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Kores K, Lešnik S, Bren U, Janežič D, Konc J. Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. J Chem Inf Model 2019; 59:2467-2478. [PMID: 30883115 DOI: 10.1021/acs.jcim.8b00981] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Resveratrol is a polyphenol known for its antioxidant and anti-inflammatory properties, which support its use as a treatment for variety of diseases. There are already known connections of resveratrol to chemoprevention of cancer because of its ability to prevent tumor initiation and inhibit tumor promotion and progression. Resveratrol is also believed to be important in cardiovascular diseases and neurological disorders, such as Alzheimer's disease. Using an inverse molecular docking approach, we sought to find new potential targets of resveratrol. Docking of resveratrol into each ProBiS predicted binding site of >38 000 protein structures from the Protein Data Bank was examined, and a number of novel potential targets into which resveratrol was docked successfully were found. These explain known actions or predict new effects of resveratrol. The results included three human proteins that are already known to bind resveratrol. A majority of proteins discovered however have no already described connections with resveratrol. We report new potential target human proteins and proteins connected with different organisms into which resveratrol can dock. Our results reveal previously unknown potential target human proteins, whose connection with cardiovascular and neurological disorders could lead to new potential treatments for variety of diseases. We believe that our research could help in future experimental studies on revestratol bioactivity in humans.
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Affiliation(s)
- Katarina Kores
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia
| | - Samo Lešnik
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia
| | - Urban Bren
- University of Maribor , Faculty for Chemistry and Chemical Technology Maribor , Smetanova ulica 17 , SI-2000 Maribor , Slovenia.,National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Dušanka Janežič
- University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
| | - Janez Konc
- National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,University of Primorska , Faculty of Mathematics, Natural Sciences and Information Technology , Glagoljaška 8 , SI-6000 Koper , Slovenia
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2
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Pachl P, Šimák O, Řezáčová P, Fábry M, Buděšínský M, Rosenberg I, Brynda J. Structure-based design of a bisphosphonate 5′(3′)-deoxyribonucleotidase inhibitor. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00235d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on previously known inhibitor–enzyme complex structures, we developed a promising inhibitor by mimicking the phosphate ion and achieved 50- and 100-fold increases in the inhibitory potency towards cdN and mdN, respectively.
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Affiliation(s)
- Petr Pachl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
| | - Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
- Department of Chemistry of Natural Compounds
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
- Institute of Molecular Genetics
| | - Milan Fábry
- Institute of Molecular Genetics
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Prague
- Czech Republic
- Institute of Molecular Genetics
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3
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Pachl P, Fábry M, Veverka V, Brynda J, Řezáčová P. Kinetic and structural characterization of an alternatively spliced variant of human mitochondrial 5'(3')-deoxyribonucleotidase. J Enzyme Inhib Med Chem 2014; 30:63-8. [PMID: 24506201 DOI: 10.3109/14756366.2013.879577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human mitochondrial 5'(3')-deoxyribonucleotidase (mdN) catalyzes dephosphorylation of nucleoside monophosphates, and thus helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Mature mdN is a 23-kDa dimeric protein with highest expression levels in the heart, brain and skeletal muscle. We have identified an alternative splice variant of the mdN gene containing an 18-nucleotide insertion encoding 6 amino acids (GKWPAT) at the 3'-end of the penultimate exon 4. We recombinantly expressed this enzyme variant and characterized its biochemical and kinetic properties as well as its three-dimensional structure. Our high-resolution (1.27 Å) crystal structure revealed that the insertion forms a loop located in the vicinity of the active site pocket and affects enzyme kinetic parameters as well as protein thermal stability.
