Role of mathematical chemodescriptors and proteomics-based biodescriptors in drug discovery

Drug Development Research

Volumn 72, Issue 2, 2011, Pages 225-233

  Basak, Subhash C ^a  

^a UNIVERSITY OF MINNESOTA DULUTH   (United States)

Author keywords

biodescriptor; chirality descriptor; differential QSAR; hierarchical QSAR; mathematical chemodescriptor

Indexed keywords

ARTICLE; CALCULATION; CHEMICAL STRUCTURE; CHIRALITY; COMPUTER MODEL; COMPUTER PREDICTION; DATA BASE; DRUG ACTIVITY; DRUG DESIGN; DRUG SCREENING; MATHEMATICAL ANALYSIS; PHARMACOPHORE; PROTEOMICS; QUANTITATIVE STRUCTURE ACTIVITY RELATION; TOXICOLOGY;

EID: 79953869361     PISSN: 02724391     EISSN: 10982299     Source Type: Journal    
DOI: 10.1002/ddr.20428     Document Type: Article

References (64)

1. Adams C, Brantner V,. 2006. Estimating the cost of new drug development: is it really 802 million dollars? Health Aff (Millwood) 25: 420-428. (Pubitemid 43529550)
2. Basak SC,. 1999. Information theoretic indices of neighborhood complexity and their applications. In:, Devillers J, Balaban AT, editors. Topological indices and related descriptors in QSAR and QSPR. Amsterdam, The Netherlands: Gordon & Breach. p 563-593.
3. Basak SC, Gute BD,. 2008. Mathematical descriptors of proteomics maps: background and applications. Curr Opin Drug Discov Devel 11: 320-326. (Pubitemid 351572441)
4. Basak SC, Mills D,. 2008. Mathematical chemistry and chemobioinformatics: a holistic view involving optimism, intractability, and pragmatism. In: Graovac A, Gutman I, Vukicevic, editors. Mathematical Methods and Modelling for Students of Chemistry and Biology. Zagreb, Croatia: University of Dubrovnik, University of Split, and Institute Ruder Boskovic. p 211-242.
5. Basak SC, Mills D,. 2009. Predicting vapor pressure of chemicals from structure: a comparison of graph theoretic versus quantum chemical descriptors. SAR QSAR Environ Res 20: 119-132.
6. Basak SC, Mills D,. 2010. Quantitative structure-activity relationships for cycloguanil analogs as PfDHFR inhibitors using mathematical molecular descriptors SAR QSAR. Environ Res 21: 215-229.
7. Basak SC, Magnuson VR, Niemi GJ, Regal RR,. 1988. Determining structural similarity of chemicals using graph-theoretic indices. Discrete Appl Math 19: 17-44. (Pubitemid 18605504)
8. Basak SC, Niemi GJ, Veith GD,. 1990. Optimal characterization of structure for prediction of properties. J Math Chem 4: 185-205.
9. Basak SC, Niemi GJ, Veith GD,. 1991. Predicting properties of molecules using graph invariants. J Math Chem 7: 243-272.
10. Basak SC, Gute BD, Drewes LR,. 1996. Predicting blood-brain transport of drugs: a computational approach. Pharm Res 13: 775-778. (Pubitemid 26156228)
11. Basak SC, Mills D, Balaban AT, Gute BD,. 2001. Prediction of mutagenicity of aromatic and heteroaromatic amines from structure: a hierarchical QSAR approach. J Chem Inf Comput Sci 41: 671-678.
12. Basak SC, Mills D, Hawkins DM, El-Masri H,. 2003. Prediction of human blood: air partition coefficient: a comparison of structure-based and property-based methods. Risk Anal 23: 1173-1184. (Pubitemid 38045097)
13. Basak SC, Mills D, Hawkins DM,. 2008. Predicting allergic contact dermatitis: a hierarchical structure-activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors. J Comput Aided Mol Design 22: 339-343.
14. Basak SC, Mills D, Natarajan R, Gute BD,. 2009. Predicting chemical reactivity and bioactivity from structure: a mathematical-cum-computational approach. In:, Chattaraj PK, editor. Chemical reactivity theory: a density functional view. Boca Raton, FL: CRC Press. p 479-502.
