- Email: [email protected]
Conformation of neolignans that bind to the arginine residue in adenosine-kinase from Leishmania donovani
Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Conformation of neolignans that bind to the arginine residue in adenosine-kinase from Leishmania donovani Maria Cristina Andreazza Costa, Lauro Euclides Soares Barata, Yuji Takahata* Instituto de Quı´mica,Universidade Estadual de Campinas, Caixa Postal 6154, Cep 13083-970-Campinas, SP, Brazil
Abstract Most probable conformation of synthetic neolignans that are active against visceral leishmaniasis is proposed. It is based upon an assumption that the receptor of the neolignans is the arginine residue in the adenosine-kinase from Leishmania donovani. A planar form (the two phenyl rings are stretched out) of the neolignans is most likely a preferred receptor site conformation. 䉷 1999 Elsevier Science B.V. All rights reserved. Keywords: Neolignans; Active conformation; Leishmaniasis; AM1 and MM methods
1. Introduction Leishmaniasis is an important tropical disease, affecting half a million people in the world, for which there are no efficient treatments at present [1]. Leishmania donovani is a species of the leishmania protozoa that are the causative agent of visceral leishmaniasis; this is fatal if untreated. Pentavalent antimonials and amphotericin B are used to the treatment, but they are not always effective and require long period of administration, which is associated with drug toxicity [2]. It has been observed that all parasitic protozoa, inclusive of L. donovani, studied to date lack the ability to synthesize purine ‘‘de novo’’. Thus they scavenge purines from the host using its own unique set of purine-salvage enzymes [3,4]. Adenosine kinase (ATP: adenosine 5 0 -phosphotransferase, EC 2.7.1.20) is one of the key enzymes of the purinesalvage pathway. It catalyses the transfer of terminal phosphate from ATP to adenosine(Ado) [5]. Little is * Corresponding author. Fax: ⫹55 019 788 3023. E-mail address: [email protected] (Y. Takahata)
known regarding the active-site structure and the molecular mecanism associated with adenosinekinase mediated Ado phosphorylation. Recently Ghosh and Datta found the evidence, for the first time, that indicates the presence of one arginine residue exclusively at the Ado-binding site of the L. donovani adenosine kinase [6]. Moreover, they demonstrated that the arginine specific regents phenylglyoxal (PGO), butane-2,3-dione and cyclohexane-1,2-dione all irreversibly inactivated the enzyme. In view of these observations, we can assume that drugs that are active against L. donovani interact with (or bind to) the arginnie residue of the adenosine kinase and inactivate the leishmanial enzyme. Once the enzyme is inactivated, L. donovani must die. Neolignans are dimers from oxidative coupling of allyl and propenyl phenols that occur in the Myristicaceae and other primitive plant families. The Virola is the most representative member of Myristicaceae occurring throughout the Americas. In 1970, initial studies of leaves of Virola surinamensis [7] showed high efficacy in the blockage tests of penetration of cercarie of Schistosoma mansoni in mice. The active substances responsible for protection were isolated
0166-1280/99/$ - see front matter 䉷 1999 Elsevier Science B.V. All rights reserved. PII: S0166-128 0(98)00560-0
282
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Fig. 1. Neolignans number 12–20 are active ‘‘in vitro’’ against visceral leishmaniasis.
and identified as the natural neolignans. Barata et al. [8] and Santos [9] synthesized 20 analogs of the active substances to determine the biological activity of neolignans. The biological tests were made by Neal and others of London School of Hygiene and Tropical
Medicine [1]. Of the 20 compounds tested in vitro, nine molecules of these showed activity against leishmaniasis, and 11 showed inactivity. The nine active neolignans are shown in Fig. 1. In previous studies, we analyzed a series of the 20 synthetic neolignans in
Fig. 2. The four local minima of the neolignans found as the most probable to be the active conformations.
