Virtual target screening to rapidly identify potential protein targets of natural products in drug discovery

Inherent biological viability and diversity of natural products make them a potentially rich source for new therapeutics. However, identification of bioactive compounds with desired therapeutic effects and identification of their protein targets is a laborious, expensive process. Extracts from organism samples may show desired activity in phenotypic assays but specific bioactive compounds must be isolated through further separation methods and protein targets must be identified by more specific phenotypic and in vitro experimental assays. Still, questions remain as to whether all relevant protein targets for a compound have been identified. The desire is to understand breadth of purposing for the compound to maximize its use and intellectual property, and to avoid further development of compounds with insurmountable adverse effects. Previously we developed a Virtual Target Screening system that computationally screens one or more compounds against a collection of virtual protein structures. By scoring each compound-protein interaction, we can compare against averaged scores of synthetic drug-like compounds to determine if a particular protein would be a potential target of a compound of interest. Here we provide examples of natural products screened through our system as we assess advantages and shortcomings of our current system in regards to natural product drug discovery

Usoda skrb vzbujajočih onesnaževal v jezerih, nastalih v vrtačah, Florida, ZDA

Zakrasele karbonatne platforme, kot je Florida, zaznamujejo hitra stopnja infiltracije, visoka prepustnost podlage in neposredna povezava z vodonosniki prek številnih vrtač. Kombinacija teh fizikalnih lastnosti prispeva k visoki občutljivosti podtalnice in vodonosnikov na kontaminacijo s skrb vzbujajočimi sintetičnimi kemikalijami. Uporaba greznic spodbuja vnos teh onesnaževal v okolje. Da bi proučili vpliv kemikalij na kraško pokrajino, so bili vzorci vode, sedimenta in vegetacije odvzeti v jezeru, nastalem v vrtači in obdanem s stanovanji, ki so opremljena z greznicami. Glavno vprašanje tega raziskovalnega projekta je, kaj se dogaja z onesnaževali iz grezničnih odplak v vodnem zajetju vrtače. Za analizo vzorcev je bila izvedena masna spektrometrija s tekočinsko kromatografijo. Ugotovljeno je bilo, da je sorazmerna količina kemikalij odvisna od 1) hidrofobnosti in polarnosti spojine, 2) mesta vzorčenja, 3) topografskega gradienta in 4) za vegetacijo, povezanosti vrste vzorca s sedimentom. Hidrogeološke študije so pokazale, da so vrtače na tem območju povezane z vodonosnikom, ki je pod njimi. Posledično skrb vzbujajoča onesnaževala predstavljajo tveganje za onesnaženje podtalnice. Ta študija je prikaz razmer v sušni sezoni Floride, to je najverjetneje obdobje z najmanjšo kontaminacijo. Vzorčenje bi bilo treba opraviti v tudi deževnem obdobju, ko izpiranje onesnaževal iz greznic lahko poveča koncentracije onesnaževal, tako v jezeru kot v vodonosnikih, kar je posebno problematično zaradi uporabnosti vode iz vodnjaka v prehranske namene. Čeprav je bila študija izvedena na Floridi, verjamemo, da so naše ugotovitve in priporočila splošno uporabni, saj se greznice uporabljajo v številnih kraških predelih sveta.Highly karstified carbonate platforms such as Florida are characterized by rapid infiltration rates, highly permeable bedrock and the direct connection to the below aquifer through the high density of sinkholes. This combination of physical features makes the groundwater and aquifers highly vulnerable to contamination from synthetic chemicals commonly referred to as contaminants of emerging concern (CECs). The use of septic tanks, otherwise referred to as onsite water treatment systems (OWTS), promotes the introduction of CECs into the environment. In order to study the impacts of CECs from OWTS on a karst landscape, water, sediment, and vegetation samples were collected in a sinkhole lake surrounded by residential housing using this waste disposal method. The main question of this research project is what is the fate of CECs from OWTSs effluent within the catchment of a sinkhole lake? Liquid chromatograph mass spectrometry was used to analyze the samples for the presence of CECs. It was found that the relative quantity of CECs in the individual constituents is dependent upon 1) the hydrophobicity and polarity of the individual compound, 2) the specific sampling site, 3) the topography gradient, and 4) for vegetation, the connectedness of the sample type to the sediment. Hydrogeological studies have found that the sinkholes of the area are all connected to the below aquifer. Consequently, these CECs pose a risk of the contamination of the groundwater. This study is a temporal snapshot, that being the dry season of Florida which is most likely the time of lowest CEC contamination. It is imperative that sampling extend into the wet season when flushing of CECs from the OWTS may increase their concentrations in both the lake but also the aquifers especially since residents use well water as their source of potable water. While this study is based in Florida, we strongly suspect that our findings and recommendations are applicable more generally as OWTS are used throughout the many karst regions of the world

Chemical Purification, Analysis and Screening core facility: overcoming challenges of natural product research in drug discovery

