Exploring Amantadine Derivatives as Urease Inhibitors: Molecular Docking and Structure–Activity Relationship (SAR) Studies

This article describes the design and synthesis of a series of novel amantadine-thiourea conjugates (3a–j) as Jack bean urease inhibitors. The synthesized hybrids were assayed for their in vitro urease inhibition. Accordingly, N-(adamantan-1-ylcarbamothioyl)octanamide (3j) possessing a 7-carbon alkyl chain showed excellent activity with IC₅₀ value 0.0085 ± 0.0011 µM indicating that the long alkyl chain plays a vital role in enzyme inhibition. Whilst N-(adamantan-1-ylcarbamothioyl)-2-chlorobenzamide (3g) possessing a 2-chlorophenyl substitution was the next most efficient compound belonging to the aryl series with IC₅₀ value of 0.0087 ± 0.001 µM. The kinetic mechanism analyzed by Lineweaver–Burk plots revealed the non-competitive mode of inhibition for compound 3j. Moreover, in silico molecular docking against target protein (PDBID 4H9M) indicated that most of the synthesized compounds exhibit good binding affinity with protein. The compound 3j forms two hydrogen bonds with amino acid residue VAL391 having a binding distance of 1.858 Å and 2.240 Å. The interaction of 3j with amino acid residue located outside the catalytic site showed its non-competitive mode of inhibition. Based upon these results, it is anticipated that compound 3j may serve as a lead structure for the design of more potent urease inhibitors.     

Protein‐Based Capacitive Biosensors: a New Tool for Structure‐Activity Relationship Studies

The present work reports a new application of a protein‐based capacitive biosensor as an in vitro assay for the selectivity study of the bacterial periplasmic protein MerP and four MerP variants. The modified MerP proteins were produced by site‐directed mutagenesis of the heavy metal associated motif (HMA). The MerP and modified MerPs selectivity for copper, zinc, cadmium and mercury bivalent ions were investigated and compared. The variations in the proteins affinity were related to the primary structure of the HMA motifs. Key amino acids for copper coordination of metalloproteins that contain the metal binding sequence Gly‐Met‐Thr‐Cys‐xxx‐xxx‐Cys were identified. The results brought insights valid for Menkes and Wilson ATPases. The protein‐based capacitive biosensors were a simple and useful tool for studying structure‐activity relationships of proteins.     

Drug Delivery Vehicles Based on Albumin–Polymer Conjugates

Albumin has been a popular building block to create nanoparticles for drug delivery purposes. The performance of albumin as a drug carrier can be enhanced by combining protein with polymers, which allows the design of carriers to encompass a broader spectrum of drugs while features unique to synthetic polymers such as stimuli‐responsiveness are introduced. Nanoparticles based on polymer–albumin hybrids can be divided into two classes: one that carries album as a bioactive surface coating and the other that uses albumin as biocompatible, although nonbioactive, building block. Nanoparticles with bioactive albumin surface coating can either be prepared by self‐assembly of albumin–polymer conjugates or by postcoating of existing nanoparticles with albumin. Albumin has also been used as building block, either in its native or denatured form. Existing albumin nanoparticles are coated with polymers, which can influence the degradation of albumin or impact on the drug release. Finally, an alternative way of using albumin by denaturing the protein to generate a highly functional chain, which can be modified with polymer, has been presented. These albumin nanoparticles are designed to be extremely versatile so that they can deliver a wide variety of drugs, including traditional hydrophobic drugs, metal‐based drugs and even therapeutic proteins and siRNA.

