Digital Commons Network^™

“Zipped Synthesis” By Cross-Metathesis Provides A Cystathionine Β‑Synthase Inhibitor That Attenuates Cellular H2S Levels And Reduces Neuronal Infarction In A Rat Ischemic Stroke Model, Christopher D. Mccune, Su Jing Chan, Matthew L. Beio, Weijun Shen, Woo Jin Chung, Laura M. Szczesniak, Chou Chai, Shu Qing Koh, Peter T.-H. Wong, David B. Berkowitz

David Berkowitz Publications

The gaseous neuromodulator H₂S is associated with neuronal cell death pursuant to cerebral ischemia. As cystathionine β-synthase (CBS) is the primary mediator of H2S biogenesis in the brain, it has emerged as a potential target for the treatment of stroke. Herein, a “zipped” approach by alkene cross-metathesis into CBS inhibitor candidate synthesis is demonstrated. The inhibitors are modeled after the pseudo-C₂-symmetric CBS product (L,L)-cystathionine. The “zipped” concept means only half of the inhibitor needs be constructed; the two halves are then fused by olefin cross-metathesis. Inhibitor design is also mechanism-based, exploiting the favorable kinetics associated with …

Mini-Ises Identifies Promising Carbafructopyranose-Based Salens For Asymmetric Catalysis: Tuning Ligand Shape Via The Anomeric Effect, Kannan R. Karukurichi, Xiang Fei, Robert A. Swyka, Sylvain Broussy, Weijun Shen, Sangeeta Dey, Sandip K. Roy, David B. Berkowitz

David Berkowitz Publications

This study introduces new methods of screening for and tuning chiral space and in so doing identifies a promising set of chiral ligands for asymmetric synthesis. The carbafructopyranosyl-1,2-diamine(s) and salens constructed therefrom are particularly compelling. It is shown that by removing the native anomeric effect in this ligand family, one can tune chiral ligand shape and improve chiral bias. This concept is demonstrated by a combination of (i) x-ray crystallographic structure determination, (ii) assessment of catalytic performance, and (iii) consideration of the anomeric effect and its underlying dipolar basis. The title ligands were identified by a new mini version of …

Exploiting Enzymatic Dynamic Reductive Kinetic Resolution (Dyrkr) In Stereocontrolled Synthesis, Gregory A. Applegate, David B. Berkowitz

David Berkowitz Publications

Over the past two decades, the domains of both frontline synthetic organic chemistry and process chemistry have seen an increase in crosstalk between asymmetric organic/organometallic approaches and enzymatic approaches to stereocontrolled synthesis. This review highlights the particularly auspicious role for dehydrogenase enzymes in this endeavor, with a focus on dynamic reductive kinetic resolutions (DYRKR) to “deracemize” building blocks, often setting two stereocenters in so doing. The scope and limitations of such dehydrogenase-mediated processes are overviewed, as are future possibilities for the evolution of enzymatic DYRKR.

Phosphatase-Inert Glucosamine 6‑Phosphate Mimics Serve As Actuators Of The Glms Riboswitch, Xiang Fei, Thomas Holmes, Julianna Diddle, Lauren Hintz, Dan Delaney, Alex Stock, Danielle Renner, Molly Mcdevitt, David B. Berkowitz, Juliane K. Soukup

David Berkowitz Publications

The glmS riboswitch is unique among generegulating riboswitches and catalytic RNAs. This is because its own metabolite, glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically participates in the RNA selfcleavage reaction, thereby providing a novel negative feedback mechanism. Given that a number of pathogens harbor the glmS riboswitch, artificial actuators of this potential RNA target are of great interest. Structural/kinetic studies point to the 2- amino and 6-phosphate ester functionalities in GlcN6P as being crucial for this actuation. As a first step toward developing artificial actuators, we have synthesized a series of nine GlcN6P analogs bearing phosphatase-inert surrogates in place …

Unleashing A “True” Pser-Mimic In The Cell, Kaushik Panigrahi, David L. Nelson, David B. Berkowitz

David Berkowitz Publications

In this issue of Chemistry & Biology, Arrendale and coworkers demonstrate a new prodrug strategy for intracellular delivery of an α, α-(difluoromethylene)phosphonate phosphoserine mimic. The deprotected pseudo-phosphopeptide releases the pro-apoptotic FOXO3a-transcription factor from its 14-3-3-adaptor protein complex, resulting in leukemic cell death.

