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Chemo-informatics - Science topic

Chemo-informatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry.
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Publications related to Chemo-informatics (2,402)
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Background Dengue virus (DENV) infection is spreading rapidly, especially in the subtropical and tropical regions, placing a huge percentage of the global population at risk and causing repeated outbreaks. DENV protease inhibition has been suggested as a viable therapeutic strategy. Using a computer-aided design approach and the structure-based dru...
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This commentary provides an overview of the publications in, and the citations to, the first twelve volumes of the Journal of Cheminformatics , covering the period 2009–2020. The analysis is based on the 622 articles that have appeared in the journal during that time and that have been indexed in the Clarivate Web of Science Core Collection databas...
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In nematodes that invade the gastro-intestinal tract of the ruminant, the process of larval exsheathment marks the transition from the free-living to the parasitic stages of these parasites. To investigate the secretome associated with larval exsheathment, a closed in vitro system that effectively reproduces the two basic components of an anaerobic...
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The purpose of this review is to introduce the reader to graph kernels, with a view of applying them in classification problems in chemoinformatics. Graph kernels are functions that allow us to infer chemical properties of molecules, which can help with tasks such as finding suitable compounds for drug design. The use of kernel methods is but one p...
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Peganum genus is rich with its high phytochemical and botanical variability. Peganum species have been used as a sedative, antitumor, analgesic and antidepressant. This paper aims to study the molecular diversity of Peganum genus and to shed more light on the structure–activity relationship of the alkaloids isolated from Peganum genus. All Peganum...
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We report the main conclusions of the first Chemoinformatics and Artificial Intelligence Colloquium, Mexico City (virtual), June 15-17, 2022. Fifteen lectures were presented during a virtual and public event with speakers from industry, academia, and non-for-profit organizations. 1,290 participants, including students and academics from more than 6...
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Five previously known anthraquinones with amino derivatives and synthesized new triazene (1-[(1E)-3,3-bis(2-hydroxyethyl)triaz-1-en-1-ol]-4-[(2-hydroxyethyl)amino]anthracene-9,10-dione) were evaluated in-silico as inhibitors of COVID-19 main protease. Preliminary screening has shown that the presence of a sulfo group in the second position of the a...
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Repurposing of amine and carboxylic acid building blocks provides an enormous opportunity to expand the accessible chemical space, because amine and acid feedstocks are typically low cost and available in high diversity. Herein, we report a copper-catalyzed deaminative esterification based on C–N activation of aryl amines via diazonium salt formati...
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Coronary artery endothelial cells (CAEC) exert an important role in the development of cardiovascular disease. Dysfunction of CAEC is associated with cardiovascular disease in subjects with type 2 diabetes mellitus (T2DM). However, comprehensive studies of the effects that a diabetic environment exerts on this cellular type are scarce. The present...
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Dear Colleagues, Research in discrete mathematics in theoretical and application aspects has significantly increased in recent decades. The first aim of this Special Issue is to encourage new theoretical results in discrete mathematics, such as results related to graph theory, theoretical computer science, and combinatorial optimization. The secon...
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Bitterness is an aversive cue elicited by thousands of chemically diverse compounds. Bitter taste may prevent consumption of foods and jeopardize drug compliance. The G protein-coupled receptors for bitter taste, TAS2Rs, have species-dependent number of subtypes and varying expression levels in extraoral tissues. Molecular recognition by TAS2R subt...
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Senescent cells accumulate within tissues during aging and secrete an array of pro-inflammatory molecules known as senescent-associated secretory phenotype (SASP), which contribute to the appearance and progression of various chronic degenerative diseases. Novel pharmacological approaches aimed at modulating or eliminating senescent cells´ harmful...
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Citation Igbokwe MC et al. (2022) In-silico study for African plants with possible beta-cell regeneration effect through inhibition of DYRK1A. Sciences of Phytochemistry. 1(2): 1-16. Abstract The continuous destruction of normal insulin-producing pancreatic beta-cells is a contributing factor in all common forms of diabetes, due to insufficient pro...
