Computation-guided asymmetric total syntheses of resveratrol dimers

Although computational simulation-based natural product syntheses are in their initial stages of development, this concept can potentially become an indispensable resource in the field of organic synthesis. Herein we report the asymmetric total syntheses of several resveratrol dimers based on a comprehensive computational simulation of their biosynthetic pathways. Density functional theory (DFT) calculations suggested inconsistencies in the biosynthesis of vaticahainol A and B that predicted the requirement of structural corrections of these natural products. According to the computational predictions, total syntheses were examined and the correct structures of vaticahainol A and B were confirmed. The established synthetic route was applied to the asymmetric total synthesis of (−)-malibatol A, (−)-vaticahainol B, (+)-vaticahainol A, (+)-vaticahainol C, and (−)-albiraminol B, which provided new insight into the biosynthetic pathway of resveratrol dimers. This study demonstrated that computation-guided organic synthesis can be a powerful strategy to advance the chemical research of natural products.

Computational predictions of adaptive aromaticity for the design of singlet fission materials

Singlet fission has attracted extensive attention from experimentalists and theoreticians due to its ability to improve photovoltaic conversion efficiency. Still, designing singlet fission materials remains challenging. In this work, we...

Hydrogen Delocalization in an Asymmetric Biomolecule: The Curious Case of Alpha-Fenchol

Rotational microwave jet spectroscopy studies of the monoterpenol α-fenchol have so far failed to identify its second most stable torsional conformer, despite computational predictions that it is only very slightly higher in energy than the global minimum. Vibrational FTIR and Raman jet spectroscopy investigations reveal unusually complex OH and OD stretching spectra compared to other alcohols. Via modeling of the torsional states, observed spectral splittings are explained by delocalization of the hydroxy hydrogen atom through quantum tunneling between the two non-equivalent but accidentally near-degenerate conformers separated by a low and narrow barrier. The energy differences between the torsional states are determined to be only 16(1) and 7(1) cm−1hc for the protiated and deuterated alcohol, respectively, which further shrink to 9(1) and 3(1) cm−1hc upon OH or OD stretch excitation. Comparisons are made with the more strongly asymmetric monoterpenols borneol and isopinocampheol as well as with the symmetric, rapidly tunneling propargyl alcohol. In addition, the third—in contrast localized—torsional conformer and the most stable dimer are assigned for α-fenchol, as well as the two most stable dimers for propargyl alcohol.

Hydrogen Delocalization in an Asymmetric Biomolecule: The Curious Case of alpha-Fenchol

Rotational microwave jet spectroscopy studies of the monoterpenol α-fenchol have so far failed to identify its second expected torsional conformer, despite computational predictions that it is only very slightly higher in energy than the most stable conformer. Vibrational FTIR and Raman jet spectroscopy investigations reveal unusually complex OH and OD stretching spectra compared to other alcohols. Via modelling of the torsional states, observed spectral splittings are explained by delocalization of the hydroxy hydrogen atom through quantum tunneling between the two non-equivalent but accidentally near-degenerate conformers separated by a low and narrow barrier. The energy differences between the torsional states are determined to be only 16(1) and 7(1) cm$^{−1}hc$ for the protiated and deuterated alcohol, respectively, which further shrink to 9(1) and 3(1) cm$^{−1}hc$ upon OH or OD stretch excitation. Comparisons are made with the more strongly asymmetric monoterpenols borneol and isopinocampheol as well as with the symmetric, rapidly tunneling propargyl alcohol. Assigned are also for α-fenchol the third – in contrast localized – torsional conformer and the most stable dimer, as well as for propargyl alcohol the two most stable dimers.

Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

Noncoding RNAs (ncRNAs) play prominent roles in the regulation of gene expression via their interactions with other biological molecules such as proteins and nucleic acids. Although much of our knowledge about how these ncRNAs operate in different biological processes has been obtained from experimental findings, computational biology can also clearly substantially boost this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules. Computational predictions are thus used as an alternative source of new insights through a process of mutual enrichment because the information obtained through experiments continuously feeds through into computational methods. The results of these predictions in turn shed light on possible interactions that are subsequently validated experimentally. This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs and lncRNAs. The ncRNA species described in this work have a special emphasis on those found in humans, but information on ncRNA of other species is also included.

