Skip to main content
SpringerLink
Log in

Natural Product-Based Drug Designing for Treatment of Human Parasitic Diseases

  • Chapter
  • First Online:
Natural Product Based Drug Discovery Against Human Parasites

Abstract

Medicinal plants are the source of various therapeutic agents, including crude extracts and pharmacologically active compounds. Many novel targets and ligands are being identified daily to treat various diseases from AIDS to Alzheimer’s to cancer with the application and techniques of drug designing. Natural products act as pillars for traditional medicine and are involved in the identification of lead compounds which could plausibly act as potential drugs in the area of parasitology. Computational biology has successfully expanded its arms in numerous ways in the process of drug discovery, from the identification of novel targets and biomarkers for rapid screening of large compounds to drug design assistance in clinical trials. The use of in silico suites like Schrodinger’s Maestro, Discovery Studio, and software like grid computing and window-based general PBPK/PD modelling for visualization software along with these, the explosion of biological data (genome sequences and information on proteins, etc.) has also led to the enhancement in the designing of effective treatment methodologies. In this chapter, we explicitly focus on the ancient drug discovery methods to advanced computational methods, which have led to an inclination of drug discovery towards a data-driven approach and using natural products to identify lead molecules and small molecule drug candidates for parasitic disease. It will also deal with the present informatics knowledge gaps and other barriers that need to be overcome for the complete reliability of computationally generated leads for drug discovery in pathogenesis. Finally, this chapter will provide a summary of commercially available important nature-based drugs and helpful software.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 219.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 279.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD (2012) Towards automated crystallographic structure refinement with phenix refine. Acta Crystallogr Sect D Biol Crystallogr 68(4):352–367

    Article  CAS  Google Scholar 

  • Alonso H, Bliznyuk AA, Gready JE (2006) Combining docking and molecular dynamic simulations in drug design. Med Res Rev 26(5):531–568

    Article  PubMed  CAS  Google Scholar 

  • Anaya AL, Cruz-Ortega R, Waller GR (2006) Metabolism and ecology of purine alkaloids. Front Biosci 11(Suppl 1):2354

    Article  PubMed  CAS  Google Scholar 

  • Angeli P, Ginès P, Wong F, Bernardi M, Boyer TD, Gerbes A, Moreau R, Jalan R, Sarin SK, Piano SJG (2015) Diagnosis and management of acute kidney injury in patients with cirrhosis: revised consensus recommendations of the International Club of Ascites. Gut 64(4):531–537

    Article  PubMed  CAS  Google Scholar 

  • Bacilieri M, Moro S (2006) Ligand-based drug design methodologies in drug discovery process: an overview. Curr Drug Discov Technol 3(3):155–165

    Article  PubMed  CAS  Google Scholar 

  • Bakan A, Bahar I (2009) The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc Natl Acad Sci U S A 106(34):14349–14354

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baldi A (2010) Computational approaches for drug design and discovery: an overview. Syst Rev Pharm 1(1):99

    Article  CAS  Google Scholar 

  • Berneche S, Roux BJN (2001) Energetics of ion conduction through the K+ channel. Nature 414(6859):73–77

    Article  PubMed  CAS  Google Scholar 

  • Brunger AT, Adams PD (2002) Molecular dynamics applied to X-ray structure refinement. Acc Chem Res 35(6):404–412

    Article  PubMed  CAS  Google Scholar 

  • Buch I, Giorgino T, De Fabritiis G (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A 108(25):10184–10189

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Carpenter KA, Huang X (2018) Machine learning-based virtual screening and its applications to Alzheimer’s drug discovery: a review. Curr Pharm Des 24(28):3347–3358

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chetry LB, Basar K, Taye K, Taka T, Tsering J, Wangpan T, Bharali MJN (2018) Medicinal plants used against gastrointestinal disorders among the Adi Tribe of Eastern Himalaya. NeBIO 9(1):93–101

    Google Scholar 

  • Das NC, Patra R, Gupta PSS, Ghosh P, Bhattacharya M, Rana MK, Mukherjee S (2021) Designing of a novel multi-epitope peptide based vaccine against Brugia malayi: an in silico approach. Infect Genet Evol 87:104633

    Article  PubMed  CAS  Google Scholar 

  • Freeman BC, Beattie G (2008) An overview of plant defenses against pathogens and herbivores. Plant Health Instruct 149:0226

    Google Scholar 

  • Fribourg M, Moreno JL, Holloway T, Provasi D, Baki L, Mahajan R, Park G, Adney SK, Hatcher C, Eltit JM (2011) Decoding the signaling of a GPCR heteromeric complex reveals a unifying mechanism of action of antipsychotic drugs. Cell 147(5):1011–1023

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ganesan A (2008) The impact of natural products upon modern drug discovery. Curr Opin Chem Biol 12(3):306–317

    Article  PubMed  CAS  Google Scholar 

  • Godreuil S, Tazi L, Bañuls AL (2007) Pulmonary tuberculosis and Mycobacterium tuberculosis: modern molecular epidemiology and perspectives. Wiley, New York

