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Journal articles on the topic 'In silico calculations'

Author: Grafiati

Published: 10 March 2023

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1

Triveni, S., C. Naresh Babu, E. Bhargav, and M. Vijaya Jyothi. "in silico Design, ADME Prediction, Molecular Docking, Synthesis of Novel Triazoles, Indazoles & Aminopyridines and in vitro Evaluation of Antitubercular Activity." Asian Journal of Chemistry 32, no. 11 (2020): 2713–21. http://dx.doi.org/10.14233/ajchem.2020.22790.

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To design and synthesize novel triazoles, indazoles and aminopyridines from various (thiophene-2-yl)prop-2-en-1-one derivatives as antitubercular leads by in silico and in vitro methods. in silco Drug design, ADME prediction and molecular docking studies were performed to assess drug likeliness and antitubercular potential of all 30 novel triazoles, indazoles and aminopyridines. in silico Drug design studies revealed that the synthetic routes applied were appropriate according to the calculations of Swiss-ADME that measure synthetic accessibility. Most of the synthesized compounds found to have considerable binding score with enoyl ACP reductase enzyme of Mycobacterium tuberculosis. All the synthesized compounds were evaluated for antitubercular potential against Drug Resistant Mycobacterium tuberculosis H37Rv strain by Luciferase reporter assay method. Most of the synthesized compounds exhibited remarkable antitubercular potential against resistant strain.

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2

Herrera-Calderon, Oscar, Andres F. Yepes-Pérez, Jorge Quintero-Saumeth, Juan Pedro Rojas-Armas, Miriam Palomino-Pacheco, José Manuel Ortiz-Sánchez, Edwin César Cieza-Macedo, et al. "Carvacrol: An In Silico Approach of a Candidate Drug on HER2, PI3Kα, mTOR, hER-α, PR, and EGFR Receptors in the Breast Cancer." Evidence-Based Complementary and Alternative Medicine 2020 (October 26, 2020): 1–12. http://dx.doi.org/10.1155/2020/8830665.

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Carvacrol is a phenol monoterpene found in aromatic plants specially in Lamiaceae family, which has been evaluated in an experimental model of breast cancer. However, any proposed mechanism based on its antitumor effect has not been reported. In our previous study, carvacrol showed a protective effect on 7,12-dimethylbenz[α]anthracene- (DMBA-) induced breast cancer in female rats. The main objective in this research was to evaluate by using in silico study the carvacrol on HER2, PI3Kα, mTOR, hER-α, PR, and EGFR receptors involved in breast cancer progression by docking analysis, molecular dynamic, and drug-likeness evaluation. A multilevel computational study to evaluate the antitumor potential of carvacrol focusing on the main targets involved in the breast cancer was carried out. The in silico study starts with protein-ligand docking of carvacrol followed by ligand pathway calculations, molecular dynamic simulations, and molecular mechanics energies combined with the Poisson–Boltzmann (MM/PBSA) calculation of the free energy of binding for carvacrol. As result, the in silico study led to the identification of carvacrol with strong binding affinity on mTOR receptor. Additionally, in silico drug-likeness index for carvacrol showed a good predicted therapeutic profile of druggability. Our findings suggest that mTOR signaling pathway could be responsible for its preventive effect in the breast cancer.

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3

Maillard, Julien F., Johann Le Maître, Christopher P. Rüger, Mark Ridgeway, Christopher J. Thompson, Benoit Paupy, Marie Hubert-Roux, Melvin Park, Carlos Afonso, and Pierre Giusti. "Structural analysis of petroporphyrins from asphaltene by trapped ion mobility coupled with Fourier transform ion cyclotron resonance mass spectrometry." Analyst 146, no. 13 (2021): 4161–71. http://dx.doi.org/10.1039/d1an00140j.

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Combination of experimentally determined collision-cross sections provided by trapped ion mobility high-resolution mass spectrometry with in-silico calculations for structural assessment of petroporphyrins within an ultra-complex crude oil matrix.

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4

Hajzer, Viktória, Roman Fišera, Attila Latika, Július Durmis, Jakub Kollár, Vladimír Frecer, Zuzana Tučeková, et al. "Stereoisomers of oseltamivir – synthesis, in silico prediction and biological evaluation." Organic & Biomolecular Chemistry 15, no. 8 (2017): 1828–41. http://dx.doi.org/10.1039/c6ob02673g.

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5

Chen, Zihao, and Kristen A. Fichthorn. "Adsorption of alkylamines on Cu surfaces: identifying ideal capping molecules using first-principles calculations." Nanoscale 13, no. 44 (2021): 18536–45. http://dx.doi.org/10.1039/d1nr05759f.

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We used dispersion-corrected density-functional theory to perform an in silico search over a series of primary alkylamines, including linear, branched, and cyclic molecules, to identify capping molecules for shape-selective Cu nanocrystal synthesis.

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6

Kawczak, Piotr, Leszek Bober, and Tomasz Bączek. "Application of QSAR Analysis and Different Quantum Chemical Calculation Methods in Activity Evaluation of Selected Fluoroquinolones." Combinatorial Chemistry & High Throughput Screening 21, no. 7 (November 15, 2018): 468–75. http://dx.doi.org/10.2174/1386207321666180827105856.

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Background: A set of antibiotic fluoroquinolones with confirmed antimicrobial activity were analyzed with the use of two types of quantum chemical calculation methods and quantitative structure-activity relationships (QSAR). Objective: The purpose of this study was to demonstrate the common and differentiating characteristics of the above-mentioned chemical compounds alike physicochemically as well as pharmacologically based on the quantum chemical calculations and microbiological activity data. Methods: During the study PCA and MLR analysis were performed, as the types of proposed chemometric approach. The semi-empirical level of in silico molecular modeling was performed for calculations of molecular descriptors. Results: QSAR models were proposed based on chosen descriptors. The relationship between the structure and microbiological activity and physicochemical parameters data was able to class and describe them with the use of statistically significant molecular descriptors. Conclusion: The applied chemometric approaches revealed the influential features of tested structures responsible for the antimicrobial activity of analyzed compounds.

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7

Aguilera-Porta, Neus, Giovanni Granucci, Jordi Muñoz-Muriedas, and Ines Corral. "Can in silico calculations assess phototoxicity of non-steroidal anti-inflammatory drugs?" Toxicology Letters 280 (October 2017): S282. http://dx.doi.org/10.1016/j.toxlet.2017.07.788.

