Double addition of phenylacetylene onto the mixed bridge phosphinito-phosphanido Pt(i) complex [(PHCy2)Pt(μ-PCy2){κ2P,O-μ-P(O)Cy2}Pt(PHCy2)](Pt-Pt)

Unveiling the mechanism of activation of the Te(IV) prodrug AS101. New chemical insights towards a better understanding of its medicinal properties

AS101 (Ammonium trichloro (dioxoethylene-O,O') tellurate) is an important hypervalent Te-based prodrug. Recently, we started a systematic investigation on AS101 with the aim to correlate its promising biological effects as a potent immunomodulator drug with multiple medicinal applications and its specific chemical properties. To date, a substantial agreement on the rapid conversion of the initial AS101 species into the corresponding TeOCl3- anion does exist, and this latter species is reputed as the pharmacologically active one. However, we realized that TeOCl3- could quickly undergo further steps of conversion in an aqueous medium, eventually producing the TeO2 species. Using a mixed experimental and theoretical investigation approach, we characterized the conversion process leading to TeO2 occurring both in pure water and in reference buffers at physiological-like pH. Our findings may offer a valuable "chemical tool" for a better description, interpretation -and optimization- of the mechanism of action of AS101 and Te-based compounds. This might be a starting point for improved AS101-based medicinal application.

The binding of diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes at DNA/RNA nucleobases: Computational evidences of an appreciable selectivity toward the AU base pairs

Multiple medicinal strategies involve modifications of the structure of DNA or RNA, which disrupt their correct functioning. Metal complexes with medicinal effects, also known as metallodrugs, are among the agents intended specifically for the attack onto nucleosides. The diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes constitute promising dual acting drugs due to their ability to release the therapeutically active bridging ligands upon their substitution by endogenous ligands. In this paper, we study the structure and the stability of the complexes formed by the diruthenium (II,III) and dirhodium (II,II) paddlewheel complexes coordinated in axial positions with the DNA/RNA nucleobases or base pairs, assuming the attainable metalation at all the accessible pyridyl nitrogens. Dirhodium complexes coordinate at the pyridyl nitrogens more strongly than the diruthenium complexes. On the other hand, we found that the diruthenium scaffold binds more selectively to nucleobase targets. Furthermore, we reveal a tighter coordination of diruthenium complex at the adenine-uracil base pair, compared to adenine-thymine, hence constituting a scarce instance of RNA-selectivity. We envision that the here reported computational outcomes may pace future experiments addressing the binding of diruthenium and dirhodium paddlewheel complexes at either single nucleobases or DNA/RNA fragments.

Diruthenium Paddlewheel Complexes Attacking Proteins: Axial versus Equatorial Coordination

Metallodrugs are an important group of medicinal agents used for the treatment of various diseases ranging from cancers to viral, bacterial, and parasitic diseases. Their distinctive features include the availability of a metal centre, redox activity, as well as the ability to multitarget. Diruthenium paddlewheel complexes are an intensely developing group of metal scaffolds, which can securely coordinate bidentate xenobiotics and transport them to target tissues, releasing them by means of substitution reactions with biomolecular nucleophiles. It is of the utmost importance to gain a complete comprehension of which chemical reactions happen with them in physiological milieu to design novel drugs based on these bimetallic scaffolds. This review presents the data obtained in experiments and calculations, which clarify the chemistry these complexes undergo once administered in the proteic environment. This study demonstrates how diruthenium paddlewheel complexes may indeed embody a new paradigm in the design of metal-based drugs of dual-action by presenting and discussing the protein metalation by these complexes.

Kinetics of Reactions of Dirhodium and Diruthenium Paddlewheel Tetraacetate Complexes with Nucleophilic Protein Sites: Computational Insights

Recently, dirhodium and diruthenium paddlewheel complexes have drawn attention as perspective anticancer drugs. In this study, the kinetics of reaction of typical paddlewheel scaffolds Rh₂(μ-O₂CCH₃)₄(H₂O)₂, Ru₂(μ-O₂CCH₃)₄(H₂O)Cl, and [Ru₂(μ-O₂CCH₃)₄(HO)Cl]^- with protein nucleophiles were investigated by means of the density functional theory. The substitution of axial ligands─water and chloride─by the models of protein residue side chains was analyzed, revealing the binding selectivity displayed by these paddlewheel metal scaffolds. The substitution of water is under a thermodynamic control, in which, although the Arg, Cys^-, and Sec^- residues are the most favorable, their binding is expected to be scarcely selective in a biological context. On the other hand, the replacement of the axial water with a more stable hydroxo ligand induces the chloride substitution in diRu complexes, which also targets Arg, Cys^-, and Sec^-, although with a moderately higher activation barrier for any examined protein residue. Additionally, the carried out characterization of the geometrical parameters of the transition states permitted determination of the impact of an increased steric hindrance of diRh and diRu complexes on their protein site selectivity. This study corroborates the idea of the substitution of the acetate ligands with biologically active, but more hindering, carboxylate ligands, in order to yield dual acting metallodrugs. This study allows us to assume that the delivery of diRu paddlewheel complexes in their monoanionic form [Ru₂(μ-O₂CR)₄(OH)Cl]^- decorated by the bulky substituents R may constitute an approach to augment the selectivity toward anticancer targets, such as TrxR in tumor cells, although under the condition that such a selectivity is operative only in high pH conditions.

