Exploring the anti-metastatic potential of sunitinib and novel analogs in colorectal cancer: insights into HIF-1α mediated metastasis by Fatemeh B. Rassouli, Maryam M. Matin, Maryam M. Matin, Farzin Hadizadeh, Farzin Hadizadeh, Masoud Nejabat, Hossein Allahverdizadeh, Hamidreza Jamali, Shahin Gharedaghi, Halimeh Hassanzadeh

“…For in vitro studies, analogs of sunitinib were synthesized, and cells were assessed for viability, migration, invasion, MMPs activity and gene expression in hypoxic condition.Results and DiscussionComputational analyses highlighted the importance of HIF-1α as a crucial mediator of metastasis in CRC. Molecular docking and dynamics simulations demonstrated favorable and stable interaction of sunitinib and three novel analogs with HIF-1α PAS-B domain. …”
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Anticonvulsant Effects of Synthetic <i>N</i>-(3-Methoxybenzyl)oleamide and <i>N</i>-(3-Methoxybenzyl)linoleamide Macamides: An In Silico and In Vivo Study by Karin Jannet Vera-López, Jorge Alberto Aguilar-Pineda, Rodrigo Martín Moscoso-Palacios, Gonzalo Davila-Del-Carpio, José Luis Manrique-Murillo, Badhin Gómez, Minerva González-Melchor, Rita Nieto-Montesinos

“…MD simulations, molecular docking, and MM/PBSA calculations were used for these purposes. …”
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Discovery of mutated oncodriver genes associated with glioblastoma originated from stem cells of subventricular zone through whole exome sequence profile analysis, and drug repurpo... by Arnob Sarker, Burhan Uddin, Reaz Ahmmed, Sabkat Mahmud, Alvira Ajadee, Md. Al Amin Pappu, Md. Abdul Aziz, Md. Nurul Haque Mollah

“…Finally, overexpressed oncodriver genes guided top-ranked six drug agents (Irinotecan, Imatinib, etoposide, pazopanib, trametinib and cabozanitinib) were recommended against GBM through molecular docking study. Most of our findings received support by the literature review also. …”
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Cortisol regulates neonatal lung development via Smoothened by Shanshan Lu, Yifei Chen, Jiawen Song, Liangliang Ren, Jun Du, Donglai Shen, Jiayin Peng, Yao Yin, Xia Li, Yuqing Wang, Yan Gao, Siman Han, Yichang Jia, Yun Zhao, Yizheng Wang

“…Methods In this study, the simulation of the molecular docking by Autodock, in vitro binding experiments, and Sonic Hedgehog (SHH) pathway examination in cells were performed to study the directly binding of cortisol to Smoothened (SMO). …”
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Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen by Mark Hutchinson, Jeffrey A. Ruffolo, Nantaporn Haskins, Michael Iannotti, Giuliana Vozza, Tony Pham, Nurjahan Mehzabeen, Harini Shandilya, Keith Rickert, Rebecca Croasdale-Wood, Melissa Damschroder, Ying Fu, Andrew Dippel, Jeffrey J. Gray, Gilad Kaplan

“…High-quality structural information remains critical for the antibody optimization process, but antibody-antigen complex structures are often unavailable and in silico antibody docking methods are still unreliable. In this study, DeepAb, a deep learning model for predicting antibody Fv structure directly from sequence, was used in conjunction with single-point experimental deep mutational scanning (DMS) enrichment data to design 200 potentially optimized variants of an anti-hen egg lysozyme (HEL) antibody. …”
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Synthesis and Evaluation of N-[1-(((3,4-Diphenylthiazol-2(3H)-ylidene)amino)methyl)cyclopentyl]acetamide Derivatives for the Treatment of Diseases Belonging to MAOs by Gülhan Turan-Zitouni, Aouatef Tabbi, Weiam Hussein, Abdullah Burak Karaduman, Begüm Nurpelin Sağlık, Yusuf Özkay

“…Also, enzyme kinetic and docking studies of compound 4b were performed against MAO-B. …”
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A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation. by Nan Wu, Zhi-Chao Xu, Kai-Dong Du, Shen Huang, Naohiro Kobayashi, Yutaka Kuroda, Yan-Hong Bai

