SERS and MD simulation studies of a kinase inhibitor demonstrate the emergence of a potential drug discovery tool

Research progress on the relationship between AURKA and tumorigenesis: the neglected nuclear function of AURKA

AURKA is a threonine or serine kinase that needs to be activated by TPX2, Bora and other factors. AURKA is located on chromosome 20 and is amplified or overexpressed in many human cancers, such as breast cancer. AURKA regulates some basic cellular processes, and this regulation is realized via the phosphorylation of downstream substrates. AURKA can function in either the cytoplasm or the nucleus. It can promote the transcription and expression of oncogenes together with other transcription factors in the nucleus, including FoxM1, C-Myc, and NF-κB. In addition, it also sustains carcinogenic signaling, such as N-Myc and Wnt signaling. This article will focus on the role of AURKA in the nucleus and its carcinogenic characteristics that are independent of its kinase activity to provide a theoretical explanation for mechanisms of resistance to kinase inhibitors and a reference for future research on targeted inhibitors.

In situ surface-enhanced Raman spectroscopy for membrane protein analysis and sensing

Membrane proteins are involved in a variety of dynamic cellular processes and exploration of the structural basis of membrane proteins is of significance for a better understanding of their functions. In situ analysis of membrane proteins and their dynamics is, however, challenging for conventional techniques. Surface-enhanced Raman spectroscopy (SERS) is powerful in protein structural characterization, allowing for sensitive, in-situ and real-time identification and dynamic monitoring under physiological conditions. In this review, the applications of SERS in probing membrane proteins are outlined, discussed and prospected. It starts with a brief introduction to membrane proteins, SERS theories and SERS-based strategies that commonly-used for membrane proteins. How to assemble phospholipid biolayers on SERS-active materials is highlighted, followed by respectively discussing about direct and indirect strategies for membrane protein sensing. SERS-based monitoring of protein-ligand interactions is finally introduced and its potential in biomedical applications is discussed in detail. The review ends with critical discussion about current challenges and limitations of this research field, and the promising perspectives in both fundamental and applied sciences.

Development of discrete interaction models for ultra-fine nanoparticle plasmonics

Plasmonics serves as a most outstanding feature of nanoparticle technology and is nowadays used in numerous applications within imaging, sensing and energy harvesting, like plasmonically enhanced solar cells, nanoparticle bioimaging, plasmon-controlled fluorescence for molecular tracking in living cells, plasmon-controlled electronic molecular devices and surface enhanced Raman spectroscopy for single molecular detection. Although plasmonics has been utilized since ancient times, the understanding of its basic interactions has not been fully achieved even under the emergence of modern nanoscience. In particular, it has been difficult to address the "ultra-fine" 1-10 nm regime, important for applications especially in bioimaging and biomedical areas, where neither classical nor quantum based theoretical methods apply. Recently, new approaches have been put forward to bridge this size gap based on semi-empirical discrete interaction models where each atom makes a difference. A primary aim of this perspective article is to review some of the most salient features of these models, and in particular focus on a recent extension - the extended discrete interaction model (Ex-DIM), where the geometric and environmental features are extended - and highlight a set of benchmark studies using this model concerning size, shape, material, temperature dependence and other characteristics of ultra-fine plasmonic nanoparticles. We also analyze new possibilities offered by the model for designing ultra-fine plasmonic particles for applications in the areas of bioimaging, biosensing, photothermal therapy, infrared light harvesting and photodetection. We foresee that future modelling activities will be closely connected to collaborative experimental work including synthesis, device fabrication and measurements with feedback and validation in a systematic fashion. With this strategy we can expect that modelling of ultra-fine plasmonics particles can be integrated in the development of novel plasmonic systems with unprecedented performance and applicability.

