Comprehensive Study on SAR of Rifamycins
J ournal of Medicinal Chemistry, 1998, Vol. 41, No. 13 2331
working conditions were as follows: gas flow, N2 at 25 mL/
min; heating rate, 10 °C/min; open sample, aluminum pan;
sample weight, 3 mg. Thermomicroscopy involved Kofler hot
stage microscopy with polarized light. The IR spectrum was
recorded with a FT-IR Bruker model IFS 48 spectrophotom-
eter, in Nujol mull and CDCl3 solution.
The 1H NMR spectra (1D and 2D) were recorded by a Bruker
DRX 500-MHz instrument at 303 K after the solubilization of
the samples in CDCl3 (concentration ) 20 mg/mL). The
chemical shift values were referred to TMS ) 0 ppm.
The assignments of rifamycins O, S, B, and SV are based
on the reported data and on 2D COSY spectra.26
release structural strains; the starting conformation was taken
from the previous step. Electrostatic contribution has been
included in the calculations, with cutoff radius of 16 Å and ꢀr
) 1.5 (independent from distance). Different protocols for
evaluating atomic partial charges have been explored, with
the aid of Gaussian92.39 Values given by the Gesteiger and
Marsili method40 and values derived by Mulliken’s analysis
performed on the results of ab initio single-point calculations
using STO-3G and 321-G basis sets were found in relevant
disagreement each other. This prompted us to use the more
robust method of potential derived charges,41 as implemented
in Gaussian92, in which atomic charges are optimized in order
to best reproduce the electrostatic potential derived by ab initio
calculation and to fit the molecular dipole moment. STO-3G
basis set was used. The program Sybyl was run on a Silicon
Graphics workstation, while Gaussian92 was run on a CRAY
T3Dv at CINECA, Bologna, Italy.
X-r a y Cr ysta llogr a p h y. Cr ysta l Da ta for Rifa m ycin O:
C
39H47NO14, M ) 753.80, triclinic, a ) 11.823(3), b ) 10.397(2),
c ) 9.501(2) Å, R ) 66.95(1), â ) 104.76(1), γ ) 115.13(1)°, V
) 967.4(4) Å3, T ) 293 K, space group P1 (no. 1), filtered Cu
KR radiation, λ ) 1.541 78 Å, Z ) 1, Dc ) 1.294 Mg/m3, F(000)
) 400, µ(Cu KR) ) 0.8234 cm-1, Siemens AED diffractometer,
θ-2θ scan, 6 < 2θ < 140°, 3677 measured reflections, 3677
unique reflections, 3151 unique observed reflections (I > 2σ
(I)). The phase problem was solved by direct methods (SIR9227),
and the structure was refined by full-matrix least-squares on
Su p p or tin g In for m a tion Ava ila ble: Listings of aniso-
tropic thermal displacement parameters, hydrogen coordi-
nates, and torsion angles for the X-ray crystal structure of
rifamycin O (12 pages). Ordering information is given on any
current masthead page.
all measured Fo with SHELXL93.28 Anisotropic thermal
2
displacement parameters were refined for all non-hydrogen
atoms. Hydrogens bonded to O2, O9, and O10, considered
important for the definition of the pharmacophore, were
located by inspection of the ∆F map and refined isotropically.
The remaining H atoms were introduced at calculated posi-
tions, riding on their carrier atoms, according to the protocols
built in the refinement program.
Final refinement on 510 parameters gave R1 ) 0.056 (on
observed data), R1 ) 0.065 (on all data), wR2 ) 0.166, gof )
1.118. Final difference Fourier map was featureless. Pro-
grams PARST95,29 ZORTEP,30 and PLUTO31 were used for
analyzing and drawing molecular structures and crystal
packing.
Refer en ces
(1) Lancini, G.; Zanichelli, W. Structure-activity relationship in
rifamycins. In Structure-activity relationship among the semi-
synthetic antibiotics; Perlman, D., Ed.; Academic Press: New
York, 1977; pp 531-600.
(2) Brufani, M.; Cerrini, S.; Fedeli, W.; Vaciago, A. Rifamycins: an
insight into biological activity based on structural investigations.
J . Mol. Biol. 1974, 87, 409-435.
(3) Brufani, M.; Cellai, L.; Cerrini, S.; Fedeli, W.; Vaciago, A.
Structure-activity relationships in the ansamycins: the crystal
structure of tolypomycinone. Mol. Pharmacol. 1978, 14, 693-
703.
(4) Brufani, M.; Cellai, L.; Cerrini, S.; Fedeli, W.; Segre, A.; Vaciago,
A. Molecular structure and activity of 3-carbomethoxy rifamycin
S. Mol. Pharmacol. 1982, 21, 394-399.
(5) Arora, S. K. Correlation of structure and activity in ansamy-
cins: molecular structure of sodium rifamycin SV. Mol. Phar-
macol. 1983, 23, 133-140.
