Elucidation of Binding Site and Chiral Specificity of Oxidovanadium Drugs with Lysozyme through Theoretical Calculations

Experimental and Computational Studies on the Interaction of DNA with Hesperetin Schiff Base CuII Complexes

The interactions with calf thymus DNA (CT-DNA) of three Schiff bases formed by the condensation of hesperetin with benzohydrazide (HHSB or L1H3), isoniazid (HIN or L2H3), or thiosemicarbazide (HTSC or L3H3) and their CuII complexes (CuHHSB, CuHIN, and CuHTSC with the general formula [CuLnH2(AcO)]) were evaluated in aqueous solution both experimentally and theoretically. UV-Vis studies indicate that the ligands and complexes exhibit hypochromism, which suggests helical ordering in the DNA helix. The intrinsic binding constants (Kb) of the Cu compounds with CT-DNA, in the range (2.3-9.2) × 106, from CuHTSC to CuHHSB, were higher than other copper-based potential drugs, suggesting that π-π stacking interaction due to the presence of the aromatic rings favors the binding. Thiazole orange (TO) assays confirmed that ligands and Cu complexes displace TO from the DNA binding site, quenching the fluorescence emission. DFT calculations allow for an assessment of the equilibrium between [Cu(LnH2)(AcO)] and [Cu(LnH2)(H2O)]+, the tautomer that binds CuII, amido (am) and not imido (im), and the coordination mode of HTSC (O-, N, S), instead of (O-, N, NH2). The docking studies indicate that the intercalative is preferred over the minor groove binding to CT-DNA with the order [Cu(L1H2am)(AcO)] > [Cu(L2H2am)(AcO)] ≈ TO ≈ L1H3 > [Cu(L3H2am)(AcO)], in line with the experimental Kb constants, obtained from the UV-Vis spectroscopy. Moreover, dockings predict that the binding strength of [Cu(L1H2am)(AcO)] is larger than [Cu(L1H2am)(H2O)]+. Overall, the results suggest that when different enantiomers, tautomers, and donor sets are possible for a metal complex, a computational approach should be recommended to predict the type and strength of binding to DNA and, in general, to macromolecules.

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.

Do bioactive 8-hydroxyquinolines oxidovanadium(IV) and (V) complexes inhibit the growth of M. smegmatis?

The antiproliferative effects of four series of V^IVO- and V^VO-based compounds containing 8-hydroxyquinoline ligands on the bacterium Mycolicibacterium smegmatis (M. smeg) were investigated. The effects on M. smeg were compared to the antiproliferative effects on the protozoan parasite Trypanosoma cruzi (T. cruzi), the causative agent for Chagas disease. In this study, we investigate the speciation of these compounds under physiological conditions as well as the antiproliferative effects on the bacterium M. smeg. We find that the complexes are more stable the less H₂O is present, and that the stability increases in lipid-like environments. Only one heteroleptic complex and two homoleptic complexes were found to show similar antiproliferative effects on M. smeg as reported for T. cruzi so the responses generally observed by M.smeg. is less than observed by the pathogen. In summary, we find that M. smeg is more sensitive to the detailed structure of the V-complex but overall these complexes are less effective against M. smeg compared to T. cruzi.

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.

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.

Study on the cytotoxic, antimetastatic and albumin binding properties of the oxidovanadium(IV) chrysin complex. Structural elucidation by computational methodologies

We have previously synthesized and characterized the chrysin coordination complex with the oxidovanadium(IV) cation (V^IVO(chrys)₂) and characterized in ethanolic solution and in solid state. Because suitable single crystals for X-ray diffraction determinations could not be obtained, in the present work, we elucidate the geometrical parameters of this complex by computational methodologies. The optimization and vibrational investigation were carried out both in ethanolic solution and in gas phase. The computational results support the experimentally proposed geometries of the V^IVO(chrys)₂ complex, thus leading to the conclusion that the complex exists as conformers with trans-octahedral geometry in ethanolic solution and as conformers with cis-octahedral geometry in the solid state. The complex also exists as conformers with trans-octahedral geometry in aqueous media. The active species formed after dissolution in DMSO showed anticancer and antimetastatic behavior in human lung cell line A549 with moderate binding (K_aca. 10⁵ M^-1) to bovine serum albumin (BSA). The interaction through hydrogen bonding and van der Waals forces resulted in a spontaneous process. Site marker competitive experiments showed binding sites for chrysin mainly located in site II (subdomain IIIA) and in site I (subdomain IIIA) for the complex. FT-IR spectral measurements showed evidences of the alterations of protein secondary structure in the presence of chrysin and V^IVO(chrys)₂.

