In Vitro Antibacterial, Antioxidant, Cytotoxicity Activity, and In Silico Molecular Modelling of Compounds Isolated from Roots of Hydnora johannis by Teshome Degfie, Milkyas Endale, Muhdin Aliye, Rajalakshmanan Eswaramoorthy, Tariku Nefo Duke, Aman Dekebo

“…Based on the data from the antioxidant study, DCM/MeOH extract (70.32%) and catechin (3) showed good antioxidant activity (65.61%) (IC50 0.25 μg/mL) relative to that of the positive control (78.21%, IC50 0.014 μg/mL) at 12.5 μg/mL. In each docking pose, catechin (3) scored higher binding affinity of −7.9, −7.2, and −6.4 kcal/mol towards PqsA, DNA gyraseB, and S. aureus PK, respectively, compared to amoxicillin (−8.1, −6.1, and −6.4 kcal/mol). …”
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In Silico Analysis Revealed Five Novel High-Risk Single-Nucleotide Polymorphisms (rs200384291, rs201163886, rs193141883, rs201139487, and rs201723157) in ELANE Gene Causing Autosom... by Khyber Shinwari, Mikhail A. Bolkov, Muhammad Yasir Akbar, Liu Guojun, Svetlana S. Deryabina, Irina A. Tuzankina, Valery. A. Chereshnev

“…We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking. This research sheds light on how ELANE failure upon mutation results in disease progression, including congenital neutropenia, and validation of these novel predicted nsSNPs is required through the wet lab.…”
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Discovering broad-spectrum inhibitors for SARS-CoV-2 variants: a cheminformatics and biophysical approach targeting the main protease by Safar M. Alqahtani

“…Accordingly, three drug molecules (BBB-26580140, BDE-32007849, and LAS-51378804) are highlighted as the best binding molecules to the main protease S1 pocket. The docking binding energy scores of BBB-26580140, BDE-32007849, and LAS-51378804 were −13.02, −13.0, and −12.56 kcal/mol, respectively. …”
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Elucidation of the Molecular Interaction between miRNAs and the Gene, Involved in Acute Myeloid Leukemia, by the Assistance of Argonaute Protein through a Computational Approach by Rohit Pritam Das, V. Badireenath Konkimalla, Surya Narayan Rath, Jagadish Hansa, Manaswini Jagdeb

“…Furthermore, the interaction between miRNAs-mRNA duplex of all chosen miRNAs are docked with AGO protein (PDB ID: 3F73, chain A) to study their interaction at molecular level through an in silico approach. …”
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Structural and free energy landscape analysis for the discovery of antiviral compounds targeting the cap-binding domain of influenza polymerase PB2 by Amr S. Abouzied, Saad Alqarni, Kareem M. Younes, Sanad M. Alanazi, Dana M. Alrsheed, Rawabi K. Alhathal, Bader Huwaimel, Akram M. Elkashlan

“…We employed a comprehensive computational approach involving virtual screening, molecular docking, and 500 ns molecular dynamics (MD) simulations. …”
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Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition by Ankita Tripathi, Dharmendra Singh, Jyotika Bhati, Deepti Singh, Jyoti Taunk, Jawaher Alkahtani, Abdulrahman Al-Hashimi, Madan Pal Singh

“…Predicted 3D (three-dimensional) structure and molecular docking revealed that 5 LcMATE proteins could bind citrate and contain amino acids related to its secretion via citrate exuding motif and other neighbouring sites. …”
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Design and In Silico and In Vitro Evaluations of a Novel Nicotinamide Derivative as a VEGFR-2 Inhibitor by Ibrahim H. Eissa, Muhammad Abd ElGayed Bkrah, Reda G. Yousef, Hazem Elkady, Eslam B. Elkaeed, Bshra A. Alsfouk, Ibrahim M. Ibrahim, Ahmed M. Metwaly, Dalal Z. Husein

“…Utilizing the density functional theory (DFT) calculations, the three-dimensional structure of the designed compound was determined, shedding light on its stability and reactivity. Molecular docking revealed its capability to inhibit VEGFR-2, which was further supported by molecular dynamics (MD) simulations confirming its binding to the target protein. …”
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Active Ingredients and Potential Mechanism of Additive Sishen Decoction in Treating Rheumatoid Arthritis with Network Pharmacology and Molecular Dynamics Simulation and Experimenta... by Ren J, Liu Z, Qi X, Meng X, Guo L, Yu Y, Dong T, Li Q

