CHAPTER 3. Vibrational Characteristics of PTP-1B Inhibitors

Transcription

1 CHAPTER 3 Vibrational Characteristics of PTP-1B Inhibitors

2 3.1 Preface Theoretical Frequency calculations were performed on the molecules chosen in this study. Initially all the geometries were optimized using with DFT method. Theory behind the frequency calculations of a molecule has been discussed in chapter on. Here we discuss the calculated frequencies, their structural significance and correlation with biological activity of the inhibitor molecules selected. PTP-1B inhibitor ligands in the present studies involve benzofuran, benzothiophene and indene molecular systems. In series S1 ligands 1 to 6 are the representative ligands and the rest are their analogues of substitute R1 with different R2 substitute. Ligands 1-3 are furans and 4-6 are thiophenes. 3.2 Result and discussion Calculated IR frequencies of some of the normal vibrations in different Benzofuran and benzothiophene derived carboxylic acid derivatives of representative molecules are reported in Table 3.1. Table 3.1: C19O22 Stretching frequencies in representative molecules in S1 Ligand Activity C19O22 Stretch Ligand Activity C19O22 Stretch (82) (76) (79) (57) (96) (77) Calculated IR frequencies of some of the normal vibrations in different Benzofuran and benzothiophene derived carboxylic acid derivatives of rest of the molecules are reported in Table

3 Table 3.2: IR frequencies of some of the normal vibrations in S1 O1C2 C19O22 Stretch O22C23 Stretch OH CO C-OH Stretch Activity (66) 1276(566) 1088(78) 1376(88) 1889(415) 1234(12) (20) 1259(443) (46) 1868(326) 1227(15) (51) 1265(469) 1076(101) (45) 1269(475) (453) (53) 1405(628) 1203(106) 1338(111) 2034(273) 1065(18) (18) 1261(309) 1075(76) 1392(142) 1818(323) 1194(144) (07) 1279(397) 1093(71) 1189(106) 1833(233) 1189(106) (05) 1284(315) 1100(152) 1286(148) 1865(234) 1157(202) (05) 1286(330) 1100(155) 1340(11) 1865(239) 1157(201) (21) 1279(473) 1061(58) 1222(102) 1849(254) 1169(170) (07) 1279( (61) 1324(20) 1849(254) 1169(138) (03) 1279(473) 1061(60) 1324(13) 1847(261) 1169(166) (05) 1278(453) 1061(64) 1324(16) 1849(250) 1169(177) (10) 1278(470) 1061(52) 1324(16) 1848(253) 1169(171) (06) 1281(348) 1094(127) 1324(05) 1868(220) 1155(194) (03) 1280(406) 1093(77) 1239(14) 1834(232) 1189(113) (10) 1278(533) 1082(84) 1229(68) 1843(184) 1164(98) (01) 1278(455) 1062(54) 1221(106) 1849(251) 1168(174) (01) 1281(512) 1094(110) 1311(03) 1856(188) 1157(153) Series S1 ligands turn out to be phenyl acetic moiety due to R2 substitution at position O22 except 7, which is acetic acid moiety and 1 to 6 have no R2 substitution at position O22. The location of ether oxygen as O22 is crucial in all these systems since it connects the non-polar, hydrophobic part of the ligand through biphenyl rings to the polar, bulky phenyl acetic substitute R2. Stretching frequency of C19O22 bond holding ether O22 is found to be interesting. Substitute R2 brings about the variation in C19O22 stretching vibration. R2 being absent in representative ligands 1-6, this vibration is assigned to 1308 cm 1. Besides the downshift this frequency is enhanced in intensity largely in rest of the ligands in series S1. This vibration is downshifted by 32, 49 and 29 cm 1 in 7, 8 and 14 (the R1 analogues of 1). This downshift in 7 and 8 turns out due to I effect from carboxylic group in 7 and 89

