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Prediction of antibacterial activity of some diarylheptanoids isolated from Garuga species by molecular mechanics and molecular orbital calculations
Journal of Molecular Structure (Theochem), 286 (1993) 259-265 0166-1280/93/$06.00 0 1993 - Elsevier Science Publishers B.V. All rights reserved
259
Prediction of antibacterial activity of some diarylheptanoids isolated from Garuga species by molecular mechanics and molecular orbital calculations Gyijrgy Mikl6s Keserii*,
Mihily
N6grBdi
Research Group for Alkaloid Chemistry of the Hungarian Academy of Sciences, P.O.B. 91, H-1521 Budapest, Hungary
(Received 1 February 1993; accepted 6 February 1993) Abstract Favoured conformations for garuganins I-III and garugamblins 1 and 2, constituents of Garuga pinnata and Garuga gamblei respectively, were calculated by molecular mechanics and semiempirical AM1 methods. Comparison of the most favoured conformations of garuganin I and II with that of rifamycin SV, a typical ansamycin antibiotic, revealed the close similarity of the last to garuganin I but not to garuganin II, regarding both the steric disposition and polarity of essential functional groups. Similar functionality of the aliphatic chains in the two classes of compounds suggest analogous mechanisms of antibacterial action. Deviation of the electrostatic potential energy maps calculated for the aromatic parts suggests lower biological activity for garuganin I.
Introduction With the dissemination of computational methods, the study of biologically active molecules without experiments has become possible. Such investigations are usually aimed at establishing structure-activity relationships and identifying structural features responsible for biological activity. For drugs recommended in folk medicine structure-activity correlations are very rare and often even the identification of the active principle in mixtures is missing. Study of folk medicine and the isolation of the active principles has become a separate field of natural product chemistry and has led to the discovery of several therapeutically valuable natural compounds. Diarylheptanoids are a rather limited group of natural products. Some open chain representatives such as curcumin have been known since the dawn of natural product chemistry, whereas macrocyclic * Corresponding author.
have been discovered only relatively recently. In the latter, the two aryl groups can be linked to each other either by an oxygen bridge, as in garuganin I, or a C-C bond, as in garuganin II. Garugamblins and garuganins are constituents of Garuga species, medicinal plants indigenous to India and used as antibacterial agents. Garuganin I [I] and III [2] isolated from Garuga pinnata, and garugamblin 1 and garugamblin 2 [3,4] found in Garuga gamblei are 14oxal[7. llmetacyclophanes; garuganin II [5] is a [7. llmetacyclophane (Fig. 1). The first group shows close similarity with ansamycin antibiotics, which are characterized by an aromatic system incorporated into a single macrocyclic ring attached to distant points of the aromatic moiety. In this paper we wish to provide by computational methods quantitative evidence for the above mentioned analogy and give thereby a tentative explanation for the biological activity of Garuga constituents. variants
GM. Keseni and M. Nbgrcidi{J.Mol. Struck (Theochem) 286 (1993) 259-265
260
R’
OMe
R-2 R3
H 0CH20 OMe H
H H OMe
Garugamblin-1 Garugamblin-2 Garuganin
I
OMe
Garuganin II
Fig. 1. Diarylheptanoid
components
of Garuga species.
Experimental Geometry optimization of garuganins and garugamblins was carried out from available X-ray data [5-71 using the MMXU program [8] on an IBM 80486 computer. Calculated minimum energy conformations of garuganins I and II are shown in Fig. 2. Calculated bond lengths compared with those arising from X-ray data are compiled in Table 1. Geometry optimization of rifamycin SV, a typical member of the ansamycin family, was performed with the MMXW program on an IBM 80486 computer starting from X-ray data [9] as input. Electrostatic potential maps were computed with the HYPERCHEM program [lo] on an IBM 80486 computer.
Results and discussion For the interpretation of the mechanism of action of biologically active compounds the simplest hypothesis is the key-lock analogy first suggested by Fischer [l 11,which has become the cornerstone of several rational drug design methods. The basic idea of this hypothesis is that the biological activity of a molecule is the result of a molecular recognition process, triggering an inter-
Fig. 2. Calculated minimum energy conformation garuganin I and (b) garuganin II.
of (a)
action between the active agent (the key) and the biomolecule of the organism responsible for the effect (the lock). In molecular recognition by steric complementarity, electrostatics plays a dominant role [12,13]. Prediction of the biological activity of a particular compound can be approached in two ways. If the structure of the biomolecule, ‘or at least of its binding site, is known, their interactions can be investigated by the so-called direct method; with the indirect method, a number of active compounds for which the same binding site is postulated are compared. Because the structure of the site of action of ansamycins, i.e. that of the two binding sites at the P-subunit of DNS-dependent RNS polymerase, has not been elucidated, in the present study we apply the indirect approach. The first member of the ansamycin group of antibiotics, i.e. rifamycin B 6 (Fig. 3), was isolated from Streptomyces mediterranei by Sensi et al. in 1959 [14]. Its total synthesis was carried out by Prelog in 1963 [15].
