The effect of silver nitrate on the alkaline phosphatase activity, TNF and IL-10 gene expression; Experimental and computational studies by Nader jadid, Ali Asghar Moshtaghie, Hashem Nayeri, Masoud Foladgar, Maryam Ostadsharif

“…However, a statistically significant alteration was detected in both groups 45 days post-injection (P < 0.005). Molecular docking analysis further revealed that the optimal binding pose for ALP, based on the docking score, was −5.28 kcal/mol, with a re-ranking score of −7.43 kcal/mol. …”
Get full text

Overcoming beta-lactam resistance in Pseudomonas aeruginosa by targeting metallo-beta-lactamase VIM-1: a one-microsecond molecular dynamics simulation study by Mohammed Salleh M. Ardawi, Samar A. Badreddine, Muhammad Yasir, Muhammad Yasir, Aiah M. Khateb, Aiah M. Khateb, Safaa A. Turkistani, Ahmed Afandi, Samah O. Noor, Adhari Alselmi, Adhari Alselmi, Vivek Dhar Dwivedi, Vivek Dhar Dwivedi, Esam I. Azhar, Esam I. Azhar

“…The virtual screening process selected four top-performing compounds (CNP0390322, CNP03905695, CNP0079056, and CNP0338283) that exhibited promising docking scores. These compounds were then subjected to re-docking and one-microsecond molecular dynamics (MD) simulations to assess their binding stability and interactions within the MBL-VIM-1 active site. …”
Get full text

Mahogany seeds extract showed potential immunomodulator by in-silico and in vivo testing by Yati Sumiyati, Alessandro Gunady, Perwira Tua, Warni Warni, Heppy Novia, Emilda

“…Docking simulation was done towards 16 bioactive contents using Protein Data Bank, PubChem, Marvinsketch, Chimera, Swissdock and pkCSM. …”
Get full text

Spectroscopic, DFT, anti-bacterial, and in-silico investigations of novel semicarbazone and thiosemicarbazone synthesised from asymmetrical chalcones by Nikita Sharma, Har Lal Singh

“…Based on the docking score and binding affinity calculation, these derivatives were found to have a greater affinity than standard antibiotics against selected the pathogens. …”
Get full text

Exploring the Mechanisms of Zhenbao Pills in the Treatment of Stroke through Network Pharmacology Combined with Mendelian Randomization by Yanhong Liu, Yunqi Hua, Xiaoe Jia

“…Furthermore, molecular docking and Gene Expression Omnibus (GEO) datasets were used for preliminary confirmation. …”
Get full text

Le port romain du quartier de Saint-Lupien à Rezé/Ratiatum (Loire-Atlantique) : origine et évolution by Jimmy Mouchard, David Guitton, Martial Monteil, Xavier Favreau, Nicolas Ménez, Matthieu Yacger

“…These structures, which served as docks along the riverbank of the main river bed, present a mixed framework, consisting of wood and stone, specifically a very elaborate and robust oak frame, including half-timbered facades and significant dry-stone filling. …”
Get full text

Current Perspectives in Detection of Bioactive Compounds From Costus spicatus Through GC–MS and LC-MS/MS: Antioxidant Properties and In Silico Analysis for Industrial Applications... by Dharmar Manimaran, Ararsa Tessema, M. Govindarajulu Yadav, S. Parthasarathi, Vasan Palanisamy

“…In this study, we performed molecular docking and found that four compounds exhibited promising binding affinities with predicted binding sites on alpha-synuclein. …”
Get full text

Multistaged In Silico Discovery of the Best SARS-CoV-2 Main Protease Inhibitors amongst 3009 Clinical and FDA-Approved Compounds by Ibrahim H. Eissa, Abdulrahman M. Saleh, Sara T. Al-Rashood, Abdul-Aziz M. M. El-Attar, Ahmed M. Metwaly

“…Levobupivacaine (2840) showed the most accurate docking and pharmacophore scores and was picked for further MD simulations experiments (RMSD, RMSF, Rg, SASA, and H-H bonding) over 100 ns. …”
Get full text

Inhibitory Effect of (2S)-Pinocembrin From Goniothalamus macrophyllus on the Prostaglandin E2 Production in Macrophage Cell Lines by Hilwan Yuda Teruna, Kamal Rullah, Rudi Hendra, Rahayu Utami, Deri Islami, Siti Munirah Mohd Faudzi, Mohd Fadhlizil Fasihi Mohd Aluwi, Kok Wai Lam

“…The docking simulations revealed that (2S)-PCB reduced PGE2 levels by suppressing mitogen-activated protein kinase (MAPK) activation through inhibiting p38 and extracellular signal-regulated kinases (ERK). …”
Get full text

Exploration of the Potential Mechanisms of Wumei Pill for the Treatment of Ulcerative Colitis by Network Pharmacology by Jinke Huang, Yijun Zheng, Jinxin Ma, Jing Ma, Mengxiong Lu, Xiangxue Ma, Fengyun Wang, Xudong Tang

“…PPI network identified 13 core target genes. The molecular docking results indicated the formation of stable bonds between the active ingredients and core target genes. …”
Get full text

