In silico studies and development of a protein-based electrochemical sensor for selective and sensitive detection of aflatoxin B1.

Proteins from different species have been docked with aflatoxin B1 (AFB1) and identified 3 proteins (prostaglandin-E(2)9-reductase from Oryctolagus uniculus, proto-oncogene serine/threonine-protein kinase Pim-1 and human immunoglobulin G (hIgG)) as potential candidates to develop an electrochemical sensor. Fluorescence spectroscopy experiments have confirmed the interaction of hIgG with AFB1 with an affinity constant of 4.6 × 105 M-1. As a proof-of-concept, hIgG was immobilized on carbon nanocomposite (carbon nanotube-nanofiber, CNT-F)-coated glassy carbon electrode (GCE). FT-IR spectra, HR-TEM and BCA assay have confirmed successful immobilization of hIgG on the electrode (hIgG@CNT-F/GCE). The preparation of this protein electrochemical sensor requires only 1 h 36 min, which is fast as compared with preparing an electro immunosensor. hIgG@CNT-F/GCE has displayed an excellent AFB1 limit of detection (0.1 ng/mL), commendable selectivity in the presence of two other mycotoxins (ochratoxin A and patulin) and the detection of  AFB1 in spiked peanuts and corn samples.

A manganese dioxide nanoparticle-bimetallic metal organic framework composite for selective and sensitive detection of vitamin D3 in human plasma.

For the first time a metal organic framework nanomaterial has been developed comprising manganese dioxide nanoparticle and iron and zinc metal ions interlinked with each other via terephthalic acid. The framework shape was identified as an elongated hexagonal nanorod (TEM) with varying functional groups (FT-IR) and diffraction patterns (XRD). The framework nanocomposite as such in aqueous acidic electrolyte solution has displayed an excellent conductivity (redox behavior) and surface excess (3.08 × 10-8 cm-2). Under the optimized conditions (0.1 M H2SO4 as electrolyte, 50 mV/s scan rate, +1.26 V (vs Ag/AgCl)), the metal organic framework coated electrode has selectively identified vitamin D3 (VD3) in the presence of various other interfering molecules and displayed excellent limit of detection (1.9 ng mL-1). The developed sensor has been applied to the determination of VD3 in extracted human plasma samples (RSD of 0.3-2.6 % and recovery of 96-102 %), and the obtained VD3 values are similar to HPLC-UV method.

Titanium particles incorporated polymer monolith microcolumn for phosphoprotein enrichment from biological samples.

In proteomic studies, selective enrichment of target phosphoproteins from biological samples is of importance. Of various enrichment methods, affinity chromatography is widely preferred method. Development of micro-affinity columns with simple strategies are in constant demand. Here in this report, for the first time, we have embedded TiO2 particles within the monolith structure in a single step. Fourier transform infrared spectroscopy and scanning electron microscope analysis has confirmed the successful incorporation of TiO2 particles within the polymer monolith. Incorporation of 3-(trimethoxy silyl) propyl methacrylate within the poly(hydroxyethyl methacrylate) based monolith composition has enhanced its rigidity and one fold phosphoprotein (α-casein) adsorption capacity. Presence of only 66.6 µg of TiO2 particles within the monolith has displayed a four-fold higher affinity to α-casein over the non-phosphoprotein i.e. bovine serum albumin. Under optimized conditions (TiO2 particle and acrylate silane), the affinity monolith has a maximum adsorption capacity of ∼ 72 mg per gram monolith. Translation of TiO2 particles-monolith into a microcolumn of 3 cm long and 19 µL volume was successful. α-casein was selectively separated from an artificial protein mixture of α-casein and BSA, α-casein spiked human plasma, and cow milk within 7 min.

Recent Progress in Development and Application of DNA, Protein, Peptide, Glycan, Antibody, and Aptamer Microarrays.

Microarrays are one of the trailblazing technologies of the last two decades and have displayed their importance in all the associated fields of biology. They are widely explored to screen, identify, and gain insights on the characteristics traits of biomolecules (individually or in complex solutions). A wide variety of biomolecule-based microarrays (DNA microarrays, protein microarrays, glycan microarrays, antibody microarrays, peptide microarrays, and aptamer microarrays) are either commercially available or fabricated in-house by researchers to explore diverse substrates, surface coating, immobilization techniques, and detection strategies. The aim of this review is to explore the development of biomolecule-based microarray applications since 2018 onwards. Here, we have covered a different array of printing strategies, substrate surface modification, biomolecule immobilization strategies, detection techniques, and biomolecule-based microarray applications. The period of 2018-2022 focused on using biomolecule-based microarrays for the identification of biomarkers, detection of viruses, differentiation of multiple pathogens, etc. A few potential future applications of microarrays could be for personalized medicine, vaccine candidate screening, toxin screening, pathogen identification, and posttranslational modifications.

