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  1. Fulltext Betamethasone Dipropionate Derivatization, Biotransformation, Molecular Docking, and ADME Analysis as Glucocorticoid Receptor
    Rashid S, Anjum S, Ahmad A, Nadeem R, Ahmed M, Shah SAA, et al.
    Biomed Res Int, 2022;2022:6865472.
    PMID: 35865666 DOI: 10.1155/2022/6865472
    Betamethasone is an important glucocorticoids (GCs), frequently used to cure allergies (such as asthma and angioedema), Crohn's disease, skin diseases (such as dermatitis and psoriasis), systemic lupus erythematosus, rheumatic disorders, and leukemia. Present investigation deals to find potential agonist of glucocorticoid receptors after biotransformation of betamethasone dipropionate (1) and to carry out the molecular docking and ADME analyses. Biotransformation of 1 was carried out with Launaea capitata (dandy) roots and Musa acuminate (banana) leaves. M. acuminate furnished low-cost value-added products such as Sananone dipropionate (2) in 5% yields. Further, biocatalysis of Sananone dipropionate (2) with M. acuminate gave Sananone propionate (3) and Sananone (4) in 12% and 7% yields, respectively. However, Sananone (4) was obtained in 37% yields from Launaea capitata. Compound 5 was obtained in 11% yield after β-elimination of propionic acid at C-17 during oxidation of compound 1. The structure elucidation of new compounds 2-5 was accomplished through combined use of X-ray diffraction and NMR (1D and 2D) studies. In addition to this, molecular docking and ADME analyses of all transformed products of 1 were also done. Compounds 1-5 showed -12.53 to -10.11 kcal/mol potential binding affinity with glucocorticoid receptor (GR) and good ADME profile. Moreover, all the compounds showed good oral bioavailability with the octanol/water partition coefficient in the range of 2.23 to 3.65, which indicated that compounds 1-5 were in significant agreement with the given criteria to be considered as drug-like.
    Matched MeSH terms: Molecular Docking Simulation
  2. Impact of polystyrene microplastics on the growth and photosynthetic efficiency of diatom Chaetoceros neogracile
    Mojiri A, Vishkaei MN, Zhou JL, Trzcinski AP, Lou Z, Kasmuri N, et al.
    Mar Environ Res, 2024 Feb;194:106343.
    PMID: 38215624 DOI: 10.1016/j.marenvres.2024.106343
    The increasing prevalence of microplastic pollution in aquatic environments has raised concerns about its impact on marine life. Among the different types of microplastics, polystyrene microplastics (PSMPs) are one of the most commonly detected in aquatic systems. Chaetoceros neogracile (diatom) is an essential part of the marine food web and plays a critical role in nutrient cycling. This study aimed to monitor the ecotoxicological impact of PSMPs on diatoms and observe enzymatic interactions through molecular docking simulations. Results showed that diatom growth decreased with increasing concentrations and exposure time to PSMPs, and the lowest photosynthetic efficiency (Fv/Fm) value was observed after 72 and 96 h of exposure to 200 mg L-1 of PSMPs. High concentrations of PSMPs led to a decrease in chlorophyll a content (up to 64.4%) and protein content (up to 35.5%). Molecular docking simulations revealed potential interactions between PSMPs and the extrinsic protein in photosystem II protein of diatoms, suggesting a strong affinity between the two. These findings indicate a detrimental effect of PSMPs on the growth and photosynthetic efficiency of diatoms and highlight the need for further research on the impact of microplastics on marine microbial processes.
    Matched MeSH terms: Molecular Docking Simulation
  3. Synthesis, molecular docking, acetylcholinesterase and butyrylcholinesterase inhibitory potential of thiazole analogs as new inhibitors for Alzheimer disease
    Rahim F, Javed MT, Ullah H, Wadood A, Taha M, Ashraf M, et al.
    Bioorg Chem, 2015 Oct;62:106-16.
