Public Access
As a service to the community, CDD hosts Public Access Data relevant to drug discovery from leading research groups around the world.
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Published: 2/12/2023 Molecules: 36876
PI: Stephan C. Schürer
SPARK Data: Compounds & Physicochemical Properties
Published: 3/28/2021 Molecules: 158809
Compound data was collected for SPARK from published and un-published sources. Data collection primarily focused on compounds tested against Gram-negative bacteria and antibiotic targets coinciding with major contributions in growth or biochemical inhibition assays. This dataset only includes compound structures, physicochemical properties, and related information. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: MIC Assays
Published: 3/27/2021 Molecules: 24585
Minimum inhibitory concentration (MIC) assay data was collected for SPARK from published and un-published sources. Data collection focused on Gram-negative bacteria. Select data was standardized and annotated by curators (Curated & Transformed Data); the un-curated data is also available (Extracted & Uploaded Data). For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: CO-ADD Contribution
Published: 3/26/2021 Molecules: 24090
The Community for Open Antimicrobial Drug Discovery (CO-ADD) at the University of Queensland contributed data to SPARK from their screening program. Additional screening data, including for non-bacterial targets, cytotoxicity, and hemolysis, can be found in their online database. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: IC50 Assays
Published: 3/26/2021 Molecules: 2539
Biochemical inhibition (IC50) assay data was collected for SPARK from published and un-published sources. Data collection focused on antibiotic targets relevant to Gram-negative bacteria. Select data was standardized and annotated by curators (Curated & Transformed Data); the un-curated data is also available (Extracted & Uploaded Data). For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: Quave Lab {Emory University} Publications
Published: 3/26/2021 Molecules: 2208
Cassandra Quave, Associate Professor of Dermatology at Emory University, deposited supplemental data from two publications (Chassagne, et al. 2021 Front Pharmacol 11:586548 and Porras, et al. 2020 ACS Chem Rev) in SPARK. The two publications provide a comprehensive review of the antibacterial activity of natural product extracts and purified compounds against clinically-relevant bacteria. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: Achaogen Contribution
Published: 3/26/2021 Molecules: 1875
Achaogen, Inc. contributed data to SPARK from their LpxC inhibitor program. The contributed data includes MIC, MIC50/90, IC50, cytotoxicity, plasma protein binding, and PK/PD assay results. This data was supported in part by Federal funding from Defense Threat Reduction Agency, Department of Defense, under Contract No. HDTRA107C0079; Military Medical Research and Development Program, Defense Health Program, Department of Defense, under Grant No. W81XWH1220040; and, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201500009C. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: Novartis Contribution
Published: 3/26/2021 Molecules: 1727
The Novartis Institutes of BioMedical Research, Inc. (NIBR) contributed data to SPARK from multiple antibiotic discovery programs, including gyrase (GyrAB), lipopolysaccharide synthesis (LpxA, LpxD, LpxK), and a comprehensive efflux panel testing known antibiotics against isogenic mutant strains of E. coli. The contributed data includes MIC, 50% bacterial growth inhibition, and IC50 assay results. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: Intracellular Accumulation Assays
Published: 3/26/2021 Molecules: 464
Bacterial intracellular accumulation assay data was collected for SPARK from published sources. Data collection focused on Gram-negative bacteria. All data was standardized and annotated by curators (Curated & Transformed Data), including converting all data into the same units. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
SPARK Data: Merck & Kyorin Contribution
Published: 3/26/2021 Molecules: 249
Merck & Co, Inc. (MSD) & Kyorin Pharmaceutical Co., Ltd. contributed data to SPARK from their joint GyrAB/ParCE inhibitor program. The contributed data includes MIC assay results. For more information on SPARK, see Thomas, et al. 2018 ACS Inf Dis 4(11):1536. SPARK data can be downloaded here and should only be used in accordance with these Terms of Use.
EDASA COVID-19 Compound Repository Available for Collaborations
Published By: Andrea Altieri, PhD Molecules: 2733
Published: 5/12/2020
EDASA Scientific, a small MedChem organization (http://www.edasascientific.
COVID-19 Mpro Active Fragments
Published By: Alex Clark Molecules: 1003
Published: 3/28/2020
Fragments found to be active against Mpro/COVID19 by crystal structure made available from Diamond Light Source, the UK's national synchrotron science facility in collaboration with Dectris (whose detectors have been used in all the MX experiments at Diamond). For the original data, please see: https://www.diamond.ac.uk/covid-19/for-scientists/Main-protease-structure-and-XChem/Downloads.html
Perlara ArkBase
Published By: Perlstein Lab Molecules: 56756
PI: Ethan Perlstein
Published: 10/27/2019
A fully open-source model-organism-based phenotypic screening data corpus comprised of drug repurposing and lead discovery screens in yeast, worm, fly and human cell models of inborn errors of metabolism such as lysosomal disease and congenital disorders of glycosylation. These data have been published in three case studies in the journals G3 (Lao et al., 2019 https://www.g3journal.org/
Serotonin receptor in vitro and in vivo activity
Published By: Nichols Molecules: 84
PI: Dave Nichols
Published: 10/14/2019
Data sets focus on brain systems that utilize dopamine or serotonin as the neurotransmitter. This includes molecular probes that have specificity for only one of the five general types of dopamine receptors (D1 - D5), as well as data sets on serotonin 5-HT1A, 5-HT2A and 5-HT2C receptors. These projects are comprised of systematic structural modification, coupled with pharmacological assay, with a view toward identifying structural determinants of the ligand binding domain in these receptors. One theme of this work has been to identify how molecules from different chemical classes can all be accommodated within the same receptor binding site.
MULTIPLE SCLEROSIS: OL Differentiation
Published By: Myelin Repair Foundation Molecules: 710
PI: Tassie Collins
Published: 10/21/2016
Acute Oligodendrocyte differentiation assay O4 immunopurified OPCs were plated at 5k/well. 1 hr after plating, test article was added and cells were incubated for four days, whereupon cells were fixed and immunostained for MBP and total nuclei (DAPI). OPC differentiation into OLs was determined by quantification of MBP staining/number of cells (identified by DAPI nuclear staining). Screening of compounds was performed in quadruplicate at 2 concentrations (10 & 2 uM; 2 & 0.4 uM; 0.4 & 0.08 uM). Data are normalized to DMSO (0% differentiation) and 40 ng/ml T3 (100% differentiation). EC50 is determined relative to the EMax of the test article. For technical details see Lariosa-Willingham, et. , al, BMC Res Notes. 2016 Sep 5;9(1):419 or contact [email protected] for detailed protocols.
MULTIPLE SCLEROSIS: OL Protection
Published By: Myelin Repair Foundation Molecules: 723
PI: Tassie Collins
Published: 10/21/2016
Oligodendrocyte Protection Assay - Viability (TNF+IFNg) Expanded OPCs were plated at 10K/well. 24 hrs after plating, test article was added, 1hr after test article addition, insult with 10U/ml IFN-gamma/1ng/ml TNF-alpha was added. Incubate 2 days, add AlamarBlue and incubate four hrs. Quantify AlamarBlue fluorescence to read out cellular viability. Data are scaled to DMSO (0% activity) and 1.1 uM quetiapine (100% activity). For technical details see Rosler, et. , al, BMC Res Notes. 2016 Sep 5;9(1):444 contact [email protected] for detailed protocols.
MULTIPLE SCLEROSIS: Myelination Assay
Published By: Myelin Repair Foundation Molecules: 715
PI: Tassie Collins
Published: 10/21/2016
Cortical Myelination Assay Cells from E18 brain cortex were prepared and plated in Neuralbasal media. Four days later, media was switched to MyM media. On day 5, test articles are added and myelination allowed to proceed for eight days. On day 13 in vitro, cells were fixed and immunostained for MBP and Olig2. Myelination was determined by quantification of MBP/Olig2+ nuclei staining and change of MBP morphology (alignment of contiguous MBP staining - fiber length). OL differentiation was determined by quantification of the MBP density x area/Olig2+ nuclei. Compounds were screened in duplicate with 4 images/well at 2 concentrations (5 & 1 uM). Data are normalized to DMSO (0% differentiation/myelination) and DAPT (100% differentiation/myelination). EC50s determined relative to response to 1 uM DAPT. For technical details see Lariosa-Willingham, et. , al, BMC Neurosci. 2016 Apr 22;17:16 or contact [email protected] for detailed protocols.
MULTIPLE SCLEROSIS: HEK293 tunicamycin protection assay
Published By: Myelin Repair Foundation Molecules: 740
PI: Tassie Collins
Published: 10/7/2016
HEK-293 protection Assay
HEK-293 cells (10K/well) are incubated for 24 hours, then test article is added. After 1 hour, 100 ng/ml tunicamycin is added. After an additional 48-hour incubation, AlamarBlue is added and fluorescence is quantified 4 hours later. Data are normalized to DMSO (0% activity) and 5 uM guanabenz (100% activity). EC50 is determined relative to the EMax of the test article. Contact [email protected] for detailed protocols.