Halocarbocyclization Entry Into The Oxabicyclo[4.3.1]Decyl Exomethylene-Δ-Lactone Cores Of Linearifolin And Zaluzanin A - Exploiting Combinatorial Catalysis, Sandeep K. Ginotra, Jacob A. Friest, David B. Berkowitz

David Berkowitz Publications

A streamlined entry into the sesquiterpene lactones (SQL) cores of linearifolin and zaluzanin A is described. Stereochemistry is controlled through transformations uncovered by ISES (In-Situ- Enzymatic-Screening). Absolute stereochemistry derives from kinetic resolution of 5- benzyloxypentene-1,2-oxide, utilizing a β-pinene-derived-Co(III)-salen. Relative stereochemistry (1,3-cis-fusion)is set via formal halometalation/carbocyclization, mediated by [Rh(O₂CC₃F₇)₂]₂/ LiBr. Subsequent ring-closing metathesis (RCM-Grubbs II) yields the title exomethylene-δ- lactone SQL-cores. In complementary fashion, RCM with Grubbs-I catalyst provides the oxabicyclo[3.3.1]nonyl-core of xerophilusin R and zinagrandinolide.

Combinatorial Catalysis Assisted By A Visible Enzymatic Beacon In Real Time: New Synthetically Versatile (Pseudo)Halometalation/Carbocyclizations, Jacob A. Friest, Sylvain Broussy, Woo Jin Chung, David B. Berkowitz

David Berkowitz Publications

Combinatorial approaches to catalysis have made an impact in targeted transformation development, including Ag-mediated carbene insertion,^[1] Sc-pybox-based asymmetric cyclopropanation,^[2] and Rh/Ir-based asymmetric hydrogenation.^[3] Useful design elements have emerged from these studies, e.g. the value of ligand self assembly,^[4] or of the inclusion of peptide-like structural elements^[5],[6],[7] in building ligand arrays. Efficient screening methods are of paramount importance for such efforts. Methods based on fluorescence,^[8] REMPI^,[9] MS,^[10] NMR,^[11] and IR thermography^[12] have appeared. A chromophore may be installed into the substrate^[13] or product^[14] of the reaction under study. Alternatively, …

Use Of A Robust Dehydrogenase From An Archael Hyperthermophile In Asymmetric Catalysis–Dynamic Reductive Kinetic Resolution Entry Into (S)-Profens, Jacob A. Friest, Yukari Maezato, Sylvain Broussy, Paul H. Blum, David B. Berkowitz

David Berkowitz Publications

Hyperthermophilic archaea are of great interest in evolutionary microbiology, owing to their ability to withstand high temperatures, and often extremes of pressure, pH and salinity. Enzymes from these organisms¹ may offer particular opportunities for asymmetric synthesis, complementary to approaches with mesophilic enzymes,² or those involving enzyme³ and pathway⁴ reengineering. However, perhaps due to a bias that hyperthermophilic enzymes have “narrow substrate specificities,”⁵ archaeal extremophiles remain a largely untapped resource in asymmetric synthesis.⁶

Herein, we disclose a remarkably general Dynamic Reductive Kinetic Resolution (DYRKR) entry into (S)-profens, including several important NSAIDs. The enzyme employed is …

Atomic Details Of Near-Transition State Conformers For Enzyme Phosphoryl Transfer Revealed By Mgf3− Rather Than By Phosphoranes, Nicola J. Baxter, Matthew W. Bowler, Tooba Alizadeh, Matthew J. Cliff, Andrea M. Hounslow, Bin Wu, David B. Berkowitz, Nicholas H. Williams, G. Michael Blackburn, Jonathan P. Waltho

