molecular docking simulation

Summary

Summary: A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.

Top Publications

  1. Marsh D, Das S, Ridell J, Smid S. Structure-activity relationships for flavone interactions with amyloid ? reveal a novel anti-aggregatory and neuroprotective effect of 2',3',4'-trihydroxyflavone (2-D08). Bioorg Med Chem. 2017;25:3827-3834 pubmed publisher
    ..Such modified flavones may facilitate drug development targeting multiple pathways in neurodegenerative disease. ..
  2. Ijiri M, Fujiya M, Konishi H, Tanaka H, Ueno N, Kashima S, et al. Ferrichrome identified from Lactobacillus casei ATCC334 induces apoptosis through its iron-binding site in gastric cancer cells. Tumour Biol. 2017;39:1010428317711311 pubmed publisher
    ..In conclusion, probiotic-derived ferrichrome induced apoptosis in gastric cancer cells. The iron binding site of ferrichrome is the structure responsible for its tumor suppressive function. ..
  3. Marastoni M, Trapella C, Scotti A, Fantinati A, Ferretti V, Marzola E, et al. Naphthoquinone amino acid derivatives, synthesis and biological activity as proteasome inhibitors. J Enzyme Inhib Med Chem. 2017;32:865-877 pubmed publisher
    ..Some analogues showed interesting inhibitory potency for the ?1 and ?5 subunits of the proteasome with IC50 values in the sub-µm range. ..
  4. Merkle P, Irving M, Hongjian S, Ferber M, Jørgensen T, Scholten K, et al. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed ?2-Microglobulin through Distinct Binding Sites. Biochemistry. 2017;56:3945-3961 pubmed publisher
  5. Rahman Y, Afrin S, Husain M, Sarwar T, Ali A, Shamsuzzaman -, et al. Unravelling the interaction of pirenzepine, a gastrointestinal disorder drug, with calf thymus DNA: An in vitro and molecular modelling study. Arch Biochem Biophys. 2017;625-626:1-12 pubmed publisher
    ..Moreover, the role of electrostatic interaction in the binding of pirenzepine to Ct-DNA cannot be precluded. ..
  6. McGee T, Yi H, Allen W, Jacobs A, Rizzo R. Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer. Bioorg Med Chem Lett. 2017;27:3177-3184 pubmed publisher
  7. Hirakis S, Malmstrom R, Amaro R. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry. 2017;56:3885-3888 pubmed publisher
    ..Brownian dynamics simulations suggest that the Flipback conformation plays a role in cAMP association to the A domain of the R subunit. ..
  8. Cornejo A, Aguilar Sandoval F, Caballero L, Machuca L, Muñoz P, Caballero J, et al. Rosmarinic acid prevents fibrillization and diminishes vibrational modes associated to ? sheet in tau protein linked to Alzheimer's disease. J Enzyme Inhib Med Chem. 2017;32:945-953 pubmed publisher
  9. Guda R, Korra R, Balaji S, Palabindela R, Eerla R, Lingabathula H, et al. Design, synthesis and biological evaluation of 8-substituted-6-hydrazonoindolo[2,1-b]quinazolin-12(6H)-one scaffolds as potential cytotoxic agents: IDO-1 targeting molecular docking studies. Bioorg Med Chem Lett. 2017;27:4741-4748 pubmed publisher
    ..73 and -11.61kcalmol-1 for T11 and T12 scaffolds, respectively towards the in vitro anti-cancer activity. ..
  10. Wang G, Chen M, Wang J, Peng Y, Li L, Xie Z, et al. Synthesis, biological evaluation and molecular docking studies of chromone hydrazone derivatives as ?-glucosidase inhibitors. Bioorg Med Chem Lett. 2017;27:2957-2961 pubmed publisher
    ..In summary, our studies shown that these chromone hydrazone derivatives are a new class of ?-glucosidase inhibitors. ..

