1
|
Štěpánová S, Andris E, Gutten O, Buděšínský M, Dejmek M, Břehová P, Rulíšek L, Kašička V. Acidity constants and protonation sites of cyclic dinucleotides determined by capillary electrophoresis, quantum chemical calculations, and NMR spectroscopy. Electrophoresis 2024; 45:687-705. [PMID: 38059733 DOI: 10.1002/elps.202300232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/11/2023] [Accepted: 11/18/2023] [Indexed: 12/08/2023]
Abstract
Cyclic dinucleotides (CDNs) are important second messengers in bacteria and eukaryotes. Detailed characterization of their physicochemical properties is a prerequisite for understanding their biological functions. Herein, we examine acid-base and electromigration properties of selected CDNs employing capillary electrophoresis (CE), density functional theory (DFT), and nuclear magnetic resonance (NMR) spectroscopy to provide benchmark pKa values, as well as to unambiguously determine the protonation sites. Acidity constants (pKa) of the NH+ moieties of adenine and guanine bases and actual and limiting ionic mobilities of CDNs were determined by nonlinear regression analysis of the pH dependence of their effective electrophoretic mobilities measured by CE in aqueous background electrolytes in a wide pH range (0.98-11.48), at constant temperature (25°C), and constant ionic strength (25 mM). The thermodynamic pKa values were found to be in the range 3.31-4.56 for adenine and 2.28-3.61 for guanine bases, whereas the pKa of enol group of guanine base was in the range 10.21-10.40. Except for systematic shifts of ∼2 pKa, the pKa values calculated by the DFT-D3//COSMO-RS composite protocol that included large-scale conformational sampling and "cross-morphing" were in a relatively good agreement with the pKas determined by CE and predict N1 atom of adenine and N7 atom of guanine as the protonation sites. The protonation of the N1 atom of adenine and N7 atom of guanine in acidic background electrolytes (BGEs) and the dissociation of the enol group of guanine in alkaline BGEs was confirmed also by NMR spectroscopy.
Collapse
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petra Břehová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
2
|
Kalvoda T, Martinek T, Jungwirth P, Rulíšek L. Hydration numbers of biologically relevant divalent metal cations from ab initio molecular dynamics and continuum solvation methods. J Chem Phys 2024; 160:084308. [PMID: 38421065 DOI: 10.1063/5.0192024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Hydration and, in particular, the coordination number of a metal ion is of paramount importance as it defines many of its (bio)physicochemical properties. It is not only essential for understanding its behavior in aqueous solutions but also determines the metal ion reference state and its binding energy to (bio)molecules. In this paper, for divalent metal cations Ca2+, Cd2+, Cu2+, Fe2+, Hg2+, Mg2+, Ni2+, Pb2+, and Zn2+, we compare two approaches for predicting hydration numbers: (1) a mixed explicit/continuum DFT-D3//COSMO-RS solvation model and (2) density functional theory based ab initio molecular dynamics. The former approach is employed to calculate the Gibbs free energy change for the sequential hydration reactions, starting from [M(H2O)2]2+ aqua complexes to [M(H2O)9]2+, allowing explicit water molecules to bind in the first or second coordination sphere and determining the most stable [M(H2O)n]2+ structure. In the latter approach, the hydration number is obtained by integrating the ion-water radial distribution function. With a couple of exceptions, the metal ion hydration numbers predicted by the two approaches are in mutual agreement, as well as in agreement with the experimental data.
Collapse
Affiliation(s)
- Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| | - Tomas Martinek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 160 00 Praha 6, Czechia
| |
Collapse
|
3
|
Osifová Z, Kalvoda T, Galgonek J, Culka M, Vondrášek J, Bouř P, Bednárová L, Andrushchenko V, Dračínský M, Rulíšek L. What are the minimal folding seeds in proteins? Experimental and theoretical assessment of secondary structure propensities of small peptide fragments. Chem Sci 2024; 15:594-608. [PMID: 38179543 PMCID: PMC10763034 DOI: 10.1039/d3sc04960d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/22/2023] [Indexed: 01/06/2024] Open
Abstract
Certain peptide sequences, some of them as short as amino acid triplets, are significantly overpopulated in specific secondary structure motifs in folded protein structures. For example, 74% of the EAM triplet is found in α-helices, and only 3% occurs in the extended parts of proteins (typically β-sheets). In contrast, other triplets (such as VIV and IYI) appear almost exclusively in extended parts (79% and 69%, respectively). In order to determine whether such preferences are structurally encoded in a particular peptide fragment or appear only at the level of a complex protein structure, NMR, VCD, and ECD experiments were carried out on selected tripeptides: EAM (denoted as pro-'α-helical' in proteins), KAM(α), ALA(α), DIC(α), EKF(α), IYI(pro-β-sheet or more generally, pro-extended), and VIV(β), and the reference α-helical CATWEAMEKCK undecapeptide. The experimental data were in very good agreement with extensive quantum mechanical conformational sampling. Altogether, we clearly showed that the pro-helical vs. pro-extended propensities start to emerge already at the level of tripeptides and can be fully developed at longer sequences. We postulate that certain short peptide sequences can be considered minimal "folding seeds". Admittedly, the inherent secondary structure propensity can be overruled by the large intramolecular interaction energies within the folded and compact protein structures. Still, the correlation of experimental and computational data presented herein suggests that the secondary structure propensity should be considered as one of the key factors that may lead to understanding the underlying physico-chemical principles of protein structure and folding from the first principles.
Collapse
Affiliation(s)
- Zuzana Osifová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University Hlavova 2030 Prague 128 00 Czech Republic
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2, 160 00, Praha 6 Czech Republic
| |
Collapse
|
4
|
Kipouros I, Stańczak A, Dunietz EM, Ginsbach JW, Srnec M, Rulíšek L, Solomon EI. Experimental Evidence and Mechanistic Description of the Phenolic H-Transfer to the Cu 2O 2 Active Site of oxy-Tyrosinase. J Am Chem Soc 2023; 145:22866-22870. [PMID: 37844210 PMCID: PMC10615789 DOI: 10.1021/jacs.3c07450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Tyrosinase is a ubiquitous coupled binuclear copper enzyme that activates O2 toward the regioselective monooxygenation of monophenols to catechols via a mechanism that remains only partially defined. Here, we present new mechanistic insights into the initial steps of this monooxygenation reaction by employing a pre-steady-state, stopped-flow kinetics approach that allows for the direct measurement of the monooxygenation rates for a series of para-substituted monophenols by oxy-tyrosinase. The obtained biphasic Hammett plot and the associated solvent kinetic isotope effect values provide direct evidence for an initial H-transfer from the protonated phenolic substrate to the Cu2O2 core of oxy-tyrosinase. The correlation of these experimental results to quantum mechanics/molecular mechanics calculations provides a detailed mechanistic description of this H-transfer step. These new mechanistic insights revise and expand our fundamental understanding of Cu2O2 active sites in biology.
Collapse
Affiliation(s)
- Ioannis Kipouros
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Agnieszka Stańczak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic
- Faculty of Science, Charles University, Albertov 2038/6, 128 00 Praha 2, Czech Republic
| | - Eleanor M. Dunietz
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague 182 23, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, United States
| |
Collapse
|
5
|
Inniss NL, Kozic J, Li F, Rosas-Lemus M, Minasov G, Rybáček J, Zhu Y, Pohl R, Shuvalova L, Rulíšek L, Brunzelle JS, Bednárová L, Štefek M, Kormaník JM, Andris E, Šebestík J, Li ASM, Brown PJ, Schmitz U, Saikatendu K, Chang E, Nencka R, Vedadi M, Satchell KJ. Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. ACS Infect Dis 2023; 9:1918-1931. [PMID: 37728236 PMCID: PMC10961098 DOI: 10.1021/acsinfecdis.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.
Collapse
Affiliation(s)
- Nicole L. Inniss
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Ján Kozic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - George Minasov
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Yingjie Zhu
- WuXi AppTec Co., Ltd, China (Shanghai) Pilot Free Trade Zone, Shanghai, 201308, China
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ludmilla Shuvalova
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Joseph S. Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL, 60439, United States
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Milan Štefek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ján Michael Kormaník
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Alice Shi Ming Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Uli Schmitz
- Structural Chemistry, Gilead Pharmaceuticals, San Mateo, CA, 94404, United States
| | - Kumar Saikatendu
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Masoud Vedadi
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| |
Collapse
|
6
|
Motlová L, Šnajdr I, Kutil Z, Andris E, Ptáček J, Novotná A, Nováková Z, Havlínová B, Tueckmantel W, Dráberová H, Majer P, Schutkowski M, Kozikowski A, Rulíšek L, Bařinka C. Comprehensive Mechanistic View of the Hydrolysis of Oxadiazole-Based Inhibitors by Histone Deacetylase 6 (HDAC6). ACS Chem Biol 2023. [PMID: 37392419 PMCID: PMC10367051 DOI: 10.1021/acschembio.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
Histone deacetylase (HDAC) inhibitors used in the clinic typically contain a hydroxamate zinc-binding group (ZBG). However, more recent work has shown that the use of alternative ZBGs, and, in particular, the heterocyclic oxadiazoles, can confer higher isoenzyme selectivity and more favorable ADMET profiles. Herein, we report on the synthesis and biochemical, crystallographic, and computational characterization of a series of oxadiazole-based inhibitors selectively targeting the HDAC6 isoform. Surprisingly, but in line with a very recent finding reported in the literature, a crystal structure of the HDAC6/inhibitor complex revealed that hydrolysis of the oxadiazole ring transforms the parent oxadiazole into an acylhydrazide through a sequence of two hydrolytic steps. An identical cleavage pattern was also observed both in vitro using the purified HDAC6 enzyme as well as in cellular systems. By employing advanced quantum and molecular mechanics (QM/MM) and QM calculations, we elucidated the mechanistic details of the two hydrolytic steps to obtain a comprehensive mechanistic view of the double hydrolysis of the oxadiazole ring. This was achieved by fully characterizing the reaction coordinate, including identification of the structures of all intermediates and transition states, together with calculations of their respective activation (free) energies. In addition, we ruled out several (intuitively) competing pathways. The computed data (ΔG‡ ≈ 21 kcal·mol-1 for the rate-determining step of the overall dual hydrolysis) are in very good agreement with the experimentally determined rate constants, which a posteriori supports the proposed reaction mechanism. We also clearly (and quantitatively) explain the role of the -CF3 or -CHF2 substituent on the oxadiazole ring, which is a prerequisite for hydrolysis to occur. Overall, our data provide compelling evidence that the oxadiazole warheads can be efficiently transformed within the active sites of target metallohydrolases to afford reaction products possessing distinct selectivity and inhibition profiles.
