A two-component approach to predicting antitumor activity from chemical structure in large-scale screening

1986 ◽  
Vol 29 (11) ◽  
pp. 2207-2212 ◽  
Author(s):  
Louis Hodes
2021 ◽  
pp. 247255522110194
Author(s):  
Paul A. Clemons ◽  
Joshua A. Bittker ◽  
Florence F. Wagner ◽  
Allison Hands ◽  
Vlado Dančík ◽  
...  

Small-molecule discovery typically involves large-scale screening campaigns, spanning multiple compound collections. However, such activities can be cost- or time-prohibitive, especially when using complex assay systems, limiting the number of compounds tested. Further, low hit rates can make the process inefficient. Sparse coverage of chemical structure or biological activity space can lead to limited success in a primary screen and represents a missed opportunity by virtue of selecting the “wrong” compounds to test. Thus, the choice of screening collections becomes of paramount importance. In this perspective, we discuss the utility of generating “informer sets” for small-molecule discovery, and how this strategy can be leveraged to prioritize probe candidates. While many researchers may assume that informer sets are focused on particular targets (e.g., kinases) or processes (e.g., autophagy), efforts to assemble informer sets based on historical bioactivity or successful human exposure (e.g., repurposing collections) have shown promise as well. Another method for generating informer sets is based on chemical structure, particularly when the compounds have unknown activities and targets. We describe our efforts to screen an informer set representing a collection of 100,000 small molecules synthesized through diversity-oriented synthesis (DOS). This process enables researchers to identify activity early and more extensively screen only a few chemical scaffolds, rather than the entire collection. This elegant and economic outcome is a goal of the informer set approach. Here, we aim not only to shed light on this process, but also to promote the use of informer sets more widely in small-molecule discovery projects.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 2813-2813
Author(s):  
Kazuya Miyashita ◽  
Noritaka Kagaya ◽  
Miho Izumikawa ◽  
Kenji Kitajima ◽  
Kyoko Watakabe-Inamoto ◽  
...  

Abstract Acute lymphoblastic leukemia (ALL) is one of the most frequently occurring cancers in infants and young children. For patients suffering from CD20-positive B-cell ALL (B-ALL) and Ph-positive ALL, overall survival rates have been greatly improved after clinical introduction of rituximab and imatinib, respectively. However, T-cell ALL (T-ALL) patients still exhibit poor prognosis, since there is no such an efficient molecular-targeted drug. It is known that LIM-only transcriptional co-factor LMO2 and its target gene HHEX are essential for self-renewal of T cell precursors and onset of T-ALL. LMO2 directly associates with LDB1 in a large DNA-containing nuclear complex and controls the transcription of T-ALL-related downstream genes. Recently, we reported that overexpression of LIM-homeodomain transcription factor Lhx2 results in liberation of Lmo2 protein from the Lmo2-Ldb1 complex followed by degradation by ubiquitin-proteasome system. We found that proliferation of 5 different human T-ALL-derived cell lines including CCRF-CEM was significantly suppressed by retroviral overexpression of Lhx2. In contrast, enforced overexpression of Lhx2 did not reduce the growth rate of B lymphoma-derived cell line Raji, oral cancer-derived cell line HSC-3, and osteosarcoma-derived cell line Saos-2. Majority of the Lhx2-transduced CCRF-CEM cells was arrested in G0 phase and subsequently underwent apoptosis. Expression of LMO2 protein and HHEX mRNA was repressed by the Lhx2 transduction. Importantly, the Lhx2-mediated growth inhibition was partially rescued by the simultaneous overexpression of Lmo2. However, both C-terminal LIM-domain and homeodomain of Lhx2 were required for the growth-suppressive activity. These data indicated that Lhx2 is capable to blocking proliferation of T-ALL-derived cells in LMO2-dependent and independent fashions. Lhx2 would be a useful molecular tool for designing a new type of anti-T-ALL drug. In order to develop a new drug that mimics the aforementioned activity of Lhx2, we performed large-scale screening of natural compound libraries to find out a compound that suppresses the proliferation of T-ALL cell line CCRF-CEM, but does not inhibit the growth of B lymphoma cell line Raji. Among 150,000 different compounds, we successfully identified 3 low-molecular-weight compounds (44D-L008, 31D-F005, 21D-D016) that fulfilled the above criteria. 44D-L008 and 31D-F005 possessed a common chemical structure. In the presence of 5μM of 44D-L008 and 31D-F005, proliferation of 5 human T-ALL cell lines including CCRF-CEM was severely blocked. On the other hand, Raji, HSC-3 and Saos-2 were completely resistant to both compounds in the same experimental settings. Intriguingly, 44D-L008 decreased viability of human skin fibroblasts in culture, whereas 31D-F005 displayed no such negative effects on skin fibroblasts, peripheral blood mononuclear cells, and peripheral blood T cells of human origin. These results indicated that small differences in the chemical structure between 44D-L008 and 31D-F005 are responsible for the side effect on normal cells. Finally, we collaborated with a hospital and found that 0.5 μM of 31D-F005 efficiently suppressed the in vitro growth of primary cancer cells of a T-ALL patient. Taken together, theses data demonstrated that 31D-F005 is a promising lead compound for a new anti-T-ALL drug. Disclosures No relevant conflicts of interest to declare.


