Discovery of potent BET bromodomain 1 stereoselective inhibitors using DNA-encoded chemical library
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Modukuri, Ram K.↗
SEARCH · Engineering Papers
Results for “stereoselectivity”
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A pyridoxal 5'-phosphate-dependent Mannich cyclase
Pyridoxal 5'-phosphate (PLP)-dependent enzymes catalyse a diverse range of chemical transformations. Despite their extraordinary functional diversity, no PLP-dependent enzyme is known to catalyse Mannich-type reactions, an important carbon–carbon bond-forming reaction in synthetic organic chemistry. Here we report the discovery of a biosynthetic enzyme LolT, a PLP-dependent enzyme catalysing a stereoselective intramolecular Mannich reaction to construct the pyrrolizidine core scaffold in loline alkaloids. Importantly, its versatile catalytic activity is harnessed for stereoselective synthesis of a variety of conformationally constrained α,α-disubstituted α-amino acids, which bear vicinal quaternary–tertiary stereocentres and various aza(bi)cyclic backbones, such as indolizidine, quinolizidine, pyrrolidine and piperidine. Furthermore, crystallographic and mutagenesis analysis and computational studies together provided mechanistic insights and structural basis for understanding LolT’s catalytic activity and stereoselectivity. As a whole, this work expands the biocatalytic repertoire of carbon–carbon bond-forming enzymes and increases our knowledge of the catalytic versatility of PLP-dependent enzymes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dirigent isoflavene-forming PsPTS2: 3D structure, stereochemical, and kinetic characterization comparison with pterocarpan-forming PsPTS1 homolog in pea
Pea (legume plant defense) phytoalexin pterocarpans (–)-maackiain and (+)-pisatin have opposite C6a and C11a configurations, but how this occurs biosynthetically is unknown. Herein, pea dirigent-protein (DP) PsPTS2, which generates 7,2'-dihydroxy-4',5'-methylenedioxyisoflav-3-ene (DMDIF), was investigated as regards stereoselectivity towards four possible 7,2'-dihydroxy-4',5'-methylenedioxyisoflavan-4-ol (DMDI) stereoisomers. Each DMDI stereoisomer configuration was determined using NMR spectroscopy, electronic circular dichroism, and molecular orbital analyses. PsPTS2 efficiently converted cis-(3R,4R)-DMDI into DMDIF, this being 20-fold faster than with the trans-(3R,4S)-isomer. The 4R-configured substrate’s near ß-axial OH orientation significantly enhanced its leaving group abilities in creating intermediate A-ring mono-quinone methide (QM), whereas the 4S-isomer’s 4-OH group α-equatorial orientation was a poorer leaving group. Substrate docking simulations also indicated that the 4R-configured ß-axial OH was closest to the Asp catalytic center, whereas the 4S-isomer’s α-equatorial OH was further away. Neither cis-(3S,4S)- nor trans-(3S, 4R)-DMDIs were substrates, even with the former having the same C3/C4 stereochemistry as (+)-pisatin. PsPTS2, assayed with cis-(3R,4R)-7,2'-dihydroxy-4'-methoxyisoflavan-4-ol [cis-(3R,4R)-DMI] and its C3/C4 stereoisomers, gave 2',7-dihydroxy-4'-methoxyisoflav-3-ene (DMIF), with the same substrate stereoselectivity. DP homologs may exist in licorice (Glycyrrhiza pallidiflora) and the tree legume Bolusanthus speciosus, as DMIF is found in both. PsPTS1 preferentially utilized cis-(3R,4R)-DMDI to give (–)-maackiain, this being 2200-fold more efficient than with cis-(3R,4R)-DMI. PsPTS1 also slowly converted trans-(3S,4R)-DMDI into (+)-maackiain, again reflecting the better 4R configured OH leaving group. Pea PsPTS2 and PsPTS1 provisionally provide a facile DP-engendered means to enable differing C6a and C11a configurations in (+)-pisatin and (–)-maackiain. Both DP transformations are considered to occur via DP-engendered generation of an identical mono-QM bound intermediate, which with PsPTS2 either re-aromatizes to give DMDIF or with PsPTS1 undergoes intramolecular cyclization to afford (–)-maackiain. Substrate docking simulations using PsPTS2 (2.5 Å resolution) and PsPTS1 (1.5 Å resolution) plausibly indicate that cis-(3R,4R)-DMDI binds in the anti-configuration in the PsPTS2 active site to afford DMDIF, and the syn-configuration in PsPTS1 to give maackiain.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Flyby reaction trajectories: Chemical dynamics under extrinsic force
