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Study of Dental Fluorosis in Subjects Related to a Phosphatic Fertilizer

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Study of Dental Fluorosis in Subjects Related to a Phosphatic Fertilizer Indian Journal of Biochemistry & Biophysics Vol. 44, December 2007, pp. 458-469 .Biological activity predictions, crystallographic comparison and hydrogen bonding analysis of cholane derivatives Rajnikant*, Dinesh and Bhavnaish Chand Condensed Matter Physics Group, Post-Graduate Department of Physics, University of Jammu, Jammu Tawi-180006, India Received 13 November 2006; revised 27 July 2007 A total of eighteen molecules of cholane derivatives (I-XVIII) (a series of steroids) have been included to predict their pharmacological effects, specific mechanisms of action, known toxicities, drug-likeness, etc, by using the statistics of multilevel neighbourhoods of atoms (MNA) descriptors for active and inactive fragments. The biological activity spectra for substances have been correlated on SAR base (structure-activity relationships data and knowledge base), which provides the different Pa (possibility of activity) and Pi (possibility of inactivity). Most of the probable activities have been characterized by Pa and Pi values, which depict that all the molecules have high value of teratogen activity. The Lipinski’s thumb rule predicts that all the cholane derivatives have stronger preponderance for “cancer-like-drug” molecules and some of their related analogous have entered in the ANCI (American National Cancer Institute) database. Some selected bond distances and bond angles of interest have been taken into account and deviation of bond distances/bond angles, vis-a-vis the substitutional group and X–H…A intra/intermolecular hydrogen bonds has been discussed in detail. X–H…A intra and intermolecular hydrogen bonds in the molecules have been described with the standard distance and angle cut-off criteria. D–θ and d–θ scatter plots for intra- and intermolecular interactions are presented for better understanding of packing interactions existing among these derivatives. There exists only one C–H…O intramolecular bifurcated hydrogen bond, while high tendency of intermolecular bifurcated hydrogen bonds based on a defined O–H…O has been observed, in which O atom acts as a prototype donor as well as acceptor. The frequency of occurrence of C–H…O hydrogen bonds is predominant (i.e. 85.7%) in intramolecular interactions, whereas in intermolecular interactions, frequency of occurrence for O–H…O interactions is 62.9%. Solvent-solute/solute-solvent interactions have also been investigated to understand more complicated processes that occur for biomolecules in aqueous solutions. The number of hydrogen donors in each derivative is less than 5, except for molecule XVIII and which has 91.3% of drug-likeness, instead of observed range of 96.5-99.3%. Keywords: Cholane, X-ray diffraction, Biological activity, Intra and intermolecular hydrogen bonds, Bifurcated hydrogen bonds, Solvent/solute interaction, Lipinski’s rule The basic cholane molecule contains a carbon skeleton or nucleus consisting of four-ring structure of which three are six-membered cyclohexane rings, one is five-membered cyclopentane ring and a side chain of five carbon atoms located at C17 position of the steroid nucleus. A representative illustration of cholane molecule is presented in Fig. 11. Generally, the C24 compounds (bile acids) are hydroxy derivatives of cholanic acid and they have a 3α- hydroxyl group (with one exception), while other Fig. 1—Basic cholane molecule (C24) with standard atomic numbering scheme hydroxyl groups may be present at C6, C7, C12 and occasionally at other carbon atoms. Bile acids play a mammals, cholic acid and chenodeoxycholic acid are key role in regulation of cholesterol metabolism the principal products. Before excretion into the bile, including synthesis, absorption, esterification, these acids conjugate with either glycine or taurine to excretion and catabolism to bile acids2. They are produce the bile salts3 which enter the small intestine produced in the liver from cholesterol and in most and facilitate lipid absorption4,5. Bile acids are largely reabsorbed from the intestine6,7 and pass back to the _______ liver in the enterohepatic circulation. Bile acid level in *Corresponding author the enterohepatic circulation regulates the rate of bile E-mail: [email protected] 8 Tel/Fax: 0191-2432051 acid synthesis . RAJNIKANT et al.: BIOLOGICAL ACTIVITY PREDICTIONS 459 Deoxycholic acid (DCA) is a bile acid having the conditions. By using a qualitative representation of unusual property of forming canal complexs with a biological activity, it is possible to compare and mix wide variety of organic compounds, including alipha- activity data for obtaining robust quantitative models. tic and aromatic hydrocarbons, fatty acids, alcohols, The