David Berkowitz Publications

Prior evidence supporting the direct observation of phosphorane intermediates in enzymatic phosphoryl transfer reactions was based on the interpretation of electron density corresponding to trigonal species bridging the donor and acceptor atoms. Close examination of the crystalline state of β-phosphoglucomutase, the archetypal phosphorane intermediate-containing enzyme, reveals that the trigonal species is not PO−3 , but is MgF−3 (trifluoromagnesate). Although MgF−3 complexes are transition state analogues rather than phosphoryl group transfer reaction intermediates, the presence of fluorine nuclei in near-transition state conformations offers new opportunities to explore the nature of the interactions, in particular the independent measures of local electrostatic and …

The Α,Α-Difluorinated Phosphonate L-Pser-Analogue: An Accessible Chemical Tool For Studying Kinase-Dependent Signal Transduction In Vitro, And In Living Cells, Kaushik Panigrahi, Marijean Eggen, Jun-Ho Maeng, Quanrong Shen, David B. Berkowitz

David Berkowitz Publications

This overview focuses on the (α,α-difluoromethylene)phosphonate mimic of phosphoserine (pCF₂Ser) and its application to the study of kinase-mediated signal transduction – pathways of great interest to drug development. The most versatile modes of access to these chemical biological tools are discussed, organized by method of PCF₂-C bond. The pCF₂-Ser mimic may be site-specifically incorporated into peptides (SPPS) and proteins (expressed protein ligation). This isopolar, dianionic pSer mimic results in a “constitutive phosphorylation” phenotype, and is seen to support native protein-protein interactions that depend upon serine phosphorylation. Signal transduction pathways studied with this chemical biological …

Use Of Fluorinated Functionality In Enzyme Inhibitor Development: Mechanistic And Analytical Advantages, David B. Berkowitz, Kannan R. Karukurichi, Roberto De La Salud-Bea, David L. Nelson, Christopher D. Mccune

David Berkowitz Publications

On the one hand, owing to its electronegativity, relatively small size, and notable leaving group ability from anionic intermediates, fluorine offers unique opportunities for mechanism-based enzyme inhibitor design. On the other, the “bio-orthogonal” and NMR-active 19-fluorine nucleus allows the bioorganic chemist to follow the mechanistic fate of fluorinated substrate analogues or inhibitors as they are enzymatically processed. This article takes an overview of the field, highlighting key developments along these lines. It begins by highlighting new screening methodologies for drug discovery that involve appropriate tagging of either substrate or the target protein itself with ¹⁹Fmarkers, that then report back …

A Set Of Phosphatase-Inert “Molecular Rulers” To Probe For Bivalent Mannose 6-Phosphate Ligand-Receptor Interactions, Xiang Fei, Christopher M. Connelly, Richard G. Macdonald, David B. Berkowitz

David Berkowitz Publications

A set of bivalent mannose 6-phosphonate “molecular rulers” has been synthesized to examine ligand binding to the M6P/IGF2R. The set is estimated to span a P-P distance range of 16–26 Å (MMFF energy minimization on the hydrated phosphonates). Key synthetic transformations include sugar triflate displacement for phosphonate installation and Grubbs I cross-metathesis to achieve bivalency. Relative binding affinities were tested by radioligand displacement assays versus PMP-BSA (pentamannose phosphate-bovine serum albumin). These compounds exhibit slightly higher binding affinities for the receptor (IC_50’s = 3.7–5 μM) than the parent, monomeric mannose 6-phosphonate ligand and M6P itself (IC₅₀ = 11.5 ± …

A Set Of Phosphatase-Inert “Molecular Rulers” To Probe For Bivalent Mannose 6-Phosphate Ligand-Receptor Interactions, Xiang Fei, Christopher M. Connelly, Richard G. Macdonald, David B. Berkowitz

David Berkowitz Publications

A set of bivalent mannose 6-phosphonate “molecular rulers” has been synthesized to examine ligand binding to the M6P/IGF2R. The set is estimated to span a P-P distance range of 16-26 Å (MMFF energy minimization on the hydrated phosphonates). Key synthetic transformations include sugar triflate displacement for phosphonate installation and Grubbs I cross-metathesis to achieve bivalency. Relative binding affinities were tested by radioligand displacement assays versus PMP-BSA (pentamannose phosphate-bovine serum albumin). These compounds exhibit slightly higher binding affinities for the receptor (IC₅₀’s = 3.7-5 &#;M) than the parent, monomeric mannose 6-phosphonate ligand and M6P itself (IC₅₀ = 11.5 …

