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1.
Biol Pharm Bull ; 47(9): 1504-1510, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39284734

RESUMEN

Signal transducer and activator of transcription 3 (STAT3) is a pleiotropic factor involved in multiple vital biological processes and a key mediator of gene transcription in response to cytokines, growth factors and aberrant activation of oncogenic signaling. STAT3 has two splicing isoforms, STAT3α and STAT3ß, derived from alternative splicing of exon 23 within pre-mRNA. STAT3ß differs from STAT3α by replacement of 55 amino-acid residues in the C-terminal transactivation domain with 7 specific amino acids. Thus, a shorter STAT3ß was originally regarded as a dominant negative isoform of STAT3α. Recently accumulating evidence from independent studies have shown STAT3 splicing isoforms confer distinct and overlapping functions in many fundamental cellular regulatory steps such as cell differentiation, inflammatory responses, and cancer progression. However, relatively little is known about the mechanisms of STAT3 pre-mRNA splicing, and it remains undiscovered which chemical compounds or bioactive substances can induce the STAT3ß expression. In this study, we generated a potent reporter for detection of alternative splicing of STAT3 pre-mRNA optimized for the screening of function-known chemical library, and successfully identified entinostat, a histone deacetylase inhibitor, as a novel inducer of STAT3ß through modulating mRNA splicing. Our findings demonstrate that alternative splicing of STAT3 can be regulated by a compound, providing an important clue for understanding the regulation mechanisms of the expression balance of STAT3 isoforms in a chemical biology approach. Entinostat is likely to be a promising seed compound for elucidating how the higher ratio of STAT3ß expression impacts on biological responses associated with Janus kinase (JAK)/STAT3 signaling pathway.


Asunto(s)
Empalme Alternativo , Benzamidas , Piridinas , Precursores del ARN , Factor de Transcripción STAT3 , Factor de Transcripción STAT3/metabolismo , Factor de Transcripción STAT3/genética , Empalme Alternativo/efectos de los fármacos , Humanos , Precursores del ARN/genética , Precursores del ARN/metabolismo , Piridinas/farmacología , Benzamidas/farmacología , Inhibidores de Histona Desacetilasas/farmacología , Células HEK293 , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo
2.
Antimicrob Agents Chemother ; : e0090924, 2024 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-39194208

RESUMEN

In vitro screening of large compound libraries with automated high-throughput screening is expensive and time-consuming and requires dedicated infrastructures. Conversely, the selection of DNA-encoded chemical libraries (DECLs) can be rapidly performed with routine equipment available in most laboratories. In this study, we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity-based selection of the DELopen library (open access for academics), containing 4.2 billion compounds. The identified inhibitors were peptide-like compounds containing an N-terminal electrophilic group able to form a covalent bond with the nucleophilic Cys145 of Mpro, as confirmed by x-ray crystallography. This DECL selection campaign enabled the discovery of the unoptimized compound SLL11 (IC50 = 30 nM), proving that the rapid exploration of large chemical spaces enabled by DECL technology allows for the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. As demonstrated further by x-ray crystallography, SLL11 was found to adopt a highly unique U-shaped binding conformation, which allows the N-terminal electrophilic group to loop back to the S1' subsite while the C-terminal amino acid sits in the S1 subsite. MP1, a close analog of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 µM) cell lines. As peptide-like compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds will be explored in the future to improve their antiviral activity.

3.
Future Med Chem ; 16(10): 1029-1051, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38910575

RESUMEN

Compound databases (DBs) are essential tools for drug discovery. The number of DBs in public domain is increasing, so it is important to analyze these DBs. In this article, the main characteristics of 64 DBs will be presented. The methodological strategy used was a literature search. To analyze the characteristics obtained in the review, the DBs were categorized into two subsections: Open Access and Commercial DBs. Open access includes generalist DBs (containing compounds of diverse origins), DBs with specific applicability, DBs exclusive to natural products and those containing compounds with specific pharmacological action. The literature review showed that there are challenges to making these repositories available, such as standardizing information curation practices and funding to maintain and sustain them.


[Box: see text].


