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Publications - Bioorganic Chemistry

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Books and chapters

Vasco, A. V.; Ricardo, M. G.; Rivera, D. G.; Wessjohann, L. A.; Ligation, Macrocyclization, and Simultaneous Functionalization of Peptides by Multicomponent Reactions (MCR) Methods Mol. Biol. 2371, 143-157, (2022) ISBN: 978-1-0716-1688-8 DOI: 10.1007/978-1-0716-1689-5_8

Multicomponent reactions (MCRs) are recently expanding the plethora of solid-phase protocols for the synthesis and derivatization of peptides. Herein, we describe a solid-phase-compatible strategy based on MCRs as a powerful strategy for peptide cyclization and ligation . We illustrate, using Gramicidin S as a model peptide, how the execution of on-resin Ugi reactions enables the simultaneous backbone N-functionalization and cyclization, which are important types of derivatizations in peptide-based drug development or for incorporation of conjugation handles, or labels.
Books and chapters

Hussain, H.; Elizbit, .; Ali, I.; Mamadalieva, N. Z.; Abbas, G.; Ali, M.; Zaman, G.; Khan, A.; Hassan, U.; Green, I. R.; Fruitful decade of Phoma secondary metabolites from 2011 to 2020: Chemistry, chemical diversity, and biological activities (Rai, M., Zimowska, B., Kövics, G.J.). Phoma: Diversity, Taxonomy, Bioactivities, and Nanotechnology 183–203, (2022) ISBN: 978-3-030-81217-1 DOI: 10.1007/978-3-030-81218-8_10

Fungi have been an extraordinary area of scientific research, and many secondary metabolites with intriguing chemical diversity along with interesting biological activities have been identified. Fungi like Phoma sp. have been investigated as a source of structurally unique metabolites over the past 10 years (2011–2020). A diverse range of natural products, viz., α-pyrone derivatives, isocoumarins, anthraquinones, xanthones, thiodiketopiperazines, cytochalasin derivatives, diphenyl ether derivatives, furopyrans, xyloketals, chromones, meroterpenoids, diterpenoids, polyketides, and alkaloids, have been reported from various Phoma spp. These metabolites illustrated phytotoxic, cytotoxic, antibacterial, antifungal, herbicidal, immunosuppressive, antiviral, antidiabetic (PTP1B inhibition), anti-Alzheimer (acetylcholinesterase inhibition), and antioxidant activities.
Books and chapters

Humberto Reyes, L.; Fernández-Niño, M.; Introductory chapter: From BioBricks to synthetic genomes (Miguel Fernández-Niño, Luis H. Reyes). Synthetic Genomics - From BioBricks to Synthetic Genomes (2022) ISBN: 978-1-83969-638-1 DOI: 10.5772/intechopen.101949

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Books and chapters

Fernández-Niño, M.; Daniela, B.-T.; Engineering microbial biofactories for a sustainable future (Catalina Lopez-Correa and Adriana Suarez-Gonzalez). Genomics and the Global Bioeconomy 25-58, (2022) DOI: 10.1016/B978-0-323-91601-1.00003-1

Engineering microbial biofactories for the transformation of industrial residues into value-added products represents a significant step toward sustainability. This chapter has two main goals: first, to review the current approaches that can be used to engineer synthetic biofactories of relevance for white biotechnology, and second, to provide clear examples of how these biofactories represent an excellent platform to transform industrial residues into value-added products. Several technologies used to engineer microbial biofactories (e.g., BioBricks design, pathway engineering, modular assembly, and chassis fine-tuning) will be discussed using a multiscale approach from genes to biofactories. The relevance of omics databases for the identification of novel biological components (genome mining) and fine-tuning their expression will also be discussed. Finally, several examples will be provided to highlight the relevance of engineering microorganisms as biofactories for a sustainable future.
Books and chapters

Ceballos, L. G.; Pacheco, D. F.; Westermann, B.; Garcia-Rivera, D.; Solid-phase heterocycle synthesis using multicomponent reactions (Erik Van der Eycken, Upendra K. Sharma). Multicomponent Reactions towards Heterocycles: Concepts and Applications 4, 139-162, (2022) ISBN: 9783527349081 DOI: 10.1002/9783527832439.ch4

Heterocycle chemistry has traditionally relied on solution-phase synthesis as technological platform to discover and produce bioactive scaffolds. With the advent of solid-phase synthesis (SPS) at the end of last century, combinatorial approaches using on-resin procedures were applied to create skeletal and appendage diversity in heterocyclic compounds. Multicomponent reactions (MCRs) were part of that endeavor for developing solid-phase protocols capable to accelerate drug discovery. This chapter highlights methodological aspects of the implementation of on-resin MCRs to produce heterocycle compounds. Different name reactions, synthetic strategies, and solid supports are analyzed with a critical view hoping to encourage the new generation of chemists to adapt the more recent multicomponent – especially catalytic – processes to the SPS technology.
Books and chapters

