Research Article The Effect of Geometrical Isomerism of 3

Research ArticleThe Effect of Geometrical Isomerism of35-Dicaffeoylquinic Acid on Its Binding Affinity toHIV-Integrase Enzyme A Molecular Docking Study

Mpho M Makola1 Ian A Dubery1 Gerrit Koorsen1 Paul A Steenkamp12

Mwadham M Kabanda34 Louis L du Preez5 and Ntakadzeni E Madala1

1Department of Biochemistry University of Johannesburg PO Box 524 Auckland Park Johannesburg 2006 South Africa2Council for Scientific and Industrial Research (CSIR) Biosciences Natural Products and Agroprocessing GroupPretoria 0001 South Africa3Department of Chemistry Faculty of Agriculture Science and Technology School of Mathematical and Physical ScienceNorth-West University Mafikeng Campus Private Bag X2046 Mmabatho 2735 South Africa4Material Science Innovation and Modelling (MaSIM) Research Focus Area Faculty of Agriculture Science and TechnologyNorth-West University Mafikeng Campus Private Bag X2046 Mmabatho 2735 South Africa5Department of Microbiological Biochemical and Food Biotechnology University of the Free State Bloemfontein South Africa

Correspondence should be addressed to Ntakadzeni E Madala emadalaujacza

Received 3 June 2016 Accepted 18 September 2016

Academic Editor Juntra Karbwang

Copyright copy 2016 Mpho M Makola et al This is an open access article distributed under the Creative Commons AttributionLicense which permits unrestricted use distribution and reproduction in any medium provided the original work is properlycited

A potent plant-derived HIV-1 inhibitor 35-dicaffeoylquinic acid (diCQA) has been shown to undergo isomerisation upon UVexposure where the naturally occurring 31199051199031198861198991199045119905119903119886119899119904-diCQA isomer gives rise to the 31198881198941199045119905119903119886119899119904-diCQA 31199051199031198861198991199045119888119894119904-diCQA and 31198881198941199045119888119894119904-diCQA isomers In this study inhibition of HIV-1 INT by UV-induced isomers was investigated using molecular docking methodsHere density functional theory (DFT) models were used for geometry optimization of the 35-diCQA isomers The YASARA andAutodock VINA software packages were then used to determine the binding interactions between the HIV-1 INT catalytic domainand the 35-diCQA isomers and the Discovery Studio suite was used to visualise the interactions between the isomers and theprotein The geometrical isomers of 35-diCQA were all found to bind to the catalytic core domain of the INT enzyme Moreoverthe 119888119894119904 geometrical isomers were found to interact with the metal cofactor of HIV-1INT a phenomenon which has been linked toantiviral potency Furthermore the 31199051199031198861198991199045119888119894119904-diCQA isomer was also found to interact with both LYS156 and LYS159 which areimportant residues for viral DNA integration The differences in binding modes of these naturally coexisting isomers may allowwider synergistic activity which may be beneficial in comparison to the activities of each individual isomer

1 Introduction

Thedevelopment of therapeutics against theHuman Immun-odeficiency Virus type 1 (HIV-1) which causes AcquiredImmunodeficiency Syndrome (AIDS) is still an active areaof research HIV-1 has among other important componentsthree enzymes that are essential for viral replication andsubsequent infection of humans namely HIV-1 protease(PROT) reverse transcriptase (RT) and integrase (INT)enzymes [1] HIV-1 INT catalyses the incorporation of viral

DNA into the host cell genome after the viral RNA has beenreverse transcribed this step is crucial in viral replicationand makes anti-HIV-1 INT inhibitors an important field ofresearch [2 3] The integrase enzyme has three domainsthe C-terminal domain (CTD) the catalytic core domain(CCD) and the N-terminal domain (NTD) [4]TheCCDhasa conserved catalytic triad the DDE motif which consistsof the residues ASP64 ASP116 and GLU152 [5] Withinthe catalytic core domain of HIV-1 INT is the divalentmetal (Mg2+ or Mn2+) cofactor that deprotonates water for

Hindawi Publishing CorporationEvidence-Based Complementary and Alternative MedicineVolume 2016 Article ID 4138263 9 pageshttpdxdoiorg10115520164138263

2 Evidence-Based Complementary and Alternative Medicine

31015840 end processing of viral cDNA a reaction that involvestransesterification [3 6] Other amino acid residues (LYS156and LYS159) are also important for viral DNA binding beforefurther processing can occur [6]

The dicaffeoylquinic acids (diCQAs) a group of plantsecondary metabolites have been found to possess specificand irreversible inhibitory activity againstHIV-1 INTmakingthem potent inhibitors [7 8] These compounds have beenisolated fromherbal plants that have beennoted for their anti-HIV activity such as Helichrysum populifolium [9] Centellaasiatica [10 11] and Aster scaber [12] The diCQAs can eitherbind to the active domain or to a flexible loop near thecatalytic site of the enzyme to inhibit viral DNA integrationto the host cell DNA [13] One such diCQA isolated fromherbal plants which has been found to be active against HIV-1 INT is 35-diCQA an ester of quinic acid and two caffeicacidmoieties substituted at the 3 and 5 positions of the quinicacid [14] From docking studies of L-chicoric acid and HIV-INT it can be assumed that the caffeic acid units are the mainpharmacophores of the diCQAs [15]

