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Journal articles on the topic 'Synthèse guidée'

Author: Grafiati

Published: 25 May 2024

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1

Colas, Maxime, and Michel Deloizy. "Le Model Based Design pour l’apprentissage par conception guidée." J3eA 22 (2023): 1009. http://dx.doi.org/10.1051/j3ea/20231009.

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Cet article présente une démarche d’apprentissage par conception guidée reposant sur des techniques de prototypage rapide dans le domaine mécatronique. La pédagogie développée se veut intégrative et auto-contenue : elle ne nécessite pas de prérequis et apporte au fur et à mesure des besoins, l’ensemble des connaissances et compétences pluridisciplinaires nécessaires à la progression cohérente du projet de conception, tant d’un point de vue mécanique, programmation, qu’en termes de technique de contrôle-commande, le tout dans un volume horaire contraint. La ligne directrice employée vise à confronter de façon permanente, progressive et itérative, modèle simulé et système réel dans un objectif de dimensionnement de partie opérative, de validation de modèle et d’algorithmes de commande en tirant partie d’outils logiciels de contrôle/commande temps-réel, de synthèse de code et de simulation multiphysique.

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2

Landry, Rodrigue, and Omer Robichaud. "Un modèle heuristique pour l’individualisation de l’enseignement." Revue des sciences de l'éducation 11, no. 2 (November 30, 2009): 295–317. http://dx.doi.org/10.7202/900496ar.

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Résumé Cet article a pour objet de montrer l’importance pour la pratique éducative d’être guidée par un cadre théorique global et cohérent. Le modèle théorique présenté s’inspire de la théorie générale des systèmes et donne à la fois une analyse et une synthèse du système éducatif. Le modèle définit les composantes universelles et essentielles de tout système d’enseignement. Ces composantes du système éducatif doivent converger vers un même but, soit l’apprentissage individualisé. Le modèle théorique présenté est surtout heuristique, cherchant à définir les principes fondamentaux d’un enseignement qui répond aux besoins éducatifs de tous les apprenants.

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PAVAGEAU, S., A.-S. BREDILLET, A. LOPEZ, and M. GLONDUS-LASSIS. "La tolérance à l’incertitude lors d’une prise de décision est une compétence complexe du médecin généraliste." EXERCER 34, no. 195 (September 1, 2023): 312–21. http://dx.doi.org/10.56746/exercer.2023.195.312.

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Contexte. L’incertitude est inhérente à l’exercice de la médecine générale. Face aux plaintes des patients, le médecin généraliste (MG) peut se sentir démuni, indécis, anxieux, et doit trouver un moyen d’intégrer cette incertitude dans sa prise de décision. Cette composante a été étudiée dans diverses études qualitatives. Objectif. Apporter une analyse compréhensive de l’incertitude dans la prise de décision en soins premiers, à partir d’une métasynthèse qualitative. Méthodes. Analyse secondaire des études qualitatives : 1) revue de la littérature avec sélection des études qualitatives selon des critères d’inclusion et de qualité ; 2) identification de thèmes clés et « translation réciproque » des différents thèmes entre les études pour aboutir à une synthèse globale, avec une nouvelle interprétation ; 3) triangulation de deux chercheurs ; 4) protocole ENTREQ et guide eMERge pour la rédaction. Résultats. Dans la synthèse des 57 articles inclus, la prise de décision médicale en situation d’incertitude a pu être comprise comme : 1) une décision qui s’appuie sur le modèle de l’approche centrée sur le patient, par une relation de confiance et en s’adaptant au patient dans sa complexité ; 2) une décision guidée par un sentiment viscéral – le « gut-feeling » – visant à écarter le danger ; 3) une décision devant être partagée, de même que l’incertitude qui l’accompagne ; 4) une décision contextualisée, influencée par la notion de pression ; 5) une situation conditionnant le ressenti des MG vis-à-vis des expériences (manque de confiance, anxiété, stress). Conclusion. Cette synthèse originale précise comment la décision médicale partagée avec le patient, son entourage et les autres professionnels, ainsi que l’approche centrée sur le patient, permettent au MG de mieux tolérer son incertitude. Elle ne disparaît pas avec l’expérience, mais la façon de l’appréhender peut s’améliorer par une posture réflexive et en lien avec les valeurs du médecin. Elle est une compétence intrinsèque complexe du métier de MG.

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4

Bouchafa, Samia. "Décision cumulative pour la vision dynamique des systèmes." Revue Française de Photogrammétrie et de Télédétection, no. 202 (April 16, 2014): 2–26. http://dx.doi.org/10.52638/rfpt.2013.48.

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Les travaux présentés dans cette synthèse portent essentiellement sur l'analyse de scènes à partir de caméras mobiles avec pour application immédiate l'apport d'une vision par ordinateur efficace dans les systèmes autonomes. Ils sont le fruit d'une décennie de recherches menées d'abord à l'INRETS (actuellement IFSTTAR : Institut français des sciences et technologies des transports, de l'aménagement et des réseaux ) puis à l'Université Paris Sud XI (Institut d'Électronique Fondamentale). L'idée initiale est que l'autonomie d'un système implique, ne serait-ce que pour raisons énergétiques, une faible variété d'opérateurs de perception, dont les algorithmes de vision. Les "primitives" extraites des images seront intrinsèquement robustes et stables vis-à-vis de perturbations variées. Elles doivent de plus anticiper, voire faciliter, un processus de décision à divers niveaux voulu systématique. Les lignes de niveaux répondent parfaitement à ces contraintes : on vérifie sans peine leur robustesse et leur abondance dans une image suggère et alimente un processus de décision cumulatif (manipulant un objet de décision unique : l'histogramme généralisé en espace de vote). Nos efforts se sont alors concentrés sur deux aspects : 1) le premier concerne la définition d'une méthodologie cohérente dans laquelle un processus primaire d'extraction de lignes de niveaux est enrichi afin de permettre la construction de primitives plus complexes guidée par un modèle de déformation de l'image. Le nombre de composants donc la forme des primitives est fonction directe du nombre de variables caractérisant le mouvement (déformation) à déterminer. 2) Le second intéresse une méthode de décision cumulative unifiée permettant de traiter des thèmes applicatifs de complexité croissante. Nos travaux se déclinent alors en trois niveaux de cumul, chacun associé de manière à un stade particulier de l'analyse d'images. Les thèmes applicatifs traités pour illustrer notre démarche sont de complexité croissante : détection et estimation du mouvement en caméra fixe, recalage d'images en caméra mobile (type de mouvement connu et profondeur des objets contrainte) puis estimation générale du mouvement propre et de la structure de la scène en caméras embarquées sur un véhicule mobile. Les résultats obtenus montrent comment un choix de primitives robustes associé à un processus de décision cumulatif permet la réutilisation des opérateurs dans plusieurs secteurs. Les systèmes proposés ont la particularité d'être compacts et cohérents, propriété recherchée dans les applications considérées.