Collapse
Affiliation(s)
- Lucia Motlová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Ivan Šnajdr
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Jakub Ptáček
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Adéla Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Zora Nováková
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Barbora Havlínová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Werner Tueckmantel
- StarWise Therapeutics LLC, University Research Park, Inc., Madison, Wisconsin 53719, United States
| | - Helena Dráberová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Mike Schutkowski
- Department of Enzymology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
| | - Alan Kozikowski
- StarWise Therapeutics LLC, University Research Park, Inc., Madison, Wisconsin 53719, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| |
Collapse
|
7
|
Andris E, Straka M, Vrána J, Růžička A, Roithová J, Rulíšek L. Can Copper(I) and Silver(I) be Hydrogen Bond Acceptors? Chemistry 2023; 29:e202203769. [PMID: 36807421 DOI: 10.1002/chem.202203769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/22/2023]
Abstract
Gold(I) centers can form moderately strong (Au⋅⋅⋅H) hydrogen bonds with tertiary ammonium groups, as has been demonstrated in the 3AuCl+ (3+ =1-(tert-butyl)-3-phenyl-4-(2-((dimethylammonio)methyl)phenyl)-1,2,4-triazol-5-ylidene) complex. However, similar hydrogen bonding interactions with isoelectronic silver(I) or copper(I) centers are unknown. Herein, we first explored whether the Au⋅⋅⋅H bond originally observed in 3AuCl+ can be strengthened by replacing Cl with Br or I. Experimental gas-phase IR spectra in the ∼3000 cm-1 region showed only a small effect of the halogen on the Au⋅⋅⋅H bond. Next, we measured the spectra of 3AgCl+ , which exhibited significant differences compared to its 3AuX+ counterparts. The difference has been explained by DFT calculations which indicated that the Ag⋅⋅⋅H interaction is only marginal in this complex, and a Cl⋅⋅⋅H hydrogen bond is formed instead. Calculations predicted the same for the 3CuCl+ complex. However, we noticed that for Ag and Cu complexes with less flexible ligands, such as dimethyl(2-(dimethylammonio)phenyl)phosphine (L7 H+ ), the computations predict the presence of the respective Ag⋅⋅⋅H and Cu⋅⋅⋅H hydrogen bonds, with a strength similar to the Au⋅⋅⋅H bond in 3AuCl+ . We, therefore, propose possible complexes where the presence of (Ag/Cu)⋅⋅⋅H bonds could be experimentally verified to broaden our understanding of these unusual interactions.
Collapse
Affiliation(s)
- Erik Andris
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| | - Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen (The, Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| |
Collapse
|
8
|
Abstract
Recent techniques of computational electrochemistry can yield redox potentials with accuracy as good as 0.1 V. Yet, many such methods are not universal, easy to use, or computationally efficient. Herein, we provide a systematic benchmarking of a relatively cheap and straightforward computational approach for fairly accurate computations of redox potentials. It is based on a combination of the conductor-like screening model for real solvents (COSMO-RS) and the density functional theory (DFT). The benchmarking is done with databases covering diverse redox systems, including transition-metal aquacomplexes and various organic and inorganic compounds. In addition, we also present our own test set aiming at maximum chemical diversity and maximum range of redox potential values. We assess the performance of the fairly efficient computational protocol combining the COSMO-RS with the BP86 DFT functional. This is done by calibrating it against different high-level state-of-the-art techniques, in particular, polarizable continuum model (PCM) connected to composite G3(MP2,CC)(+) method, domain-based pair natural orbital implementation of coupled cluster theory, or complete basis set CBS-QB3 method. We also elaborate on the absolute reduction potential value of standard hydrogen electrode to be used with COSMO-RS, and we propose the value of approx. 4.4 V. The COSMO-RS/BP86-D3(BJ) combination outperforms other methods on a wide range of redox systems. However, we show that its accuracy is based on a balanced error cancelation and, therefore, it cannot be further systematically improved. As a result, the proposed procedure represents a pragmatic choice for large-scale screening, yet it could be combined with more advanced methods for detailed studies.
Collapse
Affiliation(s)
- Lukáš Tomaník
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10Praha 6, Czech Republic
| | - Petr Slavíček
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| |
Collapse
|
9
|
Aliakbar Tehrani Z, Rulíšek L, Černý J. Molecular dynamics simulations provide structural insight into binding of cyclic dinucleotides to human STING protein. J Biomol Struct Dyn 2022; 40:10250-10264. [PMID: 34187319 DOI: 10.1080/07391102.2021.1942213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human stimulator of interferon genes (hSTING) is a signaling adaptor protein that triggers innate immune system by response to cytosolic DNA and second messenger cyclic dinucleotides (CDNs). Natural CDNs contain purine nucleobase with different phosphodiester linkage types (3'-3', 2'-2' or mixed 2'-3'-linkages) and exhibit different binding affinity towards hSTING, ranging from micromolar to nanomolar. High-affinity CDNs are considered as suitable candidates for treatment of chronic hepatitis B and cancer. We have used molecular dynamics simulations to investigate dynamical aspects of binding of natural CDNs (specifically, 2'-2'-cGAMP, 2'-3'-cGAMP, 3'-3'-cGAMP, 3'-3'-c-di-AMP, and 3'-3'-c-di-GMP) with hSTINGwt protein. Our results revealed that CDN/hSTINGwt interactions are controlled by the balance between fluctuations (conformational changes) in the CDN ligand and the protein dynamics. Binding of different CDNs induces different degrees of conformational/dynamics changes in hSTINGwt ligand binding cavity, especially in α1-helices, the so-called lid region and α2-tails. The ligand residence time in hSTINGwt protein pocket depends on different contribution of R232 and R238 residues interacting with oxygen atoms of phosphodiester groups in ligand, water distribution around interacting charged centers (in protein residues and ligand) and structural stability of closed conformation state of hSTINGwt protein. These findings may perhaps guide design of new compounds modulating hSTING activity.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Zahra Aliakbar Tehrani
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| | - Lubomír Rulíšek
- Theoretical Bioinorganic Chemistry, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Černý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic
| |
Collapse
|
10
|
Mehara J, Koovakattil Surendran A, van Wieringen T, Setia D, Foroutan-Nejad C, Straka M, Rulíšek L, Roithová J. Cationic Gold(II) Complexes: Experimental and Theoretical Study. Chemistry 2022; 28:e202201794. [PMID: 35946558 DOI: 10.1002/chem.202201794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 01/07/2023]
Abstract
Gold(II) complexes are rare, and their application to the catalysis of chemical transformations is underexplored. The reason is their easy oxidation or reduction to more stable gold(III) or gold(I) complexes, respectively. We explored the thermodynamics of the formation of [AuII (L)(X)]+ complexes (L=ligand, X=halogen) from the corresponding gold(III) precursors and investigated their stability and spectral properties in the IR and visible range in the gas phase. The results show that the best ancillary ligands L for stabilizing gaseous [AuII (L)(X)]+ complexes are bidentate and tridentate ligands with nitrogen donor atoms. The electronic structure and spectral properties of the investigated gold(II) complexes were correlated with quantum chemical calculations. The results show that the molecular and electronic structure of the gold(II) complexes as well as their spectroscopic properties are very similar to those of analogous stable copper(II) complexes.