MULTIPLE SCLEROSIS: OL Toxicity Screening
Published By: Myelin Repair Foundation Molecules: 709
PI: Tassie Collins
Published: 10/7/2016
Oligodendrocyte Toxicity Assay (TNF+IFNg)
Toxicity assay on passaged rat OPCs, plated at 10k/well incubated with drug for 2 days. Readout is AlamarBlue fluorescence after 4 hr incubation. Data are shown as percent survival relative to DMSO (100%). Max killing is with 5 ng/ml tunicamycin, which leaves ~15% cells alive. For technical details see Lariosa-Willingham, et., al, BMC Res Notes. 2016 Sep 5;9(1):419 or contact [email protected] for detailed protocols.
Green Solvents
Published By: Alex Clark Sandbox Molecules: 117
Published: 9/20/2016
Green Solvents data, used by the eponymous mobile app (http://molmatinf.com/greensolvents.html). Compiled from information published by the ACS Green Chemical Institute and GSK Solvent Guide. Published in http://pubs.acs.org/doi/abs/10.1021/sc3000509.
PARASITES: GSK Kineto Box hits with pIC50
Published By: GSK Kineto Box Project (TCAKS) Molecules: 592
PI: Pilar Manzano
Published: 6/16/2016
Using whole-cell phenotypic assays, the GlaxoSmithKline high-throughput screening (HTS) diversity set of 1.8 million compounds was screened against the three kinetoplastids most relevant to human disease, i.e. Leishmania donovani, Trypanosoma cruzi and Trypanosoma brucei. Secondary confirmatory and orthogonal intracellular anti-parasiticidal assays were conducted, and the potential for non-specific cytotoxicity determined. Hit compounds were chemically clustered and triaged for desirable physicochemical properties. The hypothetical biological target space covered by these diversity sets was investigated through bioinformatics methodologies. Consequently, three anti-kinetoplastid chemical boxes of approximately 200 compounds each were assembled. This data-set includes hit compounds and all associated screening results. http://www.nature.com/articles/srep08771
VENDOR: ASINEX PPI Library
Published By: ASINEX Molecules: 8400
PI: Mark Parisi
Published: 3/3/2016
ASINEX has been working on the design and synthesis of protein-protein interaction (PPI) libraries since 2008. The latest generation of ASINEX PPI Library comprises molecules of various sizes, frameworks, and shapes ranging from fragment-like entities to macrocyclic derivatives designed as secondary structure mimetics or as epitope mimetics.
VENDOR: ASINEX Elite Library
Published By: ASINEX Molecules: 12960
PI: Mark Parisi
Published: 3/3/2016
What issues are there after the initial “hit?” Asinex has addressed these issues with extensive ADME profiling, optimal design for easy medchem modification, and IP assessment to ensure novelty.
VENDOR: ASINEX Phenotypic Library
Published By: ASINEX Molecules: 9840
PI: Mark Parisi
Published: 3/3/2016
Asinex runs both targeted based and phenotypic assays in house and uses the experimental information it gathers to create both its target based and diverse screening sets. Through this experience, Asinex has created a phenotypic screening set; filters for this set are as follows:
MW:200-450, clogP:-1.0–7.0, clogD(pH 7.4):-5.0–4.0, Rot.Bond:0-10, HA:1-10, HD:1-5, TPSA:15-135 A, N+O:2-10, HAC:19-34, Dipole:0.3–3.30, SHP2:0.240–0.450.
VENDOR: ASINEX Diversity Library
Published By: ASINEX Molecules: 9968
PI: Mark Parisi
Published: 3/3/2016
Diversity continues to be a powerful screening tool, especially at the early “probe” stage of drug discovery. In creating this set, Asinex has applied computational tools to ensure chemical space is properly represented while also incorporating elements of its “Elite” and “BioDesign” concepts.
VENDOR: ASINEX BioDesign
Published By: ASINEX Molecules: 8041
PI: Mark Parisi
Published: 3/3/2016
ASINEX's BioDesign approach incorporates key structural features of known pharmacologically relevant natural products (e.g. alkaloids and other secondary metabolites) into synthetically feasible medicinal chemistry scaffolds.
CATALOG: Distributed Drug Discovery (D3) - IUPUI
Published By: IUPUI - D3 Enum 73K N-AcylAA-OH, -OMe, -NH2 Molecules: 73234
PI: M. J. O'Donnell and W. L. Scott
Published: 2/24/2016
A free, open-access virtual catalog/library of >73,000 molecules: (a) N-Acyl Unnatural α-Amino Acids, (b) Methyl Esters of N-Acyl Unnatural α-Amino Acids, and (c) Primary Amides of N-Acyl Unnatural α-Amino Acids. The molecules in the catalog were obtained by an enumeration based on the solid-phase combinatorial alkylation of a glycine anion equivalent with 100 R1X followed by N-acylation with 100 R2CO2H and resin cleavage (TFA, MeOH/Et3N, or TFA, respectively). The legacy data set of 48,818 molecules (above a and b sets plus R1X and R2CO2H inputs) was published on 1/1/2009. We encourage colleagues to communicate with us concerning interest in the D3 project (E-mail: [email protected]<mailto:[email protected]> or [email protected]<mailto:[email protected]>). References: J. Comb. Chem. 2009, 11, 3-13, 14-33, 34-43; J. Org. Chem. 2014, 79, 3140-51; J. Chem. Educ. 2015, 92, 819-26.
MALARIA: Biochemical screen of 5 P. falciparum kinases vs. GSK’s TCAMS
Published By: Gregory J. Crowther Molecules: 13451
PI: Gregory J. Crowther
Published: 2/3/2016
~13,500 cell-active compounds were screened for activity against five different protein kinases. GlaxoSmithKline’s Tres Cantos Antimalarial Set (TCAMS) was screened in biochemical assays of Plasmodium falciparum calcium-dependent protein kinases 1 and 4 (CDPK1/PF3D7_0217500 and CDPK4/PF3D7_0717500), mitogen-associated protein kinase 2 (MAPK2/MAP2/PF3D7_1113900), protein kinase 6 (PK6/PF3D7_1337100), and protein kinase 7 (PK7/PF3D7_0213400). Novel potent inhibitors (IC50 < 1 µM) were discovered for three of the kinases: CDPK1, CDPK4, and PK6. The PK6 inhibitors are the most potent yet discovered for this enzyme and deserve further scrutiny.
Public Dark Matter Compounds
Published By: Dark Matter Compounds Molecules: 139352
PI: Guillermo Morales
Published: 12/7/2015
Novartis found that 803,990 of their compounds had been tested in at least Novartis 100 assays and 112,872 compounds were inactive (14.0%). And an analysis of NIH data showed that 363,598 compounds had been tested in at least 100 assays where 131,726 compounds were inactive (36.2%).
Anne Mai Wassermann, Eugen Lounkine, Dominic Hoepfner, Gaelle Le Goff, Frederick J King, Christian Studer, John M Peltier, Melissa L Grippo, Vivian Prindle, Jianshi Tao, Ansgar Schuffenhauer, Iain M Wallace, Shanni Chen, Philipp Krastel, Amanda Cobos-Correa, Christian N Parker, John W Davies & Meir Glick. Dark chemical matter as a promising starting point for drug lead discovery. Nature Chemical Biology 2015, Vol. 11, pp. 958–966 (doi: 10.1038/nchembio.1936)
ADME: AZ Public ChEMBL Data
Published By: AZ Public ChEMBL Data Molecules: 5799
PI: Sean Ekins
Published: 10/5/2015
Experimental in vitro DMPK and physicochemical data on a set of publicly disclosed compounds determined at AstraZeneca. The references provided for the assays exemplify the experimental procedures used in generating the data.
https://www.ebi.ac.uk/chembl/doc/inspect/CHEMBL3301361% bound to plasma by equilibrium dialysis. Compound is incubated with whole guinea pig plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.% bound to plasma by equilibrium dialysis. Compound is incubated with whole dog plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.% bound to plasma by equilibrium dialysis. Compound is incubated with whole rat plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.% bound to plasma by equilibrium dialysis. Compound is incubated with whole mouse plasma at 37C for >5hrs. Method described in B. Testa et al (Eds.), Pharmacokinetic Profiling in Drug Research: Biological, Physicochemical, and Computational Strategies, Wiley-VCH, Weinheim, 2006, pp.119-141. Experimental range 10% to 99.95% bound.Intrinsic clearance measured in human hepatocytes following incubation at 37C. Experimental range <3 to >150 microL/min/1E6 cells. Rapid Commun. Mass Spectrom. 2010, 24, 1730-1736.Most basic pKa value (pKa B1) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Bases: >= 2.Second most acidic pKa value (pKa A2) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Acids: <= 11.
Third most basic pKa value (pKa B3) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Bases: >= 2.
Second most basic pKa value (pKa B2) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Bases: >= 2.