Photoinduced Electron-Transfer-Mediated Differential Recognition of Proteins on Plasmonic Surfaces

Photoinduced enhanced Raman spectroscopy (PIERS) has emerged as an efficient technique for enhancing the vibrational modes of analyte molecules adsorbed on a plasmonic nanoparticle-semiconductor hybrid material through chemical enhancement governed by electron transfer from the semiconductor to the plasmonic nanoparticles under an additional ultraviolet (UV) preirradiation step. The increase in chemical enhancement is imperative in analyzing and detecting pharmaceutically important moieties, such as amino acids and proteins, with a low Raman scattering cross section, even in complex biological environments. Herein, we demonstrate that UV preirradiation induced the creation of additional oxygen vacancies by introducing a low concentration (≈1%) of Ni as a dopant in the 2D platelike morphology of the BiOCl semiconductor; i.e., defect states in the semiconductor can induce charge transfer from the semiconductor to the plasmonic nanoparticles. This phenomenon facilitates electron transfer to the adsorbed analyte on the plasmonic surface. Additionally, we have shown the usefulness of this method in protein immobilization on the substrate surface, followed by the identification of a specific protein in the mixture of proteins. Proteins containing cysteine residues capture these electrons to form a surface-bound thiol group via a transient disulfide electron adduct radical. This allows differential binding of the protein molecules to the semiconductor plasmonic hybrid depending on the concentration of surface cysteine residues in proteins. Through PIERS and principal component analysis, we demonstrate the possibility of probing and distinguishing biomolecules based on their surface composition and secondary structure components even in their mixtures, thus paving the way for efficient analysis of complex biological systems.

Imaging of intracellular protein aggregates through plasmon-assisted clusteroluminescence

The formation of clusters in non-aromatic molecules can give rise to unconventional luminescence or clusteroluminescence. Typically containing heteroatoms without extended conjugation or aromatic rings, these molecules have drawn much attention owing to the prospects of label-free biological imaging. However, their applications have been limited due to the lack of knowledge of the underlying mechanism. Herein, we have elucidated the mechanism of clusteroluminescence from proteins, which were explicitly aggregated using plasmonic silver nanoparticles. The nanoparticles promoted protein aggregation and induced nitrile formation on the surface, which, along with other lone-pair-containing heteroatoms, contributed to enhanced emission in the visible range. Remarkably, this makes imaging of proteins possible with visible excitations, as co-factor-lacking proteins generally undergo electronic transitions only in the ultraviolet range. Furthermore, the inherent protein-aggregating behaviour of plasmonic nanoparticles was harnessed for imaging of intracellular Huntingtin protein aggregates overexpressed in HeLa cells through clusteroluminescence. Significant plasmon-enhanced and red-shifted fluorescence emission was observed, which helped in the imaging and localization of the intracellular aggregates. Density functional theory calculations and transient absorbance spectroscopy were used to probe the molecular interactions at the protein-nanoparticle interface and the charge transfer states, further elucidating the role of nanoparticles and the emission mechanism. This technique thus opens alternate avenues for label-free fluorescence bioimaging.

Class-specific recognition and monitoring of environmental steroid estrogens in real water systems utilizing aptamer base substitution mutagenesis approach

The same class of environmental steroid estrogens (SEs) with the highest estrogenic activity share the same chemical core structure and are often found together in the environment, posing significant risks to organismal health and environmental safety due to toxicity accumulation. In this study, a novel method for constructing the group-targeting aptasensor was developed to comprehensively analyze SEs. Through artificial intervention base substitution mutagenesis of adjacent bases T13 and C20 of the aptamer-binding domain recognizing 17β-estradiol, combined with docking calculations, the group-targeting SEs-aptamer for class-specific recognition SEs, such as estrone, estradiol, estriol, and ethinylestradiol were obtained. The binding constant of the SEs-aptamer to the SEs was 108 M-1. The established group-targeting SEs aptasensor exhibited high sensitivity within a concentration range from 0.1 to 10 nM and demonstrated strong interference resistance, as well as high stability and wide pH water applicability. It was further applied to analyze real water samples and monitor changes in SEs concentrations during the removal process by Chlorella pyrenoidosa. These successful applications have demonstrated the excellent ability of this aptasensor to monitor SE in the environment. The method offered a new approach and idea for recognizing and detecting the same class of environmental pollutants in complex systems.

