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Maia Cordeiro C, da Silva Moia G, de Oliveira MS, da Silva E Silva L, da Cruz Schneider MP, Costa SS, Baraúna RA, das Graças DA, Silva A, de Oliveira Veras AA. BioPipeline Creator-a user-friendly Java-based GUI for managing and customizing biological data pipelines. Sci Rep 2024; 14:16572. [PMID: 39019939 PMCID: PMC11255246 DOI: 10.1038/s41598-024-67409-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Bioinformatics tools are essential for performing analyses in the omics sciences. Given the numerous experimental opportunities arising from advances in the field of omics and easier access to high-throughput sequencing platforms, these tools play a fundamental role in research projects. Despite the considerable progress made possible by the development of bioinformatics tools, some tools are tailored to specific analytical goals, leading to challenges for non-bioinformaticians who need to integrate the results of these specific tools into a customized pipeline. To solve this problem, we have developed the BioPipeline Creator, a user-friendly Java-based GUI that allows different software tools to be integrated into the repertoire while ensuring easy user interaction via an accessible graphical interface. Consisting of client and server software components, BioPipeline Creator provides an intuitive graphical interface that simplifies the use of various bioinformatics tools for users without advanced computer skills. It can run on less sophisticated devices or workstations, allowing users to keep their operating system without having to switch to another compatible system. The server is responsible for the processing tasks and can perform the analysis in the user's local or remote network structure. Compatible with the most important operating systems, available at https://github.com/allanverasce/bpc.git .
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Affiliation(s)
- Cléo Maia Cordeiro
- Faculty of Computing, Federal University of Pará campus Castanhal, Pará, Brazil
| | - Gislenne da Silva Moia
- Postgraduate Program in Applied Computing, Federal University of Pará campus Tucuruí Pará, Tucuruí, Brazil
| | | | - Lucas da Silva E Silva
- Center of Genomics and System Biologics, Federal University of Pará, Belém, Pará, Brazil
| | | | - Sávio S Costa
- Biological Engineering Laboratory, Guamá Science and Technology Park, Belém, Pará, Brazil
| | - Rafael Azevedo Baraúna
- Biological Engineering Laboratory, Guamá Science and Technology Park, Belém, Pará, Brazil
| | - Diego Assis das Graças
- Biological Engineering Laboratory, Guamá Science and Technology Park, Belém, Pará, Brazil
| | - Artur Silva
- Biological Engineering Laboratory, Guamá Science and Technology Park, Belém, Pará, Brazil
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Ullah S, Rahman W, Ullah F, Ullah A, Jehan R, Iqbal MN, Ali I, Tianshun G. Identification of lead compound screened from the natural products atlas to treat renal inflammasomes using molecular docking and dynamics simulation. J Biomol Struct Dyn 2024; 42:4851-4861. [PMID: 37705295 DOI: 10.1080/07391102.2023.2254397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/04/2023] [Indexed: 09/15/2023]
Abstract
One of the most prevalent ailments is kidney disease. Effective therapies for chronic renal disease are hard to come by. As a result, there is significant clinical and social interest to predict and develop novel compounds to treat renal disorders. So, specific natural products have been employed in this study because they have protective effects against kidney diseases. When taken orally, natural products can help protect against or lessen the severity of the kidney damage caused by high fructose intake, a high-fat diet, and both Type I and Type 2 diabetes. Reduced podocyte injury, a contributor to albuminuria in diabetic nephropathy, reduces renal endothelial barrier function disruption due to hyperglycemia, as well as urinary microalbumin excretion and glomerular hyperfiltration. Multiple natural products have been shown to protect the kidneys from nephrotoxic chemicals such as LPS, gentamycin, alcohol, nicotine, lead, and cadmium, all of which can persuade acute kidney injury (AKI) or chronic kidney disease (CKD). Natural compounds inhibit regulatory enzymes for controlling inflammation-related diseases. For this, use computational methods such as drug design to identify novel flavonoid compounds against kidney diseases. Drug design via computational methods gaining admiration as a swift and effective technique to identify lead compounds in a shorter time at a low cost. In this in-silico study, we screened The Natural Product Atlas based on a structure-based pharmacophore query. Top hits were analyzed for ADMET analysis followed by molecular docking and docking validation. Finally, the lead compound was simulated for a period of 200 ns and trajectories were studied for stability. We found that NPA024823 showed promising binding and stability with the AIM2. This research work aims to predict novel anti-inflammatory compounds against kidney diseases to inhibit kidney inflammasome by targeting the AIM2 protein. So, in initial preclinical research, there will be lower failure rates that demonstrate safety profiles against predicted compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Anees Ullah
- S Khan Lab Mardan, Khyber Pakhtunkhwa, Pakistan
