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Atomistic and Coarse-grained Modeling of Pharmaceutical Formulations


Computer-aided drug design has been practised for half a century, the application of computational modeling to drug delivery and pharmaceutical formulations has emerged only in recent years. Computational pharmaceutics is able to provide rational, deductive, and knowledge-based strategies in pharmaceutics with the use of high performance computing systems. Scientists therefore apply this unique technology to build atomistic and coarse-grained models of pharmaceutical formulations, revealing more and more important mechanistic details. Alfa Chemistry provides a profound insight into the full-length molecules and its higher-level hierarchical structures through the atomistic and coarse-grained modeling.

Application of Atomistic and Coarse-grained Modeling

  • Derive parameters for higher hierarchical levels, up to the macroscale by systematically feeding information from smaller, more accurate to larger, more coarse levels.
  • Allow the study of more complex systems, up to micrometer dimension and millisecond duration.
  • Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule.Figure 1. Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule. (Marson. et al. 2016)

Modeling Process

  • Select the suitable force field to predict the thermodynamic properties of non-ionic surfactants and drugs
  • Generate an optimal atomistic and coarse-grained model for surfactants, drug molecules and solvents
  • Finally, starting from the mesoscopic scale, simulate the appearance of five simple systems with increasing complexity:
  • 1) Non-ionic surfactants in aqueous solutions
    2) Nonionic surfactants and hydrophobic drugs in aqueous solutions
    3) Nonionic surfactants, hydrophobic drugs and polar solvents in aqueous solutions
    4) Nonionic surfactants, hydrophobic drugs, preservatives and polar solvents in aqueous solutions
    5) Nonionic surfactants, hydrophobic drugs and polymeric surfactants in nonionic aqueous solutions

Our Modeling Services

At Alfa Chemistry, we have developed a multiscale (dual resolution) modeling approach combining an atomistic and coarse-grain (MARTINI) force field. In our simulations, all solute-solute interactions are treated fully atomistically, but solute-solvent and solvent-solvent interactions are treated using a coarse-grain force approach.

1. MARTINI coarse-grained (CG) model

We have developed a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules, helping to study the crystal growth of small organic molecules. We mainly apply the MARTINI model to provide a suitable level of coarsegraining since it retains information about the chemistry specific to the amino acid sequence. Alfa Chemistry uses it to investigate different biological molecules such as membrane proteins, ion channels and liposomes.

  • In this method, a CG force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal.
  • We can determine the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology.
  • Moreover, our experts can predict a new crystalline form by applying meta-dynamics to the coarse-grained model.
  • All amino acids in the MARTINI force field are modeled with a number of beads that varies depending on the steric volume of each amino acid.
  • We consider the polarity of every bead using this model.
  • A residue's hydrogen bonding capability is also characterized.

2. Atomic structure simulation

We offer analysis of static atomic structures as well as molecular dynamics simulations based on Newton's equation of motion.

  • We are capable of simulating the Newtonian equations of motion for systems with hundreds to millions of particles.
  • In addition to biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, we can also calculate the nonbonded interactions (that usually dominate simulations) for research on non-biological systems, e.g. polymers.

Alfa Chemistry's Advantages

  • Our data-driven models derived from machine learning methods can be applied to simulations of all-atom force field simulations, ab initio simulations, and coarse-grained protein folding models.
  • Our modeling can provide all potential functions, including bond length, bond angle, dihedral angle, van der Waals and Coulomb electrostatic interaction.

Our atomistic and coarse-grained models of pharmaceutical formulations services remarkably reduce the cost, promote further experiments, and accelerate the process of drug design for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Marson. et al. Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule. Soft matter. 2016, 12(39): 8246-8255.

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