Collapse
Affiliation(s)
- Jaya Mehara
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | - Adarsh Koovakattil Surendran
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | - Teun van Wieringen
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | - Deeksha Setia
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| | - Cina Foroutan-Nejad
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí. 2, 16610, Prague, Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí. 2, 16610, Prague, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí. 2, 16610, Prague, Czech Republic
| | - Jana Roithová
- Department of Spectroscopy and Catalysis, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525AJ, Nijmegen (The, Netherlands
| |
Collapse
|
11
|
Kipouros I, Stańczak A, Ginsbach JW, Andrikopoulos PC, Rulíšek L, Solomon EI. Elucidation of the tyrosinase/O 2/monophenol ternary intermediate that dictates the monooxygenation mechanism in melanin biosynthesis. Proc Natl Acad Sci U S A 2022; 119:e2205619119. [PMID: 35939688 PMCID: PMC9389030 DOI: 10.1073/pnas.2205619119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Melanins are highly conjugated biopolymer pigments that provide photoprotection in a wide array of organisms, from bacteria to humans. The rate-limiting step in melanin biosynthesis, which is the ortho-hydroxylation of the amino acid L-tyrosine to L-DOPA, is catalyzed by the ubiquitous enzyme tyrosinase (Ty). Ty contains a coupled binuclear copper active site that binds O2 to form a μ:η2:η2-peroxide dicopper(II) intermediate (oxy-Ty), capable of performing the regioselective monooxygenation of para-substituted monophenols to catechols. The mechanism of this critical monooxygenation reaction remains poorly understood despite extensive efforts. In this study, we have employed a combination of spectroscopic, kinetic, and computational methods to trap and characterize the elusive catalytic ternary intermediate (Ty/O2/monophenol) under single-turnover conditions and obtain molecular-level mechanistic insights into its monooxygenation reactivity. Our experimental results, coupled with quantum-mechanics/molecular-mechanics calculations, reveal that the monophenol substrate docks in the active-site pocket of oxy-Ty fully protonated, without coordination to a copper or cleavage of the μ:η2:η2-peroxide O-O bond. Formation of this ternary intermediate involves the displacement of active-site water molecules by the substrate and replacement of their H bonds to the μ:η2:η2-peroxide by a single H bond from the substrate hydroxyl group. This H-bonding interaction in the ternary intermediate enables the unprecedented monooxygenation mechanism, where the μ-η2:η2-peroxide O-O bond is cleaved to accept the phenolic proton, followed by substrate phenolate coordination to a copper site concomitant with its aromatic ortho-hydroxylation by the nonprotonated μ-oxo. This study provides insights into O2 activation and reactivity by coupled binuclear copper active sites with fundamental implications in biocatalysis.
Collapse
Affiliation(s)
- Ioannis Kipouros
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Agnieszka Stańczak
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague 6, Czech Republic
- Faculty of Science, Charles University, 128 00 Prague 2, Czech Republic
| | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Prokopis C. Andrikopoulos
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10, Prague 6, Czech Republic
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| |
Collapse
|
12
|
Kalvoda T, Culka M, Rulíšek L, Andris E. Exhaustive Mapping of the Conformational Space of Natural Dipeptides by the DFT-D3//COSMO-RS Method. J Phys Chem B 2022; 126:5949-5958. [PMID: 35930560 DOI: 10.1021/acs.jpcb.2c02861] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We extensively mapped energy landscapes and conformations of 22 (including three His protonation states) proteinogenic α-amino acids in trans configuration and the corresponding 484 (222) dipeptides. To mimic the environment in a protein chain, the N- and C-termini of the studied systems were capped with acetyl and N-methylamide groups, respectively. We systematically varied the main chain dihedral angles (ϕ, ψ) by 40° steps and all side chain angles by 90° or 120° steps. We optimized the molecular geometries with the GFN2-xTB semiempirical (SQM) method and performed single point density functional theory calculations at the BP86-D3/DGauss-DZVP//COSMO-RS level in water, 1-octanol, N,N-dimethylformamide, and n-hexane. For each restrained (nonequilibrium) structure, we also calculated energy gradients (in water) and natural atomic charges. The exhaustive and unprecedented QM-based sampling enabled us to construct Ramachandran plots of quantum mechanical (QM(BP86-D3)//COSMO-RS) energies calculated on SQM structures, for all 506 (484 dipeptides and 22 amino acids) studied systems. We showed how the character of an amino acid side chain influences the conformational space of single amino acids and dipeptides. With clustering techniques, we were able to identify unique minima of amino acids and dipeptides (i.e., minima on the GFN2-xTB potential energy surfaces) and analyze the distribution of their BP86-D3//COSMO-RS conformational energies in all four solvents. We also derived an empirical formula for the number of unique minima based on the overall number of rotatable bonds within each peptide. The final peptide conformer data set (PeptideCs) comprises over 400 million structures, all of them annotated with QM(BP86-D3)//COSMO-RS energies. Thanks to its completeness and unbiased nature, the PeptideCs can serve, inter alia, as a data set for the validation of new methods for predicting the energy landscapes of protein structures. This data set may also prove to be useful in the development and reparameterization of biomolecular force fields. The data set is deposited at Figshare (10.25452/figshare.plus.19607172) and can be accessed using a simple web interface at http://peptidecs.uochb.cas.cz.
Collapse
Affiliation(s)
- Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha, Czech Republic
| |
Collapse
|
13
|
Sauser L, Kalvoda T, Kavas A, Rulíšek L, Shoshan MS. Front Cover: Cyclic Octapeptides Composed of Two Glutathione Units Outperform the Monomer in Lead Detoxification (ChemMedChem 15/2022). ChemMedChem 2022. [DOI: 10.1002/cmdc.202200403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Luca Sauser
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Ayça Kavas
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Michal S. Shoshan
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| |
Collapse
|
14
|
Stańczak A, Chalupský J, Rulíšek L, Straka M. Cover Feature: Comprehensive Theoretical View of the [Cu
2
O
2
] Side‐on‐Peroxo‐/Bis‐
μ
‐Oxo Equilibria (ChemPhysChem 14/2022). Chemphyschem 2022. [DOI: 10.1002/cphc.202200434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Agnieszka Stańczak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Praha 6 Czech Republic
- Faculty of Science Charles University Albertov 2038/6 Prague 2 128 43 Czech Republic
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Praha 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Praha 6 Czech Republic
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Praha 6 Czech Republic
| |
Collapse
|
15
|
Sauser L, Kalvoda T, Kavas A, Rulíšek L, Shoshan M. Cyclic Octapeptides Composed of Two Glutathione Units Outperform the Monomer in Lead Detoxification. ChemMedChem 2022; 17:e202200152. [PMID: 35560783 PMCID: PMC9544108 DOI: 10.1002/cmdc.202200152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/11/2022] [Indexed: 11/06/2022]
Abstract
A rationally-designed scaffold of cyclic octapeptides composed of two units of the natural tripeptide glutathione (GSH) was optimized to strongly and selectively capture toxic lead ions (Pb(II)). Using state-of-the-art computational tools, a list of eleven plausible peptides was shortened to five analogs based on their calculated affinity to Pb(II) ions. We then synthesized and investigated them for their abilities to recover Pb-poisoned human cells. A clear pattern was observed from the in vitro detoxification results, indicating the importance of cavity size and polar moieties to enhance metal capturing. These, together with the apparent benefit in cyclizing the peptides, improved the detoxification of the two lead peptides by approximately two folds compared to GSH and the benchmark chelating agents against Pb poisoning. Moreover, the two peptides did not show any toxicity and, therefore, were thoroughly investigated to determine their potential as next-generation remedies for Pb poisoning.
Collapse
Affiliation(s)
- Luca Sauser
- University of Zurich: Universitat Zurich, Department of Chemistry, SWITZERLAND
| | - Tadeáš Kalvoda
- Czech Academy of Sciences: Akademie ved Ceske republiky, Institute of Organic Chemistry and Biochemistry, CZECH REPUBLIC
| | - Ayça Kavas
- University of Zurich: Universitat Zurich, Department of Chemistry, SWITZERLAND
| | - Lubomír Rulíšek
- Czech Academy of Sciences: Akademie ved Ceske republiky, Institute of Organic Chemistry and Biochemistry, CZECH REPUBLIC
| | - Michal Shoshan
- University of Zurich: Universitat Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057, Zurich, SWITZERLAND
| |
Collapse
|
16
|
Stańczak A, Chalupský J, Rulíšek L, Straka M. Comprehensive Theoretical View of the [Cu2O2] Side-on-Peroxo-/Bis-μ-Oxo Equilibria. Chemphyschem 2022; 23:e202200076. [PMID: 35532185 DOI: 10.1002/cphc.202200076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Indexed: 11/07/2022]
Abstract
Coupled binuclear copper (CBC) sites are employed by many metalloenzymes to catalyze a broad set of biochemical transformations. Typically, the CBC catalytic sites are activated by the O2 molecule to form various [Cu2O2] reactive species. This has also inspired synthesis and development of various biomimetic inorganic complexes featuring the CBC core. From theoretical perspective, the [Cu2O2] reactivity often hinges on the side-on-peroxo-dicopper(II) (P) vs. bis-μ-oxo-dicopper(III) (O) isomerism - an equilibrium that has become almost iconic in theoretical bioinorganic chemistry. Herein, we present a comprehensive calibration and evaluation of the performance of various composite computational protocols available in contemporary computational chemistry, involving coupled-cluster and multi-reference (relativistic) wave function methods, popular density functionals and solvation models. Starting with the well-studied reference [Cu2O2(NH3)6]2+ system, we compared the performance of electronic structure methods and discussed the relativistic effects. This allowed us to select several 'calibrated' DFT functionals that can be conveniently employed to study ten experimentally well-characterized [Cu2O2] inorganic systems. We mostly correctly predicted the lowest-energy structures (P vs. O) of the studied systems. In addition, we present calibration of the used electronic structure methods for prediction of the spectroscopic features of the [Cu2O2] core.