GM. Keseni and M. NbgrLid/J. Mol. Struct. (Theo&em) 286 (1993) 259-265
261
Table 1 Bond lengths(in Bngstriims) of heavy atoms in Garugu constituentscalculatedby the AM1 method; X-ray data in parentheses Bond
Garuganin I
l-2 l-3 2-3 3-4 4-5 5-6 6-7 7-20 20-3 7-8 8-9 9-10 10-11 IO-23 11-12 12-24 24-25 12-13 13-14 14-15 15-16 16-17 17-l 1-19 19-18 18-15 4-21 5-26 6-26 21-22 26-27 26-22 18-26
1.402(1.399) 1.399(1.400) 1.412(1.381) 1.394(1.385) 1.407(1.384) 1.409(1.385) 1.394(1.385) 1.388(1.376) 1.488(1.511) 1.517(1.516) 1.509(1.507) 1.463(1.472) 1.238(1.219) 1.354(1.331) 1.388(1.366) 1.423(I ,438) 1.488(1.489) 1.525(1.549) 1.486(1.509) 1.399(1.385) 1.397(1.383) 1.399(1.368) 1.400(1.354) 1.392(1.385) 1.398(1.381) 1.372(1.374) 1.376(1.376) 1.419(1.422) 1.421(1.421) _
Garuganin II 1.465(1.491) 1.406(1.382) 1.404(1.389) 1.391(1.386) 1.402(1.395) 1.396(1.370) 1.408(1.407) 1.489(1.515) 1.522(1.529) 1.508(1.520) 1.459(1.468) 1.235(1.226) 1.349(1.342) 1.387(1.357) 1.421(1.431) 1.488(1.506) 1.532(1.547) 1.492(1.506) 1.402(1.394) 1.390(1.370) 1.414(1.397) 1.402(1.395) 1.410(1.392) 1.393(1.373) I.382 (1.380) 1.374(1.370) 1.423( 1.409) 1.421(1.420) 1.370(1.370)
Oxidation of the A ring of the naphthat~ne moiety to a quinone gave rifamycin S, which was reduced to rifamycin SV [16]. The latter is a very potent inhibitor of Gram-positive bacteria with a minimum inhibitory concentration as low as 2.5 x 1OS9bg ml-‘. A derivative of rifamycin SV substituted at C-3 with a piperazine ring is marketed by Ciba-Geigy under the trade name RimactaneR. Rifamycins acting by inhibition of the RNS polymerase enzyme of bacteria have been the subject of several structure-activity studies [ 173, from which
Garuganin III
Garugamblin 1
Garugamblin 2
1.400 -
1.403(1.412) 1.399(1.397) 1.408(1.392) 1.399(1.394) 1.392(1.395) 1.402(1.399) 1.395(1.388) I.399 (1.396) 1.490(1.507) 1.513(1.524) 1.508(1.507) 1.464(1.462) 1.238(1.217) 1.355(1.351) 1.387(1.357) 1.423(1.426) 1.489(1.SOO) 1.532(1.543) 1.489(1.501) 1.403(1.403) 1.391(1.401) 1.399(1.393) 1.400(1.391) 1.400(1.399) 1.397(1.393) 1.380(1.376) -
1.404 ( 1.406) _ 1.389(1.383) 1.410(1.395) 1.387(1.375) 1.383(1.375) 1.404(1.404) 1.394(1.393) 1.396(1.392) 1.492(1.517) 1.525(1.527) 1.507(1.503) 1.468(1.471) 1.236(1.225) 1.347(1.342) 1.386(1.359) 1.424(1.435) 1.489(1.501) 1.531(1.543) 1.488(1.505) 1.402(1.397) 1.395(1.383) 1.391(1.387) 1.396(1.375) 1.392(1.385) 1.396(1.397) 1.375(1.379) 1.381(1.390) 1.434(1.438)
1.400 1.402 1.395 1.401 1.400 1.395 1.397 1.487 1.516 1.506 1.462 1.239 1.352
1.390 1.422
1.489 1.525
1.484 1.400 1.406 1.400 1.400 1.390 1.401 I .378 1.374 1.413 1.419 -
1.422(1.420) -
1.433 (1.432)
_
certain structural requirements for biological activity (as shown in Table 2) can be deduced
WI. Thus it was established that for antibacte~a~ activity oxygen functions at C-21 and C-23 were essential, whereas modifications at other points of the molecule did not entail significant changes of activity. Because the region responsible for biological activity of rifamycins could be localized to the aliphatic portion of the molecule, as a first approximation we compared the latter with the C7 chain of garuganins.
GM. Kesens’ and M. NdgnidijJ. Mol. Strut.
262
(Theo&m)
286 (1993) 259-265
l
OH S
Rilamicin B
sv
Fig. 3. Structure of the antibiotics rifamycin B, S and SV.