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8

Pitera, Jed W., and Peter A. Kollman. "Exhaustive mutagenesis in silico: Multicoordinate free energy calculations on proteins and peptides." Proteins: Structure, Function, and Genetics 41, no. 3 (2000): 385–97. http://dx.doi.org/10.1002/1097-0134(20001115)41:3<385::aid-prot100>3.0.co;2-r.

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9

Manolov, Stanimir, Iliyan Ivanov, and Dimitar Bojilov. "Microwave-assisted synthesis of 1,2,3,4-tetrahydroisoquinoline sulfonamide derivatives and their biological evaluation." Journal of the Serbian Chemical Society, no. 00 (2020): 76. http://dx.doi.org/10.2298/jsc200802076m.

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Herein we report an alternative eco-friendly method for the synthesis of 1,2,3,4-tetrahydroisoquinoline sulfonamide derivatives. All obtained compounds were screened for their in vitro inhibition of albumin denaturation, antioxidant, antitryptic, and antibacterial activity and have shown significant results. The lipophilicity was established using both reversed-phase thin layer chromatography and in silico calculations.

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10

Faletrov, Y. V., V. O. Maliugin, N. S. Frolova, and V. M. Shkumatov. "<i>In silico</i> evaluation of new affine interactions of methylcoumarin with cytochromes P450." Proceedings of the National Academy of Sciences of Belarus, Chemical Series 58, no. 2 (June 8, 2022): 186–90. http://dx.doi.org/10.29235/1561-8331-2022-58-2-186-190.

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4-methyl-7-methoxycoumarin (CumOMe) has been synthesized and in silico calculations demonstrated localization of methoxy group within 0.4 nm from Fe ion of hem groups for some structures of human CYP19 & CYP46 as well as CYP152 S. paucimobilis, CYP158 St. coelicolor, HMUO C. diphtheriae, XPLA R. rhodochrous, CYP199A4 Rh. palustris, CYP101A1 Ps. putida and CYP51 M. tuberculosis.

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11

Cioslowski, Jerzy. "Electronic Structure Calculations on Endohedral Complexes of Fullerenes: Reminiscences and Prospects." Molecules 28, no. 3 (February 1, 2023): 1384. http://dx.doi.org/10.3390/molecules28031384.

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The history of electronic structure calculations on the endohedral complexes of fullerenes is reviewed. First, the long road to the isolation of new allotropes of carbon that commenced with the seminal organic syntheses involving simple inorganic substrates is discussed. Next, the focus is switched to author’s involvement with fullerene research that has led to the in silico discovery of endohedral complexes. The predictions of these pioneering theoretical studies are juxtaposed against the data afforded by subsequent experimental developments. The successes and failures of the old and modern quantum-chemical calculations on endohedral complexes are summarized and their remaining deficiencies requiring further attention are identified.

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12

Bartuzi, Damian, Ewa Kędzierska, Agnieszka A. Kaczor, Helmut Schmidhammer, and Dariusz Matosiuk. "Novel Positive Allosteric Modulators of µ Opioid Receptor—Insight from In Silico and In Vivo Studies." International Journal of Molecular Sciences 21, no. 22 (November 11, 2020): 8463. http://dx.doi.org/10.3390/ijms21228463.

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Opioids are the drugs of choice in severe pain management. Unfortunately, their use involves serious, potentially lethal side effects. Therefore, efforts in opioid drug design turn toward safer and more effective mechanisms, including allosteric modulation. In this study, molecular dynamics simulations in silico and ‘writhing’ tests in vivo were used to characterize potential allosteric mechanism of two previously reported compounds. The results suggest that investigated compounds bind to μ opioid receptor in an allosteric site, augmenting action of morphine at subeffective doses, and exerting antinociceptive effect alone at higher doses. Detailed analysis of in silico calculations suggests that first of the compounds behaves more like allosteric agonist, while the second compound acts mainly as a positive allosteric modulator.

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13

Yang, Hui, Choon-Hong Tan, and Ming Wah Wong. "In silico characterization and prediction of thiourea-like neutral bidentate halogen bond catalysts." Organic & Biomolecular Chemistry 19, no. 32 (2021): 7051–60. http://dx.doi.org/10.1039/d1ob01092a.

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Through DFT calculations, thiourea-like halogen bond (XB)-based catalysts, with XB donor moieties connected via covalent bonds, have been designed and applied to Diels–Alder reaction and sulfa-Michael addition.

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14

Alsharif, Shada A., David Power, Ian Rouse, and Vladimir Lobaskin. "In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles." Nanomaterials 10, no. 10 (October 4, 2020): 1967. http://dx.doi.org/10.3390/nano10101967.

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The free energy of adsorption of proteins onto nanoparticles offers an insight into the biological activity of these particles in the body, but calculating these energies is challenging at the atomistic resolution. In addition, structural information of the proteins may not be readily available. In this work, we demonstrate how information about adsorption affinity of proteins onto nanoparticles can be obtained from first principles with minimum experimental input. We use a multiscale model of protein–nanoparticle interaction to evaluate adsorption energies for a set of 59 human blood serum proteins on gold and titanium dioxide (anatase) nanoparticles of various sizes. For each protein, we compare the results for 3D structures derived from experiments to those predicted computationally from amino acid sequences using the I-TASSER methodology and software. Based on these calculations and 2D and 3D protein descriptors, we develop statistical models for predicting the binding energy of proteins, enabling the rapid characterization of the affinity of nanoparticles to a wide range of proteins.

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15

Tsakiridou, Georgia, Christos Reppas, Martin Kuentz, and Lida Kalantzi. "A Novel Rheological Method to Assess Drug-Polymer Interactions Regarding Miscibility and Crystallization of Drug in Amorphous Solid Dispersions for Oral Drug Delivery." Pharmaceutics 11, no. 12 (November 22, 2019): 625. http://dx.doi.org/10.3390/pharmaceutics11120625.