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5

Chow, Jeng-Yeong, Bo-Xue Tian, Gurusankar Ramamoorthy, Brandan S. Hillerich, Ronald D. Seidel, Steven C. Almo, Matthew P. Jacobson, and C. Dale Poulter. "Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus." Proceedings of the National Academy of Sciences 112, no. 18 (April 21, 2015): 5661–66. http://dx.doi.org/10.1073/pnas.1505127112.

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Terpenoids are a large structurally diverse group of natural products with an array of functions in their hosts. The large amount of genomic information from recent sequencing efforts provides opportunities and challenges for the functional assignment of terpene synthases that construct the carbon skeletons of these compounds. Inferring function from the sequence and/or structure of these enzymes is not trivial because of the large number of possible reaction channels and products. We tackle this problem by developing an algorithm to enumerate possible carbocations derived from the farnesyl cation, the first reactive intermediate of the substrate, and evaluating their steric and electrostatic compatibility with the active site. The homology model of a putative pentalenene synthase (Uniprot: B5GLM7) from Streptomyces clavuligerus was used in an automated computational workflow for product prediction. Surprisingly, the workflow predicted a linear triquinane scaffold as the top product skeleton for B5GLM7. Biochemical characterization of B5GLM7 reveals the major product as (5S,7S,10R,11S)-cucumene, a sesquiterpene with a linear triquinane scaffold. To our knowledge, this is the first documentation of a terpene synthase involved in the synthesis of a linear triquinane. The success of our prediction for B5GLM7 suggests that this approach can be used to facilitate the functional assignment of novel terpene synthases.

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6

Arechaga, Ignacio, and Phil C. Jones. "Quick guide: ATP synthase." Current Biology 11, no. 4 (February 2001): R117. http://dx.doi.org/10.1016/s0960-9822(01)00055-0.

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7

Bodel, Catherine, Philippe Delarue, and Robert Bausière. "Architectures multiniveaux : synthèse d'un guide de choix." Revue internationale de génie électrique 6, no. 1-2 (April 30, 2003): 121–42. http://dx.doi.org/10.3166/rige.6.121-142.

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8

Bodel, Catherine, Philippe Delarue, and Robert Bausière. "Architectures multiniveaux : synthèse d'un guide de choix." Revue internationale de génie électrique 6, no. 3-4 (August 30, 2003): 351–56. http://dx.doi.org/10.3166/rige.6.351-356.

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9

Ker, De-Sheng, Sze Lei Pang, Noor Farhan Othman, Sekar Kumaran, Ee Fun Tan, Thiba Krishnan, Kok Gan Chan, Roohaida Othman, Maizom Hassan, and Chyan Leong Ng. "Purification and biochemical characterization of recombinant Persicaria minor β-sesquiphellandrene synthase." PeerJ 5 (February 28, 2017): e2961. http://dx.doi.org/10.7717/peerj.2961.

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Background Sesquiterpenes are 15-carbon terpenes synthesized by sesquiterpene synthases using farnesyl diphosphate (FPP) as a substrate. Recently, a sesquiterpene synthase gene that encodes a 65 kDa protein was isolated from the aromatic plant Persicaria minor. Here, we report the expression, purification and characterization of recombinant P. minor sesquiterpene synthase protein (PmSTS). Insights into the catalytic active site were further provided by structural analysis guided by multiple sequence alignment. Methods The enzyme was purified in two steps using affinity and size exclusion chromatography. Enzyme assays were performed using the malachite green assay and enzymatic product was identified using gas chromatography-mass spectrometry (GC-MS) analysis. Sequence analysis of PmSTS was performed using multiple sequence alignment (MSA) against plant sesquiterpene synthase sequences. The homology model of PmSTS was generated using I-TASSER server. Results Our findings suggest that the recombinant PmSTS is mainly expressed as inclusion bodies and soluble aggregate in the E. coli protein expression system. However, addition of 15% (v/v) glycerol to the protein purification buffer and removal of N-terminal 24 amino acids of PmSTS helped to produce homogenous recombinant protein. Enzyme assay showed that recombinant PmSTS is active and specific to the C15 substrate FPP. The optimal temperature and pH for the recombinant PmSTS are 30 °C and pH 8.0, respectively. The GC-MS analysis further showed that PmSTS produces β-sesquiphellandrene as a major product and β-farnesene as a minor product. MSA analysis revealed that PmSTS adopts a modified conserved metal binding motif (NSE/DTE motif). Structural analysis suggests that PmSTS may binds to its substrate similarly to other plant sesquiterpene synthases. Discussion The study has revealed that homogenous PmSTS protein can be obtained with the addition of glycerol in the protein buffer. The N-terminal truncation dramatically improved the homogeneity of PmSTS during protein purification, suggesting that the disordered N-terminal region may have caused the formation of soluble aggregate. We further show that the removal of the N-terminus disordered region of PmSTS does not affect the product specificity. The optimal temperature, optimal pH, Km and kcat values of PmSTS suggests that PmSTS shares similar enzyme characteristics with other plant sesquiterpene synthases. The discovery of an altered conserved metal binding motif in PmSTS through MSA analysis shows that the NSE/DTE motif commonly found in terpene synthases is able to accommodate certain level of plasticity to accept variant amino acids. Finally, the homology structure of PmSTS that allows good fitting of substrate analog into the catalytic active site suggests that PmSTS may adopt a sesquiterpene biosynthesis mechanism similar to other plant sesquiterpene synthases.

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10

Maceluch, J., M. Kmieciak, Z. Szweykowska-Kulińska, and A. Jarmołowski. "Cloning and characterization of Arabidopsis thaliana AtNAP57--a homologue of yeast pseudouridine synthase Cbf5p." Acta Biochimica Polonica 48, no. 3 (September 30, 2001): 699–709. http://dx.doi.org/10.18388/abp.2001_3904.

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Rat Nap57 and its yeast homologue Cbf5p are pseudouridine synthases involved in rRNA biogenesis, localized in the nucleolus. These proteins, together with H/ACA class of snoRNAs compose snoRNP particles, in which snoRNA guides the synthase to direct site-specific pseudouridylation of rRNA. In this paper we present an Arabidopsis thaliana protein that is highly homologous to Cbf5p (72% identity and 85% homology) and NAP57 (67% identity and 81% homology). Moreover, the plant protein has conserved structural motifs that are characteristic features of pseudouridine synthases of the TruB class. We have named the cloned and characterized protein AtNAP57 (Arabidopsis thaliana homologue of NAP57). AtNAP57 is a 565 amino-acid protein and its calculated molecular mass is 63 kDa. The protein is encoded by a single copy gene located on chromosome 3 of the A. thaliana genome. Interestingly, the AtNAP57 gene does not contain any introns. Mutations in the human DKC1 gene encoding dyskerin (human homologue of yeast Cbf5p and rat NAP57) cause dyskeratosis congenita a rare inherited bone marrow failure syndrome characterized by abnormal skin pigmentation, nail dystrophy and mucosal leukoplakia.