Study of steric complementarity According to AM1 calculations the conformation of the macrocyclic rings in garuganin I, garuganin III, garugamblin 1 and 2 are quite similar, so we restrict our further calculations to garuganin I. Comparing minimum energy conformations, we find that the steric disposition of the 10,lZdioxy functions in garuganin I is the same as that of the hydroxy functions at C-21 and C-23 in rifamycin SV (Fig. 4). Superposition of chains yields excellent fitting, with an average deviation of 0.07 A per atom. Although the macrocyclic ring of rifamycin SV is larger by nine members, the double bonds in the chain and the planarity of the aromatic system
impose considerable extra strain on the system, explaining the observed close similarity in the geometry of the two chains (see also Fig. 5, prepared by superimposing the two structures). Certain authors have atributed complexation of ansamycins with RNS polymerase to two factors [19-211: (i) hydrogen bonding to the active centre of the enzyme involving the oxygen atoms of the hydroxyl groups at C-l, C-8, and further at C-21 and C-23; (ii) further stabilization of the enzymesubstrate complex by T-T interactions between the naphthalene ring of ansamycin and the aromatic side-chains of the enzyme. Accepting that in the formation of the rifamycin SV-RNS polymerase complex hydrogen bonds play a decisive role, the analogous action of rifamycins and garuganin I requires that the distances of the oxygen atoms capable of hydrogen bonding Table 2 Correlation of biological activity and structural tions of the ansa bridge in ansamycins
Fig. 4. Calculated rifamycin B.
minimum
energy
conformation
of
modilica-
Structural modification
Change of activity
Deacetylation at C(25) Demethylation at C(27) Ether bridge between C(23) and C(25) Opening of macrocycle Acetonide formation involving C(21)-OH and C(23)-OH Reduction of double bonds
None None Inactivation Inactivation Inactivation Significant decrease
GM. Keserti and M. Ndgrcidi/J. Mol. Struct. (Theochem)
286 (1993) 259-265
263
ring. The C=O bond of garuganin I is fulfilling this condition, because it is oriented parallel to the meta-disubstituted aromatic ring, whereas the plane of the carbon chain in garuganin stands at an angle of 95” relative to this ring [6]. Study of electrostatic complementarity
Fig. 5. Superposition of the calculated minimum energy conformations of garuganin I and rifamycin SV. Note the geometric complementarity of the 1,3-dioxo moiety.
should be similar. In garuganin I the role of the hydroxyl groups at C-l and C-8 in rifamycin SV may be taken over by the oxygen atoms at C-3 and C-4. Close values for the O-O distances in the two molecules support this hypothesis (Table 3). Structure-activity work on ansamycins was extended in an X-ray study by Brufani and Cellai [22], who found that in the active members of the group the two planes incorporating the aliphatic chain and the aromatic rings are nearly perpendicular; further, the C=O bond extending from the ansa bridge is parallel to the plane of the aromatic Table 3 O-O distances garuganin I Distance
,OH
(in angstroms)
rifamycin
Garuganin
Rifamycin SV
20H
for
10
20Me
SV and
I
The simplest way of studying the electrostatic complementarity of molecules is the calculation of molecular electrostatic potential (MEP) surfaces [23]. Electrostatic complementarity should be valid first of all in the environment of pharrnacophores, in our case for the 1,3-difunctional part of the aliphatic chains (c.f. Fig. 5), and analogy of the MEP surfaces for the aromatic rings may provide additional evidence. Owing to the close conformational similarity of the 1,3dioxygen functions, study of electrostatic complementarity does not require the calculation of MEP surfaces, although owing to differences in the steric disposition of the aromatic rings, construction of MEP surfaces for this part of the molecules is necessary. For calculation of MEPs for garuganin I and rifamycin SV we used the models shown in Fig. 6. Calculations were carried out using AM1 single point calculations starting from the optimized geometries obtained from MM + calculations with the block diagonal method. The MEPs are shown in Fig. 7. Figure 7 reveals that electrostatic potentials in the plane of the respective aromatic rings in the environment of the phenolic hydroxyl groups attached to the aromatic ring of rifamycin SV and responsible for its pharmacological activity and that around the meta-positioned ether functions in garuganin I are distinctly different. Thus,
cH30qcH3 O-1-0-3 O-1-0-4 0-2-O-3 0-2-O-4
6.0 8.1 7.3 9.6
5.8 8.0 7.8 9.5
cH$+NHz 3
0
Fig. 6. Ring models used for the calculation of electrostatic potential maps for garuganin I and rifamycin SV.
