An integrated computational approach to identify GC minor groove binders using various molecular docking scoring functions, dynamics simulations and binding free energy calculations

Soni, Mehul N.; Kumar, Sivakumar Prasanth; Johar, Kaid; Rawal, Rakesh; Pandya, Himanshu

doi:10.1080/07391102.2019.1664331

Cited by 5 publications

(3 citation statements)

References 52 publications

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“…To address these issues, virtual screening using computer-aided drug design was initiated to select drug candidates more efficiently and cost-effectively [ 15 , 16 ]. Virtual screening is one of the most critical technologies in computer-aided drug design, through with potentially effective candidate compounds can be selected from the database containing a large number of organic compounds, and the further experimental tests with these candidate compounds can avoid the blind testing of a large number of compounds by high-throughput screening, as a result of speeding up the development of new drugs.…”

Section: Introductionmentioning

confidence: 99%

“…Herein, a method called shape feature similarity (SHAFTS) was used to carry out the 3D molecular similarity calculations [17,18], by introducing six template molecules as a basis for determining the degree of structural similarity, and performing an initial screening in the commercial database SPECS. The candidate compounds To address these issues, virtual screening using computer-aided drug design was initiated to select drug candidates more efficiently and cost-effectively [15,16]. Virtual screening is one of the most critical technologies in computer-aided drug design, through with potentially effective candidate compounds can be selected from the database con-taining a large number of organic compounds, and the further experimental tests with these candidate compounds can avoid the blind testing of a large number of compounds by high-throughput screening, as a result of speeding up the development of new drugs.…”

Section: Introductionmentioning

confidence: 99%

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Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex

et al. 2023

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In order to develop new anti-cancer drugs more efficiently and reduce side effects based on active drug targets, the virtual drug screening was carried out through the target of G-quadruplexes and 23 hit compounds were, thus, screened out as potential anticancer drugs. Six classical G-quadruplex complexes were introduced as query molecules, and the three-dimensional similarity of molecules was calculated by shape feature similarity (SHAFTS) method so as to reduce the range of potential compounds. Afterwards, the molecular docking technology was utilized to perform the final screening followed by the exploration of the binding between each compound and four different structures of G-quadruplex. In order to verify the anticancer activity of the selected compounds, compounds 1, 6 and 7 were chosen to treat A549 cells in vitro, the lung cancer epithelial cells, for further exploring their anticancer activity. These three compounds were found to be of good characteristics in the treatment of cancer, which revealed the great application prospect of the virtual screening method in developing new drugs.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex

et al. 2023

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“…Classical intercalators bind to DNA through the entire aromatic portion present in the molecule within GpG base pairs covering the entire portion top and bottom portion of the site of intercalation whereas threading intercalators act through major and minor grooves as depicted in Figure 1 (Kang et al, 2006; Liu et al, 2006). Minor and major groove binders do not alter the conformation of DNA helix majorly (Soni et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

DNA intercalators as anticancer agents

et al. 2022

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Cancer is one of the most prevailing disease conditions, which occurs due to uncontrolled cell division either due to natural mutation to the genes or due to changes induced by physical, chemical, or biological carcinogens. According to WHO, it is the second leading cause of death worldwide and has reported 10 million deaths in 2020. Hence, there arises the need for better chemotherapies and DNA intercalators are one such emerging therapy for cancer. DNA intercalating agents reversibly intercalate with the double‐helical structure of DNA by interacting with adjacent base pairs and disrupting the structure of DNA and thereby causing cell death. Here, we discuss the different classes of organo‐intercalators used in cancer therapy describing their anticancer and intercalation ability by different methods along with their structure–activity relationship and mechanism of action.

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Innovative screening for functional improved aromatic amine derivatives: Toxicokinetics, free radical oxidation pathway and carcinogenic adverse outcome pathway

Liu

et al. 2023

Journal of Hazardous Materials

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An integrated computational approach to identify GC minor groove binders using various molecular docking scoring functions, dynamics simulations and binding free energy calculations

Cited by 5 publications

References 52 publications

Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex

Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex

DNA intercalators as anticancer agents

Innovative screening for functional improved aromatic amine derivatives: Toxicokinetics, free radical oxidation pathway and carcinogenic adverse outcome pathway

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