Chemo-informatics - Science topic

The chlorine atom plays a vital role in drug design, yet the benefits of chlorine in 250 FDA-approved chlorine-containing drugs have not been studied properly. To see the “magic chloro” effect, computational studies have been carried out for 35 inhibitors, which are numbered as 12 complexes with (parent (–H), one chlorine, or two chlorine) substitu...

Shigella sonnei is a gram-negative bacterium and is the primary cause of shigellosis in advanced countries. An exceptional rise in the prevalence of the disease has been reported in Asia, the Middle East, and Latin America. To date, no preventive vaccine is available against S . sonnei infections. This pathogen has shown resistances towards both fi...

Many natural products have been acquired from plants for their helpful properties. Medicinal plants are used for treating a variety of pathologies or symptoms. The axes of many pathological processes are inflammation, oxidative stress, and senescence. This work is focused on identifying Mexican medicinal plants with potential anti-oxidant, anti-inf...

The present study aimed to investigate the decolorization of various commercial dyes through bioinformatics analysis, utilizing techniques such as molecular docking, molecular dynamics simulation, and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA). These analyses were conducted on different commercial dyes to evaluate their potential f...

Untargeted metabolomics, facilitated by mass spectrometry, represents an analytical approach aimed at globally detecting organic molecules (including metabolites and environmental pollutants) present in a particular space (e.g., cell, tissue/organ, environment). The identification of these molecules is greatly enhanced through the application of ch...

Colorectal cancer (CRC) is a frequent malignancy with a poor prognosis and a high fatality rate, unlike other malignancies. Structural improvements have been developed to better comprehend the binding of small-molecule inhibitors, reducing the side effects of chemotherapy medications. A significant functional group extensively present in both pharm...

Biological humification is the core process in sludge composting for organic matter stabilization. Characterizing dissolved organic matter (DOM) would be a promising way for tracking humification, but still needs fundamental understanding. This study evidenced the role of DOM in deciphering humification via comprehensive and expansive chemoinformat...

Frontiers in Medicinal Chemistry is a book series devoted to reviews on research topics relevant to medicinal chemistry and allied disciplines. Frontiers in Medicinal Chemistry covers developments in rational drug design, bioorganic chemistry, high-throughput screening, combinatorial chemistry, compound diversity measurements, drug absorption, drug...

Sponges are considered as one of the top spatial competitors on reef ecosystems and their success is due partly to the strong chemical defences against pathogenic microbial attacks, predators and other benthic dwelling competitors. This is the first study on the investigation of chemical defences of common intertidal marine sponges, including Pseud...

Science and art have been connected for centuries. With the development of new computational methods, new scientific disciplines have emerged, such as computational chemistry, and related fields, such as cheminformatics. Chemoinformatics is grounded on the chemical space concept: a multi-descriptor space in which chemical structures are described....

The number of databases of natural products (NPs) has increased substantially. Latin America is extraordinarily rich in biodiversity, enabling the identification of novel NPs, which has encouraged both the development of databases and the implementation of those that are being created or are under development. In a collective effort from several La...

Ischemic stroke (IS) is one of the leading causes of mortality worldwide. It is characterized by the partial or total occlusion of arteries that supply blood to the brain, leading to the death of brain cells. In recent years, natural bioactive compounds (NBCs) have shown properties that ameliorate the injury after IS and improve the patient's outco...

The emergence and immune evasion ability of SARS-CoV-2 Omicron strains, mainly BA.5.2 and BF.7 and other variants of concern have raised global apprehensions. With this context, the discovery of multitarget inhibitors may be proven more comprehensive paradigm than its one-drug-to-one target counterpart. In the current study, a library of 271 phytoc...

Predicting p K a values of small molecules has key applications in drug discovery and molecular simulation. However, current methods face challenges in rigorously interpreting experimental data and ensuring thermodynamic consistency between successive p K a values. To address these limitations, we present Uni-p K a , an accurate and reliable p K a...

An average person, if asked on the street about the subject of biomathematics, might look a little bewildered: many people, while thinking about biology, in fact think about the respective school subject and just cannot phatom the use of mathematics there. However, even common flowers such as yellow chamomiles or sunflowers show in their middles ar...

The need to identify scientific databases that can be used to design learning environments to solve authentic problems in computational chemistry, computational biology, chemoinformatics and bioinformatics becomes of great importance to developing computational thinking skills in the student. This study displays a systematic literature search condu...