The Chemical Purification, analysis and Screening core laboratories (CPAS) are located at the University of South Florida campus in Tampa. This core offers instrumentation and expertise in fractionation, purification, and various chemical analyses to support synthetic and natural products drug discovery research groups. Our main equipment are dedicated to chromatographic separation and purification (MPLC, HPLC) and mass-spectrometry for analytic detection, quantification and identification (LC-MS SQ, QqQ and QToF). The CPAS services also include Circular Dichroism spectrometry, general spectroscopic characterization (UV, FTIR), lyophilization (bench top and high capacity freeze-dryers), synthesis (microwave reactor), ADME screening (permeability and drug solubility testing), and high-throughput screening development capability (automated liquid handler and multimode plate reader). An example of three significant studies will be presented at the conference to illustrate the CPAS core facility services: 1) Identification of new bioactive compounds from mangrove endophytic fungi as potential alternatives to malaria drug resistance, 2) Myricanol isolated from Bayberry (Myrica Cerifera) and its synthetic derivatives targeting the microtubuleassociated protein tau accumulation in the Alzheimer\u27s disease and 3) New ent-labdane diterpenes with solid tumor cell lines antiproliferative properties from the endemic plant Eupatorium obtusissmum from the island of Hispaniola. The core provides research lab training workshops in advanced technology and assistance so users can operate any instruments available in the laboratories to successfully accomplish their analyses and research projects

Compounds and related methods for treatment of neurodegenerative diseases

Aspects of the invention pertain to chemical compounds, therapeutic compositions, and methods for treating neurodegenerative diseases, in particular, neurodegenerative diseases associated with abnormal accumulation of protein tau

Etude chimique et biologique des éponges marines Podospongia aff. loveni, Siphonochalina sp. et Xestospongia sp. (Isolement-bioactivité-approche de synthèse d'alcaloïdes de type benzo[de][1,6]naphthyridine isolés de Xestospongia sp.)

Le travail qui est décrit dans ce manuscrit porte sur l'isolement et la synthèse de molécules bioactives issues d'Éponges marines. Les Éponges Podospongia aff. loveni, Siphonochalina sp. et Xestospongia sp. ont été sélectionnées pour étude chimique en raison de leurs activités antifongique, anti-inflammatoire et/ ou antimicrobienne. L'élucidation structurale de ces molécules a été réalisée par les méthodes d'analyses spectrales telles que la spectrométrie de masse et les RMN du 1H et du 13C utilisant les méthodes 2D (HMQC, HMBC, COSY et NOESY). Un nouveau stérol à chaîne latérale insaturée, le 19-nor-24-oxo- 22-cholestanol a été isolé à partir de Podospongia aff. loveni.Deux sels de pyridinium ont été obtenus à partir de Siphonochalina sp. : la trigonelline et l'homarine. Ces deux composés connus se sont montrés responsables de l'activité anti-inflammatoire observée dans l'extrait brut. Huit produits appartenant à la classe des alcaloïdes à motif benzo[de][1,6]naphthyridine ont été isolés de l'Éponge Xestospongia sp.. L'aaptamine (195), l'isoaaptamine et le déméthyl(oxy)aaptamine ont été identifiés et sont connus dans la littérature pour être des molécules cytotoxiques. Parmi les cinq produits nouveaux, quatre d'entre eux possèdent de nouveaux squelettes de type triazapyrène, triazapyrénol et cyclopenta[cd]phénalène. La présence de l'aaptamine dans une Éponge du genre Xestospongia de l'ordre Haplosclerida est signalée ici pour la première fois. La dernière partie de la thèse aborde une approche de synthèse de l'aaptamine en utilisant une voie de synthèse courte et originale par rapport à celles décrites dans la littérature. La stratégie choisie est basée sur le couplage du malondialdéhyde avec des amines aromatiques. Cette voie a donné une réaction qui permet la formation du bicycle quinoléïne substitué par une éthylamine en passant par l'intermédiaire isoquinoléïne du motif benzo[de][1,6]naphthyridine.The work described in the manuscrit deals with the isolation and the synthesis of bioactive molecules from marine sponges. The sponges Podospongia aff. loveni, Siphonochalina sp. and Xestospongia sp. were selected for chemical study due to their antifungical, anti-inflammatory and/ or antibacterial activities. The elucidation of the structures of these molecules was carried out thanks to spectral analysis such as mass spectrometry, 1H and 13C NMR using 2D's methods (HMQC, HMBC, COSY and NOESY). A new sterol with unsaturated side chain, the 24-oxo-nor-19 22-cholestanol was isolated from the Podospongia aff. loveni. Two pyridinium salts were obtained from Siphonochalina sp.: the trigonelline and the homarine. These two compounds showed themselves responsible of the anti-inflammatory activity of the crude extract. Eight compounds belonging to the benzo[de][1,6]naphthyridine alkaloids family were isolated from the sponge Xestospongia sp.. The aaptamine, the isoaptamine and the demethyl(oxy)aaptamine are known as cytotoxic molecules. Among the five new compounds, four of them have exhibited new skeletons : triazapyren, tryazapyrenol and triazacylopent[cd]phenalen. The presence of aaptamine in a sponge of the genus Xestospongia of the order Haplosclerida is shown here for the first time. The last part of the thesis describes an approach of the aaptamine's synthesis using a short chemical pathway. The selected strategy is based on the coupling of the malondialdehyde with the aromatic amines. This way gave a new access to the quinoline substituted by an ethylamine via an isoquinoline intermediate.PARIS-Museum Hist.Naturelle (751052304) / SudocSudocFranceF