15. Basak SC, Mills D, Hawkins DM, Bhattacharjee AK,. 2010a. Quantitative structure-activity relationship studies of antimalarial compounds from their calculated mathematical descriptors. SAR QSAR. Environ Res 21: 103-125.
16. Basak SC, Mills D, Garg R, Bhattarai B,. 2010b. A QSAR study of HIV protease inhibitors using theoretical descriptors. Curr Computer Aided Drug Design (in press).
17. Basak SC, Mills D, Gute BD, Balaban AT, Basak K, Grunwald GD,. 2010c. Use of mathematical structural invariants in analyzing combinatorial libraries: a case study with psoralen derivatives. Curr Computer Aided Drug Design (in press).
18. Basak SC, Mills D, Hawkins DM,. 2011. Characterization of dihydrofolate reductases from multiple strains of Plasmodium falciparum using mathematical descriptors of their inhibitors. Chem Biodiversity (in press).
19. Bleicher KH, Böhm HJ, Müller K, Alanine AI,. 2003. Hit and lead generation: beyond high throughput screening. Nat Rev Drug Discov 2: 369-378. (Pubitemid 37361707)
20. Bunge M,. 1973. Method, model and matter. Dordrecht, The Netherlands: Reidel.
21. Cahn RS, Ingold CK, Prelog V,. 1956. The specification of asymmetric configuration in organic chemistry. Experientia 12: 81-124.
22. Crum-Brown A, Fraser TR,. 1868. On the connection between chemical constitution and physiological action. Part 1. On the physiological action of the ammonium bases, derived from Strychia, Brucia, Thebaia, Codeia, Morphia and Nicotia. Trans R Soc Edinb 25: 151-203.
23. DiMasi J, Hansen R, Grabowski H,. 2003. The price of innovation: new estimates of drug development costs. J Health Econ 22: 151-185. (Pubitemid 36279392)
24. Domon B, Brode S,. 2004. Implications of new proteomics strategies for biology and medicine. J Proteome Res 3: 253-260. (Pubitemid 38500992)
25. Filip PA, Balaban TS, Balaban AT,. 1987. A new approach for devising local graph invariants: derived topological indices with low degeneracy and good correlation ability. J Math Chem 1: 61-83.
26. Ghosh A, Nandy A, Nandy P, Gute BD, Basak SC,. 2009. Computational study of dispersion and extent of mutated and duplicated sequences of the H5N1 influenza neuraminidase over the period 1997-2008. J Chem Inf Model 49: 2627-2638.
27. Gund P,. 1977. Three dimensional pharmacophoric pattern searches. In:, Hahn FE, editor. Progress in molecular and subcellular biology. vol. 5. Berlin: Springer-Verlag. p 117-143.
28. Gurwitz D,. 2010. Malaria drugs: clues from malaria resistance genetics. Drug Dev Res 71: 1-3.
29. Hammett LP,. 1940. Physical organic chemistry. New York: McGraw-Hill.
30. Hansch C, Fujita T,. 1964. ρ-σ-π analysis. A method for the correlation of biological activity and chemical structure. J Am Chem Soc 86: 1616-1626.
31. Harary F,. 1969. Graph theory. Reading, MA: Addison-Wesley.
32. Hawkins DM, Basak SC, Shi X,. 2001. QSAR with few compounds and many features. J Chem Inf Comput Sci 41: 663-670.
33. Hawkins DM, Basak SC, Mills D,. 2003. Assessing model fit by cross-validation. J Chem Inf Comput Sci 43: 579-586.
34. Johnson M, Basak SC, Maggiora G,. 1988. A characterization of molecular similarity methods for property prediction. Math Comput Model 11: 630-634.
35. *, α, and β, and some methods for simplifying the generalized solvatochromic equation. J Org Chem 48: 2877-2887.
36. Keseru GM, Makara GM,. 2006. Hit discovery and hit-to-lead approaches. Drug Discov Today 11: 741-748. (Pubitemid 44038630)
37. Kier LB, Hall LH,. 1986. Molecular connectivity in structure-activity analysis. Letchworth, Hertfordshire, UK: Research Studies Press.
38. Kier LB, Hall LH,. 1990. An electrotopological-state index for atoms in molecules. Pharm Res 7: 801-807. (Pubitemid 20332531)
39. Kier LB, Hall LH,. 1999. Molecular structure description. New York: Academic Press. p 13-36.