Collapse
Affiliation(s)
- Agnieszka Stańczak
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Bioinorganic Chemistry, CZECH REPUBLIC
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Bioinorganic Chemistry, CZECH REPUBLIC
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Bioinorganic Chemistry, CZECH REPUBLIC
| | - Michal Straka
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences: Ustav organicke chemie a biochemie Akademie ved Ceske republiky, Bioinorganic Chemistry, Flemingovo nam. 2, 16610, Prague, CZECH REPUBLIC
| |
Collapse
|
17
|
Kipouros I, Stańczak A, Culka M, Andris E, Machonkin TR, Rulíšek L, Solomon EI. Evidence for H-bonding interactions to the μ-η 2:η 2-peroxide of oxy-tyrosinase that activate its coupled binuclear copper site. Chem Commun (Camb) 2022; 58:3913-3916. [PMID: 35237779 PMCID: PMC8966618 DOI: 10.1039/d2cc00750a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The factors that control the diverse reactivity of the μ-η2:η2-peroxo dicopper(II) oxy-intermediates in the coupled binuclear copper proteins remain elusive. Here, spectroscopic and computational methods reveal H-bonding interactions between active-site waters and the μ-η2:η2-peroxide of oxy-tyrosinase, and define their effects on the Cu(II)2O2 electronic structure and O2 activation.
Collapse
Affiliation(s)
- Ioannis Kipouros
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
| | - Agnieszka Stańczak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
- Faculty of Science, Charles University, Albertov 2038/6, 128 00 Praha 2, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
| | | | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, California 94025, USA
| |
Collapse
|
18
|
Bím D, Navrátil M, Gutten O, Konvalinka J, Kutil Z, Culka M, Navrátil V, Alexandrova AN, Bařinka C, Rulíšek L. Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II. J Phys Chem B 2022; 126:132-143. [PMID: 34978450 DOI: 10.1021/acs.jpcb.1c09240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol-1 can be inferred for the known kcat ≈ 1 s-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (kcat = 8.6 × 10-5 s-1 to 2.7 s-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.
Collapse
Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 2120 00 Prague, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Václav Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| |
Collapse
|
19
|
Tupec M, Culka M, Machara A, Macháček S, Bím D, Svatoš A, Rulíšek L, Pichová I. Understanding desaturation/hydroxylation activity of castor stearoyl Δ9-Desaturase through rational mutagenesis. Comput Struct Biotechnol J 2022; 20:1378-1388. [PMID: 35386101 PMCID: PMC8940945 DOI: 10.1016/j.csbj.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 01/17/2023] Open
Abstract
Rationally designed mutations in the Δ9 desaturase promoted hydroxylation activity. Proton and electron transfer to the active site is crucial for the Δ9D to desaturate Detailed analysis of all enzymatic products of the Δ9D was carried out Insight into the chemo-, and stereoselectivity of non-heme diiron enzymes was obtained
A recently proposed reaction mechanism of soluble Δ9 desaturase (Δ9D) allowed us to identify auxiliary residues His203, Asp101, Thr206 and Cys222 localized near the di-iron active site that are supposedly involved in the proton transfer (PT) to and from the active site. The PT, along with the electron transfer (ET), seems to be crucial for efficient desaturation. Thus, perturbing the major PT chains is expected to impair the native reaction and (potentially) amplify minor reaction channels, such as the substrate hydroxylation. To verify this hypothesis, we mutated the four residues mentioned above into their counterparts present in a soluble methane monooxygenase (sMMO), and determined the reaction products of mutants. We found that the mutations significantly promote residual monohydroxylation activities on stearoyl-CoA, often at the expense of native desaturation activity. The favored hydroxylation positions are C9, followed by C10 and C11. Reactions with unsaturated substrate, oleoyl-CoA, yield erythro-9,10-diol, cis-9,10-epoxide and a mixture of allylic alcohols. Additionally, using 9- and 11-hydroxystearoyl-CoA, we showed that the desaturation reaction can proceed only with the hydroxyl group at position C11, whereas the hydroxylation reaction is possible in both cases, i.e. with hydroxyl at position C9 or C11. Despite the fact that the overall outcome of hydroxylation is rather modest and that it is mostly the desaturation/hydroxylation ratio that is affected, our results broaden understanding of the origin of chemo- and stereoselectivity of the Δ9D and provide further insight into the catalytic action of the NHFe2 enzymes.
Collapse
Affiliation(s)
- Michal Tupec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Aleš Machara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Stanislav Macháček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Daniel Bím
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Aleš Svatoš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Corresponding authors.
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Corresponding authors.
| |
Collapse
|
20
|
Sauser L, Mohammed TA, Kalvoda T, Feng SJ, Spingler B, Rulíšek L, Shoshan MS. Thiolation and Carboxylation of Glutathione Synergistically Enhance Its Lead-Detoxification Capabilities. Inorg Chem 2021; 60:18620-18624. [PMID: 34860512 DOI: 10.1021/acs.inorgchem.1c03030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The natural tripeptide glutathione (GSH) is a ubiquitous compound harboring various biological tasks, among them interacting with essential and toxic metal ions. Yet, although weakly binding the poisonous metal lead (Pb), GSH poorly detoxifies it. β-Mercaptoaspartic acid is a new-to-nature novel amino acid that was found to enhance the Pb-detoxification capability of a synthetic cyclic tetrapeptide. Aiming to explore the advantages of noncanonical amino acids (ncAAs) of this nature, we studied the detoxification capabilities of GSH and three analogue peptides, each of which contains at least one ncAA that harbors both free carboxylate and thiolate groups. A thorough investigation that includes in vitro detoxification and mechanistic evaluations, metal-binding affinity, metal selectivity, and computational studies shows that these ncAAs are highly beneficial in additively enhancing Pb binding and reveals the importance of both high affinity and metal selectivity in synergistically reducing Pb toxicity in cells. Hence, such ncAAs join the chemical toolbox against Pb poisoning and pollution, enabling peptides to strongly and selectively bind the toxic metal ion.
Collapse
Affiliation(s)
- Luca Sauser
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tagwa A Mohammed
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Praha 6, Czech Republic
| | - Sheng-Jan Feng
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Spingler
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610 Praha 6, Czech Republic
| | - Michal S Shoshan
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
21
|
Novotná B, Holá L, Staś M, Gutten O, Smola M, Zavřel M, Vavřina Z, Buděšínský M, Liboska R, Chevrier F, Dobiaš J, Boura E, Rulíšek L, Birkuš G. Enzymatic Synthesis of 3'-5', 3'-5' Cyclic Dinucleotides, Their Binding Properties to the Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations. Biochemistry 2021; 60:3714-3727. [PMID: 34788017 DOI: 10.1021/acs.biochem.1c00692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The 3'-5', 3'-5' cyclic dinucleotides (3'3'CDNs) are bacterial second messengers that can also bind to the stimulator of interferon genes (STING) adaptor protein in vertebrates and activate the host innate immunity. Here, we profiled the substrate specificity of four bacterial dinucleotide synthases from Vibrio cholerae (DncV), Bacillus thuringiensis (btDisA), Escherichia coli (dgcZ), and Thermotoga maritima (tDGC) using a library of 33 nucleoside-5'-triphosphate analogues and then employed these enzymes to synthesize 24 3'3'CDNs. The STING affinity of CDNs was evaluated in cell-based and biochemical assays, and their ability to induce cytokines was determined by employing human peripheral blood mononuclear cells. Interestingly, the prepared heterodimeric 3'3'CDNs bound to the STING much better than their homodimeric counterparts and showed similar or better potency than bacterial 3'3'CDNs. We also rationalized the experimental findings by in-depth STING-CDN structure-activity correlations by dissecting computed interaction free energies into a set of well-defined and intuitive terms. To this aim, we employed state-of-the-art methods of computational chemistry, such as quantum mechanics/molecular mechanics (QM/MM) calculations, and complemented the computed results with the {STING:3'3'c-di-ara-AMP} X-ray crystallographic structure. QM/MM identified three outliers (mostly homodimers) for which we have no clear explanation of their impaired binding with respect to their heterodimeric counterparts, whereas the R2 = 0.7 correlation between the computed ΔG'int_rel and experimental ΔTm's for the remaining ligands has been very encouraging.
Collapse
Affiliation(s)
- Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic
| | - Lucie Holá
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Monika Staś
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 12800, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Florian Chevrier
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Juraj Dobiaš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB, Flemingovo náměstí 2, Prague 16610, Czech Republic
| |
Collapse
|
22
|
Abstract
We demonstrate that Ir-catalyzed C-C bond activation in biphenylenes followed by a reaction with tribenzocyclyne is a suitable method for synthesizing strained and unknown monoadducts with the tetradehydrotetrabenzo[a,c,e,i]cyclododecene scaffold ([12]annulenes). Modification of reaction conditions also furnished [12]annulene products with cis and/or trans double bonds formed by hydrogen transfer. The [9]annulene side product was formed upon the reaction of the benzyl radical with tribenzocyclyne during the Bergman cyclization. All isolated compounds were fully characterized by HRMS, NMR, and X-ray diffraction analysis.