Detail Information

Publications113 found, 100 shown here

  1. Marsh D, Das S, Ridell J, Smid S. Structure-activity relationships for flavone interactions with amyloid ? reveal a novel anti-aggregatory and neuroprotective effect of 2',3',4'-trihydroxyflavone (2-D08). Bioorg Med Chem. 2017;25:3827-3834 pubmed publisher
    ..Such modified flavones may facilitate drug development targeting multiple pathways in neurodegenerative disease. ..
  2. Ijiri M, Fujiya M, Konishi H, Tanaka H, Ueno N, Kashima S, et al. Ferrichrome identified from Lactobacillus casei ATCC334 induces apoptosis through its iron-binding site in gastric cancer cells. Tumour Biol. 2017;39:1010428317711311 pubmed publisher
    ..In conclusion, probiotic-derived ferrichrome induced apoptosis in gastric cancer cells. The iron binding site of ferrichrome is the structure responsible for its tumor suppressive function. ..
  3. Marastoni M, Trapella C, Scotti A, Fantinati A, Ferretti V, Marzola E, et al. Naphthoquinone amino acid derivatives, synthesis and biological activity as proteasome inhibitors. J Enzyme Inhib Med Chem. 2017;32:865-877 pubmed publisher
    ..Some analogues showed interesting inhibitory potency for the ?1 and ?5 subunits of the proteasome with IC50 values in the sub-µm range. ..
  4. Merkle P, Irving M, Hongjian S, Ferber M, Jørgensen T, Scholten K, et al. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed ?2-Microglobulin through Distinct Binding Sites. Biochemistry. 2017;56:3945-3961 pubmed publisher
  5. Rahman Y, Afrin S, Husain M, Sarwar T, Ali A, Shamsuzzaman -, et al. Unravelling the interaction of pirenzepine, a gastrointestinal disorder drug, with calf thymus DNA: An in vitro and molecular modelling study. Arch Biochem Biophys. 2017;625-626:1-12 pubmed publisher
    ..Moreover, the role of electrostatic interaction in the binding of pirenzepine to Ct-DNA cannot be precluded. ..
  6. McGee T, Yi H, Allen W, Jacobs A, Rizzo R. Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-heptad repeat trimer. Bioorg Med Chem Lett. 2017;27:3177-3184 pubmed publisher
  7. Hirakis S, Malmstrom R, Amaro R. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry. 2017;56:3885-3888 pubmed publisher
    ..Brownian dynamics simulations suggest that the Flipback conformation plays a role in cAMP association to the A domain of the R subunit. ..
  8. Cornejo A, Aguilar Sandoval F, Caballero L, Machuca L, Muñoz P, Caballero J, et al. Rosmarinic acid prevents fibrillization and diminishes vibrational modes associated to ? sheet in tau protein linked to Alzheimer's disease. J Enzyme Inhib Med Chem. 2017;32:945-953 pubmed publisher
  9. Guda R, Korra R, Balaji S, Palabindela R, Eerla R, Lingabathula H, et al. Design, synthesis and biological evaluation of 8-substituted-6-hydrazonoindolo[2,1-b]quinazolin-12(6H)-one scaffolds as potential cytotoxic agents: IDO-1 targeting molecular docking studies. Bioorg Med Chem Lett. 2017;27:4741-4748 pubmed publisher
    ..73 and -11.61kcalmol-1 for T11 and T12 scaffolds, respectively towards the in vitro anti-cancer activity. ..
  10. Wang G, Chen M, Wang J, Peng Y, Li L, Xie Z, et al. Synthesis, biological evaluation and molecular docking studies of chromone hydrazone derivatives as ?-glucosidase inhibitors. Bioorg Med Chem Lett. 2017;27:2957-2961 pubmed publisher
    ..In summary, our studies shown that these chromone hydrazone derivatives are a new class of ?-glucosidase inhibitors. ..