264
GM. Keseti and hf. Nbgrtidi/J. Mol. Struct. (Theo&m)
(a)
Fig. 7. Electrostatic potential maps of the aromatic ring models of (a) garuganin I and (b) rifamycin SV in the plane of the molecules. Electrostatic potential is indicated in the negative region by contour lines in steps of 5 kcal mol-’ in the range O-60 kcal mol-’ .
although steric complementarity can also be extended to the oxygen functions of the aromatic parts, the condition of electrostatic complementarity is not completely fulfilled. Therefore, it can be anticipated that the biological activity of garuganin I is lower than that of rifamycin SV. Conclusions In summary, it can be stated that garuganin I, garuganin III, garugamblin 1, and garugamblin 2,
286 (1993) 259-265
all having almost the same conformation, share several characteristic features with ansamycin antibiotics. Superposition of optimum geometries, in addition to mimicking the characteristics of the 1,3-dioxy functions, which can be regarded as the pharmacophore of ansamycins, suggests the hypothesis that garuganin I is an antibacterial compound analogous in its mechanism of action to ansamycins. Owing to differences in the electrostatic potential maps of the aromatic moieties, lower biological activity of garuganins, as compared to ansamycins, can be anticipated. A similar comparison of ansamycin SV with garuganin II, in which the aromatic moiety is of the biphenyl type, gave much weaker fitting, average deviation of 0 atoms being 1.2A per atom. This is in accordance with the finding that this compound has no reported antibacterial activity [5]. Our hypothesis contradicts that proposed by Beyer et al., who claimed an analogy between garuganin-type compounds and OF peptides [24]. This supposed analogy disregards the peptide character of the latter compounds and the fact that OF peptides act by complexation to the bacterial cell wall by means of hydrogen bonds with the peptide [25]. Because garuganin I and its congeners do not contain amino acid units, any analogy concerning structure or mechanism of action is not justified. Acknowledgements Thanks are given to Professor Gabor NaraySzabo for helpful discussions and access to HYP~CF~~ for calculating electrostatic potential maps. We also thank the Pro Renovanda Cultura Hungariae for financial support. References M.M. Haribal, AK. Mishra and B.K. Sabata, Tetrahedron, 41 (1985) 4949. A.K. Mishra, M.M. Haribal and B.K. Sabata, Phytochemistry, 24 (1985) 2463. H. Kalchhauser, H.G. Krishnamurty, A.C. Talukdar and W. S&mid, Monatsh. Chem., 119 (1988) 1047.
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4
5 6 7 8
9
10
11 12
13 14
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H. Kalchhauser and H.G. Krishnamurty, Magn. Reson. Chem., 27 (1989) 635. S. Krishnaswamy, V. Pattabhi and E.J. Gabe, Acta Crystallogr., Sect. C, 43 (1987) 527. V. Pattabhi, S. Drishnaswamy and E.J. Gabe, Acta Crystallogr., Sect. C, 40 (1984) 832. M. Nethaji, V. Pattabhi, H.G. Krishnamurty and AC. Talukdar, Acta Crystallogr., Sect. C, 46 (1990) 307. MMXST is a generalized version of Allinger’s MM2 (QCPE 343 and 318) extended by C. Still, adapted to Microsoft Fortran by G. Gajewski and K. Gilbert. L. Cellai, S. Cerrini, A. Serge, M. Brufani, W. Fedeli and A. Vaciago, J. Chem. Sot., Perkin Trans., 2 (1982) 1633. HYPERCHEM, Autodesk Inc., 2320 Marinship Way, Sausalito, CA 94965, 1992. The copy used was the authorized sample of Professor G. Naray-Szabo. E. Fisher, Ber. Dtsch. Chem. Ges., 27 (1984) 2984. P. Politzer and D.G. Tuhlar (Eds.), Chemical Applications of Atomic and Molecular Electrostatic Potentials, Plenum, New York, 1981. A. Warshel and S.T. Russel, Q. Rev. Biophys., 17 (1984) 283. P. Sensi, P. Margalith and M.T. Timbal, Farmaco Ed. Sci., 14 (1959) 146.
265
15 V. Prelog, Pure Appl. Chem., 7 (1963) 551. 16 P. Sensi, R. Ballotta, A.M. Greco and G.G. Gallo, Farmaco Ed. Sci., 16 (1961) 165. 17 W. Wehrli and M. Staehelin, Bacterial. Rev., 35 (1971) 290. 18 0. Ghisalba, P. Traxler, H. Fuhrer and W.J. Richter, J. Antibiot., 33 (1980) 847. 19 W. Wehrli and M. Staehelin, Biochim. Biophys. Acta, 182 (1969) 24. 20 M.F. Dampier and H.W. Whitlok, J. Am. Chem. Sot., 97 (1975) 6254. 21 W.R. McClure and C.L. Cech, J. Biol. Chem., 253 (1978) 8949. 22 M. Brufani and L. Cellai, in A.S. Horn and C.J. De Ranther (Eds.), X-ray Crystallography and Drug Action, Clarendon, Oxford, 1984, p. 394. 23 G. Naray-Szabb, J. Mol. Graphics, 7 (1989) 76. 24 A. Beyer, H. Kalchauser and P. Wolschann, Monatsh. Chem., 123 (1992) 417. 25 S. Sano, H. Kuroda, M. Ueno, Y. Yoshikawa, T. Nakamura and Y. Obayashi, J. Antibiot., 40 (1987) 450, 512, 519.