Book
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Computer-Aided Drug Design (CADD) is a wide area that applies scientific techniques from a variety of fields to the discovery and design of drugs. CADD represents the computational approaches and resources that aid in the design and development of novel leads, lowering drug design costs by up to 50%. Design and development of novel drugs become a m...
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Ethnopharmacology, through the description of the beneficial effects of plants, has provided an early framework for the therapeutic use of natural compounds. Natural products, either in their native form or after crude extraction of their active ingredients, have long been used by different populations and explored as invaluable sources for drug de...
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The preset neurodegenerations in Alzheimer disease (AD) are due to several mechanisms such as amyloidogenic proteolysis, neuroinflammation, mitochondrial dysfunction, neurofibrillary tangles, cholinergic dysfunction, among others. The aim of this work was to develop multitarget molecules for the treatment of AD. Therefore, a family of 64 molecules...
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Lysyl oxidase-like 2 (LOXL2) has recently been explored as extremely pivotal protein involved in angiogenesis which results in metastasis of numerous types of cancers. Hence, LOXL2 is an exciting new target for drug development against tumor progression and its spread to distant organs. Newly synthesized derivatives of natural phenolic antioxidant...
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Dynamic combinatorial libraries (DCLs) display adaptive behavior, enabled by the reversible generation of their molecular constituents from building blocks, in response to external effectors, e.g., protein receptors. So far, chemoinformatics has not yet been used for the design of DCLs-which comprise a radically different set of challenges compared...
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Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for...
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Furin is involved in the endoproteolytic processing of various protein precursors implicated in many diseases such as diabetes, obesity, atherosclerosis, cancer, Alzheimer’s disease and viral infection including COVID-19. Recently, cell entry of SARS-CoV-2 was found to require sequential cleavage of the viral spike glycoprotein (S protein) at the S...
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The concept of chemical space is a cornerstone in chemoinformatics, and it has broad conceptual and practical applicability in many areas of chemistry, including drug design and discovery. One of the most considerable impacts is in the study of structure–property relationships where the property can be a biological activity or any other characteris...
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The support vector machine (SVM) algorithm is one of the most widely used machine learning (ML) methods for predicting active compounds and molecular properties. In chemoinformatics and drug discovery, SVM has been a state-of-the-art ML approach for more than a decade. A unique attribute of SVM is that it operates in feature spaces of increasing di...
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Hepatitis C virus (HCV) is a serious disease that threatens human health. Despite consistent efforts to inhibit the virus, it has infected more than 58 million people, with 300,000 deaths per year. The HCV nonstructural protein NS5A plays a critical role in the viral life cycle, as it is a major contributor to the viral replication and assembly pro...
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Drug discovery (DD) research is a complex field with a high attrition rate. Machine learning (ML) approaches combined to chemoinformatics are of valuable input to this field. We, herein, focused on implementing multiple ML algorithms that shall learn from different molecular fingerprints (FPs) of 65 057 molecules that have been identified as active...
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There is a constant demand to develop an effective and affordable new drug entity to manage cognitive impairment. Medicinal herbs serve as natural resources for mining of new drug candidates. We used chemoinformatics to identify the bioactive compounds from Amaranthus tricolor L. a common leafy vegetable and often used in traditional medicine to ma...
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Abstract Background: Cancer is a significant public health problem worldwide and constitutes the second leading cause of death after cardiovascular disease. This study was thus designed to identify new natural compounds from Malagasy medicinal plants traditionally used to treat cancer. Methods: In silico analyses by molecular docking to model ligan...
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Histone deacetylase (HDAC) inhibitors are highly involved in the regulation of many pharmacological responses, which results in anti-inflammatory and anti-cancer effects. In the present work, chemoinformatic analyses were performed to obtain two potent and selective aminotriazoloquinazoline-based HDAC6 inhibitors. We unexpectedly obtained an aminot...
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Fingerprint (FP) representations of chemical structure continue to be one of the most widely used types of molecular descriptors in chemoinformatics and computational medicinal chemistry. One often distinguishes between two- and three-dimensional (2D and 3D) FPs depending on whether they are derived from molecular graphs or conformations, respectiv...