Dynamic effects are an important determinant of chemical reactivity and selectivity, but the deliberate manipulation of atomic motions during a chemical transformation is not straightforward. In this work, we demonstrate that extrinsic force exerted upon cyclobutanes by stretching pendant polymer chains influences product selectivity through force-imparted nonstatistical dynamic effects on the stepwise ring-opening reaction. The high product stereoselectivity is quantified by carbon-13 labeling and shown to depend on external force, reactant stereochemistry, and intermediate stability. Computational modeling and simulations show that, besides altering energy barriers, the mechanical force activates reactive intramolecular motions nonstatistically, setting up “flyby trajectories” that advance directly to product without isomerization excursions. A mechanistic model incorporating nonstatistical dynamic effects accounts for isomer-dependent mechanochemical stereoselectivity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Transformation of brucine into trifluoromethyl neobrucine using the homoleptic nickel catalyst [Ni(CF3)4]2-
The homoleptic trifluoromethyl nickel complex [Ni(CF3)4]2- catalyzes a stereoselective trifluoromethylation of brucine with Umemoto II reagent. The trifluoromethylation process proceeds with concomitant isomerization of its alkenyl double bond leading to a trifluoromethylated neobrucine-like derivative. A minor difunctionalization product was also detected from the reaction mixture, consistent with a radical addition process that is occurring in parallel. Stoichiometric reactions between the nickel(II) catalyst precursor and brucine led to no reaction. However, a stochiometric reaction with a high-valent nickel(IV) complex formed trifluoromethylated neobrucine, implicating its intermediacy.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Catalytic Dynamic Kinetic Resolutions in Tandem to Construct Two-Axis Terphenyl Atropisomers
The defined structure of molecules bearing multiple stereogenic axes is of increasing relevance to materials science, pharmaceuticals, and catalysis. However, catalytic enantioselective approaches to control multiple stereogenic axes remain synthetically challenging. Here, we report the catalytic synthesis of two-axis terphenyl atropisomers, with complementary strategies to both chlorinated and brominated variants, formed with high diastereo- and enantioselectivity. The chemistry proceeds through a sequence of two distinct dynamic kinetic resolutions: first, an atroposelective ring opening of Bringmann-type lactones produces a product with one established axis of chirality, and second, a stereoselective arene halogenation delivers the product with the second axis of chirality established. In order to achieve these results, a class of Brønsted basic guanidinylated peptides, which catalyze an efficient atroposelective chlorination, is reported for the first time. In addition, a complementary bromination is reported, which also establishes the second stereogenic axis. These bromo-terphenyls are accessible following the discovery that chiral anion phase transfer catalysis by C 2 -symmetric phosphoric acids allows catalyst control in the second stereochemistry-determining event. Accordingly, we established the fully catalyst-controlled stereodivergent synthesis of all possible chlorinated stereoisomers while also demonstrating diastereodivergence in the brominated variants, with significant levels of enantioselectivity in all cases.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Imine Reductase-Catalyzed, Radical-Mediated Asymmetric Cyano Group Migration
Functional group migration (FGM) reactions represent a fundamental class of transformations in organic chemistry, enabling the repositioning of functional moieties in nonobvious ways. However, catalytic asymmetric radical-mediated FGMs remain rare due to the inherent challenges of achieving catalyst-controlled enantioselectivity over free radical intermediates. Herein, we repurpose imine reductases (IREDs), a class of biotechnologically important enzymes known for their substrate promiscuity, to enable the first examples of catalytic asymmetric cyano group migration via a radical mechanism. An orthogonal set of radical enzymes, including PbaIREDCym and SmiIREDCym, was engineered, allowing both 1,4- and 1,5-cyano group migration reactions to occur in an enantiodivergent fashion. The use of the nonionic surfactant TPGS-1000 was found to improve both the yield and enantioselectivity of these cyano migration reactions. Furthermore, this biocatalytic process exhibited a broad substrate scope and is readily scalable, affording a rare example of chiral nonamine product assembly with imine reductases. More broadly, stereoselective radical biocatalysis with engineered IREDs and other versatile enzymes provides a potentially general solution to challenging asymmetric FGM reactions.
