Polar Surface Area Analysis Services

Polar surface area (PSA) is a simple and easy-to-calculate molecular descriptor that provides important information about the degree of molecular polarity and potential biological behavior. CD ComputaBio is an excellent service provider for PSA calculation. Our scientists combine the traditional classical 3D PSA with the improved topological polar surface area (TPSA) to provide you with accurate and efficient calculation services.

Introduction to Polar Surface Area

Polar surface area (PSA), also known as topological polar surface area (TPSA), is an important parameter commonly used in medicinal chemistry. It is defined as the sum of the surfaces of all polar atoms or molecules, mainly oxygen and nitrogen, but also the hydrogen atoms attached to them, in a compound. Related studies have shown that this parameter is well correlated with the passive transport of molecules through membranes, and therefore can predict the transport properties of drugs. In medicinal chemistry, PSA has been used to evaluate the transportability of drugs in cells. Lower PSA values usually mean that the molecule is more likely to pass through the cell membrane and be absorbed and distributed by the body. Typical PSA calculation methods include the traditional PSA method based on the three-dimensional geometric structure of the molecule and the TPSA method based on the two-dimensional topological structure of the molecule.

Fig. 1 Calculation of PSA values. Fig.1 Calculation of PSA values for different conformers, one with intramolecular hydrogen bonding (a) and one without (b). (Zadorozhnii PV, et al.; 2022)

Applications of PSA Calculation

Drug Screening and Development
In the early stages of new drug development, by calculating PSA, the transport properties of a large number of candidate compounds can be predicted, and compounds with good pharmacokinetic properties can be screened out, saving time and resources.

Computational Chemistry and Modeling
In quantitative structure-activity relationship (QSAR) studies, PSA is an important molecular descriptor that can be used to build predictive models. In addition, PSA information helps set simulation parameters and study the dynamic behavior of molecules.

Receptor Binding Studies
PSA affects the interaction of molecules with biomacromolecule receptors and helps study ligand-receptor binding mechanisms.

Predicting ADME Properties
Compounds with lower PSA are generally more lipid soluble and easily cross the intestinal epithelial cell membrane by passive diffusion. Empirical data show that compounds with PSA less than 140 Å² are more likely to be well absorbed and thus have higher oral bioavailability.

Our Services

PSA calculation is an important tool for understanding and predicting the physical and chemical properties of molecules. As a professional computational biology and chemistry service provider, CD ComputaBio uses cutting-edge algorithms to help you deal with any challenges in the PSA analysis process. Our scientists can handle PSA calculations for a wide range of complex molecules, including proteins, peptides, protein fragments, antibodies, nucleic acids, complex polycyclic compounds, and compounds containing multiple chiral centers, etc.

Accurate PSA Calculation:

Adopts advanced calculation methods, such as topology-based PSA calculation and three-dimensional molecular structure-based PSA calculation, to provide highly accurate results.
Supports high-throughput calculation of large-scale molecular libraries to meet your needs for new drug screening.

Advanced Algorithm Support:

Introduces machine learning and artificial intelligence algorithms to optimize the calculation process and improve calculation efficiency.
Develops customized algorithm solutions to provide more accurate analysis for special molecular structures.

Molecular Modeling and Simulation:

Provides molecular dynamics simulation and quantum chemical calculation to deeply explore the relationship between the polar surface area of molecules and their physicochemical properties.
Simulates the behavior of molecules in biological membranes and predicts their permeability and bioavailability.

Data Analysis and Visualization:

Provides comprehensive analysis reports, including data statistics, chart presentation, and result interpretation.
Uses professional software tools to display the polar regions of molecules, which is helpful for structure optimization and drug design.

Methods Polar Surface Area Calculation

CD ComputaBio combines the traditional classical 3D PSA with the improved topological polar surface area to provide you with accurate and efficient calculation services.

Classical 3D PSA

Accurate calculation based on three-dimensional structure: The 3D PSA method uses the molecule's actual three-dimensional conformation to calculate the surface area of all polar atoms attached to it, such as oxygen, nitrogen, and hydrogen atoms. Due to the molecule's real spatial structure being considered, the calculation results are more accurate.

In-depth analysis: Our scientists use 3D PSA tools to perform computational analyses that require high-precision assessment of molecules' interactions with biological targets, such as molecular docking and structural optimization.

Improved TPSA

Fast calculations based on 2D structures: The TPSA method calculates polar surface area based on the sum of tabulated surface contributions of polar fragments, i.e., without considering the 3D conformation, based only on connectivity information. These fragment contributions are determined by least squares fitting of single conformation 3D PSAs of 34,810 drugs from the World Drug Index.

Large-scale screening: Due to the fast calculation speed of TPSA, our scientists can use this algorithm to assist you in the screening of large-scale compound libraries.

CD ComputaBio can provide you with comprehensive, accurate, and efficient molecular PSA calculation services. Please feel free to contact us, if you have any needs or challenges in PSA calculation and analysis. Our team will wholeheartedly provide you with professional support and services to help you achieve greater results in your research.

References:

Ertl P, et al. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J Med Chem. 2000;43(20):3714-3717.
Zadorozhnii PV, et al. In Silico ADME Profiling of Salubrinal and Its Analogues. Future Pharmacology. 2022; 2(2):160-197.
Prasanna S, et al. Topological polar surface area: a useful descriptor in 2D-QSAR. Curr Med Chem. 2009;16(1):21-41.

* For Research Use Only.

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