  11. Harb L, Arooj M, Vrielink A, Mancera R. Computational site-directed mutagenesis studies of the role of the hydrophobic triad on substrate binding in cholesterol oxidase. Proteins. 2017;85:1645-1655 pubmed publisher
    ..Proteins 2017; 85:1645-1655. © 2017 Wiley Periodicals, Inc. ..
  12. Al Ashmawy A, Ragab F, Elokely K, Anwar M, Perez Leal O, Rico M, et al. Design, synthesis and SAR of new-di-substituted pyridopyrimidines as ATP-competitive dual PI3K?/mTOR inhibitors. Bioorg Med Chem Lett. 2017;27:3117-3122 pubmed publisher
  13. Pirat C, Dacquet C, Leclerc V, Hennuyer N, Beucher Gaudin M, Zanirato G, et al. Anti-diabetic activity of fused PPAR?-SIRT1 ligands with limited body-weight gain by mimicking calorie restriction and decreasing SGK1 expression. Eur J Med Chem. 2017;137:310-326 pubmed publisher
  14. Zhou Y, Yan W, Cao D, Shao M, Li D, Wang F, et al. Design, synthesis and biological evaluation of 4-anilinoquinoline derivatives as novel potent tubulin depolymerization agents. Eur J Med Chem. 2017;138:1114-1125 pubmed publisher
    ..All the results indicated that 14h could be a promising candidate for the treatment of cancer. ..
  15. Li Y, Zhao Y, Su M, Glover K, Chakravarthy S, Colbert C, et al. Structural insights into the interaction of the conserved mammalian proteins GAPR-1 and Beclin 1, a key autophagy protein. Acta Crystallogr D Struct Biol. 2017;73:775-792 pubmed publisher
    ..Thus, changes in the structure of the equatorial groove combined with the improved dimerization of pentad mutant GAPR-1 are likely to abrogate binding to Beclin 1. ..
  16. Chakka N, Andrews K, Berry L, Bregman H, Gunaydin H, Huang L, et al. Applications of parallel synthetic lead hopping and pharmacophore-based virtual screening in the discovery of efficient glycine receptor potentiators. Eur J Med Chem. 2017;137:63-75 pubmed publisher
  17. Wei J, Huo X, Yu Z, Tian X, Deng S, Sun C, et al. Phenolic acids from Balanophora involucrata and their bioactivities. Fitoterapia. 2017;121:129-135 pubmed publisher
    ..New compound 8 also could inhibit the acetyl transfer activity of GlmU moderately with the IC50 value of 18.21?M, which was a new antibacterial target. ..
  18. Kasturi S, Surarapu S, Uppalanchi S, Anireddy J, Dwivedi S, Anantaraju H, et al. Synthesis and ?-glucosidase inhibition activity of dihydroxy pyrrolidines. Bioorg Med Chem Lett. 2017;27:2818-2823 pubmed publisher
    ..The promising compounds 6i, 5o, 6o, 10a, 11a, 10f and 11f have been identified. Molecular docking simulations were done for compounds to identify important binding modes responsible for inhibition activity of ?-glucosidase. ..
  19. Sun F, Ding J, Lü X, Gao R, Lu X, Shi E, et al. Mass spectral characterization of tabun-labeled lysine biomarkers in albumin. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1057:54-61 pubmed publisher
    ..For the first time, we show that tabun-labeled lysine peptides are found in vivo and in vitro. These modified lysine peptides are good biomarkers for exposure to tabun in albumin of leporine and rat. ..
  20. Aouani I, Sellami B, Lahbib K, Cavalier J, Touil S. Efficient synthesis of novel dialkyl-3-cyanopropylphosphate derivatives and evaluation of their anticholinesterase activity. Bioorg Chem. 2017;72:301-307 pubmed publisher
    ..74µM). The diethyl-3-cyano-1-p-tolylpropylphosphate which displayed the higher dual inhibitory potency towards both cholinesterases could be considered as a potential candidate for developing new drugs to treat Alzheimer's disease. ..