UV-irradiation of the naturally occurring 31199051199031198861198991199045119905119903119886119899119904-diCQA causes the geometrical isomerism of this moleculein the caffeic acid units and gives rise to cis isomers31198881198941199045119905119903119886119899119904- diCQA 31199051199031198861198991199045119888119894119904-diCQA and 31198881198941199045119888119894119904-diCQA [1416 17] Isomerism of 35-diCQA in the quinic acid unit hasbeen shown to affect its activity against HIV-1 INT [12]however the effect of geometrical isomerism in the caffeicacid units has not been investigated for this molecule Thestereochemistry of bioactive compounds is important sincedifferent stereoisomers have different pharmacodynamics inhumans [18] This is due to the fact that target biomoleculesare stereospecific [19]Though enantiomers are often of moreconcern than other types of stereoisomers [20] the effectsof regional and geometrical isomers on biological activitystill require further investigation For instance Farrer etal found that trans platinum complexes were more activeagainst keratinocytes and human ovarian cancer cells thantheir cis counterparts [21] Furthermore photoisomerisationof cis tetrazoline oxime ethers to the trans isomers resultedin a loss of efficacy of these fungicides when used on plantsexposed to UV-irradiation [22] Given this importance ofthe stereochemistry of bioactive molecules on their activitieswe investigated the differences in the binding interactions ofHIV-INT and the UV-induced geometrical isomers of 35-diCQA

2 Methodology

21 Ligand A random conformational search approach wasused to find the lowest energy conformer for each isomerThe geometries of the four 35-diCQA isomers were thenoptimised in vacuo using density functional theory withthe B3LYP functional and the 6-311+G (d p) basis set Thecalculations were carried out on the Gaussian09 softwarepackage [23] Optimised structures were visualised using theGaussView05 software

22 Molecular Modelling All molecular modelling was per-formed using YASARA Structure [24]The intended receptor

crystal structure (PDB code 1QS4) contained two identicalchains A and B Chain A was chosen as receptor howeverit was missing residues 141ndash144 Chain B contained residues143 and 144 and these residues were inserted into chainA by first superimposing chain B onto chain A and thenremoving all other chain B residues and finally merging theresidues into chain A (all other residues were deleted) Thetwo remaining residueswere artificially added (Ile 141 andPro142) All residues in the structure except for residues 140 to145 were fixed and energy minimization was performed torelax the flexible region Subsequently all residues weremadeflexible and another energy minimization was performed onthe entire structure The resulting structure was used as thereceptor in the subsequent molecular docking experiments

23 Molecular Docking Molecular docking experimentswere prepared using YASARA [24] A rectangular box withdimensions 30 A times 30 A times 30 A was centred on the coordi-nates of the 120572-carbon of Asp 64 in the receptor moleculeThe isomer ligand molecules and the receptor molecule werekept rigid during the experiments Molecular docking exper-iments were performed using Autodock VINA [25] withthe applicationrsquos default settings Each docking experimentproduced 100 ligand-receptor pairs which were clusteredusing a RMSD cut-off of 50 A The pairs with the lowestbinding energy were considered to have the best dockingconformations The results of each experiment were viewedusing YASARA

3 Results and Discussion

Natural products have been at the forefront of drug discoveryand continue to provide viable pharmacophores and possiblescaffolds for the development of potential drugs due to theirstructural diversity Herbal plants used in traditional healingpractices are often grown in areas with high UV exposureand no standard agricultural practices have been establishedTherefore it is expected that photoisomerisation reactionsof bioactive compounds happen readily in such settings andso these active molecules may be compromised As suchit is important that these environmental effects are takeninto consideration when studying plant-derived drugs In thecurrent study as previously mentioned the effect of UV-induced geometrical isomerism of 35-diCQA was studied byconsidering structural (ligand) characteristics and biologicalactivities of these isomers using in silico studies

31 Ligand Stability Figure 1 shows the energy optimisedstructures of the 35-diCQA geometrical isomers The geom-etry optimisation of the ligands suggests that the moststable isomer in vacuo is the 31199051199031198861198991199045119888119894119904-diCQA isomer fol-lowed by the 31198881198941199045119905119903119886119899119904-diCQA isomer the naturally occur-ring 31199051199031198861198991199045119905119903119886119899119904-diCQA isomer had a relative energy of1758 kcalsdotmolminus1 (Table 1) The low energy of the mono-cisisomers can be attributed to the fact that they have moreintramolecular hydrogen bonds (IHBs) that act to stabilisetheir conformations than the 31199051199031198861198991199045119905119903119886119899119904-diCQA isomerAdditionally these mono-cis isomers have minimal stericinteractions as compared to the high energy 31198881198941199045119888119894119904-diCQA

Evidence-Based Complementary and Alternative Medicine 3

(a) (b)

(c) (d)

Figure 1 Geometry optimised structures of the geometrical isomers of 35-diCQA (a) 31199051199031198861198991199045119905119903119886119899119904-diCQA (b) 31198881198941199045119905119903119886119899119904-diCQA (c) 31199051199031198861198991199045119888119894119904-diCQA and (d) 31198881198941199045119888119894119904-diCQA

Table 1 The relative energies for the 35-diCQA geometrical isomers and the results from the rigid docking studies with the HIV-1 integraseenzyme

IsomerRelativeenergy

(kcalmol)

Free bindingenergy

(kcalmol)Contacting residues H-bonded residues

3trans5trans-diCQA 1758 minus9332ASP64 CYS65 THR66 HIS67 VAL72 ALA91GLU92 ASP116 ASN117 GLN148 ILE151

GLU152 ASN155 LYS156

CYS65 HIS67GLU152 ASN155

3cis5trans-diCQA 1320 minus8837ASP64 CYS65 GLU 92 THR 115 ASP116PHE139 ILE141 GLN148 ILE151 GLU152

ASN155 LYS156 MG1001lowastCYS65 THR66ASN117 GLU152

3trans5cis-diCQA 0000 minus9173 ASP64 THR66 HIS67 ASP116 GLN148 ILE151GLU152 ASN155 LYS156 LYS159 LYS160

ASP64 GLU92SER119 GLN148

3cis5cis-diCQA 5096 minus9082ASP64 CYS65 THR66 HIS67 VAL72 ALA91GLU92 ASP116 GLY118 GLN148 ILE151

GLU152 ASN155 MG1001lowastASP64 THR66HIS67 GLN148

lowastDivalent magnesium ion

isomer steric interactions have been shown to decreasethe stability of molecules [26] Due to the small differenceobserved in the relative energies of the isomers it can beexpected that these isomers coexist in plantmaterial with theexception of the 31198881198941199045119888119894119904-diCQA isomer (5096 kcalsdotmolminus1)which is likely to exist in a very minor concentration