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Solid dispersions provide a key technology to formulate poorly water-soluble drugs, and a main task of early development is appropriate selection of polymer. This study investigates the use of a novel rheology-based approach to evaluate miscibility and interactions of drugs with polymers regarding amorphous solid drug dispersions for oral administration. Tacrolimus was used as model drug and hydroxypropyl cellulose, ethylcellulose, Soluplus®, polyethyleneglycol 6000, Poloxamer-188 (Koliphor-188), and Eudragit® S100 were used as excipients. Solvent-based evaporation methods were used to prepare binary solid dispersions of drug and polymer. Data of the dilute solution viscosimetry were compared with in silico calculations of the Hansen solubility parameter (HSP), as well as phase separation/crystallization data obtained from X-ray diffraction and differential scanning calorimetry. HSP calculations in some cases led to false positive predictions of tacrolimus miscibility with the tested polymers. The novel rheology-based method provided valuable insights into drug-polymer interactions and likely miscibility with polymer. It is a rather fast, inexpensive, and robust analytical approach, which could be used complementary to in silico-based evaluation of polymers in early formulation development, especially in cases of rather large active pharmaceutical ingredients.

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16

Saha, Saumen, and Joydeep Chowdhury. "Binding Interaction of Juglone with Lysozyme: Spectroscopic Studies Aided by In Silico Calculations." Journal of Photochemistry and Photobiology B: Biology 193 (April 2019): 89–99. http://dx.doi.org/10.1016/j.jphotobiol.2019.02.006.

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17

Siddiqui, Shamoon Ahmad. "In silico design of organic p–n junction diodes using quantum chemical calculations." Journal of Computational Electronics 19, no. 1 (January 28, 2020): 80–90. http://dx.doi.org/10.1007/s10825-020-01447-z.

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18

Lagunes, Irene, Paloma Begines, Adrián Silva, Alexis R. Galán, Adrián Puerta, Miguel X. Fernandes, Inés Maya, José G. Fernández-Bolaños, Óscar López, and José M. Padrón. "Selenocoumarins as new multitarget antiproliferative agents: Synthesis, biological evaluation and in silico calculations." European Journal of Medicinal Chemistry 179 (October 2019): 493–501. http://dx.doi.org/10.1016/j.ejmech.2019.06.073.

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19

Artyushenko, P. V., V. A. Mironov, D. I. Morozov, I. A. Shchugoreva, N. Borbone, F. N. Tomilin, and A. S. Kichkailo. "Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2." Siberian Medical Review, no. 2 (2021): 66–67. http://dx.doi.org/10.20333/25000136-2021-2-66-67.

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The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifi cations in order to increase the binding with the RBD. Th us, a new aptamer Apt25 was designed. Th e procedure of 1) aptamer structure modeling/modifi cation, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed several times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. Th e proposed computational approach to selection and refi nement of aptamers is universal and can be used for wide range of molecular ligands and targets

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20

Garcia, Danielle R., Felipe R. Souza, Ana P. Guimarães, Martin Valis, Zbyšek Pavelek, Kamil Kuca, Teodorico C. Ramalho, and Tanos C. C. França. "In Silico Studies of Potential Selective Inhibitors of Thymidylate Kinase from Variola virus." Pharmaceuticals 14, no. 10 (October 9, 2021): 1027. http://dx.doi.org/10.3390/ph14101027.

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Continuing the work developed by our research group, in the present manuscript, we performed a theoretical study of 10 new structures derived from the antivirals cidofovir and ribavirin, as inhibitor prototypes for the enzyme thymidylate kinase from Variola virus (VarTMPK). The proposed structures were subjected to docking calculations, molecular dynamics simulations, and free energy calculations, using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method, inside the active sites of VarTMPK and human TMPK (HssTMPK). The docking and molecular dynamic studies pointed to structures 2, 3, 4, 6, and 9 as more selective towards VarTMPK. In addition, the free energy data calculated through the MM-PBSA method, corroborated these results. This suggests that these compounds are potential selective inhibitors of VarTMPK and, thus, can be considered as template molecules to be synthesized and experimentally evaluated against smallpox.

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21

Yepes-Pérez, Andres F., Oscar Herrera-Calderon, José-Emilio Sánchez-Aparicio, Laura Tiessler-Sala, Jean-Didier Maréchal, and Wilson Cardona-G. "Investigating Potential Inhibitory Effect of Uncaria tomentosa (Cat’s Claw) against the Main Protease 3CLpro of SARS-CoV-2 by Molecular Modeling." Evidence-Based Complementary and Alternative Medicine 2020 (September 30, 2020): 1–14. http://dx.doi.org/10.1155/2020/4932572.

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COVID-19 is a disease caused by severe acute respiratory syndrome coronavirus 2. Presently, there is no effective treatment for COVID-19. As part of the worldwide efforts to find efficient therapies and preventions, it has been reported the crystalline structure of the SARS-CoV-2 main protease Mpro (also called 3CLpro) bound to a synthetic inhibitor, which represents a major druggable target. The druggability of Mpro could be used for discovering drugs to treat COVID-19. A multilevel computational study was carried out to evaluate the potential antiviral properties of the components of the medicinal herb Uncaria tomentosa (Cat’s claw), focusing on the inhibition of Mpro. The in silico approach starts with protein-ligand docking of 26 Cat’s claw key components, followed by ligand pathway calculations, molecular dynamics simulations, and MM-GBSA calculation of the free energy of binding for the best docked candidates. The structural bioinformatics approaches led to identification of three bioactive compounds of Uncaria tomentosa (speciophylline, cadambine, and proanthocyanidin B2) with potential therapeutic effects by strong interaction with 3CLpro. Additionally, in silico drug-likeness indices for these components were calculated and showed good predicted therapeutic profiles of these phytochemicals. Our findings suggest the potential effectiveness of Cat’s claw as complementary and/or alternative medicine for COVID-19 treatment.

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22

Ani R, Anand P S, Sreenath B, and Deepa O S. "In Silico Prediction Tool for Drug-likeness of Compounds based on Ligand Based Screening." International Journal of Research in Pharmaceutical Sciences 11, no. 4 (October 6, 2020): 6273–81. http://dx.doi.org/10.26452/ijrps.v11i4.3310.

