Skip to main content
SpringerLink
Log in

ADPDB: A Comprehensive Knowledgebase of Manually Curated Peptides Against Dengue Virus

  • Published:
International Journal of Peptide Research and Therapeutics Aims and scope Submit manuscript

Abstract

Dengue, a significant mosquito-borne disease, presents a global health challenge with limited treatment options. Recently, there have been estimates of 390 million dengue infections annually worldwide. Thus, Dengue viruses (DENV) continue to result in a severe burden on human health all over the world. Here, we are introducing the Anti-Dengue Peptide Database (ADPDB) as a comprehensive knowledgebase dedicated to anti-dengue peptides, aiming to aid research and development efforts against the dengue virus. ADPDB consolidates information on antimicrobial peptides (AMPs) exhibiting anti-dengue activity, sourced from extensive literature curation. The database provides a user-friendly interface offering functionalities such as simple and advanced search options, data retrieval, and customizable reports. Currently housing 606 peptide entries, ADPDB encompasses peptides from various sources, including natural and synthetic origins. Name, sequence, source, target, mode of action (MoA), length, IC50, toxicity, hemolytic activity of peptides are meticulously curated, facilitating insights into their therapeutic potential. Notably, ADPDB addresses the gap in specialized databases focusing on anti-DENV peptides, aligning with the growing interest in peptide-based therapeutics. The database enables researchers, pharmaceutical industries, and clinicians to explore peptide candidates, study structure-activity relationships, and accelerate drug discovery processes. By leveraging bioinformatics-driven approaches, ADPDB aims to advance the understanding and development of peptide-based interventions against dengue. This resource is accessible via any web browser at URL: https://bblserver.org.in/adpdb/.

Graphical abstract

Graphical abstract of ADPDB (for the creation of graphical abstract, we have used the image of dengue virus (PDB ID: 1K4R by Kuhn et al in Structure of dengue virus: implications for flavivirus organization, maturation, and fusion, Cell, 108(5):717–725, 2002), image of arenicin-1 AMP (PDB ID: 2JSB by Andrä et al in Structure and mode of action of the antimicrobial peptide arenicin, Biochem J, 410(1):113–122, 2008), and image of an PubMed article (PMID: 29200948 by Chew MiawFang et al in Peptides as therapeutic agents for dengue virus, Int J Med Sci 14(13):1342–1359, 2017). The remaining images are generated and incorporated by us).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Data Availability

The master dataset of ADPDB is openly accessible in XLSX, CSV, TSV, LIST, FASTA, and TEXT formats at the URL: https://bblserver.org.in/adpdb/adpdb-download.

References

  • Andrä J, Jakovkin I, Grötzinger J, Hecht O, Krasnosdembskaya AD, Goldmann T, Gutsmann T, Leippe M (2008) Structure and mode of action of the antimicrobial peptide arenicin. Biochem J 410(1):113–122

    Article  PubMed  Google Scholar 

  • Chew MF, Poh KS, Poh CL (2017) Peptides as therapeutic agents for dengue virus. International journal of medical sciences, 14(13), p.1342

  • Chew MiawFang CM, PohKeatSeong PK, PohChitLaa PC (2017) Peptides as therapeutic agents for dengue virus. Int J Med Sci 14(13):1342–1359.

  • De La Guardia C, Lleonart R (2014) Progress in the identification of dengue virus entry/fusion inhibitors. BioMed research international, 2014

  • Diao L, Meibohm B (2013) Pharmacokinetics and pharmacokinetic–pharmacodynamic correlations of therapeutic peptides. Clin Pharmacokinet 52:855–868

    Article  CAS  PubMed  Google Scholar 

  • dos Santos Nascimento IJ, da Silva Rodrigues ÉE, da Silva MF, de Araújo-Júnior JX, de Moura RO (2022) Advances in computational methods to Discover New NS2B-NS3 inhibitors useful against Dengue and Zika Viruses. Curr Top Med Chem 22(29):2435–2462

    Article  PubMed  Google Scholar 

  • Gawde U, Chakraborty S, Waghu FH, Barai RS, Khanderkar A, Indraguru R, Shirsat T, Idicula-Thomas S (2023) CAMPR4: a database of natural and synthetic antimicrobial peptides. Nucleic Acids Res 51(D1):D377–D383

    Article  CAS  PubMed  Google Scholar 

  • Gómez EA, Giraldo P, Orduz S (2017) InverPep: a database of invertebrate antimicrobial peptides. J Global Antimicrob Resist 8:13–17

    Article  Google Scholar 

  • Hammami R, Ben Hamida J, Vergoten G, Fliss I (2009) PhytAMP: a database dedicated to antimicrobial plant peptides. Nucleic Acids Res 37(suppl1):D963–D968

