Cyclometallated Imides as Templates for the H-Bond Directed Iridium-Catalyzed Asymmetric Hydrogenation of N-Methyl, N-Alkyl and N-Aryl Imines

A combined computational and experimental approach allowed us to develop the most selective catalysts for the direct hydrogenation of N-methyl and N-alkyl imines described to date. Iridium catalysts with a cyclometallated cyclic imide group provide selectivity of up to 99% enantiomeric excess. Computational studies show that the selectivity results from the combined effect of H-bonding of the imide C=O with the substrate iminium ion and a stabilizing π-π interaction with the cyclometallated ligand. The cyclometallated ligand thus exhibits a unique mode of action, serving as a template for the H-bond directed approach of the substrate which results in enhanced selectivity. The catalyst (2) has been synthesized and isolated as a crystalline air-stable solid. X-ray analysis of 2 confirmed the structure of the catalyst and the correct position of the imide C=O groups to engage in an H-bond with the substrate. 19F-NMR real-time monitoring showed the hydrogenation of N-methyl imines catalyzed by 2 is very fast, with a TOF of approx. 3500 h-1.

Interaction with CT-DNA and in vitro cytotoxicity of two new copper(II)-based potential drugs derived from octanoic hydrazide ligands

Two copper(II) complexes [Cu(Hpmoh)(NO3)(NCS)] (1) and [Cu(peoh)(N3)]2 (2) were designed and synthesized by reaction of Cu(NO3)2·3H2O with hydrazone Schiff base ligands,abbreviated with Hpmoh and Hpeoh. Hpmoh and Hpeoh were prepared by condensation reaction of octanoic hydrazide with pyridine-2-carboxyaldehyde and 2-acetylpyridine, respectively. Complexes 1 and 2 were characterized using different analytical techniques such as FT-IR, UV-Vis, IR, EPR and single X-ray diffraction (XRD) analyses as well as computational methods (DFT). The XRD of 1 and 2 shows a mononuclear or a dinuclear structure with the copper(II) centre adopting a slightly distorted square pyramidal geometry. In water-containing solution and in DMSO, 1 and 2 undergo a partial transformation with formation of [Cu(Hpmoh)(NO3)(NCS)] (1) and [Cu(Hpmoh)(NO3)(H2O/DMSO)] (1a) in one system and [Cu(peoh)(N3)] (2a) in the other one, as supported by DFT calculations. Docking simulations confirmed that the intercalation is the preferred binding mode with DNA for 1, 1a and 2a, but suggested that the minor groove binding is also possible. A significant fluorescence quenching of the DNA-ethidium bromide conjugate was observed upon the addition of complexes 1 and 2 with a quenching constant around 104 M-1 s-1. Finally, both 1 and 2 were examined for anti-cancer activity using MDA-MB-231 (human breast adenocarcinoma) and A375 (malignant melanoma) cell lines through in vitro MTT assay which suggest comparable cancer cell killing efficacy, with the higher effectiveness of 2 due to the dissociation into two [Cu(peoh)(N3)] units.

Stabilization and Binding of [V4 O12 ]4- and Unprecedented [V20 O54 (NO3 )]n- to Lysozyme upon Loss of Ligands and Oxidation of the Potential Drug VIV O(acetylacetonato)2

High-resolution crystal structures of lysozyme in the presence of the potential drug VIV O(acetylacetonato)2 under two different experimental conditions have been solved. The crystallographic study reveals the loss of the ligands, the oxidation of VIV to VV and the subsequent formation of adducts of the protein with two different polyoxidovanadates: [V4 O12 ]4- , which interacts with lysozyme non-covalently, and the unprecedented [V20 O54 (NO3 )]n- , which is covalenty bound to the side chain of an aspartate residue of symmetry related molecules.

Implications of Protein Interaction in the Speciation of Potential VIVO-Pyridinone Drugs

Vanadium complexes (VCs) are promising agents for the treatment, among others, of diabetes and cancer. The development of vanadium-based drugs is mainly limited by a scarce knowledge of the active species in the target organs, which is often determined by the interaction of VCs with biological macromolecules like proteins. Here, we have studied the binding of [V^IVO(empp)₂] (where Hempp is 1-methyl-2-ethyl-3-hydroxy-4(1H)-pyridinone), an antidiabetic and anticancer VC, with the model protein hen egg white lysozyme (HEWL) by electrospray ionization-mass spectrometry (ESI-MS), electron paramagnetic resonance (EPR), and X-ray crystallography. ESI-MS and EPR techniques reveal that, in aqueous solution, both the species [V^IVO(empp)₂] and [V^IVO(empp)(H₂O)]⁺, derived from the first one upon the loss of a empp(-) ligand, interact with HEWL. Crystallographic data, collected under different experimental conditions, show covalent binding of [V^IVO(empp)(H₂O)]⁺ to the side chain of Asp48, and noncovalent binding of cis-[V^IVO(empp)₂(H₂O)], [V^IVO(empp)(H₂O)]⁺, [V^IVO(empp)(H₂O)₂]⁺, and of an unusual trinuclear oxidovanadium(V) complex, [V^V₃O₆(empp)₃(H₂O)], with accessible sites on the protein surface. The possibility of covalent and noncovalent binding with different strength and of interaction with various sites favor the formation of adducts with the multiple binding of vanadium moieties, allowing the transport in blood and cellular fluids of more than one metal-containing species with a possible amplification of the biological effects.

Factors driving the Ni/Cu cooperative asymmetric propargylation of aldimine esters

The factors driving the Ni⁰(binap)/Cu^I(phospherrox) cooperative asymmetric propargylation of aldimine esters are unveiled through DFT calculations. The system is fully explored accounting for conformational complexity and aggregation steps. The activation of the substrates proceeds independently, while the intercatalyst communication occurs both through indirect cooperativity, exchanging the non-innocent MeOCO₂^-, and through direct cooperation in the stereoselective C-C coupling driven by intercatalyst interactions.

