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Publications - Bioorganic Chemistry

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Publications

Bin Ware, I.; Franke, K.; Dube, M.; Ali El Enshasy, H.; Wessjohann, L. A.; Characterization and bioactive potential of secondary metabolites isolated from Piper sarmentosum Roxb. Int. J. Mol. Sci. 24, 1328, (2023) DOI: 10.3390/ijms24021328

Piper sarmentosum Roxb. (Piperaceae) is a traditional medicinal plant in South-East Asian countries. The chemical investigation of leaves from this species resulted in the isolation of three previously not described compounds, namely 4″-(3-hydroxy-3-methylglutaroyl)-2″-β-D-glucopyranosyl vitexin (1), kadukoside (2), and 6-O-trans-p-coumaroyl-D-glucono-1,4-lactone (3), together with 31 known compounds. Of these known compounds, 21 compounds were isolated for the first time from P. sarmentosum. The structures were established by 1D and 2D NMR techniques and HR-ESI-MS analyses. The compounds were evaluated for their anthelmintic (Caenorhabditis elegans), antifungal (Botrytis cinerea, Septoria tritici and Phytophthora infestans), antibacterial (Aliivibrio fischeri) and cytotoxic (PC-3 and HT-29 human cancer cells lines) activities. Methyl-3-(4-methoxyphenyl)propionate (8), isoasarone (12), and trans-asarone (15) demonstrated anthelmintic activity with IC50 values between 0.9 and 2.04 mM. Kadukoside (2) was most active against S. tritici with IC50 at 5.0 µM and also induced 94% inhibition of P. infestans growth at 125 µM. Trans-asarone (15), piperolactam A (23), and dehydroformouregine (24) displayed a dose-dependent effect against B. cinerea from 1.5 to 125 µM up to more than 80% inhibition. Paprazine (19), cepharadione A (21) and piperolactam A (23) inhibited bacterial growth by more than 85% at 100 µM. Only mild cytotoxic effects were observed.
Preprints

Illig, A.-M.; Siedhoff, N. E.; Schwaneberg, U.; Davari, M. D.; A hybrid model combining evolutionary probability and machine learning leverages data-driven protein engineering bioRxiv (2022) DOI: 10.1101/2022.06.07.495081

Protein engineering through directed evolution and (semi-)rational approaches has been applied successfully to optimize protein properties for broad applications in molecular biology, biotechnology, and biomedicine. The potential of protein engineering is not yet fully realized due to the limited screening throughput hampering the efficient exploration of the vast protein sequence space. Data-driven strategies have emerged as a powerful tool to leverage protein engineering by providing a model of the sequence-fitness landscape that can exhaustively be explored in silico and capitalize on the high diversity potential offered by nature However, as both the quality and quantity of the inputted data determine the success of such approaches, the applicability of data-driven strategies is often limited due to sparse data. Here, we present a hybrid model that combines direct coupling analysis and machine learning techniques to enable data-driven protein engineering when only few labeled sequences are available. Our method achieves high performance in predicting a protein’s fitness based on its sequence regardless of the number of sequences-fitness pairs in the training dataset. Besides reducing the computational effort compared to state-of-the-art methods, it outperforms them for sparse data situations, i.e., 50 − 250 labeled sequences available for training. In essence, the developed method is auspicious for data-driven protein engineering, especially for protein engineers who have only access to a limited amount of data for sequence-fitness landscape modeling.
Publications

Zhang, Y.; Cui, L.; Lu, Y.; He, J.; Hussain, H.; Xie, L.; Sun, X.; Meng, Z.; Cao, G.; Qin, D.; Wang, D.; Characterization of silver nanoparticles synthesized by leaves of Lonicera japonica thunb International Journal of Nanomedicine 17, 1647-1657, (2022) DOI: 10.2147/ijn.s356919

