In . J. Mol. Sci. 2014, 15, 17035-17064; doi:10.3390/ijms150917035
In e na ional Jou nal o
Molecula Sciences
ISSN 1422-0067
www.mdpi.com/jou nal/ijms
A icle
P edic ion o Mul i-Ta ge Ne wo ks o Neu op o ec i e
Compounds wi h En opy Indices and Syn hesis, Assay,
and Theo e ical S udy o New Asymme ic
1,2-Rasagiline Ca bama es
F ancisco J. Rome o Du án 1, Ne ea Alonso 1, Olga Caamaño 1, Xe a do Ga cía-Me a 1,*
Ma ilde Yañez 2, F ancisco J. P ado-P ado 1,3 and Humbe o González-Díaz 4,5,*
1 Depa men o O ganic Chemis y, Facul y o Pha macy,
Uni e si y o San iago de Compos ela (USC), San iago de Compos ela 15782, Spain;
E-Mails: coja ie . om[email p o ec ed] (F.J.R.D.); [email p o ec ed] (N.A.);
[email p o ec ed] (O.C.); [email p o ec ed] (F.J.P.-P.)
2 Depa men o Pha macology, Uni e si y o San iago de Compos ela (USC),
San iago de Compos ela 15782, Spain; E-Mail: m[email p o ec ed]
3 Biomedical Sciences Depa men , Heal h Sciences Di ision, Uni e si y o Quin ana Roo (UQROO),
Che umal 77039, Mexico
4 Depa men o O ganic Chemis y II, Facul y o Science and Technology,
Uni e si y o he Basque Coun y UPV/EHU, Leioa 48940, Spain
5 IKERBASQUE, Basque Founda ion o Science, Bilbao 48011, Spain
* Au ho s o whom co espondence should be add essed;
E-Mails: xe a do.ga cí[email p o ec ed] (X.G.-M.); humbe o.gonzálezdí[email p o ec ed] (H.G.-D.);
Tel.: +34-946-013-547 (H.G.-D.); Fax: +34-946-012-748 (H.G.-D.).
Recei ed: 11 Ma ch 2014; in e ised o m: 19 Augus 2014 / Accep ed: 21 Augus 2014 /
Published: 24 Sep embe 2014
Abs ac : In a mul i- a ge complex ne wo k, he links (Lij) ep esen he in e ac ions
be ween he d ug (di) and he a ge ( j), cha ac e ized by di e en expe imen al measu es
(Ki, Km, IC50, e c.) ob ained in pha macological assays unde di e se bounda y condi ions
(cj). In his wo k, we handle Shannon en opy measu es o de eloping a model
encompassing a mul i- a ge ne wo k o neu op o ec i e/neu o oxic compounds epo ed in
he CHEMBL da abase. The model p edic s co ec ly >8300 expe imen al ou comes wi h
Accu acy, Speci ici y, and Sensi i i y abo e 80%–90% on aining and ex e nal alida ion
se ies. Indeed, he model can calcula e di e en ou comes o >30 expe imen al measu es
in >400 di e en expe imen al p o ocolsin ela ion wi h >150 molecula and cellula
OPEN ACCESS
In . J. Mol. Sci. 2014, 15 17036
a ge s on 11 di e en o ganisms (including human). He ea e , we epo ed by he i s
ime he syn hesis, cha ac e iza ion, and expe imen al assays o a new se ies o chi al
1,2- asagiline ca bama e de i a i es no epo ed in p e ious wo ks. The expe imen al es s
included: (1) assay in absence o neu o oxic agen s; (2) in he p esence o glu ama e; and
(3) in he p esence o H2O2. Las ly, we used he new Assessing Links wi h Mo ing
A e ages (ALMA)-en opy model o p edic possible ou comes o he new compounds in
a high numbe o pha macological es s no ca ied ou expe imen ally.
Keywo ds: CHEMBL; neu op o ec i e agen s; asagiline de i a i es; asymme ic
syn hesis; mul i- a ge d ugs; molecula in o ma ion measu es; Shannon en opy;
Ma ko chains; mo ing a e ages
1. In oduc ion
En opy measu es a e uni e sal pa ame e s use ul o codi y biologically ele an in o ma ion in
many sys ems. In he 1970’s Bonche and T inajs ic e al. published wo ks abou he use o Shannon’s
en opy o calcula e a s uc u al in o ma ion pa ame e [1–4]. Kie published ano he semina wo ks on
he use o Shannon’s en opy o encoding molecula s uc u e in Chemin o ma ics s udies in 1980 [4].
Many o he au ho s used Shannon’s en opy pa ame e s o he same pu pose on small molecule
s uc u e [5–10]. G aham e al. [11–16] used en opy measu es o s udy he in o ma ion p ope ies
o o ganic molecules. En opy in o ma ion measu es we e used o desc ibe p o eins [17,18],
DNA sequences [19], p o ein ne wo ks [20], and magne ic esonance ou comes [21]. The so wa e
MARCH-INSIDE (MI) uses he heo y o Ma ko chains o calcula e he pa ame e s θk(G). These
alues a e he Shannon en opies o o de k h o a g aph G. The θk(G) alues a e use ul quan i y
in o ma ion abou he s uc u e o molecula sys ems [22]. The g aph G ep esen s a complex
molecula sys em as a ne wo k o nodes in e connec ed by links (Lij = 1) o no connec ed (Lij = 0).
MI algo i hm associa es a Ma ko ma ix o he g aph G in o de o de ine he p obabili ies o
in e ac ions ( ies o ela ionships) be ween nodes. These en opy pa ame e s θk(G) can be calcula ed
o many ypes o sys ems (molecula o o he wise). We ha e s udied small molecules, RNA
seconda y s uc u es, p o ein sequences, i al su aces, ce eb al co ex ne wo ks, me abolic ne wo ks,
hos -pa asi e ne wo ks, wo ld ading ne wo ks, social ne wo ks, e c. In molecules, we know he
in o ma ion abou links Lij (co alen bonds, hyd ogen bonds, spa ial con ac s, e c.) beyond any
easonable doub . Howe e , we can use he in o ma ion (θk(G) alues)o he sys em o p edic
in e ac ions wi h o he sys ems in a ne wo k o a highe -s uc u al le el. Fo ins ance, we use he θk(G)
alues o d ugs and a ge s s uc u e o p edic d ug– a ge in e ac ions (links) in d ug– a ge ne wo k.
In o he cases, linking pa e ns change, a e no known, o we ind con adic o y in o ma ion. This is
he case o he exis ence o di e en ela ionships be ween nodes in biological webs o social
ne wo ks. In hese cases, we can use he θk(G) alues o known ne wo ks o ind models use ul o
p edic links in new ne wo ks [23–25].
On he o he hand, he disco e y o new d ugs o he ea men o neu odegene a i e diseases such
as Alzheime ’s, Pa kison’s, and Hun ing on’s disease, F ied eich a axia and o he s, is an impo an
In . J. Mol. Sci. 2014, 15 17037
goal o medicinal chemis y [26–29]. The genes causing he edi a y o ms o some o hese diseases
ha e been iden i ied bu he molecula mechanisms o he neu onal degene a ion ha e no been o ally
unde s ood ye [30]. This pic u e, and some disappoin ing esul s in clinical ials, makes in e es ing
he p edic ion o d ug candida es wi h compu a ional echniques [31,32]. In o de o design
hese compu a ional models we need o p ocess chemical in o ma ion om public da abases.
These da abases ha e accumula ed immense da ase s o expe imen al esul s o pha macological
ials o many compounds. Fo ins ance, CHEMBL [33,34] is one o he bigges wi h mo e han
11,420,000 ac i i y da a o >1,295,500 compounds, and 9844 a ge s. This huge amoun o
in o ma ion o e s a e ile ield o he applica ion o compu a ional echniques [34,35].
The analysis o all his da a is e y complex due o he p esence o mul i- a ge , mul i-ou pu , and
mul i-scale in o ma ion. Mul i- a ge complica ion eme ges due o he exis ence o compounds wi h
mul iple a ge s [36–38]. This led o he o ma ion o complex ne wo ks o d ug– a ge in e ac ions.
We can ep esen d ug– a ge ne wo ks as a g aph wi h wo ypes o nodes d ugs (di) and a ge s ( j)
in e connec ed by links (Lij). Ba abasi e al. [39], cons uc ed a d ug– a ge ne wo k based on
Food and D ug Adminis a ion (FDA) d ugs and p o eins linked by d ug– a ge bina y associa ions.
Cse mely e al. [40], e iewed he use o ne wo ks, including d ug– a ge ne wo ks, o d ug disco e y.
Mul i-ou pu ea u e e e s o he necessi y o p edic ion o di e en expe imen al pa ame e s (IC50,
Ki, Km, e c.) o decided whe he wo nodes (d ug and a ge ) in e ac (Lij = 1) o no (Lij = 0). Mul i-scaling
e e s o he di e en s uc u al le els o he o ganiza ion o ma e . In his case, he inpu a iables
quan i y molecula in o ma ion (d ugs s uc u e) and mac omolecula in o ma ion ( a ge s). They ha e
o quan i y also cellula (cellula a ge s) and o ganism in o ma ion (specie ha exp ess he a ge ).
In hese models we ha e a high numbe o assays ca ied ou in e y di e en condi ions (cq) like ime,
concen a ions, empe a u e, cellula a ge s, issues, o ganisms, e c. In a ecen wo k, we combined he
θk(G) alues calcula ed wi h MI and he idea o Mo ing A e age (MA) ope a o s wi h a simila
pu pose [41]. In ime se ies analysis he MA ope a o s a e a e age alues o cha ac e is ic o he
sys em o di e en seasons. In ac , MA models became popula a e he ini ial wo ks o Box
and Jenkins [42]. In ime se ies analysis, MA models may combine o he ope a o s I = In eg a ed,
AR = Au o eg essi e, N = Non-linea ope a o s, o X = Exogenous e ec s. In his sense, o he s
models ha e eme ged combining di e en ope a o s: ARMA, ARIMA, VARIMA, ARIMAX,
NARMA, e c. In mul i-ou pu modeling, we calcula e he MA ope a o s as he a e age o he p ope y
o he sys em (molecula desc ip o s o o he s) o all d ugs o a ge s wi h a speci ic esponse in one
assay ca y ou unde a sub-se o condi ions (cj). Consequen ly, ou MA ope a o is no ac ing o e a
ime domain bu o e a sub-se o condi ions o he pha macological assays. The idea o applica ion o
MA ope a o s o o he domains di e en om ime is gaining adep s due o i s ad an ages.
Fo ins ance, Bo ella-Rocamo a e al. [43] de eloped a model o disease mapping using spa ial
Box–Jenkins ope a o s wi h he o m o MAs, o de ine dependence o he isk o a disease o occu .
In ou models, we use MA in ela ion wi h p ope ies o nodes o ne wo ks (d ugs, p o eins, eac ions,
laws, neu ons, e c.); which o m links Lij(cq) in speci ic sub-se o condi ions (cq). Fo his eason, we
decided o call his s a egy as ALMA (Assessing Links wi h Mo ing A e ages) models. Speck-Planche
and Co dei o epo ed di e en mul i- a ge o mul i-ou pu models using he same ype o ALMA
models [44–46].
In . J. Mol. Sci. 2014, 15 17038
In he speci ic a ea o neu odegene a i e diseases, almos all hese da ase s includes also la ge
sub-se s o assays in ol ing po en ial neu op o ec i e d ugs, a ge s, as well as d ug- a ge and/o
a ge – a ge in e ac ions. The da abase Neu oDNe has in e ac i e ools o c ea e in e ac ion ne wo ks
o wel e neu odegene a i e diseases. Acco ding o Vasaika e al. [47], i is he i s o i s kind,
which enables he cons uc ion and analysis o neu odegene a i e diseases h ough p o ein in e ac ion
ne wo ks, egula o y ne wo ks and Boolean ne wo ks. In he case o neu op o ec i e compounds, some
au ho s ha e epo ed mul i- a ge ALMA models. Ga cía e al. used opological desc ip o s o a la ge
se ies o 3370 ac i e/non-ac i e compounds o i a classi ica ion unc ion ha can p edic links Lij
(in e ac ions) o he e ogeneous se ies o GSK inhibi o s compounds wi h di e en neu ological a ge s
ele an o Alzheime ’s disease and pa asi e species. Speck-Planche e al. [48], de eloped a mul i- a ge
model using a la ge and he e ogeneous da abase o inhibi o s agains i e p o eins associa ed wi h
Alzheime ’s disease. The model co ec ly classi ied mo e han 90% o ac i e and inac i e compounds
in he ea men o Alzheime ’s disease on bo h, aining and p edic ion se ies. Se e al guidelines a e
o e ed in o he pape o show how he use o agmen -based desc ip o s can be de e minan o he
design o mul i- a ge inhibi o s o p o eins associa ed wi h Alzheime ’s disease [49].
In a ecen wo k, we used he me hod TOPS-MODE (TM) [50] o calcula e he s uc u al pa ame e s
o d ugs. The model co ec ly classi ied 4393 ou o 4915 o al cases wi h Speci ici y (Sp), Accu acy
(Ac), and Sensi i i y (Sn), o 80%–98%. We also used he me hod TM o de elop one ALMA [51]
model use ul o he p edic ion o neu op o ec i e d ugs. This da ase includes Mul i-ou pu assay
endpoin s o 2217 compounds o a leas one ou o 338 assays, wi h 148 molecula o cellula a ge s,
and 35 ypes o ac i i y measu es in 11 model o ganisms (including human). In a hi d wo k [52], we
in oduced ano he ALMA model o neu o oxici y/neu op o ec i e e ec s o d ugs based on he
me hod MI. Fi s , we used MI o calcula e molecula desc ip o s o he ype o s ochas ic spec al
momen s o all compounds. Nex , we ound a model ha classi ied co ec ly 2955/3548 o al cases on
aining and alida ion se ies wi h Ac, Sn, and Sp > 80%. Each da a poin (>8000) con ains he alues
o 37 possible measu es o ac i i y, 493 assays, 169 molecula o cellula a ge s, and 11 di e en
o ganisms (including human) o a gi en compound. The model has shown excellen esul s also in
compu a ional simula ions o high- h oughpu sc eening expe imen s, wi h Ac = 90.6% o 4671
posi i e cases. Bo h models a e able o p edic he links Lij(cq) be ween i h d ugs and j h a ge s
acco ding o he assay aq. Howe e , we do no ca ied ou a o mal cons uc ion and a compa ison o
he d ug- a ge ne wo ks o he CHEMBL da a in p e ious pape s. In any case, despi e he high
e sa ili y o en opy measu es o codi y s uc u al in o ma ion, he e is no epo o a mul i- a ge
model o d ug– a ge in e ac ions o compounds wi h neu op o ec i e/neu o oxic e ec . In his wo k,
we epo he i s mul i- a ge , mul i-ou pu , and mul i-scale ALMA model o CHEMBL da a o
neu op o ec i e/neu o oxic e ec o d ugs. Then, we cons uc and compa e o he i s ime h ee
Mul i-ou pu assay complex ne wo ks o hese CHEMBL da ase using he wo p e ious models
and he model epo ed in his wo k. F om he e, we epo ed by he i s ime he syn hesis,
cha ac e iza ion, and expe imen al assays o a new se ies o asagiline ca bama e de i a i es no
epo ed in p e ious wo ks. We ca ied ou h ee di e en expe imen al es s: assay (1) in absence o
neu o oxic agen s; (2) in he p esence o glu ama e; and (3) in he p esence o H2O2. Finally, we used
he new en opy model o p edic possible ou comes o hese compounds in a high numbe o
pha macological es s no ca ied ou expe imen ally. The esul s p esen ed he e show he high
In . J. Mol. Sci. 2014, 15 17039
po en ial o en opy pa ame e s o chemical in o ma ion o he design o neu op o ec i e d ugs, he
cons uc ion o complex bio-molecula ne wo ks, and he po en ial o ALMA models o mul i- a ge ,
mul i-ou pu , and mul i-scale modeling.
2. Resul s and Discussion
2.1. De elopmen o New Model o P edic ion o D ug–Ta ge Ne wo ks
2.1.1. Model T aining and Valida ion
We epo a model o p edic ing when he i h compound may p esen a high (Lij(cq) = 1) o no
(Lij(cq) = 0) alue o he expe imen al pa ame e used o cha ac e ize in e ac ion wi h a molecula o
cellula a ge in ol ed in a neu op o ec i e/neu odegene a i e p ocess. The ou pu Sij(cq) o ou
mul i-ou pu model depend on bo h chemical s uc u e o he i h d ug di and he se o condi ions
selec ed o pe o m he biological assay (cq) including he j h a ge , o cou se. In consonance, he
ALMA model should p edic di e en p obabili ies i we change he o ganisms (c1), he biological
assays (c2), he molecula /cellula a ge (c3), o he s anda d expe imen al pa ame e measu ed (c4), o
he same compound [53].The bes ALMA-en opy model ound in his wo k was:




