Combining the Fragment Molecular Orbital and GRID Approaches for the Prediction of Ligand-Metalloenzyme Binding Affinity: The Case Study of hCA II Inhibitors.

Polarization and charge-transfer interactions play an important role in ligand-receptor complexes containing metals, and only quantum mechanics methods can adequately describe their contribution to the binding energy. In this work, we selected a set of benzenesulfonamide ligands of human Carbonic Anhydrase II (hCA II)-an important druggable target containing a Zn2+ ion in the active site-as a case study to predict the binding free energy in metalloprotein-ligand complexes and designed specialized computational methods that combine the ab initio fragment molecular orbital (FMO) method and GRID approach. To reproduce the experimental binding free energy in these systems, we adopted a machine-learning approach, here named formula generator (FG), considering different FMO energy terms, the hydrophobic interaction energy (computed by GRID) and logP. The main advantage of the FG approach is that it can find nonlinear relations between the energy terms used to predict the binding free energy, explicitly showing their mathematical relation. This work showed the effectiveness of the FG approach, and therefore, it might represent an important tool for the development of new scoring functions. Indeed, our scoring function showed a high correlation with the experimental binding free energy (R2 = 0.76-0.95, RMSE = 0.34-0.18), revealing a nonlinear relation between energy terms and highlighting the relevant role played by hydrophobic contacts. These results, along with the FMO characterization of ligand-receptor interactions, represent important information to support the design of new and potent hCA II inhibitors.

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 FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study.

In this work, the ab initio fragment molecular orbital (FMO) method was applied to calculate and analyze the binding energy of two biscarbene-Au(I) derivatives, [Au(9-methylcaffein-8-ylidene)2]+ and [Au(1,3-dimethylbenzimidazol-2-ylidene)2]+, to the DNA G-Quadruplex structure. The FMO2 binding energy considers the ligand-receptor complex as well as the isolated forms of energy-minimum state of ligand and receptor, providing a better description of ligand-receptor affinity compared with simple pair interaction energies (PIE). Our results highlight important features of the binding process of biscarbene-Au(I) derivatives to DNA G-Quadruplex, indicating that the total deformation-polarization energy and desolvation penalty of the ligands are the main terms destabilizing the binding. The pair interaction energy decomposition analysis (PIEDA) between ligand and nucleobases suggest that the main interaction terms are electrostatic and charge-transfer energies supporting the hypothesis that Au(I) ion can be involved in π-cation interactions further stabilizing the ligand-receptor complex. Moreover, the presence of polar groups on the carbene ring, as C = O, can improve the charge-transfer interaction with K+ ion. These findings can be employed to design new powerful biscarbene-Au(I) DNA-G quadruplex binders as promising anticancer drugs. The procedure described in this work can be applied to investigate any ligand-receptor system and is particularly useful when the binding process is strongly characterized by polarization, charge-transfer and dispersion interactions, properly evaluated by ab initio methods.

Computational Studies of Au(I) and Au(III) Anticancer MetalLodrugs: A Survey.

Owing to the growing hardware capabilities and the enhancing efficacy of computational methodologies, computational chemistry approaches have constantly become more important in the development of novel anticancer metallodrugs. Besides traditional Pt-based drugs, inorganic and organometallic complexes of other transition metals are showing increasing potential in the treatment of cancer. Among them, Au(I)- and Au(III)-based compounds are promising candidates due to the strong affinity of Au(I) cations to cysteine and selenocysteine side chains of the protein residues and to Au(III) complexes being more labile and prone to the reduction to either Au(I) or Au(0) in the physiological milieu. A correct prediction of metal complexes' properties and of their bonding interactions with potential ligands requires QM computations, usually at the ab initio or DFT level. However, MM, MD, and docking approaches can also give useful information on their binding site on large biomolecular targets, such as proteins or DNA, provided a careful parametrization of the metal force field is employed. In this review, we provide an overview of the recent computational studies of Au(I) and Au(III) antitumor compounds and of their interactions with biomolecular targets, such as sulfur- and selenium-containing enzymes, like glutathione reductases, glutathione peroxidase, glutathione-S-transferase, cysteine protease, thioredoxin reductase and poly (ADP-ribose) polymerase 1.