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Affiliation(s)
- Petr Pachl
- Institute of Organic Chemistry and Biochemistry and
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4
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Pachl P, Fábry M, Rosenberg I, Simák O, Rezáčová P, Brynda J. Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors. ACTA ACUST UNITED AC 2014; 70:461-70. [PMID: 24531480 DOI: 10.1107/s1399004713030502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/06/2013] [Indexed: 11/10/2022]
Abstract
The human 5'(3')-deoxyribonucleotidases catalyze the dephosphorylation of deoxyribonucleoside monophosphates to the corresponding deoxyribonucleosides and thus help to maintain the balance between pools of nucleosides and nucleotides. Here, the structures of human cytosolic deoxyribonucleotidase (cdN) at atomic resolution (1.08 Å) and mitochondrial deoxyribonucleotidase (mdN) at near-atomic resolution (1.4 Å) are reported. The attainment of an atomic resolution structure allowed interatomic distances to be used to assess the probable protonation state of the phosphate anion and the side chains in the enzyme active site. A detailed comparison of the cdN and mdN active sites allowed the design of a cdN-specific inhibitor.
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Affiliation(s)
- Petr Pachl
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Ondřej Simák
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Pavlína Rezáčová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 37 Prague 6, Czech Republic
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5
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Šimák O, Pachl P, Fábry M, Buděšínský M, Jandušík T, Hnízda A, Skleničková R, Petrová M, Veverka V, Řezáčová P, Brynda J, Rosenberg I. Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-nucleotidases. Org Biomol Chem 2014; 12:7971-82. [DOI: 10.1039/c4ob01332h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-deoxynucleotidases.
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Affiliation(s)
- Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
- 14220 Prague 4, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Department of Chemistry of Natural Compounds
- Institute of Chemical Technology
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Radka Skleničková
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
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6
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Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A 2013; 110:E3381-7. [PMID: 23959887 DOI: 10.1073/pnas.1305519110] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the universe of protein structures is vast, these innumerable structures can be categorized into a finite number of folds. New functions commonly evolve by elaboration of existing scaffolds, for example, via domain insertions. Thus, understanding structural diversity of a protein fold evolving via domain insertions is a fundamental challenge. The haloalkanoic dehalogenase superfamily serves as an excellent model system wherein a variable cap domain accessorizes the ubiquitous Rossmann-fold core domain. Here, we determine the impact of the cap-domain insertion on the sequence and structure divergence of the core domain. Through quantitative analysis on a unique dataset of 154 core-domain-only and cap-domain-only structures, basic principles of their evolution have been uncovered. The relationship between sequence and structure divergence of the core domain is shown to be monotonic and independent of the corresponding type of domain insert, reflecting the robustness of the Rossmann fold to mutation. However, core domains with the same cap type share greater similarity at the sequence and structure levels, suggesting interplay between the cap and core domains. Notably, results reveal that the variance in structure maps to α-helices flanking the central β-sheet and not to the domain-domain interface. Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies.
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Deville-Bonne D, El Amri C, Meyer P, Chen Y, Agrofoglio LA, Janin J. Human and viral nucleoside/nucleotide kinases involved in antiviral drug activation: structural and catalytic properties. Antiviral Res 2010; 86:101-20. [PMID: 20417378 DOI: 10.1016/j.antiviral.2010.02.001] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/31/2010] [Accepted: 02/01/2010] [Indexed: 12/11/2022]
Abstract
Antiviral nucleoside and nucleotide analogs, essential for the treatment of viral infections in the absence of efficient vaccines, are prodrug forms of the active compounds that target the viral DNA polymerase or reverse transcriptase. The activation process requires several successive phosphorylation steps catalyzed by different kinases, which are present in the host cell or encoded by some of the viruses. These activation reactions often are rate-limiting steps and are thus open to improvement. We review here the structural and enzymatic properties of the enzymes that carry out the activation of analogs used in therapy against human immunodeficiency virus and against DNA viruses such as hepatitis B, herpes and poxviruses. Four major classes of drugs are considered: thymidine analogs, non-natural L-nucleosides, acyclic nucleoside analogs and acyclic nucleoside phosphonate analogs. Their efficiency as drugs depends both on the low specificity of the viral polymerase that allows their incorporation into DNA, but also on the ability of human/viral kinases to provide the activated triphosphate active forms at a high concentration at the right place. Two distinct modes of action are considered, depending on the origin of the kinase (human or viral). If the human kinases are house-keeping enzymes that belong to the metabolic salvage pathway, herpes and poxviruses encode for related enzymes. The structures, substrate specificities and catalytic properties of each of these kinases are discussed in relation to drug activation.
