Designing organometallic compounds for catalysis and therapy

Bioorganometallic chemistry is a rapidly developing area of research. In recent years organometallic compounds have provided a rich platform for the design of effective catalysts, e.g. for olefin metathesis and transfer hydrogenation. Electronic and steric effects are used to control both the thermodynamics and kinetics of ligand substitution and redox reactions of metal ions, especially Ru II. Can similar features be incorporated into the design of targeted organometallic drugs? Such complexes offer potential for novel mechanisms of drug action through incorporation of outer-sphere recognition of targets and controlled activation features based on ligand substitution as well as metal- and ligand-based redox processes. We focus here on η 6-arene, η 5-cyclopentadienyl sandwich and half-sandwich complexes of Fe II, Ru II, Os II and Ir III with promising activity towards cancer, malaria, and other conditions. © 2012 The Royal Society of Chemistry

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

Altres ajuts: COST Action CM1306Decoding 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 metalloligands with multiple vacant sites and different geometries. The study first presents a benchmark of 25 well-characterized X-ray metalloligand-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 IV O 2+ ion, to carboxypeptidase; (iii) the antiarthritic species [Au I (PEt 3 )] + 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-metalloligand docking, which could have a wide field of application, from biology and inorganic biochemistry to medicinal chemistry and pharmacology

The development of RAPTA compounds for the treatment of tumors

© 2015 Elsevier B.V. Ruthenium(II)-arene RAPTA-type compounds have been extensively explored for their medicinal properties. Herein a comprehensive review of this class of compounds is provided. A discussion of the basic RAPTA structure is given together with the ways it has been modified to elucidate the key role of each part and to afford targeted derivatives. The various mechanistic studies conducted on RAPTA compounds are described and these are linked to the observed macroscopic biological properties. Ultimately, the review shows that certain RAPTA compounds display quite unique properties that point towards a clinical investigation

An evaluation of indirubin analogues as phosphorylase kinase inhibitors

Phosphorylase kinase (PhK) has been linked with a number of conditions such as glycogen storage diseases, psoriasis, type 2 diabetes and more recently, cancer (Camus S. et al., Oncogene 2012, 31, 4333). However, with few reported structural studies on PhK inhibitors, this hinders a structure based drug design approach. In this study, the inhibitory potential of 38 indirubin analogues have been investigated. 11 of these ligands had IC50 values in the range 0.170 – 0.360 µM, with indirubin-3’-acetoxime (1c) the most potent. 7-bromoindirubin-3’-oxime (13b), an antitumor compound which induces caspase-independent cell-death (Ribas J. et al., Oncogene, 2006, 25, 6304) is revealed as a specific inhibitor of PhK (IC50 = 1.8 µM). Binding assay experiments performed using both PhK-holo and PhK-γtrnc confirmed the inhibitory effects to arise from binding at the kinase domain (γ subunit). High level computations using QM/MM-PBSA binding free energy calculations were in good agreement with experimental binding data, as determined using statistical analysis, and support binding at the ATP-binding site. The value of a QM description for the binding of halogenated ligands exhibiting -hole effects is highlighted. A new statistical metric, the ‘sum of the modified logarithm of ranks’ (SMLR), has been defined which measures performance of a model for both the “early recognition” (ranking earlier/higher) of active compounds and their relative ordering by potency. Through a detailed structure activity relationship analysis considering other kinases (CDK2, CDK5 and GSK-3α/β), 6’(Z) and 7(L) indirubin substitutions have been identified to achieve selective PhK inhibition. The key PhK binding site residues involved can also be targeted using other ligand scaffolds in future work

Iminophosphoranes As Useful Precursors To Potential Transition Metal-Based Cancer Chemotherapeutics

