Displaying publications 61 - 80 of 626 in total

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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Pomegranate peel-derived punicalagin: Ultrasonic-assisted extraction, purification, and its α-glucosidase inhibitory mechanism
    Liu Y, Kong KW, Wu DT, Liu HY, Li HB, Zhang JR, et al.
    Food Chem, 2022 Apr 16;374:131635.
    PMID: 34823934 DOI: 10.1016/j.foodchem.2021.131635
    The pomegranate peel is a by-product of pomegranate fruit rich in polyphenols. In this study, pomegranate peel polyphenols were explored using LC-MS/MS, and punicalagin was the most abundant compound. The highest yield (505.89 ± 1.73 mg/g DW) of punicalagin was obtained by ultrasonic-assisted extraction (UAE) with the ethanol concentration of 53%, sample-to-liquid ratio of 1:25 w/v, ultrasonic power of 757 W, and extraction time of 25 min. Punicalagin was further purified by the macroporous resin D101 and prep-HPLC, reaching the purity of 92.15%. The purified punicalagin had the IC50 of 82 ± 0.02 µg/mL against α-glucosidase, similar to the punicalagin standard with IC50 of 58 ± 0.014 µg/mL, both exhibiting a mixed inhibitory mechanism. Molecular docking further revealed that a steric hindrance with the intermolecular energy of -7.99 kcal/mol was formed between punicalagin and α-glucosidase. Overall, pomegranate peel is a promising source of punicalagin to develop anti-diabetic functional foods.
    Matched MeSH terms: Molecular Docking Simulation
  16. Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
    Bandyopadhyay S, Abiodun OA, Ogboo BC, Kola-Mustapha AT, Attah EI, Edemhanria L, et al.
    J Biomol Struct Dyn, 2022;40(22):11467-11483.
    PMID: 34370622 DOI: 10.1080/07391102.2021.1959401
    Medicinal plants as rich sources of bioactive compounds are now being explored for drug development against COVID-19. 19 medicinal plants known to exhibit antiviral and anti-inflammatory effects were manually curated, procuring a library of 521 metabolites; this was virtually screened against NSP9, including some other viral and host targets and were evaluated for polypharmacological indications. Leads were identified via rigorous scoring thresholds and ADMET filtering. MM-GBSA calculation was deployed to select NSP9-Lead complexes and the complexes were evaluated for their stability and protein-ligand communication via MD simulation. We identified 5 phytochemical leads for NSP9, 23 for Furin, 18 for ORF3a, and 19 for IL-6. Ochnaflavone and Licoflavone B, obtained from Lonicera japonica (Japanese Honeysuckle) and Glycyrrhiza glabra (Licorice), respectively, were identified to have the highest potential polypharmacological properties for the aforementioned targets and may act on multiple pathways simultaneously to inhibit viral entry, replication, and disease progression. Additionally, MD simulation supports the robust stability of Ochnaflavone and Licoflavone B against NSP9 at the active sites via hydrophobic interactions, H-bonding, and H-bonding facilitated by water. This study promotes the initiation of further experimental analysis of natural product-based anti-COVID-19 therapeutics.
    Matched MeSH terms: Molecular Docking Simulation
  17. Fulltext How to face COVID-19: proposed treatments based on remdesivir and hydroxychloroquine in the presence of zinc sulfate. Docking/DFT/POM structural analysis
    Ben Hadda T, Berredjem M, Almalki FA, Rastija V, Jamalis J, Emran TB, et al.
    J Biomol Struct Dyn, 2022;40(19):9429-9442.
    PMID: 34033727 DOI: 10.1080/07391102.2021.1930161
    Remdesivir and hydroxychloroquine derivatives form two important classes of heterocyclic compounds. They are known for their anti-malarial biological activity. This research aims to analyze the physicochemical properties of remdesivir and hydroxychloroquine compounds by the computational approach. DFT, docking, and POM analyses also identify antiviral pharmacophore sites of both compounds. The antiviral activity of hydroxychloroquine compound's in the presence of zinc sulfate and azithromycin is evaluated through its capacity to coordinate transition metals (M = Cu, Ni, Zn, Co, Ru, Pt). The obtained bioinformatic results showed the potent antiviral/antibacterial activity of the prepared mixture (Hydroxychloroquine/Azithromycin/Zinc sulfate) for all the opportunistic Gram-positive, Gram-negative in the presence of coronavirus compared with the complexes Polypyridine-Ruthenium-di-aquo. The postulated zinc(II) complex of hydroxychloroquine derivatives are indeed an effective antibacterial and antiviral agent against coronavirus and should be extended to other pathogens. The combination of a pharmacophore site with a redox [Metal(OH2)2] moiety is of crucial role to fight against viruses and bacteria strains. [Formula: see text]Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: Molecular Docking Simulation
  18. In silico assessment of dehalogenase from Bacillus thuringiensis H2 in relation to its salinity-stability and pollutants degradation
    Oyewusi HA, Huyop F, Wahab RA, Hamid AAA
    J Biomol Struct Dyn, 2022;40(19):9332-9346.
