hydrogen bond interaction
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Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 469
Author(s):  
Nasirudeen Idowu Abdulrashid ◽  
Suleiman Aminu ◽  
Rahma Muhammad Adamu ◽  
Nasir Tajuddeen ◽  
Murtala Bindawa Isah ◽  
...  

Sub-Saharan Africa is profoundly challenged with African Animal Trypanosomiasis and the available trypanocides are faced with drawbacks, necessitating the search for novel agents. Herein, the chemotherapeutic potential of phloroglucinol on T. congolense infection and its inhibitory effects on the partially purified T. congolense sialidase and phospholipase A2 (PLA2) were investigated. Treatment with phloroglucinol for 14 days significantly (p < 0.05) suppressed T. congolense proliferation, increased animal survival and ameliorated anemia induced by the parasite. Using biochemical and histopathological analyses, phloroglucinol was found to prevent renal damages and splenomegaly, besides its protection against T. congolense-associated increase in free serum sialic acids in infected animals. Moreover, the compound inhibited bloodstream T. congolense sialidase via mixed inhibition pattern with inhibition binding constant (Ki) of 0.181 µM, but a very low uncompetitive inhibitory effects against PLA2 (Ki > 9000 µM) was recorded. Molecular docking studies revealed binding energies of −4.9 and −5.3 kcal/mol between phloroglucinol with modeled sialidase and PLA2 respectively, while a 50 ns molecular dynamics simulation using GROMACS revealed the sialidase-phloroglucinol complex to be more compact and stable with higher free binding energy (−67.84 ± 0.50 kJ/mol) than PLA2-phloroglucinol complex (−77.17 ± 0.52 kJ/mol), based on MM-PBSA analysis. The sialidase-phloroglucinol complex had a single hydrogen bond interaction with Ser453 while none was observed for the PLA2-phloroglucinol complex. In conclusion, phloroglucinol showed moderate trypanostatic activity with great potential in ameliorating some of the parasite-induced pathologies and its anti-anemic effects might be linked to inhibition of sialidase rather than PLA2.


2021 ◽  
Author(s):  
Suresh Sampathkumar ◽  
Subramaniam Vijayakumar

Abstract The hydrogen bond interactions between methyl-imidazolium cation (MIM+) and fatty-acid anions (CmHnCOO–, where m=1–6; n-3–13) of ionic liquids are studied in both gas phase and water phase using density functional theory. The structural properties show that the presence of N–H···O and C–H···O hydrogen bonds between [MIM]+ and [CmHnCOO]– (m=1–6;n-3–13) ionic liquids. From the vibrational frequency analysis it was found that the hydrogen bond interaction between [MIM]+ and [CmHnCOO]– (m=1–6;n-3–13) ionic liquids are red-shifted in frequency. The natural bond orbital analysis show that the N–H···O hydrogen bond associated with the large charge transfer which has the higher stabilization energy (i.e. E(2) ~ 38 kcal/mol). Further, the cation/anion–water cluster (H2O)1-3 interactions show that the water molecules are preferred to interact with anions. In the case of ionic liquids–water cluster interaction, the water molecules occupies the interstitial space between cation and anion of ionic liquids which results in weakening the cation-anion interaction.


Author(s):  
Damilohun Samuel Metibemu ◽  
Oluwatoba Emmanuel Oyeneyin ◽  
Ayorinde Omolara Metibemu ◽  
Olawole Yakubu Adeniran ◽  
Idowu Olaposi Omotuyi

Background: Chronic myelogenous leukaemia (CML) constitutes about 15% of adult leukaemia and is characterized by the overproduction of immature myeloid cells. Methods: In this study, a virtual high throughput screening (vHTS) technique was employed to screen a library of phytochemicals of reported anti-cancer plants. A docking score of -10 kcalmol­1 was used as the cut-off for the selection of phyto-compounds for pharmacophore-based virtual screening. Statistically robust and thoroughly validated QSAR model (R = 0.914, R2 = 0.836, Adjusted R2 = 0.764, LOO-CV= 0.6680) was derived for the inhibition of BCR-ABL kinase domain. Results: The virtual screening, pharmacophore screening, QSAR model and molecular docking techniques applied herein revealed ellagic acid, a polyphenolic compound, as a potential competitive inhibitor of the BCR-ABL kinase domain. Ellagic acid binds to the inactive ABL state and forms similar interactions with key residues within the BCR-ABL Kinase domain as obtained in ponatinib (possesses inhibitory effects on the ABL thr-315I mutant). It forms hydrogen bond interaction with thr-315 residue (the gatekeeper residue). It is not likely to be prone to the various mutations associated with nilotinib because of its small size. Conclusion: The procedure of VHTs, Pharmacophore, QSAR, and molecular docking applied in this study could help in detecting more anti-CML compounds.


