Spodium Bonds in Biological Systems: Expanding the Role of Zn in Protein Structure and Function

Iodinated 4,4'-Bipyridines with Antiproliferative Activity Against Melanoma Cell Lines

In the last decade, biological processes involving halogen bond (HaB) as a leading interaction attracted great interest. However, although bound iodine atoms are considered powerful HaB donors, few iodinated new drugs were reported so far. Recently, iodinated 4,4'-bipyridines showed interesting properties as HaB donors in solution and in the solid state. In this paper, a study on the inhibition activity of seven halogenated 4,4'-bipyridines against malignant melanoma (MM) cell proliferation is described. Explorative dose/response proliferation assays were first performed with three 4,4'-bipyridines by using four MM cell lines and the normal BJ fibroblast cell line as control. Among them, the A375 MM cell line was the most sensitive, as determined by MTT assays, which was selected to evaluate the antiproliferative activity of all 4,4'-bipyridines. Significantly, the presence of an electrophilic iodine impacted the biological activity of the corresponding compounds. The 3,3',5,5'-tetrachloro-2-iodo-4,4'-bipyridine showed significant antiproliferation activity against the A375 cell line, and lower toxicity on BJ fibroblasts. Through in silico studies, the stereoelectronic features of possible sites determining the bioactivity were explored. These results pave the way for the utilization of iodinated 4,4'-bipyridines as templates to design new promising HaB-enabled inhibitors of MM cell proliferation.

Wolfium bonds in homodimers of MX4Y (M = Mo, W; X = F, Cl, Br; Y = O, S, Se)

The term "wolfium bond" has been recently introduced to describe the noncovalent attraction between an atom of group 6 and a nucleophile via a σ-hole binding site. Crystal structures commonly contain a motif wherein two MX4Y units are arranged in close proximity, where M represents either Mo or W, and X and Y refer to halogen and chalcogen atoms respectively. DFT calculations were thus applied to a wide range of homodimers of these molecules so as to assess their preferred arrangements, and to characterize the types of bonding that are present in each in a systematic manner. The most stable Dual-X configuration is symmetric and contains a pair of equivalent M⋯X bonds. The interaction energies range from -8 to -29 kcal mol-1, and are largest for X = F, Y = O, and M = W. The X electron donor is replaced by Y, and the two wolfium bonds are reduced to one, in the less stable Mono-Y structure, with interaction energies between -2 and -10 kcal mol-1. There is some question as to whether the weaker bonds of this type constitute true wolfium bonds.

Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research

In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.

Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations

In this study, the stability, directionality, and physical nature of Spodium bonds (SpBs, an attractive noncovalent force involving elements from group 12 and Lewis bases) between methylmercury (MeHg) and ethylmercury (EtHg) and amino acids (AAs) have been analyzed from both a structural (X-ray analysis) and theoretical (RI-MP2/def2-TZVP level of theory) point of view. More in detail, an inspection of the Protein Data Bank (PDB) reported evidence of noncovalent contacts between MeHg and EtHg molecules and electron-rich atoms (e.g., O atoms belonging to the protein backbone and S atoms from MET residues or the π-systems of aromatic AAs such as TYR or TRP). These results were rationalized through a computational study using MeHg coordinated to a thiolate group as a theoretical model and several neutral and charged electron-rich molecules (e.g., benzene, formamide, or chloride). The physical nature of the interaction was analyzed from electrostatics and orbital perspectives by performing molecular electrostatic potential (MEP) and natural bonding orbital (NBO) analyses. Lastly, the noncovalent interactions plot (NCIplot) technique was used to provide a qualitative view of the strength of the Hg SpBs and compare them to other ancillary interactions present in these systems as well as to shed light on the extension of the interaction in real space. We believe that the results derived from our study will be useful to those scientists devoted to protein engineering and bioinorganic chemistry as well as to expanding the current knowledge of SpBs among the chemical biology community.

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications

In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Why much of Chemistry may be indisputably non-bonded?

In this compendium, the wide scope of all intermolecular interactions ever known has been revisited, in particular giving emphasis the capability of much of the elements of the periodic table to form non-covalent contacts. Either hydrogen bonds, dihydrogen bonds, halogen bonds, pnictogen bonds, chalcogen bonds, triel bonds, tetrel bonds, regium bonds, spodium bonds or even the aerogen bond interactions may be cited. Obviously that experimental techniques have been used in some works, but it was through the theoretical methods that these interactions were validate, wherein the QTAIM integrations and SAPT energy partitions have been useful in this regard. Therefore, the great goal concerns to elucidate the interaction strength and if the intermolecular system shall be total, partial or non-covalently bonded, wherein this last one encompasses the most majority of the intermolecular interactions what leading to affirm that chemistry is debatably non-bonded.

Matere Bonds vs. Multivalent Halogen and Chalcogen Bonds: Three Case Studies

The term matere bond has been recently used to refer to an attractive noncovalent interaction between any element of group 7 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. The utilization of metals such as σ-hole donors is starting to attract the attention of the scientific community. In this manuscript, a comparison between matere bonds and well-known σ-hole interactions (halogen and chalcogen bonds) is carried out using three X-ray structures, retrieved from the Cambridge structural database (CSD), and density functional theory calculations (DFT). The novelty of this work resides in the utilization of a neutral Re(VII) system as the matere bond donor and multivalent chalcogen and halogen donors. In fact, as far as our knowledge extends, the description of σ-hole interactions in Se(VI) is unprecedented in the literature. The σ-hole interactions in Re(VII), Se(VI) and Cl(VII) electron acceptors are analyzed and compared using several computational tools.

