Showing papers in "3 biotech in 2022"

Hippocampus and its involvement in Alzheimer’s disease: a review

Abstract: Hippocampus is the significant component of the limbic lobe, which is further subdivided into the dentate gyrus and parts of Cornu Ammonis. It is the crucial region for learning and memory; its sub-regions aid in the generation of episodic memory. However, the hippocampus is one of the brain areas affected by Alzheimer's (AD). In the early stages of AD, the hippocampus shows rapid loss of its tissue, which is associated with the functional disconnection with other parts of the brain. In the progression of AD, atrophy of medial temporal and hippocampal regions are the structural markers in magnetic resonance imaging (MRI). Lack of sirtuin (SIRT) expression in the hippocampal neurons will impair cognitive function, including recent memory and spatial learning. Proliferation, differentiation, and migrations are the steps involved in adult neurogenesis. The microglia in the hippocampal region are more immunologically active than the other regions of the brain. Intrinsic factors like hormones, glia, and vascular nourishment are instrumental in the neural stem cell (NSC) functions by maintaining the brain's microenvironment. Along with the intrinsic factors, many extrinsic factors like dietary intake and physical activity may also influence the NSCs. Hence, pro-neurogenic lifestyle could delay neurodegeneration.

Deep learning tools for advancing drug discovery and development

Abstract: A few decades ago, drug discovery and development were limited to a bunch of medicinal chemists working in a lab with enormous amount of testing, validations, and synthetic procedures, all contributing to considerable investments in time and wealth to get one drug out into the clinics. The advancements in computational techniques combined with a boom in multi-omics data led to the development of various bioinformatics/pharmacoinformatics/cheminformatics tools that have helped speed up the drug development process. But with the advent of artificial intelligence (AI), machine learning (ML) and deep learning (DL), the conventional drug discovery process has been further rationalized. Extensive biological data in the form of big data present in various databases across the globe acts as the raw materials for the ML/DL-based approaches and helps in accurate identifications of patterns and models which can be used to identify therapeutically active molecules with much fewer investments on time, workforce and wealth. In this review, we have begun by introducing the general concepts in the drug discovery pipeline, followed by an outline of the fields in the drug discovery process where ML/DL can be utilized. We have also introduced ML and DL along with their applications, various learning methods, and training models used to develop the ML/DL-based algorithms. Furthermore, we have summarized various DL-based tools existing in the public domain with their application in the drug discovery paradigm which includes DL tools for identification of drug targets and drug-target interaction such as DeepCPI, DeepDTA, WideDTA, PADME DeepAffinity, and DeepPocket. Additionally, we have discussed various DL-based models used in protein structure prediction, de novo design of new chemical scaffolds, virtual screening of chemical libraries for hit identification, absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction, metabolite prediction, clinical trial design, and oral bioavailability prediction. In the end, we have tried to shed light on some of the successful ML/DL-based models used in the drug discovery and development pipeline while also discussing the current challenges and prospects of the application of DL tools in drug discovery and development. We believe that this review will be useful for medicinal and computational chemists searching for DL tools for use in their drug discovery projects.

Vaccine development to control the rising scourge of antibiotic-resistant Acinetobacter baumannii: a systematic review

Abstract: Acinetobacter baumannii has emerged as one of major nosocomial pathogen and global emergence of multidrug-resistant strains has become a challenge for developing effective treatment options. A. baumannii has developed resistance to almost all the antibiotics viz. beta-lactams, carbapenems, tigecycline and now colistin, a last resort of antibiotics. The world is on the cusp of post antibiotic era and the evolution of multi-, extreme- and pan-drug-resistant A. baumannii strains is its obvious harbinger. Various combinations of antibiotics have been investigated but no successful treatment option is available. All these failed efforts have led researchers to develop and implement prophylactic vaccination for the prevention of infections caused by this pathogen. In this review, the advantages and disadvantages of active and passive immunization, the types of sub-unit and multi-component vaccine candidates investigated against A. baumannii viz. whole cell organism, outer membrane vesicles, outer membrane complexes, conjugate vaccines and sub-unit vaccines have been discussed. In addition, the benefits of Reverse vaccinology are emphasized here in which the potential vaccine candidates are predicted using bioinformatic online tools prior to in vivo validations.