crystal structures can be described by descriptors esters, ethers, phenols, azo-dyes, alkaloids, camphor, Multilevel Neighbourhoods of Atoms (MNA)39. MNA methyl-orange, β-carotene and cholesterol9-11. The descriptors are based on a molecular structure sodium salt of DCA can associate with several description according to the valences and partial biological systems as a particular class of histones charges of connected atoms (including hydrogen from chromatin12, phospholipids13, proteins14,15 and atoms). They are generated as a recursively defined sequential polypeptides16. Cholic acid (CA), another sequence: important bile acid has proved particularly useful • Zero-level MNA descriptor for each atom is the as engineering component for supramolecular label A of the atom itself; chemistry17. In the crystalline state, it permits optical • Any next-level MNA descriptor for the atom is the resolution of racemic lactones18 and demonstrates sub-structure notation 19 interecalation phenomena for organic molecules . A(D1D2 Di ), where Di is the previous-level MNA descriptor for ith immediate neighbour of the In view of the relationship of various parent steroid atom A. The neighbor descriptors D D D are hydrocarbons viz., cholestane, cholane, pregnane, 1 2 i arranged in a unique manner, e.g., in lexicographic androstane, estrane, we got interested in the said order. The atom label A may include not only the series of steroids which should essentially have (i) atomic type but also any additional information about some biological activity, (ii) molecular and crystal the atom. Iterative procedure for MNA descriptor structure, (iii) molecular geometry and conforma- generation can be continued to cover the first, second, tional parameters, (iv) non-planar conformations of etc. neighbourhoods of each atom. In this manner, individual ring systems and (v) hydrogen bonding structure of any molecule is represented as a interactions. The work reported in this paper is a part set of MNA descriptors. The MNA descriptors of our on-going research on the steroids20-23. represent various structure property relationships In the present paper, a series of 18 cholane including biological activities40, mutagenecity and derivatives have been undertaken for study from the carcinogenecity41, boiling point39, drug-likeness42, etc. literature available through on-line Cambridge The three-dimensional (3D) coordinate data of all structural database (U.K.). A survey of this database the compounds have been selected as an input for the has been made to ascertain the existence of number of PASS software43 to predict the structure-activity structures reported on the cholane derivatives. We relationship. On the basis of x, y, z coordinates, have considered the structural data of only those molecular structures have been drawn and compounds, whose crystal data have been collected accordingly biological activity predictions have been by using single crystal X-ray diffractometer and a determined on the statistics of MNA descriptors for comparative study has been evolved vis-a-vis each active and inactive fragments. The biological activity other. The chemical structures of molecules I–XVIII spectra for substances have been correlated on SAR are shown in Fig. 2. The chemical name and base (structure-activity relationships data and published references of each molecule are presented knowledge base), which provides different P in Table 124-38. a (possibility of activity) and Pi (possibility of inactivity) values. Based on statistics of MNA Methodology descriptors for active and inactive compounds, two Biological activity predictions probabilities: Pa and Pi⎯probability of the compound Biological activity spectrum provides the rationale being active and inactive respectively, have been for predicting biological activity types for different calculated for each activity. Influence of these compounds. Within this concept, the biological descriptors can be positive or negative (if they are activity is considered as an intrinsic property of the found in compounds with or without particular compound, depending only on its structure. Any activity respectively) or even neutral. The Pa and Pi component of this spectrum of a given compound is values for the molecules (I-XVIII) are given in assumed to be detectable under suitable experimental Table 2. 460 INDIAN J. BIOCHEM. BIOPHYS., VOL. 44, DECEMBER 2007 Fig. 2—Chemical structures of molecules 1–XVIII RAJNIKANT et al.: BIOLOGICAL ACTIVITY PREDICTIONS 461 Table 1—Chemical name, formula and molecular weight of molecules (I–XVIII) Molec Chemical name Chemical formula Molecular Reference ule no. weight (amu) I Complex between 3α, 12α-dihydroxy-5β-cholan- C24H40O4 C2H5OH.H2O 456 24 24-oic acid (DCA), ethanol and water (3:2:1) II 3β-hydroxy-22-(4-methyl-1-pyrrolin-2-yl)-23-dinor- C27H41NO3 427 25 5α-cholane-4, 22-dione
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