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Research Article

Bioinformatics Insights on the Physicochemical Properties of Hepatitis Virus Envelope Glycoproteins

Author(s): Carlos Polanco*, Alberto Huberman, Vladimir N. Uversky, Enrique Hernández-Lemus E, Mireya Martínez-Garcia, Martha Rios Castro, Claudia Pimentel Hernández, Thomas Buhse, Gilberto Vargas-Alarcon, Francisco J. Roldan Gomez and Erika Jeannette López Oliva

Volume 21, Issue 14, 2024

Published on: 18 October, 2023

Page: [2998 - 3017] Pages: 20

DOI: 10.2174/0115701808264877231014175922

Price: $65

Abstract

Background: Globally, hepatitis B and C infect 400 million people, more than 10 times the number of people living with HIV. In 2019, it was estimated that 1.1 million people died as a result of the disease (PAHO/WHO, January 2023).

Objective: This study aimed to conduct a computational analysis of the proteins that express the hepatitis virus envelope glycoproteins in order to gain insight into their function.

Methods: Different computational tools were used to calculate the Polarity Index Method 2.0v (PIM 2.0v) profile (previously titled Polarity Index Method profile) and the Protein Intrinsic Disorder Predisposition (PIDP) analyzed for each sequence, in addition to computational tools that made it possible to revise these proteins at the genetic level.

Results: Both the PIM 2.0v profile and the PIDP profile of various hepatitis B and C virus envelope glycoproteins were able to reproduce the structural and morphological similarities that they had previously. The presence of certain patterns in each of these profiles made this accomplishment feasible.

Conclusion: Computational programs could reproduce characteristic PIM 2.0v profiles of the hepatitis B and C virus envelope glycoproteins. This information is useful for a better understanding of this emerging virus.

