Logic Structure Determination (LSD) as a Computer Assisted Structure Elucidation (Case) for Molecular Structure Determination of Cytotoxic Cembranoids from Soft Coral

Abstract

Indonesian tropical soft corals are valuable resources that produce pharmacological cytotoxic cembranoids. However, the manual structure determination in these compounds requires adequate knowledge of organic chemistry. This study presents the application of Logic Structure Determination (LSD) as a freeware Computer Assisted Structure Elucidation (CASE) for automatic molecular structure determination of cembranoid compounds from soft corals species. 12 Nuclear Magnetic Resonance (NMR) datasets of cytotoxic cembranoids were used to evaluate the accuracy of LSD in generating the possible structures. The results of this study shows that LSD generated numerous possible molecular structures as the data input files were only derived from 2D-NMR HMQC (Heteronuclear MultipleQuantum Correlation), COSY (Homonuclear Correlation Spectroscopy), and HMBC (Heteronuclear Multiple Bond Correlation). The accuracy was significantly enhanced (only 2-4 possible cembranoid structures from each NMR dataset) with the addition of H2BC (Heteronuclear 2 Bond Correlation) experimental data. This may indicate that VLRC (Very Long-Range Correlations) significantly affects LSD capability. Furthermore, LSD with direct 2 bond NMR experimental data is a reliable CASE technique for cembranoid compounds identification. In general, this freeware-CASE has the potential to be applied on other types of small molecule compounds and may serves as a solution for elucidation bottleneck step in studies on Indonesian natural products.

Deazaflavin cofactor boosts earthworms Henlea bioluminescence

“…Second, we prepared an input file for the LSD (Logical Structure Determination) software, [16][17][18] see Fig. S6.…”

Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics

“…Resorting to complementary 2D NMR spectra is one possible way to reduce the size of the chemical space explored by a CASE algorithm. 269 A 1 H-13 C H2BC (Heteronuclear 2 Bond Correlation) spectrum directly indicates the existence of a bond between two non-H atoms through a 1 J( 1 H-13 C) coupling and a 3 J( 1 H-1 H) coupling. 270 Considering both a HMBC and a H2BC spectrum, the latter allows one to classify HMBC correlations as arising from either a 2 J or a 3 J correlation, with the limitation that a 4 J( 1 H-1 H) coupling may have a significantly non-zero value and that some 2 J( 1 H-1 H) couplings may not be detected, thus leading to the incorrect interpretation of the H2BC spectra.…”

“…Resorting of complementary 2D NMR spectra is one possible way to reduce the size of the chemical space explored by a CASE algorithm . A 1 H– 13 C H2BC (Heteronuclear 2 Bond Correlation) spectrum directly indicates the existence of a bond between two non-H atoms through a 1 J ( 1 H– 13 C) coupling and a 3 J ( 1 H– 1 H) coupling .…”

Cembranoids of Soft Coral Sarcophyton from Acidified Coral Reef Environment at Shallow Water CO2 vents in Volcano Island, Banda Neira, Indonesia

“…Proton NMR analysis was conducted to find all cembranoid in the fractions, by finding the chemical shift in olefinic and oxymethine regions as according to Faraq et al (2016;. Identification of cembranoid was conducted according to Januar, Zamani, Soedharma, & Chasanah (2016b), with spectroscopic techniques (mass and nuclear magnetic resonance analyses) and LSD-CASE (Logic Structure Determination -Computer Assisted Structure Elucidation) software.…”

“…The combination of functional groups such as hydroxyl, carbonyl, epoxy, and lactone, becomes a side chain that attaches to various carbon atom positions on the main ring (Januar, Zamani, Soedharma, & Chasanah, 2016b). Cembranoid is t he main sof t coral allelochemical, with cytotoxic biological properties that may serve as a chemical weapon for predator or benthic living space competitors, such as hard coral (Lages, Fleury, Ferreira, & Pereira, 2006).…”