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Comprehensive molecular docking and dynamic simulations for drug repurposing of clinical drugs against multiple cancer kinase targets

Drug repurposing is a method to identify novel therapeutic agents from the existing drugs and clinical compounds. In the present comprehensive work, molecular docking, virtual screening and dynamics simulations were carried out for ten cancer types viz breast, colon, central nervous system, leukaemia, melanoma, ovarian, prostate, renal and lung (non-small and small cell) against validated eighteen kinase targets. The study aims to understand the action of chemotherapy drugs mechanism through binding interactions against selected targets via comparative docking simulations with the state-art molecular modelling suits such as MOE, Cresset-Flare, AutoDock Vina, GOLD and GLIDE. Chemotherapeutic drugs (n = 112) were shortlisted from standard drug databases with appropriate chemoinformatic filters. Based on docking studies it was revealed that leucovorin, nilotinib, ellence, thalomid and carfilzomib drugs possessed potential against other cancer targets. A library was built to enumerate novel molecules based on the scaffold and functional groups extracted from known drugs and clinical compounds. Twenty novel molecules were prioritised further based on drug-like attributes. These were cross docked against 1MQ4 Aurora-A Protein Kinase for prostate cancer and 4UYA Mitogen-activated protein kinase for renal cancer. All docking programs yielded similar results but interestingly AutoDock Vina yielded the lowest RMSD with the native ligand. To further validate the final docking results at atomistic level, molecular dynamics simulations were performed to ascertain the stability of the protein-ligand complex. The study enables repurposing of drugs and lead identification by employing a host of structure and ligand based virtual screening tools and techniques.Communicated by Ramaswamy H. Sarma.

Structure-activity relationship of dihydropyridines for rhabdomyosarcoma

Childhood muscle-related cancer rhabdomyosarcoma is a rare disease with a 50-year unmet clinical need for the patients presented with advanced disease. The rarity of ∼350 cases per year in North America generally diminishes the viability of large-scale, pharmaceutical industry driven drug development efforts for rhabdomyosarcoma. In this study, we performed a large-scale screen of 640,000 compounds to identify the dihydropyridine (DHP) class of anti-hypertensives as a priority compound hit. A structure-activity relationship was uncovered with increasing cell growth inhibition as side chain length increases at the ortho and para positions of the parent DHP molecule. Growth inhibition was consistent across n = 21 rhabdomyosarcoma cell line models. Anti-tumor activity in vitro was paralleled by studies in vivo. The unexpected finding was that the action of DHPs appears to be other than on the DHP receptor (i.e., L-type voltage-gated calcium channel). These findings provide the basis of a medicinal chemistry program to develop dihydropyridine derivatives that retain anti-rhabdomyosarcoma activity without anti-hypertensive effects.

Single-Molecule Electrical and Spectroscopic Profiling Protein Allostery Using a Gold Plasmonic Nanopore

Direct structural and dynamic characterization of protein conformers in solution is highly desirable but currently impractical. Herein, we developed a single molecule gold plasmonic nanopore system for observation of protein allostery, enabling us to monitor translocation dynamics and conformation transition of proteins by ion current detection and SERS spectrum measurement, respectively. Allosteric transition of calmodulin (CaM) was elaborately probed by the nanopore system. Two conformers of CaM were well-resolved at a single-molecule level using both the ion current blockage signal and the SERS spectra. The collected SERS spectra provided structural evidence to confirm the interaction between CaM and the gold plasmonic nanopore, which was responsible for the different translocation behaviors of the two conformers. SERS spectra revealed the amino acid residues involved in the conformational change of CaM upon calcium binding. The results demonstrated that the excellent spectral characterization furnishes a single-molecule nanopore technique with an advanced capability of direct structure analysis.

Surface-enhanced Raman spectroscopy for drug discovery: peptide-RNA binding

The ever-growing demand for new drugs highlights the need to develop novel cost- and time-effective techniques for drug discovery. Surface-enhanced Raman spectroscopy (SERS) is an emerging ultrasensitive and label-free technique that allows for the efficient detection and characterization of molecular interactions. We have recently developed a SERS platform for detecting a single protein molecule linked to a gold substrate (Almehmadi et al. Scientific Reports 2019). In this study, we extended the approach to probe the binding of potential drugs to RNA targets. To demonstrate the proof of concept, two 16-amino acid residue peptides with close primary structures and different binding affinities to the RNA CUG repeat related to myotonic dystrophy were tested. Three-microliter solutions of the RNA repeat with these peptides at nanomolar concentrations were probed using the developed approach, and the binding of only one peptide was demonstrated. The SER spectra exhibited significant fluctuations along with a sudden strong enhancement as spectra were collected consecutively from individual spots. Principal component analysis (PCA) of the SER spectral datasets indicated that free RNA repeats could be differentiated from those complexed with a peptide with 100% accuracy. The developed SERS platform provides a novel opportunity for label-free screening of RNA-binding peptides for drug discovery. Schematic representation of the SERS platform for drug discovery developed in this study.

