biomolecules Review Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases Irina A. Il’icheva y, Konstantin M. Polyakov y and Sergey N. Mikhailov * Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; [email protected] (I.A.I.); [email protected] (K.M.P.) * Correspondence: [email protected]; Tel.: +7-499-135-9733 Both authors contributed equally. y Received: 28 February 2020; Accepted: 1 April 2020; Published: 5 April 2020 Abstract: Nucleoside phosphorylases catalyze the reversible phosphorolysis of nucleosides to heterocyclic bases, giving α-d-ribose-1-phosphate or α-d-2-deoxyribose-1-phosphate. These enzymes are involved in salvage pathways of nucleoside biosynthesis. The level of these enzymes is often elevated in tumors, which can be used as a marker for cancer diagnosis. This review presents the analysis of conformations of nucleosides and their analogues in complexes with nucleoside phosphorylases of the first (NP-1) family, which includes hexameric and trimeric purine nucleoside phosphorylases (EC 2.4.2.1), hexameric and trimeric 50-deoxy-50-methylthioadenosine phosphorylases (EC 2.4.2.28), and uridine phosphorylases (EC 2.4.2.3). Nucleosides adopt similar conformations in complexes, with these conformations being significantly different from those of free nucleosides. In complexes, pentofuranose rings of all nucleosides are at the W region of the pseudorotation cycle that corresponds to the energy barrier to the N S interconversion. In most of the complexes, $ the orientation of the bases with respect to the ribose is in the high-syn region in the immediate vicinity of the barrier to syn anti transitions. Such conformations of nucleosides in complexes $ are unfavorable when compared to free nucleosides and they are stabilized by interactions with the enzyme. The sulfate (or phosphate) ion in the active site of the complexes influences the conformation of the furanose ring. The binding of nucleosides in strained conformations is a characteristic feature of the enzyme–substrate complex formation for this enzyme group. Keywords: nucleoside phosphorylases; X-ray structures of nucleoside phosphorylases; nucleoside conformations 1. Introduction 1.1. Nucleoside Phosphorylases as Key Enzymes in Nucleoside Metabolism Nucleoside phosphorylases (NPs) catalyze the phosphorolysis of the N-glycosidic bond in purine or pyrimidine β-d-ribo-(2’-deoxyribo)nucleosides and are found in almost all organisms. This class of enzymes includes purine nucleoside phosphorylases (PNPs; EC 2.4.2.1), 50-deoxy-50-methylthioadenosine phosphorylases (MTAPs; EC 2.4.2.28), uridine phosphorylases (UPs; EC 2.4.2.3), pyrimidine nucleoside phosphorylases (PyNPs; EC 2.4.2.2), and thymidine phosphorylases (TPs; EC 2.4.2.4). Scheme1 depicts the general scheme of phosphorolysis of nucleosides by NPs. The equilibrium of the reaction is shifted towards nucleosides, the shift being much more significant for PNPs as compared with UPs. Uridine phosphorylases catalyze phosphorolysis of both thymidine and uridine [1]. Purine nucleoside phosphorylases cleave the N-glycosidic bond in purine ribonucleosides and 2’-deoxynucleosides. Biomolecules 2020, 10, 552; doi:10.3390/biom10040552 www.mdpi.com/journal/biomolecules Biomolecules 2020, 10, 552 2 of 14 Biomolecules 2020, 10, x FOR PEER REVIEW 2 of 15 SchemeScheme 1. Phosphorolysis 1. Phosphorolysis of nucleosides of nucleosides catalyzed catalyzed by nucleosideby nucleoside phosphorylases phosphorylases (NPs). (NPs Urd—uridine,). Urd— UP—uridineuridine, UP phosphorylase,—uridine phosphorylase, PNP—purine PNP nucleoside—purine nucleoside phosphorylase, phosphorylase, Rib-1-P— Ribα-d-1-ribose-1-phosphate-P—α-D-ribose- , Pi—inorganic1-phosphate, phosphate Pi—inorganic ion. phosphate ion. ReactionsReactions that that are are catalyzed catalyzed by by nucleoside nucleoside phosphorylasesphosphorylases play play an an important important role role in maintaining in maintaining nucleosidenucleoside homeostasis homeostasis in the in the body, body, the the disruption disruption of of which which leads leads to to various various diseases. diseases. The e essentialssential role of theserole enzymes of these inenzymes metathesis in metathesis reactions reactions in the organisms in the organisms has stimulated has stimulated interest interest in their in exploration. their exploration. Numerous reviews on nucleoside phosphorylases are available. The structural Numerous reviews on nucleoside phosphorylases are available. The structural organization of these organization of these enzymes [1,2], the substrate specificity and methods for the synthesis of enzymes [1,2], the substrate specificity and methods for the synthesis of valuable nucleosides [3–6], valuable nucleosides [3–6], and