4 additional benzyl group in 8. R2 substitute is -CH2COOH in 7, whereas in 8 it is CH(CH2PhCOOH). Absence of -CH2Ph in substitute R2 in 7 relative to 8 minimize the I effect and hence the downshift. Ligand 14 being thiophene, sulphur at position S1 replace electron withdrawing furan oxygen that is in conjugation with O22. It bring about less downshift in above stretching frequency against furans 7 and 8. The downshift in furans (7-13) ranges from 49 cm 1 in 8 and 11 to 32 cm 1 in 7 whereas in thiophenes it varies from 30 cm 1 in 20 to 22 cm 1 in 16. These downshifts are attributed to two factors; one is variation in R2 substitute and second is the presence of O as furan or S as thiophene. Electron withdrawing furan oxygen causes more downshift as compared to sulphur in thiophenes. As discussed in chapter 1, the presence of hydroxyl moiety as CHOH in substitute R1 in 12 brings into the excess of twist around C4C10 bond causing its significant elongation by Å as compared to analogue 10. This reproduces the up shift in C19O22 stretching vibration of 97 cm 1 by conjugation. The ligand 12 shows the highest inhibitory activity among the furans (Log Ic50 = 1.0) in series S1. The C19O22, O22C23 and C=O from the carboxylic group in substitute R2 stretching vibrations in this series are found to be sensitive towards the inhibitory activity A in furans, thiophenes and indenes. IR frequency calculations of series S1 ligands imply that stronger binding interactions with substrate are favored with following attributesi) strengthening of the ether bond C19O22 ii) strengthening of the ether bond O22C23 in furans 7-12 and in thiophenes in which the ring at C25 in substitute R1 is not substituted. iii) weakening of the ether bond O22C23 in thiophenes and indenes wherein benzyl ring in R1 is substituted by either methoxy/ hydroxy / pyridine /thiophene/ furan moiety iv) weakening of C=O bond in furans or thiophenes v) strengthening of C=O bond in indenes Inhibitory activity versus stretching frequencies of these bonds is depicted in Figures 3.1 to 3.5. Deviations in these trends of C19O22, C=O and O22C23 stretching frequencies vs. A noticed for certain ligands are pointed out below. 90

5 1. Noticeable up-shift in C19O22 and O22C23 stretch in furans 7 wherein R2 is acetic acid instead of benzyl acetic acid moiety and in 12, one with lowest relative planarity (highest d(c4c10c11c12)). 2. Elongation of C5C24 and C4C10 bonds and shortening of C19O22 bond manifests in up shift of C=O stretching frequency in 12 relative to 15 by around 230 cm 1 engender deviation in its correlation with inhibitory activity. Downshift of 47 cm 1 is noticed in the ligand 13 because of COOH group located relatively away from ether oxygen. Presence of butyl moiety instead of phenyl as substitute R1 in 14 causes the downshift of around ~32 cm 1 in the carbonyl stretching frequency. 3. O22C23 stretch vs. A in except the indenes 24, showing up shift of 25 cm 1 and 27 showing downshift of 60 cm 1 Figure 3.1. A vs. C19O22 stretch in furans and thiophenes, 91

6 Figure 3.2. A vs. C=O stretching, furans and thiophenes. Figure 3.3 Activity A vs. C=O stretching frequency, indenes 92

7 Figure 3.4 O22C23 vs. A, (7-16) Figure. 3.5 O22C23 vs. A, (17-29) O22C23 stretching vibration in thiophenes exhibit both increasing and decreasing trend with activity. Thiophenes with higher O22C23 stretching frequency along-with furans posses enhanced intrinsic activity (Figure 3.4). Indenes and rest of the thiophenes in which benzyl moiety (as R1) is modified to 93

