1. Plant-soil feedbacks is becoming an important concept for explaining vegetation dynamics, the invasiveness of introduced exotic species in new habitats and how terrestrial ecosystems respond to ...global land use and climate change. Using a new conceptual model, we show how critical alterations in Plant-soil feedback interactions can change the assemblage of plant communities. We highlight recent advances, define terms and identify future challenges in this area of research and discuss how variations in strengths and directions of Plant-soil feedbacks can explain succession, invasion, response to climate warming and diversity-productivity relationships. 2. While there has been a rapid increase in understanding the biological, chemical and physical mechanisms and their interdependencies underlying Plant-soil feedback interactions, further progress is to be expected from applying new experimental techniques and technologies, linking empirical studies to modelling and field-based studies that can include Plant-soil feedback interactions on longer time scales that also include long-term processes such as litter decomposition and mineralization. 3. Significant progress has also been made in analysing consequences of Plant-soil feedbacks for biodiversity-functioning relationships, plant fitness and selection. 4. To further integrate Plant-soil feedbacks into ecological theory, it will be important to determine where and how observed patterns may be generalized, and how they may influence evolution. 5. Synthesis. Gaining a greater understanding of Plant-soil feedbacks and underlying mechanisms is improving our ability to predict consequences of these interactions for plant community composition and productivity under a variety of conditions. Future research will enable better prediction and mitigation of the consequences of human-induced global changes, improve efforts of restoration and conservation and promote sustainable provision of ecosystem services in a rapidly changing world.
Accurate prediction of human clearance is of critical importance in drug discovery. In this study,
in vitro
–
in vivo
extrapolation (IVIVE) of hepatic clearance was established using large sets of ...compounds for four preclinical species (mouse, rat, dog, and non-human primate) to enable better understanding of clearance mechanisms and human translation.
In vitro
intrinsic clearances were obtained using pooled liver microsomes (LMs) or hepatocytes (HEPs) and scaled to hepatic clearance using the parallel-tube and well-stirred models. Subsequently, IVIVE scaling factors (SFs) were derived to best predict
in vivo
clearance. The SFs for extended clearance classification system (ECCS) class 2/4 compounds, involving metabolic clearance, were generally small (≤ 2.6) using both LMs and HEPs with parallel-tube model, with the exception of the rodents (~ 2.4–4.6), suggesting
in vitro
reagents represent
in vivo
reasonably well. SFs for ECCS class 1A and 1B are generally higher than class 2/4 across the species, likely due to the contribution of transporter-mediated clearance that is under-represented with
in vitro
reagents. The parallel-tube model offered lower variability in clearance predictions over the well-stirred model. For compounds that likely demonstrate passive permeability-limited clearance
in vitro
, rat LM predicted
in vivo
clearance more accurately than HEP. This comprehensive analysis demonstrated reliable IVIVE can be achieved using LMs and HEPs. Evaluation of clearance IVIVE in preclinical species helps to better understand clearance mechanisms, establish more reliable IVIVE in human, and enhance our confidence in human clearance and PK prediction, while considering species differences in drug metabolizing enzymes and transporters.
Biochar application to soil is currently widely advocated for a variety of reasons related to sustainability. Typically, soil amelioration with biochar is presented as a multiple‐‘win’ strategy, ...although it is also associated with potential risks such as environmental contamination. The most often claimed benefits of biochar (i.e. the ‘wins’) include (i) carbon sequestration; (ii) soil fertility enhancement; (iii) biofuel/bioenergy production; (iv) pollutant immobilization; and (v) waste disposal. However, the vast majority of studies ignore possible trade‐offs between them. For example, there is an obvious trade‐off between maximizing biofuel production and maximizing biochar production. Also, relatively little attention has been paid to mechanisms, as opposed to systems impacts, behind observed biochar effects, often leaving open the question as to whether they reflect truly unique properties of biochar as opposed to being simply the short‐term consequences of a fertilization or liming effect. Here, we provide an outline for the future of soil biochar research. We first identify possible trade‐offs between the potential benefits. Second, to be able to better understand and quantify these trade‐offs, we propose guidelines for robust experimental design and selection of appropriate controls that allow both mechanistic and systems assessment of biochar effects and trade‐offs between the wins. Third, we offer a conceptual framework to guide future experiments and suggest guidelines for the standardized reporting of biochar experiments to allow effective between‐site comparisons to quantify trade‐offs. Such a mechanistic and systems framework is required to allow effective comparisons between experiments, across scales and locations, to guide policy and recommendations concerning biochar application to soil.