Chromatographic framework for coffee ring effect-driven separation of small molecules in surface enhanced Raman spectroscopy analysis

The applications of coffee ring effect (CRE) in analytical chemistry have been increasingly expanded from particles and macromolecules to small molecules, in particular coupled to surface-enhanced Raman spectroscopy (SERS). Despite the theory behind the formation of CRE itself from a single drop evaporation onto the dry surface is well established, the theoretical aspects of CRE-driven separation, especially the analyte-surface interactions involving small molecules, have not been conceived. Herein, we have developed a theoretical framework to describe the CRE-driven separation process of small molecules, using SERS analysis of dimethylarsinic acid (DMA^V), dimethylmonothioarsinic acid (DMMTA^V), and dimethyldithioarsinic acid (DMDTA^V) on gold nanofilm (AuNF) as an example. By combining the CRE theory for the radial flow and the Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory for mass transfer between solution and AuNF surface, we adapted the conventional chromatographic theory to derive a modified van Deemter equation for the CRE-driven separation. By using this model, we predicted the travel distances of arsenicals based on the different affinity of analytes to the AuNF and evaluated the possibility of separation of unknown analytes by CRE-based SERS, demonstrating the successful adaptation of classic chromatographic theory to CRE-driven nanochromatography.

Pharmaceutical applications of a nanospectroscopic technique: Surface-enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) is a very sensitive technique offering unique opportunities for detection and identification of molecules and molecular structures at extremely low concentrations even in complex sample matrixes. Since a nanostructured noble metal surface is required for the enhancement of Raman scattering, the acquired spectral information naturally originates from nanometer size domains making it a nanospectroscopic technique by breaking the diffraction limit of light. In this review, first Raman spectroscopy, its comparison to other related techniques, its modes and instrumentation are briefly introduced. Then, the SERS mechanism, substrates and the parameters influencing a SERS experiment are discussed. Finally, its applications in pharmaceuticals including drug discovery, drug metabolism, multifunctional chemo-photothermal-therapy-delivery-release-imaging, drug stability and drug/metabolite detection in complex biological samples are summarized and elaborated.

Divalent Ion-Induced Switch in DNA Cleavage of KpnI Endonuclease Probed through Surface-Enhanced Raman Spectroscopy

We demonstrate the remarkable ability of surface-enhanced Raman spectroscopy (SERS) to track the allosteric changes in restriction endonuclease KpnI (R.KpnI) caused by metal ions. R.KpnI binds and promiscuously cleaves DNA upon activation by Mg²⁺ ions. However, the divalent ion Ca²⁺ induces high fidelity cleavage, which can be overcome by higher concentrations of Mg²⁺ ions. In the absence of any 3D crystal structure, for the first time, we have elucidated the structural underpinnings of such a differential effect of divalent ions on the endonuclease activity. A combined SERS and molecular dynamics (MD) approach showed that Ca²⁺ ion activates an enzymatic switch in the active site, which is responsible for the high fidelity activity of the enzyme. Thus, SERS in combination with MD simulations provides a powerful tool for probing the link between the structure and activity of enzyme molecules that play vital roles in DNA transactions.

Surface-Enhanced Raman Spectroscopy as a Tool for Distinguishing Extracellular Vesicles under Autophagic Conditions: A Marker for Disease Diagnostics

Extracellular vesicles (EVs) laden with lipids, proteins, DNA, and micro-RNAs play important biological functions in intercellular communication and have pivotal roles in pathophysiological conditions. Characterization of the EVs has always been a multistep process involving large volumes, and they are heterogeneous in size and properties. A multitude of approaches is used to distinguish the EVs. Here, we report simple citrate reduced silver nanoparticles assisted surface-enhanced Raman spectroscopy (SERS) as a tool to distinguish EVs extracted from several cell lines isolated under autophagic conditions (nitrogen starvation). This study is the first report of its kind in characterizing EVs from cells under autophagic conditions using SERS. We used two cancerous cell lines, HeLa, its corresponding autophagy-deficient cell line (Atg5^-/-), and a noncancerous cell line, HEK293, to isolate EVs. Our study helps in the facile detection and differentiation of EVs isolated between two closely related human cell lines that differ by their autophagic ability. The principal component analysis (PCA) of the SERS spectra of these EVs consistently showed the presence of distinct chemical compositions of the EVs. SERS of EVs can help in probing more into the molecular level information from EVs and could become a powerful tool once coupled with improved microscopy techniques for diagnosis and therapy.