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Fig. 3. Basic structure of the amino ketones. ‘‘R’’ are the substituents in the molecules. R11 is H or Cl; R22 is –(CH2)n–NH2 or – (CH2)– O– (CH2)6 –NH2 and R24 is H or –CH3[11].
283
order to define the most probable conformer that may fit receptor [10]. Using molecular mechanics method (MM2) and Boltzmann’s distribution, we concluded that only four local minima (C, D, E, F) out of eight could correspond to the probable conformer [10]. The four probable active conformers are shown in the Fig. 2. In the present work, we want to know which conformer out of the four can best fit to the active-site of arginine residue in L. donovani adenosine kinase. We assume that the 9 active neolignans interact with the arginine residue. It is important to know active conformation of drugs. Information about the conformation helps one to understand the mechanism of drug action and help to develop new drugs. A series of amino ketone compounds are also active against leishmaniasis. These molecules are somewhat similar to the neolignans because both series of
Fig. 4. (a) Geometry of the arginine obtained by crystallographic data [12] and by AM1 calculations. (b) Geometry of the arginine after rotation of 120⬚ of the axis c, in relation to Fig. 4a. (c) Representative scheme of the adenosine. The geometry of the adenine portion was obtained from the literature [16].
284
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Table 1 DHf is the heat of formation calculated by AM1 method to conformations A and B of the arginine, where conformation A was obtained by crystallographic data. In the conformation B, the dihedral angle referent to atoms 7–2–3–4 (in the Fig. 4a) was rotated by 120⬚. The rotational barrier energy (RE) was calculated from A to B Conformation A (axis c ⫹ 62.1⬚) B (axis c ⫺ 62.7⬚)
DHf (kcal/mol) ⫺ 56.77 ⫺ 58.52
RE (kcal/mol) 3.09
compounds have two phenyl groups and a carbonyl between them. Basic structure of amino ketones are shown in the Fig. 3. It is known that a number of amino ketones are capable of inhibiting a key enzyme (2,3-oxidosqualene lanosterol cyclase) in fungal sterol biosynthesis. The amino ketones in Fig. 3 also showed activity against leishmaniasis [11]. As a result, we can assume that amino ketones are capable of inhibiting the adenosine-kinase from L. donavani. We can suppose that the amino ketones bind to the arginine residue in the adenosine-kinase from L. donavani. We compare the geometry of the amino ketones with the four possible conformation of the neolignans in order to find the most probable active conformation of the neolignans.
2. Calculations Crystallographic data for the heavy atoms of arginine are available in the literature [12]. We calculated the positions of the hydrogen atoms of arginine using the AM1 semiempirical method keeping the heavy atoms in the observed positions. The conformational analysis of the two phenyl rings of the benzophenone in the aminoketones was performed by Pauline and Wildeman [13]. A series of AM1 calculations showed that the minimum energy conformation of the benzophenone has both rings twisted by 33⬚, in agreement with crystallographic data [13]. The conformational analysis of the neolignans were performed previously [10], using molecular mechanics method-MM2. The fitting of the neolignans to the arginine was done using the PowerFit program [14]. PowerFit is a Computer-Assisted Molecular Fitting program that is designed to run on desktop computers. The computation engine of the PowerFit is based on the Steric
and Electrostatic Alignment of Kearsley and Smith [15].