Fabrication of a bi-metallic metal organic framework nanocomposite for selective and sensitive detection of triclosan.

Transition metal-ion based nanocomposites are widely used owing to their ease of synthesis and cost-effectiveness in the sensor development. In this study, we have synthesized bi-metallic (iron and zinc) metal organic framework (MOF) nanorods-nanoparticles (denoted as Fe2Zn-MIL-88B) with a well-defined structure and characterized them. The bimetallic material nanocomposite (Fe2Zn-MIL-88B, nafion (Nf), and multiwalled carbon nanotube (MWCNT)) was fabricated on the electrode (glassy carbon electrode (GCE) or screen printed carbon electrode (SPCE)) surface within 10 min at room temperature. The Fe2Zn-MIL-88B/Nf/MWCNT@GCE showed an excellent electron transfer mechanism compared to a bare GCE and bare SPCE. The Fe2Zn-MIL-88B based nanocomposite electrode triggers the oxidation of the environmental carcinogenic molecule triclosan (TCS). Under optimized conditions, the sensor has a limit of detection of 0.31 nM and high selectivity to TCS in the presence of other interfering agents. The sensor has a good day-to-day TCS detection reproducibility. Fe2Zn-MIL-88B was stable even after 11 months of synthesis and detected TCS with similar sensitivity. The fabrication of the Fe2Zn-MIL-88B/Nf/MWCNT nanocomposite was successfully translated from the GCE to SPCE. TCS was detected in human plasma and commercial products such as soaps, skin care products, shampoos, and tooth pastes.

Preparation of Affinity Chromatography Monolith in Miniaturized Format and Application for Protein Separation.

Affinity chromatography is one of the versatile technique to selectively separate target biomolecules from complex biological sources (plasma, saliva, urine, etc.). Conventional chromatography resins possess technical limitations at mini-analytical scale, which was overcome with the use of alternative material known as monoliths. This chapter discusses on the how to modify the fused silica capillary inner surface, prepare polymer monoliths within the capillary confinements, chelation of metal-ions on monoliths and protein separation from diluted human plasma using metal-ion monolith microcolumn.

Identification and structural studies of natural inhibitors against SARS-CoV-2 viral RNA methyltransferase (NSP16).

Pathogenic RNA viruses are emerging as one of the major threats and posing challenges to human community. RNA viruses have an exceptionally shorter generation time and easy to adapt in host cells. The recent emergence of SARS-CoV-2, a long RNA virus, has shown us how difficult it is to overcome this kind of pandemic without understanding the viral infection and replication mechanisms. It is essential to comprehend replications of the viral genome, including RNA polymerization and the final capping process. The mRNAs of SARS-CoV-2 coronaviruses are protected at their 5'-ends by cap structure. The cap-like system plays a significant role in viral translational process, viral RNA stability, and scatting in detecting innate immune recognition in host cells. Two coronavirus enzymes, Nsp14 and Nsp16, critically help in the formation of capping and are considered as potential drug targets for antiviral therapy. Natural and herbal medicines have a past record of treating various acute respiratory diseases. In this work, we have exploited 56000 natural compounds to screen potential inhibitors against NSP16. In silico virtual screening, docking and Molecular Dynamics (MD) simulation studies were performed to understand how these potential inhibitors are bound to NSP16. We observed that the most highly screened compound binds to protein molecules with a high dock score, primarily through hydrophobic interactions and hydrogen bonding, as previously reported for NSP16. Compound-13 (2-hydroxy-N-({1-[2-hydroxy-1-(hydroxymethyl)ethyl]piperidin-3-yl}methyl)-5-methylbenzamide) and compound-51 (N-(2-isobutoxybenzyl)-N,2-dimethyl-2,8-diazaspiro[4.5]decane-3-carboxamide) occupied in active site along with good pharmokinetices properties. In conclusion, the selected compounds could be used as a novel therapeutic against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.

A review on recent advances in the enrichment of glycopeptides and glycoproteins by liquid chromatographic methods: 2016-Present.