Probing the Paradigm of Promiscuity for N-Heterocyclic Carbene Complexes and their Protein Adduct Formation.

Metal complexes can be considered a "paradigm of promiscuity" when it comes to their interactions with proteins. They often form adducts with a variety of donor atoms in an unselective manner. We have characterized the adducts formed between a series of isostructural N-heterocyclic carbene (NHC) complexes with Ru, Os, Rh, and Ir centers and the model protein hen egg white lysozyme by X-ray crystallography and mass spectrometry. Distinctive behavior for the metal compounds was observed with the more labile Ru and Rh complexes targeting mainly a surface l-histidine moiety through cleavage of p-cymene or NHC co-ligands, respectively. In contrast, the more inert Os and Ir derivatives were detected abundantly in an electronegative binding pocket after undergoing ligand exchange of a chlorido ligand for an amino acid side chain. Computational studies supported the binding profiles and hinted at the role of the protein microenvironment for metal complexes eliciting selectivity for specific binding sites on the protein.

Determinants of the Lead(II) Affinity in pbrR Protein: A Computational Study.

Investigation of the diverse evolutionary developed mechanisms enabling bacteria to maintain homeostasis and to be resistant to lead is crucial for the discovery of novel strategies for isolation of this highly toxic metal and its subsequent elimination from contaminated environments. The metalloregulatory protein pbrR and its homologues that were identified in the Cupriavidus metallidurans CH34 chromosome are the only characterized natural metalloproteins that have a special affinity toward Pb(II) and that bind it with at least a 1000-fold selectivity over other heavy metals. The X-ray structures of apo and Pb(II)-bound pbrR have been recently reported. In the present study, the binding of Pb(II) at pbrR was investigated by means of multiscale computational modeling. Molecular dynamics simulations substantiated how conformations amenable for the Pb(II) complexation through the tris-cysteine motif are formed from the antiparallel coiled-coil packing interaction of two dimerization helices of two pbrR monomers, and the phase space of apo-pbrR has been extensively sampled. Hybrid quantum mechanics/molecular mechanics (QM/MM) calculations on metal-bound structures of pbrR also allowed us to determine the most probable protonation state for the lead binding motif and evaluate the structural features mostly affecting the Pb(II) coordination in this protein. In agreement with available experimental data, we found that pbrR may control its Pb(II) affinity, probably, by conformational changes that affect the distance between Cys78' and Cys122 and their protonation states, thus being able to switch on the Pb(II) sequestration/release-prone states in response to external stimuli. The protein structure enveloping the metal binding motif favors the thiol-thiolate-thiolate protonation state of Pb(II)-pbrR, thus probably enhancing the binding selectivity for Pb(II), compared to other metal ions.

Insight into the Substitution Mechanism of Antitumor Au(I) N-Heterocyclic Carbene Complexes by Cysteine and Selenocysteine.

We carried out a detailed theoretical study on the mechanism of the carbene ligand substitution by cysteine and selenocysteine residues in an Au(I) bis-N-heterocyclic carbene complex in order to model the initial stages of the mechanism of action of this promising class of antitumor metallodrug. Both neutral and deprotonated capped Cys and Sec species were considered as possible nucleophiles in the ligand exchange reaction on the metal center to model the corresponding protein side chains. Energies and geometric structures of the possible transition states and reactant- and product-adducts involved in the substitution process have been calculated using density functional theory and local MP2. Reaction and activation enthalpies and free energies have been evaluated and indicate a slightly exothermic and exergonic process with reasonably low barriers, 21.3 and 19.6 kcal mol-1, respectively, for capped Cys and Sec, in good agreement with the experimental data available for the reaction with free amino acids. The results suggest a mechanism for the ligand exchange reaction involving an anionic thiolate or selenothiolate species coupled to an explicit proton transfer to the leaving carbene from the acidic component of the buffer. The presence of a buffer is necessary both in in vitro experiments and under physiological conditions, and its proton reservoir behavior reveals the importance of the environmental effects in carbene substitution by biological nucleophiles.

An Insight on the Gold(I) Affinity of golB Protein via Multilevel Computational Approaches.