Author(s):  
Prerana A. Chavan ◽  
Shailaja B. Jadhav

Diabetes is a disorder which is characterized by increase in blood glucose level beyond normal value. Now days it is a metabolic disorder and considered as one of the major cause for the death of patients worldwide. Hence there is always a need for the development of newer scaffolds which are useful in treatment of diabetes. In the research computational chemistry plays an important role to discover new possible medicines. In this work, docking analysis has been carried out to study the effects of substituted pyrimidin-2-one on Dipeptidyl peptidase-4 (DPP4). Docking study shows that compound A5 having 2,4-difluorophenyl and 2-hydroxy phenyl group has a potent (IC50 28.13 µM), selective and in vitro efficacious DPP-4 inhibitor. Further molecular modeling revealed compound A5 can fit in the enzyme pocket topologically very well with the pyrimidin-2-one moiety providing hydrogen bond interaction with Glu 205 and Ser 209 of DPP-4. Based on these results, compound A5 might be a promising lead compound for further optimization in the treatment of T2DM.


2021 ◽  
Vol 7 (10) ◽  
pp. 876
Author(s):  
Geum Seok Jeong ◽  
Prima F. Hillman ◽  
Myung-Gyun Kang ◽  
Sungbo Hwang ◽  
Jong-Eun Park ◽  
...  

Using 126 endogenous lichen fungus (ELF) extracts, inhibitory activities against monoamine oxidases (MAOs) and cholinesterases (ChEs) were evaluated. Among them, extract ELF29 of the endogenous fungus Diaporthe mahothocarpus of the lichen Cladonia symphycarpia showed the highest inhibitory activity against hMAO-A. Compounds alternariol (AT), 5′-hydroxy-alternariol (HAT), and mycoepoxydiene (MED), isolated from the extract, had potent inhibitory activities against hMAO-A with IC50 values of 0.020, 0.31, and 8.68 µM, respectively. AT, HAT, and MED are reversible competitive inhibitors of hMAO-A with Ki values of 0.0075, 0.116, and 3.76 µM, respectively. The molecular docking studies suggested that AT, HAT, and MED had higher binding affinities for hMAO-A (−9.1, −6.9, and −5.6 kcal/mol, respectively) than for hMAO-B (−6.3, −5.2, and −3.7 kcal/mol, respectively). The relative tight binding might result from a hydrogen bond interaction of the three compounds with a Tyr444 residue in hMAO-A, whereas no hydrogen bond interaction was proposed in hMAO-B. In silico pharmacokinetics, the three compounds showed high gastrointestinal absorption without violating Lipinski’s five rules, but only MED showed high probability to cross the blood–brain barrier. These results suggest that AT, HAT, and MED are candidates for treating neuropsychiatric disorders, such as depression and cardiovascular disease.


2021 ◽  
Vol 11 (3) ◽  
pp. 3780-3801

The widespread global COVID-19 pandemic due to the lack of specific treatment and the urgent situation requires the use of all resources to remedy this scourge. The current study aimed to use molecular docking tools to find potential drug candidates for treatment. The pyrano[2,3-c] pyrazole 5(a-e) was targeted against the Main protease (Mpro), which plays a vital role in the replication and transcription of the Corona viral genome. The 3CL Protease (PDB ID 6LU7) was modeled, and the compounds were docked using Autodock Vina software, and ADMET data have been studied. All synthesized compounds were well engaged into the active site of the main protease with strong hydrogen bond interaction and a good score of energy. The 5b have been classed as the best inhibitor with an energy score of -6.2 kcal/mol, similar to the one given by chloroquine (-6.2Kcal/mol). Moreover, the molecular interaction studies showed that protease structure had multiple active site residues for all studied compounds. Our finding confirms the potential of these derivatives as lead compounds against the selected target protein of coronavirus, which needs further analysis and dynamic simulation studies to propose then develop a new antiviral treatment.


