In silico computation of coagulation factor II: a potential water treatment agent against gram negative bacteria
Water, as one of the main sources of life, is an important aspect to public health and safety. Up until now there have been many concerns about water pollution especially in developing countries. Heavy polluted water that is not treated well could cause many concerning diseases that can lead to deaths. Contaminants that are of chemical, physical, and biological origins are commonly found in these water sources. Gram negative bacteria (GNB) have been seen to develop multiple drug and antibiotic resistance, causing more fatal infections. This has become a major concern of public health especially as it makes water treatment more challenging. Our study investigates human coagulation factor II that is responsible for blood clotting as a possible method for water treatment against GNB. By investigating the coagulation protein interaction with several bacterial lipopolysaccharides proteins and calculating the binding affinity of the interaction, the results show factor II has a lower binding affinity compared to previously studied factor VII. This shows possibilities of factor II to hydrolyse several gram-negative bacteria to act as a potential treatment against these GNBs.
Arifin MZ, Agustriawan D, Parikesit AAP (2020). Molecular simulation oF MDM2 and E6AP proteins as P53 regulator in cervical cancer. Biointerface Research in Applied Chemistry 10(4):5875-5879. https://doi.org/10.33263/BRIAC104.875879
Chen J, Li X, Li L, Zhang T, Zhang Q, Wu F, … Song X (2019). Coagulation factors VII, IX and X are effective antibacterial proteins against drug-resistant gram-negative bacteria. Cell Research 29(9):711-724. https://doi.org/10.1038/s41422-019-0202-3
Chinnaraj M, Planer W, Pozzi N (2018). Structure of coagulation factor II: molecular mechanism of thrombin generation and development of next-generation anticoagulants. Frontiers in Medicine https://doi.org/10.3389/fmed.2018.00281
Cissé G (2019). Food-borne and water-borne diseases under climate change in low-and middle-income countries: Further efforts needed for reducing environmental health exposure risks. Acta Tropica 194:181-188. https://doi.org/10.1016/j.actatropica.2019.03.012
Conner JG, Teschler JK, Jones CJ, Yildiz FH (2016) Staying alive: Vibrio cholerae's cycle of environmental survival, transmission, and dissemination. Microbiology Spectrum 4(2):4-2. https://doi.org/10.1128/microbiolspec.VMBF-0015-2015
EMBO (2016). Protein-protein interaction prediction using docking. Retrieved 2021 June 18 from http://aidanbudd.github.io/ppisnd/trainingMaterial/allegraVia/PPI/tutorial_on_protein_docking.html
Hatami H (2013). Importance of water and water-borne diseases: on the occasion of the world water day. International Journal of Preventive Medicine 4(3):243-245.
Kozakov D, Brenke R, Comeau SR, Vajda S (2006). PIPER: an FFT‐based protein docking program with pairwise potentials. Proteins: Structure, Function, and Bioinformatics 65(2):392-406.
Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S (2017). The ClusPro web server for protein–protein docking. Nature Protocols 12(2):255.
Lungidningtyas A, Parikesit AA (2020). In silico analysis of ethanol binding activity in neuronal nicotinic acetylcholine receptors. Malaysian Journal of Applied Sciences 5(1):54-61. https://doi.org/10.37231/myjas.2020.5.1.243
National Library of Medicine (US) (2004). F2 coagulation factor II, thrombin [Homo sapiens (human)]. National Center for Biotechnology Information. Retrieved 2021 June 20 from https://www.ncbi.nlm.nih.gov/gene/2147
Our World in Data (2019). Clean Water. Retrieved 2021 June 20 from https://ourworldindata.org/water-access
Palta S, Saroa R, Palta A (2014). Overview of the coagulation system. Indian Journal of Anaesthesia 58(5):515. https://doi.org/10.4103/0019-5049.144643
Schrödinger LLC (2010). The PyMOL molecular graphics system. Version 2.3.5.
Swiech K, Picanço-Castro V, Covas DT (2017). Production of recombinant coagulation factors: Are humans the best host cells? Bioengineered 8(5):462-470.
Vangone A, Bonvin AM (2015). Contacts-based prediction of binding affinity in protein–protein complexes. Elife 4:e07454.
Waterhouse A, Bertoni M, Bienert S, Studer G, Tauriello G, Gumienny R, … Schwede T (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research 46:W296-W303.
WHO/UNICEF Joint Water Supply (2015). Sanitation monitoring programme. World Health Organization. Progress on sanitation and drinking water: 2015 update and MDG assessment.
Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A (2016). PRODIGY: a web server for predicting the binding affinity of protein–protein complexes. Bioinformatics 32(23):3676-3678.
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