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11

Zinck, Garrett E., and Joe Chappell. "Structurally Guided Reprogramming of Valerenadiene Synthase." Biochemistry 60, no. 51 (December 13, 2021): 3868–78. http://dx.doi.org/10.1021/acs.biochem.1c00523.

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12

Chen, Jonathan L., W. Matthias Leeder, Pedro Morais, Hironori Adachi, and Yi-Tao Yu. "Pseudouridylation-mediated gene expression modulation." Biochemical Journal 481, no. 1 (January 4, 2024): 1–16. http://dx.doi.org/10.1042/bcj20230096.

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RNA-guided pseudouridylation, a widespread post-transcriptional RNA modification, has recently gained recognition for its role in cellular processes such as pre-mRNA splicing and the modulation of premature termination codon (PTC) readthrough. This review provides insights into its mechanisms, functions, and potential therapeutic applications. It examines the mechanisms governing RNA-guided pseudouridylation, emphasizing the roles of guide RNAs and pseudouridine synthases in catalyzing uridine-to-pseudouridine conversion. A key focus is the impact of RNA-guided pseudouridylation of U2 small nuclear RNA on pre-mRNA splicing, encompassing its influence on branch site recognition and spliceosome assembly. Additionally, the review discusses the emerging role of RNA-guided pseudouridylation in regulating PTC readthrough, impacting translation termination and genetic disorders. Finally, it explores the therapeutic potential of pseudouridine modifications, offering insights into potential treatments for genetic diseases and cancer and the development of mRNA vaccine.

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Bolster-Foucault, Claire, Brigitte Ho Mi Fane, and Alexandra Blair. "Déterminants structurels de la stigmatisation touchant les conditions sanitaires et sociales : revue rapide et cadre conceptuel visant à guider la recherche et les interventions." Promotion de la santé et prévention des maladies chroniques au Canada 41, no. 3 (March 2021): 93–128. http://dx.doi.org/10.24095/hpcdp.41.3.03f.

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Introduction On sait que la stigmatisation est un déterminant clé de la santé et des inégalités en matière de santé en raison de ses effets sur l’accès aux ressources favorables à la santé et sur l’exposition au stress. Alors que divers rapports offrent des synthèses approfondies des mécanismes par lesquels la stigmatisation influence la santé, il n’existe aucun examen des données probantes sur les facteurs en amont de la stigmatisation touchant les conditions sanitaires et sociales. L’objectif de cette étude consiste à réaliser une synthèse des déterminants structurels connus de la stigmatisation touchant les conditions sanitaires et sociales dans les pays développés. Méthodologie Nous avons procédé à une revue rapide de la littérature. Nous avons sélectionné des ouvrages de littérature grise et de littérature en anglais et en français évalués par des pairs et publiés après 2008 à l’aide de MEDLINE, Embase, PsycINFO, Google et Google Scholar. Les titres et les résumés ont été examinés indépendamment par deux évaluateurs. Nous avons extrait divers renseignements des publications pertinentes et nous avons mené une analyse thématique de ces déterminants afin de cerner les grands domaines des déterminants structurels. Nous avons réalisé une synthèse narrative des caractéristiques de chaque étude et des déterminants ciblés. Résultats Sur les 657 publications sélectionnées, nous en avons retenu 53. Nous avons relevé 10 domaines de déterminants structurels de la stigmatisation : cadres juridiques, politiques d’aide sociale, politiques économiques, environnements social et bâti, médias et marketing, facteurs pédagogiques, politiques et pratiques en matière de soins de santé, technologie biomédicale, cadres diagnostiques et interventions en santé publique. Chaque domaine a été circonscrit et synthétisé, et nous proposons un cadre conceptuel de la manière dont les domaines cernés sont liés au processus de stigmatisation. Conclusion Au moins 10 domaines de facteurs structurels ont une influence sur la stigmatisation touchant les conditions sanitaires et sociales. On peut se servir de ces domaines pour structurer des discussions stratégiques centrées sur les moyens de réduire la stigmatisation au sein de la population.

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Lux, André. "Essai de synthèse." V. Dialectique des recherches urbaines 9, no. 1-2 (April 12, 2005): 133–40. http://dx.doi.org/10.7202/055402ar.

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Les exposés de ce colloque et les discussions qu'ils ont suscitées ramènent sans cesse à l'esprit la question de savoir ce qu'est en définitive la ville comme phénomène sociologique dans notre société. En essayant d'y répondre, les participants se sont vus forcés de soulever d'autres questions qui apparaissent liées spontanément à celle-ci. Dès lors, il faut s'interroger sur la nature de ces liens pour leur trouver une ordonnance hiérarchique. En même temps, ces questions portent sur la validité d'une présentation dichotomique des différents aspects ainsi liés d'une réalité mouvante et ambivalente. En d'autres mots, à ce stade, c'est l'opposition des concepts polaires «urbain-rural» qui est soumise à la question, d'abord en elle-même, en même temps parce qu'elle fait surgir une autre opposition entre des concepts polaires, « traditionnel-moderne », qui la concurrence dans l'explication de la dynamique concrète de la société historique, tout en étant, comme elle, à cet égard intrinsèquement controversable. Sous-jacente à cette double interrogation est la question du degré d'originalité ou, au contraire, de conformité de l'expérience québécoise en regard du modèle général (s'il en existe un) de l'urbanisation des sociétés industrielles. L'opposition entre «industriel» et «pré-industriel» vient encore compliquer le jeu des interactions entre les deux dichotomies précédentes, de manière à nous imposer le recours à tout un ensemble de nuances pour caractériser l'urbanisation de la société canadienne-française. Il est, en effet, probable qu'apparaissent des discordances d'évolution selon les paliers de la réalité sociale. Ainsi par exemple, l'objectif d'efficacité administrative qui guide les réformes institutionnelles commandées par les nouvelles structures urbaines se révèle souvent en conflit avec l'objectif de la participation démocratique qui sert de pôle, parmi d'autres, aux mutations idéologiques. Les exposés du colloque montrent enfin que peuvent exister des discordances entre les voies d'approche et les concepts utilisés par les différentes disciplines concernées par le phénomène de l'urbanisation. Celui-ci n'a donc pas nécessairement la même portée pour chacune d'entre elles et rend leur collaboration délicate. Cette collaboration est néanmoins d'autant plus indispensable que le colloque montre aussi que le problème de l'urbanisation ne peut se poser ni s'analyser correctement que dans le cadre beaucoup plus large de la problématique de l'évolution globale de notre société.