1976 ◽  
Vol 7 (4) ◽  
pp. 236-241 ◽  
Author(s):  
Marisue Pickering ◽  
William R. Dopheide

This report deals with an effort to begin the process of effectively identifying children in rural areas with speech and language problems using existing school personnel. A two-day competency-based workshop for the purpose of training aides to conduct a large-scale screening of speech and language problems in elementary-school-age children is described. Training strategies, implementation, and evaluation procedures are discussed.


2019 ◽  
Vol 19 (1) ◽  
pp. 4-16 ◽  
Author(s):  
Qihui Wu ◽  
Hanzhong Ke ◽  
Dongli Li ◽  
Qi Wang ◽  
Jiansong Fang ◽  
...  

Over the past decades, peptide as a therapeutic candidate has received increasing attention in drug discovery, especially for antimicrobial peptides (AMPs), anticancer peptides (ACPs) and antiinflammatory peptides (AIPs). It is considered that the peptides can regulate various complex diseases which are previously untouchable. In recent years, the critical problem of antimicrobial resistance drives the pharmaceutical industry to look for new therapeutic agents. Compared to organic small drugs, peptide- based therapy exhibits high specificity and minimal toxicity. Thus, peptides are widely recruited in the design and discovery of new potent drugs. Currently, large-scale screening of peptide activity with traditional approaches is costly, time-consuming and labor-intensive. Hence, in silico methods, mainly machine learning approaches, for their accuracy and effectiveness, have been introduced to predict the peptide activity. In this review, we document the recent progress in machine learning-based prediction of peptides which will be of great benefit to the discovery of potential active AMPs, ACPs and AIPs.


Diagnostics ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 869
Author(s):  
Amedeo De Nicolò ◽  
Valeria Avataneo ◽  
Jessica Cusato ◽  
Alice Palermiti ◽  
Jacopo Mula ◽  
...  

Recently, large-scale screening for COVID-19 has presented a major challenge, limiting timely countermeasures. Therefore, the application of suitable rapid serological tests could provide useful information, however, little evidence regarding their robustness is currently available. In this work, we evaluated and compared the analytical performance of a rapid lateral-flow test (LFA) and a fast semiquantitative fluorescent immunoassay (FIA) for anti-nucleocapsid (anti-NC) antibodies, with the reverse transcriptase real-time PCR assay as the reference. In 222 patients, LFA showed poor sensitivity (55.9%) within two weeks from PCR, while later testing was more reliable (sensitivity of 85.7% and specificity of 93.1%). Moreover, in a subset of 100 patients, FIA showed high sensitivity (89.1%) and specificity (94.1%) after two weeks from PCR. The coupled application for the screening of 183 patients showed satisfactory concordance (K = 0.858). In conclusion, rapid serological tests were largely not useful for early diagnosis, but they showed good performance in later stages of infection. These could be useful for back-tracing and/or to identify potentially immune subjects.