Though ligand stability in water and methanol solventincreases (results not shown) the structural conformationsof the isomers remained the same Since the main aim of thestudywas to determine differences in the binding interactionsof the isomers to the INT enzyme it suffices to use the invacuo optimised structures to avoid solvent effects


32 Docking Studies The different geometrical isomers werefound to exhibit very similar binding energies which suggestthat all the geometrical isomers are equally likely to bind toHIV-1 INT (Table 1) The docking results show that all the35-diCQA isomers bind to the catalytic domain of the HIV-1 INT enzyme (Table 1 Figure 2) by electrostatic interactionsand hydrogen bonds Figure 3 shows the localisation of theisomers in the catalytic domain of the enzyme and thehydrophobic characteristics of the catalytic domain Apartfrom the hydrogen bonds other weak interactions such aselectrostatic interactions were also shown to exist (Figure 2)The interaction of these isomers with the INT enzymethrough several forms of interactions is an indication that 35diCQA is a viable drug candidate for the inhibition of thisenzyme

The amino acid residues that interact with the isomerssummarised in Table 1 include the catalytic triad residuesASP64 ASP116 and GLU152 This is consistent with exper-imental data that showed that the diCQAs interact with theconserved catalytic domain of retroviral integrase enzymes[7] which explains the potency of the diCQAs as HIV-1INT inhibitors [27] When comparing the hydrogen bondinginteractions of the geometrical isomers important differ-ences were noted based on the type of contacting residues(Table 1) Here the 31199051199031198861198991199045119905119903119886119899119904-diCQA and 31198881198941199045119905119903119886119899119904-diCQAisomers form hydrogen bonds with GLU152 while the31199051199031198861198991199045119888119894119904-diCQA and the 31198881198941199045119888119894119904-diCQA form a hydrogenbond with ASP64This suggests that caffeoyl moiety acylatedon the 5 position of the quinic acid is essential for hydrogenbond interactions with the GLU152 and cis-isomerisationat this position diminishes this specific interaction On theother hand the caffeoyl moiety on the 3 position of thecaffeoyl moiety is important for hydrogen bond interactionswith the ASP64 and isomerisation (cis) abolishes this interac-tion Taken together a combination of these isomers wouldallow for interactions with the catalytic domain amino acidresidues that are vital for enzyme functionality Preliminarydocking results with 345-tricaffeoylquinic acid suggest thatit may possibly interact with all the residues that the individ-ual 35-diCQA isomers interact with which would explain itsgreater inhibitory activity against HIV-1 INT [8]

The lysine residues LYS156 and 159 are positioned in thecatalytic domain of HIV-1 INT and are in close proximityto the active site residues Previously site directed mutage-nesis of both these lysine residues resulted in the loss ofdisintegration activity [6] Furthermore photo-cross-linkingexperiments revealed that LYS 159 of the INT enzyme inter-acts with the viral DNA so as to orientate its phosphodiesterbond close to the active site residues for further processing[6] The naturally occurring 31199051199031198861198991199045119905119903119886119899119904-diCQA isomer andthe UV generated 31198881198941199045119905119903119886119899119904-diCQA isomer interact with LYS156 and not LYS 159 while the 31198881198941199045119888119894119904-diCQA isomer doesnot interact with any of these lysine residues (Figure 2)The 31199051199031198861198991199045119888119894119904-diCQA isomer interacts with both LYS156and LYS159 and it furthermore interacts with LYS159 viacation-pi interactions (Figure 2) In their theoretical studiesNunthaboot et al (2007) showed that the protonated formof LYS 159 is preferred when HIV-1 INT is complexed

with the inhibitor 5-CITEP [28] This protonation stateis likely to facilitate the cation-pi interactions that wereobserved between LYS159 and the catechol ring of 35-diCQA(Figure 2) [28] The importance of cation-pi interactionsfor molecular recognition and in protein-ligand interactionshas been well established [27 29 30] Our study thereforehighlights the potency of 35 diCQA as an inhibitor of thisenzyme This is well explained by these multiple forms ofinteraction which exist between the ligands and the enzymewhich suggests that the presence of all these four possibleisomers can exhibit very strong synergistic interactions withINT enzyme Moreover Hu et al suggested that contact withthe active site residues (ASP64 ASP116 and GLU152) and theaforementioned lysine residues may hint to the mimickingof viral DNA by the dicaffeoylquinic acids as a mechanismof inhibition [13] When cis-isomerisation occurs in both ofthe caffeic acid units the ligand does not interact with any ofthese lysine residues [13]

Studies done on L-chicoric acid (L-CA) isomers showeda similar binding mode to that observed in this study with35-diCQA geometrical isomers In their study Healy etal observed that cis-isomerism in both caffeic acid arms(s-ciss-cis L-CA) resulted in a conformation where bothcatechol units were well contained in the binding pocketwhich allowed for extensive hydrogen bonding to occurbetween the L-CA and the HIV-1 INT residues ASP116 andGLN148 [15] With the s-ciss-trans L-CA isomer only onecatechol ring formed a hydrogen bond with GLN148 and hadextensive contact withGLU152 [15]When comparedwith theknown inhibitor 5 CITEP the bidentate nature of L-CA andthe diCQAs allows them to occupy the same region as theinhibitor and another adjacent pocket in the catalytic domain[13 15]

Our results further indicate that cis-isomerisation at thecaffeoyl moiety attached at the 31015840 position of quinic acidseemingly allows the ligands to interact with the metalcofactor of the enzyme (Table 1 Figure 2) Here 31198881198941199045119888119894119904-diCQA and 31198881198941199045119905119903119886119899119904-diCQA isomers can be seen to havesome interaction with the Mg2+ cofactor (Table 1 Figure 4)Esposito and Craigie when comparing INT activity in thepresence of either manganese or magnesium showed thatviral DNA 31015840 processing was optimal when magnesium wasthe metal cofactor [31] Furthermore metal interaction with35-diCQAhas been shown to be important for binding of theHumanT-LymphotropicVirus Type-1 (HTLV-1) INT enzymewhich is homologous to HIV-1 INT [32] In this work it wasshown that oneMg2+ ion interacting with INT and the ligandgave optimal energies of interaction between 35-diCQA andHTLV-1 INT [32] However in the current study and contraryto Pena and colleagues 31198881198941199045119888119894119904-diCQA and 31198881198941199045119905119903119886119899119904-diCQAisomers were found to exhibit slightly lower affinity thanthose ligands that do not interact with the metal cofactor(Table 1)