Background: The leaves of L. japonica (LLJ) are widely used as medicine in China. It is rich in caffeoylquinic acids, flavonoids and iridoid glycosides and has strong reducing capacities. Therefore, it can be used as a green material to synthesize silver nanoparticles.Methods: LLJ was used as a reducing agent to produce the LLJ-mediated silver nanoparticles (LLJ-AgNPs). The structure and physicochemical properties of LLJ-AgNPs were characterized by ultraviolet spectroscopy (UV-Vis), scanning electron microscopy (SEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and x-ray powder diffraction (XRD). Antioxidant activity of LLJ-AgNPs was determined by 1,1-diphenyl-2-picrylhydrazyl (DPPH) scavenging. Antibacterial activity was determined by 96 well plates (AGAR) gradient dilution, while the anticancer potential was determined by MTT assay.Results: The results showed LLJ-AgNPs had a spherical structure with the maximum UV-Vis absorption at 400 nm. In addition, LLJAgNPs exhibited excellent antioxidant properties, where the free radical scavenging rate of LLJ-AgNPs was increased from 39% to 92% at concentrations from 0.25 to 1.0 mg/mL. Moreover, LLJ-AgNPs displayed excellent antibacterial properties against E. coli and Salmonella at room temperature, with minimum inhibitory values of 10−6 and 10−5 g/L, respectively. In addition, the synthetic LLJAgNPs exhibited a better inhibition effect in the proliferation of cancer cells (HepG2, MDA-MB −231, and Hela cells).Conclusion: The present study provides a green approach to synthesize LLJ-AgNPs. All those findings illustrated that the produced LLJ-AgNPs can be used as an economical and efficient functional material for further applications in food and pharmaceutical fields.
Publications

Zayed, A.; Abdelwareth, A.; Mohamed, T. A.; Fahmy, H. A.; Porzel, A.; Wessjohann, L. A.; Farag, M. A.; Dissecting coffee seeds metabolome in context of genotype, roasting degree, and blending in the Middle East using NMR and GC/MS techniques Food Chem. 373, 131452, (2022) DOI: 10.1016/j.foodchem.2021.131452

With a favored taste and various bioactivities, coffee has been consumed as a daily beverage worldwide. The current study presented a multi-faceted comparative metabolomics approach dissecting commercially available coffee products in the Middle East region for quality assessment and functional food purposes using NMR and GC/MS platforms. NMR metabolites fingerprinting led to identification of 18 metabolites and quantification (qNMR) of six prominent markers for standardization purposes. An increase of β-ethanolamine (MEA) reported for the first time, 5-(hydroxymethyl) furfural (5-HMF), concurrent with a reduction in chlorogenic acid, kahweol, and sucrose levels post roasting as revealed using multivariate data analyses (MVA). The diterpenes kahweol and cafestol were identified in green and roasted Coffea arabica, while 16-O-methyl cafestol in roasted C. robusta. Moreover, GC/MS identified a total of 143 metabolites belonging to 15 different chemical classes, with fructose found enriched in green C. robusta versus fatty acids abundance, i.e., palmitic and stearic acids in C. arabica confirming NMR results. These potential results aided to identify novel quality control attributes, i.e., ethanolamine, for coffee in the Middle East region and have yet to be confirmed in other coffee specimens.
Publications

Zanatta, N.; Mittersteiner, M.; Aquino, E. C.; Budragchaa, T.; Wessjohann, L. A.; Bonacorso, H. G.; Martins, M. A. P.; Synthesis of methylene-bridged trifluoromethyl azoles using 5-(1,2,3-Triazol-1-yl)enones Synthesis 54, 439-450, (2022) DOI: 10.1055/s-0040-1719837

A protocol for synthesizing triazole-containing pyrazolines and pyrazoles selectively using trifluoromethylated 5-(1,2,3-triazol-1-yl)enones as starting materials, is reported. The selectivity of the reaction was controlled by the nature of the hydrazine or derivative used: free hydrazines furnished the 1,5-regiosiomer exclusively in yields up to 98%, whereas protected hydrazines provided the 1,3-regioisomer in yields up to 77%. To demonstrate the synthetic versatility of the triazole-based enone, reactions with other unsymmetrical dinucleophiles (hydroxylamine hydrochloride and S-methyl isothiourea sulfates) allowed the selective preparation of triazole-containing isoxazoline and pyrimidine rings.
Publications