A Series of Non-Oxido VIV Complexes of Dibasic ONS Donor Ligands: Solution Stability, Chemical Transformations, Protein Interactions, and Antiproliferative Activity

A series of mononuclear non-oxido vanadium(IV) complexes, [V^IV(L^1-4)₂] (1-4), featuring tridentate bi-negative ONS chelating S-alkyl/aryl-substituted dithiocarbazate ligands H₂L^1-4, are reported. All the synthesized non-oxido V^IV compounds are characterized by elemental analysis, spectroscopy (IR, UV-vis, and EPR), ESI-MS, as well as electrochemical techniques (cyclic voltammetry). Single-crystal X-ray diffraction studies of 1-3 reveal that the mononuclear non-oxido V^IV complexes show distorted octahedral (1 and 2) or trigonal prismatic (3) arrangement around the non-oxido V^IV center. EPR and DFT data indicate the coexistence of mer and fac isomers in solution, and ESI-MS results suggest a partial oxidation of [V^IV(L^1-4)₂] to [V^V(L^1-4)₂]⁺ and [V^VO₂(L^1-4)]^-; therefore, all these three complexes are plausible active species. Complexes 1-4 interact with bovine serum albumin (BSA) with a moderate binding affinity, and docking calculations reveal non-covalent interactions with different regions of BSA, particularly with Tyr, Lys, Arg, and Thr residues. In vitro cytotoxic activity of all complexes is assayed against the HT-29 (colon cancer) and HeLa (cervical cancer) cells and compared with the NIH-3T3 (mouse embryonic fibroblast) normal cell line by MTT assay and DAPI staining. The results suggest that complexes 1-4 are cytotoxic in nature and induce cell death in the cancer cell lines by apoptosis and that a mixture of V^IV, V^V, and V^VO₂ species could be responsible for the biological activity.

Promising anticancer agents based on 8-hydroxyquinoline hydrazone copper(II) complexes

We report the synthesis and characterization of a group of benzoylhydrazones (Lⁿ) derived from 2-carbaldehyde-8-hydroxyquinoline and benzylhydrazides containing distinct para substituents (R = H, Cl, F, CH₃, OCH₃, OH and NH₂, for L^1-7, respectively; in L⁸ isonicotinohydrazide was used instead of benzylhydrazide). Cu(II) complexes were prepared by reaction of each benzoylhydrazone with Cu(II) acetate. All compounds were characterized by elemental analysis and mass spectrometry as well as by FTIR, UV-visible absorption, NMR or electron paramagnetic resonance spectroscopies. Complexes isolated in the solid state (1-8) are either formulated as [Cu(HL)acetate] (with L¹ and L⁴) or as [Cu(Lⁿ)]₃ (n = 2, 3, 5, 6, 7 and 8). Single crystal X-ray diffraction studies were done for L⁵ and [Cu(L⁵)]₃, confirming the trinuclear formulation of several complexes. Proton dissociation constants, lipophilicity and solubility were determined for all free ligands by UV-Vis spectrophotometry in 30% (v/v) DMSO/H₂O. Formation constants were determined for [Cu(LH)], [Cu(L)] and [Cu(LH_-1)] for L = L¹, L⁵ and L⁶, and also [Cu(LH_-2)] for L = L⁶, and binding modes are proposed, [Cu(L)] predominating at physiological pH. The redox properties of complexes formed with L¹, L⁵ and L⁶ are investigated by cyclic voltammetry; the formal redox potentials fall in the range of +377 to +395 mV vs. NHE. The binding of the Cu(II)-complexes to bovine serum albumin was evaluated by fluorescence spectroscopy, showing moderate-to-strong interaction and suggesting formation of a ground state complex. The interaction of L¹, L³, L⁵ and L⁷, and of the corresponding complexes with calf thymus DNA was evaluated by thermal denaturation. The antiproliferative activity of all compounds was evaluated in malignant melanoma (A-375) and lung (A-549) cancer cells. The complexes show higher activity than the corresponding free ligand, and most complexes are more active than cisplatin. Compounds 1, 3, 5, and 8 were selected for additional studies: while these complexes induce reactive oxygen species and double-strand breaks in both cancer cells, their ability to induce cell-death by apoptosis varies. Within the set of compounds tested, 8 emerges as the most promising one, presenting low IC₅₀ values, and high induction of oxidative stress and DNA damage, which eventually lead to high rates of apoptosis.

Chemoselective Ru-Catalyzed Oxidative Lactamization vs Hydroamination of Alkynylamines: Insights from Experimental and Density Functional Theory Studies

The Ru-catalyzed intramolecular oxidative amidation (lactamization) of aromatic alkynylamines with 4-picoline N-oxide as an external oxidant has been developed. This chemoselective process is very efficient to achieve medium-sized ε- and ζ-lactams (seven- and eight-membered rings) but not for the formation of common δ-lactams (six-membered rings). DFT studies unveiled the capital role of the chain length between the amine and the alkyne functionalities: the longer the connector, the more favored the lactamization process vs hydroamination.

Getting Deeper into the Molecular Events of Heme Binding Mechanisms: A Comparative Multi-level Computational Study of HasAsm and HasAyp Hemophores

Many biological systems obtain their activity by the inclusion of metalloporphyrins into one or several binding pockets. However, decoding the molecular mechanism under which these compounds bind to their receptors is something that has not been widely explored and is a field with open questions. In the present work, we apply computational techniques to unravel and compare the mechanisms of two heme-binding systems, concretely the HasA hemophores from Gram negative bacteria Serratiamarcescens (HasAsm) and Yersinia pestis (HasAyp). Despite the high sequence identity between both systems, the comparison between the X-ray structures of their apo and holo forms suggests different heme-binding mechanisms. HasAyp has extremely similar structures for heme-free and heme-bound forms, while HasAsm presents a very large displacement of a loop that ultimately leads to an additional coordination to the metal with respect to HasAyp. We combined Gaussian accelerated molecular dynamics simulations (GaMDs) in explicit solvent and protein–ligand docking optimized for metalloligands. GaMDs were first carried out on heme-free forms of both hemophores. Then, protein–ligand dockings of the heme were performed on cluster representatives of these simulations and the best poses were then subjected to a new series of GaMDs. A series of analyses reveal the following: (1) HasAyp has a conformational landscape extremely similar between heme-bound and unbound states with no to limited impact on the binding of the cofactor, (2) HasAsm presents as a slightly broader conformational landscape in its apo state but can only visit conformations similar to the X-ray of the holo form when the heme has been bound. Such behavior results from a complex cascade of changes in interactions that spread from the heme-binding pocket to the flexible loop previously mentioned. This study sheds light on the diversity of molecular mechanisms of heme-binding and discusses the weight between the pre-organization of the receptor as well as the induced motions resulting in association.