3. Results and discussion We assume that geometry of arginine residue at the active site of the leishmanial enzyme is similar to the geometry of crystallized arginine molecules. The geometry of the arginine (obtained by crystallographic data) is shown in the Fig. 4a and c displays an adenosine scheme-the substrate of the adenosinekinase. The geometry of the adenine portion of the adenosine is obtained from the literature [16]. It is known that adenine is in a perpendicular plane to the ribose ring plane [16]. If we compare the angles and distances of the guanidyl group in the arginine and those of the adenine, we observe that atoms N9, C6, N10 and N8 of the arginine can superimpose to C6, C5, N7 and C4 of the adenine through hydrogen bonds. If the axis c in the arginine of the conformation A in Fig. 4a is rotated by 120⬚, it results in the conformation B shown in Fig. 4b. The conformation B facilitates formation of an additional hydrogen bond between H15 of arginine and O17 of adenosine. We calculated the heats of formation of isolated arginine in the two conformations, A and B, using the AM1 semiempirical method (Table 1). The heat of formation of the conformation B is 1.75 kcal/mol lower than that of the conformation A. As the conformation A is the observed conformation from the crystallographic data, A must be more stable than B in crystal form. The discrepancy between the observed conformation and the calculated one may depend upon the fact that the calculated conformations are in the forms of isolated molecule while the observed one is in the form of a crystal, or it may be owing to the inaccuracy of the semiempirical method. In any case, we may be able to assume that B can be almost as stable as A. The rotation barrier is 3.09 kcal/mol which is small. These considerations suggest that the arginine residue can take the conformation B as well as A when it interacts with the substrate. If the arginine residue takes the conformation B, it interacts with the substrate by its guanidyl and amino groups. The p electrons of the two aromatic rings in the neolignans could make electrostatic interactions with the guanidyl and amino groups of arginine. For these
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
285
Table 2 dl is the distance between atoms C6 and C18 of the neolignans (compounds 12–20) in the Fig. 1. For arginine, dl is the distance between atoms C3 and C6 (Fig. 4) and for amino ketones (Fig. 3), between atoms C6 and C16. The dihedral angles, a and b are shown in the Figs. 1, 3 and 4 Compound
Conformation
˚) distance dl (A
Dihedral angles (degrees) a
b
12 C D E F
3.6 5.1 4.4 3.6
46 ⫺ 174 ⫺ 60 ⫺ 46
63 179 180 ⫺ 63
C D E F
3.4 5.1 4.5 3.4
24 ⫺ 175 ⫺ 66 ⫺ 24
64 179 180 ⫺ 64
C D E F
3.2 5.0 4.4 3.7
26 ⫺ 176 ⫺ 63 ⫺ 49
61 179 166 ⫺ 67
C D E F
3.9 5.0 4.1 3.4
65 ⫺ 177 ⫺ 60 ⫺ 42
74 161 162 ⫺ 65
C D E F
3.9 4.6 4.1 3.3
60 ⫺ 155 ⫺ 61 ⫺ 39
76 142 179 ⫺ 65
C D E F
3.4 5.3 4.8 3.8
49 ⫺ 139 ⫺ 74 ⫺ 72
45 ⫺ 177 173 ⫺ 50
C D E F
3.4 5.3 4.8 4.0
56 ⫺ 140 ⫺ 72 ⫺ 68
39 ⫺ 177 173 ⫺ 63
C D E F
3.4 4.9 4.5 3.7
52 ⫺ 160 ⫺ 69 ⫺ 57
51 177 171 ⫺ 63
C D E F
3.4 5.3 4.8 4.0 4.9 4.9
58 ⫺ 140 ⫺ 72 170 162 ⫺ 150
38 ⫺ 176 173 ⫺ 63 175 ⫺ 179
13
14
15
16
17
18
19
20
Arginine Four amino ketones
286
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Fig. 5. Fit of the neolignan 12D to arginine, produced by PowerFit program. (a) Arginine is in the conformation A obtained by crystallographic data. (b) Arginine is in the conformation B obtained after the rotation of 120⬚ on the axis c.
