Non-Covalent Interactions: Complexes of Guanidinium with DNA and RNA Nucleobases

Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms

Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm+) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm+ from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm+. We studied the binding of Gdm+ to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm+ binding. We show that Gdm+ binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm+ binding propensity, making the Gdm+ binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.

Formation of Eigen or Zundel Features at Protonated Water Cluster-Aromatic Interfaces

Interfacial interactions of protonated water clusters adsorbed at aromatic surfaces play an important role in biology, and in atmospheric, chemical and materials sciences. Here, we investigate the interaction of protonated water clusters ((H+ H2 O)n (where n=1-3)) with benzene (Bz), coronene (Cor) and dodecabenzocoronene (Dbc)). To study the structure, stability and spectral features of these complexes, computations are done using DFT-PBE0(+D3) and SAPT0 methods. These interactions are probed by AIM electron density topography and non-covalent interactions index (NCI) analyses. We suggest that the excess proton plays a crucial role in the stability of these model interfaces through strong inductive effects and the formation of Eigen or Zundel features. Also, computations reveal that the extension of the π-aromatic system and the increase of the number of water molecules in the H-bounded water network led to a strengthening of the interactions between the corresponding aromatic compound and protonated water molecules, except when a Zundel ion is formed. The present findings may serve to understand in-depth the role of proton localized at aqueous medium interacting with large aromatic surfaces such as graphene interacting with acidic liquid water. Besides, we give the IR and UV-Vis spectra of these complexes, which may help for their identification in laboratory.

Tubular Magnetic Shielding Scan (TMSS): A New Technique for Molecular Space Exploration. (i) The Case of Aromaticity of Benzene and [n]Paracyclophanes

Both traditional and novel techniques were employed in this work for magnetic shielding evaluation to shed new light on the magnetic and aromaticity properties of benzene and 12 [n]paracyclophanes with n = 3-14. Density functional theory (DFT) with the B3LYP functional and all-electron Jorge-ATZP and x2c-TZVPPall-s basis sets was utilized for geometry optimization and magnetic shielding calculations, respectively. Additionally, the 6-311+G(d,p) basis set was incorporated for the purpose of comparing the magnetic shielding results. In addition to traditional evaluations such as NICS/NICSzz-Scan, and 2D-3D σiso(r)/σzz(r) maps, two new techniques were implemented: bendable grids (BGs) and cylindrical grids (CGs) of ghost atoms (Bqs). BGs allow for the recording of magnetic shielding from the bent ring levels of [n]pCPs, while CGs provide tubular magnetic shielding scan (TMSS) maps detailing the magnetic shielding from a cylindrical region above and below the ring frame. Our findings suggest that smaller [n]pCPs with n < 6 exhibit deviations in the magnetic shielding above and below the ring, indicating a broken electron delocalization under the ring. In contrast, larger [n]pCPs tend to behave similarly to benzene in terms of magnetic shielding. Moreover, we found that shorter polymethylene chains of [n]pCPs exhibit significantly higher magnetic shielding interactions with the ring. Both of the above techniques offer new and promising tools for characterizing nonplanar aromatic compounds, thereby contributing to a deeper understanding of their magnetic and electronic properties.

The RBS1 domain of Gemin5 is intrinsically unstructured and interacts with RNA through conserved Arg and aromatic residues

Gemin5 is a multifaceted RNA-binding protein that comprises distinct structural domains, including a WD40 and TPR-like for which the X-ray structure is known. In addition, the protein contains a non-canonical RNA-binding domain (RBS1) towards the C-terminus. To understand the RNA binding features of the RBS1 domain, we have characterized its structural characteristics by solution NMR linked to RNA-binding activity. Here we show that a short version of the RBS1 domain that retains the ability to interact with RNA is predominantly unfolded even in the presence of RNA. Furthermore, an exhaustive mutational analysis indicates the presence of an evolutionarily conserved motif enriched in R, S, W, and H residues, necessary to promote RNA-binding via π-π interactions. The combined results of NMR and RNA-binding on wild-type and mutant proteins highlight the importance of aromatic and arginine residues for RNA recognition by RBS1, revealing that the net charge and the π-amino acid density of this region of Gemin5 are key factors for RNA recognition.