Apart from cis-trans isomerism other forms of isomerismof the diCQAs and related derivatives more especially onthe quinic acid unit have been shown to affect the activitythereof For instance Jiang et al showed that the addition ofsubstituents on the quinic acid unit of the diCQAs decreased


HISA 67

ASNA 155

GLUA 92

LYSA 156

GLNA 148

THRA 66

ASPA 64

CYSA 65

ALAA 91

VALA 72

ASPA 116

GLUA 152

ASNA 117

ILEA 151

Residue interactionElectrostaticvan der WaalsCovalent bondWaterMetal

OO

OO O

O

O

OO

O

O

O

H

H

H

H

(a)

GLUA 92

MGA 1001

CYSA 65

ASPA 64

ASPA 116

ASNA 155

LYSA 156

ILEA 151 GLU

A 152

ILEA 141

PHEA 139

GLNA 148

THRA 115

Residue interaction

O

O

OO

OO

O

O O

O O

OH

Electrostaticvan der WaalsCovalent bondWaterMetal

(b)

ASPA 116

GLNA 148

ILEA 151

ASPA 64

GLUA 152

ASNA 155

LYSA 156 LYS

A 160

LYSA 159

Pi

+

HISA 67

THRA 66

Residue interaction

O

O

OOO

O

OO

O

OO

O

H

H

H

H


(c)

GLUA 92

MGA 1001

ASPA 116

ASPA 64

CYSA 65

THRA 66

HISA 67 ASN

A 155

LYSA 156

GLUA 152

ILEA 151

GLNA 148

GLYA 149

ILEA 141

Residue interaction

O

O

O

OO

O

O

OO

O

OO

H

H

H

H


(d)

Figure 2 Two-dimensional representations of the interacting residues and the interaction type between HIV-1 INT and (a) 31199051199031198861198991199045119905119903119886119899119904-diCQA (b) 31198881198941199045119905119903119886119899119904-diCQA (c) 31199051199031198861198991199045119888119894119904-diCQA and (D) 31198881198941199045119888119894119904-diCQA


300minus100 000 100 200minus200minus300

Hydrophobicity

(a)


Hydrophobicity

(b)

200minus100 000 100minus200minus300 300

Hydrophobicity

(c)


Hydrophobicity

(d)

Figure 3Three-dimensional maps of the hydrophobic interactions between HIV-1 INT and (a) 31199051199031198861198991199045119905119903119886119899119904-diCQA (b) 31198881198941199045119905119903119886119899119904-diCQA (c)31199051199031198861198991199045119888119894119904-diCQA and (d) 31198881198941199045119888119894119904-diCQA isomers

their antioxidant activity [33] Furthermore regional iso-merism of the diCQA was also shown to affect theirantioxidant activity [33] Other instances where cis-transisomerisation resulted in attenuated activity of biologicallyimportant molecules includes the 120-fold increase in theanti-mycobacterium activity of cinnamic acid when thetrans isomer converts to the cis isomer [34] Generally theimplications and effects of isomerisation of molecules alsoextend beyond the pharmaceutical and nutraceutical arenaAs mentioned earlier the cis-trans photoisomerisation of thetetrazoline oxime ether group of fungicides was shown toresult in decreased efficacy when used on plants in the fieldcompared to those in green houses the consequence of whichis reduced crop production [22] The conversion of abscisicacid (a plant hormone used to prime stress resistance inplants) to its biologically inactive 2-trans isomer also places athreat on crop production [35] Likewise in the current studygeometrical isomerism of 35-diCQA attenuated the binding

interactions of the ligand Here the 31198881198941199045119905119903119886119899119904-diCQA isomercauses a slightly lower binding affinity to HIV-1 INT and cis-isomerism of the caffeic acid arm at the 31015840 position causes35-diCQA to interact with the metal cofactor highlightingthe importance of studying geometrical isomerism of naturalproducts Although we have shown experimentally that allfour isomers can exist [14] there is little evidence that allfour exist in plants such as in German chamomile [36] andAchillea millefolium L [37] which have been exposed tonatural light As such the negative results associated withthe 31198881198941199045119888119894119904-diCQA isomer can be regarded as insignificantsince its existence in nature is not well documented Usingantioxidative properties of both the positional and geomet-rical isomers it was concluded that the presence of isomersin plants is an evolutionary strategy to maximize the existingpool of metabolites in order to exhibit stronger activitieswhen needed [38] In plant defence mechanism the possibleexistence and involvement of cis of CQAs is also interesting


(a) (b)

(c) (d)

Figure 4 Ribbon structure of HIV-1 INT with the Mg2+ cofactor and the (a) 31199051199031198861198991199045119905119903119886119899119904-diCQA (b) 31198881198941199045119905119903119886119899119904-diCQA (c) 31199051199031198861198991199045119888119894119904-diCQA and (d) 31198881198941199045119888119894119904-diCQA ligand Molecular graphics were created using YASARA (httpwwwyasaraorg) and POVRay(httpwwwpovrayorg)

[39] As such studies associated with geometrical isomersshould be encouraged to fully elucidate their metabolic andpharmacological significance

