Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting.

A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.

Detoxification of comfrey (Symphytum officinale L.) extract using natural deep eutectic solvent (NADES) and evaluation of its anti-inflammatory, antioxidant, and hepatoprotective properties.

Comfrey (Symphytum officinale L.) contains rosmarinic acid which has different pharmacological activities, such as antioxidant and anti-inflammatory activities. However, the medicinal use of comfrey is limited by the hepatotoxic effect of lycopsamine in comfrey, which overshadows the health benefits of rosmarinic acid. Natural deep eutectic solvents (NADES) have a wide range of extraction properties, that provides a new approach to the detoxification of comfrey. In the present study, betaine-based and choline chloride-based NADES were screened for selective extraction of rosmarinic acid over lycopsamine. Ultrasonication was used in conjunction with NADES extraction. The chemical profile of the NADES extracts on antioxidant, anti-inflammatory and hepatotoxic activities were investigated using some chemical reagents. Betaine-urea (1:2 molar ratio, 50% water) obtained the highest content of rosmarinic acid and a low level of lycopsamine (1.934 and 0.018 mg/g, respectively). Betaine-urea was also shown to be more effective to extract rosmarinic acid compared to methanol-UAE under the same conditions, which gave lower rosmarinic acid and higher lycopsamine levels (0.007 and 0.031 mg/g, respectively). Betaine-urea extracts showed higher antioxidant and anti-inflammatory properties as compared with other NADES extracts, however, had lower hepatotoxic profile. This study recommends the use of betaine-urea to detroxify comfrey to open wider opportunities for the development of comfrey for medicinal use.

Development and validation of a UPLC-MS/MS method with volumetric absorptive microsampling to quantitate cyclophosphamide and 4-hydroxycyclophosphamide.

Cyclophosphamide (CP) is an anti-cancer alkylating prodrug, metabolized by CYP450 into its active metabolite 4-hydroxycyclophosphamide (4-OHCP). Its therapeutic effectiveness is determined by the 4-OHCP concentration. Several analytical methods in plasma and dried blood spots have been developed to analyze cyclophosphamide and 4-OHCP; however, there are many disadvantages. The objective of this study was to develop and validate the ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method by volumetric absorptive microsampling (VAMS) and 4-hydroxycyclophosphamide-d4 (4-OHCP-d4) as an internal standard. VAMS requires small sample volumes, and it is not affected by the hematocrit values; therefore, it is an efficient sampling method. The samples were derivatized with 5 µL semicarbazide hydrochloride (SCZ) and 25 µL of the resulting 4-OHCP-SCZ; 4-OHCP-d4-SCZ derivatives were absorbed by VAMS and extracted by protein precipitation. The optimum conditions were obtained using the Waters Acquity® UPLC BEH C18 (2.1 × 100 mm; 1.7 µm) column; flow rate 0.15 ml/min; mobile phase 0.01% formic acid and methanol; gradient elution mode for 6 min by positive electrospray ionization; and multiple reaction monitoring of m/z 260.7 > 140.0 for CP, 333.7 > 221.0 for 4-OHCP-SCZ, and 337.7 > 225.1 for 4-OHCP-d4-SCZ. The method met the validation requirements set by the FDA. The cyclophosphamide LLOQ value was 5 ng/mL, and the calibration curve range was 5-60,000 ng/ml. Furthermore, the 4-OHCP LLOQ value was 2.5 ng/ml, and the calibration curve range was 2.5-1,000 ng/ml.

Biodelignification of lignocellulose using ligninolytic enzymes from white-rot fungi.

Lignocellulose is the most abundant biomass available on earth, including wood and agricultural wastes such as rice straw, corn cobs, and oil palm empty bunches. The biopolymer content in lignocellulose has a great potential as feedstock for producing industrial raw materials such as glucose, sorbitol, xylose, xylitol, and other pharmaceutical excipients. Currently, scientists and governments agree that the enzymatic delignification method is an environmentally friendly green method to be applied. This review attempts to explain the proper preparation of the enzymes laccase, lignin peroxidase, and manganese peroxidase, as well as the important factors influencing their activity. The recent applications of the enzymes for detoxification of hazardous substances, proper enzyme immobilization technique, and future prospect combination with DESs extraction of lignin are also discussed.

Methods of Random Mutagenesis of Aspergillus Strain for Increasing Kojic Acid Production.

Kojic acid is an organic acid that is commonly used in the pharmaceutical and cosmetic industries. This acid compound is a secondary metabolite produced by various microorganisms, one of which is Aspergillus oryzae. Typically, improving the strain can enhance kojic acid production. A mutation is one of the tools to perform strain improvement because the change in kojic acidproducing genes effectively increases kojic acid yield. A random mutagenesis is a classic approach for inducing and producing mutants with random mutations. The mutagenesis can be generated by the individual physical and chemical mutagen, combined physical and chemical mutagens, or initiate by protoplast preparation. Aspergillus strains that are exposed to physical mutagens (e.g., UV) or chemical mutagens (e.g., N-methyl-N-nitro-N-nitrosoguanidine (NTG)) showed their abilities in increasing kojic acid production. Several new mutation methods, such as Ion Beam Implantation and Atmospheric and room temperature plasma (ARTP), also showed good responses in enhancing the production of biological products such as kojic acid. This review compared different random mutagenesis methods of Aspergillus strain with various mutagen types to provide better insight for researchers in choosing the most suitable method to increase kojic acid production.