“…To address this question, we built a structural model of tGLuc by removing the C-terminal repeat from the resolved structure of intact GLuc, and verified that the cavity-forming component in GLuc remains stable and provides an open-mouth cavity in tGLuc during 500 ns MD simulations in water. Docking simulation and a followed umbrella sampling analysis further revealed that the cavity on tGLuc has a high affinity for CTZ, with a binding energy of up to -114 kJ/mol. …”
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Pharmacological Mechanism of Zuojin Pill for Gastroesophageal Reflux Disease: A Network Pharmacology Study by Mi Lv, Jinke Huang, Jiayan Hu, Wenxi Yu, Ping Liu, Kunli Zhang, Fengyun Wang

“…Therefore, we employed network pharmacology (NP), molecular docking (MD), and molecular dynamics simulation (MDS) to investigate the pharmacological mechanisms of ZJP against GERD. …”
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Exploring the impact of deleterious missense nonsynonymous single nucleotide polymorphisms in the DRD4 gene using computational approaches by Dipto Kumer Sarker, Pallobi Ray, Fayad Bin Abdus Salam, Shaikh Jamal Uddin

“…To comprehensively understand their impact, we docked agonist dopamine and antagonist nemonapride at the binding site of the receptor, followed by 200 ns molecular dynamics simulations. …”
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Deciphering the multifaceted mechanism of Shuang Huang Lian in treating upper respiratory tract infections: A metabolomics-based network pharmacology approach by Gang Xu, Akshay Suresh Patil, Ruhan Wei, Dan Liu, Aimin Zhou, Yan Xu

“…Finally, pivotal protein targets and key active SHL components were validated through molecular docking simulations and in vitro cell culture experiments. …”
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Single-cell transcriptomics analysis reveals dynamic changes and prognostic signature in tumor microenvironment of PDAC by Yongsheng Li, Zhilong Ding, Tingxin Cheng, Yihuai Hu, Fei Zhong, Shiying Ren, Shiyan Wang

“…Furthermore, our analysis revealed significant interactions between cells at different stages of PDAC and identified three promising therapeutic agents (XR-11576, Ixabepilone, and AMONAFIDE) based on correlated genes. Finally, molecular docking studies validated their potential by confirming stable binding with key protein targets. …”
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Elucidation of α-glucosidase inhibitory activity and UHPLC-ESI-QTOF-MS based metabolic profiling of endophytic fungi Alternaria alternata BRN05 isolated from seeds of Swietenia mac... by Piyush Kumar, Sai Anand Kannakazhi Kantari, Ranendra Pratap Biswal, Prasanth Ghanta, Malleswara Dharanikota

“…A total of nineteen metabolites from EFS and twenty from EQS were tentatively identified based on MS/MS fragmentation. Molecular docking analysis revealed that twelve among these exhibited greater binding energies than that of acarbose (-6.6 kcal/mol). …”
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Angesinenolide B, A Phthalide Dimeric Peroxide, Exerts Anti-Inflammatory Properties by Suppressing MAPK/STATs Signaling Pathways and ROS Production by Zhang L, Liu Y, Wang H, Guo S, Lv J

“…Moreover, the affinities between ASB and the target proteins were verified by molecular docking analysis. In vivo, ROS generation was explored using fluorescent probe DCFH-DA, and the TNF-α and IL-6 mRNA expressions were also evaluated in CuSO4-induced zebrafish inflammation model.Results: ASB treatment was found to suppress the levels of NO, TNF-α, IL-6 and ROS, restrain the expressions of iNOS and COX-2 proteins and mRNA, as well as down-regulate MAPK and STATs signaling pathways in LPS-stimulated RAW264.7 cells. …”
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Enhancement of Doxorubicin Efficacy by Bacopaside II in Triple-Negative Breast Cancer Cells by Sima Kianpour Rad, Kenny K. L. Yeo, Runhao Li, Fangmeinuo Wu, Saifei Liu, Saeed Nourmohammadi, William M. Murphy, Yoko Tomita, Timothy J. Price, Wendy V. Ingman, Amanda R. Townsend, Eric Smith

