New Approaches for the Discovery of Pharmacologically-Active Natural Compounds

160 Pages·2019·23.848 MB·English

by  José L Medina-Franco (editor)

biomolecules
New Approaches
for the Discovery of
Pharmacologically-
Active Natural
Compounds
Edited by
José L. Medina-Franco
Printed Edition of the Special Issue Published in Biomolecules
www.mdpi.com/journal/biomolecules
New Approaches for the Discovery
of Pharmacologically-Active Natural
Compounds

New Approaches for the Discovery
of Pharmacologically-Active Natural
Compounds
SpecialIssueEditor
Jose´ L.Medina-Franco
MDPI•Basel•Beijing•Wuhan•Barcelona•Belgrade
SpecialIssueEditor
Jose´L.Medina-Franco
NationalAutonomousUniversityof
Mexico(UNAM)
Mexico
EditorialOffice
MDPI
St.Alban-Anlage66
4052Basel,Switzerland
This is a reprint of articles from the Special Issue published online in the open access journal
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Contents
AbouttheSpecialIssueEditor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Jose´L.Medina-Franco
NewApproachesfortheDiscoveryofPharmacologically-ActiveNaturalCompounds
Reprintedfrom:Biomolecules2019,9,115,doi:10.3390/biom9030115 . . . . . . . . . . . . . . . . . 1
Mar´ıa L. Del Prado-Audelo, Isaac H. Caballero-Flora´n, Jorge A. Meza-Toledo, Ne´stor
Mendoza-Mun˜oz, MaykelGonza´lez-Torres, Benjam´ınFlora´n, Herna´nCorte´sandGerardo
Leyva-Go´mez
FormulationsofCurcuminNanoparticlesforBrainDiseases
Reprintedfrom:Biomolecules2019,9,56,doi:10.3390/biom9020056. . . . . . . . . . . . . . . . . . 4
YaChen,ConradStork,SteffenHirteandJohannesKirchmair
NP-Scout:MachineLearningApproachfortheQuantificationandVisualizationoftheNatural
Product-LikenessofSmallMolecules
Reprintedfrom:Biomolecules2019,9,43,doi:10.3390/biom9020043. . . . . . . . . . . . . . . . . . 32
FernandoD.Prieto-Martı´nezandJose´L.Medina-Franco
Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4
BromodomainsUsingMolecularDockingandDynamics
Reprintedfrom:Biomolecules2018,8,61,doi:10.3390/biom8030061. . . . . . . . . . . . . . . . . . 49
MarcoA.Loza-Mejı´a,JuanRodrigoSalazarandJuanFranciscoSa´nchez-Tejeda
In Silico Studies on Compounds Derived from Calceolaria: Phenylethanoid Glycosides as
PotentialMultitargetInhibitorsfortheDevelopmentofPesticides
Reprintedfrom:Biomolecules2018,8,121,doi:10.3390/biom8040121 . . . . . . . . . . . . . . . . . 67
B.Ange´licaPilo´n-Jime´nez,FernandaI.Sald´ıvar-Gonza´lez,Ba´rbaraI.D´ıaz-EufracioandJose´
L.Medina-Franco
BIOFACQUIM:AMexicanCompoundDatabaseofNaturalProducts
Reprintedfrom:Biomolecules2019,9,31,doi:10.3390/biom9010031. . . . . . . . . . . . . . . . . . 83
Yisett Gonza´lez, Deborah Doens, He´ctor Cruz, Ricardo Santamar´ıa, Marcelino Gutie´rrez,
AlejandroLlanesandPatriciaL.Ferna´ndez
AMarineDiterpenoidModulatestheProteasomeActivityinMurineMacrophagesStimulated
withLPS
Reprintedfrom:Biomolecules2018,8,109,doi:10.3390/biom8040109 . . . . . . . . . . . . . . . . . 95
Juan Carlos Sa´nchez-Salgado, Samuel Estrada-Soto, Sara Garcı´a-Jime´nez, Sergio Montes,
JaimeGo´mez-ZamudioandRafaelVillalobos-Molina
AnalysisofFlavonoidsBioactivityforCholestaticLiverDisease: SystematicLiteratureSearch
andExperimentalApproaches
Reprintedfrom:Biomolecules2019,9,102,doi:10.3390/biom9030102 . . . . . . . . . . . . . . . . . 112
SeongSooMoon,HyeJinLee,RamyaMathiyalagan,YuJinKim,DongUkYang,DaeYoung
Lee,JinWooMin,ZulyJimenezandDeokChunYang
SynthesisofaNovelα-GlucosylGinsenosideF1byCyclodextrinGlucanotransferaseandItsIn
VitroCosmeticApplications
Reprintedfrom:Biomolecules2018,8,142,doi:10.3390/biom8040142 . . . . . . . . . . . . . . . . . 125
v
XuyangLu,ShuqinMa,YouchaoChen,DegyiYangzomandHongmaoJiang
Squalene Found in Alpine Grassland Soils under a Harsh Environment in the Tibetan
Plateau,China
Reprintedfrom:Biomolecules2018,8,154,doi:10.3390/biom8040154 . . . . . . . . . . . . . . . . . 136
vi
About the Special Issue Editor
Jose´L.Medina-FrancoholdsaBSc(1998)andanMScandPh.D.degree(2005)inChemistry.In2005,
Dr. Medina- Franco joined the University of Arizona as a postdoctoral fellow and was named
Assistant Member at the Torrey Pines Institute for Molecular Studies in Florida in August 2007.
In 2013, he conducted research at the Mayo Clinic, and in 2014, he joined UNAM as Principal
InvestigatorandFullTimeResearchProfessor. HecurrentlyleadstheDIFACQUIMresearchgroup
atUNAM.
Since 2007, Dr. Medina-Franco has been a member of the National Researcher System, National
CouncilofScienceandTechnologyinMexicoatthehighestlevel(III).In2016, hewasappointed
asResearchCollaboratoroftheMayoClinicandin2017,hewasnamedFellowoftheRoyalSociety
ofChemistry(UK).
Dr.Medina-Francohaspublishedmorethan200peer-reviewedpapers,20chaptersinbooks,andhas
issued one international patent. He has edited the books Epi-Informatics and Food Informatics.
HeservesasanAssociateEditorforthejournalsRSCAdvancesandMolecularDiversity.
Since2007,hehasbeentheprincipalinvestigatorinseveralresearchgrantsfundedbygovernment
institutionsandpharmaceuticalcompanies.
vii

