Multifunctional Small Molecule Research Articles

Inhibition of Alzheimer’s amyloid-β42 peptide aggregation by a bi-functional bis-tryptoline triazole: key insights from molecular dynamics simulations

Alzheimer’s disease (AD) is a neurodegenerative disease mainly caused by amyloid-β42 (Aβ42) peptide self-assembly in the brain. During last years, numerous multifunctional small molecules have been designed and synthesized against self-induced Aβ42 aggregation, metal-induced Aβ42 aggregation, β-secretase (BACE1), acetylcholinesterase (AChE) as well as possessing metal chelating and antioxidant activities. Recently, a bi-functional bis-tryptoline triazole (BTT) compound displaying multifunctional activity against Aβ42 aggregation and BACE1 as well as possessing metal chelating activity and antioxidant property was reported. In the present study, the molecular mechanism of Aβ42 aggregation inhibition by BTT was elucidated using molecular docking and molecular dynamics (MD) simulations. MD analysis highlighted that BTT effectively inhibits conformational transition and stabilize the native structure of Aβ42 monomer by interacting with key central hydrophobic core (CHC) region. BTT significantly enhances helical content from 46% to 57% in Aβ42 monomer, which, in turn, highlight conservation of non-aggregation prone native structure of Aβ42. The binding free energy analysis by molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method highlighted that Phe4, Leu17, Phe20, Ala21, Ala30, Ile31, Leu34, and Ile41 residues of Aβ42 participate in binding with BTT. The present study reveals the underlying inhibitory mechanism of BTT against Aβ42 aggregation and will aid in the future design of more potent inhibitors. The overall findings from the present study will be highly beneficial for the drug discovery scientists in the elucidation of the molecular mechanism of Alzheimer’s Aβ aggregation.AbbreviationsPOH2-(1-(3-Hydroxypropyl)-1H-1,2,3-triazol-4-yl)phenolPMorph2-(1-(2-morpholinoethyl)-1H-1,2,3-triazol-4-yl)phenolPTMorph2-(1-(2-thiomorpholinoethyl)-1H-1,2,3-triazol-4-yl)phenol3Dthree dimensionalAChEAcetylcholinesteraseADAlzheimer’s diseaseAβ42amyloid-β42ADTAutoDock ToolsATBAutomated Topology BuilderBACE1β–secretaseBTTbis-tryptoline triazoleCHCcentral hydrophobic coreHFHartree–FockDSSPdictionary of secondary structure of proteinsFDAFood and Drug AdministrationFELfree energy landscapeGROMACSGROningen MAchine for Chemical SimulationsLGALamarckian Genetic AlgorithmLINCSLINear Constraint SolverMDmolecular dynamicsMM–PBSAmolecular mechanics Poisson–Boltzmann surface area3JNH-HαJ-couplingDec–DETAN1–decanoyl-diethylenetriamineNFTsneurofibrillary tanglesNMRnuclear magnetic resonancePMEparticle mesh ewaldPCprincipal componentPCAprincipal component analysisPDBprotein data bankRgradius–of–gyrationRMSDroot-mean-square deviationRMSFroot–mean–square fluctuationSPCsimple point chargeVMDvisual molecular dynamicsCommunicated by Ramaswamy H. Sarma

Investigation of the molecular reactivity of bioactive oxiranylmethyloxy anthraquinones.

The design of a multitarget and multifunctional small molecule containing two functional groups reacting through different mechanisms represents an attractive goal for the medicinal chemist. The preparation of two bifunctional oxiranylmethyloxy anthraquinones, previously investigated as anticancer agents, is described here. These compounds combine a planar, DNA-intercalating and pro-oxidant anthraquinone scaffold and the alkylating epoxide functions which can covalently react with the nucleic acid. Their multilevel molecular reactivity was studied through a combination of analytical techniques: The DNA-binding properties were investigated using a mass spectrometry-based binding assay and by nuclear magnetic resonance, highlighting the formation of a covalent adduct with a nucleobase. Moreover, the contribution of the pro-oxidant redox cycling was evaluated.