Most acidic pKa value (pKa A1) determined by absorption and potentiometric titration using standard methodology from Sirius Analytical. Experimental range Acids: <= 11.
PDB Ligands
Published By: Protein Data Bank (PDB) Molecules: 16826
PI: Dale R. Cameron, Ph.D., M.C.I.C., P.Chem.
Published: 8/3/2015
Ligand information is extracted from the PDB, filtered to remove "polymer" and other related "non-free" ligands as well as metals or metal binding ligands. Updates to the filtering procedure may occur without warning. Data is provided as is with no additional curation or error correction. Links to PDB are provided by the RCSB PBD and can be cited as
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank Nucleic Acids Research, 28: 235-242.
Please report broken links, requests for additional data, etc. to the vault administrator
EBOLA: Small molecule inhibitors of Ebola virus
Published By: Nadia's Sandbox Molecules: 55
PI: Dr. Nadia Litterman
Published: 2/2/2015
This shared dataset contains 55 small molecules from the literature (up to Jan 2015) which have in vitro and or in vivo activity against the Ebola virus and various disease models. We have included an evaluation from an experienced medicinal chemist as well as results of PAINS filtering. (This work has been submitted for publication by Nadia Litterman, Christopher Lipinski and Sean Ekins to F1000Research).
VENDOR: Synthonix - Building Better Bonds
Published By: http://www.synthonix.com Molecules: 10286
Published: 1/2/2015
Synthonix helps medicinal chemists push the boundaries of drug discovery by providing a catalog of 10286 building blocks that allow them explore more challenging chemical space, and expand the range of potentially significant therapeutic targets to treat the world’s chronic and curable diseases. Synthonix, Inc : 919-875-9277; General E-mail: [email protected]; Synthonix Ltd (Europe Office): Office: +44 1223 597934; E-mail: [email protected]
PROBES: NIH Chemical Probes
Published By: Probes Vault Molecules: 319
PI: Christopher Lipinski
Published: 11/12/2014
The National Institutes of Health (NIH) has funded extensive HTS efforts, estimated more than $576 million, in both intra-mural and academic centers to identify small molecule chemical probes or tool compounds via the Molecular Libraries Screening Center Network (MLSCN) and the Molecular Library Probe Production Center Network (MLPCN). For compounds to be elected as probes, various definitions, based on a combination of potency, selectivity, solubility, and availability, have been used. To date the NIH-funded academic screening centers have discovered more than 300 chemical probes. This collection includes probe structures, targets, anti-targets, IC50 values, and other references. It also includes a variety of measures of drug-likeness including the desirability score as assigned by Dr. Chris Lipinski as described in “Computational Prediction and Validation of an Expert's Evaluation of Chemical Probes.” Litterman NK, Lipinski CA, Bunin BA, Ekins S. J Chem Inf Model. (2014)
VENDOR: Azepine Ltd. Building Blocks Collection
Published By: Azepine Ltd. Molecules: 600
PI: Julia
Published: 10/8/2014
600 building blocks, IN STOCK at competitive prices. Contact [email protected]
NEU-CSIC-GSK Kinase-Targeted HTS
Published By: Pollastri Lab - Northeastern University Molecules: 78
PI: Michael Pollastri
Published: 9/25/2014
This data set contains the published results of a high-throughput screen performed via collaboration between Northeastern University (Pollastri Laboratory), the CSIC (Navarro Laboratory), and GlaxoSmithKline Tres Cantos Laboratory (Diseases of the Developing World DPU). The article is Diaz et al, PLoS-NTDs:
DOI: 10.1371/journal.pntd.0003253
Please contact [email protected] with questions
VENDOR: Vitas-M Laboratory Stock HTS Collection
Published By: Vitas-M Laboratory Molecules: 388375
Published: 7/11/2014
Vitas-M Laboratory, LTD. Collection of HTS compounds is about 400 000 individual molecules, in stock. All of them are available for quick delivery in different formats including mg, micromole, dry powder, DMSO solution, and dry film. www.vitasmlab.com Irina Ryabushenko: [email protected]
VENDOR: Vitas-M Laboratory Building Blocks
Published By: Vitas-M Laboratory Molecules: 33297
Published: 7/10/2014
Vitas-M Laboratory, LTD. Collection of organic building blocks contains more than 33 000 identified and tested items. www.vitasmlab.com Irina Ryabushenko: [email protected]
VENDOR: Vitas-M Laboratory Scaffolds
Published By: Vitas-M Laboratory Molecules: 2898
Published: 7/8/2014
Vitas-M Laboratory, LTD. Collection of Scaffolds (Azalea project). Advanced ideas to synthesize drug-like mini-libraries. It is the best choice to acquire absolutely novel compounds that no other vendor offers. www.vitasmlab.com Irina Ryabushenko: [email protected]
VENDOR: Vitas-M Laboratory Fragments
Published By: Vitas-M Laboratory Molecules: 18631
Published: 7/8/2014
Vitas-M Laboratory, LTD. Collection of Fragments (chemical substances passed through "Rule of 3" and other special filters) for Fragments Based Drug Discovery. www.vitasmlab.com Irina Ryabushenko: [email protected]
VENDOR: Life Chemicals- GPCR library
Published By: Life Chemicals Molecules: 15948
PI: Alexandr Kucherak
Published: 6/20/2014
Similarity/pharmacophore search was based on Topomer Search prediction provided by Sybyl-X. First step - a similarity search assumed a comparison of entire stock compounds to known inhibitors derived from BindingeDB and ChemblDB. Second step - generation of 3D structures of known inhibitors and their co-alignment. This chemical spatial space was used as a template for fitting of the rest of "similar" compounds. However this is method was designed for "cherry-picking" and an alternative library can be done with virtual screening methods (all screening models a ready and proved with training sets) against such receptors - adenosine, chemokine, dopamine, gaba-, histamine, muscarinic, opioid, sphingosine. http://www.lifechemicals.com/
VENDOR: Life Chemicals- Kinase by Similarity
Published By: Life Chemicals Molecules: 62467
PI: Alexandr Kucherak
Published: 6/20/2014
Similarity search using MDL public keys and the Tanimoto similarity cut-off of 90%. Almost 25K reference compounds that tested active in 168 biological assays (more than 100 different kinase targets), were used for similarity search. All this compounds could be screened against more specific target up to the customer order. http://www.lifechemicals.com/
VENDOR: Life Chemicals- Kinase by docking
Published By: Life Chemicals Molecules: 15174
PI: Alexandr Kucherak
Published: 6/20/2014
Kinase library was prepared basing on virtual docking in a Sybyl environment. For this purpose a set of kinase structures' binding sites (about 20) were aligned and analyzed. Such superposed sites were used for structure-based pharmacophore modelling via Unity module from Sybyl-X. After all preparation an entire 3D stock was screened against this multi-pharmacophore model and in the end a top-ranking was performed. http://www.lifechemicals.com/
VENDOR: Life Chemicals- Nuclear Receptors
Published By: Life Chemicals Molecules: 9896
PI: Alexandr Kucherak
Published: 6/20/2014
Life Chemicals. Virtual docking and similarity/pharmacophore search. http://www.lifechemicals.com/
VENDOR: Life Chemicals- CNS Library
Published By: Life Chemicals Molecules: 16535
PI: Alexandr Kucherak
Published: 6/20/2014
CNS filters which are described in the literature were used as a sieve for our entire stock. As it was shown the only compounds with such parameters can have appropriate characteristics for nervous tissue permeability. All descriptors were obtained from Spreadsheets and Volsurf modules of Sybyl. (MW 200 = 350 cLogP =< 3.6 H-Bond Acceptors =< 8 H-Bond Donors =< 5 tPSA =< 120 Rotatable Bonds =< 5 LogBB1 = -3.0 to 1.0) http://www.lifechemicals.com/
VENDOR: Life Chemicals- Natural Product-like Library
Published By: Life Chemicals Molecules: 7808
PI: Alexandr Kucherak
Published: 6/20/2014
First method was based on statistical anlysis of descriptors. Previously a large database of NPs was analyzed to study NP scaffolds by arranging them in the form of a tree. Thus analysis of property distribution of more than 130 000 NP structures as well as identification of substructures typical for particular classes of natural compounds were carried out to generate a set of fragments usually present in natural compounds. This method was tested on CRC Dictionary of Natural Products (DNP) and synthetic molecules (SMs). Another method is based on scaffold similarity assessment. The number of atom signatures (from fragmnets) generated for a molecule is equal to the number of atoms that make up the molecule. Every atom signature independently represent a structural feature/fragment of the molecule, and an individual score for it is calculated. higher number of atoms from gaining higher score. To reproduce such experiment we used an implemented module Chemistry Development Kit in CDK-Taverna 2.0. It contains a NP-Likeness scorer v1.4.1 which calculates Natural Product(NP)-likeness of a molecule, i.e. the similarity of the molecule to the structure space covered by known natural products. All results were scored and ranged from -3 to +3. http://www.lifechemicals.com/
VENDOR: Life Chemicals- Screening collection
Published By: Life Chemicals Molecules: 371998
PI: Alexandr Kucherak
Published: 6/20/2014
Carefully designed, novel, drug-like small molecules with Lipinski rule of 5 and the only reason for deviation from the set of this parameters is a unique scaffold or non-standard chemistry. It is ready for application of medicinal chemistry filters like PAIN or any target-focused filters (solubility, permeability, BBB). http://www.lifechemicals.com/
VENDOR: Life Chemicals- Fragments with Guaranteed Solubility
Published By: Life Chemicals Molecules: 8241
PI: Alexandr Kucherak
Published: 6/20/2014
Fragment compounds were selected by filtering of entire LC-stock with modified “Rule of three”. Fragments have been tested for solubility in analytical laboratory. Solubility is guaranteed at 200mM concentration in DMSO, and 75% of fragments are soluble in pH7.5 buffer at 1mM concentration. http://www.lifechemicals.com/
TB: In vivo mouse efficacy from literature
Published By: TB in-vivo data2 Molecules: 778
PI: Sean Ekins, PhD
Published: 4/10/2014
Looking Back To The Future: Predicting In vivo Efficacy of Small Molecules Versus Mycobacterium tuberculosis. Selecting and translating in vitro leads for a disease into molecules with in vivo activity in an animal model of the disease is a challenge that takes considerable time and money. We demonstrate learning from in vivo active and inactive compounds using machine learning classification models (Bayesian, Support Vector Machines and recursive partitioning) consisting of 773 compounds. The Bayesian model predicted 8 out of 11 additional in vivo actives not included in the model as an external test set. Curation of seventy years of Mtb data can therefore provide statistically robust computational models to focus resources on in vivo active small molecule antituberculars. This highlights a cost effective predictor for in vivo testing elsewhere in other diseases. PMID:24665947
TB: Data for TB Mobile 2
Published By: TB Mobile 2.0 Updates Molecules: 79
PI: Sean Ekins
Published: 3/19/2014
79 compounds selected from recent papers with one or more target in TB added to TB Mobile for version 2 of the app. 20 additional molecules were used as a test set. The paper is submitted.
