Co-reporter:Weici Xu; Marcus Arieno; Henrik Löw; Kaifang Huang; Xiulan Xie; Thomas Cruchter; Qiao Ma; Jianwei Xi; Biao Huang; Olaf Wiest; Lei Gong;Eric Meggers
Journal of the American Chemical Society 2016 Volume 138(Issue 28) pp:8774-8780
Publication Date(Web):June 23, 2016
DOI:10.1021/jacs.6b02769
Based on a metal-templated approach using a rigid and globular structural scaffold in the form of a bis-cyclometalated octahedral iridium complex, an exceptionally active hydrogen-bond-mediated asymmetric catalyst was developed and its mode of action investigated by crystallography, NMR, computation, kinetic experiments, comparison with a rhodium congener, and reactions in the presence of competing H-bond donors and acceptors. Relying exclusively on weak forces, the enantioselective conjugate reduction of nitroalkenes can be executed at catalyst loadings as low as 0.004 mol% (40 ppm), representing turnover numbers of up to 20 250. A rate acceleration by the catalyst of 2.5 × 105 was determined. The origin of the catalysis is traced to an effective stabilization of developing charges in the transition state by carefully orchestrated hydrogen-bonding and van der Waals interactions between catalyst and substrates. This study demonstrates that the proficiency of asymmetric catalysis merely driven by hydrogen-bonding and van der Waals interactions can rival traditional activation through direct transition metal coordination of the substrate.
Co-reporter:Eric Hansen, Elaine Limé, Per-Ola Norrby, and Olaf Wiest
The Journal of Physical Chemistry A 2016 Volume 120(Issue 20) pp:3677-3682
Publication Date(Web):May 2, 2016
DOI:10.1021/acs.jpca.6b02757
Sulfamides, together with their simpler sulfonamide analogs, are common functional groups in a significant number of biologically active compounds. This is partly due to their unique electronic structure and conformational behavior, which mimics the tetrahedral intermediate involved in many proteases, esterases, and related enzymes. Here, the origin of these unique structural elements are analyzed in the context of a coupled, double anomeric effect using DFT calculations, including conformational scans, and NBO analysis. It is shown that these coupled interactions can be implicitly parametrized in MM3* type force fields using the quantum-guided molecular mechanics (Q2MM) method, yielding accurate force field parameters for molecular mechanics studies of sulfamides and sulfonamides.
Co-reporter:Liping Xu, Xin Zhang, Matthew S. McCammant, Matthew S. Sigman, Yun-Dong Wu, and Olaf Wiest
The Journal of Organic Chemistry 2016 Volume 81(Issue 17) pp:7604-7611
Publication Date(Web):August 3, 2016
DOI:10.1021/acs.joc.6b01317
The three-component coupling of isoprene, an alkenyl triflate, and styrenylboronic acid catalyzed by a palladium pyrox complex affords access to skipped dienes from simple chemical feedstocks. Unfortunately, the transformation proceeds with only moderate selectivity and yields. The reaction mechanism and factors responsible for the resulting regioselectivity were elucidated using M06/SDD/6-311++G(d,p) + SMD calculations. Distortion of the palladium coordination sphere in the transition structure of the migratory insertion step is found to control the 4,1- vs 1,x-selectivity. The calculated ΔΔG⧧ of 1.0 kcal/mol for this step is in excellent agreement with the experimentally observed selectivity of 1:9.9 disfavoring the 4,1-product. The transmetalation was found to be the regioselectivity determining step for the formation of the 1,2- vs 1,4-addition products. Systematic conformational searches for the transmetalation transition structure revealed a series of steric interactions between the t-Bu substituent on the ligand and the substrates in the model system that are balanced by additional repulsive interactions between the substrates and the pyridyl portion of the ligand. The combination of these effects leads to the low to moderate 1,2- vs 1,4-selectivity in the experimentally studied system.
Co-reporter:Kai Chen ; Xiaoxiao Zhang ; Yun-Dong Wu
Journal of the American Chemical Society 2014 Volume 136(Issue 33) pp:11636-11643
Publication Date(Web):July 25, 2014
DOI:10.1021/ja501548p
Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure–activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.
Co-reporter:Liping Xu ; Margaret J. Hilton ; Xinhao Zhang ; Per-Ola Norrby ; Yun-Dong Wu ; Matthew S. Sigman
Journal of the American Chemical Society 2014 Volume 136(Issue 5) pp:1960-1967
Publication Date(Web):January 11, 2014
DOI:10.1021/ja4109616
The enantioselective Pd-catalyzed redox-relay Heck arylation of acyclic alkenyl alcohols allows access to various useful chiral building blocks from simple olefinic substrates. Mechanistically, after the initial migratory insertion, a succession of β-hydride elimination and migratory insertion steps yields a saturated carbonyl product instead of the more general Heck product, an unsaturated alcohol. Here, we investigate the reaction mechanism, including the relay function, yielding the final carbonyl group transformation. M06 calculations predict a ΔΔG⧧ of 1 kcal/mol for the site selectivity and 2.5 kcal/mol for the enantioselectivity, in quantitative agreement with experimental results. The site selectivity is controlled by a remote electronic effect, where the developing polarization of the alkene in the migratory insertion transition state is stabilized by the C–O dipole of the alcohol moiety. The enantioselectivity is controlled by steric repulsion between the oxazoline substituent and the alcohol-bearing alkene substituent. The relay efficiency is due to an unusually smooth potential energy surface without high barriers, where the hydroxyalkyl-palladium species acts as a thermodynamic sink, driving the reaction toward the carbonyl product. Computational predictions of the relative reactivity and selectivity of the double bond isomers are validated experimentally.
