Eschatological scrutiny of unprofessional usage of molecular docking; how unreliability in computational methods arises from amateurish mistakes

Bagheri, Milad; Ghasemshirazi, Saeid; Abiri, Ardavan

doi:10.1016/j.bcab.2019.101224

Cited by 3 publications

(1 citation statement)

References 18 publications

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“…Molecular docking–based virtual screening is not always accurate and precise in finding the right compounds, and the compounds should be further verified with MD [46]. MD on the best compound was carried out via Desmond v5.3 package [47] by Optimized Potential for Liquid Simulations 3 (OPLS_2005) force field and Single Point Charge water model for 50 ns and 1000 frames, using NPT ensemble (constant number of atoms, constant pressure, i.e., 1.01325 bar and constant temperature, i.e., 300 K) on an orthorhombic periodic boundary condition with 0.15 M solution of NaCl to mimic the ionic strength of cellular environment [48].…”

Section: Methodsmentioning

confidence: 99%

Phlorotannins as HIV Vpu inhibitors, an in silico virtual screening study of marine natural products

Langarizadeh

Abiri

Ghasemshirazi

et al. 2020

Biotech and App Biochem

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The importance of new effective treatment methodologies for human immunodeficiency virus (HIV) is undeniable for the medical society. Viral protein U (Vpu), one of the disparaged accessory proteins of HIV, is responsible for the dissemination of viral particles, and HIV mutants lacking Vpu protein have remarkably reduced pathogenicity. Here, we explored the marine natural products to find the leading structures which can potentially inhibit the activity of Vpu in silico. To fulfill this goal, we set up a virtual screening based on molecular docking to evaluate the binding capacity of different marine products to Vpu. For validation, we used molecular dynamics simulation and monitored the root mean square deviation value and binding interactions. The results were intriguing when we realized that the hit compounds (phlorotannins) had previously been identified as reverse transcriptase and HIV protease inhibitors. This research inaugurates a new road to combat HIV by multifaceted mode of action of these marine natural products without putting the normal cells in jeopardy (with their safe toxicological profile).

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Section: Methodsmentioning

confidence: 99%