Abstract
Shape is a very important molecular feature for describing ligand molecules interacting with receptor, and other various complex chemical and biological processes. During the last years, there is a strong interest in developing several molecular shape descriptors. In this chapter we present our attempts for deriving van der Waals (vdW) shape molecular descriptors from two size molecular descriptors – the molecular vdW volume (VW) and the molecular vdW surface (SW). The ovality Θ iD , i = 1,2,3 descriptors measure the deviation of the shape of a molecule from a spherical form in one-, two-, and three dimensions, respectively, whilst the {δ,G} molecular shape parameters take into consideration the cylindrical shape of a molecule or substituent. The application of these molecular descriptors in the study of the toxicity of a series of aliphatic amines on the protozoan ciliate Tetrahymena pyriformis (Θ iD ) and for the correlation of rate constants of bimolecular nucleophilic substitution, acid-catalyzed hydrolysis of esters and esterification reactions (δ) is also reported in this chapter. The MTD (minimal topologic difference) method allows a receptor site mapping in the frame of a series of bioactive compounds. The MVD (minimal volume difference) method is an improved variant of the MTD method, which takes into account the 3D extension of a molecule. These methods are described here in some detail. The results obtained in the study of anti-carcinogenic activity of some retinoids and in the inhibition of carbonic-anhydrase (CA) by a series of sulfonamides are also presented in this chapter.
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References
Ballester PJ, Richards WG (2007) J Comput Chem 28:1711–1723
Bodor N, Gabany Z, Wong CK (1989) J Am Chem Soc 111:3783–3786
Bodor N, Buchwald P, Huang M-J (1998) SAR QSAR Environ Res 8:41–92
Bondi AJ (1964) J Phys Chem 68:441–451
Charton M (1975a) J Am Chem Soc 97:1552–1556
Charton M (1975b) J Am Chem Soc 97:3694–3697
Chiriac A, Ciubotariu D, Simon Z (1996) Quantitative Structure – Activity Relationship (QSAR) The MTD method. Mirton, Timisoara
Ciubotariu D (1987) Structure-reactivity relationships in the class of carbonic derivatives, Ph.D. thesis, Polytechnical Institute of Bucharest, Romania
Ciubotariu D, Holban Ş, Moţoc I (1975) Fac St Nat Ser Chim 3:1–8
Ciubotariu D, Holban S, Mihalas I, Simon Z, Chiriac A (1983) Fac St Nat Ser Chim 3:1–19
Ciubotariu D, Deretey E, Medeleanu M, Gogonea V, Iorga I (1990) Chem Bull PIT 35:83–98
Ciubotariu D, Gogonea V, Iorga I, Deretey E, Medeleanu M, Mureşan S, Bologa C (1993) Chem Bull Tech Timişoara 38:63–75
Ciubotariu D, Mureşan S, Gogonea V, Medeleanu M, Dragoş D (1996) In: Chiriac A, Ciubotariu D, Simon Z (eds) Quantitative Structure-Activity Relationship (QSAR). The MTD method. Mirton, Timişoara, pp 40–138
Ciubotariu D, Gogonea V, Medeleanu M (2001a) In: Diudea MV (ed) QSPR/QSAR studies by molecular descriptors. NOVA Science, Huntington, pp 281–362
Ciubotariu D, Grozav A, Gogonea V, Ciubotariu C, Medeleanu M, Dragos D, Pasere M, Simon Z (2001b) Match 44:65–92
Ciubotariu C, Medeleanu M, Ciubotariu D (2006a) Chem Bull “Politehnica” Univ Timisoara 51:13–16
Ciubotariu D, Vlaia V, Olariu T, Ciubotariu C, Medeleanu M, Dragos D, Ursica L (2006b) Generalized topological descriptors based on reciprocal distance matrix for development of toxicological QSARs, 12th International workshop quantitative structure-activity relationship environmental toxicology, 8–12 May, Lyon, p 89
Ciubotariu D, Vlaia V, Olariu T, Ciubotariu C, Medeleanu M, Ursica L, Dragos D (2006c) Molecular van der Waals descriptors for quantitative treatment of toxicological effects. 12th International workshop quantitative structure-activity relationship environmental toxicology, 8–12 May, Lyon, p 90
Cohen C (1979) Beyond the 2-D chemical structure. In: Computer assisted drug design, Olson EC, Christoffersen RE (eds), ACS Symposium Series, vol 112, Washington DC, p 371–382
Connolly ML (1985) J Am Chem Soc 107:1118
Cramer RD, Patterson DE, Bunce JD (1988) J Am Chem Soc 110(18):5959–5967
Dawson MJ, Hobbs PD, Chan RL, Chao W, Fung VA (1981) J Med Chem 24:583–592
Dawson MJ, Hobbs PD, Derdzinski K, Chan RL, Gruber J, Chao W, Smith S, Thies RW, Schiff LJ (1984) J Med Chem 27:1516–1531