Inorganics ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 67
Author(s):  
Amalia García-García ◽  
Lisset Noriega ◽  
Francisco J. Meléndez-Bustamante ◽  
María Eugenia Castro ◽  
Brenda L. Sánchez-Gaytán ◽  
...  

The interest in decavanadate anions has increased in recent decades, since these clusters show interesting applications as varied as sensors, batteries, catalysts, or new drugs in medicine. Due to the capacity of the interaction of decavanadate with a variety of biological molecules because of its high negative charge and oxygen-rich surface, this cluster is being widely studied both in vitro and in vivo as a treatment for several global health problems such as diabetes mellitus, cancer, and Alzheimer’s disease. Here, we report a new decavanadate compound with organic molecules synthesized in an aqueous solution and structurally characterized by elemental analysis, infrared spectroscopy, thermogravimetric analysis, and single-crystal X-ray diffraction. The decavanadate anion was combined with 2-aminopyrimidine to form the compound [2-ampymH]6[V10O28]·5H2O (1). In the crystal lattice, organic molecules are stacked by π–π interactions, with a centroid-to-centroid distance similar to that shown in DNA or RNA molecules. Furthermore, computational DFT calculations of Compound 1 corroborate the hydrogen bond interaction between pyrimidine molecules and decavanadate anions, as well as the π–π stacking interactions between the central pyrimidine molecules. Finally, docking studies with test RNA molecules indicate that they could serve as other potential targets for the anticancer activity of decavanadate anion.


2021 ◽  
Author(s):  
zhaofeng wu ◽  
Min Zhang ◽  
Shuai Cao ◽  
Long Wang ◽  
Zhangjie Qin ◽  
...  

Abstract Carbon quantum dots (CQDs) co-doped with N, P and S derived from expired milk was prepared by a simple hydrothermal method. Through the hydrogen bond interaction between CQDs and cellulose of pure cotton face towel (PCFT), CQDs were uniformly anchored on the cotton fibers to form a flexible all-biomass CQDs/PCFT sensor for the first time. Due to the heteroatom doping, extremely small particle size of CQDs and excellent permeability of CQDs/PCFT film, the flexible CQDs/PCFT sensor showed the high sensitivity and bending stability. In the range of 0 ~ 60o bending states, the responses of flexible CQDs/PCFT sensor to four target analytes changed by less 5%. Interestingly, due to the abundant functional groups and defects of CQDs, the flexible CQDs/PCFT sensor displayed sensing curves of different shapes for different target analytes. In this way, by establishing a database of sensing curves of target analytes, multiple analytes can be detected discriminatively by relying only on single sensor with the help of image recognition. In addition, the binary parameter method of response and response time was created, which also showed that a single sensor could achieve the discriminative detection. This work expanded the application of biomass CQDs and cellulose, and made a useful exploration for environment friendly flexible gas sensor.


2021 ◽  
Vol 9 ◽  
Author(s):  
Zhifeng Deng ◽  
Cheng Wang ◽  
Haichang Zhang ◽  
Taotao Ai ◽  
Kaichang Kou

In recent years, the wide application of fluoride materials has grown rapidly, therefore excessive discharge in the surrounding environment, especially in drinking water and organic effluent, has become a potential hazard to humans, and has even resulted in fluorosis disease. The development of a highly effective and convenient method to recognize fluoride anions in surrounding environments seems necessary and urgent. Among which, the development of a colorimetric and fluorescence fluoride chemosensor with obvious color changing allowing for naked-eye detection with high sensitivity and selectivity is more interesting and challenging. In this minireview, current novel colorimetric and fluorescence chemosensors for fluoride anions by hydrogen-bond interaction are introduced, including obvious color changing by naked-eye detection, high sensitivity and selectivity, non-pollution and fluoride extraction ability, aqueous detection, and other additional functions. Finally, the perspective of the fluoride chemosensor design concept and potential evolution trends are pointed out.


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