Kidney injury and oxidative damage alleviation by Zingiber officinale: pharmacokinetics and protective approach in a combined murine model of osteoporosis

Abstract: Ginger (Zingiber officinale) is considered as a nutraceutical spice, which possesses several health promotion and benefits. This study was carried out to investigate the phyto-chemical composition, the antioxidant capacities, the drug-likeness, and pharmacokinetic properties of ginger extract on kidney injury-associated osteoporosis in rats. Phenolic and flavonoid contents were assessed by standard chemical analysis methods and HPLC. In vivo protective effect was based on the use of female rats to evaluate the effect on renal injury as a result of combined osteoporosis using biochemical markers, oxidative status, and histological analyses. Results showed that ZO contained appreciable amounts of phenolics and flavonoids and it exhibited high scavenging activity. Ovariectomy-associated corticotherapy induced severe renal injury marked by altered biochemical markers (creatinine, urea, and uric acid), reduced GFR, significative oxidative damage signs, and disrupted antioxidant status in the combined osteoporotic rats. The histopathological examination revealed structural modifications of kidney tissues. However, all these changes were reversed following the use of ZO. These results confirm the renoprotective and antioxidant potential of ginger against renal injuries in osteoporotic rats.

Nano-biotechnology, an applicable approach for sustainable future

Abstract: Nanotechnology is one of the most emerging fields of research within recent decades and is based upon the exploitation of nano-sized materials (e.g., nanoparticles, nanotubes, nanomembranes, nanowires, nanofibers and so on) in various operational fields. Nanomaterials have multiple advantages, including high stability, target selectivity, and plasticity. Diverse biotic (e.g., Capsid of viruses and algae) and abiotic (e.g., Carbon, silver, gold and etc.) materials can be utilized in the synthesis process of nanomaterials. "Nanobiotechnology" is the combination of nanotechnology and biotechnology disciplines. Nano-based approaches are developed to improve the traditional biotechnological methods and overcome their limitations, such as the side effects caused by conventional therapies. Several studies have reported that nanobiotechnology has remarkably enhanced the efficiency of various techniques, including drug delivery, water and soil remediation, and enzymatic processes. In this review, techniques that benefit the most from nano-biotechnological approaches, are categorized into four major fields: medical, industrial, agricultural, and environmental.

Emerging uses of PLA–PEG copolymer in cancer drug delivery

Abstract: Traditional therapies need high systematic dosages that not only destroys cancerous cells but also healthy cells. To overcome this problem recent advancement in nanotechnology specifically in nanomaterials has been extensively done for various biological applications, such as targeted drug delivery. Nanotechnology, as a frontier science, has the potential to break down all the obstacles to be more effective and secure drug delivery system. It is possible to develop nanopolymer based drug carrier that can target drugs with extreme accuracy. Polymers can advance drug delivery technologies by allowing controlled release of therapeutic drugs in stable amounts over long duration of time. For controlled drug delivery, biodegradable synthetic polymers have various benefits over non-biodegradable polymers. Biodegradable polymer either are less toxic or non-toxic. Polylactic Acid (PLA) is one of the most remarkable amphipathic polymers which make it one of the most suitable materials for polymeric micelles. Amphiphilic nanomaterial, such as Polyethylene Glycol (PEG), is one of the most promising carrier for tumor targeting. PLA-PEG as a copolymer has been generally utilized as drug delivery system for the various types of cancer. Chemotherapeutic drugs are stacked into PLA-PEG copolymer and as a result their duration time delays, hence medications arrive at specific tumor site.

Therapeutic activity of fucoidan and carrageenan as marine algal polysaccharides against viruses

Abstract: Marine resources are today a renewable source of various compounds that are used in numerous industries. In recent years, considerable attention has been focused on diverse algae or their metabolites to develop several novel bioactive substances. Algae derivatives are defined as a food or part of food that has health benefits and prevention or treatment of disease. Algal sulfated polysaccharides have a high potential as a source of functional ingredients with a wide range of applications in the food and pharmaceutical industries. Fucoidan and carrageenan, as two main seaweed sulfated polysaccharides, possess numerous biological properties. These polysaccharides are highly valuable in food and healthy immune system diet and also can be applied in the pharmaceutical field. They have shown antiviral activity against SARS-CoV-2 causes COVID-19 infection by preventing virus entry into the cell or interfering with viral replication. Thus, they may provide some novel ingredients for the production of healthy functional foods, antiviral supplement formulations, or algal-based treatments for viral respiratory diseases, especially anti-COVID-19 and recommend solutions to this global health problem in the future. This article provides a review of recent researches on immune-boosting food ingredients, the antiviral activity of algae bioactive compounds, fucoidan, and carrageenan, in particular against SARS-CoV-2.

