Dilek Celebi, Hilal Akalin, Mustafa Tugrul Yilmaz, Munis Dundar
Abstract Climate change has imposed a significant struggle for survival most of the Earth’s species, highlighting the urgent need for a healthy and secure environment. Recent scientific investigations have primarily concentrated on the development and use of microorganisms as powerful biotechnological tools to address the escalating pollution that poses a severe threat to life. But this microorganisims long-term effects on biodiversity and ecosystems remain a subject of inquiry. In this comprehensive review, we aim to thoroughly evaluate the effects of microorganisms on the general ecosystem and critically assess the use of existing biotechnological tools developed to combat climate-related challenges. By shedding light on the potential implications, this review strives to contribute to a deeper understanding of the intricate interplay between microorganisms, ecosystems, and climate change mitigation.
{"title":"Impacts of Biotechnologically Developed Microorganisms on Ecosystems","authors":"Dilek Celebi, Hilal Akalin, Mustafa Tugrul Yilmaz, Munis Dundar","doi":"10.2478/ebtj-2023-0015","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0015","url":null,"abstract":"Abstract Climate change has imposed a significant struggle for survival most of the Earth’s species, highlighting the urgent need for a healthy and secure environment. Recent scientific investigations have primarily concentrated on the development and use of microorganisms as powerful biotechnological tools to address the escalating pollution that poses a severe threat to life. But this microorganisims long-term effects on biodiversity and ecosystems remain a subject of inquiry. In this comprehensive review, we aim to thoroughly evaluate the effects of microorganisms on the general ecosystem and critically assess the use of existing biotechnological tools developed to combat climate-related challenges. By shedding light on the potential implications, this review strives to contribute to a deeper understanding of the intricate interplay between microorganisms, ecosystems, and climate change mitigation.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135708021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Bioactive peptides are protein components which are inactive within the protein structure, and upon release by enzymatic hydrolysis, they exhibit special physiological functions. In the last years, the characteristics of bioactive peptides obtained from various plant, animal and microbial sources have received much attention. Bioactive peptides are produced using hydrolysis by enzymes extracted from plants or microorganisms, or digestive enzymes and fermentation by proteolytic starter cultures. The composition and sequence of the amino acids determines their different functions, including relaxing effects, solute binding properties, strengthening of the immune system, antioxidant, anti-microbial, anti-inflammatory, cholesterol-lowering and anti-hypertensive effects. Bioactive peptides are identified by different methods including membrane separation techniques and chromatography from protein hydrolysis products and using spectrometric techniques. The possibility of using bioactive peptides as health or therapeutic components depends on ensuring their bio stability, bioavailability and safety.
{"title":"Bioactive peptides: a review","authors":"Maghsoud Besharati, Maximilian Lackner","doi":"10.2478/ebtj-2023-0013","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0013","url":null,"abstract":"Abstract Bioactive peptides are protein components which are inactive within the protein structure, and upon release by enzymatic hydrolysis, they exhibit special physiological functions. In the last years, the characteristics of bioactive peptides obtained from various plant, animal and microbial sources have received much attention. Bioactive peptides are produced using hydrolysis by enzymes extracted from plants or microorganisms, or digestive enzymes and fermentation by proteolytic starter cultures. The composition and sequence of the amino acids determines their different functions, including relaxing effects, solute binding properties, strengthening of the immune system, antioxidant, anti-microbial, anti-inflammatory, cholesterol-lowering and anti-hypertensive effects. Bioactive peptides are identified by different methods including membrane separation techniques and chromatography from protein hydrolysis products and using spectrometric techniques. The possibility of using bioactive peptides as health or therapeutic components depends on ensuring their bio stability, bioavailability and safety.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135708180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Veronica Casali, Ingrid Clerc Guithon, Boudewijn van der Sanden, Olivier Stephan, Laetitia Gredy, Isabelle Vilgrain, Donald K Martin