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Drug Likeness prediction is a time-consuming and tedious process. An in-vitro method the drug development takes a long time to come to market. The failure rate is also another one to think about in this method. There are many in-silico methods currently available and developing to help the drug discovery and development process. Many online tools are available for predicting and classifying a drug after analyzing the drug-likeness properties of compounds. But most tools have their advantages and disadvantages. In this study, a tool is developed to predict the drug-likeness of compounds given as input to this software. This may help the chemists in analyzing a compound before actually preparing a compound for the drug discovery process. The tool includes both descriptor-based calculation and fingerprint-based calculation of the particular compounds. The descriptor-calculation also includes a set of rules and filters like Lipinski’s rule, Ghose filter, Veber filter and BBB likeness. The previous studies proved that the fingerprint-based prediction is more accurate than descriptor-based prediction. So, in the current study, the drug-likeness prediction tool incorporated the molecular descriptors and fingerprint-based calculations based on five different fingerprint types. The current study incorporated five different machine learning algorithms for prediction of drug-likeness and selected the algorithm, which has a high accuracy rate. When a chemist inputs a particular compound in SMILES format, the drug-likeness prediction tool predicts whether the given candidate compound is drug or non-drug.

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23

Ramasamy, Suresh, Singanan Ponnuchamy, and Sivakumar Ponnusamy. "Synthesis of Selective Bioactive Pyridylpyridones: in silico Studies and Biological Evaluations." Asian Journal of Chemistry 32, no. 5 (2020): 985–94. http://dx.doi.org/10.14233/ajchem.2020.22290.

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Twenty three substituted pyridylpyridones were designed and performed for molecular docking studies against α-amylase enzyme. The top three hit molecules were synthesized and characterized by 1H NMR, 13C NMR, ESI-mass and FT-IR spectroscopic techniques. Experimental biological applications were studied for these compounds. The DFT calculations were executed for the hit compounds. In addition, molecular electrostatic potential mapping was also executed for additional support.

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24

Kaur, Ramandeep, Rajnish Kumar, Nilambra Dogra, Ashok Kumar, Ashok Kumar Yadav, and Manoj Kumar. "Synthesis and studies of thiazolidinedione–isatin hybrids as α-glucosidase inhibitors for management of diabetes." Future Medicinal Chemistry 13, no. 5 (March 2021): 457–85. http://dx.doi.org/10.4155/fmc-2020-0022.

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Aim: Keeping in view the side effects associated with clinically used α-glucosidase inhibitors, novel thiazolidinedione–isatin hybrids were synthesized and evaluated by in vitro, in vivo and in silico procedures. Materials & methods: Biological evaluation, cytotoxicity assessment, molecular docking, binding free energy calculations and molecular dynamics studies were performed for hybrids. Results: The most potent inhibitor A-10 (IC50 = 24.73 ± 0.93 μM) was competitive in manner and observed as non-cytotoxic. A-10 possessed higher efficacy than the standard drug (acarbose) during in vivo biological testing. Conclusion: The enzyme inhibitory potential and safety profile of synthetic molecules was recognized after in vitro, in vivo, in silico and cytotoxicity studies. Further structural optimization of A-10 can offer potential hit molecules suitable for future investigations.

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25

Manolov, Stanimir, Iliyan Ivanov, and Dimitar Bojilov. "Synthesis of New 1,2,3,4-Tetrahydroquinoline Hybrid of Ibuprofen and Its Biological Evaluation." Molbank 2022, no. 1 (March 7, 2022): M1350. http://dx.doi.org/10.3390/m1350.

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Herein we report the obtaining of 1-(3,4-dihydroquinolin-1(2H)-yl)-2- (4-isobutylphenyl)propan-1-one and its characterization. The newly obtained hybrid and its derivatives (hybrids of ibuprofen with 1,2,3,4-tetrahydroisoquinoline, and piperidine) were screened for their in vitro antioxidant, antitryptic, and inhibition of albumin denaturation activity. The lipophilicity was established using both reversed-phase thin layer chromatography and in silico calculations.

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26

Ibrahim, Mahmoud A. A., Alaa H. M. Abdelrahman, Mohamed A. M. Atia, Tarik A. Mohamed, Mahmoud F. Moustafa, Abdulrahim R. Hakami, Shaden A. M. Khalifa, et al. "Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition." Marine Drugs 19, no. 7 (July 13, 2021): 391. http://dx.doi.org/10.3390/md19070391.

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The coronavirus pandemic has affected more than 150 million people, while over 3.25 million people have died from the coronavirus disease 2019 (COVID-19). As there are no established therapies for COVID-19 treatment, drugs that inhibit viral replication are a promising target; specifically, the main protease (Mpro) that process CoV-encoded polyproteins serves as an Achilles heel for assembly of replication-transcription machinery as well as down-stream viral replication. In the search for potential antiviral drugs that target Mpro, a series of cembranoid diterpenes from the biologically active soft-coral genus Sarcophyton have been examined as SARS-CoV-2 Mpro inhibitors. Over 360 metabolites from the genus were screened using molecular docking calculations. Promising diterpenes were further characterized by molecular dynamics (MD) simulations based on molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. According to in silico calculations, five cembranoid diterpenes manifested adequate binding affinities as Mpro inhibitors with ΔGbinding < −33.0 kcal/mol. Binding energy and structural analyses of the most potent Sarcophyton inhibitor, bislatumlide A (340), was compared to darunavir, an HIV protease inhibitor that has been recently subjected to clinical-trial as an anti-COVID-19 drug. In silico analysis indicates that 340 has a higher binding affinity against Mpro than darunavir with ΔGbinding values of −43.8 and −34.8 kcal/mol, respectively throughout 100 ns MD simulations. Drug-likeness calculations revealed robust bioavailability and protein-protein interactions were identified for 340; biochemical signaling genes included ACE, MAPK14 and ESR1 as identified based on a STRING database. Pathway enrichment analysis combined with reactome mining revealed that 340 has the capability to re-modulate the p38 MAPK pathway hijacked by SARS-CoV-2 and antagonize injurious effects. These findings justify further in vivo and in vitro testing of 340 as an antiviral agent against SARS-CoV-2.

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27

Szeleszczuk, Łukasz, Anna Helena Mazurek, Katarzyna Milcarz, Ewa Napiórkowska, and Dariusz Maciej Pisklak. "Can We Predict the Isosymmetric Phase Transition? Application of DFT Calculations to Study the Pressure Induced Transformation of Chlorothiazide." International Journal of Molecular Sciences 22, no. 18 (September 18, 2021): 10100. http://dx.doi.org/10.3390/ijms221810100.

