Controlling platinum, ruthenium, and osmium reactivity for anticancer drug design

The main task of the medicinal chemist is to design molecules that interact specifically with derailed or degenerating processes in a diseased organism, translating the available knowledge of pathobiochemical and physiological data into chemically useful information and structures. Current knowledge of the biological and chemical processes underlying diseases is vast and rapidly expanding. In particular the unraveling of the genome in combination with, for instance, the rapid development of structural biology has led to an explosion in available information and identification of new targets for chemotherapy. The task of translating this wealth of data into active and selective new drugs is an enormous, but realistic, challenge. It requires knowledge from many different fields, including molecular biology, chemistry, pharmacology, physiology, and medicine and as such requires a truly interdisciplinary approach. Ultimately, the goal is to design molecules that satisfy all the requirements for a candidate drug to function therapeutically. Therapeutic activity can then be achieved by an understanding of and control over structure and reactivity of the candidate drug through molecular manipulation

Vanillic acid and methoxyhydroquinone production from guaiacyl units and related aromatic compounds using Aspergillus niger cell factories

Background The aromatic compounds vanillin and vanillic acid are important fragrances used in the food, beverage, cosmetic and pharmaceutical industries. Currently, most aromatic compounds used in products are chemically synthesized, while only a small percentage is extracted from natural sources. The metabolism of vanillin and vanillic acid has been studied for decades in microorganisms and many studies have been conducted that showed that both can be produced from ferulic acid using bacteria. In contrast, the degradation of vanillin and vanillic acid by fungi is poorly studied and no genes involved in this metabolic pathway have been identified. In this study, we aimed to clarify this metabolic pathway in Aspergillus niger and identify the genes involved. Results Using whole-genome transcriptome data, four genes involved in vanillin and vanillic acid metabolism were identified. These include vanillin dehydrogenase (vdhA), vanillic acid hydroxylase (vhyA), and two genes encoding novel enzymes, which function as methoxyhydroquinone 1,2-dioxygenase (mhdA) and 4-oxo-monomethyl adipate esterase (omeA). Deletion of these genes in A. niger confirmed their role in aromatic metabolism and the enzymatic activities of these enzymes were verified. In addition, we demonstrated that mhdA and vhyA deletion mutants can be used as fungal cell factories for the accumulation of vanillic acid and methoxyhydroquinone from guaiacyl lignin units and related aromatic compounds. Conclusions This study provides new insights into the fungal aromatic metabolic pathways involved in the degradation of guaiacyl units and related aromatic compounds. The identification of the involved genes unlocks new potential for engineering aromatic compound-producing fungal cell factories.Peer reviewe

Deactivation and regeneration of solid acid and base catalyst bodies used in cascade for bio-oil synthesis and upgrading

The modes of deactivation -and the extent to which their properties can be restored- of two catalyst bodies used in cascade for bio-oil synthesis have been studied. These catalysts include a solid acid granulate (namely ZrO2/desilicated zeolite ZSM-5/attapulgite clay) employed in ex-situ catalytic fast pyrolysis of biomass, and a base extrudate (K-exchanged zeolite USY/attapulgite clay) for the subsequent bio-oil upgrading. Post-mortem analyses of both catalyst bodies with Raman spectroscopy and confocal fluorescence microscopy revealed the presence of highly poly-aromatic coke distributed in an egg-shell manner. Deactivation due to coke adsorption onto acid sites affected the zeolite ZSM-5-based catalyst, while for the base catalyst it is structural integrity loss, resulting from KOH-mediated zeolite framework collapse, the main deactivating factor. A hydrothermal regeneration process reversed the detrimental effects of coke in the acid catalyst, largely recovering catalyst acidity (∼80%) and textural properties (∼90%), but worsened the structural damage suffered by the base catalyst

Hydrogenation of levulinic acid to gamma-valerolactone over anatase-supported Ru catalysts:Effect of catalyst synthesis protocols on activity