4 Conclusion

Using molecular docking this study has shown that thegeometrical isomers that result from the UV-irradiationof 35-diCQAs have important differences in their bindinginteractions with HIV-1 INTThese differences in the bindingmodes of the isomers do not however significantly affect thebinding affinity of 35-diCQA to HIV-1 INT The differencesin their binding modes may point to a possible synergisticeffect where a combination of all these isomers would covera wider range of inhibitory activity than each individualisomer Though it is improbable that these isomers wouldbind the catalytic site all at once a ligand such as 345-tricaffeoylquinic may be a better inhibitor of HIV-1 INTFurther studies should focus on the preparation of these

individual isomers in reasonable amounts so as to validate thefindings of the current study experimentally In light of theseresults the agricultural practices governing the production ofherbal plants for their anti-HIV activity may also need to beevaluated

Competing Interests

The authors declare that they have no competing interests

References

[1] M Hill G Tachedjian and J Mak ldquoThe packaging and mat-uration of the HIV-1 pol proteinsrdquo Current HIV Research vol3 no 1 pp 73ndash85 2005

[2] K Kassahun I McIntosh D Cui et al ldquoMetabolism anddisposition in humans of raltegravir (MK-0518) an anti-AIDSdrug targeting the human immunodeficiency virus 1 integraseenzymerdquo Drug Metabolism and Disposition vol 35 no 9 pp1657ndash1663 2007


[3] D J McColl and X Chen ldquoStrand transfer inhibitors of HIV-1 integrase bringing IN a new era of antiretroviral therapyrdquoAntiviral Research vol 85 no 1 pp 101ndash118 2010

[4] A Engelman and P Cherepanov ldquoRetroviral integrase structureand DNA recombination mechanismrdquo Microbiology Spectrumvol 2 no 6 pp 1ndash22 2014

[5] R Craigie ldquoHIV integrase a brief overview from chemistry totherapeuticsrdquo The Journal of Biological Chemistry vol 276 no26 pp 23213ndash23216 2001

[6] T M Jenkins D Esposito A Engelman and R CraigieldquoCritical contacts betweenHIV-1 integrase and viral DNA iden-tified by structure-based analysis and photo-crosslinkingrdquo TheEMBO Journal vol 16 no 22 pp 6849ndash6859 1997

[7] K Zhu M L Cordeiro J Atienza W Edward Robinson Jrand S A Chow ldquoIrreversible inhibition of human immunode-ficiency virus type 1 integrase by dicaffeoylquinic acidsrdquo Journalof Virology vol 73 no 4 pp 3309ndash3316 1999

[8] H Tamura T Akioka K Ueno et al ldquoAnti-human immunode-ficiency virus activity of 345-tricaffeoylquinic acid in culturedcells of lettuce leavesrdquo Molecular Nutrition and Food Researchvol 50 no 4-5 pp 396ndash400 2006

[9] H M Heyman F Senejoux I Seibert T Klimkait V JMaharaj and J J M Meyer ldquoIdentification of anti-HIV activedicaffeoylquinic- and tricaffeoylquinic acids in Helichrysumpopulifolium by NMR-based metabolomic guided fractiona-tionrdquo Fitoterapia vol 103 pp 155ndash164 2015

[10] T Satake K Kamiya Y An T Oishi and J Yamamoto ldquoTheanti-thrombotic active constituents from Centella asiaticardquoBiological and Pharmaceutical Bulletin vol 30 no 5 pp 935ndash940 2007

[11] A Prasad M Singh N P Yadav A K Mathur and A MathurldquoMolecular chemical and biological stability of plants derivedfrom artificial seeds of Centella asiatica (L) Urban-an industri-ally important medicinal herbrdquo Industrial Crops and Productsvol 60 pp 205ndash211 2014

[12] H C Kwon C M Jung C G Shin et al ldquoA new caffeoyl quinicacid from Aster scaber and its inhibitory activity against humanimmunodeficiency virus-1 (HIV-1) integraserdquo Chemical andPharmaceutical Bulletin vol 48 no 11 pp 1796ndash1798 2000

[13] Z Hu D Chen L Dong andWM Southerland ldquoPrediction ofthe interaction of HIV-1 integrase and its dicaffeoylquinic acidinhibitor throughmolecular modeling approachrdquo Ethnicity andDisease vol 20 no 1 pp S145ndashS149 2010

[14] M M Makola P A Steenkamp I A Dubery M M Kabandaand N E Madala ldquoPreferential alkali metal adduct formationby cis geometrical isomers of dicaffeoylquinic acids allowsfor efficient discrimination from their trans isomers duringultraminushighminusperformance liquid chromatographyquadrupoletimeminusofminusflight mass spectrometryrdquo Rapid Communications inMass Spectrometry vol 30 no 8 pp 1011ndash1018 2016

[15] E F Healy J Sanders P J King and W E Robinson Jr ldquoAdocking study of l-chicoric acidwithHIV-1 integraserdquo Journal ofMolecular Graphics and Modelling vol 27 no 5 pp 584ndash5892009

[16] MN Clifford J Kirkpatrick N Kuhnert H Roozendaal and PR Salgado ldquoLCndashMS119899 analysis of the cis isomers of chlorogenicacidsrdquo Food Chemistry vol 106 no 1 pp 379ndash385 2008

[17] H Karakose R Jaiswal S Deshpande and N Kuhnert ldquoInves-tigation of the photochemical changes of chlorogenic acidsinduced by ultraviolet light inmodel systems and in agriculturalpractice with Stevia rebaudiana cultivation as an examplerdquo

Journal of Agricultural and Food Chemistry vol 63 no 13 pp3338ndash3347 2015

[18] J Mc Conathy and M J Owens ldquoStereochemistry in drugactionrdquoThe Primary Care Companion to the Journal of ClinicalPsychiatry vol 5 no 2 pp 70ndash73 2003

[19] A G Tzakos N Naqvi K Comporozos et al ldquoThe molecularbasis for the selection of captopril cis and trans conformationsby angiotensin I converting enzymerdquo Bioorganic and MedicinalChemistry Letters vol 16 no 19 pp 5084ndash5087 2006

[20] F Jamali R Mehvar and F M Pasutto ldquoEnantioselectiveaspects of drug action and disposition therapeutuc pitfallsrdquoJournal of Pharmaceutical Sciences vol 78 no 9 pp 695ndash7151989

