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Occurrence of non-canonical G-quadruplex (G4) DNA structures in the genome have been recognized as key factors in gene regulation and several other cellular processes. The mosR and ndhA genes involved in pathways of oxidation sensing regulation and ATP generation, respectively, make Mycobacterium tuberculosis (Mtb) bacteria responsible for oxidative stress inside host macrophage cells. Circular Dichroism spectra demonstrate stable hybrid G4 DNA conformations of mosR/ndhA DNA sequences. Real-time binding of mitoxantrone to G4 DNA with an affinity constant ~105–107 M−1, leads to hypochromism with a red shift of ~18 nm, followed by hyperchromism in the absorption spectra. The corresponding fluorescence is quenched with a red shift ~15 nm followed by an increase in intensity. A change in conformation of the G4 DNA accompanies the formation of multiple stoichiometric complexes with a dual binding mode. The external binding of mitoxantrone with a partial stacking with G-quartets and/or groove binding induces significant thermal stabilization, ~20–29 °C in ndhA/mosR G4 DNA. The interaction leads to a two/four-fold downregulation of transcriptomes of mosR/ndhA genes apart from the suppression of DNA replication by Taq polymerase enzyme, establishing the role of mitoxantrone in targeting G4 DNA, as an alternate strategy for effective anti-tuberculosis action in view of deadly multi-drug resistant tuberculosis disease causing bacterial strains t that arise from existing therapeutic treatments.

Application of computational tools and techniques has emerged as an invincible instrument to unravel the structure-function relationship and offered better mechanistic insights in the designing and development of new drugs along with the treatment regime. The use of in silico tools equipped modern chemist with armamentarium of extensive methods to meticulously comprehend the structural tenacity of receptor-ligand interactions and their dynamics. In silico methods offers a striking property of being less resource intensive and economically viable as compared to experimental evaluation. These techniques have proved their mettle in the designing of potential lead compounds to combat life-threatening diseases such as AIDS, cancer, tuberculosis, malaria, etc. In the present scenario, computer-aided drug designing has ascertained an essential and indispensable gizmo in therapeutic development. This review will present a brief outline of computational methods used at different facets of drug designing and its latest advancements. The aim of this review article is to briefly highlight the methodologies and techniques used in structure-based/ ligand-based drug designing viz., molecular docking, pharmacophore modeling, density functional theory, protein-hydration and molecular dynamics simulation which helps in better understanding of macromolecular events and complexities.

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G‐quadruplex defines as an evolutionarily conserved sequence, non‐canonical secondary structures found at the telomeric region and in promoter regions of various oncogenes like cMYC, CKIT, and BCL2, etc. Telomerase enzyme activity is inhibited by a small molecule that selectively interacts with G‐quadruplex. Understanding the binding mechanism of the ligand‐G quadruplex complex is crucial for assessing anti‐tumor therapeutic efficacy. We have synthesized different anthraquinone derivative‐based G4 ligands which stabilize quadruplex sequence and influence various cellular processes. We have explored the interaction of synthesized anthraquinone derivatives with G4 DNA sequences comprising human telomeric DNA sequence by using absorption, fluorescence, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR) and thermal melting. Each ligand binds to the G4 DNA in monomeric form. The absorption intensity decreases with a shift of 6‐8 nm. Fluorescence quenching studies and sensorgram indicated a significant binding affinity (Kb) in the order of 102 to 108 M−1. A shift of ~6‐10 nm indicates partial stacking of aromatic chromophores with nucleic acid bases. Similar studies with CD spectroscopy yielded Kb in the range of 103 to 107 M−1. Thermal melting profiling of DNA saturated at Drug/DNA = 5 indicated a stabilization (ΔTm) of 21 to 34 °C in presence of different ions indicating more thermal stabilization in the presence of Na+ ions as compared to K+. Molecular docking analysis concluded that external binding of the ligands to G4 DNAs. The formation of a complex G4 structure was further established by polymerase stop assay. The compounds showed in vitro cytotoxicity in cancer cells (MCF) based on a cell viability assessment which undergoes oxidative lesions at a greater extent. Apoptosis is the mechanical pathway behind the cytotoxicity of cancer cells from the live‐dead staining trials. Modifications of cellular morphs, nuclear condensation, and fragmentation were observed in fluorescence microscopy upon treatment of these compounds. qRT‐PCR highlights gene transcriptional regulation genes containing G4 sequence after treatment of ligands. Apart from damaging G4 DNA, thermal stabilization caused by selective interactions is thought to block telomerase enzyme associated with telomere end and contribute to drug‐induced death in cancerous cell types. The insights expedite therapeutic development due to the extensive possibilities of changing ensuing groups on anthraquinones to improve efficacy, reduce cell toxicity, and increase specificity for G‐quadruplex DNA.