In Silico Study of Alkaloids: Neferine and Berbamine Potentially Inhibit the SARS-CoV-2 RNA-Dependent RNA Polymerase by Rishab Marahatha, Asmita Shrestha, Kabita Sharma, Bishnu P. Regmi, Khaga Raj Sharma, Pramod Poudel, Ram Chandra Basnyat, Niranjan Parajuli

“…This study is aimed at analyzing the potential of natural alkaloids, using various computational tools, as drug candidates against SARS-CoV-2. The molecular docking analysis predicted that naturally occurring alkaloids can bind with RNA-dependent RNA-polymerase (RdRP). …”
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Insilico targeting of virus entry facilitator NRP1 to block SARS-CoV2 entry. by Nousheen Bibi, Maleeha Shah, Shahzad Khan, Muhammad Shahzad Chohan, Mohammad Amjad Kamal

“…Following virtual screening, docking studies, and evaluation of binding affinity and ADMET properties, 10 compounds were shortlisted. …”
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Interaction Effects of Tannic Acid and Gluten on Bread-Making and Its Starch Digestion by Seonghyeon Nam, Oguz K. Ozturk, Jongbin Lim

“…The interaction was systematically investigated by analyzing binding affinity, binding mode, and matrix structure of the TA–gluten complex using fluorescence quenching, molecular docking, and confocal laser scanning microscopy. TA strongly interacted with gluten via non-covalent interactions, mainly hydrogen bonds, and formed the major hydrogen bonds with six different glutamines (Q32, Q108, Q313, Q317, Q317, and Q349), which play a critical role in gluten network construction among amino acid residues of gluten. …”
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Identification of Diagnostic Genes and Effective Drugs Associated with Osteoporosis Treatment by Single-Cell RNA-Seq Analysis and Network Pharmacology by Zhanyue Zhang, Tingbao Zhang, Liangshuang Zhou, Jianzhong Guan

“…Key drugs were determined by proteins-proteins interaction and molecular docking. Results. Firstly, 15,577 cells were obtained, and 12 cell subpopulations were identified by clustering, among which 6 cell subpopulations belong to CD45+ BM-MSCs and the other subpopulations were CD45-BM-MSCs. …”
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Cuproptosis genes in predicting the occurrence of allergic rhinitis and pharmacological treatment. by Ting Yi

“…Finally, AR signature genes were used as targets for drug prediction and molecular docking to identify candidate drugs that may affect SAR.…”
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Investigating new drugs from marine seaweed metabolites for cervical cancer therapy by molecular dynamic modeling approach by Sk Injamamul Islam, Sheikh Sunzid Ahmed, Sarower Mahfuj, Gunjan Das, Md. Mohaimenul Islam Tareq, Mazen Almehmadi, Mamdouh Allahyani, Naif Alsiwiehri, Partha Biswas, Md. Nazmul Hasan, Foysal Ahammad

“…The investigations included molecular docking, ADMET test, MD simulation, and MM/GBSA analysis to identify three lead seaweed drug-like compounds: BC008 (-8.9 kcal/mol), RL379 (-8.9 kcal/mol), and BC014 (-8.7 kcal/mol). …”
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Integrative genetics and multiomics analysis reveal mechanisms and therapeutic targets in vitiligo highlighting JAK STAT pathway regulation of CTSS by Zi-yue Dong, Ming-jie He, Yong-kai Yu, Fang Wang, Peng-yuan Zhao, De-long Ran, De-shuang Fu, Qing He, Run-ping Yang, Jiang-an Zhang

“…Our GWAS-meta analysis pinpointed five druggable genes: ERBB3, RHOH, CDK10, MC1R, and NDUFAF3, and underwent drug target exploration and molecular docking. SMR analysis linked CTSS, CTSH, STX8, KIR2DL3, and GRHPR to vitiligo through pQTL and eQTL associations. …”
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Lactoferrin exhibits PEDV antiviral activity by interfering with spike-heparan sulfate proteoglycans binding and activating mucosal immune response by Peng Liu, Jinjiao Zuo, Hui Lu, Bin Zhang, Caihong Wu