259
Prediction of antibacterial activity of some diarylheptanoids isolated from Garuga species by molecular mechanics and molecular orbital calculations Gyijrgy Mikl6s Keserii*,
Mihily
N6grBdi
Research Group for Alkaloid Chemistry of the Hungarian Academy of Sciences, P.O.B. 91, H-1521 Budapest, Hungary
(Received 1 February 1993; accepted 6 February 1993) Abstract Favoured conformations for garuganins I-III and garugamblins 1 and 2, constituents of Garuga pinnata and Garuga gamblei respectively, were calculated by molecular mechanics and semiempirical AM1 methods. Comparison of the most favoured conformations of garuganin I and II with that of rifamycin SV, a typical ansamycin antibiotic, revealed the close similarity of the last to garuganin I but not to garuganin II, regarding both the steric disposition and polarity of essential functional groups. Similar functionality of the aliphatic chains in the two classes of compounds suggest analogous mechanisms of antibacterial action. Deviation of the electrostatic potential energy maps calculated for the aromatic parts suggests lower biological activity for garuganin I.
Introduction With the dissemination of computational methods, the study of biologically active molecules without experiments has become possible. Such investigations are usually aimed at establishing structure-activity relationships and identifying structural features responsible for biological activity. For drugs recommended in folk medicine structure-activity correlations are very rare and often even the identification of the active principle in mixtures is missing. Study of folk medicine and the isolation of the active principles has become a separate field of natural product chemistry and has led to the discovery of several therapeutically valuable natural compounds. Diarylheptanoids are a rather limited group of natural products. Some open chain representatives such as curcumin have been known since the dawn of natural product chemistry, whereas macrocyclic * Corresponding author.
have been discovered only relatively recently. In the latter, the two aryl groups can be linked to each other either by an oxygen bridge, as in garuganin I, or a C-C bond, as in garuganin II. Garugamblins and garuganins are constituents of Garuga species, medicinal plants indigenous to India and used as antibacterial agents. Garuganin I [I] and III [2] isolated from Garuga pinnata, and garugamblin 1 and garugamblin 2 [3,4] found in Garuga gamblei are 14oxal[7. llmetacyclophanes; garuganin II [5] is a [7. llmetacyclophane (Fig. 1). The first group shows close similarity with ansamycin antibiotics, which are characterized by an aromatic system incorporated into a single macrocyclic ring attached to distant points of the aromatic moiety. In this paper we wish to provide by computational methods quantitative evidence for the above mentioned analogy and give thereby a tentative explanation for the biological activity of Garuga constituents. variants
GM. Keseni and M. Nbgrcidi{J.Mol. Struck (Theochem) 286 (1993) 259-265
260
R’
OMe
R-2 R3
H 0CH20 OMe H
H H OMe
Garugamblin-1 Garugamblin-2 Garuganin
I
OMe
Garuganin II
Fig. 1. Diarylheptanoid
components
of Garuga species.
Experimental Geometry optimization of garuganins and garugamblins was carried out from available X-ray data [5-71 using the MMXU program [8] on an IBM 80486 computer. Calculated minimum energy conformations of garuganins I and II are shown in Fig. 2. Calculated bond lengths compared with those arising from X-ray data are compiled in Table 1. Geometry optimization of rifamycin SV, a typical member of the ansamycin family, was performed with the MMXW program on an IBM 80486 computer starting from X-ray data [9] as input. Electrostatic potential maps were computed with the HYPERCHEM program [lo] on an IBM 80486 computer.
Results and discussion For the interpretation of the mechanism of action of biologically active compounds the simplest hypothesis is the key-lock analogy first suggested by Fischer [l 11,which has become the cornerstone of several rational drug design methods. The basic idea of this hypothesis is that the biological activity of a molecule is the result of a molecular recognition process, triggering an inter-
Fig. 2. Calculated minimum energy conformation garuganin I and (b) garuganin II.
of (a)
action between the active agent (the key) and the biomolecule of the organism responsible for the effect (the lock). In molecular recognition by steric complementarity, electrostatics plays a dominant role [12,13]. Prediction of the biological activity of a particular compound can be approached in two ways. If the structure of the biomolecule, ‘or at least of its binding site, is known, their interactions can be investigated by the so-called direct method; with the indirect method, a number of active compounds for which the same binding site is postulated are compared. Because the structure of the site of action of ansamycins, i.e. that of the two binding sites at the P-subunit of DNS-dependent RNS polymerase, has not been elucidated, in the present study we apply the indirect approach. The first member of the ansamycin group of antibiotics, i.e. rifamycin B 6 (Fig. 3), was isolated from Streptomyces mediterranei by Sensi et al. in 1959 [14]. Its total synthesis was carried out by Prelog in 1963 [15].