“…ATP-binding cassette (ABC) transporter expression (<i>ABCB1</i>, <i>ABCC1</i>, <i>ABCC3</i>, and <i>ABCG2</i>) was analyzed for correlations with drug sensitivity. In silico docking assessed the binding affinity of bacopaside II to ABC transporters. …”
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Kaempferol protects against high-salt-induced hypertension and vascular endothelial injury by inhibiting ferroptosis through the ATF4/ACSL4 pathway by Qiuer Liang, Minghao Chen, Guangtian Chen, Pengli Xu, Lai Kwan Lam, Pengcheng Xie, Ting Xie, Wanqing Tu, Tianhao Liu, Xiaopeng Peng, Haoyao Yuan, Liguo Chen, Ya Xiao

“…Surface plasmon resonance and molecular docking analyses revealed that Kae directly binds to ATF4, while proteome microarray and co-immunoprecipitation assays demonstrated that ATF4 interacts with ACSL4 in HAECs. …”
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Effect of triple-frequency sono-germination and soaking treatments on techno-functional characteristics of barley by Tabussam Tufail, Huma Bader Ul Ain, Jawad Ashraf, Muhammad Safiullah Virk, Zahoor Ahmed, Mokhtar Dabbour, Tawfiq Alsulami, Suleiman Althawab, Bin Xu

“…Strong intermolecular interactions were observed in both ZQ2000 and XMLY22 samples subjected to TFUT, GE, TFUT + GE, and TS, as validated by FTIR and molecular docking analyses. The structural configuration of two barley types, ZQ2000 and XMLY22, was determined using Fourier transform infrared (FTIR) spectroscopy, which indicated an increase in α-helix and β-sheet conformation and a decrease in random coil conformation in samples treated with TFUT + GE. …”
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Celastrol boosts fluconazole efficacy against vaginal candidiasis: in vitro and in vivo evidence by Fatma Al-zahraa A. Yehia, Hisham A Abbas, Tarek M. Ibrahim, Basem Mansour, Zuhier A. Awan, Mohammed W. Al-Rabia, Wesam H. Abdulaal, Mustafa Adnan Zeyadi, Solomon Z. Okbazghi, Tarek S. Ibrahim, Wael A. H. Hegazy, Salwa E. Gomaa

“…Upon celastrol treatment, a significant decline in ABC transporters transcript levels were detected. Moreover, molecular docking demonstrated that celastrol is a potential ABC efflux transporters blocker that successfully fits into target binding pockets. …”
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Methyl 3-Bromo-4,5-dihydroxybenzoate Attenuates Inflammatory Bowel Disease by Regulating TLR/NF-κB Pathways by Jing Huang, Lei Li, Liyan Xu, Lixin Feng, Yuxin Wang, Attila Gabor SIK, Meng Jin, Rongchun Wang, Kechun Liu, Xiaobin Li

“…Network pharmacology analysis, molecular docking, transcriptomics sequencing and RT-PCR were conducted to investigate the potential mechanism. …”
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Discovery of phloridzin as a new antagonist for Di(2-ethylhexyl) phthalate-induced male reproductive toxicity based on the adverse outcome pathway network and drug-target gene set... by Huan Gao, Xue Zhang, Ziqi Liu, Xiaoge Yang, Yajie Li, Mengxing Cui, Han Wang, Xiaoyu Chen, Weiying Zhang, Zhihan Liu, Yongjiang Yu, Liping Chen, Daochuan Li, Yongmei Xiao, Wen Chen, Qing Wang

“…Further experimental results demonstrated that phloridzin provided the most effective protection against MEHP-induced apoptosis in TM3 cells probably through the p53 and MAPK signaling pathways. Molecular docking and molecular dynamics simulations suggest that STAT3 and RUNX1 may be important targets for phloridzin to antagonize MEHP-induced MRT. …”
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Baicalein induces apoptosis by inhibiting the glutamine-mTOR metabolic pathway in lung cancer by Jingyang Li, Di Zhang, Shaohui Wang, Peng Yu, Jiayi Sun, Yi Zhang, Xianli Meng, Juan Li, Li Xiang

“…The binding of baicalein to glutamine transporters and glutaminase was examined using molecular docking. The overexpression of glutamine transporters was validated using qRT–PCR and western blot analyses. …”
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