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Decatur, Wayne A., and Murray N. Schnare. "Different Mechanisms for Pseudouridine Formation in Yeast 5S and 5.8S rRNAs." Molecular and Cellular Biology 28, no. 10 (March 10, 2008): 3089–100. http://dx.doi.org/10.1128/mcb.01574-07.

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ABSTRACT The selection of sites for pseudouridylation in eukaryotic cytoplasmic rRNA occurs by the base pairing of the rRNA with specific guide sequences within the RNA components of box H/ACA small nucleolar ribonucleoproteins (snoRNPs). Forty-four of the 46 pseudouridines (Ψs) in the cytoplasmic rRNA of Saccharomyces cerevisiae have been assigned to guide snoRNAs. Here, we examine the mechanism of Ψ formation in 5S and 5.8S rRNA in which the unassigned Ψs occur. We show that while the formation of the Ψ in 5.8S rRNA is associated with snoRNP activity, the pseudouridylation of 5S rRNA is not. The position of the Ψ in 5.8S rRNA is guided by snoRNA snR43 by using conserved sequence elements that also function to guide pseudouridylation elsewhere in the large-subunit rRNA; an internal stem-loop that is not part of typical yeast snoRNAs also is conserved in snR43. The multisubstrate synthase Pus7 catalyzes the formation of the Ψ in 5S rRNA at a site that conforms to the 7-nucleotide consensus sequence present in other substrates of Pus7. The different mechanisms involved in 5S and 5.8S rRNA pseudouridylation, as well as the multiple specificities of the individual trans factors concerned, suggest possible roles in linking ribosome production to other processes, such as splicing and tRNA synthesis.

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Bailey, Constance B., Marjolein E. Pasman, and Adrian T. Keatinge-Clay. "Substrate structure–activity relationships guide rational engineering of modular polyketide synthase ketoreductases." Chemical Communications 52, no. 4 (2016): 792–95. http://dx.doi.org/10.1039/c5cc07315d.

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Structure–activity relationship studies guided stereocontrol engineering within a modular polyketide synthase ketoreductase to yield a more active enzyme whose reactivity can be explained through the Felkin–Anh model.

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Kim, Hansol, Young Ji Kang, Junseon Min, Hyeokjune Choi, and Sebyung Kang. "Development of an antibody-binding modular nanoplatform for antibody-guided targeted cell imaging and delivery." RSC Advances 6, no. 23 (2016): 19208–13. http://dx.doi.org/10.1039/c6ra00233a.

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A polyvalent antibody-binding lumazine synthase protein cage nanoparticle (ABD–AaLS) is constructed by genetically fusing lumazine synthase and antibody-binding domains. ABD–AaLS effectively displays targeting antibodies in an orientation-controlled manner.

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Grünberg, Sebastian, Lindsey A. Doyle, Eric J. Wolf, Nan Dai, Ivan R. Corrêa, Erbay Yigit, and Barry L. Stoddard. "The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1." PLOS ONE 18, no. 11 (November 8, 2023): e0291267. http://dx.doi.org/10.1371/journal.pone.0291267.

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The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or ‘PUS’ enzymes include those that rely on guide RNA molecules and others that function as ‘stand-alone’ enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.

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Zargar, Amin, Ravi Lal, Luis Valencia, Jessica Wang, Tyler William H. Backman, Pablo Cruz-Morales, Ankita Kothari, et al. "Chemoinformatic-Guided Engineering of Polyketide Synthases." Journal of the American Chemical Society 142, no. 22 (May 15, 2020): 9896–901. http://dx.doi.org/10.1021/jacs.0c02549.

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20

Cogan, Dillon P., Graham A. Hudson, Zhengan Zhang, Taras V. Pogorelov, Wilfred A. van der Donk, Douglas A. Mitchell, and Satish K. Nair. "Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis." Proceedings of the National Academy of Sciences 114, no. 49 (November 20, 2017): 12928–33. http://dx.doi.org/10.1073/pnas.1716035114.

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The [4+2] cycloaddition reaction is an enabling transformation in modern synthetic organic chemistry, but there are only limited examples of dedicated natural enzymes that can catalyze this transformation. Thiopeptides (or more formally thiazolyl peptides) are a class of thiazole-containing, highly modified, macrocyclic secondary metabolites made from ribosomally synthesized precursor peptides. The characteristic feature of these natural products is a six-membered nitrogenous heterocycle that is assembled via a formal [4+2] cycloaddition between two dehydroalanine (Dha) residues. This heteroannulation is entirely contingent on enzyme activity, although the mechanism of the requisite pyridine/dehydropiperidine synthase remains to be elucidated. The unusual aza-cylic product is distinct from the more common carbocyclic products of synthetic and biosynthetic [4+2] cycloaddition reactions. To elucidate the mechanism of cycloaddition, we have determined atomic resolution structures of the pyridine synthases involved in the biosynthesis of the thiopeptides thiomuracin (TbtD) and GE2270A (PbtD), in complex with substrates and product analogs. Structure-guided biochemical, mutational, computational, and binding studies elucidate active-site features that explain how orthologs can generate rigid macrocyclic scaffolds of different sizes. Notably, the pyridine synthases show structural similarity to the elimination domain of lanthipeptide dehydratases, wherein insertions of secondary structural elements result in the formation of a distinct active site that catalyzes different chemistry. Comparative analysis identifies other catalysts that contain a shared core protein fold but whose active sites are located in entirely different regions, illustrating a principle predicted from efforts in de novo protein design.

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Khan, Adil. "Pseudouridine in RNA: Enzymatic Synthesis Mechanisms and Functional Roles in Molecular Biology." International Journal of Environment, Agriculture and Biotechnology 8, no. 6 (2023): 284–300. http://dx.doi.org/10.22161/ijeab.86.25.

