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Total 1090 results found since Jan 2013.

Molecules, Vol. 26, Pages 7201: Greedy 3-Point Search (G3PS) & mdash;A Novel Algorithm for Pharmacophore Alignment
Molecules, Vol. 26, Pages 7201: Greedy 3-Point Search (G3PS)—A Novel Algorithm for Pharmacophore Alignment Molecules doi: 10.3390/molecules26237201 Authors: Christian Permann Thomas Seidel Thierry Langer Chemical features of small molecules can be abstracted to 3D pharmacophore models, which are easy to generate, interpret, and adapt by medicinal chemists. Three-dimensional pharmacophores can be used to efficiently match and align molecules according to their chemical feature pattern, which facilitates the virtual screening of even large compound databases. Existing alignment methods, used in computat...
Source: Molecules - November 27, 2021 Category: Chemistry Authors: Christian Permann Thomas Seidel Thierry Langer Tags: Article Source Type: research

Molecules, Vol. 23, Pages 567: Identification and Characterizations of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Scaffold Hopping- and 2D-Molecular Fingerprint-Based Similarity Search
heng Luo Kai Chen SET7, serving as the only histone methyltransferase that monomethylates ‘Lys-4’ of histone H3, has been proved to function as a key regulator in diverse biological processes, such as cell proliferation, transcriptional network regulation in embryonic stem cell, cell cycle control, protein stability, heart morphogenesis and development. What′s more, SET7 is involved inthe pathogenesis of alopecia aerate, breast cancer, tumor and cancer progression, atherosclerosis in human carotid plaques, chronic renal diseases, diabetes, obesity, ovarian cancer, prostate cancer, hepatocellular carcinoma, and ...
Source: Molecules - March 2, 2018 Category: Chemistry Authors: Hong Ding Wen Lu Jun Hu Yu-Chih Liu Chen Zhang Fu Lian Nai Zhang Fan Meng Cheng Luo Kai Chen Tags: Article Source Type: research

Molecules, Vol. 23, Pages 1876: Be Aware of Aggregators in the Search for Potential Human ecto-5 ′-Nucleotidase Inhibitors
Molecules, Vol. 23, Pages 1876: Be Aware of Aggregators in the Search for Potential Human ecto-5′-Nucleotidase Inhibitors Molecules doi: 10.3390/molecules23081876 Authors: Lucas G. Viviani Erika Piccirillo Arquimedes Cheffer Leandro de Rezende Henning Ulrich Ana Maria Carmona-Ribeiro Antonia T.-do Amaral Promiscuous inhibition due to aggregate formation has been recognized as a major concern in drug discovery campaigns. Here, we report some aggregators identified in a virtual screening (VS) protocol to search for inhibitors of human ecto-5′-nucleotidase (ecto-5′-NT/CD73), a...
Source: Molecules - July 27, 2018 Category: Chemistry Authors: Lucas G. Viviani Erika Piccirillo Arquimedes Cheffer Leandro de Rezende Henning Ulrich Ana Maria Carmona-Ribeiro Antonia T.-do Amaral Tags: Article Source Type: research

Molecules, Vol. 24, Pages 897: Insecticidal and Nematicidal Contributions of Mexican Flora in the Search for Safer Biopesticides
lo Plant metabolites have been used for many years to control pests in animals and to protect crops. Here, we reviewed the available literature, looking for the species of Mexican flora for which extracts and metabolites have shown activity against pest insects and parasitic nematodes of agricultural importance, as well as against nematodes that parasitize domestic cattle. From 1996 to 2018, the search for novel and eco-friendly biopesticides has resulted in the identification of 114 species belonging to 36 botanical families of Mexican plants with reported biological effects on 20 insect species and seven nematode spe...
Source: Molecules - March 3, 2019 Category: Chemistry Authors: Beatriz Hern ández-Carlos Marcela Gamboa-Angulo Tags: Review Source Type: research

Molecules, Vol. 25, Pages 2010: High-Throughput Computational Search for Half-Metallic Oxides
o Nardelli Half metals are a peculiar class of ferromagnets that have a metallic density of states at the Fermi level in one spin channel and simultaneous semiconducting or insulating properties in the opposite one. Even though they are very desirable for spintronics applications, identification of robust half-metallic materials is by no means an easy task. Because their unusual electronic structures emerge from subtleties in the hybridization of the orbitals, there is no simple rule which permits to select a priori suitable candidate materials. Here, we have conducted a high-throughput computational search for half-me...
Source: Molecules - April 24, 2020 Category: Chemistry Authors: Laalitha S. I. Liyanage Jagoda S ławińska Priya Gopal Stefano Curtarolo Marco Fornari Marco Buongiorno Nardelli Tags: Article Source Type: research