Co-reporter:Brandon E. Haines and Olaf Wiest
The Journal of Organic Chemistry 2014 Volume 79(Issue 6) pp:2771-2774
Publication Date(Web):February 24, 2014
DOI:10.1021/jo500222d
The SET-induced biaryl cross-coupling reaction is established as the first example of a Grignard SRN1 reaction. The reaction is examined within the mechanistic framework of dissociative electron transfer in the presence of a Lewis acid. DFT calculations show that the reaction proceeds through a radical intermediate in the form of an Mg ion-radical cage, which eludes detection in trapping experiments by reacting quickly to form an MgPh2 radical anion intermediate. A new mechanism is proposed.
Co-reporter:Brandon E. Haines, Olaf Wiest, and Cynthia V. Stauffacher
Accounts of Chemical Research 2013 Volume 46(Issue 11) pp:2416
Publication Date(Web):July 30, 2013
DOI:10.1021/ar3003267
HMG-CoA reductase (HMGR) is the target of statins, cholesterol-lowering drugs prescribed to millions of patients worldwide. More recent research indicates that HMGR could be a useful target in the development of antimicrobial agents. Over the last seven decades, researchers have proposed a series of increasingly complex reaction mechanisms for this biomedically important enzyme.The maturation of the mechanistic proposals for HMGR have paralleled advances in a diverse set of research areas, such as molecular biology and computational chemistry. Thus, the development of the HMGR mechanism provides a useful case study for following the advances in state-of-the-art methods in enzyme mechanism research. Similarly, the questions raised by these mechanism proposals reflect the limitations of the methods used to develop them.The mechanism of HMGR, a four-electron oxidoreductase, is unique and far more complex than originally thought. The reaction contains multiple chemical steps, coupled to large-scale domain motions of the homodimeric enzyme. The first proposals for the HMGR mechanism were based on kinetic and labeling experiments, drawing analogies to the mechanism of known dehydrogenases. Advances in molecular biology and bioinformatics enabled researchers to use site-directed mutagenesis experiments and protein sequencing to identify catalytically important glutamate, aspartate, and histidine residues. These studies, in turn, have generated new and more complicated mechanistic proposals.With the development of protein crystallography, researchers solved HMGR crystal structures to reveal an unexpected lysine residue at the center of the active site. The many crystal structures of HMGR led to increasingly complex mechanistic proposals, but the inherent limitations of the protein crystallography left a number of questions unresolved. For example, the protonation state of the glutamate residue within the active site cannot be clearly determined from the crystal structure. The differing protonation state of this residue leads to different proposed mechanisms for the enzyme.As computational analysis of large biomolecules has become more feasible, the application of methods such as hybrid quantum mechanics/molecular mechanics (QM/MM) calculations to the HMGR mechanism have led to the most detailed mechanistic proposal yet. As these methodologies continue to improve, they prove to be very powerful for the study of enzyme mechanisms in conjunction with protein crystallography. Nevertheless, even the most current mechanistic proposal for HMGR remains incomplete due to limitations of the current computational methodologies. Thus, HMGR serves as a model for how the combination of increasingly sophisticated experimental and computational methods can elucidate very complex enzyme mechanisms.
Co-reporter:Guillermina Estiu, Nazir Khatri, and Olaf Wiest
Biochemistry 2013 Volume 52(Issue 39) pp:
Publication Date(Web):September 3, 2013
DOI:10.1021/bi4005478
The transport of cholesterol from NPC2 to NPC1 is essential for the maintenance of cholesterol homeostasis in late endosomes. On the basis of a rigid docking model of the crystal structures of the N-terminal cholesterol binding domain of NPC1(NTD) and the soluble NPC2 protein, models of the NPC1(NTD)-NPC2-cholesterol complexes at the beginning and the end of the transport as well as the unligated NPC1(NTD)-NPC2 complex were studied using 86 ns MD simulations. Significant differences in the cholesterol binding mode and the overall structure of the two proteins compared to the crystal structures of the cholesterol binding separate units were obtained. Relevant residues for the binding are identified using MM/GBSA calculations and the influence of the mutations analyzed by modeling them in silico, rationalizing the results of previous mutagenesis experiments. From the calculated energies and the NEB (nudged elastic band) evaluation of the cholesterol transfer mechanism, an atomistic model is proposed of the transfer of cholesterol from NPC2 to NPC1(NTD) through the formation of an intermediate NPC1(NTD)-NPC2 complex.
Co-reporter:Kai Chen, Liping Xu, and Olaf Wiest
The Journal of Organic Chemistry 2013 Volume 78(Issue 10) pp:5051-5055
Publication Date(Web):April 15, 2013
DOI:10.1021/jo400406g
Histone deacetylases (HDACs) have emerged as important drug targets in epigenetics. The most common HDAC inhibitors use hydroxamic acids as zinc binding groups despite unfavorable pharmacokinetic properties. A two-stage protocol of M05-2X calculations of a library of 48 fragments in a small model active site, followed by QM/MM hybrid calculations of the full enzyme with selected binders, is used to prospectively select potential bidentate zinc binders. The energetics and interaction patterns of several zinc binders not previously used for the inhibition of HDACs are discussed.
