Insights into the Pharmacological Effects of Flavonoids: The Systematic Review of Computer Modeling

Abstract

Computer modeling is a method that is widely used in scientific investigations to predict the biological activity, toxicity, pharmacokinetics, and synthesis strategy of compounds based on the structure of the molecule. This work is a systematic review of articles performed in accordance with the recommendations of PRISMA and contains information on computer modeling of the interaction of classical flavonoids with different biological targets. The review of used computational approaches is presented. Furthermore, the affinities of flavonoids to different targets that are associated with the infection, cardiovascular, and oncological diseases are discussed. Additionally, the methodology of bias risks in molecular docking research based on principles of evidentiary medicine was suggested and discussed. Based on this data, the most active groups of flavonoids and lead compounds for different targets were determined. It was concluded that flavonoids are a promising object for drug development and further research of pharmacology by in vitro, ex vivo, and in vivo models is required.

Insights into the computer-aided drug design and discovery based on anthraquinone scaffold for cancer treatment: A systematic review

“…For the method of target protein generation, further search from the RCSB Protein Data Bank revealed that the majority of the crystal structures used in the studies were obtained via X-ray diffraction method, where this method was more commonly in use compared to NMR spectroscopy. However, X-ray crystallography was ranked as “High Risk of Bias” in the checklist as it was opined that only NMR spectroscopy captures the three-dimensional structure details in a medium close to the actual biological environment [ 49 ]. Perhaps the ranking of this domain is worth revisiting since both NMR spectroscopy and X-ray crystallography offer different pros and cons, and both tools are highly complementary [ 102 ].…”

“…Due to the lack of a standardised tool for this type of study, the risk of bias of the selected papers was assessed using a checklist previously developed and applied by Taldaev and colleagues [ 49 ], with some modifications. The assessment was carried out separately by two independent reviewers (HMC & MS).…”

“…For this review, the bias domain of “Docking Software” was removed. The authors who developed this tool ranked Glide or GOLD docking software as “low risk of bias” [ 49 ] since the Monte-Carlo algorithm and empirical scoring functions used by these two software have been shown to perform better as confirmed by in-vitro validation [ 50 ]. However, this was not always the case.…”

In silico structure-based design of peptides or proteins as therapeutic tools for obesity or diabetes mellitus: A protocol for systematic review and meta analysis

“…[21] Accordingly, computational modeling studies have been widely used in scientific investigations to predict the biological activity, toxicity, pharmacokinetics, and synthesis strategy of compounds based on the structure of the molecule. [26] There is already the prediction of systematic reviews based on protocol focusing on therapeutic targets in silico structure-based design. According to Gomes et al [38] , the reviews developed from that protocol will guide decision-making regarding the choice of targets/models in future research focused on therapeutics of obesity or diabetes mellitus.…”

“…The modeling quality will be assessed using a checklist designed based on the standardized guidelines for simulation "Strengthening the reporting of empirical simulation studies" (adapted). The risk of bias, due to the lack of a standardized tool specifically for this type of study, will be assessed based on a checklist obtained from separate literature sources, such as the checklist developed by Taldaev et al [26]…”