 
005.0007.191372.02661
·0017.0·0202.0
·4349.0·1993.0)(·4039.01396.1
2
11
111



pRN
o
ascpcS
c
e
i
i
u
i
x
ii
lqij



(1)
The s a is ical pa ame e s o he abo e equa ion in aining a e: Numbe o cases used o ain he
model (N), Canonical Reg ession Coe icien (Rc), Chi-squa e (χ2), and p-le el [54]. The p obabili y
cu -o o his Linea Disc iminan Analysis (LDA) model is ip1(cq) > 0.5 ≥ Lij(cq) = 1. I means ha
he d ug di p edic ed by he model, wi h p obabili y p > 0.5, is expec ed o gi e a posi i e ou come in
he q h assays ca y ou unde he gi en se o condi ions cq. This ALMA-en opy model p esen s
excellen pe o mance in bo h aining and ex e nal alida ion se ies wi h Sn, Sp, and Ac > 80%
(see Table 1). Values highe han 75% a e accep able o LDA-QSAR models, acco ding o
p e ious epo s [55–59].
The i s e m in he equa ion, quan i y bo h he quali y o he inpu da a p(cl) and he
in o ma ion θi5 abou he s uc u e o he d ug (see ma e ial and me hods and p e ious wo ks [51]). We
can expand he Box–Jenkins MA e ms in he ALMA equa ion in o de o clea ly depic all he
pa ame e s in ol ed:



  

  

  

  

005.0007.191372.02661
··001660.0
··020189.0
··434889.0
··199322.0
··403994.0139556.1
2
515
515
515
515
51






pRN
p
oopo
aapa
ssps
spcS
c
eee
i
i
uuu
i
xxx
i
i
xqij






(2)

In . J. Mol. Sci. 2014, 15 17040
A e inspec ion o his equa ion, we can see ha he ALMA model can p edic o he same
compound di e en sco es o di e en expe imen al pa ame e s, a ge s, assays, o e en di e en
o ganisms. In Table 2 we illus a e he alues o p obabili y o d ug– a ge in e ac ion pij(cq) p edic ed
wi h he p e ious model, o se e al examples o known d ugs o new p omising compounds. These a e
he p obabili ies wi h which he i h compound in e ac wi h he j h d ug unde he assay condi ions cq.
This is equi alen o pij(cq) > 0.5 ≥ Lij(cq)p ed = 1. Howe e , online supplemen a y ma e ial iles con ain
a comple e lis wi h many examples o posi i e and con ol cases.
Table 1. Resul s o Assessing Links wi h Mo ing A e ages (ALMA) models o en opy
measu es s. di e en spec al momen s.
Desc ip o Sub-Se S a . a % G oups Ci(mj)p ed = 1 Ci(mj)p ed = 0 Re e ence
MI-En opy
T ain
Sp 79.0 Lij(Cq)obs = 1 1092 290
This wo k
Sn 91.5 Lij(Cq)obs = 0 412 4438
Ac 88.7 To al
CV
Sp 81.3 Lij(Cq)obs = 1 379 87
Sn 92.6 Lij(Cq)obs = 0 119 1492
Ac 90.1 To al
MI spec al
momen s
T ain
Sp 84.6 Lij(Cq)obs = 1 1172 214
[52]
Sn 82.4 Lij(Cq)obs = 0 224 1051
Ac 83.5 To al
CV
Sp 83.3 Lij(Cq)obs = 1 385 77
Sn 81.6 Lij(Cq)obs = 0 78 347
Ac 82.5 To al
TM spec al
momen s
T ain
Sp 81.3 Lij(Cq)obs = 1 1533 352
[51]
Sn 98.0 Lij(Cq)obs = 0 36 1762
Ac 89.5 To al
CV
Sp 81.0 Lij(Cq)obs = 1 513 120
Sn 97.7 Lij(Cq)obs = 0 14 585
Ac 89.1 To al
MI, MARCH-INSIDE; a Sensi i i y = Sn = Posi i e Co ec /Posi i e To al; Speci ici y = Sp = Nega i e
Co ec /Nega i e To al; Accu acy = Ac = To al Co ec /To al; TM, TOPS-MODE.
Table 2. Examples p edic ed wi h he model.
Compound (i) pij(cq)Assay ID Measu e (Uni s) O ganism Ta ge P o ein
A ecoline 0.94 796814 E iciency (%) no Musca inic
ace ylcholine ecep o
Bipinna in-A 1.00 751272 Inhibi ion (%) mmu Ace ylcholine ecep o
p o ein β chain
Ca achol 0.99 796814 E iciency (%) no Musca inic
ace ylcholine ecep o
Caulophylline 0.96 838016 EC50 (nM) hsa Neu onal ace ylcholine
ecep o ; α4/β2
Ci alop am 0.99 740208 Ki (nM) mmu Dopamine anspo e
Condelphine 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
In . J. Mol. Sci. 2014, 15 17041
Table 2. Con .
Compound (i) pij(cq)Assay ID Measu e (Uni s) O ganism Ta ge P o ein
Delco ine 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
Delsoline 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
Desip amine 0.99 797692 −Log(IC50) (nM) no No epineph ine anspo e
Ela ine 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
Emopamil 1.00 817225 −Log(IC50) (nM) no Vol age-ga ed R- ype calcium
channel α-1E subuni
Epiba idine 0.94 838016 EC50 (nM) hsa Neu onal ace ylcholine
ecep o ; α4/β2
Epiba idine 0.19 825420 E icacy (%) hsa Neu onal ace ylcholine
ecep o ; α4/β2
Femoxe ine 0.99 740206 Ki (nM) mmu Dopamine anspo e
Femoxe ine 0.99 740207 Ki (nM) mmu No epineph ine anspo e
Femoxe ine 0.99 740208 Ki (nM) mmu Dopamine anspo e
Fise in 0.05 1027709 %max (%) mmu HT22 cells
Fluoxe ine 0.99 740207 Ki (nM) mmu No epineph ine anspo e
Fluoxe ine 0.99 740208 Ki (nM) mmu Dopamine anspo e
Imip amine 0.99 740206 Ki (nM) mmu Dopamine anspo e
Imip amine 0.99 740207 Ki (nM) mmu No epineph ine anspo e
Imip amine 0.99 740208 Ki (nM) mmu Dopamine anspo e
Inuline 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
Ka acoline 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
L-A ginine 0.99 755144 Ac i i y (nM) hsa Ni ic-oxide syn hase, b ain
L-NIL 0.59 752266 −Log(IC50) (nM) hsa Ni ic-oxide syn hase, b ain
L-NMMA 0.99 876477 −Log(IC50) (nM) hsa Ni ic-oxide syn hase, b ain
L-NNA 0.98 752385 −Log(IC50) (nM) hsa Ni ic-oxide syn hase, b ain
L-NNA 0.86 752276 Ki (nM) hsa Ni ic-oxide syn hase, b ain
LY-379268 0.99 714803 Ac i i y (nM) hsa Me abo opic
glu ama e ecep o 4
LY-379268 0.99 877752 Ac i i y (nM) hsa Me abo opic
glu ama e ecep o 2
LY-379268 0.99 718128 Ac i i y (nM) hsa Me abo opic
glu ama e ecep o 6
LY-389795 0.99 718128 Ac i i y (nM) hsa Me abo opic
glu ama e ecep o 6
LY-389795 0.98 715721 Ac i i y (nM) hsa Me abo opic
glu ama e ecep o 5
LY-389795 0.97 714446 Ac i i y (nM) hsa Me abo opic
glu ama e ecep o 3
In . J. Mol. Sci. 2014, 15 17042
Table 2. Con .
Compound (i) pij(cq)Assay ID Measu e (Uni s) O ganism Ta ge P o ein
Lycoc onine 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
M826 1.00 841780 Ki (nM) hsa Caspase-3
M827 1.00 841780 Ki (nM) hsa Caspase-3
Me hyllycaconi ine 1.00 750084 Ki (nM) no Neu onal ace ylcholine
ecep o p o ein α-10 subuni
NBQX 0.99 641893 −Log(IC50) (nM) no Glu ama e ecep o
iono opic, AMPA 2
NBQX 0.99 641893 −Log(IC50) (nM) no Glu ama e ecep o
iono opic, AMPA 4
NBQX 0.99 641893 −Log(IC50) (nM) no Glu ama e ecep o
iono opic, AMPA 3
NBQX 0.99 641893 −Log(IC50) (nM) mmu Glu ama e ecep o
iono opic, AMPA 1
Nipeco ic acid 0.28 785010 −Log(IC50) (nM) no GABA anspo e 1
Nipeco ic acid 0.28 785010 −Log(IC50) (nM) no GABA anspo e 2
Nipeco ic acid 0.28 785010 −Log(IC50) (nM) no GABA anspo e 3
Nipeco ic acid 0.28 785010 −Log(IC50) (nM) no Be aine anspo e
NOHA 0.04 755137 NO
o ma ion (%) no Ni ic-oxide syn hase, b ain
No epineph ine 0.98 780755 Concen a ion
(% dose·g−1) no
Nudicauline 1.00 748943 −Log(IC50) (nM) no Neu onal ace ylcholine
ecep o p o ein α-7 subuni
Omega
ni o-a ginine 0.99 752258 Ki (nM) hsa Ni ic-oxide syn hase, b ain
Oxo emo ine 0.84 798083 pD2 no Musca inic ace ylcholine
ecep o M1
Pa oxe ine 1.00 740206 Ki (nM) mmu Dopamine anspo e
RedAm-E hyl 0.33 840782 Selec i i y hsa Ni ic-oxide
syn hase, endo helial
RedAm-E hyl 0.28 840782 Selec i i y hsa Ni ic-oxide syn hase, b ain
Res e a ol 0.99 1613870 EC50 (nM) hsa Nuclea ac o NF-κB
p105 subuni
Res e a ol 0.99 1613870 EC50 (nM) hsa Nuclea ac o NF-κB
p65 subuni
S emo oline 1.00 936299 EC50 (nM) h i Nico inic ace ylcholine
ecep o α1 subuni
Thiocy isine 0.51 857972 Log Ki no Neu onal ace ylcholine
ecep o ; α4/β2
no, Ra us no egicus (Ra ); mmu, Mus musculus (Mouse); hsa, Homo sapiens (Human); and h i, Helio his i escens.
The Table 2 shows p edic ions o he same d ug in di e en se s o condi ions o assay cq, including
di e en a ge s, o ganisms, o assays. The e o e, we only ha e o subs i u e in he equa ion he alue
In . J. Mol. Sci. 2014, 15 17043
o θi5 o he compound and he espec i e alues p1(cq)·<θi5(cq)> o he MA ope a o s o each
condi ion. In he Table 3 we depic many examples o alues o MA ope a o s p1(cq)·<θi5(cq)> o
di e en condi ions.
2.1.2. Compa ison wi h O he ALMA Models
An in e es ing exe cise is he compa ison o he p esen model and he ne wo k p edic ed wi h
ou comes ob ained wi h o he me hods. Un il he bes o ou knowledge, he e a e only wo simila
models. Bo h models make use o he spec al momen s o a molecula ma ix as inpu a iables (Di) o
quan i y he molecula s uc u e o d ugs. The i s model [51] applies spec al momen s µk o o de k h
o he bond adjacency ma ix (1B) calcula ed wi h he TM app oach. The equa ion o his model is
he ollowing:






 
005.07.03683
198684.4·10·84.2·10·16.1
·10·93.2·10·84.7·10·01.7
5
4
5
4
5
4
5
4
5
4





pRN
o
ascpcS
c
ii
iii
jqij


(3)
The second model [52] employs as inpu he πik alues o he Ma ko ma ix (1Π) o a om–a om
elec on delocaliza ion calcula ed wi h he so wa e MI. In he TM me hod, we weigh ed he edges o
he molecula g aph wi h s anda d dis ances o chemical bonds whe eas he MI algo i hm employs
a om s anda d elec onega i i ies o weigh ing he nodes o molecula g aph. The equa ion o he
second model is:






 
005.0007.191372.02661
·001660.0·020189.0
·434889.0·199322.0·403994.0139556.1
2
15
555



pRN
o
ascpcS
c
e
i
i
u
i
x
ii
jqij



(4)
In bo h cases, as well as in he p esen ALMA-en opy model, we used MA e ms o quan i y he
de ia ions o he s uc u e o one compound om sub-se s o compounds wi h a posi i e ou come in
di e en condi ions cq. The h ee me hods showed excellen alues o Ac, Sp, and Sn on bo h aining
and alida ion se ies (see Table 1). Appa en ly, he TM model shows be e alues o hese pa ame e s
bu we ha e o ake in o conside a ion he di e ences in he complexi y o he da a se s used o ain
and alida e hese models. The TM-spec al momen model is able o classi y co ec ly 83%–82% o
4915 cases in o al (on aining and alida ion se ies espec i ely). The MI-spec al momen model is
able o classi y co ec ly 89%–92% o 3598 cases. No ably, he MI-en opy model is able o classi y
co ec ly 89%–92% o 8309 cases. Consequen ly, he s a is ics o he p esen model e e o a da ase
wi h mo e han wice he numbe o da a poin s p esen in p e ious models.
In . J. Mol. Sci. 2014, 15 17050
Table 5. Neu op o ec i e abili y o he new 1,2- asagiline de i a i es.
Compound Fo mula % Neu o-P o ec ion
% ANA a e.s.m. Glu ama e
b e.s.m. H2O2 c e.s.m.
2
0.0 2.8 0.0 6.5 −2.8 1.2
3
4.7 6.0 −0.2 1.6 −12.3 2.1
4
4.2 6.5 −8.1 4.9 −14.2 2.1
5
1.2 5.0 3.8 5.0 2.9 1.0
6
11.5 8.8 −4.0 5.5 −9.1 2.4
7
4.0 4.5 2.6 3.9 -6.1 1.1
8
−1.7 6.9 −5.2 5.9 −8.9 1.9
9
8.4 10.7 −5.2 2.3 −14.0 2.0
a % p o ec ion (comp 5 µM), in he Absence o Neu o oxic Agen s (ANA); b % p o ec ion (comp 5 µM)
agains Glu ama e 100 µM; c % p o ec ion (comp 5 µM) agains H2O2 100 µM.
Fi s ly, we s udied he abili y o induce a neu op o ec i e e ec in he absence o any neu o oxic
s imula ion. Secondly, we s udied he neu op o ec i e e ec in he p esence o glu ama e, a compound
ha causes a pa hological p ocess, in which neu ons a e damaged leading o apop osis when i s
ecep o s, such as he NMDA and AMPA, a e o e -ac i a ed. Las ly, he abili y o he compounds
syn hesized o p o ec om damage by H2O2, ha causes neu onal dea h by oxida i e s ess, was
analyzed. The esul s ob ained allow o deduce he exis ence o a mode a e neu op o ec i e e ec in
he absence o any oxic s imulus, p esen ing he bes esul s ype 6 and 9 ca bama e de i a i es, wi h
alues o 11.5% and 8.4%, espec i ely, ollowed by he compound 3, 4, and 7 wi h alues sligh ly
abo e 4% (see Figu e 3).