Collapse
Affiliation(s)
- Jaroslav Jacko
- Department of Organic Chemistry, Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Monika Staś
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic
| | - Martin Kotora
- Department of Organic Chemistry, Faculty of Science, Charles University, Albertov 6, 128 43 Praha 2, Czech Republic
| |
Collapse
|
23
|
Mohammed TA, Meier CM, Kalvoda T, Kalt M, Rulíšek L, Shoshan MS. Potent Cyclic Tetrapeptide for Lead Detoxification. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tagwa A. Mohammed
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Christoph M. Meier
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Martina Kalt
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Michal S. Shoshan
- Department of Chemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| |
Collapse
|
24
|
Mohammed TA, Meier CM, Kalvoda T, Kalt M, Rulíšek L, Shoshan MS. Potent Cyclic Tetrapeptide for Lead Detoxification. Angew Chem Int Ed Engl 2021; 60:12381-12385. [PMID: 33759306 DOI: 10.1002/anie.202103217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 11/05/2022]
Abstract
Lead (Pb) is a ubiquitous poisonous metal, affecting the health of vast populations worldwide. Medications to treat Pb poisoning suffer from various limitations and are often toxic owing to insufficient metal selectivity. Here, we report a cyclic tetrapeptide that selectively binds Pb and eradicates its toxic effect on the cellular level, with superior potency than state-of-the-art drugs. The Pb-peptide complex is remarkably strong and was characterized experimentally and computationally. Accompanied by the lack of toxicity and enhanced stability of this peptide, these qualities indicate its merit as a potential remedy for Pb poisoning.
Collapse
Affiliation(s)
- Tagwa A Mohammed
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Christoph M Meier
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| | - Martina Kalt
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Praha 6, Czech Republic
| | - Michal S Shoshan
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| |
Collapse
|
25
|
Pimková Polidarová M, Břehová P, Kaiser MM, Smola M, Dračínský M, Smith J, Marek A, Dejmek M, Šála M, Gutten O, Rulíšek L, Novotná B, Brázdová A, Janeba Z, Nencka R, Boura E, Páv O, Birkuš G. Synthesis and Biological Evaluation of Phosphoester and Phosphorothioate Prodrugs of STING Agonist 3',3'-c-Di(2'F,2'dAMP). J Med Chem 2021; 64:7596-7616. [PMID: 34019405 DOI: 10.1021/acs.jmedchem.1c00301] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cyclic dinucleotides (CDNs) are second messengers that bind to the stimulator of interferon genes (STING) and trigger the expression of type I interferons and proinflammatory cytokines. Here we evaluate the activity of 3',3'-c-di(2'F,2'dAMP) and its phosphorothioate analogues against five STING allelic forms in reporter-cell-based assays and rationalize our findings with X-ray crystallography and quantum mechanics/molecular mechanics calculations. We show that the presence of fluorine in the 2' position of 3',3'-c-di(2'F,2'dAMP) improves its activity not only against the wild type (WT) but also against REF and Q STING. Additionally, we describe the synthesis of the acyloxymethyl and isopropyloxycarbonyl phosphoester prodrugs of CDNs. Masking the negative charges of the CDNs results in an up to a 1000-fold improvement of the activities of the prodrugs relative to those of their parent CDNs. Finally, the uptake and intracellular cleavage of pivaloyloxymethyl prodrugs to the parent CDN is rapid, reaching a peak intracellular concentration within 2 h.
Collapse
Affiliation(s)
- Markéta Pimková Polidarová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 128 00, Czech Republic
| | - Petra Břehová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Martin Maxmilian Kaiser
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Joshua Smith
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Aleš Marek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 128 00, Czech Republic
| | - Andrea Brázdová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Náměstí 2, Prague 160 00, Czech Republic
| |
Collapse
|
26
|
Smola M, Gutten O, Dejmek M, Kožíšek M, Evangelidis T, Tehrani ZA, Novotná B, Nencka R, Birkuš G, Rulíšek L, Boura E. Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein. Angew Chem Int Ed Engl 2021; 60:10172-10178. [PMID: 33616279 PMCID: PMC8251555 DOI: 10.1002/anie.202016805] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
STING (stimulator of interferon genes) is a key regulator of innate immunity that has recently been recognized as a promising drug target. STING is activated by cyclic dinucleotides (CDNs) which eventually leads to expression of type I interferons and other cytokines. Factors underlying the affinity of various CDN analogues are poorly understood. Herein, we correlate structural biology, isothermal calorimetry (ITC) and computational modeling to elucidate factors contributing to binding of six CDNs-three pairs of natural (ribo) and fluorinated (2'-fluororibo) 3',3'-CDNs. X-ray structural analyses of six {STING:CDN} complexes did not offer any explanation for the different affinities of the studied ligands. ITC showed entropy/enthalpy compensation up to 25 kcal mol-1 for this set of similar ligands. The higher affinities of fluorinated analogues are explained with help of computational methods by smaller loss of entropy upon binding and by smaller strain (free) energy.
Collapse
Affiliation(s)
- Miroslav Smola
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Ondrej Gutten
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Milan Dejmek
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Milan Kožíšek
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Thomas Evangelidis
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Zahra Aliakbar Tehrani
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Barbora Novotná
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Radim Nencka
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Gabriel Birkuš
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Lubomír Rulíšek
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCBInstitute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610PragueCzech Republic
| |
Collapse
|
27
|
Smola M, Gutten O, Dejmek M, Kožíšek M, Evangelidis T, Tehrani ZA, Novotná B, Nencka R, Birkuš G, Rulíšek L, Boura E. Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miroslav Smola
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Ondrej Gutten
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Milan Dejmek
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Milan Kožíšek
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Thomas Evangelidis
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Zahra Aliakbar Tehrani
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Barbora Novotná
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Radim Nencka
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Gabriel Birkuš
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Lubomír Rulíšek
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Evzen Boura
- Gilead Sciences Research Centre at IOCB Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| |
Collapse
|
28
|
Gutten O, Jurečka P, Aliakbar Tehrani Z, Buděšínský M, Řezáč J, Rulíšek L. Conformational energies and equilibria of cyclic dinucleotides in vacuo and in solution: computational chemistry vs. NMR experiments. Phys Chem Chem Phys 2021; 23:7280-7294. [PMID: 33876088 DOI: 10.1039/d0cp05993e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Performance of computational methods in modelling cyclic dinucleotides - an important and challenging class of compounds - has been evaluated by two different benchmarks: (1) gas-phase conformational energies and (2) qualitative agreement with NMR observations of the orientation of the χ-dihedral angle in solvent. In gas-phase benchmarks, where CCSD(T) and DLPNO-CCSD(T) methods have been used as the reference, most of the (dispersion corrected) density functional approximations are accurate enough to justify prioritizing computational cost and compatibility with other modelling options as the criterion of choice. NMR experiments of 3'3'-c-di-AMP, 3'3'-c-GAMP, and 3'3'-c-di-GMP show the overall prevalence of the anti-conformation of purine bases, but some population of syn-conformations is observed for guanines. Implicit solvation models combined with quantum-chemical methods struggle to reproduce this behaviour, probably due to a lack of dynamics and explicitly modelled solvent, leading to structures that are too compact. Molecular dynamics simulations overrepresent the syn-conformation of guanine due to the overestimation of an intramolecular hydrogen bond. Our combination of experimental and computational benchmarks provides "error bars" for modelling cyclic dinucleotides in solvent, where such information is generally difficult to obtain, and should help gauge the interpretability of studies dealing with binding of cyclic dinucleotides to important pharmaceutical targets. At the same time, the presented analysis calls for improvement in both implicit solvation models and force-field parameters.
Collapse
Affiliation(s)
- Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10, Praha 6, Czech Republic.
| | | | | | | | | | | |
Collapse
|
29
|
Guselnikova O, Váňa J, Phuong LT, Panov I, Rulíšek L, Trelin A, Postnikov P, Švorčík V, Andris E, Lyutakov O. Plasmon-assisted click chemistry at low temperature: an inverse temperature effect on the reaction rate. Chem Sci 2021; 12:5591-5598. [PMID: 34163774 PMCID: PMC8179579 DOI: 10.1039/d0sc05898j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/05/2021] [Indexed: 11/21/2022] Open
Abstract
Plasmon assistance promotes a range of chemical transformations by decreasing their activation energies. In a common case, thermal and plasmon assistance work synergistically: higher temperature results in higher plasmon-enhanced catalysis efficiency. Herein, we report an unexpected tenfold increase in the reaction efficiency of surface plasmon-assisted Huisgen dipolar azide-alkyne cycloaddition (AAC) when the reaction mixture is cooled from room temperature to -35 °C. We attribute the observed increase in the reaction efficiency to complete plasmon-induced annihilation of the reaction barrier, prolongation of plasmon lifetime, and decreased relaxation of plasmon-excited-states under cooling. Furthermore, control quenching experiments supported by theoretical calculations indicate that plasmon-mediated substrate excitation to an electronic triplet state may play the key role in plasmon-assisted chemical transformation. Last but not least, we demonstrated the possible applicability of plasmon assistance to biological systems by AAC coupling of biotin to gold nanoparticles performed at -35 °C.