γ-Valerolactone (GVL) is a value-added renewable chemical with great potential and can be obtained from biomass by the hydrogenation of levulinic acid (LA) using metal-based catalysts, such as Ru/TiO2. We here report an in depth study of the effect of catalyst synthesis parameters on the performance of Ru/TiO2 (anatase), varying the nature of the Ru-precursor and the conditions of the calcination and/or reduction step. Catalyst performance was evaluated under batch conditions at a hydrogen pressure of 45 bar and using either water (90 °C) or dioxane (150 °C) as solvent. The experiments showed that catalyst activity depends greatly on the Ru precursor used (RuCl3, RuNO(NO3)3, Ru(NH3)6Cl3). Best results when considering the turn-over frequencies (TOF) of the catalysts were obtained using the RuNO(NO3)3 precursor, whereas RuCl3 performed better when considering the initial rate based on Ru intake. An intermediate calcination step and the use of a hydrogen-rich sweep gas during the final reduction step were shown to have a negative impact on catalyst activity. Characterization of the fresh catalysts by BET and TEM provided valuable insight in the relation between the catalyst structure and its activity

Catalytic Hydrogenation of Renewable Levulinic Acid to γ-Valerolactone:Insights into the Influence of Feed Impurities on Catalyst Performance in Batch and Flow Reactors

γ-Valerolactone (GVL) is readily obtained by the hydrogenation of levulinic acid (LA) and is considered a sustainable platform chemical for the production of biobased chemicals. Herein, the performance and stability of Ru-based catalysts (1 wt % Ru) supported on TiO2 (P25) and ZrO2 (monoclinic) for LA hydrogenation to GVL is investigated in the liquid phase in batch and continuous-flow reactors using water and dioxane as solvents. Particular attention is paid to the influence of possible impurities in the LA feed on catalyst performance for LA hydrogenation. Benchmark continuous-flow experiments at extended times on-stream showed that the deactivation profiles are distinctly different for both solvents. In dioxane, the Ru/ZrO2 catalyst is clearly more stable than Ru/TiO2, whereas the latter is slightly more stable in water. Detailed characterization studies on spent catalysts after long run times showed that the deactivation of Ru/TiO2 is strongly linked to the reduction of a significant amount of Ti4+ species of the support to Ti3+ and a decrease in the specific surface area of the support in comparison to the fresh catalyst. Ru/ZrO2 showed no signs of support reduction and displayed morphological and structural stability; however, some deposition of carbonaceous material is observed. Impurities in the LA feed such as HCOOH, H2SO4, furfural (FFR), 5-hydroxymethylfurfural (HMF), humins, and sulfur-containing amino acids impacted the catalyst performance differently. The results reveal a rapid yet reversible loss of activity for both catalysts upon HCOOH addition to LA, attributed to its preferential adsorption on Ru sites and possible CO poisoning. A more gradual drop in activity is found when cofeeding HMF, FFR, and humins for both solvents. The presence of H2SO4, cysteine, and methionine all resulted in the irreversible deactivation of the Ru catalysts. The results obtained provide new insights into the (ir)reversible (in)sensitivity of Ru-based hydrogenation catalysts to potential impurities in LA feeds, which is essential knowledge for next-generation catalyst development

Improved catalytic activity of ruthenium–arene complexes in the reduction of NAD+