8 methoxy benzyl, the activity trend appears to be reversed. The predicted value of 1061cm 1 for O22C23 vibration for is downshifted relative to benzyl analogue 15 wherein it is 1100 cm 1 (Figure 3.5). IR frequencies of O22C23 stretch show decreasing trend in their variation with activity in these ligands. The presence of methoxy benzyl moiety as substitute R1 (pair of cyclic ether oxygen instead of -OMe is present in 27) exhibits I effect and weakening the O22C23 bond. The mesp value of ether oxygen O22 in the analogue 20 is kj.mol 1 whereas in these ligands (23 to 27) it is downshifted to kj.mol 1 in 25 and kj.mol 1 in 27. The lowering of around 10 kj.mol 1 in mesp implies the reduced charge density at ether oxygen and weakening the O22C23 bond that manifest in the downshift of its IR stretching. As discussed in chapter 1, larger twist and turn of furan/thiophene rings and biphenyl rings d(c4c10c11c12) in ligand molecules elongates the C4C10 bond and discriminates positively the receptor inhibition. Ligands showing both, the higher stretching frequency C19O22 and more elongation of C4C10 bond reflect the better inhibition. Variation in these two parameters is presented in Figure 3.6 below. These variations indicate that transfer of charge density from furan/thiophene region towards central ether oxygen helps to improve the inhibitory action of the ligand. This may be helping the formation of hydrophobic region and possible π interactions at furan/thiophene rings and at the same time the increase in polar character at the opposite end. This supports the predictions by Malamas et.al. of hydrophobic and polar interactions in complexing with ptp 1b. Docking studies in present work also predict the large number of hydrogen bond interactions at the polar R2 end as compared to the opposite end. 94

9 Figure 3. 6 Elongation of C4C10 bond vs. frequency of C19O22 bond C=O (bond from the carboxylic group in substitute R2) and C19O22 stretching frequencies increase simultaneously in series S1 ligands as depicted in the figure 3.7 (R 2 = 0.97 for thiophenes and indenes) and figure 3.8 (R 2 = 0.90 for furans). This prediction is supported by the variation of esp minima at ether and carbonyl oxygen. In case of furans, the esp. minima at carbonyl O becomes more negative with minima at ether O becoming shallow. In benzothiophenes both the minima become deeper simultaneously. Figure 3. 7 C 19O 22 vs. CO stretch, S1- thiophenes and indenes 95

10 Figure 3.8 C 19O 22 vs. CO stretch, furans Series 1 R1 R3 O R1 X R2 O R3 X R4 O S O R2 Series 2 Series 3 Figure 3. 9 Atomic numbering scheme and the skeleton of series 1, 2 and 3 ligands in PTP-1B inhibitors 96

11 The stretching frequency of the two ether bonds C19O22 and O22C23 increase simultaneously in series S1 as can be seen from figure and In series S2 and S3 this feature disappear with the presence of varying substitute R1 and R2 at C18 and C20 on the biphenyl ring adjacent to ether oxygen. In series S3 downshift only is observed in C19O22 stretch in both, thiophenes and furans. Figure 3.10 C 19O 22 and O 22C 23, Series S1, Furans Figure C 19O 22 and O 22C 23, Series S1, furans, thiophenes and indenes. (8-30 except 34) C=O (from the carboxylic group) stretching frequency increases with the decrease in neighborhood C-OH stretching frequency in series S1 ligands except in 7, 9 and 10 as shown in Figure (R 2 = 0.9). 97

12 Figure 3.12 CO vs. C-OH except 7,9,10 In furans C19O22 stretching frequency linearly increases with C-OH stretching frequency as shown in figure 3.13 (with the exceptions of 7 and 12). Both These vibrations are up shifted in 7 and in 12, a large upshift of 140 cm 1 in C19O22 stretching frequency with downshift of more than 150 cm 1 in C-OH stretching frequency. No such trend is observed with the said vibrations in thiophenes and indenes. Figure C19C22 vs. C-OH b: furans, except 7 and 17 98

