NIAID ChemDB

ChemDB HIV, Opportunistic Infection and Tuberculosis Therapeutics Database
Content
Description Small molecules that have been tested against HIV and/or related opportunistic infections
Contact
Research center National Institute of Allergy and Infectious Disease (NIAID)
Release date 1989
Access
Website http://chemdb.niaid.nih.gov/

The ChemDB HIV, Opportunistic Infection and Tuberculosis Therapeutics Database is a publicly available tool developed by the National Institute of Allergy and Infectious Diseases to compile preclinical data on small molecules with potential therapeutic action against HIV/AIDS and related opportunistic infections.[1]

Characteristics and content

Since 1989, the ChemDB has been updated with information extracted from peer-reviewed published literature, conference proceedings and patents.[2] Data are compiled on compound structure, chemical properties, biological activity (e.g. targeted protein, IC50, EC50, Cytotoxicity, TI, Ki, and or MIC), and reference details (e.g. Author, Journal).[3]

The ChemDB web interface supports searching of biological, textual and chemical data using Oracle Text, the Accelrys Direct chemical search engine, and ChemAxon’s Marvin tools.[1] These tools allow web users to search the database by comparing the degree of similarity or flexibility match to chemical structures that have either been uploaded or drawn. Additional Boolean searches can be combined with structure search to include other fields on interest, including target organism or Lipinski score. In addition to the publicly available web interface, whole database downloads can be obtained by the scientific research community.[2] The database is used frequently in peer-reviewed scientific research.[4][5][6][7][8][9][10][11][12][13]

Opportunistic pathogens

Opportunistic pathogens included in this database are:[1]

SIV
FIV
Human Cytomegalovirus (HCMV)
Epstein-Barr virus
Herpes simplex virus 1
Herpes simplex virus 2
Kaposi sarcoma virus
Hepatitis A virus
Hepatitis B virus
Hepatitis C virus
Mycobacterium spp.
Pneumocystis carinni
Cryptococcus spp.
Candida spp.
Aspergillus spp.
Microsporidia
Toxoplasma gondii
Cryptosporidium parvum
Leishmania spp.
Plasmodium spp.

References

  1. 1 2 3 "Division of AIDS Anti-HIV/OI/TB Therapeutics Database". National Institutes of Health, U.S. Department of Health and Human Services. Retrieved 2012-01-24.
  2. 1 2 Rush M, Huffman D, Noble G, Whiting M, Nasr M (August 25–26, 2011). "2011 Meeting on U.S. Govt. Chem. Databases & Open Chemistry". The NIAID ChemDB HIV/AIDS Database.
  3. ↑ "Division of AIDS Anti-HIV/OI/TB Therapeutics Database". User Guide. National Institutes of Health, U.S. Department of Health and Human Services. Retrieved 2012-01-24.
  4. ↑ Hochstein C, Goshorn J, Chang F (2009). "United States National Library of Medicine Drug Information Portal". Med Ref Serv Q. 28 (2). doi:10.1080/02763860902816784. PMC 2760770Freely accessible. PMID 19384716.
  5. ↑ Cheah EL, Heng PW, Chan LW (2010). "Optimization of supercritical fluid extraction and pressurized liquid extraction of active principles from Magnolis officinalis using the Taguchi design". Sep Purif Technol. 71 (3): 293–301. doi:10.1016/j.seppur.2009.12.009.
  6. ↑ Portugal J (2009). "Evaluation of molecular descriptors for antitumor drugs with respect to noncovalent binding to DNA and antiproliferative activity". BMC Pharmacol. 9: 11. doi:10.1186/1471-2210-9-11. PMC 2758867Freely accessible. PMID 19758437.
  7. ↑ Xiong S, Fan J, Kitazato K (2010). "The antiviral protein cyanovirin-N: the current state of its production and applications". Appl Microbiol Biotechnol. 86 (3): 805–12. doi:10.1007/s00253-010-2470-1. PMID 20162270.
  8. ↑ Kremb S, Helfer M, Heller W, Hoffmann D, Wolff H, Kleinschmidt A, Cepok S, Hemmer B, Durner J, Brack-Werner R (2010). "EASY-HIT: HIV full-replication technology for broad discovery of multiple classes of HIV inhibitors". Antimicrob Agents Chemother. 54 (12): 5257–68. doi:10.1128/AAC.00515-10. PMC 2981278Freely accessible. PMID 20876377.
  9. ↑ Serafin K, Mazur P, Bak A, Laine E, Tchertanov L, Mouscadet JF, Polanski J (2011). "Ethyl malonate amides: a diketo acid offspring fragment for HIV integrase inhibition". Bioorg Med Chem. 19 (16): 5000–5. doi:10.1016/j.bmc.2011.06.054. PMID 21767953.
  10. ↑ Durdagi S, Mavromoustakos T, Papdopoulos MG (2008). "3D QSAR CoMFA/CoMSIA, molecular docking and molecular dynamics studies of fullerene-based HIV-1 PR inhibitors". Bioorg Med Chem Lett. 18 (23): 6283–9. doi:10.1016/j.bmcl.2008.09.107. PMID 18951793.
  11. ↑ Prasanna MD, Vondrasek J, Wlodawer A, Bha TN (2005). "Application of InChI to Curate, Index, and Query 3-D Structure". Proteins. 60: 001–004. doi:10.1002/prot.20469. PMID 15861385.
  12. ↑ Sánchez R, Morgado E, Grau R (2005). "A genetic code Boolean structure. I. The meaning of Boolean deduction". Bulletin of Mathematical Biology. 67: 001–014. doi:10.1016/j.bulm.2004.05.005. PMID 15691536.
  13. ↑ Zhang XW (2005). "Generation of predictive pharmacophore model for SARS-coronavirus main proteinase". Eur J Med Chem. 40: 57–62. doi:10.1016/j.ejmech.2004.09.013. PMID 15642409.
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