| | | | - Muhammad Nasir Iqbal
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology, and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Gao Tianshun
- Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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Kandeel M, Iqbal MN, Ali I, Malik S, Malik A, Sehgal SA. Comprehensive in silico analyses of flavonoids elucidating the drug properties against kidney disease by targeting AIM2. PLoS One 2023; 18:e0285965. [PMID: 37200367 DOI: 10.1371/journal.pone.0285965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/05/2023] [Indexed: 05/20/2023] Open
Abstract
Kidney disorders are among the most common diseases and there is a scarcity of effective treatments for chronic kidney disease. There has been a progressive improvement in specific flavonoids for protective effects against kidney diseases. Flavonoids inhibit the regulatory enzymes to control inflammation-related diseases. In the present study, a hybrid approach of molecular docking analyses and molecular dynamic simulation was followed by principal component analyses and a dynamics cross-correlation matrix. In the present study, the top-ranked five flavonoids were reported, and the maximum binding affinity was observed against AIM2. Molecular docking analyses revealed that Glu_186, Phe_187, Lys_245, Glu_248, Ile_263, and Asn_265 are potent residues against AIM2 for ligand-receptor interactions. Extensive in silico analyses suggested that procyanidin is a potential molecule against AIM2. Moreover, the site-directed mutagenesis for the reported interacting residues of AIM2 could be important for further in vitro analyses. The observed novel results based on extensive computational analyses may be significant for potential drug design against renal disorders by targeting AIM2.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Al-Ahsa, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelshikh University, Kafrelshikh, Egypt
| | - Muhammad Nasir Iqbal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, Pakistan
| | - Saima Malik
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abbeha Malik
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Department of Bioinformatics, University of Okara, Okara, Pakistan
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Jaapar FN, Parmin NA, Halim NHA, Hashim U, Gopinath SCB, Halim FS, Ruslinda AR, Voon CH, Uda MNA, Uda MNA, Nadzirah S, Rejali Z, Afzan A, Zakaria II. Designing DNA probe from HPV 18 and 58 in the E6 region for sensing element in the development of genosensor-based gold nanoparticles. Biotechnol Appl Biochem 2021; 69:1966-1983. [PMID: 34554606 DOI: 10.1002/bab.2260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/19/2021] [Indexed: 11/09/2022]
Abstract
The E6 region has higher protuberant probability annealing than consensus probe focusing on another region in the human papillomavirus (HPV) genome in terms of detection and screening method. Here, we designed the first multiple virus single-stranded deoxyribonucleic acid (ssDNA) for multiple detections in an early phase of screening for cervical cancer in the E6 region and became a fundamental evolution of detection electrochemical HPV biosensor. Gene profiling of the virus ssDNA sequences has been carried by high-end bioinformatics tools such as GenBank, Basic Local Alignment Searching Tools (BLAST), and Clustal OMEGA in a row. The output from bioinformatics tools resulted in 100% of similarities between our virus ssDNA probe and HPV complete genome in the databases. The cross-validation between HPV genome and our designed virus ssDNA provided high specificity and selectivity during screening methods compared with Pap smear. The DNA probe for HPV 18, 5' COOH-GAT CCA GAA GGT ACA GAC GGG GAG GGC ACG 3', while 5'COOH-GGG CGC TGT GCA GTG TGT TGG AGA CCC CGA3' as DNA probe for HPV 58 designed with 66.77% guanine (G) and cytosine (C) content for both. Our virus ssDNA probe for the HPV biosensor promises high sensitivity, specificity, selectivity, repeatability, low fluid consumption, and will be useful in mini-size diagnostic devices for cervical cancer detection.
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Affiliation(s)
- F Nadhirah Jaapar
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - N A Parmin
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - N Hamidah A Halim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Uda Hashim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia.,Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), Arau, Perlis, 02600, Malaysia
| | - F Syakirah Halim
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - A Rahim Ruslinda
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - C H Voon
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - M N A Uda
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - M N Afnan Uda
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar, Perlis, 01000, Malaysia
| | - Sh Nadzirah
- Institute of Microengineering and Nanoelectronics, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Zulida Rejali
- Department of Obstetrics and Gynaecology, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Amilia Afzan
- Department of Obstetrics and Gynaecology, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute (MGI), National Institute of Biotechnology (NIBM), Kajang, Selangor, Malaysia
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