Modeling the interactions between polyoxometalates and their environment

DFT study of α-Keggin, lacunary Keggin, and ironII-VI substituted Keggin polyoxometalates: the effect of oxidation state and axial ligand on geometry, electronic structures and oxygen transfer

Herein, the geometry, electronic structure, Fe-ligand bonding nature and simulated IR spectrum of α-Keggin, lacunary Keggin, iron(ii/iii)-substituted and the important oxidized high-valent iron derivatives of Keggin type polyoxometalates have been studied using the density functional theory (DFT/OPTX-PBE) method and natural bond orbital (NBO) analysis. The effects of different Fe oxidation states (ii-vi) and H2O/OH-/O2- ligand interactions have been addressed concerning their geometry and electronic structures. It has been revealed that the d-atomic orbitals of Fe and 2p orbitals of polyoxometalate's oxygen-atoms contribute in ligand binding. Compared with other high valent species, the considered polyoxometalate system of [PW11O39(FeVO)]4-, possesses a high reactivity for oxygen transfer.

Identification of Novel Src Inhibitors: Pharmacophore-Based Virtual Screening, Molecular Docking and Molecular Dynamics Simulations

Src plays a crucial role in many signaling pathways and contributes to a variety of cancers. Therefore, Src has long been considered an attractive drug target in oncology. However, the development of Src inhibitors with selectivity and novelty has been challenging. In the present study, pharmacophore-based virtual screening and molecular docking were carried out to identify potential Src inhibitors. A total of 891 molecules were obtained after pharmacophore-based virtual screening, and 10 molecules with high docking scores and strong interactions were selected as potential active molecules for further study. Absorption, distribution, metabolism, elimination and toxicity (ADMET) property evaluation was used to ascertain the drug-like properties of the obtained molecules. The proposed inhibitor–protein complexes were further subjected to molecular dynamics (MD) simulations involving root-mean-square deviation and root-mean-square fluctuation to explore the binding mode stability inside active pockets. Finally, two molecules (ZINC3214460 and ZINC1380384) were obtained as potential lead compounds against Src kinase. All these analyses provide a reference for the further development of novel Src inhibitors.

Organic Functionalization of Uranyl Peroxide Clusters to Impact Solubility

Benzene-1,2-diphosphonic acid (Ppb) was introduced into the uranyl peroxide cluster system, resulting in three Ppb-functionalized uranyl peroxide clusters, (UO₂)₂₀(O₂)₂₀(C₆H₄P₂O₆)₁₀^40- (U₂₀Ppb₁₀), (UO₂)₂₆(O₂)₃₃(C₆H₄P₂O₆)₆^38- (U₂₆Ppb₆), and (UO₂)₂₀(O₂)₂₄(C₆H₄P₂O₆)₆^32- (U₂₀Ppb₆). Dissolution experiments were performed for the potassium salts of U₂₀Ppb₁₀ and U₂₆Ppb₆, which revealed the capacity of U₂₀Ppb₁₀ to dissolve in the organic solvent dimethyl sulfoxide (DMSO). Unlike U₂₀Ppb₁₀, the K salt of U₂₆Ppb₆ did not dissolve in DMSO but was more soluble in water, perhaps due to the lower proportion of Ppb ligands in its structure. In this work, U₂₀Ppb₁₀ and U₂₀Ppb₆ formed as potassium salts and both adopt the fullerene topology of previously reported U₂₀. U₂₀ contains 20 uranyl peroxide units and encapsulates 12 Na cations. It is not possible for unfunctionalized U₂₀ to incorporate 12 K cations owing to space constraints, as is the case in the new clusters reported here. Transformation of U₂₀Ppb₁₀ in water over time to produce U₂₄ was observed, possibly owing to its ability to incorporate K cations, which have been associated with the formation of U₂₄.