    PMID: 26318401 DOI: 10.1016/j.bioorg.2015.08.002
    A series of thirty (30) thiazole analogs were prepared, characterized by (1)H NMR, (13)C NMR and EI-MS and evaluated for Acetylcholinesterase and butyrylcholinesterase inhibitory potential. All analogs exhibited varied butyrylcholinesterase inhibitory activity with IC50 value ranging between 1.59±0.01 and 389.25±1.75μM when compared with the standard eserine (IC50, 0.85±0.0001μM). Analogs 15, 7, 12, 9, 14, 1, 30 with IC50 values 1.59±0.01, 1.77±0.01, 6.21±0.01, 7.56±0.01, 8.46±0.01, 14.81±0.32 and 16.54±0.21μM respectively showed excellent inhibitory potential. Seven analogs 15, 20, 19, 24, 28, 30 and 25 exhibited good acetylcholinesterase inhibitory potential with IC50 values 21.3±0.50, 35.3±0.64, 36.6±0.70, 44.81±0.81, 46.36±0.84, 48.2±0.06 and 48.72±0.91μM respectively. All other analogs also exhibited well to moderate enzyme inhibition. The binding mode of these compounds was confirmed through molecular docking.
    Matched MeSH terms: Molecular Docking Simulation
  4. Synthesis of 4-thiazolidinone analogs as potent in vitro anti-urease agents
    Rahim F, Zaman K, Ullah H, Taha M, Wadood A, Javed MT, et al.
    Bioorg Chem, 2015 Dec;63:123-31.
    PMID: 26520885 DOI: 10.1016/j.bioorg.2015.10.005
    4-Thiazolidinone analogs 1-20 were synthesized, characterized by (1)H NMR and EI-MS and investigated for urease inhibitory activity. All twenty (20) analogs exhibited varied degree of urease inhibitory potential with IC50 values 1.73-69.65μM, if compared with standard thiourea having IC50 value of 21.25±0.15μM. Among the series, eight derivatives 3, 6, 8, 10, 15, 17, 19, and 20 showed outstanding urease inhibitory potential with IC50 values of 9.34±0.02, 14.62±0.03, 8.43±0.01, 7.3±0.04, 2.31±0.002, 5.75±0.003, 8.81±0.005, and 1.73±0.001μM, respectively, which is better than the standard thiourea. The remaining analogs showed good to excellent urease inhibition. The binding interactions of these compounds were confirmed through molecular docking studies.
    Matched MeSH terms: Molecular Docking Simulation
  5. Thiadiazole derivatives as New Class of β-glucuronidase inhibitors
    Salar U, Taha M, Ismail NH, Khan KM, Imran S, Perveen S, et al.
    Bioorg Med Chem, 2016 Apr 15;24(8):1909-18.
    PMID: 26994638 DOI: 10.1016/j.bmc.2016.03.020
    Thiadiazole derivatives 1-24 were synthesized via a single step reaction and screened for in vitro β-glucuronidase inhibitory activity. All the synthetic compounds displayed good inhibitory activity in the range of IC50=2.16±0.01-58.06±1.60μM as compare to standard d-saccharic acid 1,4-lactone (IC50=48.4±1.25μM). Molecular docking study was conducted in order to establish the structure-activity relationship (SAR) which demonstrated that thiadiazole as well as both aryl moieties (aryl and N-aryl) involved to exhibit the inhibitory potential. All the synthetic compounds were characterized by spectroscopic techniques (1)H, (13)C NMR, and EIMS.
    Matched MeSH terms: Molecular Docking Simulation
  6. Synthesis, α-glucosidase inhibitory, cytotoxicity and docking studies of 2-aryl-7-methylbenzimidazoles
    Taha M, Ismail NH, Imran S, Mohamad MH, Wadood A, Rahim F, et al.
    Bioorg Chem, 2016 Apr;65:100-9.
    PMID: 26894559 DOI: 10.1016/j.bioorg.2016.02.004
    Benzimidazole analogs 1-27 were synthesized, characterized by EI-MS and (1)HNMR and their α-glucosidase inhibitory activities were found out experimentally. Compound 25, 19, 10 and 20 have best inhibitory activities with IC50 values 5.30±0.10, 16.10±0.10, 25.36±0.14 and 29.75±0.19 respectively against α-glucosidase. Compound 6 and 12 has no inhibitory activity against α-glucosidase enzyme among the series. Further studies showed that the compounds are not showing any cytotoxicity effect. The docking studies of the compounds as well as the experimental activities of the compounds correlated well. From the molecular docking studies, it was observed that the top ranked conformation of all the compounds fit well in the active site of the homology model of α-glucosidase.