  21. Gao D, Li Y. Identification and preliminary structure-activity relationships of 1-Indanone derivatives as novel indoleamine-2,3-dioxygenase 1 (IDO1) inhibitors. Bioorg Med Chem. 2017;25:3780-3791 pubmed publisher
    ..We believe this study contributes a lot to the structural diversity for the future development of highly potent IDO1 inhibitors. ..
  22. Ding L, Wang Z, Sun X, Yang J, Ma C, Li W, et al. 3D-QSAR (CoMFA, CoMSIA), molecular docking and molecular dynamics simulations study of 6-aryl-5-cyano-pyrimidine derivatives to explore the structure requirements of LSD1 inhibitors. Bioorg Med Chem Lett. 2017;27:3521-3528 pubmed publisher
    ..Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300K. All the results can provide us more useful information for our further drug design. ..
  23. Mahajan S, Khairnar A, Bishnoi R, Ramya T. Microbial F-type lectin domains with affinity for blood group antigens. Biochem Biophys Res Commun. 2017;491:708-713 pubmed publisher
    ..We believe that these microbial lectins will be useful additions to the glycobiologist's toolbox for labeling, isolating and visualizing glycans. ..
  24. Wang M, Gu D, Li H, Wang Q, Kang J, Chu T, et al. Rapid prediction and identification of lipase inhibitors in volatile oil from Pinus massoniana L. needles. Phytochemistry. 2017;141:114-120 pubmed publisher
    ..The IC50 value of longifolene was 25.10 ± 0.49 ?M, indicating that this compound is the active ingredient responsible for the lipase inhibitory activity of PMLN volatile oil. ..
  25. Álvarez Almazán S, Bello M, Tamay Cach F, Martínez Archundia M, Alemán González Duhart D, Correa Basurto J, et al. Study of new interactions of glitazone's stereoisomers and the endogenous ligand 15d-PGJ2 on six different PPAR gamma proteins. Biochem Pharmacol. 2017;142:168-193 pubmed publisher
    ..An energetic analysis revealed binding free energy trends that supported known experimental findings of other authors describing better binding properties for PIO, ROSI and (S,S)-TRO than for 15d-PGJ2 and the TZD ring. ..
  26. Cavaliere F, Montanari E, Emerson A, Buschini A, Cozzini P. In silico pharmacogenetic approach: The natalizumab case study. Toxicol Appl Pharmacol. 2017;330:93-99 pubmed publisher
  27. Heller G, Aprile F, Bonomi M, Camilloni C, De Simone A, Vendruscolo M. Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide. J Mol Biol. 2017;429:2772-2779 pubmed publisher
    ..These results suggest that the binding mechanism that we report may create novel opportunities to discover drugs that target disordered proteins in their monomeric states in a specific manner. ..
  28. Shankaraiah N, Nekkanti S, Brahma U, Praveen Kumar N, Deshpande N, Prasanna D, et al. Synthesis of different heterocycles-linked chalcone conjugates as cytotoxic agents and tubulin polymerization inhibitors. Bioorg Med Chem. 2017;25:4805-4816 pubmed publisher
    ..In addition, molecular docking studies of the most active compounds 4a and 4b into the colchicine site of the tubulin, revealed the possible mode of interaction by these new conjugates. ..
  29. Nguyen T, Nguyen D, Zhao B, Le D, Choi D, Kim Y, et al. A new lignan and a new alkaloid, and ?-glucosidase inhibitory compounds from the grains of Echinochloa utilis Ohwi & Yabuno. Bioorg Chem. 2017;74:221-227 pubmed publisher
    ..1±1.3, 58.9±3.7, and 40.9±1.1?M, respectively. The results indicate that the grains of E. utilis will be useful in the treatment of diabetes control agents. ..
