BioChem, Volume 1, Issue 3 (December 2021) – 8 articles

The urgent need to fight the COVID-19 pandemic has impressively stimulated the efforts of the international scientific community, providing an extraordinary wealth of studies. After the sequence of the virus became available in early January 2020, safe and effective vaccines were developed in a time frame much shorter than everybody expected. However, additional studies are required since viral mutations have the potential of facilitating viral transmission, thus reducing the efficacy of developed vaccines. Therefore, improving the current laboratory testing methods and developing new rapid and reliable diagnostic approaches might be useful in managing contact tracing in the fight against both the original SARS-CoV-2 strain and the new, potentially fast-spreading CoV-2 variants. Mass Spectrometry (MS)-based testing methods are being explored, with the challenging promise to overcome the many limitations arising from currently used laboratory testing assays. More specifically, MALDI-MS, since its advent in the mid 1980s, has demonstrated without any doubt the great potential to overcome many unresolved analytical challenges, becoming an effective proteomic tool in several applications, including pathogen identification. With the aim of highlighting the challenges and opportunities that derive from MALDI-based approaches for the detection of SARS-CoV-2 and its variants, we extensively examined the most promising proofs of concept for MALDI studies related to the COVID-19 outbreak. Full article

Background: Diabetes is associated with chronic hyperglycaemia, long-term damage, dysfunction, and organ failure. This study aims to evaluate the antidiabetic activity of the twigs of Andrographis paniculata and its toxicological markers on Streptozotocin (STZ)-induced diabetic Albino rats. Methods: A total of thirty rats were randomly divided into five groups of six animals each. Non-diabetic animals were treated with distilled water as non-diabetic sham control group 1, while diabetic animals (group 2, 3, 4 and 5) were treated with 60 mg/kg bw STZ intravenous (iv) and 100 mg/kg body weight (bwt) of metformin orally for group 2, distilled water for group 3, and 250 and 500 mg/kg bwt of Andrograhis paniculata (A. paniculata) for groups 4 and 5, respectively. The animals were dosed for 28 days, after which they were sacrificed. Liver and kidney function tests as well as livid profile tests were used as the biomarkers of toxicological assessment. Fasting blood glucose was carried out weekly. Oral Glucose Tolerance Test (OGTT) was conducted on the 28th day of the antidiabetic assessment. Results: A. paniculata groups 4 and 5 were significant at different doses (p < 0.05) in reducing the blood glucose level in comparison with metformin. There were significant changes in total and direct bilirubin, total protein, potassium, triglyceride and inorganic phosphorus in 500 mg/kg bwt of the treated group in comparison with the metformin and diabetic group groups. A. paniculata at 500 mg/kg bwt is most effective for its antidiabetic and organ protecting effects. Full article

In the race against COVID-19 for timely therapeutic developments, mass spectrometry-based high-throughput methods have been valuable. COVID-19 manifests an extremely diverse spectrum of phenotypes from asymptomatic to life-threatening, drastic elevations in immune response or cytokine storm, multiple organ failure and death. These observations warrant a detailed understanding of associated molecular mechanisms to develop therapies. In this direction, high-throughput methods that generate large datasets focusing on changes in protein interactions, lipid metabolism, transcription, and epigenetic regulation of gene expression are extremely beneficial sources of information. Hence, mass spectrometry-based methods have been employed in several studies to detect changes in interactions among host proteins, and between host and viral proteins in COVID-19 patients. The methods have also been used to characterize host and viral proteins, and analyze lipid metabolism in COVID-19 patients. Information obtained using the above methods are complemented by high-throughput analysis of transcriptomic and epigenomic changes associated with COVID-19, coupled with next-generation sequencing. Hence, this review discusses the most recent studies focusing on the methods described above. The results establish the importance of mass spectrometry-based studies towards understanding the infection process, immune imbalance, disease mechanism, and indicate the potential of the methods’ therapeutic developments and biomarker screening against COVID-19 and future outbreaks. Full article

HIV-1 protease active site inhibitors are a key part of antiretroviral therapy, though resistance can evolve rendering therapy ineffective. Protease inhibitor resistance typically starts with primary mutations around the active site, which reduces inhibitor binding, protease affinity for substrate cleavage site residues P4-P4′, and viral replication. This is often followed by secondary mutations in the protease substrate-grooves which restore viral replication by increasing protease affinity for cleavage site residues P12-P5/P5′-P12′, while maintaining resistance. However, mutations in Gag alone can also result in resistance. The Gag resistance mutations can occur in cleavage sites (P12-P12′) to increase PR binding, as well as at non-cleavage sites. Here we show in silico that Gag non-cleavage site protease inhibitor resistance mutations can stabilize protease binding to Gag cleavage sites which contain structured subdomains on both sides: SP1/NC, SP2/p6, and MA/CA. The Gag non-cleavage site resistance mutations coordinated a network of H-bond interactions between the adjacent structured subdomains of the Gag substrates to form a substrate-clamp around the protease bound to cleavage site residues P12-P12′. The substrate-clamp likely slows protease disassociation from the substrate, restoring the cleavage rate in the presence of the inhibitor. Native Gag substrates can also form somewhat weaker substrate-clamps. This explains the 350-fold slower cleavage rate for the Gag CA/SP1 cleavage site in that the CA-SP1 substrate lacks structured subdomains on both sides of the cleavage site, and so cannot form a substrate-clamp around the PR. Full article

