Review on natural products databases: where to find data in 2020

Sorokina, Maria; Steinbeck, Christoph

doi:10.1186/s13321-020-00424-9

Cited by 283 publications

(229 citation statements)

References 127 publications

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“…We conducted virtual screens against the VEGF-A binding site on the NRP-1 b1 domain using three libraries: a ~211 K synthetic compound library (DIV) from ChemBridge; a ~257 K natural compound library (NC1) obtained from the COlleCtion of Open NatUral producTs (COCONUT) resource 63 ; and a ~20 K (NC2) natural compound library from the ZINC15 database 64 . The screens were run once without ligand-receptor interaction constraints and repeated with the constraint that compounds form a hydrogen bond to Asp 320, a key residue for coordinating the terminal arginine in the CendR motif 14 .…”

Section: Resultsmentioning

confidence: 99%

In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein

Perez‐Miller

Pátek²,

Moutal

et al. 2020

Preprint

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Neuropilin-1 (NRP-1) is a multifunctional transmembrane receptor for ligands that affect developmental axonal growth and angiogenesis. In addition to a role in cancer, NRP-1 is a reported entry point for several viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19). The furin cleavage product of SARS-CoV-2 Spike protein takes advantage of the vascular endothelial growth factor A (VEGF-A) binding site on NRP-1 which accommodates a polybasic stretch ending in a C-terminal arginine. This site has long been a focus of drug discovery efforts for cancer therapeutics. We recently showed that interruption of the VEGF-A/NRP-1 signaling pathway ameliorates neuropathic pain and hypothesize that interference of this pathway by SARS-CoV-2 spike protein interferes with pain signaling. Here, we report hits from a small molecule and natural product screen of nearly 0.5 million compounds targeting the VEGF-A binding site on NRP-1. We identified nine chemical series with lead- or drug-like physico-chemical properties. Using an ELISA, we demonstrate that six compounds disrupt VEGF-A-NRP-1 binding more effectively than EG00229, a known NRP-1 inhibitor. Secondary validation in cells revealed that almost all tested compounds inhibited VEGF-A triggered VEGFR2 phosphorylation. Two compounds displayed robust inhibition of a recombinant vesicular stomatitis virus protein that utilizes the SARS-CoV-2 Spike for entry and fusion. These compounds represent a first step in a renewed effort to develop small molecule inhibitors of the VEGF-A/NRP-1 signaling for the treatment of neuropathic pain and cancer with the added potential of inhibiting SARS-CoV-2 virus entry.

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Section: Resultsmentioning

confidence: 99%

In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein

Perez‐Miller

Pátek²,

Moutal

et al. 2020

Preprint

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“…It is also available at ChemSpider and ZINC 15 where it can be found, for instance, as a NP catalog. NuBBE DB has been recently included in the COCONUT database [ 10 ].…”

Section: Np Databases In Latin Americamentioning

confidence: 99%

“…One of the first reviews was published in 2012 [ 7 ] that included five NPs datasets (commercial and noncommercial with chemical structures available on the web). Recently, it was released the COlleCtion of Open NatUral producTs (COCONUT) database that collects over 120 databases collecting more than 400,000 nonredundant NPs and are freely accessible [ 10 ]. As part of the global efforts, different countries around the world are analyzing the information of NPs in their countries of origin.…”

mentioning

confidence: 99%

Towards a Unified Latin American Natural Products Database: LANaPD

Medina-Franco

2020

Future Sci. OA

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Around the world, the number of compound databases of natural products in the public domain is rising. This is in line with the increasing synergistic combination of natural product research and chemoinformatics. Toward this global endeavor, countries in Latin America are assembling, curating, and analyzing the contents and diversity of natural products available in their geographical regions. In this manuscript we collect and analyze the efforts that countries in Latin America have made so far to build natural product databases. We further encourage the scientific community in particular in Latin America, to continue their efforts to building quality natural product databases and, whenever possible, to make them publicly accessible. It is proposed that all compound collections could be assembled into a unified resource called LANaPD: Latin American Natural Products Database. Opportunities and challenges to build, distribute and maintain LANaPD are also discussed.

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“…For annotated mass spectral information, see Supplementary Data file. The predicted molecular formulas of the chlorine-iodine containing metabolites were searched against several external mass spectral and natural product databases, including DEREP-NP 54 and COCONUT 55 (for a full list see Supplementary Table 7). The occurrence of iodine-containing metabolites in bags 3 and 4 at the end of the E. huxleyi demise phase (day 23) was compared by plotting the extracted ion chromatogram (EIC) of the iodide fragment (m/z 126.90) in negative ionization mode using the high-energy scan function (MassLynx, version 4.1, Waters).…”

Section: Structural Characterization Of the Vdom Metabolitesmentioning

confidence: 99%

Viral infection of algal blooms leaves a halogenated footprint on the dissolved organic matter in the ocean

Kuhlisch¹,

Schleyer²,

Shahaf³

et al. 2020

Preprint

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Algal blooms are important hotspots of primary production in the ocean, forming the basis of the marine food web and fueling the pool of dissolved organic matter (DOM)1, which is the largest global inventory of reduced carbon and a market place for metabolic exchange in the ocean2. Marine viruses are key players in controlling algal bloom demise and act as major biogeochemical drivers of nutrient cycling and metabolic fluxes by shunting algal biomass from higher trophic levels to the DOM pool, a process termed the ‘viral shunt’3,4. Nevertheless, the metabolic composition of virus-induced DOM (vDOM) in the marine environment is unknown. To decode the metabolic footprint of the ‘viral shunt’, we induced a bloom of the ecologically important alga Emiliania huxleyi in the natural environment, and followed its succession using an untargeted exometabolomics approach. Here we show that algal bloom succession induces extensive and dynamic changes in the exometabolic landscape, especially during bloom demise. By correlating to a specific viral gene marker, we discovered a set of novel chlorine-iodine-containing metabolites that were induced by viral infection and copiously released during bloom demise. We further detected several of these chloro-iodo metabolites in virus-infected open ocean blooms of E. huxleyi, supporting their use as sensitive biomarkers for virus-induced demise in the natural environment. Therefore, we propose halogenation to be a hallmark of the E. huxleyi vDOM, providing insights into the profound metabolic consequences of viral infection for the marine DOM pool.

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Review on natural products databases: where to find data in 2020

Cited by 283 publications

References 127 publications

In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein

In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein

Towards a Unified Latin American Natural Products Database: LANaPD

Viral infection of algal blooms leaves a halogenated footprint on the dissolved organic matter in the ocean

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