40. Klun JA, Schmidt WF, Debboun M,. 2001. Stereochemical effects in an insect repellent. J Med Entomol 38: 809-812. (Pubitemid 33620471)
41. Kraker JJ, Hawkins DM, Basak SC, Natarajan R, Mills D,. 2007. Quantitative structure-activity relationship (QSAR) modeling of juvenile hormone activity: comparison of validation procedures. Chemometr Intell Lab Syst 87: 33-42. (Pubitemid 46654409)
42. Langham JJ, Jain AN,. 2008. Accurate and interpretable computational modeling of chemical mutagenicity. J Chem Inf Model 48: 1833-1839.
43. Lombardino JG, Lowe JA,. 2004. The role of the medicinal chemist in drug discovery-then and now. Nat Rev Drug Discov 3: 853-862. (Pubitemid 39405946)
44. Mallick P, Kuster B,. 2010. Proteomics: a pragmatic perspective. Nat Biotechnol 28: 695-709.
45. May M,. 2009. Engineering a new business. Nat Biotechnol 27: 1112-1120.
46. Muregi FW, Ishih A,. 2010. Next-generation antimalarial drugs: hybrid molecules as a new strategy in drug design. Drug Dev Res 71: 20-32.
47. Nandy A, Harle M, Basak SC,. 2006. Mathematical descriptors of DNA sequences: development and application. Arkivoc 9: 211-238. (Pubitemid 44527394)
48. Natarajan R, Basak SC,. 2009. Numerical characterization of molecular chirality of organic compounds. Curr Comp Aided Drug Design 5: 13-22.
49. Natarajan R, Basak SC,. 2011. Numerical descriptors for the characterization of chiral compounds and their applications in modeling biological and toxicological activities. Curr Top Med Chem (in press).
50. Natarajan R, Basak SC, Neumann TS,. 2007. Novel approach for the numerical characterization of molecular chirality. J Chem Inf Model 47: 771-775. (Pubitemid 46973690)
51. OW) using algorithmically- derived variables. Environ Toxicol Chem 11: 891-898.
52. Patwardhan B, Mashelkar RA,. 2009. Traditional medicine-inspired approaches to drug discovery: can Ayurveda show the way forward? Drug Discov Today 14: 804-811.
53. Primas H,. 1981. Chemistry, quantum mechanics and reductionism. Berlin: Springer-Verlag.
54. Randic M,. 1975. Characterization of molecular branching. J Am Chem Soc 97: 6609-6615.
55. Richet MC,. 1893. Note sur le rapport entre la toxicité et les propriétés physiques des corps. CR Soc Biol (Paris) 45: 775-776.
56. Robertson DG, Reily MD, Baker JD,. 2007. Metabonomics in pharmaceutical discovery and development. J Proteome Res 6: 526-539. (Pubitemid 46340156)
57. Santos-Filho OA, Hopfinger AJ, Cherkasov A, de Alencastro RB,. 2009. The receptor-dependent QSAR paradigm: an overview of the current state of the art. Med Chem (Shariqah) 5: 359-366.
58. Sinha DK, Basak SC,. 2006. Editorial, special issue. Proceedings of the Fourth Indo-U.S. Workshop on Mathematical Chemistry, January 8-12, 2005, Pune, Maharashtra, India. J Chem Inf Model 46: 1-1.
59. Taft RW,. 1952. Linear free energy relationships from rates of esterification and hydrolysis of aliphatic and ortho-substituted benzoate esters. J Am Chem Soc 74: 2729-2730.
60. Trinajstic N,. 1983. Chemical graph theory. vols.I, II. Boca Raton, FL: CRC Press.
61. Tulp M, Bohlin L,. 2004. Unconventional natural sources for future drug discovery. Drug Discov Today 9: 450-458. (Pubitemid 38510564)
62. Viswanadhan VN, Mueller GA, Basak SC, Weinstein JN,. 2001. Comparison of a neural net-based QSAR algorithm (PCANN) with hologram- and multiple linear regression-based QSAR approaches: application to 1,4-dihydropyridine-based calcium channel antagonists. J Chem Inf Comput Sci 41: 505-511.
63. Wiener H,. 1947. Structural determination of paraffin boiling points. J Am Chem Soc 69: 17-20.
64. Zhao H,. 2007. Scaffold selection and scaffold hopping in lead generation: a medicinal chemistry perspective. Drug Discov Today 12: 149-155. (Pubitemid 46188408)