Topoisomerase Ii-Drug Interaction Domains: Identification Of Substituents On Etoposide That Interact With The Enzyme, Amy M. Wilstermann, Ryan P. Bender, Murrell Godfrey, Sungjo Choi, Clemens Anklin, David B. Berkowitz, Neil Osheroff, David E. Graves

David Berkowitz Publications

Etoposide is one of the most successful chemotherapeutic agents used for the treatment of human cancers. The drug kills cells by inhibiting the ability of topoisomerase II to ligate nucleic acids that it cleaves during the double-stranded DNA passage reaction. Etoposide is composed of a polycyclic ring system (rings A–D), a glycosidic moiety at the C4 position, and a pendant ring (E–ring) at the C1 position. Although drug-enzyme contacts, as opposed to drug-DNA interactions, mediate the entry of etoposide into the topoisomerase II-drug-DNA complex, the substituents on etoposide that interact with the enzyme have not been identified. Therefore, saturation transfer …

Examination Of The New Α-(2′Z-Fluoro)Vinyl Trigger With Lysine Decarboxylase: The Absolute Stereochemistry Dictates The Reaction Course, Kannan R. Karukurichi, Roberto De La Salud-Bea, Wan Jin Jahng, David B. Berkowitz

David Berkowitz Publications

The first examination of a terminal α-fluorovinyl trigger in an amino acid decarboxylase active site is reported. To investigate the enantiospecifity of inactivation with this new AADC trigger, an enantioselective synthesis of L-α-(2′Z-fluoro)vinyllysine and its D-antipode has been developed. Control of stereochemistry is achieved through introduction of the amino acid side chain via alkylation of a chiral vinylglycine-derived dienolate. Facial selectivity is conferred by a trans-2′(β- naphthyl)-2′-propylcyclohexyl ester auxiliary, available in both antipodal forms (Comins protocol). The alkylation employs a new electrophile, N-p-methoxybenzyl-N-(2′- trimethylsilylethanesulfonyl)-4-iodobutylamine, for convergent installation of the lysine side chain. Vinyl to 2′-fluorovinyl interconversion then provides L- …

Protein Structure Similarity Clustering: Dynamic Treatment Of Pdb Structures Facilitates Clustering, Bradley D. Charette, Richard G. Macdonald, Stefan Wetzel, David B. Berkowitz, Herbert Waldmann

David Berkowitz Publications

Protein structure similarity clustering (PSSC) [1]– [3] is one of a number of potential guiding principles [4], [5] that have been introduced to focus combinatorial-library design/ protein targeting. PSSC clusters protein targets with similar ligand-binding cores in which little sequence or functional similarity is evident. Lead compounds for one member of the cluster then provide novel starting points in chemical space for ligand development for other members of the PSSC.

We describe herein a new clustering procedure that lends itself to ligand docking, molecular dynamics (MD), and the vector-alignment-search-tool (VAST) [6] algorithm. This MD-assisted approach offers an alternative to the …

Α-Vinylic Amino Acids: Occurrence, Asymmetric Synthesis, And Biochemical Mechanisms, David B. Berkowitz, Bradley D. Charette, Kannan Karukurichi, Jill M. Mcfadden

David Berkowitz Publications

This report presents an overview of the family of naturally occurring “vinylic” amino acids, namely those that feature a C–C double bond directly attached to the α-carbon, along the side chain. Strategies that have been brought to bear on the stereo-controlled synthesis of these olefinic amino acids are surveyed. The mechanistic diversity by which such “vinylic triggers” can be actuated in a PLP (pyridoxal phosphate) enzyme active site is then highlighted by discussion of vinylglycine (VG), its substituted congeners, particularly AVG [4E-(2′-aminoethoxy)vinylglycine], and a naturally occurring VG-progenitor, SMM [(S)-methylmethionine].