Asunto(s)
Productos Biológicos , Descubrimiento de Drogas , Productos Biológicos/química , Productos Biológicos/farmacología , Humanos , Bases de Datos de Compuestos Químicos , Bases de Datos Factuales , Bases de Datos Farmacéuticas
4.
Chemistry ; 30(48): e202402082, 2024 Aug 27.
Artículo en Inglés | MEDLINE | ID: mdl-38897925

RESUMEN

The construction of a chemical library based on natural products is a promising method for the synthesis of natural product-like compounds. In this study, we synthesized a terpenoid alkaloid-like compound library based on the humulene skeleton. Our strategy, which enables access to diverse ring systems such as 11-membered monocyclic, oxabicyclic, and medium-sized aza ring-containing scaffolds, involves the introduction of a nitrogen atom, an intermolecular C-O bond formation via Lewis acid-mediated epoxide-opening transannulation, and a ring-reconstruction strategy based on olefin metathesis. A cheminformatics analysis based on their structural and physicochemical properties revealed that the synthesized compounds have high three-dimensionality and high natural product likeness scores but with structural novelty. The usefulness of the terpenoid alkaloid-like compound library for drug discovery and the accessibility to structure-activity relationship studies were validated by performing an assay for osteoclast-specific tartrate-resistant acid phosphatase activity, resulting in the identification of a seed compound for bone-resorptive diseases such as osteoporosis.


Asunto(s)
Alcaloides , Sesquiterpenos Monocíclicos , Alcaloides/química , Alcaloides/síntesis química , Sesquiterpenos Monocíclicos/química , Relación Estructura-Actividad , Terpenos/química , Terpenos/síntesis química , Productos Biológicos/química , Productos Biológicos/síntesis química , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/síntesis química , Sesquiterpenos/química , Sesquiterpenos/síntesis química
5.
ACS Infect Dis ; 10(5): 1561-1575, 2024 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-38577994

RESUMEN

DNA-encoded chemical library (DEL) technology provides a time- and cost-efficient method to simultaneously screen billions of compounds for their affinity to a protein target of interest. Here we report its use to identify a novel chemical series of inhibitors of the thioesterase activity of polyketide synthase 13 (Pks13) from Mycobacterium tuberculosis (Mtb). We present three chemically distinct series of inhibitors along with their enzymatic and Mtb whole cell potency, the measure of on-target activity in cells, and the crystal structures of inhibitor-enzyme complexes illuminating their interactions with the active site of the enzyme. One of these inhibitors showed a favorable pharmacokinetic profile and demonstrated efficacy in an acute mouse model of tuberculosis (TB) infection. These findings and assay developments will aid in the advancement of TB drug discovery.


Asunto(s)
Antituberculosos , Inhibidores Enzimáticos , Mycobacterium tuberculosis , Sintasas Poliquetidas , Bibliotecas de Moléculas Pequeñas , Tioléster Hidrolasas , Animales , Humanos , Ratones , Antituberculosos/química , Antituberculosos/farmacología , Antituberculosos/uso terapéutico , Proteínas Bacterianas/antagonistas & inhibidores , Proteínas Bacterianas/química , Cristalografía por Rayos X , Modelos Animales de Enfermedad , Descubrimiento de Drogas , Evaluación Preclínica de Medicamentos , Inhibidores Enzimáticos/farmacología , Inhibidores Enzimáticos/química , Mycobacterium tuberculosis/enzimología , Mycobacterium tuberculosis/efectos de los fármacos , Sintasas Poliquetidas/metabolismo , Sintasas Poliquetidas/química , Sintasas Poliquetidas/genética , Bibliotecas de Moléculas Pequeñas/química , Bibliotecas de Moléculas Pequeñas/farmacología , Tioléster Hidrolasas/antagonistas & inhibidores , Tioléster Hidrolasas/metabolismo , Tioléster Hidrolasas/química , Tioléster Hidrolasas/genética , Tuberculosis/tratamiento farmacológico , Tuberculosis/microbiología
6.
Expert Opin Drug Discov ; 19(4): 403-414, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38300511