     

Structure–Activity Studies on the Fluorescent Indicator in a Displacement Assay for the Screening of Small Molecules Binding to RNA

A series of xanthone and thioxanthone derivatives with aminoalkoxy substituents were synthesized as fluorescent indicators for a displacement assay in the study of small‐molecule–RNA interactions. The RNA‐binding properties of these molecules were investigated in terms of the improved binding selectivity to the loop region in the RNA secondary structure relative to 2,7‐bis(2‐aminoethoxy)xanthone (X2S) by fluorimetric titration and displacement assay. An 11‐mer double‐stranded RNA and a hairpin RNA mimicking the stem loop IIB of Rev response element (RRE) RNA of HIV‐1 mRNA were used. The X2S derivatives with longer aminoalkyl substituents showed a higher affinity to the double‐stranded RNA than the parent molecule. Introduction of a methyl group on the aminoethoxy moiety of X2S effectively modulated the selectivity to the RNA secondary structure. Methyl group substitution at the C1′ position suppressed the binding to the loop regions. Substitution with two methyl groups on the amino nitrogen atom resulted in reducing the affinity to the double‐stranded region by a factor of 40 %. The effect of methyl substitution on the amino nitrogen atom was also observed for a thioxanthone derivative. Titration experiments, however, suggested that thioxanthone derivatives showed a more prominent tendency of multiple binding to RNA than xanthone derivatives. The selectivity index calculated from the affinity to the double‐stranded and loop regions suggested that the N,N‐dimethyl derivative of X2S would be suitable for the screening of small molecules binding to RRE.     

Mechanism‐Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure–Activity Relationship,Biostructural, and Kinetic Insight

The sirtuin enzymes are important regulatory deacylases in a variety of biochemical contexts and may therefore be potential therapeutic targets through either activation or inhibition by small molecules. Here, we describe the discovery of the most potent inhibitor of sirtuin 5 (SIRT5) reported to date. We provide rationalization of the mode of binding by solving co‐crystal structures of selected inhibitors in complex with both human and zebrafish SIRT5, which provide insight for future optimization of inhibitors with more “drug‐like” properties. Importantly, enzyme kinetic evaluation revealed a slow, tight‐binding mechanism of inhibition, which is unprecedented for SIRT5. This is important information when applying inhibitors to probe mechanisms in biology.     

Total Synthesis of (−)‐Zampanolide and Structure–Activity Relationship Studies on (−)‐Dactylolide Derivatives

A new total synthesis of the marine macrolide (?)‐zampanolide ( 1 ) and the structurally and stereochemically related non‐natural levorotatory enantiomer of (+)‐dactylolide ( 2 ), that is, ent‐ 2 , has been developed. The synthesis features a high‐yielding, selective intramolecular Horner–Wadsworth–Emmons (HWE) reaction to close the 20‐membered macrolactone ring of 1 and ent‐ 2 . The β‐keto phosphonate/aldehyde precursor for the ring‐closure reaction was obtained by esterification of a ω‐diethylphosphono carboxylic acid fragment and a secondary alcohol fragment incorporating the THP ring that is embedded in the macrocyclic core structure of 1 and ent‐ 2 . THP ring formation was accomplished through a segment coupling Prins‐type cyclization. Employing the same overall strategy, 13‐desmethylene‐ent‐ 2 as well as the monocyclic desTHP derivatives of 1 and ent‐ 2 were prepared. Synthetic 1 inhibited human cancer cell growth in vitro with nM IC₅₀ values, while ent‐ 2 , which lacks the diene‐containing hemiaminal‐linked side chain of 1 , is 25‐ to 260‐fold less active. 13‐Desmethylene‐ent‐ 2 as well as the reduced versions of ent‐ 2 and 13‐desmethylene‐ent‐ 2 all showed similar cellular activity as ent‐ 2 itself. The same activity level was attained by the monocyclic desTHP derivative of 1 . Oxidation of the aldehyde functionality of ent‐ 2 gave a carboxylic acid that was converted into the corresponding N‐hexyl amide. The latter showed only μM antiproliferative activity, thus being several hundred‐fold less potent than 1 .     