Among various protein post-translational modifications (PTMs), glycosylation has received special attention due to its immense role in molecular interactions, cellular signal transduction, immune response, etc. Aberration in glycan moieties of a glycoprotein is associated with cancer, diabetes, and bacterial and viral infections. In biofluids (plasma, saliva, urine, milk, etc.), glycoproteins are low in abundance and are masked by the presence of high abundant proteins. Hence, prior to their identification using mass spectrometry methods, liquid chromatography (LC)-based approaches were widely used. A general enrichment strategy involves a protein digestion step, followed by LC-based enrichment and desorption of glycopeptides, and enzymatic excision of the glycans. The focus of this review article is to highlight the articles published since 2016 that dealt with different LC-based approaches for glycopeptide and glycoprotein enrichment. The preparation of stationary phases, their surface activation, and ligand immobilization strategies have been discussed in detail. Finally, the major developments and future trends in the field have been summarized.

A conjoint multi metal-ion iminodiacetic acid monolith microfluidic chip for structural-based protein pre-fractionation.

PDMS-based multichannel microfluidic chip was designed and fabricated in a simple approach using readily available tools. UV-initiated in situ polymerization of poly(2-hydroxy ethyl methacrylate-co-di(ethylene glycol) diacrylate-co-N,N'-diallyl l-tartardiamide) in an Eppendorf tube was achieved within 40 min. This polymerization process was successfully translated to a microfluidic chip format without any further modifications. Iminodiacetic acid was successfully immobilized on aldehyde functional monoliths via Schiff base reaction and confirmed by FT-IR spectroscopy. Four transition metal ions (Co (II), Zn (II), Ni (II), and Cu (II)) were chelated individually on four IDA-monolith microfluidic chips. The conjoint metal-ion monolith microfluidic chip has displayed high permeability (9.40 × 10-13  m2 ) and a porosity of 32.8%. This affinity microfluidic chip has pre-fractioned four human plasma proteins (fibrinogen, immunoglobulin, transferrin, and human serum albumin) based on their surface-exposed histidine surface topography. A protein recovery of approximately 95% (Bradford assay data) was achieved. The multimonolith microchip can be reusable even after three protein adsorption-desorption cycles.

A micro-solid phase extraction device to prepare a molecularly imprinted porous monolith in a facile mode for fast protein separation.

A molecularly imprinted polymeric monolith was synthesized in an aqueous environment in 15 min via UV-irradiation. The imprinted monolith was composed of hydroxyethyl methacrylate as monomer, dimethyl amino ethyl methacrylate as functional monomer, methylene bisacrylamide and piperazine diacrylamide as crosslinkers and human serum albumin as template molecule. The synthesis took place in a PDMS-based device (2.5 cm long) yielding a micro-solid phase extraction column (3 × 5 mm) with two built-in fingertight connectors for an infusion pump and fraction collector. The imprinted monolith displayed the characteristic features of a porous polymeric monolith, had dimethyl amino ethyl methacrylate and human serum albumin as functional groups within the monolith and showed high permeability (0.51 × 10-13 m2). 85% of the imprinted cavities were readily available for rebinding of human serum albumin with an imprinting factor of 1.3. In comparison to a non-imprinted monolith, molecular imprinting increased human serum albumin adsorption by > 30%. Imprinted monolith displayed selectivity for human serum albumin over other competing proteins (human transferrin, ovalbumin and carbonic anhydrase) with similar or different isoelectric points and size. Human serum albumin was adsorbed (in dynamic mode) with > 98% selectivity from diluted human plasma using the imprinted monolith device. Device to device reproducibility and reusability of the device for 5 cycles showcase the imprinted monolith micro-device efficiency.

Simplification of affinity macroporous monolith microfluidic column synthesis and its ability for protein separation.

A generic multi-component approach was designed to perform simultaneous in situ polymerization and ligand immobilization to develop affinity porous polymer based chromatography resin in a facile mode. This strategy exploits the regioselective ring opening reaction between epoxy group of monomer and native functional group of ligand (i.e. amine) under aqueous condition (pH 9.7). As a proof-of-concept, reaction of iminodiacetic acid (IDA) with allyl glycidyl ether (AGE) in presence of other monomer (HEMA) and crosslinkers (DATD, PDA) for 4 h via thermal initiation process (temperature of 65 °C) was shown. Successful polymerization (both ex situ &in situ) was confirmed by visual observation, surface morphology of the polymer by scanning electron microscope and ligand immobilization by FT-IR analysis. Chelation of the metal-ion i.e. copper (Cu (II)) with IDA in the monolith showed IgG adsorption capacity (27.8 mg/g monolith) over IDA-monolith without metal-ion. The affinity column has shown efficient capture of high abundant proteins such as IgG, transferrin and albumin from human plasma.