PARASITE: MMV malaria box screen of Schistosoma mansoni
Published By: CDIPD Vault Molecules: 400
Published: 11/6/2013
Whole-organism screens of Schistosoma mansoni somules (post-infective larvae) and adults with the 400 compounds that comprise the MMV Malaria Box (http://www.mmv.org/malariabox). Only those Malaria box 'Drug-like' compounds yielding the most severe phenotypes vs. somules were tested against adults. The data are also uploaded to ChEMBL. Contact Conor Caffrey, Center for Discovery and Innovation in Parasitic Diseases (www.cdipd.org/), UCSF ([email protected]).
Kinase: Kinase Catalytic Activity (Theonie Anastassiadis Publication in Nature Biotechnology)
Published By: Kinase Catalytic Activity Molecules: 178
PI: Theonie Anastassiadis
Published: 8/30/2013
Kinase Catalytic Activity
Nature Biotechnology 2011 October 30; 29(11): 1039–1045.The library tested comprised 178 compounds known to inhibit kinases from all major protein kinase subfamiliesFor simplicity, all compounds were tested at a concentration of 0.5 µM in the presence of 10 µM ATP. 0.5 µM was chosen despite an average reported IC50 for these compounds toward their primary targets of 66 nM in order to capture weaker off-target inhibitory activity.Each kinase-inhibitor pair was tested in duplicate and results were expressed as average substrate phosphorylation as a percentage of solvent control reactions (henceforth referred to as “remaining kinase activity”).Mean remaining kinase activity for each kinase-inhibitor pair is presented. Kinase activity data was expressed as the percent remaining kinase activity in test samples compared to vehicle (dimethyl sulfoxide) reactions.
TB: Update drugs and leads with targets
Published By: TB: drugs and leads with targets - update Molecules: 38
Published: 6/14/2013
Published compounds from the recent literature for TB with known targets to be used as an update also for the TB Mobile App
KINASE: GSK Published Kinase Inhibitor Set (PKIS)
Published By: Kinome2 Molecules: 364
Published: 6/6/2013
The GSK Published Kinase Inhibitor Set (PKIS) is a set of 367 protein kinase inhibitors, which has been annotated for protein kinase family activity and is available for public screening efforts. Detailed information on the screening set can be found at the links shown below. The ChEMBL database has been the “go-to” site for bioassay data on this set. In the spirit of improving access to important data, we have gathered the PKIS data that ChEMBL has kindly made available, and processed it so it could be accessed here at the Collaborative Drug Discovery (CDD) site (much like we have done previously for the Kinase SARfari database).
The transfer to CDD makes the data available in a more “med-chemist” friendly manner. We also did some tidying up of the data set. For example there are actually only 364 compounds (some duplicates were due to salt forms or alternate names of the same molecule). We also tried to normalize target names where possible (for example, the kinases IKKA, IKKB and IKKE were called IKK-alpha, IKK-beta, IKK-epsilon for the dataset from UNC). Not that we’re perfect… we appreciate any corrections to our dataset as well!
To summarize, there are 364 compounds that have been tested against 225 targets at 0.1 and 1 uM. In this dataset, there is only one protocol, but the 225 targets are listed in one readout. Concentration is also a readout, so it is easy to limit searches to screens run at 1 and/or 0.1 uM.
Links:
1) More information on the GSK PKIS
http://www.maggichurchouseevents.co.uk/bmcs/Downloads/CBDD%20-%20Zuercher%20Bill.pdf
http://www.chordomafoundation.org/wp-content/uploads/2013/04/2013-Flanagan-Drewry.pdf
http://chembl.blogspot.co.uk/2013/05/pkis-data-in-chembl.html
2) Previous ChEMBL kinase data on CDD
https://www.collaborativedrug.com/buzz/2013/04/04/kinome-sar-for-collaborative-drug-discoverers/
KINASE: ChEMBL Kinase SARfari Compounds & BioAssay Data
Published By: CDD Vault Molecules: 54211
PI: CDD
Published: 3/27/2013
A valuable resource available at ChEMBL is the Kinase SARfari, “an integrated chemogenomics workbench focused on kinases. The system incorporates and links kinase sequence, structure, compounds and screening data”. A highly useful resource, this database makes available a large amount of SAR data for the kinase active compounds against a wide range of kinases in a broad array of assays, much of it manually mined and curated from the literature. To make this data available in the CDD interface, we took the core table of Kinase SARfari and merged it with another key table from the ChEMBL database, providing a field describing the assay utilized in each record in much greater detail than is available in native SARfari. We have now made this merged dataset available via the CDD interface. Detailed in vitro data is avaiable for 400 kinases. In addition, in vivo functional, as well as ADMET data is posted as well.
TB: ARRA
Published By: TB ARRA Molecules: 1924
PI: Bob Reynolds
Published: 3/15/2013
Data from SRI (Bob Reynolds) and Scott Franzblau group - paper submitted by Ekins et al.
Hits from previous SRI screens were used to look for similar compounds in vendor libraries, clustered and tested in vitro in a series of accepted panels of screens for new drug discovery candidates. The compounds were also used as a test set for previously generated Bayesian models built with bioactivity and cytotoxicity information.
TB: GSK
Published By: TB GSK Molecules: 177
PI: Sean Ekins, PhD
Published: 2/8/2013
Supplemental data from the Ballell et al paper ChemMedChem 2013 in press "fueling open-source drug discovery: 177 small-molecule leads against tuberculosis"
Original datasets are hosted at https://www.ebi.ac.uk/chemblntd only M.tb data is shown here but more BCG data is available at ChEMBL
TRYPANOSOME: Chagas Disease Literature Compounds
Published By: Chagas Public Data Molecules: 531
Published: 12/21/2012
Compound structures and literature references were curated for 531 molecules tested against Trypanosoma cruzi in vitro or in vivo in the published literature.