    Matched MeSH terms: Molecular Docking Simulation
  7. FT-IR, NBO, HOMO-LUMO, MEP analysis and molecular docking study of Methyl N-({[2-(2-methoxyacetamido)-4-(phenylsulfanyl)phenyl]amino}[(methoxycarbonyl) imino]methyl)carbamate
    Panicker CY, Varghese HT, Narayana B, Divya K, Sarojini BK, War JA, et al.
    Spectrochim Acta A Mol Biomol Spectrosc, 2015 Sep 5;148:29-42.
    PMID: 25863457 DOI: 10.1016/j.saa.2015.03.064
    The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of Methyl N-({[2-(2-methoxyacetamido)-4-(phenylsulfanyl) phenyl]amino} [(methoxycarbonyl)imino]methyl)carbamate have been investigated using HF and DFT levels of calculations. The geometrical parameters are in agreement with XRD data. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. Molecular electrostatic potential study was also performed. The first and second hyperpolarizability was calculated in order to find its role in nonlinear optics. Molecular docking studies are also reported. Prediction of Activity Spectra analysis of the title compound predicts anthelmintic and antiparasitic activity as the most probable activity with Pa (probability to be active) value of 0.808 and 0.797, respectively. Molecular docking studies show that both the phenyl groups and the carbonyl oxygens of the molecule are crucial for bonding and these results draw us to the conclusion that the compound might exhibit pteridine reductase inhibitory activity.
    Matched MeSH terms: Molecular Docking Simulation
  8. In silico molecular docking in DNA aptamer development
    Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M
    Biochimie, 2020 Oct 18;180:54-67.
    PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005
    Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
    Matched MeSH terms: Molecular Docking Simulation
  9. Synthesis, α-amylase inhibitory potential and molecular docking study of indole derivatives
    Taha M, Baharudin MS, Ismail NH, Imran S, Khan MN, Rahim F, et al.
    Bioorg Chem, 2018 10;80:36-42.
    PMID: 29864686 DOI: 10.1016/j.bioorg.2018.05.021
    In search of potent α-amylase inhibitor we have synthesized eighteen indole analogs (1-18), characterized by NMR and HR-EIMS and screened for α-amylase inhibitory activity. All analogs exhibited a variable degree of α-amylase inhibition with IC50 values ranging between 2.031 ± 0.11 and 2.633 ± 0.05 μM when compared with standard acarbose having IC50 values 1.927 ± 0.17 μM. All compounds showed good α-amylase inhibition. Compound 14 was found to be the most potent analog among the series. Structure-activity relationship has been established for all compounds mainly based on bringing about the difference of substituents on phenyl ring. To understand the binding interaction of the most active analogs molecular docking study was performed.
    Matched MeSH terms: Molecular Docking Simulation
  10. Fulltext Triazoloquinazolines as a new class of potent α-glucosidase inhibitors: in vitro evaluation and docking study
    Abuelizz HA, Anouar EH, Ahmad R, Azman NIIN, Marzouk M, Al-Salahi R
    PLoS One, 2019;14(8):e0220379.
    PMID: 31412050 DOI: 10.1371/journal.pone.0220379
    Previously, we synthesized triazoloquinazolines 1-14 and characterized their structure. In this study, we aimed to evaluate the in vitro activity of the targets 1-14 as α-glucosidase inhibitors using α-glucosidase enzyme from Saccharomyces cerevisiae type 1. Among the tested compounds, triazoloquinazolines 14, 8, 4, 5, and 3 showed the highest inhibitory activity (IC50 = 12.70 ± 1.87, 28.54 ± 1.22, 45.65 ± 4.28, 72.28 ± 4.67, and 83.87 ± 5.12 μM, respectively) in relation to that of acarbose (IC50 = 143.54 ± 2.08 μM) as a reference drug. Triazoloquinazolines were identified herein as a new class of potent α-glucosidase inhibitors. Molecular docking results envisaged the plausible binding interaction between the target triazoloquinazolines and α-glucosidase enzyme and indicated considerable interaction with the active site residues.