Tumor necrosis factor α (TNF-α) induces the nuclear factor κB (NF-κB) signaling pathway via TNF receptor 1 (TNF-R1). We recently reported that isopanduratin A inhibited the TNF-α-induced NF-κB signaling pathway in human lung adenocarcinoma A549 cells. In the present study, we found that isopanduratin A did not inhibit the interleukin-1α-induced NF-κB signaling pathway in A549 cells. Isopanduratin A down-regulated the expression of TNF-R1 in these cells. We also revealed that isopanduratin A down-regulated the cell surface expression of TNF-R1 by promoting the cleavage of TNF-R1 into its soluble forms. TAPI-2, an inhibitor of TNF-α-converting enzyme, suppressed the inhibitory activity of isopanduratin A against the TNF-α-induced activation of NF-κB. The mitogen-activated protein (MAP) kinase/extracellular signal-regulated kinase (ERK) kinase inhibitor U0126, but not the p38 MAP kinase inhibitor SB203580, blocked the ectodomain shedding of TNF-R1 induced by isopanduratin A. Consistent with this result, isopanduratin A induced the rapid phosphorylation of ERK, but not p38 MAP kinase. Isopanduratin A also promoted the phosphorylation of eukaryotic initiation factor 2α (eIF2α). The present results indicate that isopanduratin A inhibits TNF-α-induced NF-κB signaling pathway by promoting ERK-dependent ectodomain shedding of cell surface TNF-R1, and also decreases cellular TNF-R1 levels through the phosphorylation of eIF2α in A549 cells. Full article

This paper proposes a neuro-fuzzy system to model $\beta$-glucosidase activity based on the reaction’s pH level and temperature. The developed fuzzy inference system includes two input variables (pH level and temperature) and one output (enzyme activity). The multi-input fuzzy inference system was developed in two stages: first, developing a single input-single output fuzzy inference system for each input variable (pH, temperature) separately, using the robust adaptive network-based fuzzy inference system (ANFIS) approach. The neural network learning techniques were used to tune the membership functions based on previously published experimental data for $\beta$-glucosidase. Second, each input’s optimized membership functions from the ANFIS technique were embedded in a new fuzzy inference system to simultaneously encompass the impact of temperature and pH level on the activity of $\beta$-glucosidase. The required base rules for the developed fuzzy inference system were created to describe the antecedent (pH and temperature) implication to the consequent (enzyme activity), using the singleton Sugeno fuzzy inference technique. The simulation results from the developed models achieved high accuracy. The neuro-fuzzy approach performed very well in predicting $\beta$-glucosidase activity through comparative analysis. The proposed approach may be used to predict enzyme kinetics for several nonlinear biosynthetic processes. Full article

α-Lipoic acid (LA) has the specific absorption band at 330 nm and is quite vulnerable to UV irradiation, affording a variety of compounds including polymeric materials and hydrogen sulfide. A better understanding of the photochemical reaction of LA has already been carried out focusing mainly on the reaction product analysis derived from LA. We re-investigated the photochemical reaction of LA focusing our attention on the fate of hydrogen sulfide (H₂S) produced in the photochemical reaction procedure. The photoirradiation of LA in the presence of oxidized glutathione (GSSG) formed glutathione trisulfide (GSSSG) and a reduced form of glutathione (GSH). Similar results were obtained in the co-presence of cystine and dimethyl disulfide. The concentration of H₂S was reaching the maximum concentration, which was gradually decreasing within 10 min after photoirradiation, while the concentration of GSSSG was increasing with the decrease of H₂S concentration. The structural confirmation of GSSSG and the plausible mechanism for the formation of GSSSG are proposed based on the time-dependent and pH-dependent profile of the photoirradiation. Full article

The male reproductive system is highly susceptible to noxious influences, such as oxidative stress, inflammation, drugs, and even diseases that can induce germ cell damage and alterations in spermatogenesis. All of these factors, which are caused by actions at the testicular level and/or at the excurrent ducts and accessory glands, significantly affect sperm parameters and male fertility. For this reason, it is of major importance to investigate possible ways to protect the male reproductive system since males are exposed to these toxic factors constantly. For centuries, natural products have been used by humans in folk medicine as therapeutic agents, and because of their beneficial properties for human health, plenty of them have been introduced to the pharmaceutical market as supplementary therapies. The present review aims to compile available information regarding different natural exogenous factors that demonstrate potential useful activity in the male reproductive system. The studies presented here reopen the perspective of using natural products as protective agents and eventually as new supplementary therapeutic options for the recovery of hampered spermatogenesis and/or male infertility. Full article