Structural Reshaping of the Zinc-Finger Domain of the SARS-CoV-2 nsp13 Protein Using Bismuth(III) Ions: A Multilevel Computational Study

The identification of novel therapeutics against the pandemic SARS-CoV-2 infection is an indispensable new address of current scientific research. In the search for anti-SARS-CoV-2 agents as alternatives to the vaccine or immune therapeutics whose efficacy naturally degrades with the occurrence of new variants, the salts of Bi³⁺ have been found to decrease the activity of the Zn²⁺-dependent non-structural protein 13 (nsp13) helicase, a key component of the SARS-CoV-2 molecular tool kit. Here, we present a multilevel computational investigation based on the articulation of DFT calculations, classical MD simulations, and MIF analyses, focused on the examination of the effects of Bi³⁺/Zn²⁺ exchange on the structure and molecular interaction features of the nsp13 protein. Our calculations confirmed that Bi³⁺ ions can replace Zn²⁺ in the zinc-finger metal centers and cause slight but appreciable structural modifications in the zinc-binding domain of nsp13. Nevertheless, by employing an in-house-developed ATOMIF tool, we evidenced that such a Bi³⁺/Zn²⁺ exchange may decrease the extension of a specific hydrophobic portion of nsp13, responsible for the interaction with the nsp12 protein. The present study provides for a detailed, atomistic insight into the potential anti-SARS-CoV-2 activity of Bi³⁺ and, more generally, evidences the hampering of the nsp13–nsp12 interaction as a plausible therapeutic strategy.

The Zn²⁺/Bi³⁺ exchange in the zinc finger domains of SARS-CoV-2 nsp13 hampers the viral machinery

Anti-Staphylococcal Activity of the Auranofin Analogue Bearing Acetylcysteine in Place of the Thiosugar: An Experimental and Theoretical Investigation

Auranofin (AF, hereafter) is an orally administered chrysotherapeutic agent approved for the treatment of rheumatoid arthritis that is being repurposed for various indications including bacterial infections. Its likely mode of action involves the impairment of the TrxR system through the binding of the pharmacophoric cation [AuPEt₃]⁺. Accordingly, a reliable strategy to expand the medicinal profile of AF is the replacement of the thiosugar moiety with different ligands. Herein, we aimed to prepare the AF analogue bearing the acetylcysteine ligand (AF-AcCys, hereafter) and characterize its anti-staphylococcal activity. Biological studies revealed that AF-AcCys retains an antibacterial effect superimposable with that of AF against Staphylococcus aureus, whereas it is about 20 times less effective against Staphylococcus epidermidis. Bioinorganic studies confirmed that upon incubation with human serum albumin, AF-AcCys, similarly to AF, induced protein metalation through the [AuPEt₃]⁺ fragment. Additionally, AF-AcCys appeared capable of binding the dodecapeptide Ac-SGGDILQSGCUG-NH₂, corresponding to the tryptic C-terminal fragment (488–499) of hTrxR. To shed light on the pharmacological differences between AF and AF-AcCys, we carried out a comparative experimental stability study and a theoretical estimation of bond dissociation energies, unveiling the higher strength of the Au–S bond in AF-AcCys. From the results, it emerged that the lower lipophilicity of AF-AcCys with respect to AF could be a key feature for its different antibacterial activity. The differences and similarities between AF and AF-AcCys are discussed, alongside the opportunities and consequences that chemical structure modifications imply.

Anti-Staphylococcal Activity of the Auranofin Analogue Bearing Acetylcysteine in Place of the Thiosugar: An Experimental and Theoretical Investigation

