Chemometrics in investigation of small molecule-biomacromolecule interactions: A review

Thiazolyl hydrazineylidenyl indolones as unique potential multitargeting broad-spectrum antimicrobial agents

The emergence of pathogenic and drug-resistant microorganisms seriously threatens public safety. This work constructed a unique type of thiazolyl hydrazineylidenyl indolones (THIs) to combat global microbial multidrug-resistance. Bioactive evaluation discovered that some target THIs displayed much superior antimicrobial efficacy than clinical chloromycetin, norfloxacin, cefdinir or fluconazole against the tested strains. Eminently, butyl THI 6c displayed a broad antimicrobial spectrum with low MICs of 0.25-1 μg/mL. The highly active THI 6c not only showed low cytotoxicity and hemolysis, rapidly bactericidal ability, good antibiofilm activity and promising pharmacokinetic properties, but also could significantly impede the development of bacterial resistance. Preliminary exploration of antibacterial mechanism revealed that THI 6c could effectively penetrate the cell membrane of MRSA and embed DNA to form 6c‒DNA supramolecular complex and thus hinder DNA replication. Moreover, THI 6c could reduce cell metabolic activity, which might be attributed to the fact that THI 6c could target the pyruvate kinase of MRSA and interfere with the function of the enzyme. These results provided powerful information for further developing thiazolyl hydrazineylidenyl indolones as new broad-spectrum antimicrobial agents.

Ultrasensitive biosensing of thiram based on detection of the DNA damage induced by thiram: Application to investigation of protective effects of extra virgin olive oil against DNA damage

In this work, a novel electrochemical biosensor was fabricated based on modification of a glassy carbon electrode (GCE) with nafion-DNA/gold nanoparticles/poly-ethylenedioxy pyrrole/multi-walled carbon nanotubes-ionic liquid (NF-DNA/Au NPs/PEDOP/MWCNTs-IL/GCE) with the aim of amperometric detection of the DNA damage induced by thiram (TH). By incubation of the biosensor with the TH, the TH was intercalated within DNA, and the exposed DNA released negative charges at the surface of the biosensor which repelled the probe molecules and caused the amperometric response of the biosensor to be decreased. Protective effects of extra virgin olive oil (EVOO) on the DNA damage induced by the TH were investigated by recording amperometric responses of the biosensor in the presence of EVOO, and the results confirmed that the response of the biosensor didn't change to confirm the protective effects of the EVOO on preventing the DNA damage induced by the TH. A novel and sensitive electroanalytical method was developed for determination of the TH in two linear ranges including 1-6 pM and 7-10 pM based on amperometric detection of the DNA damage induced by the TH which gave a LOD of 0.31 pM. The developed methodology in this work was successful in detection of the DNA damage induced by TH, detection of protective effects of EVOO on preventing DNA damage and determination of the TH in real matrices.

Affinity binding of COVID-19 drug candidates (chloroquine/hydroxychloroquine) and serum albumin: Based on photochemistry and molecular docking

Chloroquine (CQ) and hydroxychloroquine (HCQ) show good efficacy in the treatment of SARS-CoV-2 in the early stage, while they are no longer recommended due to their side effects. As an important drug delivery carrier, serum albumin (SA) is closely related to the efficacy of drugs. Here, the affinity behaviour of chloroquine and hydroxychloroquine with two SA were investigated through the multispectral method of biochemistry and computer simulation. The results showed that the intrinsic emission of both SA was quenched by CQ and HCQ in a spontaneous exothermic entropy reduction static process, which relied mainly on hydrogen bonding and van der Waals forces. The lower binding constants suggested weak binding between the two drugs and SA, which might lead to differences in efficacy and possibly even to varying side effects. Binding site recognition demonstrated that CQ preferred to bind to the two sites of both SA, while HCQ tended to bind to site I of SA. The results of conformational studies demonstrated that CQ and HCQ could affect the structure of both SA by slightly increasing the α-helix content of SA. Finally, we combine the results from experimental start with molecular simulations to suggest drug modifications to guide the design of drugs. This work has important implications for guiding drug design improvements to select CQ derivatives with fewer side effects for the treatment of COVID-19.

Determination of Characteristic Volatile Component Fingerprint of Peucedanum Praeruptorum Dunn at Different Harvest Periods Based on HS-GC-IMS

BACKGROUND

Peucedanum praeruptorum Dunn (PPD) is a Chinese herbal medicine with medicinal value. Clinical studies have shown that PPD has protective effects against wind-heat, cough, asthma, cardiovascular diseases, and cancer. Therefore, cultivation of PPD is becoming more common. However, it has been difficult to determine the optimal harvest period for botanical Chinese medicines such as PPD.

OBJECTIVES

Odor characteristics are directly related to the chemical components contained in traditional Chinese medicines. In particular, for traditional Chinese medicines such as PPD that are rich in volatile components, higher quality usually means more beneficial volatile components. The purpose of this study was to analyze changes in PPD volatile components across different harvest periods, and provide the basis for the identification of the ideal harvest period to ensure PPD quality.

METHODS

We measured the volatile components of PPD at different harvest periods using HS-GC-IMS to characterize its volatile component fingerprint at different harvest periods.

RESULTS

We identified 80 volatile components in PPD across five harvest periods, and combined complex heatmap and PCA methods distinguish the characteristics of the different harvest periods, and used ion mobility spectrometry to determine the volatile organic compounds (VOCs), which mainly included compounds such as olefins, esters, alcohols, aldehydes, and ketones, and determined that the abundance of volatile components reached a peak in December.