Abstract An increasingly relevant functional measurement is a liquid biopsy to assist in the diagnosis of cancers. The existing approach for liquid biopsy is to utilize microfluidic chips for the isolation of circulating tumor cells (CTCs) or exosomes or extracellular vesicles (EV) from patient samples, and then for the analysis of the cargo contained inside the CTCs, exosomes or EVs. However, such an analysis does not provide a real-time liquid biopsy, since there is a long delay between the time of sample collection and the results from the analysis. Microfluidic chip-formats also provide the capability to mimic tissue functions from the analysis of small numbers of cells cultured in the chip. Analysis of the secreted molecules from such cells could provide a measurement of the secretome, which could be analogous to a liquid biopsy. A 3D structural organization of cells in microfluidic chips is usually in the form of organoids or spheroids. The analysis of organoids or spheroids is well-adapted for immunohistochemistry or ELISA-type identification of surface markers, but not for real-time analysis of secreted molecules since the fluid and molecules in the interior volume of the organoid or spheroid is not accessible in real-time. We have recently proposed an alternative novel design for a microfluidic chip format comprising 3D micro-niches that provide a real-time analysis of secretions produced directly from small numbers of cells. The microfluidic chip with 3D micro-niches then analyses the secretions from these monolayers in real-time (“secretome”). The microfluidic chip includes electronic biosensors that provide real-time measurement of secreted molecules. This short review concludes with a proposition for the means to utilize this novel microfluidic chip to function as a real-time and quantifiable diagnostic screening device to differentiate cancerous cells from healthy cells.
{"title":"Is a real-time quantifiable liquid biopsy achievable using a microfluidic lab-on-chip ?","authors":"Veronica Casali, Ingrid Clerc Guithon, Boudewijn van der Sanden, Olivier Stephan, Laetitia Gredy, Isabelle Vilgrain, Donald K Martin","doi":"10.2478/ebtj-2023-0014","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0014","url":null,"abstract":"Abstract An increasingly relevant functional measurement is a liquid biopsy to assist in the diagnosis of cancers. The existing approach for liquid biopsy is to utilize microfluidic chips for the isolation of circulating tumor cells (CTCs) or exosomes or extracellular vesicles (EV) from patient samples, and then for the analysis of the cargo contained inside the CTCs, exosomes or EVs. However, such an analysis does not provide a real-time liquid biopsy, since there is a long delay between the time of sample collection and the results from the analysis. Microfluidic chip-formats also provide the capability to mimic tissue functions from the analysis of small numbers of cells cultured in the chip. Analysis of the secreted molecules from such cells could provide a measurement of the secretome, which could be analogous to a liquid biopsy. A 3D structural organization of cells in microfluidic chips is usually in the form of organoids or spheroids. The analysis of organoids or spheroids is well-adapted for immunohistochemistry or ELISA-type identification of surface markers, but not for real-time analysis of secreted molecules since the fluid and molecules in the interior volume of the organoid or spheroid is not accessible in real-time. We have recently proposed an alternative novel design for a microfluidic chip format comprising 3D micro-niches that provide a real-time analysis of secretions produced directly from small numbers of cells. The microfluidic chip with 3D micro-niches then analyses the secretions from these monolayers in real-time (“secretome”). The microfluidic chip includes electronic biosensors that provide real-time measurement of secreted molecules. This short review concludes with a proposition for the means to utilize this novel microfluidic chip to function as a real-time and quantifiable diagnostic screening device to differentiate cancerous cells from healthy cells.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135707860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Obsessive-Compulsive Disorder (OCD) is a psychiatric illness that produces significant psychological distress in patients. Individuals with OCD have recurring unwanted thoughts or sensations which make them obsessed with something and feel to do something repetitively as a compulsion. In general detection of OCD is performed by symptoms analysis. However, the symptoms are significantly visible at a later stage. Even individuals with OCD have less faith in the analysis of the symptoms as long as it is not affecting their life negatively. As a result, they start their treatment at a later stage and the treatment process becomes longer. However, it is observed that if the detection is performed through laboratory analysis through some biomarkers then the patients have more faith in the detection process and can start their treatment well in advance. Therefore laboratory detection of OCD can play a vital role in OCD treatment effectiveness. Most of the laboratory detection process proposed in the literature uses Machine Learning on related biomarkers. However, the prediction accuracy rate is not enough. This research aims to analyze the approaches to pediatric OCD based on machine learning using neuroimaging biomarkers and oxidative stress biomarkers. The challenges in OCD detection and prediction using neuroimaging biomarkers, oxidative stress biomarkers, and Machine Learning models have been described. Further, it analyzes the performance of different machine learning models that were used for OCD detection and highlights the research gap to improve prediction accuracy.