Heme-containing enzymes and proteins are important for many biological and biotechnological processes. However, very little is known about heme-binding mechanisms. To shed light on this, we report a multi-level approach combining Gaussian accelerated molecular dynamics and protein−ligand dockings optimized for metallic moieties. The protocol unveils the difference in heme recruitment between HasAsm and HasAyp hemophores and shows its possible applicability to other heme-binding proteins.

Multiple and Variable Binding of Pharmacologically Active Bis(maltolato)oxidovanadium(IV) to Lysozyme

The interaction with proteins of metal-based drugs plays a crucial role in their transport, mechanism, and activity. For an active ML_n complex, where L is the organic carrier, various binding modes (covalent and non-covalent, single or multiple) may occur and several metal moieties (M, ML, ML₂, etc.) may interact with proteins. In this study, we have evaluated the interaction of [V^IVO(malt)₂] (bis(maltolato)oxidovanadium(IV) or BMOV, where malt = maltolato, i.e., the common name for 3-hydroxy-2-methyl-4H-pyran-4-onato) with the model protein hen egg white lysozyme (HEWL) by electrospray ionization mass spectrometry, electron paramagnetic resonance, and X-ray crystallography. The multiple binding of different V-containing isomers and enantiomers to different sites of HEWL is observed. The data indicate both non-covalent binding of cis-[VO(malt)₂(H₂O)] and [VO(malt)(H₂O)₃]⁺ and covalent binding of [VO(H₂O)_3–4]²⁺ and cis-[VO(malt)₂] and other V-containing fragments to the side chains of Glu35, Asp48, Asn65, Asp87, and Asp119 and to the C-terminal carboxylate. Our results suggest that the multiple and variable interactions of potential V^IVOL₂ drugs with proteins can help to better understand their solution chemistry and contribute to define the molecular basis of the mechanism of action of these intriguing molecules.

The interaction of [V^IVO(malt)₂] (BMOV, malt = maltolato) with hen egg white lysozyme (HEWL) reveals the multiple binding of different V-containing isomers and enantiomers to different sites and non-covalent and covalent binding of cis-[VO(malt)₂(H₂O)], [VO(malt)(H₂O)₃]⁺, [VO(H₂O)₃₋₄]²⁺, and cis-[VO(malt)₂] to Glu, Asp, and Asn residues.

Binding of VIV O2+ , VIV OL, VIV OL2 and VV O2 L Moieties to Proteins: X-ray/Theoretical Characterization and Biological Implications

Vanadium compounds have frequently been proposed as therapeutics, but their application has been hampered by the lack of information on the different V-containing species that may form and how these interact with blood and cell proteins, and with enzymes. Herein, we report several resolved crystal structures of lysozyme with bound V^IV O²⁺ and V^IV OL²⁺ , where L=2,2'-bipyridine or 1,10-phenanthroline (phen), and of trypsin with V^IV O(picolinato)₂ and V^V O₂ (phen)⁺ moieties. Computational studies complete the refinement and shed light on the relevant role of hydrophobic interactions, hydrogen bonds, and microsolvation in stabilizating the structure. Noteworthy is that the trypsin-V^V O₂ (phen) and trypsin-V^IV O(OH)(phen) adducts correspond to similar energies, thus suggesting a possible interconversion under physiological/biological conditions. The obtained data support the relevance of hydrolysis of V^IV and V^V complexes in the several types of binding established with proteins and the formation of different adducts that might contribute to their pharmacological action, and significantly widen our knowledge of vanadium-protein interactions.

Controlling oncogenic KRAS signaling pathways with a Palladium-responsive peptide

RAS oncoproteins are molecular switches associated with critical signaling pathways that regulate cell proliferation and differentiation. Mutations in the RAS family, mainly in the KRAS isoform, are responsible for some of the deadliest cancers, which has made this protein a major target in biomedical research. Here we demonstrate that a designed bis-histidine peptide derived from the αH helix of the cofactor SOS1 binds to KRAS with high affinity upon coordination to Pd(II). NMR spectroscopy and MD studies demonstrate that Pd(II) has a nucleating effect that facilitates the access to the bioactive α-helical conformation. The binding can be suppressed by an external metal chelator and recovered again by the addition of more Pd(II), making this system the first switchable KRAS binder, and demonstrates that folding-upon-binding mechanisms can operate in metal-nucleated peptides. In vitro experiments show that the metallopeptide can efficiently internalize into living cells and inhibit the MAPK kinase cascade.