Auranofin (AF, hereafter) is an orally administered chrysotherapeutic agent approved for the treatment of rheumatoid arthritis that is being repurposed for various indications including bacterial infections. Its likely mode of action involves the impairment of the TrxR system through the binding of the pharmacophoric cation [AuPEt₃]⁺. Accordingly, a reliable strategy to expand the medicinal profile of AF is the replacement of the thiosugar moiety with different ligands. Herein, we aimed to prepare the AF analogue bearing the acetylcysteine ligand (AF-AcCys, hereafter) and characterize its anti-staphylococcal activity. Biological studies revealed that AF-AcCys retains an antibacterial effect superimposable with that of AF against Staphylococcus aureus, whereas it is about 20 times less effective against Staphylococcus epidermidis. Bioinorganic studies confirmed that upon incubation with human serum albumin, AF-AcCys, similarly to AF, induced protein metalation through the [AuPEt₃]⁺ fragment. Additionally, AF-AcCys appeared capable of binding the dodecapeptide Ac-SGGDILQSGCUG-NH₂, corresponding to the tryptic C-terminal fragment (488-499) of hTrxR. To shed light on the pharmacological differences between AF and AF-AcCys, we carried out a comparative experimental stability study and a theoretical estimation of bond dissociation energies, unveiling the higher strength of the Au-S bond in AF-AcCys. From the results, it emerged that the lower lipophilicity of AF-AcCys with respect to AF could be a key feature for its different antibacterial activity. The differences and similarities between AF and AF-AcCys are discussed, alongside the opportunities and consequences that chemical structure modifications imply.

Reactions of Arsenoplatin-1 with Protein Targets: A Combined Experimental and Theoretical Study

Arsenoplatin-1 (AP-1) is a dual-action anticancer metallodrug with a promising pharmacological profile that features the simultaneous presence of a cisplatin-like center and an arsenite center. We investigated its interactions with proteins through a joint experimental and theoretical approach. The reactivity of AP-1 with a variety of proteins, including carbonic anhydrase (CA), superoxide dismutase (SOD), myoglobin (Mb), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and human serum albumin (HSA), was analyzed by means of electrospray ionization mass spectrometry (ESI MS) measurements. In accordance with previous observations, ESI MS experiments revealed that the obtained metallodrug–protein adducts originated from the binding of the [(AP-1)-Cl]⁺ fragment to accessible protein residues. Remarkably, in two cases, i.e., Mb and GAPDH, the formation of a bound metallic fragment that lacked the arsenic center was highlighted. The reactions of AP-1 with various nucleophiles side chains of neutral histidine, methionine, cysteine, and selenocysteine, in neutral form as well as cysteine and selenocysteine in anionic form, were subsequently analyzed through a computational approach. We found that the aquation of AP-1 is energetically disfavored, with a reaction free energy of +19.2 kcal/mol demonstrating that AP-1 presumably attacks its biological targets through the exchange of the chloride ligand. The theoretical analysis of thermodynamics and kinetics for the ligand-exchange processes of AP-1 with His, Met, Cys, Sec, Cys^–, and Sec^– side chain models unveils that only neutral histidine and deprotonated cysteine and selenocysteine are able to effectively replace the chloride ligand in AP-1.

The interaction of arsenoplatin-1 (AP-1), a promising dual-action anticancer metallodrug featuring the simultaneous presence of a cisplatin-like center and an arsenite center, with proteins was studied via a synergetic experimental and theoretical approach. The reactivity of AP-1 with a variety of proteins was analyzed through ESI MS measurements and, at the same time, the reactions of AP-1 with molecular models of the side chains of histidine, methionine, cysteine, and selenocysteine were analyzed through a computational approach.

Tetranuclear rollover cyclometalated organoplatinum-rhenium compounds; C-I oxidative addition and C-C reductive elimination using a rollover cycloplatinated dimer

The novel tetranuclear Pt(IV)-Re(VII) complex [Pt₂Me₄(OReO₃)₂(PMePh₂)₂(µ-bpy-2H)], 4, is synthesized through the reaction of silver perrhenate with a new rollover cycloplatinated(IV) complex [Pt₂Me₄I₂(PMePh₂)₂(µ-bpy-2H)], 3. In complex 4, while 2,2'-bipyridine (bpy) acts as a linker between two Pt metal centers, oxygen acts as a mono-bridging atom between Pt and Re centers through an unsupported Pt(IV)-O-Re(VII) bridge. The precursor rollover cycloplatinated(IV) complex 3 is prepared by the MeI oxidative addition reaction of the rollover cycloplatinated(II) complex [Pt₂Me₂(PMePh₂)₂(µ-bpy-2H)], 2. Complex 2 shows a metal-to-ligand charge-transfer band in the visible region, which was used to investigate the kinetics and mechanism of its double MeI oxidative addition reaction. Based on the experimental findings, the classical S_N2 mechanism was suggested for both steps and supported by computational studies. All complexes are fully characterized using multinuclear NMR spectroscopy and elemental analysis. Attempts to grow crystals of the rollover cycloplatinated(IV) dimer 3 yielded a new dimer rollover cyclometalated complex [Pt₂I₂(PMePh₂)₂(µ-bpy-2H)], 5, presumably from the C-C reductive elimination of ethane. The identity of complex 5 was confirmed by single crystal X-ray diffraction analysis.