Molecules, Vol. 26, Pages 4323: Search for Novel Lead Inhibitors of Yeast Cytochrome bc1, from Drugbank and COCONUT
uc In this work we introduce a novel filtering and molecular modeling pipeline based on a fingerprint and descriptor similarity procedure, coupled with molecular docking and molecular dynamics (MD), to select potential novel quoinone outside inhibitors (QoI) of cytochrome bc1 with the aim of determining the same or different chromophores to usual. The study was carried out using the yeast cytochrome bc1 complex with its docked ligand (stigmatellin), using all the fungicides from FRAC code C3 mode of action, 8617 Drugbank compounds and 401624 COCONUT compounds. The introduced drug repurposing pipeline consists of compou...
Source: Molecules - July 16, 2021 Category: Chemistry Authors: Ozren Jovi ć Tomislav Šmuc Tags: Article Source Type: research

Molecules, Vol. 26, Pages 4420: Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search
iao RNA molecules participate in many important biological processes, and they need to fold into well-defined secondary and tertiary structures to realize their functions. Like the well-known protein folding problem, there is also an RNA folding problem. The folding problem includes two aspects: structure prediction and folding mechanism. Although the former has been widely studied, the latter is still not well understood. Here we present a deep reinforcement learning algorithms 2dRNA-Fold to study the fastest folding paths of RNA secondary structure. 2dRNA-Fold uses a neural network combined with Monte Carlo tree sear...
Source: Molecules - July 22, 2021 Category: Chemistry Authors: Kangkun Mao Yi Xiao Tags: Article Source Type: research

Molecules, Vol. 27, Pages 65: Dealing with the Ambiguity of Glycan Substructure Search
Lisacek The level of ambiguity in describing glycan structure has significantly increased with the upsurge of large-scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as an appropriate solution for navigating these data. However, navigation is not sufficient and the model should also enable advanced search and comparison. A new ontology with a tree logical structure is introduced to represent glycan structures irrespective of the precision of molecular details. The model heavily relies on the GlycoCT encoding of glycan structures. Its implementation in the GlySTreeM knowledge...
Source: Molecules - December 23, 2021 Category: Chemistry Authors: Vincenzo Daponte Catherine Hayes Julien Mariethoz Frederique Lisacek Tags: Article Source Type: research

Molecules, Vol. 27, Pages 3280: In Search of Synergistic Insect Repellents: Modeling of Muscarinic GPCR Interactions with Classical and Bitopic Photoactive Ligands
Nowak Insect vector-borne diseases pose serious health problems, so there is a high demand for efficient molecules that could reduce transmission. Using molecular docking and molecular dynamics (MD) simulation, we studied a series of compounds acting on human and insect muscarinic acetylcholine receptors (mAChRs), a novel target of synergistic agents in pest control. We characterized early conformational changes of human M1 and fruit fly type-A mAChR G protein-coupled receptors (GPCRs) in response to DEET, IR3535, and muscarine binding based on the MD analysis of the activation microswitches known to form the signal tr...
Source: Molecules - May 20, 2022 Category: Chemistry Authors: Beata Niklas Bruno Lapied Wieslaw Nowak Tags: Article Source Type: research

Molecules, Vol. 28, Pages 1240: Energy Level Prediction of Organic Semiconductors for Photodetectors and Mining of a Photovoltaic Database to Search for New Building Units
Mustafa Kamal Due to the large versatility in organic semiconductors, selecting a suitable (organic semiconductor) material for photodetectors is a challenging task. Integrating computer science and artificial intelligence with conventional methods in optimization and material synthesis can guide experimental researchers to develop, design, predict and discover high-performance materials for photodetectors. To find high-performance organic semiconductor materials for photodetectors, it is crucial to establish a relationship between photovoltaic properties and chemical structures before performing synthetic procedures i...
Source: Molecules - January 27, 2023 Category: Chemistry Authors: Jehad Saleh Sajjad Haider Muhammad Saeed Akhtar Muhammad Saqib Muqadas Javed Sayed Elshahat Ghulam Mustafa Kamal Tags: Article Source Type: research