There is increasing awareness of epigenetics's importance in understanding disease etiologies and developing novel therapeutics. An increasing number of publications in the past few years reflect the renewed interest in epigenetic processes and their relationship with food chemicals. However, there needs to be a recent study that accounts for the m...

There is an increasing awareness of the importance of epigenetics to understand disease etiologies and develop novel therapeutics. Concomitantly, the renewed interest in epigenetic processes and their relationship with food chemicals has been reflected by an increasing number of publications in the past few years. However, there is a lack of a rece...

The RNA-binding protein human antigen R (HuR) regulates stability, translation, and nucleus-to-cytoplasm shuttling of its target mRNAs. This protein has been progressively recognized as a relevant therapeutic target for several pathologies, like cancer, neurodegeneration, as well as inflammation. Inhibitors of mRNA binding to HuR might thus be bene...

Aim. To analyze commercially available fluorine containing compounds for the possibility of their use in the 19F NMR FAXS method. Materials and methods. The selection of fluorine-containing fragments for the study was performed using 3.9 million instock screening compounds and 248,000 in-stock building-blocks from Enamine Ltd library. The selection...

Drug-Induced Liver Injury (DILI), also known as Hepatotoxicity, refers to unexpected liver damage triggered by common medications, which harms hepatocytes and other liver cells. This damage can either be intrinsic, appearing shortly after drug exposure, or idiosyncratic, emerging from intricate interactions of individual and environmental factors w...

G9a is a histone-lysine methyltransferase that performs the mono-and dimethylation of lysine 9 at histone 3 of the nucleosome. It belongs to the SET PKMT family, and its methylations are related to promoter repression and activation. G9a is a promising epigenetic target. Despite the fact that there are several G9a inhibitors under development, ther...

With the growing amount of chemical data stored digitally, it has become crucial to represent chemical compounds accurately and consistently. Harmonized representations facilitate the extraction of insightful information from datasets, and are advantageous for machine learning applications. To achieve consistent representations throughout datasets,...

Motivation: Next Generation Sequencing technologies make it possible to detect rare genetic variants in individual patients. Currently, more than a dozen software and web services have been created to predict the pathogenicity of variants related with changing of amino acid residues. Despite considerable efforts in this area, at the moment there i...

Candida albicans is the most common pathogen responsible for both spontaneous and recurrent candidiasis. The available treatment of Candida infections has several adverse effects, and the development of new drugs is critical. The current study looked at the synthesis of anti-Candida metabolites by Streptomyces sp. HC14 recovered from a soft coral....

The RNA-binding protein Human antigen R (HuR) regulates stability, translation, and nucleus-to-cytoplasm shuttling of its target mRNAs. The protein has been progressively recognized as a relevant therapeutic target for several pathologies like cancer, neurodegeneration, as well as inflammation. Inhibitors of mRNA binding to HuR might thus be benefi...

Chagas disease is caused by the parasite Trypanosoma cruzi. One of the two first-line drugs for treatment is nifurtimox, a nitrofuran that exhibits high toxicity. Therefore, the need arises to investigate new therapeutic options, and, in this sense, our objective was to study compounds that maintain the trypanocidal activity associated with the fur...

Citation: Raslan, M.A.; Raslan, S.A.; Shehata, E.M.; Mahmoud, A.S.; Sabri, N.A. Advances in the Applications of Bioinformatics and Chemoinformatics. Abstract: Chemoinformatics involves integrating the principles of physical chemistry with computer-based and information science methodologies, commonly referred to as "in silico techniques", in order...

Plants of the Phoradendron genus have been traditionally used for their lipid- and glucose-lowering effects. However, the compounds responsible for these effects and the overall chemical profile of these plants have not been thoroughly investigated. We aimed to characterize the metabolome of leaves, stems, and aerial parts of the Phoradendron brach...

In modern drug discovery, the combination of chemoinformatics and quantitative structure-activity relationship (QSAR) modeling has emerged as a formidable alliance, enabling researchers to harness the vast potential of machine learning (ML) techniques for predictive molecular design and analysis. This review delves into the fundamental aspects of c...

The South Shetland Trough, Antarctica, is an underexplored region for microbiological and biotechnological exploitation. Herein, we describe the isolation and characterisation of the novel bacterium Lacinutrix shetlandiensis sp. nov. WUR7 from a deep-sea environment. We explored its chemical diversity via a metabologenomics approach, wherein the OS...