Hydroxycinnamic Acids as DNA‐Cleaving Agents in the Presence of CuII Ions: Mechanism,Structure–Activity Relationship,and Biological Implications

The effectiveness of hydroxycinnamic acids (HCAs), that is, caffeic acid (CaA), chlorogenic acid (ChA), sinapic acid (SA), ferulic acid (FA), 3‐hydroxycinnamic acid (3‐HCA), and 4‐hydroxycinnamic acid (4‐HCA), as pBR322 plasmid DNA‐cleaving agents in the presence of Cu^II ions was investigated. Compounds bearing o‐hydroxy or 3,5‐dimethoxy groups on phenolic rings (CaA, SA, and ChA) were remarkably more effective at causing DNA damage than the compounds bearing no such groups; furthermore, CaA was the most active among the HCAs examined. The involvement of reactive oxygen species (ROS) and Cu^I ions in the DNA damage was affirmed by the inhibition of the DNA breakage by using specific scavengers of ROS and a Cu^I chelator. The interaction between CaA and Cu^II ions and the influence of ethylenediaminetetraacetic acid (EDTA), the solvent, and pH value on the interaction were also studied to help elucidate the detailed prooxidant mechanism by using UV/Vis spectroscopic analysis. On the basis of these observations, it is proposed that it is the CaA phenolate anion, instead of the parent molecule, that chelates with the Cu^II ion as a bidentate ligand, hence facilitating the intramolecular electron transfer to form the corresponding CaA semiquinone radical intermediate. The latter undergoes a second electron transfer with oxygen to form the corresponding o‐quinone and a superoxide, which play a pivotal role in the DNA damage. The intermediacy of the semiquinone radical was supported by isolation of its dimer from the Cu^II‐mediated oxidation products. Intriguingly, CaA was also the most cytotoxic compound among the HCAs toward human promyelocytic leukemia (HL‐60) cell proliferation. Addition of exogenous Cu^II ions resulted in an effect dichotomy on cell viability depending on the concentration of CaA; that is, low concentrations of CaA enhanced the cell viability and, conversely, high concentrations of CaA almost completely inhibited the cell proliferation. On the other hand, when superoxide dismutase was added before, the two stimulation effects of exogenous Cu^II ions were significantly ameliorated, thus clearly indicating that the oxidative‐stress level regulates cell proliferation and death. These findings provide direct evidence for the antioxidant/prooxidant mechanism of cancer chemoprevention.     

Evaluation of the Structure–Activity Relationship of Rifabutin and Analogs: A Drug–Membrane Study

This work focuses on the influence of rifabutin and two novel analogs, namely, N′‐acetyl‐rifabutin and N′‐butanoyl‐rifabutin, on the biophysical properties of lipid membranes. Monolayers and multilamellar vesicles composed of egg L ‐α‐phosphatidylcholine:cholesterol in a molar ratio of 4:1 are chosen to mimic biological membranes. Several accurate biophysical techniques are used to establish a putative relationship between the chemical structure of the antimycobacterial compounds and their activity on the membranes. A combination of in situ experimental techniques, such as Langmuir isotherms, Brewster angle microscopy, polarization‐modulated infrared reflection–absorption spectroscopy, and small‐angle X‐ray scattering, is used to assess the drug–membrane interaction. A relationship between the effect of a drug on the organization of the membranes and their chemical structure is found and may be useful in the development of new drugs with higher efficacy and fewer toxic effects.     

Monoamine Oxidase (MAO) as a Potential Target for Anticancer Drug Design and Development

Monoamine oxidases (MAOs) are oxidative enzymes that catalyze the conversion of biogenic amines into their corresponding aldehydes and ketones through oxidative deamination. Owing to the crucial role of MAOs in maintaining functional levels of neurotransmitters, the implications of its distorted activity have been associated with numerous neurological diseases. Recently, an unanticipated role of MAOs in tumor progression and metastasis has been reported. The chemical inhibition of MAOs might be a valuable therapeutic approach for cancer treatment. In this review, we reported computational approaches exploited in the design and development of selective MAO inhibitors accompanied by their biological activities. Additionally, we generated a pharmacophore model for MAO-A active inhibitors to identify the structural motifs to invoke an activity.     