CONCLUSIONS

The fingerprint determination of characteristic volatile components based on HS-GC-IMS can distinguish PPD in different harvest periods.

HIGHLIGHTS

We used HS-GC-IMS to determine the characteristic fingerprint of volatile components from PPD across different harvest periods. This approach differs from past studies, which have determined the optimal harvest time of medicinal materials based on only the content of a single active ingredient.

Chemometrics-assisted electrochemical biosensing of cholesterol as the sole precursor of steroids by a novel electrochemical biosensor

This project was performed with the aims of increasing the sensitivity of differential pulse voltammetry (DPV) which itself is a sensitive electroanalytical technique, and also to compare the area under peak (univariate calibration), height of peak (univariate calibration) and whole of vector (multivariate calibration) for calibration purposes. These topics were investigated by fabrication of a novel electrochemical biosensor for determination of cholesterol (CHO). The procedure used in this project was based on the synthesis of molecularly imprinted polymers (MIPs) to the preconcentration of CHO and its biosensing by a rotating glassy carbon electrode (GCE) modified by co-immobilization of cholesterol oxidase (CO), cholesterol esterase (CE) and horseradish peroxidase (HP) onto multiwalled carbon nanotubes-ionic liquid (COCEHP/MWCNTs-IL/GCE). The results showed that the hydrodynamic DPV (HYDPV) was much more sensitive than DPV and using the area under peak for univariate calibration purposes was more suitable than height of peak. Adsorption at the electrode surface is an important trouble which affects the height and position of voltammetric peaks, but the area under peak is not affected by adsorption therefore, it can be more suitable for univariate calibration purposes. The biosensor response was also calibrated by chronoamperometry and the results confirmed that the HYDPV was more sensitive than chronoamperometry. The next attempt was based on recording the biosensor responses based on second-order HYDPV data and modeling of them (whole of vectors) by three-way calibration methods which showed the best performance among the tested methods for determination of CHO. The biosensor response was long-term stable, repeatable and reproducible which was successfully applied to the analysis of serum sample towards determination of CHO whose results were comparable with a reference method.

Sensitive and selective simultaneous biosensing of nandrolone and testosterone as two anabolic steroids by a novel biosensor assisted by second-order calibration

Recently, our research group have focused on an interesting project in which a novel dual template molecularly imprinted (DTMIP) biosensor was fabricated and assisted by second-order differential pulse voltammetric (DPV) data for simultaneous determination of nandrolone decanoate (ND) and testosterone decanoate (TS). An indium tin oxide (ITO) was modified with multiwalled carbon nanotubes-graphene-ionic liquid (MWCNT-Gr-IL) and then, the fullerene C₆₀ was casted onto the surface of MWCNT-Gr-IL/ITO and electrochemically reduced. Finally, DTMIPs were electrosynthesized by electropolymerization of 4-aminobenzoic acid (ABA) as monomer with ND and TS as template molecules to obtain the final structure of the biosensor (DTMIP/C₆₀/MWCNT-Gr-IL/ITO). Structure of the biosensor was electrochemically and microscopically characterized. The ND and TS generated two severely overlapped DPVs at the surface of the biosensor which forced us to assist the biosensor with three-way calibration by second-order DPV data to simultaneous determine them. Two second-order algorithms including multivariate curve resolution alternating least squares (MCR-ALS) and parallel factor analysis2 (PARAFAC2) were used to build second-order calibration models and evaluation of their performance in the analysis of synthetic samples showed more superiority of the MCR-ALS than PARAFC2 which motivated us to select PARAFC2 for the analysis of urine samples as real cases. Application of the biosensor assisted by PARAFC2 for the analysis of urine samples towards simultaneous determination of ND and TS was successful.

Forensic Analysis of Textile Synthetic Fibers Using a FT-IR Spectroscopy Approach

Synthetic fibers are one of the most valuable trace lines of evidence that can be found in crime scenes. When textile fibers are analyzed properly, they can help in finding a linkage between suspect, victim, and the scene of the crime. Various analytical techniques are used in the examination of samples to determine relationships between different fabric fragments. In this exploratory study, multivariate statistical methods were investigated in combination with machine learning classification models as a method for classifying 138 synthetic textile fibers using Fourier transform infrared spectroscopy, FT-IR. The data were first subjected to preprocessing techniques including the Savitzky–Golay first derivative method and Standard Normal Variate (SNV) method to smooth the spectra and minimize the scattering effects. Principal Component Analysis (PCA) was built to observe unique patterns and to cluster the samples. The classification model in this study, Soft Independent Modeling by Class Analogy (SIMCA), showed correct classification and separation distances between the analyzed synthetic fiber types. At a significance level of 5%, 97.1% of test samples were correctly classified.

Resolving interactions of miglitol with normal and glycated human serum albumin by multivariate methods

This article reports results of one of our projects related to the investigation of interactions of miglitol (MIG) with normal human serum albumin (HSA) and glycated HSA (GHSA) with the help of recording spectroscopic and electrochemical data. The experimental data were analyzed by conventional and chemometric methods to extract useful information for comprehensive justifications of the interactions of the MIG with HSA and GHSA. Hard- and soft-modeling chemometric methods were used to extract quantitative and qualitative information. Then, molecular docking techniques were used to further investigation of the binding of the MIG with HSA and GHSA and the extracted results were compatible with those obtained by experimental methods. Finally, according to the binding of the BV with HSA and GHSA, second-order differential pulse voltammetric data were recorded and calibrated with three-way calibration methods for exploiting second-order advantage for determination of the GHSA in the presence of the HSA to develop a novel chemometrics assisted-electroanalytical method for diagnostic and monitoring of diabetic.