Co-reporter:Gui-Juan Cheng;Li-Juan Song;Dr. Yun-Fang Yang;Dr. Xinhao Zhang;Dr. Olaf Wiest;Dr. Yun-Dong Wu
ChemPlusChem 2013 Volume 78( Issue 9) pp:943-951
Publication Date(Web):
DOI:10.1002/cplu.201300117
Abstract
A detailed computational study of a copper-catalyzed aerobic cross-dehydrogenative coupling reaction has been conducted. To select a reliable method to describe the thermochemistry of a single electron transfer (SET) process, benchmark calculations have been performed. M06/6-311+g(d,p) is appropriate to evaluate the thermochemistry of the SET process for the system involving iminium species. The computational results support an SET mechanism, but also uncover an alternative mechanism in which O2 is directly involved in a hydrogen-abstracting step. A comparative study with tert-butylhydroperoxide (TBHP) as the oxidant has also been performed. The computations reveal several competitive pathways, including a radical pathway, a CuIII pathway, and an SET mechanism for the Cu/TBHP system.
Co-reporter:Joshua M. Lee ; Paul Helquist
Journal of the American Chemical Society 2012 Volume 134(Issue 36) pp:14973-14981
Publication Date(Web):August 14, 2012
DOI:10.1021/ja3052975
The basis for diastereoselectivity in Lewis-acid-catalyzed Mukaiyama aldol reactions was studied using density functional theory. By exploring the conformations of the transition structures for the diastereodifferentiating step of seven different reactions, simple models were generated. The effects of varying the substituents on the enol carbon and the α-carbon of the silyl enol ether from methyl to tert-butyl groups and the substituent on the aldehyde from methyl to phenyl groups were investigated by comparison of the transition structures for different reactions. Expanding on the previous qualitative models by Heathcock and Denmark, we found that while the pro-anti pathways take place via antiperiplanar transition structures, the pro-syn pathways prefer synclinal transition structures. The relative steric effects of the Lewis acid and trimethyl silyl groups and the influence of E/Z isomerism on the aldol transition state were investigated. By calculating 36 transition structures at the M06/6-311G*//B3LYP/6-31G* level of theory and employing the IEFPCM polarizable continuum model for solvation effects, this study expands the mechanistic knowledge and provides a model for understanding the diastereoselectivity in Lewis-acid-catalyzed Mukaiyama aldol reactions.
Co-reporter:Qian Peng, Jeffrey W. Pavlik, W. Robert Scheidt, and Olaf Wiest
Journal of Chemical Theory and Computation 2012 Volume 8(Issue 1) pp:214-223
Publication Date(Web):November 29, 2011
DOI:10.1021/ct2006456
Nuclear resonance vibrational spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP2– = octaethylporphyrinatio dianion) was performed. A test set of 21 methodology combinations including eight functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86, and ωB97X-D) and five basis set (VTZ, TZVP, and Lanl2DZ for iron and 6-31G* and 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e2), which can be used to simulate the vibrational density of states (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-of-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.
Co-reporter:Brandon E. Haines, C. Nicklaus Steussy, Cynthia V. Stauffacher, and Olaf Wiest
Biochemistry 2012 Volume 51(Issue 40) pp:
Publication Date(Web):September 12, 2012
DOI:10.1021/bi3008593
HMG-CoA reductase catalyzes the four-electron reduction of HMG-CoA to mevalonate and is an enzyme of considerable biomedical relevance because of the impact of its statin inhibitors on public health. Although the reaction has been studied extensively using X-ray crystallography, there are surprisingly no computational studies that test the mechanistic hypotheses suggested for this complex reaction. Theozyme and quantum mechanical (QM)/molecular mechanical (MM) calculations up to the B3LYP/6-31g(d,p)//B3LYP/6-311++g(2d,2p) level of theory were employed to generate an atomistic description of the enzymatic reaction process and its energy profile. The models generated here predict that the catalytically important Glu83 is protonated prior to hydride transfer and that it acts as the general acid or base in the reaction. With Glu83 protonated, the activation energies calculated for the sequential hydride transfer reactions, 21.8 and 19.3 kcal/mol, are in qualitative agreement with the experimentally determined rate constant for the entire reaction (1 s–1 to 1 min–1). When Glu83 is not protonated, the first hydride transfer reaction is predicted to be disfavored by >20 kcal/mol, and the activation energy is predicted to be higher by >10 kcal/mol. While not involved in the reaction as an acid or base, Lys267 is critical for stabilization of the transition state in forming an oxyanion hole with the protonated Glu83. Molecular dynamics simulations and MM/Poisson–Boltzmann surface area free energy calculations predict that the enzyme active site stabilizes the hemithioacetal intermediate better than the aldehyde intermediate. This suggests a mechanism in which cofactor exchange occurs before the breakdown of the hemithioacetal. Slowing the conversion to aldehyde would provide the enzyme with a mechanism to protect it from solvent and explain why the free aldehyde is not observed experimentally. Our results support the hypothesis that the pKa of an active site acidic group is modulated by the redox state of the cofactor. The oxidized cofactor and deprotonated Glu83 are closer in space after hydride transfer, indicating that indeed the cofactor may influence the pKa of Glu83 through an electrostatic interaction. The enzyme is able to catalyze the transfer of a hydride to the structurally and electronically distinct substrates by maintaining the general shape of the active site and adjusting the electrostatic environment through acid–base chemistry. Our results are in good agreement with the well-studied hydride transfer reactions catalyzed by liver alcohol dehydrogenase in calculated energy profile and reaction geometries despite different mechanistic functionalities.