TRYPANOSOME: Optimization of specific chemical series against human African Trypanosomiasis (HAT)
Published By: Chagas Public Data Molecules: 5559
Published: 12/12/2012
SCYNEXIS Inc, as a member of the DNDi HAT Lead Optimization Consortium developed and screened 4926 compounds for activity against T. brucei. Compound structures and in vitro activity data against T. brucei brucei are included. Cytotoxicity data and activity against the related eukaryotic parasites T. brucei rhodesiense, L. donavani, and P. falciparum for a subset of 34 compounds. All of the reported compound series are no longer in development for HAT as they were found to have poor selectivity or properties incompatible with in vivo activity. http://www.dndi.org/diseases-projects/open-innovation/1011-hat-001
TRYPANOSOME: DNDi-Optimization of fenarimol series for treatment of Chagas disease
Published By: Chagas Public Data Molecules: 743
Published: 12/9/2012
The DNDi Lead Optimization Consortium, including Epichem, Murdoch University, and CDCO, developed and screened an SAR series based on the plant fungicide fenarimol. DNDi made public compound structures, T. cruzi activity data, and L-6 cell toxicity data for 743 compounds from this series in ChEMBL-NTD. Compounds and biological assay data are included here in CDD Public. http://www.dndi.org/diseases-projects/open-innovation/1012-chagas-001
TRYPANOSOME: Broad Primary HTS to Identify Inhibitors of T.Cruzi Replication
Published By: Chagas Public Data Molecules: 303230
Published: 12/6/2012
The Broad Institute performed a high-throughput screen of 303,224 compounds in duplicate in the recombinant Tulahuen strain of Trypanosoma cruzi stably expressing beta-galactosidase reporter co-cultured with host cell, mouse fibroblast NIH3T3. Of the 4,394 hits, 4,063 were further evaluated for inhibitory activity and host cell toxicity. Finally, 27 compounds were selected as potential probe compounds and further validated. Data from the primary screen and subsequent secondary assays were deposited PubChem. Chemical compounds and biological assay data for the primary screen and six secondary assays from PubChem are included here in CDD Public. http://www.ncbi.nlm.nih.gov/pubmed/21634083
TB: Guzman et al., M.tb. MurE ligase inhibitors
Published By: CDD - Sean Ekins Molecules: 8
PI: Sean Ekins
Published: 12/6/2012
Whole cell and target based screening data from the following TB publication: Guzman JD, Gupta A, Evangelopoulos D, Basavannacharya C, Pabon LC, Plazas EA, Muñoz DR, Delgado WA, Cuca LE, Ribon W, Gibbons S, Bhakta S. J Antimicrob Chemother. 2010 Oct;65(10):2101-7. Anti-tubercular screening of natural products from Colombian plants: 3-methoxynordomesticine, an inhibitor of MurE ligase of Mycobacterium tuberculosis.
VENDOR: NIH Clinical Collection 2 array (281 molecules)
Published By: NIH Clinical Collections Molecules: 281
PI: Project Manager: Mei Steele
Published: 11/21/2012
The NIH Clinical Collection 2 are plated arrays 281 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research.
VENDOR: NIH Clinical Collection array (446 molecules)
Published By: NIH Clinical Collections Molecules: 446
PI: Project Manager: Mei Steele
Published: 11/21/2012
The NIH Clinical Collection is plated array of 446 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research.
TB: Drugs and leads with targets - data used in mobile app
Published By: SRI molecules and targets for mobile app Molecules: 707
Published: 10/23/2012
Updated Data curated for TB targets with in vivo essentiality
information from TBDB, Biocyc, Metacyc, PDB and Pubmed as well as
other references by Malabika Sarker at Stanford Research Institute.
Gyanu Lamichhane at Johns Hopkins University provided essentiality
information.ref.http://www.ncbi.nlm.nih.gov/pubmed/22477069
Explore this dataset on mobile: https://itunes.apple.com/app/tb-mobile/id567461644
TOX: Drugs and chemicals classified by hepatotoxicity
Published By: CDD Vault Molecules: 83072
PI: CDD
Published: 7/16/2012
A list of drugs and chemicals with a classification scheme based on clinical data for hepatotoxicity has been assembled by Pfizer (Hu 2008) previously in order to evaluate an in vitro human hepatocyte imaging assay technology (HIAT), resulting in a concordance of 75% with clinical hepatotoxicity. This same dataset of compounds that do or do not cause drug induced Liver injury (DILI) has been used along with molecular descriptors for in silico prediction via Bayesian models.
TB: SRI Molecules with Whole-Cell Activity Against TB
Published By: SRI Group Vault Molecules: 23
PI: Sean Ekins, PhD
Published: 4/24/2012
Molecules evaluated in Pharm Res. 2012 Apr 4. PMID: 22477069
Combining Cheminformatics Methods and Pathway Analysis to Identify Molecules with Whole-Cell Activity Against Mycobacterium Tuberculosis.
Sarker M, Talcott C, Madrid P, Chopra S, Bunin BA, Lamichhane G, Freundlich JS, Ekins S.
MALARIA: MMV Malaria Box
Published By: Public: Malaria Box Molecules: 400
Published: 3/29/2012
Molecules from MMV Malaria Box, ChEMBL-NTD (https://www.ebi.ac.uk/chemblntd) : MMV Malaria Box, Simon Macdonald, Paul Willis, Paul Kowalczyk, Thomas Spangenberg, Jeremy Burrows and Tim Wells. Medicines for Malaria Venture (MMV), PO Box 1826, 20, rte de Pré-Bois, 1215 Geneva 15, Switzerland and SCYNEXIS Inc. P.O. Box 12878 Research Triangle Park, North Carolina 27709-2878 USA.
All compounds in the Malaria Box have been screened in vitro against 3D7 (chloroquine (CQ) sensitive but sulfadoxine resistant strain of P. falciparum) and cytotoxicity assays were performed on human embryonic kidney cell lines (HEK-293). Data are expressed as EC50 in nM for the falciparum data.
ADME: ADMEdata.com - A Commercial Repository of High Quality ADME Data
Published By: G2 Research ADMEdata.com Molecules: 1760
PI: George Grass
Published: 1/13/2012
Examples of: Caco-2 Permeability, Equilibrium Solubility @ 5pH Values, Protein Binding Human, Protein Binding Rat, Rabbit Intestinal Permeability, Human Blood Plasma Partitioning & Hematocrit. For full data sets and models, directly contact George Glass, Pharm.D. Ph.D at [email protected] (distributed via CDD)
VENDOR: Porse Building Blocks Collection
Published By: CDD Vault Molecules: 29241
PI: CDD
Published: 1/13/2012
Porse File Chemical Co. is devoted to custom novel compound synthesis for drug discovery, and provides a wide product range with competitive prices and good quality. The current set is a selected subset of 1554 new diverse compounds and building blocks in the Morpholine, Piperidine, Piperazine, Pyrimidine, amino acid and API families. www.porsefinechemical.com, [email protected] +86-20-28069055
PARASITES: Schistosoma mansoni schistosomula: Microsource Spectrum & Killer Collections
Published By: Brian Suzuki's Sandbox Molecules: 119
Published: 10/5/2011
Schistosoma mansoni schistosomula: Phenotypic Screen of the Microsource Spectrum & Killer Collections.
PI: Conor R. Caffrey
Published: 10/5/2011
CDD: Public Data 119 hits
As part of a drug re-purposing (re-positioning) strategy to identify novel anti-parasitics at the UCSF Sandler Center for Drug Discovery, we developed a partially automated whole organism (phenotypic) screen for the bloodfluke that causes the infectious tropical disease, schistosomiasis. We screened the 1,260 compounds of the above-stated collections that include drugs, drug-like compounds, natural products and miscellaneous compounds. We report the phenotypic alterations in larval stages (schistosomula) of Schistosoma mansoni using simple descriptors to convey the multiple and dynamic responses of the parasite to compound insult. Full quantification of the phenotypic responses is ongoing. The data presented pertain to only the ‘hit’ compounds; the full listing of compounds in the respective collections can be obtained from Microsource Discovery Systems Inc. Contact [email protected] for more details. Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening. Abdulla MH, Ruelas DS, Wolff B, Snedecor J, Lim KC, Xu F, Renslo AR, Williams J, McKerrow JH, Caffrey CR. PLoS Negl Trop Dis. 2009 Jul 14;3(7):e478.PMID: 19597541
TB: SRI Kinase Library Phenotypic Screen
Published By: CDD Vault Molecules: 23823
PI: CDD
Published: 8/29/2011
Kinase targets are being pursued in a variety of diseases beyond
cancer, including immune and metabolic as well as viral, parasitic,
fungal and bacterial. In particular, there is a relatively recent
interest in kinase and ATP-binding targets in Mycobacterium
tuberculosis in order to identify inhibitors and potential drugs for
essential proteins that are not targeted by current drug regimens.
Herein, we report the high throughput screening results for a targeted
library of approximately 26,000 compounds that was designed based on current kinase inhibitor scaffolds and known kinase binding sites. The phenotypic data presented herein may form the basis for selecting scaffolds/compounds for further enzymatic screens against specific kinase or other ATP-binding targets in Mycobacterium tuberculosis based on the apparent activity against the whole bacteria in vitro.PMID: 21708485
Tuberculosis (Edinb). 2011 Jun 25. [Epub ahead of print]
Copyright © 2011 Elsevier Ltd. All rights reserved.
Contact Melinda Sosa for more details: [email protected]
High throughput screening of a library based on kinase inhibitor
scaffolds against Mycobacterium tuberculosis H37Rv.
Reynolds RC, Ananthan S, Faaleolea E, Hobrath JV, Kwong CD, Maddox C, Rasmussen L, Sosa MI, Thammasuvimol E, White EL, Zhang W, Secrist JA 3rd.
Source: Southern Research Institute, 2000 Ninth Avenue South,
Birmingham, AL 35205, USA.