Hepatic uptake transporters solute carriers (SLCs), including organic anion transporting polypeptide (OATP) 1B1, OATP1B3, OATP2B1, sodium-dependent taurocholate cotransporting polypeptide (NTCP), and ...organic anion (OAT2) and organic cation (OCT1) transporters, play a key role in determining the systemic and liver exposure of chemically diverse drugs. Here, we established a phenotyping approach to quantify the contribution of the six SLCs, and passive diffusion, to the overall uptake using plated human hepatocytes (PHHs). First, selective inhibitor conditions were identified by screening about 20 inhibitors across the six SLCs using single-transfected human embryonic kidney 293 cells. Data implied rifamycin SV (20
M) inhibits three OATPs, while rifampicin (5
M) inhibits OATP1B1/1B3 only. Further, hepatitis B virus myristoylated-preS1 peptide (0.1
M), quinidine (100
M), and ketoprofen (100-300
M) are relatively selective against NTCP, OCT1, and OAT2, respectively. Second, using these inhibitory conditions, the fraction transported (
) by the individual SLCs was characterized for 20 substrates with PHH. Generally, extended clearance classification system class 1A/3A (e.g., warfarin) and 1B/3B compounds (e.g., statins) showed predominant OAT2 and OATP1B1/1B3 contribution, respectively. OCT1-mediated uptake was prominent for class 2/4 compounds (e.g., metformin). Third, in vitro
values were corrected using quantitative proteomics data to obtain "scaled
" Fourth, in vitro-in vivo extrapolation of the scaled OATP1B1/1B3
was assessed, leveraging statin clinical drug-drug interaction data with rifampicin as the perpetrator. Finally, we outlined a novel stepwise strategy to implement phenotypic characterization of SLC-mediated hepatic uptake for new molecular entities and drugs in a drug discovery and development setting.
Prospective predictions of human hepatic clearance for anionic/zwitterionic compounds, which are oftentimes subjected to transporter-mediated uptake, are challenging in drug discovery. We evaluated ...the utility of preclinical species, rats and cynomolgus monkeys nonhuman primates (NHPs), to predict the human hepatic clearance using a diverse set of acidic/zwitterionic drugs. Preclinical clearance data were generated following intravenous dosing in rats/NHPs and compared to the human clearance data (n = 18/27). Single-species scaling of NHP clearance with an allometric exponent of 0.50 allowed for good prediction of human clearance (fold error ∼2.1, bias ∼1.0), with ∼86% predictions within 3-fold. In comparison, rats underpredicted the clearance of lipophilic acids, while overprediction was noted for hydrophilic acids. Finally, an in vitro clearance assay based on human hepatocytes, which is routinely used in discovery setting, markedly underpredicted human clearance (bias ∼0.12). Collectively, this study provides insights into the usefulness of the preclinical models in enabling pharmacokinetic optimization for acid/zwitterionic drug candidates.
Peptide agonists of the glucagon-like peptide-1 receptor (GLP-1R) have revolutionized diabetes therapy, but their use has been limited because they require injection. Herein, we describe the ...discovery of the orally bioavailable, small-molecule, GLP-1R agonist PF-06882961 (danuglipron). A sensitized high-throughput screen was used to identify 5-fluoropyrimidine-based GLP-1R agonists that were optimized to promote endogenous GLP-1R signaling with nanomolar potency. Incorporation of a carboxylic acid moiety provided considerable GLP-1R potency gains with improved off-target pharmacology and reduced metabolic clearance, ultimately resulting in the identification of danuglipron. Danuglipron increased insulin levels in primates but not rodents, which was explained by receptor mutagensis studies and a cryogenic electron microscope structure that revealed a binding pocket requiring a primate-specific tryptophan 33 residue. Oral administration of danuglipron to healthy humans produced dose-proportional increases in systemic exposure (NCT03309241). This opens an opportunity for oral small-molecule therapies that target the well-validated GLP-1R for metabolic health.
