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Negative Image-Based Screening: Rigid Docking Using Cavity Information.

Pekka A Postila^1,2, Sami T Kurkinen^1,2, Olli T Pentikäinen^3,4

¹Institute of Biomedicine, Integrative Physiology and Pharmacology, University of Turku, Turku, Finland.

Methods in Molecular Biology (Clifton, N.J.)

|March 24, 2021

Summary

Negative image-based screening offers a rapid and computationally efficient alternative to flexible docking for drug discovery. This rigid docking method aligns target protein cavities with ligand conformers, proving effective in virtual screening experiments.

Keywords:

Cavity detection Flexible molecular docking Negative image-based screening (NIB)Rigid molecular docking Virtual screening

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Area of Science:

Computational chemistry
Drug discovery
Structural biology

Background:

Molecular docking is crucial for rational drug discovery, involving flexible ligand binding pose sampling.
Flexible docking offers accurate pose geometries but is computationally intensive and may require post-processing for enrichment.

Purpose of the Study:

To introduce and explain the Negative Image-based (NIB) screening methodology.
To discuss the strengths and weaknesses of NIB screening in drug discovery.

Main Methods:

NIB screening utilizes a rigid docking approach, aligning target protein cavity shape/electrostatics with ab initio-generated ligand 3D conformers.
This method is ultrafast and computationally light, validated by extensive benchmarking.

Main Results:

NIB screening demonstrates effectiveness and computational efficiency compared to flexible docking.
The methodology allows for rapid screening without extensive rescoring or post-processing.

Conclusions:

NIB screening presents a practical and powerful alternative for virtual screening in drug discovery.
Its speed and low computational cost make it suitable for large-scale screening campaigns.