Soboleva, A.; Vashurina, N.; Frolov, A.; Individual glycation sites as biomarkers of Type 2 diabetes mellitus (Dr. Anca Pantea Stoian). IntechOpen (2021) ISBN: 978-1-83881-903-3 DOI: 10.5772/intechopen.95532

Type 2 diabetes mellitus (T2DM) is a widely spread metabolic disease, the initial stages of which are asymptomatic and have no clinically recognizable manifestation. At the molecular level, T2DM is manifested with essential non-enzymatic structural changes of intra- and extracellular proteins, mostly represented with oxidation and glycation of multiple residues. Protein glycation is one of the most universal markers of T2DM, and is recognized as an indirect, but adequate indicator of plasma glucose levels over prolonged periods of time. Unfortunately, glycated hemoglobin (HbA1c) – the universally accepted T2DM marker, is insensitive for short-term excursions of blood glucose, which are known to precede the onset of disease. Therefore, new generation biomarkers, giving access to the time dimension of Maillard reaction in blood, are desired. In this context, establishment of individual glycation sites of plasma proteins as new T2DM biomarkers might be a promising approach. Indeed, involvement of proteins with different half-life times in such analysis will make the time dimension of protein glycation in blood available and will allow early recognition of blood sugar fluctuations, occurring within few weeks or even days.
Books and chapters

Burgos-Toro, A.; Dippe, M.; Vásquez, A. F.; Pierschel, E.; Wessjohann, L. A.; Fernández-Niño, M.; Multi-Omics data mining: A novel tool for BioBrick design (Iva Ribic). IntechOpen (2021) DOI: 10.5772/intechopen.101351

Currently, billions of nucleotide and amino acid sequences accumulate in free-access databases as a result of the omics revolution, the improvement in sequencing technologies, and the systematic storage of shotgun sequencing data from a large and diverse number of organisms. In this chapter, multi-omics data mining approaches will be discussed as a novel tool for the identification and characterization of novel DNA sequences encoding elementary parts of complex biological systems (BioBricks) using omics libraries. Multi-omics data mining opens up the possibility to identify novel unknown sequences from free-access databases. It also provides an excellent platform for the identification and design of novel BioBricks by using previously well-characterized biological bricks as scaffolds for homology searching and BioBrick design. In this chapter, the most recent mining approaches will be discussed, and several examples will be presented to highlight its relevance as a novel tool for synthetic biology.
Books and chapters

Restrepo, S.; Samper, C.; di Palma, F.; Hodson, E.; Torres, M.; Reol, E. M.; Eddi, M.; Wessjohann, L.; Jaramillo, G. P.; et al., .; Colombia hacia una sociedad del conocimiento. Reflexiones y propuestas 1-450, (2020) ISBN: 978-958-5135-12-3

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Books and chapters

Francioso, A.; Franke, K.; Villani, C.; Mosca, L.; d’Erme, M.; Frischbutter, S.; Brandt, W.; Sanchez-Lamar, A.; Wessjohann, L.; Insights into the Phytochemistry of the Cuban Endemic Medicinal Plant Phyllanthus orbicularis: Fideloside, a Novel Bioactive 8-C-glycosyl 2,3-Dihydroflavonol (Pinarosa Avato). Molecules 79-92, (2020) ISBN: 978-3-03928-746-8 DOI: 10.3390/books978-3-03928-747-5

Phyllanthus orbicularis (Phyllanthaceae) is an endemic evergreen tropical plant of Cuba that grows in the western part of the island and is used in traditional medicine as an infusion. The aqueous extract of this plant presents a wide range of pharmacological activitiessuch as antimutagenic, antioxidant and antiviral effects. Given the many beneficial effects and the great interest in the development of new pharmacological products from natural sources, the aim of this work was to investigate the phytochemistry of this species and to elucidate the structure of the main bioactive principles. Besides thepresence of several known polyphenols, the major constituent was hitherto not described. The chemical structure of this compound, here named Fideloside, was elucidated by means of HR-ESIMS/MSn, 1D/2D NMR, FT-IR, and ECD as (2R,3R)-(−)-3’,4 ,5,7-tetrahydroxydihydroflavonol-8-C- -D-glucopyranoside. The compound, as well as the plant aqueous preparations, showed promising bioactive properties, i.e., anti-inflammatory capacity in human explanted monocytes, corroborating future pharmacological use for this new natural C-glycosyl flavanonol.
Books and chapters

Deising, H. B.; Amorim, R.; De Oliveira Silva, A.; Raschke, A.; Eisermann, I.; Wirsel, S. G. R.; Csuk, R.; Schmitz, L. M.; Arnold, N.; Antagonistic Microorganisms in Plant Protection: Consumers’ Friends or Foes? (Deising, H. B. et al., eds.). Modern Fungicides and Antifungal Compounds IX, 217-228, (2020)

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