Co-reporter:Pauline Bourbon, Qian Peng, Guillermo Ferraudi, Cynthia Stauffacher, Olaf Wiest, and Paul Helquist
The Journal of Organic Chemistry 2012 Volume 77(Issue 6) pp:2756-2762
Publication Date(Web):February 23, 2012
DOI:10.1021/jo2025527
The syntheses and photophysical/photochemical properties of two amide-tethered coumarin-labeled nicotinamides are described. Photochemical studies of 6-bromo-7-hydroxycoumarin-4-ylmethylnicotinamide (BHC-nicotinamide) revealed an unexpected solvent effect. This result is rationalized by computational studies of the different protonation states using TD-DFT with the M06L/6-311+G** method with implicit and explicit solvation models. Molecular orbital energies responsible for the λmax excitation show that the functionalization of the coumarin ring results in a strong red-shift from 330 to 370 nm when the pH of solution is increased from 3.06 to 8.07. From this MO analysis, a model for solvent interactions has been proposed. The BHC-nicotinamide proved to be photochemically stable, which is also interpreted in terms of NBO calculations. The results provide a set of principles for the rational design of either photostable labeling reagents or photolabile cage compounds.
Co-reporter:Chun-Shan Zuo;Yun-Dong Wu
Journal of Physical Organic Chemistry 2011 Volume 24( Issue 12) pp:1157-1165
Publication Date(Web):
DOI:10.1002/poc.1840
Abstract
The structures and conformational energies of twelve MeN-, O-, S-, MeP-, CO-bridged homocalix[4]arenes and two kinds of O-bridged alternate hybrid-calix[4]arenes have been calculated at the B3LYP/6-31G* level of theory. The 1,3-alternate or twisted-1,3-alternate conformations are found to be the lowest energy structures in all cases except for MeP-bridged calix[4]pyridine and calix[4]benzene, for which the twist-pinched cone and partial cone are the most stable conformations, respectively. The conformational energy differences calculated between the lowest energy and the next conformation are on the order of 2.0–3.0 kcal/mol, but smaller for the S- and MeP-bridged compounds. Analysis of the structures and relative energies shows that the phenyl hydrogens have electrostatic attractions with the lone pairs of the heteroatoms and steric repulsions with the methyl groups on bridgehead groups. Conversely, the lone electron pair in the pyridyl compounds engage in a repulsive electrostatic interaction. The interactions of 1,3-aromatic rings play a minor but important role in the relative stability sequence. This detailed understanding of the factors governing the conformational space of hetero calixarences can be used to design conformationally biased analogs of these interesting compounds. Copyright © 2011 John Wiley & Sons, Ltd.
Co-reporter:Andrew T. Johnson, Mark K. Schlegel, Eric Meggers, Lars-Oliver Essen, and Olaf Wiest
The Journal of Organic Chemistry 2011 Volume 76(Issue 19) pp:7964-7974
Publication Date(Web):August 12, 2011
DOI:10.1021/jo201469b
Glycol nucleic acid (GNA), with a nucleotide backbone comprising of just three carbons and the stereocenter derived from propylene glycol (1,2-propanediol), is a structural analog of nucleic acids with intriguing biophysical properties, such as formation of highly stable antiparallel duplexes with high Watson–Crick base pairing fidelity. Previous crystallographic studies of double stranded GNA (dsGNA) indicated two forms of backbone conformations, an elongated M-type (containing metallo-base pairs) and the condensed N-type (containing brominated base pairs). A herein presented new crystal structure of a GNA duplex at 1.8 Å resolution from self-complementary 3′-CTCBrUAGAG-2′ GNA oligonucleotides reveals an N-type conformation with alternating gauche–anti torsions along its (O3′–C3′–C2′–O2′) backbone. To elucidate the conformational state of dsGNA in solution, molecular dynamic simulations over a period of 20 ns were performed with the now available repertoire of structural information. Interestingly, dsGNA adopts conformational states in solution intermediate between experimentally observed backbone conformations: simulated dsGNA shows the all-gauche conformation characteristic of M-type GNA with the higher helical twist common to N-type GNA structures. The so far counterintuitive, smaller loss of entropy upon duplex formation as compared to DNA can be traced back to the conformational flexibility inherent to dsGNA but missing in dsDNA. Besides extensive interstrand base stacking and conformational preorganization of single strands, this flexibility contributes to the extraordinary thermal stability of GNA.
Co-reporter:Guillermina Estiu, Nathan West, Ralph Mazitschek, Edward Greenberg, James E. Bradner, Olaf Wiest
Bioorganic & Medicinal Chemistry 2010 Volume 18(Issue 11) pp:4103-4110
Publication Date(Web):1 June 2010
DOI:10.1016/j.bmc.2010.03.080
Histone deacetylases are key regulators of gene expression and have recently emerged as important therapeutic targets for cancer and a growing number of non-malignant diseases. Many widely studied inhibitors of HDACs such as SAHA are thought to have low selectivity within or between the human HDAC isoform classes. Using an isoform-selective assay, we have shown that a number of the known inhibitors have in fact a low activity against HDAC8. Based on the wealth of structural information available for human HDAC8, we use a combination of docking and molecular dynamics simulations to determine the structural origin of the experimental results. A close relationship is found between the activity and the high surface malleability of HDAC8. These results provide a rationale for the recently described ‘linkerless’ HDAC8 selective inhibitors and design criteria for HDAC8 selective inhibitors.