Identifying conformational changes of aptamer binding to theophylline: A combined biolayer interferometry, surface-enhanced Raman spectroscopy, and molecular dynamics study

Theophylline is a potent bronchodilator for the treatment of asthma, bronchitis, and emphysema. Its narrow therapeutic window (20-100 μM) demands that the blood concentration of theophylline be monitored carefully, which can be achieved by aptamer capture. Thus, an understanding of what occurs when aptamers bind to theophylline is critical for identifying a high-affinity and high-specificity aptamer, which improve the sensitivity and selectivity of theophylline detection. Consequently, there is an urgent need to develop a simple, convenient, and nondestructive method to monitor conformational changes during the binding process. Here, we report the determination of the affinity of a selected aptamer and theophylline via biolayer interferometry (BLI) experiments. Additionally, using surface-enhanced Raman spectroscopy (SERS), the conformational changes on theophylline-aptamer binding were identified from differences in the SER spectra. Finally, molecular dynamics (MD) simulations were used to identify the specific conformational changes of the aptamer during the binding process. Such a combined BLI-SERS-MD method provides an in-depth understanding of the theophylline-aptamer binding processes and a comprehensive explanation for conformational changes, which helps to select, design, and modify an aptamer with high affinity and specificity. It can also be used as a scheme for the study of other aptamer-ligand interactions, which can be applied to the detection, sensing, clinical diagnosis, and treatment of diseases.

Rapid, Label-free Optical Spectroscopy Platform for Diagnosis of Heparin-Induced Thrombocytopenia

The use of surface-enhanced Raman spectroscopy (SERS) to determine spectral markers for the diagnosis of heparin-induced thrombocytopenia (HIT), a difficult-to-diagnose immune-related complication that often leads to limb ischemia and thromboembolism, is proposed. The ability to produce distinct molecular signatures without the addition of labels enables unbiased inquiry and makes SERS an attractive complementary diagnostic tool. A capillary-tube-derived SERS platform offers ultrasensitive, label-free measurement as well as efficient handling of blood serum samples. This shows excellent reproducibility, long-term stability and provides an alternative diagnostic rubric for the determination of HIT by leveraging machine-learning-based classification of the spectroscopic data. We envision that a portable Raman instrument could be combined with the capillary-tube-based SERS analytical tool for diagnosis of HIT in the clinical laboratory, without perturbing the existing diagnostic workflow.

Shedding Light on the Trehalose-Enabled Mucopermeation of Nanoparticles with Label-Free Raman Spectroscopy

Nanoparticle-based drug delivery systems have attracted significant interest owing to their promise as tunable platforms that offer improved intracellular release of cargo therapeutics. However, significant challenges remain in maintaining the physiological stability of the mucosal matrix due to the nanoparticle-induced reduction in the matrix diffusivity and promotion of mucin aggregation. Such aggregation also adversely impacts the permeability of the nanoparticles, and thus, diminishes the efficacy of nanoparticle-based formulations. Here, an entirely complementary approach is proposed to the existing nanoparticle functionalization methods to address these challenges by using trehalose, a naturally occurring disaccharide that offers exceptional protein stabilization. Plasmon-enhanced Raman spectroscopy and far-red fluorescence emission of the plasmonic silver nanoparticulate clusters are harnessed to create a unique dual-functional, aggregating, and imaging agent that obviates the need of an additional reporter to investigate mucus-nanoparticle interactions. These spectroscopy-based density mapping tools uncover the mechanism of mucus-nanoparticle interactions and establish the protective role of trehalose microenvironment in minimizing the nanoparticle aggregation. Thus, in contrast to the prevailing belief, these results demonstrate that nonfunctionalized nanoparticles may rapidly penetrate through mucus barriers, and by leveraging the bioprotectant attributes of trehalose, an in vivo milieu for efficient mucosal drug delivery can be generated.