{"title":"Machine Learning Approaches for Obsessive Compulsive Disorder Detection","authors":"Kabita Patel, Ajaya K. Tripathy","doi":"10.2478/ebtj-2023-0012","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0012","url":null,"abstract":"Abstract Obsessive-Compulsive Disorder (OCD) is a psychiatric illness that produces significant psychological distress in patients. Individuals with OCD have recurring unwanted thoughts or sensations which make them obsessed with something and feel to do something repetitively as a compulsion. In general detection of OCD is performed by symptoms analysis. However, the symptoms are significantly visible at a later stage. Even individuals with OCD have less faith in the analysis of the symptoms as long as it is not affecting their life negatively. As a result, they start their treatment at a later stage and the treatment process becomes longer. However, it is observed that if the detection is performed through laboratory analysis through some biomarkers then the patients have more faith in the detection process and can start their treatment well in advance. Therefore laboratory detection of OCD can play a vital role in OCD treatment effectiveness. Most of the laboratory detection process proposed in the literature uses Machine Learning on related biomarkers. However, the prediction accuracy rate is not enough. This research aims to analyze the approaches to pediatric OCD based on machine learning using neuroimaging biomarkers and oxidative stress biomarkers. The challenges in OCD detection and prediction using neuroimaging biomarkers, oxidative stress biomarkers, and Machine Learning models have been described. Further, it analyzes the performance of different machine learning models that were used for OCD detection and highlights the research gap to improve prediction accuracy.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135708016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The study has developed a model splicing construct assay system based on splicing misregulation, one of the major molecular features associated with myotonic dystrophy. The splicing construct assay has double reporters for intron 2 splicing in chloride channel (CLCN1). The CLCN1 transgene splicing construct assay was used to transfect wild type and DM fibroblast cell lines and the clones generated showed that it enabled quantification of splicing efficiency in transgene construct. Validation of the DM fibroblasts containing transgene splicing construct was performed by differentiating the DM fibroblasts into myoblasts which exhibited a switch in CLCN1 splicing construct which was consistent with that associated with myotonic dystrophy (DM) condition. The myoblast derived from fibroblasts cell-based gene-splicing assay was subsequently applied in therapeutic screening in small throughput screens of 113 compounds which identified Protein Kinase C inhibitors- hypericin and Ro-31-8220 as potential therapeutic agents. The CLCN1 gene-splicing assay is a good model system for application in therapeutic screening in myotonic dystrophy because its double reporters facilitated quantification of effect putative drug on correction of misregulated splicing.
{"title":"A Cell-Based Double Reporter Gene Splicing Assay for Therapeutic Screening in Myotonic Dystrophy","authors":"I. Udosen, J. Granados, J. Brook","doi":"10.2478/ebtj-2023-0011","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0011","url":null,"abstract":"Abstract The study has developed a model splicing construct assay system based on splicing misregulation, one of the major molecular features associated with myotonic dystrophy. The splicing construct assay has double reporters for intron 2 splicing in chloride channel (CLCN1). The CLCN1 transgene splicing construct assay was used to transfect wild type and DM fibroblast cell lines and the clones generated showed that it enabled quantification of splicing efficiency in transgene construct. Validation of the DM fibroblasts containing transgene splicing construct was performed by differentiating the DM fibroblasts into myoblasts which exhibited a switch in CLCN1 splicing construct which was consistent with that associated with myotonic dystrophy (DM) condition. The myoblast derived from fibroblasts cell-based gene-splicing assay was subsequently applied in therapeutic screening in small throughput screens of 113 compounds which identified Protein Kinase C inhibitors- hypericin and Ro-31-8220 as potential therapeutic agents. The CLCN1 gene-splicing assay is a good model system for application in therapeutic screening in myotonic dystrophy because its double reporters facilitated quantification of effect putative drug on correction of misregulated splicing.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48008108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Suparerk Oonchit, B. Cherdhirunkorn, P. Tharabenjasin, N. Pabalan, Kumpol Chintanavilas, Robert S Marks, Yardnapar Parcharoen, C. Pechyen