Mo(VI) Potential Metallodrugs: Explaining the Transport and Cytotoxicity by Chemical Transformations

The transport and cytotoxicity of molybdenum-based drugs have been explained with the concept of chemical transformation, a very important idea in inorganic medicinal chemistry that is often overlooked in the interpretation of the biological activity of metal-containing systems. Two monomeric, [MoO₂(L¹)(MeOH)] (1) and [MoO₂(L²)(EtOH)] (2), and two mixed-ligand dimeric Mo^VIO₂ species, [{MoO₂(L^1-2)}₂(μ-4,4'-bipy)] (3-4), were synthesized and characterized. The structures of the solid complexes were solved through SC-XRD, while their transformation in water was clarified by UV-vis, ESI-MS, and DFT. In aqueous solution, 1-4 lead to the penta-coordinated [MoO₂(L^1-2)] active species after the release of the solvent molecule (1 and 2) or removal of the 4,4'-bipy bridge (3 and 4). [MoO₂(L^1-2)] are stable in solution and react with neither serum bioligand nor cellular reductants. The binding affinity of 1-4 toward HSA and DNA were evaluated through analytical and computational methods and in both cases a non-covalent interaction is expected. Furthermore, the in vitro cytotoxicity of the complexes was also determined and flow cytometry analysis showed the apoptotic death of the cancer cells. Interestingly, μ-4,4'-bipy bridged complexes 3 and 4 were found to be more active than monomeric 1 and 2, due to the mixture of species generated, that is [MoO₂(L^1-2)] and the cytotoxic 4,4'-bipy released after their dissociation. Since in the cytosol neither the reduction of Mo^VI to Mo^V/IV takes place nor the production of reactive oxygen species (ROS) through Fenton-like reactions of 1-4 with H₂O₂ occurs, the mechanism of cytotoxicity should be attributable to the direct interaction with DNA that happens with a minor-groove binding which results in cell death through an apoptotic mechanism.

Successes and challenges in multiscale modelling of artificial metalloenzymes: the case study of POP-Rh2 cyclopropanase

Molecular modelling applications in metalloenzyme design are still scarce due to a series of challenges. On top of that, the simulations of metal-mediated binding and the identification of catalytic competent geometries require both large conformational exploration and simulation of fine electronic properties. Here, we demonstrate how the incorporation of new tools in multiscale strategies, namely substrate diffusion exploration, allows taking a step further. As a showcase, the enantioselective profiles of the most outstanding variants of an artificial Rh₂-based cyclopropanase (GSH, HFF and RFY) developed by Lewis and co-workers (Nat. Commun., 2015, 6, 7789 and Nat. Chem., 2018, 10, 318-324) have been rationalized. DFT calculations on the free-cofactor-mediated process identify the carbene insertion and the cyclopropanoid formation as crucial events, the latter being the enantiodetermining step, which displays up to 8 competitive orientations easily altered by the protein environment. The key intermediates of the reaction were docked into the protein scaffold showing that some mutated residues have direct interaction with the cofactor and/or the co-substrate. These interactions take the form of a direct coordination of Rh in GSH and HFF and a strong hydrophobic patch with the carbene moiety in RFY. Posterior molecular dynamics sustain that the cofactor induces global re-arrangements of the protein. Finally, massive exploration of substrate diffusion, based on the GPathFinder approach, defines this event as the origin of the enantioselectivity in GSH and RFY. For HFF, fine molecular dockings suggest that it is likely related to local interactions upon diffusion. This work shows how modelling of long-range mutations on the catalytic profiles of metalloenzymes may be unavoidable and software simulating substrate diffusion should be applied.

Introducing the penicillamine moiety into a metallopeptide mimicking the NiSOD enzyme: electronic and kinetic effects

The novel NiSOD related metallopeptide incorporates penicillamine moiety in the active center which alters both the electronic and kinetic features.

Spectroscopic/Computational Characterization and the X-ray Structure of the Adduct of the VIVO-Picolinato Complex with RNase A

The structure, stability, and enzymatic activity of the adduct formed upon the reaction of the V-picolinato (pic) complex [VIVO(pic)2(H2O)], with an octahedral geometry and the water ligand in cis to the V═O group, with the bovine pancreatic ribonuclease (RNase A) were studied. While electrospray ionization-mass spectrometry, circular dichroism, and ultraviolet-visible absorption spectroscopy substantiate the interaction between the metal moiety and RNase A, electron paramagnetic resonance (EPR) allows us to determine that a carboxylate group, stemming from Asp or Glu residues, and imidazole nitrogen from His residues are involved in the V binding at acidic and physiological pH, respectively. Crystallographic data demonstrate that the VIVO(pic)2 moiety coordinates the side chain of Glu111 of RNase A, by substituting the equatorial water molecule at acidic pH. Computational methods confirm that Glu111 is the most affine residue and interacts favorably with the OC-6-23-Δ enantiomer establishing an extended network of hydrogen bonds and van der Waals stabilizations. By increasing the pH around neutrality, with the deprotonation of histidine side chains, the binding of the V complex to His105 and His119 could occur, with that to His105 which should be preferred when compared to that to the catalytically important His119. The binding of the V compound affects the enzymatic activity of RNase A, but it does not alter its overall structure and stability.

Ferromagnetic Coupling in Oxidovanadium(IV)-Porphyrin Radical Dimers

Three different oxidovanadium(IV) porphyrin dimers with anti, cis, and trans arrangements of the two rings have been synthesized by changing the bridge between the porphyrin macrocycles. This provides a unique opportunity to investigate the role of the bridge and spatial arrangement between the two V^IVO centers for their electronic communication and magnetic coupling. They were characterized by the combined application of XRD analysis, UV-vis and electron paramagnetic resonance (EPR) spectroscopy, cyclic voltammetry, magnetic susceptibility, and DFT calculations. One- and two-electron oxidations produce mono- and dication diradical species, respectively, which display an unusual ferromagnetic interaction between the unpaired spins of vanadium(IV) and porphyrin π-cation radical, in contrast to other metalloporphyrin dimers. The oxidized species show a dissimilar behavior between cis and trans isomers. The ferromagnetic coupling occurs between the porphyrin π-cation radical and the unpaired electron of the V^IVO ion on the d_xy orbital, orthogonal to the porphyrin-based molecular orbitals a_1u and a_2u.

Stereoselective Self-Assembly of DNA Binding Helicates Directed by the Viral β-Annulus Trimeric Peptide Motif

Combining coordination chemistry and peptide engineering offers extraordinary opportunities for developing novel molecular (supra)structures. Here, we demonstrate that the β-annulus motif is capable of directing the stereoselective assembly of designed peptides containing 2,2′-bipyridine ligands into parallel three-stranded chiral peptide helicates, and that these helicates selectively bind with high affinity to three-way DNA junctions.