During the past two decades, gold(III), platinum(II), palladium(II) and ruthenium(II) compounds have been investigated as potential anticancer drugs. Our group at Brooklyn College reported on the cytotoxic properties of neutral and cationic gold(III), palladium(II) and platinum(II) complexes with iminophosphoranes (IM) or iminophosphine ligands of the general formula R3P=NR\u27. These IM ligands have been very useful to synthesize and stabilize compounds of d8 transition metals which displayed higher toxicity against leukemia, prostate cancer and ovarian cancer cells when compared to normal T-lymphocytes. They also seemed to have a mode of action different from that of cisplatin. This thesis describes the synthesis of coordination and organometallic, gold(III), platinum(II), palladium(II) and ruthenium(II) complexes with different iminophosphorane ligands, the study of their stability in solution by different techniques and of their interaction with biological targets (mostly DNA and HSA). I have also included data on the biological activity of these compounds (in vitro and for selected complexes in vivo) to understand their potential as cancer chemotherapeutics. Most of these compounds have displayed excellent anticancer properties by a mode of action different from that currently accepted for cisplatin and, in some cases, have displayed a lower toxicity, better activity or better permeability in vivo. These results are described in three different chapters as summarized below. In Chapter III, I describe the synthesis and characterization of a series of coordination gold(III), palladium(II), and platinum(II) complexes with a luminescent IM ligand derived from 8-aminoquinoline [Ph3P=N-C9H6N]. The coordination palladium(II) and platinum(II) compounds can evolve further, under appropriate conditions, to give stable cyclometalated endo species [Mκ3-C,N,N-C6H4(PPh2=N-8-C9H6N}Cl] (M = Pd, Pt) by C-H activation of the phenyl group of the PPh3 fragment. The compounds have been evaluated for their antiproliferative properties in a human ovarian cancer cell line (A2780S), in human lung cancer cells (A-549) and in a non-tumorigenic human embryonic kidney cell line (HEK-293T). Most compounds have been more toxic to the ovarian cancer cell line than to the non-tumorigenic cell line. The new complexes interact with human serum albumin (HSA) faster than cisplatin. Studies of the interactions of the compounds with DNA indicate that, in some cases, they exert anticancer effects in vitro based on different mechanisms of action with respect to cisplatin. The stability of cyclometallated compounds is markedly higher than that of coordination complexes. In Chapter IV, I describe the synthesis, characterization and stability studies of new organometallic gold(III) and platinum(II) complexes containing cyclometalated IM ligands. Most compounds are more cytotoxic to a number of human cancer cell lines than cisplatin. A cationic Pt(II) derivative ([Pt{κ2-C,N-C6H4(PPh2=N(C6H5)(COD)](PF6)) displays IC50 values in the sub-micromolar range. Its cell death mechanism is mainly through caspase-dependent apoptosis but it triggers caspase-independent cell death when apoptosis is blocked. Permeability studies by two different assays: in vitro caco-2 monolayers and a rat perfusion model have revealed a high permeability profile for this compound (comparable to that of metoprolol or caffeine) and an estimated oral fraction absorbed of 100% which potentially makes it a good candidate for oral administration. Lastly in Chapter V, I describe the synthesis, characterization and stability studies of a series of organometallic ruthenium(II) complexes containing iminophosphorane ligands. These cationic compounds with chloride as counterion are highly soluble in water (70-100 mg/mL). Most compounds (especially the highly water-soluble compound- ([(η6-p-cymene)Ru{(Ph3P=N-CO-2-N-C5H4)-κ-N,O}Cl]Cl) are more cytotoxic to a number of human cancer cell lines than cisplatin. Initial mechanistic studies indicate that the cell death type for these compounds is mainly through canonical or caspase-dependent apoptosis, non-dependent on p53, and that the compounds do not interact with DNA or inhibit protease cathepsin B. In vivo experiments of ([(η6-p-cymene)Ru{(Ph3P=N-CO-2-N-C5H4)-κ-N,O}Cl]Cl) on MDA-MB-231 xenografts in NOD.CB17-Prkdc SCID/J mice showed an impressive tumor reduction (shrinkage) of 56% after 28 days of treatment (14 doses of 5 mg/kg every other day) with low systemic toxicity. Pharmacokinetic studies showed a quick absorption in plasma with preferential accumulation in the breast tumor tissues when compared to kidney and liver, which may explain its high efficacy in vivo