Co-reporter:S.T. Henriksen, J. Liu, G. Estiu, Z.N. Oltvai, O. Wiest
Bioorganic & Medicinal Chemistry 2010 Volume 18(Issue 14) pp:5148-5156
Publication Date(Web):15 July 2010
DOI:10.1016/j.bmc.2010.05.060
The rapid spread on multidrug-resistant strains of Staphylococcus aureus requires not just novel treatment options, but the development of faster methods for the identification of new hits for drug development. The exponentially increasing speed of computational methods makes a more extensive use in the early stages of drug discovery attractive if sufficient accuracy can be achieved. Computational target identification using systems-level methods suggested the histidine biosynthesis pathway as an attractive target against S. aureus. Potential inhibitors for the pathway were identified through docking, followed by ensemble rescoring, that is sufficiently accurate to justify immediate testing of the identified compounds by whole-cell assays, avoiding the need for time-consuming and often difficult intermediary enzyme assays. This novel strategy is demonstrated for three key enzymes of the S. aureus histidine biosynthesis pathway, which is predicted to be essential for bacterial biomass productions. Virtual screening of a library of ∼106 compounds identified 49 potential inhibitors of three enzymes of this pathway. Eighteen representative compounds were directly tested on three S. aureus- and two Escherichia coli strains in standard disk inhibition assays. Thirteen compounds are inhibitors of some or all of the S. aureus strains, while 14 compounds weakly inhibit growth in one or both E. coli strains. The high hit rate obtained from a fast virtual screen demonstrates the applicability of this novel strategy to the histidine biosynthesis pathway.
Co-reporter:Y. Shen;J. Liu;G. Estiu;B. Isin;Y-Y. Ahn;D-S. Lee;A-L. Barabási;V. Kapatral;O. Wiest;Z. N. Oltvai
PNAS 2010 Volume 107 (Issue 3 ) pp:1082-1087
Publication Date(Web):2010-01-19
DOI:10.1073/pnas.0909181107
Advances in genome analysis, network biology, and computational chemistry have the potential to revolutionize drug discovery
by combining system-level identification of drug targets with the atomistic modeling of small molecules capable of modulating
their activity. To demonstrate the effectiveness of such a discovery pipeline, we deduced common antibiotic targets in Escherichia coli and Staphylococcus aureus by identifying shared tissue-specific or uniformly essential metabolic reactions in their metabolic networks. We then predicted
through virtual screening dozens of potential inhibitors for several enzymes of these reactions and showed experimentally
that a subset of these inhibited both enzyme activities in vitro and bacterial cell viability. This blueprint is applicable
for any sequenced organism with high-quality metabolic reconstruction and suggests a general strategy for strain-specific
antiinfective therapy.
Co-reporter:Vincenzo Verdolino, Aaron Forbes, Paul Helquist, Per-Ola Norrby, Olaf Wiest
Journal of Molecular Catalysis A: Chemical 2010 324(1–2) pp: 9-14
Publication Date(Web):
DOI:10.1016/j.molcata.2010.02.026
Co-reporter:Yu Lan, Lujiang Deng, Jing Liu, Can Wang, Olaf Wiest, Zhen Yang and Yun-Dong Wu
The Journal of Organic Chemistry 2009 Volume 74(Issue 14) pp:5049-5058
Publication Date(Web):May 26, 2009
DOI:10.1021/jo900919v
Density functional theory calculations and experimental studies have been carried out on the intramolecular Pauson−Khand-Type reaction mediated by a PdCl2-thiourea catalyst, which proceeds under mild reaction conditions and provides a useful alternative to traditional Pauson−Khand reactions. The classical mechanism of the Pauson−Khand reaction involving the alkyne/alkene C−C bond formation as the key step has been found to be energetically unfavorable and is not in line with the experimental observations. A novel reaction mechanism has been proposed for the reaction. The first step involves the cis-halometalation of the alkyne, followed by sequential alkene and carbonyl insertion. The rate-determining fourth step is an intramolecular C−Cl oxidative addition, leading to a PdIV intermediate. A C−C bond formation by reductive elimination completes the reaction. The mechanism is in agreement with the key experimental observations including (1) the need of a chloride for catalytic activity and the absence of catalysis with Pd(OAc)2 alone; (2) the rate acceleration by the addition of LiCl; both with PdCl2 and Pd(OAc)2 catalysts; and (3) the preferred formation of the trans diastereomer in substituted cases. The cis halometalation and the formation and stability of the PdIV intermediate is studied in detail and provides general insights into these novel steps.
Co-reporter:Guillermina Estiu ; Edward Greenberg ; Christopher B. Harrison ; Nicholas P. Kwiatkowski ; Ralph Mazitschek ; James E. Bradner
Journal of Medicinal Chemistry 2008 Volume 51(Issue 10) pp:2898-2906
Publication Date(Web):April 16, 2008
DOI:10.1021/jm7015254
The development of class- and isoform-selective histone deacetylase (HDAC) inhibitors is highly desirable for the study of the complex interactions of these proteins central to transcription regulation as well as for the development of selective HDAC inhibitors as drugs in epigenetics. To provide a structural basis for the rational design of such inhibitors, a combined computational and experimental study of inhibition of three different histone deacetylase isoforms, HDAC1, -6, and -8, with three different hydroxamate inhibitors is reported. While SAHA was found to be unselective for the inhibition of class I and class II HDACs, the other inhibitors were found to be selective toward class II HDACs. Molecular dynamics simulations indicate that this selectivity is caused by both the overall shape of the protein surface leading to the active site and specific interactions of an aspartate residue in a polar loop and two phenylalanines and a methionine in a nonpolar loop. Monitoring the specific interactions as a function of the simulation time identifies a key sulfur−π interaction. The implications of the structural motifs for the design of class II-selective HDAC inhibitors are discussed.
