Computational Chemistry Driven Solution to Rubriflordilactone B

Road Map Toward Computer-Guided Total Synthesis of Natural Products. The Dysiherbol A Case Study: What if Serendipity Hadn't Intervened?

We present a computational study inspired by the story of dysiherbol A, a natural product whose putative structure was found incorrect through synthesis by a completely fortuitous event. While the carbon connectivity and chemical environment between both structures remain similar, the real dysiherbol A has a different molecular weight than that reported for the natural product. Had the synthesis groups not been favored by fortune, it could be speculated that a substantial amount of time and effort would have been required to solve the structural puzzle. Within the realm of computer-guided total synthesis of natural products, the question arose whether a synthesis group could have in silico reassigned the structure before embarking on the experimental adventure. To address this query, we evaluated some state-of-the-art computational procedures based on their computational demand and ease of implementation for nonexpert users with basic skills in computational chemistry (including HOSE, CASCADE, ANN-PRA, ML-J-DP4, DP4, and DP4+). While discussing the strengths and limitations of these methods, this case study provides a roadmap of what could be done before venturing into complex and time-demanding total synthesis projects.

Brasilterpenes A-E, Bergamotane Sesquiterpenoid Derivatives with Hypoglycemic Activity from the Deep Sea-Derived Fungus Paraconiothyrium brasiliense HDN15-135

Five bergamotane sesquiterpenoid derivatives, brasilterpenes A-E (1-5), bearing an unreported spiral 6/4/5 tricyclic ring system, were isolated from the deep sea-derived ascomycete fungus Paraconiothyrium brasiliense HDN15-135. Their structures, including absolute configurations, were established by extensive spectroscopic methods complemented by single-crystal X-ray diffraction analyses, electronic circular dichroism (ECD), and density-functional theory (DFT) calculations of nuclear magnetic resonance (NMR) data including DP4+ analysis. The hypoglycemic activity of these compounds was assessed using a diabetic zebrafish model. Brasilterpenes A (1) and C (3) significantly reduced free blood glucose in hyperglycemic zebrafish in vivo by improving insulin sensitivity and suppressing gluconeogenesis. Moreover, the hypoglycemic activity of compound 3 was comparable to the positive control, anti-diabetes drug rosiglitazone. These results suggested brasilterpene C (3) had promising anti-diabetes potential.

Diastereoselective Synthesis of the ABCD Ring System of Rubriflordilactone B

A novel nine-step diastereoselective route to the ABCD ring system of the natural product rubriflordilactone B is reported. Use of an α-substituted butenolide derived from maleic anhydride facilitated a 1,4-conjugate addition to provide a diene. The order in which a ring-closing metathesis and enolate oxidation were performed on this compound dictated the relative stereochemistry of the target. The final product exhibited anisotropic effects during room-temperature NMR studies, requiring elevated-temperature experiments to confirm its identity.

Do Double-Hybrid Exchange-Correlation Functionals Provide Accurate Chemical Shifts? A Benchmark Assessment for Proton NMR

A benchmark density functional theory (DFT) study of ¹H NMR chemical shifts for data sets comprising 200 chemical shifts, including complex natural products, has been carried out to assess the performance of DFT methods. Two new benchmark data sets, NMRH33 and NMRH148, have been established. The meta-GGA revTPSS performs remarkably well against the NMRH33 benchmark set (mean absolute deviation (MAD), 0.10 ppm; maximum deviation (max), 0.26 ppm) with the smallest MAD of all evaluated functionals. The best-performing double-hybrid density functional (DHDF), revDSD-BLYP (MAD, 0.16 ppm; max, 0.35 ppm), performs similarly to hybrid-GGA methods (e.g., mPW1PW91/6-311G(d) (MAD, 0.15 ppm; max, 0.36 ppm)), but at a considerably higher computational cost. The results indicate that currently available double-hybrid DFT methods offer no benefit over GGA (including hybrid and meta) functionals in the calculation of ¹H NMR chemical shifts.

Litosetoenins A-E, Diterpenoids from the Soft Coral Litophyton setoensis, Backbone-Rearranged through Divergent Cyclization Achieved by Epoxide Reactivity Inversion

Litosetoenins A-E (1-5), five new ring-rearranged serrulatane-type diterpenoids with a common tricyclo[3.0.4]decane core, along with a known diterpenoid glycoside (6), a related known diterpenoid (7), and four known sesquiterpenoids (8-11), were isolated from a Balinese soft coral Litophyton setoensis. Spirolitosetoenin A (5a) and isospirolitosetoenin A (5b), featuring an unprecedented spiro[4,5]decane core, were obtained after treatment of compound 5 with HCl in methanol. The structures of new compounds were elucidated by extensive spectroscopic analysis, quantum mechanical nuclear magnetic resonance approach, and chemical methods. A plausible biosynthetic pathway involving an unusual divergent biogenesis was proposed.