GM. Keseni and M. NbgrLid/J. Mol. Struct. (Theo&em) 286 (1993) 259-265
261
Table 1 Bond lengths(in Bngstriims) of heavy atoms in Garugu constituentscalculatedby the AM1 method; X-ray data in parentheses Bond
Garuganin I
l-2 l-3 2-3 3-4 4-5 5-6 6-7 7-20 20-3 7-8 8-9 9-10 10-11 IO-23 11-12 12-24 24-25 12-13 13-14 14-15 15-16 16-17 17-l 1-19 19-18 18-15 4-21 5-26 6-26 21-22 26-27 26-22 18-26
1.402(1.399) 1.399(1.400) 1.412(1.381) 1.394(1.385) 1.407(1.384) 1.409(1.385) 1.394(1.385) 1.388(1.376) 1.488(1.511) 1.517(1.516) 1.509(1.507) 1.463(1.472) 1.238(1.219) 1.354(1.331) 1.388(1.366) 1.423(I ,438) 1.488(1.489) 1.525(1.549) 1.486(1.509) 1.399(1.385) 1.397(1.383) 1.399(1.368) 1.400(1.354) 1.392(1.385) 1.398(1.381) 1.372(1.374) 1.376(1.376) 1.419(1.422) 1.421(1.421) _
Garuganin II 1.465(1.491) 1.406(1.382) 1.404(1.389) 1.391(1.386) 1.402(1.395) 1.396(1.370) 1.408(1.407) 1.489(1.515) 1.522(1.529) 1.508(1.520) 1.459(1.468) 1.235(1.226) 1.349(1.342) 1.387(1.357) 1.421(1.431) 1.488(1.506) 1.532(1.547) 1.492(1.506) 1.402(1.394) 1.390(1.370) 1.414(1.397) 1.402(1.395) 1.410(1.392) 1.393(1.373) I.382 (1.380) 1.374(1.370) 1.423( 1.409) 1.421(1.420) 1.370(1.370)
Oxidation of the A ring of the naphthat~ne moiety to a quinone gave rifamycin S, which was reduced to rifamycin SV [16]. The latter is a very potent inhibitor of Gram-positive bacteria with a minimum inhibitory concentration as low as 2.5 x 1OS9bg ml-‘. A derivative of rifamycin SV substituted at C-3 with a piperazine ring is marketed by Ciba-Geigy under the trade name RimactaneR. Rifamycins acting by inhibition of the RNS polymerase enzyme of bacteria have been the subject of several structure-activity studies [ 173, from which
Garuganin III
Garugamblin 1
Garugamblin 2
1.400 -
1.403(1.412) 1.399(1.397) 1.408(1.392) 1.399(1.394) 1.392(1.395) 1.402(1.399) 1.395(1.388) I.399 (1.396) 1.490(1.507) 1.513(1.524) 1.508(1.507) 1.464(1.462) 1.238(1.217) 1.355(1.351) 1.387(1.357) 1.423(1.426) 1.489(1.SOO) 1.532(1.543) 1.489(1.501) 1.403(1.403) 1.391(1.401) 1.399(1.393) 1.400(1.391) 1.400(1.399) 1.397(1.393) 1.380(1.376) -
1.404 ( 1.406) _ 1.389(1.383) 1.410(1.395) 1.387(1.375) 1.383(1.375) 1.404(1.404) 1.394(1.393) 1.396(1.392) 1.492(1.517) 1.525(1.527) 1.507(1.503) 1.468(1.471) 1.236(1.225) 1.347(1.342) 1.386(1.359) 1.424(1.435) 1.489(1.501) 1.531(1.543) 1.488(1.505) 1.402(1.397) 1.395(1.383) 1.391(1.387) 1.396(1.375) 1.392(1.385) 1.396(1.397) 1.375(1.379) 1.381(1.390) 1.434(1.438)
1.400 1.402 1.395 1.401 1.400 1.395 1.397 1.487 1.516 1.506 1.462 1.239 1.352
1.390 1.422
1.489 1.525
1.484 1.400 1.406 1.400 1.400 1.390 1.401 I .378 1.374 1.413 1.419 -
1.422(1.420) -
1.433 (1.432)
_
certain structural requirements for biological activity (as shown in Table 2) can be deduced
WI. Thus it was established that for antibacte~a~ activity oxygen functions at C-21 and C-23 were essential, whereas modifications at other points of the molecule did not entail significant changes of activity. Because the region responsible for biological activity of rifamycins could be localized to the aliphatic portion of the molecule, as a first approximation we compared the latter with the C7 chain of garuganins.
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262
(Theo&m)
286 (1993) 259-265
l
OH S
Rilamicin B
sv
Fig. 3. Structure of the antibiotics rifamycin B, S and SV.