“…It was hypothesized that lactoferrin can impede PEDV by blocking its binding to heparan sulfate proteoglycans (HSPG) on the surface of target cells, and molecular docking experiments was conducted to identify the binding sites between lactoferrin and HSPG. …”
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Enhanced targeted treatment of cervical cancer using nanoparticle-based doxycycline delivery system by Sadia Anjum, Ayesha Akhtar, Saleh M. Aldaqal, Maisa S. Abduh, Hammad Ahmad, Riaz Mustafa, Faiza Naseer, Maryam Sadia, Tahir Ahmad

“…Abstract This study investigates a nanoparticle-based doxycycline (DOX) delivery system targeting cervical cancer cells via the CD44 receptor. Molecular docking revealed a strong binding affinity between hyaluronic acid (HA) and CD44 (binding energy: -7.2 kJ/mol). …”
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Evaluation of polyphenol and antioxidant properties of Blumea balsamifera extract as potential therapeutic for breast cancer by Kamila Fairuz Sarah, Annisa Yuslinda, Rosyadah Nuraini, Hermanto Feri Eko, Widyananda Muhammad Hermawan, Dwijayanti Dinia Rizqi, Widodo Nashi

“…The results showed a total phenolic content of 103.85+1.5 mgGAE/g and a total flavonoid content of 225.99+17.68 mgQE/g, with an antioxidant activity of 255.17+13.11µg/mL. 11 compounds were identified, but only four (Aurantio-obtusin, Isorhamnetin, Quercetin, and Hemiphloin) were computationally analysed. Molecular docking and dynamics simulation indicate that these phytochemicals bind to their target, possibly limiting their activity. …”
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(5E,7E)-4,5,6 Trihydroxy-3-(hydroxymethyl)tetrahydro-2H-pyran-2-ylheptadeca-5,7-dienoate from Euclea crispa (L.) Inhibits Ovarian Cancer Cell Growth by Controlling Apoptotic and Me... by Chella Perumal Palanisamy, Bo Cui, Hongxia Zhang, Selvaraj Jayaraman, Ponnulakshmi Rajagopal, Vishnu Priya Veeraraghavan

“…The results of molecular docking analysis showed the binding affinity with CXCR4 and HER2. …”
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Lowering the affinity of single-chain monovalent BBB shuttle scFc-scFv8D3 prolongs its half-life and increases brain concentration by Andrés de la Rosa, Nicole G. Metzendorf, Jonathan Efverström, Ana Godec, Dag Sehlin, Jamie Morrison, Greta Hultqvist

“…Initially, in silico protein-protein docking analysis was performed to identify amino acids (AAs) likely to contribute to 8D3s TfR binding affinity. …”
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Identification of potent TMPRSS4 inhibitors through structural modeling and molecular dynamics simulations by Ismail Hdoufane, Mehdi Oubahmane, Youssef Habibi, Christelle Delaite, Mohammed M. Alanazi, Driss Cherqaoui

“…FDA-approved, clinical/preclinical drugs and natural products were docked to the pocket of TMPRSS4. Moreover, through a systematic analysis, MD simulations and MM-GBSA binding free energy calculations revealed that the best candidates Ergotamine, S55746, NPC478048, Lifirafenib, and NPC77101 are highly stable drug candidates in complex with TMPRSS4, displaying low RMSD and RMSF values with strong binding stability. …”
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Guanidines Conjugated with Cell-Penetrating Peptides: A New Approach for the Development of Antileishmanial Molecules by João Victor Marcelino de Souza, Natalia C. S. Costa, Maria C. O. Arruda Brasil, Luana Ribeiro dos Anjos, Renata Priscila Barros de Menezes, Eduardo Henrique Zampieri, Jhonatan Santos de Lima, Angela Maria Arenas Velasquez, Luciana Scotti, Marcus Tullius Scotti, Marcia A. S. Graminha, Eduardo R. Pérez Gonzalez, Eduardo Maffud Cilli