  30. Di Pietro O, Juárez Jiménez J, Muñoz Torrero D, Laughton C, Luque F. Unveiling a novel transient druggable pocket in BACE-1 through molecular simulations: Conformational analysis and binding mode of multisite inhibitors. PLoS ONE. 2017;12:e0177683 pubmed publisher
    ..Overall, these findings pave the way for the exploration of novel functionalities in the design of optimized BACE-1 multisite inhibitors. ..
  31. Fechtner S, Singh A, Chourasia M, Ahmed S. Molecular insights into the differences in anti-inflammatory activities of green tea catechins on IL-1? signaling in rheumatoid arthritis synovial fibroblasts. Toxicol Appl Pharmacol. 2017;329:112-120 pubmed publisher
    ..Therefore, varying EC content in green tea may reduce the anti-inflammatory effects of other potential catechins in green tea. ..
  32. Falsini M, Squarcialupi L, Catarzi D, Varano F, Betti M, Dal Ben D, et al. The 1,2,4-Triazolo[4,3-a]pyrazin-3-one as a Versatile Scaffold for the Design of Potent Adenosine Human Receptor Antagonists. Structural Investigations to Target the A2A Receptor Subtype. J Med Chem. 2017;60:5772-5790 pubmed publisher
    ..Docking studies at hAR structures were performed to rationalize the observed affinity data. ..
  33. Guzik K, Zak K, Grudnik P, Magiera K, Musielak B, Törner R, et al. Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1. J Med Chem. 2017;60:5857-5867 pubmed publisher
  34. Parker M, Ramaswamy R, van Gordon K, Powell C, Bosch J, Boulanger M. The structure of Plasmodium falciparum 3D7_0606800 reveals a bi-lobed architecture that supports re-annotation as a Venus Flytrap protein. Protein Sci. 2017;26:1878-1885 pubmed publisher
    ..falciparum surface protein PfVFT1 provides intriguing functional insight and establishes a structural template that could prove valuable for malaria vaccine engineering studies...
  35. Kohara T, Nakayama K, Watanabe K, Kusaka S, Sakai D, Tanaka H, et al. Discovery of novel 2-(4-aryl-2-methylpiperazin-1-yl)-pyrimidin-4-ones as glycogen synthase kinase-3? inhibitors. Bioorg Med Chem Lett. 2017;27:3733-3738 pubmed publisher
  36. Gao S, Zang J, Gao Q, Liang X, Ding Q, Li X, et al. Design, synthesis and anti-tumor activity study of novel histone deacetylase inhibitors containing isatin-based caps and o-phenylenediamine-based zinc binding groups. Bioorg Med Chem. 2017;25:2981-2994 pubmed publisher
    ..163, 0.396 and 0.605µM, respectively), compound 9n with IC50 values of 0.032, 0.256 and 0.311µM for HDAC1, 2 and 3 respectively, showed a moderate HDAC1 selectivity. ..
  37. Liang J, Labadie S, Zhang B, Ortwine D, Patel S, Vinogradova M, et al. From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors. Bioorg Med Chem Lett. 2017;27:2974-2981 pubmed publisher
    ..96?M), meeting our criteria for an in vivo tool compound from a new scaffold. ..
  38. Martinez Murillo P, Tran K, Guenaga J, Lindgren G, Adori M, Feng Y, et al. Particulate Array of Well-Ordered HIV Clade C Env Trimers Elicits Neutralizing Antibodies that Display a Unique V2 Cap Approach. Immunity. 2017;46:804-817.e7 pubmed publisher
    ..These vaccine-elicited mAbs target the V2 cap, demonstrating a means to accomplish tier 2 virus neutralization by penetrating the dense N-glycan shield. ..