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Isosymmetric structural phase transition (IPT, type 0), in which there are no changes in the occupation of Wyckoff positions, the number of atoms in the unit cell, and the space group symmetry, is relatively uncommon. Chlorothiazide, a diuretic agent with a secondary function as an antihypertensive, has been proven to undergo pressure-induced IPT of Form I to Form II at 4.2 GPa. For that reason, it has been chosen as a model compound in this study to determine if IPT can be predicted in silico using periodic DFT calculations. The transformation of Form II into Form I, occurring under decompression, was observed in geometry optimization calculations. However, the reverse transition was not detected, although the calculated differences in the DFT energies and thermodynamic parameters indicated that Form II should be more stable at increased pressure. Finally, the IPT was successfully simulated using ab initio molecular dynamics calculations.

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28

Fischer, Michael. "Interaction of water with (silico)aluminophosphate zeotypes: a comparative investigation using dispersion-corrected DFT." Physical Chemistry Chemical Physics 18, no. 23 (2016): 15738–50. http://dx.doi.org/10.1039/c6cp02289h.

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The adsorption of water in six structurally different aluminophosphates and their silicoaluminophosphate analogues is investigated using dispersion-corrected density-functional theory calculations. In addition to predicting the interaction energies, the structural changes of the materials upon water adsorption are assessed.

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29

Jacoby, Edgar, Herman Van Vlijmen, Olivier Querolle, Ian Stansfield, Lieven Meerpoel, Matthias Versele, George Hynd, and Ricardo Attar. "FEP+ calculations predict a stereochemical SAR switch for first-in-class indoline NIK inhibitors for multiple myeloma." Future Drug Discovery 2, no. 3 (July 1, 2020): FDD43. http://dx.doi.org/10.4155/fdd-2020-0004.

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In the search for first-in-class NIK inhibitors for multiple myeloma, we discovered an azaindoline hit class generated from a biochemical NIK autophosphorylation high-throughput screening assay which was optimized to the final cyanoindoline compound class. During the hit-to-lead phase, a prominent stereochemical SAR switch was observed which was accurately predicted by in silico FEP+ calculations. Crystallographic and computational analysis showed that for both stereoisomers comparable contacts, both in nature and number, could be formed by the switching hydroxyl group, making this system particularly interesting from an interaction energy viewpoint. We provide a detailed analysis of our FEP+ and WaterMap calculations and show how this type of computational chemistry methods are useful during hit-to-lead and lead optimization phases.

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Georgiou, Nikitas, Antigoni Cheilari, Danai Karta, Eleni Chontzopoulou, Janez Plavec, Demeter Tzeli, Stamatia Vassiliou, and Thomas Mavromoustakos. "Conformational Properties and Putative Bioactive Targets for Novel Thiosemicarbazone Derivatives." Molecules 27, no. 14 (July 16, 2022): 4548. http://dx.doi.org/10.3390/molecules27144548.

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The structure assignment and conformational analysis of the thiosemicarbazones, DKI21 and DKI24, were performed through homonuclear and heteronuclear 2D Nuclear Magnetic Resonance (NMR) spectroscopy (2D-COSY, 2D-NOESY, 2D-ROESY, 2D-HSQC, and 2D-HMBC) and quantum mechanics (QM) calculations, using Functional Density Theory (DFT). In addition, utilizing a combination of 2D-NOESY and 2D-ROESY spectra an exo structure was established for both of the analogs. This experimental results were confirmed by theoretical mechanistic studies, as the lowest minima conformations derived through DFT calculations were compatible with the spatial correlations observed in the 2D-NOESY and 2D-ROESY spectra. Finally, molecular binding experiments were performed to detect the potential targets for DKI21 and DKI24, derived from SwissAdme. In silico molecular binding experiments showed favorable binding energy values for the most of the enzymes studied. The ADMET calculations, using the preADMET and pKCSm software, showed that the two molecules appear as possible drug leads.

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Nada, Hossam, Ahmed Elkamhawy, and Kyeong Lee. "Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations." PeerJ 10 (October 7, 2022): e14120. http://dx.doi.org/10.7717/peerj.14120.

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The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.

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Singh, Kalpana Virendra, Ramchander Merugu, and Jeeven Singh Solanki. "ZIKA VIRUS SERENE PROTEASE COMPLEX (NS2B-NS3) INHIBITION BY 2-AMINO-5-{[(1Z)-AMINO({[(Z)-BENZOYL]IMINO})METHYL]AMINO}-N-(5-AMINO-7-{[CARBAMOYL(PHENYL)METHYL]AMINO}-6-OXOHEPTYL)PENTANAMIDE, IN SILICO STUDIES." Asian Journal of Pharmaceutical and Clinical Research 10, no. 5 (May 1, 2017): 210. http://dx.doi.org/10.22159/ajpcr.2017.v10i5.17286.

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Objective: The present in silico study is taken to report 2-amino-5-{[(1Z) -amino ({[(Z) -benzoyl] imino}) methyl] amino} -N-(5-amino-7-{[carbamoyl (phenyl) methyl] amino} -6-oxoheptyl) pentanamide as Zika virus (ZIKV) NS2B-NS3 protease inhibitor.Methods: In silico studies performed on online docking servers. NS2B-NS3 serine protease from ZIKV with PDB ID: 5GJ4 a hydrolase with total structure weight of 102878.54 is selected as the target. Docking server is used for carrying out docking calculations. Lamarckian genetic algorithm and the Solis and Wets local search methods are used for performing docking simulations. Free energy calculations, hydrogen bond (HB) formation, polar and hydrophobic interactions and HB plot are studied in this study.Results: Binding pocket is found on a serine protease NS2B chain A. Binding site predictions propose NKK as the suitable ligand for binding, which has structure closely related to the proposed ligand2-amino-5-{[(1Z) -amino ({[(Z) -benzoyl] imino}) methyl] amino} -N-(5-amino-7-{[carbamoyl (phenyl) methyl] amino} -6-oxoheptyl) pentanamide. Free energy of binding is - 4.08 kcal/Mol and inhibition constant (Ki) is very less 1.02 mm. The ligand binds to chain A of NS2B and chain B of NS3 serine protease. The legend is bound to serine protease complex through strong HB, formed between THR 60 (A) and N6 of ligand, GLU62 (A) and N8 of ligand, ARG 55 (A) and N3 of ligand and ASN108 (B) and N7 of ligand apart from polar and hydrophobic interactions.Conclusion: Docking studies performed establishes the proposed ligand2-amino-5-{[(1Z)-amino ({[(Z)-benzoyl] imino}) methyl] amino} -N-(5- amino-7-{[carbamoyl (phenyl) methyl] amino}-6-oxoheptyl) pentanamide as a molecule which can be used for the inhibition of ZIKV NS2B-NS3 serine protease.Keywords: Zika virus, NS2B-NS3 protease, Inhibition, In silico.