RESUMEN

INTRODUCTION: Large chemical spaces (CSs) include traditional large compound collections, combinatorial libraries covering billions to trillions of molecules, DNA-encoded chemical libraries comprising complete combinatorial CSs in a single mixture, and virtual CSs explored by generative models. The diverse nature of these types of CSs require different chemoinformatic approaches for navigation. AREAS COVERED: An overview of different types of large CSs is provided. Molecular representations and similarity metrics suitable for large CS exploration are discussed. A summary of navigation of CSs in generative models is provided. Methods for characterizing and comparing CSs are discussed. EXPERT OPINION: The size of large CSs might restrict navigation to specialized algorithms and limit it to considering neighborhoods of structurally similar molecules. Efficient navigation of large CSs not only requires methods that scale with size but also requires smart approaches that focus on better but not necessarily larger molecule selections. Deep generative models aim to provide such approaches by implicitly learning features relevant for targeted biological properties. It is unclear whether these models can fulfill this ideal as validation is difficult as long as the covered CSs remain mainly virtual without experimental verification.


Asunto(s)
Algoritmos , Quimioinformática , Humanos
7.
Microbiol Spectr ; 12(4): e0409523, 2024 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-38376363

RESUMEN

Candida albicans, one of the most prevalent human fungal pathogens, causes diverse diseases extending from superficial infections to deadly systemic mycoses. Currently, only three major classes of antifungal drugs are available to treat systemic infections: azoles, polyenes, and echinocandins. Alarmingly, the efficacy of these antifungals against C. albicans is hindered both by basal tolerance toward the drugs and the development of resistance mechanisms such as alterations of the drug's target, modulation of stress responses, and overexpression of efflux pumps. Thus, the need to identify novel antifungal strategies is dire. To address this challenge, we screened 3,049 structurally-diverse compounds from the Boston University Center for Molecular Discovery (BU-CMD) chemical library against a C. albicans clinical isolate and identified 17 molecules that inhibited C. albicans growth by >80% relative to controls. Among the most potent compounds were CMLD013360, CMLD012661, and CMLD012693, molecules representing two distinct chemical scaffolds, including 3-hydroxyquinolinones and a xanthone natural product. Based on structural insights, CMLD013360, CMLD012661, and CMLD012693 were hypothesized to exert antifungal activity through metal chelation. Follow-up investigations revealed all three compounds exerted antifungal activity against non-albicans Candida, including Candida auris and Candida glabrata, with the xanthone natural product CMLD013360 also displaying activity against the pathogenic mould Aspergillus fumigatus. Media supplementation with metallonutrients, namely ferric or ferrous iron, rescued C. albicans growth, confirming these compounds act as metal chelators. Thus, this work identifies and characterizes two chemical scaffolds that chelate iron to inhibit the growth of the clinically relevant fungal pathogen C. albicansIMPORTANCEThe worldwide incidence of invasive fungal infections is increasing at an alarming rate. Systemic candidiasis caused by the opportunistic pathogen Candida albicans is the most common cause of life-threatening fungal infection. However, due to the limited number of antifungal drug classes available and the rise of antifungal resistance, an urgent need exists for the identification of novel treatments. By screening a compound collection from the Boston University Center for Molecular Discovery (BU-CMD), we identified three compounds representing two distinct chemical scaffolds that displayed activity against C. albicans. Follow-up analyses confirmed these molecules were also active against other pathogenic fungal species including Candida auris and Aspergillus fumigatus. Finally, we determined that these compounds inhibit the growth of C. albicans in culture through iron chelation. Overall, this observation describes two novel chemical scaffolds with antifungal activity against diverse fungal pathogens.