A tumor-targeted Ganetespib-zinc phthalocyanine conjugate for synergistic chemo-photodynamic therapy

Therapeutic effects of photodynamic therapy (PDT) are limited by the selectivity of photosensitizer (PS). Herein, a novel tumor-targeted drug-PS conjugate (Gan-ZnPc) which integrated with zinc phthalocyanine (ZnPc) and Ganetespib has been developed. ZnPc is a promising PS with remarkable photosensitization ability. Ganetespib is a heat shock protein 90 (Hsp90) inhibitor with preferential tumor selectivity and conjugated to ZnPc as a tumor-targeted ligand. The multifunctional small molecule conjugate, Gan-ZnPc, could be bound to extracellular Hsp90 and then selectively internalized into the tumor cells, followed by the generation of abundant intracellular reactive oxygen species (ROS) upon irradiation. Besides, Gan-ZnPc can arrest cell proliferation and induce apoptosis by the inhibition of Hsp90. Herein, with combination of the inhibition of Hsp90 and the generation of cytotoxic ROS, Gan-ZnPc implements tumor selectivity, concentrated PDT and chemotherapy in a synergistic manner, which results in highly effective anti-tumor activity in vitro and in vivo.

Friction- and Wear-Reducing Properties of Multifunctional Small Molecules

Nitrogen- and oxygen-containing compounds were designed empirically and subsequently synthesized, and their rheology, friction, and wear performance as multifunctional base oils (MFBOs) were evaluated. Two of the compounds displayed good viscosity/rheology profiles without the addition of polymeric viscosity modifiers, displaying high viscosity indexes (VIs) above 200. Furthermore, all three MFBOs had lower coefficients of friction compared to well-established and accepted benchmarks. The most significant advancement is their impressive wear improvement by a factor of 5.5 to 70 compared to either of the benchmarks, which is attributed to the polar nature of the base oil which promotes boundary lubrication with metal surfaces. Moreover, these compounds were easily synthesized in one step from commercial starting materials. This work demonstrates that a careful design could provide the features/performance/functions of base oil, rheology modifiers (or VI improvers), and antiwear and friction-reducing additives, all-in one molecule.

Azo-dyes based small bifunctional molecules for metal chelation and controlling amyloid formation.

Chemical tools are needed to discover new effective drugs for tackling multifaceted complex neurodegenerative diseases like Alzheimer's disease (AD). Multifunctional nature of two compounds, 5-((4-nitro-phenyl)diazenyl)quinolin-8-ol (HL1) and 4-((4-nitrophenyl)diazenyl)benzene-1,3-diol (HL2) is reported w.r.t. their ability to bind Cu2+ ions and amyloid aggregates related to AD. HL1 and HL2 have half congo-red type azo-stilbene structural framework incorporated with metal chelating groups, designed to chelate metal ions from metal-amyloid species. Metal binding studies of HL1 and HL2 are established by the methods of Job's Plot, UV-vis spectra with metal ions and stability constant determination. In addition, their metal complexes are isolated, purity checked by elemental analysis, spectroscopically characterized and their structural analyses were obtained from DFT based calculations including binding energy determination. Chicken egg white Lysozyme (CEWL) was used as a model peptide for fibrillation studies. HL1 is found as an excellent colorimetric sensor for amyloid fibrils. Inhibitory effect of HL1 and HL2 and their isolated metal complexes L1-Cu and L2-Cu on CEWL fibrillation was studied using ThT and ANS fluorescence assay along with TEM imaging. In addition, the cell toxicity studies on these compounds suggest that although azo dyes may be non-toxic but having a nitro-substitution lead to significant cell toxicity. Overall, these results suggest that this new class of multifunctional small molecules can interact with amyloids as well as metal ions and could be potential anti-aggregation metal chelating agents.

From small molecules to polymer fibers: Photopolymerization with electrospinning on the fly

The electrospun fibers were manufactured from multifunctional small molecules through in-situ photopolymerization during the electrospinning process. In this study, Tetrabutylammonium Bromide (TBAB) was added to enhance the conductivity of the solution in order to improve spinnability. The synchronous matching of photopolymerization and electrospinning was investigated by real-time Infrared Spectroscopy (RTIR). The surface morphology of fibers was studied by SEM, and the chemical structure of fibers was characterized by FTIR. The residual of photoinitiator was investigated using UV–vis absorption spectroscopy, and the solvent resistance of fibers was characterized by soaking in different solvents. It provides an approach to prepare electrospun fibers from small molecules without using any solvents or heat.