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.

Influence of temperature on the equilibria of oxidovanadium(IV) complexes in solution

The equilibria in the solution of three different oxidovanadium(IV) complexes, VO(dhp)₂ (dhp = 1,2-dimethyl-3-hydroxy-4(1H)-pyridinonato), VO(ma)₂ (ma = maltolato) and VO(pic)₂(H₂O) (pic = picolinato), were examined in the temperature range of 120-352 K through a combination of instrumental (EPR spectroscopy) and computational techniques (DFT methods). The results revealed that a general equilibrium exists: VOL₂ + H₂O ⇄ cis-VOL₂(H₂O) ⇄ trans-VOL₂(H₂O), where cis and trans refer to the relative position of H₂O and the oxido ligand. The equilibrium is more or less shifted to the right depending on the ligand, the temperature, the ionic strength and the coordinating properties of the solvent. With VO(dhp)₂, only the square pyramidal species exists at 298 K in aqueous solution, while at 120 K the cis- and trans-VO(dhp)₂(H₂O) species are also present. The complex of maltol exists almost exclusively in the form cis-VO(ma)₂(H₂O) in aqueous solution at 298 K, while the trans species can be revealed only at higher temperatures, where the EPR linewidth significantly decreases. The equilibria involving 1-methylimidazole (MeIm), a model for the side chain His coordination, are also influenced by temperature, with its coordination being favored by decreasing the temperature. The implications of these results in the study of the (vanadium complex)-protein systems are discussed and the interaction with myoglobin (Mb) is examined as a representative example.

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.

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) (V10O286-; 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) (Nb10O286-; 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, VIVO2+, 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 VIVO2+ 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.

Photoactive PtII and PdII complexes of N,N-diethyl-N′-3,4,5-trimethoxybenzoylthiourea: synthesis, crystal structures, DFT and cytotoxicity studies

New trans-Pd^II/Pt^II acylthiourea complexes prepared by photo-induced isomerism are found to be more cytotoxic than cis-Pd^II/Pt^II against human prostate cancer and normal embryonic kidney cell lines.

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.

The latest automated docking technologies for novel drug discovery

INTRODUCTION

Molecular docking has been consolidated as one of the most important methods in the molecular modeling field. It has been recognized as a prominent tool in the study of protein-ligand complexes, to describe intermolecular interactions, to accurately predict poses of multiple ligands, to discover novel promising bioactive compounds. Molecular docking methods have evolved in terms of their accuracy and reliability; but there are pending issues to solve for improving the connection between the docking results and the experimental evidence.

AREAS COVERED

In this article, the author reviews very recent innovative molecular docking applications with special emphasis on reverse docking, treatment of protein flexibility, the use of experimental data to guide the selection of docking poses, the application of Quantum mechanics(QM) in docking, and covalent docking.

EXPERT OPINION

There are several issues being worked on in recent years that will lead to important breakthroughs in molecular docking methods in the near future These developments are related to more efficient exploration of large datasets and receptor conformations, advances in electronic description, and the use of structural information for guiding the selection of results.

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.

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.

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.

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.

Interaction of Vanadium(IV) Species with Ubiquitin: A Combined Instrumental and Computational Approach

The interaction of V^IVO²⁺ ion and five V^IVOL₂ compounds with potential pharmacological application, where L indicates maltolate (ma), kojate (koj), acetylacetonate (acac), 1,2-dimethyl-3-hydroxy-4(1 H)-pyridinonate (dhp), and l-mimosinate (mim), with ubiquitin (Ub) was studied by EPR, ESI-MS, and computational (docking and DFT) methods. The free metal ion V^IVO²⁺ interacts with Glu, Asp, His, Thr, and Leu residues, but the most stable sites (named 1 and 2) involve the coordination of (Glu16, Glu18) and (Glu24, Asp52). In the system with V^IVOL₂ compounds, the type of binding depends on the vanadium concentration. When the concentration is in the mM range, the binding occurs with cis-VOL₂(H₂O), L = ma, koj, dhp, and mim, or with VO(acac)₂: in the first case, the equatorial coordination of His68, Glu16, Glu18, or Asp21 residues yields species with formula n[VOL₂]-Ub where n = 2-3, while with VO(acac)₂ only noncovalent surface interactions are revealed. When the concentration of V is on the order of micromolar, the mono-chelated species VOL(H₂O)₂⁺ with L = ma, koj, acac, dhp, and mim, favored by the hydrolysis, interact with Ub, and adducts with composition n[VOL]-Ub ( n = 1-2) are observed with the contemporaneous coordination of (Glu18, Asp21) or (Glu16, Glu18), and (Glu24, Asp52) or (Glu51, Asp52) donors. The results of this work suggest that the combined application of spectroscopic, spectrometric, and computational techniques allow the complete characterization of the ternary systems formed by a V compound and a model protein such as ubiquitin. The same approach can be applied, eventually changing the spectroscopic/spectrometric techniques, to study the interaction of other metal species with other proteins.