Molecules, Vol. 20, Pages 14118-14138: Search for Antiprotozoal Activity in Herbal Medicinal Preparations; New Natural Leads against Neglected Tropical Diseases
Sleeping sickness, Chagas disease, Leishmaniasis, and Malaria are infectious diseases caused by unicellular eukaryotic parasites (“protozoans”). The three first mentioned are classified as Neglected Tropical Diseases (NTDs) by the World Health Organization and together threaten more than one billion lives worldwide. Due to the lack of research interest and the high increase of resistance against the existing treatments, the search for effective and safe new therapies is urgently required. In view of the large tradition of natural products as sources against infectious diseases [1,2], the aim of the present study is to ...
Source: Molecules - August 4, 2015 Category: Chemistry Authors: Núria MontesinoMarcel KaiserReto BrunThomas Schmidt Tags: Article Source Type: research

Molecules, Vol. 20, Pages 17132-17151: Comparative Analysis of Virtual Screening Approaches in the Search for Novel EphA2 Receptor Antagonists
The EphA2 receptor and its ephrin-A1 ligand form a key cell communication system, which has been found overexpressed in many cancer types and involved in tumor growth. Recent medicinal chemistry efforts have identified bile acid derivatives as low micromolar binders of the EphA2 receptor. However, these compounds suffer from poor physicochemical properties, hampering their use in vivo. The identification of compounds able to disrupt the EphA2-ephrin-A1 complex lacking the bile acid scaffold may lead to new pharmacological tools suitable for in vivo studies. To identify the most promising virtual screening (VS) protocol aim...
Source: Molecules - September 17, 2015 Category: Chemistry Authors: Donatella CallegariDaniele PalaLaura ScalviniMassimiliano TognoliniMatteo IncertiSilvia RivaraMarco MorAlessio Lodola Tags: Article Source Type: research

Molecules, Vol. 22, Pages 1808: A Search for Dual Action HIV-1 Reverse Transcriptase, Bacterial RNA Polymerase Inhibitors
otr Paneth Using molecular modeling approach, potential antibacterial agents with triazole core were proposed. A moderate to weak level of antibacterial activity in most of the compounds have been observed, with best minimal inhibitory concentration (MIC) value of 0.003 mg/mL, as shown by the 15 against S. epidermidis. Studied compounds were also submitted to the antifungal assay. The best antifungal activity was detected for 16 with MIC at 0.125 and 0.25 mg/mL against C. albicans and C. parapsilosis, respectively.
Source: Molecules - October 25, 2017 Category: Chemistry Authors: Agata Paneth Tomasz Fr ączek Agnieszka Grzegorczyk Dominika Janowska Anna Malm Piotr Paneth Tags: Article Source Type: research

Molecules, Vol. 23, Pages 568: Search for Fibrous Aggregates Potentially Useful in Regenerative Medicine Formed under Physiological Conditions by Self-Assembling Short Peptides Containing Two Identical Aromatic Amino Acid Residues
This study investigates the propensity of short peptides to self-organize and the influence of aggregates on cell cultures. The dipeptides were derived from both enantiomers of identical aromatic amino acids and tripeptides were prepared from two identical aromatic amino acids with one cysteine or methionine residue in the C-terminal, N-terminal, or central position. The formation or absence of fibrous structures under physiological conditions was established using Congo Red and Thioflavine T assays as well as by microscopic examination using normal and polarized light. The in vitro stability of the aggregates in buffered ...
Source: Molecules - March 2, 2018 Category: Chemistry Authors: Justyna Fraczyk Wojciech Lipinski Agata Chaberska Joanna Wasko Kamil Rozniakowski Zbigniew Kaminski Maciej Bogun Zbigniew Draczynski Elzbieta Menaszek Ewa Stodolak-Zych Marta Kaminska Beata Kolesinska Tags: Article Source Type: research

Molecules, Vol. 23, Pages 953: Search for Partner Proteins of A. thaliana Immunophilins Involved in the Control of Plant Immunity
A. Bruskin The involvement of plant immunophilins in multiple essential processes such as development, various ways of adapting to biotic and abiotic stresses, and photosynthesis has already been established. Previously, research has demonstrated the involvement of three immunophilin genes (AtCYP19-1/ROC3, AtFKBP65/ROF2, and AtCYP57) in the control of plant response to invasion by various pathogens. Current research attempts to identify host target proteins for each of the selected immunophilins. As a result, candidate interactors have been determined and confirmed using a yeast 2-hybrid (Y2H) system for protein&a...
Source: Molecules - April 19, 2018 Category: Chemistry Authors: Inna A. Abdeeva Gennady V. Pogorelko Liliya G. Maloshenok Maria V. Mokrykova Oksana V. Fursova Sergey A. Bruskin Tags: Article Source Type: research