Study of steric complementarity According to AM1 calculations the conformation of the macrocyclic rings in garuganin I, garuganin III, garugamblin 1 and 2 are quite similar, so we restrict our further calculations to garuganin I. Comparing minimum energy conformations, we find that the steric disposition of the 10,lZdioxy functions in garuganin I is the same as that of the hydroxy functions at C-21 and C-23 in rifamycin SV (Fig. 4). Superposition of chains yields excellent fitting, with an average deviation of 0.07 A per atom. Although the macrocyclic ring of rifamycin SV is larger by nine members, the double bonds in the chain and the planarity of the aromatic system
impose considerable extra strain on the system, explaining the observed close similarity in the geometry of the two chains (see also Fig. 5, prepared by superimposing the two structures). Certain authors have atributed complexation of ansamycins with RNS polymerase to two factors [19-211: (i) hydrogen bonding to the active centre of the enzyme involving the oxygen atoms of the hydroxyl groups at C-l, C-8, and further at C-21 and C-23; (ii) further stabilization of the enzymesubstrate complex by T-T interactions between the naphthalene ring of ansamycin and the aromatic side-chains of the enzyme. Accepting that in the formation of the rifamycin SV-RNS polymerase complex hydrogen bonds play a decisive role, the analogous action of rifamycins and garuganin I requires that the distances of the oxygen atoms capable of hydrogen bonding Table 2 Correlation of biological activity and structural tions of the ansa bridge in ansamycins
Fig. 4. Calculated rifamycin B.
minimum
energy
conformation
of
modilica-
Structural modification
Change of activity
Deacetylation at C(25) Demethylation at C(27) Ether bridge between C(23) and C(25) Opening of macrocycle Acetonide formation involving C(21)-OH and C(23)-OH Reduction of double bonds
None None Inactivation Inactivation Inactivation Significant decrease
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286 (1993) 259-265
263
ring. The C=O bond of garuganin I is fulfilling this condition, because it is oriented parallel to the meta-disubstituted aromatic ring, whereas the plane of the carbon chain in garuganin stands at an angle of 95” relative to this ring [6]. Study of electrostatic complementarity
Fig. 5. Superposition of the calculated minimum energy conformations of garuganin I and rifamycin SV. Note the geometric complementarity of the 1,3-dioxo moiety.
should be similar. In garuganin I the role of the hydroxyl groups at C-l and C-8 in rifamycin SV may be taken over by the oxygen atoms at C-3 and C-4. Close values for the O-O distances in the two molecules support this hypothesis (Table 3). Structure-activity work on ansamycins was extended in an X-ray study by Brufani and Cellai [22], who found that in the active members of the group the two planes incorporating the aliphatic chain and the aromatic rings are nearly perpendicular; further, the C=O bond extending from the ansa bridge is parallel to the plane of the aromatic Table 3 O-O distances garuganin I Distance
,OH
(in angstroms)
rifamycin
Garuganin
Rifamycin SV
20H
for
10
20Me
SV and
I
The simplest way of studying the electrostatic complementarity of molecules is the calculation of molecular electrostatic potential (MEP) surfaces [23]. Electrostatic complementarity should be valid first of all in the environment of pharrnacophores, in our case for the 1,3-difunctional part of the aliphatic chains (c.f. Fig. 5), and analogy of the MEP surfaces for the aromatic rings may provide additional evidence. Owing to the close conformational similarity of the 1,3dioxygen functions, study of electrostatic complementarity does not require the calculation of MEP surfaces, although owing to differences in the steric disposition of the aromatic rings, construction of MEP surfaces for this part of the molecules is necessary. For calculation of MEPs for garuganin I and rifamycin SV we used the models shown in Fig. 6. Calculations were carried out using AM1 single point calculations starting from the optimized geometries obtained from MM + calculations with the block diagonal method. The MEPs are shown in Fig. 7. Figure 7 reveals that electrostatic potentials in the plane of the respective aromatic rings in the environment of the phenolic hydroxyl groups attached to the aromatic ring of rifamycin SV and responsible for its pharmacological activity and that around the meta-positioned ether functions in garuganin I are distinctly different. Thus,
cH30qcH3 O-1-0-3 O-1-0-4 0-2-O-3 0-2-O-4
6.0 8.1 7.3 9.6
5.8 8.0 7.8 9.5
cH$+NHz 3
0
Fig. 6. Ring models used for the calculation of electrostatic potential maps for garuganin I and rifamycin SV.