Advances in surface-enhanced Raman spectroscopy (SERS) substrates for lipid and protein characterization: sensing and beyond

Surface-enhanced Raman spectroscopy (SERS) has become an essential ultrasensitive analytical tool for biomolecular analysis of small molecules, macromolecular proteins, and even cells. SERS enables label-free, direct detection of molecules through their intrinsic Raman fingerprint. In particular, protein and lipid bilayers are dynamic three-dimensional structures that necessitate label-free methods of characterization. Beyond direct detection and quantitation, the structural information contained in SERS spectra also enables deeper biophysical characterization of biomolecules near metallic surfaces. Therefore, SERS offers enormous potential for such systems, although making measurements in a nonperturbative manner that captures the full range of interactions and activity remains a challenge. Many of these challenges have been overcome through advances in SERS substrate development, which have expanded the applications and targets of SERS for direct biomolecular quantitation and biophysical characterization. In this review, we will first discuss different categories of SERS substrates including solution-phase, solid-supported, tip-enhanced Raman spectroscopy (TERS), and single-molecule substrates for biomolecular analysis. We then discuss detection of protein and biological lipid membranes. Lastly, biophysical insights into proteins, lipids and live cells gained through SERS measurements of these systems are reviewed.

Investigation of the binding sites and orientation of Norfloxacin on bovine serum albumin by surface enhanced Raman scattering and molecular docking

Norfloxacin (NFX) is an antibacterial agent belonging to the fluoroquinolone family of drugs, known to bind bovine serum albumin (BSA). Surface-enhanced Raman scattering (SERS) and fluorescence spectroscopy in combination with molecular docking were explored to investigate the binding interaction between NFX with Bovine serum albumin (BSA) at a physiological condition. This study focused on identifying the binding site and relevant interaction mechanisms between NFX and BSA. Spectrophotometric titration with molecular docking results demonstrated that the binding site of NFX on BSA was located in sub-domain IIA. The principle binding site was identified within a hydrophobic cavity which is surrounded by the residues Leu 197, Arg 198, Ser 201, Ala 209, Trp 213, Ser 343, Leu 346, Lys 350, Ser 453, Leu 480, Val 481, and the binding force was mainly hydrophobic interaction and hydrogen bond interaction. In addition, the absorptive orientation of the NFX molecule on the colloidal surface underwent a set of changes during the process of NFX binding to BSA.

Label-free SERS in biological and biomedical applications: Recent progress, current challenges and opportunities

To achieve an insightful look within biomolecular processes on the cellular level, the development of diseases as well as the reliable detection of metabolites and pathogens, a modern analytical tool is needed that is highly sensitive, molecular-specific and exhibits fast detection. Surface-enhanced Raman spectroscopy (SERS) is known to meet these requirements and, within this review article, the recent progress of label-free SERS in biological and biomedical applications is summarized and discussed. This includes the detection of biomolecules such as metabolites, nucleic acids and proteins. Further, the characterization and identification of microorganisms has been achieved by label-free SERS-based approaches. Eukaryotic cells can be characterized by SERS in order to gain information about the outer cell wall or to detect intracellular molecules and metabolites. The potential of SERS for medically relevant detection schemes is emphasized by the label-free detection of tissue, the investigation of body fluids as well as applications for therapeutic and illicit drug monitoring. The review article is concluded with an evaluation of the recent progress and current challenges in order to highlight the direction of label-free SERS in the future.

SERS Quantification and Characterization of Proteins and Other Biomolecules

Changes in protein expression levels and protein structure may indicate genomic mutations and may be related to some diseases. Therefore, the precise quantification and characterization of proteins can be used for disease diagnosis. Compared with several other alternative methods, surface-enhanced Raman scattering (SERS) spectroscopy is regarded as an excellent choice for the quantification and structural characterization of proteins. Herein, we review the main advance of using plasmonic nanostructures as SERS sensing platform for this purpose. Three design approaches, including direct SERS, indirect SERS, and SERS-encoded nanoparticles, are discussed in the direction of developing new precise approaches of quantification and characterization of proteins. While this Review is focused on proteins, in order to highlight concepts of SERS-based sensors also detection of other biomolecules will be discussed.

In vivo confocal Raman spectroscopy and molecular dynamics analysis of penetration of retinyl acetate into stratum corneum

OBJECTIVE

The purpose of this study is to elucidate the behavior of retinyl acetate in penetrating human skin without the presence of enhancers by using confocal Raman spectroscopy and molecular dynamics simulation.

