Joaquín Barroso-Flores

A Multi-State, Allosterically-Regulated Molecular Receptor With Switchable Selectivity

A biomimetic, ion-regulated molecular receptor was synthesized via the Weak-Link Approach (WLA). This structure features both a calix[4]arene moiety which serves as a molecular recognition unit and an activity regulator composed of hemilabile phosphine alkyl thioether ligands (P,S) chelated to a Pt(II) center. The host-guest properties of the ion-regulated receptor were found to be highly dependent upon the coordination of the Pt(II) center, which is controlled through the reversible coordination of small molecule effectors. The environment at the regulatory site dictates the charge and the structural conformation of the entire assembly resulting in three accessible binding configurations: one closed, inactive state and two open, active states. One of the active states, the semiopen state, recognizes a neutral guest molecule, while the other, the fully open state, recognizes a cationic guest molecule. Job plots and (1)H NMR spectroscopy titrations were used to study the formation of these inclusion complexes, the receptor binding modes, and the receptor binding affinities (Ka) in solution. Single crystal X-ray diffraction studies provided insight into the solid-state structures of the receptor when complexed with each guest molecule. The dipole moments and electrostatic potential maps of the structures were generated via DFT calculations at the B97D/LANL2DZ level of theory. Finally, we describe the reversible capture and release of guests by switching the receptor between the closed and semiopen configurations via elemental anion and small molecule effectors.

In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study.

The use of functionalized calix- and thia-calix[n]arenes is proposed as the basis for our in silico design of a suitable drug carrier for the tyrosine kinase inhibitor, Imatinib. Their mutual electronic properties and interaction energies, Eint, were assessed with the use of Density Functional Theory (DFT) methods under the NBODel methodology. Three structural variables for the host molecules were considered: R = {SO3H (1), t-Bu (2), i-Pr (3), COOH (4), (CH2)2OH (5), (CH2)2NH2 (6)}; b = {CH2, S}; n = {5, 6, 8}, and two possible orientations for the insertion of Imatinib within the macrocycle cavity: pyridine moiety pointing inward (N1) and piperazine pointing inward (N2). In total, we explored 72 different assemblies. Initial molecular mechanics geometry optimizations with the UFF potential were undertaken for every host-guest complex, with further optimization at the B97D/6-31G(d,p) level of theory. Using the same optimized structures, Molecular Dynamics (MD) simulations were carried out on all 72 assemblies using the General Amber Force Field and the AMBER 12 MD package. Electronic parameters were fitted using the RESP method, and the complexes were run for 100 ns. Potential of mean force was obtained for the most stable systems using umbrella sampling and the Weighted Histogram Analysis Method. Calix[n]arenes families 1 and 5 (R = SO3H and (CH2)2OH, respectively) with n = 6 constitute the most promising candidates to become drug carriers within our parameter space due to their more negative Eint values and increased flexibility to allow the inclusion of the drug.

A mixed DFT‐MD methodology for the in silico development of drug releasing macrocycles. Calix and thia‐calix[N]arenes as carriers for Bosutinib and Sorafenib

Interaction energies between a family of 36 calix[n]arenes, their corresponding thia‐ analogues, and two commercially available second generation tyrosine kinase III inhibitors—Bosutinib and Sorafenib—were calculated through DFT methods at the B97D/6‐31G(d,p) level of theory, based on Natural Population Analysis, for the in silico development of suitable drug carriers based on the aforementioned macrocycles which can increase their bioavailability and in turn their pharmaceutical efficiency. Molecular Dynamics simulations (production runs: +500 ns) using the General Amber Force Field were also carried out in order to assess the releasing process of these drugs in an explicit aqueous environment. In total, 144 host–guest complexes are examined. According to our results, five‐membered SO3H and i–Pr functionalized‐calixarenes are the best candidates for Sorafenib‐carriers while six‐membered ones SO3H and C2H4NH2 functionalized– are the lead candidates for Bosutinib‐carriers.

Ab initio calculations of electronic interactions in inclusion complexes of calix- and thiacalix[n]arenes and block s cations

Ab initio calculations at the HF/6-31G(d) level of theory were performed on a series of thiacalix[4]arenes and calix[6]arenes in presence and in absence of monovalent (Li+, Na+ and Cs+) and divalent cations (Ca2+ and Ba2+) respectively, in order to evaluate their particular bonding properties as host systems towards electrically charged species. NBO, as well as NBO deletion calculations were undertaken to evaluate the energy difference in the circular hydrogen bonding at the lower rim once an ion was placed inside the cavity. Disruption of this H-bonded system is dependent on the position of the ion within the guest and not on its ionic ratio. The basis set superposition error and the NBO deletion energy between the host and guest species were calculated in order to assess the interaction energy between them.

Reactivity of electrophilic chlorine atoms due to σ-holes: a mechanistic assessment of the chemical reduction of a trichloromethyl group by sulfur nucleophiles

σ-Holes are shown to promote the electrophilic behavior of chlorine atoms in a trichloromethyl group when bound to an electron-withdrawing moiety. A halogen bond-type non-covalent interaction between a chlorine atom and a negatively charged sulfur atom takes place, causing the abstraction of such a chlorine atom while leaving a carbanion, subsequently driving the chemical reduction of the trichloromethyl group to a sulfide in a stepwise process. The mechanism for the model reaction of trichloromethyl pyrimidine 1 with thiophenolate and thiophenol to yield phenylsulfide 4 was followed through 1H-NMR and studied using DFT transition state calculations, and the energy profile for this transformation is fully discussed. MP2 calculations of the electrostatic potential were performed for a series of trichloromethyl compounds in order to assess the presence of σ-holes and quantify them by means of the maximum surface electrostatic potential. Such calculations showed that the chlorine atoms behave as electrophilic leaving groups toward a nucleophilic attack, opening a new possibility in the synthetic chemistry of the trichloromethyl group.