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Affiliation(s)
- Dominique Deville-Bonne
- Enzymologie Moléculaire et Fonctionnelle, UR4 Université Pierre et Marie Curie, 7 quai St Bernard, 75252 Paris Cedex 05, France.
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8
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Koch K, Chen Y, Feng JY, Borroto-Esoda K, Deville-Bonne D, Gallois-Montbrun S, Janin J, Moréra S. Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:776-92. [PMID: 20183617 DOI: 10.1080/15257770903155899] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tenofovir is an acyclic phosphonate analog of deoxyadenylate used in AIDS and hepatitis B therapy. We find that tenofovir diphosphate, its active form, can be produced by human nucleoside diphosphate kinase (NDPK), but with low efficiency, and that creatine kinase is significantly more active. The 1.65 A x-ray structure of NDPK in complex with tenofovir mono- and diphosphate shows that the analogs bind at the same site as natural nucleotides, but in a different conformation, and make only a subset of the Van der Waals and polar interactions made by natural substrates, consistent with their comparatively low affinity for the enzyme.
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Affiliation(s)
- Kerstin Koch
- Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Universite Paris-Sud, Orsay, France
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9
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Dudev T, Lim C. Competition between protein ligands and cytoplasmic inorganic anions for the metal cation: a DFT/CDM study. J Am Chem Soc 2007; 128:10541-8. [PMID: 16895422 DOI: 10.1021/ja063111s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Many of the essential metalloproteins are located in the cell, whose cytoplasmic fluid contains several small inorganic anions, such as Cl-, NO2-, NO3-, H2PO4-, and SO4(2-), that play an indispensable role in determining the cell's volume, regulating the cell's pH, signal transduction, muscle contraction, as well as cell growth and metabolism. However, the physical principles governing the competition between these abundant, intracellular anions and protein or nucleic acid residues in binding to cytoplasmic metal cations such as Na+, K+, Mg2+, and Ca2+ are not well understood; hence, we have delineated the physicochemical basis for this competition using density functional theory in conjunction with the continuum dielectric method. The results show that the metal cation can bind to its target protein against a high background concentration of inorganic anions because (i) desolvating a negatively charged Asp/Glu carboxylate in a protein cavity costs much less than desolvating an inorganic anion in aqueous solution and (ii) the metal-binding site acts as a polydentate ligand that uses all its ligating entities to bind the metal cation either directly or indirectly. The results also show that the absolute hydration free energy of the "alien" anion as well as the net charge and relative solvent exposure of the metal-binding protein cavity are the key factors governing the competition between protein and inorganic ligands for a given cytoplasmic metal cation. Increasing the net negative charge of the protein cavity, while decreasing the number of available amide groups for metal binding, protects the metal-bound ligands from being dislodged by cellular anions, thus revealing a "protective" role for carboxylate groups in a protein cavity, in addition to their role in high affinity metal-binding.