Collapse
Affiliation(s)
- Olga Guselnikova
- Department of Solid State Engineering, University of Chemistry and Technology 166 28 Prague Czech Republic
- Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University Lenin Avenue 30 Tomsk 634050 Russia
| | - Jiří Váňa
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice Studentská 573 532 10 Pardubice Czech Republic
| | - Linh Trinh Phuong
- Department of Solid State Engineering, University of Chemistry and Technology 166 28 Prague Czech Republic
| | - Illia Panov
- Group of Advanced Materials and Organic Synthesis, Institute of Chemical Process Fundamentals, Czech Academy of Sciences Rozvojová 1/135 165 02 Prague Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Andrii Trelin
- Department of Solid State Engineering, University of Chemistry and Technology 166 28 Prague Czech Republic
| | - Pavel Postnikov
- Department of Solid State Engineering, University of Chemistry and Technology 166 28 Prague Czech Republic
- Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University Lenin Avenue 30 Tomsk 634050 Russia
| | - Václav Švorčík
- Department of Solid State Engineering, University of Chemistry and Technology 166 28 Prague Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 166 10 Prague 6 Czech Republic
| | - Oleksiy Lyutakov
- Department of Solid State Engineering, University of Chemistry and Technology 166 28 Prague Czech Republic
- Research School of Chemistry & Applied Biomedical Sciences, National Research Tomsk Polytechnic University Lenin Avenue 30 Tomsk 634050 Russia
| |
Collapse
|
30
|
Vavřina Z, Gutten O, Smola M, Zavřel M, Aliakbar Tehrani Z, Charvát V, Kožíšek M, Boura E, Birkuš G, Rulíšek L. Protein-Ligand Interactions in the STING Binding Site Probed by Rationally Designed Single-Point Mutations: Experiment and Theory. Biochemistry 2021; 60:607-620. [PMID: 33586948 DOI: 10.1021/acs.biochem.0c00949] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
STING protein (stimulator of interferon genes) plays an important role in the innate immune system. A number of potent compounds regulating its activity have been reported, mostly derivatives of cyclic dinucleotides (CDNs), natural STING agonists. Here, we aim to provide complementary information to large-scale "ligand-profiling" studies by probing the importance of STING-CDN protein-ligand interactions on the protein side. We examined in detail six typical CDNs each in complex with 13 rationally devised mutations in STING: S162A, S162T, Y167F, G230A, R232K, R232H, A233L, A233I, R238K, T263A, T263S, R293Q, and G230A/R293Q. The mutations switch on and off various types of protein-ligand interactions: π-π stacking, hydrogen bonding, ionic pairing, and nonpolar contacts. We correlated experimental data obtained by differential scanning fluorimetry, X-ray crystallography, and isothermal titration calorimetry with theoretical calculations. This enabled us to provide a mechanistic interpretation of the differences in the binding of representative CDNs to STING. We observed that the G230A mutation increased the thermal stability of the protein-ligand complex, indicating an increased level of ligand binding, whereas R238K and Y167F led to a complete loss of stabilization (ligand binding). The effects of the other mutations depended on the type of ligand (CDN) and varied, to some extent. A very good correlation (R2 = 0.6) between the experimental binding affinities and interaction energies computed by quantum chemical methods enabled us to explain the effect of the studied mutations in detail and evaluate specific interactions quantitatively. Our work may inspire development of high-affinity ligands against the common STING haplotypes by targeting the key (sometimes non-intuitive) protein-ligand interactions.
Collapse
Affiliation(s)
- Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague 110 00, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Zahra Aliakbar Tehrani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic.,Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Vilém Charvát
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, Prague 16610, Czech Republic
| |
Collapse
|
31
|
Culka M, Kalvoda T, Gutten O, Rulíšek L. Mapping Conformational Space of All 8000 Tripeptides by Quantum Chemical Methods: What Strain Is Affordable within Folded Protein Chains? J Phys Chem B 2021; 125:58-69. [PMID: 33393778 DOI: 10.1021/acs.jpcb.0c09251] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To gain more insight into the physicochemical aspects of a protein structure from the first principles, conformational space of all 8000 "capped" tripeptides (i.e., N-Ac-X1X2X3-NH-CH3, where Xi is one of the 20 natural amino acids) was investigated computationally. An enormous dataset (denoted P-CONF_1.6M and containing close to 1 600 000 conformers in total) has been obtained by employing a composite protocol combining density functional theory, semiempirical quantum mechanics (SQM), and state-of-the-art solvation methods with 1000 K molecular dynamics (MD) used to generate initial structures (200 snapshots for each tripeptide). This allowed us to present the first rigorous QM-based glimpse at the vast conformational space spanned by small protein fragments. The same computational procedure was repeated for tripeptide fragments taken from the SCOPe database of three-dimensional protein folds, by restraining them to their geometry in a protein. Such complementary data allowed us to compare the distribution of conformational strain energies of unrestrained tripeptidic fragments "in solvent" with those in existing protein chains. Besides providing a rigorous (ab initio) proof of a few well-known concepts and hypotheses concerning protein structures, such as the distribution of (φ, ψ) angles in Ramachandran plots, we have made several observations that came as a certain surprise: (1) distribution of conformational energies does not significantly differ between the "unbiased/unrestrained" conformers obtained from MD sampling in solvent and the biased conformers, i.e., those of a given tripeptide obtained from protein structures; (2) conformational (strain) energy window up to ∼20 to 25 kcal·mol-1 is readily available to tripeptide fragments within the context of a protein chain; (3) overpopulation in certain regions of Ramachandran plot was observed for the unbiased conformers. Last but not least, the massive dataset of accurate (DFT-D3//COSMO-RS) conformational (free) energies of ∼1.6 M peptide conformers, P-CONF_1.6M, obtained throughout this work may serve as excellent dataset for calibrating and benchmarking of popular force fields.
Collapse
Affiliation(s)
- Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Tadeáš Kalvoda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| |
Collapse
|
32
|
Andris E, Segers K, Mehara J, Rulíšek L, Roithová J. Closed Shell Iron(IV) Oxo Complex with an Fe–O Triple Bond: Computational Design, Synthesis, and Reactivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Erik Andris
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Koen Segers
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Jaya Mehara
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| |
Collapse
|
33
|
Andris E, Segers K, Mehara J, Rulíšek L, Roithová J. Frontispiz: Closed Shell Iron(IV) Oxo Complex with an Fe–O Triple Bond: Computational Design, Synthesis, and Reactivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202085162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Erik Andris
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Koen Segers
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Jaya Mehara
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| |
Collapse
|
34
|
Andris E, Segers K, Mehara J, Rulíšek L, Roithová J. Closed Shell Iron(IV) Oxo Complex with an Fe-O Triple Bond: Computational Design, Synthesis, and Reactivity. Angew Chem Int Ed Engl 2020; 59:23137-23144. [PMID: 32926539 PMCID: PMC7756500 DOI: 10.1002/anie.202009347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/11/2022]
Abstract
Iron(IV)-oxo intermediates in nature contain two unpaired electrons in the Fe-O antibonding orbitals, which are thought to contribute to their high reactivity. To challenge this hypothesis, we designed and synthesized closed-shell singlet iron(IV) oxo complex [(quinisox)Fe(O)]+ (1+ ; quinisox-H=(N-(2-(2-isoxazoline-3-yl)phenyl)quinoline-8-carboxamide). We identified the quinisox ligand by DFT computational screening out of over 450 candidates. After the ligand synthesis, we detected 1+ in the gas phase and confirmed its spin state by visible and infrared photodissociation spectroscopy (IRPD). The Fe-O stretching frequency in 1+ is 960.5 cm-1 , consistent with an Fe-O triple bond, which was also confirmed by multireference calculations. The unprecedented bond strength is accompanied by high gas-phase reactivity of 1+ in oxygen atom transfer (OAT) and in proton-coupled electron transfer reactions. This challenges the current view of the spin-state driven reactivity of the Fe-O complexes.
Collapse
Affiliation(s)
- Erik Andris
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610Praha 6Czech Republic
| | - Koen Segers
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Jaya Mehara
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610Praha 6Czech Republic
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| |
Collapse
|
35
|
Andris E, Segers K, Mehara J, Rulíšek L, Roithová J. Frontispiece: Closed Shell Iron(IV) Oxo Complex with an Fe–O Triple Bond: Computational Design, Synthesis, and Reactivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/anie.202085162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Erik Andris
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Koen Segers
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Jaya Mehara
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| |
Collapse
|
36
|
Bím D, Chalupský J, Culka M, Solomon EI, Rulíšek L, Srnec M. Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ 9-Desaturase. J Am Chem Soc 2020; 142:10412-10423. [PMID: 32406236 DOI: 10.1021/jacs.0c01786] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.
Collapse
Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic.,Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic
| |
Collapse
|
37
|
Culka M, Rulíšek L. Interplay between Conformational Strain and Intramolecular Interaction in Protein Structures: Which of Them Is Evolutionarily Conserved? J Phys Chem B 2020; 124:3252-3260. [PMID: 32237747 DOI: 10.1021/acs.jpcb.9b11784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
By computing strain energies of peptide fragments within protein structures and their intramolecular interaction energies, we attempt to reveal general biophysical trends behind the secondary structure formation in the context of protein evolution. Our "protein basis set" consisted of 1143 representatives of different folds obtained from curated SCOPe database, and for each member of the set, the strain and intramolecular energy was calculated on the "rolling tripeptide" basis, employing the DFT-D3/COSMO-RS method for the former and the QM-calibrated force field method (MM) for the latter. The calculated data, strain and interactions, were correlated with the conservation of amino acid residues in secondary structure elements and also with the level of the residue burial within the protein three-dimensional structure. It allowed us to formulate several observations concerning fundamental differences between two main secondary structure motifs: α-helices and β-strands. We have shown that a strong interaction is one of the determining characteristics of the β-sheet formation, at least at the level of tripeptides (and likely penta- or heptapeptides, too), and that the β-strand is a prevailing secondary structure in the strongly-interacting regions of the protein folds conserved by evolution. On the other hand, low strain was neither proven to be an important physicochemical property conserved by evolution nor does it correlate with the propensity for the α-helix and β-strand. Finally, it has been demonstrated that the strong interaction has a certain level of connection with residue burial; however, we demonstrate that these two characteristics should be rather regarded as two complementary factors. These findings represent an important contribution to understanding protein folding from first principles, which is a complementary approach to ongoing efforts to solve the protein folding problem by knowledge-based approaches and machine-learning.