In . J. Mol. Sci. 2014, 15 17051
Figu e 3. Resul s o he expe imen al assay o neu op o ec i e e ec o he new compounds.
2.2.2. Using ALMA-En opy Model o P edic ing New D ugs in O he Assays
We used he ALMA-en opy model o p edic ing he mo e p obable esul s o all he new asagiline
de i a i es syn hesized in his wo k, in >500 assays no ca ied ou expe imen ally. When he
molecula desc ip o s (en opy indices) o he new asagiline de i a i es we e in oduced in ou model,
we ob ained he p obable in e ac ion wi h di e en a ge s. The model p edic s ha mos o hem could
in e ac wi h he subuni s A and B o he 5-hid oxy- yp amine ype 3 ecep o s (5-HT3Rs), see Table 6.
These esul s seem o be consis en wi h he li e a u e, since he an agonis s o 5-HT3Rs ha e been
ela ed o neu op o ec i e p ope ies in i o and in i o [66]. In ac , his could be a po en ial
mechanism o neu op o ec ion added o se e al desc ibed mechanisms o asagiline de i a i es [67,68].
Rasagiline is also known o p omo ing se o onine gic ac i i y by o he ways, which is a clinically
ele an ac in ce ain ci cums ances [69]. All in one highligh s he in ica e ela ionships o hese
d ugs wi h he 5-hid oxy- yp amine (se o onine) sys em.
Table 6. Some p edic i e esul s o in e ac ion be ween compound 6 wi h 5HT3Rs and
o he a ge s.
Si(cj) Meassu e Assay ID Ta ge ID Ta ge a Neu o oxic Agen
2.097 pA2 617971 1899 5HT3aR ANA
2.097 pA2 617969 1899 5HT3aR ANA
2.097 pA2 617971 3895 5HT3bR ANA
2.097 pA2 617969 3895 5HT3bR ANA
1.78 Selec i i y 848737 3568 bNOS H2O2
1.78 Selec i i y 840777 3568 bNOS H2O2
1.78 Selec i i y 755901 3568 bNOS H2O2
1.17 Ac i i y (%) 866501 2586 nAChRβ-3 H2O2
0.42 pIC50 (nM) 710048 3772 mGluR1 Glu
a nAChRβ-3 = neu onal ace hyl-choline ecep o β3, mGluR1 = me abo opic glu ama e ecep o ype 1.
In . J. Mol. Sci. 2014, 15 17052
In any case, we need o analyze hese esul s wi h cau ion. In ou p e ious wo ks [51,52], we
p edic ed wi h new models and con i med expe imen ally ha some asagiline de i a i es (simila o
he de i a i es s udied in his wo k) p esen ed ac i i y o e glu ama e ecep o s (GluRs) pa hway.
In he i s o hese wo ks [51], we s udy expe imen al measu es o neu op o ec i e capaci y o new
1,3- asagiline de i a i es. All he compounds, excep one o hem, had a high p o ec i e ac i i y
agains damage media ed by H2O2. The bes one o all, a monop opa gyl ans de i a i e, showed also
a high neu op o ec i e ac ion in all h ee ype o assays. Ou i s model p edic ed o his compound
high p obabili y o ac i i y in ela ionship wi h ace ylcholine and GABA, in addi ion o GluRs.
In coincidence, ace ylcholine ecep o s (AChRs) ha e been associa ed wi h neu op o ec i e p op ie ies
in se e al ecen expe imen al wo ks, and he e a e also epo s o associa ion o GABA and GluRs
wi h neu op o ec i e abili y [70,71]. Nu i o a e al. [72], discussed a neu op o ec i e s a egy
in ol ing e og ade elease o glu ama e.
In ou second wo k [52], we s udied wo ypes o subs i uen g oups (p opa gyl g oups a ached o
he ni ogen and a ca bama e o es he g oup ins ead o hyd oxyl). The compounds also p esen ed wo
di e en chi ali y pa e ns bu wi h 1,3 subs i u ions pa e n. The compounds o his second se ies we e
ac i e expe imen ally in he absence and p esence o neu o oxic agen s. The bes compound o his
second se ies, a dip opa gyl de i a i e, was p edic ed o ha e b ain ni ic oxide syn hase (bNOS) as
he mos p obable a ge and ce ain p obabili y o mul i- a ge ligand. Again, bNOS was associa ed
expe imen ally wi h neu op o ec i e ac ion in se e al wo ks [73,74].
The compounds s udied his hi d wo k p esen simila subs i uen g oups and s e eochemis y bu
one 1,2 subs i u ion pa e n. Based on he p e ious esul s, we should expec a simila expe imen al
ac i i y and p edic ions. Howe e , in he p e ious sec ion we shown expe imen ally ha he p esen se
o compounds seems no o be e y ac i e o e GluRs and he model p edic s he highe sco es o
ac i i y o e 5-HT3Rs ins ead o he expec ed ecep o s. As we s a ed in he p e ious pa ag aph,
5-HT3Rs ha e been ela ed o neu op o ec i e p ope ies in i o and in i o [66]. A plausible
hypo hesis (penden o u he expe imen al con i ma ion) is he a ia ion in ecep o a ini y ( om
GluRs o 5-HT3Rs pa hway) due o he change om 1,3 o 1,2 subs i u ion pa e n. F om ou poin o
iew, hese co espondences be ween a ge s ha ou equa ions p edic , and he e e ences ci ed om
he li e a u e could indica e biological plausibili y o ou models.
3. Ma e ials and Me hods
3.1. Compu a ional Me hods
3.1.1. ALMA-En opy Models
ALMA models may be classi ied as a gene al ype o model o assessing he links in di e en
sys ems. They a e adap able o all molecula desc ip o s and/o g aphs in a ian s o desc ip o s o
complex ne wo ks. In gene al, we e e o a desc ip o Dik o ype k h o he i h sys em (compound o
d ug di in his case) ep esen ed by a ma ix M. In ac , in his wo k we a e going o compa e he
model based on en opy alues θik o a Ma ko ma ix 1Π wi h o he ALMA models based on o he
in a ian s o he same ma ix 1Π, o in a ian s o he bond adjacency ma ix 1B. Consequen ly, we
desc ibe i s he gene al equa ions o he model using a gene ic desc ip o , o g aph heo e ical
In . J. Mol. Sci. 2014, 15 17053
in a ian Dik, and la e we gi e he speci ic equa ion o he en opy model based on θik alues. The
aim o his model is o link he sco es Sij(cq) wi h he molecula desc ip o s Dik o a
gi en compound di and he Box–Jenkins MA ope a o s w i en in he o m o de ia ion e ms
ΔDik(cq) = Dik – <Dik(cq)>. The model has he ollowing gene al o m:


 























5
1
5
0
5
0
0
5
1
5
0
5
0
0
5
1
5
0
0
'')('
'')('
)(''''''
q
q
k
k
q
k
i
q
k
i
qk
k
k
k
i
lk
q
q
k
k
q
k
i
jk
k
k
k
i
lk
q
q
q
k
ijjk
k
k
q
k
kqij
cDcpDaDcpaa
cDaDcpaa
cSaSaacS
(5)
The ou pu dependen a iable is Sij(cq) = Sij(cl, c2, c3, c4, c5) = Sij(cl, aq, o , j, sx). The a iable Sij(cq)
is a nume ical sco e o he biological ac i i y o he i h d ug (di) s. he j h a ge measu ed in one assay
ca ied ou unde he se o q h condi ions cq. Ou hypo hesis is H0: we can calcula e he ou pu Si(cq) as
a linea combina ion o sco es. We ha e wo ypes o sco es. The i s ype a e he sco es
'Sik = 'ak·p(cl)·iDk ha accoun o he quali y o da a p(cl) and o con ibu ions o he k h molecula
desc ip o s o he inal ac i i y sco e Sij(cq). In ac , we used he p obabili y p(c1) = 1.0; 0.75; o 0.5
o da a cu a ed in CHEMBL da abase a le els o expe , in e media e, o au o-cu a ion le el,
espec i ely. The second ype a e sco es ''Sijk(cq>1) = ''ak·ΔDik(cj) o he con ibu ions o de ia ions
ΔDik(cq) = (Dik − <Dik(cq)>) o he desc ip o s o di om he a e age o hose o ac i e molecules
Lij(cq) = 1 o di e en cq. In gene al, cj e e s o di e en Mul i-ou pu assay condi ions, e.g., a ge s,
assays, cellula lines, o ganisms, o gans, e c. In his sense, c0 = is he accu acy o he da a o his
assay, c1 = au is he assay pe se, c2 = o is he o ganism ha exp ess he a ge , c3 = j is he j h cellula
o molecula a ge , and c5 = sx is s anda d expe imen al measu e o ac i i y. Then, he pa ame e Dik
and ΔDik(cq) a e he inpu independen a iables and Lij(cq) = 1 is he inpu dependen a iable. He e,
<Dik(cq)> is he a e age o he k h desc ip o s Dik o all i h compounds conside ed as ac i e (Lij(cq) = 1)
in an assay ca y ou unde he se o condi ions cq. The pa ame e s ΔDik(cq) a e simila o he MA used
in ime se ies analysis o Bob–Jenkins ARIMA models and o he s [42]. This ype o MA model has
been used be o e o sol e di e en p oblems in Chemin o ma ics be o e. I means ha , i s ly, we sum
he alues o Dik o all he nj d ugs wi h Lij(cq) = 1 in he assay ca y ou in he condi ions cj. Nex , we
di ide his sum by he numbe o compounds nj wi h his condi ion.
 




q
ni
i
q
k
i
q
q
k
icD
n
cD
1
1 (6)
In . J. Mol. Sci. 2014, 15 17054
In his model, we used only one molecula desc ip o θi5. This is he Shannon en opy o o de k = 5
calcula ed wi h MI. We do no use low-o de en opies k = 0, 1, 2, 3, and 4. Acco dingly, he gene al
equa ion is:


 













5
1
555
0
5
1
55
50
5
1
55
50
'')('
'')('
)('''')(''
q
q
q
i
qqk
i
lk
q
q
q
i
jk
i
l
q
q
qijjkliqij
ccpacpaa
cacpaa
cSacSaacS
i