Simple Coordination Geometry Descriptors Allow to Accurately Predict Metal-Binding Sites in Proteins

With more than a third of the genome encoding for metal-containing biomolecules, the in silico prediction of how metal ions bind to proteins is crucial in chemistry, biology, and medicine. To date, algorithms for metal-binding site prediction are mainly based on sequence analysis. Those methods have reached enough quality to predict the correct region of the protein and the coordinating residues involved in metal-binding, but they do not provide three-dimensional (3D) models. On the contrary, the prediction of accurate 3D models for protein-metal adducts by structural bioinformatics and molecular modeling techniques is still a challenge. Here, we present an update of our multipurpose molecular modeling suite, GaudiMM, to locate metal-binding sites in proteins. The approach is benchmarked on 105 X-ray structures with resolution lower than 2.0 Å. Results predict the correct binding site of the metal in the biological scaffold for all the entries in the data set. Generated 3D models of the protein-metal coordination complexes reach root-mean-square deviation values under 1.0 Å between calculated and experimental structures. The whole process is purely based on finding poses that satisfy metal-derived geometrical rules without needing sequence or fine electronic inputs. Additional post-optimizations, including receptor flexibility, have been tested and suggest that more extensive searches, required when the host structures present a low level of pre-organization, are also possible. With this new update, GaudiMM is now able to look for metal-binding sites in biological scaffolds and clearly shows how explicitly considering the geometric particularities of the first coordination sphere of the metal in a docking process provides excellent results.

Hydrophobicity may enhance membrane affinity and anti-cancer effects of Schiff base vanadium(v) catecholate complexes

Anti-cancer activities of vanadium compounds have generated recent interest because of a combination of desirable properties for chemotherapy, i.e., strong cytotoxicities, anti-metastatic activities and relatively low systemic toxicities. Certain hydrophobic vanadium(v) Schiff base/catecholate compounds, which as shown herein, have increased stability in aqueous media and affinity for membrane interfaces. Depending on their hydrophobicity, they may be able to enter cells intact. In this manuscript, two hydrophobic V(v) catecholate substituted analogues, [VO(Hshed)(cat)] and [VO(Hshed)(dtb)], (Hshed = N-(salicylideneaminato)-N'-(2-hydroxyethyl)-1,2-ethanediamine, cat = pyrocatechol, and dtb = 3,5-di(tert-butyl)catechol and the vanadium(v) precursor [V(O)2(Hshed)]) were synthesized for their ability to interact with membranes and their anti-cancer effects. Using 51V and 1H NMR spectroscopy, the presence and location of the free ligand, H2shed, and the three V(v) complexes were examined in a model membrane microemulsion system. The stability of the three complexes was measured in aqueous solution, cell media and an inhomogeneous microemulsion system. Our results demonstrated that free ligand H2shed and the intact V(v) complexes associated with the interface but that the V-complexes hydrolyzed to some extent because oxovanadates were observed by 51V NMR spectroscopy and decreasing complex by absorption spectroscopy in cell media. When determining the effects of V(v) catecholate complexes on bone cancer cells, the strongest effects were observed with the more stable hydrophobic complex [VO(Hshed)(dtb)] that was able to best associate and penetrate the model membrane system intact. These studies are consistent with the membrane permeability studies being a good predictor for in vitro cytotoxicity assays because [VO(Hshed)(dtb)] can pass through the cellular membrane intact, which may enhance its anti-cancer activities.

Integrated ESI-MS/EPR/computational characterization of the binding of metal species to proteins: vanadium drug–myoglobin application

An integrated strategy based on ESI-MS spectrometry, EPR spectroscopy and docking/QM computational methods is applied to the systems formed by V^IVO²⁺ ions and four potential V^IVOL₂ drugs and myoglobin. This approach is generizable to other metals and proteins.

Effect of secondary interactions, steric hindrance and electric charge on the interaction of VIVO species with proteins

The effect of secondary interactions (hydrogen bonds and van der Waals contacts), steric hindrance and electric charge, on the binding of V^IV complexes formed by pipemidic and 8-hydroxyquinoline-5-sulphonic acids with ubiquitin and lysozyme is studied.