264
GM. Keseti and hf. Nbgrtidi/J. Mol. Struct. (Theo&m)
(a)
Fig. 7. Electrostatic potential maps of the aromatic ring models of (a) garuganin I and (b) rifamycin SV in the plane of the molecules. Electrostatic potential is indicated in the negative region by contour lines in steps of 5 kcal mol-’ in the range O-60 kcal mol-’ .
although steric complementarity can also be extended to the oxygen functions of the aromatic parts, the condition of electrostatic complementarity is not completely fulfilled. Therefore, it can be anticipated that the biological activity of garuganin I is lower than that of rifamycin SV. Conclusions In summary, it can be stated that garuganin I, garuganin III, garugamblin 1, and garugamblin 2,
286 (1993) 259-265
all having almost the same conformation, share several characteristic features with ansamycin antibiotics. Superposition of optimum geometries, in addition to mimicking the characteristics of the 1,3-dioxy functions, which can be regarded as the pharmacophore of ansamycins, suggests the hypothesis that garuganin I is an antibacterial compound analogous in its mechanism of action to ansamycins. Owing to differences in the electrostatic potential maps of the aromatic moieties, lower biological activity of garuganins, as compared to ansamycins, can be anticipated. A similar comparison of ansamycin SV with garuganin II, in which the aromatic moiety is of the biphenyl type, gave much weaker fitting, average deviation of 0 atoms being 1.2A per atom. This is in accordance with the finding that this compound has no reported antibacterial activity [5]. Our hypothesis contradicts that proposed by Beyer et al., who claimed an analogy between garuganin-type compounds and OF peptides [24]. This supposed analogy disregards the peptide character of the latter compounds and the fact that OF peptides act by complexation to the bacterial cell wall by means of hydrogen bonds with the peptide [25]. Because garuganin I and its congeners do not contain amino acid units, any analogy concerning structure or mechanism of action is not justified. Acknowledgements Thanks are given to Professor Gabor NaraySzabo for helpful discussions and access to HYP~CF~~ for calculating electrostatic potential maps. We also thank the Pro Renovanda Cultura Hungariae for financial support. References M.M. Haribal, AK. Mishra and B.K. Sabata, Tetrahedron, 41 (1985) 4949. A.K. Mishra, M.M. Haribal and B.K. Sabata, Phytochemistry, 24 (1985) 2463. H. Kalchhauser, H.G. Krishnamurty, A.C. Talukdar and W. S&mid, Monatsh. Chem., 119 (1988) 1047.
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5 6 7 8
9
10
11 12
13 14
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H. Kalchhauser and H.G. Krishnamurty, Magn. Reson. Chem., 27 (1989) 635. S. Krishnaswamy, V. Pattabhi and E.J. Gabe, Acta Crystallogr., Sect. C, 43 (1987) 527. V. Pattabhi, S. Drishnaswamy and E.J. Gabe, Acta Crystallogr., Sect. C, 40 (1984) 832. M. Nethaji, V. Pattabhi, H.G. Krishnamurty and AC. Talukdar, Acta Crystallogr., Sect. C, 46 (1990) 307. MMXST is a generalized version of Allinger’s MM2 (QCPE 343 and 318) extended by C. Still, adapted to Microsoft Fortran by G. Gajewski and K. Gilbert. L. Cellai, S. Cerrini, A. Serge, M. Brufani, W. Fedeli and A. Vaciago, J. Chem. Sot., Perkin Trans., 2 (1982) 1633. HYPERCHEM, Autodesk Inc., 2320 Marinship Way, Sausalito, CA 94965, 1992. The copy used was the authorized sample of Professor G. Naray-Szabo. E. Fisher, Ber. Dtsch. Chem. Ges., 27 (1984) 2984. P. Politzer and D.G. Tuhlar (Eds.), Chemical Applications of Atomic and Molecular Electrostatic Potentials, Plenum, New York, 1981. A. Warshel and S.T. Russel, Q. Rev. Biophys., 17 (1984) 283. P. Sensi, P. Margalith and M.T. Timbal, Farmaco Ed. Sci., 14 (1959) 146.
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15 V. Prelog, Pure Appl. Chem., 7 (1963) 551. 16 P. Sensi, R. Ballotta, A.M. Greco and G.G. Gallo, Farmaco Ed. Sci., 16 (1961) 165. 17 W. Wehrli and M. Staehelin, Bacterial. Rev., 35 (1971) 290. 18 0. Ghisalba, P. Traxler, H. Fuhrer and W.J. Richter, J. Antibiot., 33 (1980) 847. 19 W. Wehrli and M. Staehelin, Biochim. Biophys. Acta, 182 (1969) 24. 20 M.F. Dampier and H.W. Whitlok, J. Am. Chem. Sot., 97 (1975) 6254. 21 W.R. McClure and C.L. Cech, J. Biol. Chem., 253 (1978) 8949. 22 M. Brufani and L. Cellai, in A.S. Horn and C.J. De Ranther (Eds.), X-ray Crystallography and Drug Action, Clarendon, Oxford, 1984, p. 394. 23 G. Naray-Szabb, J. Mol. Graphics, 7 (1989) 76. 24 A. Beyer, H. Kalchauser and P. Wolschann, Monatsh. Chem., 123 (1992) 417. 25 S. Sano, H. Kuroda, M. Ueno, Y. Yoshikawa, T. Nakamura and Y. Obayashi, J. Antibiot., 40 (1987) 450, 512, 519.