Interactions between DNA and the acridine intercalator: A computational study

Author(s)

Miranda, Thaynara Guimaraes ; Ciribelli, Nicolas Nascimento ; Bihain, Murielly Fernanda Ribeiro ; Pereira, Anna Karla dos Santos ; Cavallini, Grasiele Soares ; Pereira, Douglas Henrique

• Document type: Journal article
• Source: COMPUTATIONAL BIOLOGY AND CHEMISTRY; v. 109, p. 14-pg., 2024-02-21.

Abstract

Cancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and makes replication impossible. In this context, this study aimed to computationally investigate how acridine intercalators interact with DNA by evaluating the mechanism of interactions, binding, and interaction energies using quantum mechanics calculations. Molecular electrostatic potential (MEP) analysis revealed that acridine has well- distributed negative charges in the center of the molecule, indicative of a dominant electron-rich region. Acridine exhibits welldefined pi orbitals (HOMO and LUMO) on the aromatic rings, suggesting that charge transfer occurs within the molecule and may be responsible for the pharmacological activity of the compound. Structural analysis revealed that acridine interacts with DNA mainly through hydrogen bonds between HAcridine ... ODNA with bond lengths ranging from 2.370 angstrom to 3.472 angstrom. The Binding energy (Delta EBind) showed that acridine interacts with DNA effectively for all complexes and the electronic energy results (E+ZPE) for complexes revealed that the complexes are more stable when the DNA-centered acridine molecule. The Laplacian-analysis topological QTAIM parameter ( backward difference 2 rho(r)) and total energy (H(r)) categorized the interactions as being non-covalent in nature. The RGD peak distribution in the NCI analysis reveals the presence of van der Waals interactions, predominantly between the intercalator and DNA. Accordingly, we confirm that acridine/DNA interactions are relevant for understanding how the intercalator acts within nucleic acids. (AU)

• FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
• Grantee: Munir Salomao Skaf
• Support Opportunities: Research Grants - Research, Innovation and Dissemination Centers - RIDC
• FAPESP's process: 17/11485-6 - Computational and theoretical developments based on ab initio methods and the Density Functional Theory
• Grantee: Rogério Custodio
• Support Opportunities: Regular Research Grants