Multifunctional Small Molecule Fluorophore for Long‐Duration Tumor‐Targeted Monitoring and Dual Modal Phototherapy

In this work, a specific tumor‐targeted small molecular fluorophore for synchronous long‐duration cancer imaging, photodynamic therapy, and photothermal therapy is synthesized. This novel fluorophore exhibits specific targeting ability in certain tumors (U87MG, MDA‐MB‐231, A549, etc.) based on its inherent structure and efficiently generates local hyperthermia and reactive oxygen species simultaneously for imaging‐guided precise cancer therapy combining the photothermic and photodynamic effects under laser irradiation. Meanwhile, compared to traditional near infrared fluorophore, this novel fluorophore with significantly enhanced stability against photobleaching can prolong the time of tumor imaging and improve the phototherapy efficiency. This work presents a potential strategy to develop small‐molecule‐based cancer theranostic agents for simultaneous cancer targeting, imaging, and therapy.

On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry.

Proximity enhancement is a central chemical tenet underpinning an exciting suite of small-molecule toolsets that have allowed us to unravel many biological complexities. The leitmotif of this opus is “tethering”—a strategy in which a multifunctional small molecule serves as a template to bring proteins/biomolecules together. Scaffolding approaches have been powerfully applied to control diverse biological outcomes such as protein–protein association, protein stability, activity, and improve imaging capabilities. A new twist on this strategy has recently appeared, in which the small-molecule probe is engineered to unleash controlled amounts of reactive chemical signals within the microenvironment of a target protein. Modification of a specific target elicits a precisely timed and spatially controlled gain-of-function (or dominant loss-of-function) signaling response. Presented herein is a unique personal outlook conceptualizing the powerful proximity-enhanced chemical biology toolsets into two paradigms: “multifunctional scaffolding” versus “on-demand targeting”. By addressing the latest advances and challenges in the established yet constantly evolving multifunctional scaffolding strategies as well as in the emerging on-demand precision targeting (and related) systems, this Perspective is aimed at choosing when it is best to employ each of the two strategies, with an emphasis toward further promoting novel applications and discoveries stemming from these innovative chemical biology platforms.

Newly Emerging Theranostic Agents for Simultaneous Cancertargeted Imaging and Therapy

The development of multifunctional theranostic agents has become an intriguing venture for personalized oncology, because they can integrate tumor diagnosis and therapy. One approach explored to obtain such multifunctional theranostic agents is through the chemical conjugation of anticancer drugs and contrast agents with various cancer-targeted ligands. The other approach is based on the nanoplatform, in which cancer-targeted nanostructures achieve simultaneous cancer specific detection and therapeutics either by EPR effect or by conjugation of target ligands. Interestingly, a newly emerging strategy from multifunctional small molecules to develop cancertargeted theranostic agents has been reported recently. In consideration of the urgent need and rapid development of theranostic agents in cancer therapy, herein we review the currently adopted and newly emerging approaches for their preparation, and highlight the promises and challenges in each approach, hoping to offer useful insights in developing more specific and efficient cancer theranostic agents suitable for clinical use.

Adjudin protects rodent cochlear hair cells against gentamicin ototoxicity via the SIRT3-ROS pathway.

Hearing loss resulting from hair cell degeneration is a common disease that affects millions of people worldwide. Strategies to overcome the apparent irreversible hair cell loss in mammals become paramount for hearing protection. Here we reported that, by using a well-established gentamicin-induced hair cell loss model in vitro, adjudin, a multi-functional small molecule drug, protected cochlear hair cells from gentamicin damage. Immunohistochemistry, Western blotting and quantitative RT-PCR analyses revealed that adjudin exerted its otoprotective effects by up-regulating the level of Sirt3, a member of Sirtuin family protein located in mitochondria, which regulates reactive oxygen species (ROS) production in cochlear cells and inhibits the production of ROS and apoptotic cells induced by gentamicin. Sirt3 silencing experiments confirmed that Sirt3-ROS signaling axis mediated hair cell protection against gentamicin by adjudin, at least in part. Furthermore, adjudin's otoprotection effects were also observed in an in vivo gentamicin-injured animal model. Taken together, these findings identify adjudin as a novel otoprotective small molecule via elevating Sirt3 levels and Sirt3 may be of therapeutic value in hair cell protection from ototoxic insults.