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33

Velihina, Yevheniia, Nataliya Obernikhina, Stepan Pilyo, Maryna Kachaeva, Oleksiy Kachkovsky, and Volodymyr Brovarets. "In silico study of binding affinity of nitrogenous bicyclic heterocycles: fragment-to-fragment approach." Ukr. Bioorg. Acta 2020, Vol. 15, N2 15, no. 2 (December 30, 2020): 49–59. http://dx.doi.org/10.15407/bioorganica2020.02.049.

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The binding affinity of model aromatic amino acids and heterocycles and their derivatives condensed with pyridine were investigated in silico and are presented in the framework of fragment-to-fragment approach. The presented model describes interaction between pharmacophores and biomolecules. Scrupulous data analysis shows that expansion of the π-electron system by heterocycles annelation causes the shifting up of high energy levels, while the appearance of new the dicoordinated nitrogen atom is accompanied by decreasing of the donor-acceptor properties. Density Functional Theory (DFT) wB97XD/6-31(d,p)/calculations of π-complexes of the heterocycles 1-3 with model fragments of aromatic amino acids, which were formed by π-stack interaction, show an increase in the stabilization energy of π-complexes during the moving from phenylalanine to tryptophan. DFT calculation of pharmacophore complexes with model proton-donor amino acid by the hydrogen bonding mechanism (H-B complex) shows that stabilization energy (DE) increases from monoheterocycles to their condensed derivatives. The expansion of the π-electron system by introducing phenyl radicals to the oxazole cycle as reported earlier [18] leads to a decrease in the stabilization energy of the [Pharm-BioM] complexes in comparison with the annelated oxazole by the pyridine cycle.

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Back, Seoin, Jonggeol Na, Kevin Tran, and Zachary W. Ulissi. "In silico discovery of active, stable, CO-tolerant and cost-effective electrocatalysts for hydrogen evolution and oxidation." Physical Chemistry Chemical Physics 22, no. 35 (2020): 19454–58. http://dx.doi.org/10.1039/d0cp03017a.

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Based on databases of density functional theory (DFT) calculations, we evaluate multiple aspects of catalysts to discover active, stable, CO-tolerant and cost-effective hydrogen evolution and oxidation catalysts.

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35

Sethi, Aaftaab, Swetha Sanam, Sharon Munagalasetty, Sivaraman Jayanthi, and Mallika Alvala. "Understanding the role of galectin inhibitors as potential candidates for SARS-CoV-2 spike protein: in silico studies." RSC Advances 10, no. 50 (2020): 29873–84. http://dx.doi.org/10.1039/d0ra04795c.

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36

Chagnes, Alexandre, Aurélien Moncomble, and Gérard Cote. "In-Silico Calculations as a Helpful Tool for Designing New Extractants in Liquid-Liquid Extraction." Solvent Extraction and Ion Exchange 31, no. 5 (March 5, 2013): 499–518. http://dx.doi.org/10.1080/07366299.2013.775884.

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37

Tayfuroglu, Omer, Abdulkadir Kocak, and Yunus Zorlu. "In Silico Investigation into H2 Uptake in MOFs: Combined Text/Data Mining and Structural Calculations." Langmuir 36, no. 1 (December 19, 2019): 119–29. http://dx.doi.org/10.1021/acs.langmuir.9b03618.

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38

Bienboire-Frosini, Cécile, Rajesh Durairaj, Paolo Pelosi, and Patrick Pageat. "The Major Cat Allergen Fel d 1 Binds Steroid and Fatty Acid Semiochemicals: A Combined In Silico and In Vitro Study." International Journal of Molecular Sciences 21, no. 4 (February 18, 2020): 1365. http://dx.doi.org/10.3390/ijms21041365.

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The major cat allergen Fel d 1 is a tetrameric glycoprotein of the secretoglobin superfamily. Structural aspects and allergenic properties of this protein have been investigated, but its physiological function remains unclear. Fel d 1 is assumed to bind lipids and steroids like the mouse androgen-binding protein, which is involved in chemical communication, either as a semiochemical carrier or a semiochemical itself. This study focused on the binding activity of a recombinant model of Fel d 1 (rFel d 1) towards semiochemical analogs, i.e., fatty acids and steroids, using both in silico calculations and fluorescence measurements. In silico analyses were first adopted to model the interactions of potential ligands, which were then tested in binding assays using the fluorescent reporter N-phenyl-1-naphthylamine. Good ligands were fatty acids, such as the lauric, oleic, linoleic, and myristic fatty acids, as well as steroids like androstenone, pregnenolone, and progesterone, that were predicted by in silico molecular models to bind into the central and surface cavities of rFel d 1, respectively. The lowest dissociation constants were shown by lauric acid (2.6 µM) and androstenone (2.4 µM). The specific affinity of rFel d 1 to semiochemicals supports a function of the protein in cat’s chemical communication, and highlights a putative role of secretoglobins in protein semiochemistry.

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39

Schmidt, Denis, Magdalena M. Scharf, Dominique Sydow, Eva Aßmann, Maria Martí-Solano, Marina Keul, Andrea Volkamer, and Peter Kolb. "Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening." Molecules 26, no. 3 (January 26, 2021): 629. http://dx.doi.org/10.3390/molecules26030629.

