Molecular docking and 4D-QSAR model of methanone derivatives by electron conformational-genetic algorithm method

Tüzün, Burak; Sarıpınar, Emin

doi:10.1007/s13738-019-01835-8

Cited by 40 publications

(15 citation statements)

References 35 publications

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“…It should be noted that the most important factor affecting the biological activities of molecules is the interactions between molecules and proteins in enzymes. [ 41,42 ] As these interactions increase, the biological activity of the molecule increases. These interactions include hydrogen bonds, polar and hydrophobic interactions, π–π interactions, and halogen interactions, [ 43–49 ] and they are presented in Figures 2–4.…”

Section: Resultsmentioning

confidence: 99%

“…It should be noted that as the interactions between molecules and proteins in enzymes increase, the molecule attaches more to the enzyme, which increases the biological activity of the molecule. [ 32,41,42,50 ] Another parameter obtained from molecular docking calculations is Glide ligand efficiency, which is the numerical value of the effectiveness of new cyanopyridine derivatives containing phenylurea against enzymes. Another parameter is Glide H‐bond, which is the numerical value of the number of hydrogen bonds that occur in interactions between molecules and proteins in enzymes.…”

Section: Resultsmentioning

confidence: 99%

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Synthesis, molecular docking, and biological activities of new cyanopyridine derivatives containing phenylurea

Gezegen

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Dinçer

et al. 2020

Archiv der Pharmazie

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A new class of cyanopyridine derivatives (10a–e and 11a–e) containing the phenylurea unit was synthesized and tested against some metabolic enzymes including acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and α‐glycosidase (α‐Gly). The new cyanopyridine derivatives showed Ki values in the range of 40.73 ± 6.54 to 87.05 ± 16.98 µM against AChE, 29.17 ± 4.88 to 124.03 ± 22.43 µM against BChE, and 3.66 ± 0.93 to 26.33 ± 5.05 µM against α‐Gly. These inhibition effects were compared with standard enzyme inhibitors like tacrine (for AChE and BChE) and acarbose (for α‐Gly). Also, these cyanopyridine derivatives with the best inhibition score were docked into the active site of the indicated metabolic enzymes. Finally, molecular docking calculations were made to compare the biological activities of the compounds against AChE (−8.81 kcal/mol for molecule 11d), BChE (−3.52 kcal/mol for molecule 11d), and α‐Gly (−2.98 kcal/mol for molecule 11a). After molecular docking calculations, the ADME/T analysis was performed to examine the future drug use properties of the new cyanopyridine derivatives containing phenylurea.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Synthesis, molecular docking, and biological activities of new cyanopyridine derivatives containing phenylurea

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et al. 2020

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“…Being more radical as a result of all these situations affects the stability of the radical and causes the formation of more stable radicals [25]. Among the theoretical calculations made, the most reliable and accurate method used to compare the activities of molecules is molecular docking [48][49][50]. This method compares the activities of molecules with their interactions with proteins.…”

Section: Resultsmentioning

confidence: 99%

Examination of anti-oxidant properties and molecular docking parameters of some compounds in human body

Tüzün¹

2020

Turkish Computational and Theoretical Chemistry

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There are many hormones and molecules in the human body. Many of these take place in different jobs and tasks. Some of these hormones are serotonin (A1), testosterone (A2), dopamine (A3), adrenaline (A4), methylcytosine (A5) and creatine (A6). The anti-oxidant properties of these molecules in both gas and water phases of the HF/6-31++G(d,p) basis set were calculated with the Gaussian package program. After this process, molecular docking calculations were made to compare the activities of molecules against proteins with anti-oxidant properties whose name are human peroxiredoxin-5 (HP5) and bovine xanthine oxidase (BXO), were compared.

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“…Obviously, the selection of pertinent parameters (optimization) is a challenging issue of the structure-activity modeling process. Finally, the performance (robustness and predictive power) of the generated EC-GA models should be verified internally/externally using the training/test subset populations as recommended by the Organization for Economic Co-operation and Development (OECD) principles and Concordance Correlation Coefficient (CCC) criteria [ 93 , 94 , 95 ].…”

Section: 4d-qsar Dialects: Towards ‘Magic Bullet’mentioning

confidence: 99%

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

Bąk

2021

IJMS

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A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.

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Molecular docking and 4D-QSAR model of methanone derivatives by electron conformational-genetic algorithm method

Cited by 40 publications

References 35 publications

Synthesis, molecular docking, and biological activities of new cyanopyridine derivatives containing phenylurea

Synthesis, molecular docking, and biological activities of new cyanopyridine derivatives containing phenylurea

Examination of anti-oxidant properties and molecular docking parameters of some compounds in human body

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

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