Development of a metal/chelate polyhydroxyethylmethacrylate monolith capillary for selective depletion of immunoglobulin G from human plasma for proteomics.

In this study, we report the development of a new poly HEMA (HEMA-co-DEGDA-co-DATD) monolith capillary functionalized with "IDA-Cu (II) complex". Of the two tested crosslinkers (methylene bisacrylamide (MBAAm) and diethylene glycol diacrylate (DEGDA)), presence of DEGDA has enhanced the monolith rigidity. Structural assembly of these monoliths are organized with highly interconnected large globule like structures and dominated by macropore region. Iminodiacetic acid (IDA) immobilization was performed using two chemical approaches (i. aldehyde - secondary amine reaction and ii. epoxy - sec. amine reaction). FT-IR analysis confirmed successful IDA immobilization in both cases. For the first time, a reaction of sec. amine ligand with aldehyde functional material was successfully reported. Overall, the Cu (II)-IDA monolith capillary showed good permeability (3.05×10 -13m2), high IgG adsorption capacity and reusablilty even after 5 consecutive adsorption-desorption cycles. The amount of protein (IgG/HSA) adsorbed on Cu (II)-IDA monolith prepared via the two chemistries is almost similar. Using this affinity monolith capillary, we selectively depleted ∼95% of IgG from human plasma (dilution of 1:16).

Preparation and characterization of a Cu (II)-IDA poly HEMA monolith syringe for proteomic applications.

Herein, we report the preparation of a metal-chelate immobilized hydrophilic poly hydroxyethylmethacrylate-based monolith of 100 µL volume in a plastic syringe. The monolith is elastic in nature, contains well interconnected pores with a permeability (k) of 1.3 × 10-12  m2 . Immobilization of iminodiacetic acid (IDA) is performed via schiff base reaction. Adsortion of IgG on this copper-IDA monolith is of langmuir isotherm with a maximum adsorption capacity of ∼25 mg IgG per g monolith. IgG adsorption capacity of this affinity monolith remained unaffected with increase of flow rate. This proposed metal-chelate monolith in syringe format has the potential for application in proteomics.

A structure based plasma protein pre-fractionation using conjoint immobilized metal/chelate affinity (IMA) system.

The potential of immobilized metal/chelate affinity (IMA) in a continuous fashion, referred as conjoint approach, to pre-fractionate plasma proteins (in their native state) prior to LC-MS analysis was investigated in this study. Four transition metal-ions (Co (II), Zn (II), Ni (II) and Cu (II)) were individually chelated with IDA (iminodiacetic acid) coated CIM (Convective Interaction Media) disks and placed in a single housing in the following sequential order: IDA-Co (II)→IDA-Zn (II)→IDA-Ni (II)→IDA-Cu (II). The rationale behind this order is to retain proteins based on their specific requirement for surface exposed histidine topography. This structural pre-fractionation hypothesis was successfully proven using four human plasma proteins (fibrinogen, IgG, transferrin, and albumin) with varying histidine topographies. This conjoint IMA pre-fractionation strategy not only fractionated proteins (from plasma) based on their native surface histidine topography, but also identified 157 proteins from human plasma. The advantage of our conjoint IMA is its ability to fractionate proteins in their native state and reduce plasma complexity in a single step by employing single buffer system.

A review on recent developments for biomolecule separation at analytical scale using microfluidic devices.

Microfluidic devices with their inherent advantages like the ability to handle 10(-9) to 10(-18) L volume, multiplexing of microchannels, rapid analysis and on-chip detection are proving to be efficient systems in various fields of life sciences. This review highlights articles published since 2010 that reports the use of microfluidic devices to separate biomolecules (DNA, RNA and proteins) using chromatography principles (size, charge, hydrophobicity and affinity) along with microchip capillary electrophoresis, isotachophoresis etc. A detailed overview of stationary phase materials and the approaches to incorporate them within the microchannels of microchips is provided as well as a brief overview of chemical methods to immobilize ligand(s). Furthermore, we review research articles that deal with microfluidic devices as analytical tools for biomolecule (DNA, RNA and protein) separation.