Effect and mechanism of fluorofenidone on organ fibrosis

Fibrosis can occur in different organs with high incidence rate and great danger. It still lacks effective drugs for prevention of fibrosis. Fluorofenidone is a newly developed drug with anti-fibrotic activity, which provides a new hope for treating the progressive fibrotic diseases. Recent studies have shown that fluorofenidone is a multifunctional small molecule with anti-inflammatory, antioxidative and anti-apoptotic eff ects. It can inhibit the activation and proliferation of myofibroblasts, promote the degradation of extracellular matrix and regulate the cellular signal transmission. Fluorofenidone can be applied to attenuate the progression of renal, hepatic and pulmonary fibrosis.

Synthetic Flavonoids, Aminoisoflavones: Interaction and Reactivity with Metal-Free and Metal-Associated Amyloid-β Species.

Metal ion homeostasis in conjunction with amyloid-β (Aβ) aggregation in the brain has been implicated in Alzheimer's disease (AD) pathogenesis. To uncover the interplay between metal ions and Aβ peptides, synthetic, multifunctional small molecules have been employed to modulate Aβ aggregation in vitro. Naturally occurring flavonoids have emerged as a valuable class of compounds for this purpose due to their ability to modulate both metal-free and metal-induced Aβ aggregation. Although, flavonoids have shown anti-amyloidogenic effects, the structural moieties of flavonoids responsible for such reactivity have not been fully identified. In order to understand the structure-interaction-reactivity relationship within the flavonoid family for metal-free and metal-associated Aβ, we designed, synthesized, and characterized a set of isoflavone derivatives, aminoisoflavones (1-4), that displayed reactivity (i.e., modulation of Aβ aggregation) in vitro. NMR studies revealed a potential binding site for aminoisoflavones between the N-terminal loop and central helix on prefibrillar Aβ different from the non-specific binding observed for other flavonoids. The absence or presence of the catechol group differentiated the binding affinities and enthalpy/entropy balance between aminoisoflavones and Aβ. Furthermore, having a catechol group influenced the binding mode with fibrillar Aβ. Inclusion of additional substituents moderately tuned the impact of aminoisoflavones on Aβ aggregation. Overall, through these studies, we obtained valuable insights on the requirements for parity among metal chelation, intermolecular interactions, and substituent variation for Aβ interaction.

Characterization of a novel multifunctional resveratrol derivative for the treatment of atrial fibrillation

Atrial fibrillation (AF) is the most common cardiac arrhythmia and is associated with an increased risk for stroke, heart failure and cardiovascular-related mortality. Candidate targets for anti-AF drugs include a potassium channel K(v)1.5, and the ionic currents I(KACh) and late I(Na), along with increased oxidative stress and activation of NFAT-mediated gene transcription. As pharmacological management of AF is currently suboptimal, we have designed and characterized a multifunctional small molecule, compound 1 (C1), to target these ion channels and pathways. We made whole-cell patch-clamp recordings of recombinant ion channels, human atrial I(Kur), rat atrial I(KACh), cellular recordings of contractility and calcium transient measurements in tsA201 cells, human atrial samples and rat myocytes. We also used a model of inducible AF in dogs. C1 inhibited human peak and late K(v)1.5 currents, frequency-dependently, with IC₅₀ of 0.36 and 0.11 μmol·L(-1) respectively. C1 inhibited I(KACh)(IC₅₀ of 1.9 μmol·L(-1)) and the Na(v)1.5 sodium channel current (IC₅₀s of 3 and 1 μmol·L(-1) for peak and late components respectively). C1 (1 μmol·L(-1)) significantly delayed contractile and calcium dysfunction in rat ventricular myocytes treated with 3 nmol·L(-1) sea anemone toxin (ATX-II). C1 weakly inhibited the hERG channel and maintained antioxidant and NFAT-inhibitory properties comparable to the parent molecule, resveratrol. In a model of inducible AF in conscious dogs, C1 (1 mg·kg(-1)) reduced the average and total AF duration. C1 behaved as a promising multifunctional small molecule targeting a number of key pathways involved in AF.