Molecular dynamics simulation of the Pb(II) coordination in biological media via cationic dummy atom models

The coordination of Pb(II) in aqueous solutions containing thiols is a pivotal topic to the understanding of the pollutant potential of this cation. Based on its hard/soft borderline nature, Pb(II) forms stable hydrated ions as well as stable complexes with the thiol groups of proteins. In this paper, the modeling of Pb(II) coordination via classical molecular dynamics simulations was investigated to assess the possible use of non-bonded potentials for the description of the metal–ligand interaction. In particular, this study aimed at testing the capability of cationic dummy atom schemes—in which part of the mass and charge of the Pb(II) is fractioned in three or four sites anchored to the metal center—in reproducing the correct coordination geometry and, also, in describing the hard/soft borderline character of this cation. Preliminary DFT calculations were used to design two topological schemes, PB3 and PB4, that were subsequently implemented in the Amber force field and employed in molecular dynamics simulation of either pure water or thiol/thiolate-containing aqueous solutions. The PB3 scheme was then tested to model the binding of Pb(II) to the lead-sensing protein pbrR. The potential use of CDA topological schemes in the modeling of Pb(II) coordination was here critically discussed.

Reactivity of arsenoplatin complex versus water and thiocyanate: a DFT benchmark study

Seven different density functionals, including GGAs, meta-GGAs, hybrids and range-separated hybrids, and considering Grimme’s empirical dispersion correction (M06-L, M06-2X, PBE0, B3LYP, B3LYP-D3, CAM-B3LYP, ωB97X) have been tested for their performance in the prediction of molecular structures, energies and energy barriers for a class of newly developed antitumor platinum complexes involving main group heavy elements such as arsenic. The calculated structural parameters, energies and energy barriers have been compared to the available experimental data. The results show that range-separated hybrid functionals CAM-B3LYP and ωB97X give good results in predicting both geometrical parameters and isomerization energies and barrier heights and are promising new tools for the theoretical study of novel platinum(II) arsenic compounds.

A mixed-valence diruthenium(II,III) complex endowed with high stability: from experimental evidence to theoretical interpretation

We herein report the synthesis and multi-technique characterization of [Ru2Cl((2-phenylindol-3-yl)glyoxyl-l-leucine-l-phenylalanine)4], a novel diruthenium(ii,iii) complex obtained by reacting [Ru2(μ-O2CCH3)4Cl] with a dual indolylglyoxylyl dipeptide anticancer agent. We soon realised that the compound is very stable under several different conditions including aqueous buffers or organic solvents. It is also completely unreactive toward proteins. The high stability is also suggested by cellular experiments in a glioblastoma cell line. Indeed, while the parent ligand exerts high cytotoxic effects in the low μM range, the complex is completely non-cytotoxic against the same line, most probably because of the lack of ligand release. To investigate the reasons for such high stability, we carried out DFT calculations that are fully consistent with the experimental findings. The results highlight that the stability of [Ru2Cl((2-phenylindol-3-yl)glyoxyl-l-leucine-l-phenylalanine)4] relies on the nature of the ligand, including its steric hindrance that prevents the reaction of any nucleophilic group with the Ru2 core. Ligand displacement is the key step to allow reactivity with the biological targets of metal-based prodrugs. Accordingly, we discuss the implications of some important aspects that should be considered when active molecules are chosen as ligands for the synthesis of paddle-wheel-like complexes with medicinal applications.

Mechanistic Insights Into the Anticancer Properties of the Auranofin Analog Au(PEt3)I: A Theoretical and Experimental Study

Au(PEt₃)I (AF-I hereafter), the iodide analog of the FDA-approved drug auranofin (AF hereafter), is a promising anticancer agent that produces its pharmacological effects through interaction with non-genomic targets such as the thioredoxin reductase system. AF-I is endowed with a very favorable biochemical profile showing potent in vitro cytotoxic activity against several cancer types including ovarian and colorectal cancer. Remarkably, in a recent publication, some of us reported that AF-I induces an almost complete and rapid remission in an orthotopic in vivo mouse model of ovarian cancer. The cytotoxic potency does not bring about highly severe side effects, making AF-I very well-tolerated even for higher doses, even more so than the pharmacologically active ones. All these promising features led us to expand our studies on the mechanistic aspects underlying the antitumor activity of AF-I. We report here on an integrated experimental and theoretical study on the reactivity of AF-I, in comparison with auranofin, toward relevant aminoacidic residues or their molecular models. Results point out that the replacement of the thiosugar moiety with iodide significantly affects the overall reactivity toward the amino acid residues histidine, cysteine, methionine, and selenocysteine. Altogether, the obtained results contribute to shed light into the enhanced antitumoral activity of AF-I compared with AF.