Co-reporter:Patrick J. Donoghue, Paul Helquist, Per-Ola Norrby and Olaf Wiest
Journal of Chemical Theory and Computation 2008 Volume 4(Issue 8) pp:1313-1323
Publication Date(Web):July 26, 2008
DOI:10.1021/ct800132a
The rhodium catalyzed asymmetric hydrogenation of enamides to generate amino acid products and derivatives is a widely used method to generate unnatural amino acids. The choice of a chiral ligand is of utmost importance in this reaction and is often based on high throughput screening or simply trial and error. A virtual screening method can greatly increase the speed of the ligand screening process by calculating expected enantiomeric excesses from relative energies of diastereomeric transition states. Utilizing the Q2MM method, new molecular mechanics parameters are derived to model the hydride transfer transition state in the reaction. The new parameters were based off of structures calculated at the B3LYP/LACVP** level of theory and added to the MM3* force field. The new parameters were validated against a test set of experimental data utilizing a wide range of bis-phosphine ligands. The computational model agreed with experimental data well overall, with an unsigned mean error of 0.6 kcal/mol against a set of 18 data points from experiment. The major errors in the computational model were due either to large energetic errors at high e.e., still resulting in qualitative agreement, or cases where large steric interactions prevent the reaction from proceeding as expected.
Co-reporter:Lauren L. O'Neil and Olaf Wiest
Organic & Biomolecular Chemistry 2008 vol. 6(Issue 3) pp:485-492
Publication Date(Web):13 Dec 2007
DOI:10.1039/B713318A
Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may be considerably lower. Using a selective, non-covalent assay for base flipping, the sequence dependence of base flipping in DNA sequences containing an abasic site has been studied. The dissociation constants of the zinc–cyclen complex to small molecules and single strands of DNA as well as the equilibrium constants for base flipping have been determined for these sequences. Molecular dynamics simulations of the zinc-cyclen complex bound to both single- and double-stranded DNA have been performed in an attempt to rationalize the differences in the dissociation constants obtained for the two systems. The results are compared to previous studies of base flipping in DNA containing an abasic site.
Co-reporter:Patrick J. Donoghue;Elsa Kieken;Paul Helquist
Advanced Synthesis & Catalysis 2007 Volume 349(Issue 17-18) pp:
Publication Date(Web):21 NOV 2007
DOI:10.1002/adsc.200700374
The intramolecular hydroamination of carbon-carbon π-bonds is an effective method for the rapid construction of nitrogen heterocycles. The rapid evaluation of suitable ligands using virtual screening will aid in the development of a stereoselective analogue of the reaction by predicting effective substrate/ligand combinations. Electronic structure calculations of the relevant transition structures for different nucleophiles and alkynes at the B3LYP/LACVP* level of theory are presented. They provide the basis for the development of a transition state force field by the Q2MM method, which is discussed in detail. The parameter development and performance for the transition state force field is presented.
Co-reporter:Patrick J. Donoghue Dr.
Chemistry - A European Journal 2006 Volume 12(Issue 27) pp:
Publication Date(Web):28 JUL 2006
DOI:10.1002/chem.200600554
Electron transfer is the simplest reaction possible, yet it has a profound impact on the structure and reactivity of organic compounds. These changes allow a new look at some of the fundamental concepts that are used to explain organic chemistry, such as symmetry, aromaticity, and bonding. The results from high-level electronic structure calculations are used to analyze the mechanistic differences in the pericyclic reactions of simple hydrocarbons and their radical cation counterparts. The importance of state symmetry correlation, Jahn–Teller distortions, delocalization, and fractional bonding for the reaction pathways of hydrocarbon radical cations is discussed.