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[1]
Papavramidou, N.; Fee, E.; Christopoulou-Aletra, H. Jaundice in the hippocratic corpus. J. Gastrointest. Surg., 2007, 11(12), 1728-1731.
[2]
Roholm, K.; Iversen, P. Changes in the liver in acute epidemic hepatitis (catarrhal jaundice) based on 38 aspiration biopsies. Acta Pathol. Microbiol. Scand., 1939, 16(4), 427-442.
[http://dx.doi.org/10.1111/j.1600-0463.1939.tb06050.x]
[3]
Lürman, A. Eine ikterusepidemie; Berliner klinische Wochenschrift 1885.
[4]
Jehn, J. Eine icterusepidemie in wahrscheinlichem Zusammenhang mit vorausgegangener revaccination. Dtsch. Med. Wochenschr., 1885, 11(20), 339-341, 354-356.
[http://dx.doi.org/10.1055/s-0028-1142335]
[5]
Flaum, A.; Malmros, H.; Persson, E. Eine nosocomiale ikterus-epidemie. Acta Med. Scand., 1926(Suppl. 16), 544-553.
[6]
Drucker, E.; Alcabes, P.G.; Marx, P.A. The injection century: Massive unsterile injections and the emergence of human pathogens. Lancet, 2001, 358(9297), 1989-1992.
[http://dx.doi.org/10.1016/S0140-6736(01)06967-7] [PMID: 11747942]
[7]
World Health Organization. Prevention and control of viral hepatitis infection framework for global action. 2012. Available from: http://www.who.int/csr/disease/hepatitis/GHP_Framework_En.pdf
[8]
Caccamo, G.; Saffioti, F.; Raimondo, G. Hepatitis B virus and hepatitis C virus dual infection. World J. Gastroenterol., 2014, 20(40), 14559-14567.
[http://dx.doi.org/10.3748/wjg.v20.i40.14559] [PMID: 25356020]
[9]
Feinstone, S.M.; Kapikian, A.Z.; Purcell, R.H.; Alter, H.J.; Holland, P.V. Transfusion-associated hepatitis not due to viral hepatitis type A or B. N. Engl. J. Med., 1975, 292(15), 767-770.
[http://dx.doi.org/10.1056/NEJM197504102921502] [PMID: 163436]
[10]
Liang, T.J.; Hepatitis, B. The virus and disease. Hepatology, 2009, 49(S5), S13-S21.
[http://dx.doi.org/10.1002/hep.22881] [PMID: 19399811]
[11]
Hoofnagle, J.H. Course and outcome of hepatitis C. Hepatology, 2002, 36(5), S21-S29.
[PMID: 12407573]
[12]
Choo, Q.L.; Kuo, G.; Weiner, A.J.; Overby, L.R.; Bradley, D.W.; Houghton, M. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science, 1989, 244(4902), 359-362.
[http://dx.doi.org/10.1126/science.2523562] [PMID: 2523562]
[13]
Bukh, J.; Purcell, R.H.; Miller, R.H. At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. Proc. Natl. Acad. Sci., 1993, 90(17), 8234-8238.
[http://dx.doi.org/10.1073/pnas.90.17.8234] [PMID: 8396266]
[14]
Bukh, J. The history of hepatitis C virus (HCV): Basic research reveals unique features in phylogeny, evolution and the viral life cycle with new perspectives for epidemic control. J. Hepatol., 2016, 65(1), S2-S21.
[http://dx.doi.org/10.1016/j.jhep.2016.07.035] [PMID: 27641985]
[15]
Apweiler, R.; Bairoch, A.; Wu, C.H.; Barker, W.C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M.J.; Natale, D.A.; O’Donovan, C.; Redaschi, N.; Yeh, L.S. UniProt: The Universal Protein knowledgebase. Nucleic Acids Res., 2004, 32(90001), 115D-119.
[http://dx.doi.org/10.1093/nar/gkh131] [PMID: 14681372]
[16]
Romero, P.; Obradovic, Z.; Li, X.; Garner, E.C.; Brown, C.J.; Dunker, A.K. Sequence complexity of disordered protein. Proteins, 2001, 42(1), 38-48.
[http://dx.doi.org/10.1002/1097-0134(20010101)42:1<38:AID-PROT50>3.0.CO;2-3] [PMID: 11093259]
[17]
Peng, K.; Radivojac, P.; Vucetic, S.; Dunker, A.K.; Obradovic, Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics, 2006, 7(1), 208.
[http://dx.doi.org/10.1186/1471-2105-7-208] [PMID: 16618368]
[18]
Peng, K.; Vucetic, S.; Radivojac, P.; Brown, C.J.; Dunker, A.K.; Obradovic, Z. Optimizing long intrinsic disorder predictors with protein evolutionary information. J. Bioinform. Comput. Biol., 2005, 3(1), 35-60.
