Bioinformatics and Biology Insights最新文献

{"title":"Antibacterial Activity of Economically Important Medicinal Plants in Pakistan Against Different Bacterial Strains.","authors":"Adil Ali,&nbsp;Muhammad Ali,&nbsp;Zonaira Nisar,&nbsp;Syed Muhammad Ali Shah,&nbsp;Imtiaz Mustafa,&nbsp;Jaweria Nisar,&nbsp;Rizwan Asif","doi":"10.1177/11779322231189374","DOIUrl":"https://doi.org/10.1177/11779322231189374","url":null,"abstract":"<p><p>The emergence of medication resistance and unfavorable side effects from existing antibiotics has prompted the quest for novel antimicrobial agents over the last 2 decades. Plant extracts have been shown to have antibacterial effects in numerous studies. The objective of this study was the evaluation of the antibacterial effect of economically important medicinal plants found in Pakistan. <i>Onosma bracteatum</i> (flowers and leaves), <i>Viola odorata</i> (flowers and leaves), <i>Cuscuta reflexa</i> (whole plant), <i>Swertia chirata</i> (whole plant), and <i>Fagonia arabica</i> (whole plant) were used against <i>Bacillus subtilis, Escherichia coli</i>, and <i>Pseudomonas aeruginosa.</i> Water and ethanol extracts were obtained from different parts of the plants. To evaluate the antibacterial effect of these plants, qualitative assay agar well diffusion method was performed. The minimum inhibitory concentration (MIC) was determined by the broth micro dilution method. Results revealed that the highest inhibition zone (18 mm) was shown by ethanol extract of <i>V odorata</i> flower against <i>P aeruginosa</i>. Ethanol extract of <i>C reflexa</i> plants is best for all 3 tested microbes (<i>P aeruginosa, B subtilis</i>, and <i>E coli</i>). The results concluded that all these plants have abilities to fight against these tested bacteria. Ethanol extract of <i>V odorata</i> flower has the highest activity against <i>P aeruginosa</i>.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231189374"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a7/b3/10.1177_11779322231189374.PMC10392215.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9932957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>S</i>-Adenosyl-l-Homocysteine Exhibits Potential Antiviral Activity Against Dengue Virus Serotype-3 (DENV-3) in Bangladesh: A Viroinformatics-Based Approach.","authors":"Dipok Kumer Shill,&nbsp;Shafina Jahan,&nbsp;Mohammad Mamun Alam,&nbsp;Md Belayet Hasan Limon,&nbsp;Muntasir Alam,&nbsp;Mohammed Ziaur Rahman,&nbsp;Mustafizur Rahman","doi":"10.1177/11779322231158249","DOIUrl":"https://doi.org/10.1177/11779322231158249","url":null,"abstract":"<p><p>Dengue outbreak is one of the concerning issues in Bangladesh due to the annual outbreak with the alarming number of death and infection. However, there is no effective antiviral drug available to treat dengue-infected patients. This study evaluated and screened antiviral drug candidates against dengue virus serotype 3 (DENV-3) through viroinformatics-based analyses. Since 2017, DENV-3 has been the predominant serotype in Bangladesh. We selected 3 non-structural proteins of DENV-3, named NS3, NS4A, and NS5, as antiviral targets. Protein modeling and validation were performed with VERIFY-3D, Ramachandran plotting, MolProbity, and PROCHECK. We found 4 drug-like compounds from DRUGBANK that can interact with these non-structural proteins of DENV-3. Then, the ADMET profile of these compounds was determined by admetSAR2, and molecular docking was performed with AutoDock, SWISSDOCK, PatchDock, and FireDock. Furthermore, they were subjected to molecular dynamics (MD) simulation study using the DESMOND module of MAESTRO academic version 2021-4 (force field OPLS_2005) to determine their solution's stability in a predefined body environment. Two drug-like compounds named Guanosine-5'-Triphosphate (DB04137) and <i>S</i>-adenosyl-l-homocysteine (DB01752) were found to have an effective binding with these 3 proteins (binding energy > 33.47 KJ/mole). We found NS5 protein was stable and equilibrated in a 100 ns simulation run along with a negligible (<3Å) root-mean-square fluctuation value. The root-mean-square deviation value of the <i>S</i>-adenosyl-l-homocysteine-NS5 complex was less than 3Å, indicating stable binding between them. The global binding energy of <i>S</i>-adenosyl-l-homocysteine with NS5 was -40.52 KJ/mole as ∆G. Moreover, these 2 compounds mentioned above are non-carcinogenic according to their ADMET (chemical absorption, distribution, metabolism, excretion, and toxicity) profile (in silico). These outcomes suggest the suitability of <i>S</i>-adenosyl-l-homocysteine as a potential drug candidate for dengue drug discovery research.