Pharmacophore modeling, docking and the integrated use of a ligand- and structure-based virtual screening approach for novel DNA gyrase inhibitors: synthetic and biological evaluation studies

Mathpal, Deepti; Masand, Mukesh; Thomas, Anisha; Ahmad, Irfan; Zaman, Gaffar Sarwar; Kamal, Mehnaz; Jawaid, Talha; Sharma, Pramod Kumar; Gupta, Madan M.; Kumar, Santosh; Srivastava, Swayam Prakash; Balaramnavar, Vishal M.

doi:10.1039/d1ra05630a

Cited by 9 publications

(9 citation statements)

References 51 publications

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“…A lower or higher negative docking score indicates less energy in the pose [11,16]. The other criterion was used to predict affinity.…”

Section: Discussionmentioning

confidence: 99%

“…Using the Molegro virtual docker [11], the (4KZV) carbohydrate region domain of the protein receptor mincle was imported into the software. All water molecules and external hydrogen bonds were removed for a concise visualization of the binding site.…”

Section: Methodsmentioning

confidence: 99%

“…In this project, we visually and statistically examined how exactly these glycolipids/ligands bind to the carbohydrate domain of the c-type lectin molecule using a process called molecular docking [6][7][8][9]. Docking is a computational procedure in which various software packages generate different positions at which ligands bind to their receptors [9][10][11].…”

Section: Introductionmentioning

confidence: 99%

“…Molegro Virtual Studio and Discovery Studio Docking software were used in this study [11]. ChemDraw and ChemDraw3D were used for ligand preparation and construction because protein preparation using docking software is time consuming.…”

Section: Introductionmentioning

confidence: 99%

“…The aftermath of such interactions can result in a complex that enhances, activates, or inhibits biological functions [9]. All docking software possess an algorithm to identify the active site, and it explores the best possible binding position of the ligands [9,11].…”

Section: Introductionmentioning

confidence: 99%

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It Is Possible Molecular Docking of Carbohydrates to a Mycobacterium tuberculosis Molecule?

Soodeen,

Justiz-Vaillant,

Jalsa

2023

Preprint

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Mincle, a C-type lectin, is expressed predominantly in macrophages, where it plays a role in the macrophage response to various microorganisms such as mycobacteria. Docking is a computational procedure in which various software packages generate different positions at which ligands bind to their receptors. Discovery Studio docking was used in Molegro Virtual Studios. ChemDraw and ChemDraw3D were used for ligand preparation and construction because the protein preparation performed using docking software was a very lengthy process. Mincle plays a novel and non-redundant role in the induction of inflammatory signaling in response to mycobacteria. One disadvantage of Molegro studio docking is that it does not show the metallic atoms with which it interacts but rather shows hydrogen bonding and amino acid interactions. Hypothetically, trehalose dimycolate (TDM) and trehalose dibenzenate (TDB) detected by macrophages ultimately lead to CARD9 signaling, thereby producing pro-inflammatory cytokines and chemokines that have the potential to be used therapeutically.

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“…A lower or higher negative docking score indicates less energy in the pose [11,16]. The other criterion was used to predict affinity.…”

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%