Co-reporter:Adam P.R Zabell, Steven Corden, Paul Helquist, Cynthia V Stauffacher, Olaf Wiest
Bioorganic & Medicinal Chemistry 2004 Volume 12(Issue 8) pp:1867-1880
Publication Date(Web):15 April 2004
DOI:10.1016/j.bmc.2004.01.042
The human low molecular weight protein tyrosine phosphatase (HCPTP) is ubiquitously expressed as two isoforms in a wide range of human cells and may be involved in regulating the metastatic nature of epithelial tumors. A homology model is presented for the HCPTP-B isoform based on known X-ray crystal structures of other low molecular weight PTPs. A comparison of the two isoform structures indicates the possibility of developing isoform-specific inhibitors of HCPTP. Molecular dynamics simulations with CHARMM have been used to study the binding modes of the known adenine effector and phosphate in the active site of both isoforms. This analysis led to the design of the initial lead compound, based on an azaindole ring moiety, which was then also evaluated computationally. A comparison of these simulations indicates the need for a phosphonate group on the indole and provides insight into inhibitor binding modes. Compounds with varying degrees of structural similarity to the azaindole have been synthesized and tested for inhibition with each isoform. These molecular systems were examined with the program AutoDock, and comparisons made with the kinetics and the explicit simulations to validate AutoDock as a screening tool for potential inhibitors. Two compounds were experimentally found to have sub-millimolar inhibition, but the greater solubility of one reinforces the need for experimental testing alongside computational analysis.Graphic
Co-reporter:Di-Fei Wang, Olaf Wiest, Paul Helquist, Hsuan-Yin Lan-Hargest, Norbert L. Wiech
Bioorganic & Medicinal Chemistry Letters 2004 Volume 14(Issue 3) pp:707-711
Publication Date(Web):9 February 2004
DOI:10.1016/j.bmcl.2003.11.062
Quantitative structure–activity relationships (QSAR) for a series of new trichostatin A (TSA)-like hydroxamic acids for the inhibition of cell proliferation of the PC-3 cell line have been developed using molecular descriptors from Qikprop and electronic structure calculations. The best regression model shows that the PM3 atomic charge on the carbonyl carbon in the CONHOH moiety(Qco), globularity (Glob), and the hydrophilic component of the solvent-accessible surface area (FISA) describe the IC50 of 19 inhibitors of the PC-3 cell line with activities ranging over five orders of magnitude with an R2=0.92 and F=59.2. This information will be helpful in the further design of novel anticancer drugs for treatment of prostate cancer and other diseases affected by HDAC inhibition.Quantitative structure–activity relationships (QSAR) for a series of new trichostatin A (TSA)-like hydroxamic acids for the inhibition of PC3 cell proliferation line have been developed.
Co-reporter:A Jayne Oliver, Olaf Wiest, Paul Helquist, Marvin J Miller, Martin Tenniswood
Bioorganic & Medicinal Chemistry 2003 Volume 11(Issue 20) pp:4455-4461
Publication Date(Web):October 2003
DOI:10.1016/S0968-0896(03)00427-9
Prostate specific membrane antigen (PSMA) is a 110 kDa type II transmembrane protein that is expressed exclusively by prostate tumor cells and as such is a clear cellular target in the development of a new method for fast and reliable diagnosis of prostate cancer. PSMA is highly homologous to the neuropeptidase NAALADase, and it has been shown that inhibitors of NAALADase also strongly bind to PSMA. In an effort to better understand the structural basis of the inhibitory activity of more than 60 NAALADase inhibitors synthesized and tested by our group, we used Monte Carlo calculations employing the Merck Molecular Force Field to explore the conformational space available to a set of PSMA inhibitors. Conformational analysis indicated that the lower the number of unique conformations accessible by an inhibitor, the greater the biological activity displayed by the compound against LnCAP cells. This suggests that the difference in activity is largely entropy based. The key conformations associated with high activity are used to develop a simple pharmacophore model that led to the design of new, conformationally restricted analogues with potentially high activity in rational drug design.Graphic
Co-reporter:Jonas Oxgaard
European Journal of Organic Chemistry 2003 Volume 2003(Issue 8) pp:
Publication Date(Web):27 MAR 2003
DOI:10.1002/ejoc.200390204
The effect of substituents on the rearrangement of vinylcyclopropane radical cation to cyclopentene was explored by density functional theory. Correlations have been established between the activation energy of the system and the nature, as well as the position, of the substituents. It was found that radical- or cation-stabilizing substituents in select positions reduce the activation energy for the rearrangement substantially, while activation energies for competing hydrogen shifts were largely left unchanged. We have identified positions in the vinylcyclopropane where substitution is necessary, and others that can be substituted less discriminately. The mechanism of the rearrangement changes from stepwise to concerted when a strongly cation-stabilizing substituent is used, because the first step in the stepwise reaction becomes a barrierless ring opening of a strained cyclopropane. Steric effects were also explored and have been found to be of crucial importance for the success of a rearrangement. Finally, a simple set of rules has been devised to predict the outcome of oxidation of a vinylcyclopropane without requiring detailed mechanistic investigations. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Co-reporter:Julie Peller Dr. ;Prashant V. Kamat Dr.
Chemistry - A European Journal 2003 Volume 9(Issue 21) pp:
Publication Date(Web):3 NOV 2003
DOI:10.1002/chem.200204469
Oxidative transformations by the hydroxyl radical are significant in advanced oxidation processes for the breakdown of organic pollutants, yet mechanistic details of the reactions are lacking. A combination of experimental and computational methods has been employed in this study to elucidate the reactivity of the hydroxyl radical with the widely used herbicide 2,4-D (2,4-dichlorophenoxyacetic acid). The experimental data on the reactivity of the hydroxyl radical in the degradation of the herbicide 2,4-D were obtained from γ-radiolysis experiments with both 18O-labeled and unlabeled water. These were complemented by computational studies of the .OH attack on 2,4-D and 2,4-DCP (2,4-dichlorophenol) in the gas phase and in solution. These studies firmly established the kinetically controlled attack ipso to the ether functionality as the main reaction pathway of .OH and 2,4-D, followed by homolytic elimination of the ether side chain. In addition, the majority of the early intermediates in the reaction between the hydroxyl radical and 2,4-DCP, the major intermediate, were identified experimentally. While the hydroxyl radical attacks 2,4-D by .OH-addition/elimination on the aromatic ring, the oxidative breakdown of 2,4-DCP occurs through .OH addition followed by either elimination of chlorine or formation of the ensuing dichlorophenoxyl radical.
Co-reporter:Jaouad El-Bahraoui Dr. Dr.;Derek Feichtinger Dr.;Dietmar A. Plattner Dr.