Several bacterial species have evolutionary developed protein systems specialized in the control of intracellular gold ion concentration. In order to prevent the detrimental consequences that may be induced even at very low concentrations, bacteria such as Salmonella enterica and Cupriavidus metallidurans utilize Au-specific merR-type transcriptional regulators that detect these toxic ions and control the expression of specific resistance factors. Among these highly specialized proteins, golB has been investigated in depth, and X-ray structures of both apo and Au(I)-bound golB have been recently reported. Here, the binding of Au(I) at golB was investigated by means of multilevel computational approaches. Molecular dynamics simulations evidenced how conformations amenable for the Au(I) chelation through the Cys-XX-Cys motif on helix 1 are extensively sampled in the phase space of apo-golB. Hybrid QM/MM calculations on metal-bound structures of golB also allowed to characterize the most probable protonation state for gold binding motif and to assess the structural features mostly influencing the Au(I) coordination in this protein. Consistently with experimental evidence, we found that golB may control its Au(I) affinity by conformational changes that affect the distance between Cys10 and Cys13, thus being able to switch between the Au(I) sequestration/release-prone states in response to external stimuli. The protein structure enveloping the metal binding motif favors the thiol-thiolate protonation state of Au(I)-golB, thus probably enhancing the binding selectivity for Au(I) compared to other cations.

Insights into the Mechanisms of Aquaporin-3 Inhibition by Gold(III) Complexes: the Importance of Non-Coordinative Adduct Formation.

Following our recent reports on the inhibition of the water and glycerol channel aquaglyceroporin-3 (AQP3) by the coordination complex [AuIII(1,10-phenanthroline)Cl2] (Auphen), a series of six new Au(III) complexes featuring substituted 1,10-phenanthroline ligands (1-6) have been synthesized and characterized. The speciation of the compounds studied in buffered solution by UV-visible spectrophotometry showed that most of the complexes remain stable for several hours. Quantum mechanics (QM) studies of the hydrolysis processes of the compounds suggest that they are thermodynamically less prone to exchange the chlorido ligands with H2O or OH- in comparison to Au(III) bipyridyl complexes. Preliminary data on the antiproliferative activity against A549 human lung cancer cells indicate that the compounds are able to inhibit cell proliferation in vitro. Stopped-flow spectroscopy showed that these complexes potently inhibit glycerol permeation in human red blood cells (hRBC) through AQP3 blockage. The QM investigation of the ligand exchange with methanethiol, used as a model of Cys40 of AQP3, was carried out for some derivatives and showed that the affinity of the compounds' binding for thiols is higher in comparison to the Aubipy complex ([AuIII(bipy)Cl2]PF6, bipy = 2,2'-bipyridine). In addition, both noncovalent and coordinative binding of complex 3 ( [AuIII(5-chloro-1,10-phenanthroline)Cl2]PF6) to the protein channel has been investigated in comparison to the benchmark Auphen and Aubipy using a computational workflow, including QM, molecular dynamics (MD), and quantum mechanics/molecular mechanics (QM/MM) approaches. Finally, atoms in molecules (AIM) and natural bond orbital (NBO) analyses corroborate the MD predictions, providing quantification of the noncoordinative interactions between the compounds and AQP3. AQP3 inhibition is the result of protein conformational changes, upon coordinative gold binding, which induce pore closure. The importance of noncoordinative adducts in modulating the AQP3 inhibition properties of the investigated Au(III) compounds has been elucidated, and these interactions should be further considered in the future design of isoform-selective AQP inhibitors.

Reactivity of Gold(I) Monocarbene Complexes with Protein Targets: A Theoretical Study.

Neutral N⁻heterocyclic carbene gold(I) compounds such as IMeAuCl are widely used both in homogeneous catalysis and, more recently, in medicinal chemistry as promising antitumor agents. In order to shed light on their reactivity with protein side chains, we have carried out density functional theory (DFT) calculations on the thermodynamics and kinetics of their reactions with water and various nucleophiles as a model of plausible protein binding sites such as arginine, aspartic acid, asparagine, cysteine, glutamic acid, glutamine, histidine, lysine, methionine, selenocysteine, and the N-terminal group. In agreement with recent experimental data, our results suggest that IMeAuCl easily interacts with all considered biological targets before being hydrated-unless sterically prevented-and allows the establishment of an order of thermodynamic stability and of kinetic reactivity for its binding to protein residues.