Organic anion transporters (OATs) are important in the renal secretion, and thus, the clearance, of many drugs; and their functional change can result in pharmacokinetic variability. In this study, ...we applied transport rates measured in vitro using OAT-transfected human embryonic kidney cells to predict human renal secretory and total renal clearance of 31 diverse drugs. Selective substrates to OAT1 (tenofovir), OAT2 (acyclovir and ganciclovir), and OAT3 (benzylpenicillin, oseltamivir acid) were used to obtain relative activity factors (RAFs) for these individual transporters by relating in vitro transport clearance (after physiologic scaling) to in vivo secretory clearance. Using the estimated RAFs (0.64, 7.3, and 4.1, respectively, for OAT1, OAT2, and OAT3, respectively) and the in vitro active clearances, renal secretory clearance and total renal clearance were predicted with average fold errors (AFEs) of 1.89 and 1.40, respectively. The results show that OAT3-mediated transport play a predominant role in renal secretion for 22 of the 31 drugs evaluated. This mechanistic static approach was further applied to quantitatively predict renal drug-drug interactions (AFE ∼1.6) of the substrate drugs with probenecid, a clinical probe OAT inhibitor. In conclusion, the proposed in vitro-in vivo extrapolation approach is the first comprehensive attempt toward mechanistic modeling of renal secretory clearance based on routinely employed in vitro cell models.
Current challenges with the in vitro-in vivo extrapolation (IVIVE) of hepatic uptake clearance involving organic anion-transporting polypeptide (OATP) 1B1/1B3 hinder drug design strategies. Here we ...evaluated the effect of 100% human plasma on the uptake clearance using transfected human embryonic kidney (HEK) 293 cells and primary human hepatocytes and assessed IVIVE. Apparent unbound uptake clearance (PS
) increased significantly (
< 0.05) in the presence of plasma (vs. buffer incubations) for about 50% of compounds in both OATP1B1-transfected and wild-type HEK cells. Thus, plasma showed a minimal effect on the uptake ratios. With cultured human hepatocytes, plasma significantly (
< 0.05) increased PS
for 11 of 19 OATP1B substrates (median change of 2.1-fold). Cell accumulation in HEK cells and hepatocytes was also increased for tolbutamide, which is not an OATP substrate. Plasma-to-buffer ratio of PS
obtained in hepatocytes showed a good correlation with unbound fraction in plasma, and the relationship was best described by a "facilitated-dissociation" model. IVIVE was evaluated for the 19 OATP1B substrates using hepatocyte data in the presence of buffer and plasma. PS
from buffer incubations markedly underpredicted hepatic intrinsic clearance (calculated via well stirred and parallel tube models) with an estimated bias of 0.10-0.13. Predictions improved when using PS
from plasma incubations; however, considerable systemic underprediction was still apparent (0.19-0.26 bias). Plasma data with a global scaling factor of 3.8-5.3 showed good prediction accuracy (95% predictions within 3-fold; average fold error = 1.7, bias = 1). In summary, this study offers insight into the effect of plasma on the uptake clearance and its scope in improving IVIVE. SIGNIFICANCE STATEMENT: Our study using diverse anionic compounds shows that human plasma facilitates organic anion-transporting polypeptide 1B-mediated as well as passive uptake clearance, particularly for the highly bound compounds. Leveraging data from transfected human embryonic kidney 293 cells and primary human hepatocytes, we further evaluated mechanisms involved in the observed plasma-facilitated uptake transport. Enhanced hepatic uptake rate in the presence of plasma could be of relevance, as such mechanisms likely prevail in vivo and emphasize the need to maintain physiologically relevant assay conditions to achieve improved translation of transport data.
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