Impact of Cu(II) and Al(III) on the conformational landscape of amyloidβ1-42

Metal ions have been found to play an important role in the formation of extracellular β-amyloid plaques, a major hallmark of Alzheimer's disease. In the present study, the conformational landscape of Aβ42 with Al(iii) and Cu(ii) has been explored using Gaussian accelerated molecular dynamics. Both metals reduce the flexibility of the peptide and entail a higher structural organization, although to different degrees. As a general trend, Cu(ii) binding leads to an increased α-helix content and to the formation of two α-helices that tend to organize in a U-shape. By contrast, most Al(iii) complexes induce a decrease in helical content, leading to more extended structures that favor the appearance of transitory β-strands.

The binding modes of VIVO2+ ions in blood proteins and enzymes

The binding modes of VIVO2+ ions to hemoglobin (Hb), human serum transferrin (hTf), immunoglobulin G (IgG), vanadium bromoperoxidase (VBrPO) and VIVO2+-substituted imidazoleglycerol-phosphatase dehydratase (IGPD) were determined by a combined approach of full DFT and MM techniques. These results reproduce and explain the experimental spectroscopic (EPR and ESEEM) data.

Synthesis and characterization of new Pd(ii) and Pt(ii) complexes with 3-substituted 1-(2-pyridyl)imidazo[1,5-a]pyridine ligands

Several palladium(ii) and platinum(ii) complexes (1-20) of general formula [M(Lⁿ)(X)(Y)] [M = Pd, X = Y = Cl (1-Cl-4-Cl), X = Y = OAc (1-OAc-4-OAc); M = Pt: X = Y = Cl (5-8); M = Pd, X = Cl, Y = CH₃ (9-12); M = Pt, X = Cl, Y = CH₃ (13-16) or X = Y = CH₃ (17-20); n = 1-4] have been synthesized by reaction of different Pd(ii) and Pt(ii) derivatives with various 3-substituted 1-(2-pyridyl)-imidazo[1,5-a]pyridines; i.e.Lⁿ = 1-(2-pyridyl)-3-arylimidazo[1,5-a]pyridine (aryl = Phenyl, L¹; 2-o-Tolyl, L²; Mesityl, L³) and 1-(2-pyridyl)-3-benzylimidazo[1,5-a]pyridine (L⁴). Detailed spectroscopic investigation (including IR, mono- and bi-dimensional ¹H NMR) and elemental analysis has been performed for all these species, allowing their complete characterization. Lⁿ act as N,N-bidentate ligands and coordinate the metal centers in a chelate fashion through the pyridyl (N_py) and the pyridine-like nitrogen atom of the imidazo[1,5-a]pyridine group (N_im). The X-ray structural analysis performed on two of Pd(ii) and three Pt(ii) complexes, namely [Pd(L²)(CH₃)Cl] (10), [Pd(L³)(CH₃)Cl] (11) and [Pt(L¹)Cl₂] (5), [Pt(L⁴)Cl₂] (8), [Pt(L²)(CH₃)Cl] (14) confirmed the spectroscopic and analytical data. Finally DFT studies unveiled the structural reasons behind the inertia of the synthesised compounds toward metalation, identified as the higher angle steric strain in comparison with the analogous bipyridine complexes.

Copper(II) N,N,O-Chelating Complexes as Potential Anticancer Agents

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (−H, −Cl, and −Br) have been synthesized and characterized. The experimental and computational data obtained suggest that all three complexes exist in the dimeric form in the solid state and adopt the same conformation. The mass spectrometry and electron paramagnetic resonance results indicate that the dimeric structure coexists with the monomeric form in solution upon solvent (dimethyl sulfoxide and water) coordination. The three synthesized Cu(II) complexes exhibit high potentiality as ROS generators, with the Cu(II)/Cu(I) redox potential inside the biological redox window, and thus being able to biologically undergo Cu(II)/Cu(I) redox cycling. The formation of ROS is one of the most promising reported cell death mechanisms for metal complexes to offer an inherent selectivity to cancer cells. In vitro cytotoxic studies in two different cancer cell lines (HeLa and MCF7) and in a normal fibroblast cell line show promising selective cytotoxicity for cancer cells (IC₅₀ about 25 μM in HeLa cells, which is in the range of cisplatin and improved with respect to carboplatin), hence placing this N,N,O-chelating salphen-like metallic core as a promising scaffold to be explored in the design of future tailor-made Cu(II) cytotoxic compounds.

Three novel dinuclear Cu(II) complexes based on a N,N,O-chelating salphen-like ligand scaffold and bearing varying aromatic substituents (−H, −Cl, and −Br) have been synthesized and characterized. They three exhibit high potentiality as reactive oxygen species (ROS) generators, with the Cu(II)/Cu(I) redox potential inside the biological redox window. In vitro studies in two different cancer cell lines (HeLa and MCF7) and in a normal fibroblast cell line show promising selective cytotoxicity for cancer cells.

Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*

Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as Fe^II and Co^II . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled Fe^II helicate was internalized and selectively stains DNA replication factories in functional cells.

Rationalizing the Decavanadate(V) and Oxidovanadium(IV) Binding to G-Actin and the Competition with Decaniobate(V) and ATP