Dawson MI, Chao W, Hobbs PD, Delair T (1990) In: Dawson MI, Okamura WH (eds) Chemistry and biology of synthetic retinoids. CRC Press, Boca Raton, pp 385–466
Demidovich BP, Maron IA (1987) Computational mathematics. MIR Publishers, Moscow, pp 649–656
Edvinsson T, Arteca GA, Elvingson C (2003) J Chem Inf Comput Sci 43:126–133
Gavezotti A (1983) J Am Chem Soc 105(16):5220–5225
Gogonea V (1996) An approach to solvent effect modelling by the combined scaled-particle theory and dielectric continuum-medium method, Ph.D. thesis, Toyohashi University of Technology, Japan
Gogonea V, Motsenigos A, Ciubotariu D, Deretey E, Chiriac A, Simon Z (1981) Molecular mechanics and molecular shape descriptors. 2. Comparative treatment of four methods for molecular surface calculation, Preprint, University of Timisoara, Ser. Chimie. 1–12
Gogonea V, Ciubotariu D, Deretey E, Popescu M, Iorga I, Medeleanu M (1991) Rev Roum Chim 36:465–471
Golbraikh A, Tropsha A (2002) J Comput Aided Mol Des 16:357–369
HyperChem version 7.0 (2002), HyperCube Inc., Gainesville
Kortagere S, Krasowski MD, Ekins S (2009) Trends Pharmacol Sci 30:138–147
Lee DJ, Lee TD (1982) Statistics and computer methods in BASIC. Van Nostrand Reinhold, New York, p 15
Mangelsdorf DJ, Umesono K, Evans RM (1994) In: Sporn MB, Roberts AB, Goodman DS (eds) The retinoids, biology, chemistry, and medicine. Raven, New York, pp 319–349
Menziani MC, De Benedetti PG (1992) Struct Chem 3:215–219
Meyer AY (1985) J Chem Soc Perkin Trans II:1161–1169
Mezey PG (1993) Shape in chemistry. An introduction to molecular shape and topology. VCH Publishers, New York
Motoc I (1983) In: Charton M, Motoc I (eds) Steric effects in drug design. Springer, Berlin, pp 93–106
Moţoc I, Holban S, Ciubotariu D, Simon Z (1975) Fac St Nat Ser Chim 16:1–8
Muresan S, Bologa C, Medeleanu M, Gogonea V, Dragos D, Ciubotariu D (1994) Chem Bull Tech Univ Timişoara 39:23–33
Mureşan S, Ciubotariu D, Simon Z (1993) unpublished data
Niculescu-Duvaz I, Ciubotariu D, Simon Z, Voiculetz N (1991) In: Voiculetz N, Balaban AT, Niculescu-Duvăz I, Simon Z (eds) Modeling of cancer genesis and prevention. CRC Press, Boca Raton, pp 157–214
Niculescu–Duvăz I, Simon Z, Voiculetz N (1990) In: Dawson MI, & Okamura WH (eds) Chemistry and biology of synthetic retinoids. CRC Press, Boca Raton, pp 575–606
Pearlmann RS (1983) SAREA: van der Waals (and accessible) surface area of molecules, program QCPE No. 413
Purvis GD (2008) J Comput Aided Mol Des 22:461–468
Sherman MI (1986) In: Dawson P, Nakamura M (eds) Retinoids and cell differentiation. CRC Press, Boca Raton, chapter 8
Simon Z, Bădilescu I, Chiriac A, Ciubotariu D, Szabadai Z (1978) In: Francke R, Oehme P (eds) Quantitative structure-activity analysis. Akademie Verlag, Berlin, pp 161–167
Simon Z, Chiriac A, Holban S, Ciubotariu D, Mihalas GI (1984) Minimum steric difference. The MTD method for QSAR studies. Research Studies Press, Letchworth/New York
Sporn MB, Roberts AB, si Goodman DS (1994) The retinoids. biology, chemistry, and medicine. Raven Press, New York, pp 319–349
Todeschini R, Consonni V (2000) Handbook of molecular descriptors. Wiley-VCH, New York
Todeschini R, Gramatica P (1997) Quant Struct Act Relat 16:113–119
Vlaia V (2010) Contributions to the toxicity study of substances by means of quantitative structure – activity relationships, PhD thesis, Romanian Academy
Vlaia V, Olariu T, Urşica L, Ciubotariu C, Medeleanu M, Ciubotariu D (2005) Farmacia 6:89–101
Vlaia V, Olariu T, Ciubotariu C, Medeleanu M, Vlaia L, Ciubotariu D (2009) Revista de Chimie (Bucureşti) 60(12):1357–1361
Vrânceanu Gh, Hangan Th, Teleman C (1967) Geometrie elementară din punct de vedere modern. Ed. Tehnică, Bucureşti, pp 56–78
Wadell H (1935) J Geol 43:250–280
Wilson JA, Bender A, Kaya T, Clemons P (2009) J Chem Inf Model 49:2231–2241
Zauhar RJ, Moyna G, Tian LF, Li ZJ, Welsh WJ (2003) J Med Chem 46:5674–5690
Zyrianov Y (2005) J Chem Inf Model 45:657–672
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Ciubotariu, D., Vlaia, V., Ciubotariu, C., Olariu, T., Medeleanu, M. (2011). Molecular Shape Descriptors: Applications to Structure-Activity Studies. In: Putz, M. (eds) Carbon Bonding and Structures. Carbon Materials: Chemistry and Physics, vol 5. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1733-6_15
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