(7)
This ype o mo ing a e age o de ia ion-like models was coined by us as he ALMA models, and
has been used be o e o sol e di e en p oblems [54,75–77]. In o de o seek he model we used he
echnique Linea Disc iminan Analysis (LDA) implemen ed in he so wa e package STASTICA 6.0 [78].
The s a is ical pa ame e s used o co obo a e he model we e: Numbe o cases in aining (N), and
o e all alues o Sp, Sn, and Ac [54].
3.1.2. CHEMBL Da ase
We downloaded om he public da abase CHEMBL a gene al da a se composed o >8000
Mul i-ou pu assay endpoin s ( esul s o mul iple assays) [33,34]. We assigned a alue o he obse ed
(obs) class a iable Lij(cq)obs = 1 (ac i e compound) o Lij(cq)obs = 0 (non-ac i e compounds) o e e y
i h d ug biologically assayed in di e en condi ions cj. The da ase used o ain and alida e he model
includes N = 3548 s a is ical cases, o med by Nd = 3091 unique d ugs which ha e been assayed each
one in a leas one ou o 37 possible s anda d ype measu es de e mined in, a leas , one ou o
493 assays. Each assay in ol es, in u n, a leas one ou o 169 molecula o cellula a ge s exp essed
in he issues o a leas one ou o 11 di e en o ganisms (including human).
3.2. Expe imen al Me hods: Chemis y
3.2.1. Syn hesis o 1,2-Rasagiline De i a i es
Mel ing poin s a e unco ec ed and we e de e mined in Reiche Ko le The mopan (Reiche ,
Vienna, Aus ia) o in capilla y ubes on a Büchi 510 appa a us (BÜCHI Labo echnik AG, Flawil,
Swi ze land). In a ed spec a we e eco ded on a JASCO FT/IR-4100 spec opho ome e (JASCO
Analy ical Ins umen s, Eas on, PA, USA). The 1H-NMR spec a (300 MHz) and 13C-NMR spec a
(75 MHz) we e eco ded in a B uke AMX spec ome e (B uke BioSpin Co po a ion, F emon , CA,
USA), using TMS as in e nal e e ence (chemical shi s in δ alues, J. in Hz). EI Mass spec a we e
eco ded on a HEWLETT-PACKARD 5988A spec ome e (Hewle -Packa d Company, Palo Al o,
CA, USA). FABMS we e ob ained using MICROMASS AUTOSPEC mass spec ome e (WATERS,
Mil o d, MA, USA) and ESIMS we e de e mined on a BRUKER AMAZON ETD spec ome e (B uke
BioSpin Co po a ion). We pe o med mic oanalyses in a Pe kin-Elme 240B elemen al analyze
(Pe kinElme , Wal ham, MA, USA) by he Mic oanalysis Se ice o he Uni e si y o San iago
de Compos ela. The speci ic o a ion was measu ed wi h a PERKIN-ELMER 241 pola ime e
In . J. Mol. Sci. 2014, 15 17055
(Pe kinElme ), and i is exp essed in (°) (dm−1) (g−1) (mL). Mos o he eac ions we e moni o ed by
TLC on p e-coa ed silica gel pla es (Me ck 60 F254, 0.25 mm, Me ck KGaA, Da ms ad , Ge many).
Syn hesized p oduc s we e pu i ied by lash column ch oma og aphy on silica gel (Me ck 60,
230–240 mesh, Me ck KGaA) and c ys allized i necessa y. Sol en s we e d ied by dis illa ion p io use.
Compound (3): (1S,2R)-(+)-cis-1-(N-P opa gylamino)-2-indanol (2) and (1S,2R)-(+)-cis-1-(N,N-
dip opa gylamino)-2-indanol. A mix u e o 1 (0.20 g, 1.34 mmol), K2CO3 (0.18 g, 1.34 mmol) and
MeCN (7 mL) was s i ed a oom empe a u e unde a gon o 5 min. A solu ion o p opa gyl b omide
(0.3 mL, 2.7 mmol) dissol ed in MeCN (2 mL) was added d opwise wi h s i ing. A e being s i ed
o 24 h, he sol en was e apo a ed and he esidue was dissol ed in E OAc (10 mL). The o ganic
laye was washed wi h NaOH 2N (3 × 10 mL) and d ied (Na2SO4). The emo al o excess o sol en
o gi e a whi e solid, ha was pu i ied by lash column ch oma og aphy using hexane/E OAc (3:1) as
eluen o gi e, in i s place 3 (170 mg, yield 56%) as a whi e solid and in second place 2 (90 mg, yield
36%) as a whi e solid.
(+)-cis-2. M.p. 106–108 °C.[∝]
º = +38° (25 °C, 0.25, CHCl3). IR ν = 3277, 2906, 1421, 1339,
1140, 1051, 731 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.32–7.22 (m, 4H, Ha om), 4.51–4.47 (m, 1H,
2-H), 4.31–4.29 (m, 1H, 1-H), 3.69–3.52 (AB sys em , 1H, J = 17.2 Hz, CH2), 3.68–3.51 (AB sys em,
1H, J. = 17.2 Hz, CH2), 3.11–2.96 (m, 2H, 3α-H, 3β-H), 2.67 (b . s., 1H, D2O exch., OH), 2.31 ( , 1H,
J. = 2.2 Hz, CH). 13C RMN (75 MHz, CDCl3) δ = 141.85 (C-3a), 141.05 (C-7a), 128.17, 126.79,
125.58 and 123.94 (CHa om), 82.27 (C≡CH), 71.90 (C-2), 70.87 (C≡CH), 64.78 (C-1), 39.59 (CH2),
37.16 (C-3). MS (EI): m/z (%): 186 (2) [M−1]+, 168 (5) [M+–H2O], 148 (100) [M+–p opa gyl], 130
(21), 115 (10), 103 (31), 77 (11). Anal. calcd. o C12H13NO (187.24): C 76.98, H 7.00, N 7.48; ound
C 76.63, H 7.12, N 7.36.
(+)-cis-3. M.p. 106–109 °C. [∝]
º = +72° (25 °C, 0.25, CHCl3). IR ν = 3279, 2894, 1339, 1244,
1137 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.52–7.50 (m, 1H, 7-H), 7.29–7.18 (m, 3H, 4-H, 5-H,
6-H), 4.52 (dd, 1H, J. = 13.2, 6.9 Hz, 2-H), 4.42–4.40 (m, 1H, 1-H), 3.74 (b . s., 1H, D2O exch., OH),
3.65–3.39 (AB sys em, 2H, J. = 17.1 Hz, CH2), 3.64–3.38 (AB sys em, 2H, J. = 17.1 Hz, CH2),
3.24–2.79 (pa AB o an ABM sys em, 2H, JAB = 16.4 Hz, JAM =7.2 Hz, JBM = 6.1 Hz, 3α-H, 3β-H),
2.29 ( , 2H, J. = 2.3 Hz, 2 × CH). 13C RMN (75 MHz, CDCl3) δ = 141.47 (C-3a), 138.15 (C-7a),
128.68, 127.04, 126.65 and 125.46 (CHa om), 80.37 (2 × C≡CH), 72.87 (C-2), 71.39 (2 × C≡CH), 68.37
(C-1), 41.04 (2 × CH2), 40.31 (C-3). MS (EI): m/z (%): 226 (2) [M+1]+, 225 (5) [M+], 224 (4) [M−1]+,
208 (2) [M+–H2O], 186 (100) [(M−1)+–p opa gyl], 133 (32), 116 (35), 77 (29). Anal. calcd. o
C15H15NO (225.29): C 79.97, H 6.71, N 6.22; ound C 79.81, H 6.92, N 6.29.
Compound (4): (1S,2R)-(−)-cis-1-(N,N-Dip opa gylamino)-2-indanyl ace a e. A mix u e o 3 (0.08 g,
0.36 mmol), ace ic anhyd ide (66 μL, 0.72 mmol), E 3N (100 μL, 0.72 mmol), DMAP (a ca aly ic
amoun ) in MeCN (5 mL), unde a gon, was s i ed a oom empe a u e o 3 h. The sol en was
emo ed and he esidue was pa i ioned be ween E OAc (10 mL) and H2O (10 mL), and he o ganic
laye was washed wi h a sa u a ed solu ion o NaCl (3 × 10 mL), d ied (Na2SO4) and e apo a ed, o
gi e 4 (as a whi e solid (76 mg, yield 80%). M.p. 52–53 °C. [∝]
º = −70.6° (25 °C, 0.25, CHCl3).
IR ν = 3239, 2890, 1729, 1210, 1035 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.49–7.46 (m, 1H, 7-H),
7.31–7.21 (m, 3H, 4-H, 5-H, 6-H), 5.68 (d , 1H, J. = 5.4, 2.4 Hz, 2-H), 4.61 (d, 1H, J. = 5.4 Hz, 1-H),
3.77–3.63 (AB sys em, 2H, J. = 17.5 Hz, CH2), 3.76–3.62 (AB sys em, 2H, J. = 17.3 Hz, CH2),

