TL;DR
Recent developments in QM-based molecular docking and HTD are reviewed, focusing on cases where QM is used explicitly in docking workflows.
This chapter describes a structure-based computational approach to perform high-throughput ligand screens of chemical libraries using open-source software programs and illustrates this workflow with the enzymatic molecular target NAD(P)H:quinone oxidoreductase1 (NQO1), which is overexpressed in a number of human solid tumors.
This comprehensive review examines the fundamental principles underlying molecular docking and molecular dynamics simulations, their diverse applications in pharmaceutical development, and the significant limitations that currently constrain their predictive accuracy and applicability.
Key QM applications-torsional profiles, spectra prediction, reactivity analysis, and modeling of non-covalent interactions-highlighting their impact and limitations are reviewed, illustrating the trade-off between speed and accuracy.
This chapter reviews how QM methods can guide synthesis planning by complementing chemist expertise, literature precedent, and computer-assisted synthesis planning (CASP) tools and demonstrates how QM-driven synthesis planning can support the identification of synthetically accessible drug candidates and advance progress in making the compounds.
Molecular docking is an important step in drug discovery, enabling the evaluation of receptor-ligand affinity while reducing experimental costs and increasing the number of possible tests. However, the high computational cost associated with molecular docking remains a limiting factor that can restrict both the experimental precision and the scale of the problems being addressed. To improve the future applicability of molecular docking, recent works have proposed the use of quantum algorithms based on Gaussian Boson Sampling quantum computers and also gate-based quantum computers. In this work, we propose the use of Quantum Circuit Evolution (QCE) for solving the molecular docking problem, a gate based and gradient-free quantum evolutionary method whose evolution is driven by the random application of unitary operations to a quantum circuit. The proposed algorithm demonstrated the ability to find the best solution to the problem in fewer steps than the methods presented in previous studies, exhibiting fast and stable convergence.
An integrated computational strategy involving pharmacophore mapping, molecular docking, molecular dynamics simulations, and density functional theory (DFT) analysis was employed to identify potential SaFtsZ inhibitors, highlighting compound 15 as a computationally predicted scaffold for the development of SaFtsZ-targeted antibacterial agents.