Wittmund, M.; Cadet, F.; Davari, M. D.; Learning epistasis and residue coevolution patterns: Current trends and future perspectives for advancing enzyme engineering ACS Catal. 12, 14243-14263, (2022) DOI: 10.1021/acscatal.2c01426

Engineering proteins and enzymes with the desired functionality has broad applications in molecular biology, biotechnology, biomedical sciences, health, and medicine. The vastness of protein sequence space and all the possible proteins it represents can pose a considerable barrier for enzyme engineering campaigns through directed evolution and rational design. The nonlinear effects of coevolution between amino acids in protein sequences complicate this further. Data-driven models increasingly provide scientists with the computational tools to navigate through the largely undiscovered forest of protein variants and catch a glimpse of the rules and effects underlying the topology of sequence space. In this review, we outline a complete theoretical journey through the processes of protein engineering methods such as directed evolution and rational design and reflect on these strategies and data-driven hybrid strategies in the context of sequence space. We discuss crucial phenomena of residue coevolution, such as epistasis, and review the history of models created over the past decade, aiming to infer rules of protein evolution from data and use this knowledge to improve the prediction of the structure− function relationship of proteins. Data-driven models based on deep learning algorithms are among the most promising methods that can account for the nonlinear phenomena of sequence space to some degree. We also critically discuss the available models to predict evolutionary coupling and epistatic effects (classical and deep learning) in terms of their capabilities and limitations. Finally, we present our perspective on possible future directions for developing data-driven approaches and provide key orientation points and necessities for the future of the fast-evolving field of enzyme engineering.
Publications

Weigel, B.; Ludwig, J.; Weber, R. A.; Ludwig, S.; Lennicke, C.; Schrank, P.; Davari, M. D.; Nagia, M.; Wessjohann, L. A.; Heterocyclic and alkyne terpenoids by terpene synthase‐mediated biotransformation of non‐natural prenyl diphosphates: Access to new fragrances and probes ChemBioChem 23, e202200211, (2022) DOI: 10.1002/cbic.202200211

Terpene synthase-mediated biotransformation of eleven synthetic sulfur- or oxygen-containing non-natural prenyl diphosphates resulted in the formation of five novel terpenoids and analogues. Uniquely, they trap intermediate steps and form heterocycles or compounds with alkyne side chains. Computational modelling differentiates convertible from inconvertible substrates and thereby provides an understanding of the detailed molecular mechanism of terpene cyclases. Two terpene cyclases were used as biocatalytic tool, namely, limonene synthase from Cannabis sativa (CLS) and 5-epi-aristolochene synthase (TEAS) from Nicotiana tabacum. They showed significant substrate flexibility towards non-natural prenyl diphosphates to form novel terpenoids, including core oxa- and thia-heterocycles and alkyne-modified terpenoids. We elucidated the structures of five novel monoterpene-analogues and a known sesquiterpene-analogue. These results reflected the terpene synthases′ ability and promiscuity to broaden the pool of terpenoids with structurally complex analogues. Docking studies highlight an on-off conversion of the unnatural substrates.
Publications

Vasco, A. V.; Ceballos, L. G.; Wessjohann, L. A.; Rivera, D. G.; Multicomponent functionalization of the octreotide peptide macrocyclic scaffold Eur. J. Org. Chem. 2022, e202200687, (2022) DOI: 10.1002/ejoc.202200687

