molecules Article Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin Veronika Furlan 1, Janez Konc 2,* and Urban Bren 1,2,* 1 Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia; [email protected] 2 National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia * Correspondence: [email protected] (J.K.); [email protected] (U.B.); Tel.: +386-1-476-0273 (J.K.); +386-2-229-4421 (U.B.) Academic Editors: Mircea V. Diudea and Claudiu N. Lungu Received: 29 October 2018; Accepted: 17 December 2018; Published: 18 December 2018 Abstract: Research efforts are placing an ever increasing emphasis on identifying signal transduction pathways related to the chemopreventive activity of curcumin. Its anticarcinogenic effects are presumably mediated by the regulation of signaling cascades, including nuclear factor κB (NF-κB), activator protein 1 (AP-1), and mitogen-activated protein kinases (MAPK). By modulating signal transduction pathways, curcumin induces apoptosis in malignant cells, thus inhibiting cancer development and progression. Due to the lack of mechanistic insight in the scientific literature, we developed a novel inverse molecular docking protocol based on the CANDOCK algorithm. For the first time, we performed inverse molecular docking of curcumin into a collection of 13,553 available human protein structures from the Protein Data Bank resulting in prioritized target proteins of curcumin. Our predictions were in agreement with the scientific literature and confirmed that curcumin binds to folate receptor β, DNA (cytosine-5)-methyltransferase 3A, metalloproteinase-2, mitogen-activated protein kinase 9, epidermal growth factor receptor and apoptosis-inducing factor 1. We also identified new potential protein targets of curcumin, namely deoxycytidine kinase, NAD-dependent protein deacetylase sirtuin-1 and -2, ecto-50-nucleotidase, core histone macro-H2A.1, tyrosine-protein phosphatase non-receptor type 11, macrophage colony-stimulating factor 1 receptor, GTPase HRas, aflatoxin B1 aldehyde reductase member 3, aldo-keto reductase family 1 member C3, amiloride-sensitive amine oxidase, death-associated protein kinase 2 and tryptophan-tRNA ligase, that may all play a crucial role in its observed anticancer effects. Moreover, our inverse docking results showed that curcumin potentially binds also to the proteins cAMP-specific 30,50-cyclic phosphodiesterase 4D and 17-β-hydroxysteroid dehydrogenase type 10, which provides a new explanation for its efficiency in the treatment of Alzheimer’s disease. We firmly believe that our computational results will complement and direct future experimental studies on curcumin’s anticancer activity as well as on its therapeutic effects against Alzheimer’s disease. Keywords: curcumin; anticarcinogenic effects; anti-neuroinflammatory effects; mechanistic insights; inverse molecular docking 1. Introduction With the availability of an ever increasing number of three-dimensional protein structures and the onset of high-performance computing systems, molecular docking provides a fast, low-cost alternative to the experimental screening of large compound libraries [1]. In molecular docking, many small molecules are typically docked into a given protein and their binding free energies are estimated with Molecules 2018, 23, 3351; doi:10.3390/molecules23123351 www.mdpi.com/journal/molecules Molecules 2018, 23, 3351 2 of 19 Molecules 2018, 23, x 2 of 20 the aim to reduce the time and effort required to identify new candidate drug molecules for further estimateddevelopment with [2 ].the The aim calculation to reduce of thethe bindingtime and free effort energies required is simplified to identify using new various candidate assumptions drug moleculesand estimated for further by a valuedevelopment also known [2]. The as calculation “score” given of the to binding the docked free energies binding is conformations simplified using [3]. variousHowever, assumptions a small molecule and estimated drug may by a interact value also with known many as other “score” proteins given (off-targets), to the docked which binding can conformationshave significant [3]. impacts However, on drug’s a small overall molecule biological drug activity,may interact efficacy, with promiscuity, many other and proteins side-effects. (off- targets),In inverse which docking, can a singlehave smallsignificant molecule impacts is docked on intodrug’s a collection overall ofbiologic proteinal structuresactivity, enablingefficacy, promiscuity,early prediction and of side-effects. a drugs side-effects, In inverse as docking, well as toxicity. a single Inverse small dockingmolecule therefore is docked plays into an a importantcollection ofrole protein in modern structures drug