“…This target is very important for the viability and virulence of the parasite within the host cell. Docking studies confirmed the higher interaction of the conjugate with CPP and suggested that other proteins, such as trypanothione reductase, could be targeted. …”
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Chrysoeriol ameliorates hyperglycemia by regulating the carbohydrate metabolic enzymes in streptozotocin-induced diabetic rats by Baskaran Krishnan, Abirami Ramu Ganesan, Ravindran Balasubramani, Dinh Duc Nguyen, Soon Woong Chang, Shaoyun Wang, Jianbo Xiao, Balamuralikrishnan Balasubramanian

“…In addition, the molecular docking of chrysoeriol against glycolytic enzymes including hexokinase, glucose-6-phosphate dehydrogenase, pyruvate kinase, using Argus software shows chrysoeriol had greatest ligand binding energy as equivalent to glibenclamide, as a standard drug. …”
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Smad1 Promotes Tumorigenicity and Chemoresistance of Glioblastoma by Sequestering p300 From p53 by Lingli Gong, Daxing Xu, Kaixiang Ni, Jie Li, Wei Mao, Bo Zhang, Zhening Pu, Xiangming Fang, Ying Yin, Li Ji, Jingjing Wang, Yaling Hu, Jiao Meng, Rui Zhang, Jiantong Jiao, Jian Zou

“…Acetylation of K373 is found to be essential for Smad1's oncogenic function but does not confer chemoresistance in the absence of p53. Through molecular docking, it is discovered that Smad1 and p53 both interact with the acetyltransferase domain of p300, but at different amino acid sites. …”
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Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from <i>Taenia solium</i> Using Computational and Bioinformatics Tools by César Sánchez-Juárez, Roberto Flores-López, Lluvia de Carolina Sánchez-Pérez, Ponciano García-Gutiérrez, Lucía Jiménez, Abraham Landa, Rafael A. Zubillaga

“…Representative structures from these simulations and a putative binding site with low conservation relative to human GSTs, identified via the SILCS methodology, were employed for virtual screening through ensemble docking against a commercial compound library. The two compounds were found to reduce the enzyme’s activity by 50–70% under assay conditions, while showing a reduction of only 30–35% for human mu-class GSTM1, demonstrating selectivity for Ts25GST. …”
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Theoretical Investigation of the Structural, Spectroscopic, Electronic, and Pharmacological Properties of 4-Nerolidylcathecol, an Important Bioactive Molecule by Renyer A. Costa, Earle Silva A. Junior, Jaqueline de A. Bezerra, Josiana Moreira Mar, Emerson S. Lima, Maria Lucia B. Pinheiro, Diego V. C. Mendonça, Guilherme Braule P. Lopes, Adjane Dalvana S. Branches, Kelson M. T. Oliveira

“…The comparative IR studies revealed that intermolecular hydrogen bonds that stabilize dimeric forms are plausible and also allowed the assignment of several characteristic vibrations. Molecular docking calculations with DNA topoisomerase I-DNA complex (TOPO-I), glyceraldehyde 3-phospate dehydrogenase (GAPDH), and Plasmodium falciparum lactate dehydrogenase (PfLDH) showed binding free energies of −6.3, −6.5, and −7.6 kcal/mol, respectively, which indicates that 4NRC is a good competitive inhibitor for these enzymes.…”
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Comparative analysis of physicochemical properties, ginsenosides content and α-amylase inhibitory effects in white ginseng and red ginseng by Huairui Wang, Yao Cheng, Xue Zhang, Yingping Wang, Hui Zhao

“…Quantitative analysis of multi-components by a single-marker (QAMS) method and anti-α-amylase activity test were used to assess variations of chemical ingredients and pharmacological activity between white and red ginseng. Finally, molecular docking studies were carried out to screen out the most effective compound against α-amylase. …”
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Label-free (fluorescence-free) sensing of a single DNA molecule on DNA origami using a plasmon-enhanced WGM sensor by Ghamari Shahin, Chiarelli Germán, Kołątaj Karol, Subramanian Sivaraman, Acuna Guillermo P., Vollmer Frank

“…By leveraging the strong electromagnetic fields generated within the nanogap of the plasmonic dimer, this platform enables the detection of transient hybridization events between DNA docking strands and freely diffusing complementary sequences. …”
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