A critical review on the use of DP4+ in the structural elucidation of natural products: the good, the bad and the ugly. A practical guide

Covering: 2015 up to the end of 2020Even in the golden age of NMR, the number of natural products being incorrectly assigned is becoming larger every day. The use of quantum NMR calculations coupled with sophisticated data analysis provides ideal complementary tools to facilitate the elucidation process in challenging cases. Among the current computational methodologies to perform this task, the DP4+ probability is a popular and widely used method. This updated version of Goodman's DP4 synergistically combines NMR calculations at higher levels of theory with the Bayesian analysis of both scaled and unscaled data. Since its publication in late 2015, the use of DP4+ to solve controversial natural products has substantially grown, with several predictions being confirmed by total synthesis. To date, the structures of more than 200 natural products were determined with the aid of DP4+. However, all that glitters is not gold. Besides its intrinsic limitations, on many occasions it has been improperly used with potentially important consequences on the quality of the assignment. Herein we present a critical revision on how the scientific community has been using DP4+, exploring the strengths of the method and how to obtain optimal results from it. We also analyze the weaknesses of DP4+, and the paths to by-pass them to maximize the confidence in the structural elucidation.

Structural characterisation of natural products by means of quantum chemical calculations of NMR parameters: new insights

In this review, we focus in all aspects of NMR simulation of natural products, from the fundamentals to the new computational toolboxes available, combining advanced quantum chemical calculations with upstream data processing and machine learning.

Nine prenylated acylphloroglucinols with potential anti-depressive and hepatoprotective activities from Hypericum scabrum

In our screening program for new biologically active secondary metabolites, nine new polycyclic polyprenyled acylphloroglucinols, hyperscabins D-L, together with three known compounds, were obtained from the aerial parts of Hypericum scabrum. The chemical structures of 1-9 were characterized by extensive spectroscopic analyses, nuclear magnetic resonance calculation with DP4+ probability analysis, and the electronic circular dichroism spectra were calculated. Compound 1 was an unusual prenylated acylphloroglucinol decorated with a 5-oxaspiro [4,5] deca-1,9-dione skeleton. Compound 2 was a newly identified spirocyclic polyprenylated acylphloroglucinol possessing a rare 5,5-spiroketal segment. Compounds 3, 8, and 10 (10 μM) exhibited pronounced hepatoprotective activity against d-galactosamine-induced WB-F344 cell damage in vitro assays. All test compounds (1, 3, and 7-12) demonstrated potential inhibitory effects at 10 μM against noradrenalinet ([³H]-NE) reuptake in rat brain synaptosome.

NMR Calculations with Quantum Methods: Development of New Tools for Structural Elucidation and Beyond

Structural elucidation is an important and challenging stage in the discovery of new organic molecules. Single-crystal X-ray analysis provides the most unquestionable results, though in practice the availability of suitable crystals limits its broad use. On the other hand, NMR spectroscopy has become the leading and universal technique to accomplish the task. Despite continuous advances in the field, the misinterpretation of NMR data is commonplace, evidenced by the large number of erroneous structures being published in top journals. Quantum calculations of NMR chemical shifts and scalar coupling constants emerged as ideal complements to facilitate the elucidation process when experimental NMR data is inconclusive. Since seminal reports demonstrated that affordable DFT methods provide NMR predictions accurate enough to differentiate among closely related isomers, the discipline has experienced substantial growth. The impact has been felt in different areas, and nowadays the results of such calculations are routinely seen in high impact literature.This Account describes our investigations in the field of quantum NMR calculations, focusing on the development of tools for structural elucidation and practical applications. We pioneered the use of artificial intelligence methods in the development of novel strategies of structural validation. Our first generation of trained artificial neural networks (ANNs) showed excellent ability to identify mistakes at the atom connectivity level, whereas the use of multidimensional pattern recognition pushed the performance to the stereochemical limit. In a conceptually different approach, we developed DP4+, an updated version of the DP4 probability used to determine the most likely structure among two or more candidates when one set of experimental data is available. Increasing the level of theory in NMR calculations and including unscaled data in the formalism improved the performance of the method, further validated to settle the configuration of challenging motifs such as spiroepoxides or Mosher's derivatives. One of the limitations of DP4+ is related to the relatively large computational cost involved in obtaining DFT-optimized geometries, which led to the development of a fast variant including the valuable information provided by coupling constants (J-DP4 method).These tools were explored to suggest the most probable structure of controversial natural or unnatural products originally misassigned, with some predictions further validated by synthesis (as in the case of pseudorubriflordilactone B). The possibility of predicting the structure of a natural product without requiring authentic sample was investigated in collaboration with Prof. Pilli (UNICAMP, Brazil) in the computer-guided total synthesis and stereochemical revisions of several natural products. Despite these advances, there remain considerable challenges, such as the case of configurational assessment of polar systems featuring multiple intramolecular hydrogen bonding interactions because of the poor energy predictions provided by most DFT methods. In our latest work, we tackle this problem by averaging the results provided by randomly generated ensembles, paving the way for a new paradigm in quantum NMR-assisted structural elucidation.