Validation and Applications of Protein-Ligand Docking Approaches Improved for Metalloligands with Multiple Vacant Sites

Decoding the interaction between coordination compounds and proteins is of fundamental importance in biology, pharmacy, and medicine. In this context, protein- ligand docking represents a particularly interesting asset to predict how small compounds could interact with biomolecules, but to date, very little information is available to adapt these methodologies to metal-containing ligands. Here, we assessed the predictive capability of a metal-compatible parameter set for the docking program GOLD for metallo ligands with multiple vacant sites and different geometries. The study first presents a benchmark of 25 well-characterized X-ray metallo ligand-protein adducts. In 100% of the cases, the docking solutions are superimposable to the X-ray determination, and in 92% the value of the root-mean-square deviation between the experimental and calculated structures is lower than 1.5 Å. After the validation step, we applied these methods to five case studies for the prediction of the binding of pharmacological active metal species to proteins: (i) the anticancer copper(II) complex [Cu^II(Br)(2-hydroxy-1-naphthaldehyde benzoyl hydrazine)(indazole)] to human serum albumin (HSA); (ii) one of the active species of antidiabetic and antitumor vanadium compounds, V^IVO²⁺ ion, to carboxypeptidase; (iii) the antiarthritic species [Au^I(PEt₃)]⁺ to HSA; (iv) the antitumor oxaliplatin to ubiquitin; (v) the antitumor ruthenium(II) compound RAPTA-PentaOH to cathepsin B. The calculations suggested that the binding modes are in good agreement with the partial information retrieved from spectroscopic and spectrometric analysis and allowed us, in certain cases, to propose additional hypotheses. This method is an important update in protein-metallo ligand docking, which could have a wide field of application, from biology and inorganic biochemistry to medicinal chemistry and pharmacology.

VIVO complexes with antibacterial quinolone ligands and their interaction with serum proteins

Quinolone derivatives are among the most commonly prescribed antibacterials in the world and could also attract interest as organic ligands in the design of metal complexes with potential pharmacological activity. In this study, five compounds, belonging to the first (nalidixic acid or Hnal), second (ciprofloxacin or Hcip, and norfloxacin or Hnor) and third generation (levofloxacin or Hlev, and sparfloxacin or Hspar) of quinolones, were used as ligands to bind the V^IVO²⁺ ion. In aqueous solution, mono- and bis-chelated species were formed as a function of pH, with cis-[VOH_xL₂(H₂O)]^x+ and [VOH_xL₂]^x+, x = 0-2, being the major complexes at pH 7.4. DFT calculations indicate that the most stable isomers are the octahedral OC-6-32 and the square pyramidal SPY-5-12, in equilibrium with each other. To the best of our knowledge, this is the first case that an equilibrium between a penta-coordinated square pyramidal complex and a hexa-coordinated octahedral complex is observed in solution for ligands forming six-membered chelated rings. Nalidixic acid forms the solid compound [VO(nal)₂(H₂O)], to which a cis-octahedral geometry was assigned. The interaction with 1-methylimidazole (MeIm) causes a shift of the equilibrium SPY-5 + H₂O ⇄ OC-6 toward the right after the formation of cis-[VOH_xL₂(MeIm)]^x+, where MeIm replaces an equatorial water ligand. The study of the systems containing [VO(nal)₂(H₂O)] and the serum proteins - albumin (HSA), apo-transferrin (apo-hTf) and holo-transferrin (holo-hTf) - indicates that HSA and holo-hTf form the mixed species {VO(nal)₂}_y(HSA) and {VO(nal)₂}_y(holo-hTf), where y = 1-3 denotes the number of VO(nal)₂ moieties bound to accessible histidines (His105, His367, His510 for HSA, and His25, His349, His606 for holo-hTf), whereas apo-hTf yields VO(nal)₂(apo-hTf) with the coordination of the His289 residue only. Docking calculations suggest that the specific conformation of apo-hTf and the steric hindrance of the cis-VO(nal)₂ moiety interfere with its interaction with all the surface His residues and the formation of a hydrogen bond network which could stabilize the binding sites.

Prediction of the interaction of metallic moieties with proteins: An update for protein-ligand docking techniques

In this article, we present a new approach to expand the range of application of protein-ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high-quality X-ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein-ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X-ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes-proteins interactions when the X-ray structure is not available. This work could be the first step for novel applicability of docking techniques in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most protein-ligand docking programs nowadays available. © 2017 Wiley Periodicals, Inc.