“…The binding mode between the key ingredients and key targets was elucidated using molecular docking and molecular dynamics simulation.Results: In all, 75 ASSD active ingredients and 1258 RA targets were analyzed, of which kaempferol, luteolin, and quercetin were considered key components that mainly act through inflammation-related pathways, such as the PI3K-AKT, TNF, and IL-17 signaling pathways, to ameliorate RA. …”
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Computational Study of the Phytochemical Constituents from Uncaria tomentosa Stem Bark against SARS-CoV-2 Omicron Spike Protein by Oscar Herrera-Calderon, Abdulrahman M. Saleh, Andres F. Yepes-Perez, Nada H. Aljarba, Saad Alkahtani, Gaber El-Saber Batiha, Renan Dilton Hañari-Quispe, Haydee Chavez, Josefa Bertha Pari-Olarte, Eddie Loyola-Gonzales, José Santiago Almeida-Galindo, José Francisco Kong-Chirinos, Taoufiq Benali

“…The aim in this computational study was to determine the main phytochemical constituents from U. tomentosa stem bark against the SARS-CoV-2 Omicron spike protein based on molecular modeling. A molecular docking was carried out on the isolated phytochemicals in a previous work against the SARS-CoV-2 Omicron spike protein-binding domain (PDB ID: 7T9K). …”
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Microbial-based natural products as potential inhibitors targeting DNA gyrase B of Mycobacterium tuberculosis: an in silico study by Tilal Elsaman, Magdi Awadalla Mohamed, Malik Suliman Mohamed, Eyman Mohamed Eltayib, Abualgasim Elgaili Abdalla

“…Consequently, targeting this enzyme is of particular interest in developing new drugs for the treatment of drug-resistant tuberculosis, including multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB).MethodsIn the present study, multiple computational tools were adopted to screen a microbial-based natural products database (NPAtlas) for potential inhibitors of the ATPase activity of MBT DNA gyrase.Results and discussionTwelve hits were initially identified as the top candidates based on their docking scores (ranging from −9.491 to −10.77 kcal/mol) and binding free energies (−60.37 to −73.21 kcal/mol). …”
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Rutaecarpine alleviates hepatic ischemia‒reperfusion injury in liver transplantation by inhibiting inflammatory response and oxidative stress by Yan Liu, Yan Liu, Feng Qi, Lun-Jian Xiang, Zhu-Jun Yi, Sheng-Wei Li

“…Mechanistically, bioinformatics analysis and in vivo and in vitro experiments revealed that PDE4B may be a key target by which Rut exerts its protective effect, and molecular docking and cellular thermal shift assay confirmed this result. …”
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Antibacterial and antibiofilm activities of kaffir lime essential oils and their active constituents against Staphylococcus aureus focusing on sortase A by Chayapol Pontanayodsakorn, Chatchakorn Eurtivong, Pimsumon Jiamboonsri

“…However, terpinen-4-ol exhibited weak SrtA inhibition with docking score of 32.58 and in vitro SrtA inhibition of 46.14 ± 3.58 % at 1 % v/v. …”
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Baicalein inhibits PRRSV through direct binding, targeting EGFR, and enhancing immune response by Jing Wu, Qi Lu, Jing Hou, Yueqin Qiu, Min Tian, Li Wang, Kaiguo Gao, Xuefen Yang, Zongyong Jiang

“…The results of molecular docking and dynamics (MD) simulations confirmed that baicalein has a high binding affinity for EGFR, with a measured value of − 7.935 kcal/mol. …”
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Mechanistic insights into pachymic acid’s action on triple-negative breast Cancer through TOP2A targeting by Ming Liu, Li Zheng, Yang Zhang, Jinhui Tian

“…We conducted a pan-cancer analysis, tumor immune microenvironment analysis, and molecular docking. We performed cell experimental, included cytotoxicity assay, apoptosis analysis, proliferation assay, and migration and invasion assays. …”
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Non-Steroidal Anti-Inflammatory Drugs Are Inhibitors of the Intestinal Proton-Coupled Amino Acid Transporter (PAT1): Ibuprofen and Diclofenac Are Non-Translocated Inhibitors by Carsten Uhd Nielsen, Sebastian Jakobsen, Maria L. Pedersen

