Pharmacophores of the Dual Acting α, β-Blockers As Deduced, from Molecular Dynamics Simulations
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J. Biosci., Vol. 21, Number 5, September 1996, pp 599–611. © Printed in India. Pharmacophores of the dual acting α, β-blockers as deduced, from molecular dynamics simulations SHANTARAM KAMATH and EVANS COUTINHO* Bombay College of Pharmacy, Kalina, Santacruz (E), Bombay 400 098, India MS received 12 February 1996; revised 5 June 1996 Abstract. The dual acting α, β-blockers have an important place in the management of hypertension. Molecular dynamics simulations have been carried out on all stereoisomers of seven dual acting α,β-blockers namely adimolol, amosulalol, bucindolol, carvedilol, labetalol, medroxalol and primidolol. Three families of conformations have been identified for the group of compounds. The pharmacophores for α and β-activity have been constructed for two of these families. Keywords. α, β-blockers; pharmacophores; conformation; molecular dynamics. 1. Introduction The sympathetic nervous system is involved in the homeostatic regulation of a wide variety of functions such as heart rate, force of contraction of the heart, vasomotor tone, blood pressure, bronchial airway tone and carbohydrate and fatty acid metabolism (Hoffman and Lefkowitz 1992). The sympathetic nervous system is subdivided into the α and β-subsystems (Hieble et al 1995). The hyperactivity of this system leads to various cardiovascular disturbances, such as hypertension, shock, cardiac failure and arryth- mias, asthma, allergy and anaphylaxis. These conditions can he corrected by drugs that intervene at either the α or β-pathways (Ruffolo et al 1995). Dual acting α, β-receptor antagonists have the advantage that reflex tachycardia associated with antagonism of α-receptors is minimized by concomitant antagonism of β-receptors (Comer et al 1981). A recent approach in drug design, begins with the identification of the pharmaco- phores (the 3D arrangement of binding sites on a drug) for a class of compounds. The pharmacophores are then used in conjuction with 3D searching of databases to retrieve and identify previously unknown compounds that match the pharmacophores. The identified compounds act as leads in the development of highly potent and specific drugs (Vorpagel et al 1994). We have in this study identified the pharmacophores (both α and β) of the dual acting α, β-blockers using all stereoisomer of the seven drugs namely: adimolol (Maj et al 1987), amosulalol (Honda et al 1985), bucindolol (Korolkovas 1988), carvedilol (Cubeddu et al 1977), labetalol (Brogden et al 1978), medroxalol (Elliot et al 1984) and primidolol (Korolkovas 1988) (figure 1). The activity profile of some of these drugs is given in table 1, from which it is noted that a specific activity α or β, is associated with a particular stereoisomer (Cheng et al 1980; Brittain et al 1981, 1982; Gold et al 1982; Honda et al 1986a, b; Doggrel 1987; Nicols et al 1989). The first step in trying to build a pharmacophore, is to identify conformations common to the group of compounds and unique for a particular activity (α or β). This has been approached by molecular dynamics (MD) simulations for all stereoisomers of the seven compounds. *Corresponding author. 599 600 Shantaram Kamath and Evans Coutinho Figure 1. Chemical structures of the seven dual acting α,β-blockers. (A) Adimolol. (B) Amosulalol. (C) Bucindolol. (D) Carvedilol. (E) Labetalol. (F) Medroxalol. (G) Primidolol. In labetalol and medroxalol, the first and second chiral centers are labelled ‘a’ and ‘b’ respectively. 2. Methodology MD calculations were done on a Silicon Graphics IRIS Indigo computer with molecular modeling software from BIOSYM Technologies (USA). Simulations were carried out with Discover (v 2·9) and Insight II (v 2·3) was used for the graphical display. The energy was computed with the CVFF forcefield (Dauber-Osguthorpe et al 1988). A scalar dielectric constant of 1·0 was set for the Coulombic interactions. The bond stretching was expressed by a simple harmonic approximation. Cross-terms which denote coupling between the internal degrees of freedom were not included in the Pharmacophores of the dual acting α, β-blockers 601 Table 1. Relationship between stereoisomer and block- ing activity. +No data available for adimolol, bucindolol and primidolol. For medroxalol the activity of the four stereoisomers has been established, but their absolute configurations have not been determined. energy expression. The calculations were done for the protonated forms of the compounds. For adimolol, amosulalol, bucindolol, carvedilol and primidolol which have one chiral center, both the R and S stereoisomers were studied, while for labetalol and medroxalol which have two chiral centres, the four stereoisomers RR, SS, RS and SR were considered. Thus the calculations were done for a total of 18 molecules. MD simulations were carried out with the following protocol: each