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231158249"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/40/40/10.1177_11779322231158249.PMC9974618.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10847932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LC-MS Analysis, Computational Investigation, and Antimalarial Studies of <i>Azadirachta indica</i> Fruit.","authors":"Kolade O Faloye,&nbsp;Stephen A Adesida,&nbsp;Samuel A Oguntimehin,&nbsp;Adetola H Adewole,&nbsp;Olajide B Omoyeni,&nbsp;Sunday J Fajobi,&nbsp;Jeremiah P Ugwo,&nbsp;Isaac D Asiyanbola,&nbsp;Victoria O Bamimore,&nbsp;Emmanuel G Fakola,&nbsp;Olayemi J Oladiran,&nbsp;Michael Spiteller","doi":"10.1177/11779322231154966","DOIUrl":"https://doi.org/10.1177/11779322231154966","url":null,"abstract":"<p><p>Malaria is a deadly disease that continues to pose a threat to children and maternal well-being. This study was designed to identify the chemical constituents in the ethanolic fruit extract of <i>Azadirachta indica</i>, elucidate the pharmacological potentials of identified phytochemicals through the density functional theory method and carry out the antimalarial activity of extract using chemosuppression and curative models. The liquid chromatography-mass spectrometry (LC-MS) analysis of the ethanolic extract was carried out, followed by the density functional theory studies of the identified phytochemicals using B3LYP and 6-31G (d, p) basis set. The antimalarial assays were performed using the chemosuppression (4 days) and curative models. The LC-MS fingerprint of the extract led to the identification of desacetylnimbinolide, nimbidiol, O-methylazadironolide, nimbidic acid, and desfurano-6α-hydroxyazadiradione. Also, the frontier molecular orbital properties, molecular electrostatic potential, and dipole moment studies revealed the identified phytochemicals as possible antimalarial agents. The ethanolic extract of <i>A indica</i> fruit gave 83% suppression at 800 mg/kg, while 84% parasitaemia clearance was obtained in the curative study. The study provided information about the phytochemicals and background pharmacological evidences of the antimalarial ethnomedicinal claim of <i>A indica</i> fruit. Thus, isolation and structure elucidation of the identified phytochemicals from the active ethanolic extract and extensive antimalarial studies towards the discovery of new therapeutic agents is recommended for further studies.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231154966"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b8/cb/10.1177_11779322231154966.PMC9969453.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9385358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic Evidence of Multiple Introductions of SARS-CoV-2 in Mauritania.","authors":"Abdelmalick Abdelmalick,&nbsp;Sofia Sehli,&nbsp;Abdellah Idrissi Azami,&nbsp;Nihal Habib,&nbsp;Najib Al Idrissi,&nbsp;Lahcen Belyamani,&nbsp;Ahmed Houmeida,&nbsp;Hassan Ghazal","doi":"10.1177/11779322231167927","DOIUrl":"https://doi.org/10.1177/11779322231167927","url":null,"abstract":"<p><p>The rapid and global spread of the novel coronavirus severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has raised serious public health concerns, including in Mauritania. We sequenced and analyzed the entire genome of 13 SARS-CoV-2 virus strains isolated from polymerase chain reaction (PCR)-positive symptomatic patients sampled from March 3 to May 31, 2021 to better understand SARS-CoV-2 introduction, propagation, and evolution in Mauritania. A phylogenetic tree using available data from the EpiCoV GISAID database and a variant network with