interactions to be feasible, the position of the rings in the neolignans has to coincide with the guanidyl and amino groups. The distance between atoms C3 and C6 ˚ . The distance between the two of arginine is 4.9 A phenyl rings in neolignans can be measured as the distance between the atoms C6 and C18 of the molecule as seen in Fig. 1. The distances between the two rings in the four different conformations, B, C, D, and F of Fig. 2 for each of the nine active compounds as well as corresponding values of the four amino ketones were calculated. Dihedral angles a and b of the compounds were also evaluated. These results are listed in Table 2. The conformation D is the only one that exhibits a distance between the two rings close to ˚ for all the nine neolignans. The dihedral angles 5.0 A a and b of the conformation D of each neolignans are also close to those of arginine. The conformation 12D, for instance, must fit well to the arginine. The distances between the two phenyl rings for the conformations C, E and F of the neolignans, however, are ˚ for most of cases. The substantially smaller than 5.0 A distance between the two phenyl rings in each amino
˚ which is identical to the distance ketone is 4.9 A between C3 and C6 of arginine. The conformation D of the neolignans is approximately planar, like amino ketone conformation. This conformation produces the adequate position of the rings to fit to arginine. The other conformations C, E and F have the torsional angles, a or b, close to 60⬚, which cause the neolignan to take bent conformation and to make the distance between the two phenyl rings short. This prohibits the neolignans to fit to arginine. The neolignan 12 in its conformation D (12D) was fitted to arginine in its two different conformations, A and B (see Fig. 4), using the PowerFit computer program. The results of the calculations are schematically drawn in Fig. 5. The total energy for the optimal fitting between 12D and the conformation A was ⫺ 900.8 kcal/mol, while the corresponding value of the optimal fitting between 12D and the conformation B was ⫺ 982.0 kcal/mol. The pair between 12D and the conformation B of arginine is favored over the pair between 12D and the conformation A. We conclude that; (1) the neolignans that are
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
active against visceral leishmaniasis take their conformations in the form of D (as shown in Fig. 2), (2) the conformation B of the arginine may be preferred over to the conformation A to pair with the active neolignans. Acknowledgements We thank Dr. Yoshiyuki Hase for helping us the use of PowerFit computer program and stimulating discussions. Financial supports from FAPESP and CNPq as well as computational aids from CENAPAD are acknowledged. References [1] A. Paine, L.E.S. Barata, R.A. Neal, S.L. Croft, J.D. Phillipson, L.S. Santos, P.H. Ferri, Anti-leishmanial activity of neolignans from Virola species and synthetic analogues related to neolignans (unpublished data). [2] L. Rey, in: S.A. Guanabara Koogan (Ed.), Parasitologia, 2, RJ, Rio de Janeiro, 1991 Chap. 19.
287
[3] D.L. Looker, R.L. Beren, J.J. Marr, Mol. Biochem. Parasitol. 9 (1983) 15–28. [4] M. Gottlieb, Parasitol. Today 5 (1989) 257–260. [5] A. Kornberg, W.E. Pricer Jr, J. Biol. Chem. 193 (1951) 481– 495. [6] L. Ghosh, A.K. Datta, Biochem. J. 298 (1994) 295–301. [7] L.E.S. Barata, Isolamento e Sı´ntese de Neolignanas de Virola surinamensis, Ph.D. Thesis, Universidade Estadual de Campinas-SP, Brazil, 1976. [8] L.E.S. Barata, P.M. Baker, O.R. Gottlibe, E.A. Ruveda, Phytochemistry 17 (1978) 783. [9] L.S. Santos, Ph.D. Thesis, Universidade Estadual de Campinas, Campinas, SP, Brazil, 1991. [10] M.C.A. Costa, Y. Takahata, J. Comput. Chem. 18 (1997) 712– 721. [11] A. Gebre-Hiwot, D. Frommel, J. Antimicr. Chemoth. 32 (1993) 837–842. [12] G.N. Ramachandran, S.K. Mazumdar, K. Venkatesan, A.V. Lakshminarayanan, J. Mol. Biol. 15 (1966) 232–242. [13] J. Pauline, T.A. Wildman, J. Phys. Chem. 95 (1991) 20–25. [14] PowerFit User manual, 1997, Microsimulations, 478 Green Mountain Road, Mahwah, NJ 07430, USA. http://www.microsimulations.com. [15] S. Kearsley, G. Smith, Tetrahedron Computer Methodology 3 (1992) 615–633. [16] A.L. Lehninger, in: Edgard Blu¨cher (Ed.), Bioquı´mica, , 1976 pp. 214, 215.