13 R2 substitute i.e. phenyl acetyl moiety commence the downshift in the stretching frequency of ether bond C19O22 in S1 as well as in S2. Downshift is around 20 to 30 cm 1 in the series S1and that in S2 is around 20 to 90 cm. 1 Same stretch is found to be lower in furans than the thiophenes in all the three series. The stretching frequency ranges from 1259 cm 1 in 8 to 1405 cm 1 in 12 in S1 furans and in thiophenes from 1278 cm 1 in 20, 21, 26, 27 to 1286 cm 1 in 16. In S2 furans it varies from 1243 cm 1 in 41 and 42 to 1339 cm 1 in 30. Series S3 compounds are sulphono biphenyls where analogous ether carbon C23 in S1 and S2 is replaced by S, to which is attached a pair of electronegative oxygen atoms, is in turn attached to phenyl ring that is substituted with R1 and R2 at meta and para positions respectively. Similar to S1 and S2 in series S3 also C19O22 stretch is downshifted in furans as compared to thiophenes. C19O22 stretch in the representative furan 68, oscillates at 1187cm 1 The ligands 66 and 69 show this band at the same position as in 68 but is downshifted in 70 to 1175 cm 1 due to two methyl substitutes as R1 and R2 at the adjacent biphenyl ring. An up shift of 42, 55 and 33 cm 1 is observed in 67, 71 and 72. The up shift seems to be due to absence of withdrawing COOH group as R2 in 67, presence of donating -NO2 in 71 and cyclopentyl in 72 as R3. 99

14 Table 3.3 IR frequencies of some of the normal vibrations in S2 Molecule A O1C2 C19O22Stretch O22C23 Stretch OH CO C-OH Stretch (05) 1328(91) (30) (05) 1339(59) (48) (06) 1314(199) 1096(166) 1331(31) 1867(217) 1159(201) (05) 1315(95) 1056(40) 1061(80) 1335(09) 1861(225) (06) 1244(194) 1038(120) 1221(136) 1831(177) 1071(175) (06) 1274(85) 1041(75) 1308(01) 1850(275) 1160(126) (05) 1273(250) 1041(198) 1311(117) 1859(245) 1161(64) (06) 1275(113) 1003(119) 1388(15) 1846(171) 1197(166) (05) 1268(63) 1042(78) 1249(33) 1886(416) 1398(332) (06) 1276(123) 1038(93) 1249(04) 1885(412) 1395(301) (06) 1244(182) 1055(86) 1239(27) 1887(377) 1401(427) (05) 1243(198) 1056(72) 1237(15) 1886(369) 1401(427) (04) 1243(178) 1056(65) 1232(07) 188 (367) 1402(423) (06) 1261(138) 1107(63) 1192(115) 1847(237) 1401(41) (06) 1258(145) 1120(112) 1183(08) 1858(254) 1428(47) (05) 1266(119) 1043(85) 1223(13) 1883(382) 1397(303) (06) 1265(179) 1043(89) 1221(17) 1885(383) 1395(306) 100

15 (05) 1268(115) 1049(67) 1223(21) 1884(387) 1401(335) (07) 1262(152) 1085(88) 1331(43) 1861(248) 14328(41) (05) 1291(213) 1036(105) 1347(24) 1848(249) 1427(97) (73) 1290(158) 1045(145) 1221(65) 1848(201) 1383(23) (79) 1277(114) 1004(105) 1235(47) 1849(183) 1386(35) (74) 1247(166) 1044(145) 1223(48) 1850(171) 1387(20) (69) 1266(135) 1046(166) 1309(05) 1843(220) 1418(51) (79) 1281(109) 1022(113) 1048(79) 1211(153) 1835(230) 1419(49) (81) 1276(94) 991(131) 1211(95) 1839(180) 1391(27) (77) 1282(81) 1024(118) 1206(163) 1837(223) 1407(40) (35) 1202(112) 1029(120) 1317(10) 1849(234) 1433(27) (75) 1242(180) 1034(51) 1305(60) 1864(215) 1355(122) (68) 1283(271) 1104(19) 1200(219) 1850(371) 1424(49) (69) 1285(352) 1056(94) 1218(37) 1882(306) 1404(359) 101