    Article  CAS  PubMed  Google Scholar 

  • Jhong JH, Yao L, Pang Y, Li Z, Chung CR, Wang R, Li S, Li W, Luo M, Ma R, Huang Y (2022) dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. Nucleic Acids Res 50(D1):D460–D470

    Article  CAS  PubMed  Google Scholar 

  • Khan A, Khan S, Ahmad S, Anwar Z, Hussain Z, Safdar M, Rizwan M, Waseem M, Hussain A, Akhlaq M, Khan T (2021a) HantavirusesDB: Vaccinomics and RNA-based therapeutics database for the potentially emerging human respiratory pandemic agents. Microb Pathog 160:105161

    Article  CAS  PubMed  Google Scholar 

  • Khan A, Zia T, Suleman M, Khan T, Ali SS, Abbasi AA, Mohammad A, Wei DQ (2021b) Higher infectivity of the SARS-CoV‐2 new variants is associated with K417N/T, E484K, and N501Y mutants: an insight from structural data. J Cell Physiol 236(10):7045–7057

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khan T, Khan A, Wei DQ (2021c) MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses. Database 2021:pbaab063

    Article  Google Scholar 

  • Khan T, Khan A, Nasir SN, Ahmad S, Ali SS, Wei DQ (2021d) CytomegaloVirusDb: multi-omics knowledge database for cytomegaloviruses. Comput Biol Med 135:104563

    Article  CAS  PubMed  Google Scholar 

  • Khan T, Abdullah M, Toor TF, Almajhdi FN, Suleman M, Iqbal A, Ali L, Khan A, Waheed Y, Wei DQ (2022a) Evaluation of the whole proteome of achromobacterxylosoxidans to identify vaccine targets for mRNA and peptides-based vaccine designing against the emerging respiratory and lung cancer-causing bacteria. Front Med 8:p825876

    Article  Google Scholar 

  • Khan T, Khan A, Ansari JK, Najmi MH, Wei DQ, Muhammad K, Waheed Y (2022b) Potential immunogenic activity of computationally designed mRNA-and peptide-based prophylactic vaccines against MERS, SARS-CoV, and SARS-CoV-2: a reverse vaccinology approach. Molecules 27(7):2375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khan T, Muzaffar A, Shoaib RM, Khan A, Waheed Y, Wei DQ (2022c) Towards specie-specific ensemble vaccine candidates against mammarenaviruses using optimized structural vaccinology pipeline and molecular modelling approaches. Microbial Pathogenesis, 172, p.105793

  • Khan T, Suleman M, Ali SS, Sarwar MF, Ali I, Ali L, Khan A, Rokhan B, Wang Y, Zhao R, Wei DQ (2022d) Subtractive proteomics assisted therapeutic targets mining and designing ensemble vaccine against Candida auris for immune response induction. Computers in Biology and Medicine, 145, p.105462

  • Kuhn RJ, Zhang W, Rossmann MG, Pletnev SV, Corver J, Lenches E, Jones CT, Mukhopadhyay S, Chipman PR, Strauss EG, Baker TS (2002) Structure of dengue virus: implications for flavivirus organization, maturation, and fusion. Cell 108(5):717–725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee MF, Anasir MI, Poh CL (2023) Development of novel antiviral peptides against dengue serotypes 1–4. Virology 580:10–27

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Chen Z (2008) RAPD: a database of recombinantly-produced antimicrobial peptides. FEMS Microbiol Lett 289(2):126–129

    Article  CAS  PubMed  Google Scholar 

  • Lim SP, Wang QY, Noble CG, Chen YL, Dong H, Zou B, Yokokawa F, Nilar S, Smith P, Beer D, Lescar J (2013) Ten years of dengue drug discovery: progress and prospects. Antiviral Res 100(2):500–519

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Zhu Y, Sun X, Ma T, Lao X, Zheng H (2023) DRAVP: A Comprehensive Database of Antiviral Peptides and Proteins. Viruses, 15(4), p.820

  • Mathur D, Kaur H, Dhall A, Sharma N, Raghava GP (2021) SAPdb: a database of short peptides and the corresponding nanostructures formed by self-assembly. Comput Biol Med 133:104391

    Article  CAS  PubMed  Google Scholar 

  • Mondal RK, Sen D, Arya A, Samanta SK (2023) Developing anti-microbial peptide database version 1 to provide comprehensive and exhaustive resource of manually curated AMPs. Scientific Reports, 13(1), p.17843

  • Obi JO, Gutiérrez-Barbosa H, Chua JV, Deredge DJ (2021) Current trends and limitations in dengue antiviral research. Tropical Medicine and Infectious Disease, 6(4), p.180