Synthesis and biological evaluation of a targeted DNA-binding transcriptional activator with HDAC8 inhibitory activity

Development of multifunctional transcriptional activators is of increasing importance as they could trigger complicated gene networks. Recently, we developed a differential gene activating multifunctional small molecule SAHA-PIP (Sδ) by conjugating a histone deacetylase (HDAC) inhibitor, SAHA, to a selective DNA-binding pyrrole-imidazole polyamide (PIP). Epigenetic activity of Sδ was attributed to the active metal-binding (–NHOH) domain of SAHA. We synthesized a derivative of Sδ, called Jδ to evaluate the role of surface recognition domain (–phenyl) of SAHA in Sδ-mediated transcriptional activation. In vitro studies revealed that Jδ displayed potent inhibitory activity against HDAC8. Jδ retained the pluripotency gene-inducing ability of Sδ when used alone and in combination with Sδ; a notable increase in the pluripotency gene expression was observed. Interestingly, Jδ significantly induced the expression of HDAC8-controlled Otx2 and Lhx1. Our results suggest that the epigenetic activity of our multifunctional molecule could be altered to improve its efficiency as a transcriptional activator for intricate gene network(s).

Diaryl Hydrazones as Multifunctional Inhibitors of Amyloid Self-Assembly

The design and application of an effective, new class of multifunctional small molecule inhibitors of amyloid self-assembly are described. Several compounds based on the diaryl hydrazone scaffold were designed. Forty-four substituted derivatives of this core structure were synthesized using a variety of benzaldehydes and phenylhydrazines and characterized. The inhibitor candidates were evaluated in multiple assays, including the inhibition of amyloid β (Aβ) fibrillogenesis and oligomer formation and the reverse processes, the disassembly of preformed fibrils and oligomers. Because the structure of the hydrazone-based inhibitors mimics the redox features of the antioxidant resveratrol, the radical scavenging effect of the compounds was evaluated by colorimetric assays against 2,2-diphenyl-1-picrylhydrazyl and superoxide radicals. The hydrazone scaffold was active in all of the different assays. The structure-activity relationship revealed that the substituents on the aromatic rings had a considerable effect on the overall activity of the compounds. The inhibitors showed strong activity in fibrillogenesis inhibition and disassembly, and even greater potency in the inhibition of oligomer formation and oligomer disassembly. Supporting the quantitative fluorometric and colorimetric assays, size exclusion chromatographic studies indicated that the best compounds practically eliminated or substantially inhibited the formation of soluble, aggregated Aβ species, as well. Atomic force microscopy was also applied to monitor the morphology of Aβ deposits. The compounds also possessed the predicted antioxidant properties; approximately 30% of the synthesized compounds showed a radical scavenging effect equal to or better than that of resveratrol or ascorbic acid.

Molecular and phenotypic expression of decorin as modulator of angiogenesis in human potentially malignant oral lesions and oral squamous cell carcinomas

Decorin is an extracellular matrix, multifunctional small proteoglycan molecule in tumor stroma that has been shown to be modulator of angiogenesis. No clinical data is available so far on decorin expression and survival outcome of oral cancer. The aim of the present study was to examine molecular and phenotypic expression of two angiogenesis modulators viz. decorin and vascular endothelial growth factor-A (VEGF-A) in human potentially malignant oral lesions (PMOLs) and oral squamous cell carcinomas (OSCC) in relation to clinico-pathological variables and survival outcome. Tissue biopsies were obtained from 72 PMOLs, 108 OSCC and 52 healthy controls. The PMOLs included cases of leukoplakias and oral submucous fibrosis. Immunohistochemistry was performed using antibodies against decorin, VEGF-A and CD-31. Messenger-ribonucleic acid (mRNA) expression was analyzed by using real-time polymerase chain reaction. Cytoplasmic staining of decorin was observed in the basal layer of epithelium in 53 (73.61%) cases of PMOLs and in peritumoral stroma in 55 (50.92%) cases of OSCC. None of the cases showed nuclear expression of decorin. Decorin expression both at phenotypic and molecular level was found to be down-regulated from PMOLs to OSCC. Lymph node metastasis and reduced decorin expression independently correlated with overall survival in OSCC. VEGF-A expression had no significant impact on survival outcome. Micro vessel density and VEGF-A expression were significantly associated with reduced decorin expression in tumor stroma suggesting, decorin as angiogenic modulator in OSCC. Down-regulation of decorin expression and the presence of lymph node metastasis were adverse factor independently affecting overall survival in OSCC.