16 Table 3.4 IR frequencies of some of the normal vibrations in S3 A O1C2 C19O22 S23C24 O-S-O sym O-S-O A sym CO C-OH OH wag (60) 1187(66) (255) 1372(127) 1854(264) 1111(38) 1333(271) (63) 1229(62) (396) 1358(102) (33) 1155(396) (60) 1187(45) (209) 1364(241) 1805(282) 1148(221) 1216(163) (61) 1189(35) (201) 1364(198) 1838(328) 1141(255) 1265(99) (72) (157) 1356(98) 1762(408) 1207(307) 1207(307) (76) 1242(119) (51) 1347(170) 1805(335) 1146(242) 1210(171) (62) 1220(30) (212) 1365(127) 1763(355) 1176(97) 1208(266) (05) (198) 1365(221) 1805(282) 1147(218) 1216(172) (05) 1241(126) (113) 1343(182) 1805(305) 1156(190) 1219(188) (05) 1251(113) (91) 1362(190) 1805(303) 1148(230) 1217(185) (02) 1226(85) (278) 1367(151) 1833(308) 1104(68) 1197(50) (59) (131) 1336(183) 1834(379) 1100(69) 1197(43) (07) (129) 1345(32) 1833(363) 1075(155) 1102(55) 1197(61) (10) 1216(184) (269) 1368(132) (127) 1105(74) 1203(316) 102

17 In furans, C=O stretching in reference inhibitor (9), has been assigned to 1868 cm 1 An up shift as well as downshift in frequency for this vibration has been noticed with the R1 substitution. A largest up-shift of 166 cm 1 is predicted for phenyl hydroxymethyl (12) functionality. On the other hand for the benzoic acid substituted R2 derivative (13) a downshift of 50 cm 1 results. In thiophene ligands 15 and in 16, it is predicted at 1865 cm 1 Rest of the group shows a downshift of 16 cm 1 and does not show a significant variation. Indene ligands show decrease in this frequency from 1834(25) to 1868(24) cm 1 Increasing C=O stretching frequency in series S1 and S3 with decrease in adjacent C-OH frequency is depicted in figure 3.14 and In series S2 this trend disappears due to presence of varying R1 and R2 substitutes. In series S3 the R1 and R2 substitutes are OH and COOH moieties respectively in almost all the ligands, hence not affecting the variation of C=O and C-OH stretching frequency. Figure.3.14 C=O vs.c-oh stretching frequency

18 Figure 3.15 C=O vs. -OH stretching frequency S Vibrational Frequency IR Plots IR plots of calculated frequencies for the series S1, S2 and S3 ligands in cm -1 (scaled) vs. intensity in km/mol have been presented in the table 3.5 below that highlight the features such as specific frequency modes and their intensities discussed in this chapter. 104

19 Table 3.5: IR plots Series S

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25

26 Table 3.5: IR plots Series S

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35 Table 3.6: IR plots Series S

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39 Conclusions: Benzofuran, benzothiophene biphenyl molecules show better correlation with inhibitory activity in following cases- 1. Molecules showing up shift in C19O22 stretching frequencies and thus strengthening of the ether bond C19O Molecules showing up shift in the ether bond O22C23 in furans and in thiophenes in which R1 is unsubstituted benzyl moiety. Down shift in frequency of O22C23 ether bond in thiophenes and indenes having Substituted benzyl ring in R1; either with electron withdrawing or donating moiety favors the activity. 3. Presence of phenyl acetyl group at the polar end connecting to ether oxygen O22 although reduce C19O22 frequencies, favors the binding with enzyme. This may be attributed to presence of highly polar carboxyl group as well as the phenyl ring. Carboxyl brings in the hydrogen bond interactions with amino acid residues from the receptor enzyme. The phenyl ring may facilitate π interactions with the enzyme residues. 125