Conformation of neolignans that bind to the arginine residue in adenosine-kinase from Leishmania donovani Maria Cristina Andreazza Costa, Lauro Euclides Soares Barata, Yuji Takahata* Instituto de Quı´mica,Universidade Estadual de Campinas, Caixa Postal 6154, Cep 13083-970-Campinas, SP, Brazil
Abstract Most probable conformation of synthetic neolignans that are active against visceral leishmaniasis is proposed. It is based upon an assumption that the receptor of the neolignans is the arginine residue in the adenosine-kinase from Leishmania donovani. A planar form (the two phenyl rings are stretched out) of the neolignans is most likely a preferred receptor site conformation. 䉷 1999 Elsevier Science B.V. All rights reserved. Keywords: Neolignans; Active conformation; Leishmaniasis; AM1 and MM methods
1. Introduction Leishmaniasis is an important tropical disease, affecting half a million people in the world, for which there are no efficient treatments at present [1]. Leishmania donovani is a species of the leishmania protozoa that are the causative agent of visceral leishmaniasis; this is fatal if untreated. Pentavalent antimonials and amphotericin B are used to the treatment, but they are not always effective and require long period of administration, which is associated with drug toxicity [2]. It has been observed that all parasitic protozoa, inclusive of L. donovani, studied to date lack the ability to synthesize purine ‘‘de novo’’. Thus they scavenge purines from the host using its own unique set of purine-salvage enzymes [3,4]. Adenosine kinase (ATP: adenosine 5 0 -phosphotransferase, EC 2.7.1.20) is one of the key enzymes of the purinesalvage pathway. It catalyses the transfer of terminal phosphate from ATP to adenosine(Ado) [5]. Little is * Corresponding author. Fax: ⫹55 019 788 3023. E-mail address: [email protected] (Y. Takahata)
known regarding the active-site structure and the molecular mecanism associated with adenosinekinase mediated Ado phosphorylation. Recently Ghosh and Datta found the evidence, for the first time, that indicates the presence of one arginine residue exclusively at the Ado-binding site of the L. donovani adenosine kinase [6]. Moreover, they demonstrated that the arginine specific regents phenylglyoxal (PGO), butane-2,3-dione and cyclohexane-1,2-dione all irreversibly inactivated the enzyme. In view of these observations, we can assume that drugs that are active against L. donovani interact with (or bind to) the arginnie residue of the adenosine kinase and inactivate the leishmanial enzyme. Once the enzyme is inactivated, L. donovani must die. Neolignans are dimers from oxidative coupling of allyl and propenyl phenols that occur in the Myristicaceae and other primitive plant families. The Virola is the most representative member of Myristicaceae occurring throughout the Americas. In 1970, initial studies of leaves of Virola surinamensis [7] showed high efficacy in the blockage tests of penetration of cercarie of Schistosoma mansoni in mice. The active substances responsible for protection were isolated
0166-1280/99/$ - see front matter 䉷 1999 Elsevier Science B.V. All rights reserved. PII: S0166-128 0(98)00560-0
282
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Fig. 1. Neolignans number 12–20 are active ‘‘in vitro’’ against visceral leishmaniasis.
and identified as the natural neolignans. Barata et al. [8] and Santos [9] synthesized 20 analogs of the active substances to determine the biological activity of neolignans. The biological tests were made by Neal and others of London School of Hygiene and Tropical
Medicine [1]. Of the 20 compounds tested in vitro, nine molecules of these showed activity against leishmaniasis, and 11 showed inactivity. The nine active neolignans are shown in Fig. 1. In previous studies, we analyzed a series of the 20 synthetic neolignans in
Fig. 2. The four local minima of the neolignans found as the most probable to be the active conformations.
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Fig. 3. Basic structure of the amino ketones. ‘‘R’’ are the substituents in the molecules. R11 is H or Cl; R22 is –(CH2)n–NH2 or – (CH2)– O– (CH2)6 –NH2 and R24 is H or –CH3[11].