On the binding modes of metal NHC complexes with DNA secondary structures: implications for therapy and imaging

Organometallic compounds currently occupy an important place in the field of medicinal inorganic chemistry due to the unique chemical properties of metal coordination compounds. Particularly, metal compounds ligated by N-heterocyclic carbenes (NHC) have shown high potential for biomedical applications as antimicrobial and anticancer agents during the recent 15 years. Although further studies are necessary to validate the modes of action of this family of compounds, a number of biological targets have been identified, including DNA secondary structures. This perspective review aims at providing an overview of the most representative examples of metal NHC complexes reacting with nucleic acids via different binding modes. It is organized according to the type of DNA secondary structure targeted by metal NHCs, highlighting the possible advantages of biomedical applications, including therapy and imaging

Structural and functional analysis of cathepsin B1 from the blood fluke, Schistosoma mansoni

Schistosomóza je závažné infekční onemocnění postihující více než 200 milionů lidí v oblasti tropů a subtropů. Původcem je parazit krevnička, který žije v cévách člověka a živiny získává degradací hemoglobinu z krve hostitele působením trávicích proteas. V současnosti je k dispozici pouze jediný lék proti schistosomóze a hrozba vzniku rezistence vyvolává potřebu vývoje nových terapeutik. Katepsin B1 (SmCB1) je klíčovou trávicí proteasou krevničky střevní (Schistosoma mansoni) a představuje cílovou molekulu pro terapeutický zásah. Tato práce podává komplexní charakterizaci SmCB1 zaměřenou na vztah struktury a aktivity a na inhibiční regulaci s využitím šesti vyřešených krystalografických struktur molekulárních forem a komplexů SmCB1. SmCB1 je syntetizován ve formě neaktivního zymogenu, ve kterém N-koncový propeptid působí jako přirozený intramolekulární inhibitor blokující aktivní místo. Detailní biochemickou a strukturní analýzou byl identifikován nový unikátní mechanismus procesu aktivace zymogenu, při kterém je propeptid odštěpen, a byla popsána regulace tohoto procesu pomocí glykosaminoglykanů. Studium proteolytické aktivity SmCB1 prokázalo, že se jedná o enzym působící jako endopeptidasa i exopeptidasa a představuje tak účinný nástroj pro trávení hemoglobinu hostitele. Významná část práce se...Schistosomiasis is a serious infectious disease that afflicts over 200 million people in tropical and subtropical regions. It is caused by Schistosoma blood flukes that live in human blood vessels and obtain nutrients from host hemoglobin, which is degraded by digestive proteases. Current therapy relies on a single drug and concern over resistance necessitates new drug development. In Schistosoma mansoni, cathepsin B1 (SmCB1) is a critical digestive protease that is a target molecule for therapeutic interventions. This thesis provides a comprehensive characterization of SmCB1 focused on structure-activity relationships and inhibitory regulation based on six crystal structures solved for SmCB1 molecular forms and complexes. SmCB1 is biosynthesized as an inactive zymogen in which the N-terminal propeptide operates as a natural intra-molecular inhibitor by blocking the active site. Detailed biochemical and structural analyses have identified a new and, so far, unique mechanism of SmCB1 zymogen activation through which the propeptide is proteolytically removed and the regulatory role of glycosaminoglycans in this process has been described. A study of SmCB1 proteolytic activity has revealed that the enzyme acts in two modes, as endopeptidase and exopeptidase, which makes it an efficient tool for host...Katedra biochemieDepartment of BiochemistryPřírodovědecká fakultaFaculty of Scienc

Insight into cancer targets and ligand binding landscape using bioinformatics and integrated molecular modeling tools.