Stereochemical revision of xylogranatin F by GIAO and DU8+ NMR calculations

This manuscript describes predicted NMR shifts for the limonoid natural product xylogranatin F. The ¹ H and ¹³ C NMR shifts of four diastereomers were evaluated by GIAO and hybrid DFT/parametric DU8+ methods. The results of the ¹ H and ¹³ C NMR calculations for both the GIAO method and the DU8+ calculations suggest the revised structure that was recently reassigned by chemical synthesis. Furthermore, we show that while DU8+ provides superior accuracy with less computation time, GIAO points to the correct structure with more distinguishable data in this case study.

Recent progress in the synthesis of limonoids and limonoid-like natural products

Recent progress in syntheses of limonoids and limonoid-like natural products is reviewed. The current “state-of-art” advance on novel synthetic strategy are summarized and future outlook will be presented.

Convergent Total Syntheses of (-)-Rubriflordilactone B and (-)-pseudo-Rubriflordilactone B

A highly convergent strategy for the synthesis of the natural product (-)-rubriflordilactone B, and the proposed structure of (-)-pseudo-rubriflordilactone B, is described. Late stage coupling of diynes containing the respective natural product FG rings with a common AB ring aldehyde precedes rhodium-catalyzed [2+2+2] alkyne cyclotrimerization to form the natural product skeleton, with the syntheses completed in just one further operation. This work resolves the uncertainty surrounding the identity of pseudo-rubriflordilactone B and provides a robust platform for further synthetic and biological investigations.

Synthesis of amino acid derivatives of 5-alkoxy-3,4-dihalo-2(5H)-furanones and their preliminary bioactivity investigation as linkers

A series of amino acid derivatives are successfully synthesized via a metal-free C-N coupling reaction of 5-alkoxy-3,4-dihalo-2(5H)-furanones and amino acids. Their structures are well characterized with ¹H NMR, ¹³C NMR, ESI-MS and elemental analysis. As potential linkers of the 2(5H)-furanone unit with other drug moieties containing a hydroxyl or amino group, the effect of amino acids is investigated by comparison with other 2(5H)-furanone compounds by constructing C-O/C-S bonds. The preliminary results of the biological activity assay by the MTT method on a series of cancer cell lines in vitro reveal that the introduction of amino acids basically has no toxic effect. This can lead to these 2(5H)-furanone derivatives being further well-linked with other bioactive moieties with amino or hydroxy groups as expected. Thus, the biological activity assay gives a direction for the design of bioactive 2(5H)-furanones based on these amino acid linkers.

(+)- and (-)-Alternarilactone A: Enantiomers with a Diepoxy-Cage-like Scaffold from an Endophytic Alternaria sp

The enantiomers (+)- and (-)-alternarilactone A (1), the first examples of dibenzo-α-pyrones bearing a diepoxy-cage-like moiety, were isolated from the endophytic fungus Alternaria sp. hh930. The deficiency in ¹H-¹H COSY and HMBC correlations caused by the highly oxidized caged system of 1 and the deceptive and ambiguous signals such as "W" couplings in NMR data increased the risk of structure misassignment of 1. By performing a quantum chemical calculation of the NMR chemical shifts together with a DP4+ probability analysis and single-crystal X-ray crystallographic experiment, their structures were unambiguously determined, and their absolute configurations were determined by ECD calculations.

A concise Friedländer/Buchwald–Hartwig approach to the total synthesis of quindoline, a bioactive natural indoloquinoline alkaloid, and toward the unnatural 10-methylquindoline

Friedländer and Buchwald–Hartwig reactions were used to achieve an efficient total synthesis of quindoline and a new synthesis of the unnatural 10-methylquindoline. DFT calculations were employed to explain the outcome of a failed key transformation.

Quick construction of a C–N bond from arylsulfonyl hydrazides and Csp2–X compounds promoted by DMAP at room temperature

A mild C–N coupling reaction with arylsulfonyl hydrazides and 2(5H)-furanones shows good yields, excellent reaction regioselectivity and functional group tolerance.