biomolecules
Editorial
New Approaches for the Discovery of
Pharmacologically-Active Natural Compounds
JoséL.Medina-Franco
DepartmentofPharmacy,NationalAutonomousUniversityofMexico,MexicoCity04510,Mexico;
[email protected];Tel.:[phone]
Received:21March2019;Accepted:22March2019;Published:23March2019
Naturalproductscontinuetobeamajorsourceofactivecompounds. Naturalproductsfrom
differentsourceshaveprovidedalargenumberofmoleculesapprovedforclinicaluseorthathave
beenusedasthestartingpointsofoptimizationprograms[1,2]. Similarly,naturalproductshave
inspiredthesynthesisanddevelopmentofbiologicallyactivemolecules[3,4].However,identifying
pharmacologicallyactivenaturalproductsinanefficientandsystematicmannerisnotaneasytask.
Tothisend,abroadrangeofexperimentalandcomputationalapproacheshaveemergedandevolved
inrecentyears,boostedbytheprogressinthetechnologicaladvancesofscreeningstrategies.Inmany
cases,bothexperimentalandtheoreticalmethodsareusedinsynergy[5,6].
Thisspecialissueincludesninepapersincludingeightfullarticlesandonereviewpaperfrommore
than45scientistsfromaroundtheworld. Thepapersillustratethedevelopmentand/orapplication
ofabroadrangeofcomputationalandexperimentaltechniquesappliedtonaturalproductresearch.
Asdescribedbelow,severalpapersalsointegrateeitherthecreationortheminingofcompound
databases and web-based resources open to the scientific community interested in research into
naturalproducts.
TheissuebeginswiththearticlebyPrieto-Martínezetal. describingthecomputationaland
experimentalcharacterizationoftheflavonoidamentoflavoneasanovelinhibitorofbromodomain4[7].
The computational studies were performed with docking using four algorithms. This work is
an example of a successful synergistic combination of informatic methods with natural products
and experimental validation. The work of González et al. discussed the biological activity of a
diterpenoidpreviouslyextractedfromtheoctocoralPseudopterogorgiaacerosa[8]. Themarinenatural
productinhibitedtheproteasomalchymotrypsin-likeactivityofmurinemacrophagesinthepresence
oflipopolysaccharide,butnotinitsabsence. Theauthorsalsoconducteddockingsimulationsthat
providedahypothesisregardingtheinhibitoryactivityofthechymotrypsin-likeactivity.Loza-Mejíaetal.
reported on an in silico study of secondary metabolites isolated from plants of the Calceolaria
genusasbioinsecticides[9]. Thecompoundsweredockedwiththreemoleculartargets, namely;
acetylcholinesterase,prophenoloxidase,andtheecdysonereceptor.Thefindingsoftheinformatics
studies were in good agreement with previously published experimental results. In the same
work, theauthorsconcludedthatverbascosideisapromisingcandidateforthedevelopmentof
amultitargetinsecticide. SooMoonetal. presentedtheresultsofthesynthesisofnewderivatives
ofginsenosidesthataredistinctivetriterpenoidalsaponinsconsideredtoberesponsibleformost
ofthepharmacologicalactivitiesofPanaxginseng(Koreanginseng). Oneofthenewlysynthesized
compounds,α-glycosylatedginsenosideF1hadincreasedsolubility,lowercytotoxicitytowardhuman
dermalfibroblastcells,andhighertyrosinaseactivityandultravioletA(UVA)-inducedinhibitory
activityagainstmatrixmetalloproteinase-1thantheparentginsenosideF1.Theauthorsconcluded
thatthenewcompoundhaspotentialinterestincosmeticapplications[10].Intheirresearcharticle,
Luetal.reportedtheidentificationofsqualeneinfivealpinegrasslandssoilsfromtheTibetanPlateau,
whichischaracterizedbyhighaltitude,strongsolarradiation,drought,lowtemperatures,andthinair.
Tothisend,theresearchteamusedthepyrolysisgaschromatography–massspectrometrytechnique
Biomolecules2019,9,115;doi:10.3390/biom9030115 1 www.mdpi.com/journal/biomolecules