(6) Arora, S. K.; Main, P. Correlation of structure and activity in
ansamycins: molecular structure of cyclized rifamycin SV. J .
Antibiot. 1984, 37, 178-181.
All the calculations were performed on an ENCORE91
computer of the Centro di Studio per la Strutturistica Diffrat-
tometrica del CNR in Parma.
Sta tistica l An a lysis of Str u ctu r a l Da ta . The Cambridge
Structural Database32 was searched to retrieve structural data
for all rifamycins characterized by X-ray diffraction.11,12,14-22
In some cases6,16 coordinates were not deposited and were
kindly provided by authors. To these (16 active, 9 nonactive),
data concerning rifamycin O were added, for a total of 26
independent molecules. Table 8 reports quantitative measures
of in vitro activity taken from literature for the compounds
included in the analysis. In the course of the analysis we found
that three rifamycins (five independent molecules) appear in
the literature and in the Cambridge Structural Database with
the wrong absolute configuration, seriously affecting the
discussions based on torsion angles. In the present work all
values have been revised and fixed. Principal Component
Analysis has been performed on a set of 26 Z-scaled structural
variables (defined in the Results and Discussion) by the SAS
package.37 Calculations were performed on RISC/6000 and
Silicon Graphics workstations of the Centro di Calcolo Elettro-
nico at the University of Parma.
Molecu la r Mod elin g. The energies for the rearrange-
ments of torsion angles C16-C17-C18-C19 (T4), C18-C19-
C20-C21 (T6), and C25-C26-C27-C28 (T13) have been
evaluated. The crystal structures of rifamycin O and rifamycin
S20 have been used as starting models. Intramolecular hy-
drogen bonds observed in the solid state have been preserved;
the remaining hydrogens have been placed at typical positions,
according to the geometry of their carrier atoms. Energy
profiles have been calculated by the program Sybyl,38 using
the standard Tripos force field. Each profile corresponds to
the energy variations accompanying the modifications of T4,
T6, and T13, respectively. The rearrangement paths have
been divided into 35 steps of 10°; in each case the initial value
was chosen to be about 10-20° away from the value found in
the crystal. After updating the torsion angle involved in the
rearrangement, the molecular geometry was optimized to
(7) Arora, S. K. Correlation of structure and activity in ansamy-
cins: structure, conformation and interactions of antibiotic
rifamycin S. J . Med. Chem. 1985, 28, 1099-1102.
(8) Bacchi, A.; Mori, G.; Pelizzi, G.; Pelosi, G.; Nebuloni, M.;
Panzone, G. B. Polymorphism-structure relationships of rifamex-
il, an antibiotic rifamycin derivative. Mol. Pharmacol. 1995, 47,
611-623.
(9) Buergi, H. B.; Dunitz, J . D. From crystal statics to chemical
dynamics. Acc. Chem. Res. 1983, 16, 153-161.
(10) Klebe, G. The use of crystal data together with other experi-
mental and computational results to discuss structure-reactivity
and activity relationships. Struct. Chem. 1990, 1, 597-616.
(11) Arora, S. K. Structural investigations of mode of action of drugs.
III. Structure of rifamycin S iminomethyl ether. Acta Crystallogr.
Sect. B 1981, 37, 152-157.
(12) Bartolucci, C.; Cellai, L.; Cerrini, S.; Lamba, D.; Segre, A. L.;
Brizzi, V.; Brufani, M. 21. Synthesis, reactivity studies, and
X-ray crystal structure of (11R)-25-O-deacetyl-11-deoxo-11-hy-
droxy-21,23-O-isopropylidenerifamycin S. Helv. Chim. Acta 1990,
73, 185-198.
(13) Cellai, L.; Cerrini, S.; Segre, A.; Brufani, M.; Fedeli, W.; Vaciago,
A. Comparative study of the conformations of rifamycins in
solution and in the solid state by Proton Nuclear Magnetic
Resonance and X-rays. J . Org. Chem. 1982, 47, 2652-2661.
(14) Cellai, L.; Cerrini, S.; Segre, A.; Brufani, M.; Fedeli, W.; Vaciago,
A. A study on the structures of 3-methoxycarbonylrifamycins
by X-ray crystallography and 1H nuclear magnetic resonance
spectroscopy. J . Chem. Soc., Perkin Trans. 2 1982, 1633-1640.
(15) Gadret, M.; Goursolle, M.; Leger, J . M.; Colleter, J . C. Structure
cristalline de la rifampicine. Acta Crystallogr. Sect. B 1975, 31,
1454-1462.
(16) Brufani, M.; Cellai, L.; Cerrini, S.; Fedeli, W.; Marchi, E.; Segre,
A.; Vaciago, A. X-ray crystal structure of 4-deoxy-3′-bromopyrido-
[1′,2′-1,2]imidazo[5,4-c] rifamycin S. J . Antibiot. 1984, 37, 1623-
1627.