2021 ◽  
Vol 22 (15) ◽  
pp. 7773
Author(s):  
Neann Mathai ◽  
Conrad Stork ◽  
Johannes Kirchmair

Experimental screening of large sets of compounds against macromolecular targets is a key strategy to identify novel bioactivities. However, large-scale screening requires substantial experimental resources and is time-consuming and challenging. Therefore, small to medium-sized compound libraries with a high chance of producing genuine hits on an arbitrary protein of interest would be of great value to fields related to early drug discovery, in particular biochemical and cell research. Here, we present a computational approach that incorporates drug-likeness, predicted bioactivities, biological space coverage, and target novelty, to generate optimized compound libraries with maximized chances of producing genuine hits for a wide range of proteins. The computational approach evaluates drug-likeness with a set of established rules, predicts bioactivities with a validated, similarity-based approach, and optimizes the composition of small sets of compounds towards maximum target coverage and novelty. We found that, in comparison to the random selection of compounds for a library, our approach generates substantially improved compound sets. Quantified as the “fitness” of compound libraries, the calculated improvements ranged from +60% (for a library of 15,000 compounds) to +184% (for a library of 1000 compounds). The best of the optimized compound libraries prepared in this work are available for download as a dataset bundle (“BonMOLière”).


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Koji Kawamura ◽  
Suzune Nishikawa ◽  
Kotaro Hirano ◽  
Ardianor Ardianor ◽  
Rudy Agung Nugroho ◽  
...  

AbstractAlgal biofuel research aims to make a renewable, carbon–neutral biofuel by using oil-producing microalgae. The freshwater microalga Botryococcus braunii has received much attention due to its ability to accumulate large amounts of petroleum-like hydrocarbons but suffers from slow growth. We performed a large-scale screening of fast-growing strains with 180 strains isolated from 22 ponds located in a wide geographic range from the tropics to cool-temperate. A fast-growing strain, Showa, which recorded the highest productivities of algal hydrocarbons to date, was used as a benchmark. The initial screening was performed by monitoring optical densities in glass tubes and identified 9 wild strains with faster or equivalent growth rates to Showa. The biomass-based assessments showed that biomass and hydrocarbon productivities of these strains were 12–37% and 11–88% higher than that of Showa, respectively. One strain, OIT-678 established a new record of the fastest growth rate in the race B strains with a doubling time of 1.2 days. The OIT-678 had 36% higher biomass productivity, 34% higher hydrocarbon productivity, and 20% higher biomass density than Showa at the same cultivation conditions, suggesting the potential of the new strain to break the record for the highest productivities of hydrocarbons.


Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1089-1099
Author(s):  
Gwenaël Ruprich-Robert ◽  
Véronique Berteaux-Lecellier ◽  
Denise Zickler ◽  
Arlette Panvier-Adoutte ◽  
Marguerite Picard

Abstract Peroxins (PEX) are proteins required for peroxisome biogenesis. Mutations in PEX genes cause lethal diseases in humans, metabolic defects in yeasts, and developmental disfunctions in plants and filamentous fungi. Here we describe the first large-scale screening for suppressors of a pex mutation. In Podospora anserina, pex2 mutants exhibit a metabolic defect [inability to grow on medium containing oleic acid (OA medium) as sole carbon source] and a developmental defect (inability to differentiate asci in homozygous crosses). Sixty-three mutations able to restore growth of pex2 mutants on OA medium have been analyzed. They fall in six loci (suo1 to suo6) and act as dominant, allele-nonspecific suppressors. Most suo mutations have pleiotropic effects in a pex2+ background: formation of unripe ascospores (all loci except suo5 and suo6), impaired growth on OA medium (all loci except suo4 and suo6), or sexual defects (suo4). Using immunofluorescence and GFP staining, we show that peroxisome biogenesis is partially restored along with a low level of ascus differentiation in pex2 mutant strains carrying either the suo5 or the suo6 mutations. The data are discussed with respect to β-oxidation of fatty acids, peroxisome biogenesis, and cell differentiation.


Fitoterapia ◽  
2021 ◽  
pp. 104909
Author(s):  
Yuan Xiong ◽  
Guang-Hao Zhu ◽  
Hao-Nan Wang ◽  
Qing Hu ◽  
Li-Li Chen ◽  
...  

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