non-Mauritanian sequences were constructed. Variant analysis of the 13 Mauritanian SARS-CoV-2 genome sequences indicated an average mutational percentage of 0.39, which is similar to that in other countries. Phylogenetic analysis revealed multiple spatiotemporal introductions, mainly from Europe (France, Belgium) and Africa (Senegal, Côte d'Ivoire), which also provided evidence of early community transmission. A total of 2 unique mutations, namely, NSP6_Q208K and NSP15_S273T, were detected in the <i>NSP6</i> and <i>NSP15</i> genes, respectively, confirming the aforementioned introduction of SARS-CoV-2 in Mauritania. These findings highlight the relevance of continuous genomic monitoring strategies for understanding virus transmission dynamics and acquiring knowledge to address forthcoming sources of infection in Africa.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231167927"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/86/1f/10.1177_11779322231167927.PMC10130938.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9386557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Alteration of Akkermansiaceae/Lachnospiraceae Ratio Is a Microbial Feature of Antibiotic-Induced Microbiota Remodeling.","authors":"Pei-Chen Chen,&nbsp;Ming-Shian Lin,&nbsp;Tien-Ching Lin,&nbsp;Ting-Wei Kang,&nbsp;Jhen-Wei Ruan","doi":"10.1177/11779322231166229","DOIUrl":"https://doi.org/10.1177/11779322231166229","url":null,"abstract":"<p><p>Antibiotic treatment has been shown to cause gut microbiota dysbiosis. However, lacking critical features defining gut microbiota dysbiosis makes it challenging to prevent. By co-occurrence network analysis, we found that despite short antibiotic courses eliminating certain microbial taxa, the <i>Akkermansia</i> genus played the role of a high-centrality hub to maintain microbiota homeostasis. When the antibiotic courses continued, the elimination of <i>Akkermansia</i> induced a significant microbiota remodeling of the gut microbiota networks. Based on this finding, we found that under long-term antibiotic stress, the gut microbiota was rearranged into a stable network with a significantly lower <i>Akkermansiaceae</i>/<i>Lachnospiraceae</i> (A/L) ratio and no microbial hub. By functional prediction analysis, we confirmed that the gut microbiota with a low A/L ratio also had enhanced mobile elements and biofilm-formation functions that may be associated with antibiotic resistance. This study identified A/L ratio as an indicator of antibiotic-induced dysbiosis. This work reveals that besides the abundance of specific probiotics, the hierarchical structure also critically impacts the microbiome function. Co-occurrence analysis may help better monitor the microbiome dynamics than only comparing the differentially abundant bacteria between samples.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231166229"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0b/6c/10.1177_11779322231166229.PMC10108413.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9378176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selective Non-toxics Inhibitors Targeting DHFR for Tuberculosis and Cancer Therapy: Pharmacophore Generation and Molecular Dynamics Simulation.","authors":"Ghyzlane El Haddoumi,&nbsp;Mariam Mansouri,&nbsp;Houda Bendani,&nbsp;Mohammed Walid Chemao-Elfihri,&nbsp;Jouhaina Kourou,&nbsp;Hanane Abbou,&nbsp;Lahcen Belyamani,&nbsp;Ilham Kandoussi,&nbsp;Azeddine Ibrahimi","doi":"10.1177/11779322231171778","DOIUrl":"https://doi.org/10.1177/11779322231171778","url":null,"abstract":"<p><p>Dihydrofolate reductase (DHFR) is a crucial enzyme that catalyzes the conversion of folic acid. Its reserved properties and significance in both human (h-DHFR) and mycobacterium (mt-DHFR) make it a challenging target for developing drugs against cancer and bacterial infections. Although methotrexate (MTX) is commonly used for cancer therapy and bacterial infections, it has a toxic profile. In this study, we aimed to identify selective and non-toxic inhibitors against h-DHFR and mt-DHFR using an in silico approach. From a data set of 8 412 inhibitors, 11 compounds passed the toxicity and