    Matched MeSH terms: Molecular Docking Simulation
  11. Fulltext Synthesis of Chromen-4-One-Oxadiazole Substituted Analogs as Potent β-Glucuronidase Inhibitors
    Taha M, Rahim F, Ali M, Khan MN, Alqahtani MA, Bamarouf YA, et al.
    Molecules, 2019 Apr 18;24(8).
    PMID: 31003424 DOI: 10.3390/molecules24081528
    Chromen-4-one substituted oxadiazole analogs 1-19 have been synthesized, characterized and evaluated for β-glucuronidase inhibition. All analogs exhibited a variable degree of β-glucuronidase inhibitory activity with IC50 values ranging in between 0.8 ± 0.1-42.3 ± 0.8 μM when compared with the standard d-saccharic acid 1,4 lactone (IC50 = 48.1 ± 1.2 μM). Structure activity relationship has been established for all compounds. Molecular docking studies were performed to predict the binding interaction of the compounds with the active site of enzyme.
    Matched MeSH terms: Molecular Docking Simulation
  12. Fulltext Synthesis, anti-leishmanial and molecular docking study of bis-indole derivatives
    Taha M, Uddin I, Gollapalli M, Almandil NB, Rahim F, Farooq RK, et al.
    BMC Chem, 2019 Dec;13(1):102.
    PMID: 31410413 DOI: 10.1186/s13065-019-0617-4
    We have synthesized new series of bisindole analogs (1-27), characterized by 1HNMR and HR-EI-MS and evaluated for their anti-leishmanial potential. All compounds showed outstanding inhibitory potential with IC50 values ranging from 0.7 ± 0.01 to 13.30 ± 0.50 µM respectively when compared with standard pentamidine with IC50 value of 7.20 ± 0.20 µM. All analogs showed greater potential than standard except 10, 19 and 23 when compared with standard. Structure activity relationship has been also established for all compounds. Molecular docking studies were carried out to understand the binding interaction of active molecules.
    Matched MeSH terms: Molecular Docking Simulation
  13. Plant Bioactive Peptides: Current Status and Prospects Towards Use on Human Health
    Chai TT, Ee KY, Kumar DT, Manan FA, Wong FC
    Protein Pept Lett, 2021;28(6):623-642.
    PMID: 33319654 DOI: 10.2174/0929866527999201211195936
    Large numbers of bioactive peptides with potential applications in protecting against human diseases have been identified from plant sources. In this review, we summarized recent progress in the research of plant-derived bioactive peptides, encompassing their production, biological effects, and mechanisms. This review focuses on antioxidant, antimicrobial, antidiabetic, and anticancer peptides, giving special attention to evidence derived from cellular and animal models. Studies investigating peptides with known sequences and well-characterized peptidic fractions or protein hydrolysates will be discussed. The use of molecular docking tools to elucidate inter-molecular interactions between bioactive peptides and target proteins is highlighted. In conclusion, the accumulating evidence from in silico, in vitro and in vivo studies to date supports the envisioned applications of plant peptides as natural antioxidants as well as health-promoting agents. Notwithstanding, much work is still required before the envisioned applications of plant peptides can be realized. To this end, future researches for addressing current gaps were proposed.
    Matched MeSH terms: Molecular Docking Simulation
  14. New insights into the cholesterol esterase- and lipase-inhibiting potential of bioactive peptides from camel whey hydrolysates: Identification, characterization, and molecular interaction
    Baba WN, Mudgil P, Baby B, Vijayan R, Gan CY, Maqsood S
    J Dairy Sci, 2021 Jul;104(7):7393-7405.