Asunto(s)
Productos Biológicos , Micosis , Xantonas , Humanos , Candida albicans , Antifúngicos/farmacología , Antifúngicos/uso terapéutico , Micosis/tratamiento farmacológico , Farmacorresistencia Fúngica , Quelantes/farmacología , Quelantes/uso terapéutico , Aspergillus fumigatus , Hierro , Xantonas/uso terapéutico , Pruebas de Sensibilidad Microbiana
8.
Anal Biochem ; 687: 115452, 2024 04.
Artículo en Inglés | MEDLINE | ID: mdl-38158105

RESUMEN

Low-molecular drug discovery using DNA-encoded chemical library (DEL) is a powerful technology, although improving the partitioning efficiency of affinity ligands from DEL remains a challenge. Here, we assessed the usefulness of microbead-assisted capillary electrophoresis (MACE) for partitioning peptide-oligonucleotide conjugates (POCs), in which high selection pressure is applied because of different mobility of target-modified beads and POCs during CE. Despite their different charge characteristics, all POCs were well separated from the beads. When bead extraction was performed, the tagged DNA amplification was observed only in the couple of a ligand/target, suggesting proficiently specific partitioning of peptide ligands was accomplished using MACE.


Asunto(s)
Oligonucleótidos , Péptidos , Microesferas , Péptidos/química , Oligonucleótidos/química , Electroforesis Capilar/métodos , ADN/química , ADN de Cadena Simple
9.
Chem Asian J ; 18(21): e202300652, 2023 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-37721712

RESUMEN

Covalent crosslinking probes have arisen as efficient toolkits to capture and elucidate biomolecular interaction networks. Exploiting the potential of crosslinking in DNA-encoded chemical library (DEL) selection methods significantly boosted bioactive ligand discovery in complex physiological contexts. Herein, we incorporated o-nitrobenzyl alcohol (o-NBA) as a photo-activated lysine-selective crosslinker into divergent DEL formats and achieved covalent capture of ligand-target interactions featuring improved crosslinking efficiency and site-specificity. In addition, covalent DEL selection was realized with the modularly designed o-NBA-functionalized mock libraries.


Asunto(s)
Lisina , Bibliotecas de Moléculas Pequeñas , Bibliotecas de Moléculas Pequeñas/química , Ligandos , ADN/química
10.
Molecules ; 28(15)2023 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-37570623

RESUMEN

Protein-protein interactions (PPIs) are associated with various diseases; hence, they are important targets in drug discovery. However, the physicochemical empirical properties of PPI-targeted drugs are distinct from those of conventional small molecule oral pharmaceuticals, which adhere to the "rule of five (RO5)". Therefore, developing PPI-targeted drugs using conventional methods, such as molecular generation models, is challenging. In this study, we propose a molecular generation model based on deep reinforcement learning that is specialized for the production of PPI inhibitors. By introducing a scoring function that can represent the properties of PPI inhibitors, we successfully generated potential PPI inhibitor compounds. These newly constructed virtual compounds possess the desired properties for PPI inhibitors, and they show similarity to commercially available PPI libraries. The virtual compounds are freely available as a virtual library.


Asunto(s)
Descubrimiento de Drogas , Mapeo de Interacción de Proteínas , Descubrimiento de Drogas/métodos
11.
Metabolites ; 13(5)2023 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-37233666

RESUMEN

Due to the continued emergence of resistance and a lack of new and promising antibiotics, bacterial infection has become a major public threat. High-throughput screening (HTS) allows rapid screening of a large collection of molecules for bioactivity testing and holds promise in antibacterial drug discovery. More than 50% of the antibiotics that are currently available on the market are derived from natural products. However, with the easily discoverable antibiotics being found, finding new antibiotics from natural sources has seen limited success. Finding new natural sources for antibacterial activity testing has also proven to be challenging. In addition to exploring new sources of natural products and synthetic biology, omics technology helped to study the biosynthetic machinery of existing natural sources enabling the construction of unnatural synthesizers of bioactive molecules and the identification of molecular targets of antibacterial agents. On the other hand, newer and smarter strategies have been continuously pursued to screen synthetic molecule libraries for new antibiotics and new druggable targets. Biomimetic conditions are explored to mimic the real infection model to better study the ligand-target interaction to enable the designing of more effective antibacterial drugs. This narrative review describes various traditional and contemporaneous approaches of high-throughput screening of natural products and synthetic molecule libraries for antibacterial drug discovery. It further discusses critical factors for HTS assay design, makes a general recommendation, and discusses possible alternatives to traditional HTS of natural products and synthetic molecule libraries for antibacterial drug discovery.