Effect of gamma irradiation on the caffeoylquinic acid derivatives content, antioxidant activity, and microbial contamination of Pluchea indica leaves.

Pluchea indica (L.) Less. leaf has a long history of being used as a food and in traditional medicines. Although gamma irradiation is an effective decontamination method, it must be performed appropriately to preserve the bioactive constituents and biological activities of the plant. This study investigated the influence of gamma irradiation on the caffeoylquinic acid derivatives content, antioxidant capacity, and microbial burden of P. indica leaf. Dried P. indica leaf powder was exposed to gamma rays from cobalt-60 at the absorbed doses of 2.5, 5.0, 7.5, and 10 kGy. After a maceration of P. indica leaf with 70% ethanol, the content of six caffeoylquinic acid derivatives (CQAs) in the extract was assayed using high-performance liquid chromatography. The antioxidant capacity of the ethanolic extract was also determined using the DPPH, ABTS, and ferric reducing antioxidant power (FRAP) methods. The total aerobic bacteria and total yeast and mold counts were investigated using the Petrifilm method at 0 and 3 months after irradiation. Doses of 5-10 kGy significantly increased the CQA level (P < 0.05). The antioxidant activity was enhanced significantly at 2.5-10 kGy (P < 0.05). Doses of 2.5-10 kGy also effectively reduced the microbial load (P < 0.05). Among the irradiation doses, 10 kGy showed the best results. Thus, gamma irradiation at 10 kGy is useful in increasing CQA content and antioxidant capacity as well as reducing the microbial load of P. indica leaf.

Method Development and Validation for Measuring O6-Methylguanine in Dried Blood Spot Using Ultra High-Performance Liquid Chromatography Tandem Mass Spectrometry.

BACKGROUND: Cyclophosphamide is a nitrogen mustard chemotherapy drug that damages DNA through alkylation in the DNA base and produces DNA adducts. Alkylation that occurs in the N7 position of guanine base has a cytotoxic effect which is useful for cancer therapy. However, the alkylation that occurs in the O6 position of guanine bases can have mutagenic and carcinogenic effects that can trigger secondary cancer. This carcinogenic compound can be found in very low concentrations in cancer patients who had been receiving alkylating agents as their anticancer therapy. Analysis of O6-methylguanine can be one of the ways of therapeutic drug monitoring to avoid secondary cancer risk. This study aims to develop a sensitive, selective, and validated analytical method using Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS). METHODS: Analysis of O6-methylguanine was done in Dried Blood Spot (DBS) and using allopurinol as an internal standard. The optimal analysis conditions were obtained using a C18 Acquity® Bridged Ethylene Hybrid (BEH) column (1.7 µm, 100 mm x 2.1 mm); mobile phase was 0.05% formic acid - acetonitrile (95:5 v/v); flow rate 0.1 mL/minute; gradient elution for 6 minutes; and detection at m/z 165.95 > 149 for O6-methylguanine and m/z 136.9 > 110 for allopurinol. RESULTS: The present study has fulfilled the FDA validation parameter requirements. The method provides rapid, sensitive, and selective analysis of O6-methylguanine using UPLC-MS/MS with a linear concentration range between 0.5-20 ng/mL.

Development and Validation of Doxorubicin Hydrochloride and Doxorubicinol Quantification Method in Dried Blood Spot by Liquid Chromatography-Tandem Mass Spectrometry.

Dried blood spot as biosampling method offers a less invasive and easier procedure. This study aimed to develop the validated analytical method of doxorubicin hydrochloride and doxorubicinol simultaneously in dried blood spot with hexamethylphosphoramide as the internal standard. A total of 30 µL blood was spotted on DBS paper and dried for 3 hours before it was extracted by protein precipitation method using water and methanol. The separation was performed on column Acquity UHPLC BEH C-18 (2.1 × 100 mm; 1.7 µm), with 0.15 mL/min flow rate and using 0.1% acetic acid and acetonitrile as mobile phase in gradient elution for 7 min. Quantification analysis was performed by a triple quadrupole mass spectrometry with electrospray ionization (ESI) in positive ion mode. The multiple reaction monitoring (MRM) was set at m/z 544.22 > 397.06 for doxorubicin hydrochloride; m/z 546.22 > 361.05 for doxorubicinol; and m/z 180.03 > 135.16 for hexamethylphosphoramide. The lower limit of quantitation was 10 ng/mL for doxorubicin and 4 ng/mL for doxorubicinol. Concentration range acquired was 10-200 ng/mL for doxorubicin and 4-100 ng/mL for doxorubicinol. The precision and accuracy were within acceptable criteria of <15%. Dried blood spot samples acquired was stable for at least 30 days before analysis. This method fulfilled the validation requirement refers to Bioanalytical Method Validation Guideline of European Medicines Agency 2011 and US Food and Drug Administration 2018.