drug-likeness tests, and their interaction with h-DHFR and mt-DHFR was studied by performing molecular docking. To evaluate the inhibitory activity of the compounds against mt-DHFR, five known reference ligands and the natural ligand (dihydrofolate) were used to generate a pharmacophoric map. Two potential selective inhibitors for mt-DHFR and h-DHFR were selected for further investigation using molecular dynamics for 100 ns. As a result, BDBM18226 was identified as the best compound selective for mt-DHFR, non-toxic, with five features listed in the map, with a binding energy of -9.6 kcal/mol. BDBM50145798 was identified as a non-toxic selective compound with a better affinity than MTX for h-DHFR. Molecular dynamics of the two best ligands suggest that they provide more stable, compact, and hydrogen bond interactions with the protein. Our findings could significantly expand the chemical space for new mt-DHFR inhibitors and provide a non-toxic alternative toward h-DHFR for the respective treatment of tuberculosis and cancer therapy.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231171778"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a9/7d/10.1177_11779322231171778.PMC10170603.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9473443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into Omicron's Low Fusogenicity through <i>In Silico</i> Molecular Studies on Spike-Furin Interactions.","authors":"Spencer Mark Mondol,&nbsp;Md Hasib,&nbsp;Md Belayet Hasan Limon,&nbsp;A S M Rubayet Ul Alam","doi":"10.1177/11779322231189371","DOIUrl":"https://doi.org/10.1177/11779322231189371","url":null,"abstract":"<p><p>The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we <i>in silico</i> targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion. To comprehend the epistatic effect of N679 K and P681 H mutations on the spike protein, we <i>in silico</i> constructed three types of spike protein sequences by changing the respective amino acids on 679 and 681 positions (P681 H, N679 K, K679 N-H681 P variants). We then analyzed the binding affinity of furin and spike (Furin-Wild, Furin-Omicron, Furin-P681 H, Furin-N679 K, and Furin-K679 N/H681 P) complexes. Omicron and P681 H variants showed a similar higher binding energy trend compared to the wild type and N679 K. The variation in hydrogen, hydrophobic, and salt bridge bonds between spike protein and furin provided an explanation for the observed low fusogenicity of Omicron. The fate of the epistasis in furin binding and possible cleavage depends on the efficient interaction between FCS in spike and furin catalytic triad, and in addition, the loss of the hydrogen bond between Arg 681 (spike) and Asn 295 (furin) along with inhibitor-like ineffective higher affinity plays an important role in the enzymatic activity.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231189371"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/20/b3/10.1177_11779322231189371.PMC10387760.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9928767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural-Based Virtual Screening of FDA-Approved Drugs Repository for NSP16 Inhibitors, Essential for SARS-COV-2 Invasion Into Host Cells: Elucidation From MM/PBSA Calculation.","authors":"Subodh Kumar,&nbsp;Harvinder Singh,&nbsp;Manisha Prajapat,&nbsp;Phulen Sarma,&nbsp;Anusuya Bhattacharyya,&nbsp;Hardeep Kaur,&nbsp;Gurjeet Kaur,&nbsp;Nishant Shekhar,&nbsp;Karanveer Kaushal,&nbsp;Kalpna Kumari,&nbsp;Seema Bansal,&nbsp;Saniya Mahendiratta,&nbsp;Arushi Chauhan,&nbsp;Ashutosh Singh,&nbsp;Rahul Soloman Singh,&nbsp;Saurabh Sharma,&nbsp;Prasad Thota,&nbsp;Pramod Avti,&nbsp;Ajay Prakash,&nbsp;Anurag Kuhad,&nbsp;Bikash Medhi","doi":"10.1177/11779322231171777","DOIUrl":"https://doi.org/10.1177/11779322231171777","url":null,"abstract":"<p><p>NSP16 is one of the structural proteins of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) necessary for its entrance to the host cells. It exhibits 2'O-methyl-transferase (2'O-MTase) activity of NSP16 using methyl group from S-adenosyl methionine (SAM) by methylating the 5-end of virally encoded mRNAs and shields viral RNA, and