Biocatalysis↗
Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using ‘Ene’‐Reductases with Photoredox Catalysts
Abstract Flavin‐dependent ‘ene’‐reductases (EREDs) are highly selective catalysts for the asymmetric reduction of activated alkenes. This function is, however, limited to enones, enoates, and nitroalkenes using the native hydride transfer mechanism. Here we demonstrate that EREDs can reduce vinyl pyridines when irradiated with visible light in the presence of a photoredox catalyst. Experimental evidence suggests the reaction proceeds via a radical mechanism where the vinyl pyridine is reduced to the corresponding neutral benzylic radical in solution. DFT calculations reveal this radical to be “dynamically stable”, suggesting it is sufficiently long‐lived to diffuse into the enzyme active site for stereoselective hydrogen atom transfer. This reduction mechanism is distinct from the native one, highlighting the opportunity to expand the synthetic capabilities of existing enzyme platforms by exploiting new mechanistic models.
Nakano, Yuji↗
Modulating Electrostatic Interactions in Ion Pair Intermediates To Alter Site Selectivity in the C−O Deoxygenation of Sugars
Abstract Controlling which products one can access from the predefined biomass‐derived sugars is challenging. Changing from CH 2 Cl 2 to the greener alternative toluene alters which C−O bonds in a sugar are cleaved by the tris(pentafluorophenyl)borane/HSiR 3 catalyst system. This increases the diversity of high‐value products that can be obtained through one‐step, high‐yielding, catalytic transformations of the mono‐, di‐, and oligosaccharides. Computational methods helped identify this non‐intuitive outcome in low dielectric solvents to non‐isotropic electrostatic enhancements in the key ion pair intermediates, which influence the reaction coordinate in the reactivity‐/selectivity‐determining step. Molecular‐level models for these effects have far‐reaching consequences in stereoselective ion pair catalysis.
Lowe, Jared M.↗
Photoenzymatic Hydrogenation of Heteroaromatic Olefins Using 'Ene'-Reductases with Photoredox Catalysts
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99 GENERAL AND MISCELLANEOUS↗
Tighter Confinement Increases Selectivity of d-Glucose Isomerization Toward l-Sorbose in Titanium Zeolites
Aqueous-phase isomerization of D-glucose to D-fructose and L-sorbose is catalyzed in parallel by Lewis acidic Ti sites in siliceous frameworks. Glucose isomerization rates (per Ti, 373 K) are undetectable when Ti sites are confined within mesoporous voids (Ti-MCM-41, TiO 2 -SiO 2 ) and increase to detectable values when Ti sites are confined within the smaller 12-membered ring (12-MR) micropores of Ti-Beta. Furthermore, isomerization rates decrease to lower values (by ≈20×) with further decreases in micropore size as Ti sites are confined within 10-MR pores (Ti-MFI, Ti-CON), likely because of intrapore reactant diffusion restrictions, and reach undetectable values within the 8-MR pores of Ti-CHA as size exclusion prevents glucose from accessing active sites. Remarkably, the selectivity toward l -sorbose over d -fructose increases systematically as spatial constraints around Ti sites become tighter, and is >10 on Ti-MFI. These findings demonstrate the marked influence of confinement around Ti active sites on the selectivity between parallel stereoselective sugar isomerization pathways.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Diastereoselective Hydrogenation of Tetrasubstituted Olefins using a Heterogeneous Pt‐Ni Alloy Catalyst
Abstract Stereoselective hydrogenation of tetrasubstituted olefins is an attractive method to access compounds with two contiguous stereocenters. However, homogeneous catalysts for enantio‐ and diastereoselective hydrogenation exhibit low reactivity toward tetrasubstituted olefins due to steric crowding between the ligand scaffold and the substrate. Monometallic heterogeneous catalysts, on the other hand, provide accessible surface active sites for hindered olefins but exhibit unpredictable and inconsistent stereoinduction. In this work, we develop a Pt−Ni bimetallic alloy catalyst that can diastereoselectively hydrogenate unactivated, sterically‐bulky tetrasubstituted olefins, utilizing the more oxophilic Ni atoms to adsorb a hydroxyl directing group and direct facially‐selective hydrogen addition to the olefin via the Pt atoms. Structure‐activity studies on several Pt−Ni compositions underscore the importance of exposing a uniform PtNi alloy surface to achieve high diastereoselectivity and minimize side reactions. The optimized Pt−Ni/SiO 2 catalyst exhibits good functional group tolerance and broad scope for tetrasubstituted olefins in a cyclopentene scaffold, generating cyclopentanol products with three contiguous stereocenters. The synthetic utility of the method is demonstrated in a four‐step synthesis of (1R,2S)‐(+)‐cis‐methyldihydrojasmonate with high yield and enantiopurity.
