Article
Biochemistry & Molecular Biology
Sevil Kalin, Ferah Comert Onder
Summary: This study aimed to identify potential inhibitor candidates against RSK1 through ligand pharmacophore mapping and structure-based virtual screening. Several compounds with potential inhibitory activity were found through molecular docking and molecular dynamics simulations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Banoth Karan Kumar, Faheem, Kondapalli Venkata Gowri Chandra Sekhar, Rupal Ojha, Vijay Kumar Prajapati, Aravinda Pai, Sankaranarayanan Murugesan
Summary: This study identified potential ligands that may act as inhibitors of SARS-CoV-2 M-pro through computational screening. The molecules SN00293542 and SN00382835 showed the highest docking scores and demonstrated stability through molecular dynamics studies.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Farideh Sadeghkhani, Zahra Hajihassan, Sajjad Gharaghani
Summary: This study identified two potential TLR8 agonists with favorable pharmacological features, which could be used for future experimental studies. The compounds showed advantages over Motolimod, and their flexibility and energy levels were compared to provide insights for further research.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biology
Hossam Nada, Kyeong Lee, Lizaveta Gotina, Ae Nim Pae, Ahmed Elkamhawy
Summary: Dysregulation of DDR1 has been linked to various cancers and diseases, prompting the development of specific DDR1 inhibitors. VU6015929, a novel DDR1 kinase inhibitor, showed promising properties and was identified as a potential candidate through computational modeling and virtual screening.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Muthu Kumar Thirunavukkarasu, Ramanathan Karuppasamy
Summary: The study screened a candidate with high binding affinity in MEK protein from a library of 11,808 compounds, and suggested that Nebivolol may be an excellent candidate for MEK inhibition in NSCLC patients in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Arooma Maryam, Abdul Rauf Siddiqi, Sundeep Chaitanya Vedithi, Abdulilah Ece, Rana Rehan Khalid
Summary: Through e-pharmacophore based screening and molecular dynamics simulation, we have discovered compounds that selectively inhibit PDE5A compared to PDE6A. These compounds stably bind to PDE5A and show weaker binding to PDE6A. After optimization and therapeutic interventions, this compound may become a promising PDE5A selective inhibitor.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biology
Kumarappan Chidambaram
Summary: In this study, researchers used E-pharmacophore modeling to screen the eMolecules database and identified potential drug candidates against Alzheimer's disease with enhanced physicochemical and pharmacokinetic properties. Molecular dynamics simulation and MMPBSA analysis revealed the stability and binding free energy of these compounds. Furthermore, Qikprop analysis indicated that the selected compounds have good drug-likeness and pharmacokinetic properties.
Article
Biochemistry & Molecular Biology
Chandu Ala, Renuka Parshuram Joshi, Pragya Gupta, Sivaprakash Ramalingam, Murugesan Sankaranarayanan
Summary: In this study, a structure-based virtual screening was performed to identify four potential compounds that can inhibit DNMT1. Additional in vitro and in vivo studies are needed to confirm their clinical effectiveness.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Vibhu Jha, Salvatore Galati, Valerio Volpi, Lidia Ciccone, Filippo Minutolo, Flavio Rizzolio, Carlotta Granchi, Giulio Poli, Tiziano Tuccinardi
Summary: ACLY is an important enzyme involved in fatty acid synthesis and could be a promising target for anticancer drug design. Through virtual screening, compound VS1 with potential inhibitory activity was identified, showing a 2.5 times higher potency than the reference inhibitor 2-hydroxycitrate.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Simla Olgac, Abdurrahman Olgac, Idil Yenicesu, Yesim Ozkan
Summary: Cardiovascular diseases are a leading cause of death globally, highlighting the need for safe and effective antithrombotic drugs. This study identified two promising compounds as potential antiplatelet agents, which could serve as starting points for the design of new, potent, and selective GPVI receptor antagonists.
BIOORGANIC CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Harutyun Sahakyan
Summary: Virtual screening based on molecular docking is a useful method for computer-aided drug design, reducing time and cost of drug development. However, the low accuracy of scoring functions in docking methods is a limitation, necessitating more rigorous calculation methods.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2021)
Article
Biochemistry & Molecular Biology
Shweta Mishra, Mithun Singh Rajput, Devashish Rathore, Rashmi Dahima
Summary: Multi-agent therapies are important in treating diseases and have developed 3D pharmacophore models for FFAR-1, FFAR-4, and PPAR-G. These models suggest key structural elements necessary for binding affinity and have identified potential inhibitors for further investigation in anti-diabetic activities through molecular docking and MM-GBSA calculations.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Engineering, Biomedical
Yongzhao Xiong, Xinchang Gao, Daodong Pan, Ting Zhang, Lulu Qi, Ning Wang, Yufen Zhao, Yali Dang
Summary: A novel model combining common feature pharmacophore and molecular docking was established for rapid screening of umami peptides, successfully identifying twenty previously unreported dipeptides with umami taste. Experimental validation confirmed their umami activity, demonstrating the practicality of this screening strategy.
