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Conformational Diversity-Driven Crystallization of Daptomycin: A Multi-Scale Approach with Experimental Validation.

Qingshi Wen1, Ke Zhang1, Li Huang1

  • 1College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing 211816, China.

Pharmaceutics
|June 26, 2026
PubMed
Summary

Crystallizing the flexible antibiotic daptomycin is challenging. Researchers found that limiting its conformational diversity with specific solvents, like acetone, promotes crystallization, offering a rational screening method.

Keywords:
COSMO-RSconformational diversitydaptomycinmolecular dynamicssolubility

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Area of Science:

  • Chemical Engineering
  • Crystallization Science
  • Pharmaceutical Sciences

Background:

  • Daptomycin, a critical lipopeptide antibiotic, is difficult to crystallize due to its flexibility and complex ionization.
  • Existing literature lacks reports on daptomycin single crystals or highly crystalline powders.
  • Understanding daptomycin's solubility and crystallization mechanisms is crucial for developing rational screening pathways.

Purpose of the Study:

  • To elucidate the thermodynamic and kinetic factors governing daptomycin solubility and crystallization.
  • To establish a rational, reduced-trial-and-error pathway for daptomycin crystallization.

Main Methods:

  • Systematic measurement of daptomycin solubility in eight pure solvents using a static gravimetric method.
  • Integration of experimental data with Conductor-like Screening Model for Real Solvents (COSMO-RS) and molecular dynamics (MD) simulations.
  • Analysis of solvent effects on daptomycin conformational diversity and stability.

Main Results:

  • Solubility trends correlated with solvent electrostatic and hydrogen-bonding properties.
  • Molecular dynamics simulations identified the number of dominant conformational clusters as the key crystallization factor.
  • Acetone yielded crystalline powders by restricting daptomycin conformers (12 clusters), while methanol produced amorphous precipitates (53 clusters).

Conclusions:

  • The 'number of conformational clusters' effectively predicts crystallization solvent performance, bridging thermodynamics and kinetics.
  • This descriptor enables rapid screening of crystallization solvents for complex, flexible molecules.
  • The study provides a rational framework for crystallizing challenging macromolecules, moving beyond traditional trial-and-error methods.