The experimental data collected over the past 15 years on the interaction of decavanadate(V) (V₁₀O₂₈^6-; V₁₀), a polyoxometalate (POM) with promising anticancer and antibacterial action, with G-actin, were rationalized by using several computational approaches (docking, density functional theory (DFT), and molecular dynamics (MD)). Moreover, a comparison with the isostructural and more stable decaniobate(V) (Nb₁₀O₂₈^6-; Nb₁₀) was carried out. Four binding sites were identified, named α, β, γ, and δ, the site α being the catalytic nucleotide site located in the cleft of the enzyme at the interface of the subdomains II and IV. It was observed that the site α is preferred by V₁₀, whereas Nb₁₀ is more stable at the site β; this indicates that, differently from other proteins, G-actin could contemporaneously bind the two POMs, whose action would be synergistic. Both decavanadate and decaniobate induce conformational rearrangements in G-actin, larger for V₁₀ than Nb₁₀. Moreover, the binding mode of oxidovanadium(IV) ion, V^IVO²⁺, formed upon the reduction of decavanadate(V) by the -SH groups of accessible cysteine residues, is also found in the catalytic site α with (His161, Asp154) coordination; this adduct overlaps significantly with the region where ATP is bound, accounting for the competition between V₁₀ and its reduction product V^IVO²⁺ with ATP, as previously observed by EPR spectroscopy. Finally, the competition with ATP was rationalized: since decavanadate prefers the nucleotide site α, Ca²⁺-ATP displaces V₁₀ from this site, while the competition is less important for Nb₁₀ because this POM shows a higher affinity for β than for site α. A relevant consequence of this paper is that other metallodrug-protein systems, in the absence or presence of eventual inhibitors and/or competition with molecules of the organism, could be studied with the same approach, suggesting important elements for an explanation of the biological data and a rational drug design.

Integrated experimental/computational approaches to characterize the systems formed by vanadium with proteins and enzymes

An integrated instrumental/computational approach to characterize metallodrug–protein adducts at the molecular level is reviewed. A series of applications are described, focusing on potential vanadium drugs with a generalization to other metals.

Covalent and non-covalent binding in vanadium–protein adducts

An integrated method, generalizable to any metals and proteins, based on ESI-MS, EPR and molecular modelling was applied to study the covalent and non-covalent binding of the potential drug [V^IVO(nalidixato)₂(H₂O)] to lysozyme and cytochrome c.

Ambiphilic boryl groups in a neutral Ni(ii) complex: a new activation mode of H2

The concept of metal–ligand cooperation opens new avenues for the design of catalytic systems that may offer alternative reactivity patterns to the existing ones. Investigations of this concept with ligands bearing a boron center in their skeleton established mechanistic pathways for the activation of small molecules in which the boron atom usually performs as an electrophile. Here, we show how this electrophilic behavior can be modified by the ligand trans to the boron center, evincing its ambiphilic nature. Treatment of diphosphinoboryl (PBP) nickel–methyl complex 1 with bis(catecholato)diboron (B₂Cat₂) allows for the synthesis of nickel(ii) bis-boryl complex 3 that promotes the clean and reversible heterolytic cleavage of dihydrogen leading to the formation of dihydroborate nickel complex 4. Density functional theory analysis of this reaction revealed that the heterolytic activation of H₂ is facilitated by the cooperation of both boryl moieties and the metal atom in a concerted mechanism that involves a Ni(ii)/Ni(0)/Ni(ii) process. Contrary to 1, the boron atom from the PBP ligand in 3 behaves as a nucleophile, accepting a formally protic hydrogen, whereas the catecholboryl moiety acts as an electrophile, receiving the attack from the hydride-like fragment. This manifests the dramatic change in the electronic properties of a ligand by tuning the substituent trans to it and constitutes an unprecedented cooperative mechanism that involves two boryl ligands in the same molecule operating differently, one as a Lewis acid and the other one as a Lewis base, in cooperation with the metal. In addition, reactivity towards different nucleophiles such as amines or ammonia confirmed the electrophilic nature of the Bcat moiety, allowing the formation of aminoboranes.

A bis(boryl)nickel complex promotes the facile and reversible activation of H₂ through a cooperative mechanism that involves the metal and both boryl moieties in a concerted five-center process.

BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization

With a large amount of research dedicated to decoding how metallic species bind to proteins, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal-binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parameterization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 90 metal-binding X-ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems whose structures (either experimental or theoretical) are not optimal for metal-binding sites. We report here its application on three different challenging cases: (i) the modulation of metal-binding sites during conformational transition in human serum albumin, (ii) the identification of possible routes of metal migration in hemocyanins, and (iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding. BioMetAll is an open-source application available at https://github.com/insilichem/biometall.

An Artificial Hemoprotein with Inducible Peroxidase- and Monooxygenase-Like Activities

A novel inducible artificial metalloenzyme obtained by covalent attachment of a manganese(III)-tetraphenylporphyrin (MnTPP) to the artificial bidomain repeat protein, (A3A3')Y26C, is reported. The protein is part of the αRep family. The biohybrid was fully characterized by MALDI-ToF mass spectrometry, circular dichroism and UV/Vis spectroscopies. The peroxidase and monooxygenase activities were evaluated on the original and modified scaffolds including those that have a) an additional imidazole, b) a specific αRep bA3-2 that is known to induce the opening of the (A3A3') interdomain region and c) a derivative of the αRep bA3-2 inducer extended with a His₆ -Tag (His₆ -bA3-2). Catalytic profiles are highly dependent on the presence of co-catalysts with the best activity obtained with His₆ -bA3-2. The entire mechanism was rationalized by an integrative molecular modeling study that includes protein-ligand docking and large-scale molecular dynamics. This constitutes the first example of an entirely artificial metalloenzyme with inducible peroxidase and monooxygenase activities, reminiscent of allosteric regulation of natural enzymatic pathways.

Chiral Cyclobutane-Containing Cell-Penetrating Peptides as Selective Vectors for Anti-Leishmania Drug Delivery Systems

Two series of new hybrid γ/γ-peptides, γ-CC and γ-CT, formed by (1S,2R)-3-amino-2,2,dimethylcyclobutane-1-carboxylic acid joined in alternation to a Nα-functionalized cis- or trans-γ-amino-l-proline derivative, respectively, have been synthesized and evaluated as cell penetrating peptides (CPP) and as selective vectors for anti-Leishmania drug delivery systems (DDS). They lacked cytotoxicity on the tumoral human cell line HeLa with a moderate cell-uptake on these cells. In contrast, both γ-CC and γ-CT tetradecamers were microbicidal on the protozoan parasite Leishmania beyond 25 μM, with significant intracellular accumulation. They were conjugated to fluorescent doxorubicin (Dox) as a standard drug showing toxicity beyond 1 μM, while free Dox was not toxic. Intracellular accumulation was 2.5 higher than with Dox-TAT conjugate (TAT = transactivator of transcription, taken as a standard CPP). The conformational structure of the conjugates was approached both by circular dichroism spectroscopy and molecular dynamics simulations. Altogether, computational calculations predict that the drug-γ-peptide conjugates adopt conformations that bury the Dox moiety into a cavity of the folded peptide, while the positively charged guanidinium groups face the solvent. The favorable charge/hydrophobicity balance in these CPP improves the solubility of Dox in aqueous media, as well as translocation across cell membranes, making them promising candidates for DDS.