12.
Biochimie ; 212: 143-152, 2023 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37088408

RESUMEN

Zika virus (ZIKV) infection is associated with severe neurological disorders and congenital malformation. Despite efforts to eradicate the disease, there is still neither vaccine nor approved drugs to treat ZIKV infection. The NS2B-NS3 protease is a validated drug target since it is essential to polyprotein virus maturation. In the present study, we describe an experimental screening of 2,320 compounds from the chemical library of the Muséum National d'Histoire Naturelle of Paris on ZIKV NS2B-NS3 protease. A total of 96 hits were identified with 90% or more of inhibitory activity at 10 µM. Amongst the most active compounds, five were analyzed for their inhibitory mechanisms by kinetics assays and computational approaches such as molecular docking. 2-(3-methoxyphenoxy) benzoic acid (compound 945) show characteristics of a competitive inhibition (Ki = 0.49 µM) that was corroborated by its molecular docking at the active site of the NS2B-NS3 protease. Taxifolin (compound 2292) behaves as an allosteric inhibitor whereas 3,8,9-trihydroxy-2-methyl-1H-phenalen-1-one (compound 128), harmol (compound 368) and anthrapurpurin (compound 1499) show uncompetitive inhibitions. These new NS2B-NS3 protease inhibitors are valuable hits to further hit-to-lead optimization.


Asunto(s)
Infección por el Virus Zika , Virus Zika , Humanos , Simulación del Acoplamiento Molecular , Proteínas no Estructurales Virales/química , Serina Endopeptidasas/química , Inhibidores de Proteasas/farmacología , Inhibidores de Proteasas/química , Péptido Hidrolasas , Antivirales/farmacología , Antivirales/química
13.
Pharmaceuticals (Basel) ; 16(3)2023 Mar 08.
Artículo en Inglés | MEDLINE | ID: mdl-36986512

RESUMEN

The concept of privileged structure has been used as a fruitful approach for the discovery of novel biologically active molecules. A privileged structure is defined as a semi-rigid scaffold able to display substituents in multiple spatial directions and capable of providing potent and selective ligands for different biological targets through the modification of those substituents. On average, these backbones tend to exhibit improved drug-like properties and therefore represent attractive starting points for hit-to-lead optimization programs. This article promotes the rapid, reliable, and efficient synthesis of novel, highly 3-dimensional, and easily functionalized bio-inspired tricyclic spirolactams, as well as an analysis of their drug-like properties.

14.
Front Mol Neurosci ; 16: 1336004, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-38249296

RESUMEN

Ion channels play a crucial role in a variety of physiological and pathological processes, making them attractive targets for drug development in diseases such as diabetes, epilepsy, hypertension, cancer, and chronic pain. Despite the importance of ion channels in drug discovery, the vastness of chemical space and the complexity of ion channels pose significant challenges for identifying drug candidates. The use of in silico methods in drug discovery has dramatically reduced the time and cost of drug development and has the potential to revolutionize the field of medicine. Recent advances in computer hardware and software have enabled the screening of ultra-large compound libraries. Integration of different methods at various scales and dimensions is becoming an inevitable trend in drug development. In this review, we provide an overview of current state-of-the-art computational chemistry methodologies for ultra-large compound library screening and their application to ion channel drug discovery research. We discuss the advantages and limitations of various in silico techniques, including virtual screening, molecular mechanics/dynamics simulations, and machine learning-based approaches. We also highlight several successful applications of computational chemistry methodologies in ion channel drug discovery and provide insights into future directions and challenges in this field.