“…The molecular interaction between NSAIDs and hPAT1 was investigated using an AlphaFold2 model and molecular docking. <b>Results:</b> NSAIDs such as ibuprofen, diclofenac, and flurbiprofen inhibited proline uptake via hPAT1, with IC₅₀ values of 954 (logIC₅₀ 2.98 ± 0.1) µM, 272 (logIC₅₀ 2.43 ± 0.1) µM, and 280 (logIC₅₀ 2.45 ± 0.1) µM, respectively. …”
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Repurposing the Antidiabetic Drugs Glyburide, Gliquidone, and Glipizide in Combination with Benznidazole for <i>Trypanosoma cruzi</i> Infection by Citlali Vázquez, Rusely Encalada, Isabel Jiménez-Galicia, Rogelio Gómez-Escobedo, Gildardo Rivera, Benjamín Nogueda-Torres, Emma Saavedra

“…<b>Background/Objective</b>: Glyburide, glipizide, and gliquidone, hypoglycemic drugs for diabetes treatment, were previously predicted to bind to dihydrofolate reductase-thymidylate synthase from <i>T. cruzi</i> by in silico docking analysis; they also showed antiproliferative effects against <i>T. cruzi</i> epimastigotes, the stage of the insect vector. …”
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Theoretical Study of Sphingomyelinases from <i>Entamoeba histolytica</i> and <i>Trichomonas vaginalis</i> Sheds Light on the Evolution of Enzymes Needed for Survival and Colonizati... by Fátima Berenice Ramírez-Montiel, Sairy Yarely Andrade-Guillen, Ana Laura Medina-Nieto, Ángeles Rangel-Serrano, José A. Martínez-Álvarez, Javier de la Mora, Naurú Idalia Vargas-Maya, Claudia Leticia Mendoza-Macías, Felipe Padilla-Vaca, Bernardo Franco

“…AlphaFold3 models predicted the occupancy of cobalt ions in the active site of the aSMase6 enzyme. Cavity blind docking showed that the substrate is pushed outward of the active site when cobalt is bound instead of magnesium ions. …”
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Typical and atypical metabolic characteristics of three iridaceae isoflavone components: in vitro and in silico studies by Jifeng Gu, Jifeng Gu, Huishan Zhang, Mei Wang, Yuyang Zhou, Yuyang Zhou, Zhipeng Deng, Rong Shi

“…However, the metabolic characteristics of isoflavone aglycones remain unclear.MethodsIn this study, human liver microsomes (HLMs) and Cytochrome P450 (CYP) recombinant enzymes were used to study the metabolic stability, identify the metabolic pathways and enzyme kinetics of these three components, and elucidate their possible binding sites through molecular docking.ResultsWhen tectorigenin, irigenin, and irisflorentin were co-incubated with HLMs and CYP recombinant enzymes, hydroxylation metabolite for tectorigenin, demethylated metabolite for irigenin, and 6,7-dihydroxy-5,3′,4′,5′-tetramethoxy isoflavone originating from irisflorentin were identified. …”
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Mechanisms underlying the effects of cyanogenesis on development and reproduction of Tetranychus urticae: Insights from enzyme activity and gene expression aspects by Mufeng Wu, Xiao Liang, Ying Liu, Chunling Wu, Xingkui An, Zihua Zhao, Guifeng Hao, Ijiti Oluwole Gregory, Zhihong Li, Qing Chen

“…Linamarin-β-GLU (lima bean-derived) presented prompt HCN release, and molecular docking indicated higher binding energy and more robust binding sites compared with other two groups, i.e., lotaustralin-β-GLU (lima bean-derived) and amygdalin-β-GLU (almond-derived). …”
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Increased TSPO alleviates neuropathic pain by preventing pyroptosis via the AMPK-PGC-1α pathway by Baolong Li, Kaiming Yu, Xiongyao Zhou, Jialu Sun, Le Qi, Weiye Li, Tuo Yang, Weizhen Li, Ningning Wang, Xiaosong Gu, Shusen Cui, Rangjuan Cao

“…Through drug screening, molecular docking, and behavioral assays, we identified zopiclone as a promising TSPO-targeting drug for pain treatment. …”
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