Plants incorporate acquired carbon and nitrogen into amino acid metabolism, whereby the building blocks of proteins and the precursors of various metabolites are produced. This fundamental demand requires tight amino acid metabolism to sustain physiological homeostasis. There is increasing evidence that amino acid metabolism undergoes plastic alter...

Cosmetics form an important part of our daily lives, and it is therefore important to understand the basic physicochemical properties, metabolic pathways, and toxicological and safe concentrations of these cosmetics molecules. Therefore, comprehensive cosmetic ingredients bioinformatics platform (CCIBP) was developed here, which is a unique compreh...

Moringa oleifera, also known as kelor, this plant is better known to have benefits in the field of health including having properties as an antioxidant and anticancer. Several previous studies have revealed the potential of Moringa oleifera in the health sector such as anti-inflammatory, wound healing, antidiabetic, and antiviral. This study aims t...

Science and art have been connected for centuries. With the development of new computational methods, new scientific disciplines have emerged, such as computational chemistry, and related fields, such as chemoinformatics that use informatic methods to solve chemical problems focusing on small molecules. Chemoinformatics is grounded on the chemical...

Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA...

In the realm of modern drug discovery, the integration of chemoinformatics and quantitative structure-activity relationship (QSAR) modeling has emerged as a formidable alliance, enabling researchers to harness the vast potential of machine learning (ML) techniques for predictive molecular design and analysis. This review delves into the fundamental...

DXR (1-deoxy-d-xylulose-5-phosphate reductoisomerase) is an essential enzyme in the Methylerythritol 4-phosphate (MEP) pathway, which is used by M. tuberculosis and a few other pathogens. This essential enzyme in the isoprenoid synthesis pathway has been previously reported as an important target for antibiotic drug design. However, till now, there...

Alzheimer's disease (AD) has become a major public health concern and the fifth major cause of death among the aging population globally. In this study, the total phenols and flavonoids contents (TPC and TFC) and in vitro antioxidant actions of the methanol extract and the various fractions of Aframomum melegueta were evaluated using 2,2-diphenyl-2...

Aim: This study aimed to develop a chemoinformatic tool for extracting natural product information from academic literature. Materials & methods: Machine learning graph embeddings were used to extract knowledge from a knowledge graph, connecting properties, molecular data and BERTopic topics. Results: Metapath2Vec performed best in extracting compo...

A catalyst selection method for the optimization of an asymmetric, vinylogous Mukaiyama aldol reaction is described. A large library of commercially available and synthetically accessible copper-bis(oxazoline) catalysts was constructed in silico. Conformer-dependent, grid-based descriptors were calculated for each catalyst, defining a chemical feat...

Ion channels play important roles in fundamental biological processes, such as electric signaling in cells, muscle contraction, hormone secretion, and regulation of the immune response. Targeting ion channels with drugs represents a treatment option for neurological and cardiovascular diseases, muscular degradation disorders, and pathologies relate...

Natural Products (NP) are essential for the discovery of novel drugs and products for numerous biotechnological applications. The NP discovery process is expensive and time-consuming, having as major hurdles dereplication (early identification of known compounds) and structure elucidation, particularly the determination of the absolute configuratio...

Introduction: This paper proposes DBsimilarity to organize structural databases into Similarity Networks to better understand the rich information available. Method: DBsimilarity was written in Jupyter Notebooks to be easy to follow and values readability. It converts SDF files into CSV files, adds chemoinformatics data, constructs a MZMine custom...

Leishmaniasis, a category 1 neglected protozoan disease caused by a kinetoplastid pathogen called Leishmania, is transmitted through dipteran insect vectors (phlebotomine, sand flies) in three main clinical forms: fatal visceral leishmaniasis, self-healing cutaneous leishmaniasis, and mucocutaneous leishmaniasis. Generic pentavalent antimonials hav...

The sustainable management of the environment and crop production in modern agriculture involves dealing with challenges from climate change, environmental pollution, depletion of natural resources, as well as pressure to cope with dependence on agricultural inputs. Balancing crop productivity with environmental sustainability is one of the main ch...

Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discover...

Pristine environments, such as caves, are unique habitats that are isolated from human activity and are exposed to extreme environmental conditions. These environments are rich sources of microbial diversity, and the microorganisms that thrive in these conditions have developed unique survival skills. One such skill is the biosynthesis of secondary...

Chemoinformatics is an independent inter-discipline with a broad impact in drug design and discovery, medicinal chemistry, biochemistry, analytical and organic chemistry, natural products, and several other areas in chemistry. Through collaborations, scientific exchanges, and participation in international research networks, Latin American scientis...