Noncovalent Interactions Involving Group 6 in Biological Systems: The Case of Molybdopterin and Tungstopterin Cofactors

In this study we propose to coin the term Wolfium bond (WfB) to refer to a net attractive force (noncovalent interaction) between any element of group 6 and electron donor atoms (neutral molecules or anions) and to differentiate it from a coordination bond (metal‐ligand interaction). We provide evidence of the existence of this interaction by inspecting the X‐ray crystal structure of proteins containing Molybdopterin and Tungstopterin cofactors from the Protein Data Bank (PDB). The plausible biological role of the interaction as well as its physical nature (antibonding Wf‐Ligand orbital involved) are also analyzed by means of ab initio calculations (RI‐MP2/def2‐TZVP level of theory), Atoms in Molecules (AIM), Natural Bond Orbital (NBO) and Noncovalent Interactions plot (NCIplot) analyses.

Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Understanding the noncovalent interactions (NCIs) among the residues of proteins and nucleic acids, and between drugs and proteins/nucleic acids, etc., has extraordinary relevance in biomolecular structure and function. It helps in interpreting the dynamics of complex biological systems and enzymatic activity, which is esential for new drug design and efficient drug delivery. NCIs like hydrogen bonding (H-bonding) and π-stacking have been researchers' delight for a long time. Prominent among the recently discovered NCIs are halogen, chalcogen, pnictogen, tetrel, carbo-hydrogen, and spodium bonding, and n → π* interaction. These NCIs have caught the imaginations of various research groups in recent years while explaining several chemical and biological processes. At this stage, a holistic view of these new ideas and findings lying scattered can undoubtedly trigger our minds to explore more. The present review attempts to address NCIs beyond H-bonding and π-stacking, which are mainly n → σ*, n → π* and σ → σ* type interactions. Five of the seven NCIs mentioned earlier are linked to five non-inert end groups of the modern periodic table. Halogen (group-17) bonding is one of the oldest and most explored NCIs, which finds its relevance in biomolecules due to the phase correction and inhibitory properties of halogens. Chalcogen (group 16) bonding serves as a redox-active functional group of different active sites of enzymes and acts as a nucleophile in proteases and phosphates. Pnictogen (group 15), tetrel (group 14), triel (group 13) and spodium (group 12) bonding does exist in biomolecules. The n → π* interactions are linked to backbone carbonyl groups and protein side chains. Thus, they are crucial in determining the conformational stability of the secondary structures in proteins. In addition, a more recently discovered to and fro σ → σ* type interaction, namely carbo-hydrogen bonding, is also present in protein-ligand systems. This review summarizes these grand epiphanies routinely used to elucidate the structure and dynamics of biomolecules, their enzymatic activities, and their application in drug discovery. It also briefs about the future perspectives and challenges posed to the spectroscopists and theoreticians.

Insight into Spodium–π Bonding Characteristics of the MX2···π (M = Zn, Cd and Hg; X = Cl, Br and I) Complexes—A Theoretical Study

The spodium–π bonding between MX₂ (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C₂H₂/C₂H₄ acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX₂⋯C₂F₂ complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.

Investigation of the Nature of Intermolecular Interactions in Tetra(thiocyanato)corrolato-Ag(III) Complexes: Agostic or Hydrogen Bonded?

Tetra(thiocyanato)corrolato-Ag(III) complexes presented here constitute a new class of metallo-corrole complexes. The spectroscopic properties of these complexes are quite unusual and interesting. For example, the absorption spectra of these β-substituted corrolato-Ag(III) complexes are very different from those of the β-unsubstituted corrolato-Ag(III) derivatives. Single-crystal XRD analysis of a representative tetra(thiocyanato)corrolato-Ag(III) derivative reveals C-H···Ag interactions. The C-H···Ag interactions are rarely demonstrated in the crystal lattice of a discrete coordination/organometallic compound. Optimization of the hydrogen positions of the crystal structure discloses the geometrical parameters of the said interaction as a Ag···H distance of 2.597 Å and ∠C-H···Ag of 109.62°. The natural bond orbital analysis provides information about the donor-acceptor orbitals involved in the interactions and their interaction energies. It was observed that the σ_C-H orbital overlaps with the vacant d-orbital of Ag with an interaction energy of 17.93 kJ/mol. The filled d-orbital of Ag overlaps with the σ*_C-H orbital with an interaction energy of 4.79 kJ/mol. The highlights of this work are that the H···Ag distance is outside of the distance range for the typical agostic interaction but fitted with the weak H-bond distance. However, the ∠C-H···Ag angle is within the range of the agostic interaction. Both crystallographic data and electronic structure calculations reveal that these kinds of intermolecular interactions in square-planar d⁸ Ag(III) complexes are intermediate in nature. Thus, they cannot be categorically called either hydrogen bonding or agostic interaction.

Coordination versus spodium bonds in dinuclear Zn(ii) and Cd(ii) complexes with a dithiophosphate ligand

Two new d10-metal dithiophosphate complexes have been synthesized in purely aqueous media and characterized by elemental and spectral analyses. DFT calculations, QTAIM and NCI Plot index methods are preformed to differentiate the coordination and spodium bonds in the complexes.