Aggregation and Supramolecular Self-Assembly of Low-Energy Red Luminescent Alkynylplatinum(II) Complexes for RNA Detection, Nucleolus Imaging, and RNA Synthesis Inhibitor Screening

As an important nuclear substructure, the nucleolus has received increasing attention because of its significant functions in the transcription and processing of ribosomal RNA in eukaryotic cells. In this work, we introduce a proof-of-concept luminescence assay to detect RNA and to accomplish nucleolus imaging with the use of the supramolecular self-assembly of platinum(II) complexes. Noncovalent interactions between platinum(II) complexes and RNA can be induced by the introduction of a guanidinium group into the complexes, and accordingly, a high RNA affinity can be achieved. Interestingly, the aggregation affinities of platinum(II) complexes enable them to display remarkable luminescence turn-on upon RNA binding, which is a result of the strengthening of noncovalent Pt(II)···Pt(II) and π-π stacking interactions. The complexes exhibit not only intriguing spectroscopic changes and luminescence enhancement after RNA binding but also specific nucleolus imaging in cells. As compared to fluorescent dyes, the low-energy red luminescence and large Stokes shifts of platinum(II) complexes afford a high signal-to-background autofluorescence ratio in nucleolus imaging. Additional properties, including long phosphorescence lifetimes and low cytotoxicity, have endowed the platinum(II) complexes with the potential for biological applications. Also, platinum(II) complexes have been adopted to monitor the dynamics of the nucleolus induced by the addition of RNA synthesis inhibitors. This capability allows the screening of inhibitors and can be advantageous for the development of antineoplastic agents. This work provides a novel strategy for exploring the application of platinum(II) complex-based cell imaging agents based on the mechanism of supramolecular self-assembly. It is envisaged that platinum(II) complexes can be utilized as valuable probes because of the aforementioned appealing advantages.

Screening and Preliminary Biochemical and Biological Studies of [RuCl(p-cymene)(N,N-bis(diphenylphosphino)-isopropylamine)][BF4] in Breast Cancer Models

Breast cancer is the second leading cause of cancer death worldwide. Despite progress in drug discovery, identification of the correct population is the limiting factor to develop new compounds in the clinical setting. Therefore, the aim of this study is to evaluate the effects of a new metallodrug, [RuCl(p-cymene)(N,N-bis(diphenylphosphino)-isopropylamine)][BF₄] (pnpRu-14), as a lead pnp-Ru compound by screening and preliminary biochemical and biological studies in different breast cancer subtypes. The results show that complex pnpRu-14 is much more effective in promoting in vitro cytotoxic effects on HER2+ and RH+/HER2- breast cancer than the reference metallodrugs cisplatin, carboplatin, or RAPTA-C. It is important to highlight that pnpRu-14 shows an impressive cytotoxicity against BT474 cells. Caspase-dependent apoptosis is the mechanism of action for these compounds. In addition, treatment of SKBR3, BT474, T47D, and MCF7 cancer cells with pnpRu-14 caused an accumulation of cells in the G0/G1 phase cells. The human serum albumin, DNA, and H1 histones binding properties of the lead compound are reported. Pharmacokinetic and biodistribution studies show a quick absorption of pnpRu-14 in serum with no significant accumulation in any of the tested organs. This work provides evidence to support the preclinical and clinical development of pnpRu-14 in breast cancer.

DNA/Lysozyme-binding affinity study of novel peptides from TAT (47-57) and BRCA1 (782-786) in vitro by spectroscopic analysis

SISLL-TAT and TAT-SISLL were synthesized by modifying the N- or C-termini of cell-penetrating peptides as transacting activator of transcription TAT (47-57) by attaching BRCA1 (782-786) (SISLL). The novel peptides were synthesized through Fmoc solid-phase synthesis procedures and characterized by LCQ Fleet MS, ¹H NMR and ¹³C NMR. SISLL-TAT and TAT-SISLL displayed forceful antibacterial activities against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Salmonella typhimurium with low hemolysis. SISLL-TAT showed better antibacterial activity than TAT-SISLL, with the minimum inhibitory concentration (MIC) values of 10-33 μg·mL^-1. The results of the DNA-binding activities showed that both SISLL-TAT and TAT-SISLL could interact with DNA via the minor groove mode, and the binding constants were 4.97 × 10⁵ L·mol^-1 and 4.42 × 10⁵ L·mol^-1 at 310 K, respectively. Circular dichroism analysis showed slight transformation of the lysozyme secondary structure caused by SISLL-TAT and TAT-SISLL. We also found that the novel peptides SISLL-TAT and TAT-SISLL targeted bacterial DNA resulting in cell death. This explains the antibacterial mechanism of SISLL-TAT and TAT-SISLL, and is a solid theoretical basis for further designing novel and highly effective antibiotics for clinical application.

Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies

Amino acid and nucleic acid interactions are central in biology and may have played a role in the evolutionary development of protein-based life from an early "RNA Universe." To explore the possible role of single amino acids in promoting nucleic acid folding, single-molecule Förster resonance energy transfer experiments have been implemented with a DNA hairpin construct (7 nucleotide double strand with a 40A loop) as a simple model for secondary structure formation. Exposure to positively charged amino acids (arginine and lysine) is found to clearly stabilize the secondary structure. Kinetically, each amino acid promotes folding by generating a large increase in the folding rate with little change in the unfolding rate. From analysis as a function of temperature, arginine and lysine are found to significantly increase the overall exothermicity of folding while imposing only a small entropic penalty on the folding process. Detailed investigations into the kinetics and thermodynamics of this amino acid-induced folding stability reveal arginine and lysine to interact with nucleic acids in a manner reminiscent of monovalent cations. Specifically, these observations are interpreted in the context of an ion atmosphere surrounding the nucleic acid, in which amino acid salts stabilize folding qualitatively like small monovalent cations but also exhibit differences because of the composition of their side chains.

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.

Structural basis for ligand binding to the guanidine-II riboswitch

The guanidine-II riboswitch, also known as mini-ykkC, is a conserved mRNA element with more than 800 examples in bacteria. It consists of two stem-loops capped by identical, conserved tetraloops that are separated by a linker region of variable length and sequence. Like the guanidine-I riboswitch, it controls the expression of guanidine carboxylases and SugE-like genes. The guanidine-II riboswitch specifically binds free guanidinium cations and functions as a translationally controlled on-switch. Here we report the structure of a P2 stem-loop from the Pseudomonas aeruginosa guanidine-II riboswitch aptamer bound to guanidine at 1.57 Å resolution. The hairpins dimerize via the conserved tetraloop, which also contains the binding pocket. Two guanidinium molecules bind near the dimerization interface, one in each tetraloop. The guanidinium cation is engaged in extensive hydrogen bonding to the RNA. Contacts include the Hoogsteen face of a guanine base and three nonbridging phosphate oxygens. Cation-π interactions and ionic interactions also stabilize ligand binding. The guanidine-II riboswitch utilizes the same recognition strategies as the guanidine-I riboswitch while adopting an entirely different and much smaller RNA fold.

Structural basis for guanidine sensing by the ykkC family of riboswitches

Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.3 Å crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii The riboswitch folds into a boot-shaped structure, with a coaxially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation-π stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium-binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches and pave the way for a deeper understanding of guanidine detoxification-a previously unappreciated aspect of bacterial physiology.

Phenyl-guanidine derivatives as potential therapeutic agents for glioblastoma multiforme: catalytic syntheses, cytotoxic effects and DNA affinity

Glioblastoma is a highly malignant form of brain tumor. In the work described here, several substituted phenyl-guanidine derivatives were developed for application in glioblastoma treatment.

Aromatic Amino Acids-Guanidinium Complexes through Cation-π Interactions

Continuing with our interest in the guanidinium group and the different interactions than can establish, we have carried out a theoretical study of the complexes formed by this cation and the aromatic amino acids (phenylalanine, histidine, tryptophan and tyrosine) using DFT methods and PCM-water solvation. Both hydrogen bonds and cation-π interactions have been found upon complexation. These interactions have been characterized by means of the analysis of the molecular electron density using the Atoms-in-Molecules approach as well as the orbital interactions using the Natural Bond Orbital methodology. Finally, the effect that the cation-π and hydrogen bond interactions exert on the aromaticity of the corresponding amino acids has been evaluated by calculating the theoretical NICS values, finding that the aromatic character was not heavily modified upon complexation.

On the interaction between the imidazolium cation and aromatic amino acids. A computational study

Phe, Tyr and Trp form parallel complexes with cation⋯π interactions. His complexes are the strongest, but without making contact with the aromatic cloud.

Guanidine complexes of platinum: a theoretical study

We have studied theoretically the complexes of model N-phenylguanidine/ium derivatives with PtCl3(-) and PtCl2 in different coordinating modes (mono- and bidentate) with different N atoms of the guanidine/ium moiety using the B3LYP/6-31+G** and LANL2DZ mixed basis set. This will aid the understanding of the complexation between platinum and the guanidine or guanidinium moiety in order to design dual anticancer agents that combine a guanidine-based DNA minor groove binder and a cisplatin-like moiety. Calculated interaction and relative energies, analysis of the electron density, and examination of the orbital interactions indicate that the most stable type of complex is that with a monodentate interaction between PtCl3(-) and guanidinium established through one of the NH2 groups. Next, we optimized the structure of three bis-guanidinium diaromatic systems developed in our group as DNA minor groove binders and their complexation with PtCl3(-), finding that the formation of Pt complexes of these minor groove binders is favorable and would produce stable monodentate coordinated systems.