Insight into the Electrochemical Reduction Mechanism of Pt(IV) Anticancer Complexes.

We carried out a theoretical study on the mechanism of electrochemical reduction of the prototypical platinum(IV) anticancer complex [Pt(NH3)2(CH3COO)2Cl2] to the corresponding platinum(II) [Pt(NH3)2Cl2] derivative. Energies and geometric structures of the original Pt(IV) complex and all possible Pt(III) and Pt(II) intermediates and transition states involved in the reduction process have been calculated using density functional theory and Møller-Plesset perturbation theory. This study allowed us to formulate a detailed mechanism for the two-electron reduction of the [PtIV(NH3)2(CH3COO)2Cl2] complex. The results show that, in agreement with the experimental evidence from cyclic voltammetry, the initial one-electron reduction of the [PtIV(NH3)2(CH3COO)2Cl2] complex occurs through a stepwise mechanism via a metastable hexacoordinated platinum(III) [PtIII(NH3)2(CH3COO)2Cl2]- intermediate and a subsequent acetate ligand detachment with an activation free energy of 5.1 kcal mol-1. On the other hand, the second electron reduction of the resulting pentacoordinated [PtIII(NH3)2(CH3COO)Cl2] species occurs through a barrierless concerted process to the final [PtII(NH3)2Cl2] derivative.

A Multi-Level Theoretical Study to Disclose the Binding Mechanisms of Gold(III)-Bipyridyl Compounds as Selective Aquaglyceroporin Inhibitors.

Structural studies have paved the avenue to a deeper understanding of aquaporins (AQPs), small ancient proteins providing efficient transmembrane pathways for water, small uncharged solutes such as glycerol, and possibly gas molecules. Despite the numerous studies, their roles in health and disease remain to be fully disclosed. The recent discovery of AuIII complexes as potent and selective inhibitors of aquaglyceroporin isoforms paves the way to their possible therapeutic application. The binding of the selective human AQP3 inhibitor, the cationic complex [Au(bipy)Cl2 ]+ (Aubipy), to the protein channel has been investigated here by means of a multi-level theoretical workflow that includes QM, MD and QM/MM approaches. The hydroxo complex was identified as the prevalent form of Aubipy in physiological media and its binding to AQP3 studied by MD. Both non-covalent and coordinative Aubipy-AQP3 adducts were simulated to probe their role in the modulation of water channel functionality. The electronic structures of representative Aubipy-AQP3 adducts were then analysed to unveil the role played by the metal moiety in their stabilisation. This study spotlights the overall importance of three key aspects for AQP3 inhibition: 1) water speciation of the AuIII complex, 2) stability of non-covalent adducts and 3) conformational changes induced within the pore by the coordinative binding of AuIII . The obtained results are expected to orient future developments in the design of isoform-selective AuIII inhibitors.

Cisplatin Primary Complex with l-Histidine Target Revealed by IR Multiple Photon Dissociation (IRMPD) Spectroscopy.

The primary complex obtained from cisplatin and l-histidine in water has been detected and isolated by electrospray ionization. The so-obtained cis-[PtCl(NH3 )2 (histidine)]+ complex has been characterized in detail by high-resolution mass spectrometry (MS), tandem MS, IR multiple photon dissociation (IRMPD) spectroscopy, and by quantum chemical calculations. The structural features revealed by IRMPD spectroscopy indicate that platinum binds to the imidazole group, which presents tautomeric forms. Thus, depending on the position of the amino acid pendant on the imidazole ring, isomeric complexes are formed that are remarkably different with respect to the ease with which they undergo fragmentation when activated either by energetic collisions or by multiple IR photon absorption. It is shown here how IRMPD kinetics can allow their relative proportions to be estimated.

Circular and Chainlike Copper(II)-Lanthanide(III) Complexes Generated by Assembly Reactions of Racemic and Chiral Copper(II) Cross-Linking Ligand Complexes with LnIII(NO3)3·6H2O (LnIII = GdIII, TbIII, DyIII).