Abstract This study aimed to modify screen-printed carbon micro-electrode surfaces by coating them with multiwall carbon-based nanotubes conjugated with chitosan and then validated the formed multiwall carbon-based nanotubes-chitosan coated screen printed carbon micro-electrode for the detection of homocysteine, a biomarker analyte known as a risk indicator in cardiovascular disease. The microstructure surface and crystallographic structure stability of the formed multiwall carbon-based nanotubes-chitosan obtained at formed multiwall carbon-based nanotubes per chitosan ratios of 1:1, 2:1, 3:1, and 4:1 were examined via field emission scanning electron microscopy, X-ray radiation, Raman spectroscopy, surface area and pore size, and thermogravimetric analyses. Homocysteine solutions at 30–100 µM were measured by cyclic voltammetry using the different formed multiwall carbon-based nanotubes-chitosan compositions as sensor electrodes. That with an optimal formed multiwall carbon-based nanotubes per chitosan ratio of 4:1 showed the highest crystallinity and electrical conductivity and gave a high coefficient of determination (R2 = 0.9036) between the homocysteine concentration and the oxidation current detection over an operating range of 30–100 µM. This new composite microelectrode for detecting homocysteine concentration makes it a promising candidate for clinical applications.
{"title":"Electrode surfaces based on multiwall carbon nanotubes-chitosan composites validated in the detection of homocysteine biomarkers for cardiovascular disease risk monitoring","authors":"Suparerk Oonchit, B. Cherdhirunkorn, P. Tharabenjasin, N. Pabalan, Kumpol Chintanavilas, Robert S Marks, Yardnapar Parcharoen, C. Pechyen","doi":"10.2478/ebtj-2023-0010","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0010","url":null,"abstract":"Abstract This study aimed to modify screen-printed carbon micro-electrode surfaces by coating them with multiwall carbon-based nanotubes conjugated with chitosan and then validated the formed multiwall carbon-based nanotubes-chitosan coated screen printed carbon micro-electrode for the detection of homocysteine, a biomarker analyte known as a risk indicator in cardiovascular disease. The microstructure surface and crystallographic structure stability of the formed multiwall carbon-based nanotubes-chitosan obtained at formed multiwall carbon-based nanotubes per chitosan ratios of 1:1, 2:1, 3:1, and 4:1 were examined via field emission scanning electron microscopy, X-ray radiation, Raman spectroscopy, surface area and pore size, and thermogravimetric analyses. Homocysteine solutions at 30–100 µM were measured by cyclic voltammetry using the different formed multiwall carbon-based nanotubes-chitosan compositions as sensor electrodes. That with an optimal formed multiwall carbon-based nanotubes per chitosan ratio of 4:1 showed the highest crystallinity and electrical conductivity and gave a high coefficient of determination (R2 = 0.9036) between the homocysteine concentration and the oxidation current detection over an operating range of 30–100 µM. This new composite microelectrode for detecting homocysteine concentration makes it a promising candidate for clinical applications.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47943351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lei Tian, D. Luo, Rui Li, Pengrui Jiao, Zhiwei Zhou, Robert S Marks, Qun Sun
Abstract Bacteroides xylanisolvens Y-11 and Bifidobacterium longum y37 isolated from human gut were found to inhibit each other's growth after co-culturing in previous studies. To further reveal the potential mechanism of mutual inhibition between them, ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to investigate the metabolic changes of the strains after monoculture and co-culture, and the key differential metabolites were subject to the validation. The results showed that the types and amounts of metabolites were significantly changed during co-culture, with hydrocarbons and their derivatives, organic acids and esters being the main differential metabolites, which posed a greater influence on the metabolism of B. xylanisolvens Y-11 than on B. longumy y37. Further studies suggest that cycloserine and succinic acid may be the main metabolites that inhibit the growth of both strains, and the decrease of pH may be the main reason for succinic acid to inhibit the growth of the two strains. Moreover, B. longum y37 played a dominant role in the co-culture and its metabolites influenced the growth of B. xylanisolvens Y-11 to a greater extent. This study provides a new perspective for further understanding of the interaction between intestinal microbes and the influence of intestinal microecology on the occurrence and development of diseases.