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Pseudouridine, a common modified nucleotide, is prevalent in bacterial tRNA, rRNA, and snRNA. Initially identified in rRNA and tRNA, its presence extends to snRNA. Despite being the first identified and most prevalent RNA modification, its biosynthesis and diverse roles remain insufficiently understood. This extensively occurring modified nucleotide influences structural and functional attributes in various RNA categories. The isomerization process involves a carbon–carbon bond formation, and Pumilio family proteins (PUFs) are potential Ψ reader proteins. Pseudouridine, a ubiquitous constituent in structural RNAs, is notably absent in mRNA or viral RNAs. Its enzymatic isomerization occurs at the polynucleotide level, independently of cofactors. Compared to uridine, pseudouridine prefers the C3-endo conformation, enhancing stability in specific structural motifs. Evolutionarily conserved in major spliceosomal snRNAs, it plays a crucial role in spliceosome assembly and splicing. Pseudouridine (ψ), comprising 0.2–0.6% of uridines in mammalian mRNA, is enzymatically generated by pseudouridine synthases. Five pseudouridine synthase families orchestrate its site-specific isomerization. In eukaryotic and archaeal organisms, specific synthases rely on noncoding RNAs, like box H/ACA small nucleolar/scaRNPs. These modifications contribute to RNA structural stabilization and functional efficacy. In pre-mRNA and mRNA they guide splicing processes and protect against degradation, acting as a defense mechanism against viral infections. This review delves into the detection, structure, functions, and applications of pseudoridine in RNA. Methodologies like High-performance liquid chromatography, mass spectrometry, thin layer chromatography, enzyme-linked Immunosorbent assay, capillary electrophoresis, northern blotting, reverse transcript polymerase chain reaction and RNA bisulfite sequencing. establish a robust framework. Pseudouridine's roles in reinforcing RNA structures, modulating translation, and its potential in mRNA.

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Hansen, Frederik T., Jens L. Sørensen, Henriette Giese, Teis E. Sondergaard, and Rasmus J. N. Frandsen. "Quick guide to polyketide synthase and nonribosomal synthetase genes in Fusarium." International Journal of Food Microbiology 155, no. 3 (April 2012): 128–36. http://dx.doi.org/10.1016/j.ijfoodmicro.2012.01.018.

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Dong, Shi-Hui, Mila Nhu-Lam, Rajesh Nagarajan, and Satish K. Nair. "Structure-Guided Biochemical Analysis of Quorum Signal Synthase Specificities." ACS Chemical Biology 15, no. 6 (May 4, 2020): 1497–504. http://dx.doi.org/10.1021/acschembio.0c00142.

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Balazs, Amber Y. S., Nichola L. Davies, David Longmire, Martin J. Packer, and Elisabetta Chiarparin. "Nuclear magnetic resonance free ligand conformations and atomic resolution dynamics." Magnetic Resonance 2, no. 1 (June 23, 2021): 489–98. http://dx.doi.org/10.5194/mr-2-489-2021.

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Abstract. Knowledge of free ligand conformational preferences (energy minima) and conformational dynamics (rotational energy barriers) of small molecules in solution can guide drug design hypotheses and help rank ideas to bias syntheses towards more active compounds. Visualization of conformational exchange dynamics around torsion angles, by replica exchange with solute tempering molecular dynamics (REST-MD), gives results in agreement with high-resolution 1H nuclear magnetic resonance (NMR) spectra and complements free ligand conformational analyses. Rotational energy barriers around individual bonds are comparable between calculated and experimental values, making the in-silico method relevant to ranking prospective design ideas in drug discovery programs, particularly across a series of analogs. Prioritizing design ideas, based on calculations and analysis of measurements across a series, efficiently guides rational discovery towards the “right molecules” for effective medicines.

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Adhikari, Kamal, I.-Wen Lo, Chun-Liang Chen, Yung-Lin Wang, Kuan-Hung Lin, Saeid Malek Zadeh, Rajesh Rattinam, Yi-Shan Li, Chang-Jer Wu, and Tsung-Lin Li. "Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase." Biomolecules 10, no. 5 (May 9, 2020): 738. http://dx.doi.org/10.3390/biom10050738.

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Plant type III polyketide synthases produce diverse bioactive molecules with a great medicinal significance to human diseases. Here, we demonstrated versatility of a stilbene synthase (STS) from Pinus Sylvestris, which can accept various non-physiological substrates to form unnatural polyketide products. Three enzymes (4-coumarate CoA ligase, malonyl-CoA synthetase and engineered benzoate CoA ligase) along with synthetic chemistry was practiced to synthesize starter and extender substrates for STS. Of these, the crystal structures of benzoate CoA ligase (BadA) from Rhodopseudomonas palustris in an apo form or in complex with a 2-chloro-1,3-thiazole-5-carboxyl-AMP or 2-methylthiazole-5-carboxyl-AMP intermediate were determined at resolutions of 1.57 Å, 1.7 Å, and 2.13 Å, respectively, which reinforces its capacity in production of unusual CoA starters. STS exhibits broad substrate promiscuity effectively affording structurally diverse polyketide products. Seven novel products showed desired cytotoxicity against a panel of cancer cell lines (A549, HCT116, Cal27). With the treatment of two selected compounds, the cancer cells underwent cell apoptosis in a dose-dependent manner. The precursor-directed biosynthesis alongside structure-guided enzyme engineering greatly expands the pharmaceutical repertoire of lead compounds with promising/enhanced biological activities.

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Gilroy, Kyle D., Hsin-Chieh Peng, Xuan Yang, Aleksey Ruditskiy, and Younan Xia. "Symmetry breaking during nanocrystal growth." Chemical Communications 53, no. 33 (2017): 4530–41. http://dx.doi.org/10.1039/c7cc01121k.

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Lancaster, Jason, Ashot Khrimian, Sharon Young, Bryan Lehner, Katrin Luck, Anna Wallingford, Saikat Kumar B. Ghosh, et al. "De novo formation of an aggregation pheromone precursor by an isoprenyl diphosphate synthase-related terpene synthase in the harlequin bug." Proceedings of the National Academy of Sciences 115, no. 37 (August 23, 2018): E8634—E8641. http://dx.doi.org/10.1073/pnas.1800008115.

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Insects use a diverse array of specialized terpene metabolites as pheromones in intraspecific interactions. In contrast to plants and microbes, which employ enzymes called terpene synthases (TPSs) to synthesize terpene metabolites, limited information from few species is available about the enzymatic mechanisms underlying terpene pheromone biosynthesis in insects. Several stink bugs (Hemiptera: Pentatomidae), among them severe agricultural pests, release 15-carbon sesquiterpenes with a bisabolene skeleton as sex or aggregation pheromones. The harlequin bug, Murgantia histrionica, a specialist pest of crucifers, uses two stereoisomers of 10,11-epoxy-1-bisabolen-3-ol as a male-released aggregation pheromone called murgantiol. We show that MhTPS (MhIDS-1), an enzyme unrelated to plant and microbial TPSs but with similarity to trans-isoprenyl diphosphate synthases (IDS) of the core terpene biosynthetic pathway, catalyzes the formation of (1S,6S,7R)-1,10-bisaboladien-1-ol (sesquipiperitol) as a terpene intermediate in murgantiol biosynthesis. Sesquipiperitol, a so-far-unknown compound in animals, also occurs in plants, indicating convergent evolution in the biosynthesis of this sesquiterpene. RNAi-mediated knockdown of MhTPS mRNA confirmed the role of MhTPS in murgantiol biosynthesis. MhTPS expression is highly specific to tissues lining the cuticle of the abdominal sternites of mature males. Phylogenetic analysis suggests that MhTPS is derived from a trans-IDS progenitor and diverged from bona fide trans-IDS proteins including MhIDS-2, which functions as an (E,E)-farnesyl diphosphate (FPP) synthase. Structure-guided mutagenesis revealed several residues critical to MhTPS and MhFPPS activity. The emergence of an IDS-like protein with TPS activity in M. histrionica demonstrates that de novo terpene biosynthesis evolved in the Hemiptera in an adaptation for intraspecific communication.