also controls its replication as well as infection. In the present study, we used in silico approaches of drug repurposing to target and inhibit the SAM binding site in NSP16 using Food and Drug Administration (FDA)-approved small molecules set from Drug Bank database. Among the 2 456 FDA-approved molecules, framycetin, paromomycin, and amikacin were found to be significant binders against the SAM binding cryptic pocket of NSP16 with docking score of -13.708, -14.997 and -15.841 kcal/mol, respectively. Classical molecular dynamics (MD) simulation and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA)-based binding free energy calculation depicted that all these three framycetin, paromomycin, and amikacin might be promising therapeutic leads towards SARS-CoV-2 infections via host immune escape inhibition pathway.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231171777"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7e/50/10.1177_11779322231171777.PMC10392196.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9932956","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Potential of Ameliorating COVID-19 and Sequelae From <i>Andrographis paniculata</i> via Bioinformatics.","authors":"Hien Thi Nguyen,&nbsp;Van Mai Do,&nbsp;Thanh Thuy Phan,&nbsp;Dung Tam Nguyen Huynh","doi":"10.1177/11779322221149622","DOIUrl":"https://doi.org/10.1177/11779322221149622","url":null,"abstract":"<p><p>The current coronavirus disease 2019 (COVID-19) outbreak is alarmingly escalating and raises challenges in finding efficient compounds for treatment. Repurposing phytochemicals in herbs is an ideal and economical approach for screening potential herbal components against COVID-19. <i>Andrographis paniculata</i>, also known as Chuan Xin Lian, has traditionally been used as an anti-inflammatory and antibacterial herb for centuries and has recently been classified as a promising herbal remedy for adjuvant therapy in treating respiratory diseases. This study aimed to screen Chuan Xin Lian's bioactive components and elicit the potential pharmacological mechanisms and plausible pathways for treating COVID-19 using network pharmacology combined with molecular docking. The results found terpenoid (andrographolide) and flavonoid (luteolin, quercetin, kaempferol, and wogonin) derivatives had remarkable potential against COVID-19 and sequelae owing to their high degrees in the component-target-pathway network and strong binding capacities in docking scores. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the PI3K-AKT signaling pathway might be the most vital molecular pathway in the pathophysiology of COVID-19 and long-term sequelae whereby therapeutic strategies can intervene.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322221149622"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/3c/37/10.1177_11779322221149622.PMC9841859.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9114842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking.","authors":"Md Anisur Rahman,&nbsp;Md Al Amin,&nbsp;Most Nilufa Yeasmin,&nbsp;Md Zahidul Islam","doi":"10.1177/11779322231186481","DOIUrl":"https://doi.org/10.1177/11779322231186481","url":null,"abstract":"<p><p>The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to \"Smoking and COVID-19: a scoping review,\" about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis. We have applied all important methods namely protein-protein interaction, hub-protein interaction, drug-protein interaction, tf-gene interaction, and gene-MiRNA interaction of bioinformatics to analyze to understand deeply the connection between both smoking and COVID-19 severity. We have also analyzed Pathways and Gene Ontology where 5 significant signaling pathways were validated with previous literature. Also, we verified 7 hub-proteins, and finally, we validated a total of 7 drugs with the previous study.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231186481"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d0/0c/10.1177_11779322231186481.PMC10350588.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9831677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}