[21] N J Farrer J AWoods L Salassa et al ldquoA potent trans-diimineplatinum anticancer complex photoactivated by visible lightrdquoAngewandte ChemiemdashInternational Edition vol 49 no 47 pp8905ndash8908 2010

[22] M Freneau P de Sainte Claire NHoffmann et al ldquoPhototrans-formation of tetrazoline oxime ethers photoisomerization vsphotodegradationrdquo RSC Advances vol 6 no 7 pp 5512ndash55222016

[23] M J Frisch G W Trucks H B Schlegel et al Gaussian 09Revision C01 Gaussian Inc Wallingford Conn USA 2009

[24] E Krieger and G Vriend ldquoYASARA viewmdashmolecular graphicsfor all devicesmdashfrom smartphones to workstationsrdquo Bioinfor-matics vol 30 no 20 pp 2981ndash2982 2014

[25] O Trott andA J Olson ldquoAutoDockVINA improving the speedand accuracy of docking with a new scoring function efficientoptimization and multithreadingrdquo Journal of ComputationalChemistry vol 31 no 2 pp 455ndash461 2010

[26] M L Vueba M E Pina F Veiga J J Sousa and L A E B DeCarvalho ldquoConformational study of ketoprofen by combinedDFT calculations and Raman spectroscopyrdquo International Jour-nal of Pharmaceutics vol 307 no 1 pp 56ndash65 2006

[27] S A DePriest D Mayer C B Naylor and G R Marshall ldquo3D-QSAR of angiotensin-converting enzyme and thermolysininhibitors a comparison of CoMFA models based on deducedand experimentally determined active site geometriesrdquo Journalof the American Chemical Society vol 115 no 13 pp 5372ndash53841993

[28] N Nunthaboot S Pianwanit V Parasuk S Kokpol andP Wolschann ldquoTheoretical study on the HIV-1 integraseinhibitor 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-propenone (5CITEP)rdquo Journal of Molecular Structure vol844-845 pp 208ndash214 2007

[29] C L Padgett A P Hanek H A Lester D A Dougherty andS C R Lummis ldquoUnnatural amino acid mutagenesis of theGABAA receptor binding site residues reveals a novel cation-120587 interaction between GABA and 1205732Tyr97rdquo The Journal ofNeuroscience vol 27 no 4 pp 886ndash892 2007

[30] D A Dougherty ldquoThe cationminus120587 interactionrdquo Accounts ofChemical Research vol 46 no 4 pp 885ndash893 2013

[31] D Esposito and R Craigie ldquoHIV integrase structure andfunctionrdquoAdvances in Virus Research vol 52 pp 319ndash333 1999

[32] A Pena J Yosa Y Cuesta-Astroz O Acevedo L Lareo andF Garcıa-Vallejo ldquoInfluence of Mg2+ ions on the interactionbetween 35-dicaffeoylquinic acid and HTLV-I integraserdquo Uni-versitas Scientiarum vol 17 no 1 pp 5ndash15 2012

[33] X-W Jiang J-P Bai Q Zhang et al ldquoCaffeoylquinic acidderivatives from the roots of Arctium lappa L (burdock) andtheir structure-activity relationships (SARs) of free radical


scavenging activitiesrdquo Phytochemistry Letters vol 15 pp 159ndash163 2016

[34] Y-L Chen S-T Huang F-M Sun et al ldquoTransformation ofcinnamic acid from trans- to cis-form raises a notable bacte-ricidal and synergistic activity against multiple-drug resistantMycobacterium tuberculosisrdquo European Journal of Pharmaceu-tical Sciences vol 43 no 3 pp 188ndash194 2011

[35] W Liu X Han Y Xiao et al ldquoSynthesis photostability andbioactivity of 23-cyclopropanated abscisic acidrdquo Phytochem-istry vol 96 pp 72ndash80 2013

[36] R Guimaraes L Barros M Duenas et al ldquoInfusion anddecoction of wild German chamomile bioactivity and char-acterization of organic acids and phenolic compoundsrdquo FoodChemistry vol 136 no 2 pp 947ndash954 2013

[37] M I Dias L Barros M Duenas et al ldquoChemical compositionof wild and commercial Achillea millefolium L and bioactivityof the methanolic extract infusion and decoctionrdquo Food Chem-istry vol 141 no 4 pp 4152ndash4160 2013

[38] T Ramabulana R D Mavunda P A Steenkamp L A PiaterI A Dubery and N E Madala ldquoPerturbation of pharmaco-logically relevant polyphenolic compounds in Moringa oleiferaagainst photo-oxidative damages imposed by gamma radia-tionrdquo Journal of Photochemistry and Photobiology B Biology vol156 pp 79ndash86 2016

[39] M I Mhlongo L A Piater P A Steenkamp N E Madala andI A Dubery ldquoMetabolomic fingerprinting of primed tobaccocells provide the first evidence for the biological origin of cis-chlorogenic acidrdquo Biotechnology Letters vol 37 no 1 pp 205ndash209 2015

Submit your manuscripts athttpwwwhindawicom

Stem CellsInternational

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014


MEDIATORSINFLAMMATION

of


Behavioural Neurology

EndocrinologyInternational Journal of



Disease Markers


BioMed Research International

OncologyJournal of



Oxidative Medicine and Cellular Longevity


PPAR Research

The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014

Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Journal of

ObesityJournal of



Computational and Mathematical Methods in Medicine

OphthalmologyJournal of


Diabetes ResearchJournal of



Research and TreatmentAIDS


Gastroenterology Research and Practice


Parkinsonrsquos Disease

Evidence-Based Complementary and Alternative Medicine

Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom


31015840 end processing of viral cDNA a reaction that involvestransesterification [3 6] Other amino acid residues (LYS156and LYS159) are also important for viral DNA binding beforefurther processing can occur [6]