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Lim, Soo-Hwan, Jong-In Baek, Byeong-Min Jeon, Jung-Woo Seo, Min-Sung Kim, Ji-Young Byun, Soo-Hoon Park, et al. "CRISPRi-Guided Metabolic Flux Engineering for Enhanced Protopanaxadiol Production in Saccharomyces cerevisiae." International Journal of Molecular Sciences 22, no. 21 (October 31, 2021): 11836. http://dx.doi.org/10.3390/ijms222111836.

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Protopanaxadiol (PPD), an aglycon found in several dammarene-type ginsenosides, has high potency as a pharmaceutical. Nevertheless, application of these ginsenosides has been limited because of the high production cost due to the rare content of PPD in Panax ginseng and a long cultivation time (4–6 years). For the biological mass production of the PPD, de novo biosynthetic pathways for PPD were introduced in Saccharomyces cerevisiae and the metabolic flux toward the target molecule was restructured to avoid competition for carbon sources between native metabolic pathways and de novo biosynthetic pathways producing PPD in S. cerevisiae. Here, we report a CRISPRi (clustered regularly interspaced short palindromic repeats interference)-based customized metabolic flux system which downregulates the lanosterol (a competing metabolite of dammarenediol-II (DD-II)) synthase in S. cerevisiae. With the CRISPRi-mediated suppression of lanosterol synthase and diversion of lanosterol to DD-II and PPD in S. cerevisiae, we increased PPD production 14.4-fold in shake-flask fermentation and 5.7-fold in a long-term batch-fed fermentation.

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Huang, He, Huiying Li, Pavel Martásek, Linda J. Roman, Thomas L. Poulos, and Richard B. Silverman. "Structure-Guided Design of Selective Inhibitors of Neuronal Nitric Oxide Synthase." Journal of Medicinal Chemistry 56, no. 7 (March 28, 2013): 3024–32. http://dx.doi.org/10.1021/jm4000984.

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Jez, Joseph M., Marianne E. Bowman, and Joseph P. Noel. "Structure-Guided Programming of Polyketide Chain-Length Determination in Chalcone Synthase†." Biochemistry 40, no. 49 (December 2001): 14829–38. http://dx.doi.org/10.1021/bi015621z.

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Leferink, Nicole G. H., Kara E. Ranaghan, Jaime Battye, Linus O. Johannissen, Sam Hay, Marc W. Kamp, Adrian J. Mulholland, and Nigel S. Scrutton. "Taming the Reactivity of Monoterpene Synthases To Guide Regioselective Product Hydroxylation." ChemBioChem 21, no. 7 (April 2020): 985–90. http://dx.doi.org/10.1002/cbic.201900672.

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Massenet, Séverine, Yuri Motorin, Denis L. J. Lafontaine, Eduard C. Hurt, Henri Grosjean, and Christiane Branlant. "Pseudouridine Mapping in the Saccharomyces cerevisiae Spliceosomal U Small Nuclear RNAs (snRNAs) Reveals that Pseudouridine Synthase Pus1p Exhibits a Dual Substrate Specificity for U2 snRNA and tRNA." Molecular and Cellular Biology 19, no. 3 (March 1, 1999): 2142–54. http://dx.doi.org/10.1128/mcb.19.3.2142.

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ABSTRACT Pseudouridine (Ψ) residues were localized in theSaccharomyces cerevisiae spliceosomal U small nuclear RNAs (UsnRNAs) by using the chemical mapping method. In contrast to vertebrate UsnRNAs, S. cerevisiae UsnRNAs contain only a few Ψ residues, which are located in segments involved in intermolecular RNA-RNA or RNA-protein interactions. At these positions, UsnRNAs are universally modified. When yeast mutants disrupted for one of the several pseudouridine synthase genes (PUS1,PUS2, PUS3, and PUS4) or depleted in rRNA-pseudouridine synthase Cbf5p were tested for UsnRNA Ψ content, only the loss of the Pus1p activity was found to affect Ψ formation in spliceosomal UsnRNAs. Indeed, Ψ44 formation in U2 snRNA was abolished. By using purified Pus1p enzyme and in vitro-produced U2 snRNA, Pus1p is shown here to catalyze Ψ44 formation in the S. cerevisiae U2 snRNA. Thus, Pus1p is the first UsnRNA pseudouridine synthase characterized so far which exhibits a dual substrate specificity, acting on both tRNAs and U2 snRNA. As depletion of rRNA-pseudouridine synthase Cbf5p had no effect on UsnRNA Ψ content, formation of Ψ residues in S. cerevisiae UsnRNAs is not dependent on the Cbf5p-snoRNA guided mechanism.

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Chen, Yang, and Yu Cao. "The sphingomyelin synthase family: proteins, diseases, and inhibitors." Biological Chemistry 398, no. 12 (November 27, 2017): 1319–25. http://dx.doi.org/10.1515/hsz-2017-0148.

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AbstractSphingomyelin (SM) is among the most important biomolecules in eukaryotes and acts as both constructive components and signal carrier in physiological processes. SM is catalyzed by a membrane protein family, sphingomyelin synthases (SMSs), consisting of three members, SMS1, SMS2 and SMSr. SMSs modulate sphingomyelin and other sphingolipids levels, thereby regulating membrane mobility, ceramide-dependent apoptosis and DAG-dependent signaling pathways. SMSs was found associated with various diseases. Downregulation of SMS2 activity results in protective effects against obesity, atherosclerosis and diabetes and makes SMS2 inhibitors potential medicines. Structural guided specific drug design could be the next breakthrough, discriminating SMS2 from other homologs.

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Nishimura, Sho, Kazune Nakamura, Miyako Yamamoto, Daichi Morita, Teruo Kuroda, and Takanori Kumagai. "Genome Sequence-Guided Finding of Lucensomycin Production by Streptomyces achromogenes Subsp. streptozoticus NBRC14001." Microorganisms 10, no. 1 (December 26, 2021): 37. http://dx.doi.org/10.3390/microorganisms10010037.

