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Innovative Medicines & Omics Femtomolar inhibition of pseudoeriocitrin

efficacy than eriocitrin. However, the high binding femtoseconds. This environment is full of various
affinity of pseudoeriocitrin to several proteins tested in solvents and thousands of different molecules which are
this study raises concerns about its potential toxicity. If often not considered in docking. However, these factors
the femtomolar inhibition effect of pseudoeriocitrin is may influence protein movement, the probability of the
attributed to its chemical properties, we predict that this protein encountering the ligand, and the potential energy
high level of inhibitory affinity may be due to the following involved. In addition, different molecules, including water,
characteristics: exhibit significant energy variations due to continuous
(i) The heterocyclic center structure exhibits a planar vibrational and rotational motions. The modes of atomic
geometry motion are typically excluded from the calculation used to
(ii) The core structure of the ligand (the combined cyclic determine free binding energy. Temperature fluctuation
structures at the center) is broad and comprises four in the environment and the time required for the protein
rings to reach its minimum energy state are also overlooked in
(iii) The side chains attached to the core structure feature docking simulations. In the future, enhanced simulation
hydroxyl groups or oxygen atoms capabilities may allow for more comprehensive analyses
(iv) The positioning of the 3,4,5-trihydroxy-6-methyloxan- within the same process.
2-yl and 3,4-dihydroxyphenyl groups is perpendicular Experimental results are crucial for understanding
to the plane of the core structure
(v) The center of the ligand is rigid over a wide area, and crystalline structures and translating them into
the side groups are connected to the heterocyclic the computational realm through software, such as
center through sigma bonds. Gaussian. This enables a comparison of theoretical
and practical study results regarding their consistency.
The presence of radical oxygen atoms in pseudoeriocitrin In a thorough experimental study by Gatfaoui
contributes to the formation of multiple hydrogen bonds. et al., 1,3-Benzenedimethanaminium bis(trioxonitrate)
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Further research is required to determine if normal double- (BD[NO ] ) was synthesized and characterized, with its
3 2
bonded oxygen atoms can produce a similar inhibition biological activity – particularly its antibacterial activity
effect. – was predicted by molecular docking. Highest occupied
In a previous study by Ramalingam et al., a new drug molecular orbital (HOMO) and lowest unoccupied
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candidate named isopropyl1-benzoyl-4-(benzoyloxy)- molecular orbital (LUMO) analyses were performed to
2,6-diphenyl-1,2,5,6-tetrahydropyridine-3-carboxylate elucidate charge transfer within the molecule. Molecular
(IDPC) was synthesized and characterized using Fourier electrostatic potential (MEP) was calculated to examine
transform infrared spectroscopy (FT-IR) and nuclear the intermolecular hydrogen bond interactions in detail.
magnetic resonance (NMR) techniques. The compound The study is significant as it demonstrates the consistency
was then investigated through molecular docking to between the experimental and computational results. The
assess its affinity for severe acute respiratory syndrome findings indicate that in silico docking simulations can be
coronavirus 2 (SARS-CoV-2) receptors. The analysis supported by characterization techniques such as X-ray
revealed frontier orbital energies and a low energy gap, diffraction (XRD) and FT-IR. Furthermore, HOMO-
indicating a tendency for intramolecular charge transfer LUMO analyses should be included in the accuracy test
and excellent bioactivity for the compound. The study also of the targeted chemical structure. In this study, various
demonstrated the presence of hydrogen bonding, covalent fungal proteins were used as targets for docking, which
and non-covalent interactions, and electron delocalization were carried out with 10 poses, through the iGEMDOCK
within the molecule. The strong binding affinity observed program, similar to our study. The results revealed
between the active sites of the SARS-CoV-2 main protease numerous π-anion and π-alkyl interactions, including
receptor and the IDPC ligand was attributed primarily to charge transfer, in the binding region of BD(NO ) with
3 2
hydrogen bonding and π-cationic interactions involving target proteins, as well as hydrogen bonds involving
the phenyl ring and carbonyl oxygen groups. In the various atoms. The presence of aromatic structures and
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present study, in silico predictions also suggest a potential oxygen atoms in the ligand played an important role in
connection between oxygen radicals and strong binding facilitating these interactions. Overall, aromatic rings
affinity. significantly contributed to the aromatic interactions and
Common limitations of in silico docking arise from increased binding affinity in our study.
the assumption that the environment in which chemical Oxygen-rich polyphenols are the active ingredients
interactions are predicted is stationary. In reality, the in many drugs due to their ability to reversibly inhibit
biological environment is dynamic and changes over enzymes. However, phenolic compounds containing

Volume 2 Issue 2 (2025) 91 doi: 10.36922/imo.6026