    PMID: 33934858 DOI: 10.3168/jds.2020-19868
    Novel antihypercholesterolemic bioactive peptides (BAP) from peptic camel whey protein hydrolysates (CWPH) were generated at different time, temperature, and enzyme concentration (%). Hydrolysates showed higher pancreatic lipase- (PL; except 3 CWPH) and cholesterol esterase (CE)-inhibiting potential, as depicted by lower half-maximal inhibitory concentration values (IC50 values) compared with nonhydrolyzed camel whey proteins (CWP). Peptide sequencing and in silico data depicted that most BAP from CWPH could bind active site of PL, whereas as only 3 peptides could bind the active site of CE. Based on higher number of reactive residues in the BAP and greater number of substrate binding sites, FCCLGPVPP was identified as a potential CE-inhibitory peptide, and PAGNFLPPVAAAPVM, MLPLMLPFTMGY, and LRFPL were identified as PL inhibitors. Molecular docking of selected peptides showed hydrophilic and hydrophobic interactions between peptides and target enzymes. Thus, peptides derived from CWPH warrant further investigation as potential candidates for adjunct therapy for hypercholesterolemia.
    Matched MeSH terms: Molecular Docking Simulation
  15. Investigations of adsorption behavior and anti-inflammatory activity of glycine functionalized Al12N12 and Al12ON11 fullerene-like cages
    Aghaei M, Ramezanitaghartapeh M, Javan M, Hoseininezhad-Namin MS, Mirzaei H, Rad AS, et al.
    Spectrochim Acta A Mol Biomol Spectrosc, 2021 Feb 05;246:119023.
    PMID: 33049473 DOI: 10.1016/j.saa.2020.119023
    The adsorption behavior of the amino acid, glycine (Gly), via the carboxyl, hydroxyl, and amino groups onto the surfaces of Al12N12 and Al16N16 fullerene-like cages were computationally evaluated by the combination of density functional theory (DFT) and molecular docking studies. It was found that Gly can chemically bond with the Al12N12 and Al16N16 fullerene-like cages as its amino group being more favorable to interact with the aluminum atoms of the adsorbents compared to carboxyl and hydroxyl groups. Oxygen and carbon doping were reported to reduce steric hindrance for Glycine interaction at Al site of Al12ON11/Gly and Al12CN11/Gly complexes. Interaction was further enhanced by oxygen doping due to its greater electron withdrawing effect. Herein, the Al12ON11/Gly complex where two carbonyl groups of Gly are bonded to the aluminum atoms of the Al12N12 fullerene-like cage is the most stable interaction configuration showing ∆adsH and ∆adsG values of -81.74 kcal/mol and -66.21 kcal/mol, respectively. Computational studies also revealed the frequency shifts that occurred due to the interaction process. Molecular docking analysis revealed that the Al12N12/Gly (-11.7 kcal/mol) and the Al12ON11/Gly (-9.2 kcal/mol) complexes have a good binding affinity with protein tumor necrosis factor alpha (TNF-α). TNF-α was implicated as a key cytokine in various diseases, and it has been a validated therapeutic target for the treatment of rheumatoid arthritis. These results suggest that the Al12N12/Gly complex in comparison with the Al16N16/Gly, Al12ON11/Gly, and the Al12CN11/Gly complexes could be efficient inhibitors of TNF-α.
    Matched MeSH terms: Molecular Docking Simulation
  16. Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation
    Bahaman AH, Wahab RA, Abdul Hamid AA, Abd Halim KB, Kaya Y
    J Biomol Struct Dyn, 2021 Apr;39(7):2628-2641.