[http://dx.doi.org/10.1142/S0219720005000886] [PMID: 15751111]
[19]
Okamoto, H.; Imai, M.; Shimozaki, M.; Hoshi, Y.; Iizuka, H.; Gotanda, T.; Tsuda, F.; Miyakawa, Y.; Mayumi, M. Nucleotide sequence of a cloned hepatitis B virus genome, subtype ayr: Comparison with genomes of the other three subtypes. J. Gen. Virol., 1986, 67(11), 2305-2314.
[http://dx.doi.org/10.1099/0022-1317-67-11-2305] [PMID: 3783127]
[20]
Inchauspe, G.; Zebedee, S.; Lee, D.H.; Sugitani, M.; Nasoff, M.; Prince, A.M. Genomic structure of the human prototype strain H of hepatitis C virus: Comparison with American and Japanese isolates. Proc. Natl. Acad. Sci., 1991, 88(22), 10292-10296.
[http://dx.doi.org/10.1073/pnas.88.22.10292] [PMID: 1658800]
[21]
Zhou, J.; Oldfield, C.J.; Yan, W.; Shen, B.; Dunker, A.K. Identification of intrinsic disorder in complexes from the protein data bank. ACS Omega, 2020, 5(29), 17883-17891.
[http://dx.doi.org/10.1021/acsomega.9b03927] [PMID: 32743159]
[22]
Gautam, A.; Singh, H.; Tyagi, A.; Chaudhary, K.; Kumar, R.; Kapoor, P.; Raghava, G.P.S. CPPsite: A curated database of cell penetrating peptides. Database, 2012, 2012(0), bas015.
[http://dx.doi.org/10.1093/database/bas015] [PMID: 22403286]
[23]
Polanco, C.; Castañón-González, J.A.; Uversky, V.N.; Buhse, T.; Samaniego Mendoza, J.L.; Calva, J.J. Electronegativity and intrinsic disorder of preeclampsia-related proteins. Acta Biochim. Pol., 2017, 64(1), 99-111.
[PMID: 27824362]
[24]
Polanco, C.; Huberman, A.; Hernández-Lemus, E.; Uversky, V.N.; Rios Castro, M.; Martnez-Garcia, M.; Vargas-Alarcón, G.; Buhse, T.; Pimentel Hernández, C.; Zazueta, C.; Roldan Gomez, F.R.; López Oliva, E.J. Bioinformatics-based characterization of the variability of MPOX virus proteins. Lett. Drug Des. Discov., 2024.
[25]
Dayhoff, G.W.; Uversky, V.N. Rapid prediction and analysis of protein intrinsic disorder. Protein Sci., 2022, 31(12), e4496.
[26]
Mészáros, B.; Erdős, G.; Dosztányi, Z. IUPred2A: Context-dependent prediction of protein disorder as a function of redox state and protein binding. Nucleic Acids Res., 2018, 46(W1), W329-W337.
[http://dx.doi.org/10.1093/nar/gky384] [PMID: 29860432]
[27]
Brettin, T.; Davis, J.J.; Disz, T.; Edwards, R.A.; Gerdes, S.; Olsen, G.J.; Olson, R.; Overbeek, R.; Parrello, B.; Pusch, G.D.; Shukla, M.; Thomason, J.A., III; Stevens, R.; Vonstein, V.; Wattam, A.R.; Xia, F. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep., 2015, 5(1), 8365.
[http://dx.doi.org/10.1038/srep08365] [PMID: 25666585]
[28]
Romero, P.R.; Zaidi, S.; Fang, Y.Y.; Uversky, V.N.; Radivojac, P.; Oldfield, C.J.; Cortese, M.S.; Sickmeier, M.; LeGall, T.; Obradovic, Z.; Dunker, A.K. Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. Proc. Natl. Acad. Sci., 2006, 103(22), 8390-8395.
[http://dx.doi.org/10.1073/pnas.0507916103] [PMID: 16717195]
[29]
Sharifnia, Z.; Bandehpour, M.; Kazemi, B.; Zarghami, N. Design and development of modified mRNA encoding the core antigen of the hepatitis C virus: A possible application in vaccine production. Iran. Biomed. J., 2019, 23(1), 57-67.
[http://dx.doi.org/10.29252/ibj.23.1.57] [PMID: 30056690]
[30]
McGregor, J.; Hardy, J.M.; Lay, C.S.; Boo, I.; Piontek, M.; Suckow, M.; Coulibaly, F.; Poumbourios, P.; Center, R.J.; Drummer, H.E. Virus-like particles containing the E2 core domain of hepatitis C virus generate broadly neutralizing antibodies in guinea pigs. J. Virol., 2022, 96(5), e01675-e21.
[http://dx.doi.org/10.1128/jvi.01675-21] [PMID: 34986001]
[31]
