Tautomerism and ionization

The interactions between a ligand and a target protein can be significantly affected as a result of tautomerism and ionization, potentially having a direct impact when identifying new hits for a given receptor. Hence, the enumeration of the tautomeric and protonation (ionization) states are an important step in in-silico drug discovery tasks such as virtual screening.

Tautomers are isomers differing only in the positions of hydrogen atoms and electrons. Even a simple molecule can have several different tautomeric forms. Moreover, acid/base equilibrium, which explores different protonation states by assigning formal charges to those chemical moieties that are likely to be charged (e.g., phosphate or guanidine) under different conditions,  produces additional forms called protomers.

Many factors can influence the tautomeric and protonation equilibriums, such as concentration, temperature, and pH. Tautomers and protomers differ in shape, functional groups, surface, and hydrogen bonding. Therefore, tautomerism and protonation may result in alternative binding modes with the corresponding impact on ligand/protein interactions.

For instance, Polgar and co-workers have studied the impact of ligand protonation on virtual screening against BACE1 [1]. As an additional proof of the importance of these factors, the widely used ZINC database is processed to generate relevant tautomers and protomers between pH 5 and 9.5.

However, a lot of works do not consider these aspects when building databases or when performing virtual screening due to the perceived underlying complexity.

Chirality

In addition, chirality is also a crucial factor in drug discovery. The presence of an asymmetric carbon atom  (chiral carbon) causes two stereoisomers (non-superposable mirror images of each other), which can show a remarkable difference in the effect of their biological action.

For example, ephedrine has been used for asthma, whereas its enantiomer,  pseudoephedrine, is a nasal/sinus decongestant.

Ephedrine on the left side which is the (S) isomer and pseudoephedrine on the right side which is the (R) isomer

As other examples related to chirality, only the (S) isomer of ibuprofen is effective, whereas the (R) isomer has no anti-inflammatory action and the antihypertensive drug methyldopa owes its effect exclusively to the (S) isomer.  

Ibuprofen on the left side and methyldopa on the right side which both are (S) isomers.

In conclusion, tautomerism, ionization and chirality are factors that affect the interactions between a ligand and a target protein and they should be handled properly in in-silico drug design projects.

[1]  Tímea Polgár, Csaba Magyar, István Simon, and György M. Keserü. “Impact of Ligand Protonation on Virtual Screening against β-Secretase (BACE1)”. Journal of Chemical Information and Modeling 2007 47 (6), 2366-2373. DOI: 10.1021/ci700223p

The post Are you considering tautomerism, ionization and chirality when identifying new hits? appeared first on Pharmacelera | Pushing the limits of computational chemistry.

IYZ and LY2 are two bioactive inhibitors of Pim-1. The main described interactions between the protein and these molecules are hydrophobic. This can be appreciated in the reference molecule in the picture below (blue residues: Lys67, Asp186, Val52, Ile185, Leu44, Phe49,  Leu174, Ala65), which also shows one hydrogen bond interaction (orange residue: Lys67).   

Tools using hydrophobic parameters derived from solvation models, such as a quantum mechanical (QM) version of the MST continuum method used in PharmScreen, favours this type of ligand-target interactions.

The similarity-property principle suggests that analogous compounds will likely share similar biological properties. Indeed, defining the adequate properties that define the biological interactions are fundamental to explore similarity studies. In this case, hydrophobicity is an essential interaction to be considered when a ligand-based drug design process is performed.

Alignment

In order to verify it, we have aligned IYZ against LY2 using both traditional interaction fields and PharmScreen´s hydrophobic interaction fields and the results have been compared with the crystal structure.

The picture below shows the alignment of both approaches with respect to the reference molecule in purple.When comparing this with the crystallized molecule, the alignment performed considering traditional interaction fields misses the correct pose of the molecule, while PharmScreen is able to find the bioactive overlay using hydrophobic interaction fields, as shown in the picture below.

Hence, when searching for new potential hits in ligand-based in-silico approaches, it is crucial to use models for molecular alignment and similarity that use hydrophobic properties in situations in which hydrophobicity dominates the interaction between a ligand and a protein, as the one shown in this example.

[1] C. J. Saris, J. Domen, and A. Berns, “The pim-1 oncogene encodes two related protein-serine/threonine kinases by alternative initiation at AUG and CUG.,” EMBO J., vol. 10, no. 3, pp. 655–64, Mar. 1991.

[2] J. J. Gu, Z. Wang, R. Reeves, and N. S. Magnuson, “PIM1 phosphorylates and negatively regulates ASK1-mediated apoptosis.,” Oncogene, vol. 28, no. 48, pp. 4261–71, Dec. 2009.

[3] Y. Tursynbay, J. Zhang, Z. Li, T. Tokay, Z. Zhumadilov, D. Wu, and Y. Xie, “Pim-1 kinase as cancer drug target: An update.,” Biomed. reports, vol. 4, no. 2, pp. 140–146, Feb. 2016.

The post Alignment of PIM-1 Inhibitors with PharmScreen appeared first on Pharmacelera | Pushing the limits of computational chemistry.