  • Palanichamy Kala M, John S, A.L. and, Rathore AP (2023) Dengue: Update on Clinically Relevant Therapeutic Strategies and Vaccines. Current Treatment Options in Infectious Diseases, pp.1–26

  • Qureshi A, Thakur N, Kumar M (2013) HIPdb: a database of experimentally validated HIV inhibiting peptides. PLoS ONE 8(1):e54908

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qureshi A, Thakur N, Tandon H, Kumar M (2014) AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Res 42(D1):D1147–D1153

    Article  CAS  PubMed  Google Scholar 

  • Reginald K, Chan Y, Plebanski M, Poh CL (2018) Development of peptide vaccines in dengue. Curr Pharm Design 24(11):1157–1173

    Article  CAS  Google Scholar 

  • Seebah S, Suresh A, Zhuo S, Choong YH, Chua H, Chuon D, Beuerman R, Verma C (2007) Defensins knowledgebase: a manually curated database and information source focused on the defensins family of antimicrobial peptides. Nucleic Acids Res 35(suppl1):D265–D268

    Article  CAS  PubMed  Google Scholar 

  • Shi G, Kang X, Dong F, Liu Y, Zhu N, Hu Y, Xu H, Lao X, Zheng H (2022) DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides. Nucleic Acids Res 50(D1):D488–D496

    Article  CAS  PubMed  Google Scholar 

  • Shukla R, Ahuja R, Beesetti H, Garg A, Aggarwal C, Chaturvedi S, Nayyar K, Arora U, Lal AA, Khanna N (2023) Sinococuline, a bioactive compound of Cocculus hirsutus has potent anti-dengue activity. Scientific Reports, 13(1), p.1026

  • Théolier J, Fliss I, Jean J, Hammami R (2014) MilkAMP: a comprehensive database of antimicrobial peptides of dairy origin. Dairy Sci Technol 94:181–193

    Article  Google Scholar 

  • Wang G, Li X, Wang Z (2016) APD3: the antimicrobial peptide database as a tool for research and education. Nucleic Acids Res 44(D1):D1087–D1093

    Article  CAS  PubMed  Google Scholar 

  • Whitmore L, Wallace B (2004) The Peptaibol database: a database for sequences and structures of naturally occurring peptaibols. Nucleic Acids Res 32(suppl1):D593–D594

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Q, Chen X, Li B, Lu C, Yang S, Long J, Chen H, Huang J, He B (2022) A database of anti-coronavirus peptides. Scientific Data, 9(1), p.294

  • Zhao X, Wu H, Lu H, Li G, Huang Q (2013) LAMP: a database linking antimicrobial peptides. PLoS ONE 8(6):e66557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zouhir A, Taieb M, Lamine MA, Cherif A, Jridi T, Mahjoubi B, Mbarek S, Fliss I, Nefzi A, Sebei K, Hamida B, J (2017) ANTISTAPHYBASE: database of antimicrobial peptides (AMPs) and essential oils (EOs) against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus aureus. Arch Microbiol 199:215–222

    Article  CAS  PubMed  Google Scholar 

  • Zouhir A, Souiai O, Harigua E, Cherif A, Chaalia AB, Sebei K (2023) ANTIPSEUDOBASE: Database of Antimicrobial Peptides and Essential Oils Against Pseudomonas. International Journal of Peptide Research and Therapeutics, 29(3), p.37

Download references

Acknowledgements

Rajat Kumar Mondal and Ananya Anurag Anand are thankful to MoE-GoI for their fellowship. We are extremely thankful to IIIT-A for providing the infrastructural facility i.e. Central Computing Facility.

Funding

There was no funding available for this project.

Author information

Authors and Affiliations

  1. Biochemistry and Bioinformatics Laboratory, Department of Applied Sciences, Indian Institute of Information Technology, Allahabad (IIIT-A), Devghat, Jhalwa, Prayagraj, Uttar Pradesh, 211012, India

    Rajat Kumar Mondal, Ananya Anurag Anand & Sintu Kumar Samanta

Authors
  1. Rajat Kumar Mondal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ananya Anurag Anand
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sintu Kumar Samanta
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

R.K.M.: Conceptualization, Resources, Investigation and Data Curation & Analysis, Validation, Writing; A.A.A.: Resources, Data Mining & Curation, Data Analysis and Writing; S.K.S.: Conceptualization, Formal Analysis, Supervision, Writing-review & Editing.

Corresponding author

Correspondence to Sintu Kumar Samanta.

Ethics declarations

Competing Interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mondal, R.K., Anand, A.A. & Samanta, S.K. ADPDB: A Comprehensive Knowledgebase of Manually Curated Peptides Against Dengue Virus. Int J Pept Res Ther 30, 36 (2024). https://doi.org/10.1007/s10989-024-10610-0

Download citation

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10989-024-10610-0

Keywords

Search

Navigation