Angewandte Chemie 2001 Volume 113(Issue 11) pp:
Publication Date(Web):28 MAY 2001
DOI:10.1002/1521-3757(20010601)113:11<2131::AID-ANGE2131>3.0.CO;2-N
Warum ist sie so selektiv, die asymmetrische Jacobsen-Katsuki-Epoxidierung? Dichtefunktionalrechnungen brachten hier neue Erkenntnisse: Axiale Koordination am Metallzentrum erhöht nicht nur die Reaktionsgeschwindigkeit, sondern führt überdies zu hochgradig nichtplanaren Konformationen des aktiven Katalysators (siehe Strukturbild).
Co-reporter:Katrin Schroeter Dipl.-Chem.;Detlef Schröder Dr.;Helmut Schwarz Dr. Dr. h. c. mult.;G. Devi Reddy Dr. Dr.;Claudio Carra Dipl.-Chem.;Thomas Bally Dr.
Chemistry - A European Journal 2000 Volume 6(Issue 23) pp:
Publication Date(Web):10 NOV 2000
DOI:10.1002/1521-3765(20001201)6:23<4422::AID-CHEM4422>3.0.CO;2-V
The ion chemistry of anti-o,o′-dibenzene (1) was examined in the gaseous and the condensed phase. From a series of comparative ion cyclotron resonance (ICR) mass spectrometry experiments which involved the interaction of Cu+ with 1, benzene, or mixtures of both, it was demonstrated that 1 can be brought into the gas phase as an intact molecule under the experimental conditions employed. The molecular ions, formally 1.+ and 1.−, were investigated with a four-sector mass spectrometer in metastable-ion decay, collisional activation, charge reversal, and neutralization–reionization experiments. Surprisingly, the expected retrocyclization to yield two benzene molecules was not dominant for the long-lived molecular ions; however, other fragmentations, such as methyl and hydrogen losses, prevailed. In contrast, matrix ionization of 1 in freon (77 K) by γ-radiation or in argon (12 K) by X-irradiation leads to quantitative retrocyclization to the cationic dimer of benzene, 2.+. Theoretical modeling of the potential-energy surface for the retrocyclization shows that only a small, if any, activation barrier is to be expected for this process. In another series of experiments, metal complexes of 1 were investigated. 1/Cr+ was formed in the ion source and examined by metastable ion decay and collisional activation experiments, which revealed predominant losses of neutral benzene. Nevertheless, comparison with the bis-ligated [(C6H6)2Cr]+ complex provided evidence for the existence of an intact 1/Cr+ under these experimental conditions. No evidence for the existence of 1/Fe+ was obtained, which suggests that iron mediates the rapid retrocyclization of 1/Fe+ into the bis-ligated benzene complex [(C6H6)2Fe]+.
Die Ionenchemie von anti-o,o′-Dibenzol 1 wurde sowohl in der Gasphase als auch in kondensierter Phase untersucht. Ionen-Cyclotron-Resonanz-Massenspektrometrie mit Hilfe von Cu+-Ionen zeigten, dass 1 unter den experimentellen Bedingungen als intaktes Molekül in der Gasphase existiert. Die Molekülionen, formal 1.+ und 1.−, wurden mit einem Viersektor-Massenspektrometer untersucht und verschiedenen Stoßexperimenten unterworfen. Erstaunlicherweise war die erwartete Retrocyclisierung, die zu zwei Benzolmolekülen führen sollte, nicht der Hauptprozess, sondern andere Fragmentierungen, wie Methyl- und Wasserstoffverluste überwogen. Im Gegensatz dazu führte die Matrixionisierung von 1 durch γ-Strahlung in freon (77 K) oder durch Röntgenstrahlung in Argon (12 K) zu quantitativer Retrocyclisierung unter Bildung des kationischen Benzoldimers, 2.+. Die theoretische Modellierung der Retrocyclisierungs-Potentialenergiefläche zeigt, dass eine nur geringe Barriere für diesen Prozess erwartet werden kann. In einer weiteren Reihe von Experimenten wurden kationische Metallkomplexe von 1 untersucht. Gasphasenexperimente ergaben, dass im Falle des Chroms der Komplex 1/Cr+ erzeugbar war, während für Eisen eine schnelle Retrocyclisierung zum bisligierten Benzolkomplex [(C6H6)2Fe]+ vorherscht.
Co-reporter:Lauren L. O'Neil and Olaf Wiest
Organic & Biomolecular Chemistry 2008 - vol. 6(Issue 3) pp:NaN492-492
Publication Date(Web):2007/12/13
DOI:10.1039/B713318A
Base flipping is the movement of a DNA base from an intrahelical, base-stacked position to an extrahelical, solvent-exposed position. As there are favorable interactions for an intrahelical base, both hydrogen bonding and base stacking, base flipping is expected to be energetically prohibitive for an undamaged DNA duplex. For damaged DNA bases, however, the energetic cost of base flipping may be considerably lower. Using a selective, non-covalent assay for base flipping, the sequence dependence of base flipping in DNA sequences containing an abasic site has been studied. The dissociation constants of the zinc–cyclen complex to small molecules and single strands of DNA as well as the equilibrium constants for base flipping have been determined for these sequences. Molecular dynamics simulations of the zinc-cyclen complex bound to both single- and double-stranded DNA have been performed in an attempt to rationalize the differences in the dissociation constants obtained for the two systems. The results are compared to previous studies of base flipping in DNA containing an abasic site.