Article
Biochemistry & Molecular Biology
Andres Felipe Vasquez, Luis Alberto Gomez, Andres Gonzalez Barrios, Diego M. Riano-Pachon
Summary: Antifolates like methotrexate block nucleic acid synthesis and cell proliferation, but their classical structure is ineffective against melanoma. A study combining virtual screening and cell-based assays identified promising non-classical hDHFR inhibitors, with compounds C1 and C2 exhibiting activity against melanoma cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
David Bacelar Costa Junior, Janay Stefany Carneiro Araujo, Larissa de Mattos Oliveira, Flavio Simas Moreira Neri, Paulo Otavio Lourenco Moreira, Alex Gutterres Taranto, Amanda Luisa Fonseca, Fernando de Pilla Varotti, Franco Henrique Andrade Leite
Summary: Malaria, caused by Plasmodium spp., remains a significant public health issue with drug resistance limiting chemotherapy. By exploring essential therapeutic targets of the parasite, a potential new antimalarial molecule with activity comparable to artemether was identified through virtual screening. This molecule, previously used in traditional Chinese medicine, may offer a repurposing opportunity to expedite drug development. Molecular dynamics studies confirmed the stability of molecular interactions, paving the way for further research on new derivatives for in vitro and in vivo evaluation.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Psychology, Clinical
Glenn D. Walters, Dorothy L. Espelage
Summary: This study tested a four-path mediation model and found that bullying victimization can lead to an increase in hostility, expansion of delinquent peer associations, and growth in pro-bullying attitudes, all of which contribute to future bullying perpetration.
PSYCHOLOGY OF VIOLENCE
(2023)
Article
Criminology & Penology
Glenn D. Walters
Summary: The current study supports the idea that firesetting may serve as a developmental antecedent to future offending. Cognitive impulsivity, but not cognitive insensitivity, was found to mediate the relationship between firesetting and offense variety. These findings are in line with theory and suggest that firesetting may belong on the antisocial spectrum.
PSYCHOLOGY CRIME & LAW
(2023)
Article
Criminology & Penology
Glenn D. Walters, Jonathan Kremser, Lindsey Runell
Summary: This study aimed to investigate whether sex moderates the indirect effect of depression on delinquency through cognitive impulsivity, and if so, whether this effect is stronger in girls than in boys. The results revealed that the pathway from depression to cognitive impulsivity to delinquency was moderated by sex, whereas the direct effect of depression on delinquency was not. Further analysis indicated that this pathway was significant only in girls. This study demonstrates the importance of integrating concepts from different theories using mediation and moderation, including the cognitive theory of depression and gendered pathways perspective from feminist criminology.
Article
Criminology & Penology
Glenn D. Walters, Lindsey Runell, Jonathan Kremser
Summary: This study used path analysis to examine the mediating role of cognitive insensitivity in the relationship between bullying perpetration and delinquency. The results showed that cognitive insensitivity successfully mediated this relationship, while peer delinquency and the peer x insensitivity interaction did not. The findings suggest that involvement in bullying behavior may lead to an increase in antisocial thinking, which in turn stimulates future engagement in delinquent behavior.
CRIME & DELINQUENCY
(2023)
Article
Criminology & Penology
Glenn D. Walters, Lindsey Runell, Jonathan Kremser
Summary: The goal of this study was to examine the relationship between cognitive insensitivity and cognitive impulsivity in antisocial thought process over two years, with a focus on delinquent youth. The study found that the correlation between cognitive insensitivity and impulsivity significantly increased from the beginning to the end of the two-year period. This increase was only evident in youth with above average delinquency scores, suggesting that the intertwining of these dimensions occurs specifically in delinquent youth over time.
PSYCHOLOGY CRIME & LAW
(2023)
Article
Chemistry, Physical
Zafer Bulut, Nurgul Abul, Ayse Halic Poslu, Ilhami Gulcin, Abdulilah Ece, Erol Ercag, Omer Koz, Gamze Koz
Summary: A series of novel uracil-appended benzylic amines were synthesized through reductive amination with moderate to good yields (30-84% yields). The compounds were characterized using FT-IR, H-1 NMR, C-13 NMR spectroscopy and elemental analysis. The inhibition abilities of the compounds were evaluated against acetylcholinesterase (AChE) and human carbonic anhydrase I and II (hCA I and II) isoenzymes.
JOURNAL OF MOLECULAR STRUCTURE
(2023)
Article
Mechanics
Sudip Chowdhury, Arnab Banerjee, Sondipon Adhikari
Summary: This article introduces the concepts of additional inerter-based viscoelastic mass dampers (AIVMD) and additional viscoelastic mass damper inerters (AVMDI). H-2 and H-infinity optimization schemes are used to derive the optimal closed-form solutions for these dampers analytically. A parametric study is conducted to investigate the sensitivity of the optimal design parameters with other system parameters. The results suggest that higher damper mass ratio, inerter mass ratio, and stiffness ratio are recommended for designing optimal novel dampers with robust vibration reduction capacities.