{"title":"The metabolic mechanism of growth inhibition by co-culture of Bacteroides xylanisolvens Y-11 and Bifidobacterium longum y37","authors":"Lei Tian, D. Luo, Rui Li, Pengrui Jiao, Zhiwei Zhou, Robert S Marks, Qun Sun","doi":"10.2478/ebtj-2023-0008","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0008","url":null,"abstract":"Abstract Bacteroides xylanisolvens Y-11 and Bifidobacterium longum y37 isolated from human gut were found to inhibit each other's growth after co-culturing in previous studies. To further reveal the potential mechanism of mutual inhibition between them, ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to investigate the metabolic changes of the strains after monoculture and co-culture, and the key differential metabolites were subject to the validation. The results showed that the types and amounts of metabolites were significantly changed during co-culture, with hydrocarbons and their derivatives, organic acids and esters being the main differential metabolites, which posed a greater influence on the metabolism of B. xylanisolvens Y-11 than on B. longumy y37. Further studies suggest that cycloserine and succinic acid may be the main metabolites that inhibit the growth of both strains, and the decrease of pH may be the main reason for succinic acid to inhibit the growth of the two strains. Moreover, B. longum y37 played a dominant role in the co-culture and its metabolites influenced the growth of B. xylanisolvens Y-11 to a greater extent. This study provides a new perspective for further understanding of the interaction between intestinal microbes and the influence of intestinal microecology on the occurrence and development of diseases.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45239946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV), also known as SARS-CoV-2, have caused global epidemics with high morbidity and mortality. Active research on finding effective drugs against 2019-nCoV/SARS-CoV-2 is going on. In silico screening represents the best approach for hits identification and could shorten the time and reduce cost compared to de novo drug discovery. Recently, CoV2 mutations have been a big concern in India, particularly on non-structural proteins (NSPs) and Spike Protein (B.1.617) which are the key targets that play a pivotal role in mediating viral replication and transcription. Herein, this study analyzed the NSPs and spike’s structural aspects of mutant strains of SARS-CoV-2. The three-dimensional structures of NSPs and S Spike proteins were retrieved from the protein data bank or modeled. And a dataset of an antiviral compound library containing 490,000 drug-like ligands and structurally diverse biologically active scaffolds was used for our studies. Initially, the molecular alignment was performed for library compounds with the reference drug molecule to find targets that match the field points. Antiviral compounds having a similarity score >0.6; were selected for further docking studies with wild and mutant NSPs and S Spike protein of SARS-CoV-2 variant B.1.617. The docking studies identified a potent analog MA-11, which exhibited the highest binding affinity towards wild and mutant proteins. Further, molecular dynamics simulation studies of selected compounds confirmed their perfect fitting into NSP12 and spike active sites and offer direction for further lead optimization and rational drug design.