  39. Wang L, Bao B, Song G, Chen C, Zhang X, Lu W, et al. Discovery of unsymmetrical aromatic disulfides as novel inhibitors of SARS-CoV main protease: Chemical synthesis, biological evaluation, molecular docking and 3D-QSAR study. Eur J Med Chem. 2017;137:450-461 pubmed publisher
    ..A possible binding mode was generated via molecular docking simulation and a comparative field analysis (CoMFA) model was constructed to understand the structure-activity ..
  40. Narva S, Chitti S, Amaroju S, Bhattacharjee D, Rao B, Jain N, et al. Design and synthesis of 4-morpholino-6-(1,2,3,6-tetrahydropyridin-4-yl)-N-(3,4,5-trimethoxyphenyl)-1,3,5-triazin-2-amine analogues as tubulin polymerization inhibitors. Bioorg Med Chem Lett. 2017;27:3794-3801 pubmed publisher
    ..Molecular docking studies were also carried out to understand the binding pattern. The studies suggested that 8jhas a good binding affinity of -7.949 towards nocodazole binding site of tubulin while nocodazole has -7.462. ..
  41. Lou Y, Zhou K, Shi J, Pan D. Characterizing the binding interaction of fungicide boscalid with bovine serum albumin (BSA): A spectroscopic study in combination with molecular docking approach. J Photochem Photobiol B. 2017;173:589-597 pubmed publisher
  42. Costas Lago M, Besada P, Rodríguez Enríquez F, Viña D, Vilar S, Uriarte E, et al. Synthesis and structure-activity relationship study of novel 3-heteroarylcoumarins based on pyridazine scaffold as selective MAO-B inhibitors. Eur J Med Chem. 2017;139:1-11 pubmed publisher
    ..Docking simulations provided insights into enzyme inhibitor interactions and allowed us to rationalize the observed structure-activity relationships (SARs). ..
  43. Zanyatkin I, Stroylova Y, Tishina S, Stroylov V, Melnikova A, Haertle T, et al. Inhibition of Prion Propagation by 3,4-Dimethoxycinnamic Acid. Phytother Res. 2017;31:1046-1055 pubmed publisher
    ..We suggest that DMCA is a perspective dietary compound for prophylaxis of neurodegenerative diseases that needs further research. Copyright © 2017 John Wiley & Sons, Ltd. ..
  44. Partyka A, Kurczab R, Canale V, Satała G, Marciniec K, Pasierb A, et al. The impact of the halogen bonding on D2 and 5-HT1A/5-HT7 receptor activity of azinesulfonamides of 4-[(2-ethyl)piperidinyl-1-yl]phenylpiperazines with antipsychotic and antidepressant properties. Bioorg Med Chem. 2017;25:3638-3648 pubmed publisher
    ..625mg/kg, i.p.). ..
  45. Sasaki T, Mita M, Ikari N, Kuboyama A, Hashimoto S, Kaneko T, et al. Identification of key amino acid residues in the hTGR5-nomilin interaction and construction of its binding model. PLoS ONE. 2017;12:e0179226 pubmed publisher
    ..Our study promotes a better understanding of the structure of TGR5, and it may be useful in developing and screening new TGR5 agonists. ..
  46. Pandey A, Dixit U, Kholodovych V, Comollo T, Pandey V. The ?1'-?2' Motif of the RNase H Domain of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Is Responsible for Conferring Open Conformation to the p66 Subunit by Displacing the Connection Domain from the Polymerase Cleft. Biochemistry. 2017;56:3434-3442 pubmed publisher
    ..The unstable elongated p66 molecule may then readily dimerize with p51 to assume a stable dimeric conformation. ..
  47. Quéméner A, Maillasson M, Arzel L, Sicard B, Vomiandry R, Mortier E, et al. Discovery of a Small-Molecule Inhibitor of Interleukin 15: Pharmacophore-Based Virtual Screening and Hit Optimization. J Med Chem. 2017;60:6249-6272 pubmed publisher
    ..One of them was selected as a hit and optimized by a structure-activity relationship approach, leading to the first small-molecule IL-15 inhibitor with sub-micromolar activity. ..