In . J. Mol. Sci. 2014, 15 17056
3.17–2.93 (pa AB o an ABM sys em, 2H, JAB = 17.2 Hz, JAM = 5.7 Hz, JBM = 2.5 Hz, 3α-H, 3β-H),
2.21 ( , 2H, J. = 2.4 Hz, 2 × CH), 2.02 (s, 3H, CH3). 13C NMR (75 MHz, CDCl3) δ = 170.40 (COCH3),
140.01 (C-3a), 139.48 (C-7a), 128.07, 126.97, 125.24 and 125.13 (CHa om), 81.21 (2 × C≡CH), 77.04
(C-2), 71.74 (2 × C≡CH), 68.94 (C-1), 39.99 (2 × CH2), 37.68 (C-3), 21.70 (CH3). MS (FAB):
m/z (%): 269 (6) [M+2]+, 268 (26) [M+1]+, 225 (2) [M+–ace yl], 197 (18), 169 (12), 154 (88), 137
(100). Anal. calcd. o C17H17NO2 (267.32): C 76.38, H 6.41, N 5.24; ound C 76.12, H 6.68, N 5.36.
Compound (5): (1S,2R)-(−)-cis-1-(N,N-Dip opa gylamino)-2-indanyl benzoa e. To a solu ion o o
3 (0.08 g, 0.36 mmol), DMAP (a ca aly ic amoun ) in MeCN (5 mL), a 0 °C and unde a gon, was
added d opwise a solu ion o benzoyl chlo ide (82 μL, 0.72 mmol) and E 3N (100 μL, 0.72 mmol).
The mix u e was s i ed a oom empe a u e o 2 h. he sol en was e apo a ed and he esidue
was dissol ed in CH2Cl2 (10 mL). The laye o ganic was washed wi h a sa u a ed solu ion o NaCl
(3 × 10 mL), d ied (Na2SO4) and e apo a ed, o gi e a yellow oil ha was pu i ied by lash column
ch oma og aphy using hexane–E OAc (6:1) as eluen o gi e 5 (73 mg, yield 73%) as a yellow oil.
[∝]
º = −85.6° (25 °C, 0.25, CHCl3). IR ν = 3289, 2842, 1714, 1267, 1108, 1069 cm−1. 1H NMR
(300 MHz, CDCl3) δ = 7.95–7.92 (m, 2H, 2'-H, 6'-H), 7.56–7.50 (m, 7H, 3'-H, 4'-H, 5'-H, 4 × Ha om),
6.00 (d , 1H, J. = 5.6, 2.6 Hz, 2-H), 4.74 (d, 1H, J. = 5.3 Hz, 1-H), 3.75 (d, 4H, J. = 2.3 Hz, 2 × CH2),
3.29–3.06 (pa AB o an ABM sys em, 2H, JAB = 17.0 Hz, JAM = 5.7 Hz, JBM = 2.7 Hz, 3α-H, 3β-H),
2.15 ( , 2H, J. = 2.1 Hz, 2 × CH). 13C NMR (75 MHz, CDCl3) δ = 166.36 (CO), 140.30 (C-3a), 139.81
(C-7a), 133.16 (C'-4), 130.72 (C'-1), 129.83, 128.61, 128.39, 127.28, 125.49 and 125.43 (4 × CHa om,
4 × C'-H), 81.30 (2 × C≡CH), 77.75 (C-2), 72.20 (2 × C≡CH), 69.17 (C-1), 40.40 (2 × CH2), 38.13
(C-3). MS (FAB): m/z (%): 331 (11) [M+2]+, 330 (40) [M+1]+, 231 (68), 186 (3), 154 (95), 137 (100),
105 (25). Anal. calcd. o C22H19NO2 (329.39): C 80.22, H 5.81, N 4.25; ound C 80.05, H 6.01, N 4.34.
3.2.2. Reac ion o Ca bamyla ion
To a s i ed and ice-cooled solu ion o 2 o 3 (0.43 mmol) in ace oni ile (5 mL) was added he
N,N-dialkylca bamyl chlo ide (0.73 mmol), ollowed by a d opwise addi ion o NaH (60% in oil,
0.56 mmol). The eac ion mix u e was s i ed o 24 h a oom empe a u e unde a gon. A e
e apo a ion o he sol en in acuo, wa e (10 mL) was added and ex ac ed wi h e he (3 × 10 mL).
The o ganic phase was washed wi h dilu e KOH (pH 10–11), d ied and e apo a ed o d yness
in acuo. Pu i ica ion by column ch oma og aphy (Hexane:E OAc 4:1) a o ded:
Compound (6): (1S,2R)-(−)-cis-1-(N-P opa gylamino)-2-indanyl dime hylca bama e. This compound
was ob ained as a yellow solid (100 mg, yield 73%). M.p. 119–122 °C. [∝]
º = −50.4° (23 °C, 0.25,
CHCl3). IR ν = 3264, 2923, 1693, 1388, 1184, 1047 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.40–7.39
(m, 1H, 7-H), 7.28–7.13 (m, 3H, 4-H, 5-H, 6-H), 5.52–5.48 (m, 1H, 2-H), 4.38 (d, 1H, J = 5.0 Hz,
1-H), 3.61–3.46 (AB sys em, 1H, J. = 16.8 Hz, CH2), 3.60–3.45 (AB sys em, 1H, J. = 16.8 Hz, CH2),
3.19–3.04 (AB sys em, 1H, J = 16.5 Hz, 3α-H), 3.17–3.03 (AB sys em, 1H, J. = 16.5 Hz, 3β-H),
2.90–2.80 (m, 6H, 2 × CH3), 2.62 ( , 1H, J. = 2.5 Hz, CH), 2.25 (b . s., 1H, D2O exch., NH). 13C NMR
(75 MHz, CDCl3) δ = 155.97 (CO), 142.09 (C-3a), 139.75 (C-7a), 127.97, 126.69, 124.93 and 124.66
(CHa om), 82.17 (C≡CH), 76.00 (C-2), 71.64 (C≡CH), 63.28 (C-1), 37.46 (CH2), 36.35 (C-3), 29.94
In . J. Mol. Sci. 2014, 15 17057
and 29.67 (2 × CH3). MS (FAB): m/z (%): 258 (1) [M]+, 257 (6) [M−1]+, 168 (100), 116 (80), 72 (80).
Anal. calcd. o C15H18N2O2 (258.32): C 69.74, H 7.02, N 10.84; ound C 69.65, H 7.13, N 10.93.
Compound (7): (1S,2R)-(−)-cis-1-(N-P opa gylamino)-2-indanyl die hylca bama e. Isa yellow solid
(98 mg, yield 66%). M.p. 68–69 °C. [∝]
º = −37.6° (23 °C, 0.25, CHCl3). IR ν = 3242, 2972, 1677,
1425, 1270, 1173, 1066 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.42–7.39 (m, 1H, 7-H),
7.29–7.21 (m, 3H, 4-H, 5-H, 6-H), 5.54 (d , 1H, J. = 5.3, 3.6 Hz, 2-H), 4.41–4.39 (m, 1H, 1-H),
3.63–3.49 (AB sys em, 1H, J. = 16.8 Hz, CH2), 3.62–3.48 (AB sys em, 1H, J. = 16.8 Hz, CH2),
3.29–3.09 (m, 6H, 3α-H, 3β-H, 2 × CH2CH3), 2.25 ( , 1H, J. = 2.4 Hz, CH), 1.93 (b . s., 1H, D2O
exch., NH), 1.28–1.01 (m, 6H, 2 × CH2CH3). 13C NMR (75 MHz, CDCl3) δ = 155.18 (CO), 142.24
(C-3a), 139.80 (C-7a), 127.91, 126.65, 124.88 and 124.61 (CHa om), 82.19 (C≡CH), 75.64 (C-2), 71.54
(C≡CH), 63.52 (C-1), 41.92 and 41.30 (2 × CH2CH3), 37.45 (CH2), 36.50 (C-3), 13.99 and 13.51
(2 × CH2CH3). MS (FAB): m/z (%): 288 (18) [M+2]+, 287 (100) [M+1]+, 286 (8) [M]+, 285 (6)
[M−1]+, 231 (21), 154 (27), 137 (26). Anal. calcd. o C17H22N2O2 (286.37): C 71.30, H 7.74, N 9.78;
ound 71.12, H 7.99, N 9.92.
Compound (8): (1S,2R)-(−)-cis-1-(N,N-Dip opa gylamino)-2-indanyl dime hylca bama e. Was
ob ained as a whi e solid (76 mg, yield 58%). M.p. 109–112 °C. [∝]
º = −38° (25 °C, 0.25, CHCl3).
IR ν = 3292, 2922, 1685, 1397, 1272, 1186, 1050 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.48 ( , 1H,
J = 3.9 Hz, 7-H), 7.27–7.22 (m, 3H, 4-H, 5-H, 6-H), 5.61 (d , 1H, J. = 5.6, 3.3 Hz, 2-H), 4.63–4.61 (m,
1H, 1-H), 3.67–3.66 (m, 4H, 2 × CH2), 3.16–2.97 (AB sys em, 1H, J. = 16.8 Hz, 3α-H), 3.14–2.96
(AB sys em, 1H, J. = 16.8 Hz, 3β-H), 2.91–2.81 (m. 6H, 2 × CH3), 2.21 ( , 1H, J. = 2.2 Hz, 2 × CH)
13C NMR (75 MHz, CDCl3) δ = 155.98 (CO), 140.05 (C-3a), 139.82 (C-7a), 127.96, 126.76, 125.39
and 125.10 (CHa om), 81.10 (2 × C≡CH), 77.36 (C-2), 71.91 (2 × C≡CH), 68.31 (C-1), 40.24 (2 × CH2),
37.94 (C-3), 36.49 and 36.14 (2 × CH3). MS (FAB): m/z (%): 298 (19) [M+2]+, 297 (100) [M+1]+, 296
(4) [M]+, 295 (9) [M−1]+, 231 (30), 204 (21), 154 (31), 137 (39). Anal. calcd. o C18H20N2O2
(296.36): C 72.95, H 6.80, N 9.45; ound 72.78, H 7.01, N 9.53.
Compound (9): (1S,2R)-(−)-cis-1-(N,N-Dip opa gylamino)-2-indanyl die hylca bama e. This
compound was ob ained as an oil (70 mg, yield 49%). [∝]
º = −18.6° (25 °C, 0.25, CHCl3).