Arafa, M.; Besheer, T.; El-Eraky, A.M.; Abo El-khair, S.M.; Elsamanoudy, A.Z. Genetic variants of XRCC1 and risk of hepatocellular carcinoma in chronic hepatitis C patients. Br. J. Biomed. Sci., 2019, 76(2), 64-69.
[http://dx.doi.org/10.1080/09674845.2019.1594487] [PMID: 31025604]
[32]
Barooah, P.; Saikia, S.; Kalita, M.J.; Bharadwaj, R.; Sarmah, P.; Bhattacharyya, M.; Goswami, B.; Medhi, S. IL-10 polymorphisms and haplotypes predict susceptibility to hepatocellular carcinoma occurrence in patients with hepatitis C virus infection from Northeast India. Viral Immunol., 2020, 33(6), 457-467.
[http://dx.doi.org/10.1089/vim.2019.0170] [PMID: 32352886]
[33]
Schöbel, A.; Nguyen-Dinh, V.; Schumann, G.G.; Herker, E. Hepatitis C virus infection restricts human LINE-1 retrotransposition in hepatoma cells. PLoS Pathog., 2021, 17(4), e1009496.
[http://dx.doi.org/10.1371/journal.ppat.1009496] [PMID: 33872335]
[34]
Tran, G. The role of hepatitis C virus in the pathogenesis of hepatocellular carcinoma. Biosci. Horiz., 2008, 1(2), 167-175.
[http://dx.doi.org/10.1093/biohorizons/hzn020]
[35]
Grakoui, A.; Wychowski, C.; Lin, C.; Feinstone, S.M.; Rice, C.M. Expression and identification of hepatitis C virus polyprotein cleavage products. J. Virol., 1993, 67(3), 1385-1395.
[http://dx.doi.org/10.1128/jvi.67.3.1385-1395.1993] [PMID: 7679746]
[36]
Hijikata, M.; Kato, N.; Ootsuyama, Y.; Nakagawa, M.; Shimotohno, K. Gene mapping of the putative structural region of the hepatitis C virus genome by in vitro processing analysis. Proc. Natl. Acad. Sci., 1991, 88(13), 5547-5551.
[http://dx.doi.org/10.1073/pnas.88.13.5547] [PMID: 1648221]
[37]
Cocquerel, L.; Meunier, J.C.; Pillez, A.; Wychowski, C.; Dubuisson, J. A retention signal necessary and sufficient for endoplasmic reticulum localization maps to the transmembrane domain of hepatitis C virus glycoprotein E2. J. Virol., 1998, 72(3), 2183-2191.
[http://dx.doi.org/10.1128/JVI.72.3.2183-2191.1998] [PMID: 9499075]
[38]
Kettinen, H.; Grace, K.; Grunert, S.; Clarke, B.; Rowlands, D.; Jackson, R. Mapping of the internal ribosome entry site at the 5′ end of the hepatitis C virus genome In Viral Hepatitis and Liver Disease. Proceedings of the International Symposium on Viral Hepatitis and Liver Disease: Molecules Today, More Cures Tomorrow, Tokyo1993, pp. 125-131.
[39]
Deng, L.P.; Gui, X.E.; Zhang, Y.X.; Gao, S.C.; Yang, R.R. Impact of human immunodeficiency virus infection on the course of hepatitis C virus infection: A meta-analysis. World J. Gastroenterol., 2009, 15(8), 996-1003.
[http://dx.doi.org/10.3748/wjg.15.996] [PMID: 19248201]
[40]
Chan, D.P.C.; Sun, H.Y.; Wong, H.T.H.; Lee, S.S.; Hung, C.C. Sexually acquired hepatitis C virus infection: A review. Int. J. Infect. Dis., 2016, 49, 47-58.
[http://dx.doi.org/10.1016/j.ijid.2016.05.030] [PMID: 27270138]
[41]
Jian, Wu Y.; Shu Chen, L.; Gui Qiang, W. Effects of fatty liver and related factors on the efficacy of combination antiviral therapy in patients with chronic hepatitis C. Liver Int., 2006, 26(2), 166-172.
[http://dx.doi.org/10.1111/j.1478-3231.2005.01219.x] [PMID: 16448454]
[42]
Lampert, B.C.; Kissling, K. Approaches and strategies to manage the hepatitis C virus-positive heart donor. Curr. Opin. Organ Transplant., 2022, 27(3), 229-234.
[http://dx.doi.org/10.1097/MOT.0000000000000984] [PMID: 35649114]
[43]
Zarkasi, K.A.; Abdullah, N.; Abdul Murad, N.A.; Ahmad, N.; Jamal, R. Genetic factors for coronary heart disease and their mechanisms: A meta-analysis and comprehensive review of common variants from genome-wide association studies. diagnostics, 2022, 12(10), 2561.