Resveratrol Analogues as Selective Estrogen Signaling Pathway Modulators: Structure–Activity Relationship

Resveratrol is a plant-derived phytoalexin found in grapes, red wine and many other plants used in Asian folk medicine. It is extensively studied for pleiotropic biological activity. The most crucial are anticancer and chemopreventive properties. Resveratrol has also been reported to be an antioxidant and phytoestrogen. The phytoestrogenic activity of resveratrol was assayed in different in vitro and in vivo models. Although these works brought some, on the first look, conflicting results, it is commonly accepted that resveratrol interacts with estrogen receptors and functions as a mixed agonist/antagonist. It is widely accepted that the hydroxyl groups are crucial for resveratrol’s cytotoxic and antioxidative activity and are responsible for binding estrogen receptors. In this work, we assayed 11 resveratrol analogues, seven barring methoxy groups and six hydroxylated analogues in different combinations at positions 3, 4, 5 and 3′,4′,5′. For this purpose, recombined estrogen receptors and estrogen-dependent MCF-7 and Ishikawa cells were used. Our study was supported by in silico docking studies. We have shown that, resveratrol and 3,4,4′5′-tetrahydroxystilbene, 3,3′,4,5,5′-pentahydroxystilbene and 3,3′,4,4′,5,5′-hexahydroxystilbene may act as selective estrogen receptor modulators.     

A New Iron‐Based Carbon Monoxide Oxidation Catalyst: Structure–Activity Correlation

A new iron‐based catalyst for carbon monoxide oxidation, as a potential substitute for precious‐metal systems, has been prepared by using a facile impregnation method with iron tris‐acetylacetonate as a precursor on γ‐Al₂O₃. Light‐off and full conversion temperatures as low as 235 and 278 °C can be reached. However, the catalytic activity strongly depends on the loading; lower loadings perform better than higher ones. The different activities can be explained by variations of the structures formed. The structures are thoroughly characterized by a multimethodic approach by using X‐ray diffraction, Brunauer–Emmett–Teller surface areas, and Mössbauer spectroscopy combined with diffuse reflectance UV/Vis and X‐ray absorption spectroscopy. Consequently, isolated tetrahedrally coordinated Fe³⁺ centers and phases of AlFeO₃ are identified as structural requirements for high activity in the oxidation of carbon monoxide.     

A Quantitative Structure–Activity Relationship Study of Calpeptin (Calpain Inhibitor) as an Anticancer Agent

Calpeptin analogs show anticancer properties with inhibition of calpain. In this work, we applied a quantitative structure–activity relationship (QSAR) model on 34 calpeptin derivatives to select the most appropriate compound. QSAR was employed to generate the models and predict the more significant compounds through a series of calpeptin derivatives. The HyperChem, Gaussian 09, and Dragon software programs were used for geometry optimization of the molecules. The 2D and 3D molecular structures were drawn by ChemDraw (Ultra 16.0) and Chem3D (Pro16.0) software. The Unscrambler program was used for the analysis of data. Multiple linear regression (MLR‐MLR), partial least‐squares (MLR‐PLS1), principal component regression (MLR‐PCR), a genetic algorithm‐artificial neural networks (GA‐ANN), and a novel similarity analysis‐artificial neural network (SA‐ANN) method were used to create QSAR models. Among the three MLR models, MLR‐MLR provided better statistical parameters. The R² and RMSE of the prediction were estimated as 0.8248 and 0.26, respectively. Nevertheless, the constructed model using GA‐ANN revealed the best statistical parameters among the studied methods (R² test = 0.9643, RMSE test = 0.0155, R² train = 0.9644, RMSE train = 0.0139). The GA‐ANN model is found to be the most favorable method among the statistical methods and can be employed for designing new calpeptin analogs as potent calpain inhibitors in cancer treatment.     

Total Synthesis of Aspergillomarasmine A and Related Compounds: A Sulfamidate Approach Enables Exploration of Structure–Activity Relationships

The fungal secondary metabolite aspergillomarasmine A (AMA) has recently been identified as an inhibitor of metallo‐β‐lactamases NDM‐1 and VIM‐2. Described herein is an efficient and practical route to AMA and its related compounds by a sulfamidate approach. In addition, a series of derivatives has been prepared and tested for biological activity in an effort to explore preliminary structure activity relationships. While it was determined that natural LLL isomer of AMA remains the most effective inactivator of NDM‐1 enzyme activity both in vitro and in cells, the structure is highly tolerant of the changes in the stereochemistry at positions 3, 6, and 9.