15.
Beilstein J Org Chem ; 18: 1355-1378, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36247982

RESUMEN

This perspective is an attempt to document the problems that medicinal chemists are facing in drug discovery. It is also trying to identify relevant/possible, research areas in which academics can have an impact and should thus be the subject of grant calls. Accordingly, it describes how hit discovery happens, how compounds to be screened are selected from available chemicals and the possible reasons for the recurrent paucity of useful/exploitable results reported. This is followed by the successful hit to lead stories leading to recent and original antibacterials which are, or about to be, used in human medicine. Then, illustrated considerations and suggestions are made on the possible inputs of academic medicinal chemists. This starts with the observation that discovering a "good" hit in the course of a screening campaign still rely on a lot of luck - which is within the reach of academics -, that the hit to lead process requires a lot of chemistry and that if public-private partnerships can be important throughout these stages, they are absolute requirements for clinical trials. Concerning suggestions to improve the current hit success rate, one academic input in organic chemistry would be to identify new and pertinent chemical space, design synthetic accesses to reach these and prepare the corresponding chemical libraries. Concerning hit to lead programs on a given target, if no new hits are available, previously reported leads along with new structural data can be pertinent starting points to design, prepare and assay original analogues. In conclusion, this text is an actual plea illustrating that, in many countries, academic research in medicinal chemistry should be more funded, especially in the therapeutic area neglected by the industry. At the least, such funds would provide the intensive to secure series of hopefully relevant chemical entities which appears to often lack when considering the results of academic as well as industrial screening campaigns.

16.
Heliyon ; 8(8): e10108, 2022 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-36033279

RESUMEN

Obesity is one of the most common global health problems for all age groups with obese people at risk of a variety of associated health complications. Consequently, there is a need to develop new therapies that lower body fat without the side effects. However, obesity is a complex and systemic disease, so that in vitro results are not easily translatable to clinical situations. A promising way to circumnavigate these issues is to reposition already approved drugs for new treatments, enabling a more streamlined drug discovery process due to the availability of pre-existing pharmacological and toxicological datasets. Chemical libraries, such as the Prestwick Chemical Library of 1200 FDA approved drugs, are available for this purpose. We have developed a simple semi-automated whole-organism approach to screening the Prestwick Chemical Library for those compounds which reduce fat content using the model organism Caenorhabditis elegans. Our whole-organism approach to high-throughput screening identified 9 "lead" compounds that reduced fat within 2 weeks in the model. Further screening and analysis provided 4 "hit" compounds (Midodrine, Vinpocetine, Fenoprofen and Lamivudine) that showed significant promise as drugs to reduce fat levels. The effects of these candidates were found to further reduce fat content in nematodes where an nhr-49/PPAR mutation resulted in "overweight" worms. Upon unblinding the "hit" compounds, they were found to have recently been shown to have anti-obesity effects in mammalian models too. In developing a whole-animal chemical screen to identify pharmacological agents as potential anti-obesity compounds, we demonstrate how chemical libraries can be rapidly and relatively cheaply profiled for active hits. Using the nematode Caenorhabditis elegans thus enables drugs to be assessed for applicability in humans and provides a new incentive to explore drug repurposing as a feasible and efficient way to identify new anti-obesity compounds.

17.
Bioorg Med Chem Lett ; 75: 128948, 2022 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-35987508

RESUMEN

The c-MET receptor tyrosine kinase has received considerable attention as a cancer drug target yet there remains a need for inhibitors which are selective for c-MET and able to target emerging drug-resistant mutants. We report here the discovery, by screening a DNA-encoded chemical library, of a highly selective c-MET inhibitor which was shown by X-ray crystallography to bind to the kinase in an unprecedented manner. These results represent a novel mode of inhibiting c-MET with a small molecule and may provide a route to targeting drug-resistant forms of the kinase whilst avoiding potential toxicity issues associated with broad kinome inhibition.


Asunto(s)
Antineoplásicos , Proteínas Proto-Oncogénicas c-met , Antineoplásicos/farmacología , Línea Celular Tumoral , ADN , Inhibidores de Proteínas Quinasas/química , Bibliotecas de Moléculas Pequeñas/química
18.
Mol Inform ; 41(11): e2200116, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-35916110

RESUMEN

Technological advances and practical applications of the chemical space concept in drug discovery, natural product research, and other research areas have attracted the scientific community's attention. The large- and ultra-large chemical spaces are associated with the significant increase in the number of compounds that can potentially be made and exist and the increasing number of experimental and calculated descriptors, that are emerging that encode the molecular structure and/or property aspects of the molecules. Due to the importance and continued evolution of compound libraries, herein, we discuss definitions proposed in the literature for chemical space and emphasize the convenience, discussed in the literature to use complementary descriptors to obtain a comprehensive view of the chemical space of compound data sets. In this regard, we introduce the term chemical multiverse to refer to the comprehensive analysis of compound data sets through several chemical spaces, each defined by a different set of chemical representations. The chemical multiverse is contrasted with a related idea: consensus chemical space.