Purpurolide A, 5/5/5 Spirocyclic Sesquiterpene Lactone in Nature from the Endophytic Fungus Penicillium purpurogenum

Purpurolide A (1), an unprecedent sesquiterpene lactone with a rarely encountered 5/5/5 spirocyclic skeleton, along with two new 6/4/5/5 tetracyclic sesquiterpene lactones (2 and 3), were isolated from the cultures of the endophytic fungus Penicillium purpurogenum IMM003. The structures and absolute configurations of 1-3 were established by spectroscopic analysis, single-crystal X-ray diffraction, and calculations of the ¹³C NMR and ECD data. Compounds 1-3 showed significant inhibitory activity against pancreatic lipase.

Method Calibration or Data Fitting?

We investigate by explicit parameter optimization to what extent basis sets of polarized double-ζ quality can introduce compensating errors in five different density functional methods. It is shown that minor changes in the contraction coefficients of the valence functions in the basis sets can have a significant impact and allow different density functional methods to achieve very similar performances. This holds for nuclear magnetic shielding constants and for isomerization energies, barrier heights, and noncovalent interactions. It is furthermore shown that errors due to neglect of vibrational and solvent effects can be absorbed in the combined method and basis set errors. These findings hold for data sets consisting of 50-150 data points. This raises the question of whether the common practice of identifying combinations of density functional methods and basis sets that have a good performance against a selected set of reference data should be considered as data fitting in the combined parameter space spanned by the method and basis set.

NMR and experimental reinvestigation of the condensation reaction between γ-methylene-α,β-unsaturated aldehydes and propargyl aldehydes

An experimental and computational study of the reaction between γ-methylene enals and propargyl aldehydes uncovered a deconjugative aldol condensation.

Structural revision of two unusual rhamnofolane diterpenes, curcusones I and J, by means of DFT calculations of NMR shifts and coupling constants

The structures of two unusual rhamnofolane diterpenes, curcusones I and J, have been revised using quantum calculations of NMR shifts.

Total syntheses of schilancidilactones A and B, schilancitrilactone A, and 20-epi-schilancitrilactone A via late-stage nickel-catalyzed cross coupling

The first total syntheses of schilancidilactones A and B, schilancitrilactone A, and 20-epi-schilancitrilactone A have been accomplished using a nickel-catalyzed cross coupling of alkyl bromide with vinyl stannane as the final step. The other key steps include late-stage C(sp3)-H bromination, the oxidative cleavage of a diol to provide the requisite ketone and ester for schilancidilactones A and B, and Dieckmann-type condensation to generate the A ring of schilancitrilactone A and 20-epi-schilancitrilactone A.

Navigating the Chiral Pool in the Total Synthesis of Complex Terpene Natural Products

The pool of abundant chiral terpene building blocks (i.e., "chiral pool terpenes") has long served as a starting point for the chemical synthesis of complex natural products, including many terpenes themselves. As inexpensive and versatile starting materials, such compounds continue to influence modern synthetic chemistry. This review highlights 21st century terpene total syntheses which themselves use small, terpene-derived materials as building blocks. An outlook to the future of research in this area is highlighted as well.

NF-κB inhibitors, unique γ-pyranol-γ-lactams with sulfide and sulfoxide moieties from Hawaiian plant Lycopodiella cernua derived fungus Paraphaeosphaeria neglecta FT462

LC-UV/MS-based metabolomic analysis of the Hawaiian endophytic fungus Paraphaeosphaeria neglecta FT462 led to the identification of four unique mercaptolactated γ-pyranol-γ-lactams, paraphaeosphaerides E-H (1-4) together with one γ-lactone (5) and the methyl ester of compound 2 (11). The structures of the new compounds (1-5 and 11) were elucidated through the analysis of HRMS and NMR spectroscopic data. The absolute configuration was determined by chemical reactions with sodium borohydride, hydrogen peroxide, α-methoxy-α-(trifluoromethyl)phenylacetyl chlorides (Mosher reagents), and DP4 + NMR calculations. All the compounds were tested against STAT3, A2780 and A2780cisR cancer cell lines, E. coli JW2496, and NF-κB. Compounds 1 and 3 strongly inhibited NF-κB with IC50 values of 7.1 and 1.5 μM, respectively.

Verbenanone, an octahydro-5H-chromen-5-one from a Hawaiian-Plant Associated Fungus FT431

A new secondary metabolite verbenanone (1) with a unique (4aS,8aS)-octahydro-5H-chromen-5-one moiety has been obtained from the endophytic fungus FT431, which was isolated from the native Hawaiian plant Verbena sp. The structure of compound 1 was characterized based on NMR and MS spectroscopic analysis. The absolute configuration (AC) of compound 1 was determined by Mosher acids. Compound 1 was tested against A2780 and A2780cisR, but it was inactive.