Collapse
Affiliation(s)
- Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| |
Collapse
|
38
|
Hudeček O, Benoni R, Reyes-Gutierrez PE, Culka M, Šanderová H, Hubálek M, Rulíšek L, Cvačka J, Krásný L, Cahová H. Dinucleoside polyphosphates act as 5'-RNA caps in bacteria. Nat Commun 2020; 11:1052. [PMID: 32103016 PMCID: PMC7044304 DOI: 10.1038/s41467-020-14896-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
It has been more than 50 years since the discovery of dinucleoside polyphosphates (NpnNs) and yet their roles and mechanisms of action remain unclear. Here, we show that both methylated and non-methylated NpnNs serve as RNA caps in Escherichia coli. NpnNs are excellent substrates for T7 and E. coli RNA polymerases (RNAPs) and efficiently initiate transcription. We demonstrate, that the E. coli enzymes RNA 5′-pyrophosphohydrolase (RppH) and bis(5′-nucleosyl)-tetraphosphatase (ApaH) are able to remove the NpnN-caps from RNA. ApaH is able to cleave all NpnN-caps, while RppH is unable to cleave the methylated forms suggesting that the methylation adds an additional layer to RNA stability regulation. Our work introduces a different perspective on the chemical structure of RNA in prokaryotes and on the role of RNA caps. We bring evidence that small molecules, such as NpnNs are incorporated into RNA and may thus influence the cellular metabolism and RNA turnover. Nicotinamide adenine dinucleotide and coenzyme A serve as a 5′-cap of prokaryotic RNA. Here the authors report that methylated and non-methylated dinucleoside polyphosphates (NpnNs) exist as Escherichia coli RNA caps which can be cleaved by 5′-pyrophosphohydrolase (RppH) and bis(5′-nucleosyl)-tetraphosphatase (ApaH).
Collapse
Affiliation(s)
- Oldřich Hudeček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Roberto Benoni
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Paul E Reyes-Gutierrez
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Hana Šanderová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Libor Krásný
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Hana Cahová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.
| |
Collapse
|
39
|
Novotná B, Vaneková L, Zavřel M, Buděšínský M, Dejmek M, Smola M, Gutten O, Tehrani ZA, Pimková Polidarová M, Brázdová A, Liboska R, Štěpánek I, Vavřina Z, Jandušík T, Nencka R, Rulíšek L, Bouřa E, Brynda J, Páv O, Birkuš G. Enzymatic Preparation of 2'-5',3'-5'-Cyclic Dinucleotides, Their Binding Properties to Stimulator of Interferon Genes Adaptor Protein, and Structure/Activity Correlations. J Med Chem 2019; 62:10676-10690. [PMID: 31715099 DOI: 10.1021/acs.jmedchem.9b01062] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cyclic dinucleotides are second messengers in the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway, which plays an important role in recognizing tumor cells and viral or bacterial infections. They bind to the STING adaptor protein and trigger expression of cytokines via TANK binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) and inhibitor of nuclear factor-κB (IκB) kinase (IKK)/nuclear factor-κB (NFκB) signaling cascades. In this work, we describe an enzymatic preparation of 2'-5',3'-5'-cyclic dinucleotides (2'3'CDNs) with use of cyclic GMP-AMP synthases (cGAS) from human, mouse, and chicken. We profile substrate specificity of these enzymes by employing a small library of nucleotide-5'-triphosphate (NTP) analogues and use them to prepare 33 2'3'CDNs. We also determine affinity of these CDNs to five different STING haplotypes in cell-based and biochemical assays and describe properties needed for their optimal activity toward all STING haplotypes. Next, we study their effect on cytokine and chemokine induction by human peripheral blood mononuclear cells (PBMCs) and evaluate their cytotoxic effect on monocytes. Additionally, we report X-ray crystal structures of two new CDNs bound to STING protein and discuss structure-activity relationship by using quantum and molecular mechanical (QM/MM) computational modeling.
Collapse
Affiliation(s)
- Barbora Novotná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Lenka Vaneková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Martin Zavřel
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Miroslav Smola
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Zahra Aliakbar Tehrani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Markéta Pimková Polidarová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Andrea Brázdová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Radek Liboska
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ivan Štěpánek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Zdeněk Vavřina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Science , Charles University , Prague 110 00 , Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic.,Faculty of Food and Biochemical Technology , University of Chemistry and Technology , Prague 166 28 , Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Evžen Bouřa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Ondřej Páv
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| | - Gabriel Birkuš
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences and Gilead Sciences Research Centre at IOCB , Flemingovo nam. 2 , Prague 16610 , Czech Republic
| |
Collapse
|
40
|
Ajenjo J, Klepetářová B, Greenhall M, Bím D, Culka M, Rulíšek L, Beier P. Preparation of (Pentafluorosulfanyl)benzenes by Direct Fluorination of Diaryldisulfides: Synthetic Approach and Mechanistic Aspects. Chemistry 2019; 25:11375-11382. [DOI: 10.1002/chem.201902651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Javier Ajenjo
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of ScienceCharles University Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Blanka Klepetářová
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | | | - Daniel Bím
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Petr Beier
- Institute of Organic Chemistry and Biochemistry, of the Czech Academy of Sciences Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| |
Collapse
|
41
|
Abstract
Protein folds are determined by the interplay between various (de)stabilizing forces, which can be broadly divided into a local strain of the protein chain and intramolecular interactions. In contrast to the α-helix, the β-sheet secondary protein structure is significantly stabilized by long-range interactions between the individual β-strands. It has been observed that quite diverse amino acid sequences can form a very similar small β-sheet fold, such as in the three-β-strand WW domain. Employing "calibrated" quantum-chemical methods, we show herein on two sequentially diverse examples of the WW domain that the internal strain energy is higher in the β-strands and lower in the loops, while the interaction energy has an opposite trend. Low strain energy computed for peptide sequences in the loop 1 correlates with its postulated early formation in the folding process. The relatively high strain energy within the β-strands (up to 8 kcal mol-1 per amino acid residue) is compensated by even higher intramolecular interaction energy (up to 15 kcal mol-1 per residue). It is shown in a quantitative way that the most conserved residues across the structural family of WW domains have the highest contributions to the intramolecular interaction energy. On the other hand, the residues in the regions with the lowest strain are not conserved. We conclude that the internal interaction energy is the physical quantity tuned by evolution to define the β-sheet protein fold.
Collapse
Affiliation(s)
- Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 Praha 6 , Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 Praha 6 , Czech Republic
| |
Collapse
|
42
|
Brůža Z, Kratochvíl J, Harvey JN, Rulíšek L, Nováková L, Maříková J, Kuneš J, Kočovský P, Pour M. Cover Feature: A New Insight into the Stereoelectronic Control of the Pd
0
‐Catalyzed Allylic Substitution: Application for the Synthesis of Multisubstituted Pyran‐2‐ones via an Unusual 1,3‐Transposition (Chem. Eur. J. 34/2019). Chemistry 2019. [DOI: 10.1002/chem.201901743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Zbyněk Brůža
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jiří Kratochvíl
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jeremy N. Harvey
- Department of ChemistryKatholieke Universiteit, Leuven 3001 Leuven Belgium
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences 16610 Prague 6 Czech Republic
| | - Lucie Nováková
- Department of Analytical ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jana Maříková
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jiří Kuneš
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Pavel Kočovský
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
- Department of Organic Chemistry, Faculty of Natural, SciencesCharles University 12843 Prague 2 Czech Republic
| | - Milan Pour
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| |
Collapse
|
43
|
Brůža Z, Kratochvíl J, Harvey JN, Rulíšek L, Nováková L, Maříková J, Kuneš J, Kočovský P, Pour M. A New Insight into the Stereoelectronic Control of the Pd
0
‐Catalyzed Allylic Substitution: Application for the Synthesis of Multisubstituted Pyran‐2‐ones via an Unusual 1,3‐Transposition. Chemistry 2019; 25:8053-8060. [DOI: 10.1002/chem.201900323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/15/2019] [Indexed: 11/12/2022]
Affiliation(s)
- Zbyněk Brůža
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jiří Kratochvíl
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jeremy N. Harvey
- Department of ChemistryKatholieke Universiteit, Leuven 3001 Leuven Belgium
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences 16610 Prague 6 Czech Republic
| | - Lucie Nováková
- Department of Analytical ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jana Maříková
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Jiří Kuneš
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| | - Pavel Kočovský
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
- Department of Organic Chemistry, Faculty of Natural, SciencesCharles University 12843 Prague 2 Czech Republic
| | - Milan Pour
- Department of Organic and Bioorganic ChemistryFaculty of PharmacyCharles University Hradec Králové 50005 Czech Republic
| |
Collapse
|
44
|
Culka M, Galgonek J, Vymětal J, Vondrášek J, Rulíšek L. Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective. J Phys Chem B 2019; 123:1215-1227. [PMID: 30645123 DOI: 10.1021/acs.jpcb.8b09245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
By combining bioinformatics with quantum-chemical calculations, we attempt to address quantitatively some of the physical principles underlying protein folding. The former allowed us to identify tripeptide sequences in existing protein three-dimensional structures with a strong preference for either helical or extended structure. The selected representatives of pro-helical and pro-extended sequences were converted into "isolated" tripeptides-capped at N- and C-termini-and these were subjected to an extensive conformational sampling and geometry optimization (typically thousands to tens of thousands of conformers for each tripeptide). For each conformer, the QM(DFT-D3)/COSMO-RS free-energy value was then calculated, Gconf(solv). The Δ Gconf(solv) is expected to provide an objective, unbiased, and quantitatively accurate measure of the conformational preference of the particular tripeptide sequence. It has been shown that irrespective of the helical vs extended preferences of the selected tripeptide sequences in context of the protein, most of the low-energy conformers of isolated tripeptides prefer the R-helical structure. Nevertheless, pro-helical tripeptides show slightly stronger helix preference than their pro-extended counterparts. Furthermore, when the sampling is repeated in the presence of a partner tripeptide to mimic the situation in a β-sheet, pro-extended tripeptides (exemplified by the VIV) show a larger free-energy benefit than pro-helical tripeptides (exemplified by the EAM). This effect is even more pronounced in a hydrophobic solvent, which mimics the less polar parts of a protein. This is in line with our bioinformatic results showing that the majority of pro-extended tripeptides are hydrophobic. The preference for a specific secondary structure by the studied tripeptides is thus governed by the plasticity to adopt to its environment. In addition, we show that most of the "naturally occurring" conformations of tripeptide sequences, i.e., those found in existing three-dimensional protein structures, are within ∼10 kcal·mol-1 from their global minima. In summary, our "ab initio" data suggest that complex protein structures may start to emerge already at the level of their small oligopeptidic units, which is in line with a hierarchical nature of protein folding.