    PMID: 32248752 DOI: 10.1080/07391102.2020.1751713
    Literature has shown that oil palm leaves (OPL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by the Trichoderma species. However, mechanism of β-glucosidase and xylanase selectivity to degrade lignin, hemicellulose and cellulose in OPL for NC production remains relatively vague. The study aimed to comprehend this aspect by an in silico approach of molecular docking, molecular dynamics (MD) simulation and Molecular-mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis, to compare interactions between the β-glucosidase- and xylanase from Trichoderma asperellum UC1 in complex with each substrate. Molecular docking of the enzyme-substrate complex showed residues Glu165-Asp226-Glu423 and Arg155-Glu210-Ser160 being the likely catalytic residues of β-glucosidase and xylanase, respectively. The binding affinity of β-glucosidase for the substrates are as follows: cellulose (-8.1 kcal mol-1) > lignin (-7.9 kcal mol-1) > hemicellulose (-7.8 kcal mol-1), whereas, xylanase showed a corresponding preference for; hemicellulose (-6.7 kcal mol-1) > cellulose (-5.8 kcal mol-1) > lignin (-5.7 kcal mol-1). Selectivity of both enzymes was reiterated by MD simulations where interactions between β-glucosidase-cellulose and xylanase-hemicellulose were the strongest. Notably low free-binding energy (ΔGbind) of β-glucosidase and xylanase in complex with cellulose (-207.23 +/- 47.13 kJ/mol) and hemicellulose (-131.48 +/- 24.57 kJ/mol) were observed, respectively. The findings thus successfully identified the cellulose component selectivity of the polymer-acting β-glucosidase and xylanase of T. asperellum UC1.Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: Molecular Docking Simulation
  17. Synthesis of novel N-(1,3-thiazol-2-yl)benzamide clubbed oxadiazole scaffolds: Urease inhibition, Lipinski rule and molecular docking analyses
    Athar Abbasi M, Raza H, Aziz-Ur-Rehman, Zahra Siddiqui S, Adnan Ali Shah S, Hassan M, et al.
    Bioorg Chem, 2019 03;83:63-75.
    PMID: 30342387 DOI: 10.1016/j.bioorg.2018.10.018
    Present work aimed to synthesize some unique bi-heterocyclic benzamides as lead compounds for the in vitro inhibition of urease enzyme, followed by in silico studies. These targeted benzamides were synthesized in good yields through a multi-step protocol and their structures were confirmed by IR, 1H NMR, 13C NMR, EI-MS and elemental analysis. The in vitro screening results showed that most of the ligands exhibited good inhibitory potentials against the urease. Chemo-informatics analysis envisaged that all these compounds obeyed the Lipinski's rule. Molecular docking results showed that 7h exhibited good binding energy value (-8.40 kcal/mol) and was bound within the active region of urease enzyme. From the present investigation, it was inferred that some of these potent urease inhibitors might serve as novel templates in drug designing.
    Matched MeSH terms: Molecular Docking Simulation
  18. Discovery of new targeting agents against GAPDH receptor for antituberculosis drug delivery
    Noh MAA, Fazalul Rahiman SS, A Wahab H, Mohd Gazzali A
    J Basic Clin Physiol Pharmacol, 2021 Jun 25;32(4):715-722.
    PMID: 34214294 DOI: 10.1515/jbcpp-2020-0435
    OBJECTIVES: Tuberculosis (TB) remains a public health concern due to the emergence and evolution of multidrug-resistant strains. To overcome this issue, reinforcing the effectiveness of first line antituberculosis agents using targeted drug delivery approach is an option. Glyceraldehyde-3-Phosphate Dehydrogenase (GADPH), a common virulence factor found in the pathogenic microorganisms has recently been discovered on the cell-surface of Mycobacterium tuberculosis, allowing it to be used as a drug target for TB. This study aims to discover active small molecule(s) that target GAPDH and eventually enhance the delivery of antituberculosis drugs.

    METHODS: Ten ligands with reported in vitro and/or in vivo activities against GAPDH were evaluated for their binding interactions through molecular docking studies using AutoDock 4.2 program. The ligand with the best binding energy was then modified to produce 10 derivatives, which were redocked against GAPDH using previous protocols. BIOVIA Discovery Studio Visualizer 2019 was used to explore the ligand-receptor interactions between the derivatives and GAPDH.

    RESULTS: Among the 10 ligands, curcumin, koningic acid and folic acid showed the best binding energies. Further analysis on the docking of two folic acid derivatives, F7 (γ-{[tert-butyl-N-(6-aminohexyl)]carbamate}folic acid) and F8 (folic acid N-hydroxysuccinimide ester) showed that the addition of a bulky substituent at the carboxyl group of the glutamic acid subcomponent resulted in improved binding energy.

    CONCLUSIONS: Folic acid and the two derivatives F7 and F8 have huge potentials to be developed as targeting agents against the GAPDH receptor. Further study is currently on-going to evaluate the effectiveness of these molecules in vitro.