FDA APPROVED: NCGC Pharmaceutical Collection (NPC) V1.1.0
Published By: NCGC Pharmaceutical Collection NPC V1.1.0 Molecules: 14579
PI: Noel Southall
Published: 8/8/2011
The NCGC Pharmaceutical Collection: A Comprehensive Resource of Clinically Approved Drugs Enabling Repurposing and Chemical Genomics. Huang, R., Southall, N., Wang, Y., Yasgar, A., Shinn, P., Jadhav, A., Nguyen, D., Austin, C. Sci Transl Med 27 April 2011: Vol. 3, Issue 80, p. 80ps16.
http://stm.sciencemag.org/content/3/80/80ps16.abstract
VENDOR: BioBlocks Catalog with Pricing Information
Published By: BioBlocks Molecules: 2971
PI: Doug Murphy
Published: 8/3/2011
2989 compounds.
BioBlocks offers a focused collection of over 2200 scaffolds, building blocks and fragments which are pre-qualified as drug components. The majority of these compounds are uniquely offered by BioBlocks and have found applications ranging from intermediates for drug discovery to surrogate amino acids in peptide chemistry.
Up-to-date details about BioBlocks building blocks are available at www.bioblocks.com
TOX: Drug induced liver injury data (DILI)
Published By: BBB Molecules: 519
Published: 4/29/2011
Drug induced liver injury data - training set is experimental data from Jim Xu and test set represents literature data.
published in Drug Metab Dispos. 2010 Dec;38(12):2302-8. Epub 2010 Sep 15. A predictive ligand-based Bayesian model for human drug-induced liver injury.
Ekins S, Williams AJ, Xu JJ.
TB: Target database for In vivo essential genes
Published By: SRI TB Target Database Molecules: 314
PI: Sean Ekins
Published: 4/21/2011
Data curated for TB targets with in vivo essentiality information from TBDB, Biocyc, Metacyc, PDB and Pubmed as well as other references collated by Dr. Malabika Sarker at Stanford Research Institute. Dr. Gyanu Lamichhane at Johns Hopkins University is kindly acknowledged for providing essentiality information.
**please note there are no small molecules associated with this dataset**
VENDOR: Enamine Representative Diverse Screening Library
Published By: Enamine Molecules: 200000
PI: Dmytro Mykytenko
Published: 4/12/2011
Original 200K diverse screening library was generated especially for Collaborative Drug
Discovery users from the world’s largest stock of commercially available screening compounds
(over 1.7 M species). The library features exclusive drug-like compounds with refined ADME
properties. Our high quality compounds can be cherry-picked and supplied immediately in
different formats.
REPOSITIONING, FDA APPROVED: Drugs Repurposed using HTS methods
Published By: In vitro repurposing Molecules: 109
Published: 3/18/2011
Drugs identified with new uses using HTS methods. This table greatly extends a previously published version "Ekins S, Williams AJ, Krasowski MD, Freundlich JS. In silico repositioning of approved drugs for rare and neglected diseases Drug Discov Today. 2011 Mar 1. PMID: 21376136 doi:10.1016/j.drudis.2011.02.016 The table lists molecules, Old use / target, new use/ target, how discovered and references.
Abbreviations: CCR5, Chemokine receptor 5; DHFR, Dihydrofolate reductase; DOA, Drugs of abuse, FDA, Food and Drug Administration; GLT1, Glutamate transporter 1; HSP-90, Heat shock protein 90; JHCCL, John Hopkins Clinical Compound Library; Mtb, Mycobacterium tuberculosis; NK-1, neurokinin- 1 receptor; OCTN2.
REPOSITIONING, FDA APPROVED: Orphan-designated products
Published By: Rare disease repurposing Molecules: 76
Published: 3/18/2011
FDA Table 2 - from the FDA resource, the rare disease research database (RDRD), which lists Orphan-designated products (http://www.fda.gov/ForIndustry/DevelopingProductsforRareDiseasesConditions/HowtoapplyforOrphanProductDesignation/ucm216147.htm) with at least one marketing approval for a rare disease indication. This data was analyzed by Ekins and Williams (paper submitted).
REPOSITIONING, FDA APPROVED: Orphan-designated products
Published By: Rare disease repurposing Molecules: 105
Published: 3/18/2011
FDA Table 1 - from the FDA resource, the rare disease research database (RDRD), which lists Orphan-designated products (http://www.fda.gov/ForIndustry/DevelopingProductsforRareDiseasesConditions/HowtoapplyforOrphanProductDesignation/ucm216147.htm) with at least one marketing approval for a common disease indication.
The FDA did not associate the data with molecule structures.
VENDOR: Colorado Center for Drug Discovery Pilot Library
Published By: C2D2 Public Molecules: 2240
PI: Greg Miknis, Associate Director
Published: 3/7/2011
The library contains structurally diverse small molecules which conform to drug like criteria. Several chemotypes are represented and the library is designed to be applicable to a wide variety of potential targets.
To request information about the collection, please send a request to [email protected]
LIPID: Lipid Maps Structure Database
Published By: Lipid Maps Database Molecules: 22215
PI: Lipidomics Gateway
Published: 2/11/2011
The Lipid Maps (http://www.lipidmaps.org/) structures were annotated with 5 common ions (H+,2H++, K+, Na+, NH4+) including mammalian fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterol lipids, and prenol lipids. The structures and ions are searchable by structure and MW to facilitate identification of novel lipids.
TB: Mycobacterium drugome
Published By: virtual metabolites Molecules: 274
Published: 11/5/2010
Dataset of 274 drugs (approved for human use in US and Europe) from a publication by Kinnings et al., PLoS Computational Biology vol 6: e1000976 (2010)
Drugs co-crystallized with at least one structure in PDB.This dataset can be used with the other TB screening datasets in CDD to determine which of these approved drugs have activity against Mtb (from the literature.
TB: Inhibitors of non-replicating Mtb from the literature
Published By: CDD - Sean Ekins Molecules: 26
PI: Sean Ekins
Published: 10/28/2010
Structures and data from published papers:
Darby and Nathan J Antimicrob Chemother 2010: 65: 1424-1427
Bryk et al., Cell Host and Microbe 2008: 3: 137-145
Lin et al., Arch Biochem Biophys. 2010 501: 214-220
Lin et al., J Biol Chem 2008: 283: 34423-34431
de Cavalho et al: J Med Chem 2009: 52: 5789-5792
Lin et al., Nature 2009: 461: 621-626
VENDOR: Astatech, Inc. Building Block Collection
Published By: Astatech, Inc. Molecules: 6140
Published: 10/15/2010
AstaTech, Inc. offers advanced and novel intermediates to facilitate the drug discovery process. Our broad selection includes building blocks, novel amines, protected amines, unnatural amino acids, ketones, aldehydes, heterocycles, isatoic anhydrides, boroinc acids and chiral intermediates. Contact [email protected] for ordering information.
VENDOR: Chemik 2010 Catalogue
Published By: CDD Vault Molecules: 3889
PI: CDD
Published: 10/5/2010
Chemik has successfully assisted drug discovery companies like Wyeth on their early phase projects. We provide the raw material and key intermediates from grams to multi-tons for them. With 10-years of experience in this field, we can help our customers develop a new intermediate in 4-6 weeks with competitive pricing, great quality and continuous service.
MALARIA: Phenanthrene and Anthracene Aminoalcohols
Published By: CDD Vault Molecules: 35
PI: CDD
Published: 9/21/2010
Antimalarial data vs P. berghei in mice for halogen-substituted anthracene and phenanthrene N-di- and mono-alkylsubstituted aminoalcohol hydrochlorides. Twenty-seven compounds showed activity (Increase in Mean Survival Time >6 days); eight compounds were curative (IMST > 60 days). Table includes PubMed IDs for details and syntheses.
TB: BCG/MTB Activity
Published By: Novartis: TB Data Molecules: 283
PI: Srinivasa Rao
Published: 9/15/2010
Aerobic BCG Activty (MIC50)- 274 compounds
Aerobic MTB Activity (MIC50)- 283 compounds
Anaerobic BCG ATP Activity (IC50)- 283 compounds
Anaerobic MTB ATP Activity (IC50)- 283 compounds
Cytotoxicity (CC50)- 223 compoundskeywords: Mycobacterium tuberculosis, Mycobacterium bovis, TB
MALARIA: JHU JHCCL Plasmodium falciparum inhibition
Published By: Johns Hopkins - Sullivan (2008) Molecules: 2693
Published: 6/4/2010
Percent inhibition of 2663 approved drugs at 10 microM
TB, MALARIA: Bayesian predictions for GSK malaria hits
Published By: GSK Data Bayesian Models (Ekins, et al.) Molecules: 13355
PI: Sean Ekins
Published: 5/28/2010
Predictions for the GSK malaria hits (published by Gamo et al., Nature 465: 305-310 (2010)) using the Bayesian models (published by Ekins et al., Mol BioSyst 6: 840-851 (2010)).