METHODS

In this study, in vivo confocal Raman spectroscopy was combined with molecular dynamics simulation to investigate the transdermal permeation of the aqueous suspension of retinyl acetate.

RESULTS

Permeation was measured after 30min, and retinyl acetate was found up to 20μm deep inside the stratum corneum. The delivery of retinyl acetate inside a skin membrane model was studied by molecular dynamics. The membrane model that was used represented normal young skin containing a lipid bilayer with 25% ceramide, 36% fatty acid, 30% cholesterol, and 6% cholesterol sulfate.

CONCLUSION

Spectroscopy data indicate that retinyl acetate permeates into the stratum corneum. Molecular dynamics data showed that retinyl acetate permeates in the membrane model and that their final location is deep inside the lipid bilayer. We showed, for the first time, a correlation between Raman permeation data and computational data.

A Dual Non-ATP Analogue Inhibitor of Aurora Kinases A and B, Derived from Resorcinol with a Mixed Mode of Inhibition

Aurora kinases are the most commonly targeted mitotic kinases in the intervention of cancer progression. Here, we report a resorcinol derivative, 5-methyl-4-(2-thiazolylazo) resorcinol (PTK66), a dual inhibitor of Aurora A and Aurora B kinases. PTK66 is a surface binding non-ATP analogue inhibitor that shows a mixed pattern of inhibition against both of Aurora A and B kinases. The in vitro IC50 is approximately 47 and 40 μm for Aurora A and Aurora B kinases, respectively. In cellular systems, PTK66 exhibits a substantially low cytotoxicity at micromolar concentrations but it can induce aneuploidy under similar dosages as a consequence of Aurora kinase inhibition. This result was corroborated by a drop in the histone H3 (S10) phosphorylation level detected via Western blot analysis using three different cell types. Altogether, our findings indicate that the ligand containing resorcinol backbone is one of the novel scaffolds targeting the Aurora family of kinases, which could be a target for antineoplastic drug development.

Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse

This report proposes a label-free, versatile approach for screening drugs of abuse using a combination of protein tethering and surface-enhanced Raman spectroscopy.

Revealing the trehalose mediated inhibition of protein aggregation through lysozyme-silver nanoparticle interaction

We propose a facile and robust carbohydrate-mediated method for the prevention of nanoparticle induced denaturation and aggregation of proteins. Using label-free plasmon-enhanced Raman spectroscopy measurements, the mechanistic principles of trehalose stabilization in a model protein-nanoparticle system are elucidated for the first time, facilitating its further application in diagnostic and therapeutic nanoplex development.

Using surface enhanced Raman scattering to analyze the interactions of protein receptors with bacterial quorum sensing modulators

Many members of the LuxR family of quorum sensing (QS) transcriptional activators, including LasR of Pseudomonas aeruginosa, are believed to require appropriate acyl-homoserine lactone (acyl-HSL) ligands to fold into an active conformation. The failure to purify ligand-free LuxR homologues in nonaggregated form at the high concentrations required for their structural characterization has limited the understanding of the mechanisms by which QS receptors are activated. Surface-enhanced Raman scattering (SERS) is a vibrational spectroscopy technique that can be applied to study proteins at extremely low concentrations in their active state. The high sensitivity of SERS has allowed us to detect molecular interactions between the ligand-binding domain of LasR (LasRLBD) as a soluble apoprotein and modulators of P. aeruginosa QS. We found that QS activators and inhibitors produce differential SERS fingerprints in LasRLBD, and in combination with molecular docking analysis provide insight into the relevant interaction mechanism. This study reveals signal-specific structural changes in LasR upon ligand binding, thereby confirming the applicability of SERS to analyze ligand-induced conformational changes in proteins.

Solution processed nanomanufacturing of SERS substrates with random Ag nanoholes exhibiting uniformly high enhancement factors

An Ag film exhibits an enhanced Raman signal over unusually large areas due to surface plasmons around its nanoholes. The SERS signal is increased by optical interference effects and the uniformity of the signal is improved by electrical activation.

Size and distribution control of surface plasmon enhanced photoluminescence and SERS signal in Ag–GaN hybrid systems

In the present experiment, two GaN nanowall network (NWN) samples with different porosity were grown on c-sapphire substrates using plasma assisted molecular beam epitaxy (PA-MBE).