283
order to define the most probable conformer that may fit receptor [10]. Using molecular mechanics method (MM2) and Boltzmann’s distribution, we concluded that only four local minima (C, D, E, F) out of eight could correspond to the probable conformer [10]. The four probable active conformers are shown in the Fig. 2. In the present work, we want to know which conformer out of the four can best fit to the active-site of arginine residue in L. donovani adenosine kinase. We assume that the 9 active neolignans interact with the arginine residue. It is important to know active conformation of drugs. Information about the conformation helps one to understand the mechanism of drug action and help to develop new drugs. A series of amino ketone compounds are also active against leishmaniasis. These molecules are somewhat similar to the neolignans because both series of
Fig. 4. (a) Geometry of the arginine obtained by crystallographic data [12] and by AM1 calculations. (b) Geometry of the arginine after rotation of 120⬚ of the axis c, in relation to Fig. 4a. (c) Representative scheme of the adenosine. The geometry of the adenine portion was obtained from the literature [16].
284
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Table 1 DHf is the heat of formation calculated by AM1 method to conformations A and B of the arginine, where conformation A was obtained by crystallographic data. In the conformation B, the dihedral angle referent to atoms 7–2–3–4 (in the Fig. 4a) was rotated by 120⬚. The rotational barrier energy (RE) was calculated from A to B Conformation A (axis c ⫹ 62.1⬚) B (axis c ⫺ 62.7⬚)
DHf (kcal/mol) ⫺ 56.77 ⫺ 58.52
RE (kcal/mol) 3.09
compounds have two phenyl groups and a carbonyl between them. Basic structure of amino ketones are shown in the Fig. 3. It is known that a number of amino ketones are capable of inhibiting a key enzyme (2,3-oxidosqualene lanosterol cyclase) in fungal sterol biosynthesis. The amino ketones in Fig. 3 also showed activity against leishmaniasis [11]. As a result, we can assume that amino ketones are capable of inhibiting the adenosine-kinase from L. donavani. We can suppose that the amino ketones bind to the arginine residue in the adenosine-kinase from L. donavani. We compare the geometry of the amino ketones with the four possible conformation of the neolignans in order to find the most probable active conformation of the neolignans.
2. Calculations Crystallographic data for the heavy atoms of arginine are available in the literature [12]. We calculated the positions of the hydrogen atoms of arginine using the AM1 semiempirical method keeping the heavy atoms in the observed positions. The conformational analysis of the two phenyl rings of the benzophenone in the aminoketones was performed by Pauline and Wildeman [13]. A series of AM1 calculations showed that the minimum energy conformation of the benzophenone has both rings twisted by 33⬚, in agreement with crystallographic data [13]. The conformational analysis of the neolignans were performed previously [10], using molecular mechanics method-MM2. The fitting of the neolignans to the arginine was done using the PowerFit program [14]. PowerFit is a Computer-Assisted Molecular Fitting program that is designed to run on desktop computers. The computation engine of the PowerFit is based on the Steric
and Electrostatic Alignment of Kearsley and Smith [15].