  48. Yan Y, Wang W, Sun Z, Zhang J, Ji C. Protein-Ligand Empirical Interaction Components for Virtual Screening. J Chem Inf Model. 2017;57:1793-1806 pubmed publisher
    ..The trained PLEIC-SVM model is able to capture important interaction patterns between ligand and protein residues for one specific target, which is helpful in discarding false positives in postdocking filtering. ..
  49. Teske K, Rai G, Nandhikonda P, Sidhu P, Feleke B, Simeonov A, et al. Parallel Chemistry Approach to Identify Novel Nuclear Receptor Ligands Based on the GW0742 Scaffold. ACS Comb Sci. 2017;19:646-656 pubmed publisher
  50. Fernández Sainz J, Pacheco Liñán P, Granadino Roldán J, Bravo I, Garzón A, Rubio Martinez J, et al. Binding of the anticancer drug BI-2536 to human serum albumin. A spectroscopic and theoretical study. J Photochem Photobiol B. 2017;172:77-87 pubmed publisher
    ..Thermodynamic analysis showed that the main protein-drug interactions are of the van der Waals type although the presence of amide and ether groups in BI-2536 could also allow H-bonding with some residues in the subdomain IIA pocket. ..
  51. Bandyopadhyay N, Pradhan A, Das S, Naskar J. Comparative study of an osazone based ligand and its palladium(II) complex with human serum albumin: A spectroscopic, thermodynamic and molecular docking approach. J Photochem Photobiol B. 2017;173:1-11 pubmed publisher
    ..These parameters indicate that the binding processes are spontaneous both for LH2 and 1. Molecular docking analyses reveal that both LH2 and 1 reside in domain-I of HSA. ..
  52. Fan M, Zhang G, Pan J, Gong D. An inhibition mechanism of dihydromyricetin on tyrosinase and the joint effects of vitamins B6, D3 or E. Food Funct. 2017;8:2601-2610 pubmed publisher
    ..This study may provide a scientific foundation for screening effective tyrosinase inhibitors. ..
  53. Fan C, Huang Y. Identification of novel potential scaffold for class I HDACs inhibition: An in-silico protocol based on virtual screening, molecular dynamics, mathematical analysis and machine learning. Biochem Biophys Res Commun. 2017;491:800-806 pubmed publisher
    ..Biological assay results demonstrated that two of them exhibited HDAC-inhibitory activity and are thus considerable for structure modification to further improve their bio-activity. ..
  54. Charron C, Hou J, McFarland M, Dhanvantari S, Kovacs M, Luyt L. Structure-Activity Study of Ghrelin(1-8) Resulting in High Affinity Fluorine-Bearing Ligands for the Ghrelin Receptor. J Med Chem. 2017;60:7256-7266 pubmed publisher
    ..This is not only the highest affinity ghrelin analogue reported but also the shortest ghrelin analogue capable of binding GHS-R1a with better affinity than ghrelin(1-28). ..
  55. Yadav P, Antonyraj C, Basheer Ahamed S, Srinivas S. Understanding Russell's viper venom factor V activator's substrate specificity by surface plasmon resonance and in-silico studies. PLoS ONE. 2017;12:e0181216 pubmed publisher
    ..This study suggests a transition in RVV-V from the native rigid to the distorted flexible structure and paves a way to design a new peptide substrate/inhibitor. ..
  56. Mould D, Alli C, Bremberg U, Cartic S, Jordan A, Geitmann M, et al. Development of (4-Cyanophenyl)glycine Derivatives as Reversible Inhibitors of Lysine Specific Demethylase 1. J Med Chem. 2017;60:7984-7999 pubmed publisher
    ..67 ?M in a surrogate cellular biomarker assay. Moreover, this derivative does not display the same level of hERG liability as observed with 1 and represents a promising lead for further development...