Cut offs for activity (220,000 model >0.31, 2,200 model > -1.37 are classed as actives in the whole cell screen).
MALARIA: St. Jude Children's Research Hospital Whole Cell Malaria Dataset
Published By: St. Jude - Malaria/Trypanosome Bioactives Molecules: 1524
PI: Kip Guy
Published: 5/26/2010
Supplemental data for Nature Article published by St. Jude CRH (Guiguemde, W, et al. Chemical genetics of Plasmodium falciparum. Nature 465, 311-315 (20 May 2010)), including 1524 structures tested in a primary screen, with additional data in eight protocols: Bland-Altman analysis, calculated ADMET properties, Phylochemogenetic screen, Sensitivity, Synergy, and Enzyme Assays, as well as a Thermal Melt Analysis.
MALARIA: Novartis GNF-Pf Dataset
Published By: Novartis Malaria Molecules: 5695
Published: 5/21/2010
Plasmodium falciparum strains 3d7 (drug-susceptible) and W2 (chloroquine-, quinine-, pyrimethamine-, cycloguanil-, and sulfadoxine-resistant), obtained from MR4, were tested in an erythrocyte-based infection assay for susceptibility to inhibition of proliferation by selected compounds.
VENDOR: ASINEX Novel Anti-Malaria Screening Set
Published By: ASINEX Molecules: 1
PI: Mark Parisi
Published: 5/20/2010
CONFIDENTIAL DATA SET: 594 Novel compounds from ASINEX. Please see the attached file which elaborates on ASINEX design.
FOR ACCESS: New CDD users- your registration will be passed through an approval process before access to the dataset is granted. Existing CDD users- please contact [email protected]
VENDOR: ASINEX Tres Cantos (GSK) Antimalarial Subset
Published By: ASINEX Molecules: 278
PI: Mark Parisi
Published: 5/20/2010
278 ASINEX active anti Malaria data matching GSK data.
AVAILABLE FOR IMMEDIATE SCREENING.The corresponding dataset is proprietary and owned by ASINEX.For more information, please contact Mark Parisi:Email: [email protected]
Telephone: 1-877-ASINEX1
Fax: 1-336-721-1618
MALARIA: Tres Cantos Antimalarial Set (TCAMS)
Published By: GSK Anti-Malarial Data Molecules: 13471
PI: Javier Gamo
Published: 5/19/2010
Screening of approximately 2 million compounds in GlaxoSmithKline’s screening library identified over 13,500 inhibitors of proliferation of P. falciparum in human erythrocytes. The work was carried out at Tres Cantos Medicine Development Campus, GlaxoSmithKline, Severa Ochoa 2, 28760 Tres Cantos, Spain.
TB: Sacchettini et. al. review - additional antituberculosis agents
Published By: PK Molecules: 18
Published: 2/5/2010
Non-approved antituberculosis agents from Figure 1 in Sacchettini J.C., Rubin E.J. and Freundlich J.S. Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis, Nature Reviews Microbiology, 6, 41-52, (2008).
TB: Tuberculosis Small Molecule Patent Data
Published By: TB Patent Data Molecules: 20775
PI: Collaborative Drug Discovery
Published: 1/27/2010
Structures and patent information regarding tuberculosis research from the US Patent and Trademark Office, European Patent Office, and World Intellectual Property Organization.
TB: Makarov et al., NM4TB consortia
Published By: CDD - Sean Ekins Molecules: 32
PI: Sean Ekins
Published: 1/21/2010
Structure activity relationship data for 1,3-benzothiazin-4-ones (BTZ). Data obtained from the paper "Benzothiazinones Kill Mycobacterium tuberculosis by Blocking Arabinan Synthesis" published in Science by Makarov et al., 2009 and colleagues at the NM4TB consortia (PMID: 19299584).
VENDOR: TimTec Diversity Set
Published By: TimTec Molecules: 9998
PI: Vendor
Published: 1/5/2010
Screening library of 10,000 diverse drug like compounds
VENDOR: TimTec OGT-Inhibitors Analogs SET
Published By: TimTec Molecules: 334
PI: Vendor
Published: 1/5/2010
O-GlcNAc Transferase Inhibitors Analogs SET
VENDOR: TimTec ActiTarg-K, Kinase Modulators
Published By: TimTec Molecules: 6212
PI: Vendor
Published: 1/5/2010
ActiTarg-K, counts over 6,000 compounds providing a high value screening library of drug-like molecules for identifying synthesis direction for new protein kinase inhibitors
VENDOR: TimTec Natural Product Derivatives Library
Published By: TimTec Molecules: 3001
PI: Vendor
Published: 1/5/2010
NDL-3000 Natural Derivatives from TimTec
VENDOR: TimTec Natural Product Library
Published By: TimTec Molecules: 479
PI: Vendor
Published: 1/5/2010
NPL Pure Natural Products from TimTec
VENDOR: Screening Library
Published By: AsisChem Molecules: 43121
Published: 10/26/2009
A collection of over 40,000 drug-like, small molecule compounds available for your custom selection. All compounds are in stock up to 25mg.
VENDOR: Building Blocks
Published By: AsisChem Molecules: 176
Published: 10/26/2009
A collection of compounds useful in drug discovery. All compounds if not in stock are available within a few weeks for amounts up to 10 grams.
TB: TAACF - NIAID CB2 Library
Published By: Southern Research Institute Molecules: 102634
PI: Robert Goldman
Published: 9/30/2009
Results of screening a commercial (ChemBridge) compound library for the ability to inhibit the growth of M. tuberculosis strain H37Rv. See PMID: 19758845
TB: EthR inhibitors (Willand et al.)
Published By: CDD - Sean Ekins Molecules: 5
PI: Sean Ekins
Published: 9/28/2009
Drug-like inhibitors of the transcriptional repressor EthR. Molecules and data from Willand et al Nature Medicine 15: 537-544 (2009) PMID: 19412174
VENDOR, ADME: Benchmark Data from a Set of Structurally Diverse Commercial Drugs.
Published By: NM4TB: Karlen Group Site Molecules: 24
PI: Anders Karlen
Published: 6/11/2009
A multivariate analysis of drugs on the Swedish market was the basis for the selection of a small, physicochemically diverse set of 24 drug compounds. Factors such as structural diversity, commercial availability, price, and a suitable analytical technique for quantification were considered in the selection. Lipophilicity, pKa, solubility, and permeability across human Caco-2 cell monolayers were measured for the compiled data set. We anticipate that this data set can serve as a benchmark set for validation of new experimental techniques or in silico models. It can also be used as a diverse starting data set for the development of new computational models.
Data taken from:
Presentation of a structurally diverse and commercially available drug data set for correlation and benchmarking studies.
Sköld C, Winiwarter S, Wernevik J, Bergström F, Engström L, Allen R, Box K, Comer J, Mole J, Hallberg A, Lennernäs H, Lundstedt T, Ungell AL, Karlén A.
J Med Chem. 2006 Nov 16;49(23):6660-71.
TB: Absorption Data from Published Literature
Published By: CDD: TB Curated Literature Molecules: 24
Published: 5/28/2009
TB Absorption Data from reference article
Inhibition of siderophore biosynthesis by 2-triazole substituted analogues of 5'-O-[N-(salicyl)sulfamoyl]adenosine: antibacterial nucleosides effective against Mycobacterium tuberculosis.
Gupte, A.; Boshoff, H. I.; Wilson, D. J.; Neres, J.; Labello, N. P.; Somu, R. V.; Xing, C.; Barry, C. E.; Aldrich, C. C.
J Med Chem (2008) Vol 51, No 23, pp 7495-7507Permeability data.
TB: Pharmacokinetic Data from Published Literature
Published By: CDD: TB Curated Literature Molecules: 28
Published: 5/28/2009
TB Pharmacokinetic Data from Published Literature sources. SAR data for 28 unique, as well as common compounds.
Data includes PubMed citations, targets, cells and organisms tested, bioavailability, Vm, Vd, Cmax, etc.
TB: Toxicity Data from Published Literature
Published By: CDD: TB Curated Literature Molecules: 638
Published: 5/28/2009
TB Toxicity Data from Published Literature sources. SAR data for 638 unique, as well as common compounds from PubMed references.
Data includes PubMed citations, targets, cells and organisms testes, cell viability, LD50, CC50, MNTD, etc.
TB: Efficacy Data from Published Literature
Published By: CDD: TB Curated Literature Molecules: 6768
Published: 5/28/2009
TB Efficacy Data from Published Literature sources. SAR data for 6771 unique, as well as common compounds from over 300 PubMed references.
Data includes PubMed citations, targets, cells and organisms testes, MIC, % Inhibition, EC50-EC100, IC50, etc.
TB: MLSMR
Published By: Southern Research Institute Molecules: 214507
PI: Robert Goldman
Published: 5/8/2009
A diverse collection of over 200,000 compounds collected by the Molecular Libraries Small Molecule Repository (MLSMR) were made available to the Southern Research Molecular Libraries Screening Center in Spring 2008 for primary testing against Mtb H37Rv. The most active compounds from this primary screen were selected and tested at 10 concentrations in both a dose response assay against H37Rv as well as a cytotoxicity counterscreen using vero cells.