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While selective inhibition is one of the key assets for a small molecule drug, many diseases can only be tackled by simultaneous inhibition of several proteins. An example where achieving selectivity is especially challenging are ligands targeting human kinases. This difficulty arises from the high structural conservation of the kinase ATP binding sites, the area targeted by most inhibitors. We investigated the possibility to identify novel small molecule ligands with pre-defined binding profiles for a series of kinase targets and anti-targets by in silico docking. The candidate ligands originating from these calculations were assayed to determine their experimental binding profiles. Compared to previous studies, the acquired hit rates were low in this specific setup, which aimed at not only selecting multi-target kinase ligands, but also designing out binding to anti-targets. Specifically, only a single profiled substance could be verified as a sub-micromolar, dual-specific EGFR/ErbB2 ligand that indeed avoided its selected anti-target BRAF. We subsequently re-analyzed our target choice and in silico strategy based on these findings, with a particular emphasis on the hit rates that can be expected from a given target combination. To that end, we supplemented the structure-based docking calculations with bioinformatic considerations of binding pocket sequence and structure similarity as well as ligand-centric comparisons of kinases. Taken together, our results provide a multi-faceted picture of how pocket space can determine the success of docking in multi-target drug discovery efforts.

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40

Bell, David R., Jeffrey K. Weber, Wang Yin, Tien Huynh, Wei Duan, and Ruhong Zhou. "In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers." Proceedings of the National Academy of Sciences 117, no. 15 (March 31, 2020): 8486–93. http://dx.doi.org/10.1073/pnas.1913242117.

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Nucleic acid aptamers hold great promise for therapeutic applications due to their favorable intrinsic properties, as well as high-throughput experimental selection techniques. Despite the utility of the systematic evolution of ligands by the exponential enrichment (SELEX) method for aptamer determination, complementary in silico aptamer design is highly sought after to facilitate virtual screening and increased understanding of important nucleic acid–protein interactions. Here, with a combined experimental and theoretical approach, we have developed two optimal epithelial cellular adhesion molecule (EpCAM) aptamers. Our structure-based in silico method first predicts their binding modes and then optimizes them for EpCAM with molecular dynamics simulations, docking, and free energy calculations. Our isothermal titration calorimetry experiments further confirm that the EpCAM aptamers indeed exhibit enhanced affinity over a previously patented nanomolar aptamer, EP23. Moreover, our study suggests that EP23 and the de novo designed aptamers primarily bind to EpCAM dimers (and not monomers, as hypothesized in previous published works), suggesting a paradigm for developing EpCAM-targeted therapies.

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41

Ahmed, Muhammad Naeem, Mehreen Ghias, Syed Wadood Ali Shah, Mohammad Shoaib, Muhammad Nawaz Tahir, Muhammad Ashfaq, Mahmoud A. A. Ibrahim, Hina Andleeb, Diego M. Gil, and Antonio Frontera. "X-ray characterization, Hirshfeld surface analysis, DFT calculations, in vitro and in silico lipoxygenase inhibition (LOX) studies of dichlorophenyl substituted 3-hydroxy-chromenones." New Journal of Chemistry 45, no. 42 (2021): 19928–40. http://dx.doi.org/10.1039/d1nj04340d.

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This work reports the synthesis, X-ray characterization and theoretical study of dichlorophenyl substituted 3-hydroxy-chromenones focusing on the low prevalence of halogen bonds and in vitro and in silico lipoxygenase inhibition (LOX) studies.

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42

Ogunyemi, Babatunde Temitope, and Ogunyemi Olajide Oderinlo. "In-silico investigation of oxoaporphine alkaloids of Xylopia aethiopica against SARS-COV-2 main protease." AROC in Natural Products Research 02, no. 01 (February 26, 2022): 01–12. http://dx.doi.org/10.53858/arocnpr02010112.

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Background: The ongoing coronavirus pandemic poses a significant social, economic, and health threat worldwide. The situation is exacerbated further by vaccine hesitancy and the ongoing development of mutant strains that could lead to drug resistance. It is therefore critical to find new anti-viral chemotherapeutic agents to reduce or end the epidemic. This study aimed to investigate the antiprotease activity of the oxoaporphine alkaloids in Xylopia aethiopica. Methods: Computational techniques such as molecular docking were used to probe the oxoaporphine alkaloids in the plant for their ability to inhibit the main protease of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The docking score calculations which quantifies the predictive binding affinity of both ligand and target was carried out using Auto-Dock Vina software. Results: The results showed that oxoaporphine alkaloids had a better binding affinity than hydroxychloroquine sulfate (standard). Similarly, the values of the chemical descriptors obtained for these alkaloids revealed notable profiles, and these alkaloids also have good oral bioavailability according to rule of five. Conclusion: These findings imply that these plant-based alkaloids could be investigated further as prospective leads against SARS-CoV-2 main protease. Furthermore, structural-activity relationships on these compounds could be an effective way to mitigate the predicted side effects

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43

Spirtovic-Halilovic, Selma, Mirsada Salihovic, Hurija Dzudzevic-Cancar, Snezana Trifunovic, Suncica Roca, Dzenita Softic, and Davorka Zavrsnik. "DFT study and microbiology of some coumarin-based compounds containing a chalcone moiety." Journal of the Serbian Chemical Society 79, no. 4 (2014): 435–43. http://dx.doi.org/10.2298/jsc130628077s.

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In the present investigation, a series of coumarin-based compounds containing a chalcone moiety were studied for their in vitro and in silico properties. DFT global chemical reactivity descriptors (chemical hardness, total energy, electronic chemical potential and electrophilicity) are calculated for four synthesized compounds and used to predict their relative stability and reactivity. The antibacterial activities of all compounds have been screened against Bacillus subtilis (ATCC No. 6633) and Bacillus cereus (ATCC No. 11778). Quantum-chemical calculations indicate that antibacterial activity correlates well with chemical reactivity descriptors of molecules.

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44

El Hassab, Mahmoud A., Tamer M. Ibrahim, Aly A. Shoun, Sara T. Al-Rashood, Hamad M. Alkahtani, Amal Alharbi, Razan O. Eskandrani, and Wagdy M. Eldehna. "In silico identification of potential SARS COV-2 2′-O-methyltransferase inhibitor: fragment-based screening approach and MM-PBSA calculations." RSC Advances 11, no. 26 (2021): 16026–33. http://dx.doi.org/10.1039/d1ra01809d.