The 1:1 assembly reaction of the racemic form of the cross-linking ligand complex Na[CuIILdpen(1R2R/1S2S)] with LnIII(NO3)3·6H2O gave the centrosymmetric circular (CuIILnIII)2 complex [CuIILdpen(1R2R/1S2S)LnIII(NO3)2]2 (1Ln: Ln = Gd, Tb, Dy), while the reaction of the enantiopure form Na[CuIILdpen(1R2R)] with LnIII(NO3)3·6H2O gave the chiral chainlike (CuIILnIII)1∞ complex [CuIILdpen(1R2R)LnIII(NO3)2(CH3CN)]1∞·CH3CN (2Ln: Ln = Gd, Tb, Dy), where {CuIILdpen(1R2R)}- is (N-((1R,2R)-2-(((E)-3-ethoxy-2-oxybenzylidene)amino)-1,2-diphenylethyl)-2-oxybenzamide)copper(II) and {CuIILdpen(1R2R/1S2S)}- is the racemic mixture of {CuIILdpen(1R2R)}- and {CuIILdpen(1S2S)}-. The copper(II) component functions as a cross-linking ligand complex and bridges two LnIII ions at two phenoxo oxygen atoms and one ethoxy oxygen atom, as well as at an amido oxygen atom. For 1Ln, two binuclear species of [CuIILdpen(1R2R)LnIII(NO3)2] and [CuIILdpen(1S2S)LnIII(NO3)2] with opposite chiralities are linked by two amido oxygen atoms O3 and O3* to form a centrosymmetric circular structure with Gd-Cu = 3.370(1) Å and Gd-Cu* = 5.627(1) Å. For 2Ln, binuclear species with the same chirality are bridged by Gd-O3* = 2.228(5) Å to form a chiral chainlike structure with Gd-Cu = 3.3348(9) Å and Gd-Cu* = 6.2326(9) Å. The bridged angles through the amido group of Gd-O3*═C7* are 133.9(5) and 177.6(4)° for 1Gd and 2Gd, respectively. The magnetic susceptibilities of 1Gd and 2Gd were analyzed by the spin-only Hamiltonian on the basis of the circular tetranuclear (-CuIIGdIII-)2 and linear chainlike (-CuIIGdIII-)1∞ structures, respectively. The CuII-GdIII magnetic interactions through two phenoxo bridges and a three-atom N-C═O bridge, J1 and J2, are both ferromagnetic to be J1 = +4.6 cm-1 and J2 = +1.8 cm-1 for 1Gd and J1 = +4.2 cm-1 and J2 = +0.037 cm-1 for 2Gd. The J2 value of 2Gd is much smaller than that of 1Gd. When the temperature was lowered, 1Ln and 2Ln (Ln = Tb, Dy) showed a decrease in the χMT vs T plot due to crystal field effects on the LnIII ion (Stark splitting) and an increase due to the ferromagnetic CuII-LnIII interaction. The magnetization values of 1Ln and 2Ln (Ln = Tb, Dy) without liquid paraffin are considerably larger than the corresponding values with liquid paraffin, indicating the presence of strong magnetic anisotropy. 1Tb and 1Dy showed frequency dependence of ac magnetic susceptibility under zero external dc magnetic field, showing the behavior of single-molecule magnets (SMMs). 2Tb and 2Dy showed no frequency dependence under a zero external magnetic field but showed a meaningful frequency dependence under an external magnetic field. Their energy barriers, Δ/kB, estimated by the Arrhenius plots are 29.4(6) and 20.6(3) K for 1Tb and 2Tb under dc bias fields of 0 and 1000 Oe, respectively, and those of 1Dy and 2Dy are 13.1(9) K and 16.4(2) K under dc bias fields of 0 and 1000 Oe, respectively.

Cisplatin and transplatin interaction with methionine: bonding motifs assayed by vibrational spectroscopy in the isolated ionic complexes.