Nearly all living cells undergo DNA replication in order to duplicate their genome; this multi-step biological process is tightly regulated by different cellular machineries and numerous multi-protein complexes. MCM2 (Minichromosome maintenance protein 2) is a key player in this game and its expression profile has been strongly correlated with can...

Antibiotics are drugs that have revolutionized the world scenario for the treatment of infectious diseases caused by bacteria and have reduced morbidity and mortality rates worldwide. Due to the increase in population and veterinary treatment, the use of medicines for health and treatment in animals has increased considerably. In this context, the...

Chemoinformatics is the combination of physical chemistry theory with computer and information science techniques "in silico techniques" to a variety of descriptive and prescriptive chemistry issues, including applications to biology, drug discovery, and related molecular areas. On the other hand, machine learning has become a vital tool for drug d...

GUIDEMOL is a Python computer program based on the RDKit software to process molecular structures and calculate molecular descriptors with a graphical user interface using the tkinter package. It can calculate descriptors already implemented in RDKit as well as grid representations of 3D molecular structures using the electrostatic potential or vox...

Efficient chemical library design for high-throughput virtual screening and drug design requires a pre-screening filter pipeline capable of labeling aggregators, pan-assay interference compounds (PAINS), and rapid elimination of swill (REOS); identifying or excluding covalent binders; flagging moieties with specific bio-evaluation data; and incorpo...

Epithelial cell transforming 2 (ECT2) is a potential oncogene and a number of recent studies have correlated it with the progression of several human cancers. Despite this elevated attention for ECT2 in oncology-related reports, there is no collective study to combine and integrate the expression and oncogenic behavior of ECT2 in a panel of human c...

This review presents an analysis of different algorithms for predicting the sensory ability of organic compounds towards metal ions based on their chemical formula. A database of chemosensors containing information on various classes of suitable compounds, including dipyrromethenes, BODIPY, Schiff bases, hydrazones, fluorescein, rhodamine, phenanth...

Peptides are a re-emerged strategy to fight a plethora of diseases and their utility has been expanded to new areas. Now sequence-based peptide design opens up new possibilities to develop peptidic molecular entities. However, its methodological limitations (e.g., its inefficiency in designing large peptides and that do not allow the analysis of po...

Background: The increasing amount of chemical reaction data makes traditional ways to navigate its corpus less effective, while the demand for novel approaches and instruments is rising. Recent data science and machine learning techniques support the development of new ways to extract value from the available reaction data. On the one side, Comput...

Structural diversification of lead molecules is a key component of drug discovery to explore close-in chemical space. Late stage functionalizations (LSFs) are versatile methodologies capable of installing functional handles on richly decorated intermediates to deliver numerous diverse products in a single reaction. Predicting the regioselectivity o...

Structural diversification of lead molecules is a key component of drug discovery to explore chemical space. Late stage functionalizations (LSFs) are versatile methodologies capable of installing functional handles on richly decorated intermediates to deliver numerous diverse products in a single reaction. Predicting the regioselectivity of LSF is...

High uric acid is associated with gout, hypertension, metabolic syndrome, cardiovascular disease, and kidney disease. URAT1 (SLC22A12), originally discovered in mice as Rst, is generally considered a very selective uric acid transporter compared to other closely-related kidney uric acid transporters such as OAT1 (SLC22A6, NKT) and OAT3 (SLC22A8). W...

Essential oils (EOs) are a promising source for novel environmentally safe insecticides. However, the structural diversity of their compounds poses challenges to accurately elucidate their biological mechanisms of action. We present a new chemoinformatics methodology aimed at predicting the impact of essential oil (EO) compounds on the molecular ta...

Background: Coronary Heart Disease (CHD), commonly known as the silent killer, impacted the severity of COVID-19 patients during the pandemic era. Thrombosis or blood clots create the buildup of plaque on the coronary artery walls of the heart, which leads to coronary heart disease. Cyclooxygenase 1 (COX-1) is involved in the production of prostacy...

Chemical libraries and compound data sets are among the main inputs to start the drug discovery process at universities, research institutes, and the pharmaceutical industry. The approach used in the design of compound libraries, the chemical information they possess, and the representation of structures, play a fundamental role in the development...

Bacterial infections are increasingly problematic due to the rise of antimicrobial resistance. Consequently, the rational design of materials naturally resistant to biofilm formation is an important strategy for preventing medical device-associated infections. Machine learning (ML) is a powerful method to find useful patterns in complex data from a...