The dicaffeoylquinic acids (diCQAs) a group of plantsecondary metabolites have been found to possess specificand irreversible inhibitory activity againstHIV-1 INTmakingthem potent inhibitors [7 8] These compounds have beenisolated fromherbal plants that have beennoted for their anti-HIV activity such as Helichrysum populifolium [9] Centellaasiatica [10 11] and Aster scaber [12] The diCQAs can eitherbind to the active domain or to a flexible loop near thecatalytic site of the enzyme to inhibit viral DNA integrationto the host cell DNA [13] One such diCQA isolated fromherbal plants which has been found to be active against HIV-1 INT is 35-diCQA an ester of quinic acid and two caffeicacidmoieties substituted at the 3 and 5 positions of the quinicacid [14] From docking studies of L-chicoric acid and HIV-INT it can be assumed that the caffeic acid units are the mainpharmacophores of the diCQAs [15]

UV-irradiation of the naturally occurring 31199051199031198861198991199045119905119903119886119899119904-diCQA causes the geometrical isomerism of this moleculein the caffeic acid units and gives rise to cis isomers31198881198941199045119905119903119886119899119904- diCQA 31199051199031198861198991199045119888119894119904-diCQA and 31198881198941199045119888119894119904-diCQA [1416 17] Isomerism of 35-diCQA in the quinic acid unit hasbeen shown to affect its activity against HIV-1 INT [12]however the effect of geometrical isomerism in the caffeicacid units has not been investigated for this molecule Thestereochemistry of bioactive compounds is important sincedifferent stereoisomers have different pharmacodynamics inhumans [18] This is due to the fact that target biomoleculesare stereospecific [19]Though enantiomers are often of moreconcern than other types of stereoisomers [20] the effectsof regional and geometrical isomers on biological activitystill require further investigation For instance Farrer etal found that trans platinum complexes were more activeagainst keratinocytes and human ovarian cancer cells thantheir cis counterparts [21] Furthermore photoisomerisationof cis tetrazoline oxime ethers to the trans isomers resultedin a loss of efficacy of these fungicides when used on plantsexposed to UV-irradiation [22] Given this importance ofthe stereochemistry of bioactive molecules on their activitieswe investigated the differences in the binding interactions ofHIV-INT and the UV-induced geometrical isomers of 35-diCQA

2 Methodology

21 Ligand A random conformational search approach wasused to find the lowest energy conformer for each isomerThe geometries of the four 35-diCQA isomers were thenoptimised in vacuo using density functional theory withthe B3LYP functional and the 6-311+G (d p) basis set Thecalculations were carried out on the Gaussian09 softwarepackage [23] Optimised structures were visualised using theGaussView05 software

22 Molecular Modelling All molecular modelling was per-formed using YASARA Structure [24]The intended receptor

crystal structure (PDB code 1QS4) contained two identicalchains A and B Chain A was chosen as receptor howeverit was missing residues 141ndash144 Chain B contained residues143 and 144 and these residues were inserted into chainA by first superimposing chain B onto chain A and thenremoving all other chain B residues and finally merging theresidues into chain A (all other residues were deleted) Thetwo remaining residueswere artificially added (Ile 141 andPro142) All residues in the structure except for residues 140 to145 were fixed and energy minimization was performed torelax the flexible region Subsequently all residues weremadeflexible and another energy minimization was performed onthe entire structure The resulting structure was used as thereceptor in the subsequent molecular docking experiments

23 Molecular Docking Molecular docking experimentswere prepared using YASARA [24] A rectangular box withdimensions 30 A times 30 A times 30 A was centred on the coordi-nates of the 120572-carbon of Asp 64 in the receptor moleculeThe isomer ligand molecules and the receptor molecule werekept rigid during the experiments Molecular docking exper-iments were performed using Autodock VINA [25] withthe applicationrsquos default settings Each docking experimentproduced 100 ligand-receptor pairs which were clusteredusing a RMSD cut-off of 50 A The pairs with the lowestbinding energy were considered to have the best dockingconformations The results of each experiment were viewedusing YASARA

3 Results and Discussion

Natural products have been at the forefront of drug discoveryand continue to provide viable pharmacophores and possiblescaffolds for the development of potential drugs due to theirstructural diversity Herbal plants used in traditional healingpractices are often grown in areas with high UV exposureand no standard agricultural practices have been establishedTherefore it is expected that photoisomerisation reactionsof bioactive compounds happen readily in such settings andso these active molecules may be compromised As suchit is important that these environmental effects are takeninto consideration when studying plant-derived drugs In thecurrent study as previously mentioned the effect of UV-induced geometrical isomerism of 35-diCQA was studied byconsidering structural (ligand) characteristics and biologicalactivities of these isomers using in silico studies

31 Ligand Stability Figure 1 shows the energy optimisedstructures of the 35-diCQA geometrical isomers The geom-etry optimisation of the ligands suggests that the moststable isomer in vacuo is the 31199051199031198861198991199045119888119894119904-diCQA isomer fol-lowed by the 31198881198941199045119905119903119886119899119904-diCQA isomer the naturally occur-ring 31199051199031198861198991199045119905119903119886119899119904-diCQA isomer had a relative energy of1758 kcalsdotmolminus1 (Table 1) The low energy of the mono-cisisomers can be attributed to the fact that they have moreintramolecular hydrogen bonds (IHBs) that act to stabilisetheir conformations than the 31199051199031198861198991199045119905119903119886119899119904-diCQA isomerAdditionally these mono-cis isomers have minimal stericinteractions as compared to the high energy 31198881198941199045119888119894119904-diCQA


(a) (b)

(c) (d)




(kcalmol)

Free bindingenergy























HISA 67

ASNA 155

GLUA 92

LYSA 156

GLNA 148

THRA 66

ASPA 64

CYSA 65

ALAA 91

VALA 72

ASPA 116

GLUA 152

ASNA 117

ILEA 151


OO

OO O

O

O

OO

O

O

O

H

H

H

H

(a)