Asunto(s)
Productos Biológicos , Bibliotecas de Moléculas Pequeñas , Bibliotecas de Moléculas Pequeñas/química , Relación Estructura-Actividad , Estructura Molecular , Descubrimiento de Drogas
19.
Eur J Med Chem ; 240: 114505, 2022 Oct 05.
Artículo en Inglés | MEDLINE | ID: mdl-35839689

RESUMEN

Structurally diverse small compounds are utilized to obtain hit compounds that have suitable pharmacophores in appropriate three-dimensional conformations for the target drug receptors. We have focused on the 1,3,5-trioxazatriquinane skeleton, which has a rigid bowl-like structure enabling the diverse orientation of side chain units, leading to a novel small-scale focused library based on the skeleton. In the library screening for the orexin receptor, some of the compounds showed orexin receptor antagonistic activity with a high hit rate of 7%. By optimizing the hit compounds, we discovered a potent dual orexin receptor antagonist, 38b, and a selective orexin 1 receptor antagonist, 41b carrying the same plane structure. Both compounds showed reasonable brain permeability and beneficial effects when administered intraperitoneally to wild-type mice. Docking simulations of their eutomers, (-)-38b and (+)-41b, with orexin receptors suggested that the interaction between the 1,3,5-trioxazatriquinane core structure and the hydrophobic subpocket in orexin receptors enables a U-shape structure, which causes tight van der Waals interactions with the receptors similar to SB-334867, a selective orexin 1 receptor antagonist. These results indicate that the library approach utilizing the 1,3,5-trioxazatriquinanes bearing multiple effective residues (TriMERs) might be useful for the hit discovery process targeting not only opioid and orexin receptors but other G-protein coupled receptors.


Asunto(s)
Antagonistas de los Receptores de Orexina , Animales , Compuestos Heterocíclicos de 4 o más Anillos , Ratones , Antagonistas de los Receptores de Orexina/química , Antagonistas de los Receptores de Orexina/farmacología , Receptores de Orexina , Orexinas , Relación Estructura-Actividad
20.
J Gen Virol ; 103(6)2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35731650

RESUMEN

Oncolytic adenoviruses (OAds) have attracted much attention as novel anticancer agents. Numerous studies have examined the antitumour effects of combinational use of an OAd and anticancer agents; however, few chemical compounds enhancing OAd infection have been reported. In this study, we screened a food and drug administration (FDA)-approved drug library containing 1134 small chemical compounds to identify chemical compounds that enhance OAd replication in human tumour cells. We found that domperidone, a dopamine D2 receptor antagonist, significantly enhanced the replication of an OAd in human tumour cells, including human pancreatic tumour cells, by two-fivefold, resulting in improvement of OAd-mediated tumour cell killing activities. The E1A mRNA levels were significantly increased in domperidone-pre-treated cells following OAd infection, which contributed to the promotion of OAd replication. However, mRNA levels of the dopamine D2 receptor (DRD2), which is known to be a target molecule of domperidone, were undetectable in most of the tumour cells by real-time reverse transcription (RT)-PCR analysis, indicating that domperidone promoted OAd replication by acting on a molecule other than DRD2. This study provides important clues for the improvement of OAd-mediated cancer therapy.


Asunto(s)
Infecciones por Adenoviridae , Antineoplásicos , Viroterapia Oncolítica , Virus Oncolíticos , Adenoviridae/genética , Línea Celular Tumoral , Domperidona/farmacología , Antagonistas de Dopamina/farmacología , Humanos , Viroterapia Oncolítica/métodos , Virus Oncolíticos/genética , ARN Mensajero/genética
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