Aggregation Patterns in Low- and High-Charge Anions Define Opposite Solubility Trends

Molecular dynamics simulations in aqueous solution reveal the existence of two distinct patterns of aggregation in low and high charge density Lindqvist-type polyoxometalates (POMs). Our results indicate the presence of contact and solvent-shared ion pairs and specific and preferential interactions of alkalis with POMs. Highly charged POMs are capable of breaking apart the Li⁺ and Cs⁺ solvation shell, thus enhancing the formation of long-lived alkali-POM contact ion pairs, where alkalis act as an electrostatic "glue" forming large oligomers. Stronger ion pair interactions for Li⁺ than for Cs⁺ promote lower solubility for Li⁺ than for Cs⁺, evoking anomalous solubility trends. Lower charge density POMs are not capable of disrupting the Li⁺ solvation shell and only solvent-shared ion pairs are formed, whereas for Cs⁺, contact ion pairs exist. The large number of oxygen atoms in the POM surface enhances the hydrogen bonds between POM and water, thus promoting aggregation. In this case, aggregation follows normal solubility trends. Thus, aggregation depends on the strength of ion pair interactions, the capacity of POM to disrupt alkali's solvation shell, and the contact surface area between the solvent and POM.

Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site-directed mutagenesis

The class A G-protein-coupled receptors (GPCRs) Orexin-1 (OX1) and Orexin-2 (OX2) are located predominantly in the brain and are linked to a range of different physiological functions, including the control of feeding, energy metabolism, modulation of neuro-endocrine function, and regulation of the sleep-wake cycle. The natural agonists for OX1 and OX2 are two neuropeptides, Orexin-A and Orexin-B, which have activity at both receptors. Site-directed mutagenesis (SDM) has been reported on both the receptors and the peptides and has provided important insight into key features responsible for agonist activity. However, the structural interpretation of how these data are linked together is still lacking. In this work, we produced and used SDM data, homology modeling followed by MD simulation, and ensemble-flexible docking to generate binding poses of the Orexin peptides in the OX receptors to rationalize the SDM data. We also developed a protein pairwise similarity comparing method (ProS) and a GPCR-likeness assessment score (GLAS) to explore the structural data generated within a molecular dynamics simulation and to help distinguish between different GPCR substates. The results demonstrate how these newly developed methods of structural assessment for GPCRs can be used to provide a working model of neuropeptide-Orexin receptor interaction.

Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites

Obesity is an increasingly common disease. While antagonism of the melanin-concentrating hormone-1 receptor (MCH-1R) has been widely reported as a promising therapeutic avenue for obesity treatment, no MCH-1R antagonists have reached the market. Discovery and optimization of new chemical matter targeting MCH-1R is hindered by reduced HTS success rates and a lack of structural information about the MCH-1R binding site. X-ray crystallography and NMR, the major experimental sources of structural information, are very slow processes for membrane proteins and are not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of these methods to impact the drug discovery process for GPCR targets in "real-time", and hence, there is an urgent need for other practical and cost-efficient alternatives. We present here a conceptually pioneering approach that integrates GPCR modeling with design, synthesis, and screening of a diverse library of sugar-based compounds from the VAST technology (versatile assembly on stable templates) to provide structural insights on the MCH-1R binding site. This approach creates a cost-efficient new avenue for structure-based drug discovery (SBDD) against GPCR targets. In our work, a primary VAST hit was used to construct a high-quality MCH-1R model. Following model validation, a structure-based virtual screen yielded a 14% hit rate and 10 novel chemotypes of potent MCH-1R antagonists, including EOAI3367472 (IC50 = 131 nM) and EOAI3367474 (IC50 = 213 nM).

Structure, properties and reactivity of polyoxometalates: a theoretical perspective

In the thematic review dedicated to polyoxometalate (POM) chemistry published in Chemical Reviews in 1998, no contribution was devoted to theory. This is not surprising because computational modelling of molecular metal-oxide clusters was in its infancy at that time. Nowadays, the situation has completely changed and modern computational methods have been successfully applied to study the structure, electronic properties, spectroscopy and reactivity of POM clusters. Indeed, the progress achieved during the past decade has been spectacular and herein we critically review the most important papers to provide the reader with an almost complete perspective of the field.