In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants by Saurav Katuwal, Siddha Raj Upadhyaya, Rishab Marahatha, Asmita Shrestha, Bishnu P. Regmi, Karan Khadayat, Saroj Basnet, Ram Chandra Basnyat, Niranjan Parajuli

“…The top 10 best-docked coumarins were further analyzed to understand their binding interactions against the spike proteins of other variants (wild-type, Alpha, Beta, Gamma, and Delta), and these studies also demonstrated decent binding energies. …”
Get full text

Molecular Mechanism of Targeted Inhibition of Pancreatic Lipase and Cholesterol Esterase by Hempseed Peptides by YIN Hao, ZHU Jiangxiong, ZHAO Haiyun, ZHONG Yu, WANG Danfeng, DENG Yun

“…Further analysis using molecular docking simulations showed that hydrogen bonding, salt bridges, and cation-π interactions played crucial roles in peptide-enzyme binding. …”
Get full text

Sculpting multi-epitope vaccine against Monkeypox viral strains using immunoinformatics by Zaira Rehman, Ammad Fahim, Maryam Irtash

“…Based on docking scores and physicochemical profile the vaccine construct V1 with beta defensin adjuvant was selected for further analysis. …”
Get full text

Interaction of toll-like receptors and ACE-2 with different variants of SARS-CoV-2: A computational analysis by Azadeh Zahmatkesh, Elham Salmasi, Reza Gholizadeh

“…Methods: The RNA motifs for TLR7, TLR8 and a CpG motif for TLR9 were analyzed in different variants. Molecular docking and molecular dynamics (MD) simulations were performed to investigate receptor-ligand interactions. …”
Get full text

A Computational Approach towards the Development of Newer Anticancer Agents by Javed I. Sheikh, H. D. Juneja, V. N. Ingle

“…In silico molecular docking analyses of the novel 1-(2', 4'-dihydroxy-5'-chlorophenyl)-3-aryl-propane-1, 3-diones were performed in the active sites of enzyme cytochrome P450 reductase to obtain new anticancer agents computationally. 1-(2', 4'-dihydroxy-5'-chlorophenyl)-3-(4"-methoxy-phenyl)-propane-1, 3-dione (3f) was found to have maximum affinity for the active sites of enzyme.…”
Get full text

SUCCESSFUL TREATMENT OF PERIPROSTHESIS INFECTION BY TIGECYCLINE by S. K. Yarovoy, R. A. Khromov

“…In terms of the ineffectiveness of glycopeptides and carbapenems inflammatory process was docked with the help of new antibacterial agents "Tigecyclin" belonging to the class of glycylcyclines, structurally similar to tetracycline.The article is supplemented with a short analysis of the current data on antimicrobial resistance the most likely causative agents of infectious-inflammatory complications after Falloprosthesis. …”
Get full text

Direct and Indirect Drug Design Approaches for the Development of Novel Tricyclic Antipsychotics: Potential 5-HT2A Antagonist by Mahantesh Namdev Jadhav, Ganesh Rajendra Kokil, Shilpa Sudhakar Harak, Sanjay Baburao Wagh

“…Development of novel hybrid atypical tricyclic antipsychotic pharmacophore was achieved using direct (by measuring docking score of designed molecules on modelled 5- receptor) and indirect (current, clinically available therapeutic agents’ data) drug design approaches.…”
Get full text

New insights into the mechanism of triphenyl phosphate and its metabolite diphenyl phosphate in diabetic kidney disease by Ting Fang, Qiaoyan Liu, Xinxin Huangfu, Hongkai Zhu, Hongwen Sun, Liming Chen

“…This study aims to investigate the potential impact of TPHP and its metabolite diphenyl phosphate (DPHP) on diabetic kidney disease using various methods, including network toxicology, molecular docking, and cell experiments like CCK8 assay and real-time-PCR. …”
Get full text

Hydroxysafflor Yellow A Inhibits LPS-Induced NLRP3 Inflammasome Activation via Binding to Xanthine Oxidase in Mouse RAW264.7 Macrophages by Xiaolong Xu, Yuhong Guo, Jingxia Zhao, Ning Wang, Junying Ding, Qingquan Liu

“…In this study, we predicted the potential interaction between HSYA and xanthine oxidase (XO) via PharmMapper inverse docking and confirmed the binding inhibition via inhibitory test (IC50 = 40.04 μM). …”
Get full text

Phytochemical study and evaluation of the antidiabetic and antihyperglycemic activities of the fruit extracts of Physalis peruviana L. (Solanaceae) by Damien S.T. Tshibangu, Fortune S. Kavugho, Carlos N. Kabengele, Adrien T. Masunda, Gédéon N. Bongo, Giresse N. Kasiama, Domaine T. Mwanangombo, Clément L. Inkoto, Clément M. Mbadiko, Benjamin Z. Gbolo, Désiré M. Musuyu, Dorothée D. Tshilanda, Jean Paul K.N. Ngbolua, Pius T. Mpiana

“…(PP) fruit extracts as well as to determine the structure-activity relationship of some molecules from this plant using molecular docking. Medically, the plant has been used traditionally to treat diabetes and other diseases.The methanolic extract showed the highest yield of 12.01 %, while the lower yield of 2.74 % was observed in the ethyl acetate one. …”
Get full text