Selective depletion of neuropathy-related antibodies from human serum by monolithic affinity columns containing ganglioside mimics.

Monolithic columns containing ganglioside GM2 and GM3 mimics were prepared for selective removal of serum anti-ganglioside antibodies from patients with acute and chronic immune-mediated neuropathies. ELISA results demonstrated that anti-GM2 IgM antibodies in human sera and a mouse monoclonal anti-GM2 antibody were specifically and selectively adsorbed by monolithic GM2 mimic columns and not by blank monolithic columns or monolithic GM3 mimic columns. In control studies, serum antibodies against the ganglioside GQ1b from another neuropathy patient were not depleted by monolithic GM2 mimic columns. Fluorescence microscopy with FITC-conjugated anti-human immunoglobulin antibodies showed that the immobilized ganglioside mimics were evenly distributed along the column. The columns were able to capture ∼95% of the anti-GM2 antibodies of patients after only 2 min of incubation. A monolithic column of 4.4 µL can deplete 28.2 µL of undiluted serum. These columns are potential diagnostic and therapeutic tools for neuropathies related to anti-ganglioside antibodies.

Bioaffinity chromatography on monolithic supports.

Affinity chromatography on monolithic supports is a powerful analytical chemical platform because it allows for fast analyses, small sample volumes, strong enrichment of trace biomarkers and applications in microchips. In this review, the recent research using monolithic materials in the field of bioaffinity chromatography (including immunochromatography) is summarized and discussed. After giving an introduction into affinity chromatography, information on different biomolecules (antibodies, enzymes, lectins, aptamers) that can act as ligands in bioaffinity chromatography is presented. Subsequently, the history of monoliths, their advantages, preparation and formats (disks, capillaries and microchips) as well as ligand immobilization techniques are mentioned. Finally, analytical and preparative applications of bioaffinity chromatography on monoliths are presented. During the last four years 37 papers appeared. Protein A and G are still most often used as ligands for the enrichment of immunoglobulins. Antibodies and lectins remain popular for the analysis of mainly smaller molecules and saccharides, respectively. The highly porous cryogels modified with ligands are applied for the sorting of different cells or bacteria. New is the application of aptamers and phages as ligands on monoliths. Convective interaction media (epoxy CIM disks) are currently the most used format in monolithic bioaffinity chromatography.

A three-phase microfluidic chip for rapid sample clean-up of alkaloids from plant extracts.

A three-phase microchip was developed for the rapid and efficient small-scale purification of alkaloids from plant extracts. As part of the development of such a three-phase microchip, first a two-phase microchip with two channels (3.2 cm and 9.3 cm) was used to study the extraction efficiency of strychnine nitrate and strychnine at various flow rates. Strychnine was extracted from a basic aqueous phase to a chloroform phase (extraction) or strychnine was extracted from a chloroform phase into an acidic aqueous phase (back extraction). Subsequently, the "simultaneous extraction and back extraction" of strychnine was carried out in a three-phase microchip. The experimental extraction rate and yield were compared with model data. At a residence time of 25 sec, 79.5% of strychnine was extracted into the acidic aqueous phase using the three-phase microchip. In general, a good correlation was found between experimental results and model data for both two- and three-phase extractions. Finally, the three-phase microchip was employed in the purification of alkaloids (strychnine and brucine) from Strychnos seed extracts.

Single step synthesis of carbohydrate monolithic capillary columns for affinity chromatography of lectins.

Carbohydrate monolithic beds were synthesized in a single step in capillary columns to study affinity chromatography of lectins. In this method, carbohydrates (beta-galactose, beta-glucose, and alpha-mannose) with an easy to synthesize alkene terminated tetraethylene glycol spacer were used as functional monomers along the monomer 2-hydroxyethyl methacrylate (HEMA). As crosslinkers (+)-N,N'-diallyltartardiamide (DATD) and piperazine diacrylamide (PDA, 1,4-bisacryloyl-piperazine) were used. SEM showed the successful formation of monolithic beds in the capillary columns. The permeability of the columns was high. The specific interaction of the lectins Con A, Lens culinaris (LCA) and Arachis hypogaea (PNA) with the carbohydrate stationary phase was studied by frontal affinity chromatography (FAC). Con A and LCA were successfully eluted from the column using 0.1 M methyl-alpha-mannopyranoside and PNA with 0.1 M beta-galactose. Dissociation constants (Kd) for carbohydrate-lectin interactions were determined and compared with literature.