The replacement of the disulfide bridge by other types of side chain linkages has been a continuous endeavor in the development of cyclic peptide drugs with improved metabolic stability. Octreotide is a potent and selective somatostatin analog that has been used as an anticancer agent, in radiolabeled conjugates for the localization of tumors and as targeting moiety in peptide-drug conjugates. Here, we describe an onresin methodology based on a multicomponent macrocyclization that enables the substitution of the disulfide bond by a tertiary lactam bridge functionalized with a variety of exocyclic moieties, including lipids, fluorophores, and charged groups. Conformational analysis in comparison with octreotide provides key information on the type of functionalization permitting the conformational mimicry of the bioactive peptide.
Publications

Tousif, M. I.; Nazir, M.; Saleem, M.; Tauseef, S.; Shafiq, N.; Hassan, L.; Hussain, H.; Montesano, D.; Naviglio, D.; Zengin, G.; Ahmad, I.; Psidium guajava L. an incalculable but underexplored food crop: Its phytochemistry, ethnopharmacology, and industrial applications Molecules 27, 7016, (2022) DOI: 10.3390/molecules27207016

Psidium guajava L. (guava) is a small tree known for its fruit flavor that is cultivated almost around the globe in tropical areas. Its fruit is amazingly rich in antioxidants, vitamin C, potassium, and dietary fiber. In different parts of the world, this plant holds a special place with respect to fruit and nutritional items. Pharmacological research has shown that this plant has more potential than just a fruit source; it also has beneficial effects against a variety of chronic diseases due to its rich nutritional and phytochemical profile. The primary goal of this document is to provide an updated overview of Psidium guajava L. and its bioactive secondary metabolites, as well as their availability for further study, with a focus on the health benefits and potential industrial applications. There have been several studies conducted on Psidium guajava L. in relation to its use in the pharmaceutical industry. However, its clinical efficacy and applications are still debatable. Therefore, in this review a detailed study with respect to phytochemistry of the plant through modern instruments such as GC and LC-MS has been discussed. The biological activities of secondary metabolites isolated from this plant have been extensively discussed. In order to perform long-term clinical trials to learn more about their effectiveness as drugs and applications for various health benefits, a structure activity relationship has been established. Based on the literature, it is concluded that this plant has a wide variety of biopharmaceutical applications. As a whole, this article calls for long-term clinical trials to obtain a greater understanding of how it can be used to treat different diseases.
Publications

Sun, X.; Chen, L.; Yan, H.; Cui, L.; Hussain, H.; Xie, L.; Liu, J.; Jiang, Y.; Meng, Z.; Cao, G.; Park, J.; Wang, D.; An efficient high‐speed counter‐current chromatography method for the preparative separation of potential antioxidant from Paeonia lactiflora Pall. combination of in vitro evaluation and molecular docking J Sep Sci 45, 1856-1865, (2022) DOI: 10.1002/jssc.202200082

Paeonia lactiflora Pall., one of the most famous classical herbal medicine, has been used to treat diseases for over 1200 years. In this research, the functional ingredients were purified by online-switch two-dimensional high-speed counter-current chromatography combined with inner-recycling and continuous injection mode. The antioxidant activity was evaluated by investigating the 2,2’-azobis (2-amidinopropane) dihydrochloride-induced oxidant damage in vitro and confirmed through molecular docking. n-Butanol/ethyl acetate/water (2:3:5, v/v) solvent system was used for the first dimensional separation and optimized the sample loading. Two pure compounds and a polyphenol-enriched fraction were separated. The polyphenol-enriched fraction was separated with a solvent system n-hexane/ethyl acetate/methanol/water (2:8:4:6, v/v) with continuous injection mode. Five compounds were successfully separated, including gallic acid (1), methyl gallate (2), albiflorin (3), paeoniflorin (4), and ethyl gallate (5). Their structures were identified by mass spectrometry and nuclear magnetic resonance. The results from antioxidant effect showed that albiflorin had stronger antioxidant activity. Molecular docking results indicated that the affinity energy of the identified compounds ranged from -3.79 to -8.22 kcal/mol and albiflorin showed the lowest affinity energy. Overall, all those findings suggested that the strong antioxidant capacity of albiflorin can be potentially used for treatment of diseases that caused by oxidation.
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