MALARIA: Johns Hopkins Clinical Compound Library
Published By: Johns Hopkins - Sullivan (2008) Molecules: 1878
Published: 4/28/2009
Drugs were screened at a concentration of 10 μM. Synchronized ring stage parasites from chloroquine-sensitive 3D7 or multidrug resistant Dd2 were cultured in RPMI 1640 medium with 10% human serum and incubated for either 48 or 96 h in the presence of drug and [3H]-hypoxanthine. A 96 well plate with 0.2 mL of culture material per well at 0.2% parasitemia and 2-4% hematocrit, gives a radioactive incorporation signal of approximately 10,000 cpm at 48 h and 20,000 cpm at 96 h with background counts less than 500 cpm. Screening experiments were performed in duplicate and percent inhibition is reported as the average of two experiments.
TB: Literature Review
Published By: TB Literature Data Molecules: 49
PI: Ballel, et al.
Published: 4/17/2009
Tuberculosis SAR data compiled in a survey of agents active against M. tuberculosis, including those with both known and unknown modes of action (Ballel, et al. “New Small-Molecule Synthetic Antimycobacterials” in Antimicrobial agents and chemotherapy, June 2005). Updated 4/17 with TubercuList/TBDB/other target links and improved references.
TB: Sacchettini et al., review
Published By: CDD - Sean Ekins Molecules: 14
PI: Sean Ekins
Published: 2/18/2009
First and second line antituberculosis agents from Tables 1 and 2 in Sacchettini J.C., Rubin E.J. and Freundlich J.S. Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis, Nature Reviews Microbiology, 6, 41-52, (2008).
VENDOR: IUPUI - Distributed Drug Discovery (D3) Public Data
Published By: IUPUI - D3 Enum 73K N-AcylAA-OH, -OMe, -NH2 Molecules: 48818
PI: M. J. O'Donnell and W. L. Scott
Published: 1/1/2009
An open-access virtual catalog of acylated unnatural amino acids and their methyl esters. We encourage our colleagues to communicate with us concerning interest in the Distributed Drug Discovery project and synthetic methodology, which are described in a series of three papers in the Journal of Combinatorial Chemistry (in press).
VENDOR: ASINEX Building Blocks
Published By: ASINEX Molecules: 6745
PI: Mark Parisi
Published: 12/23/2008
Drug like Building Blocks, if you are considering a lead optimization program, our Building Blocks may prove to be exactly what you are looking for.
PARASITES: scents
Published By: CDD - Sean Ekins Molecules: 228
PI: Sean Ekins
Published: 12/21/2008
Molecule and structure name data for scents from a book by Roman Kaiser, "meaningful scents around the world" published by Wiley-VCH in 2006. Molecule number relates to their numbering in the book.
TOX: toxcast
Published By: CDD - Sean Ekins Molecules: 306
PI: Sean Ekins
Published: 12/18/2008
EPA toxcast library of compounds (mostly pesticides) available at http://www.epa.gov/ncct/dsstox/DataFiles.html
http://www.epa.gov/ncct/toxcast/
FDA APPROVED, TOX: Maximum recommended daily dose
Published By: CDD - Sean Ekins Molecules: 1215
PI: Sean Ekins
Published: 12/10/2008
An FDA database which contains maximum recommended daily dose values for over 1200 pharmaceuticals. The dataset represents some of the molecules used in the following publication Matthews, E.J., et al., Current Drug Discovery Technologies, 1(1): 61-76. (2004)
VENDOR: Ayurvedic Traditions vis-a-vis Current Healthcare & Wellness Needs
Published By: Falguni Dasgupta: Personal Data Compilation Molecules: 37
PI: Falguni Dasgupta
Published: 10/30/2008
Traditional use of Indian medicinal plants and their extracts is discussed with reference to modern perspectives with the objective of finding common grounds, re-evaluation of claims and creating opportunities in Healthcare and Wellness in conformity with regulatory requirements as well as finding New Drug "Leads."
PARASITES: Sandler-UCSF Celera Cysteine Protease Inhibitor Library
Published By: McKerrow Group Molecules: 1860
PI: Jim McKerrow
Published: 10/23/2008
In vitro T. cruzi and T. brucei parasite and specific enzyme screens.
FDA APPROVED: Approved Drugs
Published By: Johns Hopkins Clinical Compound Library Molecules: 2815
PI: David Sullivan
Published: 10/16/2008
FDA approved drugs with defined molecular structure including 763 molecules from the Physicians’ Desk Reference, 780 from DrugBank, 1151 in the Orange Book 2007, and 1007 from Dr. Chris Lipinski’s FDA list
VENDOR: ASINEX GPCR Focused Library
Published By: ASINEX Molecules: 3502
PI: Mark Parisi
Published: 10/2/2008
High Quality exceptionally drug like GPCR oriented set available at a discounted rate to the CDD community. This library incorporates our medicinal chemistry expertise and our ability to identify privileged fragments from literature and assemble them in an unprecedented way.
GPCR: PDSP Ki Database
Published By: PDSP Ki Database Molecules: 20026
PI: Bryan Roth
Published: 9/16/2008
Over 47,000 Ki values against 699 GPCR targets from the NIMH Psychoactive Drug Screening Program (PDSP) Database
VENDOR: ASINEX Synergy Libraries
Published By: ASINEX Molecules: 25008
PI: Mark Parisi
Published: 4/26/2008
ASINEX has developed a new high diversity library rich in drug like pharmacophore fragments. The design of the library is based on two forms of Synergy. The first is the inter-relationship between diverse and targeted oriented techniques, and the second involves the convergence of multi-step key intermediates (6-9 steps) in order to create sophisticated compounds. See the PDF below for more details.
TOX: Structures with Known Toxicity Profiles's Public Data
Published By: Structures with Known Toxicity Profiles Molecules: 135
PI: Sean Ekins, PhD
Published: 3/28/2008
Tissue specific toxicity profiles of known compounds with references
PROMISCUOUS INHIBITORS: Shoichet published promiscuous inhibitors
Published By: Shoichet published promiscuous inhibitors Molecules: 111
PI: Brian Shoichet
Published: 3/26/2008
Aggregates creating "false positives" by self-association of organic molecules in aqueous solutions
TOX: UC Davis - Hammock's Public Data
Published By: UC Davis - Hammock Molecules: 714
PI: Bruce Hammock
Published: 3/17/2008
Inhibitors of soluble epoxide hydrolases (sEH) - these enzymes have 3 main functions: detoxification, catabolism and regulation of signaling molecules.
MALARIA, TRYPANOSOME: St. Jude Public Data
Published By: St. Jude - Malaria/Trypanosome Bioactives Molecules: 2426
PI: Kip Guy
Published: 3/5/2008
Open access results from Kip Guy’s laboratory at St. Jude Children’s Research Hospital including HTS of bioactives against malaria and T. brucei
MALARIA: Drexel Public Data
Published By: Drexel University Molecules: 195
PI: Jean-Claude Bradley
Published: 3/2/2008
Results from an ongoing open data collaboration between
Drexel (Ugi-4CC products) and UCSF (antimalarial screening). This data set represents an example of how researchers can choose to publish selected results openly. (By default, in contrast, all groups are private.)
MALARIA: U.S. Army Survey
Published By: U.S. Army Malaria Literature Survey Molecules: 12318
Published: 2/29/2008
An extensive collection of antimalarial drug animal SAR data, including chemical structures, bioactivity data, pharmacological data, and toxicity data (Published originally by the U.S. Army in 1946 as “A Survey of Malaria Drugs”)
MALARIA: PlasmoDB
Published By: UPenn - Malaria Literature Data Molecules: 120
PI: David Roos
Published: 2/19/2008
PlasmoDB of malaria inhibitors compiled from the literature, including chemical structure, PlasmoDB Gene Identifier, Target Gene Name, and references against P. falciparum, P. vivax, P. berghei, P. yoelii, P. chabaudi, P. vinckei petteri
MALARIA: Natural Products (NPPDB)
Published By: National Center for Natural Products Research Molecules: 426
PI: Babu Tekwani
Published: 2/15/2008
Antimalarial database of flavone natural products, including antimalarial and cytotoxicity data (University of Mississippi, National Center for Natural Products Research)
TB: TAACF Assay Results
Published By: TB Early Phase Drug Discovery Program Molecules: 812
PI: Bernard Munos
Published: 2/12/2008
Antibacterial activity of a publicly available library of 812 compounds against Mycobacterium tuberculosis (H37Rv) in Alamar Blue whole cell assay
FDA APPROVED: Orphan Drugs
Published By: Known drugs Molecules: 1721
PI: Christopher Lipinski
Published: 10/26/2007
FDA approved drugs with designated indications, sponsor name and chemical structures (when available)