Endophytic fungi: a potential source of industrial enzyme producers

Abstract: Microbial enzymes have gained interest for their widespread use in various industries and medicine due to their stability, ease of production, and optimization. Endophytic fungi in plant tissues produce a wide range of secondary metabolites and enzymes, which exhibit a variety of biological activities. The present review illustrates promising applications of enzymes produced by endophytic fungi and discusses the characteristic features of the enzymes, application of the endophytic fungal enzymes in therapeutics, agriculture, food, and biofuel industries. Endophytic fungi producing ligninolytic enzymes have possible biotechnological applications in lignocellulosic biorefineries. The global market of industrially important enzymes, challenges, and future prospects are illustrated. However, the commercialization of endophytic fungal enzymes for industrial purposes is yet to be explored. The present review suggests that endophytic fungi can produce various enzymes and may become a novel source for upscaling the production of enzymes of industrial use.

Drought tolerance improvement in Solanum lycopersicum: an insight into “OMICS” approaches and genome editing

Abstract: Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. “Omics” techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through “omics” and “multi-omics” technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.

Fabrication of a sensing platform for identification of tumor necrosis factor-alpha: a biomarker for neonatal sepsis

Abstract: Neonatal sepsis is a prime cause of neonatal deaths across the globe. Presently, various medical tests and biodevices are available in neonatal care. These diagnosis platforms possess several limitations such as being highly expensive, time-consuming, or requiring skilled professionals for operation. These limitations can be overcome through biosensor development. This work discusses the assembling of an electrochemical sensing platform that is designed to detect the level of tumor necrosis factor-alpha (TNF-α). The sensing platform was moderated with nanomaterials molybdenum disulfide nanosheets (MoS2NSs) and silicon dioxide-modified iron oxide nanoparticles (Fe3O4@SiO2NPs). The integration of nanomaterials helps in accomplishing the improved characteristics of the biosensor in terms of conductivity, selectivity, and sensitivity. Further, the molecularly imprinted polymer (MIP) approach was incorporated for sensing the presence of TNF-α on the surface of the working electrode. The electrochemical response of the electrode was recorded at different conditions. A broad concentration range was selected to optimize the biosensor from 0.01 pM to 100 nM. The sensitivity of the biosensor was higher and it exhibits a lower detection limit (0.01 pM).

Identification of antiviral peptide inhibitors for receptor binding domain of SARS-CoV-2 omicron and its sub-variants: an in-silico approach

Abstract: Omicron, a variant of concern (VOC) of SARS-CoV-2, emerged in South Africa in November 2021. Omicron has been continuously acquiring a series of new mutations, especially in the spike (S) protein that led to high infectivity and transmissibility. Peptides targeting the receptor-binding domain (RBD) of the spike protein by which omicron and its variants attach to the host receptor, angiotensin-converting enzyme (ACE2) can block the viral infection at the first step. This study aims to identify antiviral peptides from the Antiviral peptide database (AVPdb) and HIV-inhibitory peptide database (HIPdb) against the RBD of omicron by using a molecular docking approach. The lead RBD binder peptides obtained through molecular docking were screened for allergenicity and physicochemical criteria (isoelectric point (pI) and net charge) required for peptide-based drugs. The binding affinity of the best five peptide inhibitors with the RBD of omicron was validated further by molecular dynamics (MD) simulation. Our result introduces five antiviral peptides, including AVP1056, AVP1059, AVP1225, AVP1801, and HIP755, that may effectively hinder omicron-host interactions. It is worth mentioning that all the three major sub-variants of omicron, BA.1 (B.1.1.529.1), BA.2 (B.1.1.529.2), and BA.3 (B.1.1.529.3), exhibits conserved ACE-2 interacting residues. Hence, the screened antiviral peptides with similar affinity can also interrupt the RBD-mediated invasion of different major sub-variants of omicron. Altogether, these peptides can be considered in the peptide-based therapeutics development for omicron treatment after further experimentation.The online version contains supplementary material available at 10.1007/s13205-022-03258-4.