    PMID: 34014147 DOI: 10.1080/07391102.2021.1927846
    Increased scientific interest has led to the rise in biotechnological uses of halophilic and halotolerant microbes for hypersaline wastewater bioremediation. Hence, this study performed molecular docking, molecular dynamic (MD) simulations, and validation by Molecular Mechanic Poisson-Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis H2. We aimed to identify the interactions of DehH2 with substrates haloacids, haloacetates, and chlorpyrifos under extreme salinity (35% NaCl). MD simulations revealed that DehH2 preferentially degraded haloacids and haloacetates (-6.3 to -4.7 kcal/mol) by forming three or four hydrogen bonds to the catalytic triad, Asp125, Arg201, and Lys202. Conversely, chlorpyrifos was the least preferred substrate in both MD simulations and MM-PBSA calculations. MD simulation results ranked the DehH2-L-2CP complex (RMSD □0.125-0.23 nm) as the most stable while the least was the DehH2-chlorpyrifos complex (RMSD 0.32 nm; RMSF 0.0 - 0.29). The order of stability was as follows: DehH2-L-2CP > DehH2-MCA > DehH2-D-2CP > DehH2-3CP > DehH2-2,2-DCP > DehH2-2,3-DCP > DehH2-TCA > DehH2-chlorpyrifos. The MM-PBSA calculations further affirmed the DehH2-L-2CP complex's highest stability with the lowest binding energy of -45.14 kcal/mol, followed closely by DehH2-MCA (-41.21 kcal/mol), DehH2-D-2CP (-31.59 kcal/mol), DehH2-3CP (-30.75 kcal/mol), DehH2-2,2- DCP (-29.72 kcal/mol), DehH2-2,3-DCP (-22.20 kcal/mol) and DehH2-TCA (-18.46 kcal/mol). The positive binding energy of the DehH2-chlorpyrifos complex (+180.57 kcal/mol) proved the enzyme's non-preference for the substrate. The results ultimately illustrated the unique specificity of the DehH2 to degrade the above-said pollutants under a hypersaline condition.Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: Molecular Docking Simulation
  19. Fulltext Carbapenem resistance gene crisis in A. baumannii: a computational analysis
    Zahra N, Zeshan B, Ishaq M
    BMC Microbiol, 2022 Dec 03;22(1):290.
    PMID: 36463105 DOI: 10.1186/s12866-022-02706-8
    Acinetobacter baumannii (A. baumannii) is one of the members of ESKAPE bacteria which is considered multidrug resistant globally. The objective of this study is to determine the protein docking of different antibiotic resistance gene (ARGs) in A. baumannii. In silico analysis of antibiotic resistance genes against carbapenem are the blaOXA-51, blaOXA-23, blaOXA-58, blaOXA-24, blaOXA-143, NMD-1 and IMP-1 in A. baumannii. The doripenem, imipenem and meropenem were docked to blaOXA-51 and blaOXA-23 using PyRx. The top docking energy was -5.5 kcal/mol by imipenem and doripenem and meropenem showed a binding score of -5. 2 kcal/mol each and blaOXA-23 energy was -4.3 kcal/mol by imipenem and meropenem showed a binding score of -2.3 kcal/mol, while doripenem showed the binding score of -3.4 kcal/mol. Similarly, doripenem imipenem and meropenem were docked to blaOXA-58, IMP-1, Rec A and blaOXA-143, with docking energy was -8.8 kcal/mol by doripenem and meropenem each while imipenem showed a binding score of -4.2 kcal/mol and with IMP-1 demonstrated their binding energies. was -5.7 kcal/mol by meropenem and doripenem showed a binding score of -5.3 kcal/mol, while imipenem showed a binding score of -4.5 kcal/mol. And docking energy was -4.9 kcal/mol by imipenem and meropenem showed binding energy of -3.6 kcal/mol each while doripenem showed a binding score of -3.9 kcal/mol in RecA and with blaOXA-143 docking energy was -3.0 kcal/mol by imipenem and meropenem showed a binding score of -1.9 kcal/mol, while doripenem showed the binding score of -2.5 kcal/mol respectively. Doripenem, imipenem, and meropenem docking findings with blaOXA-24 confirmed their binding energies. Doripenem had the highest docking energy of -5.5 kcal/mol, meropenem had a binding score of -4.0 kcal/mol, and imipenem had a binding score of -3.9 kcal/mol. PyRx was used to dock the doripenem, imipenem, and meropenem to NMD-1. Docking energies for doripenem were all - 4.0 kcal/mol, whereas meropenem had docking energy of -3.3 kcal/mol and imipenem was -1.50 kcal/mol. To the best of our knowledge the underlying mechanism of phenotypic with genotypic resistance molecular docking regarding carbapenem resistance A. baumannii is unclear. Our molecular docking finds the possible protein targeting mechanism for carbapenem-resistant A.baumannii.
    Matched MeSH terms: Molecular Docking Simulation
  20. Novel antihypertensive peptides from lupin protein hydrolysate: An in-silico identification and molecular docking studies
    Fadimu GJ, Gan CY, Olalere OA, Farahnaky A, Gill H, Truong T
    Food Chem, 2023 May 01;407:135082.
    PMID: 36493485 DOI: 10.1016/j.foodchem.2022.135082
    Application of non-thermal treatment to proteins prior to enzymatic hydrolysis can facilitate the release of novel bioactive peptides (BPs) with unique biological activities. In this study, lupin protein isolate was pre-treated with ultrasound and hydrolysed using alcalase and flavourzyme to produce alcalase hydrolysate (ACT) and flavourzyme hydrolysate(FCT). These hydrolysates were fractionated into 1, 5, and 10 kDa molecular weight fractions using a membrane ultrafiltration technique. The in vitro angiotensin-converting enzyme (ACE) studies revealed that unfractionated ACT (IC50 = 3.21 mg mL-1) and FCT (IC50 = 3.32 mg mL-1) were more active inhibitors of ACE in comparison to their ultrafiltrated fractions with IC50 values ranging from 6.09 to 7.45 mg mL-1. Molecular docking analysis predicted three unique peptides from ACT (AIPPGIPY, SVPGCT, and QGAGG) and FCT (AIPINNPGKL, SGNQGP, and PPGIP) as potential ACE inhibitors. Thus, unique BPs with ACE inhibitory effects might be generated from ultrasonicated lupin protein.
    Matched MeSH terms: Molecular Docking Simulation
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