric form without needing any additional catalytic activity. We find that in this scenario the enzyme lowers the activation energy so much that there is no energy barrier left in the tautomerization, even if the quantum correlations quickly decay.
Collapse
Affiliation(s)
- Onur Pusuluk
- Department of Physics, İstanbul Technical University, Maslak, Istanbul 34469, Turkey
| | - Tristan Farrow
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| | - Cemsinan Deliduman
- Department of Physics, Mimar Sinan Fine Arts University, Bomonti, Istanbul 34380, Turkey
| | - Keith Burnett
- University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Vlatko Vedral
- Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- Centre for Quantum Technologies, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| |
Collapse
|
50
|
Pohl R, Socha O, Šála M, Rejman D, Dračínský M. The Control of the Tautomeric Equilibrium of Isocytosine by Intermolecular Interactions. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Radek Pohl
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague Czech Republic
| |
Collapse
|