metabolism in biological systems [7–10] have been considered. and metabolismThe biosynthesis in biological of nitro systemsgenous [bases7–10] and have nucleosides been considered. in most of organisms can proceed by two Thepathways biosynthesis. De novo of synthesis nitrogenous utilizes bases some and amino nucleosides acids and insmall most organic of organisms molecules can as proceedprecursors by. two pathways.This biochemical De novo synthesispathway uses utilizes numerous some aminoenzymes acids and andit has small a high organic requirement molecules for energy. as precursors. The This biochemicalsteps of the de pathway novo synthesis uses numerous are virtually enzymes the same and in all it organisms. has a high An requirement alternative salvage for energy. pathway, The steps of thewhich de novo repeatedly synthesis utilizes are virtually fragments the of sameRNA, inis energy all organisms. saving and An italternative varies in different salvage organisms. pathway, In which repeatedlyall organisms, utilizes reactions fragments catalyzed of RNA, by isnucleoside energy savingphosphorylases and it varies play the in dikeyfferent role in organisms. the salvage In all organisms,pathway reactions. The regulation catalyzed of bynucleoti nucleosidede metabolism phosphorylases and biosynthesis play the are key considered role in the in salvage relation pathway. to Escherichia coli and Salmonella enterica in [9] and in [10] for mammalian. The regulation of nucleotide metabolism and biosynthesis are considered in relation to Escherichia coli Purinergic signaling modulates fundamental pathophysiological processes, such as tissue and Salmonella enterica in [9] and in [10] for mammalian. homeostasis, wound healing, neurodegeneration, immunity, inflammation, and cancer [11]. Many Purinergiccancer processes signaling in humans modulates are accompanied fundamental by the pathophysiologicaldisturbance of pyrimidine processes, metabolism. such Colon as tissue homeostasis,carcinoma woundcells [12], healing,melanoma neurodegeneration,tumors [13], breast adenocarcinoma immunity, cells inflammation, [14], ascites hepatoma and cancer, and [11]. ManyEhrlich cancer ascites processes carcinoma in humans cells [15 are] have accompanied increased levels by theof uridine disturbance phosphorylase of pyrimidine activity. metabolism. Recent Colonexperiments carcinoma in cells mice [12 [16],] melanoma showed that tumors the disruption [13], breast of uridine adenocarcinoma homeostasis cells causes [14 cancer], ascites diseases. hepatoma, and EhrlichNucleoside ascites phosphorylase carcinoma inhibitors cells [15] provide have increased the poten levelstial to ofcorrect uridine metabolic phosphorylase defects in humans activity. [8 Recent]. experimentsThese in i micenhibitors [16] can showed also be that applied the disruption in the therapy of uridine of human homeostasis parasitic diseases. causes This cancer area diseases. of Nucleosideapplication phosphorylase is based on inhibitors the fact that provide most theof parasites potential are to correctnot able metabolic to synthesize defects purines in humans and [8]. pyrimidines de novo because their genomes lack genes encoding necessary enzymes. Hence, These inhibitors can also be applied in the therapy of human parasitic diseases. This area of significant differences between parasite and human nucleoside phosphorylases provide the basis for application is based on the fact that most of parasites are not able to synthesize purines and pyrimidines the selective inhibition of parasite enzymes. 5′-Methylthioimmucillin-H was developed as a specific de novoinhibitor because for Plasmodium their genomes falciparum lack genes PNP and encoding it was proposed necessary for enzymes. the treatment Hence, of malaria significant [17,18 di]. ffTheerences betweenhelminth parasite parasite and Schistosoma human nucleoside mansoni also phosphorylases cannot synthesize provide purines the de basis novo for [19 the]. Hence, selective the search inhibition of parasitefor inhibitors enzymes. that 5’-Methylthioimmucillin-H are specific for Schistosoma wasmansoni developed PNP is asa achallenging specific inhibitor problem. for AnotherPlasmodium falciparumimportantPNP problem and it is was the proposedsearch for inhibitors for the treatmentspecific for ofGiardia malaria lamblia [17 UP,18, ].because The helminth this helminth parasite Schistosomaparasite mansoniis unablealso to synthesize cannot synthesizepyrimidines purinesde novo [ de20]. novo [19]. Hence, the search for inhibitors that are specificX-Ray crystallography for Schistosoma is mansonione of thePNP most is commonly a challenging used techniques problem. for Another studying important the structure problem-