[http://dx.doi.org/10.3390/diagnostics12102561] [PMID: 36292250]
[44]
Te, H.S.; Jensen, D.M. Epidemiology of hepatitis B and C viruses: A global overview. Clin. Liver Dis., 2010, 14(1), 1-21. [vii].
[http://dx.doi.org/10.1016/j.cld.2009.11.009] [PMID: 20123436]
[45]
Melikoki, V.; Kourlaba, G.; Kanavaki, I.; Fessatou, S.; Papaevangelou, V. Seroprevalence of hepatitis C in children without identifiable risk-factors: A systematic review and meta-analysis. J. Pediatr. Gastroenterol. Nutr., 2021, 72(6), e140-e148.
[http://dx.doi.org/10.1097/MPG.0000000000003099] [PMID: 33633077]
[46]
Abdel-Gawad, M.; Abd-elsalam, S.; Abdel-Gawad, I.; Tag-Adeen, M.; El-Sayed, M.; Abdel-Malek, D. Seroprevalence of hepatitis C virus infection in children: A systematic review and META‐ANALYSIS. Liver Int., 2022, 42(6), 1241-1249.
[http://dx.doi.org/10.1111/liv.15212] [PMID: 35220648]
[47]
Sperry, A.B.; Bennett, A.; Wen, J. Hepatitis B and C in children. Clin. Liver Dis., 2022, 26(3), 403-420.
[http://dx.doi.org/10.1016/j.cld.2022.03.005] [PMID: 35868682]
[48]
Benova, L.; Mohamoud, Y.A.; Calvert, C.; Abu-Raddad, L.J. Vertical transmission of hepatitis C virus: Systematic review and meta-analysis. Clin. Infect. Dis., 2014, 59(6), 765-773.
[http://dx.doi.org/10.1093/cid/ciu447]
[49]
World Health Organization(WHO). Global health sector strategies on, respectively, HIV, viral hepatitis, and sexually transmitted infections for the period 2022–2023. 2022. Available from https://www.who.int/publications/i/item/9789240053779
[50]
Indolfi, G.; Guido, M.; Azzari, C.; Resti, M. Histopathology of hepatitis C in children, a systematic review: Implications for treatment. Expert Rev. Anti Infect. Ther., 2015, 13(10), 1225-1235.
[http://dx.doi.org/10.1586/14787210.2015.1070668] [PMID: 26202832]
[51]
Basit, H.; Tyagi, I.; Koirala, J. Hepatitis C. [Updated 2023 Mar 26]. In: StatPearls [Internet]; Treasure Island (FL): StatPearls Publishing, 2023.
[52]
Pisano, M.B.; Giadans, C.G.; Flichman, D.M.; Ré, V.E.; Preciado, M.V.; Valva, P. Viral hepatitis update: Progress and perspectives. World J. Gastroenterol., 2021, 27(26), 4018-4044.
[http://dx.doi.org/10.3748/wjg.v27.i26.4018]
[53]
Saraceni, C.; Birk, J. A review of hepatitis B virus and hepatitis C virus immunopathogenesis. J. Clin. Transl. Hepatol., 2021, 000(000), 000.
[http://dx.doi.org/10.14218/JCTH.2020.00095] [PMID: 34221927]
[54]
Ott, J.J.; Stevens, G.A.; Groeger, J.; Wiersma, S.T. Global epidemiology of hepatitis B virus infection: New estimates of age-specific HBsAg seroprevalence and endemicity. Vaccine, 2012, 30(12), 2212-2219.
[http://dx.doi.org/10.1016/j.vaccine.2011.12.116]
[55]
Dusheiko, G.; Agarwal, K.; Maini, M.K. New approaches to chronic hepatitis B. N. Engl. J. Med., 2023, 388(1), 55-69.
[http://dx.doi.org/10.1056/NEJMra2211764] [PMID: 36599063]
[56]
Khanam, A.; Chua, J.V.; Kottilil, S. Immunopathology of chronic hepatitis B infection: Role of innate and adaptive immune responses in disease progression. Int. J. Mol. Sci., 2021, 22(11), 5497.
[http://dx.doi.org/10.3390/ijms22115497] [PMID: 34071064]
[57]
Zheng, J.R.; Wang, Z.L.; Feng, B. Hepatitis B functional cure and immune response. Front. Immunol., 2022, 13, 1075916-1075916.
[http://dx.doi.org/10.3389/fimmu.2022.1075916] [PMID: 36466821]
[58]
Chigbu, D.; Loonawat, R.; Sehgal, M.; Patel, D.; Jain, P. Hepatitis C virus infection: Host-virus interaction and mechanisms of viral persistence. Cells, 2019, 8(4), 376.
[http://dx.doi.org/10.3390/cells8040376] [PMID: 31027278]

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