discoveryenabling andearly design. prediction of a drugs side-effects, as well as toxicity. Inverse dockingCurcumin therefore (diferuloylmethane) plays an important is derived role in modern from the drug rhizome discovery of the plant and Curcumadesign. longa (Zingiberaceae family)Curcumin native to (diferuloylmethane) Southeast Asia and representsis derived the from main the component rhizome of of the the turmeric plant spice Curcuma [4]. C. longa (containsZingiberaceae a class family) of compounds native to Southeast known as Asia curcuminoids, and represents namely the main curcumin, component demethoxycurcumin, of the turmeric spiceand bisdemethoxycurcumin [4]. C. longa contains [ 5a]. Curcuminoidsclass of compounds consist ofknow twon methoxylated as curcuminoids, phenolic namely groups curcumin, connected demethoxycurcumin,by two α,β unsaturated and carbonyl bisdemethoxycurcumin groups that exist [5 in]. anCurcuminoids enol form at consist physiological of two pHmethoxylated [6]. As the phenolicmain curcuminoid, groups connected curcumin by comprises two α,β unsaturated approximately carbonyl 2% to5% groups of the that turmeric exist spicein an andenol is form largely at physiologicalresponsible both pH for[6]. itsAs yellowthe main color curcuminoid, and its therapeutic curcumin effects comprises [4]. Curcuminapproximately is known 2% to to5% possess of the turmericantioxidant, spice antiseptic, and is analgetic,largely responsible antimicrobial, both anti-inflammatory for its yellow color as well and as its anticarcinogenic therapeutic effects properties [4]. Curcuminand is considered is known pharmacologically to possess antioxidant, safe [4 ].antiseptic Reported, analgetic, biological antimicrobial, activities of curcumin anti-inflammatory are presented as wellin Figure as anticarcinogenic1. properties and is considered pharmacologically safe [4]. Reported biological activities of curcumin are presented in Figure 1. Figure 1. Structural formula and reported biological effects of curcumin [7–18]. Figure 1. Structural formula and reported biological effects of curcumin [7–18]. 1.1. Anticarcinogenic, Antioxidant and Anti-Inflammatory Properties of Curcumin 1.1. Anticarcinogenic, Antioxidant and Anti-Inflammatory Properties of Curcumin Curcumin was found to prevent inflammatory diseases, such as the bowel disease, pancreatitis, arthritis,Curcumin and chronic was found anterior to prevent uveitis [ 5inflammatory]. Inhibition of dise carcinogenesisases, such as was the demonstrated bowel disease, by pancreatitis,in vivo and arthritis,in vitro studies and chronic at all threeanterior stages: uveitis Tumor [5]. initiation,Inhibition tumor of carcinogenesis promotion (proliferation), was demonstrated and progression by in vivo and(angiogenesis in vitro studies and formation at all three of metastases)stages: Tumor [19]. initiation, Curcumin tumor also possessespromotion a (proliferation), strong antioxidant and progressionactivity and (angiogenesis acts as a potent and scavengerformation of metastases) a variety of [19]. reactive Curcumin oxygen also and possesses nitrogen a speciesstrong antioxidantincluding superoxide activity and anion acts as radicals, a potent hydroxyl scavenger radicals of a variety [20] as of well reactive as nitrogen oxygen dioxideand nitrogen radicals species [21]. includingAdditionally, superoxide it was demonstrated anion radicals, that hydroxyl reduced radicals•NO generation [20] as well following as nitrogen curcumin dioxide treatment radicals [21]. may • Additionally,relieve neuroinflammation it was demonstrated associated that with reduced degenerative NO generation conditions following such as curcumin Alzheimer’s treatment disease may [22]. relieveHowever, neuroinflammation degradation products associated of curcumin with degenerative might also conditions be responsible such as for Alzheimer’s its observed disease biological [22]. However,effects [23 ].degradation products of curcumin might also be responsible for its observed biological effectsDue [23]. to its lipophilicity, curcumin is able to cross the nuclear membrane and take part in epigeneticDue to regulation its lipophilicity, [24]. Curcumin curcumin was is reportedable to tocross target the chromatin-modifying nuclear membrane and enzymes take histonepart in epigenetic regulation [24]. Curcumin was reported to target chromatin-modifying enzymes histone acetyltransferases (HATs) and histone deacetylases (HDACs). The balance between acetylation and deacetylation of histone proteins indeed plays a crucial role in the regulation of gene expression [12]. Molecules 2018, 23, 3351 3 of 19 acetyltransferases (HATs) and histone deacetylases (HDACs). The balance between