Chemistry↗
Structural Basis of Sequential Enantioselective Epoxidation by a Flavin‐Dependent Monooxygenase in Lasalocid A Biosynthesis
Abstract Polyether polyketides are a structurally diverse group of natural products known for their antimicrobial and antiproliferative activities. Lasalocid A is a canonical natural polyether produced by the soil bacteriumStreptomyces lasalocidi. In lasalocid A biosynthesis, a polyene polyketide intermediate is converted into a bisepoxide by the flavin‐dependent monooxygenase enzyme Lsd18. Remarkably, Lsd18 acts on two distinct C═C groups in the substrate molecule, forming two (R,R) epoxides. We have determined the X‐ray crystal structures of Lsd18 in the substrate‐free, substrate‐bound, and product‐bound forms. Our work has revealed that Lsd18 has an extra‐large substrate‐binding pocket that allows the polyene to adopt different conformations within the enzyme pocket. This feature enables Lsd18 to epoxidate both of the C═C groups. Additionally, a subpocket located near the Lsd18 active site controls stereoselectivity by dictating which face of the C═C group is placed next to the flavin. Molecular understanding of how Lsd18 transforms a polyene into a bisepoxide during lasalocid A biosynthesis lays the foundation for the production of designer polyethers for drug development.
Chemistry↗
A Chemoselective and Stereodivergent Platform of Heme‐Nitrene Transferases to Access Chiral Aryl‐β‐Amino Esters and An Investigation of the Sequence‐Activity Landscape
Engineered biocatalysts can utilize nitrene precursors to access enantioenriched amination products, yet they have not been applied to produce valuable, enantiomerically enriched noncanonical β-amino esters. Current approaches to synthesizing β-amino acids rely on pre-oxidized precursors and multistep synthetic approaches involving various protecting groups. We engineered a platform of heme enzymes for stereoselective C–H bond amination of readily available carboxylic ester derivatives to install primary amines. A directed evolution campaign coupled with sequencing of over 1000 variants enabled us to develop engineered variants that use either O-pivaloylhydroxylamine triflic acid (PONT) or hydroxylamine hydrochloride (H 2 NOH∙HCl) as aminating reagents. An analysis of the resulting sequence–activity dataset revealed additional improvements that could be made to the final variant, highlighting the utility of sequencing data to guide future steps in directed evolution campaigns. Furthermore, the evolved nitrene transferases expand the scope of accessible chiral β-amino acid building blocks for peptidomimetic applications and provide new starting points for the design and synthesis of enantioenriched β-amino acid motifs.
amino ester building blocks↗
Importance of Engineered and Learned Molecular Representations in Predicting Organic Reactivity, Selectivity, and Chemical Properties
Machine-readable chemical structure representations are foundational in all attempts to harness machine learning for the prediction of reactivities, selectivities, and chemical properties directly from molecular structure. The featurization of discrete chemical structures into a continuous vector space is a critical phase undertaken before model selection, and the development of new ways to quantitatively encode molecules is an active area of research. Here, we highlight the application and suitability of different representations, from expert-guided “engineered” descriptors to automatically “learned” features, in different prediction tasks relevant to organic and organometallic chemistry, where differing amounts of training data are available. These tasks include statistical models of stereo- and enantioselectivity, thermochemistry, and kinetics developed using experimental and quantum chemical data. The use of expert-guided molecular descriptors provides an opportunity to incorporate chemical knowledge, domain expertise, and physical constraints into statistical modeling. In applications to stereoselective organic and organometallic catalysis, where data sets may be relatively small and 3D-geometries and conformations play an important role, mechanistically informed features can be used successfully to obtain predictive statistical models that are also chemically interpretable. We provide an overview of several recent applications of this approach to obtain quantitative models for reactivity and selectivity, where topological descriptors, quantum mechanical calculations of electronic and steric properties, along with conformational ensembles, all feature as essential ingredients of the molecular representations used. Alternatively, more flexible, general-purpose molecular representations such as attributed molecular graphs can be used with machine learning approaches to learn the complex relationship between a structure and prediction target. This approach has the potential to out-perform more traditional representation methods such as “hand-crafted” molecular descriptors, particularly as data set sizes grow. One area where this is particularly relevant is in the use of large sets of quantum mechanical data to train quantitative structure–property relationships. A general approach toward curating useful data sets and training highly accurate graph neural network models is discussed in the context of organic bond dissociation enthalpies, where this strategy outperforms regression using precomputed descriptors. Finally, we describe how graph neural network predictions can be incorporated into mechanistically informed statistical models of chemical reactivity and selectivity. Once trained, this approach avoids the expensive computational overhead associated with quantum mechanical calculations, while maintaining chemical interpretability. We illustrate examples for which fast predictions of bond dissociation enthalpy and of the identities of radicals formed through cleavage of a molecule’s weakest bond are used in simple physical models of site-selectivity and reactivity.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Photobiocatalysis for Abiological Transformations