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Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
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Hunsucker SA, Mitchell BS, Spychala J. The 5'-nucleotidases as regulators of nucleotide and drug metabolism. Pharmacol Ther 2005; 107:1-30. [PMID: 15963349 DOI: 10.1016/j.pharmthera.2005.01.003] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2005] [Indexed: 11/19/2022]
Abstract
The 5'-nucleotidases are a family of enzymes that catalyze the dephosphorylation of nucleoside monophosphates and regulate cellular nucleotide and nucleoside levels. While the nucleoside kinases responsible for the initial phosphorylation of salvaged nucleosides have been well studied, many of the catabolic nucleotidases have only recently been cloned and characterized. Aside from maintaining balanced ribo- and deoxyribonucleotide pools, substrate cycles that are formed with kinase and nucleotidase activities are also likely to regulate the activation of nucleoside analogues, a class of anticancer and antiviral agents that rely on the nucleoside kinases for phosphorylation to their active forms. Both clinical and in vitro studies suggest that an increase in nucleotidase activity can inhibit nucleoside analogue activation and result in drug resistance. The physiological role of the 5'-nucleotidases will be covered in this review, as will the evidence that these enzymes can mediate resistance to nucleoside analogues.
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Affiliation(s)
- Sally Anne Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Himo F, Guo JD, Rinaldo-Matthis A, Nordlund P. Reaction Mechanism of Deoxyribonucleotidase: A Theoretical Study. J Phys Chem B 2005; 109:20004-8. [PMID: 16853585 DOI: 10.1021/jp0546150] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction mechanism of human deoxyribonucleotidase (dN) is studied using high-level quantum-chemical methods. dN catalyzes the dephosphorylation of deoxyribonucleoside monophosphates (dNMPs) to their nucleoside form in human cells. Large quantum models are employed (99 atoms) based on a recent X-ray crystal structure. The calculations support the proposed mechanism in which Asp41 performs a nucleophilic attack on the phosphate to form a phospho-enzyme intermediate. Asp43 acts in the first step as an acid, protonating the leaving nucleoside, and in the second step as a base, deprotonating the lytic water. No pentacoordinated intermediates could be located.
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Affiliation(s)
- Fahmi Himo
- Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, ALBANOVA, SE-106 91 Stockholm, Sweden
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Lewis W, Haase CP, Miller YK, Ferguson B, Stuart T, Ludaway T, McNaught J, Russ R, Steltzer J, Santoianni R, Long R, Fiermonte G, Palmieri F. Transgenic expression of the deoxynucleotide carrier causes mitochondrial damage that is enhanced by NRTIs for AIDS. J Transl Med 2005; 85:972-81. [PMID: 15951836 DOI: 10.1038/labinvest.3700301] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) are antiretrovirals for AIDS with limiting mitochondrial side effects. The mitochondrial deoxynucleotide carrier (DNC) transports phosphorylated nucleosides for mitochondrial DNA replication and can transport phosphorylated NRTIs into mitochondria. Transgenic mice (TG) that exclusively overexpress DNC in the heart tested DNC's role in mitochondrial dysfunction from NRTIs. Two TG lines were created that overexpressed the human DNC gene in murine myocardium. Cardiac and mitochondrial structure and function were examined by magnetic resonance imaging, echocardiography, electrocardiography, transmission electron microscopy, and plasma lactate. Antiretroviral combinations (HAART) that contained NRTIs (stavudine (2', 3'-didehydro-2', 3'-deoxythymidine or d4T)/lamivudine/indinavir; or zidovudine (3' azido-3'-deoxythymidine or AZT)/lamivudine/indinavir; 35 days) were administered to simulate AIDS therapy. In parallel, a HAART combination without NRTIs (nevirapine/efavirenz/indinavir; 35 days) served as an NRTI-sparing, control regimen. Untreated DNC TGs exhibited normal cardiac function but abnormal mitochondrial ultrastructure. HAART that contained NRTIs caused cardiomyopathy in TGs with increased left ventricle mass and volume, heart rate variability, and worse mitochondrial ultrastructural defects. In contrast, treatment with an NRTI-sparing HAART regimen caused no cardiac changes. Data suggest the DNC is integral to mitochondrial homeostasis in vivo and may relate mechanistically to mitochondrial dysfunction in patients treated with HAART regimens that contain NRTIs.
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Affiliation(s)
- William Lewis
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA.
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