New VIV, VIVO, VVO, and VVO2 Systems: Exploring their Interconversion in Solution, Protein Interactions, and Cytotoxicity

The synthesis and characterization of one oxidoethoxidovanadium(V) [V^VO(L¹)(OEt)] (1) and two nonoxidovanadium(IV) complexes, [V^IV(L^2-3)₂] (2 and 3), with aroylhydrazone ligands incorporating naphthalene moieties, are reported. The synthesized oxido and nonoxido vanadium complexes are characterized by various physicochemical techniques, and their molecular structures are solved by single crystal X-ray diffraction (SC-XRD). This revealed that in 1 the geometry around the vanadium atom corresponds to a distorted square pyramid, with a O₄N coordination sphere, whereas that of the two nonoxido V^IV complexes 2 and 3 corresponds to a distorted trigonal prismatic arrangement with a O₄N₂ coordination sphere around each "bare" vanadium center. In aqueous solution, the V^VO moiety of 1 undergoes a change to V^VO₂ species_, yielding [V^VO₂(L¹)]^- (1'), while the nonoxido V^IV-compounds 2 and 3 are partly converted into their corresponding V^IVO complexes, [V^IVO(L^2-3)(H₂O)] (2' and 3'). Interaction of these V^VO₂, V^IVO, and V^IV systems with two model proteins, ubiquitin (Ub) and lysozyme (Lyz), is investigated through docking approaches, which suggest the potential binding sites: the interaction is covalent for species 2' and 3', with the binding to Glu16, Glu18, and Asp21 for Ub, and His15 for Lyz, and it is noncovalent for species 1', 2, and 3, with the surface residues of the proteins. The ligand precursors and complexes are also evaluated for their in vitro antiproliferative activity against ovarian (A2780) and prostate (PC3) human cancer cells and in normal fibroblasts (V79) to check the selectivity of the compounds for cancer cells.

ESI-MS Study of the Interaction of Potential Oxidovanadium(IV) Drugs and Amavadin with Model Proteins

In this study, the binding to lysozyme (Lyz) of four important VIV compounds with antidiabetic and/or anticancer activity, [VIVO(pic)2(H2O)], [VIVO(ma)2], [VIVO(dhp)2], and [VIVO(acac)2], where pic-, ma-, dhp-, and acac- are picolinate, maltolate, 1,2-dimethyl-3-hydroxy-4(1H)-pyridinonate, and acetylacetonate anions, and of the vanadium-containing natural product amavadin ([VIV(hidpa)2]2-, with hidpa3- N-hydroxyimino-2,2'-diisopropionate) was investigated by ElectroSpray Ionization-Mass Spectrometry (ESI-MS). Moreover, the interaction of [VIVO(pic)2(H2O)], chosen as a representative VIVO2+ complex, was examined with two additional proteins, myoglobin (Mb) and ubiquitin (Ub), to compare the data. The examined vanadium concentration was in the range 15-150 μM, i.e., very close to that found under physiological conditions. With pic-, dhp-, and hidpa3-, the formation of adducts n[VIVOL2]-Lyz or n[VIVL2]-Lyz is favored, while with ma- and acac- the species n[VIVOL]-Lyz are detected, with n dependent on the experimental VIV/protein ratio. The behavior of the systems with [VIVO(pic)2(H2O)] and Mb or Ub is very similar to that of Lyz. The results suggested that under physiological conditions, the moiety cis-VIVOL2 (L = pic-, dhp-) is bound by only one accessible side-chain protein residue that can be Asp, Glu, or His, while VIVOL+ (L = ma-, acac-) can interact with the two equatorial and axial sites. If the VIV complex is thermodynamically stable and does not have available coordination positions, such as amavadin, the protein cannot interact with it through the formation of coordination bonds and, in such cases, noncovalent interactions are predicted. The formation of the adducts is dependent on the thermodynamic stability and geometry in aqueous solution of the VIVO2+ complex and affects the transport, uptake, and mechanism of action of potential V drugs.

Biospeciation of Potential Vanadium Drugs of Acetylacetonate in the Presence of Proteins

Among vanadium compounds with potential medicinal applications, [V^IVO(acac)₂] is one of the most promising for its antidiabetic and anticancer activity. In the organism, however, interconversion of the oxidation state to +III and +V and binding to proteins are possible. In this report, the transformation of V^III(acac)₃, V^IVO(acac)₂, and V^VO₂(acac)2- after the interaction with two model proteins, lysozyme (Lyz) and ubiquitin (Ub), was studied with ESI-MS (ElectroSpray Ionization-Mass Spectroscopy), EPR (Electron Paramagnetic Resonance), and computational (docking) techniques. It was shown that, in the metal concentration range close to that found in the organism (15–250 μM), V^III(acac)₃ is oxidized to V^IVO(acac)⁺ and V^IVO(acac)₂, which—in their turn—interact with proteins to give n[V^IVO(acac)]–Protein and n[V^IVO(acac)₂]–Protein adducts. Similarly, the complex in the +IV oxidation state, V^IVO(acac)₂, dissociates to the mono-chelated species V^IVO(acac)⁺ which binds to Lyz and Ub. Finally, V^VO₂(acac)2- undergoes complete dissociation to give the 'bare' V^VO2+ ion that forms adducts n[V^VO₂]–Protein with n = 1–3. Docking calculations allowed the prediction of the residues involved in the metal binding. The results suggest that only the V^IVO complex of acetylacetonate survives in the presence of proteins and that its adducts could be the species responsible of the observed pharmacological activity, suggesting that in these systems V^IVO²⁺ ion should be used in the design of potential vanadium drugs. If V^III or V^VO₂ potential active complexes had to be designed, the features of the organic ligand must be adequately modulated to obtain species with high redox and thermodynamic stability to prevent oxidation and dissociation.