Modular, robust and extendible multicellular circuit design in yeast

Division of labor between cells is ubiquitous in biology but the use of multi-cellular consortia for engineering applications is only beginning to be explored. A significant advantage of multi-cellular circuits is their potential to be modular with respect to composition but this claim has not yet been extensively tested using experiments and quantitative modeling. Here, we construct a library of 24 yeast strains capable of sending, receiving or responding to three molecular signals, characterize them experimentally and build quantitative models of their input-output relationships. We then compose these strains into two- and three-strain cascades as well a four-strain bistable switch and show that experimentally measured consortia dynamics can be predicted from the models of the constituent parts. To further explore the achievable range of behaviors, we perform a fully automated computational search over all two-, three- and four-strain consortia to identify combinations that realize target behaviors including logic gates, band-pass filters and time pulses. Strain combinations that are predicted to map onto a target behavior are further computationally optimized and then experimentally tested. Experiments closely track computational predictions. The high reliability of these model descriptions further strengthens the feasibility and highlights the potential for distributed computing in synthetic biology.

Human MLH1/3 variants causing aneuploidy, pregnancy loss, and premature reproductive aging

Embryonic aneuploidy from mis-segregation of chromosomes during meiosis causes pregnancy loss. Proper disjunction of homologous chromosomes requires the mismatch repair (MMR) genes MLH1 and MLH3, essential in mice for fertility. Variants in these genes can increase colorectal cancer risk, yet the reproductive impacts are unclear. To determine if MLH1/3 single nucleotide polymorphisms (SNPs) in human populations could cause reproductive abnormalities, we use computational predictions, yeast two-hybrid assays, and MMR and recombination assays in yeast, selecting nine MLH1 and MLH3 variants to model in mice via genome editing. We identify seven alleles causing reproductive defects in mice including female subfertility and male infertility. Remarkably, in females these alleles cause age-dependent decreases in litter size and increased embryo resorption, likely a consequence of fewer chiasmata that increase univalents at meiotic metaphase I. Our data suggest that hypomorphic alleles of meiotic recombination genes can predispose females to increased incidence of pregnancy loss from gamete aneuploidy.

Preliminary analysis of a neotropical plant extract antiviral potential against Chikungunya and Mayaro viruses

Chikungunya and Mayaro fevers are viral infectious diseases, without vaccine or treatment, that causes fever and arthralgia. Establishing novel antiviral tools capable of preventing or treating Chikungunya virus (CHIKV), and Mayaro virus (MAYV) infections are needed. The use of plant-based compounds that affect the replication cycles of these viruses has been proposed as a promising strategy. Chiococca alba (L.) Hitchc. is a neotropical plant used by Yucatec Mayas traditional healers, mainly, as antipyretic and antirheumatic. To evaluate the potential of C. alba methanolic extracts against CHIKV and MAYV through preliminary analysis in vitro and in silico . The cytotoxicity profile of two C. alba roots methanolic extracts in Vero cells was performed by lysosomal viability using the neutral red assay, and the antiviral potential was determined by plaque assay. We further assessed, through in silico computational predictions, the possible interactions between the active site of the nsP2 proteases of these viruses with some secondary metabolites present in C. alba extracts, identified by High-Performance Liquid Chromatography (HPLC). Our partial phytochemical analysis revealed the presence of flavonoids, and phenolic acids in the C. alba extracts. Our in vitro assays showed that both C. alba extracts inhibited more than 70% of CHIKV and MAYV activities at 60 µg/mL concentration. Based on our in silico computational predictions, the flavonoids naringin and vitexin showed the greatest affinity energies with the CHIKV and MAYV nsP2 proteases, revealing the great potential of these compounds as viral inhibitors. The findings described here indicates that C. alba extracts, or their secondary metabolites, as a potential source of novel antiviral compounds.