Assessing Environmental Risk Posed by Pharmaceuticals and Personal Care Products in Shallow Lakes, Florida, USA—Part B

The use of pharmaceuticals and personal care products (PPCPs) is steadily growing as the world’s population both increases and ages. Many of these products are released into the environment via municipal wastewater treatment plants and onsite wastewater treatment systems (septic tanks). Consequently, it is essential to ascertain whether these contaminants pose any risk to aquatic organisms who live in the water bodies receiving this waste. Risk quotients (RQ) are a commonly used method to do so. For our pilot study, we undertook such analysis for three trophic levels: algae, crustaceans, and fish from two small lakes, one fed by septic tanks and the other not. This research was conducted in 2021 from the end of the dry season and through most of the wet season in west central Florida, USA. Of the 14 PPCPs measured, six had RQs that posed a risk to all three trophic levels. This risk increased during the wet season. Both lakes, regardless of whether they directly received PPCPs from septic tanks or not, had some level of risk. However, the lake without septic tanks had a smaller risk, both in elevated RQs and the occurrence to the various species. Of the PPCPs measured, DEET, caffeine, and theophylline posed the greatest risk

Seasonality of Pharmaceuticals and Personal Care Products in Shallow Lakes, Florida, USA—Part A

Shallow lakes are highly vulnerable to pollution due to their small water volume. Those that receive effluent from the drainfields of onsite wastewater treatment systems (septic tanks) may contain pharmaceuticals and personal care products (PPCPs) that escaped removal during treatment. This study examined the effects of seasonal rainfall variability on the assemblages and concentrations of fourteen PPCPs in two shallow lakes in West–Central Florida, USA: one surrounded by residents equipped with septic tanks and the other located within a nature preserve. Water samples were collected weekly during an 18-week interval from April to August 2021. Liquid chromatography–mass spectrometry analyses revealed the omnipresence of five PPCPs: theophylline, caffeine, cotinine, DEET, and testosterone, although acetaminophen, ibuprofen, and sulfamethoxazole were also common. Of all the PPCPs detected, theophylline, DEET, and acetaminophen concentrations were higher during the wet season in the septic tank-influenced lake, while caffeine, cotinine, and testosterone concentrations decreased. In the lake located in the nature preserve, theophylline, caffeine, and acetaminophen levels increased in the wet season. In contrast, cotinine, DEET, and testosterone levels decreased. Overall, more compounds were detected during the wet season, with highly hydrophobic PPCPs (fluoxetine, atorvastatin, and octocrylene) only present during this period

Fate of Contaminants of Emerging Concern in a Sinkhole Lake, Florida, USA

Highly karstified carbonate platforms such as Florida are characterized by rapid infiltration rates, highly permeable bedrock and the direct connection to the below aquifer through the high density of sinkholes. This combination of physical features makes the groundwater and aquifers highly vulnerable to contamination from synthetic chemicals commonly referred to as contaminants of emerging concern (CECs). The use of septic tanks, otherwise referred to as onsite water treatment systems (OWTS), promotes the introduction of CECs into the environment. In order to study the impacts of CECs from OWTS on a karst landscape, water, sediment, and vegetation samples were collected in a sinkhole lake surrounded by residential housing using this waste disposal method. The main question of this research project is what is the fate of CECs from OWTSs effluent within the catchment of a sinkhole lake? Liquid chromatograph mass spectrometry was used to analyze the samples for the presence of CECs. It was found that the relative quantity of CECs in the individual constituents is dependent upon 1) the hydrophobicity and polarity of the individual compound, 2) the specific sampling site, 3) the topography gradient, and 4) for vegetation, the connectedness of the sample type to the sediment. Hydrogeological studies have found that the sinkholes of the area are all connected to the below aquifer. Consequently, these CECs pose a risk of the contamination of the groundwater. This study is a temporal snapshot, that being the dry season of Florida which is most likely the time of lowest CEC contamination. It is imperative that sampling extend into the wet season when flushing of CECs from the OWTS may increase their concentrations in both the lake but also the aquifers especially since residents use well water as their source of potable water. While this study is based in Florida, we strongly suspect that our findings and recommendations are applicable more generally as OWTS are used throughout the many karst regions of the world.</jats:p