3. Results and discussion We assume that geometry of arginine residue at the active site of the leishmanial enzyme is similar to the geometry of crystallized arginine molecules. The geometry of the arginine (obtained by crystallographic data) is shown in the Fig. 4a and c displays an adenosine scheme-the substrate of the adenosinekinase. The geometry of the adenine portion of the adenosine is obtained from the literature [16]. It is known that adenine is in a perpendicular plane to the ribose ring plane [16]. If we compare the angles and distances of the guanidyl group in the arginine and those of the adenine, we observe that atoms N9, C6, N10 and N8 of the arginine can superimpose to C6, C5, N7 and C4 of the adenine through hydrogen bonds. If the axis c in the arginine of the conformation A in Fig. 4a is rotated by 120⬚, it results in the conformation B shown in Fig. 4b. The conformation B facilitates formation of an additional hydrogen bond between H15 of arginine and O17 of adenosine. We calculated the heats of formation of isolated arginine in the two conformations, A and B, using the AM1 semiempirical method (Table 1). The heat of formation of the conformation B is 1.75 kcal/mol lower than that of the conformation A. As the conformation A is the observed conformation from the crystallographic data, A must be more stable than B in crystal form. The discrepancy between the observed conformation and the calculated one may depend upon the fact that the calculated conformations are in the forms of isolated molecule while the observed one is in the form of a crystal, or it may be owing to the inaccuracy of the semiempirical method. In any case, we may be able to assume that B can be almost as stable as A. The rotation barrier is 3.09 kcal/mol which is small. These considerations suggest that the arginine residue can take the conformation B as well as A when it interacts with the substrate. If the arginine residue takes the conformation B, it interacts with the substrate by its guanidyl and amino groups. The p electrons of the two aromatic rings in the neolignans could make electrostatic interactions with the guanidyl and amino groups of arginine. For these
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
285
Table 2 dl is the distance between atoms C6 and C18 of the neolignans (compounds 12–20) in the Fig. 1. For arginine, dl is the distance between atoms C3 and C6 (Fig. 4) and for amino ketones (Fig. 3), between atoms C6 and C16. The dihedral angles, a and b are shown in the Figs. 1, 3 and 4 Compound
Conformation
˚) distance dl (A
Dihedral angles (degrees) a
b
12 C D E F
3.6 5.1 4.4 3.6
46 ⫺ 174 ⫺ 60 ⫺ 46
63 179 180 ⫺ 63
C D E F
3.4 5.1 4.5 3.4
24 ⫺ 175 ⫺ 66 ⫺ 24
64 179 180 ⫺ 64
C D E F
3.2 5.0 4.4 3.7
26 ⫺ 176 ⫺ 63 ⫺ 49
61 179 166 ⫺ 67
C D E F
3.9 5.0 4.1 3.4
65 ⫺ 177 ⫺ 60 ⫺ 42
74 161 162 ⫺ 65
C D E F
3.9 4.6 4.1 3.3
60 ⫺ 155 ⫺ 61 ⫺ 39
76 142 179 ⫺ 65
C D E F
3.4 5.3 4.8 3.8
49 ⫺ 139 ⫺ 74 ⫺ 72
45 ⫺ 177 173 ⫺ 50
C D E F
3.4 5.3 4.8 4.0
56 ⫺ 140 ⫺ 72 ⫺ 68
39 ⫺ 177 173 ⫺ 63
C D E F
3.4 4.9 4.5 3.7
52 ⫺ 160 ⫺ 69 ⫺ 57
51 177 171 ⫺ 63
C D E F
3.4 5.3 4.8 4.0 4.9 4.9
58 ⫺ 140 ⫺ 72 170 162 ⫺ 150
38 ⫺ 176 173 ⫺ 63 175 ⫺ 179
13
14
15
16
17
18
19
20
Arginine Four amino ketones
286
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
Fig. 5. Fit of the neolignan 12D to arginine, produced by PowerFit program. (a) Arginine is in the conformation A obtained by crystallographic data. (b) Arginine is in the conformation B obtained after the rotation of 120⬚ on the axis c.