A Formal [3,3]-Sigmatropic Rearrangement Route To Quaternary Α-Vinyl Amino Acids: Use Of Allylic N-Pmp Trifluoroacetimidates, David B. Berkowitz, Bin Wu, Huijie Li

David Berkowitz Publications

Pd(II)-mediated rearrangement of allylic N-PMP (p-methoxyphenyl) trifluoroacetimidates provides the first formal sigmatropic route to quaternary, α-vinylic amino acids, potential suicide substrates for PLP-enzymes. The amino acid side chains enter via transition metal-mediated C-C bond constructions, including (i) Cu(I)-mediated conjugate addition (Ala); (ii) Pd(0)/AsPh₃-mediated Stille coupling (Allyl-Gly, Phe, DOPA, m-Tyr) and (iii) Pd(0)/Pt-Bu₃-mediated Negishi coupling (Leu). In the synthesis of the DOPA decarboxylase inactivator, α-vinyl-m-tyrosine, the new N-PMP trifluoroacetimidate rearranges much more efficiently than the corresponding trichloroacetimidate.

In Situ Enzymatic Screening (Ises) Of P,N-Ligands For Ni(0)- Mediated Asymmetric Intramolecular Allylic Amination, David B. Berkowitz, Weijun Shen, Gourhari Maiti

David Berkowitz Publications

An in situ enzymatic screening (ISES) approach to rapid catalyst evaluation recently pointed to Ni(0) as a new candidate transition metal for intramolecular allylic amination. This led to further exploration of chiral bidentate phosphine ligands for such transformations. Herein, a variety of P,N-ligands are examined for this Ni(0)-chemistry, using a model reaction leading into the vinylglycinol scaffold. On the one hand, an N,N-bis(2-diphenylphosphinoethyl)alkylamine (‘PNP’) ligand proved to be the fastest ligand yet seen for this Ni(0)-transformation. On the other, phosphinooxazoline (PHOX) ligands of the Pfaltz–Helmchen– Williams variety gave the highest enantioselectivities (up to 51% ee) among P,N-ligands …

A Convenient Synthesis Of L-Α-Vinylglycine From L-Homoserine Lactone, David B. Berkowitz, Marianne K. Smith

David Berkowitz Publications

A procedure for the synthesis ofL-IX-vinylglycine from L-homoserine lactone is described. The route developed is convenient (only one chromatography step is required) and efficient (72 %; ≥ 95 % optical yield over 4 steps). Key features include the use of acid-labile protecting groups for the amino (Boc) and carboxyl (diphenylmethyl ester) groups, and the use of the phenylselenolate equivalent derived from sodium borohydride and diphenyl diselenide for L-homoserine lactone cleavage.

Enantiomerically Enriched Α-Methyl Amino Acids. Use Of An Acyclic, Chiral Alanine-Derived Dianion With A High Diastereofacial Bias., David B. Berkowitz, Marianne K. Smith

David Berkowitz Publications

Hindered esters derived from N-benzoylalanine and the following chiral alcohols have been synthesized: (1) (−)-isopinocampheol; (2) (−)-trans-2-phenylcyclohexanol and (3) (−)-8-phenylmenthol. Sequential treatment of these esters with LDA (1.2 equiv.) and n-butyllithium (2.4 equiv.) at −78°C in THF generates the corresponding chiral dianions. Alkylation of each of these with benzyl bromide reveals that only the (−)-8-phenylmenthyl auxiliary confers a high diastereofacial bias upon its derivative dianion. In fact, that dianion (6) consistently displays diastereomeric ratios in the range of 89:11 to 94:6 for alkylations with a spectrum of nine alkyl halides. If one recrystallization step is …

Free Α-Oxiranyl Amino Acids, David B. Berkowitz, Michelle L. Pedersen

David Berkowitz Publications

Analogues of natural amino acids, in which the α-proton is replaced by an unsubstituted epoxide ring, are potential mechanism-based inhibitors for pyridoxal phosphate dependent enzymes.¹ Yet, free α-oxiranyl amino acids have remained elusive until now. The synthesis of an α-(phenyl-substituted)oxiranyl amino ester has been reported. However, the accessibility and stability of the corresponding free, zwitterionic α-oxiranyl amino acid remained an open question.⁹