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Dengue fever is the most common and important arthropod-borne viral illness in humans. However, no effective medications or vaccinations exist to prevent this condition. The dengue viral (DENV) protease non-structural protein (NS) 2B-3 is a possible target for antiviral treatment. Based on the lead compound reported in our earlier study, eight phth...
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Antibiotic resistance is a major threat to public health. The development of chemo-informatic tools to guide medicinal chemistry campaigns in the efficint design of antibacterial libraries is urgently needed. We present AB-DB, an open database of all-atom force-field parameters, molecular dynamics trajectories, quantum-mechanical properties, and cu...
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The rigidity and flexibility of small molecules are complementary in 3-dimensional ligand-protein interaction. Therefore, the chemical library with conformational diversity would be a valuable resource for investigating the influence of skeletal flexibility on the biological system. In this regard, we designed and synthesized ten conformationally d...
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Given the observable toxicity of lithium carbonate, neuropharmacology requires effective and non-toxic lithium salts. In particular, these salts can be employed as neuroprotective agents since lithium ions demonstrate neuroprotective properties through inhibition of glycogen synthetase kinase-3β and other target proteins, increasing concentrations...
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A central question in origins of life research is how non-entailed chemical processes, which simply dissipate chemical energy because they can do so due to immediate reaction kinetics and thermodynamics, enabled the origin of highly-entailed ones, in which concatenated kinetically and thermodynamically favorable processes enhanced some processes ov...
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Abstract: Background & aim: The use of Chemoinformatics for drug discovery and development plays an important role in introducing new and more effective drugs, optimizing the properties of existing drugs and the growth of drug-related industries, as well as the health of human, animal and plant communities. Therefore, the purpose of the present stu...
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Among the various types of cancer, lung cancer is the second most-diagnosed cancer worldwide. The kinesin spindle protein, Eg5, is a vital protein behind bipolar mitotic spindle establishment and maintenance during mitosis. Eg5 has been reported to contribute to cancer cell migration and angiogenesis impairment and has no role in resting, non-divid...
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The retrospective evaluation of virtual screening approaches and activity prediction models are important for methodological development. However, for fair comparison, evaluation data sets must be carefully prepared. In this research, we compiled structure–activity–relationship matrix-based data sets for 15 biological targets along with many divers...
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The obtainment of new luminophores for molecular sensorics of biosystems is becoming one of the urgent tasks in the field of chemical synthesis. The solution to each practical problem imposes its own limitations in the design of new structures with practically useful properties. The relationship between the structure and spectral properties is stil...
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Discovering new reactions, optimizing their performance, and extending the synthetically accessible chemical space are critical drivers for major technological advances and more sustainable processes. The current wave of machine intelligence is revolutionizing all data‐rich disciplines. Machine intelligence has emerged as a potential game‐changer f...
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Myracrodruon urundeuva Fr. Allem. (Anacardiaceae) is a tree popularly known as the “aroeira-do-sertão”, native to the caatinga and cerrado biomes, with a natural dispersion ranging from the Northeast, Midwest, to Southeast Brazil. Its wood is highly valued and overexploited, due to its characteristics such as durability and resistance to decaying....
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Background: Traditional Chinese medicine (TCM) has been widely used in the treatment of human diseases. However, the synergistic effects of multiple TCM prescriptions in the treatment of stroke have not been thoroughly studied. Objective of the study: This study aimed to reveal the mechanisms underlying the synergistic effects of these TCM prescrip...
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Ionic liquids (ILs) have great potential for application in energy storage and conversion devices. They have been identified as promising electrolytes candidates in various battery systems. However, the practical application of many ionic liquids remains limited due to the unfavorable melting points (Tm) which constrain the operating temperatures o...
Cover Page
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Dear Colleagues, The use of In-silico technologies for drug discovery began in the early 2000s with applications such as predicting ADMET, bacterial mutagenicity,hERG inhibition, molecular docking and in-depth docking simulations. The field has been continuously expanding ever since and the tasks at hand have become more complex and led to develop...