Cisplatin and transplatin (cis- and trans-[PtCl2(NH3)2]) have been allowed to react with methionine (Met) in water solution in a study aimed to characterize the monofunctional complex primarily formed. The thioether function of methionine is known to have a very high affinity for square planar platinum(ii) and sulfur-containing biomolecules have been proposed as a cisplatin drug reservoir on the way to platination at DNA. Both cisplatin and transplatin yield [PtCl(NH3)2Met]+ complexes, delivered by electrospray ionization in the gas phase and sampled as isolated species using tools based on mass spectrometry. The collision induced dissociation spectra of both cis-[PtCl(NH3)2Met]+ and trans-[PtCl(NH3)2Met]+ are quite similar and also the transport properties assayed by ion mobility mass spectrometry do not allow any appreciable discrimination. However, the vibrational spectra obtained by IR multiple photon absorption (IRMPD) spectroscopy show distinct features. Their analysis, supported by quantum chemical calculations, has revealed that while cisplatin attack is mainly directed to the sulfur atom of Met, transplatin shows a more balanced partition between sulfur and nitrogen binding. Among the vibrational signatures characterizing cis-[PtCl(NH3)2Met]+ and trans-[PtCl(NH3)2Met]+ complexes, the asymmetric NH2 stretching of the α-amino group of the amino acid at ca. 3440 cm-1 is peculiar and diagnostic of S-platination. IRMPD kinetics evaluated at this frequency support the prevailing S-attack by cisplatin while approximately a 1 : 2 ratio of S- versus N-coordination is observed by transplatin, to be possibly related to the trans effect at the platinum center.

Cisplatin Binding to Biological Ligands Revealed at the Encounter Complex Level by IR Action Spectroscopy.

Cisplatin [cis-diamminedichloroplatinum(II)] was the first platinum-based antineoplastic agent and is still a cornerstone for the treatment of various solid tumors. Reactive events responsible for cisplatin activity are unveiled here at the molecular level. Simple ligands (L) representing ubiquitous functional groups in the biological environment likely to be encountered by administered cisplatin have been allowed to react with cis-[PtCl(NH3)2 (H2O)](+), the primary intermediate from cisplatin hydrolysis. The substitution reactions have been examined by a combined experimental and computational approach and the structural features of the substitution product, cis-[PtCl(NH3)2(L)](+), have been probed by IR multiple-photon dissociation (IRMPD) spectroscopy. Furthermore, IRMPD spectroscopy has been exploited to elucidate the structure of [PtCl(NH3)2(L)(H2O)](+) clusters, also obtained by electrospray ionization (ESI) from the aqueous solution and representing the major focus of this investigation. These ions conform to the encounter complex of cis-[PtCl(NH3)2 (H2O)](+) with the incoming ligand and represent the first direct evidence of a prototypical Eigen-Wilkins encounter complex in solution, lying on the reaction coordinate for ligand substitution and extracted by ESI for mass spectrometric analysis. Activated [PtCl(NH3)2(L)(H2O)](+) ions dissociate by the loss of either H2O or L, the former process implying a ligand substitution event. IRMPD spectroscopy has thus revealed both structural details and reaction dynamics at the level of the isolated encounter complex.

Activation and Reactivity of a Bispidine Analogue of Cisplatin: A Theoretical Investigation.

The reactivity of a bispidine, 3,7-diazabicyclo[3.3.1]nonane, analogue of cisplatin, a new anticancer drug with promising properties, is theoretically investigated to clarify the in vitro reactivity and in vivo mechanism of action of this compound. Thermodynamics and kinetics of the first and second aquation steps and of the reaction of the generated mono- and diaqua species with guanine, the main target of the platinum based antitumor compounds, have been studied. In agreement with the experimental evidence, the bispidine analogue is significantly less reactive than cisplatin toward aquation but the formed aquaspecies show a good reactivity with guanine, consistently with the promising anticancer properties of these new compounds.

Investigation of the molecular similarity in closely related protein systems: The PrP case study.

The amyloid conversion is a massive detrimental modification affecting several proteins upon specific physical or chemical stimuli characterizing a plethora of diseases. In many cases, the amyloidogenic stimuli induce specific structural features to the protein conferring the propensity to misfold and form amyloid deposits. The investigation of mutants, structurally similar to their native isoform but inherently prone to amyloid conversion, may be a viable strategy to elucidate the structural features connected with amyloidogenesis. In this article, we present a computational protocol based on the combination of molecular dynamics (MD) and grid-based approaches suited for the pairwise comparison of closely related protein structures. This method was applied on the cellular prion protein (PrP(C)) as a case study and, in particular, addressed to the quali/quantification of the structural features conferred by either E200K mutations and treatment with CaCl(2), both able to induce the scrapie conversion of PrP. Several schemes of comparison were developed and applied to this case study, and made up suitable of application to other protein systems. At this purpose an in-house python codes has been implemented that, together with the parallelization of the GRID force fields program, will spread the applicability of the proposed computational procedure.