MECHANICS BASED DESIGN OF STRUCTURES AND MACHINES
(2023)
Article
Criminology & Penology
Glenn D. Walters, Lindsey Runell, Jonathan Kremser
Summary: Prior research has found that social variables are associated with delinquent and criminal outcomes through antisocial cognition. This study investigates the connection between a person's perception of parental support/monitoring and peer delinquency, and whether this connection is influenced by cognitive insensitivity. The findings suggest that cognitive insensitivity mediates the relationship between parental monitoring and peer delinquency, supporting the idea that aspects of antisocial thinking play a role in the relationship between social variables and delinquent outcomes.
CRIMINAL JUSTICE STUDIES
(2023)
Article
Criminology & Penology
Glenn. D. D. Walters
Summary: The purpose of this study was to investigate the relationship between moral agency and peer delinquency in adolescents. The study found that a change in moral agency could predict a change in peer delinquency, and vice versa. The findings also revealed that the peer selection effect was stronger than the peer influence effect in early adolescence.
JOURNAL OF DEVELOPMENTAL AND LIFE-COURSE CRIMINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Cagla Efeoglu, Sena Taskin, Ozge Selcuk, Begum Celik, Ece Tumkaya, Abdulilah Ece, Hayati Sari, Zeynel Seferoglu, Furkan Ayaz, Yahya Nural
Summary: This study synthesized new naphthoquinone thiazole hybrids and tested their anti-inflammatory immunomodulatory activities. The compounds showed promising potential in inhibiting the production of pro-inflammatory cytokines and may serve as anti-inflammatory drugs. In silico screening and molecular dynamics simulation suggested that the potential target of these compounds could be PI3K.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Hulya Celik Onar, Eda Mehtap Ozden, Hava Dudu Taslak, Ilhami Gulcin, Abdulilah Ece, Erol Ercag
Summary: In this study, a series of coumarin-chalcone derivatives were synthesized and characterized. The compounds showed promising antioxidant potency and inhibition against human carbonic anhydrases, acetylcholinesterase, and alpha-glycosidase enzymes. Molecular docking and dynamics simulations provided insights into the activity against acetylcholinesterase. The synthesized compounds were also characterized electrochemically.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Biochemistry & Molecular Biology
Ozcan Gulec, Cuneyt Turkes, Mustafa Arslan, Yeliz Demir, Busra Dincer, Abdulilah Ece, Sukru Beydemir
Summary: In this study, a library of beta-lactam-substituted benzenesulfonamides was synthesized and characterized. These compounds showed potent inhibition of carbonic anhydrases and acetylcholinesterase. Some compounds also exhibited anticancer activity, surpassing the efficacy of commonly used drugs. Molecular docking and dynamics simulations revealed the possible mechanisms of action. Overall, these compounds have the potential to be developed into effective and safe inhibitors for various diseases.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Arooma Maryam, Abdul Rauf Siddiqi, Sundeep Chaitanya Vedithi, Abdulilah Ece, Rana Rehan Khalid
Summary: Through e-pharmacophore based screening and molecular dynamics simulation, we have discovered compounds that selectively inhibit PDE5A compared to PDE6A. These compounds stably bind to PDE5A and show weaker binding to PDE6A. After optimization and therapeutic interventions, this compound may become a promising PDE5A selective inhibitor.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Medicinal
Omur Guven, Belgin Sever, Faika Basoglu-Unal, Abdulilah Ece, Hiroshi Tateishi, Ryoko Koga, Mohamed O. Radwan, Nefise Demir, Mustafa Can, Mutlu Dilsiz Aytemir, Jun-ichiro Inoue, Masami Otsuka, Mikako Fujita, Halilibrahim Ciftci, Hasan Demirci
Summary: TRAF6 is a protein with important biological functions, and its structural studies play a crucial role in the development of new therapeutic drugs. By analyzing the structure and mechanism of TRAF6, we have identified new compounds that interact with its key regions and demonstrated their favorable pharmacokinetic properties, making them potential TRAF6 inhibitors in the future.
Article
Chemistry, Medicinal
Cuneyt Caglayan, Yusuf Temel, Cuneyt Turkes, Adnan Ayna, Abdulilah Ece, Sukru Beydemir
Summary: This study investigated the inhibition mechanisms of several enzymes by methotrexate (MTX), as well as the potential protective effects of the antioxidant morin. The results suggest that morin may mitigate the adverse effects of MTX by increasing the activity of important regulatory enzymes. Furthermore, molecular dynamic simulations provided insights into the stability and key amino acid residues involved in the enzyme-binding pockets.
ARCHIV DER PHARMAZIE
(2023)