IR ν = 3292, 2928, 1688, 1425, 1270, 1167, 1062 cm−1. 1H NMR (300 MHz, CDCl3) δ = 7.49 ( , 1H,
J = 4.2 Hz, 7-H), 7.28–7.23 (m, 3H, 4-H, 5-H, 6-H), 5.59 (d , 1H, J. = 5.8, 3.9 Hz, 2-H), 4.62 (d, 1H,
J. = 5.8 Hz, 1-H), 3.71–3.57 (m, 4H, 2 × CH2), 3.35–3.23 (m, 4H, 2 × CH2CH3), 3.17–2.98 (AB
sys em, 1H, J. = 16.8 Hz, 3α-H), 3.15–2.97 (AB sys em, 1H, J = 16.8 Hz, 3β-H), 2.21 ( , 2H, J. = 2.2 Hz,
2 × CH), 1.12–1.01 (m, 6H, 2 × CH2CH3). 13C NMR (75 MHz, CDCl3) δ = 155.21 (CO), 139.98
(C-3a), 139.86 (C-7a), 128.00, 126.74, 125.55 and 125.01 (CHa om), 81.06 (2 × C≡CH), 76.58 (C-2),
71.97 (2 × C≡CH), 67.99 (C-1), 41.65 and 41.12 (2 × CH2CH3), 40.14 (2 × CH2), 37.81 (C-3), 13.97
and 13.47 (2 × CH2CH3). MS (FAB): m/z (%): 326 (20) [M+2]+, 325 (92) [M+1]+, 324 (2) [M]+,
323 (8) [M−1]+, 288 (89), 230 (51), 154 (71), 137 (100). Anal. calcd. o C20H24N2O2 (324.42): C 74.04,
H 7.46, N 8.64; ound 73.89, H 7.61, N 8.75.
In . J. Mol. Sci. 2014, 15 17058
3.3. Expe imen al Me hods: Biology
3.3.1. Cul u e o Ra Co ical Neu ons
Emb yos we e selec ed om 19 o 20 days p egnan a s by caesa ean sec ion. Meninges we e
emo ed and co ex was isola ed a e he dissec ion o he b ain. The agmen s ob ained om se e al
emb yos we e subjec ed o mechanic diges ion. We e-suspended he cells in a Neu obasal medium
wi h 2% B-27. We seeded in 48-well pla es a a densi y o 100,000 cells/mL. Neu onal cul u es we e
allowed o g ow o 8–10 days. Incuba ions wi h di e en CSF we e done when he mic oscope
showed he exis ence o a dense neu onal ne wo k. Emb yos we e selec ed om 19 o 20 days
p egnan a s, which we e decapi a ed and emb yos we e ex ac ed om he womb by caesa ean
sec ion. Meninges we e emo ed and a po ion o mo o co ex was isola ed a e he dissec ion o he
b ain. F agmen s ob ained om se e al emb yos we e subjec ed o mechanic diges ion and cells we e
e-suspended in Neu obasal medium wi h 2% B-27 and seeded in 48-well pla es a a densi y o
100,000 cells/mL. Neu onal cul u es we e allowed o g ow o 8–10 days and when he mic oscope
showed he exis ence o a dense neu onal ne wo k, incuba ions wi h di e en CSF we e done [79].
3.3.2. Measu emen o Neu onal Viabili y
We used he MTT educ ion assay ollowing he p ocedu e p e iously desc ibed [65]. A e he
app op ia e incuba ions wi h he compounds alone, o co-incuba ed wi h 100 µM H2O2 o glu ama e,
0.5 mg/mL MTT we e added o each well and incuba ion was pe o med a 37 °C o 2 h. Fo mazan
sal o med was dissol ed in DMSO, and colo ime ic de e mina ion we e pe o med a 540 nm. Con ol
cells wi hou compounds o oxic s imulus we e conside ed 100% iabili y. Neu onal iabili y
a e exposu e o compounds o di e en ea men s was exp essed as% o con ol wi hin each
indi idual expe imen . G aph Pad P ism So wa e (G aphPad So wa e, San Diego, CA, USA) was
used o pe o m s a is ical analyses and g aphical p esen a ion. Expe imen s we e ep oduced a leas
h ee imes. Da a we e exp essed as mean ± S.E.M. alues. G oups we e compa ed by ANOVA/Dunne ’s
es . A p- alue ≤0.05 was accep ed as he limi o s a is ical signi icance.
4. Conclusions
We can use Shannon en opy measu es o de eloping p edic i e models o mul i- a ge ne wo ks
o neu op o ec i e/neu o oxic compounds. In doing so, we can use Box–Jenkins ope a o s o
molecula desc ip o s o ob ain mul i- a ge , mul i-scale, and mul i-ou pu models able o p edic
di e en ou comes o mul iple combina ions o ou pu expe imen al measu es, expe imen al
p o ocols, o ganisms, and molecula and cellula a ge s. One o hese models has been demons a ed
he e o be use ul as a complemen a y ool in he o ganic syn hesis and e alua ion o he mul i- a ge
biological ac i i y o new compounds wi h po en ial neu op o ec i e ac i i y. The model is also a e y
use ul ool o p edic complex ne wo ks o d ug- a ge in e ac ions wi h possible applica ions o he
s udy o non-linea e ec s in he biological ac i i y o neu op o ec i e d ugs.
In . J. Mol. Sci. 2014, 15 17059
Acknowledgmen s
The au ho s hank he Xun a de Galicia o inancial suppo o his wo k unde
p ojec 07CSA008203PR.
Au ho Con ibu ions
Syn hesis, iden i ica ion, pu i ica ion, and cha ac e iza ion o new o ganic compounds: Xe a do
Ga cía-Me a, Olga Caamaño, and Ne ea Alonso; Pha macological assays: Ma ilde Yañez; Da a e ie al
and p ep ocessing, chemin o ma ics calcula ions, s a is ical analysis, complex ne wo k analysis,
p edic i e s udy: F ancisco J. Rome o Du án, F ancisco J. P ado-P ado and Humbe o González-Díaz;
W i ing o pape : F ancisco J. Rome o Du án, Xe a do Ga cía-Me a, and Humbe o González-Díaz.
Supplemen a y In o ma ion
Supplemen a y ma e ial iles which con ain de ailed lis s o he alues o pa ame e s a e a ailable
upon eques s o he co esponding au ho .
Con lic o In e es
The au ho s decla e no con lic o in e es .
Re e ences
1. Mekenyan, O.; Bonche , D.; T inajs ic, N. Chemical g aph heo y modeling he he modynamic
p ope ies o molecules. In e n. J. Quan um Chem. Symp. 1980, 18, 369–380.
2. Bonche , D.; T inajs ic, N. In o ma ion heo y, dis ance ma ix, and molecula b anching.
J. Chem. Phys. 1977, 67, 4517–4533.
3. Bonche , D.; Kamenski, D.; Kamenska, V. Symme y and in o ma ion con en o chemical
s uc u es. Bull. Ma h. Biol. 1976, 38, 119–133.
4. Kie , L.B. Use o molecula negen opy o encode s uc u e go e ning biological ac i i y.
J. Pha m. Sci. 1980, 69, 807–810.
5. S ahu a, F.L.; Godden, J.W.; Bajo a h, J. Di e en ial Shannon en opy analysis iden i ies
molecula p ope y desc ip o s ha p edic aqueous solubili y o syn he ic compounds wi h high
accu acy in bina y QSAR calcula ions. J. Chem. In . Compu . Sci. 2002, 42, 550–558.
6. S ahu a, F.L.; Godden, J.W.; Xue, L.; Bajo a h, J. Dis inguishing be ween na u al p oduc s and
syn he ic molecules by desc ip o Shannon en opy analysis and bina y QSAR calcula ions.
J. Chem. In . Compu . Sci. 2000, 40, 1245–1252.
7. Roy, K.; Saha, A. Compa a i e QSPR s udies wi h molecula connec i i y, molecula negen opy
and au indicespa I: Molecula he mochemical p ope ies o di e se unc ional acyclic
compounds. J. Mol. Model. 2003, 9, 259–270.
8. Ag awal, V.K.; Khadika , P.V. Modelling o ca bonic anhyd ase inhibi o y ac i i y o
sul onamides using molecula negen opy. Bioo g. Med. Chem. Le . 2003, 13, 447–453.