Sulfur-Assisted Phenyl Migration from Phosphorus to Platinum in PtW2 and PtMo2 Clusters Containing Thioether-Functionalized Short-Bite Ligands of the Bis(diphenylphosphanyl)amine-Type.

The reactivity of dichloroplatinum(II) complexes containing thioether-functionalized bis(diphenylphosphanyl)amines of formula (Ph2P)2N(CH2)2SR (R = (CH2)5CH3, CH2Ph) toward group 6 carbonylmetalates Na[M(CO)3Cp] (M = Mo or W, Cp = cyclopentadienyl) was explored. Reactions with two or more equivalents of Na[M(CO)3Cp] (M = Mo or W) afforded the trinuclear complexes of general formula [PtPh{M(CO)3Cp}{µ-P(Ph)N(CH2CH2SR)(PPh2)-κ(3)P,P,S}M(CO)2Cp] (3 M = Mo, R = (CH2)5CH3; 4 M = Mo, R = CH2Ph; 9 M = W, R = (CH2)5CH3; 10 M = W, R = CH2Ph), the structure of which consists of a six-membered platinacycle condensed with a four-membered M-P-N- P cycle, together with small amounts of isomeric PtM2 clusters [PtM2(CO)5Cp2{(Ph2P)2N(CH2CH2SR)-κ(2)P,P}] (5 M = Mo, R = (CH2)5CH3; 6 M = Mo, R = CH2Ph; 11 M = W, R = (CH2)5CH3; 12 M = W, R = CH2Ph) in which the ligand (Ph2P)2NR solely chelates the Pt atom or bridges an M-Pt bond as in [PtM2(CO)5Cp2{µ-(Ph2P)2N(CH2CH2SR)-κ(2)P,P}] (7 M = Mo, R = (CH2)5CH3; 8 M = Mo, R = CH2Ph; 13 M = W, R = (CH2)5CH3; 14 M = W, R = CH2Ph). The synthesis of the trinuclear complexes 3, 4, 9, and 10 entails an unexpected P-phenyl bond cleavage reaction and phenyl migration onto Pt. When only 1 equiv of Na[M(CO)3Cp] (M = Mo or W) was used, the heterodinuclear products of monosubstitution [PtCl{M(CO)3Cp}{Ph2PN(R)PPh2-P,P}] (15 M = Mo, R = (CH2)5CH3; 16 M = Mo, R = CH2Ph; 17 M = W, R = (CH2)5CH3; 18 M = W, R = CH2Ph) were obtained, which are the precursors to the bicyclic products 3, 4, 9, and 10, respectively. Density functional calculations were performed to study the thermodynamics of the formation of all the new complexes, to evaluate the relative stabilities of the isomeric chelated and bridged forms, and to trace the mechanism of formation of the phosphanido-bridged products 3, 4, 9, and 10. It was concluded that Pt(II) complexes containing a thioether-functionalized short-bite ligand, [PtCl2{Ph2PN(R)PPh2}], react with Na[M(CO)3Cp] to yield first heterodinuclear Pt-M and then heterotrinuclear PtM2 complexes resulting from the activation of a P-C bond in one of the PPh2 groups and phenyl migration to Pt. The critical role of an intramolecular thioether group was demonstrated.

TiCl4-promoted condensation of methyl acetoacetate, isobutyraldehyde, and indole: a theoretical and experimental study.

The mechanism of the TiCl4-promoted condensation of methyl acetoacetate, isobutyraldehyde, and indole was studied by a combination of theoretical and experimental techniques. The energy profile of plausible reaction paths was evaluated by DFT calculations, and various reaction intermediates were isolated or observed in solution by NMR spectroscopy. Theoretical and experimental results indicate that the reaction proceeds in three steps, all promoted by titanium: (1) formation of the enolate ion of methyl acetoacetate, (2) Knoevenagel condensation of the enolate ion and aldehyde, and (3) Michael addition of indole to the Knoevenagel adduct. The study sheds light on the role of titanium in the reaction, providing a mechanistic model for analogous reactions.