Solution NMR structure of the peptide 536_2 from medicinal leech Hirudo medicinalis in dodecylphosphocholine micelles

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

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Medicinal leech antimicrobial peptides lacking toxicity represent a promising alternative strategy to combat antibiotic-resistant pathogens.

Grafskaia, E.N.Nadezhdin, K.D.Talyzina, I.A.Polina, N.F.Podgorny, O.V.Pavlova, E.R.Bashkirov, P.V.Kharlampieva, D.D.Bobrovsky, P.A.Latsis, I.A.Manuvera, V.A.Babenko, V.V.Trukhan, V.M.Arseniev, A.S.Klinov, D.V.Lazarev, V.N.

(2019) Eur J Med Chem 180: 143-153

  • DOI: https://doi.org/10.1016/j.ejmech.2019.06.080
  • Primary Citation of Related Structures:  
    6RRL, 6RRO, 6RSM

  • PubMed Abstract: 

    The rise of antibiotic resistance has necessitated the development of alternative strategies for the treatment of infectious diseases. Antimicrobial peptides (AMPs), components of the innate immune response in various organisms, are promising next-generation drugs against bacterial infections. The ability of the medicinal leech Hirudo medicinalis to store blood for months with little change has attracted interest regarding the identification of novel AMPs in this organism. In this study, we employed computational algorithms to the medicinal leech genome assembly to identify amino acid sequences encoding potential AMPs. Then, we synthesized twelve candidate AMPs identified by the algorithms, determined their secondary structures, measured minimal inhibitory concentrations against three bacterial species (Escherichia coli, Bacillus subtilis, and Chlamydia thrachomatis), and assayed cytotoxic and haemolytic activities. Eight of twelve candidate AMPs possessed antimicrobial activity, and only two of them, 3967 (FRIMRILRVLKL) and 536-1 (RWRLVCFLCRRKKV), exhibited inhibition of growth of all tested bacterial species at a minimal inhibitory concentration of 10 μmol. Thus, we evidence the utility of the developed computational algorithms for the identification of AMPs with low toxicity and haemolytic activity in the medicinal leech genome assembly.

  • Organizational Affiliation

    Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141700, Russia.


Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
peptide 536_211Hirudo medicinalisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation16-34-00936 mol a

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Other