GLUA 92

MGA 1001

CYSA 65

ASPA 64

ASPA 116

ASNA 155

LYSA 156

ILEA 151 GLU

A 152

ILEA 141

PHEA 139

GLNA 148

THRA 115

Residue interaction

O

O

OO

OO

O

O O

O O

OH


(b)

ASPA 116

GLNA 148

ILEA 151

ASPA 64

GLUA 152

ASNA 155

LYSA 156 LYS

A 160

LYSA 159

Pi

+

HISA 67

THRA 66

Residue interaction

O

O

OOO

O

OO

O

OO

O

H

H

H

H


(c)

GLUA 92

MGA 1001

ASPA 116

ASPA 64

CYSA 65

THRA 66

HISA 67 ASN

A 155

LYSA 156

GLUA 152

ILEA 151

GLNA 148

GLYA 149

ILEA 141

Residue interaction

O

O

O

OO

O

O

OO

O

OO

H

H

H

H


(d)




Hydrophobicity

(a)


Hydrophobicity

(b)


Hydrophobicity

(c)


Hydrophobicity

(d)





(a) (b)

(c) (d)



4 Conclusion



Competing Interests


References

















































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















(a) (b)

(c) (d)




(kcalmol)

Free bindingenergy























HISA 67

ASNA 155

GLUA 92

LYSA 156

GLNA 148

THRA 66

ASPA 64

CYSA 65

ALAA 91

VALA 72

ASPA 116

GLUA 152

ASNA 117

ILEA 151


OO

OO O

O

O

OO

O

O

O

H

H

H

H

(a)

GLUA 92

MGA 1001

CYSA 65

ASPA 64

ASPA 116

ASNA 155

LYSA 156

ILEA 151 GLU

A 152

ILEA 141

PHEA 139

GLNA 148

THRA 115

Residue interaction

O

O

OO

OO

O

O O

O O

OH


(b)

ASPA 116

GLNA 148

ILEA 151

ASPA 64

GLUA 152

ASNA 155

LYSA 156 LYS

A 160

LYSA 159

Pi

+

HISA 67

THRA 66

Residue interaction

O

O

OOO

O

OO

O

OO

O

H

H

H

H


(c)

GLUA 92

MGA 1001

ASPA 116

ASPA 64

CYSA 65

THRA 66

HISA 67 ASN

A 155

LYSA 156

GLUA 152

ILEA 151

GLNA 148

GLYA 149

ILEA 141

Residue interaction

O

O

O

OO

O

O

OO

O

OO

H

H

H

H


(d)




Hydrophobicity

(a)


Hydrophobicity

(b)


Hydrophobicity

(c)


Hydrophobicity

(d)





(a) (b)

(c) (d)



4 Conclusion



Competing Interests


References

















































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

























HISA 67

ASNA 155

GLUA 92

LYSA 156

GLNA 148

THRA 66

ASPA 64

CYSA 65

ALAA 91

VALA 72

ASPA 116

GLUA 152

ASNA 117

ILEA 151


OO

OO O

O

O

OO

O

O

O

H

H

H

H

(a)

GLUA 92

MGA 1001

CYSA 65

ASPA 64

ASPA 116

ASNA 155

LYSA 156

ILEA 151 GLU

A 152

ILEA 141

PHEA 139

GLNA 148

THRA 115

Residue interaction

O

O

OO

OO

O

O O

O O

OH


(b)

ASPA 116

GLNA 148

ILEA 151

ASPA 64

GLUA 152

ASNA 155

LYSA 156 LYS

A 160

LYSA 159

Pi

+

HISA 67

THRA 66

Residue interaction

O

O

OOO

O

OO

O

OO

O

H

H

H

H


(c)

GLUA 92

MGA 1001

ASPA 116

ASPA 64

CYSA 65

THRA 66

HISA 67 ASN

A 155

LYSA 156

GLUA 152

ILEA 151

GLNA 148

GLYA 149

ILEA 141

Residue interaction

O

O

O

OO

O

O

OO

O

OO

H

H

H

H


(d)




Hydrophobicity

(a)


Hydrophobicity

(b)


Hydrophobicity

(c)


Hydrophobicity

(d)





(a) (b)

(c) (d)



4 Conclusion



Competing Interests


References

















































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















HISA 67

ASNA 155

GLUA 92

LYSA 156

GLNA 148

THRA 66

ASPA 64

CYSA 65

ALAA 91

VALA 72

ASPA 116

GLUA 152

ASNA 117

ILEA 151


OO

OO O

O

O

OO

O

O

O

H

H

H

H

(a)

GLUA 92

MGA 1001

CYSA 65

ASPA 64

ASPA 116

ASNA 155

LYSA 156

ILEA 151 GLU

A 152

ILEA 141

PHEA 139

GLNA 148

THRA 115

Residue interaction

O

O

OO

OO

O

O O

O O

OH


(b)

ASPA 116

GLNA 148

ILEA 151

ASPA 64

GLUA 152

ASNA 155

LYSA 156 LYS

A 160

LYSA 159

Pi

+

HISA 67

THRA 66

Residue interaction

O

O

OOO

O

OO

O

OO

O

H

H

H

H


(c)

GLUA 92

MGA 1001

ASPA 116

ASPA 64

CYSA 65

THRA 66

HISA 67 ASN

A 155

LYSA 156

GLUA 152

ILEA 151

GLNA 148

GLYA 149

ILEA 141

Residue interaction

O

O

O

OO

O

O

OO

O

OO

H

H

H

H


(d)




Hydrophobicity

(a)


Hydrophobicity

(b)


Hydrophobicity

(c)


Hydrophobicity

(d)





(a) (b)

(c) (d)



4 Conclusion



Competing Interests


References

















































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of


















Hydrophobicity

(a)


Hydrophobicity

(b)


Hydrophobicity

(c)


Hydrophobicity

(d)





(a) (b)

(c) (d)



4 Conclusion



Competing Interests


References

















































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















(a) (b)

(c) (d)



4 Conclusion



Competing Interests


References

















































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of






























































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of





























of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of





















of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of
















Documents

Research Article The Effect of Geometrical Isomerism of 3