    Google Scholar 

  • Grabley S, Thiericke R (1998) Drug discovery from nature. Springer Science & Business Media, New York

    Google Scholar 

  • Gupta C, Prakash D, Gupta S (2013) Relationships between bioactive food components and their health benefits, 1st edn. Food Science Publisher, Richardson, pp 66–85

    Google Scholar 

  • Harpole TJ, Delemotte L (2018) Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations. Biochim Biophys Acta Biomembr 1860(4):909–926

    Article  PubMed  CAS  Google Scholar 

  • Kinghorn AD (2002) The role of pharmacognosy in modern medicine. Expert Opin Pharmacother 3(2):77–79

    Article  PubMed  Google Scholar 

  • Kumar A, Voet A, Zhang KYJ (2012) Fragment based drug design: from experimental to computational approaches. Curr Med Chem 19(30):5128–5147

    Article  PubMed  CAS  Google Scholar 

  • Lin L, Harnly J, Greco L, Bruno MN (2008) LC-MS profiling and quantification of food phenolic components using a standard analytical approach for all plants. Food Sci Technol 99:1–103

    Google Scholar 

  • Lindorff-Larsen K, Best RB, DePristo MA, Dobson CM, Vendruscolo M (2005) Simultaneous determination of protein structure and dynamics. Nature 433(7022):128–132

    Article  PubMed  CAS  Google Scholar 

  • Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) How fast-folding proteins fold. Science 334(6055):517–520

    Article  PubMed  CAS  Google Scholar 

  • Linnemann C, Van Buuren MM, Bies L, Verdegaal EM, Schotte R, Calis JJ, Behjati S, Velds A, Hilkmann H, Atmioui DE, Visser M (2015) High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma. Nat Med 21(1):81–85

    Article  PubMed  CAS  Google Scholar 

  • Lopes FV, Stroppa PHF, Marinho JA, Soares RR, Azevedo LA, Goliatt PVC, Abramo C, da Silva AD (2021) 1,2,3-Triazole derivatives: synthesis, docking, cytotoxicity analysis and in vivo antimalarial activity. Chem Biol Interact 350:109688

    Article  Google Scholar 

  • Mazid M, Khan T, Mohammad F (2011) Role of secondary metabolites in defense mechanisms of plants. Biol Med 3(2):232–249

    CAS  Google Scholar 

  • McKerrow JH (2005) Designing drugs for parasitic diseases of the developing world. PLoS Med 2(8):e210

    Article  PubMed  PubMed Central  Google Scholar 

  • Mertens R (2019) 2 The lock-and-key analogy in Emil Fischer’s program on sugar fermentation, 1890–1907. In: The construction of analogy-based research programs. transcript-Verlag, pp 39–76

    Chapter  Google Scholar 

  • Merz KM Jr, Ringe D, Reynolds CH (2010) Drug design: structure-and ligand-based approaches. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Mirjalili V, Feig M (2013) Protein structure refinement through structure selection and averaging from molecular dynamics ensembles. Journal of chemical theory and computation 9(2):1294–1303

    Article  PubMed  CAS  Google Scholar 

  • Nguyen HD, Hall CK (2004) Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. Proc Natl Acad Sci 101(46):16180–16185

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nichols A (2011) Causal inference for binary regression. Stata conference Chicago (version June 14, 2011)

    Google Scholar 

  • Pathak, N., M. Prajneshu, LK Shaban Ahmad, A. Bhaduri, 2012 A. Dhandapani and O Sharma "Phytochemical analysis and antifungal activity of weed extracts against rhizoctonia root rot in buckwheat (Fagopyrum tataricum) Biopestic Int. 16(2):125-131

    Google Scholar 

  • Pokorný J (2007) Are natural antioxidants better—and safer—than synthetic antioxidants? Eur J Lipid Sci Technol 109(6):629–642

    Article  Google Scholar 

  • Ramlal A, Ahmad S, Kumar L, Khan FN, Chongtham R (2021) From molecules to patients: the clinical applications of biological databases and electronic health records. In: Translational bioinformatics in healthcare and medicine. Elsevier, Amsterdam, pp 107–125

    Chapter  Google Scholar 

  • Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE (2012) Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins Struct Funct Bioinform 80(8):2071–2079

    Article  CAS  Google Scholar 

  • Roy M, Kaushik S, Jyoti A, Srivastava VK (2021) Probing the peculiarity of EhRabX10, a pseudoRab GTPase, from the enteric parasite Entamoeba histolytica through in silico modeling and docking Studies. BioMed Res Int 2021:9913625

    Article  PubMed  PubMed Central  Google Scholar 

  • Salsbury FR Jr (2010) Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Curr Opin Pharmacol 10(6):738–744

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schulze-Kaysers N, Feuereisen M, Schieber A (2015) Phenolic compounds in edible species of the Anacardiaceae family—a review. RSC Adv 5(89):73301–73314