  57. Teder T, Lõhelaid H, Samel N. Structural and functional insights into the reaction specificity of catalase-related hydroperoxide lyase: A shift from lyase activity to allene oxide synthase by site-directed mutagenesis. PLoS ONE. 2017;12:e0185291 pubmed publisher
    ..We propose that the corresponding residues in cHPL, Phe150 and Ser177, are involved in a proper coordination of the epoxy allylic radical intermediate necessary for aldehyde formation in the hydroperoxide lyase reaction. ..
  58. Yoshioka H, Yamada A, Nishiyama Y, Kagechika H, Hashimoto Y, Fujii S. Development of nonsteroidal glucocorticoid receptor modulators based on N-benzyl-N-(4-phenoxyphenyl)benzenesulfonamide scaffold. Bioorg Med Chem. 2017;25:3461-3470 pubmed publisher
    ..These findings open up new possibilities for developing novel nonsteroidal GR modulators with distinctive activity profiles. ..
  59. Glyde R, Ye F, Darbari V, Zhang N, Buck M, Zhang X. Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation. Mol Cell. 2017;67:106-116.e4 pubmed publisher
    ..We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. ..
  60. Ross M, Fidai I, Cowan J. Analysis of Structure-Activity Relationships Based on the Hepatitis?C Virus SLIIb Internal Ribosomal Entry Sequence RNA-Targeting GGHYRFK?Cu Complex. Chembiochem. 2017;18:1743-1754 pubmed publisher
    ..Together, the data yielded insights into structure-function relationships that will guide future optimization efforts. ..
  61. Kundu P, Chattopadhyay N. Interaction of a bioactive pyrazole derivative with calf thymus DNA: Deciphering the mode of binding by multi-spectroscopic and molecular docking investigations. J Photochem Photobiol B. 2017;173:485-492 pubmed publisher
    ..In-silico molecular docking simulation corroborates the experimental findings and depicts that DSDP favorably binds to the minor groove region ..
  62. Le Cann F, Delehouze C, Leverrier Penna S, Filliol A, Comte A, Delalande O, et al. Sibiriline, a new small chemical inhibitor of receptor-interacting protein kinase 1, prevents immune-dependent hepatitis. FEBS J. 2017;284:3050-3068 pubmed publisher
    ..Finally, Sib protects mice from concanavalin A-induced hepatitis. These results reveal the small-molecule Sib as a new RIPK1 inhibitor potentially of interest for the treatment of immune-dependent hepatitis...
  63. Zheng Z, Zhao Z, Li S, Lu X, Jiang M, Lin J, et al. Altenusin, a Nonsteroidal Microbial Metabolite, Attenuates Nonalcoholic Fatty Liver Disease by Activating the Farnesoid X Receptor. Mol Pharmacol. 2017;92:425-436 pubmed publisher
    ..In summary, we have uncovered a new class of nonsteroidal FXR agonist that shows promise in treating NAFLD and the associated metabolic syndrome. ..
  64. Chrysanthopoulos P, Mujumdar P, Woods L, Dolezal O, Ren B, Peat T, et al. Identification of a New Zinc Binding Chemotype by Fragment Screening. J Med Chem. 2017;60:7333-7349 pubmed publisher
  65. Spiliotopoulos D, Wamhoff E, Lolli G, Rademacher C, Caflisch A. Discovery of BAZ2A bromodomain ligands. Eur J Med Chem. 2017;139:564-572 pubmed publisher
    ..The binding modes of compounds 1 and 3 are compatible with ligand growing for optimization of affinity for BAZ2A and selectivity against the close homologue BAZ2B. ..
  66. Nittinger E, Inhester T, Bietz S, Meyder A, Schomburg K, Lange G, et al. Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces. J Med Chem. 2017;60:4245-4257 pubmed publisher
    ..On the basis of these results, we derived interaction geometries to improve current computational models. It is expected that these observations will be useful in designing new chemical structures for biological applications. ..
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