Collapse
Affiliation(s)
- Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 2 , 166 10 , Praha 6 , Czech Republic
| |
Collapse
|
45
|
Straka M, Andris E, Vícha J, Růžička A, Roithová J, Rulíšek L. Spectroscopic and Computational Evidence of Intramolecular AuI
⋅⋅⋅H+
−N Hydrogen Bonding. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811982] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Michal Straka
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo náměstí 2 16610 Prague 6 Czech Republic
| | - Erik Andris
- Department of Organic Chemistry; Faculty of Science; Charles University; Hlavova 2030/8 12843 Prague 2 Czech Republic
| | - Jan Vícha
- Centre of Polymer Systems; Tomas Bata University in Zlín; tř. Tomáše Bati 5678 76001 Zlín Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry; Faculty of Chemical Technology; University of Pardubice; 53210 Pardubice Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry; Faculty of Science; Charles University; Hlavova 2030/8 12843 Prague 2 Czech Republic
- Institute for Molecules and Materials; Radboud University; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Flemingovo náměstí 2 16610 Prague 6 Czech Republic
| |
Collapse
|
46
|
Straka M, Andris E, Vícha J, Růžička A, Roithová J, Rulíšek L. Spectroscopic and Computational Evidence of Intramolecular Au I ⋅⋅⋅H + -N Hydrogen Bonding. Angew Chem Int Ed Engl 2019; 58:2011-2016. [PMID: 30600866 PMCID: PMC6519277 DOI: 10.1002/anie.201811982] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/21/2018] [Indexed: 11/10/2022]
Abstract
Despite substantial evidence of short Au⋅⋅⋅H−X contacts derived from a number of X‐ray structures of AuI compounds, the nature of AuI⋅⋅⋅H bonding in these systems has not been clearly understood. Herein, we present the first spectroscopic evidence for an intramolecular AuI⋅⋅⋅H+−N hydrogen bond in a [Cl−Au−L]+ complex, where L is a protonated N‐heterocyclic carbene. The complex was isolated in the gas phase and characterized with helium‐tagging infrared photodissociation (IRPD) spectra, in which H+−N‐mode‐derived bands evidence the intramolecular AuI⋅⋅⋅H+−N bond. Quantum chemical calculations reproduce the experimental IRPD spectra and allow to characterize the intramolecular Au⋅⋅⋅H+−N bonding with a short rAu⋅⋅⋅H distance of 2.17 Å and an interaction energy of approximately −10 kcal mol−1. Various theoretical descriptors of chemical bonding calculated for the Au⋅⋅⋅H+−N interaction provide strong evidence for a hydrogen bond of moderate strength.
Collapse
Affiliation(s)
- Michal Straka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Erik Andris
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12843, Prague 2, Czech Republic
| | - Jan Vícha
- Centre of Polymer Systems, Tomas Bata University in Zlín, tř. Tomáše Bati 5678, 76001, Zlín, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, 53210, Pardubice, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030/8, 12843, Prague 2, Czech Republic.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| |
Collapse
|
47
|
Barinka C, Novakova Z, Hin N, Bím D, Ferraris DV, Duvall B, Kabarriti G, Tsukamoto R, Budesinsky M, Motlova L, Rojas C, Slusher BS, Rokob TA, Rulíšek L, Tsukamoto T. Structural and computational basis for potent inhibition of glutamate carboxypeptidase II by carbamate-based inhibitors. Bioorg Med Chem 2018; 27:255-264. [PMID: 30552009 DOI: 10.1016/j.bmc.2018.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/07/2018] [Accepted: 11/14/2018] [Indexed: 02/04/2023]
Abstract
A series of carbamate-based inhibitors of glutamate carboxypeptidase II (GCPII) were designed and synthesized using ZJ-43, N-[[[(1S)-1-carboxy-3-methylbutyl]amino]carbonyl]-l-glutamic acid, as a molecular template in order to better understand the impact of replacing one of the two nitrogen atoms in the urea-based GCPII inhibitor with an oxygen atom. Compound 7 containing a C-terminal 2-oxypentanedioic acid was more potent than compound 5 containing a C-terminal glutamic acid (2-aminopentanedioic acid) despite GCPII's preference for peptides containing an N-terminal glutamate as substrates. Subsequent crystallographic analysis revealed that ZJ-43 and its two carbamate analogs 5 and 7 with the same (S,S)-stereochemical configuration adopt a nearly identical binding mode while (R,S)-carbamate analog 8 containing a d-leucine forms a less extensive hydrogen bonding network. QM and QM/MM calculations have identified no specific interactions in the GCPII active site that would distinguish ZJ-43 from compounds 5 and 7 and attributed the higher potency of ZJ-43 and compound 7 to the free energy changes associated with the transfer of the ligand from bulk solvent to the protein active site as a result of the lower ligand strain energy and solvation/desolvation energy. Our findings underscore a broader range of factors that need to be taken into account in predicting ligand-protein binding affinity. These insights should be of particular importance in future efforts to design and develop GCPII inhibitors for optimal inhibitory potency.
Collapse
Affiliation(s)
- Cyril Barinka
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic.
| | - Zora Novakova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Niyada Hin
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Daniel Bím
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Dana V Ferraris
- McDaniel College, 2 College Hill, Westminster MD 21157, United States
| | - Bridget Duvall
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Gabriel Kabarriti
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Reiji Tsukamoto
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Milos Budesinsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Lucia Motlova
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Camilo Rojas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States; Department of Molecular and Comparative Pathobiology, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States; Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Tibor András Rokob
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Magyar Tudósok körútja 2, Hungary
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic.
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD 21205, United States; Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, United States.
| |
Collapse
|
48
|
Nguyen HTH, Andrikopoulos PC, Rulíšek L, Shaffer CJ, Tureček F. Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase. J Am Soc Mass Spectrom 2018; 29:1706-1720. [PMID: 29736598 DOI: 10.1007/s13361-018-1980-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/24/2018] [Accepted: 04/24/2018] [Indexed: 06/08/2023]
Abstract
We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H-X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS3) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H)+ complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H-X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Huong T H Nguyen
- Department of Chemistry, Bagley Hall, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Prokopis C Andrikopoulos
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
- Laboratory of Biomolecular Recognition, Institute of Biotechnology, Czech Academy of Sciences, 252 50, Vestec, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10, Prague, Czech Republic
| | - Christopher J Shaffer
- Department of Chemistry, Bagley Hall, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
- Valspar Corporation, Minneapolis, MN, USA
| | - František Tureček
- Department of Chemistry, Bagley Hall, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
| |
Collapse
|
49
|
Řezáč J, Bím D, Gutten O, Rulíšek L. Toward Accurate Conformational Energies of Smaller Peptides and Medium-Sized Macrocycles: MPCONF196 Benchmark Energy Data Set. J Chem Theory Comput 2018; 14:1254-1266. [DOI: 10.1021/acs.jctc.7b01074] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jan Řezáč
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Daniel Bím
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- Gilead Sciences Research Center and The Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| |
Collapse
|
50
|
Andris E, Andrikopoulos PC, Schulz J, Turek J, Růžička A, Roithová J, Rulíšek L. Aurophilic Interactions in [(L)AuCl]...[(L′)AuCl] Dimers: Calibration by Experiment and Theory. J Am Chem Soc 2018; 140:2316-2325. [DOI: 10.1021/jacs.7b12509] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Erik Andris
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-128 43 Prague 2, Czech Republic
| | - Prokopis C. Andrikopoulos
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, CZ-166 10 Prague 6, Czech Republic
| | - Jiří Schulz
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-128 43 Prague 2, Czech Republic
| | - Jan Turek
- Department
of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic
| | - Aleš Růžička
- Department
of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, CZ-532 10 Pardubice, Czech Republic
| | - Jana Roithová
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, CZ-128 43 Prague 2, Czech Republic
| | - Lubomír Rulíšek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, CZ-166 10 Prague 6, Czech Republic
| |
Collapse
|