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Information on microbial genome sequences is a powerful resource for accessing natural products with significant activities. We herein report the unveiling of lucensomycin production by Streptomyces achromogenes subsp. streptozoticus NBRC14001 based on the genome sequence of the strain. The genome sequence of strain NBRC14001 revealed the presence of a type I polyketide synthase gene cluster with similarities to a biosynthetic gene cluster for natamycin, which is a polyene macrolide antibiotic that exhibits antifungal activity. Therefore, we investigated whether strain NBRC14001 produces antifungal compound(s) and revealed that an extract from the strain inhibited the growth of Candida albicans. A HPLC analysis of a purified compound exhibiting antifungal activity against C. albicans showed that the compound differed from natamycin. Based on HR-ESI-MS spectrometry and a PubChem database search, the compound was predicted to be lucensomycin, which is a tetraene macrolide antibiotic, and this prediction was supported by the results of a MS/MS analysis. Furthermore, the type I polyketide synthase gene cluster in strain NBRC14001 corresponded well to lucesomycin biosynthetic gene cluster (lcm) in S. cyanogenus, which was very recently reported. Therefore, we concluded that the antifungal compound produced by strain NBRC14001 is lucensomycin.

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Major, Dan Thomas, and Michal Weitman. "Electrostatically Guided Dynamics—The Root of Fidelity in a Promiscuous Terpene Synthase?" Journal of the American Chemical Society 134, no. 47 (November 15, 2012): 19454–62. http://dx.doi.org/10.1021/ja308295p.

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36

Bellaiche, N., and E. Azoulay. "Cone beam et troisième molaire mandibulaire incluse." Revue d'Orthopédie Dento-Faciale 53, no. 1 (February 2019): 21–34. http://dx.doi.org/10.1051/odf/2019004.

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Les patients, comme les chirurgiens-dentistes, attendent beaucoup de l’orthodontiste pour les guider dans la prédiction d’évolution des dents de sagesse (DDS). L’imagerie est un outil clé pour la prise de décision et l’analyse pré-opératoire. Cet article est une synthèse des découvertes fortuites radiologiques liées à la troisième molaire mandibulaire et montre l’intérêt du CBCT. La pathologie associée à la troisième molaire est plus souvent observée dans le CBCT que dans la panoramique. Plus de troisièmes molaires seraient enlevées si les résultats pathologiques étaient basés sur le CBCT.

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Mabesoone, Mathijs F. J., Stefan Leopold-Messer, Hannah A. Minas, Clara Chepkirui, Pornsuda Chawengrum, Silke Reiter, Roy A. Meoded, et al. "Evolution-guided engineering of trans -acyltransferase polyketide synthases." Science 383, no. 6689 (March 22, 2024): 1312–17. http://dx.doi.org/10.1126/science.adj7621.

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Bacterial multimodular polyketide synthases (PKSs) are giant enzymes that generate a wide range of therapeutically important but synthetically challenging natural products. Diversification of polyketide structures can be achieved by engineering these enzymes. However, notwithstanding successes made with textbook cis -acyltransferase ( cis -AT) PKSs, tailoring such large assembly lines remains challenging. Unlike textbook PKSs, trans -AT PKSs feature an extraordinary diversity of PKS modules and commonly evolve to form hybrid PKSs. In this study, we analyzed amino acid coevolution to identify a common module site that yields functional PKSs. We used this site to insert and delete diverse PKS parts and create 22 engineered trans -AT PKSs from various pathways and in two bacterial producers. The high success rates of our engineering approach highlight the broader applicability to generate complex designer polyketides.

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38

Horisberger, Denis, and Micheline Meylan. "Le guide des stations forestières du canton de Vaud: synthèse pour les praticiens | The guide to forest stations in canton Vaud: a summary for practioners." Schweizerische Zeitschrift fur Forstwesen 160, s1 (December 1, 2009): s43—s53. http://dx.doi.org/10.3188/szf.2009.s0043.

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The guide to forest stations in canton Vaud is a collection of references and applications intended for forest practitioners. This computer-based instrument constantly incorporates new information. The guide is conceived on transparent bases that can be repeated and thus called in question. It offers a simplified process for determining vegetation groups and evaluating their productivity. It is completed by some suggestions for a choice of species adapted to the station which takes into account their suitability for any given station, climate changes and the present composition of forest stands.

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Shimizu, T., Y. Nakanishi, Y. Nakagawa, I. Tsujino, N. Takahashi, S. Hashimoto, and N. Nemoto. "Thymidylate Synthase Expression can Guide Treatment Selection for Advanced Non-Small Cell Lung Cancer Patients." Annals of Oncology 23 (September 2012): ix407. http://dx.doi.org/10.1016/s0923-7534(20)33835-7.

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40

Guerriero, Gea, Sylvain Legay, and Jean-Francois Hausman. "Alfalfa Cellulose Synthase Gene Expression under Abiotic Stress: A Hitchhiker’s Guide to RT-qPCR Normalization." PLoS ONE 9, no. 8 (August 1, 2014): e103808. http://dx.doi.org/10.1371/journal.pone.0103808.

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41

Gould, Matthew K., Sam Dean, and Achim C. Schnaufer. "How to survive and thrive without mitochondrial DNA: A protozoan's guide to ATP synthase modification." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1797 (July 2010): 32. http://dx.doi.org/10.1016/j.bbabio.2010.04.114.

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42

Morris, Francine, Ryan Vierling, Lauren Boucher, Jürgen Bosch, and Caren L. Freel Meyers. "DXP Synthase-Catalyzed CN Bond Formation: Nitroso Substrate Specificity Studies Guide Selective Inhibitor Design." ChemBioChem 14, no. 11 (July 3, 2013): 1309–15. http://dx.doi.org/10.1002/cbic.201300187.

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43

Mank, Nicholas, Amy Arnette, Vince Klapper, Lesa Offermann, and Maksymilian Chruszcz. "Structure of dihydrodipicolinate synthase from the commensal bacteriumBacteroides thetaiotaomicronat 2.1 Å resolution." Acta Crystallographica Section F Structural Biology Communications 71, no. 4 (March 20, 2015): 449–54. http://dx.doi.org/10.1107/s2053230x15004628.

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Dihydrodipicolinate synthase (DapA) catalyzes the first committed step of the diaminopimelate biosynthetic pathway of lysine. It has been shown to be an essential enzyme in many bacteria and has been the subject of research to generate novel antibiotics. However, this pathway is present in both pathogenic and commensal bacteria, and antibiotics targeting DapA may interfere with normal gut colonization.Bacteroides thetaiotaomicronis a Gram-negative commensal bacterium that makes up a large proportion of the normal microbiota of the human gut. The structure of DapA fromB. thetaiotaomicron(BtDapA) has been determined. This structure will help to guide the generation of selectively active antibiotic compounds targeting DapA.