Harnessing biocatalysts for novel abiological transformations is a longstanding goal of synthetic chemistry. Combining the merits of biocatalysis and photocatalysis allows for selective transformations fueled by visible light and offers many advantages including new reactivity, high enantioselectivity, greener syntheses, and high yields. Photoinduced electron or energy transfer enables synthetic methodologies that complement conventional two electron processes or offer orthogonal pathways for developing new reactions. Enzymes are well suited and can be tuned by directed evolution to exert control over radical intermediates thereby suppressing undesirable reactions and delivering high chemo- and stereoselectivities. Within the past decade, the combination of biocatalysis and photocatalysis was mainly focused on exploiting light-regenerated cofactors to increase native enzymatic activity. However, recent developments have demonstrated that the combination can unlock new-to-nature chemistry. Particularly, the discovery and application of new strategies are well poised to expand the applications of photobiocatalysis. In the past three years, our lab has been studying the combinations of photocatalysis and biocatalysis which can be applied to create new synthetic methodologies and solve challenges in synthetic organic chemistry. Our efforts have expanded the strategies for combining external photocatalysts with enzymes through the construction of a synergistic cooperative stereoconvergent reduction system consisting of photosensitized energy transfer and ene-reductase catalyzed alkene reduction. Additionally, our efforts have also extended the capability of cofactor-dependent photoenzymatic systems to include enantioselective bimolecular radical hydroalkylations of alkenes by irradiating electron donor-acceptor complexes comprised of enzymatic redox active cofactors and unnatural substrates. In this Account, we highlight strategies developed by our group and others for combining biocatalysis and photocatalysis with the aim of introducing nonnatural reactivity to enzymes. Presently, strategies applied to achieve this goal include the repurposing of newly discovered photoactive enzymes, the elucidation of new photoreactivity within cofactor-dependent enzymes, the combination of external photocatalysts with enzymes, and the construction of artificial photoenzymes. By demonstrating the successful application of these strategies for achieving selective new-to-nature transformations, we hope to spur interest in the expanding the scope of photobiocatalytic systems through the use and extension of these strategies and creation of new strategies. In addition, we hope to elucidate the intuition in synergizing the unique capabilities of biocatalysis and photocatalysis so that photobiocatalysis can be recognized as a potential solution to difficult challenges in synthetic organic chemistry.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Tuning Enzyme Thermostability via Computationally Guided Covalent Stapling and Structural Basis of Enhanced Stabilization
Enhancing the thermostability of enzymes without impacting their catalytic function represents an important yet challenging goal in protein engineering and biocatalysis. We recently introduced a novel method for enzyme thermostabilization that relies on the computationally guided installation of genetically encoded thioether “staples” into a protein via cysteine alkylation with the noncanonical amino acid O-2-bromoethyl tyrosine (O2beY). Here, we demonstrate the functionality of an expanded set of electrophilic amino acids featuring chloroacetamido, acrylamido, and vinylsulfonamido side-chain groups for protein stapling using this strategy. Using a myoglobin-based cyclopropanase as a model enzyme, our studies show that covalent stapling with pchloroacetamido-phenylalanine (pCaaF) provides higher stapling efficiency and enhanced stability (thermodynamic and kinetic) compared to the other stapled variants and the parent protein. Interestingly, molecular simulations of conformational flexibility of the cross-links show that the pCaaF staple allows fewer energetically feasible conformers than the other staples, and this property may be a broader indicator of stability enhancement. Using this strategy, pCaaF-stapled variants with significantly enhanced stability against thermal denaturation (ΔT m ' = +27 °C) and temperature-induced heme loss (ΔT 50 = +30 °C) were obtained while maintaining high levels of catalytic activity and stereoselectivity. Crystallographic analyses of singly and doubly stapled variants provide key insights into the structural basis for stabilization, which includes both direct interactions of the staples with protein residues and indirect interactions through adjacent residues involved in heme binding. This work expands the toolbox of protein stapling strategies available for protein stabilization.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