    Article  CAS  Google Scholar 

  • Sellami M, Slimeni O, Pokrywka A, Kuvačić G, Hayes LD, Milic M, Padulo J (2018) Herbal medicine for sports: a review. J Int Soc Sports Nutr 15(1):1–14

    Article  Google Scholar 

  • Siracusa L, Ruberto G (2019) Not only what is food is good—polyphenols from edible and nonedible vegetable waste. In: Polyphenols in plants. Elsevier, Amsterdam, pp 3–21

    Chapter  Google Scholar 

  • Snow CD, Nguyen H, Pande VS, Gruebele M (2002) Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420(6911):102–106

    Article  PubMed  CAS  Google Scholar 

  • Speck-Planche A, Luan F, Cordeiro NDS (2012) Role of ligand-based drug design methodologies toward the discovery of new anti-Alzheimer agents: futures perspectives in Fragment-Based Ligand Design. Curr Med Chem 19(11):1635–1645

    Article  PubMed  CAS  Google Scholar 

  • Sudipta K, Lokesh P, Rashmi W, Vijay R, Ssn K (2012) Phytochemical screening and in vitro antimicrobial activity of Bougainvillea spectabilis flower extracts. Int J Phytomed 4(3):375

    Google Scholar 

  • Sun-Waterhouse D (2011) The development of fruit-based functional foods targeting the health and wellness market: a review. Int J Food Sci Technol 46(5):899–920

    Article  CAS  Google Scholar 

  • Swamy BP, Shamsudin NAA, Abd Rahman SN, Mauleon R, Ratnam W, Cruz MTS, Kumar A (2017) Association mapping of yield and yield-related traits under reproductive stage drought stress in rice (Oryza sativa L.). Rice 10(1):1–13

    Article  Google Scholar 

  • Tan L, Yan W, McCorvy JD, Cheng J (2018) Biased ligands of G protein-coupled receptors (GPCRs): structure–functional selectivity relationships (SFSRs) and therapeutic potential. J Med Chem 61(22):9841–9878

    Article  PubMed  CAS  Google Scholar 

  • Tebani A, Afonso C, Marret S, Bekri S (2016) Omics-based strategies in precision medicine: toward a paradigm shift in inborn errors of metabolism investigations. Int J Mol Sci 17(9):1555

    Article  PubMed  PubMed Central  Google Scholar 

  • Thomford NE, Senthebane DA, Rowe A, Munro D, Seele P, Maroyi A, Dzobo K (2018) Natural products for drug discovery in the 21st century: innovations for novel drug discovery. Int J Mol Sci 19(6):1578

    Article  PubMed  PubMed Central  Google Scholar 

  • Wacker D, Stevens RC, Roth BL (2017) How ligands illuminate GPCR molecular pharmacology. Cell 170(3):414–427

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wink M (2008) Plant secondary metabolism: diversity, function and its evolution. Nat Prod Commun 3(8):1934578X0800300801

    Google Scholar 

  • Zhang L, Tan J, Han D, Zhu H (2017) From machine learning to deep learning: progress in machine intelligence for rational drug discovery. Drug Discov Today 22(11):1680–1685

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science, Jamia Millia Islamia, New Delhi, India

    Shaban Ahmad, Avtar Kishan, Pragya Chitkara & Mansaf Alam

  2. Department of Clinical Laboratory Sciences, College of Applied Medical Science, Najran University, Najran, Saudi Arabia

    Saeed A. Asiri

  3. Plant Molecular Biology Division, International Center for Genetic Engineering and Biotechnology, New Delhi, India

    Murugesh Eswaran

  4. Department of Botany, Hansraj College, University of Delhi, New Delhi, India

    Sahil Mehta

Authors
  1. Shaban Ahmad
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Avtar Kishan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pragya Chitkara
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Saeed A. Asiri
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Murugesh Eswaran
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sahil Mehta
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Mansaf Alam
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mansaf Alam .

Editor information

Editors and Affiliations

  1. Department of Plant Molecular Biology & Delhi School of Climate Change, University of Delhi (South Campus), New Delhi, Delhi, India

    Archana Singh

  2. Department of Chemistry & Delhi School of Public Health, Hansraj College, University of Delhi, Delhi, India

    Brijesh Rathi

  3. Department of Zoology & Delhi School of Public Health, Kirorimal College, University of Delhi, Delhi, India

    Anita K. Verma

  4. Molecular Biology Research Laboratory, Department of Zoology & Delhi School of Public Health, Deshbandhu College, University of Delhi, New Delhi, Delhi, India

    Indrakant K. Singh

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Ahmad, S. et al. (2023). Natural Product-Based Drug Designing for Treatment of Human Parasitic Diseases. In: Singh, A., Rathi, B., Verma, A.K., Singh, I.K. (eds) Natural Product Based Drug Discovery Against Human Parasites. Springer, Singapore. https://doi.org/10.1007/978-981-19-9605-4_3

Download citation

Publish with us

Policies and ethics

Search

Navigation