interactions to be feasible, the position of the rings in the neolignans has to coincide with the guanidyl and amino groups. The distance between atoms C3 and C6 ˚ . The distance between the two of arginine is 4.9 A phenyl rings in neolignans can be measured as the distance between the atoms C6 and C18 of the molecule as seen in Fig. 1. The distances between the two rings in the four different conformations, B, C, D, and F of Fig. 2 for each of the nine active compounds as well as corresponding values of the four amino ketones were calculated. Dihedral angles a and b of the compounds were also evaluated. These results are listed in Table 2. The conformation D is the only one that exhibits a distance between the two rings close to ˚ for all the nine neolignans. The dihedral angles 5.0 A a and b of the conformation D of each neolignans are also close to those of arginine. The conformation 12D, for instance, must fit well to the arginine. The distances between the two phenyl rings for the conformations C, E and F of the neolignans, however, are ˚ for most of cases. The substantially smaller than 5.0 A distance between the two phenyl rings in each amino
˚ which is identical to the distance ketone is 4.9 A between C3 and C6 of arginine. The conformation D of the neolignans is approximately planar, like amino ketone conformation. This conformation produces the adequate position of the rings to fit to arginine. The other conformations C, E and F have the torsional angles, a or b, close to 60⬚, which cause the neolignan to take bent conformation and to make the distance between the two phenyl rings short. This prohibits the neolignans to fit to arginine. The neolignan 12 in its conformation D (12D) was fitted to arginine in its two different conformations, A and B (see Fig. 4), using the PowerFit computer program. The results of the calculations are schematically drawn in Fig. 5. The total energy for the optimal fitting between 12D and the conformation A was ⫺ 900.8 kcal/mol, while the corresponding value of the optimal fitting between 12D and the conformation B was ⫺ 982.0 kcal/mol. The pair between 12D and the conformation B of arginine is favored over the pair between 12D and the conformation A. We conclude that; (1) the neolignans that are
M.C.A. Costa et al. / Journal of Molecular Structure (Theochem) 464 (1999) 281–287
active against visceral leishmaniasis take their conformations in the form of D (as shown in Fig. 2), (2) the conformation B of the arginine may be preferred over to the conformation A to pair with the active neolignans. Acknowledgements We thank Dr. Yoshiyuki Hase for helping us the use of PowerFit computer program and stimulating discussions. Financial supports from FAPESP and CNPq as well as computational aids from CENAPAD are acknowledged. References [1] A. Paine, L.E.S. Barata, R.A. Neal, S.L. Croft, J.D. Phillipson, L.S. Santos, P.H. Ferri, Anti-leishmanial activity of neolignans from Virola species and synthetic analogues related to neolignans (unpublished data). [2] L. Rey, in: S.A. Guanabara Koogan (Ed.), Parasitologia, 2, RJ, Rio de Janeiro, 1991 Chap. 19.
287
[3] D.L. Looker, R.L. Beren, J.J. Marr, Mol. Biochem. Parasitol. 9 (1983) 15–28. [4] M. Gottlieb, Parasitol. Today 5 (1989) 257–260. [5] A. Kornberg, W.E. Pricer Jr, J. Biol. Chem. 193 (1951) 481– 495. [6] L. Ghosh, A.K. Datta, Biochem. J. 298 (1994) 295–301. [7] L.E.S. Barata, Isolamento e Sı´ntese de Neolignanas de Virola surinamensis, Ph.D. Thesis, Universidade Estadual de Campinas-SP, Brazil, 1976. [8] L.E.S. Barata, P.M. Baker, O.R. Gottlibe, E.A. Ruveda, Phytochemistry 17 (1978) 783. [9] L.S. Santos, Ph.D. Thesis, Universidade Estadual de Campinas, Campinas, SP, Brazil, 1991. [10] M.C.A. Costa, Y. Takahata, J. Comput. Chem. 18 (1997) 712– 721. [11] A. Gebre-Hiwot, D. Frommel, J. Antimicr. Chemoth. 32 (1993) 837–842. [12] G.N. Ramachandran, S.K. Mazumdar, K. Venkatesan, A.V. Lakshminarayanan, J. Mol. Biol. 15 (1966) 232–242. [13] J. Pauline, T.A. Wildman, J. Phys. Chem. 95 (1991) 20–25. [14] PowerFit User manual, 1997, Microsimulations, 478 Green Mountain Road, Mahwah, NJ 07430, USA. http://www.microsimulations.com. [15] S. Kearsley, G. Smith, Tetrahedron Computer Methodology 3 (1992) 615–633. [16] A.L. Lehninger, in: Edgard Blu¨cher (Ed.), Bioquı´mica, , 1976 pp. 214, 215.