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The transcriptional regulators YAP (Yes-associated protein) and TAZ (transcriptional co-activator with PDZ-binding motif) are the major downstream effectors in the Hippo pathway and are involved in cancer progression through modulation of the activity of TEAD (transcriptional enhanced associate domain) transcription factors. To exploit the advantag...
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Research in chemistry increasingly requires interdisciplinary work prompted by, among other things, advances in computing, machine learning, and artificial intelligence. Everyone working with molecules, whether chemist or not, needs an understanding of the representation of molecules in a machine‐readable format, as this is central to computational...
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As a continuation of our research on the chemical reactivity, pharmacokinetics and ADMET properties of cyclopeptides of marine origin with potential therapeutic abilities, in this work our already presented integrated molecular modeling protocol has been used for the study of the chemical reactivity and bioactivity properties of the Veraguamides A–...
Preprint
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Collecting labeled data for many important tasks in chemoinformatics is time consuming and requires expensive experiments. In recent years, machine learning has been used to learn rich representations of molecules using large scale unlabeled molecular datasets and transfer the knowledge to solve the more challenging tasks with limited datasets. Var...
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Objective: To explore the mechanism of edaravone in the treatment of oxidative stress in rats with cerebral infarction based on quantitative proteomics technology. Method: The modified Zea Longa intracavitary suture blocking method was utilized to make rat CI model. After modeling, the rat was intragastrically given edaravone for 7 days, once a...
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As a frequent cause of colitis and nosocomial infections, Clostridium difficile continues to be an important pathogen of concern. Up to the authors’ knowledge, no specific medication is available to counteract the effect of C. difficile toxins. This study aimed to identify the most potential antagonists against the two major toxins of C. difficile:...
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The selection of experimental conditions leading to a reasonable yield is an important and essential element for the automated development of a synthesis plan and the subsequent synthesis of the target compound. The classical QSPR approach, requiring one-to-one correspondence between chemical structure and a target property, can be used for optimal...
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Inhibitors of DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug discovery. They are also chemical tools to understand the biochemistry of epigenetic processes. Herein, we report five distinct inhibitors of DNMT1 characterized in enzymatic inhibition assays that did not show activity with DNMT3B. It was concluded that the d...
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Background Vaccination programs have been launched worldwide to halt the spread of COVID-19. However, the identification of existing, safe compounds with combined treatment and prophylactic properties would be beneficial to individuals who are waiting to be vaccinated, particularly in less economically developed countries, where vaccine availabilit...
Preprint
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We have previously shown that prenyl and aliphatic triazoles are interesting motifs to prepare new chemical entities for antiparasitic and antituberculosis drug development. In this opportunity a new series of prenyl-1,2,3-triazoles were prepared from isoprenyl azides and different alkynes looking for new antimalarial drug candidates. The compounds...
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Nanotoxicology is a relatively new field of research concerning the study and application of nanomaterials to evaluate the potential for harmful effects in parallel with the development of applications. Nanotoxicology as a field spans materials synthesis and characterisation, assessment of fate and behaviour, exposure science, toxicology / ecotoxic...
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Humans are now in a bioinformatics and chemo informatics century, where we can foresee data across domains like as healthcare, the environmental, technology, and public health. The use of information sharing in silico methodologies has impacted sickness administration by predicting the absorption, distribution, metabolism, excretion, and toxicity (...
Preprint
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The majority of bioactive molecules act on membrane proteins or intracellular targets and therefore needs to partition into or cross biological membranes. Natural products often exhibit lipid modifications to facilitate critical molecule-membrane interactions and in many cases their bioactivity is markedly reduced upon removal of a lipid group. How...
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Breast cancer is one of the most common malignancies in women worldwide. Traditional Chinese medicine has been used as adjunctive or complementary therapy for breast cancer. Diterpenoids from Euphorbia fischeriana Steud. have been demonstrated to possess anti-breast-cancer activity. This research was aimed to systematically explore the diterpenoids...
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Food compounds with a bitter taste have a role in human health, both for their capability to influence food choice and preferences and for their possible systemic effect due to the modulation of extra-oral bitter taste receptors (TAS2Rs). Investigating the interaction of bitter food compounds with TAS2Rs is a key step to unravel their complex effec...