Recent advances in the bio-application of microalgae-derived biochemical metabolites and development trends of photobioreactor-based culture systems

Abstract: Microalgae are microscopic algae in sizes ranging from a few micrometers to several hundred micrometers. On average, half of the oxygen in the atmosphere is produced by the photosynthetic process of microalgae, so the role of these microorganisms in the life cycle of the planet is very significant. Pharmaceutical products derived from microalgae and commercial developments of a variety of supplements extracted from them originate from a variety of their specific secondary metabolites. Many of these microalgae are a reservoir of unique biological compounds including carotenoids, antioxidants, fatty acids, polysaccharides, enzymes, polymers, peptides, pigments, toxins and sterols with antimicrobial, antiviral, antifungal, antiparasitic, anticoagulant, and anticancer properties. The present work begins with an introduction of the importance of microalgae in renewable fuels and biodiesel production, the development of healthy food industry, and the creation of optimal conditions for efficient biomass yield. This paper provides the latest research related to microalgae-derived substances in the field of improving drug delivery, immunomodulatory, and anticancer attributes. Also, the latest advances in algal biocompounds to combat the COVID-19 pandemic are presented. In the subject of cultivation and growth of microalgae, the characteristics of different types of photobioreactors, especially their latest forms, are fully discussed along with their advantages and obstacles. Finally, the potential of microalgae biomass in biotechnological applications, biofuel production, as well as various biomass harvesting methods are described.

Bioactive properties of ZnO nanoparticles synthesized using Cocos nucifera leaves

Abstract: Biosynthesis of zinc oxide nanoparticles has been reported using Cocos nucifera leaf (CNL) extract along with estimation of their antimicrobial potential before and after calcination using different micro-organisms. UV–visible spectra of ZnO nanoparticles showed absorption maxima at 383 nm and 363 nm, respectively, with 3.237 eV and 3.416 eV, respectively, as the corresponding band gap energies. FESEM and TEM images showed spherical morphologies of ZnO nanoparticles within the size range 109–215 nm. XRD analysis confirmed the formation of hexagonal wurtzite structures. ATR-IR spectra revealed the presence of stretching vibrations of N–H, O–H, C=C, C=O and NH2 groups along with C–H and N–H deformation involving biomolecules from CNL extract responsible for reduction and stabilization of ZnO nanoparticles. Uncalcinated ZnO nanoparticles displayed antibacterial activities only against S. aureus and P. aeruginosa whereas calcinated ZnO nanoparticles did not show antibacterial activities against E. coli, S. aureus, P. aeruginosa and B. subtilis. ZnO nanoparticles were not active against Penicillium spp., Fusarium oxysporum, Aspergillus flavus, Rhizoctonia solani as well as HCT-116 cancer cells before as well as after calcination. Antimicrobial nature and biocompatibility of ZnO nanoparticles were influenced by different parameters of the nanoparticles along with micro-organisms and the human cells. Non-antimicrobial properties of ZnO nanoparticles can be treated as a pre-requisite for its biocompatibility due to its inert nature. These ZnO nanoparticles can serve a dual purpose by facilitating use as antibacterial agent against susceptible micro-organisms as well as a biocompatible carrier molecule in drug delivery applications.

Chemical investigation and screening of anti-cancer potential of Syzygium aromaticum L. bud (clove) essential oil nanoemulsion

Abstract: This study was done to improve the medicinal properties of Syzygium Aromaticum L by processing S. Aromaticum L. bud essential oil (SABE) to the Nanoemulsion drug delivery system (SABE-NE) and investigating its anti-tumor and apoptotic impacts against the human HT-29 colon cancer cells. Applying the ultra-sonication method and characterization by DLS and FESEM analysis facilitates the nanoemulsification procedure. Human cancer (HT-29) and normal (HFF) cell lines were then evaluated based on the SABE-NE apoptotic and cytotoxic effects. In an in vitro section, flow cytometry method, Cas3 gene profile, AO/PI cell staining, and MTT assays are used to analyze the apoptotic and cytotoxic activities. In further analysis, liver lipid peroxidation and antioxidant genes expression (SOD, CAT, and GPx) investigate alterations in mice organs. As a result, produced 131.2 nm SABE-NE induces apoptosis response and cellular death (Cas3 up-regulation and enhanced SubG1 peaks). Subsequently, the HT-29 cells' viability can reduce significantly, while HFF cells indicate confined cytotoxic impacts. Moreover, in vivo test results on mice livers demonstrate the cytoprotective properties of SABE-NE (reduced lipid peroxidation and increased antioxidant enzymes gene expression and nondetectable cytotoxic impacts). We produced a novel nanoemulsion drug delivery system called SABE-NE, a cell-specific apoptotic inducer. We thus can be utilized as an efficient anti-cancer compound for human colon cancer treatment. However, further supplementary studies are required to verify and approve its cell-specific anti-tumor activity.