    Matched MeSH terms: Molecular Docking Simulation
  19. Fulltext The Efficacy of Traditional Medicinal Plants in Modulating the Main Protease of SARS-CoV-2 and Cytokine Storm
    Choe J, Har Yong P, Xiang Ng Z
    Chem Biodivers, 2022 Nov;19(11):e202200655.
    PMID: 36125969 DOI: 10.1002/cbdv.202200655
    Selected traditional medicinal plants exhibit therapeutic effects in coronavirus disease (Covid-19) patients. This review aims to identify the phytochemicals from five traditional medicinal plants (Glycyrrhiza glabra, Nigella sativa, Curcuma longa, Tinospora cordifolia and Withania somnifera) with high potential in modulating the main protease (Mpro) activity and cytokine storm in Covid-19 infection. The Mpro binding affinity of 13 plant phytochemicals were in the following order: Withanoside II>withanoside IV>withaferin A>α-hederin>withanoside V>sitoindoside IX>glabridin>liquiritigenin, nigellidine>curcumin>glycyrrhizin>tinocordiside>berberine. Among these phytochemicals, glycyrrhizin, withaferin A, curcumin, nigellidine and cordifolioside A suppressed SARS-CoV-2 replication and showed stronger anti-inflammatory activities than standard Covid-19 drugs. Both preclinical and clinical evidences supported the development of plant bioactive compounds as Mpro inhibitors.
    Matched MeSH terms: Molecular Docking Simulation
  20. Fulltext Virtual screening of functional foods and dissecting their roles in modulating gene functions to support post COVID-19 complications
    Afroz S, Fairuz S, Joty JA, Uddin MN, Rahman MA
    J Food Biochem, 2021 12;45(12):e13961.
    PMID: 34676581 DOI: 10.1111/jfbc.13961
    COVID-19 has become the focal point since 2019 after the outbreak of coronavirus disease. Many drugs are being tested and used to treat coronavirus infections; different kinds of vaccines are also introduced as preventive measure. Alternative therapeutics are as well incorporated into the health guidelines of some countries. This research aimed to look into the underlying mechanisms of functional foods and how they may improve the long-term post COVID-19 cardiovascular, diabetic, and respiratory complications through their bioactive compounds. The potentiality of nine functional foods for post COVID-19 complications was investigated through computational approaches. A total of 266 bioactive compounds of these foods were searched via extensive literature reviewing. Three highly associated targets namely troponin I interacting kinase (TNNI3K), dipeptidyl peptidase 4 (DPP-4), and transforming growth factor beta 1 (TGF-β1) were selected for cardiovascular, diabetes, and respiratory disorders, respectively, after COVID-19 infections. Best docked compounds were further analyzed by network pharmacological tools to explore their interactions with complication-related genes (MAPK1 and HSP90AA1 for cardiovascular, PPARG and TNF-alpha for diabetes, and AKT-1 for respiratory disorders). Seventy-one suggested compounds out of one-hundred and thirty-nine (139) docked compounds in network pharmacology recommended 169 Gene Ontology (GO) items and 99 Kyoto Encyclopedia of Genes and Genomes signaling pathways preferably AKT signaling pathway, MAPK signaling pathway, ACE2 receptor signaling pathway, insulin signaling pathway, and PPAR signaling pathway. Among the chosen functional foods, black cumin, fenugreek, garlic, ginger, turmeric, bitter melon, and Indian pennywort were found to modulate the actions. Results demonstrate that aforesaid functional foods have attenuating roles to manage post COVID-19 complications. PRACTICAL APPLICATIONS: Functional foods have been approaching a greater interest due to their medicinal uses other than gastronomic pleasure. Nine functional food resources have been used in this research for their traditional and ethnopharmacological uses, but their directive-role in modulating the genes involved in the management of post COVID-19 complications is inadequately studied and reported. Therefore, the foods types used in this research may be prioritized to be used as functional foods for ameliorating the major post COVID-19 complications through appropriate science.
    Matched MeSH terms: Molecular Docking Simulation
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