Doctoral Degree. University of KwaZulu-Natal, Durban.The alarming rate of varying types of cancer diseases in human remains a global burden requiring drastic treatment in which, a prominent method of combating it is through enzymebased drug design. Metastatic castration-resistant prostate cancer (mCRPC) and triple-negative breast cancer (TNBC) are deadly forms of prostate and breast cancers, respectively. The later cancerous growth has been linked to non-receptor tyrosine (Src/p38) kinase as a potential targeted enzyme for possible chemotherapeutic control while, mCRPC have recently been linked to retinoic acid-related orphan-receptor gamma (ROR-γ). Most studies on ROR-γ usually relate it as an orphan due to low or zero possibility to identify potential inhibitor for this receptor. Amazingly, promising inhibitors of ROR-γ and their therapeutic potential were currently identified and evaluated experimentally, among which inhibitor XY018 has appreciable bioactivity. However, molecular understanding of the conformational features of XY018-ROR-γ complex is still elusive. Herein, we provide the first account of conformation details of XY018-ROR-γ using multiple computational approaches. Comparative molecular dynamics (MD) simulation of XY018-ROR-γ and hydroxycholesterol bound ROR-γ (HC9-ROR-γ) were carried out. This was widened to binding free energy calculation (MM/GBSA), principal component analysis (PCA), root mean square fluctuation (RMSF), radius of gyration (RoG) and ligand-residue interaction network. In addition, the in silico study was optimized to predict toxicity and biological activity of the identified ligand. Findings from this study revealed that: (1) hydrophobic packing contributes significantly to binding free energy, (2) Ile136 and Leu60 exhibited high hydrogen-bond in both systems, (3) XY018-ROR-γ displayed a relatively high loop region residue fluctuation compared to ROR- γ bound to natural ligand HC9-ROR-γ, (4) electrostatic interactions are potential binding force in XY018-ROR-γ complex compared to HC9-ROR-γ, (5) XY018-ROR-γ assumes a rigid conformation which is highlighted by a decrease in residual fluctuation, (6) XY018 could potentially induce pseudoporphyria, nephritis, and interstitial nephritis but potentially safe in renal failure. In vivo examination of UM-164 as a bioactive moiety against Src/p38 kinase was recently reported in literature. This ligand is a promising lead compound for developing the first targeted therapeutic strategy against triple-negative breast cancer (TNBC). However, the conformational features of UM-164 in complex with Src remained poorly explored towards the rational design of novel Src dual inhibitor. Similar to XY018-ROR-γ investigation, a comprehensive account on the conformational features of Src-UM-164 and the influence of UM-164 binding to the Src using different computational approaches was also provided. This was carried out through MD simulation, principal component analysis (PCA), thermodynamic calculations, dynamic cross-correlation (DCCM) analysis and ligand-residue interaction network profile, as well as toxicity testing. Analysis of results from this investigation revealed that: (1) the binding of UM-164 to Src induces a more stable and compact conformation on the protein structure; (2) UM-164 binding to Src induces highly correlated motions in the protein; (3) high fluctuation exhibited by the loops in Src-UM-164 system support the experimental evidence that UM-164 binds the DFGout inactive conformation of Src; (4) a relatively high binding free energy estimated for the Src-UM-164 system is affirmative of its experimental potency; (5) hydrophobic packing contributes significantly to the drug binding in Src-UM-164; (6) a relatively high H-bond formation in Src-UM-164 indicates enhanced drug-protein interaction; (7) UM-164 is relatively less toxic than Dasatinib, therefore, is potentially safer. Furthermore, a mutant form of Src was also investigated due to its drug resistivity character. Thr91 mutation was found to induce a complete loss of protein conformation required for drug fitness in c-Src. Computational studies were carried out on this mutant enzyme in complex with UM-164 as described in Src wild-type. A notable observation from binding free energy analysis results is that, a reduction in binding affinity up to -13.416 kcal/mol was estimated for this mutated candidate compared to the wild-type-UM-164. This entire work provides an invaluable contribution to the understanding of dynamics of the orphan nuclear receptor (ROR-γ) and non-receptor tyrosine kinase (Src) which could largely contribute to the design of novel inhibitors to minimise the chances of drug resistance in castrated resistance prostate cancer and triple negative breast cancer, respectively.List of abbreviations on page xiii