Development and validation of rapid and cost-effective protocol for estimation of amylose and amylopectin in maize kernels

Abstract: Maize possesses wide variation in amylose and amylopectin which assumes significance as a part of both food-chain and different industrial applications. Estimation of amylose and amylopectin in maize kernels is important for developing suitable hybrids. The existing protocols for estimation of amylose and amylopectin in maize are elaborate and lengthy, and involve high cost. Here, we developed a rapid and cost-effective method for estimation of amylose and amylopectin in maize kernels. 10% toluene and 80% ethanol were used for removal of proteins (~ 10%) and lipids (~ 4%) from maize flour. The over-estimation of amylose was minimized using NaOH with KI to stop free KI to bind with amylopectin. Standards were improved by mixing amylose and amylopectin in different concentrations (0–100%), rather than using amylose or amylopectin alone. Standard curve generated regression equation of y = 90.436x + 0.8535 with R2 = 0.9989. Two types of samples viz., (1) protein, amylose and amylopectin (2) amylose and amylopectin, showed that starch fractions were highly comparable to expected values with correlation coefficient (r) of 0.9998 and mean standard deviation of 0.54. The protocol successfully estimated wide range of amylose (2.79–50.04%) and amylopectin (59.96–97.21%) among diverse maize inbreds including amylose extender1 (ae1) and waxy1 (wx1) mutants. Present protocol required 75% less time and 92.5% less cost compared to existing protocols. The newly developed method would be highly useful in developing maize hybrids high in amylose or amylopectin. This is the first report of rapid and cost-effective protocol for estimation of starch fractions in maize kernels.

Enhanced keratinase production by Bacillus subtilis amr using experimental optimization tools to obtain feather protein lysate for industrial applications

Abstract: The poultry industry produces millions of tons of feathers waste that can be transformed into valuable products through bioprocess. The study describes the enhanced keratinase and feather hydrolysate production by Bacillus subtilis AMR. The metabolism of each microorganism is unique, so optimization tools are essential to determine the best fermentation parameters to obtain the best process performance. The evaluation of different propagation media indicated the constitutive production of two keratinases of approximately 80 kDa. The combination of Mn2+, Ca2+, and Mg2+ at 0.5 mM improved the keratinolytic activity and feather degradation 1.5-fold, while Cu2+ inhibited the enzymatic activity completely. Replace yeast extract for sucrose increased the feather hydrolysate production three times. The best feather concentration for hydrolysate production was 1.5% with an inoculum of 108 CFU/mL and incubation at 30 °C. None of the inorganic additional nitrogen sources tested increased hydrolysate production, although (NH4)2SO4 and KNO3 improved enzymatic activity. The optimization process improved keratinolytic activity from 205.4 to 418.7 U/mL, the protein concentration reached 10.1 mg/mL from an initial concentration of 3.9 mg/mL, and the feather degradation improved from 70 to 96%. This study characterized keratinase and feather hydrolysate production conditions offering valuable information for exploring and utilizing AMR keratinolytic strain for feather valorization.The online version contains supplementary material available at 10.1007/s13205-022-03153-y.

Cerium oxide nanostructures: properties, biomedical applications and surface coatings

Abstract: Cerium oxide nanoparticles have significantly improved catalytic properties and are of increasing interest in the nanoparticle research field hence the current trends in cerium oxide nanoparticles are reviewed here. Unlike previous reviews which have focused primarily on the biosynthesis of cerium oxide nanoparticles, their properties, and applications, this review will focus on the unique physical, chemical, and biological properties of cerium oxide nanoparticles, the role of oxygen vacancies or defects in the lattice structure, the ratio of oxidation states in determining their catalytic properties and applications in biosensing, drug or gene delivery, etc. have been discussed. Furthermore, the limitations of the bare form of cerium oxide nanoparticles and the advances in the field of surface coating by different ligands to overcome the issues of bare nanoparticles have been discussed. The review concludes with a discussion on the environmental aspects and toxicity of cerium oxide nanoparticles and their potential future in practical applications.