{"title":"Insilico Screening for Identification of Hits against SARS-Cov-2 Variant of Concern B.1.617 and NSP12 Mutants by Molecular Docking and Simulation Studies","authors":"Vinuthna Vani Madishetti, Sudhakar Reddy, S. Kalagara, Ashish Garg, Sreenivas Enaganti, Sardar Hussain","doi":"10.2478/ebtj-2023-0009","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0009","url":null,"abstract":"Abstract Human coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV) and 2019 novel coronavirus (2019-nCoV), also known as SARS-CoV-2, have caused global epidemics with high morbidity and mortality. Active research on finding effective drugs against 2019-nCoV/SARS-CoV-2 is going on. In silico screening represents the best approach for hits identification and could shorten the time and reduce cost compared to de novo drug discovery. Recently, CoV2 mutations have been a big concern in India, particularly on non-structural proteins (NSPs) and Spike Protein (B.1.617) which are the key targets that play a pivotal role in mediating viral replication and transcription. Herein, this study analyzed the NSPs and spike’s structural aspects of mutant strains of SARS-CoV-2. The three-dimensional structures of NSPs and S Spike proteins were retrieved from the protein data bank or modeled. And a dataset of an antiviral compound library containing 490,000 drug-like ligands and structurally diverse biologically active scaffolds was used for our studies. Initially, the molecular alignment was performed for library compounds with the reference drug molecule to find targets that match the field points. Antiviral compounds having a similarity score >0.6; were selected for further docking studies with wild and mutant NSPs and S Spike protein of SARS-CoV-2 variant B.1.617. The docking studies identified a potent analog MA-11, which exhibited the highest binding affinity towards wild and mutant proteins. Further, molecular dynamics simulation studies of selected compounds confirmed their perfect fitting into NSP12 and spike active sites and offer direction for further lead optimization and rational drug design.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47006932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Background: Current threats connected to the ongoing depletion of fossil resources and elevated levels of greenhouse gases accelerating climate change and global warming provoke a renaissance of biotechnological production of various organic bulk chemicals, which, particularly during the second half of the 20th century, were almost exclusively produced from fossil resources via chemosynthetic processes. Scope: Besides the manufacture of bioethanol, a product obtained by microbial fermentation, biogenic production of solvents and energy carriers like acetone, isopropanol, 2,3-butanediol, or 1-butanol, hence, processes known since the beginning of the last century, experiences now a substantial revival. Summary of new synthesis and conclusions reached in the review: The review illustrates how to produce these products by resorting to fossil raw materials instead of petrochemical production processes, and how this can be accomplished by the cultivation of anaerobic organisms, namely facultatively anaerobic yeasts and bacteria (production of ethanol or 2,3-butanediol), and strictly anaerobic Clostridia (1-butanol, acetone, or isopropanol) on renewable resources. Moreover, novel methods for producing biodiesel-like methyl-esters of aerobically produced bacterial polyhydroxyalkanoate biopolyester building blocks combine the synthesis of microbial biopolyesters from wastewater with the progress of innovative renewable energy carriers. The biochemical background, the current state of research and development, and the status of industrialization of these processes are reviewed. Conclusion: Challenges to make these bioprocesses, based on inexpensive renewable resources, competitive with or even superior to petrochemical production routes in terms of sustainability, scalability, and economic feasibility still exist: however, they can be overcome by the concerted action of various scientific disciplines.
{"title":"Biotechnological Approaches to Generate Biogenic Solvents and Energy Carriers from Renewable Resources","authors":"M. Koller","doi":"10.2478/ebtj-2023-0007","DOIUrl":"https://doi.org/10.2478/ebtj-2023-0007","url":null,"abstract":"Abstract Background: Current threats connected to the ongoing depletion of fossil resources and elevated levels of greenhouse gases accelerating climate change and global warming provoke a renaissance of biotechnological production of various organic bulk chemicals, which, particularly during the second half of the 20th century, were almost exclusively produced from fossil resources via chemosynthetic processes. Scope: Besides the manufacture of bioethanol, a product obtained by microbial fermentation, biogenic production of solvents and energy carriers like acetone, isopropanol, 2,3-butanediol, or 1-butanol, hence, processes known since the beginning of the last century, experiences now a substantial revival. Summary of new synthesis and conclusions reached in the review: The review illustrates how to produce these products by resorting to fossil raw materials instead of petrochemical production processes, and how this can be accomplished by the cultivation of anaerobic organisms, namely facultatively anaerobic yeasts and bacteria (production of ethanol or 2,3-butanediol), and strictly anaerobic Clostridia (1-butanol, acetone, or isopropanol) on renewable resources. Moreover, novel methods for producing biodiesel-like methyl-esters of aerobically produced bacterial polyhydroxyalkanoate biopolyester building blocks combine the synthesis of microbial biopolyesters from wastewater with the progress of innovative renewable energy carriers. The biochemical background, the current state of research and development, and the status of industrialization of these processes are reviewed. Conclusion: Challenges to make these bioprocesses, based on inexpensive renewable resources, competitive with or even superior to petrochemical production routes in terms of sustainability, scalability, and economic feasibility still exist: however, they can be overcome by the concerted action of various scientific disciplines.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":null,"pages":null},"PeriodicalIF":1.7,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46527641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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