Alzheimer's Disease: Emerging Trends in Small Molecule Therapies

Alzheimer's disease (AD) is a highly complex and rapidly progressive neurodegenerative disorder characterized by the systemic collapse of cognitive function and formation of dense amyloid plaques and neurofibrillary tangles. AD pathology is derived from the cholinergic, amyloid and tau hypotheses, respectively. Current pharmacotherapy with known anti-cholinesterases, such as Aricept® and Exelon®, only offer symptomatic relief without any disease-modifying effects. It is now clear that in order to prevent the rapid progression of AD, new therapeutic treatments should target multiple AD pathways as opposed to the traditional "one drug, one target" approach. This review will focus on the recent advances in medicinal chemistry aimed at the development of small molecule therapies that target various AD pathological routes such as the cholinesterases (AChE and BuChE), amyloidogenic secretases (β/γ- secretase), amyloid-β aggregation, tau phosphorylation and fibrillation and metal-ion redox/reactive oxygen species (ROS). Some notable ring templates will be discussed along with their structure-activity relationship (SAR) data and their multiple modes of action. These emerging trends signal a paradigm shift in anti-AD therapies aimed at the development of multifunctional small molecules as disease-modifying agents (DMAs).

Multifunctional small molecule for controlled assembly of oligomeric nanoparticles and crosslinked polymers

One multifunctional small molecule can undergo a natural condensation reaction under the control of reducing agent to generate amphiphilic oligomers which quickly self-assemble supramolecular nanoparticles or form crosslinked, reversibly degradable polymers.

GDP-Capture Compound — A novel tool for the profiling of GTPases in pro- and eukaryotes by capture compound mass spectrometry (CCMS)

The functional isolation of proteome subsets based on small molecule-protein interactions is an increasingly popular and promising field in functional proteomics. Entire protein families may be profiled on the basis of their common interaction with a metabolite or small molecule inhibitor. This is enabled by novel multifunctional small molecule probes. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate Capture Compound-protein conjugates from complex biological samples for direct trypsinisation and protein identification by liquid chromatography/mass spectrometry (CCMS). We here present the synthesis and application of a novel GDP-Capture Compound for the functional enrichment of GTPases, a pivotal protein family that exerts key functions in signal transduction. We present data from CCMS experiments on two biological lysates from Escherichia coli and from human-derived Hek293 cells. The GDP-Capture Compound robustly captures a wide range of different GTPases from both systems and will be a valuable tool for the proteomic profiling of this important protein family.

Construction of Supramolecular Structures via. Hydrogen Bonds. Supramolecular Liquid-Crystalline Networks Built through Hydrogen Bonds.

Liquid-crystalline supramolecular networks have been obtained by self-assembly through the formation of hydrogen bonds. Hydrogen-bonded networks built from 4, 4'-bipyridine and polyacrylates containing a side-chain benzoic acid show smectic A phases. The complexation of poly(acrylic acid) and bis(imidazolyl) mesogenic compounds also leads to mesomorphic networks. Self-assembly of multifunctional small molecules having benzoic acids and pyridyl moieties affords H-bonded networks which exhibit nematic and smectic phases. Liquid-crystalline polymer alloys have been prepared from a thermotropic polyester containing a lateral pyridyl group and poly(4-vinylphenol). The interaction through H bonds between these polymers results in the formation of the miscible blends that show nematic phases. These networks exhibit thermoreversible phase transitions due to the dynamic nature of H bond.