molecule was built in a fully extended conformation and minimized by 100 steps of steepest descents to remove any strain present in the starting conformation. The molecule was then ‘heated’ to 1000 K, in steps of 100 K. At each new temperature, a 1 As of equilibration was used. On reaching 1000K, the molecule was equilibrated for sufficient time and the kinetic energy was monitored for convergence to ensure complete equilibration. Dynamics was con- tinued for a further period of 100 ps. Frames from the MD trajectory were stored every 1 ps, to give a total of 100 structures, which were processed later. Newton’s equations of motion were integrated with the Verlet algorithm, using an integration time step of 1·0 fs. During equilibration, the temperature was controlled by direct velocity scaling, while during data collection, a weak coupling to a temperature bath with a time constant of 0.1 ps was used. Each of the 100 stored structures, were ‘cooled’ subsequently to 600 K and 300 K. At each new temperature, the molecule was equilibrated for 3 ps, and dynamics resumed for 2 ps. The final ‘300 K structures’ were energy minimized, initially with 50 steps of steepest descents, followed by 1000 steps of conjugate gradients, at the end of which most structures had a derivative of 0·001 Kcal/mol/Å or lower. An examination of the 100 structures for each molecule suggested that the conforma- tions could be nicely grouped into families using the criteria of distance and plane– plane angles between the two aromatic rings. Such a classification identified three major families for the class of compounds. 3. Results and discussion The first family (I) is characterized by a nearly parallel arrangement of the two aromatic rings. The average plane–plane angle (taken over all 18 molecules) is 17°. The two planes are separated on an average by 42 Å. This family is the lowest in energy compared to the 602 Shantaram Kamath and Evans Coutinho Figures 2. other two families (II and III) and also contains the global minimum structure of each molecule (figure 2). We had reported this conformation as the most stable structure in a previous molecular mechanics study for this class of compounds (Coutinho 1995). In the second family (II), the two aromatic rings are tilted at an average angle of 47° (figure 3). The interplanar distance is 5·4 Å. This family is generally the first local minimum and approximately 3·1 Kcal/mol higher in energy than family I. Pharmacophores of the dual acting α, β-blockers 603 Figure 3. The third family (III) can be described by a perpendicular arrangement of the two aromatic rings (figure 3) and forms the second local minimum in the potential energy hypersurface. The two rings are 6·5 Å apart. This family is on an average, 3·3 Kcal/mol higher than family I. The positions of the first and second local minima 604 Shantaram Kamath and Evans Coutinho Figure 4. Figures 2–4. Chemical structures of families I–III. For the sake of brevity only a single stereoisomer of each drug has been shown. (A) S-adimolol. (B) S-amosulalo. (C) S-bucindolol. (D) R-carvedilol. (E) SS-labetalol. (F) RS-medroxalol. (G) S-primidolol. Broken lines indicate hydrogen bonds. i.e., families II and III, are interchanged for S-adimolol, all four stereoisomers of labetalol and RS and SR stereoisomers of medroxalol. For these molecules family III is more stable than family II. The conformational details for families I, II and III are listed in table 2. Pharmacophores of the dual acting α, β-blockers 605 606 Shantaram Kamath and Evans Coutinho Figure 5. 3.1 Construction of the pharmacophores The pharmacophores of families I and III were then determined. Four descriptor centers namely the centroids of each aromatic ring (a1 and a2), the oxygen atom of the alcoholic OH group (o) and nitrogen atom of the NH2 group (n) were used for the description of the binding of these molecules to the receptor (4-point binding). The pharmacophore for α-activity in family I was constructed by first superimposing structures of S-amosulalol (Doggrel 1987; Honda et al 1985, 1986a, b), S and R carvedilol (Nicols et al 1989) and SS- and SR-labetalol (Brittain et al 1981, 1982; Gold et al 1982) using the four descriptors of binding mentioned above and is shown in figure 5a. Then, for each binding point say a1, a centroid (A1) was computed for the distribution of the a1 points in the superimposed structures. This was likewise repeated for the remaining three binding sites a2, o and n, from which were derived, the three Pharmacophores of the dual acting α, β-blockers 607 Figure 6. Figures 5 and 6. Construction of the α-pharmacophore (a) and the β-pharmacophore (b) of families I (5) and III (6) (see text). On the right are the distances between the pharmaeophore centers A1, A2, O and N. Distances are in Å. centroids A2, O and N respectively. These four points A1, A2, O and N along with their specific inter-distances define the α-pharmacophore and is shown alongside in figure 5a.