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44

Kim, Woojoo E., Katherine Charov, Mária Džunková, Eric D. Becraft, Julia Brown, Frederik Schulz, Tanja Woyke, James J. La Clair, Ramunas Stepanauskas, and Michael D. Burkart. "Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics." ACS Chemical Biology 16, no. 5 (May 6, 2021): 813–19. http://dx.doi.org/10.1021/acschembio.1c00157.

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45

Duan, Jingqi, Ling Li, Jing Lu, Wei Wang, and Keqiong Ye. "Structural Mechanism of Substrate RNA Recruitment in H/ACA RNA-Guided Pseudouridine Synthase." Molecular Cell 34, no. 4 (May 2009): 427–39. http://dx.doi.org/10.1016/j.molcel.2009.05.005.

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46

Muller, S., J. B. Fourmann, C. Loegler, B. Charpentier, and C. Branlant. "Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA: 55-synthase and RNA-guided RNA: -synthase activities." Nucleic Acids Research 35, no. 16 (August 17, 2007): 5610–24. http://dx.doi.org/10.1093/nar/gkm606.

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47

Cardinal, M., J. Crain, MT Do, M. Fréchette, S. McFaull, R. Skinner, and W. Thompson. "Note de synthèse - Étude sur les blessures, édition 2012 : Pleins feux sur la sécurité routière et dans les transports." Maladies chroniques et blessures au Canada 32, no. 4 (September 2012): 254–55. http://dx.doi.org/10.24095/hpcdp.32.4.08f.

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Le rapport Étude sur les blessures, édition 2012 : Pleins feux sur la sécurité routière et dans les transports, le premier rapport de santé publique à l'échelle nationale en la matière, présente une synthèse des statistiques provenant de diverses sources sur les blessures survenues dans les réseaux routiers et de transport. Il établit le profil des blessures chez les Canadiens et les Canadiennes âgés de 24 ans et moins, explique les risques et les facteurs de protection et formule des recommandations sur les mesures à prendre. Les conclusions servent à guider l'élaboration de programmes ciblés de prévention des blessures.

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48

Biteau, Nicolas G., Vincent Roy, Cyril Nicolas, Hubert F. Becker, Jean-Christophe Lambry, Hannu Myllykallio, and Luigi A. Agrofoglio. "Synthesis and Structure–Activity Relationship Studies of Pyrido [1,2-E]Purine-2,4(1H,3H)-Dione Derivatives Targeting Flavin-Dependent Thymidylate Synthase in Mycobacterium Tuberculosis." Molecules 27, no. 19 (September 21, 2022): 6216. http://dx.doi.org/10.3390/molecules27196216.

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In 2002, a new class of thymidylate synthase (TS) involved in the de novo synthesis of dTMP named Flavin-Dependent Thymidylate Synthase (FDTS) encoded by the thyX gene was discovered; FDTS is present only in 30% of prokaryote pathogens and not in human pathogens, which makes it an attractive target for the development of new antibacterial agents, especially against multi-resistant pathogens. We report herein the synthesis and structure-activity relationship of a novel series of hitherto unknown pyrido[1,2-E]purine-2,4(1H,3H)-dione analogues. Several synthetics efforts were done to optimize regioselective N1-alkylation through organopalladium cross-coupling. Modelling of potential hits were performed to generate a model of interaction into the active pocket of FDTS to understand and guide further synthetic modification. All those compounds were evaluated on an in-house in vitro NADPH oxidase assays screening as well as against Mycobacterium tuberculosis ThyX. The highest inhibition was obtained for compound 23a with 84.3% at 200 µM without significant cytotoxicity (CC50 > 100 mM) on PBM cells.

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Bukhari, Ali A., and Ranjit K. Goudar. "Thymidylate Synthase as a Predictive Biomarker for Pemetrexed Response in NSCLC." Lung Cancer International 2013 (December 25, 2013): 1–7. http://dx.doi.org/10.1155/2013/436409.

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In recent years, major strides in cancer research have made it possible to select personalized chemotherapy recommendations based on an individual patient’s tumor biology. The prognostic and/or predictive ability of biomarkers seeks to tailor the use of targeted chemotherapy and can result in improved clinical outcomes with reduced toxicity. A proliferation of new technology and pharmacotherapeutics in the setting of current FDA Clinical Laboratory Improvement Amendment (CLIA) standards has resulted in a recent surge in direct-to-physician biomarker tests. However, in the absence of clinical validation, there is the concern that the biomarkers may be utilized prematurely, resulting in improper chemotherapy selection and patient harm. Thymidylate synthase (TS) has been marketed as a predictive biomarker for the use of pemetrexed in NSCLC. We will examine the evidence behind the use of TS as a predictive biomarker to predict response to pemetrexed in NSCLC. At this time, the evidence does not currently support using TS assays to guide chemotherapy selection outside of a clinical research protocol.

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Liu, Hongshuang, Senbiao Fang, Lin Zhao, Xiao Men, and Haibo Zhang. "A Single Active-Site Mutagenesis Confers Enhanced Activity and/or Changed Product Distribution to a Pentalenene Synthase from Streptomyces sp. PSKA01." Bioengineering 10, no. 3 (March 22, 2023): 392. http://dx.doi.org/10.3390/bioengineering10030392.

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Pentalenene is a ternary cyclic sesquiterpene formed via the ionization and cyclization of farnesyl pyrophosphate (FPP), which is catalyzed by pentalenene synthase (PentS). To better understand the cyclization reactions, it is necessary to identify more key sites and elucidate their roles in terms of catalytic activity and product specificity control. Previous studies primarily relied on the crystal structure of PentS to analyze and verify critical active sites in the active cavity, while this study started with the function of PentS and screened a novel key site through random mutagenesis. In this study, we constructed a pentalenene synthetic pathway in E. coli BL21(DE3) and generated PentS variants with random mutations to construct a mutant library. A mutant, PentS-13, with a varied product diversity, was obtained through shake-flask fermentation and product identification. After sequencing and the functional verification of the mutation sites, it was found that T182A, located in the G2 helix, was responsible for the phenotype of PentS-13. The site-saturation mutagenesis of T182 demonstrated that mutations at this site not only affected the solubility and activity of the enzyme but also affected the specificity of the product. The other products were generated through different routes and via different carbocation intermediates, indicating that the 182 active site is crucial for PentS to stabilize and guide the regioselectivity of carbocations. Molecular docking and molecular dynamics simulations suggested that these mutations may induce changes in the shape and volume of the active cavity and disturb hydrophobic/polar interactions that were sufficient to reposition reactive intermediates for alternative reaction pathways. This article provides rational explanations for these findings, which may generally allow for the protein engineering of other terpene synthases to improve their catalytic efficiency or modify their specificities.

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