Piperazine-based HIV-1 entry inhibitors: Massive in silico library design and screening for gp120 attachment inhibitors.

HIV-1 attachment, despite being an ideal target stage to stop infection from the beginning, remains as one of the HIV lifecycle phases with less amount of designed and commercially available inhibitors. To contribute to the urgently needed discovery of new active compounds that could become part of the current highly active antiretroviral therapy, and as an attempt to explore a massive chemical space, high-throughput virtual screening of 16.3 million combinatorially generated and piperazine-cored compounds, was accomplished. Docking calculations, molecular dynamics simulations, and QSAR analyses were carried out to assess the suitability of each ligand to bind gp120 envelope glycoprotein, thus preventing it from binding to CD4 co-receptor. Ligand 255 stands out as a promising candidate to be tested beyond computational methodologies, and the 4,5,6,7-tetrahydroindole fragment is reported as a better group to bind inside the Phe43 cavity than the substituted indoles reported in the literature.

The OECD Principles for (Q)SAR Models in the Context of Knowledge Discovery in Databases (KDD)

The steps followed in the knowledge discovery in databases (KDD) process are well documented and are widely used in different areas where exploration of data is used for decision making. In turn, while different workflows for developing quantitative structure-activity relationship (QSAR) models have been proposed, including combinatorial use of QSAR, there is now agreement on common requirements for building trustable predictive models. In this work, we analyze and confront the steps involved in KDD and QSAR and present how they comply with the OECD principles for the validation, for regulatory purposes, of QSAR models.

A Redox-Switchable, Allosteric Coordination Complex

A redox-regulated molecular tweezer complex was synthesized via the weak-link approach. The PtII complex features a redox-switchable hemilabile ligand (RHL) functionalized with a ferrocenyl moiety, whose oxidation state modulates the opening of a specific coordination site. Allosteric regulation by redox agents gives reversible access to two distinct structural states-a fully closed state and a semi-open state-whose interconversion was studied via multinuclear NMR spectroscopy, cyclic voltammetry, and UV-vis-NIR spectroscopy. Two structures in this four-state system were further characterized via SCXRD, while the others were modeled through DFT calculations. This fully reversible, RHL-based system defines an unusual level of electrochemical control over the occupancy of a specific coordination site, thereby providing access to four distinct coordination states within a single system, each defined and differentiated by structure and oxidation state.

An Allosterically Regulated, Four-State Macrocycle

Macrocycles capable of host-guest chemistry are an important class of structures that have attracted considerable attention because of their utility in chemical separations, analyte sensing, signal amplification, and drug delivery. The deliberate design and synthesis of such structures are rate-limiting steps in utilizing them for such applications, and coordination-driven supramolecular chemistry has emerged as a promising tool for rapidly making large classes of such systems with attractive molecular recognition capabilities and, in certain cases, catalytic properties. A particularly promising subset of such systems are stimuli-responsive constructs made from hemilabile ligands via the weak-link approach (WLA) to supramolecular coordination chemistry. Such structures can be reversibly toggled between different shapes, sizes, and charges based upon small-molecule and elemental-anion chemical effectors. In doing so, one can deliberately change their recognition properties and both stoichiometric and catalytic chemistries, thereby providing mimics of allosteric enzymes. The vast majority of structures made to date involve two-state systems, with a select few being able to access three different states. Herein, we describe the synthesis of a new allosterically regulated four-state macrocycle assembled via the WLA. The target structure was made via the stepwise assembly of ditopic bidentate hemilabile N-heterocyclic carbene thioether (NHC,S) and phosphino thioether (P,S) ligands at PtII metal nodes. The relatively simple macrocycle displays complex dynamic behavior when addressed with small-molecule effectors, and structural switching can be achieved with several distinct molecular cues. Importantly, each state was fully characterized by multinuclear NMR spectroscopy and, in some cases, single-crystal X-ray diffraction studies and density functional theory computational models. This new structure opens the door to complex multicue switching reminiscent of multistate chemoswitches that could be important in controlling stoichiometric and catalytic transformations as well as generating molecular logic systems.

Real-Time Visualization of Cell Membrane Damage Using Gadolinium-Schiff Base Complex-Doped Quantum Dots

Despite the importance of cell membranes for maintenance of integrity of cellular structures, there is still a lack of methods that allow simple real-time visualization of their damage. Herein, we describe gadolinium-Schiff base-doped quantum dots (GdQDs)-based probes for a fast facile spatial labeling of membrane injuries. We found that GdQDs preferentially interact through electron-rich and hydrophobic residues with a specific sequence motif of NHE-RF2 scaffold protein, exposed upon membrane damage. Such interaction results in a fast formation of intensively fluorescent droplets with a higher resolution and in a much shorter time compared to immunofluorescence using organic dye. GdQDs have high stability, brightness, and considerable cytocompatibility, which enable their use in long-term experiments in living cultures. To the best of our knowledge, this is the first report, demonstrating a method allowing real-time monitoring of membrane damage and recovery without any special requirements for instrumentation. Because of intensive brightness and simple signal pattern, GdQDs allow easy examination of interactions between cellular membranes and cell-penetrating peptides or cytostatic drugs. We anticipate that the simple and flexible method will also facilitate the studies dealing with host-pathogen interactions.