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45

Wang, Honglei, Yanliang Zhao, Huixuan Zhao, Junxia Yang, Dong Zhai, Lei Sun, and Weiqiao Deng. "In silico design of metal-free hydrophosphate catalysts for hydrogenation of CO₂ to formate." Physical Chemistry Chemical Physics 24, no. 5 (2022): 2901–8. http://dx.doi.org/10.1039/d1cp04582b.

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The metal-free catalysts composed of K3−nHnPO4 (n = 0, 1, 2) and B(C6F5−mHm)3 (m = 0, 3, 5) are studied using DFT calculations, where this emerging Lewis pair catalyst is considered as a new class of candidate catalysts for reducing CO2 to formate.

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46

Czaja, Kornelia, Jacek Kujawski, Elżbieta Jodłowska-Siewert, Paulina Szulc, Tomasz Ratajczak, Dominika Krygier, Marcin K. Chmielewski, and Marek K. Bernard. "On the Interactions of Fused Pyrazole Derivative with Selected Amino Acids: DFT Calculations." Journal of Chemistry 2017 (2017): 1–9. http://dx.doi.org/10.1155/2017/8124323.

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Due to the increasing prevalence of neoplasms, there is a permanent need for new selective cytostatic compounds. Anticancer drugs can act in different ways, affecting protein expression and synthesis, including disruption of signaling pathways within cells. Continuing our previous research aiming at elucidating the mechanism of pyrazole’s anticancer activity, we carried out in silico studies on the interactions of fused pyrazole derivative with alanine, lysine, glutamic acid, and methionine. The objective of the study is to improve our understanding of the possible interactions of pyrazole derivatives with the above-mentioned amino acids. For this purpose, we apply the DFT formalism (optimization using the B3LYP, CAM-B3LYP, PBE0, and M06L functionals) and interaction energy calculations (counterpoise corrected method based on the basis set superposition error, BSSE) together with QTAIM approach and estimation of the 1H NMR chemical shifts of analyzed pyrazole derivative using different basis sets and DFT functionals in CPCM solvation model (and water used as a solvent).

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47

Oladipo, Segun Daniel, Tunde Lewis Yusuf, Sizwe Joshua Zamisa, Gideon Femi Tolufashe, Kolawole Ayodapo Olofinsan, Zikhona Tywabi-Ngeva, and Nonhlangabezo Mabuba. "Synthesis, crystal structure with free radical scavenging activity and theoretical studies of Schiff bases derived from 1-naphthylamine, 2,6-diisopropylaniline, and substituted benzaldehyde." European Journal of Chemistry 12, no. 2 (June 30, 2021): 204–15. http://dx.doi.org/10.5155/eurjchem.12.2.204-215.2088.

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Three Schiff bases 1-(4-chlorophenyl)-N-(naphthalen-1-yl)methanimine (1), 1-(4-methoxy phenyl)-N-(naphthalen-1-yl)methanimine (2), and 1-(4-chlorophenyl)-N-(2,6-diisopropyl phenyl)methanimine (3) were synthesized and characterized by elemental analysis, 1H and 13C NMR, FT-IR and UV-Visible spectroscopic techniques. The crystal structure of compound 3 was obtained and it revealed that the compound crystallized in a monoclinic space group P21/n and there exists an intermolecular hydrogen bond in a phenyl-imine form with C-H⋯N. Crystal data for C19H22ClN: a = 7.28280(10) Å, b = 9.94270(10) Å, c = 24.0413(2) Å, β = 97.0120(10)°, V = 1727.83(3) Å3, Z = 4, μ(Mo Kα) = 0.215 mm-1, Dcalc = 1.1526 g/cm3, 14038 reflections measured (12.42° ≤ 2Θ ≤ 52.74°), 3448 unique (Rint = 0.0223, Rsigma = 0.0182) which were used in all calculations. The final R1 was 0.0337 (I≥2u(I)) and wR2 was 0.0927 (all data). The free radical scavenging activities of all three compounds were assayed using DPPH, FRAP, and OH assays. According to results obtained, compound 2 shows effective DPPH- (IC50 = 22.69±0.14 μg/mL), FRAP+ (IC50 = 28.44±0.12 μg/mL), and OH- (IC50 = 27.97±0.16 μg/mL) scavenging activities compared with compounds 1 and 3 but less than standard antioxidant compound Trolox (TRO). Additionally, theoretical calculations for the three complexes were performed by using density functional theory (DFT) calculations at the B3LYP/6-31++G(2d,2p) level in the ground state to obtain an optimized geometrical structure and to perform an electronic, molecular electronic potential surface and natural bond orbital (NBO) analysis. The geometrical calculation obtained was found to be consistent with the experimental geometry. Further analysis was conducted using the in silico technique to predict the drug likeness, molecular and ADME properties of these molecules.

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Cotuá, José, and Sandra Cotes. "In silico Study of Solvent Effects on the Intramolecular Hydrogen Bond of Hydroxy Proline." Oriental Journal Of Chemistry 38, no. 3 (June 30, 2022): 676–80. http://dx.doi.org/10.13005/ojc/380318.

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The hydrogen bond strength and stabilization energy of hydroxyproline–water complexes were investigated by performing density-functional theory calculations. In particular, the hydrogen bond formation between carbonyl groups serving as proton acceptors and amino groups as proton donors in the hydroxyproline–water was examined. Hydroxyproline-water exhibit higher energy of their hydrogen bond when the carbonyl groups of their hydroxyproline moieties acts as a proton acceptor. Furthermore, the infrared spectra of isolated water and hydroxyproline molecules were compared with those of the hydroxyproline–water complexes, and the observed frequency shifts were discussed.

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He, Xianran, Yousong Nie, Min Zhong, Shaolei Li, Xiaolong Li, Yi Guo, Zhenming Liu, et al. "New organoselenides (NSAIDs-Se derivatives) as potential anticancer agents: Synthesis, biological evaluation and in silico calculations." European Journal of Medicinal Chemistry 218 (June 2021): 113384. http://dx.doi.org/10.1016/j.ejmech.2021.113384.

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Izquierdo, Rodolfo, Néstor Cubillan, Mayamaru Guerra, and Merlín Rosales. "Substituted heterocycles as new candidates for liquid organic hydrogen carriers: In silico design from DFT calculations." International Journal of Hydrogen Energy 46, no. 34 (May 2021): 17853–70. http://dx.doi.org/10.1016/j.ijhydene.2021.02.201.

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