Catalytic Regioselective Isomerization of 2,2-Disubstituted Oxetanes to Homoallylic Alcohols

The selective isomerization of strained heterocyclic compounds is an important tool in organic synthesis. An unprecedented regioselective isomerization of 2,2-disubstituted oxetanes into homoallylic alcohols is described. The use of tris(pentafluorophenyl)borane (B(C₆ F₅ )₃ )_, a commercially available Lewis acid was key to obtaining good yields and selectivities since other Lewis acids afforded mixtures of isomers and substantial polymerization. The reaction took place under exceptionally mild reaction conditions and very low catalyst loading (0.5 mol %). DFT calculations disclose the mechanistic features of the isomerization and account for the high selectivity displayed by the B(C₆ F₅ )₃ catalyst. The synthetic applicability of the new reaction is demonstrated by the preparation of γ-chiral alcohols using iridium-catalyzed asymmetric hydrogenation.

Computational insight into the interaction of oxaliplatin with insulin

In an organism, cisplatin and its derivatives are known to interact with proteins besides their principal DNA target. These off-target interactions have major therapeutic consequences including undesired side effects, loss of bioavailability and emergence of resistance. Insulin is one of the prototypical protein targets of platinum drugs as it has been seen to be involved in bioavailability reduction and might also determine resistance in certain cancer lines. However, despite the interest in understanding the nature of the oxaliplatin-insulin adducts, no 3D models have been achieved so far. In this study, we apply our recent computational multiscale protocol optimized for bioinorganic interactions to provide structural insights into these systems. To do so, the initial structures are predicted by blind protein-metalloligand docking calculations optimized to account for a metal-containing species, and then refined using a Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) integrated protocol. The results are consistent with experimental information obtained from fragment analysis, and also provide novel structural information like conformational changes occurring upon binding and potential effects on the biological functions of the protein. This study opens an avenue towards applying similar strategies to a wide ensemble of metallodrug-protein/peptide systems for which no structural data are available.

Bonding rearrangements in organometallic reactions: from orbitals to curly arrows

Reaction mechanisms include a description of both the nuclear and electronic rearrangements along the energetically most favourable pathway. Extracting the nuclear rearrangements from the outcome of quantum chemical calculations is straightforward, while it is more intricate for the electronic rearrangements. This is particularly true when changes in the bonding pattern are of interest, just as in the arrow-pushing formalism used in chemical schemes. Here, we report on our use of a simple and highly visual procedure to recover the bonding rearrangements along a reaction pathway from DFT calculations and to draw curly arrows. We show that the procedure allows us discern among mechanistic proposals in the context of organometallic reactions featuring the forming and breaking of bonds.

Chemistry of mixed-ligand oxidovanadium(IV) complexes of aroylhydrazones incorporating quinoline derivatives: Study of solution behavior, theoretical evaluation and protein/DNA interaction

A series of eight hexacoordinated mixed-ligand oxidovanadium(IV) complexes [VO(L^x)(L^N-N)] (1-8), where L^x = L¹ - L⁴ are four differently substituted ONO donor aroylhydrazone ligands and L^N-N are N,N-donor bases like 2,2'-bipyridine (bipy) (1, 3, 5 and 7) and 1,10-phenanthroline (phen) (2, 4, 6 and 8), have been reported. All synthesized complexes have been characterized by various physicochemical techniques and molecular structures of 1 and 6 were determined by X-ray crystallography. With a view to evaluate the biological activity of the V^IVO species, the behavior of the systems V^IVO²⁺/L^x, V^IVO²⁺/L^x/bipy and V^IVO²⁺/L^x/phen was studied as a function of pH in a mixture of H₂O/DMSO 50/50 (v/v). DFT calculations allowed finding out the relative stability of the tautomeric forms of the ligands, and predicting the structure of vanadium complexes and their EPR parameters. To study their interaction with proteins, firstly the ternary systems V^IVO²⁺/L^1,2 with 1-methylimidazole, which is a good model for histidine binding, were examined. Subsequently the interaction of the complexes with lysozyme (Lyz), cytochrome c (Cyt) and bovine serum albumin (BSA) was studied. The results indicate that the complexes showed moderate binding affinity towards BSA, while no interaction takes place with lysozyme and cytochrome c. This could be explained with the higher number of accessible coordinating and polar residues for BSA than for Lyz and Cyt. Further, the complexes were also evaluated for their DNA binding propensity through UV-vis absorption titration and fluorescence spectral studies. These results were consistent with BSA binding affinity and showed moderate binding affinity towards CT-DNA.

GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm

Protein-ligand docking is a widely used method to generate solutions for the binding of a small molecule with its target in a short amount of time. However, these methods provide identification of physically sound protein-ligand complexes without a complete view of the binding process dynamics, which has been recognized to be a major discriminant in binding affinity and ligand selectivity. In this paper, a novel piece of open-source software to approach this problem is presented, called GPathFinder. It is built as an extension of the modular GaudiMM platform and is able to simulate ligand diffusion pathways at atomistic level. The method has been benchmarked on a set of 20 systems whose ligand-binding routes were studied by other computational tools or suggested from experimental "snapshots". In all of this set, GPathFinder identifies those channels that were already reported in the literature. Interestingly, the low-energy pathways in some cases indicate novel possible binding routes. To show the usefulness of GPathFinder, the analysis of three case systems is reported. We believe that GPathFinder is a software solution with a good balance between accuracy and computational cost, and represents a step forward in extending protein-ligand docking capacities, with implications in several fields such as drug or enzyme design.