A series of neutral Ru-II half-sandwich complexes of the type [(eta(6)-arene)Ru(N,N')Cl] where the arene is para-cymene (p-cym), hexamethylbenzene (hmb), biphenyl (bip), or benzene (bn) and N,N' is N-(2-aminoethyl) -4-(trifluoromethyl)benzenesulfonamide (TfEn), N-(2-aminoethyl)-4-toluenesulfonamide (TsEn), or N-(2-aminoethyl)-methylenesulfonamide (MsEn) were synthesized and characterized. X-ray crystal structures of [(p-cym)Ru(MsEn)Cl] (1), [(hmb)Ru(TsEn)Cl] (5), [(hmb)Ru(TfEn)Cl] (6), [(bip)Ru(MsEn)Cl] (7), and [(bip)Ru(TsEn)Cl] (8) have been determined. The complexes can regioselectively catalyze the transfer hydrogenation of NAD(+) to give 1,4-NADH in the presence of formate. The turnover frequencies (TOF) when the arene is varied decrease in the order bn > bip > p-cym > hmb for complexes with the same N,N' chelating ligand. The TOF decreased with variation in the N,N' chelating ligand in the order TfEn > TsEn > MsEn for a given arene. [(bn)Ru(TfEn)Cl] (12) was the most active, with a TOP of 10.4 h(-1). The effects of NAD(+) and formate concentration on the reaction rates were determined for [(p-cym)Ru(TsEn)Cl] (2). Isotope studies implicated the formation of [(arene)Ru(N,N')(H)] as the rate-limiting step. The coordination of formate and subsequent CO2 elimination to generate the hydride were modeled computationally by density functional theory (DFT). CO2 elimination occurs via a two-step process with the coordinated formate first twisting to present its hydrogen toward the metal center. The computed barriers for CO2 release for arene = benzene follow the order MsEn > TsEn > TfEn, and for the Ms En system the barrier followed bn < hmb, both consistent with the observed rates. The effect of methanol on transfer hydrogenation rates in aqueous solution was investigated. A study of pH dependence of the reaction in D2O gave the optimum pH* as 7.2 with a TOF of 1.58 h(-1) for 2. The series of compounds reported here show an improvement in the catalytic activity by an order of magnitude compared to the ethylenediamine analogues

Conjugation of Organoruthenium(II) 3-(1H-Benzimidazol-2-yl)pyrazolo[3,4-b]pyridines and Indolo[3,2-d]benzazepines to Recombinant Human Serum Albumin: a Strategy To Enhance Cytotoxicity in Cancer Cells

Five organoruthenium complexes [RuCl(η6-arene)(L)]Cl with a modified arene ligand, namely, 4-formylphenoxyacetyl-η6-benzylamide, and L = 3-(1H-benzimidazol-2-yl)-1H-pyrazolo[3,4-b]pyridines or indolo[3,2-d]benzazepines were synthesized and conjugated to recombinant human serum albumin in order to improve their drug targeting and delivery to cancer cells, and a marked increase in cytotoxicity was observed

Dichomitus squalens partially tailors its molecular responses to the composition of solid wood

White-rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed-wood forests containing both soft- and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood [guaiacyl (G) lignin and higher mannan content] and hardwood [syringyl/guaiacyl (S/G) lignin and higher xylan content] using semi-natural solid cultures. Spruce (softwood) and birch (hardwood) sticks were degraded by D. squalens as measured by oxidation of the lignins using 2D-NMR. The fungal response as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition. Mannanolytic transcripts and proteins were more abundant in spruce cultures, while a proportionally higher xylanolytic activity was detected in birch cultures. Both wood types induced manganese peroxidases to a much higher level than laccases, but higher transcript and protein levels of the manganese peroxidases were observed on the G-lignin rich spruce. Overall, the molecular responses demonstrated a stronger adaptation to the spruce rather than birch composition, possibly because D. squalens is mainly found degrading softwoods in nature, which supports the ability of the solid wood cultures to reflect the natural environment.Peer reviewe

Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways

The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential cleavage pathways and resulting fragments that are formed during depolymerization of lignin oligomers containing two to six monomers. We have developed a chemical discovery technique to identify the chemically relevant putative fragments in eight known polymeric linkage types of lignin. Obtaining these structures is a crucial precursor to the development of any further kinetic modeling. We have developed this approach by adapting steered molecular dynamics calculations under constant force and varying the points of applied force in the molecule to diversify the screening approach. Key observations include relationships between abundance and breaking frequency, the relative diversity of potential pathways for a given linkage, and the observation that readily cleaved bonds can destabilize adjacent bonds, causing subsequent automatic cleavage.Massachusetts Institute of Technology (Research Support Corporation, Reed Grant)United States. Dept. of Energy. Computational Science Graduate Fellowship Program (DOE-CSGF)Burroughs Wellcome Fund (Career Award at the Scientific Interface